CancerSEA-X: A Single-cell Resource for Tumor Microenvironment Cell States Across over 30 Cancer Types

Single-cell studies have significantly advanced our understanding of the transcriptional and functional heterogeneity in cancers. Recent studies have identified distinct states of cancer, immune, and stromal cells in the tumor microenvironment (TME), with growing evidence highlighting their clinical significance and therapeutic potential. Here, we present CancerSEA-X, an expanded version of CancerSEA that offers a comprehensive atlas of TME cell states. CancerSEA-X integrates 25 cancer cell states, 105 immune cell states, and 26 stromal cell states from systematically curated publications. Combining 239 single-cell datasets across 32 cancer types, encompassing over 9 million cells from 2120 patients, CancerSEA-X provides functional activity spectra and cancer-specific gene associations for these 156 cell states. These cell state-gene relationships were mapped onto networks, providing a systematic view of the TME. To improve usability, we redesigned the user interface to feature cell state characterization, state-gene correlation analysis, and interactive visualization of cell state-gene networks, enabling researchers to comprehensively explore these states and their functional relevance. Overall, CancerSEA-X serves as a valuable platform for investigating TME cell states, deepening our understanding of cancer heterogeneity, and potentially advancing the design of more effective clinical therapies. CancerSEA-X is freely available at http://biocc.hrbmu.edu.cn/CancerState.