Genetic variation in arsenic (+3 oxidation state) methyltransferase (AS3MT), arsenic metabolism and risk of basal cell carcinoma in a European population

Exposure to inorganic arsenic increases the risk of basal cell carcinoma (BCC). Arsenic metabolism is a susceptibility factor for arsenic toxicity, and specific haplotypes in arsenic (+3 oxidation state) methyltransferase (AS3MT) have been associated with increased urinary fractions of the most toxic arsenic metabolite, methylarsonic acid (MMA). The aim of this study is to elucidate the association of AS3MT haplotypes with arsenic metabolism and the risk of BCC. Four AS3MT polymorphisms were genotyped in BCC cases (N = 529) and controls (N = 533) from Eastern Europe with low to moderate arsenic exposure (lifetime average drinking water concentration: 1.3 µg/L, range 0.01–167 µg/L). Urinary metabolites [inorganic arsenic (iAs), MMA, dimethylarsinic acid (DMA)] were analyzed by HPLC‐ICPMS. Five AS3MT haplotypes (based on rs3740400 A/C, rs3740393 G/C, rs11191439 T/C and rs1046778 T/C) had frequencies >5%. Individuals with the CCTC haplotype had lower %iAs (P = 0.032) and %MMA (P = 0.020) in urine, and higher %DMA (P = 0.033); individuals with the CGCT haplotype had higher %MMA (P < 0.001) and lower %DMA (P < 0.001). All haplotypes showed increased risk of BCC with increasing arsenic exposure through drinking water (ORs 1.1–1.4, P values from <0.001 to 0.082), except for the CCTC haplotype (OR 1.0, CI 0.9–1.2, P value 0.85). The results suggest that carriage of AS3MT haplotypes associated with less‐efficient arsenic methylation, or lack of AS3MT haplotypes associated with a more‐efficient arsenic methylation, results in higher risk of arsenic‐related BCC. The fact that AS3MT haplotype status modified arsenic metabolism, and in turn the arsenic‐related BCC risk, supports a causal relationship between low‐level arsenic exposure and BCC. Environ. Mol. Mutagen. 56:60–69, 2015. © 2014 The Authors. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society     

Human NPY promoter variation rs16147:T>C as a moderator of prefrontal NPY gene expression and negative affect

Studies in humans and animals suggest a role for NPY in the mediation of behavioral stress responses. Here, we examined whether the NPY promoter variant rs16147:T>C is functional for expression of NPY in a brain region relevant for behavioral control, anxiety and depression, the anterior cingulate cortex. In silico analysis of DNA structural profile changes produced by rs16147 variation suggests allelic differences in protein binding at the rs16147 site. This was confirmed by electrophoretic mobility shift assay, demonstrating that the rs16147 C‐allele has strongly reduced affinity for a yet unknown factor compared to the T‐allele. Analyzing 107 human post‐mortem brain samples we show that allelic variation at rs16147 contributes to regulation of NPY mRNA and peptide levels in this region. Specifically, the C‐allele leads to increased gene expression. In agreement with the molecular findings, rs16147:T>C is associated with anxiety and depressive symptoms in 314 young adults via a gene x environment interaction with early childhood adversity, replicating the recent finding of rs16147‐C as a risk factor for stress related psychopathology. Our results show the importance of rs16147:T>C for regulation of NPY gene expression and brain function. © 2010 Wiley‐Liss, Inc.     

Dysbindin‐1 gene contributes differentially to early‐ and adult‐onset forms of functional psychosis

Dysbindin‐1 is a relatively ubiquitous protein in the brain which is involved in the modulation of synaptic homeostasis. The dysbindin‐1 gene (DTNBP1) has been associated with schizophrenia and bipolar disorder diagnoses. However, its contribution to the severity of the clinical and neurocognitive expression of these disorders remains controversial. We aimed to explore the association between DTNBP1 and the phenotypes which are more directly linked with the underlying biology, such as age at onset and neurocognitive impairment. The present family sample comprised 894 Caucasian individuals: 268 patients affected by functional psychosis [58% with illness onset before 18 years, mean age at onset (SD): 14.71 (2.10)], 483 parents and 143 siblings. Ten DTNBP1 single nucleotide polymorphisms were genotyped in all individuals and their transmission disequilibrium was tested in relation to: (i) the risk for psychosis; (ii) patients' age at onset; and (iii) familial neurocognitive performance (including IQ estimation and executive functioning). In early‐onset families a 5‐marker haplotype encompassing exons 2–4 and the surrounding introns was significantly over‐transmitted to cases, while in adult‐onset families two haplotypes corresponding to the region between introns 4 and 7 were over‐transmitted to cases. Estimated IQ was associated with the rs760666 marker in the whole sample, whereas a significant association between executive functioning and the rs2619522 marker appeared in early‐onset families. Our findings confirm the role of the dysbindin‐1 gene in the risk for functional psychosis and show a differential haplotypic risk pattern in families with early as opposed to adult onset in the affected offspring. © 2011 Wiley‐Liss, Inc.     

Genome‐wide association analysis of age at onset in schizophrenia in a European‐American sample

We performed a genome‐wide association analysis to identify genetic variants influencing age at onset (AAO) and examine gene × gender interactions for AAO in schizophrenia (SCZ) using a European‐American sample (1,162 cases). Linear regression model in PLINK was used to test for associations with AAO while the GxE option was chosen to test for the influence of gene × gender interactions. The most significant association with AAO was observed with SNP rs7819815 (P = 3.10 × 10^?7) at 8q24.22. The next best signal was at 4q25 in COL25A1 gene (rs17039583, P = 4.30 × 10^?6) and the third region was at 4p16.1 (rs17407555, P = 4.56 × 10^?6, near RAF1P1, and rs4697924, P = 1.23 × 10^?5 within WDR1 gene). Conditional analysis on chromosome 4 indicated that 4p16.1 and 4q25 loci were independent. Furthermore, 2 SNPs (rs16834822 and rs16834824) at 1q43 in RYR2 showed strong associations in the female sample (P = 2.10 × 10^?6 and 2.33 × 10^?6, respectively) and strong gene × gender interactions in influencing AAO (P = 9.23 × 10^?7 and 1.15 × 10^?6, respectively) while the second best region showing gene × gender interaction was at 7q22.3 (rs179863, P = 2.33 × 10^?6). Using an independent sample of 1,068 cases, we could not replicate the associations for above top SNPs; however, we found nominal significance associations for their flanking SNPs (P < 0.05). These findings provide evidence of several genetic variants influencing AAO of SCZ. © 2011 Wiley‐Liss, Inc.     

Evaluation of the relationships of the WBP1L gene with schizophrenia and the general psychopathology scale based on a case–control study

WBP1L is a target of microRNA 137 (miR‐137) and has been considered a candidate gene for schizophrenia (SCZ). To investigate the relationships between WBP1L and SCZ and its related symptom scales, a total of 5,993 Chinese Han subjects, including 2,128 SCZ patients and 3,865 controls, were enrolled. In addition, an independent sample set for replication study including 1,052 SCZ patients and 2,124 controls were also recruited. Thirty‐two tag single nucleotide polymorphisms (SNPs) located within gene region of WBP1L were selected for genotyping and analyzing. The expression quantitative trait loci (eQTL) effects for the targeted SNPs were investigated with gene expression data from multiple human tissues. Rs4147157 (OR = 0.84, p = 1.51 × 10^?5) and rs284854 (OR = 1.14, p = 7.00 × 10^?4) were significantly associated with SCZ disease status and these association signals were replicated in our replication sample. A significant association was identified between rs4147157 and the general (β = ?.66, p = .001) and total (β = ?.8, p = .0042) scores of positive and negative syndrome scale scores in SCZ patients. Both SNPs were significant eQTL for genes around WBP1L in human brain tissues including ARL3 and AS3MT. To conclude, SNPs rs4147157 and rs284854 were associated with SCZ in the Chinese Han population. Additionally, rs4147157 was significantly associated with specific symptom features of SCZ.     

Association analysis of polymorphisms at the interleukin‐1 locus in essential hypertension

Infection with microorganisms such as Helicobacter pylori and Chlamidia pneumoniae has been associated with coronary heart disease (CAD) and hypertension (HT). Infection increases the release of pro‐inflammatory cytokines, thus facilitating interactions that lead to vascular damage and other effects. We hypothesized that genetically determined differences in activity or responsiveness of cytokine(s) might contribute to HT. The interleukin‐1 gene (IL1) cluster on chromosome 2q14 contains three related genes (IL1A, IL1B, and IL1RN) located within a 430‐kb region. These encode IL‐1α and IL‐1β, as well as their endogenous receptor antagonist, IL‐1ra. The IL1RN gene has a penta‐allelic 86‐bp tandem repeat in intron 2. Allele IL1RN* 2 is associated with a wide range of chronic inflammatory and autoimmune conditions, and its combination with the ? 31T variant of an IL1B C(? 31)T polymorphism constitutes a pro‐inflammatory haplotype that leads to vigorous IL‐1β production. We therefore tested each of these polymorphisms for association with HT. Subjects were white Anglo‐Celtic residents of Sydney, Australia. Frequencies of IL1B C(? 31)T genotypes CC, CT, and TT were 0.50, 0.40, and 0.10 in normotensive (NT) and 0.46, 0.46, and 0.08 in HT, respectively (χ² = 1.2, P = 0.55). T allele frequency in NT (0.30) was similar to that in HT (0.31). For the IL1RN variant, frequencies of alleles IL1RN* 1 and * 2 and combined minor alleles * 3, * 4, and * 5 were 0.61, 0.36, and 0.03 in NT and 0.54, 0.36, and 0.10 in HT, respectively (χ² = 11, P = 0.004). In conclusion, no association of the IL1B C(? 31)T with HT was found, whereas combined frequency of the minor alleles of the IL1RN polymorphism was increased in the HT cohort studied. © 2001 Wiley‐Liss, Inc.     

A functional variant on 20q13.33 related to glioma risk alters enhancer activity and modulates expression of multiple genes

Genome‐wide association studies (GWAS) have identified single‐nucleotide polymorphisms (SNPs) associated with glioma risk on 20q13.33, but the biological mechanisms underlying this association are unknown. We tested the hypothesis that a functional SNP on 20q13.33 impacted the activity of an enhancer, leading to an altered expression of nearby genes. To identify candidate functional SNPs, we identified all SNPs in linkage disequilibrium with the risk‐associated SNP rs2297440 that mapped to putative enhancers. Putative enhancers containing candidate functional SNPs were tested for allele‐specific effects in luciferase enhancer activity assays against glioblastoma multiforme (GBM) cell lines. An enhancer containing SNP rs3761124 exhibited allele‐specific effects on activity. Deletion of this enhancer by CRISPR‐Cas9 editing in GBM cell lines correlated with an altered expression of multiple genes, including STMN3, RTEL1, RTEL1‐TNFRSF6B, GMEB2, and SRMS. Expression quantitative trait loci (eQTL) analyses using nondiseased brain samples, isocitrate dehydrogenase 1 (IDH1) wild‐type glioma, and neurodevelopmental tissues showed STMN3 to be a consistent significant eQTL with rs3761124. RTEL1 and GMEB2 were also significant eQTLs in the context of early CNS development and/or in IDH1 wild‐type glioma. We provide evidence that rs3761124 is a functional variant on 20q13.33 related to glioma/GBM risk that modulates the expression of STMN3 and potentially other genes across diverse cellular contexts.     

The CHRNA5/CHRNA3/CHRNB4 Nicotinic Receptor Regulome: Genomic Architecture,Regulatory Variants,and Clinical Associations

Functionally related genes often cluster into a genome region under coordinated regulation, forming a local regulome. To understand regulation of the CHRNA5/CHRNA3/CHRNB4 nicotinic receptor gene cluster, we integrate large‐scale RNA expression data (brain and peripheral) from GTEx (Genotype Tissue Expression), clinical associations (GRASP), and linkage disequilibrium data (1000 Genomes) to find candidate SNPs representing independent regulatory variants. CHRNA3, CHRNA5, CHRNB4 mRNAs, and a well‐expressed CHRNA5 antisense RNA (RP11‐650L12.2) are co‐expressed in many human tissues, suggesting common regulatory elements. The CHRNA5 enhancer haplotype tagged by rs880395 not only increases CHRNA5 mRNA expression in all tissues, but also enhances RP11‐650L12.2 and CHRNA3 expression, suggesting DNA looping to multiple promoters. However, in nucleus accumbens and putamen, but not other brain regions, CHRNA3 expression associates uniquely with a haplotype tagged by rs1948 (located in the CHRNB4 3′UTR). Haplotype/diplotype analysis of rs880395 and rs1948 plus rs16969968 (a nonsynonymous CHRNA5 risk variant) in GWAS (COGEND, UW‐TTURC, SAGE) yields a nicotine dependence risk profile only partially captured by rs16969968 alone. An example of local gene clusters, this nicotinic regulome is controlled by complex genetic variation, with broad implications for interpreting GWAS.     

Lack of association between G‐protein coupled receptor kinase 5 gene and Parkinson's disease

The major component of Lewy Bodies (LB), the pathological hallmark of Parkinson's disease (PD) is α‐synuclein, most prominently phosphorylated at serine 129. G‐protein coupled receptor kinase 5 (GRK5) has been reported to phosphorylate α‐synuclein in vitro, enhancing the α‐synuclein toxicity to dopaminergic neurons in Drosophila model. Moreover, GRK5 was found in LBs from brain of PD patients. A genetic association study performed in the Japanese population revealed haplotypic association of the GRK5 gene with susceptibility to sporadic PD. We aimed at investigating whether four polymorphisms within the GRK5 gene (rs871196, rs2420616, rs7069375, rs4752293) could represent a risk factor for sporadic PD in Southern Italy. We genotyped 446 patients with PD and 450 controls for these markers and did not find any significant association with the disease at allelic, genotypic and haplotypic level. Our results indicate that the GRK5 gene does not confer risk to sporadic PD in our sample from Southern Italy. © 2010 Wiley‐Liss, Inc.     

Gene‐based evaluation of low‐frequency variation and genetically‐predicted gene expression impacting risk of keloid formation

Keloids are benign dermal tumors occurring approximately 20 times more often in individuals of African descent as compared to individuals of European descent. While most keloids occur sporadically, a genetic predisposition is supported by both familial aggregation of some keloids and large differences in risk among populations. Despite Africans and African Americans being at increased risk over lighter‐skinned individuals, little genetic research exists into this phenotype. Using a combination of admixture mapping and exome analysis, we reported multiple common variants within chr15q21.2‐22.3 associated with risk of keloid formation in African Americans. Here we describe a gene‐based association analysis using 478 African American samples with exome genotyping data to identify genes containing low‐frequency variants associated with keloids, with evaluation of genetically‐predicted gene expression in skin tissues using association summary statistics. The strongest signal from gene‐based association was located in C15orf63 (P‐value = 6.6 × 10^?6) located at 15q15.3. The top result from gene expression was increased predicted DCAF4 expression (P‐value = 5.5 × 10^?4) in non–sun‐exposed skin, followed by increased predicted OR10A3 expression in sun‐exposed skin (P‐value = 6.9 × 10^?4). Our findings identify variation with putative roles in keloid formation, enhanced by the use of predicted gene expression to support the biological roles of variation identified only though genetic association studies.     

A functional variant in the miR‐142 promoter modulating its expression and conferring risk of Alzheimer disease

Noncoding RNAs have been widely recognized as essential mediators of gene regulation. However, in contrast to protein‐coding genes, much less is known about the influence of noncoding RNAs on human diseases. Here we examined the association of genetic variants located in primary microRNA sequences and long noncoding RNAs (lncRNAs) with Alzheimer disease (AD) by leveraging data from the largest genome‐wide association meta‐analysis of late‐onset AD. Variants annotated to 5 miRNAs and 10 lncRNAs (in seven distinct loci) exceeded the Bonferroni‐corrected significance threshold (p < 1.02 × 10^?6). Among these, a leading variant (rs2526377:A>G) at the 17q22 locus annotated to two noncoding RNAs (MIR142 and BZRAP1‐AS) was significantly associated with a reduced risk of AD and fulfilled predefined criteria for being a functional variant. Our functional genomic analyses revealed that rs2526377 affects the promoter activity and decreases the expression of miR‐142. Moreover, differential expression analysis by RNA‐Seq in human iPSC‐derived neural progenitor cells and the hippocampus of miR‐142 knockout mice demonstrated multiple target genes of miR‐142 in the brain that are likely to be involved in the inflammatory and neurodegenerative manifestations of AD. These include TGFBR1 and PICALM, of which their derepression in the brain due to reduced expression levels of miR‐142‐3p may reduce the risk of AD.     

Genome‐wide analysis of allelic imbalances reveals 4q deletions as a poor prognostic factor and MDM4 amplification at 1q32.1 in hepatoblastoma

In a single‐nucleotide polymorphism array‐based analysis of 56 hepatoblastoma (HB) tumors, allelic imbalances were detected in 37 tumors (66%). Chromosome gains were found in 1q (28 tumors), 2q (24), 6p (8), 8q (8), 17q (6), and 20pq (10), and losses in 1p (6), 4q (9), and 16q (4). Fine mapping delineated the shortest overlapping region (SOR) of gains at 1q32.1 (1.3 Mb) and 2q24.2‐q24.3 (4.8 Mb), and losses at 4q34.3‐q35.2 (8.7 Mb) and 4q32.3 (1.6 Mb). Uniparental disomy of 11pter‐11p15.4 (IGF2) and loss of 11pter‐p14.1 were found in 11 and 2 tumors, respectively. Expression of HTATIP2 (11p15.1) was absent in 9 of 20 tumors. Amplification was identified in four tumors at 1q32.1, where the candidate oncogene MDM4 is located. In the 4q32.3‐SRO, ANXA10S, a variant of the candidate tumor suppressor ANXA10, showed no expression in 19 of 24 tumors. Sequence analysis of ANXA10S identified a missense mutation (E36K, c.106G>A) in a HB cell line. Multivariate analysis revealed that both 4q deletion and RASSF1A methylation (relative risks: 4.21 and 7.55, respectively) are independent prognostic factors. Our results indicate that allelic imbalances and gene expression patterns provide possible diagnostic and prognostic markers, as well as therapeutic targets in a subset of HB. © 2010 Wiley‐Liss, Inc.     

The Role of microRNA‐146a (miR‐146a) and its Target IL‐1R‐Associated Kinase (IRAK1) in Psoriatic Arthritis Susceptibility

MicroRNAs have shown different expression patterns in immune diseases. The present study explores the association of miRNA‐146a variant rs2910164 and of two IRAK1 (target of miR‐146a) polymorphisms rs3027898 and rs1059703 with psoriasic arthritis (PsA). Twenty‐nine PsA and 66 controls were enrolled in the study. To study if the statistical significant differences between patients with PsA and controls are independent to psoriasis, we expanded the study in 49 patients with ankylosing spondylitis (AS). Strong statistical significant difference was observed in IRAK1 rs3027898 polymorphism distribution between patients with PsA and controls (P = 0.003), as between patients with AS and controls (P < 0.001). Marginally significant difference was observed in distribution of IRAK1 rs1059703 genotypes between patients with PsA and controls (P = 0.058), but no difference was observed in miRNA‐146a rs2910164 distribution (P = 0.394). This is the first study that addresses IRAK1 rs3027898 polymorphism association with PsA susceptibility, but further studies could help to understand the extent of the proposed association.     

Genome‐wide compound heterozygosity analysis highlighted 4 novel susceptibility loci for congenital heart disease in Chinese population

Genome‐wide association studies (GWASs) have achieved great success in deciphering the genetic cause of congenital heart disease (CHD). However, the heritability of CHD remains to be clarified, and numerous genetic factors responsible for occurrence of CHD are yet unclear. In this study, we performed a genome‐wide search for relaxed forms of compound heterozygosity (CH) in association with CHD using our existing GWAS data including 2265 individuals (957 CHD cases and 1308 controls). CollapsABEL was used to iteratively test the association between the CH genotype and the CHD phenotype in a sliding window manner. We highlighted 17 genetic loci showing suggestive CH‐like associations with CHD (P < 5 × 10^?8), among which 4 genetic loci had expression quantitative trait loci (eQTL) effects in blood (P_eQTL < 0.01). After conditional association analysis, each loci had only 1 independently effective signal reaching the significance threshold (rs2071477/rs3129299 at 6p21.32, P = 2.47 × 10^?10; rs10773097/rs2880921 at 12q24.31, P = 3.30 × 10^?8; rs73032040/rs7259476 at 19q13.11, P = 1.14 × 10^?8; rs10416386/rs4239517 at 19q13.31, P = 1.15 × 10^?9), together explained 7.83% of the CHD variance. Among these 4 associated loci, outstanding candidates for CHD‐associated genes included UBC, CFM2, ZNF302, LYPD3 and CADM4. Although replication studies with larger sample size are warranted, the first CH GWAS of CHD may extend our current knowledge of the genetic contributions to CHD in the Han Chinese population.     

The rs6983267 SNP and long non‐coding RNA CARLo‐5 are associated with endometrial carcinoma

The single nucleotide polymorphism (SNP) rs6983267 and cancer‐associated region long non‐coding RNA (CARLo‐5) are associated with various human cancers. This study aimed to investigate the expression of CARLo‐5 in endometrial carcinoma (EC) and its relationship with clinicopathological features and patient survival. The association of the rs6983267 SNP with EC risk and its involvement in the regulation of CARLo‐5 expression in EC were investigated. The rs6983267 SNP was genotyped by polymerase chain reaction (PCR) and ligase detection reaction in 543 EC patients and 584 controls. The expression of CARLo‐5 in 108 EC tissues and 66 normal endometrial tissues (NETs) was determined using quantitative real‐time PCR. The genotype and allele distributions of the rs6983267 SNP differed significantly between patients and controls. There was a significant correlation between the rs6983267 genotypes and lymph node metastasis of EC patients (P = 0.026). CARLo‐5 expression was significantly higher in EC tissues than in NETs (P < 0.001) and significantly associated with FIGO stage (P = 0.029) and lymph node metastasis (P = 0.030). Patients with high CARLo‐5 expression had significantly shorter overall survival than those with low CARLo‐5 expression (P = 0.003). The rs6983267 genotype was significantly correlated with CARLo‐5 expression (P < 0.05). In conclusion, CARLo‐5 was identified as a pro‐oncogenic lncRNA that may play an important role in EC progression and represent a prognostic marker for EC. The expression of CARLo‐5 was significantly correlated with the rs6983267 genotype associated with increased susceptibility to EC. Environ. Mol. Mutagen. 57:508–515, 2016. © 2016 Wiley Periodicals, Inc.