Shannon Telesco

A functional genomics predictive network model identifies regulators of inflammatory bowel disease

A major challenge in inflammatory bowel disease (IBD) is the integration of diverse IBD data sets to construct predictive models of IBD. We present a predictive model of the immune component of IBD that informs causal relationships among loci previously linked to IBD through genome-wide association studies (GWAS) using functional and regulatory annotations that relate to the cells, tissues, and pathophysiology of IBD. Our model consists of individual networks constructed using molecular data generated from intestinal samples isolated from three populations of patients with IBD at different stages of disease. We performed key driver analysis to identify genes predicted to modulate network regulatory states associated with IBD, prioritizing and prospectively validating 12 of the top key drivers experimentally. This validated key driver set not only introduces new regulators of processes central to IBD but also provides the integrated circuits of genetic, molecular, and clinical traits that can be directly queried to interrogate and refine the regulatory framework defining IBD.

High-Throughput Characterization of Blood Serum Proteomics of IBD Patients with Respect to Aging and Genetic Factors

To date, no large scale, systematic description of the blood serum proteome has been performed in inflammatory bowel disease (IBD) patients. By using microarray technology, a more complete description of the blood proteome of IBD patients is feasible. It may help to achieve a better understanding of the disease. We analyzed blood serum profiles of 1128 proteins in IBD patients of European descent (84 Crohn’s Disease (CD) subjects and 88 Ulcerative Colitis (UC) subjects) as well as 15 healthy control subjects, and linked protein variability to patient age (all cohorts) and genetic components (genotype data generated from CD patients). We discovered new, previously unreported aging-associated proteomic traits (such as serum Albumin level), confirmed previously reported results from different tissues (i.e., upregulation of APOE with aging), and found loss of regulation of MMP7 in CD patients. In carrying out a genome wide genotype-protein association study (proteomic Quantitative Trait Loci, pQTL) within the CD patients, we identified 41 distinct proteomic traits influenced by cis pQTLs (underlying SNPs are referred to as pSNPs). Significant overlaps between pQTLs and cis eQTLs corresponding to the same gene were observed and in some cases the QTL were related to inflammatory disease susceptibility. Importantly, we discovered that serum protein levels of MST1 (Macrophage Stimulating 1) were regulated by SNP rs3197999 (p = 5.96E-10, FDR<5%), an accepted GWAS locus for IBD. Filling the knowledge gap of molecular mechanisms between GWAS hits and disease susceptibility requires systematically dissecting the impact of the locus at the cell, mRNA expression, and protein levels. The technology and analysis tools that are now available for large-scale molecular studies can elucidate how alterations in the proteome driven by genetic polymorphisms cause or provide protection against disease. Herein, we demonstrated this directly by integrating proteomic and pQTLs with existing GWAS, mRNA expression, and eQTL datasets to provide insights into the biological processes underlying IBD and pinpoint causal genetic variants along with their downstream molecular consequences.

Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn's Disease Cohort Inform IBD Genetic Association Loci.

OBJECTIVES:Genome-wide association studies (GWAS) have identified loci reproducibly associated with inflammatory bowel disease (IBD) and other immune-mediated diseases; however, the molecular mechanisms underlying most of genetic susceptibility remain undefined. Expressional quantitative trait loci (eQTL) of disease-relevant tissue can be employed in order to elucidate the genes and pathways affected by disease-specific genetic variance.METHODS:In this study, we derived eQTLs for human whole blood and intestine tissues of anti-tumor necrosis factor-resistant Crohn’s disease (CD) patients. We interpreted these eQTLs in the context of published IBD GWAS hits to inform on the disease process.RESULTS:At 10% false discovery rate, we discovered that 5,174 genes in blood and 2,063 genes in the intestine were controlled by a nearby single-nucleotide polymorphism (SNP) (i.e., cis-eQTL), among which 1,360 were shared between the two tissues. A large fraction of the identified eQTLs were supported by the regulomeDB database, showing that the eQTLs reside in regulatory elements (odds ratio; OR=3.44 and 3.24 for blood and intestine eQTLs, respectively) as opposed to protein-coding regions. Published IBD GWAS hits as a whole were enriched for blood and intestine eQTLs (OR=2.88 and 2.05; and P value=2.51E-9 and 0.013, respectively), thereby linking genetic susceptibility to control of gene expression in these tissues. Through a systematic search, we used eQTL data to inform 109 out of 372 IBD GWAS SNPs documented in National Human Genome Research Institute catalog, and we categorized the genes influenced by eQTLs according to their functions. Many of these genes have experimentally validated roles in specific cell types contributing to intestinal inflammation.CONCLUSIONS:The blood and intestine eQTLs described in this study represent a powerful tool to link GWAS loci to a regulatory function and thus elucidate the mechanisms underlying the genetic loci associated with IBD and related conditions. Overall, our eQTL discovery approach empirically identifies the disease-associated variants including their impact on the direction and extent of expression changes in the context of disease-relevant cellular pathways in order to infer the functional outcome of this aspect of genetic susceptibility.

Gut microbiota density influences host physiology and is shaped by host and microbial factors

To identify factors that regulate gut microbiota density and the impact of varied microbiota density on health, we assayed this fundamental ecosystem property in fecal samples across mammals, human disease, and therapeutic interventions. Physiologic features of the host (carrying capacity) and the fitness of the gut microbiota shape microbiota density. Therapeutic manipulation of microbiota density in mice altered host metabolic and immune homeostasis. In humans, gut microbiota density was reduced in Crohn’s disease, ulcerative colitis, and ileal pouch-anal anastomosis. The gut microbiota in recurrent Clostridium difficile infection had lower density and reduced fitness that were restored by fecal microbiota transplantation. Understanding the interplay between microbiota and disease in terms of microbiota density, host carrying capacity, and microbiota fitness provide new insights into microbiome structure and microbiome targeted therapeutics.

Su1763 Distinctive Gene Expression Profiles in the Whole Blood of Patients With Moderate to Severe Ulcerative Colitis and Crohn's Disease

Introduction The aim of this study was to define whole blood (WB) gene expression profiles in moderate to severe ulcerative colitis (UC) and Crohn’s disease (CD) patients, and to elucidate modulated genes and pathways that are shared by and also unique to each disease. Gene expression profiling of UC and CD WB has not been compared in a study of this size, and the subset of non-overlapping genes identified could potentially lead to a means to discriminate between these two forms of IBD. A molecular diagnostic assay based on gene expression from readily accessible tissue (WB) would have great utility in differentiating between UC and CD, a common diagnostic dilemma. Methods WB samples were collected from a subset of patients in one of two clinical trials: PURSUIT-SC, a study to evaluate safety and efficacy of induction therapy with SC golimumab in patients with moderate to severe UC, and CERTIFI, a study to evaluate safety and efficacy of ustekinumab therapy in patients with moderate to severe CD. In both studies, samples (n = 69 UC, 204 CD) were collected at baseline for mRNA expression profiling using Affymetrix HG-U133+ PM arrays. Samples from healthy volunteers were obtained independently of the trials. Changes in gene expression of > 1.5-fold and false detection rate (FDR) p-value Results There was overlap in the significant changes in gene expression observed in the WB of UC and CD patients compared to normal controls. Of the 1229 differentially expressed transcripts in UC, 63% (45% relative to CD) overlapped with those in CD WB. Over-expressed genes in UC and CD included CD177, IL1R1, IL17RA, MMPs, and other genes involved in systemic inflammation, cellular cytotoxicity, and lymphocyte migration. However, significant proportions of genes (37% of UC gene changes, or 55% of CD) were uniquely expressed in either disease. Genes expressed specifically in UC included regulators of cell death and survival, eg BCL2A1, and several integrin isoforms. Differentially expressed genes specific to CD included IL23A, genes involved in ubiquitination and autophagy, eg ATG9B, and several chemokines. Pathways unique to CD involved B-cell receptor signalling and protein degradation, while oncogenic mechanisms were more predominant in pathways uniquely upregulated in UC. Conclusion Despite sharing many of the same upregulated transcripts, WB of CD and UC patients also demonstrated significant proportions of differentially expressed genes. Transcriptional profiles in circulating immune cells found in WB may serve as a surrogate for relaying the state of less-accessible luminal tissues in UC and CD patients, and have the potential to aid in differential diagnosis of these diseases. Disclosure of Interest S. Telesco Employee of: Janssen R&D, LLC, K. Li Employee of: Janssen R&D, LLC, C. Marano Employee of: Janssen R&D, LLC, C. Gasink Employee of: Janssen R&D, LLC, K. Ma Employee of: Janssen R&D, LLC, R. Strauss Employee of: Janssen R&D, LLC, C. Brodmerkel Employee of: Janssen R&D, LLC

978 Whole Blood mRNA Expression Profiling of Crohn's Disease in the Certifi Ustekinumab Study Discriminates Clinical Subtypes

Introduction Objective markers of Crohn’s Disease (CD) activity have been sought as diagnostic, phenotypic, prognostic and disease activity markers. Complications such as stricture and fistula and characteristics such as TNF-antagonist responsiveness have been suggested as discreet mechanistic CD subtypes. This study explored the ability of genome wide expression profiling in whole blood to differentiate CD sub-populations. Methods In the previously reported Phase 2b ustekinumab CERTIFI study of patients with moderate to severely active CD who had failed or were intolerant to TNF-antagonists, whole blood samples were collected from a subset for mRNA expression profiling using Affymetrix HG-U133+ PM arrays. Baseline expression profiles were compared between patient sub-groups characterised by defined baseline disease attributes; and compared with those from samples obtained independently from healthy subjects. Expression modulations of > +/-1.5x and false discovery rate (FDR) p-value Results Patients (n = 204) with moderate to severe CD had significant expression modulations in 1725 transcripts in the whole blood compared with healthy subjects (n = 49), including genes involved in inflammatory response and connective tissue disorders. A panel of 20 transcripts (including GAB2 and IL18R1) discriminated patients with only colonic (n = 49) vs. strictly ileal (n = 60) disease involvement. Significantly different expression modulations of 169, 321, and 151 transcripts, respectively, were identified in patients with high baseline CRP (>10 mg/dL, n = 97), faecal calprotectin (>850 mg/g, n = 80) or lactoferrin (>100 mg/g, n = 89) compared with patients with low baseline CRP ( 15 yrs] vs. short [ Conclusion Genome-wide expression profiling of peripheral blood samples provides the understanding of CD at the molecular level in circulation. This is a new, non-invasive method that can be used to identify systemic markers of local pathological alterations in CD and to discriminate clinically between different CD sub-types. Disclosure of Interest K. Li Employee of: Janssen R&D, LLC, C. Brodmerkel Employee of: Janssen R&D, LLC, S. Telesco Employee of: Janssen R&D, LLC, K. Ma Employee of: Janssen R&D, LLC, C. Gasink Employee of: Janssen R&D, LLC