Proficiency of data interpretation: identification of signaling SNPs/specific loci for coronary artery disease

Genetic Variants at PRKCG Splice and UTR Sites Promote Cancer Susceptibility by Disrupting Epigenetic and miRNA Regulatory Network

The changes in the protein kinase C gamma gene (PRKCG) expression are associated with both coding and non-coding variants. No studies have specifically established the association between PRKCG 3'UTR, 5'UTR, donor and acceptor splice variants with post-transcriptional changes through utilizing in-silico tools. The current study intends to uncover this linkage. In total, 419 3' and 5'UTR variants were retrieved. 325 of these variant IDs were annotated as functionally significant. 18 variants impacted the transcription factors binding and therefore influenced the post-transcriptional regulatory activity while 7 variants affected regulatory mechanisms through histone modifications. 2 rsIDs (rs373228, rs446795) potentially impacted the interactions with RNA binding proteins. In addition to that, PRKCG showed high expression in brain cells and had variable expression in TCGA tumors, respectively. Furthermore, 5 3' UTR variants were identified to be targeted by miRNAs. In total, 5 of these miRNAs (hsa-miR-663a, hsa-miR-324-5p, hsa-miR-646, hsa-miR-1205 and hsa-miR-4270) that targeted 3'UTRs (rs57483118, rs181418157 and rs60891969) showed differential expressions in distinct cancer types. The presence of 3'UTR variants likely altered the secondary structure of mRNA. The 7 rsIDs at 3' UTR site caused the loss of function of authentic splice site at 10 positions was noted; at 1 position, gain of function was observed while at 2 positions no effect was identified. Moreover, the loss of donor and acceptor splice site was evident. Our results highlight the importance of non-coding regions that might boost our research capacity to predict and construct targeted therapeutic approaches.

Genetic polymorphism in untranslated regions of PRKCZ influences mRNA structure, stability and binding sites

BACKGROUND

Variations in untranslated regions (UTR) alter regulatory pathways impacting phenotype, disease onset, and course of disease. Protein kinase C Zeta (PRKCZ), a serine-threonine kinase, is implicated in cardiovascular, neurological and oncological disorders. Due to limited research on PRKCZ, this study aimed to investigate the impact of UTR genetic variants' on binding sites for transcription factors and miRNA. RNA secondary structure, eQTLs, and variation tolerance analysis were also part of the study.

METHODS

The data related to PRKCZ gene variants was downloaded from the Ensembl genome browser, COSMIC and gnomAD. The RegulomeDB database was used to assess the functional impact of 5' UTR and 3'UTR variants. The analysis of the transcription binding sites (TFBS) was done through the Alibaba tool, and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) was employed to identify pathways associated with PRKCZ. To predict the effect of variants on microRNA binding sites, PolymiRTS was utilized for 3' UTR variants, and the SNPinfo tool was used for 5' UTR variants.

RESULTS

The results obtained indicated that a total of 24 variants present in the 3' UTR and 25 variants present in the 5' UTR were most detrimental. TFBS analysis revealed that 5' UTR variants added YY1, repressor, and Oct1, whereas 3' UTR variants added AP-2alpha, AhR, Da, GR, and USF binding sites. The study predicted TFs that influenced PRKCZ expression. RNA secondary structure analysis showed that eight 5' UTR and six 3' UTR altered the RNA structure by either removal or addition of the stem-loop. The microRNA binding site analysis highlighted that seven 3' UTR and one 5' UTR variant altered the conserved site and also created new binding sites. eQTLs analysis showed that one variant was associated with PRKCZ expression in the lung and thyroid. The variation tolerance analysis revealed that PRKCZ was an intolerant gene.

CONCLUSION

This study laid the groundwork for future studies aimed at targeting PRKCZ as a therapeutic target.

A bidirectional link between metabolic syndrome and elevation in alanine aminotransferase in elderly female: a longitudinal community study

Pre-obesity, as a significant risk factor for the progression of metabolic syndrome (MS), has become a prevalent public health threat globally. In this three-year longitudinal study of pre-obese women at baseline, the goal was to clarify the female-specific bidirectional relationship between the risk of MS and blood alanine aminotransferase. In this manuscript, the MS score was determined using the following equation: MS score = 2*waist/height + fasting glucose/5.6 + TG/1.7 + SBP/130-HDL/1.02 for men and 1.28 for women, which is highly related to the risk of MS. With 2,338 participants, a hierarchical nonlinear model with random effects was utilized to analyze the temporal trends of serum characteristics from 2017 to 2019. A bivariate cross-lagged panel model (CLPM) was employed to estimate the structural relations of frequently measured variables at three different time points to determine the directionality of the relationship between the risk of MS and serum characteristics. MassARRAY Analyzer 4 platforms were used to evaluate and genotype candidate SNPs. In this study, the MS score only rose with age in females; it was positively correlated with serum alanine aminotransferase (ALT) in females; the CLPM revealed that the MS score in 2017 predicted ALT in 2018 (β = 0.066, p < 0.001); and ALT in 2018 predicted an MS score in 2019 (β = 0.037, p < 0.050); both relationships were seen in females. Additionally, the MS score in elderly females with NAFLD was related to the rs295 in the lipoprotein lipase (LPL) gene (p = 0.042). Our work showed that there may be female-specific causal correlations between elevated ALT and risk of MS and that the polymorphism rs295 in LPL may serve as a marker for the prognosis of MS. The genetic roles of rs295 in the LPL gene in the onset of MS and the development of ALT in the elderly Chinese Han population are thus provided by this, offering one potential mechanism.

Investigation of UTR Variants by Computational Approaches Reveal Their Functional Significance in PRKCI Gene Regulation

Single nucleotide polymorphisms (SNPs) are associated with many diseases including neurological disorders, heart diseases, diabetes, and different types of cancers. In the context of cancer, the variations within non-coding regions, including UTRs, have gained utmost importance. In gene expression, translational regulation is as important as transcriptional regulation for the normal functioning of cells; modification in normal functions can be associated with the pathophysiology of many diseases. UTR-localized SNPs in the PRKCI gene were evaluated using the PolymiRTS, miRNASNP, and MicroSNIper for association with miRNAs. Furthermore, the SNPs were subjected to analysis using GTEx, RNAfold, and PROMO. The genetic intolerance to functional variation was checked through GeneCards. Out of 713 SNPs, a total of thirty-one UTR SNPs (three in 3' UTR region and twenty-nine in 5' UTR region) were marked as ≤2b by RegulomeDB. The associations of 23 SNPs with miRNAs were found. Two SNPs, rs140672226 and rs2650220, were significantly linked with expression in the stomach and esophagus mucosa. The 3' UTR SNPs rs1447651774 and rs115170199 and the 5' UTR region variants rs778557075, rs968409340, and 750297755 were predicted to destabilize the mRNA structure with substantial change in free energy (∆G). Seventeen variants were predicted to have linkage disequilibrium with various diseases. The SNP rs542458816 in 5' UTR was predicted to put maximum influence on transcription factor binding sites. Gene damage index(GDI) and loss of function (o:e) ratio values for PRKCI suggested that the gene is not tolerant to loss of function variants. Our results highlight the effects of 3' and 5' UTR SNP on miRNA, transcription and translation of PRKCI. These analyses suggest that these SNPs can have substantial functional importance in the PRKCI gene. Future experimental validation could provide further basis for the diagnosis and therapeutics of various diseases.

Association of the rs2111234, rs3135499, rs8057341 polymorphisms in the NOD2 gene with leprosy: A case-control study in the Norte de Santander, Colombia population

BACKGROUND

Leprosy is a chronic infectious disease caused by Mycobacterium leprae. The development of leprosy involves several factors, including the causative agent, the individual host's immune response, environmental factors, and the genetic background of the host. Specifically, the host's innate immune response, encoded by genes, determines their susceptibility to developing leprosy post-infection. Polymorphic variants in the nucleotide-binding oligomerization domain 2 (NOD2) gene are associated with leprosy among populations in a variety of endemic areas around the world. Colombia, a country located in the tropical zone, has several leprosy-endemic regions, including Norte de Santander. The aim of this study was to analyze the rs7194886, rs2111234, rs3135499, and rs8057341 single nucleotide polymorphisms (SNPs) in the NOD2 gene using a case-control study to determine whether they confer greater or lesser susceptibility to the development of leprosy.

METHODOLOGY

The TaqMan qPCR amplification system was used for SNPs detection.

FINDINGS

An association between the A-rs8057341 SNP (p = 0,006286) and resistance to leprosy was found. However, the rs3135499 (p = 0,9063) and rs2111234 (p = 0.1492) were not found to be associated with leprosy susceptibility. In addition, the rs7194886 SNP was not found to be in Hardy-Weinberg equilibrium (HWE) in the study population. The GAG haplotype, consisting of SNPs rs2111234-G, rs3135499-A, and rs8057341G, acts as a susceptibility factor for the development of leprosy in women. SNPs rs3135499 and rs8057341 are functionally related to decreased NOD2 expression according to an in-silico analysis.

CONCLUSIONS

The SNPs rs8057341-A was related with resistance to leprosy and the haplotype rs2111234-G, rs3135499-A and rs8057341-G SNPs was related with susceptibility in the Norte de Santander Colombia, studied population.

Association of rs2954029 and rs6982502 Variants with Coronary Artery Disease by HRM Technique: A GWAS Replication Study in an Iranian Population

BACKGROUND

Genome-wide association studies (GWAS) have been the primary tool for an unbiased study of the genetic background of coronary artery disease (CAD). They have identified a list of single-nucleotide polymorphisms (SNPs) associated with coronary artery disease (CAD). In this study, we aimed to replicate the association of rs2954029 and rs6982502, a GWAS identified SNP, to CAD in an Iranian population.

METHODS

A sample of 285 subjects undergoing coronary angiography, including 134 CAD patients and 151 healthy. The genotype determination of rs2954029 and rs6982502 SNPs performed using the high-resolution melting analysis (HRM) technique.

RESULTS

Our results revealed that the TT genotype of rs2954029 (p= 0.009) and rs6982502 (p< 0.001) were significantly higher in CAD patients compared with controls. Binary logistic regression showed that rs6982502 and rs2954029 increase the risk of CAD incidence (2.470 times, p= 0.011, 95% CI= [1.219-4.751], and 2.174 times, p= 0.033, 95% CI= [1.066-4.433] respectively). After adjusting for confounders, we found that rs6982502 and rs2954029 are significantly associated with CAD risk.

CONCLUSION

These data showed that the TT genotype of rs2954029 and rs6982502 is associated with the risk of CAD in a hospital-based sample of the Iranian population, which has replicated the result of recent GWAS studies.

ADA gene haplotype is associated with coronary-in-stent-restenosis

BACKGROUND

Cardiovascular diseases (CVDs) are the most common and the first cause of death worldwide. While some studies have investigated the association of the Adenosine Deaminase (ADA) gene with CDVs, its roles on in-stent restenosis (ISR) has not been studied.

METHODS AND RESULTS

In this study, we investigated the role of ADA gene variants in both genetic and haplotype models on the risk of ISR. 91 samples were included in this study. The subjects were divided into two groups regarding having or not-having ISR (n = 40 ISR+ and n = 51 ISR-). The genotyping for G22A (rs73598374) and A4223C (rs452159) polymorphisms was performed using PCR-RFLP method. Statistical analysis was performed by SPSS v. 20 and Haploview 4.2 softwares. The basic demographic conditions in ISR groups were statistically similar. There was a significant association between A allele of rs452159 ISR groups after adjustment (allelic model: P value = 0.028, OR(95%CI) = 0.366(0.149-0.899)), while rs73598374 polymorphism shows no significant association with ISR. In haplotype analysis, the GA (G:rs73598374/A:rs452159) haplotype decreased the risk of ISR (P value = 00.025, OR(95%CI) = 0.382(0.161-0.907)).

CONCLUSIONS

This study suggests that A allele of ADA rs452159 polymorphism and GA (G:rs73598374/A:rs452159) haplotype may be related to decreased risk of ISR in CAD patients receiving drug-eluting stent and offers more observational studies on ADA variants in other populations to generate a potential haplotype panel for ISR risk assessment.

Structure analysis of deleterious nsSNPs in human PALB2 protein for functional inference

Partner and Localizer of BRCA2 or PALB2 is a typical tumor suppressor protein, that responds to DNA double stranded breaks through homologous recombination repair. Heterozygous mutations in PALB2 are known to contribute to the susceptibility of breast and ovarian cancer. However, there is no comprehensive study characterizing the structural and functional impacts of SNPs located in the PALB2 gene. Therefore, it is of interest to document a comprehensive analysis of coding and non-coding SNPs located at the PALB2 loci using in silico tools. The data for 1455 non-synonymous SNPs (nsSNPs) located in the PALB2 loci were retrieved from the dbSNP database. Comprehensive characterization of the SNPs using a combination of in silico tools such as SIFT, PROVEAN, PolyPhen, PANTHER, PhD-SNP, Pmut, MutPred 2.0 and SNAP-2, identified 28 functionally important SNPs. Among these, 16 nsSNPs were further selected for structural analysis using conservation profile and protein stability. The most deleterious nsSNPs were documented within the WD40 domain of PALB2. A general outline of the structural consequences of each variant was developed using the HOPE project data. These 16 mutant structures were further modelled using SWISS Model and three most damaging mutant models (rs78179744, rs180177123 and rs45525135) were identified. The non-coding SNPs in the 3' UTR region of the PALB2 gene were analyzed for altered miRNA target sites. The comprehensive characterization of the coding and non-coding SNPs in the PALB2 locus has provided a list of damaging SNPs with potential disease association. Further validation through genetic association study will reveal their clinical significance.

Association of Metabolic Syndrome with Aerobic Exercise and LPL rs3779788 Polymorphism in Taiwan Biobank Individuals

PURPOSE

The Lipoprotein lipase (LPL) gene is a significant contributor to dyslipidemia. It has shown associations with several conditions including atherosclerosis, obesity, and metabolic syndrome (MetS). We assessed the interactive association between MetS and rs3779788 of the LPL gene based on aerobic exercise.

MATERIALS AND METHODS

Data were available for 7532 Taiwan Biobank (TWB) participants recruited between 2008 and 2016. We used multiple logistic regression to determine the odds ratios (OR) for MetS and their 95% confident intervals (C.I.). Potential variables included LPL rs3779788, aerobic exercise, sex, age, education, marital status, body mass index (BMI), smoking, alcohol consumption, midnight snacking, vegetarian diet, coffee, dietary fat, and tea drinking.

RESULTS

Aerobic exercise was protective against MetS (OR, 0.858; 95% C.I., 0.743-0.991). Compared to CC/CT genotype, the OR for developing MetS was 0.875, (95% C.I., 0.571-1.341) in TT individuals. The test for interaction was significant for the rs3779788 variant and aerobic exercise (p = 0.0484). In our group analyses, the OR for MetS was 0.841 (95% C.I., 0.727-0.974) in CC/CT and 4.076 (95% C.I., 1.158-14.346) in TT individuals who did aerobic exercise compared to those who did not.

CONCLUSION

Our study indicated that aerobic exercise improved metabolic syndrome in Taiwanese adults with rs3779788 CC/CT genotype relative to those with TT genotype.

Identification of Genetic Factors Underlying the Association between Sodium Intake Habits and Hypertension Risk

The role of sodium in hypertension remains unresolved. Although genetic factors have a significant impact on high blood pressure, studies comparing genetic susceptibility between people with low and high sodium diets are lacking. We aimed to investigate the genetic variations related to hypertension according to sodium intake habits in a large Korean population-based study. Data for a total of 57,363 participants in the Korean Genome and Epidemiology Study Health Examination were analyzed. Sodium intake was measured by a semi-quantitative food frequency questionnaire. We classified participants according to sodium intake being less than or greater than 2 g/day. We used logistic regression to test single-marker variants for genetic association with a diagnosis of hypertension, adjusting for age, sex, body mass index, exercise, alcohol, smoking, potassium intake, principal components 1, and principal components 2. Significant associations were defined as p < 5 × 10-8. In participants whose sodium intake was greater than 2 g/day, chromosome 6 open reading frame 10 (C6orf10)-human leukocyte antigen (HLA)-DQB1 rs6913309, ring finger protein (RNF)213 rs112735431, glycosylphosphatidylinositol anchored molecule-like (GML)- cytochrome P450 family 11 subfamily B member 1(CYP11B1) rs3819496, myosin light chain 2 (MYL2)-cut like homeobox 2 (CUX2) rs12229654, and jagged1 (JAG1) rs1887320 were significantly associated with hypertension. In participants whose intake was less than 2 g/day, echinoderm microtubule-associated protein-like 6(EML6) rs67617923 was significantly associated with hypertension. Genetic susceptibility associated with hypertension differed according to sodium intake. Identifying gene variants that contribute to the dependence of hypertension on sodium intake status could make possible more individualized nutritional recommendations for preventing cardiovascular diseases.

Association Study of Coronary Artery Disease-Associated Genome-Wide Significant SNPs with Coronary Stenosis in Pakistani Population

Genome-wide association studies (GWAS) of coronary artery disease (CAD) have revealed multiple genetic risk loci. We assessed the association of 47 genome-wide significant single-nucleotide polymorphisms (SNPs) at 43 CAD loci with coronary stenosis in a Pakistani sample comprising 663 clinically ascertained and angiographically confirmed cases. Genotypes were determined using the iPLEX Gold technology. All statistical analyses were performed using R software. Linkage disequilibrium (LD) between significant SNPs was determined using SNAP web portal, and functional annotation of SNPs was performed using the RegulomeDB and Genotype-Tissue Expression (GTEx) databases. Genotyping comparison was made between cases with severe stenosis (≥70%) and mild/minimal stenosis (<30%). Five SNPs demonstrated significant associations: three with additive genetic models PLG/rs4252120 (p = 0.0078), KIAA1462/rs2505083 (p = 0.005), and SLC22A3/rs2048327 (p = 0.045) and two with recessive models SORT1/rs602633 (p = 0.005) and UBE2Z/rs46522 (p = 0.03). PLG/rs4252120 was in LD with two functional PLG variants (rs4252126 and rs4252135), each with a RegulomeDB score of 1f. Likewise, KIAA1462/rs2505083 was in LD with a functional SNP, KIAA1462/rs3739998, having a RegulomeDB score of 2b. In the GTEx database, KIAA1462/rs2505083, SLC22A3/rs2048327, SORT1/rs602633, and UBE2Z/rs46522 SNPs were found to be expression quantitative trait loci (eQTLs) in CAD-associated tissues. In conclusion, five genome-wide significant SNPs previously reported in European GWAS were replicated in the Pakistani sample. Further association studies on larger non-European populations are needed to understand the worldwide genetic architecture of CAD.

Molecular Relationships between Bronchial Asthma and Hypertension as Comorbid Diseases

Comorbidity, a co-incidence of several disorders in an individual, is a common phenomenon. Their development is governed by multiple factors, including genetic variation. The current study was set up to look at associations between isolated and comorbid diseases of bronchial asthma and hypertension, on one hand, and single nucleotide polymorphisms associated with regulation of gene expression (eQTL), on the other hand. A total of 96 eQTL SNPs were genotyped in 587 Russian individuals. Bronchial asthma alone was found to be associated with rs1927914 (TLR4), rs1928298 (intergenic variant), and rs1980616 (SERPINA1); hypertension alone was found to be associated with rs11065987 (intergenic variant); rs2284033 (IL2RB), rs11191582 (NT5C2), and rs11669386 (CARD8); comorbidity between asthma and hypertension was found to be associated with rs1010461 (ANG/RNASE4), rs7038716, rs7026297 (LOC105376244), rs7025144 (intergenic variant), and rs2022318 (intergenic variant). The results suggest that genetic background of comorbidity of asthma and hypertension is different from genetic backgrounds of both diseases manifesting isolated.