Pluto Bioinformatics

GSE146784: T cells and Dendritic cells from MC38 tumors treated with anti-PD-1 or anti-PD-1 plus D18

Bulk RNA sequencing

We treated mice bearing MC38 tumors with anti-PD-1 antibody (twice each week) or D18 (once one week). CD4+ T cells, CD8+ T cells and DCs were respectively isolated from tumors by FACS and RNA-seq performed. The goals of this study are to identify the activated cellular pathways in different subtype cells with the combination treatment. Samples were sequenced on an Illumina Hiseq 4000 instrument. The sequence reads were aligned to mouse mm10 reference genome using STAR (2.4.0) and then assembled and quantified by HTSeq (0.6.1) with Gencode M8 as annotation. DESeq2 was used for differential gene expression analysis among subgroups. Hierarchical clustering and principal component analysis were plotted applying FactoMineR and gplots libraries in R. log2 [FPKM] was calculated for each gene. We found that Granzyme, IFN, TNF were up-regulated and the related interferon induction pathway was activated in CD8+ T cells; the Th1 pathway and interferon signaling pathway were activated in CD4+ T cells; the expression of interferon-related and antigen-presenting machinery-related genes were increased in DCs by the combination treatment. SOURCE: Liangliang Wang (abcwangliang@126.com) - Tsinghua University