GSE120163
Next Generation Sequencing Facilitates Quantitative Analysis of CD45 positive immune cell Transcriptomes in four treated groups after hydrodynamic transfections
Purpose: The goals of this study are to compare the transcriptome profilings (RNA-seq) of CD45 positive immune cells in the control, polyIC, anti-PD-L1 and combination groups. Methods: All the CD45 positive immune cells of the mouse liver in control, polyIC, anti-PD-L1 and combination groups at day 24 were isolated, after hydrodynamic trasfection of c-Myc and N-ras at day 0. Then the mRNA profiles were generated by sequencing, in triplicate, using  Illumina HiSeq 4000. RNA-seq generated raw data were aligned to the GRCm38 mouse reference genome using Star program (2.3.0). Gene differential expression analysis was performed using Cuffdiff to obtain the expression levels of genes in each sample.Gene Set Enrichment Analysis (GSEA) analysis was performed for pathway analysis online (software.broadinstitute.org/gsea). Results: By comparing to the control group, the number of differentially expressed genes and the overlaps in other groups were listed by Venn diagram. There were a total of 1654 differentially expressed genes specifically in the combination group. Gene set enrichment analysis (GSEA) of these 1654 genes demonstrated that the immune cells in the combination groups were particularly associated with adaptive and innate immune system and the progresses of antigen processing and presentations. The key genes involved in interferon-g (IFg) signaling pathway and some key genes, as indicators of anti-tumor cytotoxic function, were listed by heatmap. Conclusions: The RNA-seq data further confirmed that combination of polyIC and PD-L1 Ab dramatically enhanced the anti-tumor immunity in the liver, especially the adaptive immune response. Overall design: The mRNA profiles of CD45 positive immune cells from mouse liver in control, polyIC, anti-PD-L1 and combination groups at day 24 after hydrodynamic trasfection of c-Myc and N-ras (day 0) were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.