Project description:Transcriptomic analysis of the colon from a wildtype 8 week old female mice in C57BL6 background. In particular, we characterized the expression of genes encoding known receptors for Regenerating islet-derived proteins (REG3III) among the different colonic intestinal epithelial cell subsets under steady state. Colonic DCLK1+ tuft cell-containing spots had the highest expression levels of genes encoding various REG3III receptors.
Project description:To perform a global analysis of high fiber diet-induced changes in gene expression in various compartments of the colonic microenvironment, we employed a spatial transcriptomic analysis using the 10X Genomics® platform. This technique allowed for visualization of gene expression in histological cross-sections of the distal colon with spatial information and therefore enabled detection of differentially expressed genes simultaneously in diverse cell types, together with information about their anatomical location in the tissue. Distal colon samples were processed using a Visium Spatial Gene Expression Slide & Reagent Kit (PN-1000184, 10X Genomics) as per the manufacturer’s instructions. Unbiased clustering divided the colon into four distinct zones: epithelium, lamina propria & submucosa, muscularis, and neuronal plexus, as visualized by hematoxylin and eosin (H&E) staining.
Project description:The incidence of sporadic early-onset colon cancer (EOCC) has increased worldwide. The molecular mechanisms in the tumor and the tumor microenvironment in EOCC are not fully understood. The aim of this study is to unravel unique spatial transcriptomic and proteomic profiles in tumor epithelial cells and cancer-associated fibroblasts (CAFs). Sporadic colon cancer FFPE tissue samples were divided into patients diagnosed with EOCC (<50 yrs) and late-onset colon cancer (LOCC, ≥50 yrs). Spatial transcriptomic analysis of 112 areas of interest (AOIs) were performed using Nanostring GeoMx digital spatial profiling. The data generated was combined with in silico analysis and functional assays to characterize FAP(+) CAFs at the EOCC tumor invasive margin.
Project description:The limitation of single-cell or bulk transcriptomic profiling is the lack of spatial topographical context. Spatial transcriptomics (ST) allows sequencing of polyadenylated transcripts from a tissue section which can be spatially mapped onto the histological brightfield image using an array of barcoded oligo-dT capturing probes. Using the 10X Visium platform, here, we unbiasedly characterized the spatial transcriptomic landscape of murine colon in steady state and during mucosal healing upon dextran sodium sulfate (DSS) induced injury
Project description:The limitation of single-cell or bulk transcriptomic profiling is the lack of spatial topographical context. Spatial transcriptomics (ST) allows sequencing of polyadenylated transcripts from a tissue section which can be spatially mapped onto the histological brightfield image using an array of barcoded oligo-dT capturing probes. Using the 10X Visium platform, here, we unbiasedly characterized the spatial transcriptomic landscape of murine colon during mucosal healing upon dextran sodium sulfate (DSS) induced injury in mice in which B cell has been depleted and control.
Project description:We applied a spatially resolved, high-dimensional transcriptomic approach to study MPM morpho-logical evolution. 139 regions across 8 biphasic MPMs (B-MPMs) were profiled using the GeoMx™Digital Spatial Profiler and Cancer Transcriptome Atlas to compare epithelioid and sarcomatoid components transcriptional profile and reconstruct the positional context of transcriptional activities and the spatial topology of MPM cells interactions.