CD14 polymorphisms,microbial exposure and allergic diseases: a systematic review of gene–environment interactions

Asthma and allergy may develop as a result of interactions between environmental factors and the genetic characteristics of an individual. This review aims to summarize the available evidence for, and potential effects of, an interaction between polymorphisms of the CD14 gene and exposure to microbes on the risk of asthma and allergic diseases. We searched PubMed, MEDLINE and Global Health databases, finding 12 articles which met inclusion criteria. Most studies reported a significant interaction between CD14 polymorphisms and microbial exposure. When stratified by age at microbial exposure (early life vs adult life), there was evidence of a protective effect of gene–environment interaction against atopy in children, but not adults. We also found different effects of interaction depending on the type of microbial exposures. There was no strong evidence for asthma and eczema. Future studies should consider a three‐way interaction between CD14 gene polymorphisms, microbial exposures and the age of exposure.     

Polymorphisms in drug‐metabolizing enzymes and risk to head and neck cancer: Evidence for gene–gene and gene–environment interaction

A case–control study involving 750 cases with squamous‐cell carcinoma of the head and neck (HNSCC) and an equal number of healthy controls was initiated to investigate the association of polymorphisms in the drug metabolizing genes cytochrome P450 1A1 (CYP1A1), CYP1B1, CYP2E1 and glutathione S‐transferase M1 (GSTM1) with the risk of developing cancer. Attempts were also made to identify the role and nature of gene–gene and gene–environment interactions in modifying the susceptibility to HNSCC. Polymorphisms in drug metabolizing CYPs or GSTM1 showed modest associations with cancer risk. However, cases carrying haplotypes with variant alleles of both CYP1A1*2A and *2C or CYP1B1*2 and *3 or CYP2E1*5B and *6 were at significant risk of developing HNSCC. Likewise, cases carrying a combination of variant genotypes of CYPs and GSM1 (null) were at higher risk (up to 5‐fold) of developing HNSCC. HNSCC risk also increased several‐fold in cases carrying variant genotypes of CYPs who were regular tobacco smokers (8–18‐fold), tobacco chewers (3–7‐fold), or alcohol users (2–4‐fold). Statistical analysis revealed a more than multiplicative interaction between combinations of the variant genotypes of CYPs and GSTM1 (null) and between variant genotypes and tobacco smoking or chewing or alcohol consumption, in both case–control and case‐only designs. The data thus suggest that although polymorphisms in carcinogen‐metabolizing CYPs may be a modest risk factor for developing HNSCC, gene–gene, and gene–environment interactions play a significant role in modifying the susceptibility to HNSCC. Environ. Mol. Mutagen. 55:134–144, 2014. © 2013 Wiley Periodicals, Inc.     

Genetic variation in UGT genes modify the associations of NSAIDs with risk of colorectal cancer: Colon cancer family registry

The use of non‐steroidal anti‐inflammatory drugs (NSAIDs) is associated with reduced risk of colorectal neoplasia. Previous studies have reported that polymorphisms in NSAID‐metabolizing enzymes central to NSAID metabolism including UDP‐glucuronosyltransferases (UGT) and cytochrome P450 (CYP) 2C9 may modify this protective effect. We investigated whether 35 functionally relevant polymorphisms within CYP2C9 and UGT genes were associated with colorectal cancer risk or modified the protective effect of NSAIDs on colorectal cancer susceptibility, using 1,584 colorectal cancer cases and 2,516 unaffected sibling controls from the Colon Cancer Family Registry. A three‐SNP genotype in UGT1A6 (G–A–A; Ala7–Thr181–Arg184) and the Asp85 variant in UGT2B15 increased the risk of colorectal cancer (OR 3.87; 95% CI 1.04–14.45 and OR 1.34; 95% CI 1.10–1.63, respectively). We observed interactions between UGT1A3 Thr78Thr (A>G) and NSAID use (P‐interaction = 0.02), a three‐SNP genotype within UGT2B4 and ibuprofen use (P‐interaction = 0.0018), as well as UGT2B15 Tyr85Asp (T>G) and aspirin use (P‐interaction = 0.01). The interaction with the UGT2B4 and the UGT2B15 polymorphisms were noteworthy at the 25% FDR level. This study highlights the need for further pharmacogenetic studies to identify individuals who might benefit from NSAID use as part of developing effective strategies for prevention of colorectal neoplasia. © 2014 Wiley Periodicals, Inc.     

UGT1A1 基因多态性与转移性结直肠癌伊立替康化疗毒性及疗效的关系

目的: 探讨 UGT1A1 ^*28和 UGT1A1 ^*6基因多态性与伊立替康治疗转移性结直肠癌患者的不良反应和疗效之间的关系。方法: 外周血中抽提基因组DNA,采用PCR扩增目的基因片段,直接测序法分析2010年4月至2012年3月在我院做基因检测的207例消化道肿瘤患者 UGT1A1 ^*28和 UGT1A1 ^*6基因多态性的分布情况,并对其中56例采用含伊立替康方案化疗的转移性结直肠癌患者出现的不良反应情况、肿瘤进展时间及化疗疗效进行观察并记录,比较不同基因型患者之间的差异。结果: 207例消化道肿瘤患者中, UGT1A1 ^*28位点野生型TA6/6有164例(79.2%),杂合突变型TA6/7有41例(19.8%),纯合突变型TA7/7有2例(1.0%); UGT1A1 ^*6位点野生型G/G有154例(74.4%),杂合突变型G/A有51例(24.6%),纯合突变型A/A有2例(1.0%)。在56例转移性结直肠癌患者中,^*6位点突变型(G/A和A/A)可以增加发生3级以上腹泻(38.9% vs 7.9%,P<0.05)和中性粒细胞减少(61.1% vs 29.0%,P<0.05)的风险;^*28位点突变型(6/7和7/7)可以增加发生3级以上血小板减少(33.3% vs 2.1%,P<0.05)的风险;肿瘤进展时间和化疗疗效在^*28和^*6位点各基因型之间差异无统计学意义。结论: 在采用含伊立替康方案化疗的转移性结直肠癌患者中, UGT1A1 ^*6位点突变型增加发生3级以上腹泻和中性粒细胞减少的风险; UGT1A1 ^*28位点突变型增加发生3级以上血小板减少的风险。     

Haplotype analysis of three polymorphisms of the COL2A1 gene and associations with generalised radiological osteoarthritis

It was investigated whether radiographic osteoarthritis (ROA) is associated with specific haplotypes of the COL2A1 gene. Radiographs of knees, hips, hands, and spine were scored for the presence of ROA in subjects of 55–70 years from a population-based cohort study, the Rotterdam study. Cases had ROA in 3 or more joint groups; controls, from the same population, had ROA in less than 3 joint groups. Allele frequencies of 3 dimorphisms ( Hae III, Hin dIII, Mae II) and a VNTR polymorphism of the COL2A1 gene were determined. The VNTR allele 14R2 and the Hin dIII polymorphism showed a significant association. Haplotype analysis of the Hae III, Hin dIII and VNTR polymorphisms showed that a specific haplotype (1-2-14R2) is strongly associated with ROA in 3 or more joint groups (OR = 5.3, 95% CI 2.3–12.7). Our results suggest that a specific haplotype of the COL2A1 locus may predispose to generalised ROA.     

Catalog of 86 single-nucleotide polymorphisms (SNPs) in three uridine diphosphate glycosyltransferase genes: UGT2A1, UGT2B15, and UGT8

We report here three high-density maps of variations found among 48 Japanese individuals in three uridine diphosphate glycosyltransferase (UGT) genes, UGT2A1, UGT2B15, and UGT8. A total of 86 single-nucleotide polymorphisms (SNPs) were identified through systematic screening of genomic regions containing these genes: 8 in 5' flanking regions, 7 in coding regions, 67 in introns, 3 in 3' untranslated regions, and 1 in a 3' flanking region. We also discovered 14 variations of other types. Of the 86 SNPs, 63 (73%) were considered to be novel on the basis of comparison of our data with the Database of SNPs (dbSNP) of the National Center for Biotechnology Information. Among the seven SNPs identified in exonic sequences, five were non-synonymous changes that would result in amino-acid substitutions. The collection of SNPs derived from this study will serve as an additional resource for studies of complex genetic diseases and responsiveness to drug therapy.     

Genetic and gene–environment interaction effects on preschoolers' social behaviors

This study examined effects from a specific dopamine receptor gene (DRD4), environmental influences from parents and peers, and the interaction between them, on aggressive and prosocial behaviors of preschoolers. Children were classified as DRD4‐L (n = 27) if they had at least one DRD4 allele with six to eight repeats and as DRD4‐S (n = 35) if not. Parent–child interactions were coded when children were 3–4 years old. Peer interaction data and parent questionnaires were collected at age 5. DRD4‐L children shared less with each other and parents were less sensitive during parent–twin triadic interactions. Also, genotype interacted with peer aggression to affect children's aggression during a peer play interaction at age 5, and genotype interacted with prior parental sensitivity to affect later externalizing problems. Thus, children having a certain genetic disposition may be more sensitive to certain environmental stimuli and therefore more likely to exhibit aggressive behaviors under more stressful circumstances. © 2009 Wiley Periodicals, Inc. Dev Psychobiol 51: 451–464, 2009     

Copy‐number variations (CNVs) of the human sex steroid metabolizing genes UGT2B17 and UGT2B28 and their associations with a UGT2B15 functional polymorphism

UGT2B17 and UGT2B28 are among the most commonly deleted genes in humans and encode members of the uridine diphosphate (UDP)‐glucuronosyltransferase 2B (UGT2B) subfamily. They are involved, along with UGT2B15, in the catabolism of sex‐steroid hormones. Despite the recent biomedical interest in UGT2B17 and UGT2B28 copy‐number variations (CNVs) within human populations, the impact of their gene dosage has been hampered by the lack of precise molecular identification of the common deletion breakpoints within high homology sequence regions on chromosome 4. We have characterized these common deletions and report their coexistence in Caucasians, along with the p.D85Y (rs1902023:G>T) functional polymorphism of UGT2B15. Segmental duplications of 4.9 kb for UGT2B17 and 6.8 kb for UGT2B28 comprise purine‐rich recombination sites located 117 kb and 108 kb apart on both ends of the deletions. CNVs of UGT2B17 and UGT2B28 occur in Caucasians at 27% and 13.5%, respectively. While only 43% have two copies of both genes, 57% harbor at least one deletion. Their co‐occurrence on 5% of chromosomes creates a 225‐kb genomic gap. CNVs of both UGT2B17 and UGT2B28, with the co‐occurrence of UGT2B15:p.D85Y, generate seven distinct haplotypes. Restricting the analyses to CNV of the UGT2B17 gene without evaluating UGT2B28 CNV, along with the genotype of UGT2B15, may over‐ or underestimate the impact of each gene under physiological conditions or disease states. Hum Mutat 30:1–10, 2009. © 2009 Wiley‐Liss, Inc.     

GSTP1 is a hub gene for gene–air pollution interactions on childhood asthma

There is growing evidence that multiple genes and air pollutants are associated with asthma. By identifying the effect of air pollution on the general population, the effects of air pollution on childhood asthma can be better understood. We conducted the Taiwan Children Health Study (TCHS) to investigate the influence of gene–air pollution interactions on childhood asthma. Complete monitoring data for the ambient air pollutants were collected from Taiwan Environmental Protection Agency air monitoring stations. Our results show a significant two‐way gene–air pollution interaction between glutathione S‐transferase P (GSTP1) and PM₁₀ on the risk of childhood asthma. Interactions between GSTP1 and different types of air pollutants have a higher information gain than other gene–air pollutant combinations. Our study suggests that interaction between GSTP1 and PM₁₀ is the most influential gene–air pollution interaction model on childhood asthma. The different types of air pollution combined with the GSTP1 gene may alter the susceptibility to childhood asthma. It implies that GSTP1 is an important hub gene in the anti‐oxidative pathway that buffers the harmful effects of air pollution.     

The associations between CYP24A1 polymorphisms and cancer susceptibility: A meta-analysis and trial sequential analysis

Purpose

Published data have shown that vitamin D may have a protective effect on cancer development. CYP24A1, the main enzyme responsible for the degradation of active vitamin D, plays an important role in many cancer related cellular processes. Up to now, relationships between CYP24A1 polymorphisms and cancer susceptibility have been widely investigated, whereas the results are inconsistent. The aim of present meta-analysis was to explore the associations between CYP24A1 polymorphisms and cancer susceptibility.

The effect of CYP1A1 polymorphisms on the risk of lung cancer: a global meta-analysis based on 71 case-control studies

The cytochrome P450 1A1 (CYP1A1) is a phase I enzyme involved in many oxidative reactions that has attracted considerable attention as a candidate gene for lung cancer susceptibility based on its function as a key factor required for bioactivation of carcinogenic polycyclic aromatic hydrocarbons and catechol oestrogen formation. In the past decade, the relationship between CYP1A1 and lung cancer has been reported in various ethnic groups; however, these studies have yielded contradictory results. To investigate this inconsistency, we performed a meta-analysis of 71 studies involving a total of 30 368 subjects for the MspI and Ile-Val polymorphism of the CYP1A1 gene to evaluate the effect of CYP1A1 on genetic susceptibility for lung cancer. In a combined analysis, the summary per-allele odds ratios for lung cancer of the MspI and Ile-Val polymorphism were 1.19 [95% confidence interval (CI): 1.11-1.28] and 1.20 (95% CI: 1.08-1.33), respectively. Significant results were also observed using dominant or recessive genetic model. In the subgroup analysis by ethnicity, significantly increased risks were found for the MspI and Ile-Val polymorphism among East Asians in almost all genetic models. However, only marginal significant associations were detected for the MspI polymorphism among Caucasians and other population, while no significant associations were observed for the Ile-Val polymorphism in Caucasians and other population. This meta-analysis demonstrated that the MspI and Ile-Val polymorphism of CYP1A1 is a risk factor associated with increased lung cancer susceptibility, but these associations vary in different ethnic populations.     

Exploring multilocus associations of inflammation genes and colorectal cancer risk using hapConstructor

Background  

In candidate-gene association studies of single nucleotide polymorphisms (SNPs), multilocus analyses are frequently of high dimensionality when considering haplotypes or haplotype pairs (diplotypes) and differing modes of expression. Often, while candidate genes are selected based on their biological involvement in a given pathway, little is known about the functionality of SNPs to guide association studies. Investigators face the challenge of exploring multiple SNP models to elucidate which variants, independently or in combination, might be associated with a disease of interest. A data mining module, hapConstructor (freely-available in Genie software) performs systematic construction and association testing of multilocus genotype data in a Monte Carlo framework. Our objective was to assess its utility to guide statistical analyses of haplotypes within a candidate region (or combined genotypes across candidate genes) beyond that offered by a standard logistic regression approach.     

MicroRNA–mRNA interactions in colorectal cancer and their role in tumor progression

MicroRNAs (miRNA/miR) play an important role in gene regulatory networks through targeting mRNAs. They are involved in diverse biological processes such as cell proliferation, differentiation, angiogenesis, and apoptosis. Due to their pivotal effects on multiple genes and pathways, dysregulated miRNAs have been reported to be associated with different diseases, including colorectal cancer (CRC). Recent evidence indicates that aberrant miRNA expression is tightly linked with the initiation and progression of CRC. To elucidate the influence of miRNA regulation in CRC, it is critical to identify dysregulated miRNAs, their target mRNA genes and their involvement in gene regulatory and signaling networks. Various experimental and computational studies have been conducted to decipher the function of miRNAs involved in CRC. Experimental studies that are used for this purpose can be classified into two categories: direct/individual and indirect/high‐throughput gene expression studies. Here we review miRNA target identification studies related to CRC with an emphasis on experimental data based on Luciferase reporter assays. Recent advances in determining the function of miRNAs and the signaling pathways they are involved in have also been summarized. The review helps bioinformaticians and biologists to find extensive information about downstream targets of dysregulated miRNAs, and their pro‐/anti‐CRC effects. © 2015 Wiley Periodicals, Inc.