Informatics and Data Management Core

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Gastrointestinal (Gl) neuromuscular disorders are characterized by motility dysfunctions. Gl motility is mainly regulated by three types of neuro-effector cells, Smooth muscle cells (SMCs), Interstitial cells of Cajal (ICC), and PDGFRa+ cells, all of which are electrically coupled to form the integrated network referred as SIP syncytium. To understand Gl motility, SIP cells should be studied together because each of these cells modifies the behaviors ofthe other cells. This Program seeks to uncover a variety of elements in SIP cells that affect Gl motility in beneficial or pathological ways: 1) molecular mechanisms of pacemaker activity and regulation of responses to neurotransmission; 2) purine signaling and metabolism pathways; and 3) phenotypic and genetic changes of ICC after loss and restoration of c-KIT expression. Each of these projects will interact with the informatics and data management capabilities provided by the Core. The Core employs next-generation sequencing (mRNA-seq) that provides gene expression profiles of each SIP cell type on a genome-wide scale with very high resolution. The genome-wide transcripts will provide all genes, isoforms, and splice variants that are expressed in each cell type. In addition, they will also identify changes in expression levels for individual genes, isoforms, and splice variants with superior resolution in pathologically changed SIP cells. This powerful genome-wide approach to study gene expression will reveal: 1) patterns of changes in the entire transcriptome of SIP cells; 2) identify cell-specific genes, isoforms, and splice variants; 3) examine individual transcripts for functional studies; 4) link transcriptional information to potential physiologic functions ofthe cells; and 5) identify genes that control phenotypic changes ofthe cells. RELEVANCE (See instructions): The discovery of important elements that are anticipated with the transcriptome study ofthe SIP cells will provide a road map to study in detail the functions of each cell type and aid in the development of hypotheses that will progress to human studies, which will stimulate the development of clinical therapeutics to treat human subjects with motility disorders where these cell types may be pathologically involved.