Next Article in Journal
Effect of Maternal Retinol Status at Time of Term Delivery on Retinol Placental Concentration, Intrauterine Transfer Rate, and Newborn Retinol Status
Next Article in Special Issue
Glycosylation Alterations in Multiple Sclerosis Show Increased Proinflammatory Potential
Previous Article in Journal
Investigating Core Signaling Pathways of Hepatitis B Virus Pathogenesis for Biomarkers Identification and Drug Discovery via Systems Biology and Deep Learning Method
Previous Article in Special Issue
Changes in Circulating Extracellular Vesicles in Patients with ST-Elevation Myocardial Infarction and Potential Effects of Remote Ischemic Conditioning—A Randomized Controlled Trial
Open AccessReview

Immunoglobulins or Antibodies: IMGT® Bridging Genes, Structures and Functions

IMGT®, The International ImMunoGeneTics Information System®, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
*
Authors to whom correspondence should be addressed.
Biomedicines 2020, 8(9), 319; https://doi.org/10.3390/biomedicines8090319
Received: 7 August 2020 / Revised: 23 August 2020 / Accepted: 25 August 2020 / Published: 31 August 2020
(This article belongs to the Special Issue Immunoglobulins in Inflammation)

Abstract

IMGT®, the international ImMunoGeneTics® information system founded in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science at the interface between immunogenetics and bioinformatics. For the first time, the immunoglobulin (IG) or antibody and T cell receptor (TR) genes were officially recognized as ‘genes’ as well as were conventional genes. This major breakthrough has allowed the entry, in genomic databases, of the IG and TR variable (V), diversity (D) and joining (J) genes and alleles of Homo sapiens and of other jawed vertebrate species, based on the CLASSIFICATION axiom. The second major breakthrough has been the IMGT unique numbering and the IMGT Collier de Perles for the V and constant (C) domains of the IG and TR and other proteins of the IG superfamily (IgSF), based on the NUMEROTATION axiom. IMGT-ONTOLOGY axioms and concepts bridge genes, sequences, structures and functions, between biological and computational spheres in the IMGT® system (Web resources, databases and tools). They provide the IMGT Scientific chart rules to identify, to describe and to analyse the IG complex molecular data, the huge diversity of repertoires, the genetic (alleles, allotypes, CNV) polymorphisms, the IG dual function (paratope/epitope, effector properties), the antibody humanization and engineering.
Keywords: IMGT; immunogenetics; immunoinformatics; immunoglobulin; antibody; IG and TR antigen receptors; IMGT-ONTOLOGY; IMGT Collier de Perles; IMGT unique numbering; adaptive immune repertoire IMGT; immunogenetics; immunoinformatics; immunoglobulin; antibody; IG and TR antigen receptors; IMGT-ONTOLOGY; IMGT Collier de Perles; IMGT unique numbering; adaptive immune repertoire
Table of content:
  • 1. Introduction
  • 2. Immunoglobulin (IG) or Antibody Molecular Genetics
  • 2.1. Human Immunoglobulin (IG) or Antibody Structure and Dual Function
  • 2.1.1. Immunoglobulin Fab and Fc Basic Structure
  • 2.1.2. B Cell Differentiation
  • 2.1.3. Membrane Immunoglobulins and B Cell Receptor
  • 2.1.4. Secreted IG
  • 2.2. Human IG Classes and Subclasses: Heavy and Light Chain Types
  • 2.2.1. IG Heavy Chain Types
  • 2.2.2. IG Light Chain Types
  • 2.3. IG Chain Variable and Constant Domains
  • 2.3.1. IG Variable Domains
  • 2.3.2. IG Constant Domains
  • 2.4. Synthesis and Expression of the Immunoglobulins (IG) or Antibodies
  • 2.4.1. IG Molecular Synthesis Characteristics
  • 2.4.2. Synthesis of the H-mu Chains: D-J and V-D-J Rearrangements in the IGH Locus
  • 2.4.3. Synthesis of the L-kappa and L-lambda Chains: V-J Rearrangements in the IGK and IGL Loci
  • 2.5. Origin of the Variable Domain Diversity of the Immunoglobulins
  • 2.5.1. Overview
  • 2.5.2. Combinatorial Diversity
  • 2.5.3. Junctional Diversity
  • 2.5.4. Somatic Hypermutations
  • 2.6. Expression of the Heavy Chains and IG Classes
  • 2.6.1. Coexpression of the Membrane H-mu and H-delta Chains
  • 2.6.2. Expression of H-gamma, H-epsilon and H-alpha chains: Class Switch Recombination
  • 2.6.3. Expression of H-delta Chains from IgM IgD+ Cells
  • 2.6.4. Expression of Membrane and Secreted Immunoglobulins
  • 2.7. Regulation of the Rearrangements and Chain Expression
  • 2.7.1. Allelic and Isotypic Exclusion. Rearrangement Chronology
  • 2.7.2. Regulation of the IG Gene Expression: Enhancers
  • 2.8. Structural and Biological Properties of the Secreted Immunoglobulins
  • 2.8.1. IgM
  • 2.8.2. IgD
  • 2.8.3. IgG
  • 2.8.4. IgA
  • IgA1 and IgA2
  • Secretory IgA
  • IgA Effector Function
  • 2.8.5. IgE
  • 3. Immunoglobulin Genes: IMGT® Gene and Allele Nomenclature
  • 3.1. IMGT® Standardized Genes and Alleles (CLASSIFICATION)
  • 3.1.1. IG and TR Genes and Concepts of Classification: Birth of IMGT® and Immunoinformatics
  • 3.1.2. Homo sapiens IG Genes and Concepts of Identification and Description
  • 3.2. Homo sapiens IGH Locus and Genes
  • 3.2.1. Organization of the Homo sapiens IGH Locus
  • 3.2.2. IGHC Multigene Deletions and Gene Order, IGHC and IGHV Copy Number Variation (CNV) Haplotypes
  • 3.2.3. IGH Orphons
  • 3.2.4. Potential Homo sapiens IGH Genomic Repertoire
  • 3.3. Homo sapiens IGK Locus and Genes
  • 3.3.1. Organization of the Homo sapiens IGK Locus
  • 3.3.2. IGK Orphons
  • 3.3.3. Potential Homo sapiens IGK Genomic Repertoire
  • 3.3.4. Homo sapiens IGKC Allotypes (Km Alleles)
  • 3.4. Homo sapiens IGL Locus and Genes
  • 3.4.1. Organization of the Homo sapiens IGL Locus
  • 3.4.2. IGL Orphons
  • 3.4.3. Potential Homo sapiens IGL Genomic Repertoire
  • 3.4.4. Homo sapiens IGL Isotypes
  • 4. Immunoglobulin Structures: IMGT Unique Numbering and IMGT® Collier de Perles
  • 4.1. IMGT Unique Numbering and IMGT Colliers de Perles for V-DOMAIN (NUMEROTATION)
  • 4.1.1. V Domain Definition and Main Characteristics
  • 4.1.2. V-DOMAIN IMGT Colliers de Perles
  • 4.1.3. V-DOMAIN Strands and Loops (FR-IMGT and CDR-IMGT)
  • 4.1.4. V-DOMAIN Conserved Amino Acids
  • 4.1.5. V-DOMAIN Delimitation
  • 4.1.6. Protein Displays for the V-REGION and J-REGION
  • 4.2. IMGT Unique Numbering and IMGT Colliers de Perles for C Domain (NUMEROTATION)
  • 4.2.1. C Domain Definition and Main Characteristics
  • 4.2.2. C Domain IMGT Colliers de Perles
  • 4.2.3. C Domain Strands and loops
  • 4.2.4. C Domain Conserved Amino Acids
  • 4.2.5. C Domain Genomic Delimitation
  • 4.2.6. C-REGION Protein Displays
  • 5. IMGT® Databases and Tools for IG Sequences and Structures
  • 5.1. IMGT®, the International ImMunoGeneTics Information System®
  • 5.2. IMGT® Nucleotide Sequence and Repertoire Analysis
  • 5.2.1. IMGT/V-QUEST for Nucleotide Sequence Analysis
  • 5.2.2. IMGT/HighV-QUEST
  • 5.3. IMGT® Amino Acid Sequence Analysis and Representation
  • 5.3.1. IMGT/DomainGapAlign
  • 5.3.2. IMGT/Collier-de-Perles Tool
  • 5.4. IMGT® Structure and Amino Acid Databases
  • 5.4.1. IMGT/3Dstructure-DB
  • 5.4.2. IMGT/2Dstructure-DB
  • 5.4.3. IMGT/mAb-DB
  • 6. Using the IMGT Numbering for V and C-Domain for Antibody Description and Engineering
  • 6.1. Antibody V-DOMAIN Humanization by IMGT-CDR Grafting
  • 6.1.1. CDR-IMGT Delimitation for Grafting
  • 6.1.2. Amino acid Interactions between FR-IMGT and CDR-IMGT
  • 6.2. Only-Heavy-Chain Antibodies
  • 6.2.1. Dromedary IgG2 and IgG3
  • 6.2.2. Human Heavy Chain Diseases (HCD)
  • 6.2.3. Nurse Shark IgN
  • 6.3. Contact Analysis of TR-Mimic Antibodies and TR
  • 6.4. Antibody C-Domain Post-Translational Modifications, Engineering and Allotypes
  • 6.4.1. N-linked Glycosylation Sites CH2 N84.4
  • 6.4.2. Knobs-into-Holes
  • 6.4.3. Interface Ball-and-Socket-Like Joints
  • 6.4.4. IGHG Alleles and Gm Allotypes
  • 6.4.5. IGHG Engineered Variants and Effector Properties
  • 7. Conclusions

1. Introduction

The adaptive immune response is found in all extant vertebrate species from fishes to humans and was acquired by jawed vertebrates or gnathostomata more than 450 million years ago. It is characterized by a remarkable immune specificity and memory which are the properties of the B and T cells, and by an extreme diversity of their specific antigen receptors [1]. These antigen receptors of the adaptive immune response comprise the immunoglobulins (IG) or antibodies of the B cells and plasmocytes [2], and the T cell receptors (TR) of the T cells [3]. The IG recognize antigens in their native (unprocessed) form, whereas the TR recognize processed antigens, which are presented as peptides by the highly polymorphic major histocompatibility (MH, in humans HLA for human leucocyte antigens) proteins. Immunoglobulins or antibodies serve a dual role in immunity: they both recognize antigens on the surface of foreign bodies such as bacteria and viruses, and trigger elimination mechanisms such as cell lysis and phagocytosis, to rid the body of these invading cells and particles [2]. The potential antigen receptor repertoire of each individual is estimated to comprise about 2 × 1012 different IG and TR, and the limiting factor is only the number of B and T cells that an organism is genetically programmed to produce [1] This huge diversity results from the complex molecular synthesis of the IG and TR chains and more particularly of their variable domains which, at their N-terminal end, recognize and bind the antigens [2,3].
IMGT®, the international ImMunoGeneTics information system® (http://www.imgt.org) [1], was created in 1989 by Marie-Paule Lefranc at Montpellier, France, Laboratoire d’ImmunoGénétique Moléculaire (LIGM) des Prof G. and M-P. Lefranc (Université de Montpellier and CNRS) to manage the huge diversity of the IG and TR repertoires. For the first time, immunoglobulin (IG) or antibody and T cell receptor (TR) variable (V), diversity (D), joining (J) and constant (C) genes were officially recognized as ‘genes’ as well as were conventional genes [2,3,4,5]. By its creation, IMGT® marks the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics [1]. The IMGT® information system has been online since 1995 (first Internet connexion of IMGT/LIGM-DB occurred at the 9th International Congress of Immunology (ICI) in San Francisco, CA (USA), 23–29 July 1995), marking the 7-year anniversary of the first Internet France-USA connexion on July 28, 1988). IMGT® [6,7,8,9,10,11,12,13,14,15,16,17,18] is an integrated system for genes, sequences and structures of the IG or antibodies, TR and MH of the adaptive immune responses of the jawed vertebrates, as well as of other proteins of the IG superfamily (IgSF) [19] and MH superfamily (MhSF) of vertebrates and invertebrates [20]. Immunoinformatics [1] builds and organizes molecular immunogenetics knowledge to be managed and shared in IMGT®. The accuracy and consistency of IMGT® data and the coherence between the different IMGT® components (databases, tools and Web resources), are based on the IMGT Scientific chart rules, generated from the seven axioms and concepts of IMGT-ONTOLOGY, the first ontology for immunogenetics and immunoinformatics [21,22,23,24,25,26,27,28,29]. As examples, IMGT Scientific chart rules comprise the IMGT® standardized keywords (IDENTIFICATION axiom [30,31] and concepts of identification), the IMGT® standardized labels [32,33,34] (DESCRIPTION axiom [34,35] and concepts of description), the IMGT® gene and allele nomenclature [1,2,3,4,5,36] (CLASSIFICATION axiom [37,38] and concepts of classification), the IMGT unique numbering [39,40,41,42,43,44,45,46] and IMGT Colliers de Perles [47,48,49,50,51,52] (NUMEROTATION axiom [53] and concepts of numerotation).
The IMGT® information system comprises seven databases [54,55,56,57,58,59,60], 17 tools [61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80] and more than 25,000 pages of Web resources. IMGT® dababases are specialized in sequences (i.e, IMGT/LIGM-DB [54,55]), genes and alleles (IMGT/GENE-DB [56]), two-dimensional (2D) (IMGT/2Dstructure-DB) and three-dimensional (3D) structures (IMGT/3Dstructure-DB) [57,58,59]. IMGT/mAb-DB [60] allows querying therapeutic monoclonal antibodies (IG, mAb), fusion proteins for immunological applications (FPIA), composite proteins for clinical applications (CPCA) and related proteins (RPI) of therapeutic interest (with links to amino acid sequences in IMGT/2Dstructure-DB and, if available, to 3D structures in IMGT/3Dstructure-DB). IMGT® tools include (i) for nucleotide sequence analysis, IMGT/V-QUEST [61,62,63,64,65,66] and the integrated IMGT/JunctionAnalysis [67,68] and IMGT/Automat [69,70] tools, and for next generation sequencing, the high-throughput version IMGT/HighV-QUEST [66,71,72,73,74,75] and the downloadable IMGT/StatClonotype [76,77] package (statistical pairwise analysis of the diversity and expression of the IMGT clonotypes (AA) [73] and repertoire comparison in adaptive immune responses), (ii) for genomic analysis, IMGT/LIGMotif [78] (identification and description of new genes in genomic sequences), (iii) for amino acid sequence analysis per domain, IMGT/DomainGapAlign [58,79,80], and (iv) for graphical representations of domains, the IMGT/Collier-de-Perles tool [51] (e.g., IMGT Colliers de Perles of the variable (V), constant (C), groove (G) domains) [39,40,41,42,43,44,45,46,47,48,49,50,51,52]). IMGT® Web resources (‘the IMGT Marie-Paule page’) comprise the IMGT Repertoire (IG and TR, MH and RPI), IMGT Scientific chart, IMGT Education (IMGT Lexique, Aide-mémoire (amino acid physicochemical properties [81], splicing sites), tutorials, etc.). Since 2003, IMGT® has been widely used in the analysis of therapeutic antibodies for humanization and/or engineering [6,9,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100]. The IMGT nomenclature has been endorsed by the International Union of Immunological Societies (IUIS) [84,85] and used, since 2006, in the description of the therapeutic antibodies published by the World Health Organisation (WHO) International Nonproprietary Names (INN) programme [86,87].
We first present the immunoglobulin (IG) or antibody structure and dual function based on molecular genetics in humans. We then highlight the two founding breakthroughs of immunoinformatics, the IMGT® IG and TR gene and allele nomenclature (illustrated here, by the description of the Homo sapiens IGH, IGK and IGL loci), and the IMGT unique numbering and IMGT® Collier de Perles (illustrated here, by the IG V and C domains). We then show how IMGT® databases and IMGT® tools intrinsically bridge IG and TR genes, sequences and structures, according to three axes, the genomic locus description from fish to humans, the analysis of the huge diversity of the adaptive immune repertoires, the IG and TR engineering for therapeutical and clinical applications. Using IMGT state of the art, we illustrate with immunoglobulin (IG) or antibody examples.

2. Immunoglobulin (IG) or Antibody Molecular Genetics

2.1. Human Immunoglobulin (IG) or Antibody Structure and Dual Function

2.1.1. Immunoglobulin Fab and Fc Basic Structure

The discovery of the action of proteolytic enzymes on IgG1 by Porter in 1959 [101] provided the first great insight into antibody structure. The general Y shaped configuration of an immunoglobulin corresponds to two Fab (fragment antigen binding) arms and an Fc (fragment crystallizable) region (Figure 1). These fragments are obtained by papain-digestion of IgG1 or by recombinant engineering. The immunoglobulins (IG) or antibodies share a basic four-chain structure composed of two identical heavy chains of 50–70 kDa and two identical light chains of 25 kDa. An IG comprises 12 domains (for example, IgG1, Figure 1) or 14 domains (IgM or IgE). The heavy chain (i.e., H-gamma1) is made of a variable heavy (VH) domain at the N-terminal end and of three constant heavy (CH) domains with a hinge between CH1 and CH2 (or four CH domains, for the heavy chains H-mu and H-epsilon) (Table 1). The light chain (L-kappa or L-lambda) is made of a variable light (VL) domain (V-kappa or V-lambda) at the N-terminal end and of a constant domain (C-kappa or C-lambda) at the C-terminal end.
The two identical Fab arms of an immunoglobulin (IG) or antibody, each comprises the two N-terminal domains VH-CH1 of the heavy chain associated with the light chain (VL-CL). Each Fab arm is involved, by the N-terminal VH and VL domains, in the antigen recognition and binding (Figure 2).
The Fc region, formed by the C-terminal domains CH2-CH3 of the two heavy H-gamma1 chains, interacts with effector molecules such as the complement component C1q and the Fc receptors [2]. The binding of these effector molecules to the Fc of antibodies coated at the surface of foreign antigens trigger elimination processes. Activation of the classical complement cascade generates a variety of potent biological molecules, which promote phagocytosis, chemotaxis and formation of the membrane attack complex, resulting in cell lysis. The pathway is triggered by the interaction of C1, a protein complex of C1q, C1r and C1s, with antigen-antibody complexes. It is the C1q head region which interacts directly with the immunoglobulin Fc. Binding of antibody-antigen complexes or aggregated immunoglobulins to the Fc receptors triggers cell functions which serve important roles against pathogenic agents as well as in the regulation of antibody production.

2.1.2. B Cell Differentiation

Immunoglobulins are expressed as membrane immunoglobulins (mIG) on the surface of the B lymphocytes (mature B cells and memory B cells) as part of a B cell receptor (BcR) or as soluble immunoglobulins secreted by plasma cells [2] (Figure 3).
The different stages of B cell differentiation from the hematopoietic stem cells into mature B cells which express IgM and IgD, occur in the bone marrow and are antigen independent [2] (Figure 3). The final differentiation stages, from the mature B cells into memory cells or plasma cells that express or secrete IG from various classes or subclasses occur in the germinal centers of the secondary lymphoid organs, and are antigen dependent, and generally requires cooperation between B and T cells [2] (Figure 3).

2.1.3. Membrane Immunoglobulins and B Cell Receptor

The B cell reeptor BcR (Figure 4) comprises an antigen recognition unit constituted by a membrane immunoglobulin (mIG), on mature B cells (IgM, IgD) or on memory B cells (IgM, IgA, IgG, IgE), anchored in the membrane and a signalling coreceptor constituted by two heterodimers CD79A (Ig-alpha, mb-1, MB-1)/CD79B (Ig-beta, B29). The CD79A/CD79B dimers ensure the signal transmission when the membrane IG binds to an antigen. The CD79A and CD79B chains are composed of a single IgSF C-like domain and exist at the cell surface as a disulfide-linked heterodimer and contain, in their cytoplasmic region (CY), an immunoreceptor tyrosine-based activation motif (ITAM) (Figure 4) (IMGT® http://www.imgt.org, IMGT Repertoire (RPI) > IMGT RPI entries from gene to protein > IgSF other than IG or TR > CD79A; ibid > CD79B).
ITAM (indicated by YLYL in Figure 4) are rich in tyrosines and with a consensus (D/E)xxYxx(L/I)x6–8Yxx(L/I) [102]. Cross-linking of the BcR induces the tyrosylphosphorylation of the ITAM on the cytoplasmic region of CD79A and CD79B, and the signalling cascade leading to B cell activation, by recruitment of signalling molecules which belong to at least two families of protein tyrosine kinases (PTK), the Syk family and the Tec family, and provide signal transmission.

2.1.4. Secreted IG

Secreted IgG, IgD and IgE are monomeric, whereas IgM occurs as a pentamer. IgA occurs predominantly as a monomer in the serum and as a dimer in seromucous secretions.

2.2. Human IG Classes and Subclasses: Heavy and Light Chain Types

2.2.1. IG Heavy Chain Types

Human immunoglobulins (IG) or antibodies are divided into five classes: IgM, IgD, IgG, IgA and IgE—each with distinct heavy chains (H-mu, H-delta, H-gamma, H-alpha and H-epsilon, respectively) which differ by their physicochemical properties, antigenic determinants, biological functions and effector properties (Table 2) [103,104,105,106,107,108].
The IgG and IgA classes in humans are further subdivided into four subclasses (IgG1, IgG2, IgG3 and IgG4) and two subclasses (IgA1 and IgA2), respectively, on their heavy chain characteristics (H-gamma1, H-gamma2, H-gamma3 and H-gamma4, H-alpha1 and H-alpha2). Thus, in humans, there is a total of nine heavy chain isotypes (H-mu, H-delta, H-gamma3, H-gamma1, H-alpha1, H-gamma2, H-gamma4, H-epsilon, H-alpha2) (Table 3). The inter H-L and inter H-H disulfide bridges (numbers and positions of the involved cysteines) characterize the human IG classes or subclasses (Table 4).
The nine isotypes are defined by the heavy chain constant region which is encoded by one of the nine functional IGHC genes (IGHM, IGHD, IGHG3, IGHG1, IGHA1, IGHG2, IGHG4, IGHE and IGHA2), listed in the order 5′–3′ in the IGH locus (IMGT®, http//www.imgt.org, IMGT Repertoire (IG and TR)). The kappa or lambda light chains may associate to any heavy chain isotype. Further allotypic variants of certain subclasses or class have also been identified which represent genetic markers for the gamma1, gamma2, gamma3, alpha2 and epsilon heavy chains, and are, consequently called G1m, G2m, G3m, A2m and Em allotypes [83] (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 2. Proteins and alleles > 4. Allotypes > Human (Homo sapiens) IGHC). The allotypes are polymorphic markers detected by serological methods, and are present in different individuals of the same species [83]. The Gm and Am allotypic determinants, inherited in fixed combinations or Gm-haplotypes, are useful tools in the characterization of populations [83,109,110] and genetics of immunoglobulins [111,112,113,114,115,116,117].

2.2.2. IG Light Chain Types

The two light chain types, L-kappa and L-lambda, are common to all five classes. Either light chain type can associate with any of the heavy chain types, but in any particular immunoglobulin, both light and both heavy chains are identical. The kappa to lambda ratio in the serum of healthy individuals is approximately 2 to 1. Four lambda isotypes have been identified by the presence or absence of serological markers (Mcg, Kern and Oz) [2] (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 2. Proteins and alleles > 5. Isotypes: Human (Homo sapiens) IGLC). Three Km allotypes have been characterized [83,109,110] (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 2. Proteins and alleles > 4. Allotypes: Human (Homo sapiens) IGKC).

2.3. IG Chain Variable and Constant Domains

2.3.1. IG Variable Domains

The basic structure of an immunoglobulin (IG) or antibody comprises two identical heavy chains, associated with two identical light chains, kappa or lambda (Figure 5). Each chain folds up into domains of approximately 100 to 110 amino acids. There are two domains for a light chain, and four or five domains for a heavy chain. The N-terminal domain of the light and heavy chains is the variable (V) domain which exhibits an enormous diversity between different IG. Each V domain comprises a beta-sheet framework (FR-IMGT) [33] supporting three hypervariable loops or complementarity determining region (CDR-IMGT) 1, 2 and 3 [32], which are spatially close to each other and constitute the recognition and antigen binding site (Figure 2). The variable domain of a light chain, designated V-KAPPA or V-LAMBDA depending on the light chain type, is a V-J-REGION encoded by two rearranged genes (IGKV and IGKJ, or IGLV and IGLJ, respectively) (Table 1).

2.3.2. IG Constant Domains

The other domains, designated as constant (C) domains, are identical between chains from the same class, subclass and with the same allotypes. The constant region or C-REGION of the heavy chain is encoded by one of the IGHC genes, and comprises three or four constant domains (CH1, CH2 and CH3, with a flexible hinge region between CH1 and CH2, for the H-gamma, H-alpha and H-delta chains of the IgG, IgA and IgD, CH1 to CH4 for the H-mu and H-epsilon chains) [118]. The hinge region located between the CH1 and CH2 of the H-gamma chains is encoded by one exon (for H-gamma1, H-gamma2 and H-gamma4) or several exons (2 for H-delta, 2-5 usually 4 for H-gamma3 [119,120]). In IgM and IgE, the CH2 replaces the hinge, and the CH3 and CH4 correspond to the CH2 and CH3 in IgG, IgD and IgA (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 1. Locus and genes > 5. Gene exon/intron organization IGHC: Human) [2]. The C-REGION of the light chain is encoded by the IGKC gene (for the kappa chains), or one of the IGLC genes (for the lambda chains) [2], and comprises a unique constant domain (C-KAPPA or C-LAMBDA, respectively).
In intact immunoglobulins, the domains usually associate into pairs through multiple non-covalent lateral interactions. However the CH2 of the IgG, IgD and IgA, and the equivalent CH3 of the IgM and IgE are unpaired but stabilized with interposed N-linked, branched carbohydrate chains. All human IG heavy chains are glycosylated [121] (IMGT® http://www.imgt.org, IMGT Education > IMGT Lexique > Immunoglobulin (IG) or antibody glycosylation). The number of potential N-glycosylation sites per heavy chain is reported in Table 3. The positions of the Asn (N) of the potential N-glycosylation sites are highlighted in the IGHC Protein display (N in green) or are identified by the underlined N-X-S/T (Asn-X-Ser/Thr) motif where X is any AA except Pro). O-glycosylation characterizes the hinge of the H-delta and H-alpha1 chains.
The molecular structure of the IG chains in domains (12 for IgG, IgD and IgA, 14 for IgM and IgE) is extensively used for the construction and expression of engineered antibodies (IMGT® http://www.imgt.org, IMGT/mAb-DB) [60].

2.4. Synthesis and Expression of the Immunoglobulins (IG) or Antibodies

2.4.1. IG Molecular Synthesis Characteristics

The variable domain of a heavy chain, designated as VH, is a V-D-J-REGION encoded by three rearranged genes (IGHV, IGHD and IGHJ) (Table 1). In humans, the genes encoding the heavy chains and the light chains, kappa and lambda, are located in the IGH, IGK and IGL loci on chromosome 14 (14q32.33), 2 (2p11.2) and 22 (22q11.2), respectively [2]. The synthesis of the IG heavy and light chains requires gene rearrangements, at the DNA level [122,123,124], in the IGH, IGK and IGL loci during the B cell differentiation in bone marrow (Figure 3). The synthesis of the chains of the antigen receptors, immunoglobulin (IG) or antibody [1,2], and T cell receptors (TR) [1,3], includes several molecular mechanisms that occur at the DNA level and are unique to the B and T cells (Figure 6): (a) combinatorial V-D-J or V-J rearrangements of the variable (V), diversity (D) and joining (J) genes (b) N-diversity resulting from the exonuclease trimming at the ends of the V, D, and J genes and the random addition of nucleotides at the V-(D)-J junctions before the gene ligation, and (c) later, during B cell differentiation, for the IG, somatic hypermutations (SHM) in the rearranged V-(D)-J genes. During the transcription in B or T cells, the rearranged V-(D)-J gene which codes the V domain is spliced to a C gene that codes the C region. Chronologically in B cells, the synthesis of the H-mu chains precedes that of the light chains.

2.4.2. Synthesis of the H-Mu Chains: D-J and V-D-J Rearrangements in the IGH Locus

The IGH locus comprises variable (V), diversity (D), joining (J) and constant (C) genes. The variable domain of a heavy chain, or VH, is a V-D-J-REGION generated by the junction at the DNA level of three genes: a variable gene IGHV, a diversity gene IGHD and a joining gene IGHJ (Figure 7). The synthesis requires two successive rearrangements. First, one of the IGHD genes is joined to one of the IGHJ genes with deletion of the intermediary DNA as an excision loop, then one of the IGHV genes is joined to the partially rearranged D-J gene to generate a completely rearranged IGHV-D-J gene. This second rearrangement is also accompanied by the formation of an excision loop which is cleaved off. The rearranged IGHV-D-J gene is transcribed with the IGHM gene, the most 5′ IGHC gene in the locus, into a IGHV-D-J-M (or IGHV-D-J-Cmu) pre-messenger RNA. The IGHM gene encodes the four domains (CH1 to CH4) of the H-mu constant region. After splicing of the pre-messager RNA, translation of the messenger RNA, and elimination of the signal peptide by a peptidase in the endoplasmic reticulum, a mature H-mu chain is produced [2].

2.4.3. Synthesis of the L-Kappa and L-Lambda Chains: V-J Rearrangements in the IGK and IGL Loci

The kappa (IGK) locus and the lambda (IGL) locus comprise variable (V), joining (J) and constant (C) genes. The variable domain of a L-kappa or L-lambda chain, V-KAPPA or V-LAMBDA, is a V-J-REGION, generated by the junction, at the DNA level, of two genes: a variable and a joining genes, with deletion of the intermediary DNA to create a rearranged IGKV-J gene in the IGK locus (Figure 8), or a IGLV-J gene in the IGL locus.
The rearranged IGKV-J (or IGLV-J) gene is transcribed with the IGKC gene (or one of the IGLC genes) into a IGKV-J-C (or IGLV-J-C) pre-messenger RNA. The unique IGKC gene, or one of the functional IGLC genes, with their single exon, encodes the single domain of the constant region of the L-kappa or L-lambda chains, respectively. After splicing of the pre-messenger RNA, translation of the messenger RNA and elimination of the signal peptide from the polypeptide chain in the endoplasmic reticulum, a mature L-kappa (or L-lambda) chain is produced [2].

2.5. Origin of the Variable Domain Diversity of the Immunoglobulins

2.5.1. Overview

The diversity of the variable domains of the immunoglobulin chains arises mainly from combinatorial diversity, V-J and V-D-J junctional diversity and somatic hypermutations [2]. In addition, within an immunoglobulin, the pairing of the variable domains of the heavy chain (VH) and of the light chain (VL, V-KAPPA or V-LAMBDA), to form the antigen recognition and binding site, creates an additional degree of diversity [2].

2.5.2. Combinatorial Diversity

The combinatorial diversity is created by the somatic V-D-J and V-J rearrangements. The somatic IGKV-J, IGLV-J and IGHV-D-J rearrangements require the presence of recombination signal (RS) sequences which are located in 3′ of the V genes, 5′ of the J genes, and on both sides of the D genes [2,125] (Figure 9). The RS comprise two highly preserved motifs, a palindromic heptamer and a nonamer rich in “a” or “t”, separated by a not conserved spacer of 12 ±1 or 23 ±1 nucleotides. They are recognized by the recombinase enzymes (recombination activating 1 (RAG1) and recombination activating 2 (RAG2)) [126,127]. Efficient rearrangements occur between RS of different lengths, that is one with a 12 ± 1 spacer, and another one with a 23 ± 1 spacer (12/23 joining rule) [128] (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 1. Locus and genes > 7. Gene tables > Recombination signals sequence logos; ibid: IMGT Education > Tutorials > Immunoglobulins and B cells > Molecular genetics of immunoglobulins). The potential repertoire resulting from the combinatorial diversity depends on the number of V, D and J genes, and on their functionality.

2.5.3. Junctional Diversity

The junctional diversity is represented by the V-J junction diversity of the L-kappa chains which creates variability of the amino acid at position 115 (IMGT unique numbering) of the rearranged CDR3 [125,129], and by the N-diversity (N, for nucleotides) essentially observed at the V-D-J junctions of the IG heavy chains, and which represents the major source of the CDR3 diversity. In 1982 Alt and Baltimore proposed a model that explains the mechanism of N-diversity [130]. It results from the excision of nucleotides by an exonuclease at the ends of the V, D and J genes during rearrangement (3′ end of the V-REGION, 5′ end of the J-REGION and/or both ends of the D-REGION), followed by the addition of nucleotides randomly via the DNA nucleotidylexotransferase (DNTT, terminaldeoxynucleotidyltransferase TdT) [131]. This addition of nucleotides preferentially involves ‘g’ nucleotides and is template independent. If the ends of the coding regions are intact (no deletion due to the exonuclease), P-nucleotides may be observed adjacent to these coding regions [132]. P-nucleotides are short sequences of 1 to 3 nucleotides palindromic (inverted repeat) to the intact coding end (3′ end of the V-REGION, 5′ end of the J-REGION and/or both ends of the D-REGION. P-nucleotides result from the dissymmetric opening of the hairpin formed at the extremities of the coding regions during V-J or V-D-J rearrangements [133].

2.5.4. Somatic Hypermutations

Somatic hypermutations (SHM) appear during the B cell maturation in the germinal centers of the secondary lymphoid organs (spleen and lymph nodes) (Figure 3). They specifically affect the IG rearranged V-J and V-D-J genes during the antigen dependent stages of differentiation and represent a major mechanism for the generation of diversity of the variable domains of antibodies. This process of somatic hypermutation involves the introduction, to a high rate of point mutations in rearranged VH and VL (V-KAPPA or V-LAMBDA) sequences [134,135,136,137,138,139]. Other genes expressed in B cells are not changed by the mechanisms of somatic hypermutation. SHM occurs at a frequency estimated 10−3 per base in a B cell which is roughly 106 times more as frequent as the rate of spontaneous mutations in other cells. Somatic hypermutation shares with class-switch recombination (CSR) common mechanisms: they are both initiated by activation induced cytidine deaminase (AICDA, AID) which necessitates transcription to target single-strand DNA. AICDA induces the deamination of cytosine (c) to uracil (u). The replication system transforms the uridine in thymidine leading to a c > t transition (and g > a transition on the opposite strand). In SHM, the uracil is removed by uracil DNA glycosylase (UNG), and this abasic site is further processed by either the DNA base excision repair (BER) pathway or the DNA mismatch repair (MMR) systems. The DNA lesions are repaired by error-prone DNA polymerases, leading to nucleotide transitions and transversions [139].

2.6. Expression of the Heavy Chains and IG Classes

2.6.1. Coexpression of the Membrane H-Mu and H-Delta Chains

During its differentiation, an immature B cell becomes a naive mature B cell which expresses simultaneously membrane IgM and IgD classes (Figure 3). The VH domains of the H-mu and H-delta chains are identical, and are encoded by the same rearranged V-D-J-REGION. The mechanism of expression of the H-delta isotype differs from the expression of other isotypes in that its expression depends on a splicing mechanism and not on the class switching mechanism like the other isotypes. IgD is coexpressed with IgM on the surface of naive mature B cells (only case where two different IG classes are expressed by the same cell).
The IGHM and IGHD genes are located nearby in the IGH locus. B cells which express IgM and IgD produce two types of RNA premessengers of the IGH-V-D-J-gene, the first ones ending after the IGHM gene, and the second ones, containing IGHM and IGHD, ending after the IGHD gene and long of about 20 kilobases (kb) (the distance separating IGHM and IGHD being 6 kb in the human IGH locus). The RNA premessengers ending after the IGHM gene are spliced to produce mature IGHV-D-J-Cmu mRNA, translated into membrane H-mu chains. The RNA premessengers ending after the IGHD gene undergo splicing which removes the IGHM gene and produces mature IGHV-D-J-Cdelta mRNA, translated into membrane H-delta chains [140,141,142]. It is not excluded that this long premessager is also used to produce H-mu chains.

2.6.2. Expression of H-Gamma, H-Epsilon and H-Alpha Chains: Class Switch Recombination

The mature B cells which enter the lymph nodes express the IgM and IgD classes (Figure 3). After antigenic stimulation, activated B cells proliferate and can differentiate to produce other isotypes: the class switch recombination (CSR) occurs in the lymph nodes when B cells mature as a result of B and T cell cooperation. The activated B lymphocyte by its major histocompatibiliy MH2 proteins comes into contact with a T lymphocyte CD4 +. Recognition of B cell peptide/MH2 (p/MH2) by the T cell receptor (TR) leads to the T cell activation (expression of cytokines and of CD40LG on the T cell surface). The interaction between the CD40 (TNFRSF5) constitutively expressed on the B cell and its ligand CD40LG expressed on the surface of activated T cell leads to the expression of cytokin receptors on B cells, which in presence of the interleukins secreted by the T cell, provide the signal for the B cell to switch from IgM and IgD to IgG (IgG1, IgG2, IgG3 or IgG4) or IgA (IgA1 or IgA2) or IgE classes. This switch results in a change of the constant region of the heavy chain, while maintaining the expression of the same antibody specificity. In the switch recombination, the rearranged IGHV-D-J gene, previously associated with the IGHM gene in a H-mu messenger RNA of a B cell expressing IgM, is brought into the proximity of one of the other IGHC genes, downstream (more in 3′) in the locus, for example IGHG1 [2] (Figure 10).
The switch recombination occurs between switch sequences located at about 2 kb in 5′ of each IGHC gene (except IGHD) (Figure 10). The switch sequences, of about 2 kb, are composed of 20–80 nucleotide motifs repeated in tandem. These motifs contain short ‘gggct’ and ‘gagct’ repeats and, near the recombination site, ‘tggg’ or ‘tgag’. The class switch involves the recombination of the Smu sequence with the S sequence of another IGHC gene, for example with a Sgamma sequence in the case of a switching from IgM to IgG, resulting in the deletion of the IGHC genes located between Smu and the Sgamma of the IGHG gene used (Figure 10). This occurs by the formation of excision loops which are cleaved off [143,144,145,146,147]. For example, in the case of switching from IgM to IgG1 (Figure 10), the IGHM, IGHD and IGHG3 genes are deleted [2].
At the molecular level, CSR shares a number of features with SHM. It necesitates transcription of the C regions which starts from a small exon (called I) located upstream of each switch region, resulting in a sterile J-C transcript which does not encode any protein. As mentioned above, CSR is also initiated by AICDA. Transcription allows the separation of both DNA strands which are then targeted by deamination of multiple ‘c’ nucleotides by AICDA. This is followed by generation of single-strand breaks by the BER system (single-strand break by the apurinic/apyrimidic endonuclease 1 (APE1) at a UNG abasic site), which may be converted into double-strand breaks by the MMR proteins. After loop excision of the intervening sequence, fusion of the switch regions is thought to be mediated by the non-homologous end-joining (NHEJ) system [148,149].

2.6.3. Expression of H-Delta Chains from IgM IgD+ Cells

Only a minority of normal plasma cells and rare B cell malignancies express exclusively IgD (IgMIgD+ B cells). The low frequency has been explained by the lack of a recognizable switch sequence between IGHM (Cmu) and IGHD (Cdelta). However, a region, designated as sigma delta, contains a relatively high content of pentameric repeats with an extremely “g-rich” area and appears to function as a vestigial switch recombination site leading to the expression of delta chains in germinal center B cells and plasma cells [150,151,152].

2.6.4. Expression of Membrane and Secreted Immunoglobulins

Heavy chains of membrane and secreted immunoglobulins differ in their C-terminal region. The heavy chains of the membrane IG on the B cell surface have a hydrophobic C-terminal end which holds them anchored in the plasma membrane, whereas the heavy chains of the plasma cell secreted IG have an hydrophilic end [153]. Expression of membrane and secreted IG results from an alternative splicing of the heavy chain transcripts (Figure 11).
The C-terminal region of the membrane H-mu chain is encoded by two small exons, M1 and M2 located at about 2 kb in 3′ of the CH4 exon [154], M1 encodes 39 amino acids, whereas M2 only encodes two amino acids (Figure 11). These 41 amino acids represent the anchor region of the membrane H-mu chain which comprises an extracellular region (CO) of 13 amino acids between the CH4 domain and the membrane, a hydrophobic transmembrane region (TM) of 27 amino acids and a short cytoplasmic region (CY) of one amino acid. The C-terminal region of the secreted H-mu chain comprises 20 amino acids encoded by the 3′ end of the CH4 exon (designated as CHS) [2].
For the synthesis of a membrane H-mu chain, it is the poly A site located in 3′of the M2 exon, and the splicing site located in the CH4 exon, at the 5′ limit of CHS which are used (Figure 11). This splicing deletes the CHS sequence and its stop codon, as well as the sequence between CH4 and M1, and between M1 and M2. For the synthesis of a secreted H-mu chain, it is the poly A site located 103 bp from the 3′ end of the CH4 exon, and the stop codon at the 3′ end of CH4 which are used (Figure 11). One cell can therefore present the two H-mu RNA precursors and the relative expression of a H-mu chain, membrane or secreted, depends on a control in the selection of the polyA site used [155]. The organization of the 3′ region of the IGHD gene differs due to the presence of a small independent CHS exon located at 1.9 kb in 3′ of the CH3 exon, and which encodes the nine last amino acids of the secreted H-delta chains. The M1 and M2 exons, located at 0.8 kb and 1.1 kb in 3′ of CHS, respectively, encode the TM and CY, M1 encodes 53 amino acids whereas M2 encodes two amino acids. The expression of the membrane and secreted H-delta chain depends on the selection of the poly A used: poly A in 3′ of the IGHD exon M2, for the synthesis of the membrane H-delta chain, or poly A in 3′ of CHS for the synthesis of the secreted H-delta chain [156].
The expression of the membrane and secreted H-gamma, H-alpha and H-epsilon chains follows the same mechanisms as those described for the H-mu chain, the CHS being part of a domain (CH3 or CH4 depending on the IGHC gene).

2.7. Regulation of the Rearrangements and Chain Expression

2.7.1. Allelic and Isotypic Exclusion. Rearrangement Chronology

The B cells, and the plasma cells which derive from them, display: - allelic exclusion: in most cases, the only productive genes are either those of the paternal chromosome, or those of the maternal chromosome, but usually not the two together (functional haploidy); - isotypic exclusion: a single type of light chain, L-kappa or L-lambda, and usually a single type de heavy chain belonging to a given subclass, are synthesised.
Molecular analysis has shown that the excluded allele is usually either not rearranged, or unproductively rearranged (IGK locus in B cells synthesising a lambda chain) [157,158].
During the B cell differentiation, the IGH locus on one chromosome 14 undergoes first a D-J, then a V-D-J rearrangement. A productive rearrangement allows the synthesis of a H-mu chain in the cytoplasm of the pre-B cells.The H-mu chain is expressed at the surface of the pre-B cells in association with a lambda-like chain (IGLL1) and a V-pre-B (VPREB1) chain, which constitute together the pre-B cell receptor [159,160] (Figure 3) [2].
The expression of the surface IgM at a later stage requires the synthesis of L-kappa or L-lambda chains, that is a productive V-J rearrangement of the IGK or IGL loci. It is the expression of the pre-B cell receptor at the surface of a pre-B cell which gives the signal which inhibits further IGHV-D-J rearrangements on chromosome 14 (Figure 12), and the signal which starts the light chain V-J rearrangements. Chronologically the V-J rearrangements of the IGK locus usually precede those of the IGL locus [157,158]. A chromosome 2 will be rearranged first. If the resulting rearrangement is productive, L-kappa chains will be synthesized, which will allow the expression of IgM, the other chromosome 2 and both chromosomes 22 remaining germline. If the first rearrangement is unproductive, the other chromosome 2, then the chromosome 22 will be rearranged until a productive rearrangement allows the synthesis of a light chain. Thus, in a B cell which produces antibodies, generally only one chromosome 14 is productively rearranged (expressing a productive H-mu chain) whereas only one chromosome 2 or 22 is productively rearranged (expressing a productive L-kappa or L-lambda chain). IG genes on the other chromosomes are either germline, or rearranged but unproductive, or deleted.

2.7.2. Regulation of the IG Gene Expression: Enhancers

In order to synthesize complete IG heavy and light chains, the rearranged IGHV-D-J and IGKV-J (or IGLV-J) genes are transcribed with the IGHM gene and with the IGKC (or one IGLC) genes, respectively. The transcription level, low in the first B cell development stages, becomes very high in the plasma cells which result from the clonal proliferation [161]. The V genes possess a promoter sequence in 5′ of L-PART1 (exon encoding the first part of the leader peptide) [162] and can be transcribed before they rearrange. These germline transcripts correspond to an opening, and therefore to better accessibility of the chromatin before the rearrangements. However, that transcription remains low. The C genes can also be transcribed from promoter sequences located upstream of the J genes but again the level of transcription is low and the transcripts are degraded in the nucleus [163].
Murine and human IG transcription enhancers are the first enhancers described in the DNA of eucaryote cells [164,165,166,167]. By different approaches several groups have simultaneously shown that a DNA segment located between the most 3′ IGHJ and the switch Smu sequence is not only able to increase the transcription, but also possesses the properties of the enhancers previously described in the viruses. These enhancers (i) activate the transcription whatever their orientation and their position (in 5′ or 3′) relative to the gene promoter, (ii) only activate the promoters located in cis, that is on the same chromosome, and (iii) activate in vitro genes others than those to which they are normally associated in vivo and increase their transcription, even when located at a distance of several kb [168].
The presence of an enhancer in the Homo sapiens IG loci has been demonstrated between the most 3′ IGHJ and the IGHM gene [169], and between the most 3′ IGKJ and the IGKC gene [170,171]. When a IGHV-D-J or IGKV-J rearrangement occur, the promoter sequence in 5′ of the IGHV or IGKV genes is not modified, but this promoter is now closer to the enhancer sequences located in 3′ of the IGHJ or IGKJ genes. By decreasing the distance between the V gene promoter and the enhancer, the IGHV-D-J and IGKV-J rearrangements allow the interaction of factors binding to these sequences, and consequently an increased trancription of the IGHV-D-J-Cmu and IGKV-J-Ckappa transcripts. During the switch recombination, the IGH enhancer, being localized at more than 1 kb upstream from the Smu sequence, is retained in the locus and can therefore be used for the expression of all the heavy chain classes and subclasses. A second enhancer has been described in 3′ of the IGKC gene [172]. Two 3′ enhancers have been characterized in the Homo sapiens IGH locus, one downstream of IGHA1, and another one downstream of IGHA2, within 25 kb of each gene, respectively [173]. These enhancers were duplicated along with part of the IGH locus [114,174,175,176], which occurred between about 30 and 60 million years ago. An enhancer has also been localized in the Homo sapiens IGL locus in 3′ of IGLC7, the most 3′ IGLC gene [177]. This enhancer consists of three modules located 6, 9.8 and 11.7 kb downstream of IGLC7 [178].

2.8. Structural and Biological Properties of the Secreted Immunoglobulins

2.8.1. IgM

IgM represents about 10% of total serum immunoglobulins in human and is largely confined to the intravascular pool. It exists almost exclusively as a polymeric form (pentamer) made of five monomer units associated with the polypeptide designated as J (joining) chain [179]. IgM is the predominant antibody produced early in the immune response. Pentameric IgM is decavalent with small antigens but only pentavalent with larger antigens, presumably due to steric hindrance (Table 2). A disulfide bridge connects the H-mu chains between CH2 and CH3. Disulfide bridges between the CH3 and the tailpieces of the different monomers are involved in the IgM polymerization. A single J chain is present per IG. This amounts to 1.5% of pentameric IgM. The conserved features of the J chain (16 kDa) is the presence of a N-glycosylation site Asn-Ile-Ser and of eight cysteines. Six of the cysteines form three intradisulfide bridges, and two are linked to the penultimate cysteine of two H-mu chains. The five ‘Fc’ (or paired CH3 and CH4 of each monomer) are arranged into a planar pentamer (Fc5) (IMGT/3Dstructure-DB PDB 2rcj) [180]. Electron microscope studies have revealed that uncomplexed IgM has a planar and ”star” conformation with the 10 Fab arms protruding out from the Fc5. On binding to an antigenic surface, the F(ab’)2 dislocate out of the plane of the central Fc5 disc, giving a “staple” or “crab-like” (“table-like”) conformation [104]. In this latter conformation, IgM is a very efficient activator of the classical complement pathway. C1q interacts directly with the CH3 domain of the IgM.

2.8.2. IgD

IgD represents less than 1% of total serum immunolobulins. IgD has a long and extended hinge region of 58 amino acids encoded by two exons, which allows great flexibility in the relative position of the two Fab arms. The hinge N-terminus half of 34 AA encoded by the first exon is heavily O-glycosylated (four to seven oligosaccharides). The hinge C-terminus half of 24 AA encoded by the second exon is rich in charged amino acids (2 Arg, 6 Lys, 9 Glu) and is very susceptible to proteolytic attack, whch makes serum IgD unstable (Table 2).

2.8.3. IgG

IgG is the major antibody class in normal human serum forming about 70% of the total immunoglobulins. IgG is a monomer and is evenly distributed between intravascular and extravascular pools. IgG is the predominant antibody of the secondary immune responses. There are four subclasses in humans.
The effector molecules binding IgG Fc are C1q, the Fcgamma receptors (FcγR) present on the surface of many cells of the immune system, the neonatal Fc receptor (FCGRT, FcRn) which transports maternal IgG to the foetus, and the bacterial Fc receptors, protein A and protein G, which are believed to mask the bacteria through immobilized immunoglobulins on their surface.
C1q interacts directly with the CH2 domain of IgG. Binding to monomeric IgG is weak, but when several IgG bind to, and effectively aggregate at an antigenic surface, two or more C1q heads may bind simultaneously leading to tighter binding and activation of the complement cascade. There are marked differences in ability to activate complement: IgG1 and IgG3 activate well, IgG2 less well, IgG4 not at all (Table 2).
Three classes of human FcγR have been described: FcγRI (CD64) are receptors with high affinity for IgG Fc and possess three C-like extracellular domains, FcγRII (CD32) and FcγRIII (CD16) are receptors with lower affinity and possess two C-like domains [181]. FcγRI, FcγRII and FcγRIII on macrophages and Natural Killer (NK) cells mediate antibody-dependent cell-mediated cytotoxicity (ADCC) and phagocytosis, whilst FcγRI, FcγRII and possibly FcγRIII on neutrophils are able to trigger release of activated oxygen species. The cellular responses also comprise endocytosis, enhanced antigen presentation and regulation of the antibody production, depending on the particular FcγR isoform and the type of cell [181]. FcγRI (CD64) displays high affinity for monomeric human IgG1 and IgG3, whilst the affinity for human IgG4 is about 10-fold lower and human IgG2 does not bind. The human FcγRII (CD32) binds IgG1 and IgG3. IgG4 does not bind, whilst the binding of IgG2 is controlled by an allotypic determinant in certain forms of the receptor. FcγRI and FcγRII appear to recognize overlapping but non-identical sites in the lower hinge region of IgG.
The crystal structures of the Fc of human IgG1 in complex with Staphylococcus aureus protein A [182], or in complex with streptococcal protein G [183], and that of Fc of rat in complex with FCGRT (FcRn) [184] revealed binding sites at the interface between the CH2 and CH3 Fc domains. The crystal structure of the human IgG1 Fc fragment-FcγRIII complex shows that FcγRIII binds to the two CH2 domains and lower hinge of the Fc [185].

2.8.4. IgA

IgA1 and IgA2

IgA forms about 15–20% of total serum immunoglobulins where it occurs as a monomer. IgA is the predominant immunoglobulin in seromucous secretions such as saliva, tracheobronchial secretions, colostrum, milk and genitourinary secretions, where it is found in a dimeric form known as secretory IgA (sIgA). There are two subclasses of IgA, with IgA1 being the predominant (80–90%) subclass in serum. In contrast to serum IgA, secretory IgA shows roughly equal proportions of the two subclasses. The two IgA subclasses differ in the hinge: IgA1 has an effective structural hinge of 19 amino acids containing eight potential glycosylation sites, whereas IgA2 has a short structural hinge of six amino acids including five prolines which, by its nature, is resistant to proteolysis. A further peculiarity of IgA2 is that for most molecules (allotype A2m1), the light chain is disulfide bridged, not to the heavy chain but to the light chain of the other Fab unit. The CH2 domain of both IgA suclasses has seven cysteines. Two are involved in the usual intradomain disulfide bridge, another two in a second intradomain bridge and one is thought to be free, possibly for interaction with secretory component. The remaining two form inter-H disulfide bridges. There is a further intradomain disulfide linkage in CH1 in addition to the conserved domain disulfide.

Secretory IgA

The dimer involves J chain (16 kDa) and another polypeptide known as secretory component (SC) (70 kDa). Selective transport of polymeric IgA through epithelial cells depends on the incorporation of the J chain into the polymers. Two of the J chain cysteines are linked to the penultimate cysteine of the alpha chains. The J chain, which was identified initially in human IgA [186] amounts to 4% of dimeric human IgA. The SC, unlike IG and J chain which are produced by plasma cells, is synthesized in epithelial cells. With extra segments to attach it to the epithelial cell membrane, SC serves as a receptor for polymeric IG (poly-IG) containing J chain, i.e., IgA (or IgM). After endocytosis and transport, cleavage of the poly-IG/poly-IG receptor complex releases poly-IG (poly-IG with the J-chain) associated with SC. This process is particularly important for secretory IgA release. The poly-IG receptor is composed, in its poly-IG binding portion (i.e., SC) of five highly conserved C-like domains of approximately 100 amino acids. SC (70 kDa) probably interacts non-covalently with the Fc and J chain and forms a single disulfide bridge to one of the monomers of dimeric IgA.

IgA Effector Function

IgA can activate the alternative complement pathway and bind to specific FcαR. FcαR is present on monocytes, macrophages, neutrophils and eosinophils and can mediate ADCC, phagocytosis and degranulation. FcαR has two extracellular C-like domains and spans the membrane once. FcαR binds at a site in the IgA CH2 domain.

2.8.5. IgE

IgE [187,188,189], though a trace IG in serum, is found bound to receptors, specific for the IgE Fc, on the cell surface of mast cells and basophils in all individuals. IgE is involved in protection against helminthic parasites [190] but is most commonly associated with atopic allergies. The ability of IgE-Fc to undergo conformational changes is critical for IgE function [191]. IgE binds to two principal receptors, FCER1 (FcεRI, tetrameric IgE Fc receptor I), the “high affinity” receptor for the IgE Fc, on the surface of mast cells and basophils, and FCER2 (IgE Fc receptor II, FcεRII, CD23), the “low affinity“ receptor for IgE Fc, a Ca2+ -dependent C-type lectin and a B cell specific antigen [192].
FCER1 is tetrameric and consists of an alpha chain (FCER1A, IgE Fc binding site) chain, a beta chan (FCER1B, which amplifies the signal), and two disulfide linked gamma chains (FCER1G, where the downstream signal initiates). FCERI is expressed on tissue mast cells, blood basophils, airway epithelial and smooth muscle cells and intestinal epithelial cells [193,194]. Aggregation of the receptors by binding of multivalent antigens, such as pollen, to prebound IgE results in cell degranulation and release of pre-formed mediators of inflammation causing an allergic response and an immediate hypersensitivity response that, if intense, can cause anaphylactic shock and even death. The FCERIA binding site on IgE involves CH3 (next to the interface between CH2 and CH3). The crystal structure of the human IgE Fc and its high-affinity FCERIA reveals that the receptor binds one Fc asymmetrically. The CH3 of each chain of the Fc is bound to two different sites of the C-like domain [D2] of FCERIA (IMGT/3Dstructure-DB, PDB code: 1f6a) [195].The IgE Fc is highly flexible adopting an acutely bent conformation when unbound (IMGT/3Dstructure-DB: PDB code: 2y7q) [196], partially bent conformation in a complex with omalizumab Fab (IMGT/3Dstructure-DB, PDB code: 5g64) [197], fully extended in a complex with aεFab (IMGT/3Dstructure-DB, PDB code: 4j4p) [198] and with the 8D6 Fab (IMGT/3Dstructure-DB, PDB code: 6eyo) [199].
FCER2 (FcεRII, CD23), the low-affinity receptor for IgE is present on monocytes, B cells, T cells, gut and airway epithelial cells, plays a role in cytotoxicity against parasites such as schistosomes. FCER2 has essential roles in B cell growth and differentiation, and the regulation of IgE production [200,201,202,203]. It also exists as a soluble secreted form [204], then functioning as a potent mitogenic growth factor. The interaction between IgE and FCER2 appears to require the presence of the IgE CH2, CH3 and CH4 domains, the latter serving to promote the dimerization of the two epsilon chains, necessary for receptor binding. Crystal structure of IgE bound to its B cell FCER2 reveals a mechanism of reciprocal allosteric inhibition with the high affinity receptor FCER1 (IMGT/3Dsructure-DB, PDB code: 4gko) [205].
Antibodies classically bind antigens via their complementarity determining regions, but an alternative mode of interaction involving V-domain framework regions has been observed for some B cell “superantigens”. The crystal structure of an antibody from an allergic individual, bindng to the grass pollen allergen Phl p 7 has shown that both modes of interaction were employed simultaneously with binding of two antigen molecules (IMGT/3Dstructure-DB, PDB code: 5otj) [206].

3. Immunoglobulin Genes: IMGT® Gene and Allele Nomenclature

3.1. IMGT® Standardized Genes and Alleles (Classification)

3.1.1. IG and TR Genes and Concepts of Classification: Birth of IMGT® and Immunoinformatics

The creation of IMGT® in 1989 by Marie-Paule Lefranc (LIGM, UM, CNRS), during the 10th Human Genome Mapping Workshop (HGM10, New Haven, CT, USA, 11–17 June 1989) gave birth to immunoinformatics, a new science at the interface between immunogenetics and bioinformatics [1]. Indeed, for the first time, immunoglobulin (IG) or antibody and T cell receptor (TR) variable (V), diversity (D), joining (J), and constant (C) genes were officially recognized as “genes” as well as were the conventional genes, with the entry of all genes of the Homo sapiens TRG locus in the HGM database [207,208]. This major breakthrough allowed IG and TR genes and alleles of the complex and highly diversified adaptive immune responses to be managed in genomic databases and tools. IMGT® gene and allele names are based on the concepts of classification of ‘Group’, ‘Subgroup’, ‘Gene’ and ‘Allele’ [37,38,84,85]. ‘Group’ allows to classify a set of genes which belong to the same multigene family, within the same species or between different species. For example, there are 10 groups for the IG of higher vertebrates: IGHV, IGHD, IGHJ, IGHC, IGKV, IGKJ, IGKC, IGLV, IGLJ, IGLC. ‘Subgroup’ allows to identify a subset of genes which belong to the same group, and which, in a given species, share at least 75% identity at the nucleotide level, e.g., Homo sapiens IGHV1 subgroup. Subgroups, genes and alleles are always associated to a species name (84,85). An allele is a polymorphic variant of a gene, which is characterized by the mutations of its sequence at the nucleotide level, identified in its core sequence (V-REGION, D-REGION, J-REGION, C-REGION) and compared to the gene allele reference sequence, designated as allele *01. For example, Homo sapiens IGHV1-2*01 is the allele *01 of the Homo sapiens IGHV1-2 gene that belongs to the Homo sapiens IGHV1 subgroup which itself belongs to the IGHV group (84,85) (Figure 13). For the IGH locus, the constant genes are designated by the letter (and eventually number) corresponding to the encoded isotypes (IGHM, IGHD, IGHG3…), instead of using the letter C. IG and TR genes and alleles are not italicized in publications.
The IMGT IG and TR gene names [1,2,3,4,5] were approved by the Human Genome Organisation (HUGO) Nomenclature Committee (HGNC) in 1999 and were endorsed by the WHO-IUIS Nomenclature Subcommittee for IG and TR [84,85]. The IMGT IG and TR gene names, with the allele *01 of the IMGT reference sequences, have been provided since 1999, via HGNC, to NCBI (first ‘LocusLink’, then ‘Entrez Gene’, now superseded by ‘Gene’) [2,3,4,5].
IMGT human IG and TR gene names have been integrated in the CLASSIFICATION axiom [37,38] of IMGT-ONTOLOGY [29] (IMGT® http://www.imgt.org, IMGT Index > IMGT-ONTOLOGY), on the NCBO BioPortal and, on the same site, in the HUGO ontology and in the National Cancer Institute (NCI) Metathesaurus. Since 2006, IMGT gene and allele names have been used for the description of the therapeutic mAb and FPIA from the WHO-INN programme [86,87]. Amino acid sequences of the IMGT human IG and TR constant genes (e.g., Homo sapiens IGHM, IGHG1, IGHG2) were provided to UniProt in 2008, and those of the IMGT human IG variable genes with their IMGT gene definition (e.g., P23083, Homo sapiens IGHV1-2, Immunoglobulin heavy variable 1-2), in 2016. There are reciprocal direct links between the gene entries of IMGT/GENE-DB [56], the IMGT® gene database, and HGNC, NCBI Gene, Ensembl, Vega and UniProt.

3.1.2. Homo sapiens IG Genes and Concepts of Identification and Description

To date (July 25, 2020), four hundred sixty-five IG genes have been identified in Homo sapiens, 389 of them in Major Locus and 76 in orphon sets [56] (Table 5). Genes of the major loci participate to the IG chain synthesis whereas those of the orphon sets do not.
Given the complexity of the IG synthesis which generates a huge diversity of sequences, thirty-two molecular entity types have been defined. They are identified with IMGT standardized keywords [30], based on the “GeneType”, “ConfigurationType”, and “MoleculeType” which define them (IDENTIFICATION axiom [30,31]). The ten most classical IG and TR entity types are shown in Table 6. To each molecular entity type corresponds a molecular entity prototype. These prototypes are described with IMGT standardized labels [34] (DESCRIPTION axiom [34,35]). The V-GENE and V-D-J-GENE are shown as examples (Figure 14). Other prototypes are available on the IMGT® web site (IMGT® http://www.imgt.org, IMGT Scientific chart > 1. Sequence and 3D structure identification and description > IMGT prototypes table). The ten molecular entity types are reported in the IG synthesis in Figure 15, bridging genes, sequences and proteins.

3.2. Homo sapiens IGH Locus and Genes

3.2.1. Organization of the Homo sapiens IGH Locus

The Homo sapiens IGH locus is located on chromosome 14 [209], at the telomeric extremity of the long arm [210,211], at band 14q32.33 [2]. The orientation of the locus has been determined by the analysis of translocations, involving the IGH locus, in leukemia and lymphoma. The Homo sapiens IGH locus spans 1250 kb [2] (Figure 16). It consists of 123 to 129 IGHV genes [212,213,214,215,216,217,218] depending on the haplotypes, 27 IGHD genes, belonging to seven subgroups [219,220,221,222,223], nine IGHJ genes [223,224] and, in the most frequent haplotype, 11 IGHC genes [114,119,120,154,174,175,225,226,227,228,229,230,231,232,233,234,235,236]. Eighty-two to 88 IGHV genes belong to seven subgroups [2,237], whereas 41 pseudogenes, which are too divergent to be assigned to subgroups, have ben assigned to the clans.

3.2.2. IGHC Multigene Deletions and Gene Order, IGHC and IGHV Copy Number Variation (CNV) Haplotypes

IGHC haplotypes have been identified in Homo sapiens, which correspond to IGHC copy number variations (IGHC CNV) with absence of the corresponding IG classes and subclasses in healthy indiduals having IGHC deletions on both chromosomes (either homozygous for a same deletion, or heterozygous for two different deletions). These IGHC CNV deletions are designed I to VI according to the chronogical order in which they were found (Figure 17).
The first two identified deletions, deletion I (del G1-EP1-A1-GP-G2-G4) [113,114] and deletion II (del EP1-A1-GP) [115] allowed ordering of the Homo sapiens IGHC genes by determinng the relative positions of two cosmids [174,175]. Deletion III (del A1-GP-G2-G4-E) [116,238] includes the IGHE gene and corresponds to the complete absence of the IgA1, IgG2, IgG4 subclasses and of the IgE class as demonstrated by the gene deletion molecular analysis in the healthy and homozygous individual T17 [116]. The mechanism of these IGHC multigene deletions [113,114,115,116,239,240], several of them found in conguineous families [241,242]. involves, as demonstrated for one of them, highly homologous hot spots of recombination [176]. CNV with IGHC multigene duplication or triplication were detected by Southern analysis and pulsed field gel electrophoresis (PFGE) [117,243,244,245,246].
The IGHV cluster comprises several CNV reported in Figure 17B. As an example, the genome assembly from GRCh38 from the hydatidiform mole CHORI-17 BAC library corresponds to a new haplotype (haplotype B) in the highly polymorphic region by insertion/deletion between IGHV4-34 and IGHV4-28 [247] (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 2. Locus representations > IGH Locus representation: Human (Homo sapiens) Polymorphism by insertion/deletion between IGHV4-34 and IGHV4-28 (haplotypes A to F)). In addition, eight CNV-containing haplotypes were identified from a panel of nine diploid genomes of diverse ethnic origin [247]. These polymorphisms confirm the diversity of genomic IGH alleles and/or CNV polymorphisms identified in extensive studies of different populations, as restriction fragment length polymorphism (RFLP) alleles [117,248,249,250,251]

3.2.3. IGH Orphons

Thirty-five IGH genes have been found outside the main locus in other chromosomal localizations. These genes designated as orphons cannot contribute in the synthesis of the immunoglobulin chains, even if they have an ORF. Nine IGHV orphons and 10 IGHD orphons have been described on chromosome 15 (15q11.2), and 16 IGHV orphons on chromosom 16 (16p11.2) [218]. In addition one IGHC processed gene, IGHEP2 (so far, the only processed IG gene described in the major loci) is localized on chromosome 9 (9p24.2-p24.1) [252] (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 1. Locus and genes > 7. Gene tables > IGHV > Human > Gene table: Human (Homo sapiens) IGHV orphons; ibid: IGHD; ibid: IGHC).

3.2.4. Potential Homo sapiens IGH Genomic Repertoire

The potential genomic IGH repertoire per haploid genome comprises 38 to 46 functional IGHV genes belonging to six or seven subgroups depending on the haplotypes [2,237], 23 IGHD, 6 IGHJ and, in the most frequent haplotype, nine IGHC genes (Table 7). The total number of human IGH genes per haploid genome in the major locus is 170-176 of which 76-84 genes are functional.
The potential repertoire of the Homo sapiens IGH V-CLUSTER is shown in Table 7A and that of the IGH D-J-C-CLUSTER in Table 7B. The IGHV subgroups (Table 7A) are listed per subgroup and inside each subgroup, in an ascending numerical order. Only the IGHV subgroups with at least one functional allele are shown, excepted for the IGHV8 subgroup recently assigned with an ORF. The CDR-IMGT lengths (in number of AA or codons) are shown between square brackets, with lengths of the CDR1-IMGT, CDR2-IMGT and CDR3-IMGT separated by dots. The allele functionality is indicated by F: functional, (F): when the accession number refers to rearranged genomic DNA or cDNA and the corresponding germline gene has not yet been isolated, ORF: open reading frame, P: pseudogene. In the column ‘Nb of alleles P’, the number of pseudogenes with V-REGION in-frame and the number of pseudogenes with frameshift(s) are shown separated by a dot, between parentheses. Copy number variations (CNV) are numbered from 5′ to 3′ in the locus (Figure 16), with ‘i’ for an insertion, ‘d’ for a deletion, ‘e’ for an exchange.The IGHD, IGHJ and IGHC genes of the D-J-C-CLUSTER (Table 7B) are listed according to the gene order. All the IGHD genes have at least one in-frame reading frame without stop-codons, however four genes are assigned to ORF owing to an unusual 5′D-HEPTAMER. Only the six functional IGHJ genes are shown. The IGHEP1 (4 P) and the IGHGP (2 ORF, 1P) are listed owing to the structural organization of the IGHC genes in two duplicated clusters. Gene order is according to the IMGT Locus gene order (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 1. Locus and Genes > 3. Locus descriptions > Locus gene order > IGH).

3.3. Homo sapiens IGK Locus and Genes

3.3.1. Organization of the Homo sapiens IGK Locus

The Homo sapiens IGK locus is located on chromosome 2 [253], on the short arm [254], at band at 2p11.2 [2]. The orientation of the locus has been determined by the analysis of translocations, involving the IGK locus, in leukemia and lymphoma. The Homo sapiens IGK locus spans 1820 kb [2] (Figure 18). It consists of 76 IGKV genes belonging to seven subgroups [237,255,256,257,258,259,260,261], five IGKJ genes [261,262,263] and a unique IGKC gene [263]. The 76 IGKV genes are organized in two clusters separared by 800 kb [2]. The IGKV distal cluster in 5′ of the locus and in the most centromeric position) spans 400 kb and comprises 36 genes. The IGKV proximal cluster (in 3′ of the locus, closer to IGKC, aand in the most telomeric position) spans 600 kb and comprises 40 genes.
The potential genomic IGK repertoire per haploid genome comprises 31-35 functional IGKV genes belonging to five subgroups, the five IGKJ genes and the unique IGKC gene [2,264]. One rare IGKV haplotype has been described which contains only the proximal cluster. This haplotype comprises the 40 proximal IGKV genes belonging to seven subgroups, of which 17–19 are functional and belong to five subgroups [2]. If both the proximal and distal IGKV clusters are present, the total number of human IGK genes per haploid genome is 82 of which 37 to 41 are functional. If only the proximal IGKV cluster is present, the total number of genes per haploid genome is 46 of which 23-25 genes are functional [2].

3.3.2. IGK Orphons

Twenty-five IGKV orphons have been identified and sequenced: two on the short arm of chromosome two but outside of the major IGK locus, 12 on the long arm of chromosome 2, five on chromosome 22, one on chromosome 1, one on chromosome 15, and four outside of chromosome 2 [2,261] (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 1. Locus and genes > 7. Gene tables > IGKV > Human > Gene table: Human (Homo sapiens) IGKV orphons).

3.3.3. Potential Homo sapiens IGK Genomic Repertoire

The potential repertoire of the Homo sapiens IGK V-CLUSTER is shown in Table 8A and that of the IGK J-C-CLUSTER in Table 8B. The IGKV subgroups (Table 8A) are listed per subgroup and inside each subgroup in an ascending numerical order, first the proximal cluster, then the distal cluster. Only the IGKV subgroups with at least one functional allele are shown. The CDR-IMGT lengths (in number of AA or codons) are shown between square brackets, with lengths of the CDR1-IMGT, CDR2-IMGT and CDR3-IMGT separated by dots. The allele functionality is indicated by F: functional, [F]: when the accession number refers to genomic DNA, but not known as being germline or rearranged, ORF: open reading frame, P: pseudogene. In the column ‘Nb of alleles P’, the number of pseudogenes with V-REGION in-frame and the number of pseudogenes with frameshift(s) are shown separated by a dot, between parentheses. Seven novel IGKV alleles were characterized [265] following the sequencing of the IGK locus from the CH17 hydatidiform mole BAC library. Gene order is according to the IMGT Locus gene order (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 1. Locus and Genes > 3. Locus descriptions > Locus gene order > IGK).

3.3.4. Homo sapiens IGKC Allotypes (Km Alleles)

Homo sapiens IGKC allotypes are designated as Km (for ‘kappa marker’) (previously Inv) [83] The three Km allotypes Km1, Km2 and Km3 defined three Km alleles Km3 (or Km-1, Km-2 serologically), Km1,2 and Km1 which correspond to IGKC amino acid changes at position 45.1 and 101, according to the IMGT unique numbering for C-DOMAIN [42]. Km3. has Ala A45.1 and Val V101 and corresponds to four IGKC alleles (¨*01,*02;*03 and *05), Km1,2 has Ala A45.1 and Leu L101 (IGKC*04 allele) and Km1 has Val V45.1 and Leu L101 (IGKC*06) allele [83] (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 2. Proteins and alleles 4. Allotypes; ibid. 2. Alignments of alleles > IGKC > Mammalia > human (Homo sapiens)).

3.4. Homo sapiens IGL Locus and Genes

3.4.1. Organization of the Homo sapiens IGL Locus

The Homo sapiens IGL locus is located on chromosome 22 [266], on the long arm, at band 22q11.2 [2], The human IGL locus spans 1050 kb [2] (Figure 19). The orientation of the locus has been determined by the analysis of translocations, involving the IGL locus, in leukemia and lymphoma [267]. Sequencing of the long arm of chromosome 22 showed that it encompasses about 35 megabases of DNA and that the IGL locus is localized at six megabases from the centromere [268]. Although the correlation between DNA seqences and chromosomal bands was not yet been made, the localization of the IGL locus could be refined at 22q11.2. The human IGL locus consists of 73-74 IGLV genes [237,269,270,271,272,273], localized on 900 kb, seven to 11 IGLJ and seven to 11 IGLC genes depending on the haplotypes, each IGLC gene being preceded by one IGLJ gene [274,275,276,277]. Fifty-six-57 genes belong to 11 subgroups, whereas 17 pseudogenes which are too divergent to be assigned to subgroups, have been assigned to the clans. The potential genomic IGL repertoire per haploid genome comprises 29-33 functional IGLV gnes in the 7-IGL gene haplotype [2,278,279]. One, two, three or four additional IGLC genes, each one probably preceded by one IGLJ, have been shown to characterize IGLC haplotypes with eight, nine, 10 or 11 genes [280,281], but these genes have not yet been sequenced. The total number of human IGL genes per haploid genome is 87–96 of which 37–43 are functional [2].

3.4.2. IGL Orphons

Six orphons have been identified, four (two IGLV, two IGLC) on chromosome 22q outside of the major IGL locus and two IGLV on chromosome 8 [282]. A processed gene, IGLJ-C/OR18, has been found on chromosome 18 [283].

3.4.3. Potential Homo sapiens IGL Genomic Repertoire

The potential repertoire of the Homo sapiens IGL V-CLUSTER in shown in Table 9A and that of the IGL J-C-CLUSTER in Table 9B. The IGLV subgroups (Table 9A) are listed per subgroup and inside each subgroup, in an ascending numerical order. Only the IGLV subgroups with at least one functional allele are shown. The CDR-IMGT lengths (in number of AA or codons) are shown between square brackets, with lengths of the CDR1-IMGT, CDR2-IMGT and CDR3-IMGT separated by dots. The allele functionality is indicated by F: functional, ORF: open reading frame, P: pseudogene. In the column ‘Nb of alleles P’, the number of pseudogenes with V-REGION in-frame and the number of pseudogenes with frameshift(s) are shown separated by a dot, between parentheses. IGLV alleles increase the diversity of the lambda light chain repertoire in the human population [284,285,286,287]. Four novel IGLV alleles and one IGLC allele were characterized [265] following the sequencing of the IGL locus from the CH17 hydatidiform mole BAC library. Limited CNV polymorphism by insertion and/or deletion seems to indicate that the V-CLUSTER of the human IGL locus has undergone less evolutionary shuffling that the human IGH or IGL loci [284]. However, CNV with a variable number of additional J-C cassettes, from one to four, have been identified by Southern blot analysis. These additional J-C cassettes are localized between the J2-C2 and J3-C3 cassettes. Gene order is according to the IMGT Locus gene order (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 1. Locus and Genes > 3. Locus descriptions > Locus gene order > IGL).

3.4.4. Homo sapiens IGL Isotypes

The Homo sapiens IGL C-REGION, encoded by 4-5 IGLC genes in the 7-IGLC gene haplotype, belong to four serological isotypic forms. These lambda isotypes differ by limited amino acid changes which produce the Oz, Kern (Ke) and Mcg serological markers [2,276,279] (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 2. Proteins and alleles > 5. Isotypes > IGLC > Mammalia: human (Homo sapiens) IGLC). Mcg+ proteins have Asn N1 and Thr T3 (positions according to the IMGT unique numbering for C-DOMAIN [42]) whereas Mcg proteins have Ala 1 and Ser 3. Position 82 initially described as characteristic of the Mcg marker is not involved. Ke+ proteins have Gly G45 whereas Ke proteins have Ser S45. Oz+ proteins have Lys K100 whereas Oz proteins have Arg R100 [276,279].

4. Immunoglobulin Structures: IMGT Unique Numbering and IMGT® Collier de Perles

4.1. IMGT Unique Numbering and IMGT Colliers de Perles for V-DOMAIN (NUMEROTATION)

4.1.1. V Domain Definition and Main Characteristics

The V domain includes the V-DOMAIN of the IG and of the TR, which corresponds to the V-J REGION or V-D-J-REGION encoded by V-(D)-J rearrangements [2,3], and the V-LIKE-DOMAIN of the IgSF other than IG and TR. The V domain description of any receptor, any chain and any species is based on the IMGT unique numbering for V domain (V-DOMAIN and V-LIKE-DOMAIN) [39,40,41,44,45,46].
A V domain comprises about 100 amino acids and is made of nine antiparallel beta strands (A, B, C, C′, C″, D, E, F and G) linked by beta turns (AB, CC′, C″D, DE and EF) and three loops (BC, C′C″ and FG), forming a sandwich of two sheets [ABED] [GFCC’C”] [39,40,41,44,45,46]. The sheets are closely packed against each other through hydrophobic interactions giving a hydrophobic core, and joined together by a disulfide bridge between a first highly conserved cysteine (1st-CYS) in the B strand (in the first sheet) and a second equally conserved cysteine (2nd-CYS) in the F strand (in the second sheet) [39,40,41,44,45,46].

4.1.2. V-DOMAIN IMGT Colliers de Perles

The loop and strands are visualized in the IMGT Colliers de Perles [47,48,49,50,51,52] which can be displayed on 1 layer (closer to the amino acid sequence) (Figure 20) or on 2 layers (closer to the 3D structure) (Figure 21). The three loops, BC, C’C” and FG (or CDR1-IMGT, CDR2-IMGT and CDR3-IMGT for a V-DOMAIN) are delimited by the IMGT anchors. The six anchors belong to strands and comprise positions 26 and 39 (anchors of the BC loop or CDR1-IMGT), 55 and 66 (anchors of the C’-C’’ loop or CDR2-IMGT), 104 and 118 (anchors of the FG loop or CDR3-IMGT), and are shown in square in the IMGT Colliers de Perles. The CDR3-IMGT anchors are highly conserved, they are C104 (2nd-CYS, in F strand) and F118 or W118 (J-PHE or J-TRP in G strand). The JUNCTION of an IG or TR V-DOMAIN includes the anchors 104 and 118 and is therefore two amino acids longer than the corresponding CDR3-IMGT (positions 105-117).

4.1.3. V-DOMAIN Strands and Loops (FR-IMGT and CDR-IMGT)

The V domain strands and loops and their delimitations and lengths, based on the IMGT unique numbering for V domain [39,40,41,44,45,46], are shown in Table 10. In the IG and TR V-DOMAIN, the three hypervariable loops BC, C’C” and FG involved in the ligand recognition (native antigen for IG and pMH for TR) are designated complementarity determining regions (CDR-IMGT), whereas the strands form the framework region (FR-IMGT), which includes FR1-IMGT, FR2-IMGT, FR3-IMGT and FR4-IMGT (Table 10). Correspondences between the IMGT unique numbering for V-DOMAIN [39,40,41] with other numberings, e.g., Kabat [118], or canonical structures [288,289,290], are available in the IMGT Scientific chart (IMGT® http://www.imgt.org, IMGT Scientific chart > Numbering > Correspondence between V numberings).
For a V domain, the BC loop (or CDR1-IMGT in a V-DOMAIN) encompasses positions 27 to 38, the C’C’’ loop (or CDR2-IMGT in a V-DOMAIN) positions 56 to 65, and the FG loop (or CDR3-IMGT) positions 105 to 117. In a V-DOMAIN, the CDR3-IMGT encompasses the V-(D)-J junction that results from a V-J or V-D-J rearrangement [2,3] and is more variable in sequence and length than the CDR1-IMGT and CDR2-IMGT that are encoded by the V gene region only. For CDR3-IMGT of length >13 AA, additional IMGT positions are added at the top of the loop between 111 and 112 (Table 11) (IMGT® http://www.imgt.org, IMGT Scientific chart > 2. Numbering > IMGT unique numbering for V-DOMAIN and V-LIKE-DOMAIN).
In biological data, the lengths of the loops and strands are given by the number of occupied positions (unoccupied positions or ‘IMGT gaps’ are represented with hatches in the IMGT Colliers de Perles (Figure 20A) or by dots in alignments). The CDR-IMGT lengths are given in number of amino acids (or codons), into brackets and separated by dots: for example VH [8.8.13] means that the BC, C’C” and FG loops (or CDR1-IMGT, CDR2-IMGT and CDR3-IMGT for a V-DOMAIN) have a length of 8, 8 and 13 amino acids (or codons), respectively. Similarly [25.17.38.11] means that the FR1-IMGT, FR2-IMGT, FR3-IMGT and FR4-IMGT have a length of 25, 17, 38 and 11 amino acids (or codons), respectively. Together, the four FR of a VH domain usually comprise 91 amino acids and the individual FR-IMGT lengths are [25.17.38.11], whereas the four FR of a VL domain usually comprise 89 amino acids and the individual FR-IMGT lengths are [26.17.36.10] (Figure 20A).

4.1.4. V-DOMAIN Conserved Amino Acids

A V domain has five characteristic amino acids at given positions (positions with bold (online red) letters in the IMGT Colliers de Perles). Four of them are highly conserved and hydrophobic [81] and are common to the C domain: 23 (1st-CYS), 41 (CONSERVED-TRP), 89 (hydrophobic) and 104 (2nd-CYS). These amino acids contribute to the two major features shared by the V and C domain: the disulfide bridge (between the two cysteines 23 and 104) and the internal hydrophobic core of the domain (with the side chains of tryptophan W41 and amino acid 89). The fifth position, 118, is an anchor of the FG loop. It is occupied, in the V domains of IgSF other than IG or TR [19], by amino acids with diverse physicochemical properties [81]. In contrast, in IG and TR V-DOMAIN, the position 118 is occupied by remarkably conserved amino acids which consist in a phenylalanine or a tryptophan encoded by the J-REGION and therefore designated J-TRP or J-PHE 118. The bulky aromatic side chains of J-TRP and J-PHE are internally orientated and structurally contribute to the V-DOMAIN hydrophobic core [40,41].

4.1.5. V-DOMAIN Delimitation

A criterion used in the IMGT® characterization of a V domain is its delimitation taking into account the exon delimitations, whenever appropriate. This IMGT® genomic approach integrates the strands A and G which are usually absent of structural alignments [45]. The exon rule is not used for the delimitation of the 5′ end of the first N-terminal domain of proteins with a leader. In those cases, the 5′ end of the first N-terminal domain corresponds to the proteolytic site between the leader (L-REGION) and the coding region of the mature protein. This is the case of the V-DOMAIN of the IG and TR chains. The IG V-DOMAIN (VH, V-KAPPA, V-LAMBDA) is therefore delimited in 5′ by the proteolytic site which delimits the 5′ end of the V-REGION and in 3′ by the splicing site of the J-REGION of the rearranged V-D-J (for IGH) or V-J (for IGK or IGL) [45].

4.1.6. Protein Displays for the V-REGION and J-REGION

The V-REGION of the IGHV, IGKV and IGLV genes in germline configuration are displayed in Protein displays (Figure 22) [2,237], with the FR1-IMGT, CDR1-IMGT, FR2-IMGT, CDR2-IMGT, FR3-IMGT and germline CDR3-IMGT.
The J-REGION of the IGHJ, IGKJ and IGLJ genes in germline configuration are displayed in Protein displays, aligned on the conserved J-MOTIF ‘F/WGXG’ (where F is J-PHE, W is J-TRP, G, glycine, X, any amino acid, and G, glycine) [2,237] (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 2. Proteins and alleles > 1. Protein displays > V-REGION > IGHV, ibid. > IGKV, ibid. > IGLV; ibid. > J-REGION > IGHJ, ibid. IGKJ, ibid. IGLJ). The translation of the IGH D-REGION in the six frames are displayed in Alignments of alleles [2,223] (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > Proteins and alleles > 2. Alignments of alleles > IGHD > Mammalia: human (Homo sapiens) > IGHD overview).

4.2. IMGT Unique Numbering and IMGT Colliers de Perles for C Domain (NUMEROTATION)

4.2.1. C Domain Definition and Main Characteristics

The C domain includes the C-DOMAIN of the IG and of the TR [2,3] and the C-LIKE-DOMAIN of the IgSF other than IG and TR. The C domain description of any receptor, any chain and any species is based on the IMGT unique numbering for C domain (C-DOMAIN and C-LIKE-DOMAIN) [42,44,45,46]. A C domain comprises about 90-100 amino acids and is made of seven antiparallel beta strands (A, B, C, D, E, F and G), linked by beta turns (AB, DE and EF), a transversal strand (CD) and two loops (BC and FG), and forming a sandwich of two sheets [ABED] [GFC] [42,44,45,46]. A C domain has a topology and a three-dimensional structure similar to that of a V domain but without the C’ and C’’ strands and the C’C’’ loop, which is replaced by a transversal CD strand [42].

4.2.2. C Domain IMGT Colliers de Perles

The lengths of the strands and loops are visualized in the IMGT Colliers de Perles [48,49,50,51,52], on one layer (Figure 20B) and two layers (Figure 23). There are six IMGT anchors in a C domain (four of them identical to those of a V domain): positions 26 and 39 (anchors of the BC loop), 45 and 77 (by extension, anchors of the CD strand as there is no C’-C’’ loop in a C domain [42], and 104 and 118 (anchors of the FG loop).

4.2.3. C Domain Strands and Loops

The C domain strands, turns and loops and their delimitations and lengths, based on the IMGT unique numbering for C domain [42,44,45,46], are shown in Table 12. Correspondences between the IMGT unique numbering with other numberings (Eu, Kabat [118]) are available in the IMGT Scientific chart (IMGT® http://www.imgt.org, IMGT Scientific chart > Numbering > Correspondence between C numberings).

4.2.4. C Domain Conserved Amino Acids

A C domain has five characteristic amino acids at given positions (positions with bold (online red) letters in the IMGT Colliers de Perles). Four of them are highly conserved and hydrophobic [81] and are common to the V domain: 23 (1st-CYS), 41 (CONSERVED-TRP), 89 (hydrophobic) and 104 (2nd-CYS). As mentioned above, these amino acids contribute to the two major features shared by the V and C domain: the disulfide bridge (between the two cysteines 23 and 104) and the internal hydrophobic core of the domain (with the side chains of tryptophan W41 and amino acid 89). The fifth position, 118, is diverse and is characterized as being a FG loop anchor.

4.2.5. C Domain Genomic Delimitation

In IMGT®, the C domains (C-DOMAIN and C-LIKE-DOMAIN) are delimited taking into account the exon delimitation, whenever appropriate. The exon/intron organization of the Homo sapiens IGHC genes shows that each CH C-domain corresponds to one exon [2] (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 1. Locus and genes > 5. Gene exon/intron organization > IGHC > Human). As for the V domain, this IMGT® genomic approach integrates the strands A and G which are usually absent of structural alignments [45].

4.2.6. C-REGION Protein Displays

The Protein display of the C-REGION of the IGKC and IGLC corresponds to the C-KAPPA and C-LAMBDA domains (Figure 24A,B).The Protein display of the C-REGION of the IGHC genes (Figure 24C) is shown per CH domain and comprises, in addition to the 3 or 4 CH domains, the hinge region for the H-alpha, H-delta and H-gamma chains and, for the membrane IG (mIG), the region CO + TM + CY (encompassing the connecting region (CO), the transmembrane region (TM) and the cytoplasmic region (CY) (Table 1) with delimitation of the exons M or M1 and M2 [2]) and for the secreted IG (sIG), the CHS (expressed instead of CO + TM + CY).

5. IMGT® Databases and Tools for IG Sequences and Structures

5.1. IMGT®, the International ImMunoGeneTics Information System®

IMGT®, the international ImMunoGeneTics information system® comprises seven databases [54,55,56,57,58,59,60] and 17 tools [61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80] and >25,000 pages of Web resources (Figure 25) [1,94].

5.2. IMGT® Nucleotide Sequence and Repertoire Analysis

5.2.1. IMGT/V-QUEST for Nucleotide Sequence Analysis

IMGT/V-QUEST [61,62,63,64,65,66] is the IMGT® online tool for the analysis of IG and TR nucleotide sequence analysis [1]. The entry type corresponds to user nucleotide sequences of V domains (1-50 sequences per analysis), from rearranged gDNA or cDNA. IMGT/V-QUEST identifies the variable (V), diversity (D) and junction (J) genes in rearranged IG and TR sequences and, for the IG, the nucleotide (nt) mutations and amino acid (AA) changes resulting from somatic hypermutations by comparison with the IMGT/V-QUEST reference directories sets. (links available from the IMGT/V-QUEST Welcome page). The IMGT/V-QUEST reference directory sets include IMGT reference sequences (one per allele) from functional (F) genes and alleles, open reading frame (ORF) and pseudogenes (P) alleles with in-frame V-REGION. The tool integrates IMGT/JunctionAnalysis [67,68] for the detailed characterization of the V-D-J or V-J junctions, and IMGT/Automat [69,70] for a complete sequence annotation. The IMGT/V-QUEST tool functionalities include:
(1)
Introduction of IMGT gaps, according to the IMGT unique numbering for V-DOMAIN (Section 4),
(2)
Identification of the closest V, D and J genes and alleles, according to the IMGT gene and allele nomenclature (Section 3) (e.g., for Homo sapiens [2,4]) (Figure 26A),
(3)
IMGT/JunctionAnalysis results [67,68] (Figure 26B),
(4)
Description of mutations and amino acid changes [65].
The amino acid (AA) changes are described for the hydropathy (three classes), volume (five classes) and physicochemical properties (11 classes) [81] (IMGT® http://www.imgt.org, IMGT Education > IMGT Aide-mémoire > Amino acids > IMGT classes of the 20 common amino acids). S40 > G (++−) means that the two AA involved in the change (S > G) at codon 40 belong to the same hydropathy (+) and volume (+) classes but to different physicochemical properties (−) classes [81]. This qualification of AA replacement has led to the identification of four types of AA changes: very similar (+++), similar (++−, +−+), dissimilar (−−+, −+−, +−−), and very dissimilar (−−−).
(5)
Identification of indels and their correction [65] (option),
(6)
IMGT/Automat annotation [69,70] (annotations are those found in IMGT/LIGM-DB flatfiles),
(7)
IMGT Colliers de Perles [51].
Users can choose the option ‘Search for insertions and deletions in V-REGION’ [65] (1-50 sequences per run) in Advanced parameters. The option ‘Analysis of single chain Fragment variable (scFv) [75], available in Advanced functionalities, allows the analysis of long read scFv sequences from combinatorial libraries containing two V-DOMAIN. Customized parameters and results provided by IMGT/V-QUEST and IMGT/JunctionAnalysis have been described elsewhere [61,62,63,64,65,66].
IMGT/V-QUEST is frequently used by clinicians for the analysis of the somatic hypermutations in leukemia, lymphoma and myeloma, and more particularly in chronic lymphocytic leukemia (CLL) [291,292,293] in which the percentage of mutations in the patient VH has a prognostic value. The sequences of the V-(D)-J junctions determined by IMGT/JunctionAnalysis are also used in the characterization of stereotypic patterns in CLL and B cell lymphoproliferations [291,292,293,294] and for the junction synthesis of specific probes for the follow-up of residual diseases in leukemias and lymphomas.

5.2.2. IMGT/HighV-QUEST

IMGT/HighV-QUEST basic functionalities for NGS repertoire analysis: IMGT/HighV-QUEST [66,71,72,73,74] is the high-throughput version of IMGT/V-QUEST. It is so far the only online portal available for the direct analysis of long IG and TR sequences from next generation sequencing (NGS) [1]. The submitted entries are user long read nucleotide sequences of V domains (1,000,000 sequences per run). IMGT/HighV-QUEST uses the same algorithms and IMGT reference directories (and therefore provides the same degree of resolution and high quality results) as IMGT/V-QUEST. The tool works for the IG of any species for which an IMGT reference directory is available [1]. The option ‘Analysis of single chain Fragment variable (scFv)’ allows the analysis of scFv long read sequences which contain two V domains [75], and the repertoire analysis of phage display scFv combinatorial libraries [295,296]. The IMGT/HighV-QUEST basic functionalities include:
(1).
Introduction of IMGT gaps, according to the IMGT unique numbering for V-DOMAIN [41] (Section 4),
(2).
Identification of indels and their correction [65] (by default),
(3).
Identification of the closest V, D and J genes and alleles, according to the IMGT gene and allele nomenclature (Section 3) (e.g., for Homo sapiens [2,4]),
(4).
IMGT/JunctionAnalysis results [67,68],
(5).
Description of mutations and amino acid changes [65],
(6).
IMGT/Automat annotation [69,70].
The IMGT/HighV-QUEST output is provided in eleven results files in CVS format (results equivalent to those of the Excel file from IMGT/V-QUEST online) (Table 13). A twelfth file ‘scFv’ is only present if ‘Analysis of single chain Fragment variable (scFv)’ was selected in Advanced functionalities).
The outputs of the IMGT/HighV-QUEST can be statistically analysed (two batches up to 1 million sequences, comprising outputs of different sets) for the identification and characterization of the IMGT clonotypes (AA) online [73] (Figure 27) and their comparison between sets.
An IMGT clonotype (AA) is defined by:
  • a unique V-(D)-J-rearrangement (V and J genes and alleles) (nt)
  • a unique CDR3-IMGT (AA)
  • conserved anchors 104, 118 (C104, W118 or F118)
The IMGT clonotype (AA) definition includes the IMGT names of the V, D, J genes and alleles, the CDR3-IMGT length (AA), the CDR3-IMGT sequence (AA), and the anchors 104 and 118 of the junction (i.e., for VH, ‘C, W’ for 2nd-CYS 104 and J-TRP 118, respectively) [73].
IMGT clonotype (AA and nt) results per locus are provided in 10 sections (HTML pages) (IMGT® http://www.imgt.org, IMGT/HighV-QUEST > Documentation):
(1).
IMGT clonotypes (AA) per Nb
(2).
IMGT clonotypes (AA) per Nb with detailed clonotypes (nt)
(3).
IMGT clonotypes (AA) per V gene
(4).
IMGT clonotypes (AA) per V gene with detailed clonotypes (nt)
(5).
IMGT clonotypes (AA) per CDR3-IMGT length (AA)
(6).
IMGT clonotypes (AA) per CDR3-IMGT length (AA) with detailed clonotypes (nt)
(7).
IMGT clonotypes (AA) by CRD3-IMGT sequence (AA) alphabetical order with detailed clonotypes (nt)
(8).
IMGT clonotype (AA) diversity and expression histograms: per V, (D), J-GENE and per CDR3-IMGT length
(9).
IMGT clonotype (AA) diversity and expression tables: per V, (D), J-GENE and per CDR3-IMGT length
(10).
V gene and allele table: Rearrangements, Nb of sequences and Nb IMGT clonotypes (AA) per V-GENE and allele
Figure 27 shows a very small part of a list of 64,093 unique IMGT clonotypes (AA) identified in a case study. The display is based on the CDR3-IMGT length and corresponds to 5. and 6. in the list above. Each IMGT clonotype (AA) of a dataset, identified and defined by IMGT/HighV-QUEST, has an ‘Exp. ID’ identifier. For example, #45307, with an Exp. ID ‘45307-Xall’, is defined by a CDR3-IMGT length (AA) of ‘14 AA’, a CDR3-IMGT sequence (AA) ‘TRDGPVAVHWFFAL’, the ‘IGHV6-1*01 F – IGHD2-8*02 F – IGHJ2*01 F’ rearrangement, and conserved anchors 104 and 118 ‘C, W’. The IMGT clonotype (AA) representative sequence [73] has a V-REGION which is 97.64% identical to that of the germline IGHV6-1*01 and a length of 422 nt. The link to a ‘Sequence ID’ gives access to the representative sequence in FASTA format; the three following numbers indicates the number of sequences assigned to an IMGT clonotype (AA) (‘1 copy’, ‘More than 1’ and Total) [73]. ‘Sequences file’ gives access to a file containing the ‘1 copy’ sequences assigned to a given IMGT clonotype (AA), in FASTA format. In Figure 27B, IMGT clonotypes (AA) (in the pink horizontal lines) are displayed with the corresponding IMGT clonotypes (nt). For example, the ‘IMGT clonotype (AA)’ #45325, with an Exp. ID ‘45325_Xall’, is defined as above (CDR3-IMGT length (AA) ‘14 AA’, CDR3-IMGT sequence (AA) ‘ARDLCDYGLCYFDY’, ‘IGHV1-18*04 F-IGHD4-17*01 F-IGHJ4*02 F’ rearrangement, conserved anchors 104 and 118 ‘C, W’, V-REGION representative sequence 97.91% identical to that of the germline IGHV1-18*04, and length of 414 nt. ‘Sequence ID’, the three following numbers, ‘Sequences file’ are as above. The header for the description of the VH clonotypes (nt) is given at the top. The nb of different CDR3-IMGT (nt) indicates the nb of IMGT clonotypes (nt) for a given IMGT clonotype (AA) (e.g., 2 for #41328). The CDR3-IMGT sequence (nt) is shown with the number of different nucleotides (‘Nb diff nt’) by comparison with that of the representative sequence, ‘0′ indicates that the CDR3-IMGT sequence (nt) is identical to that of the IMGT clonotype (AA) representative sequence. For #41328, there is an IMGT clonotype (nt) with 4 nt differences (‘c’ instead of ‘t’ at position 9, ‘c’ instead of ‘a’ at position 12, ‘t’ instead of ‘c’ at position 30 and ‘c’ instead of ‘t’ at position 33) compared to the CDR3-IMGT of the representative sequence. #41328 also shows an example of ‘several alleles’ (for V and J) (2 alleles for IGHV) assigned to an IMGT clonotype (AA).
To date (July 10, 2020), more than 21 billion of sequences were analysed by IMGT/HighV-QUEST, by 3177 users from 46 countries (43% users from USA, 34% from EU, 22% from other parts of the world).
Results from the IMGT/HighV-QUEST statistical analysis and IMGT clonotypes (AA) characterization can be analysed by the downloadable package IMGT/StatClonotype [76,77] which provides pairwise evaluation and visualisation comparison of NGS IG and TR IMGT clonotype (AA) diversity or expression (Figure 28).

5.3. IMGT® Amino Acid Sequence Analysis and Representation

5.3.1. IMGT/DomainGapAlign

IMGT/DomainGapAlign [58,79,80] is the IMGT® online tool for the analysis of amino acid sequences and 2D structures of domains (e.g., V and C for IG) [1]. It is very popular in antibody humanization as it allows the comparison of the user V domain against reference sequences of V-REGION and J-REGION of genes and alleles of Homo sapiens and other vertebrate species (e.g., mouse, rat) and the delimitation and characterization of the FR-IMGT and CDR-IMGT.
IMGT/DomainGapAlign analyses amino acid domain sequences by comparison with the IMGT reference directory sets (translation of the germline V and J genes and of the C gene domains]. These reference amino acid sequences can be displayed by querying IMGT/DomainDisplay online. Several amino acid sequences can be analysed simultaneously in IMGT/DomainGapAlign, provided that they belong to the same domain type.
IMGT/DomainGapAlign displays the user V domain sequences aligned with the closest V and J regions, with IMGT gaps and delimitations of the strands and loops and the FR-IMGT and CDR-IMGT, according to the IMGT unique numbering [41]. If several closest genes and/or alleles are identified, the user can select the display of each corresponding alignment. The user amino acid sequence is displayed, according to the IMGT color menu, with the delimitations of the V-REGION, J-REGION, and for VH domains, (N-D)-REGION (identified by the tool by comparison with the delimitations of the closest V and J gene and allele). The characteristics of the AA changes [81] are shown in strands and loops and in FR-IMGT and CDR-IMGT. Clicking on the user sequence name in the alignment gives access to the IMGT/Collier-de-Perles tool which automatically provides the IMGT Collier de Perles of the analysed VH or VL domain (V-D-J region or V-J region, respectively) with highlighted amino acid differences (in pink circles online) with the closest germline sequence.
IMGT/DomainGapAlign analyses the user C domain sequences with similar functionalities: alignments and identification of the genes and alleles with the closest C domain, delimitation of the C-DOMAIN in the user sequence, characteristics of the AA changes in strands, turns and loops, IMGT Collier de Perles of the C-DOMAIN with highlighted amino acid differences (in pink circles online) with the closest reference sequence.
The IMGT/DomainGapAlign tool functionalities include:
(1).
Introduction of IMGT gaps, according to the IMGT unique numbering for V-DOMAIN [41] or for C-DOMAIN [42] (Section 4),
(2).
Identification of the closest V, D and J genes and alleles, according to the IMGT gene and allele nomenclature (Section 3) (e.g., for Homo sapiens [2,4]) (Figure 29A),
(3).
Delimitations of the domains, according to the IMGT unique numbering for V-DOMAIN [41] or for C-DOMAIN [42] (Section 4) (Figure 29B),
(4).
Description of AA changes (Figure 29C),
(5).
IMGT Collier de Perles [47,48,49,50] with highlighted AA changes (pink circles online) created by the IMGT/Collier-de-Perles tool [51].
IMGT/DomainGapAlign is widely used for the amino acid sequence analysis and standardized comparison for antibody humanisation and engineering using IMGT gene and allele nomenclature and IMGT unique numbering [88,89,90,91,92,93,94,95,96,97,98,99,100]. in the annotation of the IMGT/2Dstructure-DB and IMGT/3Dstructure-DB [57,58,59] entries with reciprocal links to IMGT/mAb-DB [60], and for the WHO INN description of therapeutic monoclonal antibodies [86,87].

5.3.2. IMGT/Collier-de-Perles Tool

The IMGT/Collier-de-Perles tool [51], on the IMGT® Web site at http://www.imgt.org (IMGT tools), allows the user to draw IMGT Colliers de Perles [47,48,49,50], on one or two layers, starting from their own domain amino acid sequences. Sequences have to be gapped according to the IMGT unique numbering (using for example IMGT/DomainGapAlign [58,79,80]). IMGT/Collier-de-Perles tool can be customized to display the CDR-IMGT according to the IMGT color menu and the amino acids according to their hydropathy or volume, or to the eleven IMGT physicochemical classes [81]. (IMGT® http://www.imgt.org, IMGT Education > IMGT Aide-Mémoire > Amino acids > IMGT classes of the 20 common amino acids). IMGT color menu for the CDR-IMGT of a V-DOMAIN indicates the type of rearrangement, V-J or V-D-J [2,3]. Thus, the IMGT color menu for CDR1-IMGT, CDR2-IMGT and CDR3-IMGT, is red, orange and purple for VH (encoded by a V-D-J-REGION resulting from a V-D-J rearrangement), and blue, green and greenblue for V-KAPPA or V-LAMBDA (encoded by a V-J-REGION resulting from a V-J rearrangement). The IMGT/Collier-de-Perles tool is incorporated in IMGT/V-QUEST [61,62,63,64,65,66] (users start from IG and TR V domain nucleotide sequences), IMGT/DomainGapAlign [58,79,80] (users start from V, C and G amino acid sequences).
IMGT Colliers de Perles for V, C and G domains are provided in IMGT/2Dstructure-DB (for amino acid sequences in the database) and in IMGT/3Dstructure-DB (on two layers with hydrogen bonds for the V or C domains or with the pMH contact sites for the G domains, for 3D structures) [57,58,59].

5.4. IMGT® Structure and Amino Acid Databases

5.4.1. IMGT/3Dstructure-DB

IMGT/3Dstructure-DB [57,58,59], on the IMGT® Web site at http://www.imgt.org, provides IMGT annotations and contact analysis of three-dimensional structure data of IG, TR, MH, and RPI and their complexes. The ‘PDB code’ (four letters and/or numbers, e.g., 1n8z) is used as ‘IMGT entry ID’ for the 3D structures obtained from the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) [297]. The IMGT/3Dstructure-DB card (per entry) provides eight search/display options: ‘Chain details’, ‘Contact analysis’, ‘Paratope and epitope’ [298,299], ‘3D visualization Jmol or QuickPDB’, ‘Renumbered IMGT files’, ‘IMGT numbering comparison’, ‘References and links’, ‘Printable card’.
‘Chain details’ provides detailed IMGT annotation which includes the IMGT gene and allele identification (CLASSIFICATION), region and domain delimitations (DESCRIPTION) and amino acid (AA) positions according to the IMGT unique numbering. The closest IMGT genes and alleles expressed in the AA sequences of the 3D structures are identified by aligning the AA sequences of the 3D structures with the IMGT domain reference directory. The ‘1n8z’ comprises the trastruzumab Fab chains (L-KAPPA ‘1n8z_A’ and the VH-CH1 ‘1n8z_B’ (Figure 30). The Fab is in complex with the Homo sapiens ERRB2 (erb-b2 receptor tyrosine kinase 2, HER2, NEU, CD340) (Ligand ‘1n8z_C’) [300].
‘Contact analysis’ includes the ‘Domain pair contacts’ and the contacts between amino acids at given positions or ‘IMGT [email protected]’. Domain pair contacts between the trastuzumab Fab V-KAPPA [D1] 1n8z_A and ERBB2 (‘(Ligand)’ 1n8z_C) and between the trastuzumab Fab VH [D1] 1n8z_B and ERBB2 (‘(Ligand)’ 1n8z_C) are shown in Figure 31. An ‘IMGT [email protected]’ is defined by the IMGT position numbering in a domain (or if not characterized, in the chain), the AA name (3-letter and between parentheses 1-letter abbreviation), the IMGT domain description and the IMGT chain ID, e.g., ’57 – TYR (Y) – VH – 1n8z_B’. Its characteristics are reported in an IMGT [email protected] card (or ‘[email protected]’) which includes (i) general information (PDB file numbering, IMGT file numbering, residue full name and formula), (ii) structural information ‘IMGT [email protected]’ (secondary structure, Phi and Psi angles (in degrees) and accessible surface area (ASA) (in square angstrom)) and (iii) detailed contact analysis. Contact analysis of IG/antigen complexes, is provided with detailed and standardized description of paratope/epitope in crystal structures.
‘Renumbered IMGT flat file’ allows to view (or download) an IMGT coordinate file renumbered according to the IMGT unique numbering and to which has been added the IMGT specific information. This IMGT information (identical to that provided in ‘Chain details’) is in the ‘REMARK 410’ lines (blue online) added in the IMGT coordinate files. Tools associated to IMGT/3Dstructure-DB include IMGT/StructuralQuery and IMGT/DomainSuperimpose, available online.
In summary, the IMGT/3Dstructure-DB provides:
(1)
Identification of the closest genes and alleles, according to the IMGT gene and allele nomenclature (Section 3) (e.g., for Homo sapiens [2,4]) (Figure 30),
(2)
IMGT/DomainGapAlign results [58,79,80],
(3)
IMGT Collier de Perles [47,48,49,50] (on two layers with hydrogen bonds for V and C) created by the IMGT/Collier-de-Perles tool [51],
(4)
Contact analysis between a pair of domains or between a domain and a ligand (Figure 31) (paratope/epitope description of IG/antigen (Figure 32) and TR/pMH complexes) [57,58,59],
(5)
Renumbered IMGT files [57,58,59],
(6)
IMGT numbering comparison [57,58,59].
In July 2020, IMGT/3Dstructure-DB contained 3985 IG structure entries (including 2152 IG/Ag complexes).

5.4.2. IMGT/2Dstructure-DB

IMGT/2Dstructure-DB was created as an extension of IMGT/3Dstructure-DB [57,58,59] to describe and analyse amino acid (AA) sequences of antibodies for which no 3D structures were available. IMGT/2Dstructure-DB uses the IMGT/3Dstructure-DB informatics frame and interface, which allow one to analyse, manage, and query IG, TR, and MH, as well as other IgSF and MhSF and engineered proteins (FPIA, CPCA), as polymeric receptors made of several chains, in contrast to the IMGT/LIGM-DB sequence database that analyses and manages sequences individually [54,55]. The AA sequences are analyzed with the IMGT® criteria of standardized identification [30,31], description [32,33,34,35], nomenclature [37,38] and numerotation [39,40,41,42,43,44,45,46].
The current IMGT/2Dstructure-DB entries include 336 AA sequences of antibodies from Kabat [118] (those for which there were no available nucleotide sequences), and AA sequences of mAb and FPIA from IMGT/mAb-DB [60] and the WHO-INN programme [86,87]. Queries can be made on an individual entry, using the Entry ID or the Molecule name. Thus a ‘trastuzumab’ query in ‘Molecule name’ allows to retrieve 18 results: five INN from IMGT/2Dstructure-DB, and thirteen 3D structures (of which “1nz8”) from IMGT/3Dstructure-DB. The same query interface is used for IMGT/2Dstructure-DB and IMGT/3Dstructure-DB.
The IMGT/2Dstructure-DB cards provide standardized IMGT information on chains and domains and IMGT Colliers de Perles on one or two layers, identical to that provided for the sequence analysis in IMGT/3Dstructure -DB, however the information on experimental structural data (hydrogene bonds in IMGT Collier de Perles on two layers, Contact analysis) is only available in the corresponding IMGT/3Dstructure-DB cards, if the antibodies have been cristallised.

5.4.3. IMGT/mAb-DB

IMGT/mAb-DB [60], has been developed to provide an easy access to therapeutic antibody amino acid sequences (links to IMGT/2Dstructure-DB) and structures (links to IMGT/3Dstructure-DB, if 3D structures are available). IMGT/mAb-DB data include monoclonal antibodies (mAb, INN suffix -mab, being defined by the presence of at least an IG variable domain) and fusion proteins for immune applications (FPIA, for example, a receptor or membrane ligand fused to a Fc) from the WHO INN programme [86,87]. This database also includes a few composite proteins for clinical applications (CPCA) (e.g., protein or peptide fused to a Fc for only increasing their half-life; INN prefix ef- recently adopted for these CPCA) and some related proteins of the immune system (RPI) used, unmodified, for clinical applications.

6. Using the IMGT Numbering for V and C-Domain for Antibody Description and Engineering

6.1. Antibody V-DOMAIN Humanization by IMGT-CDR Grafting

6.1.1. CDR-IMGT Delimitation for Grafting

For many years, the main source of specific monoclonal antibodies [301] has been from mouse or rat species, owing to the difficulty of obtaining human monoclonal antibodies by the hybridoma methodology. The objective of antibody humanization has been to graft at the DNA level the CDR of an antibody V domain, from mouse (or other species) and of a given specificity, onto the V domain framework of a human antibody, thus preserving the specificity of the original (murine or other species) antibody while decreasing its immunogenicity [302]. The Contact analysis of IG/Ag complexes in IMGT/3Dstructure-DB [57,58,59] and their analysis [303] demonstrate the preponderance of the CDR-IMGT amino acids in the paratope [298] (Figure 31; Figure 32). IMGT/DomainGapAlign [58,79,80] has become the IMGT reference tool for antibody humanization design based on CDR grafting. Indeed, it precisely defines the CDR-IMGT to be grafted and helps selecting the most appropriate human FR-IMGT by providing the alignment of the amino acid sequences between the mouse (or other species) and the closest human V-DOMAIN [90,91,92,93,94,95,96,97,98,99,100] (IMGT® http://www.imgt.org, The IMGT Biotechnology page > Antibody humanization).
Analyses performed on humanized therapeutic antibodies underline the importance of a correct delimitation of the CDR and FR. As an example, two amino acid changes were required in the first version of the humanized VH of alemtuzumab, in order to restore the specificity and affinity of the original rat antibody. The positions of these amino acid changes (S28 > F and S35 > F) are now known to be located in the CDR1-IMGT and should have been directly grafted, but at the time of this mAb humanization they were considered as belonging to the FR according to the Kabat numbering [118]. In contrast, positions 66-74 were, at the same time, considered as belonging to the CDR according to the Kabat numbering, whereas they clearly belong to the FR2-IMGT and the corresponding sequence should have been ‘human’ instead of being grafted from the ‘rat’ sequence (IMGT® http://www.imgt.org, The IMGT Biotechnology page > Antibody humanization > Alemtuzumab).

6.1.2. Amino Acid Interactions between FR-IMGT and CDR-IMGT

IMGT Colliers de Perles from crystallized 3D structures in IMGT/3Dstructure-DB [57,58,59] highlight two conserved hydrogen bonds between FR-IMGT and CDR-IMGT positions: FR2-IMGT 39 with CDR2-IMGT 56 (or 57) and FR2-IMGT 40 with CDR3-IMGT 105 (Figure 21). Antibody engineering and humanization should therefore preserve these bondings which stabilize the loops. It is also worthwhile to note that, in VH CDR3, the stem of the CDR3 loop is stabilized by a conserved salt bridge between R106 (arginine contributed by the 3′V-REGION) and D116 (aspartate contributed by the 5′J-REGION of the Homo sapiens IGHJ2, IGHJ3, IGHJ4, IGHJ5 or IGHJ6) (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 2. Proteins and alleles > 2. Alignments of alleles > IGHJ > Mammalia > human (Homo sapiens)).

6.2. Only-Heavy-Chain Antibodies

6.2.1. Dromedary IgG2 and IgG3

The dromedary or Arabian camel (Camelus dromedarius) IGHV3 genes belong to two sets based on four AA differences which have been linked to two antibody formats expressed in Camelidae: the conventional IG (H2L2) and the “only-heavy-chain” IG (H2, i.e., no light chain and only two identical H-gamma chains lacking CH1) [304] (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 2. Proteins and alleles > 1. Protein displays > V-REGION > IGHV > Arabian camel (Camelus dromedarius)). The AA differences characteristic of each set are located at four FR2-IMGT positions, 42, 49, 50 and 52 (42 in the C strand, 49, 50 and 52 in the C’ strand), and belong to the [GFCC’C”] sheet at the hydrophobic VH-VL interface in conventional antibodies of Camelidae as well as of any vertebrate species [1] whereas, in camelid ‘only-heavy-chain’ antibodies (no light chains, and therefore no VL), these positions are exposed to the environment with, through evolution, a selection of hydrophilic amino acids [305].
The first set of IGHV3 genes is expressed in conventional tetrameric IgG1 that constitute 25% of circulating antibodies. The second set is expressed in ‘only-heavy-chain’ IgG2 and IgG3 that constitute 75% of the circulating antibodies [304]. The respective H-gamma2 and H-gamma3 chains are both characterized by the absence of the CH1 domain owing to a splicing defect [306]. It is the absence of CH1 which is responsible for the lack of association of the light chains (see 6.1.2) (Figure 33) (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 1. Locus and Genes > 7. Gene tables; ibid., IMGT Biotechnology page > Characteristics of the camelidae (camel, llama) antibody synthesis). Only-heavy-chain antibodies is a feature of the Camelidae IG as they have also been found in the Bactrian camel (Camelus bactrianus) of Central Asia and in the llama (Lama glama) and alpaca (Vicugna pacos) of South America. The genetic event (splicing defect) responsible for the lack of CH1 occurred in their common ancestor before the radiation between the ‘camelini’ and ‘lamini’, dating approximately 11 million years (Ma) ago.
The V domains of Camelidae ‘only-heavy-chain’ antibodies have characteristics for potential pharmaceutical applications (e.g., specificities with binding to protein clefts for those with extended CDR3, easy production and selection of single-domain format with novel specificities). They are designated as VHH domain when they have to be distinguished from conventional VH (the V sequence criterion is based on the four AA at positions 42, 49, 50 and 52, particularly 49 and 50, with E49 (or Q49) and R50 in VHH, and G49 and L50 (or P50) in VH. A more complete knowledge of the germline genes is required to identify somatic mutations from genetic polymorphisms, for the other positions. Most llama VHH have normal or long CDR3-IMGT and, as expected from Arabian camel, have E49 (or Q49) and R50 (i.e., llama anti-TNF 5m2i [8.8.16] and 5m2m [12.8.18] [307], or llama anti-HIV 5hm1 [8.7.14] [308]). However some llama VHH, defined as having no paired VL, were found unexpectedly to have the conventional G49 and L50, and to be characterized by a short CDR3-IMGT of 8 amino acids and Arg R118 (instead of J-TRP W118) (i.e., 5m2j [8.8.8] [307]). The selection of the J-REGION R118 (instead of W118, in the IGHJ 118-121 ‘W-G-X-G’ motif, G strand of the V domain) and that of the V-REGION R50 (instead of L50 or P50, in the IGHV, C’ strand of the V domain) represent therefore two different evolutionary paths which make the G-F-C-C’ layer of the VHH more hydrophilic (Figure 21). The term ‘nanobody’ initially used for describing a single-domain format antibody is not equivalent to VHH, as it has been used for V domains other than VHH and for constructs containing more than one V domain and is a registered mark (VH and/or VHH) (e.g., caplacizumab, ozoralizumab) (IMGT® http://www.imgt.org, IMGT/mAb-DB > caplacizumab; ibid. ozoralizumab).

6.2.2. Human Heavy Chain Diseases (HCD)

The camelidae ‘only-heavy-chain’ antibodies synthesis is remarkably reminiscent of what is observed in human heavy chain diseases (HCD). These proliferative disorders of B lymphoid cells produce truncated monoclonal immunoglobulin heavy chains which lack associated light chains. In most HCD, the absence of the heavy chain CH1 domain by deletion or splicing defect may be responsible for the lack of assembly of the light chain [309]. Similar observations have also been reported in mouse variants [309] (IMGT® http://www.imgt.org, IMGT Education > Pathology of the immune system > Molecular defects in Immunoglobulin Heavy Chain Diseases (HCD); ibid., IMGT Lexique > Heavy Chain Diseases (HCD)).

6.2.3. Nurse Shark IgN

A convergence mechanism in evolution is observed in nurse shark Ginglymostoma cirratum (‘Gincir’ in the IMGT 6-letter abbreviaton code for species) IgN antibodies (or IgNAR, ‘immunoglobulin new antigen receptor’) [310] which are ‘only-heavy-chain’ antibodies (H2 homodimeric H-nu chains without CH1, and no associated light chains). The IGHV genes expressed in the Gincir H-nu chains belong to the IGHV2 subgroup and are characterized by the absence of the CDR2-IMGT owing to a deletion that encompasses position 54 to 67. The Gincir IGH genes are organized in duplicated cassettes, and those that express IgN comprise Gincir IGHV2 subgroup genes and an IGHN constant gene (IMGT® http://www.imgt.org, IMGT Repertoire (IG and TR) > 2. Proteins and alleles > 1. Protein displays > IGHV > nurse shark (Ginglymostoma cirratum), ibid., IGHC; ibid., > 1. Locus and genes > 7. Gene tables > IGHV > Chondrichthyes > nurse shark (Ginglymostoma cirratum), ibid., IGHC).

6.3. Contact Analysis of TR-Mimic Antibodies and TR

The IMGT unique numbering has recently allowed the contact analysis comparison between an antibody and a T cell receptor, with a same ligand [311]. Both immunoglobulin, IG Fab 3M4E5, a TR-mimic antibody, and the T cell receptor, TR 1G4_a58b61, target the NY-ESO-1 peptide SLLMWITQC presented by HLA-A*02:01 [312] (Figure 34). IMGT Colliers de Perles on one and two layers and contact analyses of the IG/pMH1 (3gjf, for Fab 3M4E5) and TR/pMH1 (2p5e, for 1G4_a58b61) complexes [311] are available in IMGT/3Dstructure-DB, based on the unique numbering V-DOMAIN for IG and TR [40,41,42], and the IMGT unique numbering for G-DOMAIN for MH [43]. They allow to visualize the features and differences in the antigen recognition by an antibody and a TR targeting the same p/MH antigen (Figure 34). The contacts of the NY-ESO-1 peptide SLLMWITQC with the MH1 HLA-A*02:01 groove are similar in the two peptide-HLA complexes as expected [313,314,315].

6.4. Antibody C-Domain Post-Translational Modifications, Engineering and Allotypes

The constant region of the IG heavy chain is made of several CH domains, which are analysed and described in IMGT® using the IMGT unique numbering [42,44,45,46]. This allows a universal standardized comparison of sequences and 3D structures between C domains of any chain, any receptor and any species. Examples of post-translational modifications (glycosylations), effector properties and engineering at the C-DOMAIN level are given in the following subsections.

6.4.1. N-Linked Glycosylation Sites CH2 N84.4

The N-linked glycosylation site present in the CH2 domain of the constant region of the four human IG H-gamma chains is located at CH2 N84.4. As shown in the IMGT Collier de Perles, this asparagine is localized at the DE turn (Figure 35).
The human glycans are mainly classified as ‘biantennary complex’ structure with a core fucose (Fuc) and are often terminated with N-acetylneuraminic acid (Neu5Ac), a sialic acid (Figure 36). The largest N-linked oligosaccharide structure found in human IgG is shown in Figure 36A (left panel). The conserved heptasaccharide core is composed of two N-acetylglucosamine (GlcNAc), three mannose (Man) and two other GlcNAc residues that are β-1,2 linked to α-6 Man and α-3 Man, forming two arms. The bisecting N-acetylglucosamine (GlcNac, NAG) represents around 10% of human IgG glycoforms. The four most abundant glycans in mAb biopharmaceuticals are shown in Figure 36A (right panel). The Fc oligosaccharides are terminated by zero, one or two galactoses and are called G0, G1 or G2, respectively. For G1F, Gal can be on the α1,3-arm or on the α1,6-arm. Additional fucose (Fuc), galactose (Gal), N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc) residues may be present or not, particularly depending on the expression system. Mammalian cell expression systems are the favorite methods for the commercial production of monoclonal antibodies because their protein glycosylation machinery closely resembles that in human. The current marketed antibodies are mainly expressed in CHO (Chinese Hamster Ovary), SP2/0 (mouse myeloma cells), NS0 (Non-Secreting mouse myeloma cells) and hybridomas (Figure 36B).
The graphical representation of the 36 possible structures of IG N-glycans expressed in human cells are available in the IMGT Lexique, with correspondence between the ‘GA’ nomenclature, based on the number of galactose (G) (0, 1 or 2) and sialic acid (A) (0, 1 or 2) at the terminal ends of the arms of the IG N-glycans, and the ‘HN’ nomenclature based on the number of carbohydrates in the glycan composition (H: number of hexoses, N: number of N-acetyl glucosamine), with, if present, S number of sialic acids (IMGT® http://www.imgt.org, IMGT Lexique > Immunoglobulin (IG) or antibody glycosylation).

6.4.2. Knobs-into-Holes

The knobs-into-holes methodology has been proposed for obtaining bispecific antibodies [309]. The aim is to increase interactions between the CH3 domain of two H-gamma1 chains that belong to antibodies with a different specificity to obtain bispecific antibodies. The two amino acids CH3 T22 (B strand) and Y86 (E strand) selected for changes belong to the [ABED] sheet, at the interface of the two Homo sapiens IGHG1 CH3 domains (Figure 37). Interactions of these two amino acids are described in ‘Contact analysis’ in IMGT/3Dstructure-DB [57,58,59] (Figure 37A). The knobs-into-holes methodology consists into an amino acid change on one CH3 domain (here, T22 > Y) that creates a knob, and another amino acid change on the other CH3 domain (here, Y86 > T) that creates a hole, thus favoring increased interactions between the CH3 of the two H-gamma1 chains at both positions 22 and 86 [316] (IMGT® http://www.imgt.org, The IMGT Biotechnology page > Bispecific antibodies > Knobs-into-holes amino acid changes). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).

6.4.3. Interface Ball-and-Socket-Like Joints

The comparison of the interface between the CH2 and CH3 domains from 3D structures of Homo sapiens IGHG2 Fc with the interface in 3D structures of IGHG1 Fc revealed that in all Fc of gamma chains the movement of the CH2 results from a pivoting around a highly conserved ball-and-socket-like joint [317]. Using the IMGT unique numbering for C-domain, the CH2 L15 side chain (last position of the A strand, next to the AB turn) (the ‘ball’) interacts with a pocket (the ‘socket’) formed by CH3 M107, H108, E109 and H115 (FG loop) (Figure 38). The interface is stabilized by two hydrogen bonds: CH2 L15 (O) and CH3 H115 (ND1), CH2 K125 (O) and CH3 Y29 (OH), and by two salt bridges: CH2 K12 (A strand) and CH3 E40 (C strand), CH2 K123 (G strand) and CH3 E109 (FG) (Figure 38). These amino acids are well conserved between the Homo sapiens gamma isotypes and the IGHG genes and alleles except for IGHG3 H115 that shows a polymorphism associated to different G3m allotypes [83]. This ball-and-socket-like joint is a structural feature similar but reversed to that previously described at the VH and CH1 domain interface [318], in which the VH L12, T125 and S127 form the ‘socket’ whereas the CH1 F29 and P30 form the ‘ball’ (IMGT® http://www.imgt.org, IMGT Repertoire > 2. Proteins and alleles > 1. Protein displays > C-DOMAIN with CHS, M and HINGE regions; ibid., IMGT Repertoire > 2. Proteins and alleles > 2. Alignments of alleles > IGHC; ibid., IMGT/3Dstructure-DB > query on Fab).

6.4.4. IGHG Alleles and Gm Allotypes

Allotypes are polymorphic markers of an IG subclass that correspond to amino acid changes and are detected serologically by antibody reagents [83]. In therapeutic antibodies (human, humanized or chimeric), allotypes may represent potential immunogenic epitopes [82], as demonstrated by the presence of antibodies in individuals immunized against these allotypes [83]. For the H-gamma chains, the allotypes are designated as Gm (for gamma marker), and for the H-gamma1 chains as G1m [83]. The allotypes G1m, G2m and G3m are carried by the constant region of the H-gamma1, H-gamma2 and H-gamma3 chains, encoded by the IGHG1, IGHG2 and IGHG3 genes, respectively.
The H-gamma1 chains may express four G1m alleles (combinations of G1m allotypes): G1m3, G1m3,1, G1m17,1, and G1m17,1,2 (and in Negroid populations three additional G1m alleles, Gm17,1,27, Gm17,1,28 and Gm17,1,27,28) [83]. The correspondence between the G1m alleles and IGHG1 alleles is shown in Table 14.
Amino acids involved in the expression of G1m allotypes and localized on the CH1 and CH3 domains of H-gamma1 chains are shown in IMGT Colliers de Perles on two layers and in 3D structures (Figure 39). In the CH1, the lysine at position 120 (K120) in strand G corresponds to the G1m17 allotype [83]. The isoleucine I103 (strand F) is specific of the H-gamma1 chain isotype. If an arginine is expressed at position 120 (R120), the simultaneous presence of R120 and I103 corresponds to the expression of the G1m3 allotype [83]. For isotypes other than H-gamma1, R120 corresponds to the expression of the nG1m17 isoallotype (an isoallotype or nGm is detected by antibody reagents that identify this marker as an allotype in one IgG subclass and as an isotype for other subclasses). In the CH3, the aspartate D12 and leucine L14 (strand A) correspond to G1m1, whereas glutamate E12 and methionine M14 correspond to the nG1m1 isoallotype [83]. A glycine at position 110 corresponds to G1m2, whereas an alanine does not correspond to any allotype (G1m2-negative chain).
Trastuzumab has been engineered in order to obtain the less immunogenic (being most frequent in different populations) allotype G1m17 (CH1 K120), associated to the nG1m1 (CH3 E12, M14) [319], defined using the generic description, as IGHG1*03v, G1m3 > G1m17, nG1m1 (CH1 R120 > K, CH3 E12,M14). The G1m allotypes have been confirmed serologically [82].
The H-gamma2 chains express only one allotype G2m23. G2m23 and the H-gamma2 chains are either G2m23 or G2m. (two dots indicate that a specimen was tested and found to be negative for G2m23 [83]. G2m23 is localized on CH2. Amino acid sequence and 3D structure comparisons show that the G2m23 allotype is correlated with CH2 M45.1, whereas the absence of the allotype (G2m..) is correlated with valine V45.1 [83]. The G2m23-positive H-gamma2 chains are also characterized by the presence of threonine T92 in the CH1, whereas the G2m23-negative chains and the H-gamma chains of other IgG subclasses have proline P92 in the CH1. Being located on the CH1 domain this amino acid change is not involved in the expression of the G2m23 allotype, but owing to the strong linkage on the same chain, the CH1 T92 codon has been used for the molecular characterization of the G2m23 chains [83].
The H-gamma3 chains are the most polymorphic IG chains in humans. Thirteen G3m allotypes are characterized: G3m5, G3m6, G3m10, G3m11, G3m13, G3m14, G3m15, G3m16, G3m21, G3m24, G3m26, G3m27, G3m28 [83]. Three isoallotypes (nG3m5, nG3m11, and nG3m21) have also been characterized. Two G3m allotypes are located on the CH2 of gamma3 chains, G3m16 (W83) and G3m21 (L82), nG3m21 (P82) [83]. The other G3m allotypes form two mosaics on the CH3 [83] (Figure 40). A first mosaic includes G3m11 (S44), nG3m11 (N44), G3m10 (S44, I101)/G3m24 (S44, V101), G3m27 (I101), G3m6 (S44, E98)/G3m13 (S44, Q98). The second mosaic includes G3m 26 (R115), G3m5 (R115, F116)/nG3m5 (H115, Y116)/G3m28 (R115, Y116), G3m14 (M84, R115, F116) and G3m15 (M39, H115, Y116) [83] (Figure 40). The combination of expressed allotypes correspond to haplotypes represented in the IMGT G3m allele butterfly’ representation [83] (Figure 41).
The therapeutical antibody omodenbamab (INN L123, 2020) is an Homo sapiens immunoglobulin G3-kappa, anti-Staphylococcus aureus SpA (Staphylococcal protein A). The C region of the H-gamma3 chains is encoded by IGHG3*01, G3m5* (G3m5,10,11,13,14,26,27) with CH3 S44 (439), M84 (452), Q98 (474), I101 (477), R115 (490) and F116 (491).

6.4.5. IGHG Engineered Variants and Effector Properties

Amino acids in the IGHG constant regions of the IG heavy chains are frequently engineered to modify the effector properties of the therapeutic monoclonal antibodies. Amino acids changes are engineered at positions involved in antibody-dependent cellular (ADCC), antibody-dependent cellular phagocytosis (ADCP), complement-dependent cytotoxicity (CDC), half-life increase, half-IG exchange, and B cell inhibition by coengagement of antigen and FcγR on the same cell [320,321] (IMGT® http://www.imgt.org, The IMGT Biotechnology page > Amino acid positions involved in ADCC, ADCP, CDC, half-life and half-IG exchange).
The IMGT engineered variant nomenclature (Table 15) has been set up for an easier comparison between engineered antibodies [311]. The IMGT engineered variant name comprises the species, the gene name, the letter ‘v’ with a number (e.g., Homo sapiens IGHG1v1), and then the domain(s) with AA change(s) defined by the letter of the novel AA and position in the domain, e.g., CH2, P1.4. In Table 15, correspondence with the Eu numbering is shown between parentheses, whereas in antibody descriptions (i.e., INN proposed and recommended lists), positons between parentheses are those in the antibody chains. The IMGT engineered variants are classified by comparison with the allele *01 of the gene and, if the effects are independent on the alleles, as a reference for the description of the amino acid (AA) changes for the other alleles. In those cases, the same variant (v) number is used for any allele of the same gene in the same species.
Examples of Fc engineered variants from Table 15 [311], found frequently in therapeutical antibodies, include for ADCC and CDC reduction of IgG1, the variant G1v4: CH2 A114 (329), for ADCC and CDC reduction of IgG2, the variant G2v3: CH2 A1.2 (235), A1 (237), S2 (238), A30 (268), L92 (309), S115 (330), S116 (331), and for ADCC and CDC reduction of IgG4, the variant G4v4: CH2 A1.3 (234), A1.2 (235). Half-life increase of IgG1 is obtained with the variant G1v21: CH2 Y15.1 (252), T16 (254), E18 (256). IGHG4 half-IG exchange reduction is obtained with the variant G4v5: h P10 (228). An absence of H-gamma N-glycosylation is obtained by one of the variants affecting the CH2 N84.4, for example, G4v36: CH2 Q84.4 (297).

7. Conclusions

IMGT® bridging genes, structures and functions provides a unique frame for three research axes: deciphering the IG and TR locus, genes and alleles in genomes of vertebrates from fish to humans, identifying clonality and exploring high-throughput repertoires with IMGT/HighV-QUEST and exploiting data from IMGT/mAb-DB, IMGT/2Dstructure-DB and IMGT/3Dstructure-DB towards targeted and customized therapeutic antibodies. Regarding the first axis, IMGT® genomic annotated data are classically displayed in IMGT Repertoire Web Resources (Locus description, Locus representation, Gene tables, Alignments of alleles). So far the number of higher vertebrate species present in the IMGT Web Resources reaches forty. The curated IG and TR genes and alleles are entered in the IMGT/GENE-DB database and the corresponding IMGT® reference directories and used for coherent gene and sequence annotations of IG and TR loci of newly sequenced genomes. Thus the annotation of the IG and TR loci [78,322,323,324,325,326,327] are key to the study and comparison of the expressed adaptive immune repertoires, in normal or pathological situations. The IMGT standardized IG and TR genes and alleles in different species [328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362] offer a unique opportunity for comparison of immune responses and of potential applications in veterinary and human medicine.
IMGT/V-QUEST is the reference tool for the clonality sequence analysis in leukemia and lymphoma [291,292,293,294,363,364,365,366], which has been extended to veterinary species owing to the availability and IMGT® biocuration of the IG and TR loci [346,349,350,351], and the IMGT reference directories. Exploring hight-throughput repertoires with IMGT/HighV-QUEST provides standardized NGS analysis of IG and TR repertoires in experimental engineered (combinatorial libraries) or in physiological conditions (vaccination, immunodeficiency, autoimmune diseases, cancers and infectious diseases). IMGT/HighV-QUEST is particularly well adapted for the analysis of complete V domains of the IG and TR repertoires from B and T subsets, in many experiments and from many individuals (humans or other vertebrate species). It allows the analysis of the content of scFv combinatorial phage display libraries which are classically screened for identification of novel therapeutic antibody specificities [367,368,369,370,371].
Given the importance of the interactions in the antibody specificity and affinity on the one hand and in the antibody pharmacokinetics/pharmacodynamics and half-life on the other hand, the IMGT® integrated and standardized approach provides the genetic knowledge for allowing antibody informatics to answer the needs of targeted and customized therapy in the context of personalized medicine. The INN definition for the -mab integrates the format, target(s), IMGT gene and allele nomenclature, the CDR-IMGT lengths delimitation, the post-translational modifications and the engineered AA changes [60,86,87].
The extension of the IMGT unique numbering to the IgSF [372,373,374,375,376] and to the MhSF [377,378,379] proteins other than IG or TR has opened new perspectives for the standardized description of the polymorphism of the antigens (epitopes belonging to V, C or G domains) and of the Fc receptors (FCGR of the IgSF, FCGRT of the MhSF) and for the characterization of their interactions (antibody/antigen, FcR/antibody). The F domain (for Fibronectin type III domain), the S domain (for Scavenger, of the Scavenger receptor superfamly SrSF) and the A domain (for Apple domain) have been standardized with an IMGT unique numbering. Mass spectrometry has shown promising results in the analysis of the IGHG3 polymorphism and that anti-malarial variable domains [380,381,382]. Using the IMGT unique numbering per domain is the bridge between the biological and computational spheres.

Author Contributions

Conceptualization, methodology, validation, investigation, resources, data curation, writing, review and editing, visualization, project administration, ontology, funding acquisition, M.-P.L. and G.L. All authors have read and agreed to the published version of the manuscript.

Funding

IMGT® was funded in part by the BIOMED1 (BIOCT930038), Biotechnology BIOTECH2 (BIO4CT960037), 5th PCRDT Quality of Life and Management of Living Resources (QLG2-2000-01287), and 6th PCRDT Information Science and Technology (ImmunoGrid, FP6 IST-028069) programmes of the European Union (EU). IMGT® received financial support from the GIS IBiSA, the Agence Nationale de la Recherche (ANR) Labex MabImprove (ANR-10-LABX-53-01), the Région Occitanie Languedoc-Roussillon (Grand Plateau Technique pour la Recherche (GPTR), BioCampus Montpellier. IMGT® is currently supported by the Centre National de la Recherche Scientifique (CNRS), the Ministère de l’Enseignement Supérieur, de la Recherche et de l’Innovation (MESRI) and the University of Montpellier.

Acknowledgments

We thank Safa Aouinti for the IMGT/StatClonotype development, Karima Cherouali and Anjana Kushwaha for the biocuration of the therapeutic monoclonal antibodies in the IMGT/mAb-DB and IMGT/2Dstructure-DB, respectively, François Ehrenmann and Souphatta Sasorith for help with the 3D structure figures. We are grateful to all members of the IMGT® team for their expertise and constant motivation during these 30 years. We thank Cold Spring Harbor Protocol Press for the pdf of the IMGT Booklet available in IMGT references. IMGT® is a registered trademark of CNRS. IMGT® is member of the International Medical Informatics Association (IMIA) and a member of the Global Alliance for Genomics and Health (GA4GH). This work was granted access to the High Performance Computing (HPC) resources of [email protected] and of Centre Informatique National de l’Enseignement Supérieur (CINES) and to Très Grand Centre de Calcul (TGCC) of the Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA) under the allocation 036029 (2010-2020) made by GENCI (Grand Equipement National de Calcul Intensif).

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Lefranc, M.-P. Immunoglobulin and T cell receptor genes: IMGT® and the birth and rise of immunoinformatics. Front. Immunol. 2014, 5, 22. [Google Scholar] [CrossRef]
  2. Lefranc, M.-P.; Lefranc, G. The Immunoglobulin FactsBook; Academic Press: London, UK, 2001; pp. 1–457. [Google Scholar]
  3. Lefranc, M.-P.; Lefranc, G. The T Cell Receptor FactsBook; Academic Press: London, UK, 2001; pp. 1–397. [Google Scholar]
  4. Lefranc, M.-P. Nomenclature of the human immunoglobulin genes. In Current Protocols in Immunology; Coligan, J.E., Bierer, B.E., Margulies, D.E., Shevach, E.M., Strober, W., Eds.; John Wiley and Sons: Hoboken, NJ, USA, 2000; pp. A.1P.1–A.1P.37. [Google Scholar]
  5. Lefranc, M.-P. Nomenclature of the human T cell Receptor genes. In Current Protocols in Immunology; Coligan, J.E., Bierer, B.E., Margulies, D.E., Shevach, E.M., Strober, W., Eds.; John Wiley and Sons: Hoboken, NJ, USA, 2000; pp. A.1O.1–A.1O.23. [Google Scholar]
  6. Lefranc, M.-P. IMGT, the international ImMunoGeneTics information system. In Immunoinformatics: Bioinformatic Strategies for Better Understanding of Immune Function; Bock, G., Goode, J., Eds.; Novartis Foundation Symposium, John Wiley and Sons: Chichester, UK, 2003; Volume 254, pp. 126, discussion 136–142, 216–222, 250–252. [Google Scholar]
  7. Lefranc, M.-P.; Giudicelli, V.; Ginestoux, C.; Chaume, D. IMGT, the international ImMunoGeneTics information system: The reference in immunoinformatics. Stud. Health Technol. Inform. 2003, 95, 74–79. [Google Scholar]
  8. Lefranc, M.-P. IMGT databases, web resources and tools for immunoglobulin and T cell receptor sequence analysis. Leukemia 2003, 17, 260–266. [Google Scholar] [CrossRef]
  9. Lefranc, M.-P. IMGT, the international ImMunoGenetics information system®. In Antibody Engineering Methods and Protocols, 2nd ed.; Lo, B.K.C., Ed.; Methods in Molecular Biology, Series of Humana Press: Totowa, NJ, USA, 2004; Volume 248, pp. 27–49. [Google Scholar] [CrossRef]
  10. Lefranc, M.-P.; Giudicelli, V.; Kaas, Q.; Duprat, E.; Jabado-Michaloud, J.; Scaviner, D.; Ginestoux, C.; Clément, O.; Chaume, D.; Lefranc, G. IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res. 2009, 33, D593–D597. [Google Scholar] [CrossRef]
  11. Lefranc, M.-P. IMGT, the international ImMunoGeneTics information system: A standardized approach for immunogenetics and immunoinformatics. Immunome Res. 2005, 20. [Google Scholar] [CrossRef]
  12. Lefranc, M.-P. IMGT®, the international ImMunoGeneTics information system® for immunoinformatics. Methods for querying IMGT® databases, tools and Web resources in the context of immunoinformatics. In Immunoinformatics: Predicting Immunogenicity in Silico; Chapter 2; Flower, D.R., Ed.; Humana Press: Totowa, NJ, USA, 2007; Volume 409, pp. 19–42. [Google Scholar] [CrossRef]
  13. Lefranc, M.-P.; Giudicelli, V.; Regnier, L.; Duroux, P. IMGT®, a system and an ontology that bridge biological and computational spheres in bioinformatics. Brief. Bioinform. 2008, 9, 263–275. [Google Scholar] [CrossRef] [PubMed]
  14. Lefranc, M.-P. IMGT®, the international ImMunoGeneTics information system® for immunoinformatics. Methods for querying IMGT® databases, tools and Web resources in the context of immunoinformatics. Mol. Biotechnol. 2008, 40, 101–111. [Google Scholar] [CrossRef]
  15. Lefranc, M.-P.; Giudicelli, V.; Ginestoux, C.; Jabado-Michaloud, J.; Folch, G.; Bellahcene, F.; Wu, Y.; Gemrot, E.; Brochet, X.; Lane, J.; et al. IMGT®, the international ImMunoGeneTics information system®. Nucleic Acids Res. 2009, 37, D1006–D1012. [Google Scholar] [CrossRef]
  16. Lefranc, M.-P. IMGT, the International ImMunoGeneTics Information System. Cold Spring Harb. Protoc. 2011, 6, 595–603. [Google Scholar] [CrossRef]
  17. Lefranc, M.-P.; Giudicelli, V.; Duroux, P.; Jabado-Michaloud, J.; Folch, G.; Aouinti, S.; Carillon, E.; Duvergey, H.; Houles, A.; Paysan-Lafosse, T.; et al. IMGT®, the international ImMunoGeneTics information system® 25 years on. Nucleic Acids Res. 2015, 43, D413–D422. [Google Scholar] [CrossRef]
  18. Lefranc, M.-P. IMGT® Information System. In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; SpringerScience+Business Media, Springer: New York, NY, USA, 2013; pp. 959–964. [Google Scholar] [CrossRef]
  19. Lefranc, M.-P. Immunoglobulin superfamily (IgSF). In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science+Business Media, Springer: New York, NY, USA, 2013. [Google Scholar] [CrossRef]
  20. Lefranc, M.-P. MH superfamily (MhSF). In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science+Business Media, Springer: New York, NY, USA, 2013. [Google Scholar] [CrossRef]
  21. Giudicelli, V.; Lefranc, M.-P. Ontology for immunogenetics: IMGT-ONTOLOGY. Bioinformatics 1999, 15, 1047–1054. [Google Scholar] [CrossRef]
  22. Giudicelli, V.; Lefranc, M.-P. IMGT-ONTOLOGY: Gestion et découverte de connaissances au sein d’IMGT. In Extraction et Gestion des Connaissances (EGC’2003); Hacid, M.-S., Kodratoff, Y., Boulanger, D., Eds.; Actes des troisièmes journées Extraction et Gestion des Connaissances, Lyon, France, 22–24 janvier 2003; Revue des Sciences et Technologies de l’Information, RSTI, série Revue d’Intelligence Artificielle- Extraction des Connaissances et Apprentissage (RIA-ECA); Hermès Science Publications: Lavoisier, Cachan, Paris, 2003; Volume 17(1-2-3), pp. 13–23. ISBN 2-7462-0631-5. [Google Scholar]
  23. Lefranc, M.-P.; Giudicelli, V.; Ginestoux, C.; Bosc, N.; Folch, G.; Guiraudou, D.; Jabado-Michaloud, J.; Magris, S.; Scaviner, D.; Thouvenin, V.; et al. IMGT-ONTOLOGY for immunogenetics and immunoinformatics. Silico Biol. 2004, 4, 17–29. [Google Scholar]
  24. Lefranc, M.-P. IMGT-ONTOLOGY and IMGT databases, tools and Web resources for immunogenetics and immunoinformatics. Mol. Immunol. 2004, 40, 647–660. [Google Scholar] [CrossRef]
  25. Lefranc, M.-P.; Clément, O.; Kaas, Q.; Duprat, E.; Chastellan, P.; Coelho, I.; Combres, K.; Ginestoux, C.; Giudicelli, V.; Chaume, D.; et al. IMGT-Choreography for Immunogenetics and Immunoinformatics. Silico Biol. 2005, 5, 45–60. [Google Scholar]
  26. Duroux, P.; Kaas, Q.; Brochet, X.; Lane, J.; Ginestoux, C.; Lefranc, M.-P.; Giudicelli, V. IMGT-Kaleidoscope, the formal IMGT-ONTOLOGY paradigm. Biochimie 2008, 90, 570–583. [Google Scholar] [CrossRef]
  27. Lefranc, M.-P. IMGT-ONTOLOGY, IMGT® databases, tools and Web resources for Immunoinformatics. In Immunoinformatics; Schoenbach, C., Ranganathan, S., Brusic, V., Eds.; Immunomics Reviews, Series of Springer Science and Business Media LLC; Springer: New York, NY, USA, 2008; Chapter 1; Volume 1, pp. 1–18. ISBN 978-0-387-72967-1. [Google Scholar]
  28. Giudicelli, V.; Lefranc, M.-P. IMGT-ONTOLOGY 2012. Frontiers in Bioinformatics and Computational Biology. Front. Genet. 2012, 3, 79. [Google Scholar] [CrossRef]
  29. Giudicelli, V.; Lefranc, M.-P. IMGT-ONTOLOGY. In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science+Business Media, Springer: New York, NY, USA, 2013; pp. 964–972. [Google Scholar] [CrossRef]
  30. Lefranc, M.-P. From IMGT-ONTOLOGY IDENTIFICATION axiom to IMGT standardized keywords: For immunoglobulins (IG), T cell receptors (TR), and conventional genes. Cold Spring Harb. Protoc. 2011, 6, 604–613. [Google Scholar] [CrossRef]
  31. Lefranc, M.-P. IMGT-ONTOLOGY, IDENTIFICATION axiom. In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science+Business Media, Springer: New York, NY, USA, 2013. [Google Scholar] [CrossRef]
  32. Lefranc, M.-P. Complementarity Determining Region (CDR-IMGT). In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science+Business Media, Springer: New York, NY, USA, 2013. [Google Scholar] [CrossRef]
  33. Lefranc, M.-P. Framework Region (FR-IMGT). In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science+Business Media, Springer: New York, NY, USA, 2013. [Google Scholar] [CrossRef]
  34. Lefranc, M.-P. From IMGT-ONTOLOGY DESCRIPTION axiom to IMGT standardized labels: For immunoglobulin (IG) and T cell receptor (TR) sequences and structures. Cold Spring Harb. Protoc. 2011, 6, 614–626. [Google Scholar] [CrossRef]
  35. Lefranc, M.-P. IMGT-ONTOLOGY, DESCRIPTION axiom. In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science+Business Media, Springer: New York, NY, USA, 2013. [Google Scholar] [CrossRef]
  36. Lefranc, M.-P. Nomenclature of the human immunoglobulin heavy (IGH) genes. Exp. Clin. Immunogenet. 2001, 18, 100–116. [Google Scholar] [CrossRef]
  37. Lefranc, M.-P. From IMGT-ONTOLOGY CLASSIFICATION axiom to IMGT standardized gene and allele nomenclature: For immunoglobulins (IG) and T cell receptors (TR). Cold Spring Harb. Protoc. 2011, 6, 627–632. [Google Scholar] [CrossRef]
  38. Lefranc, M.-P. IMGT-ONTOLOGY, CLASSIFICATION Axiom. In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science+Business Media, Springer: New York, NY, USA, 2013. [Google Scholar] [CrossRef]
  39. Lefranc, M.-P. Unique database numbering system for immunogenetic analysis. Immunol. Today 1997, 18, 509. [Google Scholar] [CrossRef]
  40. Lefranc, M.-P. The IMGT unique numbering for Immunoglobulins, T cell receptors and Ig-like domains. Immunologist 1999, 7, 132–136. [Google Scholar]
  41. Lefranc, M.-P.; Pommié, C.; Ruiz, M.; Giudicelli, V.; Foulquier, E.; Truong, L.; Thouvenin-Contet, V.; Lefranc, G. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev. Comp. Immunol. 2003, 27, 55–77. [Google Scholar] [CrossRef]
  42. Lefranc, M.-P.; Pommié, C.; Kaas, Q.; Duprat, E.; Bosc, N.; Guiraudou, D.; Jean, C.; Ruiz, M.; Da Piedade, I.; Rouard, M.; et al. IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev. Comp. Immunol. 2005, 29, 185–203. [Google Scholar] [CrossRef] [PubMed]
  43. Lefranc, M.-P.; Duprat, E.; Kaas, Q.; Tranne, M.; Thiriot, A.; Lefranc, G. IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily (MhcSF) G-LIKE-DOMAIN. Dev. Comp. Immunol. 2005, 29, 917–938. [Google Scholar] [CrossRef] [PubMed]
  44. Lefranc, M.-P. IMGT unique numbering for the Variable (V), Constant (C), and Groove (G) domains of IG, TR, MH, IgSF, and MhSF. Cold Spring Harb. Protoc. 2011, 6, 633–642. [Google Scholar] [CrossRef]
  45. Lefranc, M.-P. Immunoinformatics of the V, C, and G domains: IMGT® definitive system for IG, TR and IgSF, MH, and MhSF. In Immunoinformatics: From Biology to Informatics, 2nd ed.; De, R.K., Tomar, N., Eds.; Methods in Molecular Biology, Series of Humana Press; Springer: New York, NY, USA, 2014; Volume 1184, pp. 59–107. [Google Scholar] [CrossRef]
  46. Lefranc, M.-P. IMGT unique numbering. In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science+Business Media, Springer: New York, NY, USA, 2013; pp. 952–959. [Google Scholar] [CrossRef]
  47. Ruiz, M.; Lefranc, M.-P. IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures. Immunogenetics 2002, 53, 857–883. [Google Scholar]
  48. Kaas, Q.; Lefranc, M.-P. IMGT Colliers de Perles: Standardized sequence-structure representations of the IgSF and MhcSF superfamily domains. Curr. Bioinform. 2007, 2, 21–30. [Google Scholar] [CrossRef]
  49. Kaas, Q.; Ehrenmann, F.; Lefranc, M.-P. IG, TR and IgSf, MHC and MhcSF: What do we learn from the IMGT Colliers de Perles? Brief. Funct. Genomic. Proteomic 2007, 6, 253–264. [Google Scholar] [CrossRef]
  50. Lefranc, M.-P. IMGT Collier de Perles for the Variable (V), Constant (C), and Groove (G) domains of IG, TR, MH, IgSF, and MhSF. Cold Spring Harb. Protoc. 2011, 6, 643–651. [Google Scholar] [CrossRef]
  51. Ehrenmann, F.; Giudicelli, V.; Duroux, P.; Lefranc, M.-P. IMGT/Collier de Perles: IMGT Standardized representation of domains (IG, TR, and IgSF Variable and Constant domains, MH and MhSF Groove domains). Cold Spring Harb. Protoc. 2011, 6, 726–736. [Google Scholar] [CrossRef]
  52. Lefranc, M.-P. IMGT Collier de Perles. In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science+Business Media, Springer: New York, NY, USA, 2013; pp. 944–952. [Google Scholar] [CrossRef]
  53. Lefranc, M.-P. IMGT-ONTOLOGY, NUMEROTATION axiom. In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science+Business Media, Springer: New York, NY, USA, 2013. [Google Scholar] [CrossRef]
  54. Lefranc, M.-P.; Giudicelli, V.; Busin, C.; Malik, A.; Mougenot, I.; Déhais, P.; Chaume, D. LIGM-DB/IMGT: An integrated database of Ig and TcR, part of the Immunogenetics database. Ann. N. Y. Acad. Sci. 1995, 764, 47–49. [Google Scholar] [CrossRef]
  55. Giudicelli, V.; Duroux, P.; Ginestoux, C.; Folch, G.; Jabado-Michaloud, J.; Chaume, D.; Lefranc, M.-P. IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. Nucleic Acids Res. 2006, 34, D781–D784. [Google Scholar] [CrossRef]
  56. Giudicelli, V.; Chaume, D.; Lefranc, M.-P. IMGT/GENE-DB: A comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res. 2005, 33, D256–D261. [Google Scholar] [CrossRef]
  57. Kaas, Q.; Ruiz, M.; Lefranc, M.-P. IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic Acids Res. 2004, 32, D208–D210. [Google Scholar] [CrossRef]
  58. Ehrenmann, F.; Kaas, Q.; Lefranc, M.-P. IMGT/3Dstructure-DB and IMGT/DomainGapAlign: A database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF. Nucleic Acids Res. 2010, 38, D301–D307. [Google Scholar] [CrossRef]
  59. Ehrenmann, F.; Lefranc, M.-P. IMGT/3Dstructure-DB: Querying the IMGT Database for 3D Structures in Immunology and Immunoinformatics (IG or Antibodies, TR, MH, RPI, and FPIA). Cold Spring Harb. Protoc. 2011, 6, 750–761. [Google Scholar] [CrossRef]
  60. Poiron, C.; Wu, Y.; Ginestoux, C.; Ehrenmann, F.; Duroux, P.; Lefranc, M.-P. IMGT/mAb-DB: The IMGT® database for therapeutic monoclonal antibodies. In Proceedings of the 11èmes Journées Ouvertes de Biologie. Informatique et Mathématiques (JOBIM), Montpellier, France, 7–9 September 2010. [Google Scholar]
  61. Giudicelli, V.; Chaume, D.; Lefranc, M.-P. IMGT/V-QUEST, an integrated software for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis. Nucleic Acids Res. 2004, 32, W435–W440. [Google Scholar] [CrossRef]
  62. Giudicelli, V.; Lefranc, M.-P. Interactive IMGT on-line tools for the analysis of immunoglobulin and T cell receptor repertoires. In New Research on Immunology; Veskler, B.A., Ed.; Nova Science Publishers Inc.: New York, NY, USA, 2005; pp. 77–105. [Google Scholar]
  63. Brochet, X.; Lefranc, M.-P.; Giudicelli, V. IMGT/V-QUEST: The highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res. 2008, 36, W503–W508. [Google Scholar] [CrossRef]
  64. Giudicelli, V.; Lefranc, M.-P. IMGT® standardized analysis of immunoglobulin rearranged sequences. In Immunoglobulin Gene Analysis in Chronic Lymphocytic Leukemia; Ghia, P., Rosenquist, R., Davi, F., Eds.; Wolters Kluwer Health Italy Ltd.: Milan, Italy, 2008; Chapter 2; pp. 33–52. [Google Scholar]
  65. Giudicelli, V.; Brochet, X.; Lefranc, M.-P. IMGT/V-QUEST: IMGT standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences. Cold Spring Harb. Protoc. 2011, 6, 695–715. [Google Scholar] [CrossRef]
  66. Alamyar, E.; Duroux, P.; Lefranc, M.-P.; Giudicelli, V. IMGT® tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. In Immunogenetics; Christiansen, F., Tait, B., Eds.; Methods in Molecular Biology Series of Humana Press; Springer: New York, NY, USA, 2012; Chapter 32; Volume 882, pp. 569–604. [Google Scholar] [CrossRef]
  67. Yousfi Monod, M.; Giudicelli, V.; Chaume, D.; Lefranc, M.-P. IMGT/JunctionAnalysis: The first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics 2004, 20, i379–i385. [Google Scholar] [CrossRef] [PubMed]
  68. Giudicelli, V.; Lefranc, M.-P. IMGT/JunctionAnalysis: IMGT standardized analysis of the V-J and V-D-J Junctions of the rearranged immunoglobulins (IG) and T cell receptors (TR). Cold Spring Harb. Protoc. 2011, 6, 716–725. [Google Scholar] [CrossRef] [PubMed]
  69. Giudicelli, V.; Protat, C.; Lefranc, M.-P. The IMGT strategy for the automatic annotation of IG and TR cDNA sequences: IMGT/Automat. In Proceedings of the European Conference on Computational Biology (ECCB 2003), Data and Knowledge Bases, Institut National de Recherche en Informatique et en Automatique, Paris, Poster DKB_31, ECCB 2003, Paris, France, 27–30 September 2003; pp. 103–104. [Google Scholar]
  70. Giudicelli, V.; Chaume, D.; Jabado-Michaloud, J.; Lefranc, M.-P. Immunogenetics sequence Annotation: The strategy of IMGT based on IMGT-ONTOLOGY. Stud. Health Technol. Inf. 2005, 116, 3–8. [Google Scholar]
  71. Alamyar, E.; Giudicelli, V.; Duroux, P.; Lefranc, M.-P. IMGT/HighV-QUEST: A high-throughput system and web portal for the analysis of rearranged nucleotide sequences of antigen receptors—High-throughput version of IMGT/V-QUEST. In Proceedings of the 11èmes Journées Ouvertes de Biologie, Informatique et Mathématiques (JOBIM), Montpellier, France, 7–9 September 2010. [Google Scholar]
  72. Alamyar, E.; Giudicelli, V.; Li, S.; Duroux, P.; Lefranc, M.-P. IMGT/HighV-QUEST: The IMGT® web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. Immunome Res. 2012, 8, 26. [Google Scholar]
  73. Li, S.; Lefranc, M.-P.; Miles, J.J.; Alamyar, E.; Giudicelli, V.; Duroux, P.; Freeman, J.D.; Corbin, V.; Scheerlinck, J.-P.; Frohman, M.A.; et al. IMGT/HighV-QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. Nat. Commun. 2013, 4, 2333. [Google Scholar] [CrossRef]
  74. Giudicelli, V.; Duroux, P.; Lavoie, A.; Aouinti, S.; Lefranc, M.-P.; Kossida, S. From IMGT-ONTOLOGY to IMGT/HighV-QUEST for NGS immunoglobulin (IG) and T cell receptor (TR) repertoires in autoimmune and infectious diseases. Autoimmun. Infect. Dis. 2015, 1. [Google Scholar] [CrossRef]
  75. Giudicelli, V.; Duroux, P.; Kossida, S.; Lefranc, M.-P. IG and TR single chain Fragment variable (scFv) sequence analysis: A new advanced functionality of IMGT/V-QUEST and IMGT/HighV-QUEST. BMC Immunol. 2017, 18, 35. [Google Scholar] [CrossRef]
  76. Aouinti, S.; Malouche, D.; Giudicelli, V.; Kossida, S.; Lefranc, M.-P. IMGT/HighV-QUEST statistical significance of IMGT clonotype (AA) diversity per gene for standardized comparisons of next generation sequencing immunoprofiles of immunoglobulins and T cell receptors. PLoS ONE 2015, 10, e0142353, Correction in 2016, 11, e0146702. [Google Scholar] [CrossRef]
  77. Aouinti, S.; Giudicelli, V.; Duroux, P.; Malouche, D.; Kossida, S.; Lefranc, M.-P. IMGT/StatClonotype for pairwise evaluation and visualization of NGS IG and TR IMGT clonotype (AA) diversity or expression from IMGT/HighV-QUEST. Front. Immunol. 2016, 7, 339. [Google Scholar] [CrossRef]
  78. Lane, J.; Duroux, P.; Lefranc, M.-P. From IMGT-ONTOLOGY to IMGT/LIGMotif: The IMGT® standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences. BMC Bioinform. 2010, 11, 223. [Google Scholar] [CrossRef]
  79. Ehrenmann, F.; Lefranc, M.-P. IMGT/DomainGapAlign: IMGT standardized analysis of amino acid sequences of Variable, Constant, and Groove domains (IG, TR, MH, IgSF, MhSF). Cold Spring Harb. Protoc 2011, 6, 737–749. [Google Scholar] [CrossRef] [PubMed]
  80. Ehrenmann, F.; Lefranc, M.-P. IMGT/DomainGapAlign: The IMGT® tool for the analysis of IG, TR, MHC, IgSF and MhcSF domain amino acid polymorphism. In Immunogenetics; Christiansen, F., Tait, B., Eds.; Methods in Molecular Biology Series of Humana Press; Springer: New York, NY, USA, 2012; Chapter 33; Volume 882, pp. 605–633. [Google Scholar] [CrossRef]
  81. Pommié, C.; Levadoux, S.; Sabatier, R.; Lefranc, G.; Lefranc, M.-P. IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties. J. Mol. Recognit. 2004, 17, 17–32. [Google Scholar]
  82. Jefferis, R.; Lefranc, M.-P. Human immunoglobulin allotypes: Possible implications for immunogenicity. MAbs 2009, 1, 332–338. [Google Scholar] [CrossRef] [PubMed]
  83. Lefranc, M.-P.; Lefranc, G. Human Gm, Km and Am allotypes and their molecular characterization: A remarkable demonstration of polymorphism. In Immunogenetics; Christiansen, F., Tait, B., Eds.; Methods in Molecular Biology Series of Humana Press; Springer: New York, NY, USA, 2012; Chapter 34; Volume 882, pp. 635–680. [Google Scholar] [CrossRef]
  84. Lefranc, M.-P. WHO-IUIS Nomenclature Subcommittee for immunoglobulins and T cell receptors report. Immunogenetics 2007, 59, 899–902. [Google Scholar] [CrossRef]
  85. Lefranc, M.-P. WHO-IUIS Nomenclature Subcommittee for immunoglobulins and T cell receptors report August 2007, 13th International Congress of Immunology, Rio de Janeiro, Brazil. Dev. Comp. Immunol. 2008, 32, 461–463. [Google Scholar] [CrossRef]
  86. Lefranc, M.-P. Antibody nomenclature: From IMGT-ONTOLOGY to INN definition. MAbs 2011, 3, 1–2. [Google Scholar] [CrossRef]
  87. World Health Organization International Nonproprietary Names (INN) Programme. INN for Biological and Biotechnological Substances (A Review) - 2019. Available online: http://www.who.int/medicines/services/inn/publication/en/. (accessed on 29 August 2020).
  88. Lefranc, M.-P. Antibody databases and tools: The IMGT® experience. In Therapeutic Monoclonal Antibodies: From Bench to Clinic; Chapter 4; An, Z., Ed.; John Wiley and Sons: Hoboken, NJ, USA, 2009; pp. 91–114. [Google Scholar]
  89. Lefranc, M.-P. Antibody databases: IMGT®, a French platform of world-wide interest. Bases de données anticorps: IMGT®, une plate-forme française d’intérêt mondial. Médecine Sci. 2009, 25, 1020–1023. (In French) [Google Scholar] [CrossRef]
  90. Ehrenmann, F.; Duroux, P.; Giudicelli, V.; Lefranc, M.-P. Standardized sequence and structure analysis of antibody using IMGT®. In Antibody Engineering; Kontermann, R., Dübel, S., Eds.; Springer: Berlin/Heidelberg, Germany, 2010; Chapter 2; Volume 2, pp. 11–31. [Google Scholar]
  91. Lefranc, M.-P.; Ehrenmann, F.; Ginestoux, C.; Duroux, P.; Giudicelli, V. Use of IMGT® databases and tools for antibody engineering and humanization. In Antibody Engineering; Chames, P., Ed.; Methods in Molecular Biology Series of Humana Press; Springer: New York, NY, USA, 2012; Chapter 1; Volume 907, pp. 3–37. [Google Scholar]
  92. Lefranc, M.-P. Immunoglobulins: 25 years of Immunoinformatics and IMGT-ONTOLOGY. Biomolecules 2014, 4, 1102–1139. [Google Scholar] [CrossRef]
  93. Lefranc, M.-P. IMGT® immunoglobulin repertoire analysis and antibody humanization. In Molecular Biology of B Cells, 2nd ed.; Alt, F.W., Honjo, T., Radbruch, A., Reth, M., Eds.; Academic Press, Elsevier Ltd.: London, UK, 2015; Chapter 26; pp. 481–514. ISBN 978-0-12-397933-9. [Google Scholar] [CrossRef]
  94. Lefranc, M.-P. How to use IMGT® for therapeutic antibody engineering. In Handbook of Therapeutic Antibodies, 2nd ed.; Dübel, S., Reichert, J., Eds.; Defining the Right Antibody Composition; Wiley-Blackwell: Hoboken, NJ, USA, 2014; Chapter 10; Volume 1, pp. 229–264. ISBN 978-3-527-68244-7. [Google Scholar]
  95. Alamyar, A.; Giudicelli, V.; Duroux, P.; Lefranc, M.-P. Antibody V and C domain sequence, structure and interaction analysis with special reference to IMGT®. In Monoclonal Antibodies: Methods and Protocols, 2nd ed.; Ossipow, V., Fischer, N., Eds.; Methods in Molecular Biology Series of Humana Press; Springer: New York, NY, USA, 2014; Volume 1131, pp. 337–381. [Google Scholar] [CrossRef]
  96. Lefranc, M.-P. Antibody informatics: IMGT®, the international ImMunoGeneTics information system®, the international ImMunoGeneTics information system®. Microbiol. Spectr. 2014, 2. [Google Scholar] [CrossRef]
  97. Shirai, H.; Prades, C.; Vita, R.; Marcatili, P.; Popovic, B.; Xu, J.; Overington, J.P.; Hirayama, K.; Soga, S.; Tsunoyama, K.; et al. Antibody informatics for drug discovery. Biochim. Biophys. Acta 2014, 1844, 2002–2015. [Google Scholar] [CrossRef]
  98. Lefranc, M.-P. Antibody Informatics: IMGT, the International ImMunoGeneTics Information System. In Antibodies for Infectious Diseases; Crowe, J., Boraschi, D., Rappuoli, R., Eds.; ASM Press: Washington, DC, USA, 2015; pp. 363–379. [Google Scholar] [CrossRef]
  99. Lefranc, M.-P.; Ehrenmann, F.; Kossida, S.; Giudicelli, V.; Duroux, P. Use of IMGT® databases and tools for antibody engineering and humanization. In Antibody Engineering; Nevoltris, D., Chames, P., Eds.; Methods in Molecular Biology Series of Humana Press; Springer: New York, NY, USA, 2018; Volume 1827, pp. 35–69. [Google Scholar] [CrossRef]
  100. Lefranc, M.-P.; Lefranc, G. IMGT® and 30 years of Immunoinformatics Insight in Antibody V and C domain structure and function. Antibodies 2019, 8, 29. [Google Scholar] [CrossRef]
  101. Porter, R.R. The hydrolysis of rabbit Y-globulin and antibodies with crystalline papain. Biochem. J. 1959, 73, 119–126. [Google Scholar] [CrossRef] [PubMed]
  102. Reth, M. Antigen receptor tail clue. Nature 1989, 338, 383–384. [Google Scholar] [CrossRef] [PubMed]
  103. Strosberg, D. Immunologie; Bach, J.F., Ed.; Flammarion Médecine-Sciences: Paris, France, 1986. [Google Scholar]
  104. Burton, D.R. Molecular Genetics of Immunoglobulin; Calabi, F., Neuberger, M.S., Eds.; Elsevier: Oxford, UK, 1987; pp. 1–50. [Google Scholar]
  105. Lefranc, M.-P.; Lefranc, G. Molecular genetics of immunoglobulin allotypes. In The Human IgG Subclasses: Molecular Analysis of Structure, Function and Regulation; Shakib, F., Ed.; Pergamon Press: Oxford, UK, 1990; pp. 43–78. [Google Scholar]
  106. Lefranc, M.-P.; Lefranc, G. Les immunoglobulines humaines. In l’Hématologie de Bernard Dreyfus; Breton-Gorius, J., Reyes, F., Rochant, H., Rosa, J., Vernant, J.P., Eds.; Flammarion Médecine-Sciences: Paris, France, 1992; pp. 197–254. [Google Scholar]
  107. Hamilton, R.G. Handbook of Human Immunology; Leffell, M.S., Donnenberg, A.D., Rose, N.R., Eds.; CRC Press: New York, NY, USA, 1997; pp. 65–109. [Google Scholar]
  108. Janeway, C.A.; Travers, P. Immunobiologie; De Boeck and Larder: Paris, France, 1997; pp. 111–151. [Google Scholar]
  109. Lefranc, G.; Loiselet, J.; Rivat, L.; Ropartz, C. Gm, Km and ISf allotypes in the Lebanese population. Acta Anthropog. 1976, 1, 34–45. [Google Scholar]
  110. Lefranc, G.; Rivat, L.; Serre, J.L.; Lalouel, J.M.; Pison, G.; Loiselet, J.; Ropartz, C.; De Lange, G.; Van Loghem, E. Common and uncommon immunoglobulin haplotypes among Lebanese communities. Hum. Genet. 1978, 41, 197–209. [Google Scholar] [CrossRef]
  111. Lefranc, G.; Rivat, L.; Rivat, C.; Loiselet, J.; Ropartz, C. Evidence for “deleted” or “silent” genes homozygous at the locus coding for the constant region of the gamma3 chain. Am. J. Hum. Genet. 1976, 28, 51–61. [Google Scholar]
  112. Geha, R.S.; Malakian, A.; Lefranc, G.; Chayban, D.; Serre, J.L. Immunologic reconstitution in severe combined immunodeficiency following transplantation with parental bone marrow. Pediatrics 1976, 58, 451–455. [Google Scholar]
  113. Lefranc, G.; Chaabani, H.; Van Loghem, E.; Lefranc, M.-P.; De Lange, G.; Helal, A.N. Simultaneous absence of the human IgG1, IgG2, IgG4 and IgA1 subclasses: Immunological and immunogenetical considerations. Eur. J. Immunol. 1983, 13, 240–244. [Google Scholar] [CrossRef]
  114. Lefranc, M.-P.; Lefranc, G.; Rabbitts, T.H. Inherited deletion of immunoglobulin heavy chain constant region genes in normal human individuals. Nature 1982, 300, 760–762. [Google Scholar] [CrossRef]
  115. Lefranc, M.-P.; Lefranc, G.; de Lange, G.; Out, T.A.; van den Broek, P.J.; van Nieuwkoop, J.; Radl, J.; Helal, A.N.; Chaabani, H.; van Loghem, E.; et al. Instability of the human immunoglobulin heavy chain constant region locus indicated by different inherited chromosomal deletions. Mol. Biol. Med. 1983, 1, 207–217. [Google Scholar]
  116. Wiebe, V.; Helal, A.; Lefranc, M.-P.; Lefranc, G. Molecular analysis of the T17 immunoglobulin CH multigene deletion (del A1-GP-G2-G4-E). Hum. Genet. 1994, 93, 520–528. [Google Scholar] [CrossRef]
  117. Osipova, L.P.; Posukh, O.L.; Wiebe, V.P.; Miyazaki, T.; Matsumoto, H.; Lefranc, G.; Lefranc, M.-P. BamHI-SacI RFLP and Gm analysis of the immunoglobulin IGHG genes in the Northern Selkups (West Siberia): New haplotypes with deletion, duplication and triplication. Hum. Genet. 1999, 105, 530–541. [Google Scholar] [CrossRef] [PubMed]
  118. Kabat, E.A.; Wu, T.T.; Reid-Miller, M.; Perry, H.; Gottesman, K. Sequences of Proteins of Immunological Interest, 4th ed.; U.S. Dept. of Health and Human Services, Public Health Service, National Institutes of Health: Washington, DC, USA, 1987; pp. 165–492.
  119. Huck, S.; Fort, P.; Crawford, D.H.; Lefranc, M.-P.; Lefranc, G. Sequence of a human immunoglobulin gamma 3 heavy chain constant region gene: Comparison with the other human Cgamma genes. Nucleic Acids Res. 1986, 14, 1779–1789. [Google Scholar] [CrossRef] [PubMed]
  120. Huck, S.; Lefranc, G.; Lefranc, M.-P. A human immunoglobulin IGHG3 allele (Gmb0, b1, c3, c5, u) with an IGHG4 converted region and three hinge exons. Immunogenetics 1989, 30, 250–257. [Google Scholar] [CrossRef] [PubMed]
  121. Jefferis, R.; Lund, J.; Pound, J.D. IgG-Fc-mediated effector functions: Molecular definition of interaction sites for effector ligands and the role of glycosylation. Immunol. Rev. 1998, 163, 59–76. [Google Scholar] [CrossRef]
  122. Brack, C.; Hirama, M.; Lenhard-Schuller, R.; Tonegawa, S. A complete immunoglobulin gene is created by somatic recombination. Cell 1978, 15, 1–14. [Google Scholar] [CrossRef]
  123. Tonegawa, S. Somatic generation of antibody diversity. Nature 1983, 302, 575–581. [Google Scholar] [CrossRef]
  124. Weigert, M.; Perry, R.; Kelley, D.; Hunkapiller, T.; Schilling, J.; Hood, J.L. The joining of V and J gene segments creates antibody diversity. Nature 1980, 283, 497–499. [Google Scholar] [CrossRef]
  125. Sakano, H.; Hüppi, K.; Heinrich, G.; Tonegawa, S. Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature 1979, 280, 288–294. [Google Scholar] [CrossRef]
  126. Schatz, D.G.; Oettinger, M.A.; Baltimore, D. The V(D)J recombination activating gene, RAG-1. Cell 1989, 59, 1035–1048. [Google Scholar] [CrossRef]
  127. Oettinger, M.A.; Schatz, D.G.; Gorka, C.; Baltimore, D. RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 1990, 248, 1517–1523. [Google Scholar] [CrossRef] [PubMed]
  128. Early, P.; Huang, H.; Davis, M.; Calame, K.; Hood, L. An immunoglobulin heavy chain variable region gene is generated from three segments of DNA: VH, D and JH. Cell 1980, 19, 981–992. [Google Scholar] [CrossRef]
  129. Max, E.E.; Seidman, J.G.; Leder, P. Sequences of five potential recombination sites encoded close to an immunoglobulin kappa constant region gene. Proc. Natl. Acad. Sci. USA 1979, 76, 3450–3454. [Google Scholar] [CrossRef] [PubMed]
  130. Alt, F.W.; Baltimore, D. Joining of immunoglobulin heavy chain gene segments: Implications from a chromosome with evidence of three D-JH fusions. Proc. Natl. Acad. Sci. USA 1982, 79, 4118–4122. [Google Scholar] [CrossRef]
  131. Landau, N.R.; St John, T.P.; Weissman, I.L.; Wolf, S.C.; Silverstone, A.E.; Baltimore, D. Cloning of terminal transferase cDNA by antibody screening. Proc. Natl. Acad. Sci. USA 1984, 81, 5836–5840. [Google Scholar] [CrossRef]
  132. Lafaille, J.J.; DeCloux, A.; Bonneville, M.; Takagaki, Y.; Tonegawa, S. Junctional sequences of T cell receptor gamma delta genes: Implications for gamma delta T cell lineages and for a novel intermediate of V-(D)-J joining. Cell 1989, 59, 859–870. [Google Scholar] [CrossRef]
  133. Lewis, S.M. P nucleotide insertions and the resolution of hairpin DNA structures in mammalian cells. Proc. Natl. Acad. Sci. USA 1994, 91, 1332–1336. [Google Scholar] [CrossRef]
  134. Gearhart, P.J.; Johnson, N.D.; Douglas, R.; Hood, L. IgG antibodies to phosphorylcholine exhibit more diversity than their IgM counterparts. Nature 1981, 291, 29–34. [Google Scholar] [CrossRef]
  135. Petersen-Mahrt, S.K.; Harris, R.S.; Neuberger, M.S. AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification. Nature 2002, 418, 99–103. [Google Scholar] [CrossRef]
  136. Di Noia, J.; Neuberger, M.S. Altering the pathway of immunoglobulin hypermutation by inhibiting uracil-DNA glycosylase. Nature 2002, 419, 43–48. [Google Scholar] [CrossRef]
  137. Teng, G.; Papavasiliou, F.N. Immunoglobulin somatic hypermutation. Annu. Rev. Genet. 2007, 41, 107–120. [Google Scholar] [CrossRef]
  138. Di Noia, J.M.; Neuberger, M.S. Molecular mechanisms of antibody somatic hypermutation. Annu. Rev. Biochem. 2007, 76, 1–22. [Google Scholar] [CrossRef] [PubMed]
  139. Peled, J.U.; Kuang, F.L.; Iglesias-Ussel, M.D.; Roa, S.; Kalis, S.L.; Goodman, M.F.; Scharff, M.D. The biochemistry of somatic hypermutation. Annu. Rev. Immunol. 2008, 26, 481–511. [Google Scholar] [CrossRef] [PubMed]
  140. Knapp, M.R.; Liu, C.P.; Newell, N.; Ward, R.B.; Tucker, P.W.; Strober, S.; Blattner, F. Simultaneous expression of immunoglobulin mu and delta heavy chains by a cloned B-cell lymphoma: A single copy of the VH gene is shared by two adjacent CH genes. Proc. Natl. Acad. Sci. USA 1982, 79, 2996–3000. [Google Scholar] [CrossRef] [PubMed]
  141. Maki, R.; Roeder, W.; Traunecker, A.; Sidman, C.; Wabl, M.; Raschke, W.; Tonegawa, S. The role of DNA rearrangement and alternative RNA processing in the expression of immunoglobulin delta genes. Cell 1981, 24, 353–365. [Google Scholar] [CrossRef]
  142. Kerr, W.G.; Hendershot, L.M.; Burrows, P.D. Regulation of IgM and IgD expression in human B-lineage cells. J. Immunol. 1991, 146, 3314–3321. [Google Scholar]
  143. Honjo, T.; Kataoka, T. Organization of immunoglobulin heavy chain genes and allelic deletion model. Proc. Natl. Acad. Sci. USA 1978, 75, 2140–2144. [Google Scholar] [CrossRef]
  144. Rabbitts, T.H.; Forster, A.; Dunnick, W.; Bentley, D.L. The role of gene deletion in the immunoglobulin heavy chain switch. Nature 1980, 283, 351–356. [Google Scholar] [CrossRef]
  145. Cory, S.; Adams, J.M. Deletions are associated with somatic rearrangement of immunoglobulin heavy chain genes. Cell 1980, 19, 37–51. [Google Scholar] [CrossRef]
  146. Iwasato, T.; Shimizu, A.; Honjo, T.; Yamagishi, H. Circular DNA is excised by immunoglobulin class switch recombination. Cell 1990, 62, 143–149. [Google Scholar] [CrossRef]
  147. Matsuoka, M.; Yoshida, K.; Maeda, T.; Usuda, S.; Sakano, H. Switch circular DNA formed in cytokine-treated mouse splenocytes: Evidence for intramolecular DNA deletion in immunoglobulin class switching. Cell 1990, 62, 135–142. [Google Scholar] [CrossRef]
  148. Chaudhuri, J.; Basu, U.; Zarrin, A.; Yan, C.; Franco, S.; Perlot, T.; Vuong, B.; Wang, J.; Phan, R.T.; Datta, A.; et al. Evolution of the immunoglobulin heavy chain class switch recombination mechanism. Adv. Immunol. 2007, 94, 157–214. [Google Scholar] [CrossRef] [PubMed]
  149. Stavnezer, J.; Guikema, J.E.J.; Schrader, C.E. Mechanism and regulation of class switch recombination. Annu. Rev. Immunol. 2008, 26, 261–292. [Google Scholar] [CrossRef] [PubMed]
  150. Kluin, P.M.; Kayano, H.; Zani, V.J.; Kluin-Nelemans, H.C.; Tucker, P.W.; Satterwhite, E.; Dyer, M.J. IgD class switching: Identification of a novel recombination site in neoplastic and normal B cells. Eur. J. Immunol. 1995, 25, 3504–3508. [Google Scholar] [CrossRef]
  151. Arpin, C.; de Bouteiller, O.; Razanajaona, D.; Fugier-Vivier, I.; Briere, F.; Banchereau, J.; Lebecque, S.; Liu, Y.J. The normal counterpart of IgD myeloma cells in germinal center displays extensively mutated IgVH gene, Cmu-Cdelta switch, and lambda light chain expression. J. Exp. Med. 1998, 187, 1169–1178. [Google Scholar] [CrossRef]
  152. Liu, Y.J.; de Bouteiller, O.; Arpin, C.; Briere, F.; Galibert, L.; Ho, S.; Martinez-Valdez, H.; Banchereau, J.; Lebecque, S. Normal human IgD+IgM- germinal center B cells can express up to 80 mutations in the variable region of their IgD transcripts. Immunity 1996, 4, 603–613. [Google Scholar] [CrossRef]
  153. Kehry, M.; Ewald, S.; Douglas, R.; Sibley, C.; Raschke, W.; Fambrough, D.; Hood, L. The immunoglobulin mu chains of membrane-bound and secreted IgM molecules differ in their C-terminal segments. Cell 1980, 21, 393–406. [Google Scholar] [CrossRef]
  154. Rabbitts, T.H.; Forster, A.; Milstein, C.P. Human immunoglobulin heavy chain genes: Evolutionary comparisons of C mu, C delta and C gamma genes and associated switch sequences. Nucleic Acids Res. 1981, 9, 4509–4524. [Google Scholar] [CrossRef]
  155. Nelson, K.J.; Haimovich, J.; Perry, R.P. Characterization of productive and sterile transcripts from the immunoglobulin heavy-chain locus: Processing of muM and muS mRNA. Mol. Cell Biol. 1983, 3, 1317–1332. [Google Scholar] [CrossRef]
  156. Blattner, F.R.; Tucker, P.W. The molecular biology of immunoglobulin D. Nature 1984, 307, 417–422. [Google Scholar] [CrossRef]
  157. Hollis, G.F.; Evans, R.J.; Stafford-Hollis, J.M.; Korsmeyer, S.J.; McKearn, J.P. Immunoglobulin lambda light-chain-related genes 14.1 and 16.1 are expressed in pre-B cells and may encode the human immunoglobulin omega light-chain protein. Proc. Natl. Acad. Sci. USA 1989, 86, 5552–5556. [Google Scholar] [CrossRef] [PubMed]
  158. Schiff, C.; Bensmana, M.; Guglielmi, P.; Milili, M.; Lefranc, M.-P.; Fougereau, M. The immunoglobulin lambda-like gene cluster (14.1, 16.1 and F lambda 1) contains gene(s) selectively expressed in pre-B cells and is the human counterpart of the mouse lambda 5 gene. Int. Immunol. 1990, 2, 201–207. [Google Scholar] [CrossRef] [PubMed]
  159. Hieter, P.A.; Korsmeyer, S.J.; Waldmann, T.A.; Leder, P. Human immunoglobulin kappa light-chain genes are deleted or rearranged in lambda-producing B cells. Nature 1981, 290, 368–372. [Google Scholar] [CrossRef]
  160. Korsmeyer, S.J.; Hieter, P.A.; Ravetch, J.V.; Poplack, D.G.; Waldmann, T.A.; Leder, P. Developmental hierarchy of immunoglobulin gene rearrangements in human leukemic pre-B-cells. Proc. Natl. Acad. Sci. USA 1981, 78, 7096–7100. [Google Scholar] [CrossRef]
  161. Mather, E.L.; Perry, R.P. Transcriptional regulation of immunoglobulin V genes. Nucleic Acids Res. 1981, 9, 6855–6867. [Google Scholar] [CrossRef]
  162. Bentley, D.L.; Farrell, P.J.; Rabbitts, T.H. Unrearranged immunoglobulin variable region genes have a functional promoter. Nucleic Acids Res. 1982, 10, 1841–1856. [Google Scholar] [CrossRef] [PubMed]
  163. Kemp, D.J.; Harris, A.W.; Cory, S.; Adams, J.M. Expression of the immunoglobulin C mu gene in mouse T and B lymphoid and myeloid cell lines. Proc. Natl. Acad. Sci. USA 1980, 77, 2876–2880. [Google Scholar] [CrossRef] [PubMed]
  164. Banerji, J.; Olson, L.; Schaffner, W. A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes. Cell 1983, 33, 729–740. [Google Scholar] [CrossRef]
  165. Gillies, S.D.; Morrison, S.L.; Oi, V.T.; Tonegawa, S. A tissue-specific transcription enhancer element is located in the major intron of a rearranged immunoglobulin heavy chain gene. Cell 1983, 33, 717–728. [Google Scholar] [CrossRef]
  166. Mercola, M.; Wang, X.F.; Olsen, J.; Calame, K. Transcriptional enhancer elements in the mouse immunoglobulin heavy chain locus. Science 1983, 221, 663–665. [Google Scholar] [CrossRef]
  167. Neuberger, M.S. Expression and regulation of immunoglobulin heavy chain gene transfected into lymphoid cells. EMBO J. 1983, 2, 1373–1378. [Google Scholar] [CrossRef] [PubMed]
  168. Lefranc, G.; Lefranc, M.-P. Regulation of the immunoglobulin gene transcription. Biochimie 1990, 72, 7–17. [Google Scholar] [CrossRef]
  169. Hayday, A.C.; Gillies, S.D.; Saito, H.; Wood, C.; Wiman, K.; Hayward, W.S.; Tonegawa, S. Activation of a translocated human c-myc gene by an enhancer in the immunoglobulin heavy-chain locus. Nature 1984, 307, 334–340. [Google Scholar] [CrossRef] [PubMed]
  170. Emorine, L.; Kuehl, M.; Weir, L.; Leder, P. A conserved sequence in the immunoglobulin J kappa-C kappa intron: Possible enhancer element. Nature 1983, 304, 447–449. [Google Scholar] [CrossRef] [PubMed]
  171. Gimble, J.M.; Max, E.E. Human immunoglobulin kappa gene enhancer: Chromatin structure analysis at high resolution. Mol. Cell Biol. 1987, 7, 15–25. [Google Scholar] [CrossRef]
  172. Judde, J.G.; Max, E.E. Characterization of the human immunoglobulin kappa gene 3′ enhancer: Functional importance of three motifs that demonstrate B-cell-specific in vivo footprints. Mol. Cell Biol. 1992, 12, 5206–5216. [Google Scholar] [CrossRef]
  173. Mills, F.C.; Harindranath, N.; Mitchell, M.; Max, E.E. Enhancer complexes located downstream of both human immunoglobulin Calpha genes. J. Exp. Med. 1997, 186, 845–858. [Google Scholar] [CrossRef]
  174. Flanagan, J.G.; Rabbitts, T.H. Arrangement of human immunoglobulin heavy chain constant region genes implies evolutionary duplication of a segment containing gamma, epsilon and alpha genes. Nature 1982, 300, 709–713. [Google Scholar] [CrossRef]
  175. Rabbitts, T.H.; Flanagan, J.G.; Lefranc, M.-P. Flexibility and change within the human immunoglobulin gene locus. In Genetic Rearrangement. Proceedings of the Fifth John Innes Symposium “Biological Consequences of DNA Structure and Genome Arrangement”; Chater, K.F., Cullis, C.A., Hopwood, D.A., Johnston, A.W.B., Woolhouse, H.W., Eds.; Croom Helm: London, UK, 1983; pp. 143–154. [Google Scholar]
  176. Keyeux, G.; Lefranc, G.; Lefranc, M.-P. A multigene deletion in the human IGH constant region locus involves highly homologous hot spots of recombination. Genomics 1989, 5, 431–441. [Google Scholar] [CrossRef]
  177. Blomberg, B.B.; Rudin, C.M.; Storb, U. Identification and localization of an enhancer for the human lambda L chain Ig gene complex. J. Immunol. 1991, 147, 2354–2358. [Google Scholar]
  178. Asenbauer, H.; Combriato, G.; Klobeck, H.G. The immunoglobulin lambda light chain enhancer consists of three modules which synergize in activation of transcription. Eur. J. Immunol. 1999, 29, 713–724. [Google Scholar] [CrossRef]
  179. Koshland, M.E. The coming of age of the immunoglobulin J chain. Annu. Rev. Immunol. 1985, 3, 425–453. [Google Scholar] [CrossRef] [PubMed]
  180. Perkins, S.J.; Nealis, A.S.; Sutton, B.J.; Feinstein, A. Solution structure of human Immunoglobulin, M. J. Mol. Biol. 1991, 221, 1345–1366. [Google Scholar] [CrossRef]
  181. Gessner, J.E.; Heiken, H.; Tamm, A.; Schmidt, R.E. The IgG Fc receptor family. Ann. Hematol. 1998, 76, 231–248. [Google Scholar] [CrossRef] [PubMed]
  182. Deisenhofer, J. Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution. Biochemistry 1981, 20, 2361–2370. [Google Scholar] [CrossRef]
  183. Sauer-Eriksson, A.E.; Kleywegt, G.J.; Uhlén, M.; Jones, T.A. Crystal structure of the C2 fragment of streptococcal protein G in complex with the Fc domain of human IgG. Structure 1995, 3, 265–278. [Google Scholar] [CrossRef]
  184. Burmeister, W.P.; Huber, A.H.; Bjorkman, P.J. Crystal structure of the complex of rat neonatal Fc receptor with Fc. Nature 1994, 372, 379–383. [Google Scholar] [CrossRef]
  185. Sondermann, P.; Huber, R.; Oosthuizen, V.; Jacob, U. The 3.2-A crystal structure of the human IgG1 Fc fragment-Fc gammaRIII complex. Nature 2000, 406, 267–273. [Google Scholar] [CrossRef]
  186. Halpern, M.S.; Koshland, M.E. Novel subunit in secretory IgA. Nature 1970, 228, 1276–1278. [Google Scholar] [CrossRef]
  187. Bennich, H.H.; Ishizaka, K.; Johansson, S.G.O.; Rowe, D.S.; Stanworth, D.R.; Terry, W.D. Immunoglobulin E, a new class of human immunoglobulin. World Health Organ. 1968, 38, 151–152. [Google Scholar] [CrossRef]
  188. Ishizaka, K.; Ishizaka, T.; Hornbrook, M.M. Physicochemical properties of reaginic antibody. V. Correlation of reaginic activity with E globulin antibody. J. Immunol. 1966, 97, 840–853. [Google Scholar] [PubMed]
  189. Platts-Mills, T.A.; Heymann, P.W.; Commins, S.P.; Woodfolk, J.A. The discovery of IgE 50 years later. Ann. Allergy Asthma Immunol. 2016, 116, 179–182. [Google Scholar] [CrossRef] [PubMed]
  190. Fitzsimmons, C.M.; Falcone, F.H.; Dunne, D.W. Helminth Allergens, Parasite-Specific IgE, and Its Protective Role in Human Immunity. Front. Immunol. 2014, 5, 61. [Google Scholar] [CrossRef] [PubMed]
  191. Sutton, B.J.; Davies, A.M.; Bax, H.J.; Karagiannis, S.N. IgE antibodies: From structure to function and clinical translation. Antibodies 2019, 8, 19. [Google Scholar] [CrossRef]
  192. Sutton, B.J.; Davies, A.M. Structure and dynamics of IgE-receptor interactions: Fc epsilonRI and CD23/Fc epsilonRII. Immunol. Rev. 2015, 268, 222–235. [Google Scholar] [CrossRef]
  193. Kraft, S.; Kinet, J.-P. New developments in Fc epsilonRI regulation, function and inhibition. Nat. Rev. Immunol. 2007, 7, 365–378. [Google Scholar] [CrossRef]
  194. Untersmayr, E.; Bises, G.; Starkl, P.; Bevins, C.L.; Scheiner, O.; Boltz-Nitulescu, G.; Wrba, F.; Jensen-Jarolim, E. The high affinity IgE receptor Fc epsilonRI is expressed by human intestinal epithelial cells. PLoS ONE 2010, 5, e9023. [Google Scholar] [CrossRef]
  195. Garman, S.C.; Wurzburg, B.A.; Tarchevskaya, S.S.; Kinet, J.P.; Jardetzky, T.S. Structure of the Fc fragment of human IgE bound to its high-affinity receptor Fc epsilonRI alpha. Nature 2000, 406, 259–666. [Google Scholar] [CrossRef]
  196. Wan, T.; Beavil, R.L.; Fabiane, S.M.; Beavil, A.J.; Sohi, M.K.; Keown, M.; Young, R.J.; Henry, A.J.; Owens, R.J.; Gould, H.J.; et al. The crystal structure of IgE Fc reveals an asymmetrically bent conformation. Nat. Immunol. 2002, 3, 681–686. [Google Scholar] [CrossRef]
  197. Davies, A.M.; Allan, E.G.; Keeble, A.H.; Delgado, J.; Cossins, B.P.; Mitropoulou, A.N.; Pang, M.O.Y.; Ceska, T.; Beavil, A.J.; Craggs, G.; et al. Allosteric mechanism of action of the therapeutic anti-IgE antibody omalizumab. J. Biol. Chem. 2017, 292, 9975–9987. [Google Scholar] [CrossRef]
  198. Drinkwater, N.; Cossins, B.P.; Keeble, A.H.; Wright, M.; Cain, K.; Hailu, H.; Oxbrow, A.; Delgado, J.; Shuttleworth, L.K.; Kao, M.W.; et al. Human immunoglobulin E flexes between acutely bent and extended conformations. Nat. Struct. Mol. Biol. 2014, 21, 397–404. [Google Scholar] [CrossRef]
  199. Chen, J.-B.; Ramadani, F.; Pang, M.O.Y.; Beavil, R.L.; Holdom, M.D.; Mitropoulou, A.N.; Beavil, A.J.; Gould, H.J.; Chang, T.-W.; Sutton, B.J.; et al. Structural basis for selective inhibition of immunoglobulin E-receptor interactions by an anti-IgE antibody. Sci. Rep. 2018, 8, 11548. [Google Scholar] [CrossRef] [PubMed]
  200. Yukawa, K.; Kikutani, H.; Owaki, H.; Yamasaki, K.; Yokota, A.; Nakamura, H.; Barsumian, E.L.; Hardy, R.R.; Suemura, M.; Kishimoto, T. A B cell-specific differentiation antigen, CD23, is a receptor for IgE (Fc epsilon R) on lymphocytes. J. Immunol. 1987, 138, 2576–2580. [Google Scholar] [PubMed]
  201. Bonnefoy, J.Y.; Aubry, J.P.; Peronne, C.; Wijdenes, J.; Banchereau, J. Production and characterization of a monoclonal antibody specific for the human lymphocyte low affinity receptor for IgE: CD 23 is a low affinity receptor for IgE. J. Immunol. 1987, 138, 2970–2978. [Google Scholar] [PubMed]
  202. Conrad, D.H.; Ford, J.W.; Sturgill, J.L.; Gibb, D.R. CD23: An overlooked regulator of allergic disease. Curr. Allergy Asthma Rep. 2007, 7, 331–337. [Google Scholar] [CrossRef]
  203. Palaniyandi, S.; Liu, X.; Periasamy, S.; Ma, A.; Tang, J.; Jenkins, M.; Tuo, W.; Song, W.; Keegan, A.D.; Conrad, D.H.; et al. Inhibition of CD23-mediated IgE transcytosis suppresses the initiation and development of allergic airway inflammation. Mucosal Immunol. 2015, 8, 1262–1274. [Google Scholar] [CrossRef]
  204. Cooper, A.M.; Hobson, P.S.; Jutton, M.R.; Kao, M.W.; Drung, B.; Schmidt, B.; Fear, D.J.; Beavil, A.J.; McDonnell, J.M.; Sutton, B.J.; et al. Soluble CD23 controls IgE synthesis and homeostasis in human B cells. J. Immunol. 2012, 188, 3199–3207. [Google Scholar] [CrossRef]
  205. Dhaliwal, B.; Yuan, D.; Pang, M.O.; Henry, A.J.; Cain, K.; Oxbrow, A.; Fabiane, S.M.; Beavil, A.J.; McDonnell, J.M.; Gould, H.J.; et al. Crystal structure of IgE bound to its B-cell receptor CD23 reveals a mechanism of reciprocal allosteric inhibition with high affinity receptor FcεRI. Proc. Natl. Acad. Sci. USA 2012, 109, 12686–12691. [Google Scholar] [CrossRef]
  206. Mitropoulou, A.N.; Bowen, H.; Dodev, T.; Davies, A.M.; Bax, H.; Beavil, R.L.; Beavil, A.J.; Gould, H.J.; James, L.K.; Sutton, B.J. Structure of a patient-derived antibody in complex with allergen reveals simultaneous conventional and superantigen-like recognition. Proc. Natl. Acad. Sci. USA 2018, 115, E8707–E8716. [Google Scholar] [CrossRef]
  207. Lefranc, M.-P. The Human T-cell rearranging gamma (TRG) genes and the gamma T-cell receptor. Biochimie 1988, 70, 901–908. [Google Scholar] [CrossRef]
  208. Lefranc, M.P.; Rabbitts, T.H. The human T-cell receptor gamma (TRG) genes. Trends Biochem. Sci. (TIBS) 1989, 14, 214–218. [Google Scholar] [CrossRef]
  209. Croce, C.M.; Shander, M.; Martinis, J.; Cicurel, L.; D’Ancona, G.G.; Dolby, T.W.; Koprowski, H. Chromosomal location of the genes for human immunoglobulin heavy chains. Proc. Natl. Acad. Sci. USA 1979, 76, 3416–3419. [Google Scholar] [CrossRef] [PubMed]
  210. Kirsch, I.R.; Morton, C.C.; Nakahara, K.; Leder, P. Human immunoglobulin heavy chain genes map to a region of translocations in malignant B lymphocytes. Science 1982, 216, 301–303. [Google Scholar] [CrossRef] [PubMed]
  211. McBride, O.W.; Battey, J.; Hollis, G.F.; Swan, D.C.; Siebenlist, U.; Leder, P. Localization of human variable and constant region immunoglobulin heavy chain genes on subtelomeric band q32 of chromosome 14. Nucleic Acids Res. 1982, 10, 8155–8170. [Google Scholar] [CrossRef] [PubMed]
  212. Shin, E.K.; Matsuda, F.; Nagaoka, H.; Fukita, Y.; Imai, T.; Yokoyama, K.; Soeda, E.; Honjo, T. Physical map of the 3′ region of the human immunoglobulin heavy chain locus: Clustering of autoantibody-related variable segments in one haplotype. EMBO J. 1991, 10, 3641–3645. [Google Scholar] [CrossRef]
  213. Matsuda, F.; Shin, E.K.; Nagaoka, H.; Matsumura, R.; Haino, M.; Fukita, Y.; Taka-ishi, S.; Imai, T.; Riley, J.H.; Anand, R.; et al. Structure and physical map of 64 variable segments in the 3′0.8-megabase region of the human immunoglobulin heavy-chain locus. Nat. Genet. 1993, 3, 88–94. [Google Scholar] [CrossRef]
  214. Cook, G.P.; Tomlinson, I.M.; Walter, G.; Riethman, H.; Carter, N.P.; Buluwela, L.; Winter, G.; Rabbitts, T.H. A map of the human immunoglobulin VH locus completed by analysis of the telomeric region of chromosome 14q. Nat. Genet. 1994, 7, 162–168. [Google Scholar] [CrossRef]
  215. Cook, G.P.; Tomlinson, I.M. The human immunoglobulin VH repertoire. Immunol. Today 1995, 16, 237–242. [Google Scholar] [CrossRef]
  216. Matsuda, F.; Ishii, K.; Bouvagnet, P.; Kuma Ki Hayashida, H.; Miyata, T.; Honjo, T. The complete nucleotide sequence of the human immunoglobulin heavy chain variable region locus. J. Exp. Med. 1998, 188, 2151–2162. [Google Scholar] [CrossRef]
  217. Matsuda, F.; Honjo, T. The human immunoglobulin VH locus. Immunologist 1999, 7, 171–176. [Google Scholar]
  218. Pallarès, N.; Lefebvre, S.; Contet, V.; Matsuda, F.; Lefranc, M.-P. The human immunoglobulin heavy variable genes. Exp. Clin. Immunogenet. 1999, 16, 36–60. [Google Scholar] [CrossRef] [PubMed]
  219. Siebenlist, U.; Ravetch, J.V.; Korsmeyer, S.; Waldmann, T.; Leder, P. Human immunoglobulin D segments encoded in tandem multigenic families. Nature 1981, 294, 631–635. [Google Scholar] [CrossRef] [PubMed]
  220. Buluwela, L.; Albertson, D.G.; Sherrington, P.; Rabbitts, P.H.; Spurr, N.; Rabbitts, T.H. The use of chromosomal translocations to study human immunoglobulin gene organization: Mapping DH segments within 35 kb of the C mu gene and identification of a new DH locus. EMBO J. 1988, 7, 2003–2010. [Google Scholar] [CrossRef] [PubMed]
  221. Ichihara, Y.; Matsuoka, H.; Kurosawa, Y. Organization of human immunoglobulin heavy chain diversity gene loci. EMBO J. 1988, 7, 4141–4150. [Google Scholar] [CrossRef]
  222. Corbett, S.J.; Tomlinson, I.M.; Sonnhammer, E.L.; Buck, D.; Winter, G. Sequence of the human immunoglobulin diversity (D) segment locus: A systematic analysis provides no evidence for the use of DIR segments, inverted D segments, “minor” D segments or D-D recombination. J. Mol. Biol. 1997, 270, 587–597. [Google Scholar] [CrossRef]
  223. Ruiz, M.; Pallarès, N.; Contet, V.; Barbié, V.; Lefranc, M.P. The human immunoglobulin heavy diversity (IGHD) and joining (IGHJ) segments. Exp. Clin. Immunogenet. 1999, 16, 173–184. [Google Scholar] [CrossRef]
  224. Ravetch, J.V.; Siebenlist, U.; Korsmeyer, S.; Waldmann, T.; Leder, P. Structure of the human immunoglobulin mu locus: Characterization of embryonic and rearranged J and D genes. Cell 1981, 27 Pt 2, 583–591. [Google Scholar] [CrossRef]
  225. Krawinkel, U.; Rabbitts, T.H. Comparison of the hinge-coding segments in human immunoglobulin gamma heavy chain genes and the linkage of the gamma 2 and gamma 4 subclass genes. EMBO J. 1982, 1, 403–407. [Google Scholar] [CrossRef] [PubMed]
  226. White, M.B.; Shen, A.L.; Word, C.J.; Tucker, P.W.; Blattner, F.R. Human Immunoglobulin D: Genomic Sequence of the Delta Heavy Chain. Science 1985, 228, 733–737. [Google Scholar] [CrossRef]
  227. Takahashi, N.; Ueda, S.; Obata, M.; Nikaido, T.; Nakai, S.; Honjo, T. Structure of human immunoglobulin gamma genes: Implications for evolution of a gene family. Cell 1982, 29, 671–679. [Google Scholar] [CrossRef] [PubMed]
  228. Lefranc, M.-P.; Rabbitts, T.H. Human immunoglobulin heavy chain A2 gene allotype determination by restriction fragment length polymorphism. Nucleic Acids Res. 1984, 12, 1303–1311. [Google Scholar] [CrossRef] [PubMed]
  229. Ellison, J.W.; Berson, B.J.; Hood, L.E. The nucleotide sequence of a human immunoglobulin C gamma1 gene. Nucleic Acids Res. 1982, 10, 4071–4079. [Google Scholar] [CrossRef] [PubMed]
  230. Max, E.E.; Battey, J.; Ney, R.; Kirsch, I.R.; Leder, P. Duplication and deletion in the human immunoglobulin epsilon genes. Cell 1982, 29, 691–699. [Google Scholar] [CrossRef]
  231. Bensmana, M.; Huck, S.; Lefranc, G.; Lefranc, M.-P. The human immunoglobulin pseudo-gamma IGHGP gene shows no major structural defect. Nucleic Acids Res. 1988, 16, 3108. [Google Scholar] [CrossRef]
  232. Ellison, J.; Hood, L. Linkage and sequence homology of two human immunoglobulin gamma heavy chain constant region genes. Proc. Natl. Acad. Sci. USA 1982, 79, 1984–1988. [Google Scholar] [CrossRef]
  233. Ellison, J.; Buxbaum, J.; Hood, L. Nucleotide sequence of a human immunoglobulin C gamma 4 gene. DNA 1981, 1, 11–18. [Google Scholar] [CrossRef]
  234. Flanagan, J.G.; Rabbitts, T.H. The sequence of a human immunoglobulin epsilon heavy chain constant region gene, and evidence for three non-allelic genes. EMBO J. 1982, 1, 655–660. [Google Scholar] [CrossRef]
  235. Flanagan, J.G.; Lefranc, M.-P.; Rabbitts, T.H. Mechanisms of divergence and convergence of the human immunoglobulin alpha 1 and alpha 2 constant region gene sequences. Cell 1984, 36, 681–688. [Google Scholar] [CrossRef]
  236. Bensmana, M.; Chuchana, P.; Lefranc, G.; Lefranc, M.-P. Sequence of the CH1 and hinge-CH2 exons of the human immunoglobulin IGHA2 A2m(2) allele: Comparison with the nonallelic and allelic IGHA genes. Cytogenet. Cell Genet. 1991, 56, 128. [Google Scholar] [CrossRef]
  237. Scaviner, D.; Barbié, V.; Ruiz, M.; Lefranc, M.-P. Protein displays of the human immunoglobulin heavy, kappa and lambda variable and joining regions. Exp. Clin. Immunogenet. 1999, 16, 234–240. [Google Scholar] [CrossRef]
  238. Migone, N.; Oliviero, S.; de Lange, G.; Delacroix, D.L.; Boschis, D.; Altruda, F.; Silengo, L.; DeMarchi, M.; Carbonara, A.O. Multiple gene deletions within the human immunoglobulin heavy-chain cluster. Proc. Natl. Acad. Sci. USA 1984, 81, 5811–5815. [Google Scholar] [CrossRef]
  239. Lefranc, M.-P.; Lefranc, G. Human immunoglobulin heavy-chain multigene deletions in healthy individuals. FEBS Lett. 1987, 213, 231–237. [Google Scholar] [CrossRef]
  240. Lefranc, M.-P.; Hammarström, L.; Smith, C.I.; Lefranc, G. Gene Deletions in the human immunoglobulin heavy chain constant region locus: Molecular and immunological analysis. Immunodefic. Rev. 1991, 2, 265–281. [Google Scholar] [PubMed]
  241. Lefranc, M.-P.; Lefranc, G. Consanguinity. In Encyclopedia of Genetics; Brenner, S., Miller, J.H., Eds.; Academic Press: London, UK, 2002; Volume 1, pp. 456–457. ISBN 978-0-1222-7080-2. [Google Scholar]
  242. Lefranc, M.-P.; Lefranc, G. Consanguinity. In Brenner’s Encyclopedia of Genetics, 2nd ed.; Maloy, S., Hughes, K., Eds.; Academic Press: San Diego, CA, USA, 2013; Volume 2, pp. 158–162. [Google Scholar]
  243. Bottaro, A.; Cariota, U.; DeMarchi, M.; Carbonara, A.O. Pulsed-field electrophoresis screening for immunoglobulin heavy-chain constant-region (IGHC) multigene deletions and duplications. Am. J. Hum. Genet. 1991, 48, 745–756. [Google Scholar] [PubMed]
  244. Bottaro, A.; Gallina, R.; Brusco, A.; Cariota, U.; Boccazzi, C.; Barilaro, M.R.; Plebani, A.; Ugazio, A.G.; van Leeuwen, A.M.; DeLange, G.G.; et al. Familial clustering of IGHC deletions and duplications: Functional and molecular analysis. Immunogenetics 1993, 37, 356–363. [Google Scholar] [CrossRef]
  245. Brusco, A.; Cariota, U.; Bottaro, A.; Boccazzi, C.; Delange, G.; Van Leewen, A.M.; Galanello, R.; Plebani, A.; Ugazio, A.U.; Guerra, M.G.; et al. Deletions, duplications and triplications of the IGHC region in different Italian populations. Immunodeficiency 1993, 4, 243–244. [Google Scholar]
  246. Brusco, A.; Cariota, U.; Bottaro, A.; Boccazzi, C.; Plebani, A.; Ugazio, A.G.; Galanello, R.; van Leeuwen, A.M.; DeLange, G.G.; Depelchin, S.; et al. Structural and immunologic analysis of gene triplications in the Ig heavy chain constant region locus. J. Immunol. 1994, 152, 129–135. [Google Scholar]
  247. Watson, C.T.; Steinberg, K.M.; Huddleston, J.; Warren, R.L.; Malig, M.; Schein, J.; Willsey, A.J.; Joy, J.B.; Scott, J.K.; Graves, T.A.; et al. Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation. Am. J. Hum. Genet. 2013, 92, 530–546. [Google Scholar] [CrossRef]
  248. Ghanem, N.; Lefranc, M.-P.; Lefranc, G. Definition of the RFLP alleles in the human immunoglobulin IGHG gene locus. Eur. J. Immunol. 1988, 18, 1059–1065. [Google Scholar] [CrossRef]
  249. Ghanem, N.; Bensmana, M.; Dugoujon, J.M.; Constans, J.; Lefranc, M.-P.; Lefranc, G. BamHI and SacI RFLPs of the human immunoglobulin IGHG genes with reference to the Gm polymorphism in African people: Evidence for a major polymorphism. Hum. Genet. 1989, 83, 37–44. [Google Scholar] [CrossRef]
  250. Ghanem, N.; Dugoujon, J.M.; Lefranc, M.-P.; Lefranc, G. BstEII restriction fragment alleles and haplotypes of the human IGHG genes with reference to the BamHI/SacI RFLPs and to the Gm polymorphism. Exp. Clin. Immunogenet. 1989, 6, 39–54. [Google Scholar] [PubMed]
  251. Hammarström, L.; Ghanem, N.; Smith, C.I.E.; Lefranc, G.; Lefranc, M.-P. RFLP of human immunoglobulin genes. Exp. Clin. Immunogenet. 1990, 7, 7–19. [Google Scholar] [PubMed]
  252. Battey, J.; Max, E.E.; McBride, W.O.; Swan, D.; Leder, P. A processed human immunoglobulin epsilon gene has moved to chromosome 9. Proc. Natl. Acad. Sci. USA 1982, 79, 5956–5960. [Google Scholar] [CrossRef] [PubMed]
  253. Malcolm, S.; Barton, P.; Murphy, C.; Ferguson-Smith, M.A.; Bentley, D.L.; Rabbitts, T.H. Localization of human immunoglobulin kappa light chain variable region genes to the short arm of chromosome 2 by in situ hybridization. Proc. Natl. Acad. Sci. USA 1982, 79, 4957–4961. [Google Scholar] [CrossRef]
  254. McBride, O.W.; Hieter, P.A.; Hollis, G.F.; Swan, D.; Otey, M.C.; Leder, P. Chromosomal location of human kappa and lambda immunoglobulin light chain constant region genes. J. Exp. Med. 1982, 155, 1480–1490. [Google Scholar] [CrossRef]
  255. Zachau, H.G. The immunoglobulin kappa locus-or-what has been learned from looking closely at one-tenth of a percent of the human genome. Gene 1993, 135, 167–173. [Google Scholar] [CrossRef]
  256. Zachau, H.G. The human immunoglobulin k genes. Immunologist 1996, 4, 49–54. [Google Scholar]
  257. Huber, C.; Schäble, K.F.; Huber, E.; Klein, R.; Meindl, A.; Thiebe, R.; Lamm, R.; Zachau, H.G. The V kappa genes of the L regions and the repertoire of V kappa gene sequences in the human germ line. Eur. J. Immunol. 1993, 23, 2868–2875. [Google Scholar] [CrossRef]
  258. Schäble, K.F.; Zachau, H.G. The variable genes of the human immunoglobulin kappa locus. Biol. Chem. Hoppe Seyler 1993, 374, 1001–1022. [Google Scholar]
  259. Cox, J.P.; Tomlinson, I.M.; Winter, G. A directory of human germ-line V kappa segments reveals a strong bias in their usage. Eur. J. Immunol. 1994, 24, 827–836. [Google Scholar] [CrossRef]
  260. Schäble, K.; Thiebe, R.; Flügel, A.; Meindl, A.; Zachau, H.G. The human immunoglobulin kappa locus: Pseudogenes, unique and repetitive sequences. Biol. Chem. Hoppe Seyler 1994, 375, 189–199. [Google Scholar] [CrossRef] [PubMed]
  261. Barbié, V.; Lefranc, M.-P. The human immunoglobulin kappa variable (IGKV) genes and joining (IGKJ) segments. Exp. Clin. Immunogenet. 1998, 15, 171–183. [Google Scholar] [CrossRef]
  262. Hieter, P.A.; Maizel, J.V., Jr.; Leder, P. Evolution of human immunoglobulin kappa J region genes. J. Biol. Chem. 1982, 257, 1516–1522. [Google Scholar] [PubMed]
  263. Hieter, P.A.; Max, E.E.; Seidman, J.G.; Maizel, J.V., Jr.; Leder, P. Cloned human and mouse kappa immunoglobulin constant and J region genes conserve homology in functional segments. Cell 1980, 22 Pt 1, 197–207. [Google Scholar] [CrossRef]
  264. Lefranc, M.-P. Nomenclature of the human immunoglobulin kappa (IGK) genes. Exp. Clin. Immunogenet. 2001, 18, 161–174. [Google Scholar] [CrossRef]
  265. Watson, C.T.; Steinberg, K.M.; Graves, T.A.; Warren, R.L.; Malig, M.; Schein, J.; Wilson, R.K.; Holt, R.A.; Eichler, E.E.; Breden, F. Version 2. Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity. Genes Immun. 2015, 16, 24–34. [Google Scholar] [CrossRef]
  266. Erikson, J.; Martinis, J.; Croce, C.M. Assignment of the genes for human lambda immunoglobulin chains to chromosome 22. Nature 1981, 294, 173–175. [Google Scholar] [CrossRef]
  267. Emanuel, B.S.; Cannizzaro, L.A.; Magrath, I.; Tsujimoto, Y.; Nowell, P.C.; Croce, C.M. Chromosomal orientation of the lambda light chain locus: V lambda is proximal to C lambda in 22q11. Nucleic Acids Res. 1985, 13, 381–387. [Google Scholar] [CrossRef] [PubMed]
  268. Dunham, I.; Shimizu, N.; Roe, B.A.; Chissoe, S.; Hunt, A.R.; Collins, J.E.; Bruskiewich, R.; Beare, D.M.; Clamp, M.; Smink, L.J.; et al. The DNA sequence of human chromosome 22. Nature 1999, 402, 489–495. [Google Scholar] [CrossRef] [PubMed]
  269. Frippiat, J.P.; Williams, S.C.; Tomlinson, I.M.; Cook, G.P.; Cherif, D.; Le Paslier, D.; Collins, J.E.; Dunham, I.; Winter, G.; Lefranc, M.-P. Organization of the human immunoglobulin lambda light-chain locus on chromosome 22q11.2. Hum. Mol. Genet. 1995, 4, 983–991. [Google Scholar] [CrossRef] [PubMed]
  270. Kawasaki, K.; Minoshima, S.; Schooler, K.; Kudoh, J.; Asakawa, S.; de Jong, P.J.; Shimizu, N. The organization of the human immunoglobulin lambda gene locus. Genome Res. 1995, 5, 125–135. [Google Scholar] [CrossRef] [PubMed]
  271. Williams, S.C.; Frippiat, J.P.; Tomlinson, I.M.; Ignatovich, O.; Lefranc, M.-P.; Winter, G. Sequence and evolution of the human germline V lambda repertoire. J. Mol. Biol. 1996, 264, 220–232. [Google Scholar] [CrossRef] [PubMed]
  272. Kawasaki, K.; Minoshima, S.; Nakato, E.; Shibuya, K.; Shintani, A.; Schmeits, J.L.; Wang, J.; Shimizu, N. One-megabase sequence analysis of the human immunoglobulin lambda gene locus. Genome Res. 1997, 7, 250–261. [Google Scholar] [CrossRef] [PubMed]
  273. Pallarès, N.; Frippiat, J.P.; Giudicelli, V.; Lefranc, M.-P. The human immunoglobulin lambda variable (IGLV) genes and joining (IGLJ) segments. Exp. Clin. Immunogenet. 1998, 15, 8–18. [Google Scholar] [CrossRef]
  274. Hieter, P.A.; Hollis, G.F.; Korsmeyer, S.J.; Waldmann, T.A.; Leder, P. Clustered arrangement of immunoglobulin lambda constant region genes in man. Nature 1981, 294, 536–540. [Google Scholar] [CrossRef] [PubMed]
  275. Taub, R.A.; Hollis, G.F.; Hieter, P.A.; Korsmeyer, S.; Waldmann, T.A.; Leder, P. Variable amplification of immunoglobulin lambda light-chain genes in human populations. Nature 1983, 304, 172–174. [Google Scholar] [CrossRef]
  276. Dariavach, P.; Lefranc, G.; Lefranc, M.-P. Human immunoglobulin C lambda 6 gene encodes the Kern+Oz-lambda chain and C lambda 4 and C lambda 5 are pseudogenes. Proc. Natl. Acad. Sci. USA. 1987, 84, 9074–9078. [Google Scholar] [CrossRef]
  277. Vasicek, T.J.; Leder, P. Structure and expression of the human immunoglobulin lambda genes. J. Exp. Med. 1990, 172, 609–620. [Google Scholar] [CrossRef]
  278. Lefranc, M.-P. Nomenclature of the human immunoglobulin lambda (IGL) genes. Exp. Clin. Immunogenet. 2001, 18, 242–254. [Google Scholar] [CrossRef]
  279. Lefranc, M.-P.; Lefranc, G. Immunoglobulin lambda (IGL) genes of human and mouse. In Molecular Biology of B Cells; Honjo, T., Alt, F.W., Neuberger, M.S., Eds.; Academic Press, Elsevier Ltd.: Amsterdam, The Netherlands, 2004; pp. 37–59. ISBN 978-0-12-053641-2. [Google Scholar]
  280. Ghanem, N.; Dariavach, P.; Bensmana, M.; Chibani, J.; Lefranc, G.; Lefranc, M.-P. Polymorphism of immunoglobulin lambda constant region genes in populations from France, Lebanon and Tunisia. Exp. Clin. Immunogenet. 1988, 5, 186–195. [Google Scholar]
  281. Kay, P.H.; Moriuchi, J.; Ma, P.J.; Saueracker, E. An unusual allelic form of the immunoglobulin lambda constant region genes in the Japanese. Immunogenetics 1992, 35, 341–343. [Google Scholar] [CrossRef] [PubMed]
  282. Frippiat, J.P.; Dard, P.; Marsh, S.; Winter, G.; Lefranc, M.P. Immunoglobulin lambda light chain orphons on human chromosome 8q11.2. Eur. J. Immunol. 1997, 27, 1260–1265. [Google Scholar] [CrossRef] [PubMed]
  283. Hollis, G.F.; Hieter, P.A.; McBride, O.W.; Swan, D.; Leder, P. Processed genes: A dispersed human immunoglobulin gene bearing evidence of RNA-type processing. Nature 1982, 296, 321–325. [Google Scholar] [CrossRef] [PubMed]
  284. Lefranc, M.-P.; Pallarès, N.; Frippiat, J.P. Allelic polymorphisms and RFLP in the human immunoglobulin lambda light chain locus. Hum. Genet. 1999, 104, 361–369. [Google Scholar] [CrossRef]
  285. Passos Júnior, G.A.; Queiroz, R.G.; Brûlé, A. EcoRI restriction fragment-length polymorphism of the human immunoglobulin variable lambda 8 (IGLV8) subgroup reveals a gene family. Hum. Immunol. 1997, 55, 96–102. [Google Scholar] [CrossRef]
  286. da Silva, M.I.; Passos, G.A. The human immunoglobulin variable lambda locus IGLV9 gene is a monomorphic marker in the urban Brazilian population. Immunol. Lett. 1999, 69, 369–370. [Google Scholar] [CrossRef]
  287. Moraes Junta, C.; Passos, G.A. Genomic EcoRI polymorphism and cosmid sequencing reveal an insertion/deletion and a new IGLV5 allele in the human immunoglobulin lambda variable locus (22q11.2/IGLV). Immunogenetics 2003, 55, 10–15. [Google Scholar] [CrossRef]
  288. Chothia, C.; Lesk, A.M. Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 1987, 196, 901–917. [Google Scholar] [CrossRef]
  289. Chothia, C.; Lesk, A.M.; Tramontano, A.; Levitt, M.; Smith-Gill, S.J.; Air, G.; Sheriff, S.; Padlan, E.A.; Davies, D.; Tulip, W.R.; et al. Conformations of immunoglobulin hypervariable regions. Nature 1989, 342, 877–883. [Google Scholar] [CrossRef]
  290. Al-Lazikani, B.; Lesk, A.M.; Chothia, C. Standard conformations for the canonical structures of immunoglobulins. J. Mol. Biol. 1997, 273, 927–948. [Google Scholar] [CrossRef]
  291. Stamatopoulos, K.; Belessi, C.; Moreno, C.; Boudjograh, M.; Guida, G.; Smilevska, T.; Belhoul, L.; Stella, S.; Stavroyianni, N.; Crespo, M.; et al. Over 20% of patients with chronic lymphocytic leukemia carry stereotyped receptors: Pathogenetic implications and clinical correlations. Blood 2007, 109, 259–270. [Google Scholar] [CrossRef]
  292. Agathangelidis, A.; Darzentas, N.; Hadzidimitriou, A.; Brochet, X.; Murray, F.; Yan, X.J.; Davis, Z.; van Gastel-Mol, E.J.; Tresoldi, C.; Chu, C.C.; et al. Stereotyped B-cell receptors in one third of chronic lymphocytic leukemia: Towards a molecular classification with implications for targeted therapeutic interventions. Blood 2012, 119, 4467–4475. [Google Scholar] [CrossRef] [PubMed]
  293. Kostareli, E.; Gounari, M.; Janus, A.; Murray, F.; Brochet, X.; Giudicelli, V.; Pospisilova, S.; Oscier, D.; Foroni, L.; di Celle, P.F.; et al. Antigen receptor stereotypy across B-cell lymphoproliferations: The case of IGHV4-59/IGKV3-20 receptors with rheumatoid factor activity. Leukemia 2012, 26, 1127–1131. [Google Scholar] [CrossRef] [PubMed]
  294. Xochelli, A.; Bikos, V.; Polychronidou, E.; Galigalidou, C.; Agathangelidis, A.; Charlotte, F.; Moschonas, P.; Davis, Z.; Colombo, M.; Roumelioti, M.; et al. Disease-biased and shared characteristics of the immunoglobulin gene repertoires in marginal zone B cell lymphoproliferations. J. Pathol. 2019, 247, 416–421. [Google Scholar] [CrossRef] [PubMed]
  295. Hemadou, A.; Giudicelli, V.; Smith, M.L.; Lefranc, M.-P.; Duroux, P.; Kossida, S.; Heiner, C.; Hepler, N.L.; Kuijpers, J.; Groppi, A.; et al. Pacific Biosciences sequencing and IMGT/HighV-QUEST analysis of full-length single chain Fragment variable from an in vivo selected phage-display combinatorial library. Front. Immunol. 2017, 8, 1796. [Google Scholar] [CrossRef]
  296. Han, S.Y.; Antoine, A.; Howard, D.; Chang, B.; Chang, W.S.; Slein, M.; Deikus, G.; Kossida, S.; Duroux, P.; Lefranc, M.-P.; et al. Coupling of single molecule, long read sequencing with IMGT/HighV-QUEST analysis expedites identification of SIV gp140-specific antibodies from scFv phage display libraries. Front. Immunol. 2018, 9, 329. [Google Scholar] [CrossRef]
  297. Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235–242. [Google Scholar] [CrossRef]
  298. Lefranc, M.-P. Paratope. In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science+Business Media, Springer: New York, NY, USA, 2013. [Google Scholar] [CrossRef]
  299. Lefranc, M.-P. Epitope. In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science+Business Media, Springer: New York, NY, USA, 2013. [Google Scholar] [CrossRef]
  300. Cho, H.S.; Mason, K.; Ramyar, K.X.; Stanley, A.M.; Gabelli, S.B.; Denney, D.W., Jr.; Leahy, D.J. Structure of the extracellular region of HER2 alone and in complex with the Herceptin Fab. Nature 2003, 421, 756–760. [Google Scholar] [CrossRef]
  301. Köhler, G.; Milstein, C. Continuous cultures of fused cells secreting antibody of predefined specificity. Nature 1975, 256, 495–497. [Google Scholar] [CrossRef]
  302. Riechmann, L.; Clark, M.; Waldmann, H.; Winter, G. Reshaping human antibodies for therapy. Nature 1988, 332, 323–327. [Google Scholar] [CrossRef]
  303. Marillet, S.; Lefranc, M.-P.; Boudinot, P.; Cazals, F. Novel structural parameters of Ig-Ag complexes yield a quantitative description of interaction specificity and binding affinity. Front. Immunol. 2017, 8, 34. [Google Scholar] [CrossRef] [PubMed]
  304. Hamers-Casterman, C.; Atarhouch, T.; Muyldermans, S.; Robinson, G.; Hamers, C.; Bajyana Songa, E.; Bendahman, N.; Hamers, R. Naturally occurring antibodies devoid of light chains. Nature 1993, 363, 446–448. [Google Scholar] [CrossRef] [PubMed]
  305. Nguyen, V.K.; Hamers, R.; Wyns, L.; Muyldermans, S. Camel heavy-chain antibodies: Diverse germline VHH and specific mechanisms enlarge the antigen-binding repertoire. EMBO J. 2000, 19, 921–930. [Google Scholar] [CrossRef] [PubMed]
  306. Nguyen, V.K.; Hamers, R.; Wyns, L.; Muyldermans, S. Loss of splice consensus signal is responsible for the removal of the entire CH1 domain of the functional camel IgG2a heavy chain antibodies. Mol. Immunol. 1999, 36, 515–524. [Google Scholar] [CrossRef]
  307. Beirnaert, E.; Desmyter, A.; Spinelli, S.; Lauwereys, M.; Aarden, L.; Dreier, T.; Loris, R.; Silence, K.; Pollet, C.; Cambillau, C.; et al. Bivalent llama single-domain antibody fragments against tumor necrosis factor have picomolar potencies due to intramolecular interactions. Front. Immunol. 2017, 8, 867. [Google Scholar] [CrossRef]
  308. Strokappe, N.M.; Hock, M.; Rutten, L.; Mccoy, L.E.; Back, J.W.; Caillat, C.; Haffke, M.; Weiss, R.A.; Weissenhorn, W.; Verrips, T. Super potent bispecific llama VHH antibodies neutralize HIV via a combination of gp41 and gp120 epitopes. Antibodies 2019, 8, 38. [Google Scholar] [CrossRef]
  309. Lefranc, M.-P.; Lefranc, G. The constant region genes of the immunoglobulin heavy chains. Mol. Genet. (Life Sci. Adv.) 1988, 7, 39–45. [Google Scholar]
  310. Greenberg, A.S.; Avila, D.; Hughes, M.; Hughes, A.; McKinney, E.C.; Flajnik, M.F. A new antigen receptor gene family that undergoes rearrangement and extensive somatic diversification in sharks. Nature 1995, 374, 168–173. [Google Scholar] [CrossRef]
  311. Lefranc, M.-P.; Lefranc, G. Antibody sequence and structure analyses using IMGT®: 30 years of immunoinformatics. In Computer Aided Antibody Design: Methods and Protocols; Tsumoto, K., Kuroda, D., Eds.; Methods in Molecular Biology Series; Springer Nature: London, UK, in press.
  312. Holland, C.J.; Crean, R.M.; Pentier, J.M.; de Wet, B.; Lloyd, A.; Srikannathasan, V.; Lissin, N.; Lloyd, K.A.; Blicher, T.H.; Conroy, P.J.; et al. Specificity of bispecific T cell receptors and antibodies targeting peptide-HLA. J. Clin. Investig. 2020, 130, 2673–2688. [Google Scholar] [CrossRef]
  313. Kaas, Q.; Chiche, L.; Lefranc, M.-P. IMGT unique numbering for standardized contact analysis of immunoglobulin/antigen and T cell receptor/peptide/MHC complexes. In BIOINFO 2005, Proceedings of the 2005 International Joint Conference of InCoB, AASBi and KSBI; Lee, D., Wong, L., Kim, D.-W., Kim, C., Tan, T.W., Lee, K.-H., Eds.; Kaist Press: Daejeon, Korea, 2005; pp. 209–214. ISBN 89-89453-12-7. [Google Scholar]
  314. Kaas, Q.; Lefranc, M.-P. T cell receptor/peptide/MHC molecular characterization and standardized pMHC contact sites in IMGT/3Dstructure-DB. Silico Biol. 2005, 5, 505–528. [Google Scholar]
  315. Kaas, Q.; Duprat, E.; Tourneur, G.; Lefranc, M.-P. IMGT standardization for molecular characterization of the T cell receptor/peptide/MHC complexes. In Immunoinformatics; Schoenbach, C., Ranganathan, S., Brusic, V., Eds.; Immunomics Reviews, Series of Springer Science and Business Media LL; Springer: New York, NY, USA, 2008; pp. 19–49. ISBN 978-0-387-72967-1. [Google Scholar]
  316. Ridgway, J.B.; Presta, L.G.; Carter, P. Knobs-into-holes’ engineering of antibody CH3 domains for heavy chain heterodimerization. Protein Eng. 1996, 9, 617–621. [Google Scholar] [CrossRef] [PubMed]
  317. Teplyakov, A.; Zhao, Y.; Malia, T.; Obmolova, G.; Gilliland, G.L. IgG2 Fc structure and the dynamic features of the IgG CH2-CH3 interface. Mol. Immunol. 2013, 56, 131–139. [Google Scholar] [CrossRef]
  318. Lesk, A.M.; Chothia, C. Elbow motion in the immunoglobulin involves a molecular ball-and-socket joint. Nature 1988, 335, 188–190. [Google Scholar] [CrossRef] [PubMed]
  319. Carter, P.; Presta, L.; Gorman, C.M.; Ridgway, J.B.; Henner, D.; Wong, W.L.; Rowland, A.M.; Kotts, C.; Carver, M.E.; Shepard, H.M. Humanization of an anti-p185HER2 antibody for human cancer therapy. Proc. Natl. Acad. Sci. USA 1992, 89, 4285–4289. [Google Scholar] [CrossRef] [PubMed]
  320. Wang, X.; Mathieu, M.; Brezski, R.J. IgG Fc engineering to modulate antibody effector functions. Protein Cell 2018, 9, 63–73. [Google Scholar] [CrossRef]
  321. Strohl, W.R. Current progress in innovative engineered antibodies. Protein Cell 2018, 9, 86–120. [Google Scholar] [CrossRef]
  322. Elemento, O.; Gascuel, O.; Lefranc, M.-P. Reconstructing the duplication history of tandemly repeated genes. Mol. Biol. Evol. 2002, 19, 278–288. [Google Scholar] [CrossRef]
  323. Elemento, O.; Lefranc, M.-P. IMGT/PhyloGene: An online software package for phylogenetic analysis of immunoglobulin and T cell receptor genes. Dev. Comp. Immunol. 2003, 27, 763–779. [Google Scholar]
  324. Baum, P.; Pasqual, N.; Thuderoz, F.; Hierle, V.; Chaume, D.; Lefranc, M.-P.; Jouvin-Marche, E.; Marche, N.; Demongeot, J. IMGT/GeneInfo: Enhancing V(D)J recombination database accessibility. Nucleic Acids Res. 2004, 32, D51–D54. [Google Scholar] [CrossRef]
  325. Baum, T.P.; Hierle, V.; Pascal, N.; Bellahcene, F.; Chaume, D.; Lefranc, M.-P.; Jouvin-Marche, E.; Marche, P.N.; Demongeot, J. IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations. BMC Bioinform. 2006, 7, 224. [Google Scholar] [CrossRef]
  326. Bleakley, K.; Giudicelli, V.; Wu, Y.; Lefranc, M.-P.; Biau, G. IMGT standardization for statistical analyses of T cell receptor junctions: The TRAV-TRAJ example. Silico Biol. 2006, 6, 573–588. [Google Scholar]
  327. Bleakley, K.; Lefranc, M.-P.; Biau, G. Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools. BMC Bioinform. 2008, 9, 408. [Google Scholar] [CrossRef] [PubMed]
  328. Artero, S.; Lefranc, M.-P. The Teleostei Immunoglobulin Light IGL1 and IGL2 V., J and C genes. Exp. Clin. Immunogenet. 2000, 17, 162–172. [Google Scholar] [CrossRef] [PubMed]
  329. Artero, S.; Lefranc, M.-P. The Teleostei Immunoglobulin Heavy IGH genes. Exp. Clin. Immunogenet. 2000, 17, 148–161. [Google Scholar] [CrossRef] [PubMed]
  330. Martinez-Jean, C.; Folch, G.; Lefranc, M.-P. Nomenclature and overview of the Mouse (Mus musculus and Mus sp.) Immunoglobulin Kappa (IGK) Genes. Exp. Clin. Immunogenet. 2001, 18, 255–279. [Google Scholar] [CrossRef]
  331. Bosc, N.; Lefranc, M.-P. IMGT Locus in Focus: The mouse (Mus musculus) T cell receptor alpha (TRA) and delta (TRD) variable genes. Dev. Comp. Immunol. 2003, 27, 465–497. [Google Scholar] [CrossRef]
  332. Schwartz, J.C.; Lefranc, M.-P.; Murtaugh, M.-P. Organization, complexity and allelic diversity of the porcine (Sus scrofa domestica) immunoglobulin lambda locus. Immunogenetics 2012, 64, 399–407. [Google Scholar] [CrossRef] [PubMed]
  333. Schwartz, J.C.; Lefranc, M.-P.; Murtaugh, M.P. Evolution of the porcine (Sus scrofa domestica) immunoglobulin kappa locus through germline gene conversion. Immunogenetics 2012, 64, 303–311. [Google Scholar] [CrossRef]
  334. Herzig, C.; Blumerman, S.; Lefranc, M.-P.; Baldwin, C. Bovine T cell receptor gamma variable and constant genes: Combinatorial usage by circulating γδ T cells. Immunogenetics 2006, 58, 138–151. [Google Scholar] [CrossRef]
  335. Conrad, M.L.; Mawer, M.A.; Lefranc, M.-P.; McKinneli, L.; Whitehead, J.; Davis, S.K.; Pettman, R.; Koop, B.F. The genomic sequence of the bovine T cell receptor gamma TRG loci and localization of the TRGC5 cassette. Vet. Immunol. Immunopathol. 2007, 115, 346–356. [Google Scholar] [CrossRef]
  336. Massari, S.; Bellahcene, F.; Vaccarelli, G.; Carelli, G.; Mineccia, M.; Lefranc, M.-P.; Antonacci, R.; Ciccarese, S. The deduced structure of the T cell receptor gamma locus in Canis lupus familiaris. Mol. Immunol. 2009, 46, 2728–2736. [Google Scholar] [CrossRef]
  337. Herzig, T.A.; Lefranc, M.-P.; Baldwin, C.L. Annotation and classification of the bovine T cell receptor delta genes. BMC Genom. 2010, 11, 100. [Google Scholar] [CrossRef]
  338. Antonacci, R.; Mineccia, M.; Lefranc, M.-P.; Ashmaoui, H.M.; Lanave, C.; Piccinni, B.; Pesole, G.; Hassanane, M.S.; Massari, S.; Ciccarese, S. Expression and genomic analyses of Camelus dromedarius T cell receptor delta (TRD) genes reveal a variable domain repertoire enlargement due to CDR3 diversification and somatic mutation. Mol. Immunol. 2011, 48, 1384–1396. [Google Scholar] [CrossRef] [PubMed]
  339. Buonocore, F.; Castro, R.; Randelli, E.; Lefranc, M.-P.; Six, A.; Kuhl, H.; Reinhardt, R.; Facchiano, A.; Boudinot, P.; Scapigliati, G. Diversity, molecular characterization and expression of T cell receptor gamma in a teleost fish, the sea bass (Dicentrarchus labrax, L). PLoS ONE 2012, 7, e47957. [Google Scholar] [CrossRef] [PubMed]
  340. Castro, R.; Jouneau, L.; Pham, H.P.; Bouchez, O.; Giudicelli, V.; Lefranc, M.-P.; Quillet, E.; Benmansour, A.; Cazals, F.; Six, A.; et al. Teleost fish mount complex clonal IgM and IgT responses in spleen upon systemic viral infection. PLoS Pathog. 2013, 9, e1003098. [Google Scholar] [CrossRef] [PubMed]
  341. Ciccarese, S.; Vaccarelli, G.; Lefranc, M.-P.; Tasco, G.; Consiglio, A.; Casadio, R.; Linguiti, G.; Antonacci, R. Characteristics of the somatic hypermutation in the Camelus dromedarius T cell receptor gamma (TRG) and delta (TRD) variable domains. Dev. Comp. Immunol. 2014, 46, 300–313. [Google Scholar] [CrossRef] [PubMed]
  342. Piccinni, B.; Massari, S.; Caputi Jambrenghi, A.; Giannico, F.; Lefranc, M.-P.; Ciccarese, S.; Antonacci, R. Sheep (Ovis aries) T cell receptor alpha (TRA) and delta (TRD) genes and genomic organization of the TRA/TRD locus. BMC Genom. 2015, 16, 709. [Google Scholar] [CrossRef] [PubMed]
  343. Linguiti, G.; Antonacci, R.; Tasco, G.; Grande, F.; Casadio, R.; Massari, S.; Castelli, V.; Consiglio, A.; Lefranc, M.-P.; Ciccarese, S. Genomic and expression analyses of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) loci reveal a similar basic public γδ repertoire in dolphin and human. BMC Genom. 2016, 17, 634. [Google Scholar] [CrossRef]
  344. Yu, G.Y.; Mate, S.; Garcia, K.; Ward, M.D.; Brueggemann, E.; Hall, M.; Kenny, T.; Sanchez-Lockhart, M.; Lefranc, M.-P.; Palacios, G. Cynomolgus macaque (Macaca fascicularis) immunoglobulin heavy chain locus description. Immunogenetics 2016, 68, 417–428. [Google Scholar] [CrossRef] [PubMed]
  345. Deiss, T.C.; Vadnais, M.; Wang, F.; Chen, P.L.; Torkamani, A.; Mwangi, W.; Lefranc, M.-P.; Criscitiello, M.F.; Smider, V.V. Immunogenetic factors driving formation of ultralong VH CDR3 in Bos taurus antibodies. Cell Mol. Immunol. 2019, 16, 53–64. [Google Scholar] [CrossRef] [PubMed]
  346. Martin, J.; Ponstingl, H.; Lefranc, M.-P.; Archer, J.; Sargan, D.; Bradley, A. Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci. Immunogenetics 2018, 70, 223–236. [Google Scholar] [CrossRef]
  347. Magadan, S.; Krasnov, A.; Hadi Saljoqi, S.; Afanasyev, S.; Mondot, S.; Lallias, D.; Castro, R.; Salinas, I.; Sunyer, O.; Hansen, J.; et al. Standardized IMGT® nomenclature of Salmonidae IGH genes, the paradigm of Atlantic salmon and rainbow trout: From genomics to repertoires. Front. Immunol. 2019, 10, 2541. [Google Scholar] [CrossRef] [PubMed]
  348. Mondot, S.; Lantz, O.; Lefranc, M.-P.; Boudinot, P. The T cell receptor (TRA) locus in the rabbit (Oryctolagus cuniculus): Genomic features and consequences for invariant T cells. Eur. J. Immunol. 2019, 49, 2146–2158. [Google Scholar] [CrossRef] [PubMed]
  349. Pégorier, P.; Bertignac, M.; Chentli, I.; Nguefack Ngoune, V.; Folch, G.; Jabado-Michaloud, J.; Hadi-Saljoqi, S.; Giudicelli, V.; Duroux, P.; Lefranc, M.-P.; et al. IMGT® biocuration and comparative study of the T cell receptor beta locus of veterinary species based on Homo sapiens TRB. Front. Immunol. 2020, 11, 821. [Google Scholar] [CrossRef] [PubMed]
  350. Radtanakatikanon, A.; Keller, S.M.; Darzentas, N.; Moore, P.F.; Folch, G.; Nguefack Ngoune, V.; Lefranc, M.-P.; Vernau, W. Topology and expressed repertoire of the Felis catus T cell receptor loci. BMC Genomics. 2020, 21, 20. [Google Scholar] [CrossRef] [PubMed]
  351. Antonacci, R.; Massari, S.; Linguiti, G.; Caputi Jambrenghi, A.; Giannico, F.; Lefranc, M.-P.; Ciccarese, S. Evolution of the T-cell Receptor (TR) loci in the adaptive immune response: The tale of the TRG locus in mammals. Genes 2020, 11, 624. [Google Scholar] [CrossRef]
  352. Buresi, C.; Ghanem, N.; Huck, S.; Lefranc, G.; Lefranc, M.-P. Exon duplication and triplication in the human T-cell receptor gamma constant region genes and RFLP in French, Lebanese, Tunisian, and Black African populations. Immunogenetics 1989, 29, 161–172. [Google Scholar] [CrossRef] [PubMed]
  353. Dard, P.; Lefranc, M.-P.; Osipova LSanchez-Mazas, A. DNA sequence variability of IGHG3 genes associated to the main G3m haplotypes in human populations. Eur. J. Hum. Genet. 2001, 9, 765–772. [Google Scholar] [CrossRef]
  354. Raux, G.; Gilbert, D.; Joly, P.; Martel, P.; Roujeau, J.-C.; Prost, C.; Lefranc, M.-P.; Tron, F. IGHV3 associated restriction fragment length polymorphisms confer susceptibility to bullous pemphigoid. Exp. Clin. Immunogenet. 2001, 18, 59–66. [Google Scholar] [CrossRef]
  355. Chardes, T.; Chapal, N.; Bresson, D.; Bes, C.; Giudicelli, V.; Lefranc, M.-P.; Peraldi-Roux, S. The human anti-thyroid peroxidase autoantibody repertoire in Graves’ and Hashimoto’s autoimmune thyroid diseases. Immunogenetics 2002, 54, 141–157. [Google Scholar] [CrossRef]
  356. Martinez, O.; Gangi, E.; Mordi, D.; Gupta, S.; Dorevitch, S.; Lefranc, M.-P.; Prabhakar, B.S. Diversity in the Complementarity Determining Region 3 (CDR3) of Antibodies from mice with evolving anti-TSHR antibody responses. Endocrinology 2007, 148, 752–761. [Google Scholar] [CrossRef]
  357. Robert, R.; Lefranc, M.-P.; Ghochikyan, A.; Agadjanyan, M.G.; Cribbs, D.H.; Van Nostrand, W.E.; Wark, K.L.; Dolezal, O. Restricted V gene usage and VH/VL pairing of mouse humoral response against the N-terminal immunodominant epitope of the amyloid β peptide. Mol. Immunol. 2010, 48, 59–72. [Google Scholar] [CrossRef]
  358. Magdelaine-Beuzelin, C.; Kaas, Q.; Wehbi, V.; Ohresser, M.; Jefferis, R.; Lefranc, M.-P.; Watier, H. Structure-function relationships of the variable domains of monoclonal antibodies approved for cancer treatment. Crit. Rev. Oncol. Hematol. 2007, 64, 210–225. [Google Scholar] [CrossRef] [PubMed]
  359. Magdelaine-Beuzelin, C.; Vermeire, S.; Goodall, M.; Baert, F.; Noman, M.; Van Assche, G.; Ohresser, M.; Degenne, D.; Dugoujon, J.M.; Jefferis, R.; et al. IgG1 heavy chain-coding gene polymorphism (G1m allotypes) and development of antibodies-to-infliximab. Pharm. Genom. 2009, 19, 383–387. [Google Scholar] [CrossRef]
  360. Giest, S.; McWinnie, A.; Lefranc, M.-P.; Little, A.M.; Grace, S.; Mackinnon, S.; Madrigal, J.A.; Travers, P.J. CMV specific CD8+ T cells targeting different peptide / HLA combinations demonstrate varying T cell receptor diversity. Immunology 2012, 135, 27–39. [Google Scholar] [CrossRef] [PubMed]
  361. Ouled-Haddou, H.; Ghamlouch, H.; Regnier, A.; Trudel, S.; Herent, D.; Lefranc, M.-P.; Marolleau, J.; Gubler, B. Characterization of a new V gene replacement in the absence of activation-induced cytidine deaminase and its contribution to human BcR diversity. Immunology 2014, 141, 268–275. [Google Scholar] [CrossRef] [PubMed]
  362. Li, L.; Wang, X.H.; Williams, C.; Volsky, B.; Steczko, O.; Seaman, M.S.; Luthra, K.; Nyambi, P.; Nadas, A.; Giudicelli, V.; et al. A broad range of mutations in HIV-1 neutralizing human monoclonal antibodies specific for V2, V3, and the CD4 binding site. Mol. Immunol. 2015, 66, 364–374. [Google Scholar] [CrossRef] [PubMed]
  363. Abed, R.E.; Khechine, A.E.; Omri, H.E.; Youssef, S.; Laatiri, A.; Lefranc, M.-P.; Khelif, A.; Soua, Z. Chemiluminescent detection of clonal immunoglobulin and T cell receptor gene rearrangements in Tunisian lymphoid malignancies, leukemias and lymphomas. Leuk. Lymphoma 2006, 47, 1129–1137. [Google Scholar] [CrossRef] [PubMed]
  364. Besbes, S.; Hamadou, W.S.; Boulland, M.L.; Lefranc, M.-P.; Ben Youssef, Y.; Achour, B.; Khelif, A.; Fest, T.; Soua, Z. Combined IKZF1 and IG markers as new tools for diagnosis and minimal residual disease assessment in Tunisian B-ALL. Bull. Cancer 2016, 103, 822–828. [Google Scholar] [CrossRef]
  365. Langerak, A.W.; Brüggemann, M.; Davi, F.; Darzentas, N.; van Dongen, J.J.M.; Gonzalez, D.; Cazzaniga, G.; Giudicelli, V.; Lefranc, M.-P.; Giraud, M.; et al. EuroClonality-NGS consortium. High-throughput immunogenetics for clinical and research applications in immunohematology: Potential and challenges. J. Immunol. 2017, 198, 3765–3774. [Google Scholar] [CrossRef]
  366. Rosenquist, R.; Ghia, P.; Hadzidimitriou, A.; Sutton, L.-A.; Agathangelidis, A.; Baliakas, P.; Darzentas, N.; Giudicelli, V.; Lefranc, M.-P.; Langerak, A.W.; et al. Immunoglobulin gene sequence analysis in chronic lymphocytic leukemia: Updated ERIC recommendations. Leukemia 2017, 31, 1477–1481. [Google Scholar] [CrossRef] [PubMed]
  367. Chassagne, S.; Laffly, E.; Drouet, E.; Herodin, F.; Lefranc, M.-P.; Thullier, P. A high affinity macaque antibody Fab with human-like framework regions obtained from a small phage display immune library. Mol. Immunol. 2004, 41, 539–546. [Google Scholar] [CrossRef] [PubMed]
  368. Laffly, E.; Danjou, L.; Condemine, F.; Vidal, D.; Drouet, E.; Lefranc, M.-P.; Bottex, C.; Thullier, P. Selection of a macaque Fab with human-like framework regions, high affinity, and that neutralizes the protective antigen (PA) of Bacillus anthracis. Antimicrob. Agents Chemother. 2005, 49, 3414–3420. [Google Scholar] [CrossRef]
  369. Pelat, T.; Hust, M.; Laffly, E.; Condemine, F.; Bottex, C.; Vidal, D.; Lefranc, M.-P.; Dubel, S.; Thullier, P. A high affinity, human-like antibody fragment (scFv) neutralising the lethal factor (LF) of Bacillus anthracis by inhibiting PA-LF complex formation. Antimicrob. Agents Chemother. 2007, 51, 2758–2764. [Google Scholar] [CrossRef] [PubMed]
  370. Pelat, T.; Bedouelle, H.; Rees, A.R.; Crennell, S.J.; Lefranc, M.-P.; Thullier, P. Germline humanization of a non-human Primate antibody that neutralizes the anthrax toxin, by in vitro and in silico engineering. J. Mol. Biol. 2008, 384, 1400–1407. [Google Scholar] [CrossRef] [PubMed]
  371. Pelat, T.; Hust, M.; Hale, M.; Lefranc, M.-P.; Dübel, S.; Thullier, P. Isolation of a human-like antibody fragment (scFv) that neutralizes ricin biological activity. BMC Biotechnol. 2009, 9, 60. [Google Scholar] [CrossRef] [PubMed]
  372. Duprat, E.; Kaas, Q.; Garelle, V.; Lefranc, G.; Lefranc, M.-P. IMGT standardization for alleles and mutations of the V-LIKE-DOMAINs and C-LIKE-DOMAINs of the immunoglobulin superfamily. Recent Res. Dev. Hum. Genet. 2004, 2, 111–136. [Google Scholar]
  373. Bertrand, G.; Duprat, E.; Lefranc, M.-P.; Marti, J.; Coste, J. Characterization of human FCGR3B*02 (HNA-1b, NA2) cDNAs and IMGT standardized description of FCGR3B alleles. Tissue Antigens Cover 2004, 64, 119–131. [Google Scholar] [CrossRef]
  374. Bernard, D.; Hansen, J.D.; du Pasquier, L.; Lefranc, M.-P.; Benmansour, A.; Boudinot, P. Costimulatory receptors in jawed vertebrates: Conserved CD28, odd CTLA4 and multiple BTLAs. Dev. Comp. Immunol. 2007, 31, 255–271. [Google Scholar] [CrossRef]
  375. Garapati, V.P.; Lefranc, M.-P. IMGT Colliers de Perles and IgSF domain standardization for T cell costimulatory activatory (CD28, ICOS) and inhibitory (CTLA4, PDCD1 and BTLA) receptors. Dev. Comp. Immunol. 2007, 31, 1050–1072. [Google Scholar] [CrossRef]
  376. Hansen, J.D.; Pasquier, L.D.; Lefranc, M.-P.; Lopez, V.; Benmansour, A.; Boudinot, P. The B7 family of immunoregulatory receptors: A comparative and evolutionary perspective. Mol. Immunol. 2009, 46, 457–472. [Google Scholar] [CrossRef] [PubMed]
  377. Duprat, E.; Lefranc, M.-P.; Gascuel, O. A simple method to predict protein binding from aligned sequences -application to MHC superfamily and beta2-microglobulin. Bioinformatics 2006, 22, 453–459. [Google Scholar] [CrossRef] [PubMed]
  378. Frigoul, A.; Lefranc, M.-P. MICA: Standardized IMGT allele nomenclature, polymorphisms and diseases. In Recent Research Developments in Human Genetics; Pandalai, S.G., Ed.; Research Signpost: Trivandrum, India, 2005; Volume 3, pp. 95–145. ISBN 81-7736-244-5. [Google Scholar]
  379. Boudinot, P.; Mondot, S.; Jouneau, L.; Teyton, L.; Lefranc, M.-P.; Lantz, O. Restricting nonclassical MHC genes coevolve with TRAV genes used by innate-like T cells in mammals. Proc. Natl. Acad. Sci. USA 2016, 113, E2983–E2992. [Google Scholar] [CrossRef] [PubMed]
  380. Dechavanne, C.; Guillonneau, F.; Chiappetta, G.; Sago, L.; Lévy, P.; Salnot, V.; Guitard, E.; Ehrenmann, F.; Broussard, C.; Chafey, P.; et al. Mass spectrometry detection of G3m and IGHG3 alleles and follow-up of differential mother and neonate IgG3. PLoS ONE 2012, 7, e46097. [Google Scholar] [CrossRef] [PubMed]
  381. Dambrun, M.; Dechavanne, C.; Emmanuel, A.; Aussenac, F.; Leduc, M.; Giangrande, C.; Vinh, J.; Dugoujon, J.M.; Lefranc, M.-P.; Guillonneau, F.; et al. Human immunoglobulin heavy gamma chain polymorphisms: Molecular confirmation of proteomic assessment. Mol. Cell Proteom. 2017, 16, 824–839. [Google Scholar] [CrossRef]
  382. Coelho, C.H.; Nadakal, S.T.; Hurtado, P.G.; Morrison, R.; Galson, J.D.; Neal, J.; Wu, Y.; King, C.R.; Price, V.; Miura, K.; et al. Antimalarial Antibody Repertoire Defined by Plasma IG Proteomics and Single B Cell IG Sequencing. Available online: http://videocast.nih.gov/watch=37965 (accessed on 29 August 2020).
Figure 1. An immunoglobulin (IG) or antibody. The structure is that of the antibody b12, an IgG1-kappa, and so far the only complete human IG crystallized (IMGT® http://www.imgt.org, IMGT/3Dstructure-DB > Entry code (PDB): 1hzh). H-GAMMA-1 and L-KAPPA (for the chains), VH, CH1, CH2, CH3, V-KAPPA and C-KAPPA (for the domains) written in capital letters are IMGT standardized labels (DESCRIPTION) [1,34,35]. H-gamma1 and L-kappa, written in small letters in the text, corresponf to the IMGT standardized keywords (IDENTIFICATION) [1,30,31]. The two light chains are identical and the two heavy chains are identical (the different colours are only used for a better visualization). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 1. An immunoglobulin (IG) or antibody. The structure is that of the antibody b12, an IgG1-kappa, and so far the only complete human IG crystallized (IMGT® http://www.imgt.org, IMGT/3Dstructure-DB > Entry code (PDB): 1hzh). H-GAMMA-1 and L-KAPPA (for the chains), VH, CH1, CH2, CH3, V-KAPPA and C-KAPPA (for the domains) written in capital letters are IMGT standardized labels (DESCRIPTION) [1,34,35]. H-gamma1 and L-kappa, written in small letters in the text, corresponf to the IMGT standardized keywords (IDENTIFICATION) [1,30,31]. The two light chains are identical and the two heavy chains are identical (the different colours are only used for a better visualization). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g001
Figure 2. Paired VH and VL domains of an immunoglobulin (IG) or antibody. The VH and VL domains are encoded by a V-D-J-REGION and a V-J-REGION, respectively. The frameworks are colored in grey. The hypervariable loops or complementarity determining regions CDR1-IMGT, CDR2-IMGT and CDR3-IMGT are colored in red, orange and purple for VH, and in blue, green and green-blue for VL, respectively. The six loops of VH and VL constitute the antigen recognition and binding site. The highly conserved amino acids are indicated in red with their position according to the IMGT unique numbering: C23 (1st-CYS), W41 (CONSERVED-TRP), L89 (conserved hydrophobic amino acid), C104 (2nd-CYS 104), W118 (J-TRP) for VH, and F118 (J-PHE) for VL [1,40,41]. 104 and 118 are anchor positions for the CDR3-IMGT (written in red). Anchor positions are, for the CDR1-IMGT, 26 and 39 and, for the CDR2-IMGT, 55 and 66 (written in black). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 2. Paired VH and VL domains of an immunoglobulin (IG) or antibody. The VH and VL domains are encoded by a V-D-J-REGION and a V-J-REGION, respectively. The frameworks are colored in grey. The hypervariable loops or complementarity determining regions CDR1-IMGT, CDR2-IMGT and CDR3-IMGT are colored in red, orange and purple for VH, and in blue, green and green-blue for VL, respectively. The six loops of VH and VL constitute the antigen recognition and binding site. The highly conserved amino acids are indicated in red with their position according to the IMGT unique numbering: C23 (1st-CYS), W41 (CONSERVED-TRP), L89 (conserved hydrophobic amino acid), C104 (2nd-CYS 104), W118 (J-TRP) for VH, and F118 (J-PHE) for VL [1,40,41]. 104 and 118 are anchor positions for the CDR3-IMGT (written in red). Anchor positions are, for the CDR1-IMGT, 26 and 39 and, for the CDR2-IMGT, 55 and 66 (written in black). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g002
Figure 3. B cell differentiation with the antigen independent phase in the bone marrow and the antigen dependent phase in the secondary lymphoid organs [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 3. B cell differentiation with the antigen independent phase in the bone marrow and the antigen dependent phase in the secondary lymphoid organs [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g003
Figure 4. B cell receptor (BcR). The B cell receptor (BcR) on the surface of mature B cells comprises an immunoglobulin (IG) or antibody, here IgM, as a monomer H2L2, anchored in the membrane of the B cell (membrane IG or mIG) and the CD79 signalling coreceptors constituted of two heterodimers CD79A/CD79B (BcR = mIG + CD79 coreceptor). VH, CH1, CH2, CH3 and CH4 indicate the domains of the H-mu chains of the IgM. Depending on the light chain type, L-kappa or L-lambda, VL and CL correspond to V-kappa and C-kappa, or to V-lambda and C-lambda, respectively. ITAM motifs are indicated by the letters YLYL for tyrosyl (Y) and leucyl (L) amino acids. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 4. B cell receptor (BcR). The B cell receptor (BcR) on the surface of mature B cells comprises an immunoglobulin (IG) or antibody, here IgM, as a monomer H2L2, anchored in the membrane of the B cell (membrane IG or mIG) and the CD79 signalling coreceptors constituted of two heterodimers CD79A/CD79B (BcR = mIG + CD79 coreceptor). VH, CH1, CH2, CH3 and CH4 indicate the domains of the H-mu chains of the IgM. Depending on the light chain type, L-kappa or L-lambda, VL and CL correspond to V-kappa and C-kappa, or to V-lambda and C-lambda, respectively. ITAM motifs are indicated by the letters YLYL for tyrosyl (Y) and leucyl (L) amino acids. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g004
Figure 5. Schematic representation of an immunoglobulin [2]. The two inter heavy chain (inter-H) disulfide bridges correspond to those of a human (Homo sapiens) IgG1. The intrachain (Cys 23-Cys 104) disulfide bridge of each of the 12 domains are not shown. The three complementarity regions (CDR1, CDR2 and CDR3) of the VH (V-D-J-region) and of the VL (V-J-region) are indicated by hatches (and numbers 1, 2, 3 for VH). V = V-REGION (in green), J = J-REGION (in yellow), D = D-REGION (or more exactly N-AND-D-REGION to take into account the N-diversity) (in red), the C-REGION is in blue (dark blue for the heavy (H) chain, light blue for the light (L) chain). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 5. Schematic representation of an immunoglobulin [2]. The two inter heavy chain (inter-H) disulfide bridges correspond to those of a human (Homo sapiens) IgG1. The intrachain (Cys 23-Cys 104) disulfide bridge of each of the 12 domains are not shown. The three complementarity regions (CDR1, CDR2 and CDR3) of the VH (V-D-J-region) and of the VL (V-J-region) are indicated by hatches (and numbers 1, 2, 3 for VH). V = V-REGION (in green), J = J-REGION (in yellow), D = D-REGION (or more exactly N-AND-D-REGION to take into account the N-diversity) (in red), the C-REGION is in blue (dark blue for the heavy (H) chain, light blue for the light (L) chain). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g005
Figure 6. Molecular synthesis of the immunoglobulins (IG) or antibodies and origin of their diversity. The gene numbers are from the human (Homo sapiens) IGH, IGK and IGL loci. The molecular mechanisms creating the diversity of the antigen receptors of the adaptive immune responses include the combinatorial diversity (V-(D)-J rearrangements), the junctional diversity (including the N-diversity), the somatic hypermutations (SHM) and the pairing of the heavy and light chains. Altogether the mechanisms of diversity that occur at the DNA level in the B cell result in about 6.3 × 106 and about 3.5 × 106 possibilities of heavy and light chains, respectively, and the pairing of one heavy chain with one light chain (the antibody is made of two identical heavy and light chains) results into a potential repertoire of 2 × 1012 different antibodies. The two inter-H-L and the inter-H-H disulfide bridges which depend on IG or antibody class or subclass are not shown. Only the core gene regions are represented. V = V-REGION (in green), D = D-REGION, J = J-REGION, C = C-REGION (in blue). The gene regions involved in the H chain V-D-J and L chain V-J rearrangements are highlighted: V (in dark green), D (in red) and J (in yellow). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 6. Molecular synthesis of the immunoglobulins (IG) or antibodies and origin of their diversity. The gene numbers are from the human (Homo sapiens) IGH, IGK and IGL loci. The molecular mechanisms creating the diversity of the antigen receptors of the adaptive immune responses include the combinatorial diversity (V-(D)-J rearrangements), the junctional diversity (including the N-diversity), the somatic hypermutations (SHM) and the pairing of the heavy and light chains. Altogether the mechanisms of diversity that occur at the DNA level in the B cell result in about 6.3 × 106 and about 3.5 × 106 possibilities of heavy and light chains, respectively, and the pairing of one heavy chain with one light chain (the antibody is made of two identical heavy and light chains) results into a potential repertoire of 2 × 1012 different antibodies. The two inter-H-L and the inter-H-H disulfide bridges which depend on IG or antibody class or subclass are not shown. Only the core gene regions are represented. V = V-REGION (in green), D = D-REGION, J = J-REGION, C = C-REGION (in blue). The gene regions involved in the H chain V-D-J and L chain V-J rearrangements are highlighted: V (in dark green), D (in red) and J (in yellow). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g006
Figure 7. Synthesis of an IG H-mu chain [2]. (a1) At the DNA level, in a first step, one of the IGHD genes is joined to one of the IGHJ genes, with deletion of the intermediary DNA, to create a partially rearranged D-J gene. (a2) In a second step, one of the IGHV genes is joined to D-J, with deletion of the intermediary DNA, to generate a completely rearranged IGHV-D-J gene. (b) The rearranged IGHV-D-J gene is transcribed with the IGHM gene into a IGHV-D-J-M (or IGHV-D-J-Cmu) pre-messenger RNA. (c) The RNA sequences corresponding to the introns and to the non-used IGHJ genes are excised by splicing, and a mature messenger which comprises the spliced coding regions and the 5′ and 3′ untranslated sequences, is obtained. (d) The messenger RNA is translated into a polypeptide chain by the ribosomes. (e) The signal peptide is cleaved off by a peptidase following the entry of the polypeptide chain in the endoplasmic reticulum, and a mature H-mu chain is produced. In DNA and pre-messenger RNA, L for Leader corresponds L-PART1 and L-PART2, and in spliced messenger RNA to L-REGION [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 7. Synthesis of an IG H-mu chain [2]. (a1) At the DNA level, in a first step, one of the IGHD genes is joined to one of the IGHJ genes, with deletion of the intermediary DNA, to create a partially rearranged D-J gene. (a2) In a second step, one of the IGHV genes is joined to D-J, with deletion of the intermediary DNA, to generate a completely rearranged IGHV-D-J gene. (b) The rearranged IGHV-D-J gene is transcribed with the IGHM gene into a IGHV-D-J-M (or IGHV-D-J-Cmu) pre-messenger RNA. (c) The RNA sequences corresponding to the introns and to the non-used IGHJ genes are excised by splicing, and a mature messenger which comprises the spliced coding regions and the 5′ and 3′ untranslated sequences, is obtained. (d) The messenger RNA is translated into a polypeptide chain by the ribosomes. (e) The signal peptide is cleaved off by a peptidase following the entry of the polypeptide chain in the endoplasmic reticulum, and a mature H-mu chain is produced. In DNA and pre-messenger RNA, L for Leader corresponds L-PART1 and L-PART2, and in spliced messenger RNA to L-REGION [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g007
Figure 8. Synthesis of a L-kappa chain [2]. (a) At the DNA level, one of the IGKV gene is joined to one of the five IGKJ genes, with deletion of the intermediary DNA, to create a rearranged IGKV-J gene. (b) The rearranged IGKV-J sequence is transcribed with the IGKC gene into a IGKV-J-C pre-messenger RNA. (c) The RNA sequences corresponding to the introns and to the non-used IGKJ genes are excised by splicing, and a mature messenger which comprises the spliced coding regions, and the 5′ and 3′ untranslated sequences, is obtained. (d) The messenger RNA is translated into a polypeptide chain by the ribosomes. (e) The signal peptide is cleaved off by a peptidase following the entry of the polypeptide chain in the endoplasmic reticulum, and a mature L-kappa chain is produced. In DNA and pre-messenger RNA, L for Leader corresponds to L-PART1 and L-PART2, and in spliced messenger RNA to L-REGION [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 8. Synthesis of a L-kappa chain [2]. (a) At the DNA level, one of the IGKV gene is joined to one of the five IGKJ genes, with deletion of the intermediary DNA, to create a rearranged IGKV-J gene. (b) The rearranged IGKV-J sequence is transcribed with the IGKC gene into a IGKV-J-C pre-messenger RNA. (c) The RNA sequences corresponding to the introns and to the non-used IGKJ genes are excised by splicing, and a mature messenger which comprises the spliced coding regions, and the 5′ and 3′ untranslated sequences, is obtained. (d) The messenger RNA is translated into a polypeptide chain by the ribosomes. (e) The signal peptide is cleaved off by a peptidase following the entry of the polypeptide chain in the endoplasmic reticulum, and a mature L-kappa chain is produced. In DNA and pre-messenger RNA, L for Leader corresponds to L-PART1 and L-PART2, and in spliced messenger RNA to L-REGION [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g008
Figure 9. Molecular events generating the junction N-diversity, in a rearrangement between a D gene and a J gene in the IGH locus. (a) The enzymatic RAG1/RAG2 protein complex recognizes the recombination signal (RS) sites and cuts the germline DNA between the heptamer and the coding region, resulting in a coding joint (below) and a signal joint (top) which is eliminated as an excision circle. (b) A hairpin is formed at each coding end, here 3′D and 5′J ends, by transesterification. (c) The haipin is cut by the protein complex (X-ray repair cross complementing 6 (XRCC6, Ku70)/ X-ray repair cross complementing 5 (XRCC5, Ku80), protein kinase DNA-activated catalytic subunit (PRKDC, DNA-PKcs, DNA-PK), DNA cross-link repair 1C (DCLRE1C, Artemis). Depending on the position of the cut-off site, a blunt end or P nucleotides are obtained. (d) An exonuclease eliminates nucleotides at the coding ends. (e) DNA nucleotidylexotransferase (DNTT, TdT, terminal deoxynucleotidyl transferase) adds N nucleotides, preferably ‘g’ and ‘c’ at random without template. (f) Finally, the rearranged DNA is repaired and ends are ligated by the ligase complex (X-ray repair cross complementing 4 (XRCC4), non-homologous end joining factor 1 (NHEJ1, Cernunnos), LIG4 (DNA ligase 4, ligase IV DNA ATP-dependent). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 9. Molecular events generating the junction N-diversity, in a rearrangement between a D gene and a J gene in the IGH locus. (a) The enzymatic RAG1/RAG2 protein complex recognizes the recombination signal (RS) sites and cuts the germline DNA between the heptamer and the coding region, resulting in a coding joint (below) and a signal joint (top) which is eliminated as an excision circle. (b) A hairpin is formed at each coding end, here 3′D and 5′J ends, by transesterification. (c) The haipin is cut by the protein complex (X-ray repair cross complementing 6 (XRCC6, Ku70)/ X-ray repair cross complementing 5 (XRCC5, Ku80), protein kinase DNA-activated catalytic subunit (PRKDC, DNA-PKcs, DNA-PK), DNA cross-link repair 1C (DCLRE1C, Artemis). Depending on the position of the cut-off site, a blunt end or P nucleotides are obtained. (d) An exonuclease eliminates nucleotides at the coding ends. (e) DNA nucleotidylexotransferase (DNTT, TdT, terminal deoxynucleotidyl transferase) adds N nucleotides, preferably ‘g’ and ‘c’ at random without template. (f) Finally, the rearranged DNA is repaired and ends are ligated by the ligase complex (X-ray repair cross complementing 4 (XRCC4), non-homologous end joining factor 1 (NHEJ1, Cernunnos), LIG4 (DNA ligase 4, ligase IV DNA ATP-dependent). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g009
Figure 10. Class switch IgM-IgG1: Smu-Sgamma1 recombination [2]. In a B cell which expresses IgM on the cell surface, a productive rearranged IGHV-D-J gene on one chromosome 14 is transcribed with the IGHM gene. Before the switch (S) recombination, all the IGHC genes are present in the IGH locus. During the switch recombination, a novel DNA rearrangement occurs in the IGH locus, between the Switch mu (Smu) sequence and another S sequence located in 5′ of a more downstream IGHC gene (for example, Sgamma1 upstream of IGHG1). This leads to the deletion of the intermediary DNA and to the loss of the IGHC genes located between the two S sequences which recombine. The enhancer (E) located between the most 3′ IGHJ and Smu is retained during the switch recombination [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 10. Class switch IgM-IgG1: Smu-Sgamma1 recombination [2]. In a B cell which expresses IgM on the cell surface, a productive rearranged IGHV-D-J gene on one chromosome 14 is transcribed with the IGHM gene. Before the switch (S) recombination, all the IGHC genes are present in the IGH locus. During the switch recombination, a novel DNA rearrangement occurs in the IGH locus, between the Switch mu (Smu) sequence and another S sequence located in 5′ of a more downstream IGHC gene (for example, Sgamma1 upstream of IGHG1). This leads to the deletion of the intermediary DNA and to the loss of the IGHC genes located between the two S sequences which recombine. The enhancer (E) located between the most 3′ IGHJ and Smu is retained during the switch recombination [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g010
Figure 11. Synthesis of a membrane and of a secreted H-mu chain [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 11. Synthesis of a membrane and of a secreted H-mu chain [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g011
Figure 12. Regulation of the immunoglobulin gene rearrangements in the pre-B cell [2]. The expression of the pre-B cell receptor gives the signal which inhibits further IGHV-D-J rearrangements on chromosome 14, and the signal which starts the IGKV-J rearrangements on chromosome 2 [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 12. Regulation of the immunoglobulin gene rearrangements in the pre-B cell [2]. The expression of the pre-B cell receptor gives the signal which inhibits further IGHV-D-J rearrangements on chromosome 14, and the signal which starts the IGKV-J rearrangements on chromosome 2 [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g012
Figure 13. Concepts of classification for IMGT gene and allele nomenclature (CLASSIFICATION axiom) [37,38]. (A) Hierarchy of the concepts of classification and their relations. The definition of the reciprocal relations between concepts can be read, from one concept to the other, either ascending the hierarchy (solid arrows) or descending the hierarchy (dotted arrows). (B) Examples of concept instances for each concept of classification. The concept instances are associated to an instance of the “Taxon” concept, and more precisely for the “Gene” and “Allele” concepts to an instance of the “Species” concept (here, Homo sapiens) [1,2,3,4,5,37,38,84,85]. The “Locus” concept is a concept of localization (LOCALIZATION axiom) [28]. It is shown with the reciprocal relations to the “Gene” concept. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 13. Concepts of classification for IMGT gene and allele nomenclature (CLASSIFICATION axiom) [37,38]. (A) Hierarchy of the concepts of classification and their relations. The definition of the reciprocal relations between concepts can be read, from one concept to the other, either ascending the hierarchy (solid arrows) or descending the hierarchy (dotted arrows). (B) Examples of concept instances for each concept of classification. The concept instances are associated to an instance of the “Taxon” concept, and more precisely for the “Gene” and “Allele” concepts to an instance of the “Species” concept (here, Homo sapiens) [1,2,3,4,5,37,38,84,85]. The “Locus” concept is a concept of localization (LOCALIZATION axiom) [28]. It is shown with the reciprocal relations to the “Gene” concept. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g013
Figure 14. Description of a V-GENE and of a V-D-J-GENE (DESCRIPTION axiom) [34,35]. IMGT standardized labels [32,33,34], generated from the concepts of description, are in capital letters (no plural), e.g., V-REGION, JUNCTION, CDR-IMGT [32], FR-IMGT [33]. Forty labels (27 for V-GENE and 33 for V-D-J-GENE of which 20 are shared) are necessary and sufficient for a complete description. The labels for the description of genomic rearranged genes in IMGT/LIGM-DB [54,55] are L-V-J-GENE and L-V-D-J-GENE. The labels “GENE-UNIT” have been created to bridge the DESCRIPTION and CLASSIFICATION axioms. Indeed they refer to genomic entities, in germline (for V, D and J) or undefined (for C) configuration, entered in IMGT/GENE-DB [56]. Exceptionally they may refer to rearranged entities (as the L-V-D-J-GENE-UNIT, shown here) when the corresponding germline genes are not yet known. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 14. Description of a V-GENE and of a V-D-J-GENE (DESCRIPTION axiom) [34,35]. IMGT standardized labels [32,33,34], generated from the concepts of description, are in capital letters (no plural), e.g., V-REGION, JUNCTION, CDR-IMGT [32], FR-IMGT [33]. Forty labels (27 for V-GENE and 33 for V-D-J-GENE of which 20 are shared) are necessary and sufficient for a complete description. The labels for the description of genomic rearranged genes in IMGT/LIGM-DB [54,55] are L-V-J-GENE and L-V-D-J-GENE. The labels “GENE-UNIT” have been created to bridge the DESCRIPTION and CLASSIFICATION axioms. Indeed they refer to genomic entities, in germline (for V, D and J) or undefined (for C) configuration, entered in IMGT/GENE-DB [56]. Exceptionally they may refer to rearranged entities (as the L-V-D-J-GENE-UNIT, shown here) when the corresponding germline genes are not yet known. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g014
Figure 15. Molecular entity types of the IG synthesis (IDENTIFICATION axiom) [16,30,31] in jawed vertebrates (Gnathostomata). (1) DNA rearrangements (is_rearranged_into). (2) Transcription (is_transcribed_into). (3) Translation (is_translated_into). IMGT standardised keywords, generated from the concepts of identification, identify the entity types based on the MoleculeType and and the ConfigurationType. The MoleculeType is gDNA, mRNA, in vitro cDNA or protein. The ConfigurationType is undefined (conventional and C-gene), germline (V-gene, D-gene and J-gene) or rearranged. The rearranged entities include V-D-J-gene (label L-V-D-J-GENE) and V-J-gene (label L-V-J-GENE) (gDNA), L-V-D-J-C-sequence and L-V-J-C-sequence (cDNA), V-D-J-C-chain and V-J-C-chain (protein) [30]. The functionality of undefined and germline entities is functional (F), open reading frame (ORF) or pseudogene (P) [30]. The functionality of rearranged entities is productive or unproductive [30] (Table 6). L= L-REGION (shown in ‘Transcriptome’) (light yellow), V = V-REGION (in green), D = D-REGION, J = J-REGION, C = C-REGION (in blue). The gene core regions involved in the V-D-J (heavy chain) and V-J (light chain) rearrangements are highlighted: V (in dark green), D (in red) and J (in orange yellow). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 15. Molecular entity types of the IG synthesis (IDENTIFICATION axiom) [16,30,31] in jawed vertebrates (Gnathostomata). (1) DNA rearrangements (is_rearranged_into). (2) Transcription (is_transcribed_into). (3) Translation (is_translated_into). IMGT standardised keywords, generated from the concepts of identification, identify the entity types based on the MoleculeType and and the ConfigurationType. The MoleculeType is gDNA, mRNA, in vitro cDNA or protein. The ConfigurationType is undefined (conventional and C-gene), germline (V-gene, D-gene and J-gene) or rearranged. The rearranged entities include V-D-J-gene (label L-V-D-J-GENE) and V-J-gene (label L-V-J-GENE) (gDNA), L-V-D-J-C-sequence and L-V-J-C-sequence (cDNA), V-D-J-C-chain and V-J-C-chain (protein) [30]. The functionality of undefined and germline entities is functional (F), open reading frame (ORF) or pseudogene (P) [30]. The functionality of rearranged entities is productive or unproductive [30] (Table 6). L= L-REGION (shown in ‘Transcriptome’) (light yellow), V = V-REGION (in green), D = D-REGION, J = J-REGION, C = C-REGION (in blue). The gene core regions involved in the V-D-J (heavy chain) and V-J (light chain) rearrangements are highlighted: V (in dark green), D (in red) and J (in orange yellow). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g015
Figure 16. Representation of the human IGH locus at 14q32.33 [2]. The boxes representing the genes are not to scale. Exons are not shown. Switch sequences are represented by a filled circle upstream of the IGHC genes. Pseudogenes which could not be assigned to subgroups with functional genes are designated by a Roman numeral between parentheses, corresponding to the clans, followed by a hyphen, and a number for the localization from 3′ to 5′ in the locus [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 16. Representation of the human IGH locus at 14q32.33 [2]. The boxes representing the genes are not to scale. Exons are not shown. Switch sequences are represented by a filled circle upstream of the IGHC genes. Pseudogenes which could not be assigned to subgroups with functional genes are designated by a Roman numeral between parentheses, corresponding to the clans, followed by a hyphen, and a number for the localization from 3′ to 5′ in the locus [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g016
Figure 17. Multigene deletions and copy number variations (CNV) in the Homo sapiens IGH locus on chromosome 14 (14q32.33). (A). IGHC-CNV deletions, either identical or different, on both chromosomes, designed I to VI according to the chronogical order in which they were found. Deletion I, first identified by the absence of the Gm1 allotypes in a 70-year old healthy Tunisian woman (TAK3), homozygous for that deletion [113,114] allowed the ordering of the Homo sapiens IGHC genes in the IGH locus [174,175]. Deletions I and II [113,114,115], found in healthy individuals from consanguinesous families, involve highly homologous spots of recombination [176], as also described in an healthy individual (T17) homozygous for deletion III and lacking IgA1, IgG2, IgG4 and IgE [116]. (B). Polymorphisms by insertion/deletion between IGHV4-34 and IGHV4-28 (haplotypes A to F). The distance between IGHV4-34 and IGHV4-28 (sequence length shown by the regular line) is indicated in kilobases (kb) for each haplotype. Haplotype A is from GRCh37 and corresponds to the main line of IMGT Locus Representation [2]. Haplotype B is from GRCh38 and corresponds to BAC clone sequences [247] from the CHORI-17 BAC library. Dotted lines indicate missing genes compared to the haplotype C. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®,the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 17. Multigene deletions and copy number variations (CNV) in the Homo sapiens IGH locus on chromosome 14 (14q32.33). (A). IGHC-CNV deletions, either identical or different, on both chromosomes, designed I to VI according to the chronogical order in which they were found. Deletion I, first identified by the absence of the Gm1 allotypes in a 70-year old healthy Tunisian woman (TAK3), homozygous for that deletion [113,114] allowed the ordering of the Homo sapiens IGHC genes in the IGH locus [174,175]. Deletions I and II [113,114,115], found in healthy individuals from consanguinesous families, involve highly homologous spots of recombination [176], as also described in an healthy individual (T17) homozygous for deletion III and lacking IgA1, IgG2, IgG4 and IgE [116]. (B). Polymorphisms by insertion/deletion between IGHV4-34 and IGHV4-28 (haplotypes A to F). The distance between IGHV4-34 and IGHV4-28 (sequence length shown by the regular line) is indicated in kilobases (kb) for each haplotype. Haplotype A is from GRCh37 and corresponds to the main line of IMGT Locus Representation [2]. Haplotype B is from GRCh38 and corresponds to BAC clone sequences [247] from the CHORI-17 BAC library. Dotted lines indicate missing genes compared to the haplotype C. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®,the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g017aBiomedicines 08 00319 g017b
Figure 18. Representation of the human IGK locus at 2p12 [2]. The boxes representing the genes are not to scale. Exons are not shown. The IGKV genes of the proximal V-CLUSTER are designated by a number for the subgroup, followed by a hyphen and a number for the localization from 3′ to 5′ in the locus. The IGKV genes of the distal duplicated V-CLUSTER are designated by the same numbers as the corresponding genes in the proximal V-CLUSTER, with the letter D added. Arrows show the IGKV genes polarity of which is opposite to that of the J-C-CLUSTER [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 18. Representation of the human IGK locus at 2p12 [2]. The boxes representing the genes are not to scale. Exons are not shown. The IGKV genes of the proximal V-CLUSTER are designated by a number for the subgroup, followed by a hyphen and a number for the localization from 3′ to 5′ in the locus. The IGKV genes of the distal duplicated V-CLUSTER are designated by the same numbers as the corresponding genes in the proximal V-CLUSTER, with the letter D added. Arrows show the IGKV genes polarity of which is opposite to that of the J-C-CLUSTER [2]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g018
Figure 19. Representation of the human IGL locus at 22q11.2 [2]. The boxes representing the genes are not to scale. Exons are not shown. (AC) refer to three distinct V-CLUSTER based on the IGLV gene subgroup content [271]. Pseudogenes which could not be assigned to subgroups with functional genes are designated by a Roman numeral between parentheses, corresponding to the clans, followed by a hyphen, and a number for the localization from 3′ to 5′ in the locus. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 19. Representation of the human IGL locus at 22q11.2 [2]. The boxes representing the genes are not to scale. Exons are not shown. (AC) refer to three distinct V-CLUSTER based on the IGLV gene subgroup content [271]. Pseudogenes which could not be assigned to subgroups with functional genes are designated by a Roman numeral between parentheses, corresponding to the clans, followed by a hyphen, and a number for the localization from 3′ to 5′ in the locus. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g019
Figure 20. IMGT Collier de Perles of IG V-DOMAIN and C-DOMAIN on one layer [40,41,42]. (A) Trastuzumab VH (on the left) and V-KAPPA (on the right). The CDR1-IMGT, CDR2-IMGT and CDR3-IMGT (corresponding to the BC, C’C” and FG loops, respectively) are represented online in red, orange and purple, for the VH and in blue, green and bluegreen, for the VL (V-KAPPA (here) or V-LAMBDA). The CDR-IMGT lengths are [8.8.13] for VH and [6.3.9] for V-KAPPA (B) Trastuzumab CH1 (on the left) and C-KAPPA (on the right). Amino acids are shown in the one-letter abbreviation. Positions at which hydrophobic amino acids (hydropathy index with positive value: I, V, L, F, C, M, A) and tryptophan (W) are found in more than 50% of analysed sequences are shown online in blue. All proline (P) are shown online in yellow. Hatched circles correspond to missing positions according to the IMGT unique numbering for V domain [40,41] or C domain [42]. Arrows indicate the direction of the beta strands and their designations in 3D structures. Anchors are shown in squares. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 20. IMGT Collier de Perles of IG V-DOMAIN and C-DOMAIN on one layer [40,41,42]. (A) Trastuzumab VH (on the left) and V-KAPPA (on the right). The CDR1-IMGT, CDR2-IMGT and CDR3-IMGT (corresponding to the BC, C’C” and FG loops, respectively) are represented online in red, orange and purple, for the VH and in blue, green and bluegreen, for the VL (V-KAPPA (here) or V-LAMBDA). The CDR-IMGT lengths are [8.8.13] for VH and [6.3.9] for V-KAPPA (B) Trastuzumab CH1 (on the left) and C-KAPPA (on the right). Amino acids are shown in the one-letter abbreviation. Positions at which hydrophobic amino acids (hydropathy index with positive value: I, V, L, F, C, M, A) and tryptophan (W) are found in more than 50% of analysed sequences are shown online in blue. All proline (P) are shown online in yellow. Hatched circles correspond to missing positions according to the IMGT unique numbering for V domain [40,41] or C domain [42]. Arrows indicate the direction of the beta strands and their designations in 3D structures. Anchors are shown in squares. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g020
Figure 21. IMGT Collier de Perles of V-DOMAIN on two layers and ribbon representation [94]. (A) Trastuzumab VH. (B) Trastuzumab V-KAPPA. The IMGT Colliers de Perles on two layers (on the left) show, in the forefront, the GFCC′C′′ strands (forming the sheet located at the interface VH/VL) and, in the back, the ABED strands. The IMGT Colliers de Perles were generated using the IMGT/Collier-de-Perles tool [51] integrated in IMGT/3Dstructure-DB [57,58,59]. The CDR1-IMGT, CDR2-IMGT and CDR3-IMGT (corresponding to the BC, C’C” and FG loops, respectively) are represented in red, orange and purple, for the VH and in blue, green and bluegreen, for the VL, here V-KAPPA. The CDR-IMGT lengths are [8.8.13] for VH and [6.3.9] for V-KAPPA. Hatched circles correspond to missing positions according to the IMGT unique numbering for V domain [40,41]. Arrows indicate the direction of the beta strands and their designations in 3D structures. Anchors are shown in squares. Hydrogen bonds (green lines online were automatically added from the experimental structural data). The disulfide bridge (orange line between C23 and C104) was also automatically added from the experimental structural data. The ribbon representation of the 3D structures (on the right) was obtained using PyMOL (http://www.pymol.org). The identifiers of the chains to which the domains belong are 1n8z_B and 1n8z_A (IMGT® http://www.imgt.org, IMGT/3Dstructure-DB). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 21. IMGT Collier de Perles of V-DOMAIN on two layers and ribbon representation [94]. (A) Trastuzumab VH. (B) Trastuzumab V-KAPPA. The IMGT Colliers de Perles on two layers (on the left) show, in the forefront, the GFCC′C′′ strands (forming the sheet located at the interface VH/VL) and, in the back, the ABED strands. The IMGT Colliers de Perles were generated using the IMGT/Collier-de-Perles tool [51] integrated in IMGT/3Dstructure-DB [57,58,59]. The CDR1-IMGT, CDR2-IMGT and CDR3-IMGT (corresponding to the BC, C’C” and FG loops, respectively) are represented in red, orange and purple, for the VH and in blue, green and bluegreen, for the VL, here V-KAPPA. The CDR-IMGT lengths are [8.8.13] for VH and [6.3.9] for V-KAPPA. Hatched circles correspond to missing positions according to the IMGT unique numbering for V domain [40,41]. Arrows indicate the direction of the beta strands and their designations in 3D structures. Anchors are shown in squares. Hydrogen bonds (green lines online were automatically added from the experimental structural data). The disulfide bridge (orange line between C23 and C104) was also automatically added from the experimental structural data. The ribbon representation of the 3D structures (on the right) was obtained using PyMOL (http://www.pymol.org). The identifiers of the chains to which the domains belong are 1n8z_B and 1n8z_A (IMGT® http://www.imgt.org, IMGT/3Dstructure-DB). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g021
Figure 22. Protein displays of the Homo sapiens IGH, IGK and IGL V-REGION. Only the *01 allele of each functional or ORF V-REGION shown. (A). IGHV genes are listed per subgroup and, for each subgroup, increasing numbers corresponding generally to their position from 3′ to 5′ in the locus [2,237]. (B). IGKV genes are listed per subgroup and, for each subgroup, increasing numbers corresponding generally to their position from 3′ to 5′ in the locus, with the letter D for genes of the distal V-CLUSTER [2,237]. The IGKV2-29 gene is not represented the *01 allele being a pseudogene. For information, the IGKV2-29*02 F differs from IGKV2D-29*01 by P49 > S, N66 > S, S107 > G, Q109 > H [2,237]. (C). IGLV genes are listed per subgroup and, for each subgroup, increasing numbers corresponding generally to their position from 3′ to 5′ in the locus [2,237]. The header of the IMGT Protein display of V-REGION comprises 7 lines. Line 1: FR-IMGT and CDR-IMGT. Line 2: start and end positions of FR-IMGT and CDR-IMGT, e.g., (1-26). Line 3: name of strands (A, B…) and loops (AB, BC…). Line 4: start and end positions of strands, e.g., (1-15). Line 5: arrows (for the strands). Line 6: positions according to the IMGT unique numbering for V-DOMAIN and V-LIKE-DOMAIN [41]. Line 7: Pipes for the start and end positions of strands and loops and highlighted positions, dots for the other positions (dots indicate gaps according to the IMGT unique numbering [41]). The four conserved amino acids 23 (1st-CYS), 41 (CONSERVED-TRP), 89 (hydrophobic) and 104 (2nd-CYS) are highlighted (C23 and C104 in pink, W41 and hydrophobic 89 in blue). N (Asn, asparagine) of potential N-glycosylation sites (NXS/T, where X is different from P) (N-linked glycosylation) is shown in green. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 22. Protein displays of the Homo sapiens IGH, IGK and IGL V-REGION. Only the *01 allele of each functional or ORF V-REGION shown. (A). IGHV genes are listed per subgroup and, for each subgroup, increasing numbers corresponding generally to their position from 3′ to 5′ in the locus [2,237]. (B). IGKV genes are listed per subgroup and, for each subgroup, increasing numbers corresponding generally to their position from 3′ to 5′ in the locus, with the letter D for genes of the distal V-CLUSTER [2,237]. The IGKV2-29 gene is not represented the *01 allele being a pseudogene. For information, the IGKV2-29*02 F differs from IGKV2D-29*01 by P49 > S, N66 > S, S107 > G, Q109 > H [2,237]. (C). IGLV genes are listed per subgroup and, for each subgroup, increasing numbers corresponding generally to their position from 3′ to 5′ in the locus [2,237]. The header of the IMGT Protein display of V-REGION comprises 7 lines. Line 1: FR-IMGT and CDR-IMGT. Line 2: start and end positions of FR-IMGT and CDR-IMGT, e.g., (1-26). Line 3: name of strands (A, B…) and loops (AB, BC…). Line 4: start and end positions of strands, e.g., (1-15). Line 5: arrows (for the strands). Line 6: positions according to the IMGT unique numbering for V-DOMAIN and V-LIKE-DOMAIN [41]. Line 7: Pipes for the start and end positions of strands and loops and highlighted positions, dots for the other positions (dots indicate gaps according to the IMGT unique numbering [41]). The four conserved amino acids 23 (1st-CYS), 41 (CONSERVED-TRP), 89 (hydrophobic) and 104 (2nd-CYS) are highlighted (C23 and C104 in pink, W41 and hydrophobic 89 in blue). N (Asn, asparagine) of potential N-glycosylation sites (NXS/T, where X is different from P) (N-linked glycosylation) is shown in green. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g022aBiomedicines 08 00319 g022b
Figure 23. IMGT Collier de Perles of C-DOMAIN on two layers and ribbon representation [94]. (A) Trastuzumab CH1. (B) Trastuzumab C-KAPPA. The IMGT Colliers de Perles on two layers (on the left) show, in the forefront, the GFC strands and, in the back, the ABED strands (located at the interface CH1/C-KAPPA), linked by the CD transversal strand. The IMGT Colliers de Perles were generated by the IMGT/Collier-de-Perles tool [51] integrated in IMGT/3Dstructure-DB [57,58,59]. Hydrogen bonds (green lines online were automatically added from the experimental structural data). The disulfide bridge (orange line between C23 and C104) was also automatically added from the experimental structural data. Amino acids are shown in the one-letter abbreviation. Positions at which hydrophobic amino acids (hydropathy index with positive value: I, V, L, F, C, M, A) and tryptophan (W) are found in more than 50% of analysed sequences are shown online in blue. All proline (P) are shown online in yellow. Hatched circles correspond to missing positions according to the IMGT unique numbering for C domain [42]. Arrows indicate the direction of the beta strands and their designations in 3D structures. Anchors are shown in squares. The ribbon representation of the 3D structures (on the right) was obtained using PyMOL (http://www.pymol.org). The identifiers of the chains to which the domains belong are 1n8z_B and 1n8z_A (IMGT® http://www.imgt.org, IMGT/3Dstructure-DB). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 23. IMGT Collier de Perles of C-DOMAIN on two layers and ribbon representation [94]. (A) Trastuzumab CH1. (B) Trastuzumab C-KAPPA. The IMGT Colliers de Perles on two layers (on the left) show, in the forefront, the GFC strands and, in the back, the ABED strands (located at the interface CH1/C-KAPPA), linked by the CD transversal strand. The IMGT Colliers de Perles were generated by the IMGT/Collier-de-Perles tool [51] integrated in IMGT/3Dstructure-DB [57,58,59]. Hydrogen bonds (green lines online were automatically added from the experimental structural data). The disulfide bridge (orange line between C23 and C104) was also automatically added from the experimental structural data. Amino acids are shown in the one-letter abbreviation. Positions at which hydrophobic amino acids (hydropathy index with positive value: I, V, L, F, C, M, A) and tryptophan (W) are found in more than 50% of analysed sequences are shown online in blue. All proline (P) are shown online in yellow. Hatched circles correspond to missing positions according to the IMGT unique numbering for C domain [42]. Arrows indicate the direction of the beta strands and their designations in 3D structures. Anchors are shown in squares. The ribbon representation of the 3D structures (on the right) was obtained using PyMOL (http://www.pymol.org). The identifiers of the chains to which the domains belong are 1n8z_B and 1n8z_A (IMGT® http://www.imgt.org, IMGT/3Dstructure-DB). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g023
Figure 24. IMGT Protein displays of the Homo sapiens IGKC, IGLC and IGHC genes. (A). IGKC Protein display. Ala A45.1 and Val V101 characterize the Km3 allotype (see Section 3.3.4). (B). IGLC Protein display. Asn N1 and Thr T3 characterize the Mcg isotype marker, Gly G45 characterizes the Ke isotype marker, and Lys K100, the Oz isotype marker (see Section 3.4.4). (C). IGHC Protein display. The IGHC Protein display is shown per domain (CH1, CH2, CH3, and for IGHM and IGHE, CH4). The CO + TM + CY of the membrane IG (mIG) is encoded by two exons, excepted for IGHA1 and IGHA2 where it is encoded by a single exon. The CHS of the sIG is colored in green. The hinge region (presented here, at the bottom of the figure) is located between CH1 and CH2. It is encoded by one exon (in IGHG1, IGHG2, IGHG4, IGHGP genes), two exons (in IGHD gene), two to five exons (in IGHG3 gene, 4 for the most common haplotype, shown here). The hinge region of the IGHA1 and IGHA2 is fused in 5′ to the CH2 domain (encoded in a H-CH2 exon) [2]. The IGHGP, although an ORF, is shown for compleness. The C-KAPPA, C-LAMBDA and CH are numbered according to the IMGT unique numbering for C-DOMAIN and C-LIKE-DOMAIN [42]. The header of the IMGT Protein display of the C-DOMAIN obtained automatically (A and B) comprises 5 lines. Line 1: name of strands (A, B…), turns and loops (AB, BC…). Line 2: start and end positions of strands, e.g., (1-15). Line 3: arrows (for the strands). Line 4: positions according to the IMGT unique numberin [42]. Missing positions (32 and 33 in the BC loop and 46 to 76) in the C domain by comparison with the V domain are not shown. Line 5: Pipes for the start and end positions of strands and loops and highlighted positions, and dots for the other positions (dots indicate gaps according to the IMGT unique numbering [42]). The four conserved amino acids 23 (1st-CYS), 41 (CONSERVED-TRP), 89 (hydrophobic) and 104 (2nd-CYS) are highlighted (C23 and C104 in pink, W41 and hydrophobic 89 in blue). The IMGT Protein display of the Homo sapiens IGHC obtained manually (C) allows to display the CHS, the CO+TM+CY and the hinge. The N-linked glycosylation motifs (NXS/T, where X is different from P) are underlined. In the automatic version for the CH displayed online, the letter N (Asn, asparagine) of potential N-glycosylation sites are shown in green. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 24. IMGT Protein displays of the Homo sapiens IGKC, IGLC and IGHC genes. (A). IGKC Protein display. Ala A45.1 and Val V101 characterize the Km3 allotype (see Section 3.3.4). (B). IGLC Protein display. Asn N1 and Thr T3 characterize the Mcg isotype marker, Gly G45 characterizes the Ke isotype marker, and Lys K100, the Oz isotype marker (see Section 3.4.4). (C). IGHC Protein display. The IGHC Protein display is shown per domain (CH1, CH2, CH3, and for IGHM and IGHE, CH4). The CO + TM + CY of the membrane IG (mIG) is encoded by two exons, excepted for IGHA1 and IGHA2 where it is encoded by a single exon. The CHS of the sIG is colored in green. The hinge region (presented here, at the bottom of the figure) is located between CH1 and CH2. It is encoded by one exon (in IGHG1, IGHG2, IGHG4, IGHGP genes), two exons (in IGHD gene), two to five exons (in IGHG3 gene, 4 for the most common haplotype, shown here). The hinge region of the IGHA1 and IGHA2 is fused in 5′ to the CH2 domain (encoded in a H-CH2 exon) [2]. The IGHGP, although an ORF, is shown for compleness. The C-KAPPA, C-LAMBDA and CH are numbered according to the IMGT unique numbering for C-DOMAIN and C-LIKE-DOMAIN [42]. The header of the IMGT Protein display of the C-DOMAIN obtained automatically (A and B) comprises 5 lines. Line 1: name of strands (A, B…), turns and loops (AB, BC…). Line 2: start and end positions of strands, e.g., (1-15). Line 3: arrows (for the strands). Line 4: positions according to the IMGT unique numberin [42]. Missing positions (32 and 33 in the BC loop and 46 to 76) in the C domain by comparison with the V domain are not shown. Line 5: Pipes for the start and end positions of strands and loops and highlighted positions, and dots for the other positions (dots indicate gaps according to the IMGT unique numbering [42]). The four conserved amino acids 23 (1st-CYS), 41 (CONSERVED-TRP), 89 (hydrophobic) and 104 (2nd-CYS) are highlighted (C23 and C104 in pink, W41 and hydrophobic 89 in blue). The IMGT Protein display of the Homo sapiens IGHC obtained manually (C) allows to display the CHS, the CO+TM+CY and the hinge. The N-linked glycosylation motifs (NXS/T, where X is different from P) are underlined. In the automatic version for the CH displayed online, the letter N (Asn, asparagine) of potential N-glycosylation sites are shown in green. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g024aBiomedicines 08 00319 g024b
Figure 25. IMGT®, the international ImMunoGenetics information system®, http://www.imgt.org [1,94]. The IMGT Web resources (>25,000 pages, the IMGT Marie-Paule page) are not shown. IMGT/mAb-DB for therapeutic monoclonal antibodies and fusion proteins for immune applications (FPIA) has been online since December 4, 2009. IMGT/HighV-QUEST portal for next generation sequencing (NGS) high-throughput sequence analysis, created in October 2010, has been available on the web since November 22, 2010. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 25. IMGT®, the international ImMunoGenetics information system®, http://www.imgt.org [1,94]. The IMGT Web resources (>25,000 pages, the IMGT Marie-Paule page) are not shown. IMGT/mAb-DB for therapeutic monoclonal antibodies and fusion proteins for immune applications (FPIA) has been online since December 4, 2009. IMGT/HighV-QUEST portal for next generation sequencing (NGS) high-throughput sequence analysis, created in October 2010, has been available on the web since November 22, 2010. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g025
Figure 26. IMGT/V-QUEST. (A). Result summary. AY513484 is the nucleotide sequence of the VH domain of humAb4D5-8 (trastuzumab) (identified in IMGT/LIGM-DB [54,55] by the clone name). Comments in red are added automatically by the IMGT/V-QUEST tool. The sequence identified by IMGT/V-QUEST as containing a V domain in the user sequence, and therefore analysed by the tool, is displayed with a green background. (B). Results of IMGT/JunctionAnalysis. The JUNCTION decryption (3′V)3′{N1}5′(D)3′{N2}5′(5′J) (labels here for one D) provides region lengths (in nt) of (3′V), (D) and (5′J) (numbers between parentheses), of {N1} and {N2} (numbers between braces), and between these regions and at the 3′ or 5′ end of V, D or J, numbers indicating, either trimmed nt (negative (−) values) or palindromic P nucleotides (positive (+) values) (trimmed or P nt are mutually exclusive) (IMGT® http://www.imgt.org, IMGT/JunctionAnalysis (doc) > IMGT/JunctionAnalysis Documentation). Color menu is according to the AA physicochemical properties [81]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 26. IMGT/V-QUEST. (A). Result summary. AY513484 is the nucleotide sequence of the VH domain of humAb4D5-8 (trastuzumab) (identified in IMGT/LIGM-DB [54,55] by the clone name). Comments in red are added automatically by the IMGT/V-QUEST tool. The sequence identified by IMGT/V-QUEST as containing a V domain in the user sequence, and therefore analysed by the tool, is displayed with a green background. (B). Results of IMGT/JunctionAnalysis. The JUNCTION decryption (3′V)3′{N1}5′(D)3′{N2}5′(5′J) (labels here for one D) provides region lengths (in nt) of (3′V), (D) and (5′J) (numbers between parentheses), of {N1} and {N2} (numbers between braces), and between these regions and at the 3′ or 5′ end of V, D or J, numbers indicating, either trimmed nt (negative (−) values) or palindromic P nucleotides (positive (+) values) (trimmed or P nt are mutually exclusive) (IMGT® http://www.imgt.org, IMGT/JunctionAnalysis (doc) > IMGT/JunctionAnalysis Documentation). Color menu is according to the AA physicochemical properties [81]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g026aBiomedicines 08 00319 g026b
Figure 27. Displays of (A) IMGT clonotypes (AA) and (B) IMGT clonotypes (nt). IMGT clonotypes (AA) and (nt) are characterized by the IMGT/HighV-QUEST statistical module [66,73]. Displays are based on CDR3-IMGT lengths. In B, the pink lines correspond to IMGT clonotypes (AA) with, below each one of them, the corresponding IMGT clonotypes (nt). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 27. Displays of (A) IMGT clonotypes (AA) and (B) IMGT clonotypes (nt). IMGT clonotypes (AA) and (nt) are characterized by the IMGT/HighV-QUEST statistical module [66,73]. Displays are based on CDR3-IMGT lengths. In B, the pink lines correspond to IMGT clonotypes (AA) with, below each one of them, the corresponding IMGT clonotypes (nt). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g027
Figure 28. Results of IMGT/StatClonotype [76,77]. Differences in proportions graph. Genes are ordered by their position in the locus with the IMGT functionality [2]. The differences in proportions graph with significance and confidence interval (CI) are shown for Homo sapiens IGH IMGT clonotypes (AA) with a given gene, between two sets of B cell populations. Negative differences in proportions are shown on the left of the vertical line (abscissa equal to 0) and positive differences are shown on the right of the vertical line. CI bars colors correspond to the test interpretation before adjustment of p - values, red (non-significant) and cyan (significant) (rawp), significant differences validated by the IMGT/StatClonotypes seven procedures (All_p): dark blue, by two or more multiple testing procedures (Min_2p): pink, and only by Benjamini & Hochberg (BH) (Only_BH): green). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 28. Results of IMGT/StatClonotype [76,77]. Differences in proportions graph. Genes are ordered by their position in the locus with the IMGT functionality [2]. The differences in proportions graph with significance and confidence interval (CI) are shown for Homo sapiens IGH IMGT clonotypes (AA) with a given gene, between two sets of B cell populations. Negative differences in proportions are shown on the left of the vertical line (abscissa equal to 0) and positive differences are shown on the right of the vertical line. CI bars colors correspond to the test interpretation before adjustment of p - values, red (non-significant) and cyan (significant) (rawp), significant differences validated by the IMGT/StatClonotypes seven procedures (All_p): dark blue, by two or more multiple testing procedures (Min_2p): pink, and only by Benjamini & Hochberg (BH) (Only_BH): green). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g028
Figure 29. IMGT/DomainGapAlign [58,79,80]. (A). Analysis of the translated AY513484 sequence (trastuzumab VH). The analysis at the amino acid level gives the same percent of identity and same score for three alleles of IGHV3-66*02 (the one identified by nucleotide analysis, as well as *01 and *04. Analysis at the amino acid level gives IGHJ4*01 as the closest IGHJ gene and allele, mentioned in the IMGT/V-QUEST comments (in red in Figure 26A). The results are presented according to the IMGT Protein display header for V-DOMAIN [41]. (B). Regions and domains identified by IMGT/DomainGapAlign in the trastuzumab VH (V-REGION in green, N-AND-D-REGION in red and J-REGION in orange) and Results summary (by comparison with the closest genes and alleles IGHV3-66*01 and IGHJ4*01). Results summary comprises the V-REGION identity percentage (81.6%), CDR-IMGT lengths [8.8.13], Number of different AA changes in CDR1-IMGT and CDR2-IMGT, FR-IMGT lengths, Number of different AA in FR-IMGT and Total number of AA change in V-DOMAIN. (C). AA changes in FR-IMGT and CDR-IMGT with similarity characteristics. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 29. IMGT/DomainGapAlign [58,79,80]. (A). Analysis of the translated AY513484 sequence (trastuzumab VH). The analysis at the amino acid level gives the same percent of identity and same score for three alleles of IGHV3-66*02 (the one identified by nucleotide analysis, as well as *01 and *04. Analysis at the amino acid level gives IGHJ4*01 as the closest IGHJ gene and allele, mentioned in the IMGT/V-QUEST comments (in red in Figure 26A). The results are presented according to the IMGT Protein display header for V-DOMAIN [41]. (B). Regions and domains identified by IMGT/DomainGapAlign in the trastuzumab VH (V-REGION in green, N-AND-D-REGION in red and J-REGION in orange) and Results summary (by comparison with the closest genes and alleles IGHV3-66*01 and IGHJ4*01). Results summary comprises the V-REGION identity percentage (81.6%), CDR-IMGT lengths [8.8.13], Number of different AA changes in CDR1-IMGT and CDR2-IMGT, FR-IMGT lengths, Number of different AA in FR-IMGT and Total number of AA change in V-DOMAIN. (C). AA changes in FR-IMGT and CDR-IMGT with similarity characteristics. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g029
Figure 30. Chain details of the trastuzumab Fab ‘1n8z’ in IMGT/3Dstructure-DB [57,58,59]. (A). L-KAPPA chain (1b8z_A). The chain sequence is identified as containing a V-KAPPA (V-REGION in green and J-REGION in orange) and a C-KAPPA (blue). (B). VH-CH1 chain (1n8z_B). The chain sequence is identified as containing a VH (V-REGION in green, N-AND-D-REGION in red and J-REGION in orange) and a CH1 (in blue). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 30. Chain details of the trastuzumab Fab ‘1n8z’ in IMGT/3Dstructure-DB [57,58,59]. (A). L-KAPPA chain (1b8z_A). The chain sequence is identified as containing a V-KAPPA (V-REGION in green and J-REGION in orange) and a C-KAPPA (blue). (B). VH-CH1 chain (1n8z_B). The chain sequence is identified as containing a VH (V-REGION in green, N-AND-D-REGION in red and J-REGION in orange) and a CH1 (in blue). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g030aBiomedicines 08 00319 g030b
Figure 31. IMGT/3Dstructure-DB Domain pair contacs [57,58,59]. (A). Domain pair contacts between trastuzumab Fab V-KAPPA (1n8z_A) and ERBB2 ((Ligand) 1n8z_C). (B). Domain pair contacts between trastuzumab Fab VH (1n8z_B) and ERBB2 ((Ligand) 1n8z_C). Positions in the CDR1-IMGT, CDR2-IMGT and CDR3-IMGT are represented in blue, green and bluegreen, for the V-KAPPA and in red, orange and purple, for the VH. Positions in the FR-IMGT are in yellow. 55 and 66 are anchors of the CDR2-IMGT. Clicking on ‘[email protected]’ gives access to the IMGT [email protected] card. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 31. IMGT/3Dstructure-DB Domain pair contacs [57,58,59]. (A). Domain pair contacts between trastuzumab Fab V-KAPPA (1n8z_A) and ERBB2 ((Ligand) 1n8z_C). (B). Domain pair contacts between trastuzumab Fab VH (1n8z_B) and ERBB2 ((Ligand) 1n8z_C). Positions in the CDR1-IMGT, CDR2-IMGT and CDR3-IMGT are represented in blue, green and bluegreen, for the V-KAPPA and in red, orange and purple, for the VH. Positions in the FR-IMGT are in yellow. 55 and 66 are anchors of the CDR2-IMGT. Clicking on ‘[email protected]’ gives access to the IMGT [email protected] card. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g031aBiomedicines 08 00319 g031b
Figure 32. IMGT/3Dstructure-DB paratope/epitope of trastuzumab/ERBB2 in 1n8z [57,58,59]. The IMGT paratope, or antigen-binding site, include the part of the VH and VL domains that recognizes (binds to) the antigen (Ag) (epitope or antigenic determinant) [298,299]. In addition to the contacts between amino acids of the CDR1-IMGT, CDR2-IMGT and CDR3-IMGT of the V-KAPPA and VH and the antigen ERBB2 (Figure 31), framework positions which are detected as having relevant contacts with the antigen are included in the paratope. This is the case, here, of the anchor positions of the CDR2-IMGT in V-KAPPA F(66_A) (Figure 31A) and in VH R(55_B) and R(66_B) (Figure 31B). These posiions are classically taken into account in V domain humanization by grafting. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 32. IMGT/3Dstructure-DB paratope/epitope of trastuzumab/ERBB2 in 1n8z [57,58,59]. The IMGT paratope, or antigen-binding site, include the part of the VH and VL domains that recognizes (binds to) the antigen (Ag) (epitope or antigenic determinant) [298,299]. In addition to the contacts between amino acids of the CDR1-IMGT, CDR2-IMGT and CDR3-IMGT of the V-KAPPA and VH and the antigen ERBB2 (Figure 31), framework positions which are detected as having relevant contacts with the antigen are included in the paratope. This is the case, here, of the anchor positions of the CDR2-IMGT in V-KAPPA F(66_A) (Figure 31A) and in VH R(55_B) and R(66_B) (Figure 31B). These posiions are classically taken into account in V domain humanization by grafting. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g032
Figure 33. Characteristics of the immunoglobulin synthesis in Camelidae. The Arabian camel (Camelus dromedarius) and the llama (Lama glama) have three IgG subclasses: the conventional IgG1 and the non-conventional IgG2 and IgG3. IgG2 and IgG3 are characterized by the absence of light chain. This lack of light chain is itself a consequence of the absence of the CH1 domain in the H-gamma 2 and H-gamma 3 chains, due to a splicing defect of the CH1 exon (non canonical DONOR-SPLICE: nat instead of ngt). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 33. Characteristics of the immunoglobulin synthesis in Camelidae. The Arabian camel (Camelus dromedarius) and the llama (Lama glama) have three IgG subclasses: the conventional IgG1 and the non-conventional IgG2 and IgG3. IgG2 and IgG3 are characterized by the absence of light chain. This lack of light chain is itself a consequence of the absence of the CH1 domain in the H-gamma 2 and H-gamma 3 chains, due to a splicing defect of the CH1 exon (non canonical DONOR-SPLICE: nat instead of ngt). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g033
Figure 34. Contact analysis and IMGT Collier de Perles of a TR-mimic antibody and of a TR targeting peptide-HLA. VH and V-LAMBDA of the IG Fab 3M4E5 and V-BETA and V-ALPHA of the TR 1G4_a58b61 target the NY-ESO-1 peptide presented by HLA-A*02:01 [311,312]. From top to bottom are shown: 1. contacts with the ligand, 2. contacts with G-ALPHA1, 3. contacts with G-ALPHA2, 4. IMGT Collier de Perles on one layer, 5. IMGT Collier de Perles on two layers with hydrogen bonds, 6. contacts of the NY-ESO-1 peptide SLLMWITQC with the MH1 HLA-A*02:01 groove [313,314,315]. The CDR1-IMGT, CDR2-IMGT and CDR3-IMGT are represented in red, orange and purple for the IG VH and the TR V-BETA, and in blue, green, bluegreen for the IG VL, here V-LAMBDA and for the TR V-ALPHA. Three-dimensional structure PDB codes are 3gjf, for Fab 3M4E5 (IG/pMH1), and 2p5e, for 1G4_a58b61 (TR/pMH1) (IMGT® http://www.imgt.org, IMGT/3Dstructure-DB). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 34. Contact analysis and IMGT Collier de Perles of a TR-mimic antibody and of a TR targeting peptide-HLA. VH and V-LAMBDA of the IG Fab 3M4E5 and V-BETA and V-ALPHA of the TR 1G4_a58b61 target the NY-ESO-1 peptide presented by HLA-A*02:01 [311,312]. From top to bottom are shown: 1. contacts with the ligand, 2. contacts with G-ALPHA1, 3. contacts with G-ALPHA2, 4. IMGT Collier de Perles on one layer, 5. IMGT Collier de Perles on two layers with hydrogen bonds, 6. contacts of the NY-ESO-1 peptide SLLMWITQC with the MH1 HLA-A*02:01 groove [313,314,315]. The CDR1-IMGT, CDR2-IMGT and CDR3-IMGT are represented in red, orange and purple for the IG VH and the TR V-BETA, and in blue, green, bluegreen for the IG VL, here V-LAMBDA and for the TR V-ALPHA. Three-dimensional structure PDB codes are 3gjf, for Fab 3M4E5 (IG/pMH1), and 2p5e, for 1G4_a58b61 (TR/pMH1) (IMGT® http://www.imgt.org, IMGT/3Dstructure-DB). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g034aBiomedicines 08 00319 g034b
Figure 35. Homo sapiens IGHG1 CH2 and N-linked glycosylation site N84.4 [94]. (A) IMGT Collier de Perles of IGHG1 CH2 on one layer (on the left) and on two layers with hydrogen bonds (on the right). The N84.4 is at the DE turn. The identifier of the chain to which the domain belongs is 1hzh_H. The IMGT Colliers de Perles on two layers show, in the forefront, the GFC strands and, in the back, the ABED strands, linked by the CD transversal strand. The IMGT Colliers de Perles were generated by the IMGT/Collier-de-Perles tool [51] integrated in IMGT/3Dstructure-DB [57,58,59]. Hydrogen bonds (green lines) and disulfide bond between C23 and C104 (orange line) were automatically added from the experimental structural data). Amino acids are shown in the one-letter abbreviation. Positions at which hydrophobic amino acids (hydropathy index with positive value: I, V, L, F, C, M, A) and tryptophan (W) are found in more than 50% of analysed sequences are shown in blue. All proline (P) are shown in yellow. Hatched circles correspond to missing positions according to the IMGT unique numbering for C domain [42]. Arrows indicate the direction of the beta strands and their designations in 3D structures. Anchors (26, 39, 45, 77, 104, 118) are shown in squares. (B) 3D structure of the IGHG1 CH2 dimer with the two carbohydrate chains. The N84.4 at the DE turn is shown on the CH2 on the left whereas the N84.4 of the CH2 on the right is hidden behind the carbohydrates. The ribbon representation of the 3D structures was obtained using PyMOL (http://www.pymol.org). The identifiers of the H-gamma1 chains to which the CH2 domains belong are 1hzh_H and 1hzh_K (IMGT® http://www.imgt.org, IMGT/3Dstructure-DB). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 35. Homo sapiens IGHG1 CH2 and N-linked glycosylation site N84.4 [94]. (A) IMGT Collier de Perles of IGHG1 CH2 on one layer (on the left) and on two layers with hydrogen bonds (on the right). The N84.4 is at the DE turn. The identifier of the chain to which the domain belongs is 1hzh_H. The IMGT Colliers de Perles on two layers show, in the forefront, the GFC strands and, in the back, the ABED strands, linked by the CD transversal strand. The IMGT Colliers de Perles were generated by the IMGT/Collier-de-Perles tool [51] integrated in IMGT/3Dstructure-DB [57,58,59]. Hydrogen bonds (green lines) and disulfide bond between C23 and C104 (orange line) were automatically added from the experimental structural data). Amino acids are shown in the one-letter abbreviation. Positions at which hydrophobic amino acids (hydropathy index with positive value: I, V, L, F, C, M, A) and tryptophan (W) are found in more than 50% of analysed sequences are shown in blue. All proline (P) are shown in yellow. Hatched circles correspond to missing positions according to the IMGT unique numbering for C domain [42]. Arrows indicate the direction of the beta strands and their designations in 3D structures. Anchors (26, 39, 45, 77, 104, 118) are shown in squares. (B) 3D structure of the IGHG1 CH2 dimer with the two carbohydrate chains. The N84.4 at the DE turn is shown on the CH2 on the left whereas the N84.4 of the CH2 on the right is hidden behind the carbohydrates. The ribbon representation of the 3D structures was obtained using PyMOL (http://www.pymol.org). The identifiers of the H-gamma1 chains to which the CH2 domains belong are 1hzh_H and 1hzh_K (IMGT® http://www.imgt.org, IMGT/3Dstructure-DB). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g035
Figure 36. (A). Largest N-linked oligosaccharide structure found in human IgG (left panel) and most abundant glycans found in mAb biopharmaceuticals (right panel). (B). Glycosylation patterns of recombinant antibodies produced in human, CHO and NS0 cells. Symbol Nomenclature for Glycans (SNFG) is according to the NCBI Glycans page https://www.ncbi.nlm.nih.gov/glycans/snfg.html. Gal: galactose, Man: mannose, Fuc: fucose, GlcNac: N-acetylglucosamine, Neu5Ac: N-acetylneuraminic acid and Neu5Gc: N-glycolylneuraminic acid. The absence of GlcNac bisecting, in glycans of recombinant antibodies produced in hamster (CHO) and mouse (NS0) cells, is marked by a white square (IMGT® http://www.imgt.org, IMGT Lexique > Immunoglobulin (IG) or antibody glycosylation). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 36. (A). Largest N-linked oligosaccharide structure found in human IgG (left panel) and most abundant glycans found in mAb biopharmaceuticals (right panel). (B). Glycosylation patterns of recombinant antibodies produced in human, CHO and NS0 cells. Symbol Nomenclature for Glycans (SNFG) is according to the NCBI Glycans page https://www.ncbi.nlm.nih.gov/glycans/snfg.html. Gal: galactose, Man: mannose, Fuc: fucose, GlcNac: N-acetylglucosamine, Neu5Ac: N-acetylneuraminic acid and Neu5Gc: N-glycolylneuraminic acid. The absence of GlcNac bisecting, in glycans of recombinant antibodies produced in hamster (CHO) and mouse (NS0) cells, is marked by a white square (IMGT® http://www.imgt.org, IMGT Lexique > Immunoglobulin (IG) or antibody glycosylation). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g036aBiomedicines 08 00319 g036b
Figure 37. Homo sapiens IGHG1 CH3 and knobs-into-holes positions [94]. (A) Contact analysis of threonine T22 and tyrosine Y86 at the interface between the two CH3 domains of the gamma1 chains. T22 and Y86 are the two positions involved in the knobs-and-holes. (B) IMGT Colliers de Perles of Homo sapiens IGHG1 CH3 on one layer (on the left) and on two layers with hydrogen bonds (on the right). T22 (in strand B) and Y86 (in strand E) are highlighted. The IMGT Colliers de Perles on two layers show, in the forefront, the GFC strands and, in the back, the ABED strands, linked by the CD transversal strand. The [ABED] sheets are at the interface between the two CH3 domains. The IMGT Colliers de Perles were generated by the IMGT/Collier-de-Perles tool [51] integrated in IMGT/3Dstructure-DB [57,58,59]. Hydrogen bonds (green lines) and disulfide bond between C23 and C104 (orange line) were automatically added from the experimental structural data. Amino acids are shown in the one-letter abbreviation. Positions at which hydrophobic amino acids (hydropathy index with positive value: I, V, L, F, C, M, A) and tryptophan (W) are found in more than 50% of analysed sequences are shown in blue. All proline (P) are shown in yellow. Hatched circles correspond to missing positions according to the IMGT unique numbering for C domain [42]. Arrows indicate the direction of the beta strands and their designations in 3D structures. Anchors (26, 39, 45, 77, 104, 118) are shown in squares. (C) 3D structure of the CH3 dimer showing the two amino acids T22 and Y86 involved in the knobs-and-holes amino acid changes (T22 > Y on one CH3 domain, Y86 > T on the other). The identifiers of the gamma1 chains to which the CH3 domains belong are 1hzh_H and 1hzh_K (IMGT® http://www.imgt.org, IMGT/3Dstructure-DB). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 37. Homo sapiens IGHG1 CH3 and knobs-into-holes positions [94]. (A) Contact analysis of threonine T22 and tyrosine Y86 at the interface between the two CH3 domains of the gamma1 chains. T22 and Y86 are the two positions involved in the knobs-and-holes. (B) IMGT Colliers de Perles of Homo sapiens IGHG1 CH3 on one layer (on the left) and on two layers with hydrogen bonds (on the right). T22 (in strand B) and Y86 (in strand E) are highlighted. The IMGT Colliers de Perles on two layers show, in the forefront, the GFC strands and, in the back, the ABED strands, linked by the CD transversal strand. The [ABED] sheets are at the interface between the two CH3 domains. The IMGT Colliers de Perles were generated by the IMGT/Collier-de-Perles tool [51] integrated in IMGT/3Dstructure-DB [57,58,59]. Hydrogen bonds (green lines) and disulfide bond between C23 and C104 (orange line) were automatically added from the experimental structural data. Amino acids are shown in the one-letter abbreviation. Positions at which hydrophobic amino acids (hydropathy index with positive value: I, V, L, F, C, M, A) and tryptophan (W) are found in more than 50% of analysed sequences are shown in blue. All proline (P) are shown in yellow. Hatched circles correspond to missing positions according to the IMGT unique numbering for C domain [42]. Arrows indicate the direction of the beta strands and their designations in 3D structures. Anchors (26, 39, 45, 77, 104, 118) are shown in squares. (C) 3D structure of the CH3 dimer showing the two amino acids T22 and Y86 involved in the knobs-and-holes amino acid changes (T22 > Y on one CH3 domain, Y86 > T on the other). The identifiers of the gamma1 chains to which the CH3 domains belong are 1hzh_H and 1hzh_K (IMGT® http://www.imgt.org, IMGT/3Dstructure-DB). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g037
Figure 38. Contact analysis and ball-and-socket interface between Homo sapiens IGHG1 CH2 and CH3 [94]. (A) Contact analysis between the CH2 and CH3 domains of the Fc gamma1 (from IMGT/3Dstructure-DB, 3ave_A). The amino acids of the CH3 BC and FG loops (left column) and those of the CH2 G strand (right column) are shown in rectangles. CH2 96 and 97 correspond to the EF turn whereas other positions are from the A strand or AB turn. Arrows indicates the two hydrogen bonds (orange on line) and the two salt bridges (green online) mentioned in the text [312]. (B) The ball-and-socket-joint of the IGHG1 CH2-CH3 interface [312] is shown using the IMGT numbering, with the ball (L15) and the socket (M107, H108, E109 and H115). The interface is stabilized by two hydrogen bonds involving on CH2, L15 (O) and K125 (O) that bind on CH3, H115 (ND1) and Y29 (OH), respectively, and by two salt bridges involving on CH2, K12 (A strand) and K123 (G strand) that interact on CH3 with E40 (C strand) and E109 (FG loop), respectively. The identifier of the gamma1 chain to which the CH2 and CH3 domains belong is 3ave_A (IMGT® http://www.imgt.org, IMGT/3Dstructure-DB). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 38. Contact analysis and ball-and-socket interface between Homo sapiens IGHG1 CH2 and CH3 [94]. (A) Contact analysis between the CH2 and CH3 domains of the Fc gamma1 (from IMGT/3Dstructure-DB, 3ave_A). The amino acids of the CH3 BC and FG loops (left column) and those of the CH2 G strand (right column) are shown in rectangles. CH2 96 and 97 correspond to the EF turn whereas other positions are from the A strand or AB turn. Arrows indicates the two hydrogen bonds (orange on line) and the two salt bridges (green online) mentioned in the text [312]. (B) The ball-and-socket-joint of the IGHG1 CH2-CH3 interface [312] is shown using the IMGT numbering, with the ball (L15) and the socket (M107, H108, E109 and H115). The interface is stabilized by two hydrogen bonds involving on CH2, L15 (O) and K125 (O) that bind on CH3, H115 (ND1) and Y29 (OH), respectively, and by two salt bridges involving on CH2, K12 (A strand) and K123 (G strand) that interact on CH3 with E40 (C strand) and E109 (FG loop), respectively. The identifier of the gamma1 chain to which the CH2 and CH3 domains belong is 3ave_A (IMGT® http://www.imgt.org, IMGT/3Dstructure-DB). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g038aBiomedicines 08 00319 g038b
Figure 39. Homo sapiens IGHG1 and G1m allotypes [83,94]. (A) IGHG1 CH1. The IMGT Collier de Perles of IGHG1 CH1 on two layers is shown with hydrogen bonds, as green lines online (on the left). K120 (strand G) corresponds to the G1m17 allotype [83]. I103 (strand F) is specific of the H-gamma1 chain isotype. The simultaneous presence of R120 and I103 corresponds to the expression of the G1m3 allotype (not shown) [83]. For isotypes other than H-gamma1, R120 corresponds to the expression of the nG1m17 isoallotype (not shown) [83]. The 3D structure of the CH1 (on the right) shows K120 (G1m17) and the H-gamma1 specific I103 [83]. (B) IGHG1 CH3. The IMGT Collier de Perles of IGHG1 CH3 on two layers is shown with hydrogen bonds, as green lines online (on the left). D12 and L14 (strand A) correspond to the G1m1 allotype, whereas E12 and M14 (not shown) correspond to the nG1m1 isoallotype [83]. G110 (not shown) corresponds to G1m2, whereas A110 (here) does not correspond to any allotype [83]. G129 and K130 represent the CHS in secreted IG. The 3D structure of the CH3 (on the right) shows the positions 12 and 14 of the G1m1/nG1m1 allotype, and position 110 of the G1m2/- allotype. The CH1 and CH3 domains are from the b12 antibody. The b12 H-gamma1 chain is encoded by the IGHG1*01 allele and expresses the G1m17,1 allotypes, based on sequence analysis (CH1 K120, CH3 D12 and L14) [83]. The presence of an A (Ala) in CH1 121 of 1hzh_H is a PDB file error. It should be a V (Val) as in 1n0x_H, and as mentioned in the IMGT note of 1hzh(IMGT® http://www.imgt.org, IMGT/3Dstructure-DB > Entry code (PDB): 1hzh). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 39. Homo sapiens IGHG1 and G1m allotypes [83,94]. (A) IGHG1 CH1. The IMGT Collier de Perles of IGHG1 CH1 on two layers is shown with hydrogen bonds, as green lines online (on the left). K120 (strand G) corresponds to the G1m17 allotype [83]. I103 (strand F) is specific of the H-gamma1 chain isotype. The simultaneous presence of R120 and I103 corresponds to the expression of the G1m3 allotype (not shown) [83]. For isotypes other than H-gamma1, R120 corresponds to the expression of the nG1m17 isoallotype (not shown) [83]. The 3D structure of the CH1 (on the right) shows K120 (G1m17) and the H-gamma1 specific I103 [83]. (B) IGHG1 CH3. The IMGT Collier de Perles of IGHG1 CH3 on two layers is shown with hydrogen bonds, as green lines online (on the left). D12 and L14 (strand A) correspond to the G1m1 allotype, whereas E12 and M14 (not shown) correspond to the nG1m1 isoallotype [83]. G110 (not shown) corresponds to G1m2, whereas A110 (here) does not correspond to any allotype [83]. G129 and K130 represent the CHS in secreted IG. The 3D structure of the CH3 (on the right) shows the positions 12 and 14 of the G1m1/nG1m1 allotype, and position 110 of the G1m2/- allotype. The CH1 and CH3 domains are from the b12 antibody. The b12 H-gamma1 chain is encoded by the IGHG1*01 allele and expresses the G1m17,1 allotypes, based on sequence analysis (CH1 K120, CH3 D12 and L14) [83]. The presence of an A (Ala) in CH1 121 of 1hzh_H is a PDB file error. It should be a V (Val) as in 1n0x_H, and as mentioned in the IMGT note of 1hzh(IMGT® http://www.imgt.org, IMGT/3Dstructure-DB > Entry code (PDB): 1hzh). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g039aBiomedicines 08 00319 g039b
Figure 40. G3m allotypes localizations on the gamma3 chains [83]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 40. G3m allotypes localizations on the gamma3 chains [83]. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g040
Figure 41. IMGT G3m allele butterfly’ representation [83]. The two mosaics on the CH3 domain are shown for each G3m allele (allotypes are described in [83]). The first mosaic around G3m11 is on the top with G3m27, G3m10/G3m24, G3m13/G3m6. The second mosaic is at the bottom with G3m26, G3m5/nG3m5/G3m28. Amino acids involved in the allotype expression and their position according to the IMGT unique numbering for C domain [42] are indicated. Two allotypes are on the CH2 domain, G3m16 (Trp W83) and G3m21 (Leu L82). Haplotypes to which the G3m alleles belong, are indicated between square brackets. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Figure 41. IMGT G3m allele butterfly’ representation [83]. The two mosaics on the CH3 domain are shown for each G3m allele (allotypes are described in [83]). The first mosaic around G3m11 is on the top with G3m27, G3m10/G3m24, G3m13/G3m6. The second mosaic is at the bottom with G3m26, G3m5/nG3m5/G3m28. Amino acids involved in the allotype expression and their position according to the IMGT unique numbering for C domain [42] are indicated. Two allotypes are on the CH2 domain, G3m16 (Trp W83) and G3m21 (Leu L82). Haplotypes to which the G3m alleles belong, are indicated between square brackets. (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org).
Biomedicines 08 00319 g041
Table 1. Immunoglobulin (IG) receptor, chain and domain structure labels and correspondence with sequence labels [34]. IMGT standardized labels are in capital letters [34,35]. They are shown for two examples of IG: A. Homo sapiens IgG1-kappa, B. Homo sapiens IgM-lambda.
Table 1. Immunoglobulin (IG) receptor, chain and domain structure labels and correspondence with sequence labels [34]. IMGT standardized labels are in capital letters [34,35]. They are shown for two examples of IG: A. Homo sapiens IgG1-kappa, B. Homo sapiens IgM-lambda.
A.
IG Structure Labels
(IMGT/3Dstructure-DB [57,58,59])
Sequence Labels (IMGT/LIGM-DB [54,55])
ReceptorChainDomain TypeDomainRegion 1
IG-GAMMA-1_KAPPAH-GAMMA-1VVHV-D-J-REGION
CCH1C-REGION 2
CCH2
CCH3
L-KAPPAVV-KAPPAV-J-REGION
CC-KAPPAC-REGION
B.
IG Structure Labels
(IMGT/3Dstructure-DB) [57,58,59]
Sequence Labels (IMGT/LIGM-DB) [54,55]
ReceptorChainDomain typeDomainRegion 1
IG-MU_LAMBDAH-MUVVHV-D-J-REGION
CCH1C-REGION 2
CCH2
CCH3
CCH4 3
L-LAMBDAVV-LAMBDAV-J-REGION
CC-LAMBDA-1C-REGION
1. The VH domain (or V-D-J-REGION) and the VL domain (V-KAPPA or V-LAMBDA) (or V-J-REGION) are encoded by rearranged V-(D)-J genes, whereas the remaining of the chain is the C-REGION (encoded by a C gene). The C-REGION comprises one C domain (C-KAPPA or C-LAMBDA) for the L chain, or several C domains (CH) for the H chain. 2. The heavy chain C-REGION also includes the HINGE-REGION for the H-ALPHA, H-DELTA and H-GAMMA chains and, for membrane IG (mIG), the CONNECTING-REGION (CO), TRANSMEMBRANE-REGION (TM) and CYTOPLASMIC-REGION (CY); for secreted IG (sIG), the C-REGION includes CHS instead of CO, TM and CY. 3. For H-MU and H-EPSILON.
Table 2. Structural and biological properties of human immunoglobulins [2].
Table 2. Structural and biological properties of human immunoglobulins [2].
PropertiesHuman IG Classes and Subclasses
IgMIgDIgGIgAIgE
IgG1IgG2IgG3IgG4IgA1IgA2
Molecular weight of secreted form (kDa) 1950 (p)170–180150150155-165150160 (m) 300 (d)160 (m) 350 (d)190
Chain composition
(with number of H2L2 monomers, if more than one)
2κ2)5 or (μ2λ2)5δ2κ2 or δ2λ2γ12κ2 or γ12λ2γ22κ2 or γ22λ2γ32κ2 or γ32λ2γ42κ2 or γ42λ2(α12κ2)1–2 or (α12λ2)1–2(α22κ2)1–2 or (α22λ2)1–2ε2κ2 or ε2λ2
Functional valency (nb of antigen binding sites)5 or 10222 or 42
Structure 2monomer (mb) pentamer (s)monomer (mb, s)monomer (mb, s)monomer (mb, s) dimer (sec)monomer (mb, s)
Inter-heavy (H-H) disulfide bridges per monomer1124112221
Other chainJ chain(16 kDa)J chain (16 kDa), secretory component (70 kDa)
Sedimentation coefficient in Svedberg unit (S)18–2076.5–7.07, 10, 13, 15, 177.9
Carbohydrate average (%)10–129–142–37–1112–13
Adult level range (age 16-60) in serum (g/L) 30.25–3.10.03-0.45–122–60.5–10.2–11.4–4.20.2–0.50.0001–0.0002
8.0-16.8
Approximate % total IG in adult serum (% of the subclass in the class)100.245–53 (70–80)11–15 (18−23)3–6 (6−8)1–4 (2–6)11–14 (90)1–4 (10)0.004
Synthetic rate (mg/kg weight/day)3.30.23333333319–293.3–5.30.002
Biological half-life (day)5–102–821–2421–247–821–245–74–61–5
Transplacental transfer00+++++++000
Complement activation classical pathway (C1q)+++0++++++0000
Complement activation alternative pathway000000+00
Binding macrophages and other phagocytic cells (FcγR or FCGR) 40+++++/–++++/–000
Binding to mast cells and basophils (FcεR or FCER)00000000+++
Binding to epithelial poly-IG receptor+00000++++++0
Reactivity with Staphyloccus protein A00++++(0) *++000
* IgG3 allotype dependent; 1. Approximate molecular weight (m = monomer, d = dimer, p = pentamer). 2. mb = membrane, s = secreted, sec = secretory. 3. Total IG adult level range (age 16–60) in serum: 9.5–21.7 g/L; 4. +/–: binding depends on the FCGR isotype and on the cell type.
Table 3. Homo sapiens immunoglobulin (IG) chain characteristics [2].
Table 3. Homo sapiens immunoglobulin (IG) chain characteristics [2].
Chain CharacteristicsHuman IG Chain Types
Heavy Chain (H)Light Chain (L)
μδγ1γ2γ3γ4α1α2εκλ
Molecular weight (kDa)7060505053-57505555702525
Number of variable (V) domains11111111111
Number of constant (C) domains43333333411
Length (in number of amino acids)Constant regionCH1 (for H) or CL (for L)10410197979897104102103107104 or 106
CH2112108109108110109101101107
CH3112108106106105106112111108
CH4111110
Hinge region058151232, 47 or 62121960
Membrane IGConnecting region (CO)132718181818323215
Transmembrane region (TM)272727272727272727
Cytoplamic region (CY)1126262626121226
Secreted IGCHS 1209222220202
N-glycosylation sites 253112124700
O-glycosylation sites 378
Allotypes [83]G1mG2mG3mG4mA2mEmKm
1. CHS corresponds to the tailpiece of secreted IG, encoded by the CHS region at the C-terminal end of the CH4 exon (for IGHM and IGHE) or of the CH3 exon (for IGHG1, IGHG2, IGHG3, IGHG4, IGHA1, IGHA2) or as a separate exon for IGHD. 2. Only indicated for the C-REGION. N-glycosylation sites may be found in some V domains. 3. O-glycosylation sites are located in the hinge regions of the H-delta and H-alpha1 chains.
Table 4. Interchain disulfide bridges. The number of inter Heavy (H)-Light (L) and inter H-H disulfide bridges is given per monomer of human (Homo sapiens) IG classes and subclasses, with positions of the cystein in the domain (IMGT unique numbering for C-DOMAIN [42]).
Table 4. Interchain disulfide bridges. The number of inter Heavy (H)-Light (L) and inter H-H disulfide bridges is given per monomer of human (Homo sapiens) IG classes and subclasses, with positions of the cystein in the domain (IMGT unique numbering for C-DOMAIN [42]).
Disulfide BridgesChainClasses and Subclasses
IgMIgDIgGIgAIgE
IgG1IgG2IgG3IgG4IgA1IgA2
Inter H-LHnumber111111111
Positions 1CH1 10CH1 11h 5CH1 10CH1 10CH1 10CH1 10CH1 123CH1 10, 11
LC-KAPPA126 (last amino acid)
C-LAMBDA126 (penultimate amino acid)
Inter H-HHnumber1124112221
Positions 1CH2: 125CH2: 1.6h 11, h 14h 4, h 5, h 8, h 11h1 13, h1 16, h2 5, h2 11, h2 14, h3 5, h3 11, h3 14, h4 5, h4 11, h4 14h 8, h 11CH2: 1.1, 1.2CH2: 1.1, 1.2CH2: 1.6, 11, 124
1. Cysteines of the hinge involved in inter-chain bridges are indicated with a small letter ‘h’, for example, Inter-H-L (h 5-CL 126), and Inter-H-H (h 11, h 14), for an Homo sapiens IgG1 – kappa, as used in the description of monoclonal antibodies, published by the WHO INN programme [86,87]). h1 to h4 numbers the IGHG3 hinge exons in the most current haplotypes.
Table 5. Number of IG genes and alleles per IMGT group in IG major loci and orphon sets.
Table 5. Number of IG genes and alleles per IMGT group in IG major loci and orphon sets.
LocusIGHIGKIGLTotal
IMGT GroupIGHVIGHDIGHJIGHCTotal IGHIGKVIGKJIGKCTotal IGKIGLVIGLJIGLCTotal IGL
Nb of genesMajor Locus159279112067751837811 111 1100389
Orphon sets261001 2373200324 303 4776
Locus total1853791224310951115821114107465
Nb of allelesMajor Locus494341991638114951281441021175941
Orphon sets49100261340 345049104
Locus total5434419936991489516214914251861045
1. Includes IGLJ2A, IGLC2A, IGLJ2B, IGLC2B, IGLJ2C, IGLC2C, IGLJ2D, IGLC2D; detected by Southern blot analysis and mapped, no sequence available. 2. Includes IGHEP2, the only known processed gene in an IG major locus in Homo sapiens. 3. Not included IGLV8/Ora which is unmapped (detected by Southern blot analysis, no sequence available). 4. Includes IGLJ-C/OR18, the only known processed IG orphon gene in Homo sapiens. (IMGT®, http://www.imgt.org, IMGT Repertoire (IG and TR) > Gene table: human (Homo sapiens)).
Table 6. The ten most classical IG and TR entity types and associated prototypes. Entity types are identified with IMGT standardized keywords [30] (IDENTIFICATION axiom [30,31]). Prototypes are described with IMGT standardized labels [34] (DESCRIPTION axiom [34,35]).
Table 6. The ten most classical IG and TR entity types and associated prototypes. Entity types are identified with IMGT standardized keywords [30] (IDENTIFICATION axiom [30,31]). Prototypes are described with IMGT standardized labels [34] (DESCRIPTION axiom [34,35]).
IDENTIFICATION (IMGT Standardized Keywords) [30] DESCRIPTION (IMGT Standardized Labels) [34]
Molecular Entity TypeConfiguration TypeMolecule TypeFunctionalityMolecular Entity Prototype
V-genegermlinegDNAF, ORF, PV-GENE
D-genegermlinegDNAF, ORF, PD-GENE
J-genegermlinegDNAF, ORF, PJ-GENE
C-geneundefinedgDNAF, ORF, PC-GENE
V-D-J-generearrangedgDNAproductive, unproductiveV-D-J-GENE
V-J-generearrangedgDNAproductive, unproductiveV-J-GENE
L-V-D-J-C-sequencerearrangedcDNAproductive, unproductiveL-V-D-J-C-SEQUENCE
L-V-J-C-sequencerearrangedcDNAproductive, unproductiveL-V-J-C-SEQUENCE
V-D-J-C-sequence or chainrearrangedproteinproductive, unproductiveH-MU, H-DELTA, H-GAMMA1, etc.
V-J-C-sequence or chainrearrangedproteinproductive, unproductiveL-KAPPA, L-LAMBDA1, etc.
Table 7. Potential Homo sapiens IGH genomic repertoire.
Table 7. Potential Homo sapiens IGH genomic repertoire.
A.Homo sapiens IGH V-CLUSTER.
IMGT IGHV SubgroupIMGT Gene Name 1CDR-IMGTNb of Alleles FNb of Alleles ORFNb of Alleles
P
Homo SapiensIGHV-CNVGene Order
IGHV1IGHV1-2[8.8.2]6 F 159
IGHV1-3[8.8.2]3 F, 1 (F) 157
IGHV1-8[8.8.2]3 FCNV5e1147
IGHV1-18[8.8.2]4 F 132
IGHV1-24[8.8.2]1 F 120
IGHV1-45[8.8.2]3 F 60
IGHV1-46[8.8.2]4 F 59
IGHV1-58[8.8.2]2 F, 1 (F) 41
IGHV1-69 a[8.8.2]17 F, 1 (F) 21
IGHV1-69D a[8.8.2] CNV1i17
IGHV1-69-2[8.8.2]2 FCNV1i18
IGHV2IGHV2-5[10.7.3]8 F (no *07) 154
IGHV2-26[10.7.3]3 F 117
IGHV2-70 b[10.7.3]19 F1 ORF 16
IGHV2-70D b[10.7.3] CNV1i20
IGHV3IGHV3-7[8.8.2]3 F, 1 (F) 150
IGHV3-9[8.8.3]3 FCNV5e1146
IGHV3-11[8.8.2]5 F1 P (0.1) 144
IGHV3-13[8.7.2]5 F 141
IGHV3-15[8.10.2]8 F 138
IGHV3-20[8.8.2]2 F2 ORF 130
IGHV3-21[8.8.2]4 F, 1 (F) 128
IGHV3-23 c[8.8.2]5 F 124
IGHV3-23D c[8.8.2] CNV4i121
IGHV3-30 d[8.8.2]19 F 109
IGHV3-30-3[8.8.2]3 FCNV3i102
IGHV3-30-5 d[8.8.2] CNV3i96
IGHV3-33[8.8.2]7 F 89
IGHV3-43 e[8.8.3]2 F 65
IGHV3-43D e[8.8.3]2 FCNV2i76
IGHV3-48[8.8.2]4 F 55
IGHV3-49[8.10.2]5 F 54
IGHV3-53[8.8.2]4 F, 1 (F) 47
IGHV3-62[8.8.2]1 F (* 04) 23 P (2.1)