Sinan U. Umu

Abstract It has been reported that microsatellite instable (MSI) tumors in colorectal cancer (CRC) exhibit stronger anti-tumor responses than microsatellite stable (MSS) tumors. Analyzing scRNA-seq data from 185 CRC patients we found that immune, structural, and cancer cells in MSS tumors with high numbers of tumor-infiltrating CD8 T cells and macrophages (TAMs; CD8hiTAMhi) and CD8lowTAMhi tumors were enriched for pathways associated with anti- and pro-tumor responses, respectively.

Abstract It has been reported that microsatellite instable (MSI) tumors in colorectal cancer (CRC) exhibit stronger anti-tumor immune responses than microsatellite stable (MSS) tumors. Using a simple classification system we recently showed that MSS tumors with both high numbers of tumor-associated macrophages (TAMs) and T cells had good prognosis, whereas high numbers of TAMs and low numbers of T cells had by far the worst prognosis.

Abstract Background: Single-cell RNA sequencing (scRNA-seq) provides high-resolution transcriptome data to understand the heterogeneity of cell populations at the single-cell level. The analysis of scRNA-seq data requires the utilization of numerous computational tools. However, non-expert users usually experience installation issues, a lack of critical functionality or batch analysis modes, and the steep learning curves of existing pipelines.