Xiaofei Yan

GABRA2 markers moderate the subjective effects of alcohol

Individual differences in subjective responses (SRs) to alcohol are moderated by genetic variants and may be risk factors for the development of alcohol use disorders. Variation in the GABAAα2 receptor subunit gene (GABRA2) has been associated with alcohol dependence (AD). Therefore, we examined whether individual differences in SRs, which reflect sensitivity to the effects of alcohol, are associated with variation in GABRA2. Sixty‐nine healthy subjects (21–30 years) underwent a laboratory‐based within‐session cumulative oral alcohol dosing procedure, achieving a mean peak blood alcohol level of 100.4 mg/dl (standard error = 2.5). Subjective assessments were obtained throughout the session, including ascending and descending limbs of the alcohol curve. We genotyped single nucleotide polymorphisms (SNPs) across the chromosome 4 region spanning GABRA2 and analyzed the effect of genotype and haplotypes on subjective responses to alcohol. Population substructure was characterized through the use of ancestry informative markers. Individual SNP analysis demonstrated that carriers of the minor alleles for SNPs rs279858, rs279844, rs279845, rs279826, rs279828 and rs279836 had lower ‘Negative’ alcohol effects scores than individuals homozygous for the common allele at each SNP (P = 0.0060, P = 0.0035, P = 0.0045, P = 0.0043, P = 0.0037 and P = 0.0061, respectively). Haplotype effects of block 1 showed concordant results with SNPs in this block (P = 0.0492 and P = 0.0150 for haplotypes 1 and 4, respectively). The minor alleles for several of these SNPs have previously been associated with AD. Our findings provide further evidence that variation within GABRA2 is associated with attenuated negative responses to alcohol, a known risk factor for vulnerability to alcohol use disorders.

Variants Identified in a GWAS Meta-Analysis for Blood Lipids Are Associated with the Lipid Response to Fenofibrate

A recent large-scale meta-analysis of genome-wide studies has identified 95 loci, 59 of them novel, as statistically significant predictors of blood lipid traits; we tested whether the same loci explain the observed heterogeneity in response to lipid-lowering therapy with fenofibrate. Using data from the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN, n = 861) we fit linear mixed models with the genetic markers as predictors and high-density lipoprotein (HDL) cholesterol, low-density lipoprotein (LDL) cholesterol, total cholesterol, and triglyceride concentrations as outcomes. For all four traits, we analyzed both baseline levels and changes in response to treatment with fenofibrate. For the markers that were significantly associated with fenofibrate response, we fit additional models evaluating potential epistatic interactions. All models were adjusted for age, sex, and study center as fixed effects, and pedigree as a random effect. Statistically significant associations were observed between the rs964184 polymorphism near APOA1 (P-value≤0.0001) and fenofibrate response for HDL and triglycerides. The association was replicated in the Pharmacogenetics of Hypertriglyceridemia in Hispanics study (HyperTG, n = 267). Suggestive associations with fenofibrate response were observed for markers in or near PDE3A, MOSC1, FLJ36070, CETP, the APOE-APOC1-APOC4-APOC2, and CILP2. Finally, we present strong evidence for epistasis (P-value for interaction =  0.0006 in GOLDN, 0.05 in HyperTG) between rs10401969 near CILP2 and rs4420638 in the APOE-APOC1-APOC4-APOC2 cluster with total cholesterol response to fenofibrate. In conclusion, we present evidence linking several novel and biologically relevant genetic polymorphisms to lipid lowering drug response, as well as suggesting novel gene-gene interactions in fenofibrate pharmacogenetics.

Perianal Crohnʼs Disease is Associated with Distal Colonic Disease, Stricturing Disease Behavior, IBD-Associated Serologies and Genetic Variation in the JAK-STAT Pathway

Background:Perianal Crohns Disease (pCD) is a particularly severe phenotype associated with poor quality of life with a reported prevalence of 12%–40%. Previous studies investigating the etiology of pCD have been limited in the numbers of subjects and the intensity of genotyping. The aim of this study was to identify clinical, serological, and genetic factors associated with pCD. Methods:We performed a case–control study comparing patients with (pCD+) and without perianal (pCD−) involvement in CD; defined as the presence of perianal abscesses or fistulae. Data on demographics and clinical features were obtained by chart review. Inflammatory bowel disease-related serology was determined by enzyme-linked immunosorbent assay. Genetic data were generated using Illumina genotyping platforms. Results:We included 1721 patients with CD of which 524 (30.4%) were pCD+ and 1197 were pPCD−. pCD was associated with distal colonic disease (Odds ratio 5.54 [3.23–9.52], P < 0.001), stricturing disease behavior (1.44 [1.14–1.81], P = 0.002) and family history of inflammatory bowel disease (4.98 [3.30–7.46], P < 0.001). pCD was associated with higher anti-sacharomyces cerevisae antibodies IgA (P < 0.001) and OmpC (P = 0.008) antibody levels. pCD was associated with known inflammatory bowel disease loci, including KIF3B, CRTC3, TRAF3IP2, JAZF1, NRIP1, MST1, FUT2, and PTGER (all P < 0.05). We also identified genetic association with genes involved in autophagy (DAPK1, P = 5.11 × 10−5), TNF alpha pathways (NUCB2, P = 8.68 × 10−5; DAPK1), IFNg pathways (DAPK1; NDFIP2, P = 8.74 × 10−5), and extracellular matrix and scaffolding proteins (USH1C, P = 8.68 × 10−5; NDFIP2; TMC07, P = 8.87 × 10−5). Pathway analyses implicated the JAK-Stat pathway (pc = 3.72 × 10−5). Conclusion:We have identified associations between pCD, more distal colonic inflammation, Crohns disease-associated serologies, and genetic variation in the JAK-Stat pathway.

Genetic associations with adverse events from anti-tumor necrosis factor therapy in inflammatory bowel disease patients

AIM To study the type and frequency of adverse events associated with anti-tumor necrosis factor (TNF) therapy and evaluate for any serologic and genetic associations. METHODS This study was a retrospective review of patients attending the inflammatory bowel disease (IBD) centers at Cedars-Sinai IBD Center from 2005-2016. Adverse events were identified via chart review. IBD serologies were measured by ELISA. DNA samples were genotyped at Cedars-Sinai using Illumina Infinium Immunochipv1 array per manufacturer’s protocol. SNPs underwent methodological review and were evaluated using several SNP statistic parameters to ensure optimal allele-calling. Standard and rigorous QC criteria were applied to the genetic data, which was generated using immunochip. Genetic association was assessed by logistic regression after correcting for population structure. RESULTS Altogether we identified 1258 IBD subjects exposed to anti-TNF agents in whom Immunochip data were available. 269/1258 patients (21%) were found to have adverse events to an anti-TNF-α agent that required the therapy to be discontinued. 25% of women compared to 17% of men experienced an adverse event. All adverse events resolved after discontinuing the anti-TNF agent. In total: n = 66 (5%) infusion reactions; n = 49 (4%) allergic/serum sickness reactions; n = 19 (1.5%) lupus-like reactions, n = 52 (4%) rash, n = 18 (1.4%) infections. In Crohn’s disease, IgA ASCA (P = 0.04) and IgG-ASCA (P = 0.02) levels were also lower in patients with any adverse events, and anti-I2 level in ulcerative colitis was significantly associated with infusion reactions (P = 0.008). The logistic regression/human annotation and network analyses performed on the Immunochip data implicated the following five signaling pathways: JAK-STAT (Janus Kinase-signal transducer and activator of transcription), measles, IBD, cytokine-cytokine receptor interaction, and toxoplasmosis for any adverse event. CONCLUSION Our study shows 1 in 5 IBD patients experience an adverse event to anti-TNF therapy with novel serologic, genetic , and pathways associations.

Application of Bayesian regression with singular value decomposition method in association studies for sequence data.

Genetic association studies usually involve a large number of single-nucleotide polymorphisms (SNPs) (k) and a relative small sample size (n), which produces the situation that k is much greater than n. Because conventional statistical approaches are unable to deal with multiple SNPs simultaneously when k is much greater than n, single-SNP association studies have been used to identify genes involved in a disease’s pathophysiology, which causes a multiple testing problem. To evaluate the contribution of multiple SNPs simultaneously to disease traits when k is much greater than n, we developed the Bayesian regression with singular value decomposition (BRSVD) method. The method reduces the dimension of the design matrix from k to n by applying singular value decomposition to the design matrix. We evaluated the model using a Markov chain Monte Carlo simulation with Gibbs sampler constructed from the posterior densities driven by conjugate prior densities. Permutation was incorporated to generate empirical p-values. We applied the BRSVD method to the sequence data provided by Genetic Analysis Workshop 17 and found that the BRSVD method is a practical method that can be used to analyze sequence data in comparison to the single-SNP association test and the penalized regression method.

Mo1750 Genetic Associations With Preferential 6TGN Metabolizers Reveal Novel Pathways Involved in Purine Metabolism

INTRODUCTION: The prevalence of inflammatory bowel disease (IBD) is increasing globally whilst genetic factors account for only a small portion of overall disease variance. Accumulating evidence has highlighted the importance of epigenetic regulation in IBD pathogenesis. We aimed to identify key epigenetic modulators of IBD in a population of increasing disease incidence and characterize the mechanisms involved. METHODS: Customized PCR array containing 128 well-defined epigenetic modulators were performed and candidate genes were validated in 96 tissues from patients with Crohns disease (CD), ulcerative colitis (UC) andmatched healthy controls using quantitative RT-PCR,Western blot and immunohistochemistry. Functional assays were performed using normal colonic epithelium cell line, NCM460, in which histone modification status and expressions of inflammatory cytokines were monitored upon small-molecule inhibition or RNA interference. RESULTS: Seven epigenetic modulators were differentially expressed in inflamed IBD tissues compared with controls. Amongst them, lysine acetyltransferase 2B (KAT2B) mRNA and protein levels were significantly down regulated in CD and UC inflamed tissues in a validation cohort (p< 0.05). KAT2B proteins were localized abundantly in nuclei of epithelial cells of non-inflamed colonic tissues but not in paired inflamed tissues. Inhibition of KAT2B by anacardic acid (AA), a specific small-molecule KAT2B antagonist, or small-interfering RNA (siRNA) in NCM460 cells reduced acetylation level of histone H4, but not histone H3 lysine 9 and lysine 14. Moreover, siRNA knockdown of KAT2B significantly decreased IL-10 but increased IL-1β and IL-18 expression in NCM460 cells, these changes were dose-dependent and influenced by AA treatment. CONCLUSION: Our findings demonstrated for the first time a novel epigenetic link between histone modification and IBD through KAT2B. Downregulation of KAT2B may promote histone deacetylation that leads to suppression of IL-10, a key anti-inflammatory cytokine critical for innate and adaptive inflammatory responses. Ongoing functional characterization of tissue or disease-specific epigenetic variations in IBD will provide insight into biological pathways that may translate into new therapeutic approaches.

Tu1920 The Role of Genetic Variation and C-Reactive Protein (CRP) in IBD

macrocystic or microcystic morphology, and impression of a pseudocyst] were noted. FNA results, including cyst fluid CEA , and cytology features of mucin, cellular atypia or cancer were recorded. Univariate analysis (Fishers exact and Mann-Whitney U test) was performed followed by multivariate logistic regression analysis to identify if CEA was an independent predictor for MCN. ROC curves were generated for CEA levels to evaluate its diagnostic characteristics. Results: 2407 pts met inclusion criteria and 1861 (77.6%) underwent EUSFNA [mean age 63 yrs, 87% Caucasians, 58% females, and mean pancreatic cyst size 26 mm]. 376 pts underwent surgery (37% Whipples surgery, 45% distal pancreatectomy, 18% others) and cancer on cytology was noted in 138 pts. Based on the gold standard, there were 440 pts with MCN (including IPMN) and 882 NMCN. On univariate analysis, the median values of CEA in MCN were significantly higher than that of NMCN (126.9 vs. 21.65, p < 0.001). On multivariate analysis, CEA [OR = 1.3 (1.1 1.6), p < 0.01] was a statistically significant predictor for MCN while adjusting for mucin on cytology, presence of solid mass on EUS, mural nodule, and multilocularity. Area under ROC curve was 0.74 (0.70 0.77, p<0.01) for CEA (cut off of 92.9 ng/ml sensitivity, 70% and specificity, 64%) (Figure). The traditional cut off of 192 ng/ml yielded a sensitivity of 59% and specificity of 73% in identifying MCN. Conclusions: This large multicenter study demonstrates that cyst fluid CEA levels have an unacceptable accuracy level in differentiating MCN and NMCN of the pancreas limiting its applicability in clinical practice. Future studies should focus on novel markers in cyst fluid to improve the risk stratification for diagnosis, cancer risk and surveillance of pancreatic cystic neoplasms. Table: AUC, Sensitivity and specificity of CEA in differentiating MCN from NMCN.

Su1931 Genetic and Serological Predictors of H. pylori Infection in Patients With Inflammatory Bowel Disease

G A A b st ra ct s suppresses the development of MGC. To clarify the molecular changes due to H. pylori eradication, in this study, we evaluated differences in molecular alterations related to carcinogenesis in background mucosa of GC between H. pylori positive and negative patients. Materials and Methods: Seventy-seven consecutive patients who underwent ER for GC were enrolled. H. pylori status was analyzed in each patient by two methods: Giemsa staining and serum H. pylori-IgG antibody. Biopsy specimens were obtained from all cases, and DNA was extracted from intestinal metaplasia (IM), a precancerous lesion, via laser capture microdissection. Microsatellite instability (MSI) was evaluated at five loci based on the Bethesda panel; promoter methylation at hMLH1, E-cadherin, p16, and APC was assessed using methylation-specific polymerase chain reaction. Reactivity of monoclonal antibody for colonic phenotype (mAb Das-1) to IM was also evaluated by an immunoperoxidase assay. Results: H. pylori status was negative in 32 of 77 participants (41.6%). The incidence of MSI and hypermethylation at hMLH1, E-cadherin, p16, and APC genes in IM for H. pylori positive and negative patients, respectively, were 47.6%, 23.7%, 10.5% and 56.1% and 36.7%, 6.7%, 3.4%, 38.7% and 35.5%. There were no significant differences in molecular alterations between H. pylori positive and negative cases. mAb Das-1 reactivity to IM was 70.5% in H. pylori positive and 71.0% in H. pylori negative patients, demonstrating no significant difference. Conclusions: Early GC occurs frequently even in H. pylori negative patients. There were no significant differences in molecular alterations in IM between H. pylori positive and negative patients, suggesting that H. pylori eradication may not change the course of molecular alterations in background mucosa once GC has occured in the stomach.