Journal Description
Antibodies
Antibodies
is an international, peer-reviewed, open access journal on immunoglobulins, published quarterly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, ESCI (Web of Science), PubMed, PMC, Embase, CAPlus / SciFinder, and other databases.
- Journal Rank: CiteScore - Q2 (Drug Discovery)
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 22.2 days after submission; acceptance to publication is undertaken in 4.6 days (median values for papers published in this journal in the first half of 2025).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
2.7 (2024);
5-Year Impact Factor:
4.7 (2024)
Latest Articles
A Robust, High-Titer, Semi-Automated, and In-Culture Antibody-Capturing Transient CHO Platform Technology
Antibodies 2025, 14(4), 87; https://doi.org/10.3390/antib14040087 (registering DOI) - 11 Oct 2025
Abstract
Background: Recent advances in antibody discovery technologies, especially progress in de novo synthesis through machine learning, have imposed a significant production challenge for the generation of a large diversity of antibodies against nearly any target of interest. There is a demand for the
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Background: Recent advances in antibody discovery technologies, especially progress in de novo synthesis through machine learning, have imposed a significant production challenge for the generation of a large diversity of antibodies against nearly any target of interest. There is a demand for the rapid production of dozens of purified antibodies in 10-milligram quantities sufficient for functional screening and molecular assessment studies. Objectives: To meet this requirement, a semi-automated production methodology and workflow was developed to bridge the miniaturized high-throughput screenings (HTSs) and the conventional custom-scale workflow by taking advantage of four new technology applications. Methods: First, it exploited a novel, simple, high-titer transient expression system, “CHO4Tx®”, which could achieve high yields in the range of 200 mg/L and above, across a variety of antibody constructs, including challenging targets. The consistently high yields from this transient CHO platform enabled the delivery of ~20 mg of crude material per 100 mL scale flask production with a throughput capacity of nineteen constructs in a single run. Secondly, we established a magnetic ProA bead in-culture antibody-capturing process, which significantly shortened the production timeline by eliminating the steps of cell centrifugation, filtration, and medium column loading. Third, we utilized the GenScript AmMag™ SA Plus semi-automation, which could handle magnetic ProA bead elution for 12 constructs within less than 1 h. Lastly, we transformed the AKTA PureTM system into an automated buffer exchange purification system with a capacity of processing 19 samples in a single run. Results and Conclusions: This new production platform was proven to be robust and could be applied for the routine production of antibodies of sufficient quality and quantity in support of cell-based assays and biophysical characterization.
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(This article belongs to the Special Issue A Festschrift Celebrating Dr. Dimiter Stanchev Dimitrov: Antibodies, Innovation, and Impact on Infectious Disease and Cancer Research)
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Open AccessArticle
Structural and Functional Characterization of Anti-SARS-CoV-2 Spike Monoclonal Antibodies Produced via Bicistronic Expression in CHO Cells
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Federico Francisco Marsili, Fernanda Bittencourt de Aquino, Hiam Rodrigo da Silva Arruda, Mayra Amorim Marques, Katia Maria dos Santos Cabral, Marcius da Silva Almeida, Guilherme Augusto Piedade de Oliveira, Andrea Queiroz Maranhão, Renato Sampaio Carvalho and Leda dos Reis Castilho
Antibodies 2025, 14(4), 86; https://doi.org/10.3390/antib14040086 - 9 Oct 2025
Abstract
Background: Recombinant monoclonal antibodies (mAbs) represent the fastest-growing sector of the biopharmaceutical industry, with their efficient expression being a key technological factor for scalability. Objectives: In this study we compared the performance of two bicistronic vectors, which alternate the positions of the light
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Background: Recombinant monoclonal antibodies (mAbs) represent the fastest-growing sector of the biopharmaceutical industry, with their efficient expression being a key technological factor for scalability. Objectives: In this study we compared the performance of two bicistronic vectors, which alternate the positions of the light and heavy chain coding genes, employing a wild-type Encephalomyocarditis virus (EMCV) IRES functional element to drive expression of the second gene. Methods: Using two neutralizing anti-SARS-CoV-2 IgG1 antibodies as model molecules, we conducted transient transfections in the commercially available ExpiCHOTM platform. Following protein A affinity purification and quantification, vectors positioning the light chain as the first cistron consistently yielded higher expression levels than those with the heavy chain upstream. To confirm the quality attributes of the mAbs, we applied a comprehensive analytical workflow, including SDS-PAGE and Western blot for molecular mass and purity, circular dichroism for secondary structure, intrinsic tryptophan fluorescence for tertiary structure, and SEC-HPLC for quaternary structure and aggregate detection. Additionally, we assessed binding affinity to the target using spot blot and surface plasmon resonance, analyzed N-glycosylation profiles by HILIC-HPLC and mass spectrometry, and examined molecular structure by transmission electron microscopy. Results and Conclusions: Together, these results provide insight into the impact of gene positioning within bicistronic vectors on mAb expression efficiency and quality, supporting optimization strategies for scalable recombinant antibody production.
Full article
(This article belongs to the Special Issue A Festschrift Celebrating Dr. Dimiter Stanchev Dimitrov: Antibodies, Innovation, and Impact on Infectious Disease and Cancer Research)
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Open AccessArticle
Monoclonal Antibodies Can Aid in the Culture-Based Detection and Differentiation of Mucorales Fungi—The Flesh-Eating Pathogens Apophysomyces and Saksenaea as an Exemplar
by
Christopher R. Thornton and Genna E. Davies
Antibodies 2025, 14(4), 85; https://doi.org/10.3390/antib14040085 - 7 Oct 2025
Abstract
Background: The frequency of necrotising cutaneous and soft tissue infections caused by the Mucorales fungi Apophysomyces and Sakasenaea is increasing. The absence of sophisticated diagnostic technologies in low- and middle-income countries (LMICs) means that detection of cutaneous mucormycosis continues to rely on culture
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Background: The frequency of necrotising cutaneous and soft tissue infections caused by the Mucorales fungi Apophysomyces and Sakasenaea is increasing. The absence of sophisticated diagnostic technologies in low- and middle-income countries (LMICs) means that detection of cutaneous mucormycosis continues to rely on culture of the infecting pathogens from biopsy and their differentiation based on morphological characteristics. However, Apophysomyces and Sakasenaea are notorious for their failure to sporulate on standard mycological media used for the identification of human pathogenic fungi. Differentiation of these pathogens and their discrimination from Aspergillus fumigatus, the most common mould pathogen of humans, is essential due to their differing sensitivities to the antifungal drugs used to treat mucormycosis. Methods: A murine IgG1 monoclonal antibody, JD4, has been developed that is specific to Apophysomyces species. In Western blotting and enzyme-linked immunosorbent assay (ELISA), mAb JD4 is shown to bind to an extracellular 15 kDa protein, readily detectable in crude antigen extracts from non-sporulating cultures of Apophysomyces. Results: When combined with a Mucorales-specific lateral-flow immunoassay (LFIA), mAb JD4 allows the differentiation of Apophysomyces from Saksenaea species and discrimination from Aspergillus fumigatus. Monoclonal antibody JD4 enables the detection and differentiation of Apophysomyces species from other fungal pathogens that cause rapidly progressive cutaneous and soft tissue mycoses in humans. When this is combined with a rapid LFIA, improvements are offered in the sensitivity and specificity of Mucorales detection based on mycological culture, which remains a gold-standard procedure for mucormycosis detection in LMICs lacking access to more sophisticated diagnostic procedures.
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(This article belongs to the Section Antibody-Based Diagnostics)
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Open AccessArticle
Novel Humanized Anti-HER3 Antibodies: Structural Characterization and Therapeutic Activity
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Alessia Muzi, Roberto Arriga, Giovanni Bulfaro, Francesca Fata, Antonella Costanzo, Valerio Chiarini, Manuela Cappelletti, Fabiana Fosca Ferrara, Federica Bucci, Linda Celeste Montemiglio, Carmelinda Savino, Emanuele Marra, Gennaro Ciliberto, Luigi Aurisicchio, Beatrice Vallone and Giuseppe Roscilli
Antibodies 2025, 14(4), 84; https://doi.org/10.3390/antib14040084 - 6 Oct 2025
Abstract
Background/Objectives: The ErbB protein family plays a critical role in the progression of various solid tumors, and HER3 has been implicated in resistance mechanisms to multiple cancer therapies due to its ability to form heterodimers with other ErbB receptors, thereby activating pathways that
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Background/Objectives: The ErbB protein family plays a critical role in the progression of various solid tumors, and HER3 has been implicated in resistance mechanisms to multiple cancer therapies due to its ability to form heterodimers with other ErbB receptors, thereby activating pathways that promote tumor growth and survival. This study aimed to generate and characterize humanized monoclonal antibodies against HER3 to inhibit its function and evaluate their potential as therapeutic agents. Methods: Murine monoclonal antibodies TK-A3 and TK-A4 were humanized and tested for binding to ErbB3 and competition with neuregulin-1β (NRG). Specificity was assessed by ELISA, and epitope identified by X-ray crystallography. Downstream signaling was analyzed by western blot for phosphorylated ErbB3, Akt, and MAPK. Antitumor activity was evaluated in vitro and in a pancreatic cancer xenograft model. A toxicology study was also conducted. Results: TK-hu A3 and TK-hu A4 bound specifically to ErbB3 without cross-reactivity to other ErbB receptors. The ErbB3-TK-hu A3 Fab structure revealed the binding epitope. Both antibodies competed with NRG, inhibiting ErbB3, Akt, and MAPK phosphorylation in a dose-dependent manner. They suppressed cancer cell survival in vitro, and TK-hu A3 significantly delayed tumor growth in vivo. The toxicology study indicated good tolerability. Conclusions: TK-hu A3 emerged as the lead candidate, showing specific HER3 targeting, strong pathway inhibition, and antitumor efficacy in vivo. Beyond standalone use, it could support novel strategies such as T-cell engagers, ADCs, CAR-T, and bispecific antibodies. These findings highlight TK-hu A3 as a promising therapy for HER3-positive, treatment-resistant cancers, meriting further development.
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(This article belongs to the Section Antibody-Based Therapeutics)
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Open AccessArticle
Generation Using Phage-Display of pH-Dependent Antibodies Against the Tumor-Associated Antigen AXL
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Tristan Mangeat, Célestine Mairaville, Myriam Chentouf, Madeline Neiveyans, Martine Pugnière, Giang Ngo, Vincent Denis, Corentin Catherine, Alexandre Pichard, Emmanuel Deshayes, Margaux Maurel, Matthieu Gracia, Anne Bigot, Vincent Mouly, Sébastien Estaran, Alain Chavanieu, Pierre Martineau and Bruno Robert
Antibodies 2025, 14(4), 83; https://doi.org/10.3390/antib14040083 - 30 Sep 2025
Abstract
Background/Objectives: Tumor-associated antigens are not tumor-specific antigens but proteins that are overexpressed by tumor cells and also weakly expressed at the surface of healthy tissues. Therefore, some side effects are observed when targeted by therapeutic antibodies, a phenomenon named “on-target, off-tumor toxicity”. As
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Background/Objectives: Tumor-associated antigens are not tumor-specific antigens but proteins that are overexpressed by tumor cells and also weakly expressed at the surface of healthy tissues. Therefore, some side effects are observed when targeted by therapeutic antibodies, a phenomenon named “on-target, off-tumor toxicity”. As tumors generate an acidic microenvironment, we investigated whether we could generate pH-dependent antibodies to increase their tumor specificity. For this proof-of-concept study, we selected the tyrosine kinase receptor AXL because we already developed several antibodies against this target. Methods: To generate a pH-dependent anti-AXL antibody, we performed classical panning of a single-chain variable fragment (scFv) library using phage display at an acidic pH throughout the process. Results: After the third round of panning, 9 scFvs, among the 96 picked clones, bound to AXL at acidic pH and showed very low binding at a neutral pH. After reformatting them into IgG, two clones were selected for further study due to their strong pH-sensitive binding. Using molecular docking and alanine scanning, we found that their binding strongly depended on two histidine residues present on AXL at positions 61 and 116. Conclusions: To conclude, we set-up an easy process to generate pH-dependent antibodies that may increase their tumor-binding specificity and potentially decrease toxicity towards healthy tissues.
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(This article belongs to the Section Antibody Discovery and Engineering)
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Open AccessReview
Serum Factors in Primary Podocytopathies
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Edward John Filippone and John L. Farber
Antibodies 2025, 14(4), 82; https://doi.org/10.3390/antib14040082 - 28 Sep 2025
Abstract
Primary podocytopathies, including minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS), are caused by a circulating factor or factors injurious to the podocyte. An immunologic origin seems likely based on responsiveness to corticosteroids or other immunosuppressive agents, including calcineurin inhibitors targeting T-cells
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Primary podocytopathies, including minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS), are caused by a circulating factor or factors injurious to the podocyte. An immunologic origin seems likely based on responsiveness to corticosteroids or other immunosuppressive agents, including calcineurin inhibitors targeting T-cells and rituximab targeting B-cells. Potential non-antibody-mediated circulating factors have been identified, including cardiotrophin-like cytokine 1, soluble urokinase plasminogen activator receptor, and angiopoietin-like 4, among others. More recent research supports a primary antibody pathogenesis, with anti-nephrin antibodies found in a significant percentage of cases. Such antibodies also predict recurrence after transplantation. Other potential antigenic targets besides nephrin include annexin, the proteosome, podocin, and CD40. Additionally, high-resolution confocal microscopy has identified punctate immunoglobulin deposits along the slit diaphragm and podocyte cell body that may or may not colocalize with abnormal punctate nephrin staining and may correlate with detectable circulating antibodies. The success of rituximab in observational studies in both native kidneys and transplants supports a primary role for autoantibodies. We discuss in detail the data supporting putative non-antibody circulating factors, as well as the recent data supporting antibody pathogenesis, which may provide some clues on treating the individual patient.
Full article
(This article belongs to the Section Humoral Immunity)
Open AccessArticle
Purification and Characterization of Immunoglobulin Y (IgY) Targeting Surface Antigen 1 (SAG1) of Toxoplasma gondii
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Enrique Adrián Herrera-Aguirre, Diana León-Núñez, Jaime Marcial-Quino, Saúl Gómez-Manzo, César Augusto Reyes-López, Yolanda Medina-Flores, Olga Mata-Ruíz, Lizbeth Xicotencatl-García, Hector Luna-Pastén, Luz Belinda Ortiz-Alegría, Nury Pérez-Hernández, Magdalena Escorcia, Dolores Correa and Fernando Gómez-Chávez
Antibodies 2025, 14(4), 81; https://doi.org/10.3390/antib14040081 - 26 Sep 2025
Abstract
Toxoplasma gondii (T. gondii) is an obligate intracellular protozoan parasite responsible for toxoplasmosis, a disease with significant health implications for humans and animals. The surface antigen 1 (SAG1) of T. gondii is a major immunodominant protein that facilitates host cell invasion,
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Toxoplasma gondii (T. gondii) is an obligate intracellular protozoan parasite responsible for toxoplasmosis, a disease with significant health implications for humans and animals. The surface antigen 1 (SAG1) of T. gondii is a major immunodominant protein that facilitates host cell invasion, making it an ideal target for diagnostic and therapeutic interventions. Immunoglobulin Y (IgY), the primary antibody in avian species, offers unique advantages over mammalian IgG, including easier animal care, lower costs, high-yield production, and potential passive immunization. Objectives: This study aimed to induce, purify, and characterize IgY antibodies targeting T. gondii SAG1 from hen egg yolks. Methods: The coding region of the mature portion of T. gondii SAG1 was amplified by PCR, cloned into the pET32a(+) vector for heterologous expression in E. coli. The recombinant SAG1 (rSAG1) was purified by affinity chromatography and used to immunize hens. IgY was extracted from egg yolks using PEG. SDS-PAGE and spectrophotometry were used to evaluate purity and concentration. By ELISA, Western blot, and flow cytometry, the specificity of IgY was assessed against recombinant and endogenous, native, and denatured SAG1. Results: Purified IgY demonstrated strong recognition of both recombinant and native SAG1 in ELISA and Western blot, and against T. gondii tachyzoites by flow cytometry. Conclusions: SAG1-specific IgY was produced in a pure form; it could be helpful in research, diagnosis, and treatment at low costs on a larger production scale, with minimal animal harm.
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(This article belongs to the Section Antibody Discovery and Engineering)
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Development of a Chicken Immunoglobulin Heavy Chain Variable Region (VH) Single-Domain Antibody (sdAb) Against Calsequestrin (CSQ) and Its Application
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Sun Lee, Seoryeong Park, Hyunji Yang, Geummi Cho, Seung Youn Lee, Donggeun Lee, Nara Tae, Dae Hee Kim and Junho Chung
Antibodies 2025, 14(3), 80; https://doi.org/10.3390/antib14030080 - 19 Sep 2025
Abstract
Background/Objectives: Calsequestrin (CSQ) is a calcium-binding protein that is highly soluble and can serve as a solubility-enhancing fusion tag in recombinant protein expression. Its unique property of calcium-induced precipitation followed by EDTA-mediated resolubilization enables efficient purification. However, the broader application of CSQ-tagged proteins
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Background/Objectives: Calsequestrin (CSQ) is a calcium-binding protein that is highly soluble and can serve as a solubility-enhancing fusion tag in recombinant protein expression. Its unique property of calcium-induced precipitation followed by EDTA-mediated resolubilization enables efficient purification. However, the broader application of CSQ-tagged proteins in research have been hampered by the lack of reliable anti-CSQ detection reagents. This study aimed to develop single-domain antibodies (sdAbs) against CSQ for use in diverse immunoassays and cell-based analyses. Methods: Single-domain antibodies were selected from phage-displayed chicken VH libraries generated from CSQ-immunized chickens. After biopanning, CSQ-specific VH sdAb clones were isolated and expressed as VH–human kappa light chain constant region (VH-Cκ) fusion proteins in E. coli. The PE06 clone was chosen for further characterization and conjugated to horseradish peroxidase (HRP) and Alexa Fluor 647 for assay applications. Results: PE06 VH-Cκ fusion protein demonstrated specific binding to CSQ-tagged proteins and enabled reliable detection in enzyme-linked immunosorbent assay (ELISA), immunoblotting, and flow cytometry. These results validated its utility as a chemically defined detection reagent for CSQ fusion proteins expressed in E. coli. Conclusions: This study establishes a CSQ-specific chicken VH sdAb as a versatile detection tool for CSQ-tagged proteins. The approach expands the utility of CSQ as a protein fusion tag and enables the development of recombinant antibodies fused with CSQ, such as scFv-CSQ constructs, for broad application in research and assay systems.
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(This article belongs to the Section Antibody Discovery and Engineering)
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Open AccessReview
Monoclonal Antibodies and Small-Molecule Therapies for Lichen Planus: Targeted Immunomodulation and Emerging Evidence
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Francois Rosset, Nadia Sciamarrelli, Luca Mastorino, Valentina Pala, Sara Boskovic, Eleonora Bongiovanni, Orsola Crespi, Yingying Liao, Simone Ribero and Pietro Quaglino
Antibodies 2025, 14(3), 79; https://doi.org/10.3390/antib14030079 - 17 Sep 2025
Abstract
Background/Objectives: Lichen planus (LP) is a chronic inflammatory disease of autoimmune origin, affecting the skin and mucous membranes. While corticosteroids and immunosuppressants are traditionally used, many cases remain refractory or intolerant to standard therapies. Recent advances in immunopathogenesis have led to the exploration
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Background/Objectives: Lichen planus (LP) is a chronic inflammatory disease of autoimmune origin, affecting the skin and mucous membranes. While corticosteroids and immunosuppressants are traditionally used, many cases remain refractory or intolerant to standard therapies. Recent advances in immunopathogenesis have led to the exploration of targeted therapies, including biologic agents and small-molecule inhibitors. Methods: This review synthesizes current evidence from case reports, case series, and observational studies on the use of monoclonal antibodies (anti-TNF-α, anti-IL-17, anti-IL-23, anti-IL-6) and JAK inhibitors in LP. A structured literature search was conducted across PubMed, Scopus, and Web of Science, focusing on studies published between 2010 and 2025. Data on mechanisms, clinical efficacy, safety, and research limitations were extracted and summarized. Results: Promising therapeutic responses were reported for IL-17 inhibitors (secukinumab, ixekizumab) and JAK inhibitors (tofacitinib, baricitinib) in mucosal and recalcitrant LP. Anti-TNF agents showed variable efficacy, while emerging targets such as BTK and IFN-γ are under investigation. Adverse events were generally mild to moderate, but long-term safety data are lacking. The absence of randomized controlled trials and standardized outcome measures limits generalizability. Conclusions: Biologic and small-molecule therapies represent a potential paradigm shift in the treatment of LP, offering targeted immunomodulation with promising efficacy in refractory cases. Further collaborative research, including randomized studies and biomarker-driven approaches, is urgently needed to validate these treatments and establish personalized care strategies.
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(This article belongs to the Section Antibody-Based Therapeutics)
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Advancing Antibody Titer Assessment in ABO-Incompatible Transplantation
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Masayuki Tasaki, Kazuhide Saito and Kota Takahashi
Antibodies 2025, 14(3), 78; https://doi.org/10.3390/antib14030078 - 15 Sep 2025
Abstract
Background: The accurate evaluation of anti-ABO antibodies is essential for risk stratification in ABO-incompatible (ABOi) transplantation. Historically, hemagglutination-based titration has been the cornerstone of such an assessment; however, different tools are being evaluated in this context. In recent years, several novel methods
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Background: The accurate evaluation of anti-ABO antibodies is essential for risk stratification in ABO-incompatible (ABOi) transplantation. Historically, hemagglutination-based titration has been the cornerstone of such an assessment; however, different tools are being evaluated in this context. In recent years, several novel methods have been reported. Methods: A narrative review was conducted using PubMed, Scopus, and Google Scholar, focusing on recent studies evaluating anti-ABO antibody measurement techniques in the context of ABOi organ transplantation. Results: In addition to the conventional tube method, techniques such as column agglutination technology, flow cytometry, and enzyme-linked immunosorbent assay are utilized for anti-ABO antibody assessment. However, any particular technique, significant interinstitutional and interoperator variabilities have been reported due to differences in the detailed protocols and the inherently subjective nature of some techniques. Moreover, these assays are based on the antibody binding to ABO antigens expressed on red blood cells, which might not accurately reflect the clinical context of organ transplantation. In recent years, technological advances have enabled the development of novel assays evaluating antibody responses specifically against the ABO antigens expressed on vascular endothelial cells. These include glycan microarrays, which differentiate responses by ABO antigen subtypes, and CD31-based microarrays, wherein recombinant CD31 proteins expressing ABO antigens are immobilized. These approaches are applied to assess clinically relevant anti-ABO antibodies in the context of ABOi organ transplantation. Conclusions: The objective evaluation of antibody titers against ABO antigens on vascular endothelial cells might not only enable a more accurate risk assessment but also facilitate meaningful comparisons between institutions.
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(This article belongs to the Special Issue Antibody-Mediated Rejection in Kidney Transplantation)
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Comparative Evaluation of Three Primary Antibody Clones for p16 Immunohistochemistry in Gynecologic Tumors
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Hiroshi Yoshida, Ayumi Sugitani, Mayumi Kobayashi-Kato, Masaya Uno and Mitsuya Ishikawa
Antibodies 2025, 14(3), 77; https://doi.org/10.3390/antib14030077 - 5 Sep 2025
Abstract
Background: p16 immunohistochemistry (IHC) serves as a surrogate marker for high-risk human papillomavirus (hrHPV) and is widely used in gynecologic pathology. However, few studies have directly compared the staining performance and reproducibility of different p16 antibody clones in this context. Methods: We retrospectively
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Background: p16 immunohistochemistry (IHC) serves as a surrogate marker for high-risk human papillomavirus (hrHPV) and is widely used in gynecologic pathology. However, few studies have directly compared the staining performance and reproducibility of different p16 antibody clones in this context. Methods: We retrospectively evaluated 176 gynecologic tumor specimens including 42 whole slide sections and 134 tissue microarray cores from the cervix, endometrium, vulva, and ovary using three fully automated p16 IHC assays: E6H4 (Ventana/Roche), JC8 (Agilent/Dako), and 6H12 (Leica). Two pathologists independently reviewed each case, and concordance and interobserver agreement were analyzed. Sensitivity, specificity, and Cohen’s κ statistics were calculated, with E6H4 serving as the reference. Results: All three antibody clones demonstrated excellent staining performance with preserved tissue morphology and minimal background artifacts. Concordance for p16 positivity/negativity was 100% across all clone pairings (95% CI: 97.9–100%). Interobserver reproducibility was also perfect, with a κ coefficient of 1.00 (95% CI: 0.94–1.00). Minor non-block staining patterns did not impair interpretability. Conclusions: Our findings indicate that E6H4, JC8, and 6H12 clones yield comparable staining results when used in conjunction with standardized automated protocols. These results support the practical interchangeability of these clones in clinical and research settings, particularly when cost, availability, or risk management require substitution. Laboratories should continue to perform internal validation and utilize external quality assurance programs when implementing p16 IHC.
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(This article belongs to the Section Antibody-Based Diagnostics)
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Open AccessReview
Infertility and Auto-Antibodies: A Review
by
Brigita Šemeklienė and Brigita Gradauskienė
Antibodies 2025, 14(3), 76; https://doi.org/10.3390/antib14030076 - 5 Sep 2025
Abstract
Infertility is a multifactorial condition with a wide range of potential causes, including anatomical, hormonal, genetic, and lifestyle-related factors. Among these, immunological mechanisms have increasingly been recognized as important contributors. The immune system plays a critical role in maintaining reproductive health, and its
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Infertility is a multifactorial condition with a wide range of potential causes, including anatomical, hormonal, genetic, and lifestyle-related factors. Among these, immunological mechanisms have increasingly been recognized as important contributors. The immune system plays a critical role in maintaining reproductive health, and its dysregulation can impair fertility in both men and women. Recent scientific studies suggest that altered immune responses, particularly those involving autoimmune reactions, may negatively affect fertility by disrupting the complex immunological balance required for successful conception and pregnancy maintenance. This review focuses on the most common autoantibodies, such as antinuclear, antisperm, antiendometrial, antiovarian, antiphospholipid, and antithyroid antibodies. Treatment options, including immunomodulatory therapy, hormone replacement therapy, and lifestyle interventions, are also reviewed.
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(This article belongs to the Special Issue Antibody and Autoantibody Specificities in Autoimmunity)
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Safety and Effectiveness of Dupilumab in Atopic Dermatitis Patients with Hematologic Comorbidities: A Multicenter, Retrospective Study
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Luca Bettolini, Stefano Bighetti, Silvia Mariel Ferrucci, Angelo Valerio Marzano, Francesca Barei, Alessandra Narcisi, Matteo Bianco, Andrea Carugno, Nicola Zerbinati, Simone Ribero, Michela Ortoncelli, Elena Pezzolo, Maddalena Napolitano, Martina Maurelli, Giampiero Girolomoni, Zeno Fratton, Enzo Errichetti, Caterina Foti, Giacomo Dal Bello, Ilaria Trave, Anna Balato, Dario Didona, Niccolò Gori, Federica Veronese, Giovanni Paolino, Franco Rongioletti, Mario Bruno Guanti, Laura Calabrese, Riccardo Balestri, Manfredo Bruni and Mariateresa Rossiadd
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Antibodies 2025, 14(3), 75; https://doi.org/10.3390/antib14030075 - 3 Sep 2025
Abstract
Background: Dupilumab, a monoclonal antibody targeting the interleukin-4 receptor α, is approved for moderate-to-severe atopic dermatitis (AD). However, its safety profile in patients with concomitant hematologic disorders remains unclear, as such populations were excluded from pivotal trials. Objective: To evaluate the safety and
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Background: Dupilumab, a monoclonal antibody targeting the interleukin-4 receptor α, is approved for moderate-to-severe atopic dermatitis (AD). However, its safety profile in patients with concomitant hematologic disorders remains unclear, as such populations were excluded from pivotal trials. Objective: To evaluate the safety and effectiveness of dupilumab in adolescents and adults with AD and underlying hematologic comorbidities. Methods: This retrospective, multicenter study included 139 patients aged ≥15 years with moderate-to-severe AD and at least one hematologic disorder, treated with dupilumab across 21 dermatology centers. Data on disease severity, laboratory markers, and hematologic outcomes were collected over a median follow-up of 52 weeks (range 4–156). Results: The most common hematologic conditions included monoclonal gammopathies, leukemias, lymphomas, myeloproliferative neoplasms, and immune cytopenias. Clinical response to dupilumab was sustained across all endpoints, with median EASI scores decreasing from 26.0 at the baseline to 1.0 at week 52. NRS pruritus and sleep scores similarly declined to 0.0 by week 52. Serum IgE levels and eosinophil counts progressively decreased. The clinical response to dupilumab was sustained across all endpoints, with significant and progressive improvements in EASI, pruritus NRS, and sleep NRS observed up to week 52, followed by long-term stability through week 156. Serum IgE levels decreased steadily at all timepoints, while eosinophil counts declined after week 4 and stabilized beyond week 52. Hematologic conditions remained stable in 82.7% of patients, resolved in 16.5%, and progressed in only one case. Twelve patients (8.6%) received a new hematologic diagnosis during follow-up; no causal relationship could be established due to the retrospective design and absence of systematic screening, and these findings should be interpreted as descriptive associations only. Conclusions: Dupilumab appears to be safe and effective in AD patients with a broad range of hematologic comorbidities, including malignancies. These findings support its use in real-world settings, though prospective studies are warranted to further assess long-term safety in this population.
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(This article belongs to the Section Antibody-Based Therapeutics)
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Structure-Guided Stapling of Dimeric Conformations and Linker Engineering Enhance Thermostability and Fine-Tune Activity of Bispecific VHH Cytokine Agonists
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Raphael Trenker, Deepti Rokkam, Andrew Morin, Priyanka Balasubrahmanyam, Verenice Paredes, Ivan Cheng, Rene de Waal Malefyt, Martin Oft, Patrick Lupardus and Sandro Vivona
Antibodies 2025, 14(3), 74; https://doi.org/10.3390/antib14030074 - 1 Sep 2025
Abstract
Background: Bispecific antibodies have emerged as a promising class of therapeutics, enabling simultaneous targeting of two distinct antigens. Single-domain antibodies (sdAbs) comprising camelid variable heavy chains (VHHs) provide a compact and adaptable platform for bispecific antibody design due to their small size and
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Background: Bispecific antibodies have emerged as a promising class of therapeutics, enabling simultaneous targeting of two distinct antigens. Single-domain antibodies (sdAbs) comprising camelid variable heavy chains (VHHs) provide a compact and adaptable platform for bispecific antibody design due to their small size and ease of linkage. Methods: Here we investigate structure-activity relationship of VHH-based cytokine surrogates by combining cell signaling and functional assays with x-ray crystallography and other biophysical techniques. Results: We describe crystal structures of four unique bispecific VHHs that engage and activate the cytokine receptor pairs IL-18Rα/IL-18Rβ and IL-2Rβ/IL-2Rγ. These bispecific VHH molecules, referred to as surrogate cytokine agonists (SCAs), create unique cytokine signals that can be tuned by linker engineering. Our structural analysis reveals multiple dimeric conformations for these bispecific SCAs, where the two VHH domains can interact to form a compact structure. We demonstrate that the dimeric conformation can be enforced via engineering of a non-native disulfide bond between the VHH subunits, thus enhancing molecular thermostability. Conclusion: Our findings have important implications for the design and engineering of bispecific VHHs or sdAbs, offering a novel strategy for tuning their activity and increasing their stability.
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(This article belongs to the Section Antibody Discovery and Engineering)
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Computational Prediction of Single-Domain Immunoglobulin Aggregation Propensities Facilitates Discovery and Humanization of Recombinant Nanobodies
by
Felix Klaus Geyer, Julian Borbeck, Wiktoria Palka, Xueyuan Zhou, Jeffrey Takimoto, Brian Rabinovich, Bernd Reifenhäuser, Karlheinz Friedrich and Harald Kolmar
Antibodies 2025, 14(3), 73; https://doi.org/10.3390/antib14030073 - 28 Aug 2025
Abstract
Background/Objectives: Single-domain immunoglobulins are small protein modules with specific affinities. Among them, the variable domains of heavy chains of heavy-chain-only antibodies (VHH) as the antigen-binding fragment of heavy-chain-only antibodies (also termed nanobodies) have been widely investigated for their applicability, e.g., therapeutics and immunodiagnostics.
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Background/Objectives: Single-domain immunoglobulins are small protein modules with specific affinities. Among them, the variable domains of heavy chains of heavy-chain-only antibodies (VHH) as the antigen-binding fragment of heavy-chain-only antibodies (also termed nanobodies) have been widely investigated for their applicability, e.g., therapeutics and immunodiagnostics. However, despite their advantageous biochemical and biophysical characteristics, protein aggregation throughout recombinant synthesis is a serious drawback in the development of nanobodies with application perspectives. Therefore, we aimed to develop a computational method to predict the aggregation propensity of VHH antibodies for the selection of promising candidates in early discovery. Methods: We employed a deep learning-based structure prediction for VHHs and derived from it likely biophysical and biochemical properties of the framework region 2 with relevance for aggregation. A total of 106 nanobody variants were produced by recombinant expression and characterized for their aggregation behavior using size exclusion chromatography (SEC). Results: Quantitative characteristics of framework region 2 patches were combined into a function that defines an aggregation score (AS) predicting the aggregation propensities of VHH variants. AS was evaluated for its capability to forecast recombinant VHH aggregation by experimentally studying VHH Fc-fusion proteins for their aggregation. We observed a clear correlation between the calculated aggregation score and the actual aggregation propensities of biochemically characterized VHHs Fc-fusion proteins. Moreover, we implemented an easily accessible pipeline of software modules to design nanobodies with desired solubility properties. Conclusions: AI-based prediction of VHH structures, followed by analysis of framework region 2 properties, can be used to predict the aggregation propensities of VHHs, providing a convenient and efficient tool for selecting stable recombinant nanobodies.
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(This article belongs to the Collection Computational Antibody and Antigen Design)
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Cost-Effective Method for Full-Length Sequencing of Monoclonal Antibodies from Hybridoma Cells
by
Sarah Döring, Georg Tscheuschner, Sabine Flemig, Michael G. Weller and Zoltán Konthur
Antibodies 2025, 14(3), 72; https://doi.org/10.3390/antib14030072 - 22 Aug 2025
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Background: Monoclonal antibodies play an important role in therapeutic and analytical applications. For recombinant expression, the coding sequences of the variable regions of the heavy and light chains are required. In addition, cloning antibody sequences, including constant regions, reduces the impact of hybridoma
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Background: Monoclonal antibodies play an important role in therapeutic and analytical applications. For recombinant expression, the coding sequences of the variable regions of the heavy and light chains are required. In addition, cloning antibody sequences, including constant regions, reduces the impact of hybridoma cell loss and ensures preservation of the naturally occurring full antibody sequence. Method: We combined amplification of IgG antibody variable regions from hybridoma mRNA with an advanced method for full-length cloning of monoclonal antibodies in a simple two-step workflow. Following Sanger sequencing and evaluation of consensus sequences, the best matching variable, diversity, and joining (V-(D-)J) gene segments were identified according to identity scores from IgBLAST reference sequences. Simultaneously, the mouse IgG subclass was determined at the DNA level based on isotype-specific sequence patterns in the CH1 domain. Knowing the DNA sequence of V-(D-)J recombination responsible for the complementary determining region 3 (CDR 3), variable region-specific primers were designed and used to amplify the corresponding antibody constant regions. Results: To verify the approach, we applied it to the hybridoma clone BAM-CCMV-29-81 and obtained identical full-length antibody sequences as with RNA Illumina sequencing. Further validation at the protein level using an established MALDI-TOF MS-fingerprinting protocol showed that five out of six genetically encoded CDR domains of the monoclonal antibody BAM-CCMV-29-81 could be efficiently correlated. Conclusion: This simple, streamlined method enables the cost-effective determination of the full-length sequence of monoclonal antibodies from hybridoma cell lines, with the added benefit of obtaining the DNA sequence of the antibody ready for recombinant expression.
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Open AccessArticle
Guidelines in the Preparation of Fully Synthetic, Human Single-Domain Antibody Phage Display Libraries
by
Mark A. Tornetta, Brian P. Whitaker, Olivia M. Cantwell, Peter N. Haytko, Eileen D. Pisors, Fulai Zhou and Mark L. Chiu
Antibodies 2025, 14(3), 71; https://doi.org/10.3390/antib14030071 - 15 Aug 2025
Abstract
Background/Objectives: The complexity of diseases such as cancer and auto-immune disorders drives the need for unique, target-driven therapeutics. A broader arsenal to generate better biologics-based therapeutics is needed to provide more efficient and effective antibody generation technologies. The critical parameter for antibody generation
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Background/Objectives: The complexity of diseases such as cancer and auto-immune disorders drives the need for unique, target-driven therapeutics. A broader arsenal to generate better biologics-based therapeutics is needed to provide more efficient and effective antibody generation technologies. The critical parameter for antibody generation is to generate as much candidate diversity to each target as possible. Method/Results: We present guidelines for having an efficient process using a fully synthetic human single-domain antibody (sdAb) phage display library. Critical milestones for success focused on library quality control (QC) assessments, evaluation of specific biopanning outputs, and construct designs that enabled efficient transition to mammalian expression. The synthetic VHO libraries produced epitope diversity better than an immunized sourced library with candidates possessing nM potencies and monodispersity > 90% via SEC. Conclusions: Synthetic human scaffold sdAb phage display libraries was constructed, biopanned, and selected candidates that could be directly transitioned for mammalian expression. The diverse VHO sets of candidates produced from many targets easily provided opportunities to make a multi-specific biological compound. Both synthetic and immunized phage selection campaign results suggested that these technologies complemented each other to generate therapeutic candidates. Finally, we demonstrated how diverse data produced from a process that used VHO synthetic libraries could accelerate drug discovery.
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(This article belongs to the Special Issue Therapeutic Antibodies: New Trends in Discovery, Developability and Characterization)
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Open AccessArticle
Comparative Molecular Dynamics Study of 19 Bovine Antibodies with Ultralong CDR H3
by
Olena Denysenko, Anselm H. C. Horn and Heinrich Sticht
Antibodies 2025, 14(3), 70; https://doi.org/10.3390/antib14030070 - 13 Aug 2025
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Background/Objectives: Cows produce antibodies with ultralong CDRH3 segments (ulCABs) that contain a disulfide-stabilized knob domain. This domain is connected to the globular core of the antibody by a β-strand stalk. In the crystal structures, the stalk protrudes from the core in an
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Background/Objectives: Cows produce antibodies with ultralong CDRH3 segments (ulCABs) that contain a disulfide-stabilized knob domain. This domain is connected to the globular core of the antibody by a β-strand stalk. In the crystal structures, the stalk protrudes from the core in an extended conformation and presents the knob at its distal end. However, the rigidity of this topology has been questioned due to the extensive crystal packing present in most ulCAB crystal structures. To gain more insight into the dynamics of ultralong CDRH3s, we performed a comparative molecular dynamics (MD) study of 19 unique ulCABs. Methods: For all 19 systems, one-microsecond MD simulations were performed in explicit solvent. The analyses included an investigation of the systems’ conformational stability and the dynamics of the knob domain as well as an energetic analysis of the intramolecular knob interactions. Results: The simulations show that the extended stalk–knob conformation observed in the crystal structures is not preserved in solution. There are significant differences in the degree of knob dynamics, the orientations of the knobs, the number of flexible stalk residues, and the frequency of the motions. Furthermore, interactions between the knob and the light chain (LC) of the ulCABs were observed in about half of the systems. Conclusions: The study reveals that pronounced knob dynamics is a general feature of ulCABs rather than an exception. The magnitude of knob motions depends on the system, thus reflecting the high sequence diversity of the CDRH3s in ulCABs. The observed knob–LC interactions might play a role in stabilizing distinct knob orientations. The MD simulations of ulCABs could also help to identify suitable knob fragments as mini-antibodies by suggesting appropriate truncation points based on flexible sites in the stalks.
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Conversion Factors to Compare Serum Concentrations of Anti-HBs, Anti-SARS-CoV-2 and Anti-Tetanus Toxin IgG
by
Aurelia Knispel and Christian Jassoy
Antibodies 2025, 14(3), 69; https://doi.org/10.3390/antib14030069 - 13 Aug 2025
Abstract
Background: The concentration of antigen-specific antibodies in serum is usually measured in international units/mL. Therefore, the actual concentration of virus-specific antibodies in sera is unknown. Objectives: The aim of the study was to determine conversion factors for concentrations of IgG against
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Background: The concentration of antigen-specific antibodies in serum is usually measured in international units/mL. Therefore, the actual concentration of virus-specific antibodies in sera is unknown. Objectives: The aim of the study was to determine conversion factors for concentrations of IgG against hepatitis B surface antigen (HBs), SARS-CoV-2 receptor binding domain (RBD) and nucleoprotein (NP) as well as tetanus toxin (Ttx) in serum and to compare antigen-specific IgG concentrations in serum samples. Methods: Absorption equivalence ELISAs were used to determine conversion factors for international units (IU) for anti-HBs, anti-SARS-CoV-2-RBD and NP and for anti-Ttx immunoglobulin G. The antigen-specific IgG concentrations in serum samples were then measured in units/mL and the ratio of IgG concentrations in the sera was determined using the conversion factors. Results: One IU of anti-HBs IgG corresponded to 24.4 BAU of anti-CoV-2 RBD IgG, 6.87 BAU of anti-CoV-2 NP and 14 mIU of anti-Ttx IgG. One BAU anti-SARS-CoV-2 NP-specific IgG is equivalent to 3.5 BAU SARS-CoV-2 RBD-specific IgG. Conversion of international units showed that median serum anti-Ttx-IgG concentrations were 50 times higher and anti-CoV-2-RBD-IgG concentrations were 390 times higher than median anti-HBs-IgG concentrations. In addition, after SARS-CoV-2 infection, the concentration of NP-specific IgG in serum was generally higher than that of RBD-specific IgG. Conclusions: The study provides conversion factors for serum concentrations of IgG against HBs, SARS-CoV-2 RBD and NP, as well as Ttx-IgG. This offers new insights into serum IgG concentrations and allows conclusions to be drawn about plasma cell pools.
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(This article belongs to the Section Humoral Immunity)
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A 3D Surface Plot for the Effective Visualization of Specific Serum Antibody Binding Properties
by
József Prechl, Ágnes Kovács, Krisztián Papp, Zoltán Hérincs and Tamás Pfeil
Antibodies 2025, 14(3), 68; https://doi.org/10.3390/antib14030068 - 13 Aug 2025
Abstract
Background: When an antigen molecule is exposed to serum, many different kinds of antibodies bind to it. The complexity of these binding events is only poorly characterized by assays that generate a single variable, generally reflecting the fractional saturation of the antigen, as
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Background: When an antigen molecule is exposed to serum, many different kinds of antibodies bind to it. The complexity of these binding events is only poorly characterized by assays that generate a single variable, generally reflecting the fractional saturation of the antigen, as the readout. Methods: We have previously devised an assay that delivers the essential biochemical variables to determine fractional saturation as the output: an equilibrium dissociation constant for affinity, the ratio of antibody concentration to the equilibrium constant and the concentration of bound antibodies under reference conditions. Here we propose a visualization method for the practical and informative display of these variables. Results: Using total antigen concentration and free and bound antibody concentration as coordinates in a three-dimensional space, a surface plot can depict the behavior of serum antibodies in the measurement range and identify the values of the key variables of binding activity. This surface display (antibody binding in 3-concentration display, Ab3cD) was used for the characterization of antibody binding to the SARS-CoV-2 spike protein in seronegative and seropositive sera. We demonstrate that this visualization scheme is suitable for presenting both individual and group differences and that epitope density changes, not commonly measured by immunoassays, are also revealed by the method. Conclusions: We recommend the use of 3D visualization whenever detailed, informative and characteristic differences in serum antibody reactivity are studied.
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(This article belongs to the Section Humoral Immunity)
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