The tumor immune microenvironmental analysis of 2,033 transcriptomes across 7 cancer types.

Scientific Reports
Sungjae KimJeong-Sun Seo

Abstract

Understanding the tumor microenvironment is important to efficiently identify appropriate patients for immunotherapies in a variety of cancers. Here, we presented the tumor microenvironmental analysis of 2,033 cancer samples across 7 cancer types: colon adenocarcinoma, skin cutaneous melanoma, kidney renal papillary cell carcinoma, sarcoma, pancreatic adenocarcinoma, glioblastoma multiforme, and pheochromocytoma / paraganglioma from The Cancer Genome Atlas cohort. Unsupervised hierarchical clustering based on the gene expression profiles separated the cancer samples into two distinct clusters, and characterized those into immune-competent and immune-deficient subtypes using the estimated abundances of infiltrated immune and stromal cells. We demonstrated differential tumor microenvironmental characteristics of immune-competent subtypes across 7 cancer types, particularly immunosuppressive tumor microenvironment features in kidney renal papillary cell carcinoma with significant poorer survival rates and immune-supportive features in sarcoma and skin cutaneous melanoma. Additionally, differential genomic instability patterns between the subtypes were found across the cancer types, and discovered that immune-competent subtypes in ...Continue Reading

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Methods Mentioned

BETA
PCA
RNA-seq

Software Mentioned

ESTIMATE
R package ‘ DESeq2
Tumor IMmune Estimation Resource ( TIMER )
R package ’ edgeR ’
GISTIC
PAAD
TIMER
ABSOLUTE
R package ‘ survminer ’

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