TISCH – a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment

Cancer immunotherapy targeting co-inhibitory pathways by checkpoint blockade shows remarkable efficacy in a variety of cancer types. However, only a minority of patients respond to treatment due to the stochastic heterogeneity of tumor microenvironment (TME). Recent advances in single-cell RNA-seq technologies enabled comprehensive characterization of the immune system heterogeneity in tumors but posed computational challenges on integrating and utilizing the massive published datasets to inform immunotherapy.

Researchers from Tongji University present Tumor Immune Single Cell Hub (TISCH), a large-scale curated database that integrates single-cell transcriptomic profiles of nearly 2 million cells from 76 high-quality tumor datasets across 27 cancer types. All the data were uniformly processed with a standardized workflow, including quality control, batch effect removal, clustering, cell-type annotation, malignant cell classification, differential expression analysis and functional enrichment analysis. TISCH provides interactive gene expression visualization across multiple datasets at the single-cell level or cluster level, allowing systematic comparison between different cell-types, patients, tissue origins, treatment and response groups, and even different cancer-types. In summary, TISCH provides a user-friendly interface for systematically visualizing, searching and downloading gene expression atlas in the TME from multiple cancer types, enabling fast, flexible and comprehensive exploration of the TME.

Overview of the TISCH workflow and features

TISCH automatically parsed and curated tumor single-cell RNA-seq datasets from GEO or Array Express databases. All datasets were then uniformly processed with a standardized workflow, including quality control, batch effect removal, cell clustering, differential expression analysis, and cell type annotation at multiple levels. Each dataset in TISCH is displayed with relevant study information, including species, treatment, the number of patients and cells, technology platform, stage and related study. In the Dataset module, TISCH provides two functions: single-dataset exploration and multiple-dataset comparison. In the Gene module, TISCH allows single gene expression visualization across multiple datasets and cell types. TISCH also supports the downloading of expression matrices, DE gene tables and meta-information for each dataset.

Availability – http://tisch.comp-genomics.org