Project description:To determine the influence of in vivo tumor growth and antitumor immune responses on the generation of tumor neoepitopes, we performed whole exome sequencing (WES) on the mT3-2D cell line, WT tumors and SCID tumors
Project description:To investigate how pancreatic malignant epithelial cells responded to anti-tumor T-cell immune responses in vivo, RNA-seq was used to examine the gene expression profiles of the mT3-2D-GFP cell line and FACS sorted mT3-2D-GFP cancer cells isolated from WT and SCID tumors.
Project description:To comprehensively assess the immune milieu of WT and SCID mT3-2D tumors, we employed NanoString nCounter immune profiling. The two groups of samples exhibited distinct immune profiles and indicated greater upregulation of immune-related genes in mT3-2D WT tumors than in SCID tumors.
Project description:WES was used to analyze the mutational landscape of KPC and Panc02, two murine pancreatic cancer cell lines. As expected, a relatively low mutational burden was identified in KPC cells.
Project description:Recently, Bailey et al (2016, Nature) defined four subtypes of pancreatic cancer that are associated with distinct histopathological characteristics and differential survival, namely, Squamous, Pancreatic Progenitor, Immunogenic, and ADEX (Aberrantly Differentiated Endocrine eXocrine). We set out to assess by RNASeq whether loss of CXCR2 was significantly associated with a specific PDAC subtype. Pancreatic tumors were harvested from KPC or KPC Cxcr2-/- mice at endpoint (n=5 v 5), RNA prepared, and RNASeq analysis carried out. Reads were analysed using the bcbio-nextgen framework (https://bcbio-nextgen.readthedocs.org/en/latest/). After quality control and adaptor trimming, reads were aligned to the mouse genome build (UCSC mouse mm10) using STAR. Counts for known genes were generated using the function featureCounts in the R/Bioconductor package \Rsubread\. The R/Bioconductor package edgeR was used to identify differentially expressed genes.