Haijian Wang

Identification of genetic variants in base excision repair pathway and their associations with risk of esophageal squamous cell carcinoma.

The etiology of esophageal squamous cell carcinoma (ESCC) has been shown to be associated with genetic and certain environmental factors that produce DNA damage. Base excision repair (BER) genes are responsible for repair of DNA damage caused by reactive oxygen species and other electrophiles and therefore are good candidate susceptibility genes for ESCC. We first screened eight BER genes for new and potential functional polymorphisms by resequencing 27 DNA samples. We then identified and genotyped for important tagging single nucleotide polymorphisms (SNPs) in a case-control study of 419 patients with newly diagnosed esophageal cancer and 480 healthy controls by frequency matching on age and sex. The association between genotypes and ESCC risk was estimated by unconditional multivariate logistic regression analysis, and stepwise regression procedure was used for constructing the final logistic regression model. We identified 129 SNPs in the eight BER genes, including 18 SNPs that cause amino acid changes. In the final model, 4 SNPs, including 2 in the coding regions (ADPRT Val762Ala and MBD4 Glu346Lys) and others in noncoding regions (LIG3 A3704G and XRCC1 T-77C), remained as significant predictors for the risk of ESCC. The adjusted odd ratios were 1.25 [95% confidence interval (CI) 1.02–1.53] for the ADPRT 762Ala allele, 1.25 (95% CI 1.02–1.53) for the MBD4 346 Lys allele, 0.78 (95% CI 0.63–0.97) for the LIG3 3704G allele, and 1.38 (95% CI 1.01–1.89) for the XRCC1–77C allele. In addition, we observed a significant gene-gene interaction between XRCC1 Gln399Arg and ADPRT Val762Ala. The results suggest that the polymorphisms in five BER genes may be associated with the susceptibility to ESCC in a Chinese population.

The G–113A polymorphism in CYP1A2 affects the caffeine metabolic ratio in a Chinese population

This study was designed to better understand genetic variation in the cytochrome P450 (CYP) gene CYP1A2 and its impact on CYP1A2 activity in Chinese subjects.

Genetic susceptibility of lung cancer associated with common variants in the 3′ untranslated regions of the adenosine triphosphate-binding cassette B1 (ABCB1) and ABCC1 candidate transporter genes for carcinogen export

Tobacco‐specific nitrosamine 4‐(methylnitrosamino)‐1‐(3‐pyridyl)‐1‐butanone (NKK) is a well defined carcinogen that can induce lung cancer. Genetic polymorphisms in its disposition pathways could modify the risk of developing lung cancer. The authors of this report previously catalogued the sequence variations of the adenosine triphosphate‐binding cassette B1 (ABCB1) and ABCC1 candidate transporter genes for carcinogen export in the Chinese population and screened out common variants with potential function in their 5′ flanking and 3′ untranslated regions. The objective of the current study was to test the hypothesis that these common variants are associated with lung cancer risk.

Molecular population genetics of human CYP3A locus: signatures of positive selection and implications for evolutionary environmental medicine.

Background The human CYP3A gene cluster codes for cytochrome P450 (CYP) subfamily enzymes that catalyze the metabolism of various exogenous and endogenous chemicals and is an obvious candidate for evolutionary and environmental genomic study. Functional variants in the CYP3A locus may have undergone a selective sweep in response to various environmental conditions. Objective The goal of this study was to profile the allelic structure across the human CYP3A locus and investigate natural selection on that locus. Methods From the CYP3A locus spanning 231 kb, we resequenced 54 genomic DNA fragments (a total of 43,675 bases) spanning four genes (CYP3A4, CYP3A5, CYP3A7, and CYP3A43) and two pseudogenes (CYP3AP1 and CYP3AP2), and randomly selected intergenic regions at the CYP3A locus in Africans (24 individuals), Caucasians (24 individuals), and Chinese (29 individuals). We comprehensively investigated the nucleotide diversity and haplotype structure and examined the possible role of natural selection in shaping the sequence variation throughout the gene cluster. Results Neutrality tests with Tajima’s D, Fu and Li’s D* and F*, and Fay and Wu’s H indicated possible roles of positive selection on the entire CYP3A locus in non-Africans. Sliding-window analyses of nucleotide diversity and frequency spectrum, as well as haplotype diversity and phylogenetically inferred haplotype structure, revealed that CYP3A4 and CYP3A7 had recently undergone or were undergoing a selective sweep in all three populations, whereas CYP3A43 and CYP3A5 were undergoing a selective sweep in non-Africans and Caucasians, respectively. Conclusion The refined allelic architecture and selection spectrum for the human CYP3A locus highlight that evolutionary dynamics of molecular adaptation may underlie the phenotypic variation of the xenobiotic disposition system and varied predisposition to complex disorders in which xenobiotics play a role.

Linkage disequilibrium and haplotype architecture for two ABC transporter genes (ABCC1 and ABCG2) in Chinese population: implications for pharmacogenomic association studies.

Information about linkage disequilibrium (LD) patterns and haplotype structures for candidate genes is instructive for the design and analysis of genetic association studies for complex diseases and drug response. ABCC1 and ABCG2 are genes coding for two multidrug resistance (MDR) associated transporters; they are also related to some pathophysiological traits. To pinpoint the LD profiles of these MDR genes in Chinese, we systemically screened 27 unrelated individuals for single nucleotide polymorphisms (SNPs) in the coding and regulatory regions of these genes, and thereby characterized their haplotype structures. Despite marked variations in haplotype diversity, LD pattern and intragenic recombination intensity between the two genes, both loci could be partitioned into several LD blocks, in which a modest number of haplotypes accounted for a high fraction of the sampled chromosomes. We concluded that each locus has its own genomic LD profile, but that they still share a common segmental LD architecture with low haplotype diversity. Our data will benefit genetic association studies of complex traits and drug response possibly related to these genes.

Comparative and evolutionary pharmacogenetics of ABCB1: complex signatures of positive selection on coding and regulatory regions.

Background As a major mediator in the complex interplay between humans and the xenobiotic environment, the ABCBI transporter gene is an obvious candidate for comparative and evolutionary pharmacogenetic studies. It has been recently reported that common variants in its coding region, which are variously associated with drug response and disease susceptibility, may have conferred differential selective sweep in various populations. Fully profiling the alletic architecture and explicitly interrogating the natural selection at ABCBI are needed to understand its evolutionary population genetics. Methods and results Using a comprehensive single nucleotide polymorphism variants in coding and regulatory regions, as well as comparable genotype data from the Environmental Genome Project, we systematically characterized the extent and length of linkage disequilibrium throughout the ABCBI locus in three major ethnic populations (African, European, and Chinese). We observed pronounced signals of recent positive selection on the derived alleles of three common single nucleotide polymorphisms coding regions: e12/1236T, e21/2677T, and e26/3435T in the Chinese, as well as on extended haplotype homozygosity were also observed for two potentially functional common variants in the 5′f/-4489G (rs17149810) in the Chinese and 5′f/-693T (rs3213619) in the Africans, respectively, which may have shaped the phylogenetically inferred star-like haplotype structure of the 5′flanking region. Conclusion Our finding reveal complex signatures of natural selection on both coding and regulatory regions of the human ABCBI gene, point to potential functional relevance of its regulatory variants, and suggest that evolutionary dynamics and transcriptional regulation may underline the phenotypic variation in xenobiotic disposition and varying predisposition to complex in which xenobiotics play a role.

Association of the variable number of tandem repeats polymorphism in the promoter region of the SMYD3 gene with risk of esophageal squamous cell carcinoma in relation to tobacco smoking

The etiology of esophageal squamous cell carcinoma (ESCC) has been shown to be multifactorial, including genetic, epigenetic, and environmental factors, such as tobacco smoking. A variable number of tandem repeats (VNTR) polymorphism in the promoter region of SMYD3, a recently characterized histone lysine methyltransferase gene that is implicated in cell proliferation and carcinogenesis, has been shown to be functional, but its association with cancer risk has not been well established because of apparently discrepant results in different populations. In this case‐control study, we genotyped 567 patients with newly diagnosed ESCC and 567 healthy controls and found an increased ESCC risk (odds ratio [OR] = 1.42, 95% confidence interval [CI] = 1.05–1.91) associated with the common SMYD3 VNTR genotype. Stratification analysis revealed that the increased risk was limited to smokers (OR = 1.99; 95% CI = 1.27–3.12). Furthermore, compared with the reference group of non‐smokers carrying the homozygous or heterozygous genotype, ORs (95% CI) of the wild genotype for non‐smokers, smokers who smoked <25, and ≥25 pack‐years were 1.03 (0.70–1.53), 2.80 (1.66–4.70), and 4.76 (2.67–8.46), respectively (P < 0.001 for trend test), suggesting an interaction between this genetic polymorphism and smoking status. These findings provide additional evidence that the common VNTR polymorphism in the promoter region of SMYD3 gene may be a susceptibility factor for human cancers such as ESCC by interacting with tobacco carcinogens. (Cancer Sci 2008; 99: 787–791)

Histone H3K9 demethylase JMJD1A modulates hepatic stellate cells activation and liver fibrosis by epigenetically regulating peroxisome proliferator-activated receptor γ

As a central event in liver fibrogenesis, hepatic stellate cell (HSC) transdifferentiation involves loss of regulation by adipogenic transcription factors such as peroxisome proliferator‐activated receptor γ; (PPARγ), which is epigenetically silenced during HSC activation. We hypothesized that JMJD1A, an H3K9 demethylase involved in adipogenic metabolism, could regulate PPARγ. In human HSC cell line, rat primary HSCs, and carbontetrachloride‐induced mouse liver fibrogenesis model, we down‐regulated the expression of JMJD1A using small interfering or short hairpin RNAs, and overexpressed its wild‐type and mutant. We analyzed the effects of JMJD1A manipulation on the histone di‐methyl‐H3K9 (H3k9me2) status of PPARγ gene and the expression of PPARγ and fibrosis markers using chromatin immunoprecipitation, real‐time quantitative RT‐PCR and Western blot, and also investigated the in vitro and in vivo consequences on liver fibrosis and necrosis by Masson or hematoxylin‐eosin staining, respectively. JMJD1A knockdown in HSCs correlated with reinforced H3K9me2 in the PPARγ gene promoter, and its down‐regulation in both mRNA and protein led to increased expression of fibrosis markers, which could be consistently rescued by JMJD1A overexpression. Jmjd1a knockdown in situ resulted in significantly increased expression of α‐smooth muscle actin (P = 0.005) and Col1a (P = 0.036), strengthened production of collagens (P = 0.028), and remarkably enhanced necrosis (P = 0.007) 4 weeks after treatment. This study suggests JMJD1A as a novel epigenetic regulator that modulates HSC activation and liver fibrosis through targeting PPARγ gene expression.—Jiang, Y., Wang, S., Zhao, Y., Lin, C., Zhong, F., Jin, L., He, F., Wang, H. Histone H3K9 demethylase JMJD1A modulates hepatic stellate cells activation and liver fibrosis by epigenetically regulating peroxisome proliferator‐activated receptor γ. FASEB J. 29, 1830‐1841 (2015). www.fasebj.org

Matrix metalloproteinase‐2 polymorphisms and clinical outcome of Chinese patients with nonsmall cell lung cancer treated with first‐line, platinum‐based chemotherapy

Matrix metalloproteinase‐2 (MMP‐2) is well known for its critical role in cell survival and cancer development. It also plays an important role in hematopoietic recovery after chemotherapy‐induced myelosuppression. In this study, the authors investigated the association of MMP‐2 polymorphisms with treatment efficacy and the occurrence of severe toxicity in patients with nonsmall cell lung cancer (NSCLC) who were receiving first‐line, platinum‐based chemotherapy.

Association Between CASP8 and CASP10 Polymorphisms and Toxicity Outcomes With Platinum-Based Chemotherapy in Chinese Patients With Non-Small Cell Lung Cancer

Caspase-8 and caspase-10 play crucial roles in both cancer development and chemotherapy efficacy. In this study, we aimed to comprehensively assess single nucleotide polymorphisms (SNPs) of the caspase-8 (CASP8) and caspase-10 (CASP10) genes in relation to toxicity outcomes with first-line platinum-based chemotherapy in patients with advanced non-small cell lung cancer (NSCLC). We genotyped 13 tag SNPs of CASP8 and CASP10 in 663 patients with advanced NSCLC treated with platinum-based chemotherapy regimens. Associations between SNPs and chemotherapy toxicity outcomes were identified in a discovery set of 279 patients and then validated in an independent set of 384 patients. In both the discovery and validation sets, variant homozygotes of CASP8 rs12990906 and heterozygotes of CASP8 rs3769827 and CASP10 rs11674246 and rs3731714 had a significantly lower risk for severe toxicity overall. However, only the association with the rs12990906 variant was replicated in the validation set for hematological toxicity risk. In a stratified analysis, we found that some other SNPs, including rs3769821, rs3769825, rs7608692, and rs12613347, were significantly associated with severe toxicity risk in some subgroups, such as in nonsmoking patients, patients with adenocarcinoma, and patients treated with cisplatin combinations. Consistent results were also found in haplotype analyses. Our results provide novel evidence that polymorphisms in CASP8 and CASP10 may modulate toxicity outcomes in patients with advanced NSCLC treated with platinum-based chemotherapy. If validated, the findings will facilitate the genotype-based selection of platinum-based chemotherapy regimens.