TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment

Abstract

The Tumor Immune Single Cell Hub 2 (TISCH2) is a resource of single-cell RNA-seq (scRNA-seq) data from human and mouse tumors, which enables comprehensive characterization of gene expression in the tumor microenvironment (TME) across multiple cancer types. As an increasing number of datasets are generated in the public domain, in this update, TISCH2 has included 190 tumor scRNA-seq datasets covering 6 million cells in 50 cancer types, with 110 newly collected datasets and almost tripling the number of cells compared with the previous release. Furthermore, TISCH2 includes several new functions that allow users to better utilize the large-scale scRNA-seq datasets. First, in the Dataset module, TISCH2 provides the cell–cell communication results in each dataset, facilitating the analyses of interacted cell types and the discovery of significant ligand–receptor pairs between cell types. TISCH2 also includes the transcription factor analyses for each dataset and visualization of the top enriched transcription factors of each cell type. Second, in the Gene module, TISCH2 adds functions for identifying correlated genes and providing survival information for the input genes. In summary, TISCH2 is a user-friendly, up-to-date and well-maintained data resource for gene expression analyses in the TME. TISCH2 is freely available at http://tisch.comp-genomics.org/.

Deciphering the role of QPCTL in glioma progression and cancer immunotherapy

“…Tumor Immune Single-cell Hub 2 (TISCH2) is an scRNA-seq database, which aims to characterize TMEs at single-cell resolution. TISCH2 ( http://tisch.comp-genomics.org ) has collected 187 sets of high-quality tumor single-cell transcriptome data and corresponding patient information from GEO and ArrayExpress ( 31 ). The data cover 50 cancer types, including 6 million cells from more than 1,500 patients.…”

Comprehensive analysis of the prognosis, tumor microenvironment, and immunotherapy response of SDHs in colon adenocarcinoma

“…Correlation analysis was applied to clarify the SDHs expression in connection with the expressions of immune-related genes. The Tumor Immune Single-Cell Hub (TISCH) database ( http://tisch.comp-genomics.org/home/ ), a scRNA-seq database focusing on the tumor microenvironment, was employed to analyze the correlations between SDHs expression and infiltrating immune cells ( 35 ). Gene expression data was gained from the GEO database (GSE146771), including 10468 single cells from 10 patients.…”

Deciphering comprehensive features of tumor microenvironment controlled by chromatin regulators to predict prognosis and guide therapies in uterine corpus endometrial carcinoma

“…Additionally, the CRRS was significantly inversely related to tumor mutation burden (TMB) (Figure 5B), and the combination of CRRS and TMB could better predict the overall survival of UCEC patients (Figure 5C). Microsatellite instability hypermutated (MSI-H) tumors account for approximately 25% to 30% of endometrial carcinomas (42), which have DNA mismatch repair defects, resulting in errors in repetitive DNA sequences known as microsatellites (41,43). As shown in Figure 5D, the MSI-H subtype had a lower CRRS.…”

“…We further verified the relationship between APOBEC3G and CD8A/ GZMB by qRT-PCR, and the results demonstrated that the two variables were positively correlated (Figure S8D). Then, we investigated the heterogeneity expression pattern of APOBEC3G, CD8A, and GZMB in different immune cells at a single-cell level using TISCH2 (UCEC-GSE139555) (43), and found that they were mainly expressed in CD8 + T cells (Figure S8E). Next, we explored associations between CRRS and signatures of antitumor immunity.…”