scverse Conference 2024

Colorectal cancer (CRC) features molecular heterogeneity and differing immune cell infiltration patterns, affecting how patients respond to therapy. However, a comprehensive understanding of immune cell phenotypes across patient subgroups is missing. Using various "scverse" tools, we dissect the CRC tumor microenvironment by integrating 4,27 million single cells from 1670 samples and 650 patients across 49 studies (77 datasets) representing 7 billion expression values. These samples encompass the full spectrum of disease progression, from normal colon to polyps, primary tumors, and metastases, covering both early and advanced stages of CRC. Additionally, to address the limited availability of neutrophil single-cell data, we supplemented the atlas by analyzing samples from 12 CRC patients using a platform that captures cells with very low transcript counts. We present a high-resolution view of CRC with 62 major cell types or states, revealing different cell-type composition patterns in CRC subtypes. The atlas allows for refined tumor classification and patient stratification into four immune phenotypes: immune desert, myeloid, B cell, and T cell subtypes. These findings could have important implications for developing improved cancer immunotherapy approaches in CRC.
https://crc.icbi.at/