Whole exome sequencing highlights variants in association with Keratoconus in Jordanian families

Subclinical parents assist in the detection of genetic variants in keratoconus by trio-based whole-exome sequencing

Purpose

To explore the genetic variants of 14 keratoconus trios containing subclinical parents.

Methods

Trio-based whole-exome sequencing was performed in 14 keratoconus trios containing subclinical parents. The variants identified in candidate genes of keratoconus were analyzed by multiple bioinformatics tools.

Results

We identified 12 variants in 10 candidate genes of keratoconus (COL5A1, TGFBI, CAST, MPDZ, WNT10A, MYOF, ERMP1, MAP3K19, COL1A1, and WNT16). All variants were novel, not previously reported, and defined as uncertain significance according to the American College of Medical Genetics and Genomics guidelines. All variants were heterozygous and autosomal dominant cosegregated in keratoconus families.

Conclusions

We found that the candidate variants identified in clinically diagnosed patients and their subclinical parents may cause keratoconus through an autosomal dominant inheritance pattern, with different variable expressivity. This study indicates that genetic testing may play an important role in identifying patients with latent keratoconus and high-risk individuals for corneal ectasia after refractive surgery.

Whole-exome sequencing screening for candidate genes and variants associated with primary sporadic keratoconus in Chinese patients

The pathogenesis of keratoconus (KC) is complex, and genetic factors play an important role. The purpose of this study was to screen and analyse candidate genes and variants in Chinese patients with primary sporadic KC. Whole-exome sequencing (WES) was performed to identify candidate genes and variants in 105 unrelated Chinese patients with primary sporadic KC. Through a series of screening processes, 54 candidate variants in 26 KC candidate genes were identified in 53 KC patients (53/105, 50.5%). These 54 candidate variants included 10 previously identified variants in 9 KC candidate genes and 44 novel variants in 20 KC candidate genes. The previously identified variants occurred in 25.7% (27/105) of patients. Of these, 4 variants (COL6A5, c.5014T > G; CAST, c.1814G > A; ZNF469, c.946G > A; and MPDZ, c.3836A > G) were identified for the first time in Chinese KC patients. The novel variants occurred in 33.3% (35/105) of patients. Of the 26 screened KC candidate genes, 11 KC candidate genes (CAT, COL12A1, FLG, HKDC1, HSPG2, PLOD1, ITGA2, TFAP2B, USH2A, WNT10A, and COL6A5) were found to be potentially pathogenic in Chinese KC patients for the first time. Gene Ontology (GO) biological process (BP) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed on the 26 KC candidate genes using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The results showed that the KC candidate genes were significantly enriched in biological processes such as collagen fibril organization and extracellular matrix (ECM) organization and in ECM-receptor interaction and protein digestion and absorption pathways. The results further expand the spectrum of KC candidate variants and provide a basis for further KC gene studies.

Association between Polymorphism rs61876744 in PNPLA2 Gene and Keratoconus in a Saudi Cohort

The genetic etiology of Keratoconus (KC) in Middle Eastern Arabs of Saudi origin is still unclear. A recent genome-wide study identified two significant loci in the region of PNPLA2 (rs61876744) and CSNK1E (rs138380) for KC that may be associated with KC in the Saudi population. In addition, polymorphisms in the apolipoprotein E (APOE) gene, namely, rs429358 and rs7412, responsible for APOE allelic variants ε2, ε3, and ε4, may influence KC via oxidative stress mechanism(s). Thus, we investigated the possible association of polymorphisms rs61876744, rs138380, rs429358, rs7412, and APOE genotypes in KC patients of the Saudi population. This study included 98 KC cases and 167 controls. Polymorphisms rs6187644 and rs138380 were genotyped using TaqMan assays, and rs429358 and rs7412 were genotyped via Sanger sequencing. Although the allele frequency of rs61876744(T) in PNPLA2 was a protective effect against KC (odds ratio (OR) = 0.64, 95% confidence interval (CI) = 0.44-0.93), the p-value (p = 0.020) was not significant for multiple testing correction (p = 0.05/4 = 0.015). However, rs6187644 genotype showed a modestly significant protective effect in the dominant model (OR = 0.53, 95% CI = 0.32-0.88, p = 0.013). Polymorphisms rs138380, rs429358, and rs7412 showed no significant allelic or genotype association with KC. However, the ε2-carriers (ε2/ε2 and ε2/ε3 genotypes) exhibited a greater than 5-fold increased risk of KC, albeit non-significantly (p = 0.055). Regression analysis showed no significant effect of age, gender, and the four polymorphisms on KC. Our results suggest that polymorphism rs6187644 in PNPLA2 might be associated with KC in the Middle Eastern Arabs of Saudi origin but warrant a large-scale association analysis at this locus.

Trio-based exome sequencing broaden the genetic spectrum in keratoconus

Keratoconus (KC) is a complex corneal disorder with genetic factors involving in its pathogenesis. The genetic etiology of KC has not been fully elucidated. In this study, we aimed to expand the genetic spectrum in KC by trio-based exome sequencing. Trio-based exome sequencing was conducted in 20 patients with KC and their unaffected parents to broaden the genetic spectrum of the disease. With a series of filtering criteria, de novo, recessive homozygous, and compound heterozygous variants in candidate genes were identified, and the candidate genes were classified for further analysis. Finally, we identified 60 variants in 32 candidate genes through trio-based exome sequencing. Among the candidate genes, 10 genes (ARHGEF10, ARHGEF17, ASPM, FLNA, NDRG1, NEB, PLS3, STARD8, SYNE1, TTN) were classified as cytoskeleton-related genes, 4 genes (COL28A1, SDK1, STAB1, TENM2) were classified as cell adhesion-related genes, and 18 genes (APLP2, BCORL1, CCNB3, FOXN1, FUT8, GALNT10, HEPH, HHIP, HMGB3, HS6ST2, JADE3, KIAA0040, MCF2L, MYOF, QRICH2, RPS6KA6, SMARCA1, TNRC6A) were classified into other genes group. Additionally, the candidate rare deleterious variants in TTN were highly repeated in 25% trios. In conclusion, the study provided new insights into the genetic spectrum of KC which might underlie the genetic etiology for the disease. The findings would improve our understanding of pathogenesis in KC and provide critical clues to future functional validation.

Family-based exome sequencing identifies candidate genes related to keratoconus in Chinese families

Background: Keratoconus (KC) is a complex corneal disorder with a strong genetic component. The present study aimed to identify candidate genes related to KC in Chinese families.

Methods: Family-based exome sequencing was performed in ten patients suffering from KC who belong to five families with two affected members in each. The candidate rare variants were identified with multi-step bioinformatics analysis. The STRING website was used to perform the protein interaction of the identified genes.

Results: Our analyses identified 32 candidate rare variants in 13 genes by family-based exome sequencing. The molecular analyses of identified genes showed that EPCAM directly interacted with CTNNB1 of the Hippo signaling pathway and focal adhesion pathway, and directly interacted with CTNNB1, CDH1 of the WNT signaling pathway. SHROOM3 directly interacted with ROCK2, ROCK1 of the focal adhesion pathway. SYNE1 directly interacted with MUSK of the extracellular matrix organization pathway. TEK directly interacted with VEGFA, SHC1, PIK3R1, GRB2 of the focal adhesion pathway. TTN directly interacted with CAPN3 of the extracellular matrix organization pathway.

Conclusion: The EPCAM, SHROOM3, SYNE1, TEK, and TTN genes were potential high-risk candidate pathogenic genes of familial KC. The findings might significantly improve our understanding of the genetic etiology of the disease, providing novel insights on KC pathogenesis.

Whole-Exome Sequencing Implicates the USP34 rs777591A > G Intron Variant in Chronic Obstructive Pulmonary Disease in a Kashi Cohort

Genetic factors are important factors in chronic obstructive pulmonary disease (COPD) onset. Plenty of risk and new causative genes for COPD have been identified in patients of the Chinese Han population. In contrast, we know considerably little concerning the genetics in the Kashi COPD population (Uyghur). This study aims at clarifying the genetic maps regarding COPD susceptibility in Kashi (China). Whole-exome sequencing (WES) was used to analyze three Uyghur families with COPD in Kashi (eight patients and one healthy control). Sanger sequencing was also used to verify the WES results in 541 unrelated Uyghur COPD patients and 534 Uyghur healthy controls. WES showed 72 single nucleotide variants (SNVs), two deletions, and small insertions (InDels), 26 copy number variants (CNVs), and 34 structural variants (SVs), including g.71230620T > A (rs12449210T > A, NC_000,016.10) in the HYDIN axonemal central pair apparatus protein (HYDIN) gene and g.61190482A > G (rs777591A > G, NC_000002.12) in the ubiquitin-specific protease 34 (USP34) gene. After Sanger sequencing, we found that rs777591“AA” under different genetic models except for the dominant model (adjusted OR = 0.8559, 95%CI 0.6568–1.115, p > .05), could significantly reduce COPD risk, but rs12449210T > A was not related to COPD. In stratified analysis of smoking status, rs777591“AA” reduced COPD risk significantly among the nonsmoker group. Protein and mRNA expression of USP34 in cigarette smoke extract-treated BEAS-2b cells increased significantly compared with those in the control group. Our findings associate the USP34 rs777591“AA” genotype as a protector factor in COPD.

Systematically Displaying the Pathogenesis of Keratoconus via Multi-Level Related Gene Enrichment-Based Review

Keratoconus (KC) is an etiologically heterogeneous corneal ectatic disorder. To systematically display the pathogenesis of keratoconus (KC), this study reviewed all the reported genes involved in KC, and performed an enrichment analysis of genes identified at the genome, transcription, and protein levels respectively. Combined analysis of multi-level results revealed their shared genes, gene ontology (GO), and pathway terms, to explore the possible pathogenesis of KC. After an initial search, 80 candidate genes, 2,933 transcriptional differential genes, and 947 differential proteins were collected. The candidate genes were significantly enriched in extracellular matrix (ECM) related terms, Wnt signaling pathway and cytokine activities. The enriched GO/pathway terms of transcription and protein levels highlight the importance of ECM, cell adhesion, and inflammatory once again. Combined analysis of multi-levels identified 13 genes, 43 GOs, and 12 pathways. The pathogenic relationships among these overlapping factors maybe as follows. The gene mutations/variants caused insufficient protein dosage or abnormal function, together with environmental stimulation, leading to the related functions and pathways changes in the corneal cells. These included response to the glucocorticoid and reactive oxygen species; regulation of various signaling (P13K-AKT, MAPK and NF-kappaB), apoptosis and aging; upregulation of cytokines and collagen-related enzymes; and downregulation of collagen and other ECM-related proteins. These undoubtedly lead to a reduction of extracellular components and induction of cell apoptosis, resulting in the loosening and thinning of corneal tissue structure. This study, in addition to providing information about the genes involved, also provides an integrated insight into the gene-based etiology and pathogenesis of KC.

Heterogeneity in biomarkers, mitogenome and genetic disorders of the Arab population with special emphasis on large-scale whole-exome sequencing

More than 25 million DNA variations have been discovered as novel including major alleles from the Arab population. Exome studies on the Saudi genome discovered > 3000 novel nucleotide variants associated with > 1200 rare genetic disorders. Reclassification of many pathogenic variants in the Human Gene Mutation Database and ClinVar Database as benign through the Arab database facilitates building a detailed and comprehensive map of the human morbid genome. Intellectual disability comes first with the combined and observed carrier frequency of 0.06779 among Saudi Arabians; retinal dystrophy is the next highest. Genome studies have discovered interesting novel candidate disease marker variations in many genes from consanguineous families. More than 7 pathogenic variants in the C12orf57 gene are prominently associated with the etiology of developmental delay/intellectual impairment in Arab ancestries. Advances in large-scale genome studies open a new outlook on Mendelian genes and disorders. In the past half-dozen years, candidate genes of intellectual disability, neurogenetic disorders, blood and bleeding disorders and rare genetic diseases have been well documented through genomic medicine studies in combination with advanced computational biology applications. The Arab mitogenome exposed hundreds of variations in the mtDNA genome and ancestral sharing with Africa, the Near East and East Asia and its association with obesity. These recent discoveries in disease markers and molecular genetics of the Arab population will have a positive impact towards supporting genetic counsellors on reaching consanguineous families to manage stress linked to genetics and precision medicine. This narrative review summarizes the advances in molecular medical genetics and recent discoveries on pathogenic variants. Despite the fact that these initiatives are targeting the genetics and genomics of disorders prevalent in Arab populations, a lack of complete cooperation across the projects needed to be revisited to uncover the Arab population's prominent disease markers. This shows that further study is needed in genomics to fully comprehend the molecular abnormalities and associated pathogenesis that cause inherited disorders in Arab ancestries.

Cascade of interactions between candidate genes reveals convergent mechanisms in keratoconus disease pathogenesis

Keratoconus is a progressive thinning, steepening and distortion of the cornea which can lead to loss of vision if left untreated. Keratoconus has a complex multifactorial etiology, with genetic and environmental components contributing to the disease pathophysiology. Studies have observed high concordance between monozygotic twins, discordance between dizygotic twins, and high familial segregation indicating the presence of a very strong genetic component in the pathogenesis of keratoconus. The use of genome-wide linkage studies on families and twins, genome-wide association studies (GWAS) on case-controls, next-generation sequencing (NGS)-based genomic screens on both familial and non-familial cohorts have led to the identification of keratoconus candidate genes with much greater success and increased resproducibility of genetic findings. This review focuses on candidate genes identified till date and attempts to understand their role in biological processes underlying keratoconus pathogenesis. In addition, using these genes I propose molecular pathways that could contribute to keratoconus pathogenesis. The pathways identified the presence of direct cross-talk between known candidate genes of keratoconus and remarkably, 28 known candidate genes have a direct relationship among themselves that involves direct protein-protein binding, regulatory activities such as activation and inhibition, chaperone, transcriptional activation/co-activation, and enzyme catalysis. This review attempts to describe these relationships and cross-talks in the context of keratoconus pathogenesis.