Project description:We harvested and sequenced the spontaneous pancreatic tumor generated by a 6-month-old KPC mouse (KrasLSL-G12D; Trp53LSL-R172H; Ptf1a-Cre).
Project description:Bulk RNA sequencing of sorted peri-pancreatic LN cDC1s from different stages of neoplastic development in the KPC mouse model of pancreatic adenocarcinoma.
Project description:To study possible CNVs and genes affected by CNVs in the cancer associated fibroblast populations of pancreatic cancers, we applied single cell sequencing technology (10x Genomics) to identify different subpopulations in murine KPC pancreatic tumors and pancreata of age- and gender-matched non-tumor bearing mice. Single cell RNA sequencing (scRNA-Seq) identified three major CAF subpopulations which were interrogated together with the ductal carcinoma population for CNVs using a previously reported inferCNV algorithm. Fibroblasts and ductal cells identified by scRNA-Seq in normal, uninvolved pancreas were used as reference and inferCNVs in both CAF and ductal carcinoma cells were validated with CNVs previously reported within a large high-resolution array comparative genomic hybridization (aCGH) of KPC tumors. CNVs were exclusively detected in the myelofibroblastic cancer associated fibroblast (myCAF) subpopulation and not in the other CAF phenotypes. In comparison to ductal carcinoma cells, myCAFs were less frequently affected by CNVs. CNVs in the myCAFs which were unique for the myCAFs and not shared with gene loci affected by CNVs in ductal carcinoma cells included known regulators of CAF activation, CAF-mediated cancer cell invasion, or antagonists of TGFβ signaling.
Project description:This study used 10X Genomics, single-cell RNA-sequencing to examine the cell types present in the KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre (KPC) mouse model for pancreatic ductal adenocarcinoma. The study analyzed tumors from 4 different mice. For each tumor, we performed flow sorting to isolate all viable cells, and to isolate a fibroblast-enriched population of cells for single-cell RNA-seq to determine the transcriptomes of individual cells in KPC pancreatic ductal adenocarcinoma tumors.
Project description:Single cell transcriptomes of CD45+ cells from KPC tumor subcutaneous allografts, either treated with PD-1+CTLA-4 checkpoint blockade or treatment-naïve.
Project description:Circulating Tumor Cells (CTCs) are shed from primary tumors into the bloodstream, mediating the hematogenous spread of cancer to distant organs. Using a pancreatic cancer mouse model, we applied a microfluidic device to isolate CTCs independently of tumor epitopes, subjecting these to single cell RNA-sequencing. This study was conducted to determine the heterogeneity of pancreatic CTCs and to compare these CTCs to matched primary tumors, cell line controls (NB508 cancer cell line and MEF non-cancer cell line), primary tumor single cells, and normal leukocytes/WBCs. We profiled RNA from 75 single cells circulating in mouse blood enriched for circulating tumor cells from 5 mice, 12 single cells from a mouse embryonic fibroblast cell line, 16 single cells from the nb508 mouse pancreatic cancer cell line, 12 single mouse white blood cells, 18 single GFP lineage-traced circulating tumor cells from two mice, 20 single GFP lineage-traced cancer cells from the primary pancreatic tumor of a mouse, and 34 dilutions to 10 or 100 picograms of total RNA from mouse primary pancreatic tumors from 4 mice.
