Susceptibility Single Nucleotide Polymorphisms Research Articles

Highlights from Recent Cancer Literature

Highlights from Recent Cancer Literature

Smart approach for cost-effective genotyping of single nucleotide polymorphisms

Single Nucleotide Polymorphisms (SNPs) are in the prime focus of genomic studies for their probable roles in diagnostics and prognosis of diseases and forensic science. SNaPshot/minisequencing reaction-based genotyping of targeted SNPs is a method of choice due to its fast and reliable detection assay. Here we described smart modifications in minisequencing reaction to make it cost-effective to detect 15 SNPs in a single assay. The target SNPs were amplified in a multiplex PCR from genomic DNA, and these multiplex PCR amplicons were utilized as a template in modified SNaPshot reaction for SNPs identification. The modified protocol was assessed for reproducibility on more than 50 human DNA samples, and it was observed that this modified method is at least five times more productive than the original protocol recommended by the manufacturer. The current smart modifications in SNaPshot reaction were successfully optimized for susceptible asthma SNPs. However, these can be applied for cost-effective genotyping of any type of genomic Single Nucleotide Polymorphisms.

Genetic association between interleukin-10 gene rs1518111 and rs3021094 polymorphisms and risk of type 1 diabetes and diabetic nephropathy in Egyptian children and adolescents.

Genetic and environmental factors have been implicated in etiopathogenesis and progression of type 1 diabetes mellitus (T1DM) and diabetic nephropathy (DN). Genetic association between interleukin-10 (IL-10) single nucleotide polymorphisms (SNPs) with T2DM and DN was recently established. We aimed to explore the potential genetic risk of IL-10 gene rs1518111 and rs3021094 SNPs in susceptibility to T1DM and DN. Cross-sectional study included 140 T1DM children, of whom 74 had DN and 90 controls. IL-10 gene rs1518111 and rs3021094 SNP were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique of the extracted genomic DNA from participants. Odds ratios (ORs) and 95% confidence intervals (CIs) were applied to explore the association between IL-10 gene polymorphisms and the risk of T1DM and DN. For rs1518111 SNP, AA genotype was associated with high risk of T1DM (OR = 4.53; CI = 2.11-9.74; p < 0.001), while A allele was associated with high risk of both T1DM (OR = 3.35; CI = 2.20-5.09; p < 0.001) and DN (OR = 2.36; CI = 1.27-4.38; p = 0.006). For rs3021094 SNP, AC genotype displayed lower risk to develop T1DM (OR = 0.35; CI = 0.13-0.94; p = 0.037), while A allele displayed higher risk to develop T1DM (OR = 1.69; CI = 1.11-2.56; p = 0.013). GA and AC haplotypes of rs1518111 and rs3021094 had lower ORs for having T1DM and DN, while GC had lower OR for having T1DM. AA genotype and A allele of IL-10 rs1518111 SNP could be linked to increased risk for T1DM and DN among Egyptian children. None of rs3021094 genotypes or alleles displayed significant association with DN. GA and AC haplotypes could be protective against T1DM and DN susceptibility.

Genome-wide long non-coding RNA association study on Han Chinese women identifies lncHSAT164 as a novel susceptibility gene for breast cancer.

Background:Single-nucleotide polymorphisms (SNPs)-associated genes and long non-coding RNAs (lncRNAs) can contribute to human disease. To comprehensively investigate the contribution of lncRNAs to breast cancer, we performed the first genome-wide lncRNA association study on Han Chinese women.Methods:We designed an lncRNA array containing >800,000 SNPs, which was incorporated into a 96-array plate by Affymetrix (CapitalBio Technology, China). Subsequently, we performed a two-stage genome-wide lncRNA association study on Han Chinese women covering 11,942 individuals (5634 breast cancer patients and 6308 healthy controls). Additionally, in vitro gain or loss of function strategies were performed to clarify the function of a novel SNP-associated gene.Results:We identified a novel breast cancer-associated susceptibility SNP, rs11066150 (Pmeta = 2.34 × 10−8), and a previously reported SNP, rs9397435 (Pmeta = 4.32 × 10−38), in Han Chinese women. rs11066150 is located in NONHSAT164009.1 (lncHSAT164), which is highly expressed in breast cancer tissues and cell lines. lncHSAT164 overexpression promoted colony formation, whereas lncHSAT164 knockdown promoted cell apoptosis and reduced colony formation by regulating the cell cycle.Conclusions:Based on our lncRNA array, we identified a novel breast cancer-associated lncRNA and found that lncHSAT164 may contribute to breast cancer by regulating the cell cycle. These findings suggest a potential therapeutic target in breast cancer.

Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease

Genetic factors underlying coronary artery disease (CAD) have been widely studied using genome-wide association studies (GWASs). However, the functional understanding of the CAD loci has been limited by the fact that a majority of GWAS variants are located within non-coding regions with no functional role. High cholesterol and dysregulation of the liver metabolism such as non-alcoholic fatty liver disease confer an increased risk of CAD. Here, we studied the function of non-coding single-nucleotide polymorphisms in CAD GWAS loci located within liver-specific enhancer elements by identifying their potential target genes using liver cis-eQTL analysis and promoter Capture Hi-C in HepG2 cells. Altogether, 734 target genes were identified of which 121 exhibited correlations to liver-related traits. To identify potentially causal regulatory SNPs, the allele-specific enhancer activity was analyzed by (1) sequence-based computational predictions, (2) quantification of allele-specific transcription factor binding, and (3) STARR-seq massively parallel reporter assay. Altogether, our analysis identified 1,277 unique SNPs that display allele-specific regulatory activity. Among these, susceptibility enhancers near important cholesterol homeostasis genes (APOB, APOC1, APOE, and LIPA) were identified, suggesting that altered gene regulatory activity could represent another way by which genetic variation regulates serum lipoprotein levels. Using CRISPR-based perturbation, we demonstrate how the deletion/activation of a single enhancer leads to changes in the expression of many target genes located in a shared chromatin interaction domain. Our integrative genomics approach represents a comprehensive effort in identifying putative causal regulatory regions and target genes that could predispose to clinical manifestation of CAD by affecting liver function.

Susceptible Single Nucleotide Polymorphisms in Exon 10 and Intron 9 of Complement Factor H Gene in Patients With Age-related Macular Degeneration

Background: Age-related macular degeneration (AMD) is the leading cause of vision loss in the elderly. Although it has been shown that Y402H polymorphism in the CFH gene was strongly associated with AMD in the Iranian population, there were no data on other single nucleotide polymorphisms (SNPs), which have the most significant association with AMD. This study aimed to investigate hot point regions in exon 10 and intron 9. Materials and Methods: One hundred and sixty-six AMD patients and 69 controls were recruited. Their blood was collected in the tubes containing EDTA. Then, DNA was extracted from the blood, and its quality was evaluated. Primers were designed for intron 9 and exon10 sequencing. A viral polymorphisms analysis software named CEQ was used for the analysis of putative polymorphisms. Results: We noticed three polymorphisms in study cases: rs7535263 and C66379A in intron 9 and rs2274700 in exon 10. Based on the McNamara’s test (rs7535263 and rs2274700) and the Phi and Cramer’s test (C66379A), a significant difference was found between the control and patient groups regarding rs7535263 and rs2274700 polymorphisms. Conclusion: We found a synonymous or silent mutation, A473A, rs2274700 in exon 10 in 85% of patients. From two intronic SNPs, just rs7535263 showed association with the disease in studied patients living in Gilan Province, Iran. Although no significant relationship was found between controls and patients regarding the C66379A allele, it would be important that no other sources have reported C66379A polymorphism in AMD yet.

Variant of SNPs at lncRNA NEAT1 contributes to gastric cancer susceptibility in Chinese Han population.

The long noncoding RNA (lncRNA) nuclear-enriched abundant transcript 1 (NEAT1) has been implicated in many tumors risk including gastric cancer. However, the association of single nucleotide polymorphisms (SNPs) at NEAT1 with gastric cancer risk has not been studied. The aim of this study was to investigate the association between SNPs in NEAT1 and gastric cancer susceptibility. In this study, four SNPs in lncRNA NEAT1 were selected for genotyping in 484 gastric cancer patients and 484 controls in Chinese Han population. Quantitative real-time PCR (qRT-PCR) was conducted to evaluate the potential function of rs3825071. Attributable risk percentage (ARP) and population attributable risk percentage (PARP) were used to assess the epidemiological effect. In the dominant model (GG), the genotypes AG + AA of rs3825071 and rs7943779 were associated with an increased risk of gastric cancer (OR = 1.72, 95%CI = 1.27-2.32 and OR = 1.63, 95%CI = 1.19-2.22). Individuals harboring ≥ 3 risk alleles have higher risk of gastric cancer (OR = 1.88, 95% CI = 1.26-2.80, P = 0.002). ARP and PARP associated with gastric cancer were 42.53% and 10.88% for rs3825071, and were 33.78% and 6.26% for rs7943779, respectively. Furthermore, compared with the genotype GG of rs3825071, the genotypes AG and AA had higher expression of NEAT1. We found that the genetic variations in NEAT1 were significantly associated with risk of gastric cancer. The G > A variant of rs3825071 may confer gastric cancer susceptibility by changed biological effects to increase the expression of NEAT1.

Genetic variant in microRNA-146a gene is associated with risk of rheumatoid arthritis

Objective To investigated the association between single nucleotide polymorphisms (SNPs) in microRNA-146a (miR-146a) gene and susceptibility of rheumatoid arthritis (RA). Methods We systemically extracted the genetic data of miR-146a from previous genome-wide association studies (GWASs) of RA. Subsequently, we performed a replication study in an independent Chinese cohort for selected variant. A meta-analysis combined the previous GWASs with the replication study was also conducted. The epigenetic annotation and cytokine assay were used for exploring potential variant function. Results The extracted genetic association data from three previous GWASs showed that the allele T of functional SNP rs2431697 increased RA susceptibility. The significant association for the SNP was also found in the Chinese replication cohort (OR = 1.24, 95% CI = 1.06–1.46, p = 8.69E-03). The estimated effect size for this SNP was larger in Asian population than that in European population (Asian meta-analysis: OR = 1.15, 95% CI = 1.09–1.22, p = 4.37E-07; Tran-ethnic meta-analysis: OR = 1.07, 95% CI = 1.04–1.10, p = 1.79E-06). The cytokine assay also showed that the risk allele T of the SNP rs2431697 is inversely associated with plasma TNF-α levels in health controls (p = .016). Conclusions In summary, this study supports that genetic variant in miR-146a gene is associated with RA risk. KEY MESSAGES The association between SNPs in miR-146a gene and susceptibility of RA was unclear. We investigated the genetic association using GWASs data and a replication study. The SNP rs2431697 in miR-146a gene is associated with RA risk.

Single Nucleotide Polymorphisms in Tumor Necrosis Factor-α and Susceptibility to HIV Infection in Local Population of Lahore Pakistan

A single nucleotide polymorphism (SNP) is observed at -308 position of the promoter region of tumor necrosis factor (TNF- α) gene due to which TNF is categorized into TNF1 and TNF2 allele. TNF2 allele is associated with higher concentration of TNF- α which in turn is associated with HIV infection. In order to know the association between TNF2 and HIV infection n =75 HIV positive samples and n=15 HIV negative samples were observed for TNF polymorphism. It was found that among the infected patients 53 patients had TNF2.The total percentage of the patients and controls having TNF2 allele was found to be 63.34.%. Chi square value was significant showing that there is a strong correlation between HIV susceptibility and TNF SNPs (-308) of the promoter region.

Mechanistic insight into the progressive retinal atrophy disease in dogs via pathway-based genome-wide association analysis.

The retinal degenerative disease, progressive retinal atrophy (PRA) is a major reason of vision impairment in canine population. Canine PRA signifies an inherently dissimilar category of retinal dystrophies which has solid resemblances to human retinis pigmentosa. Even though much is known about the biology of PRA, the knowledge about the intricate connection among genetic loci, genes and pathways associated to this disease in dogs are still remain unknown. Therefore, we have performed a genome wide association study (GWAS) to identify susceptibility single nucleotide polymorphisms (SNPs) of PRA. The GWAS was performed using a case–control based association analysis method on PRA dataset of 129 dogs and 135,553 markers. Further, the gene-set and pathway analysis were conducted in this study. A total of 1,114 markers associations with PRA trait at p < 0.01 were extracted and mapped to 640 unique genes, and then selected significant (p < 0.05) enriched 35 gene ontology (GO) terms and 5 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways contain these genes. In particular, apoptosis process, homophilic cell adhesion, calcium ion binding, and endoplasmic reticulum GO terms as well as pathways related to focal adhesion, cyclic guanosine monophosphate)-protein kinase G signaling, and axon guidance were more likely associated to the PRA disease in dogs. These data could provide new insight for further research on identification of potential genes and causative pathways for PRA in dogs.

Do Polygenic Risk Scores For Cancer Susceptibility Associate With Risk Of Radiotherapy Toxicity?

Single nucleotide polymorphisms (SNPs) associated with increased susceptibility to cancer frequently lie in genes that might also modulate response to radiation. The purpose of this study is to evaluate whether individuals at increased genetic risk of developing cancer are also more likely to develop late radiotherapy-induced toxicities. We test the hypothesis that polygenic risk scores (PRS) for cancer susceptibility alter toxicity risk among cancer patients who received radiotherapy. Analysis included 1,134 breast, 3,521 prostate, and 610 lung cancer patients from radiotherapy cohorts from the Radiogenomics and REQUITE Consortia. All patients received radiotherapy alone or as part of combination treatment and were followed prospectively for development of toxicity in relevant tissues. Germline DNA was genotyped using a genome-wide SNP array with non-typed SNPs imputed using the 1000 Genomes reference data. A PRS was generated for each patient by summing risk alleles from cancer susceptibility SNPs identified in the literature - 352 for breast, 147 for prostate, 24 for lung cancer. A weighted PRS was similarly generated for prostate and lung cancer in which each SNP was first weighted by its odds ratio for cancer susceptibility; such a score was not available for breast cancer as the odds ratios vary by estrogen receptor status. Toxicity was quantified for each patient using STAT score, which is a previously validated measure of overall radiotherapy toxicity that combines multiple individual endpoints. Multivariable logistic regression tested association between PRS and toxicity STAT score (dichotomized at the mean plus one standard deviation) at 2 years after treatment for breast and prostate and up to 1 year for lung cancer patients, controlling for clinical covariates. Individual SNPs comprising the PRS were tested in a secondary analysis. No association was found between PRS and development of late radiotherapy toxicity among breast (PRS OR = 1.01, 95% CI = 1.00 to 1.02), prostate (PRS OR = 1.01, 95% CI = 1.00 to 1.03; weighted PRS OR = 1.10, 95%CI = 0.94 to 1.28) or lung cancer patients (PRS OR = 0.95, 95% CI = 0.88 to 1.02; weighted PRS OR = 0.77, 95% CI = 0.51 to 1.14). On multivariable analysis of individual SNPs, rs138944387 was associated with breast pain (beta = 1.12; 95% CI = 0.62 to 1.61; p = 1.09x10-5) and rs17513613 was associated with risk of breast edema (beta = -0.21; 95% CI = -0.31 to -0.12; p = 2.01x10-5). Cancer patients with a high polygenic predisposition to breast, prostate or lung cancer show no evidence of an increased risk of late radiotherapy toxicity. Thus, these patients can undergo standard treatment without an anticipated excess toxicity risk. The association between individual SNPs and late toxicity requires validation in independent cohorts and functional studies to elucidate the biologic mechanism underlying this shared risk.

Relationship analysis of the miR-196a2 polymorphism (rs11614913) with colorectal cancer risk in southern Khorasan, eastern Iran

BackgroundIt has been considered that colorectal cancer (CRC) is the fourth most common cause of cancer death with multifactorial characteristics and genetic precedent can provide a comprehensive sight to its etiology. Single nucleotide polymorphisms (SNPs) in microRNAs (miRNAs /miRs) sequence are considered as prognostic markers with high specify for CRC detection and prevention. Recent researches have indicated that rs11614913 is the most common SNP related to the vulnerability to many of the cancers. This case-control study aims to quantify the correlation between rs11614913 in miR-196a2 and CRC in southeast Iranian population. MethodsTo identify the role of rs11614913 SNP in susceptibility to CRC, this case-control study is done on CRC patients (n = 52) and healthy persons (n = 120) of the same organization with a uniform gender and age dispensation compared to CRC patients and no prior background of any kind of cancer by PCR-RFLP technique. Statistical analysis is carried out utilizing SPSS (version 16). ResultsAfter the comparison of genotype and allele distribution of this SNP among case and control groups, it has not shown any statistically significant findings (P > 0.05). ConclusionWe have not discovered statistically significant association between rs11614913 polymorphism in miR-196a2 and the risk of CRC in the southeast Iranian society.

Long cryopreserved lab-adapted Plasmodium falciparum increases resistance to chloroquine but not its susceptibility

Introduction: Plasmodium falciparum (P. falciparum) is a deadly protozoan that is accountable for malaria and chloroquine was the first-line antimalarial drug before its withdrawal and replaced by artemisinin. To date, several studies showed that P. falciparum had regained its sensitivity towards chloroquine after its withdrawal for decades. By understanding the basic principle and mechanism of chloroquine resistance in P. falciparum, at the molecular level, it would be valuable prior to the re-introduction of chloroquine as a first-line anti-malarial drug for malaria treatment. Thus, this study was conducted to determine the chloroquine resistance level of long preserved lab-adapted P. falciparum strain. Methodology: By using 14 years (2006-2020) cryopreserved chloroquine-sensitive (3D7) and chloroquine-resistant (W2) lab-adapted P. falciparum strains, the strains were subjected to continuous culture for three months before in vitro drug susceptibility assay and single nucleotide polymorphisms (SNP) analysis on Pfcrt and Pfmdr-1 gene for both strains. Results: This study shows the IC50 chloroquine of lab-adapted P. falciparum 3D7 and W2 strains were at 32.98 nM and 691.21 nM, respectively and both strains showed 3-fold higher IC50 when compared to their susceptibility before cryopreserved (3D7; 13.84nM and W2; 208.27 nM). The SNPs result showed a consistent amino acid substitution at position 76 (K to T) on PfCRT and 86 (N to Y) in Pfmdr-1 gene which concordance with other studies before preservation. Conclusion: Thus, this study shows that long cryopreserved of lab-adapted P. falciparum increases the chloroquine resistance level but not exhibited any change in susceptibility.

Annotation of susceptibility SNPs associated with atrial fibrillation.

Objective: Genome-wide association studies (GWAS) and the candidate gene based association studies have identified a panel of variants associated with atrial fibrillation (AF), however, most of the identified single nucleotide polymorphisms (SNPs) were found located within intergenic or intronic genomic regions, and whether the positive SNPs have a real biological function is unknown, and the real disease causing gene need to be studied.Results: The current results of the genetic studies including common variants identified by GWAS (338 index SNPs) and candidate gene based association studies (40 SNPs) were summarized.Conclusion: Our study suggests the relationship between genetic variants and possible targeted genes, and provides insight into potential genetic pathways underlying AF incidence and development. The results may provide an encyclopedia of AF susceptibility SNPs and shed light on the functional mechanisms of AF variants identified through genetic studies.Methods: We summarized AF susceptibility SNPs identified by GWAS and candidate gene based association studies, and give a comprehensive functional annotation of all these AF susceptibility loci. by genomic annotation, microRNA binding prediction, promoter activity analysis, enhancer activity analysis, transcription factors binding activity prediction, expression quantitative trait loci (eQTL) analysis, long-range transcriptional regulatory function analysis, gene ontology and pathway enrichment analysis.

Critical Analysis of Genome-Wide Association Studies: Triple Negative Breast Cancer Quae Exempli Causa.

Genome-wide association studies (GWAS) are useful in assessing and analyzing either differences or variations in DNA sequences across the human genome to detect genetic risk factors of diseases prevalent within a target population under study. The ultimate goal of GWAS is to predict either disease risk or disease progression by identifying genetic risk factors. These risk factors will define the biological basis of disease susceptibility for the purposes of developing innovative, preventative, and therapeutic strategies. As single nucleotide polymorphisms (SNPs) are often used in GWAS, their relevance for triple negative breast cancer (TNBC) will be assessed in this review. Furthermore, as there are different levels and patterns of linkage disequilibrium (LD) present within different human subpopulations, a plausible strategy to evaluate known SNPs associated with incidence of breast cancer in ethnically different patient cohorts will be presented and discussed. Additionally, a description of GWAS for TNBC will be presented, involving various identified SNPs correlated with miRNA sites to determine their efficacies on either prognosis or progression of TNBC in patients. Although GWAS have identified multiple common breast cancer susceptibility variants that individually would result in minor risks, it is their combined effects that would likely result in major risks. Thus, one approach to quantify synergistic effects of such common variants is to utilize polygenic risk scores. Therefore, studies utilizing predictive risk scores (PRSs) based on known breast cancer susceptibility SNPs will be evaluated. Such PRSs are potentially useful in improving stratification for screening, particularly when combining family history, other risk factors, and risk prediction models. In conclusion, although interpretation of the results from GWAS remains a challenge, the use of SNPs associated with TNBC may elucidate and better contextualize these studies.

Association of Variants in PLD1, 3p24.1, and 10q11.21 Regions With Hirschsprung’s Disease in Han Chinese Population

Background and Aims: Hirschsprung’s disease (HSCR) is a rare genetically heterogeneous congenital disorder. A recent study based on whole genome sequencing demonstrated that common variants at four novel loci, which contained two intronic variants on CASQ2 and PLD1, and intergenic variants located between SLC4A7 and EOMES at 3p24.1, and between LINC01518 and LOC283028 at 10q11.21, were associated with HSCR susceptibility. To validate these associations with HSCR susceptibility, we performed a case–control study in a Han Chinese sample set.Methods: We selected four previously identified single nucleotide polymorphisms (SNPs) for replication, along with tag SNPs to cover the four associated regions. In total, 61 SNPs were genotyped in 420 HSCR patients and 1,665 healthy controls from the Han Chinese population.Results: None of the 14 tag SNPs in the CASQ2 gene region, including the previously associated rs9428225, showed an association with HSCR. Among the 24 tag SNPs from the SLC4A7-EOMES region at 3p24.1, rs2642925 [odds ratio (OR) = 1.41, 95% confidence interval (95% CI) = 1.10–1.79; PAdditive = 0.007] and the previously associated SNP rs9851320 showed a suggestive association (OR = 1.22, 95% CI = 1.01–1.47; PAdditive = 0.042). A non-synonymous SNP, rs2287579, in PLD1 showed a suggestive association with HSCR susceptibility (OR = 1.71, 95% CI = 1.18–2.46; PAdditive = 0.004). Additionally, the previously associated PLD1 SNP rs12632766 showed a suggestive significance (OR = 1.20, 95% CI = 1.01–1.42, PAdditive = 0.038). In the LINC01518-LOC283028 region at 10q11.21, three SNPs meet the study-wide significance threshold. Rs17153309 was the most associated SNP (OR = 1.60, 95% CI = 1.34–1.90; PAdditive = 1.13 × 10–7). The previously associated SNP rs1414027 also showed significant association (OR = 1.43, 95% CI = 1.20–1.70, PAdditive = 3.92 × 10–5). Two associated SNPs at 10q11.21 (rs1414027 and rs624804) were expression quantitative trait loci in digestive tract tissues from GTEx databases.Conclusions: Our results confirmed that variants of the LINC01518-LOC283028 region were associated with HSCR in the Han Chinese population. Additionally, the susceptibility of SNPs in the LINC01518-LOC283028 region were associated with the expression levels of nearby genes. These results provide new insight into the pathogenesis of HSCR.

Transmission of polycystic ovary syndrome susceptibility single-nucleotide polymorphisms and their association with phenotype changes in offspring.

Does the inheritance of polycystic ovary syndrome (PCOS) susceptibility single-nucleotide polymorphism affect the phenotype of offspring? Male offspring who inherit PCOS-related genetic variations from PCOS mothers were more susceptible to developing the metabolic abnormality in their later life. Genetic factors are considered the major etiology of PCOS. Previous studies have highlighted that offspring of women with PCOS had an increased risk of the same disease or PCOS-like symptoms. The study involved 172 children born to women with PCOS and 529 children born to non-PCOS women. All offspring were conceived by assisted reproductive technologies. The offspring ranged from 1 to 8 years old. Metabolic phenotype analyses were performed in offspring aged from 2 to 8 (N = 619). Sanger sequencing, TaqMan and Sequenom MassARRAY were used to sequence the samples. In male offspring, the fasting insulin (FINS) (P = 0.037) homeostasis model assessment of insulin resistance (HOMA-IR) (P = 0.038) and the homeostasis model assessment of pancreatic beta-cell function (HOMA-β) (P = 0.038) levels were higher in offspring of PCOS mothers compared to controls. In female offspring, PCOS offspring had a significantly higher anti-Müllerian hormone levels (P = 0.001) compared to those from control mothers. In male offspring of PCOS mothers, subjects with a T allele at rs2349415 in the gene FSHR had higher FINS (P = 0.023), HOMA-IR (P = 0.030) and HOMA-β levels (P = 0.013) than those in the homozygous CC group. The same increased trend in FINS, HOMA-IR and HOMA-β levels could be found in the CC and TC group in rs2268361 located in gene FSHR compared to the TT group (P = 0.029, P = 0.030, P = 0.046, respectively). As for rs10818854 in the DENND1A gene, the AA and AG group had a higher FINS (P = 0.037) and HOMA-β (P = 0.008) levels than the homozygous CC group. Firstly, the offspring may be too young to see any phenotype changes. Secondly, this study only analyzed the differences of genotype frequency using the dominant model instead of all three models due to the limited sample size of the homozygous model. The results, therefore, should be replicated and performed in a larger sample size population. Thirdly, environmental impacts cannot be ruled out. The findings presented in this thesis add to our understanding the changes in offspring born to PCOS women and remind us to consider early intervention to avoid more severe effects. This study was supported by the National Key Research and Development Program of China 2017YFC1001000 (to Z.-J.C.), the National Natural Science Foundation of China 81430029 (to Z.-J.C.), 81622021 and 31571548 (to H.Z.), the National Natural Science Foundation of Shandong Province JQ201816 (to H.Z.) and Shandong Provincial Key Research and Development Program 2017G006036 (to L.-L.C.) and 2018YFJH0504 (to Z.-J.C.). There are no conflicts of interest to declare. N/A.

Impact of IL-17F 7488T/C Functional Polymorphism on Progressive Rheumatoid Arthritis: Novel Insight from the Molecular Dynamic Simulations

ABSTRACT Resorption of bones and cartilage coupled with structural changes in the inflamed joints are the major hallmark of rheumatoid arthritis (RA). Genetic polymorphisms in pro-inflammatory interleukins (ILs) appear to play an important role in the susceptibility towards progressive RA. We therefore aimed to investigate the association of single nucleotide polymorphisms (SNP), present in the hotspot coding/promoter regions of IL-6, −17 and −18, with RA susceptibility or severity in a larger study cohort from Pakistan together with finding clues as to how a functional SNP impacts the predisposition towards RA. TaqMan SNP genotyping approach was first used to assess IL-6 (rs1800795), IL-17 F (rs763780), IL-17A (rs2275913), and IL-18 (rs1946518) polymorphisms in 310 subjects (150 RA and 160 control). Molecular dynamic simulations (MDS) of wild- and mutant-type IL-17A with corresponding receptor were thereafter performed using AMBER-16; Chimera 1.13 was used for analyses. Our results showed the association of two SNPs, namely IL-6 − 174 G/C [allelic (OR = 0.960, 95% CI = 0.929–0.992, p = .009)] and IL-17 F 7488 T/C [allelic (OR = 0.907, 95%CI = 0.861–0.954, p = .000)] with increased RA risk in Pakistani subjects. When mapped, IL-17 F 7488 T/C was found involved in His161→Arg161 change near the C-terminus of IL-17 F. Comparative MDS revealed enhanced stability of the mutant hence advocating a potential role of IL-17F functional SNP in RA susceptibility and/or severity. This study provides a novel structural insight for SNP-derived functional mutation and its overall impact on binding with heterotrimeric receptor complex of IL-17 receptor thereby opening new avenues for understanding the biochemical basis of the disease.

First comprehensive computational analysis of functional consequences of TMPRSS2 SNPs in susceptibility to SARS-CoV-2 among different populations

Current SARS-CoV-2 pandemy mortality created the hypothesis that some populations may be more susceptible to SARS-CoV-2. TMPRSS2 encodes a transmembrane serine protease which plays a crucial role in SARS-CoV-2 cell entry. Single nucleotide polymorphisms (SNPs) in TMPRSS2 might influence SARS-CoV2 entry into the cell. This study aimed to investigate the impact of SNPs on TMPRSS2 function and structure. In silico tools such as Ensembl, Gtex, ExPASY 2, GEPIA, CCLE, KEGG and GO were engaged to characterize TMPRSS2 and its expression profile. The functional effects of SNPs were analyzed by PolyPhen-2, PROVEN, SNAP2, SIFT and HSF. Also, Phyre2, GOR IV and PSIPRED were used to predict the secondary structure of TMPRSS2. Moreover, post-translational modification (PTM) and secretory properties were analyzed through Modpredand Phobius, respectively. Finally, miRNA profiles were investigated by PolymiRTS and miRSNPs. Out of 11,184 retrieved SNPs from dbSNP, 92 showed a different frequency between Asians and other populations. Only 21 SNPs affected the function and structure of TMPRSS2 by influencing the protein folding, PTM, splicing and miRNA function. Particularly, rs12329760 may create a de novo pocket protein. rs875393 can create a donor site, silencer and broken enhancer motifs. rs12627374 affects a wide spectrum of miRNAs profile. This study highlighted the role of TMPRSS2 SNPs and epigenetic mechanisms especially non-coding RNAs in appearance of different susceptibility to SARS-CoV-2 among different populations. Also, this study could pave the way to potential therapeutic implication of TMPRSS2 in designing antiviral drugs. Communicated by Ramaswamy H. Sarma

Transethnic Genome-Wide Association Study Provides Insights in the Genetic Architecture and Heritability of Long QT Syndrome.

Long QT syndrome (LQTS) is a rare genetic disorder and a major preventable cause of sudden cardiac death in the young. A causal rare genetic variant with large effect size is identified in up to 80% of probands (genotype positive) and cascade family screening shows incomplete penetrance of genetic variants. Furthermore, a proportion of cases meeting diagnostic criteria for LQTS remain genetically elusive despite genetic testing of established genes (genotype negative). These observations raise the possibility that common genetic variants with small effect size contribute to the clinical picture of LQTS. This study aimed to characterize and quantify the contribution of common genetic variation to LQTS disease susceptibility. We conducted genome-wide association studies followed by transethnic meta-analysis in 1656 unrelated patients with LQTS of European or Japanese ancestry and 9890 controls to identify susceptibility single nucleotide polymorphisms. We estimated the common variant heritability of LQTS and tested the genetic correlation between LQTS susceptibility and other cardiac traits. Furthermore, we tested the aggregate effect of the 68 single nucleotide polymorphisms previously associated with the QT-interval in the general population using a polygenic risk score. Genome-wide association analysis identified 3 loci associated with LQTS at genome-wide statistical significance (P<5×10-8) near NOS1AP, KCNQ1, and KLF12, and 1 missense variant in KCNE1(p.Asp85Asn) at the suggestive threshold (P<10-6). Heritability analyses showed that ≈15% of variance in overall LQTS susceptibility was attributable to common genetic variation (h2SNP 0.148; standard error 0.019). LQTS susceptibility showed a strong genome-wide genetic correlation with the QT-interval in the general population (rg=0.40; P=3.2×10-3). The polygenic risk score comprising common variants previously associated with the QT-interval in the general population was greater in LQTS cases compared with controls (P<10-13), and it is notable that, among patients with LQTS, this polygenic risk score was greater in patients who were genotype negative compared with those who were genotype positive (P<0.005). This work establishes an important role for common genetic variation in susceptibility to LQTS. We demonstrate overlap between genetic control of the QT-interval in the general population and genetic factors contributing to LQTS susceptibility. Using polygenic risk score analyses aggregating common genetic variants that modulate the QT-interval in the general population, we provide evidence for a polygenic architecture in genotype negative LQTS.