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1.
Interactions Between Vitamin D and Calcium Intake, Vitamin D Receptor Genetic Polymorphisms, and Colorectal Cancer Risk.
Zhang, X, Fang, YJ, Feng, XL, Abulimiti, A, Huang, CY, Luo, H, Zhang, CX
Digestive diseases and sciences. 2021;(6):1895-1905
Abstract
BACKGROUND Vitamin D has anticarcinogenic properties and acts through vitamin D receptor (VDR) to carry out its functions. AIMS This study explored the independent and combined effects of dietary vitamin D and calcium, and VDR genetic polymorphisms on colorectal cancer risk in a Chinese population. METHODS This ongoing case-control study recruited 488 cases with histologically confirmed colorectal cancer and 496 sex- and age-matched controls. Vitamin D and calcium intakes were assessed by a validated food frequency questionnaire, and VDR genotype was conducted for Fok I (rs2228570), Bsm I (rs1544410), Apa I (rs7975232), and Taq I (rs731236). Unconditional logistic regression was used to calculate odds ratio and 95% confidence interval after adjusting for various confounders. RESULTS No significant association was found between Fok I, Bsm I, Apa I, Taq I, and colorectal cancer risk. Higher intakes of dietary vitamin D and calcium were associated with 47% and 50% reduction in colorectal cancer risk. Significant interaction was observed between dietary vitamin D intake and Apa I polymorphisms in relation to colorectal cancer risk (Pinteraction = 0.006). Subjects with higher dietary vitamin D intake and mutant Apa I A allele had a substantially decreased risk of colorectal cancer compared to Apa I aa carriers with lower vitamin D intake. CONCLUSIONS Our study supports that Apa I may interact with dietary vitamin D intake on colorectal cancer risk. However, no interactions were found between dietary vitamin D or calcium intakes and Fok I, Bsm I, and Taq I in relation to colorectal cancer risk.
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Endometriosis Is Associated with Functional Polymorphism in the Promoter of Heme Oxygenase 1 (HMOX1) Gene.
Milewski, Ł, Ścieżyńska, A, Ponińska, J, Soszyńska, M, Barcz, E, Roszkowski, PI, Kamiński, P, Włodarski, P, Płoski, R, Malejczyk, J
Cells. 2021;(3)
Abstract
Endometriosis is a common gynecological disorder characterized by the ectopic growth of endometrial-like tissue outside the uterine cavity. Etiopathogenesis of endometriosis is poorly understood; it is plausible, however, that the disease may be associated with oxidative stress related to local heme and iron metabolism. Therefore, the aim of the study was to reveal a possible association of endometriosis with a stress-inducible heme oxygenase 1 (HMOX1). For this purpose, 228 patients with clinically confirmed endometriosis and 415 control parous women from general Polish population were examined for functional -413A>T (rs2071746) single-nucleotide polymorphism (SNP) and (GT)n dinucleotide repeat length polymorphism in the promoter of HMOX1 gene. In addition, -413A>T SNP was assessed by the specific TaqMan® SNP Genotyping Assay, and (GT)n polymorphism was determined by PCR product size analysis. We found that endometriosis is associated with an increased frequency of -413A(GT)31,32 haplotype (OR (95%CI) = 1.27 (1.01-1.60), p = 0.0381) and -413A(GT)31,32 homozygous genotype [OR (95%CI) = 1.51 (1.06-2.17), p = 0.0238]. These data suggest that endometriosis is associated with functional polymorphism of HMOX1 gene, and this gene may play a part in the pathogenesis of this disorder.
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The Roles of Reduced Folate Carrier-1 (RFC1) A80G (rs1051266) Polymorphism in Congenital Heart Disease: A Meta-Analysis.
Yi, K, Ma, YH, Wang, W, Zhang, X, Gao, J, He, SE, Xu, XM, Ji, M, Guo, WF, You, T
Medical science monitor : international medical journal of experimental and clinical research. 2021;:e929911
Abstract
BACKGROUND We performed the present study to better elucidate the correlation of reduced folate carrier-1 (RFC1) A80G (rs1051266) polymorphism with the risk of congenital heart disease (CHD). MATERIAL AND METHODS According to the designed search strategy, a systematic literature search was performed through the PubMed, Cochrane Library, Web of Science, EMBASE, CNKI, VIP, and Wan Fang databases to collect published case-control studies on the correlation between RFC1 A80G polymorphism and CHD. All relevant studies up to October 1, 2019 were identified. The odds ratio (OR) and 95% confidence interval (CI) of the genotype distribution were used as the effect indicators. RESULTS A total of 6 eligible studies was finally included in our meta-analysis, including 724 children with CHD, 760 healthy children, 258 mothers of the children with CHD, and 334 mothers of healthy control children. The meta-analysis revealed that for fetal analysis, only in the heterozygous model (GA vs GG, OR=1.36, 95% CI [1.06, 1.75], P=0.02) was RFC1 A80G polymorphism associated with risk of CHD. In maternal analysis, 3 genetic models of RFC1 A80G polymorphism increased the risk of CHD: the allelic model (A vs G, OR=1.36, 95% CI [1.07, 1.71], P=0.01), the homozygote model (AA vs GG, OR=2.99, 95%CI [1.06, 8.41], P=0.04), and the dominance model (GA+AA vs GG, OR=1.53, 95%CI [1.08, 2.16], P=0.02). CONCLUSIONS The maternal RFC1 A80G polymorphism has a strong correlation with CHD. Compared with the G allele, the A allele increases the risk of CHD by 0.36-fold.
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Vitamin D Receptor Gene Polymorphisms and the Risk of Metabolic Syndrome (MetS): A Meta-Analysis.
Totonchi, H, Rezaei, R, Noori, S, Azarpira, N, Mokarram, P, Imani, D
Endocrine, metabolic & immune disorders drug targets. 2021;(5):943-955
Abstract
BACKGROUND Several studies have assessed the association between the vitamin D receptor (VDR) polymorphism and the risk of metabolic syndrome (MetS). However, the results were inconsistent and inconclusive. Therefore, we conducted a meta-analysis to clarify the exact association between the vitamin D receptor (VDR) polymorphisms and the risk of MetS. METHODS All accessible studies reporting the association between the FokI (rs2228570) or/and TaqI (rs731236) or/and BsmI (rs1544410) or/and ApaI (rs7975232 polymorphisms of the Vitamin D Receptor and susceptibility to MetS published prior to February 2019 were systematically searched in Web of Science, Scopus, and PubMed. After that, Odds ratios (ORs) and their corresponding 95% confidence intervals (CIs) were estimated to evaluate the strength of the association in five genetic models. RESULTS A total of 9 articles based on four gene variations, and comprising 3348 participants with 1779 metabolic syndrome patients were included. The overall results suggested a significant association between BsmI (rs1544410) polymorphism and MetS susceptibility in recessive model (OR, 0.72, 95% CI, 0.55-0.95, fixed effect model), allelic model (OR, 0.83, 95% CI, 0.72-0.95, fixed effect model), and bb vs BB (OR, 0.65, 95% CI, 0.46-0.93, fixed effect). However, no significant association was identified between TaqI (rs731236) polymorphism, ApaI (rs7975232) polymorphism, and FokI (rs2228570) polymorphism and MetS. CONCLUSION This meta-analysis suggested an association between the BsmI (rs1544410) polymorphism and MetS. Indeed, BsmI (rs1544410) acts as a protective factor in the MetS. As a result, the VDR gene could be regarded as a promising pharmacological and physiological target in the prevention or treatment of the MetS.
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5.
Association of Genetic Variant at Chromosome 12q23.1 With Neuropathic Pain Susceptibility.
Veluchamy, A, Hébert, HL, van Zuydam, NR, Pearson, ER, Campbell, A, Hayward, C, Meng, W, McCarthy, MI, Bennett, DLH, Palmer, CNA, et al
JAMA network open. 2021;(12):e2136560
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Abstract
IMPORTANCE Neuropathic pain (NP) has important clinical and socioeconomic consequences for individuals and society. Increasing evidence indicates that genetic factors make a significant contribution to NP, but genome-wide association studies (GWASs) are scant in this field and could help to elucidate susceptibility to NP. OBJECTIVE To identify genetic variants associated with NP susceptibility. DESIGN, SETTING, AND PARTICIPANTS This genetic association study included a meta-analysis of GWASs of NP using 3 independent cohorts: ie, Genetics of Diabetes Audit and Research in Tayside Scotland (GoDARTS); Generation Scotland: Scottish Family Health Study (GS:SFHS); and the United Kingdom Biobank (UKBB). Data analysis was conducted from April 2018 to December 2019. EXPOSURES Individuals with NP (ie, case participants; those with pain of ≥3 months' duration and a Douleur Neuropathique en 4 Questions score ≥3) and individuals with no pain (ie, control participants) with or without diabetes from GoDARTS and GS:SFHS were identified using validated self-completed questionnaires. In the UKBB, self-reported prescribed medication and hospital records were used as a proxy to identify case participants (patients recorded as receiving specific anti-NP medicines) and control participants. MAIN OUTCOMES AND MEASURES GWAS was performed using linear mixed modeling. GWAS summary statistics were combined using fixed-effect meta-analysis. A total of 51 variants previously shown to be associated with NP were tested for replication. RESULTS This study included a total of 4512 case participants (2662 [58.9%] women; mean [SD] age, 61.7 [10.8] years) and 428 489 control participants (227 817 [53.2%] women; mean [SD] age, 62.3 [11.5] years) in the meta-analysis of 3 cohorts with European descent. The study found a genome-wide significant locus at chromosome 12q23.1, which mapped to SLC25A3 (rs369920026; odds ratio [OR] for having NP, 1.68; 95% CI, 1.40-2.02; P = 1.30 × 10-8), and a suggestive variant at 13q14.2 near CAB39L (rs7992766; OR, 1.09; 95% CI, 1.05-1.14; P = 1.22 × 10-7). These mitochondrial phosphate carriers and calcium binding genes are expressed in brain and dorsal root ganglia. Colocalization analyses using expression quantitative loci data found that the suggestive variant was associated with expression of CAB39L in the brain cerebellum (P = 1.01 × 10-14). None of the previously reported variants were replicated. CONCLUSIONS AND RELEVANCE To our knowledge, this was the largest meta-analyses of GWAS to date. It found novel genetic variants associated with NP susceptibility. These findings provide new insights into the genetic architecture of NP and important information for further studies.
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Vitamin D and Type 1 Diabetes Risk: A Systematic Review and Meta-Analysis of Genetic Evidence.
Najjar, L, Sutherland, J, Zhou, A, Hyppönen, E
Nutrients. 2021;(12)
Abstract
Several observational studies have examined vitamin D pathway polymorphisms and their association with type 1 diabetes (T1D) susceptibility, with inconclusive results. We aimed to perform a systematic review and meta-analysis assessing associations between selected variants affecting 25-hydroxyvitamin D [25(OH)D] and T1D risk. We conducted a systematic search of Medline, Embase, Web of Science and OpenGWAS updated in April 2021. The following keywords "vitamin D" and/or "single nucleotide polymorphisms (SNPs)" and "T1D" were selected to identify relevant articles. Seven SNPs (or their proxies) in six genes were analysed: CYP2R1 rs10741657, CYP2R1 (low frequency) rs117913124, DHCR7/NADSYN1 rs12785878, GC rs3755967, CYP24A1 rs17216707, AMDHD1 rs10745742 and SEC23A rs8018720. Seven case-control and three cohort studies were eligible for quantitative synthesis (n = 10). Meta-analysis results suggested no association with T1D (range of pooled ORs for all SNPs: 0.97-1.02; p > 0.01). Heterogeneity was found in DHCR7/NADSYN1 rs12785878 (I2: 64.8%, p = 0.02). Sensitivity analysis showed exclusion of any single study did not alter the overall pooled effect. No association with T1D was observed among a Caucasian subgroup. In conclusion, the evidence from the meta-analysis indicates a null association between selected variants affecting serum 25(OH)D concentrations and T1D.
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Causal Association between Periodontitis and Parkinson's Disease: A Bidirectional Mendelian Randomization Study.
Botelho, J, Machado, V, Mendes, JJ, Mascarenhas, P
Genes. 2021;(5)
Abstract
The latest evidence revealed a possible association between periodontitis and Parkinson's disease (PD). We explored the causal relationship of this bidirectional association through two-sample Mendelian randomization (MR) in European ancestry populations. To this end, we used openly accessible data of genome-wide association studies (GWAS) on periodontitis and PD. As instrumental variables for periodontitis, seventeen single-nucleotide polymorphisms (SNPs) from a GWAS of periodontitis (1817 periodontitis cases vs. 2215 controls) and eight non-overlapping SNPs of periodontitis from an additional GWAS for validation purposes. Instrumental variables to explore for the reverse causation included forty-five SNPs from a GWAS of PD (20,184 cases and 397,324 controls). Multiple approaches of MR were carried-out. There was no evidence of genetic liability of periodontitis being associated with a higher risk of PD (B = -0.0003, Standard Error [SE] 0.0003, p = 0.26). The eight independent SNPs (B = -0.0000, SE 0.0001, p = 0.99) validated this outcome. We also found no association of genetically primed PD towards periodontitis (B = -0.0001, SE 0.0001, p = 0.19). These MR study findings do not support a bidirectional causal genetic liability between periodontitis and PD. Further GWAS studies are needed to confirm the consistency of these results.
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Accurate Imputation of Untyped Variants from Deep Sequencing Data.
Torkamaneh, D, Belzile, F
Methods in molecular biology (Clifton, N.J.). 2021;:271-281
Abstract
The quality, statistical power, and resolution of genome-wide association studies (GWAS) are largely dependent on the comprehensiveness of genotypic data. Over the last few years, despite the constant decrease in the price of sequencing, whole-genome sequencing (WGS) of association panels comprising a large number of samples remains cost-prohibitive. Therefore, most GWAS populations are still genotyped using low-coverage genotyping methods resulting in incomplete datasets. Imputation of untyped variants is a powerful method to maximize the number of SNPs identified in study samples, it increases the power and resolution of GWAS and allows to integrate genotyping datasets obtained from various sources. Here, we describe the key concepts underlying imputation of untyped variants, including the architecture of reference panels, and review some of the associated challenges and how these can be addressed. We also discuss the need and available methods to rigorously assess the accuracy of imputed data prior to their use in any genetic study.
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Association of Interleukin-10 -592 C > A gene polymorphism with coronary artery disease: A case-control study and meta-analysis.
Ghalandari, M, Jamialahmadi, K, Nik, MM, Pirhoushiaran, M, Mirhafez, SR, Rooki, H, Avan, A, Ghazizadeh, H, Moohebati, M, Nohtani, M, et al
Cytokine. 2021;:155403
Abstract
BACKGROUND Coronary-artery-disease (CAD) is the leading cause of death worldwide, and hence there is a need to identify reliable markers for identifying individuals at high risk of developing CAD. Interleukin-10 (IL-10) is an anti-inflammatory cytokine that is associated with an increased risk of developing both atherosclerosis and acute coronary events. The study aimed to explore the association of a genetic variant in IL-10 with the risk of developing CAD and the severity of the disease. To further explore, a systematic review and meta-analysis was performed. The cumulative results of the relationship between IL and 10 -592 C > A polymorphism and CAD in Iranian population have also been presented. METHODS In this cross sectional study, a total of 948 individuals including 307 healthy controls and 641 patients that among cases, four hundred and fifty-five of the patients had > 50% stenosis (angiogram positive group) and 186 patients had < 50% stenosis (angiogram negative group) were recruited from the Mashhad-Stroke and Heart-Atherosclerotic-Disorders cohort. Genotyping for the IL-10 -592 C > A polymorphism was performed using a PCR-RFLP technique, and statistical analysis undertaken by univariate and multivariate analyses. PubMed, Google Scholar and Scopus were searched for papers related to this polymorphism up to October 2019. The Meta-analysiswas done based on the random effect model using a Meta-analysis. RESULTS In our study, the frequency of the variant A allele of the IL-10 -592 C > A was significantly higher in CAD patients than the control group (P value = 0.043). Moreover, subjects carrying AA genotype had a significantly higher risk of CAD (OR: 1.8, 95%CI: 1.04-3.16), p = 0.03), compared to those with the wild type genotype. The results of meta-analysis of 9336 cases and 8461 controls did not also show any significant association between IL and 10 -592 C > A and CAD in dominant and recessive genetic models but only in co-dominant model when fix effect was applied. CONCLUSION Although our research findings support a significant association of genetic polymorphism in the IL10 gene with cardiovascular diseases, this finding cannot be confirmed in meta-analysis. Further functional analysis and evaluation of this marker in a multicenter setting are needed to establish its value as a risk stratification marker.
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10.
Bitter Taste Receptors and Chronic Otitis Media.
Kaufman, AC, Colquitt, L, Ruckenstein, MJ, Bigelow, DC, Eliades, SJ, Xiong, G, Lin, C, Reed, DR, Cohen, NA
Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery. 2021;(2):290-299
Abstract
OBJECTIVE To evaluate the presence of bitter taste receptors (T2Rs) in the middle ear and to examine their relationship with chronic ear infections. STUDY DESIGN Cross-sectional study. SETTING Tertiary care hospital. METHODS This study enrolled 84 patients being evaluated for otologic surgery: 40 for chronic otitis media (COM) and 44 for other surgical procedures (controls). We collected a small piece of mucosa from 14 patients for mRNA analysis and from 23 patients for immunohistochemistry. A total of 55 patients underwent a double-blind taste test to gauge sensitivity to phenylthiocarbamide, denatonium, quinine, sucrose, and sodium chloride; 47 patients gave a salivary sample for single-nucleotide polymorphism analysis of rs1376251 (TAS2R50) and rs1726866 (TAS2R38). RESULTS Bitter taste receptors were found in all samples, but the repertoire varied among patients. T2R50 was the most consistently identified receptor by mRNA analysis. Its rs1376251 allele was related to susceptibility to COM but not the expression pattern of T2R50. Ratings of bitterness intensity of phenylthiocarbamide, a ligand for T2R38, differed significantly between the COM and control groups. CONCLUSION T2Rs were found within the middle ear of every patient sampled; the rs1376251 allele of TAS2R50 appears to be related to chronic ear infections. These receptors are an intriguing target for future research and possible drug targeting.