(HOST-MICROBIAL ANALYTICS & REPOSITORY CORE) There is growing evidence for the importance of environmental factors, such as the microbiome, playing a critical role in the pathogenesis of many digestive, liver and pancreatic diseases. There is much interest in the characterization of the microbiome to identify potential biomarkers relevant for precision medicine as well as the modification of the human microbiome as a modality to prevent and/or treat diseases. To facilitate research focused on host-microbial interactions and their relevance to digestive, liver and pancreatic diseases, the Center for Molecular Studies in Digestive and Liver Diseases (CMSDLD) has developed a Host-Microbial Analytic and Repository Core (H-MARC) with the following two Specific Aims: 1) To provide critical analytic services the characterize analytes (i.e. genomics, transcriptomics, metabolomics) in both microbes and their mammalian hosts and 2) To provide expertise that will allow CMSDLD members to extend pre-clinical in vitro and animal model research into the human clinical domain.
In Specific Aim 1, to support the analysis of the mammalian host, H-MARC will provide access to high-end instruments designed to quantify gene expression at the mRNA and protein levels as well as access to FACS for the characterization of mammalian cell populations. Genomic analysis will be provided via Penn's Next Gen Sequencing Core. To support the analysis of the microbiota, H-MARC will support experiments involving microbial cultures as well as the analysis of metabolites via targeted metabolomics. Computational and biostatistical support to analyze microbiome datasets associated with clinical metadata will also be provided through full time biostatisticians in H-MARC who will interface with the PennCHOP Microbiome Program.
In Specific Aim 2, H-MARC will support human subject research by providing a robust Human Biospecimen Repository via a LabVantage-based LIMS system as well as the collection of robust annotated clinical data for IBD phenotyping via the EPIC EMR. Importantly, to facilitate human subject research translating preclinical research into the clinical domain, H-MARC will provide advice and expertise in the development of human intervention studies. Ultimately, H-MARC services are designed to facilitate integrated analyses of host-microbial interactions at the preclinical and clinical interface.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Center Core Grants (P30)
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Special Emphasis Panel (ZDK1)
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University of Pennsylvania
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Wangensteen, Kirk J; Wang, Yue J; Dou, Zhixun et al. (2018) Combinatorial genetics in liver repopulation and carcinogenesis with a in vivo CRISPR activation platform. Hepatology 68:663-676
Andres, Sarah F; Williams, Kathy N; Rustgi, Anil K (2018) The Molecular Basis of Metastatic Colorectal Cancer. Curr Colorectal Cancer Rep 14:69-79
Serper, M; Forde, K A; Kaplan, D E (2018) Rare clinically significant hepatic events and hepatitis B reactivation occur more frequently following rather than during direct-acting antiviral therapy for chronic hepatitis C: Data from a national US cohort. J Viral Hepat 25:187-197
Avetisyan, Marina; Rood, Julia E; Huerta Lopez, Silvia et al. (2018) Muscularis macrophage development in the absence of an enteric nervous system. Proc Natl Acad Sci U S A 115:4696-4701
Kim, Yong Hoon; Marhon, Sajid A; Zhang, Yuxiang et al. (2018) Rev-erb? dynamically modulates chromatin looping to control circadian gene transcription. Science 359:1274-1277
Costea, Paul I; Hildebrand, Falk; Arumugam, Manimozhiyan et al. (2018) Enterotypes in the landscape of gut microbial community composition. Nat Microbiol 3:8-16
Correnti, Jason M; Gottshall, Lauren; Lin, Annie et al. (2018) Ethanol and C2 ceramide activate fatty acid oxidation in human hepatoma cells. Sci Rep 8:12923
Khalili, Mandana; Shuhart, Margaret C; Lombardero, Manuel et al. (2018) Relationship Between Metabolic Syndrome, Alanine Aminotransferase Levels, and Liver Disease Severity in a Multiethnic North American Cohort With Chronic Hepatitis B. Diabetes Care 41:1251-1259
Qiu, Chengxiang; Huang, Shizheng; Park, Jihwan et al. (2018) Renal compartment-specific genetic variation analyses identify new pathways in chronic kidney disease. Nat Med 24:1721-1731
Shoshkes-Carmel, Michal; Wang, Yue J; Wangensteen, Kirk J et al. (2018) Subepithelial telocytes are an important source of Wnts that supports intestinal crypts. Nature 557:242-246

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