Association between genetic variant rs2267716 of CRHR2 gene with colorectal cancer

Colorectal cancer (CRC) is the third most common cancer and one of the main causes of death around the world. Multiple lines of evidence have suggested the role of the corticotropin-releasing hormone (CRH) family in CRC induction, including the low expression of corticotropin-releasing hormone receptor 2 (CRHR2), which is an angiogenesis inhibitor and inflammatory modulator. Previous research suggests that CRHR2 expression in colonic intestinal cells can regulate migration, proliferation and apoptosis through the modulation of several pathways. The aim of this study was to analyze the association of the rs10250835, rs2267716 and rs2267717 variants of CRHR2 gene with CRC in the Mexican population in order to consider its predictive value in CRC. This cross-sectional study included a group of 187 unrelated patients with sporadic CRC and a control group of 191 healthy blood donors. DNA extraction from peripheral blood was carried out using the Miller method. Identification of the rs10250835 variant was performed using PCR-restriction fragment length polymorphism (RFLP) and the rs2267716 and rs2267717 variants using TaqMan allelic discrimination assay. The minor allele homozygous CC of the rs2267716 variant of CRHR2 showed significant difference between CRC and control group (p=0.025), as well as the GCA haplotype (p=0.007), corresponding to the rs10250835, rs2267716 and rs2267717 variants, respectively. Our results suggest that the rs2267716 variant and GCA haplotype of CRHR2 represent a risk factor for CRC development in Mexican patients.

VDR Polymorphisms in Autoimmune Connective Tissue Diseases: Focus on Italian Population

Vitamin D is an important hormone involved in various physiologic processes, and its activity is linked to binding with vitamin D receptor (VDR). Genetic polymorphisms in the VDR gene could modulate the expression or function of the receptor and, consequently, alter the effects of vitamin D. Variants in VDR gene have been associated with susceptibility to many illnesses sensitive to vitamin D administration and to autoimmune disorders, but no data are available regarding autoimmune connective tissue diseases in Italian population. We analyzed three VDR polymorphisms in 695 Italian patients with autoimmune connective tissue diseases (308 with systemic lupus erythematosus (SLE), 195 with primary Sjogren’s syndrome (pSS), and 192 with rheumatoid arthritis (RA)) and in 246 healthy controls with the aim to evaluate a possible association of VDR SNPs with susceptibility to these diseases in the Italian population. Genotyping of rs2228570, rs7975232, and rs731236 in VDR gene was performed by an allelic discrimination assay. A case/control association study and a genotype/phenotype correlation analysis have been performed. We observed a higher risk to develop SLE for rs2228570 TT genotype ( P = 0.029 , OR = 1.79 ). No association was observed between susceptibility to pSS or RA and this SNP, although this variant is significantly less present in RA patients producing autoantibodies. For rs7975232 SNP, we observed a significant association of the variant homozygous genotype with SLE ( P = 0.009 , OR = 1.82 ), pSS ( P = 0.046 , OR = 1.66 ), and RA ( P = 0.028 , OR = 1.75 ) susceptibility. Moreover, we reported associations of this genotype with clinical phenotypes of SLE and pSS. Lastly, the GG genotype of rs731236 was associated with a lower RA susceptibility ( P = 0.045 , OR = 0.55 ). Our results show that the explored VDR polymorphisms are significantly associated with autoimmune connective tissue disorders and support the hypothesis that the genetic variability of VDR gene may be involved in susceptibility to these diseases in Italian population.

Beclometasone but not fluticasone modulates PDGFD expression in the H295R adrenal cell line.

BackgroundAdrenal suppression is a clinically concerning side effect of inhaled corticosteroid (ICS) treatment in patients with asthma. Increased susceptibility to ICS-induced adrenal suppression has previously been identified in those with the rs591118 polymorphism in Platelet Derived Growth Factor D (PDGFD). The mechanism underpinning this relationship is not known.MethodsH295R cells were genotyped for rs591118 using a validated Taqman PCR allelic discrimination assay. H295R cell viability was determined after treatment with beclometasone and fluticasone (range 0-330 μM). Cortisol was measured in cell culture medium using competitive enzyme immunoassay.ResultsPDGFD protein expression in H295R cells was confirmed using Western blotting. When ACTH and forskolin were added to H295R cells, a reduction in PDGFD expression was seen which was then restored by incubation with prochloraz, a known inhibitor of steroidogenesis.A dose-dependent, decrease in PDGFD expression was observed with beclometasone (over a 24 h incubation period) but not with beclometasone incubations beyond 24 hour nor with fluticasone (at 24 or 48 hours).ConclusionsH295R cells express PDGFD protein which can be modulated by incubation with steroidogenesis agonists and antagonists and additionally with exogenous beclometasone.

Association of PNPLA3 I148M with liver disease biomarkers in Latinos

Introduction. Liver disease accounts for approximately 2 million deaths per year worldwide. The majority of liver diseases are due to complications of cirrhosis, viral hepatitis, and hepatocellular carcinoma. Increased levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) may indicate liver disease. Moreover, there are additional noninvasive liver fibrosis indices that help to estimate liver damage, including AST to ALT ratio, AST to platelet ratio index (APRI), fibrosis-4 (FIB-4) score, and nonalcoholic fatty liver disease (NAFLD) fibrosis score. The aims of the present study were to (1) perform an association analysis of the patatin-like phospholipase domain containing 3 (PNPLA3) I148M (rs738409) variant with ALT, AST, and various liver fibrosis indices, and (2) determine whether there are gender related-differences in these associations. Methods. We obtained demographic, anthropometric, and metabolic phenotypes from Latino adult participants (n = 503, 64% female, 36.4 ± 0.5 years) from the Arizona Insulin Resistance (AIR) registry. SNP genotyping of I148M was performed using the TaqMan allelic discrimination assay. We used linear regression for the association analyses of the genotypes with ALT, AST, and the various liver fibrosis indices. We included genotype, age, body mass index (BMI), and alcohol status in the linear regression model. Results. The variant I148M was in Hardy-Weinberg equilibrium, with genotype distribution: non-risk CC = 118, heterozygous CG = 246, and risk GG = 139. The G allele was significantly associated with increased ALT and AST levels (p = 7.8 x 10-7 and p = 9.7 x 10-6, respectively). Moreover, we showed that the G allele was significantly associated with higher APRI (p = 3.7 x 10-7) and FIB-4 score (p = 4.1 x 10-3). When we analyzed the data by gender, we observed similar significant trends for ALT, AST, and APRI (all, p < 0.01). In females, the G allele was significantly associated with increased FIB-4 score (p = 6.9 x 10-3), which was not observed in the males (p > 0.05). There was no association of the I148M variant with AST/ALT ratio nor NAFLD risk score, whether analyzed in all adults or by gender. Discussion/Conclusion. Our findings provide additional evidence of an association of PNPLA3 I148M with several liver disease biomarkers in male and female Latinos residing in the Southwest of the United States.

No Association of Eight TNFAIP3 Single Nucleotide Variants to Rheumatoid Arthritis in Native Mexicans

Rheumatoid arthritis (RA) is a chronic inflammatory disease of autoimmune origin associated with many genetic traits, including genes related to the control of inflammation. The A20 protein, encoded by the TNFAIP3 gene, is a negative regulator of NF-kB-mediated inflammation. Several single nucleotide variants (SNVs) of TNFAIP3 are associated with susceptibility to RA in different ethnic groups, but not in Chileans, the only Latin Americans studied thus far. Objective. To examine the association of eight TNFAIP3 SNVs, four of them not previously studied, with RA in Mexican patients. Materials . We studied 471 RA patients (ACR-EULAR 2010) and eight TNFAIP3 SNVs: including, rs10499194C/T, rs6920220G/A and rs2230926T/G, which are associated with RA in European and Asian patients, in addition to rs373421182G/C, rs139054966T/G, rs5029924C/T, rs59693083A/G and rs61593413T/A, not previously examined in RA. All SNVs were evaluated by means of an allelic discrimination assay and TaqMan probes. Results. The allelic and genotypic frequencies of all SNVs examined were similar between cases and controls, and none of them was associated with RA under the allelic, codominant, dominant, and recessive models was observed. Conclusion. Our data indicate that the TNFAIP3 SNVs evaluated herein are not risk factors for RA in Mexican subjects.

Association of HER1 and HER2 Gene Variants in the Predisposition of Colorectal Cancer

Background. Colorectal cancer (CRC) is a major health concern worldwide. A series of sequential accumulation of genetic and epigenetic changes are responsible for the initiation and progression of diseases via the normal > adenoma > carcinoma sequence. Genetic variants in crucial cancer-causing genes are known to mediate the risk of cancer. Objective. In this case-control study, we examined single nucleotide polymorphism (SNP) in HER1 (rs763317 and rs3752651) and HER2 (rs1136201 and rs1058808) genes to assess their role in the susceptibility of CRC in a Saudi population. Methods. TaqMan allelic discrimination assay was utilized to identify the genotypes in 163 normal and 143 CRC patients. Results. In the overall analysis, the rs3752651 and rs1136201 were significantly associated with the risk of CRC. Although none of the examined SNPs had any impact on the age at which CRC was diagnosed, interestingly, three SNPs showed a significant association based on gender. The rs3752651 conferred significant protection only in men, whereas rs1136201 diminished the risk and rs1058808 considerably increased the susceptibility of CRC only in women. Conclusions. Our result suggests that these SNPs in HER1 and HER2 after validation in larger cohorts of different ethnicities may be utilized as genetic screening markers for predicting colorectal cancer predisposition.

Differentiating Pigs from Wild Boars Based on NR6A1 and MC1R Gene Polymorphisms

This preliminary study aimed to differentiate domestic pigs from wild boars based on MC1R and NR6A1 polymorphisms and to identify admixture between these genomes. We studied samples obtained from wild boars from two regions of Poland and five pig breeds: Polish Landrace, Polish Large White, Złotnicka White, Pulawska and Duroc. Along the MC1R gene sequence, we identified four polymorphic loci comprising three codons. The “wild type” allele was primarily found in wild boar but also in the Duroc and Złotnicka White breeds. Non-wild type alleles were identified in the vast majority of domestic pig samples and in two wild boar samples. Based on MC1R profiles, we conducted a population study, and revealed admixture between both genomes using STRUCTURE and NETWORK Software. Interestingly, an allelic discrimination assay with NR6A1 g.748C > T TaqMan probes revealed a clear separation of samples into two groups: wild boar samples representing the C allele and domestic breeds representing the T allele. Based on the obtained results, we conclude that NR6A1 g.748C > T is an effective marker for differentiating between wild boars and domestic pigs, where this is supported by MC1R data, to identify admixed profiles. We recommend that a larger sample of genomes is studied to verify this method.

Polymorphism of NAT2, PXR, ABCB1, and GSTT1 genes among tuberculosis patients of North Eastern States of India

Background: Anti-tuberculosis drug-induced liver injury (AT-DILI) in tuberculosis (TB) patients has been linked to polymorphisms in genes encoding drug metabolism enzymes and proteins. Objective: This study aimed to monitor polymorphisms of NAT2, PXR, ABCB1, and GSTT1 genes in TB patients from three states (Manipur, Tripura, and Nagaland) in the North Eastern Region of India. Methods: Genomic DNA was isolated from the whole blood samples of TB patients (n=219; Manipur:139; Tripura: 60; Nagaland: 20). The TaqMan allelic discrimination assay and statistical tools were used to investigate single nucleotide polymorphisms (SNP) patterns in NAT2, PXR, ABCB1, and GSTT1 genes. Results: In the study population, ten distinct genotypes of the NAT2 gene and single variation in the PXR, ABCB1, and GSTT1 genes were identified. A strong linkage disequilibrium (LD) was observed between rs1801280 and rs1799931 of the NAT2 gene. Majority of the study populations were intermediate (~46.1%), rest were either slow acetylators (~35.6%) or fast acetylators. Interestingly, ~55% of the TB patients in Tripura were slow acetylators and majority in Manipur and Nagaland were of intermediate acetylator genotypes. For all of the markers investigated, the population had a greater prevalence of ancestral alleles and genotypes. According to a combinational study of the genotypes linked to AT-DILI, ~26.1% of the population possessed the risk genotypes. Conclusion: These TB patients from north eastern states of India were found as carriers of the ancestral alleles and genotypes. And the risk for AT-DILI during TB treatment is low. Expanding such studies with additional markers and larger sample sizes will be useful to generate precise population-specific pharmacogenomics details for efficient TB management.

Lack of Association of LPA Gene Polymorphisms with Coronary Artery Disease in Pakistani Subjects

Coronary artery disease (CAD) is the leading cause of death worldwide. Pakistan faces a high epidemic of CAD, and the disease burden is increasing with the passage of time. Several genetic markers have been reported to be significantly associated with CAD; one of them is the lipoprotein A gene. The aim of the current investigation was to genotype the LPA gene SNPs, rs3798220 and rs10455872, in Pakistani subjects with CAD in a case control study design. The genotyping was done by TaqMan allelic discrimination assay. The results showed that the cases had significantly higher prevalence of diabetes (64.6%), hypertension (62.1%), and smoking habits (29.5%). The level of cholesterol in cases was higher than in controls ( 208.25 ± 54.11 vs. 175.34 ± 43.51 , p ≤ 0.0001 ). The LDL-C was higher in cases than in controls ( 104.62 ± 37.94 vs. 77.05 ± 21.17 , p ≤ 0.0001 ). Similarly, triglycerides were also higher in cases than in controls ( 214.51 ± 74.60 vs. 190.54 ± 70.26 , p ≤ 0.0001 ), whereas HDL-C was lower in cases than in controls ( 45.13 ± 11.63 vs. 67.9 ± 17.57 , p ≤ 0.0001 ). For rs3798220, the risk allele (C) frequency was 0.005 in cases and 0.002 in controls. For rs10455872, the risk allele (G) frequency was 0.017 in cases and 0.014 in controls. The risk allele frequencies were not significantly different between cases and controls ( p > 0.05 ). In conclusion, these two LPA SNPs do not contribute significantly to CAD progression and cannot be used as independent risk factors for CAD in Pakistani population.

Single Nucleotide Polymorphisms of Indoleamine 2,3-Dioxygenase Influenced the Age Onset of Parkinson’s Disease

Aims Earlier studies reported alterations of the kynurenine (KYN) pathway of tryptophan (TRP) metabolism in Parkinson&rsquo;s disease (PD). The first rate-limiting enzymes indoleamine 2,3- dioxygenase (IDO) and tryptophan dioxygenase were observed upregulated, resulting elevated KYN/TRP ratios in the serum and cerebrospinal fluid samples of patients with PD. An increasing number of single nucleotide polymorphisms (SNPs) has been identified in a population of PD. However, little is known if genetic variations of the IDO contribute to disturbance of the KYN metabolism in and the pathogenesis of PD. Main methods SNP analysis of IDO1 was performed by allelic discrimination assay with fluorescently labelled TaqMan probes and a subgroup analysis was conducted according to the age of PD onset. The frame shifts variant rs34155785, intronic variant rs7820268, and promotor region variant rs9657182 SNPs of 105 PD patients without comorbidity were analyzed and compared to 129 healthy controls. Key findings No significant correlation was found in three SNPs between PD patients and healthy controls. However, the subgroup analysis revealed that A alleles of rs7820268 SNP or rs9657182 SNP carriers contribute to later onset of PD than non-carriers. Significance The study suggested that SNPs of IDO1 influenced the age onset of PD and genotyping of SNPs in certain alleles potentially serves as a risk biomarker of PD.