Single cell analysis reveals intra-tumor heterogeneity and microenvironment for clear cell renal cell carcinoma

Here we performed 3' transcriptome single cell sequencing on 7 ccRCC patients' tumor and matched 5 adjacent normal samples. We identified two different functional subgroups in ccRCC tumor epithelial cells and two different gene transcriptional programs that were associated with survival across a TCGA cohort. We found important transcriptional factor regulons that played roles in ccRCC progression. We identified macrophage and T cell clusters whose higher infiltration in tumor was associated with overall survival. We also discovered some potentially targetable inhibitory interactions among tumor epithelial cells, the infiltrating T cell and myeloid compartments. Collectively, our data provided cell clusters and gene sets for predict clinical outcome and potential targets for ccRCC therapy. Overall design: Single cell mRNA profiles of 7 primary tumors and correspongding para-tumors from 7 patients with celar cell cancer were generated by 10X Genomics plartform, without technical replication, and sequenced by NovaSeq 6000 (Illumina)