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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (31 July 2021) | Viewed by 35205

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Prof. Dr. Tomasz Żarnowski

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Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, 20-059 Lublin, Poland
Interests: management of glaucoma (wound healing, complications, new methods); neuroprotection in neuroscience (glaucoma, epilepsy); glaucoma genetics; clinico-genetical correlations; management of complicated cataracts
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Dear Colleagues,

Genetics of eye diseases has been a field of interest for many researchers in the last few decades. Technological advancement of molecular techniques allowed the spread of new approaches in search of genetic factors underlying pathological processes in ocular disorders. For years, traditional linkage analysis has been utilized to link different diseases' phenotypes with particular loci and has been successful in finding variations responsible for known pathological processes, for instance in retinoblastoma. One limitation of this approach is its reliance on prior knowledge of pathological pathways. Most eye diseases are clinically heterogenous, with many pathways still unknown. Additionally, diseases’ phenotypical heterogeneity is usually reflected by their polygenic inheritance, therefore linkage analysis, though useful in finding genes of big impact, fails to recognize whole spectrum of casual variations involved in development of complex diseases, such as glaucoma, age-related maculopathy or keratoconjunctivitis sicca. In age-related maculopathy, which is considered the most well genetically defined complex disorder, two major loci explain only half of its heritability and MYOC, one of major glaucoma-causing genes is present only in 2–4% of primary open-angle glaucoma patients. More recently, genome-wide association studies have emerged. These huge studies are more powerful in finding variations in genes of subtle effects that summarily contribute to more complex disorders, thus they are hoped, among others, to help defining heritability of polygenic eye diseases. Importance of knowledge regarding genetics of eye diseases is hard to overestimate, especially up against novel achievements of molecular manipulation techniques. Advances in sequence analysis and gene delivery methods, by both viral and nonviral vectors have recently allowed the delivery of genetic payloads in preclinical models of retinal disorders, expanding the disease-modifying power of gene therapies. Further studies regarding targets for such therapies are however still needed. Despite the number of studies contributing to different eye diseases’ genetics there is still little understood and much to be revealed.

This special issue is focused on molecular side of the topic, nevertheless clinical implications are also welcome, if connected with biomolecular experiments.

Prof. Tomasz Żarnowski
Guest Editor

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Keywords

gene phenotypes

genetic payloads

retinoblastoma

glaucoma

age-related maculopathy

keratoconjunctivitis sicca

gene delivery methods

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Genetics of Eye Disease 2.0 in International Journal of Molecular Sciences (5 articles)

Published Papers (11 papers)

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29 pages, 3071 KiB

Open AccessArticle

Next-Generation Sequencing Screening of 43 Families with Non-Syndromic Early-Onset High Myopia: A Clinical and Genetic Study

by Eva González-Iglesias, Ana López-Vázquez, Susana Noval, María Nieves-Moreno, María Granados-Fernández, Natalia Arruti, Irene Rosa-Pérez, Marta Pacio-Míguez, Victoria E. F. Montaño, Patricia Rodríguez-Solana, Angela del Pozo, Fernando Santos-Simarro and Elena Vallespín

Int. J. Mol. Sci. 2022, 23(8), 4233; https://doi.org/10.3390/ijms23084233 - 11 Apr 2022

Cited by 3 | Viewed by 3490

Abstract

Early-onset high myopia (EoHM) is a disease that causes a spherical refraction error of ≥−6 diopters before 10 years of age, with potential multiple ocular complications. In this article, we report a clinical and genetic study of 43 families with EoHM recruited in our center. A complete ophthalmological evaluation was performed, and a sample of peripheral blood was obtained from proband and family members. DNA was analyzed using a customized next-generation sequencing panel that included 419 genes related to ophthalmological disorders with a suspected genetic cause, and genes related to EoHM pathogenesis. We detected pathogenic and likely pathogenic variants in 23.9% of the families and detected variants of unknown significance in 76.1%. Of these, 5.7% were found in genes related to non-syndromic EoHM, 48.6% in genes associated with inherited retinal dystrophies that can include a syndromic phenotype, and 45.7% in genes that are not directly related to EoHM or retinal dystrophy. We found no candidate genes in 23% of the patients, which suggests that further studies are needed. We propose a systematic genetic analysis for patients with EoHM because it helps with follow-up, prognosis and genetic counseling. Full article

(This article belongs to the Special Issue Genetics of Eye Disease)

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8 pages, 1314 KiB

Open AccessArticle

Biallelic Variants in KIF17 Associated with Microphthalmia and Coloboma Spectrum

by Antonella Riva, Antonella Gambadauro, Valeria Dipasquale, Celeste Casto, Maria Domenica Ceravolo, Andrea Accogli, Marcello Scala, Giorgia Ceravolo, Michele Iacomino, Federico Zara, Pasquale Striano, Caterina Cuppari, Gabriella Di Rosa, Maria Concetta Cutrupi, Vincenzo Salpietro and Roberto Chimenz

Int. J. Mol. Sci. 2021, 22(9), 4471; https://doi.org/10.3390/ijms22094471 - 25 Apr 2021

Cited by 8 | Viewed by 2034

Abstract

Microphthalmia, anophthalmia, and coloboma (MAC) are a group of congenital eye anomalies that can affect one or both eyes. Patients can present one or a combination of these ocular abnormalities in the so called “MAC spectrum”. The KIF17 gene encodes the kinesin-like protein Kif17, a microtubule-based, ATP-dependent, motor protein that is pivotal for outer segment development and disc morphogenesis in different animal models, including mice and zebrafish. In this report, we describe a Sicilian family with two siblings affected with congenital coloboma, microphthalmia, and a mild delay of motor developmental milestones. Genomic DNA from the siblings and their unaffected parents was sequenced with a clinical exome that revealed compound heterozygous variants in the KIF17 gene (NM_020816.4: c.1255C > T (p.Arg419Trp); c.2554C > T (p.Arg852Cys)) segregating with the MAC spectrum phenotype of the two affected siblings. Variants were inherited from the healthy mother and father, are present at a very low-frequency in genomic population databases, and are predicted to be deleterious in silico. Our report indicates the potential co-segregation of these biallelic KIF17 variants with microphthalmia and coloboma, highlighting a potential conserved role of this gene in eye development across different species. Full article

(This article belongs to the Special Issue Genetics of Eye Disease)

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13 pages, 3824 KiB

Open AccessArticle

Optic Nerve Head and Retinal Abnormalities Associated with Congenital Fibrosis of the Extraocular Muscles

by Mervyn G. Thomas, Gail D. E. Maconachie, Helen J. Kuht, Wai-Man Chan, Viral Sheth, Michael Hisaund, Rebecca J. McLean, Brenda Barry, Bashir Al-Diri, Frank A. Proudlock, Zhanhan Tu, Elizabeth C. Engle and Irene Gottlob

Int. J. Mol. Sci. 2021, 22(5), 2575; https://doi.org/10.3390/ijms22052575 - 4 Mar 2021

Cited by 5 | Viewed by 3076

Abstract

Congenital fibrosis of the extraocular muscles (CFEOM) is a congenital cranial dysinnervation disorder caused by developmental abnormalities affecting cranial nerves/nuclei innervating the extraocular muscles. Autosomal dominant CFEOM arises from heterozygous missense mutations of KIF21A or TUBB3. Although spatiotemporal expression studies have shown KIF21A and TUBB3 expression in developing retinal ganglion cells, it is unclear whether dysinnervation extends beyond the oculomotor system. We aimed to investigate whether dysinnervation extends to the visual system by performing high-resolution optical coherence tomography (OCT) scans characterizing retinal ganglion cells within the optic nerve head and retina. Sixteen patients with CFEOM were screened for mutations in KIF21A, TUBB3, and TUBB2B. Six patients had apparent optic nerve hypoplasia. OCT showed neuro-retinal rim loss. Disc diameter, rim width, rim area, and peripapillary nerve fiber layer thickness were significantly reduced in CFEOM patients compared to controls (p < 0.005). Situs inversus of retinal vessels was seen in five patients. Our study provides evidence of structural optic nerve and retinal changes in CFEOM. We show for the first time that there are widespread retinal changes beyond the retinal ganglion cells in patients with CFEOM. This study shows that the phenotype in CFEOM extends beyond the motor nerves. Full article

(This article belongs to the Special Issue Genetics of Eye Disease)

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14 pages, 3244 KiB

Open AccessArticle

EPHA2 Segregates with Microphthalmia and Congenital Cataracts in Two Unrelated Families

by Philippa Harding, Maria Toms, Elena Schiff, Nicholas Owen, Suzannah Bell, Ian Christopher Lloyd and Mariya Moosajee

Int. J. Mol. Sci. 2021, 22(4), 2190; https://doi.org/10.3390/ijms22042190 - 22 Feb 2021

Cited by 7 | Viewed by 3410

Abstract

EPHA2 is a transmembrane tyrosine kinase receptor that, when disrupted, causes congenital and age-related cataracts. Cat-Map reports 22 pathogenic EPHA2 variants associated with congenital cataracts, variable microcornea, and lenticonus, but no previous association with microphthalmia (small, underdeveloped eye, ≥2 standard deviations below normal axial length). Microphthalmia arises from ocular maldevelopment with >90 monogenic causes, and can include a complex ocular phenotype. In this paper, we report two pathogenic EPHA2 variants in unrelated families presenting with bilateral microphthalmia and congenital cataracts. Whole genome sequencing through the 100,000 Genomes Project and cataract-related targeted gene panel testing identified autosomal dominant heterozygous mutations segregating with the disease: (i) missense c.1751C>T, p.(Pro584Leu) and (ii) splice site c.2826-9G>A. To functionally validate pathogenicity, morpholino knockdown of epha2a/epha2b in zebrafish resulted in significantly reduced eye size ± cataract formation. Misexpression of N-cadherin and retained fibre cell nuclei were observed in the developing lens of the epha2b knockdown morphant fish by 3 days post-fertilisation, which indicated a putative mechanism for microphthalmia pathogenesis through disruption of cadherin-mediated adherens junctions, preventing lens maturation and the critical signals stimulating eye growth. This study demonstrates a novel association of EPHA2 with microphthalmia, suggesting further analysis of pathogenic variants in unsolved microphthalmia cohorts may increase molecular diagnostic rates. Full article

(This article belongs to the Special Issue Genetics of Eye Disease)

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20 pages, 5182 KiB

Open AccessArticle

Stationary and Progressive Phenotypes Caused by the p.G90D Mutation in Rhodopsin Gene

by Nina Kobal, Tjaša Krašovec, Maja Šuštar, Marija Volk, Borut Peterlin, Marko Hawlina and Ana Fakin

Int. J. Mol. Sci. 2021, 22(4), 2133; https://doi.org/10.3390/ijms22042133 - 21 Feb 2021

Cited by 7 | Viewed by 3398

Abstract

Mutations in rhodopsin gene (RHO) are a frequent cause of retinitis pigmentosa (RP) and less often, congenital stationary night blindness (CSNB). Mutation p.G90D has previously been associated with CSNB based on the examination of one family. This study screened 60 patients. Out of these 60 patients, 32 were affected and a full characterization was conducted in 15 patients. We described the clinical characteristics of these 15 patients (12 male, median age 42 years, range 8–71) from three families including visual field (Campus Goldmann), fundus autofluorescence (FAF), optical coherence tomography (OCT) and electrophysiology. Phenotypes were classified into four categories: CSNB (N = 3, 20%) sector RP (N = 3, 20%), pericentral RP (N = 1, 6.7%) and classic RP (N = 8, 53.3% (8/15)). The phenotypes were not associated with family, sex or age (Kruskal–Wallis, p > 0.05), however, cystoid macular edema (CME) was observed only in one family. Among the subjects reporting nyctalopia, 69% (22/32) were male. The clinical characteristics of the largest p.G90D cohort so far showed a large frequency of progressive retinal degeneration with 53.3% developing RP, contrary to the previous report. Full article

(This article belongs to the Special Issue Genetics of Eye Disease)

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29 pages, 3358 KiB

Open AccessArticle

Long-Range PCR-Based NGS Applications to Diagnose Mendelian Retinal Diseases

by Jordi Maggi, Samuel Koller, Luzy Bähr, Silke Feil, Fatma Kivrak Pfiffner, James V. M. Hanson, Alessandro Maspoli, Christina Gerth-Kahlert and Wolfgang Berger

Int. J. Mol. Sci. 2021, 22(4), 1508; https://doi.org/10.3390/ijms22041508 - 3 Feb 2021

Cited by 11 | Viewed by 4486

Abstract

The purpose of this study was to develop a flexible, cost-efficient, next-generation sequencing (NGS) protocol for genetic testing. Long-range polymerase chain reaction (PCR) amplicons of up to 20 kb in size were designed to amplify entire genomic regions for a panel (n = 35) of inherited retinal disease (IRD)-associated loci. Amplicons were pooled and sequenced by NGS. The analysis was applied to 227 probands diagnosed with IRD: (A) 108 previously molecularly diagnosed, (B) 94 without previous genetic testing, and (C) 25 undiagnosed after whole-exome sequencing (WES). The method was validated with 100% sensitivity on cohort A. Long-range PCR-based sequencing revealed likely causative variant(s) in 51% and 24% of proband from cohorts B and C, respectively. Breakpoints of 3 copy number variants (CNVs) could be characterized. Long-range PCR libraries spike-in extended coverage of WES. Read phasing confirmed compound heterozygosity in 5 probands. The proposed sequencing protocol provided deep coverage of the entire gene, including intronic and promoter regions. Our method can be used (i) as a first-tier assay to reduce genetic testing costs, (ii) to elucidate missing heritability cases, (iii) to characterize breakpoints of CNVs at nucleotide resolution, (iv) to extend WES data to non-coding regions by spiking-in long-range PCR libraries, and (v) to help with phasing of candidate variants. Full article

(This article belongs to the Special Issue Genetics of Eye Disease)

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12 pages, 3125 KiB

Open AccessArticle

Genotypic Homogeneity in Distinctive Transforming Growth Factor-Beta Induced (TGFBI) Protein Phenotypes

by Sang Beom Han, Venkatraman Anandalakshmi, Chee Wai Wong, Si Rui Ng and Jodhbir S. Mehta

Int. J. Mol. Sci. 2021, 22(3), 1230; https://doi.org/10.3390/ijms22031230 - 27 Jan 2021

Cited by 2 | Viewed by 2151

Abstract

Background: To evaluate the distribution of the transforming growth factor-beta induced (TGFBI) corneal dystrophies in a multi-ethnic population in Singapore, and to present the different phenotypes with the same genotype. Methods: This study included 32 patients. Slit lamp biomicroscopy was performed for each patient to determine the disease phenotype. Genomic DNA was extracted from the blood samples and the 17 exons of the TGFBI gene were amplified by PCR and sequenced bi-directionally for genotype analysis. Results: Regarding phenotypes, the study patients comprised 11 (34.4%; 8 with R555W and 3 with R124H mutation) patients with granular corneal dystrophy type 1 (GCD1), 6 (18.8%; 5 with R124H and 1 with R124C mutation) patients with GCD2, 13 (40.6%; 7 with R124C, 2 with H626R, 2 with L550P, 1 with A620D and 1 with H572R) patients with lattice corneal dystrophy (LCD) and 2 (6.3%; 1 with R124L and 1 with R124C) patients with Reis–Bückler corneal dystrophy. Regarding genotype, R124H mutation was associated with GCD2 (5 cases; 62.5%) and GCD1 (3 cases; 37.5%). R124C mutation was associated with LCD (7 cases; 87.5%) and GCD2 (1 case; 12.5%). All the 8 cases (100%) of R555W mutation were associated with GCD1. Conclusions: Although the association between genotype and phenotype was good in most cases (65.7%; 21 of 32 patients), genotype/phenotype discrepancy was observed in a significant number. Full article

(This article belongs to the Special Issue Genetics of Eye Disease)

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12 pages, 1487 KiB

Open AccessArticle

Novel Biallelic Variants and Phenotypic Features in Patients with SLC38A8-Related Foveal Hypoplasia

by Elena R. Schiff, Vijay K. Tailor, Hwei Wuen Chan, Maria Theodorou, Andrew R. Webster and Mariya Moosajee

Int. J. Mol. Sci. 2021, 22(3), 1130; https://doi.org/10.3390/ijms22031130 - 24 Jan 2021

Cited by 11 | Viewed by 2959

Abstract

Biallelic pathogenic variants in solute carrier family 38 member 8, SLC38A8, cause a pan-ocular autosomal recessive condition known as foveal hypoplasia 2, FVH2, characterised by foveal hypoplasia, nystagmus and optic nerve chiasmal misrouting. Patients are often clinically diagnosed with ocular albinism, but foveal hypoplasia can occur in several other ocular disorders. Here we describe nine patients from seven families who had molecularly confirmed biallelic recessive variants in SLC38A8 identified through whole genome sequencing or targeted gene panel testing. We identified four novel sequence variants (p.(Tyr88*), p.(Trp145*), p.(Glu233Gly) and c.632+1G>A). All patients presented with foveal hypoplasia, nystagmus and reduced visual acuity; however, one patient did not exhibit any signs of chiasmal misrouting, and three patients had features of anterior segment dysgenesis. We highlight these findings in the context of 30 other families reported to date. This study reinforces the importance of obtaining a molecular diagnosis in patients whose phenotype overlap with other inherited ocular conditions, in order to support genetic counselling, clinical prognosis and family planning. We expand the spectrum of SLC38A8 mutations which will be relevant for treatment through future genetic-based therapies. Full article

(This article belongs to the Special Issue Genetics of Eye Disease)

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15 pages, 2982 KiB

Open AccessArticle

Clinical and Histopathological Features of Gelsolin Amyloidosis Associated with a Novel GSN Variant p.Glu580Lys

by Maja Potrč, Marija Volk, Matteo de Rosa, Jože Pižem, Nataša Teran, Helena Jaklič, Aleš Maver, Brigita Drnovšek-Olup, Michela Bollati, Katarina Vogelnik, Alojzija Hočevar, Ana Gornik, Vladimir Pfeifer, Borut Peterlin, Marko Hawlina and Ana Fakin

Int. J. Mol. Sci. 2021, 22(3), 1084; https://doi.org/10.3390/ijms22031084 - 22 Jan 2021

Cited by 10 | Viewed by 3105

Abstract

Gelsolin amyloidosis typically presents with corneal lattice dystrophy and is most frequently associated with pathogenic GSN variant p.Asp214Asn. Here we report clinical and histopathological features of gelsolin amyloidosis associated with a novel GSN variant p.Glu580Lys. We studied DNA samples of seven members of a two-generation family. Exome sequencing was performed in the proband, and targeted Sanger sequencing in the others. The heterozygous GSN variant p.Glu580Lys was identified in six patients. The patients exhibited corneal dystrophy (5/6), loose skin (5/6) and/or heart arrhythmia (3/6) and one presented with bilateral optic neuropathy. The impact of the mutation on the protein structure was evaluated in silico. The substitution is located in the fifth domain of gelsolin protein, homologous to the second domain harboring the most common pathogenic variant p.Asp214Asn. Structural investigation revealed that the mutation might affect protein folding. Histopathological analysis showed amyloid deposits in the skin. The p.Glu580Lys is associated with corneal dystrophy, strengthening the association of the fifth domain of gelsolin protein with the typical amyloidosis phenotype. Furthermore, optic neuropathy may be related to the disease and is essential to identify before discussing corneal transplantation. Full article

(This article belongs to the Special Issue Genetics of Eye Disease)

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23 pages, 11026 KiB

Open AccessArticle

Application of WES towards Molecular Investigation of Congenital Cataracts: Identification of Novel Alleles and Genes in a Hospital-Based Cohort of South India

by Dinesh Kumar Kandaswamy, Makarla Venkata Sathya Prakash, Jochen Graw, Samuel Koller, István Magyar, Amit Tiwari, Wolfgang Berger and Sathiyaveedu Thyagarajan Santhiya

Int. J. Mol. Sci. 2020, 21(24), 9569; https://doi.org/10.3390/ijms21249569 - 16 Dec 2020

Cited by 14 | Viewed by 3679

Abstract

Congenital cataracts are the prime cause for irreversible blindness in children. The global incidence of congenital cataract is 2.2–13.6 per 10,000 births, with the highest prevalence in Asia. Nearly half of the congenital cataracts are of familial nature, with a predominant autosomal dominant pattern of inheritance. Over 38 of the 45 mapped loci for isolated congenital or infantile cataracts have been associated with a mutation in a specific gene. The clinical and genetic heterogeneity of congenital cataracts makes the molecular diagnosis a bit of a complicated task. Hence, whole exome sequencing (WES) was utilized to concurrently screen all known cataract genes and to examine novel candidate factors for a disease-causing mutation in probands from 11 pedigrees affected with familial congenital cataracts. Analysis of the WES data for known cataract genes identified causative mutations in six pedigrees (55%) in PAX6, FYCO1 (two variants), EPHA2, P3H2,TDRD7 and an additional likely causative mutation in a novel gene NCOA6, which represents the first dominant mutation in this gene. This study identifies a novel cataract gene not yet linked to human disease. NCOA6 is a transcriptional coactivator that interacts with nuclear hormone receptors to enhance their transcriptional activator function. Full article

(This article belongs to the Special Issue Genetics of Eye Disease)

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11 pages, 1712 KiB

Open AccessCase Report

Posterior Polymorphous Corneal Dystrophy in a Patient with a Novel ZEB1 Gene Mutation

by Eva Fernández-Gutiérrez, Pedro Fernández-Pérez, Ana Boto-De-Los-Bueis, Laura García-Fernández, Patricia Rodríguez-Solana, Mario Solís and Elena Vallespín

Int. J. Mol. Sci. 2023, 24(1), 209; https://doi.org/10.3390/ijms24010209 - 22 Dec 2022

Cited by 2 | Viewed by 1879

Abstract

Posterior polymorphous corneal dystrophy (PPCD), a rare, bilateral, autosomal-dominant, inherited corneal dystrophy, affects the Descemet membrane and corneal endothelium. We describe an unusual presentation of PPCD associated with a previously unknown genetic alteration in the ZEB1 gene. The proband is a 64-year-old woman diagnosed with keratoconus referred for a corneal endothelium study who presented endothelial lesions in both eyes suggestive of PPCD, corectopia and iridocorneal endothelial synechiae in the right eye and intrastromal segments in the left eye. The endothelial count was 825 in the right eye and 1361 in the left eye, with typical PPCD lesions visible under specular and confocal microscopy. In the next generation sequencing genetic analysis, a heterozygous c.1A > C (p.Met1Leu) mutation was found in the ZEB1 gene (TCF8). The PPCD3 subtype is associated with corneal ectasia, and both can appear due to a pathogenic mutation in the ZEB1 gene (OMIM #189909). However, our patient had a previously unreported mutation in the ZEB1 gene, which mediates the transition between cell lines and provides a pathogenic explanation for the epithelialisation of the corneal endothelium, a characteristic of PPCD. Full article

(This article belongs to the Special Issue Genetics of Eye Disease)

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