Identification of candidate protective variants for common diseases and evaluation of their protective potential

Putative protective genomic variation in the Lithuanian population

Genomic effect variants associated with survival and protection against complex diseases vary between populations due to microevolutionary processes. The aim of this study was to analyse diversity and distribution of effect variants in a context of potential positive selection. In total, 475 individuals of Lithuanian origin were genotyped using high-throughput scanning and/or sequencing technologies. Allele frequency analysis for the pre-selected effect variants was performed using the catalogue of single nucleotide polymorphisms. Comparison of the pre-selected effect variants with variants in primate species was carried out to ascertain which allele was derived and potentially of protective nature. Recent positive selection analysis was performed to verify this protective effect. Four variants having significantly different frequencies compared to European populations were identified while two other variants reached borderline significance. Effect variant in SLC30A8 gene may potentially protect against type 2 diabetes. The existing paradox of high rates of type 2 diabetes in the Lithuanian population and the relatively high frequencies of potentially protective genome variants against it indicate a lack of knowledge about the interactions between environmental factors, regulatory regions, and other genome variation. Identification of effect variants is a step towards better understanding of the microevolutionary processes, etiopathogenetic mechanisms, and personalised medicine.

Case-Control Study of the Association between Single Nucleotide Polymorphisms of Genes Involved in Xenobiotic Detoxification and Antioxidant Protection with the Long-Term Influence of Organochlorine Pesticides on the Population of the Almaty Region

The association of genetic polymorphisms with the individual sensitivity of humans to the action of pesticide pollution is being actively studied in the world. The aim of this study was a molecular epidemiological analysis of candidate polymorphisms of genes involved in pesticide metabolism, detoxification, and antioxidant protection. Some of the selected polymorphisms also relate to susceptibility to cancer and cardiovascular, respiratory, and immune system diseases in individuals exposed to pesticides for a long time. For a case-control study of a unique cohort of people exposed to organochlorine pesticides for 10 years or more were chosen, a control cohort was selected that matched with the experimental group by the main population characteristics. PCR-PRLF and genome-wide microarray genotyping (GWAS) methods were used. We identified 17 polymorphisms of xenobiotic detoxification genes and 27 polymorphisms of antioxidant defense genes, which had a significantly high statistical association with the negative impact of chronic pesticide intoxication on human health. We also found 17 polymorphisms of xenobiotic detoxification genes and 12 polymorphisms of antioxidant defense genes that have a protective effect. Data obtained added to the list of potential polymorphisms that define a group at high risk or resistant to the negative effects of pesticides.

Adjustment of p-value expression to ontology using machine learning for genetic prediction, prioritization, interaction, and its validation in glomerular disease

The results of gene expression analysis based on p-value can be extracted and sorted by their absolute statistical significance and then applied to multiple similarity scores of their gene ontology (GO) terms to promote the combination and adjustment of these scores as essential predictive tasks for understanding biological/clinical pathways. The latter allows the possibility to assess whether certain aspects of gene function may be associated with other varieties of genes, to evaluate regulation, and to link them into networks that prioritize candidate genes for classification by applying machine learning techniques. We then detect significant genetic interactions based on our algorithm to validate the results. Finally, based on specifically selected tissues according to their normalized gene expression and frequencies of occurrence from their different biological and clinical inputs, a reported classification of genes under the subject category has validated the abstract (glomerular diseases) as a case study.

Sensitive electrochemical detection of polymorphisms in IL6 and TGFβ1 genes from ovarian cancer DNA patients using EcoRI and DNA hairpin-modified gold electrodes

Two electrochemical bioplatforms were prepared based on thiolated hairpin DNA probes tethered to AuNP-modified screen-printed electrodes to detect T > G and T > C polymorphisms, namely rs1880269 and rs1800469, present the interleukin-6 (IL6) and transforming growth factor β1 (TGFβ1) genes. The electrochemical readout was ensured by the detection of the double-stranded DNA using methylene blue as a redox probe after treatment by EcoRI restrictase. The main parameters influencing the analytical response such as the thiolated DNA probe concentration, incubation time with electrode, DNA hybridization time, EcoRI enzyme load, and its cleavage time were optimized based on the current intensity and signal-to-blank (S/B) ratio as selection criteria. Using spiked buffer solutions, the IL6 and TGFβ1 E-bioplatforms display wide ranges of linearity (1 × 10²-1 × 10⁸ fM and 5 × 10¹-1 × 10⁵ fM, respectively) and limits of detection (47.9 fM and 16.6 fM, respectively). The two bioelectrodes have also good discrimination toward 1-mismatched, two mismatched, and non-complementary sequences, when they were used 30-fold higher than the target sequences. More importantly, the two bioplatforms successfully detected the single nucleotide polymorphisms (SNPs) in scarcely diluted genomic DNA, collected from 52 donors, and showed they can reliably distinguish between heterozygous (TG and TC genotypes) and homozygous (GG and CC genotypes) patients with  respect to the control subjects (TT genotype), where the differences are statistically highly significant (p-value < 0.0001). Thus, the designed devices could be used to conduct large cohort studies targeting these mutations or extended to other SNPs.

Possible Protective Effect of LOXL1 Variant in the Cohort of Chernobyl Catastrophe Clean-Up Workers

Ionising radiation (IR) is an environmental factor known to alter genomes and therefore challenge organisms to adapt. Lithuanian clean-up workers of the Chernobyl nuclear disaster (LCWC) experienced high doses of IR, leading to different consequences. This study aims to characterise a unique protective genomic variation in a relatively healthy LCWC group. This variation influenced their individual reaction to IR and potentially protects against certain diseases such as exfoliation syndrome and glaucoma. Clinical and IR dosage data were collected using a questionnaire to characterise the cohort of 93 LCWC. Genome-wide genotyping using Illumina beadchip technology was performed. The control group included 466 unrelated, self-reported healthy individuals of Lithuanian descent. Genotypes were filtered out from the microarray dataset using a catalogue of SNPs. The data were used to perform association, linkage disequilibrium, and epistasis analysis. Phenotype data analysis showed the distribution of the most common disease groups among the LCWC. A genomic variant of statistical significance (Fishers' exact test, p = 0.019), rs3825942, was identified in LOXL1 (NM_005576.4:c.458G>A). Linkage disequilibrium and epistasis analysis for this variant identified the genes LHFPL3, GALNT6, PIH1D1, ANKS1B, and METRNL as potentially involved in the etiopathogenesis of exfoliation syndrome and glaucoma, which were not previously associated with the disease. The LOXL1 variant is mostly considered a risk factor in the development of exfoliation syndrome and glaucoma. The influence of recent positive selection, the phenomenon of allele-flipping, and the fact that only individuals with the homozygous reference allele have glaucoma in the cohort of the LCWC suggest otherwise. The identification of rs3825942 and other potentially protective genomic variants may be useful for further analysis of the genetic architecture and etiopathogenetic mechanisms of other multifactorial diseases.

Genetic Analysis in a Swiss Cohort of Bilateral Congenital Cataract

Importance

Identification of geographic population-based differences in genotype and phenotype heterogeneity are important for targeted and patient-specific diagnosis and treatment, counseling, and screening strategies.

Objective

To report disease-causing variants and their detailed phenotype in patients with bilateral congenital cataract from a single center in Switzerland and thereby draw a genetic map and perform a genotype-phenotype comparison of this cohort.

Design, Setting, and Participants

This clinical and molecular-genetic cohort study took place through the collaboration of the Department of Ophthalmology at the University Hospital Zurich and the Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland. Thirty-seven patients from 25 families with different types of bilateral congenital cataract were included. All participating family members received a comprehensive eye examination. Whole exome sequencing was performed in the index patients, followed by a filtering process to detect possible disease-associated variants in genes previously described in association with congenital cataract. Probable disease-causing variants were confirmed by Sanger sequencing in available family members. All data were collected from January 2018 to June 2020, and the molecular-genetic analyses were performed from January 2019 to July 2020.

Main Outcomes and Measures

Identification of the underlying genetic causes of bilateral congenital cataract, including novel disease-causing variants and phenotype correlation.

Results

Among the 37 patients (18 [49%] male and 19 [51%] female; mean [SD] age, 17.3 [15.9] years) from 25 families, pathogenic variants were detected in 20 families (80% detection rate), which included 13 novel variants in the following genes: BCOR, COL4A1, CRYBA2, CRYBB2, CRYGC, CRYGS, GJA3, MAF, NHS, and WFS1. Putative disease-causing variants were identified in 14 of 20 families (70%) as isolated cases and in 6 of 20 families (30%) with syndromic cases. A recessive variant in the CRYBB2 gene in a consanguineous family with 2 affected siblings showing a nuclear and sutural cataract was reported in contrast to previously published reports. In addition, the effect on splicing in a minigene assay of a novel splice site variant in the NHS gene (c.[719-2A>G]) supported the pathogenicity of this variant.

Conclusions and Relevance

This study emphasizes the importance of genetic testing of congenital cataracts. Known dominant genes need to be considered for recessive inheritance patterns. Syndromic types of cataract may be underdiagnosed in patients with mild systemic features.

Substantial anti-gout effect conferred by common and rare dysfunctional variants of URAT1/SLC22A12

Objectives

Gout, caused by chronic elevation of serum uric acid levels, is the commonest form of inflammatory arthritis. The causative effect of common and rare variants of ATP-binding cassette transporter G2 (ABCG2/BCRP) on gout risk has been studied, but little attention has been paid to the effect of common (rs121907892, p.W258X) and rare variants of urate transporter 1 (URAT1/SLC22A12) on gout, despite dysfunctional variants of URAT1 having been identified as pathophysiological causes of renal hypouricaemia.

Methods

To address this important but overlooked issue, we investigated the effects of these URAT1 variants on gout susceptibility, using targeted exon sequencing on 480 clinically defined gout cases and 480 controls of Japanese males in combination with a series of functional analyses of newly identified URAT1 variants.

Results

Our results show that both common and rare dysfunctional variants of URAT1 markedly decrease the risk of gout (OR 0.0338, reciprocal OR 29.6, P = 7.66 × 10⁻⁸). Interestingly, we also found that the URAT1-related protective effect on gout eclipsed the ABCG2-related causative effect (OR 2.30–3.32). Our findings reveal only one dysfunctional variant of URAT1 to have a substantial anti-gout effect, even in the presence of causative variants of ABCG2, a ‘gout gene’.

Conclusion

Our findings provide a better understanding of gout/hyperuricaemia and its aetiology that is highly relevant to personalized health care. The substantial anti-gout effect of common and rare variants of URAT1 identified in the present study support the genetic concept of a ‘Common Disease, Multiple Common and Rare Variant’ model.

Genetic modifiers and phenotypic variability in neuromuscular disorders

Neuromuscular disorders are mostly rare diseases with autosomal dominant, recessive, or X-linked inheritance. Interestingly, among patients carrying the same mutations, a range of phenotypic severity is reported. This phenotypic variability in neuromuscular disorders is still not fully understood. This review will focus on genetic modifiers and will briefly describe metabolic pathways, in which they are involved. Genetic modifiers are variants in the same or other genes that modulate the phenotype. Proteins encoded by genetic modifiers in neuromuscular diseases are taking part in different metabolic processes, most commonly in inflammation, growth and regeneration, endoplasmic reticulum metabolism, and cytoskeletal activities. Recent advances in omics technologies, development of computational algorithms, and establishing large international consortia intensified discovery sped up investigation of genetic modifiers. As more individuals affected by neuromuscular disorders are tested, it is often suggested that classic models of genetic causation cannot explain phenotypic variability. There is a growing interest in their discovery and identifying shared metabolic pathways can contribute to design targeted therapies. We provide an update on variants acting as genetic modifiers in neuromuscular disorders and strategies used for their discovery.

Influence of E-cadherin genetic variation in canine mammary tumour risk, clinicopathological features and prognosis

E-cadherin is a cell adhesion molecule that participates in several cellular processes that guarantee the maintenance of structural and functional integrity of epithelial tissues. E-cadherin plays an important role in mammary carcinogenesis, and various studies have demonstrated the effect of CDH1 genetic variation in risk, progression and biological behaviour of human breast cancer. Although there are some recognized genetic variations in canine CDH1 gene, their influence in canine mammary tumour development and progression has not been previously evaluated. In this study, we aim to assess the influence of CDH1 SNPs rs850805755, rs852280880 and rs852639930 in the risk, clinicopathological features and clinical outcome of canine mammary tumours. A case-control study was conducted involving 206 bitches with mammary tumours and 161 bitches free of mammary neoplasia. CDH1 SNPs rs850805755 and rs852280880 were associated with a decreased risk and a later onset of mammary tumour development. Furthermore, these SNPs were related to the development of small size carcinomas, of low histological grade and low nuclear pleomorphism. SNP rs852639930 was associated with the development of small size tumours with a non-infiltrative, non-invasive growth pattern. Data from the present investigation demonstrate that these CDH1 genetic variants could have a protective role in canine mammary tumours, by being associated with low risk of tumour development, delayed onset of the disease and less aggressive clinicopathological features.

Selecting variants of unknown significance through network-based gene-association significantly improves risk prediction for disease-control cohorts

Variants of unknown/uncertain significance (VUS) pose a huge dilemma in current genetic variation screening methods and genetic counselling. Driven by methods of next generation sequencing (NGS) such as whole exome sequencing (WES), a plethora of VUS are being detected in research laboratories as well as in the health sector. Motivated by this overabundance of VUS, we propose a novel computational methodology, termed VariantClassifier (VarClass), which utilizes gene-association networks and polygenic risk prediction models to shed light into this grey area of genetic variation in association with disease. VarClass has been evaluated using numerous validation steps and proves to be very successful in assigning significance to VUS in association with specific diseases of interest. Notably, using VUS that are deemed significant by VarClass, we improved risk prediction accuracy in four large case-studies involving disease-control cohorts from GWAS as well as WES, when compared to traditional odds ratio analysis. Biological interpretation of selected high scoring VUS revealed interesting biological themes relevant to the diseases under investigation. VarClass is available as a standalone tool for large-scale data analyses, as well as a web-server with additional functionalities through a user-friendly graphical interface.

Exploring Impact of Rare Variation in Systemic Lupus Erythematosus by a Genome Wide Imputation Approach

The importance of low frequency and rare variation in complex disease genetics is difficult to estimate in patient populations. Genome-wide association studies are therefore, underpowered to detect rare variation. We have used a combined approach of genome-wide-based imputation with a highly stringent sequence kernel association (SKAT) test and a case-control burden test. We identified 98 candidate genes containing rare variation that in aggregate show association with SLE many of which have recognized immunological function, but also function and expression related to relevant tissues such as the joints, skin, blood or central nervous system. In addition we also find that there is a significant enrichment of genes annotated for disease-causing mutations in the OMIM database, suggesting that in complex diseases such as SLE, such mutations may be involved in subtle or combined phenotypes or could accelerate specific organ abnormalities found in the disease. We here provide an important resource of candidate genes for SLE.

Alzheimer's disease phospholipase C-gamma-2 (PLCG2) protective variant is a functional hypermorph

BACKGROUND

Recent Genome Wide Association Studies (GWAS) have identified novel rare coding variants in immune genes associated with late onset Alzheimer's disease (LOAD). Amongst these, a polymorphism in phospholipase C-gamma 2 (PLCG2) P522R has been reported to be protective against LOAD. PLC enzymes are key elements in signal transmission networks and are potentially druggable targets. PLCG2 is highly expressed in the hematopoietic system. Hypermorphic mutations in PLCG2 in humans have been reported to cause autoinflammation and immune disorders, suggesting a key role for this enzyme in the regulation of immune cell function.

METHODS

We assessed PLCG2 distribution in human and mouse brain tissue via immunohistochemistry and in situ hybridization. We transfected heterologous cell systems (COS7 and HEK293T cells) to determine the effect of the P522R AD-associated variant on enzymatic function using various orthogonal assays, including a radioactive assay, IP-One ELISA, and calcium assays.

RESULTS

PLCG2 expression is restricted primarily to microglia and granule cells of the dentate gyrus. Plcg2 mRNA is maintained in plaque-associated microglia in the cerebral tissue of an AD mouse model. Functional analysis of the p.P522R variant demonstrated a small hypermorphic effect of the mutation on enzyme function.

CONCLUSIONS

The PLCG2 P522R variant is protective against AD. We show that PLCG2 is expressed in brain microglia, and the p.P522R polymorphism weakly increases enzyme function. These data suggest that activation of PLCγ2 and not inhibition could be therapeutically beneficial in AD. PLCγ2 is therefore a potential target for modulating microglia function in AD, and a small molecule drug that weakly activates PLCγ2 may be one potential therapeutic approach.

New insight into the role of the complement in the most common types of retinopathy-current literature review

Pathological neovascularisation, which is a critical component of diseases such as age-related macular degeneration (AMD), diabetic retinopathy (DR) and retinopathy of prematurity (ROP), is a frequent cause of compromised vision or blindness. Researchers continuously investigate the role of the complement system in the pathogenesis of retinopathy. Studies have confirmed the role of factors H and I in the development of AMD, and factors H and B in the development of DR. Other components, such as C2, C3, and C5, have also been considered. However, findings on the involvement of the complement system in the pathogenesis of ROP are still inconclusive. This paper presents a review of the current literature data, pointing to the novel results and achievements from research into the role of complement components in the development of retinopathy. There is still a need to continue research in new directions, and to gather more detailed information about this problem which will be useful in the treatment of these diseases.

Association Between Complement Factor C2/C3/CFB/CFH Polymorphisms and Age-Related Macular Degeneration: A Meta-Analysis

BACKGROUND

Several previous studies have assessed the contribution of polymorphisms in genes encoding the complement factors C2/C3/CFB/CFH with the risk of age-related macular degeneration (AMD), however the results have been inconsistent. We conducted a meta-analysis to systematically review the potential association between complement factor polymorphisms and AMD.

METHODS

Studies that investigated associations between C2 (rs547154 and rs9332739), C3 (rs1047286), CFB (rs4151667 and rs641153), and CFH (rs551397 and rs2274700) polymorphisms and AMD were identified by searching PubMed, EMBASE, Web of Science, and Cochrane Library databases for articles published prior to January 1, 2018. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated to evaluate the association between these polymorphisms and AMD using Stata 12.0 software. Q and I² statistics were used to evaluate between-study heterogeneity. Publication bias analyses were conducted using Begg's test. We also conducted an ethnic subgroup analysis.

RESULTS

A total of 53 studies that included data for 53,774 patients and 56,973 healthy controls were evaluated. The pooled ORs for rs551397, rs2274700, rs4151667, rs641153, rs1047286, rs9332739, and rs547154 in the heterozygote model were 0.53 (95% CI: 0.45-0.61), 0.53 (95% CI: 0.40-0.70), 0.54 (95% CI: 0.46-0.63), 0.48 (95% CI: 0.4-0.57), 1.42 (95% CI: 1.22-1.66), 0.5 (95% CI: 0.45-0.56), and 0.52 (95% CI: 0.43-0.62), respectively.

CONCLUSION

Our findings from this analysis confirmed the protective role of C2/CFB/CFH polymorphisms in the development of AMD, but showed that the single nucleotide polymorphism in C3 was a high-risk factor for AMD. The racial analysis results suggested that the effect of variant alleles was stronger in Caucasians than Asians.