Today our new computational method for assigning cell types of the tumour microenvironment has been published in Nature Methods. The microenvironment is the set of immune and structural cells that surround and interact with tumours, and has important consequences for both patient prognosis and response to therapy. Recently, single-cell RNA-sequencing (scRNA-seq) has given us the ability to measure the gene expression programs in single tumour cells, but until now we have lacked the tools to assign these to the constituent cell types of the tumour microenvironment. Our new computational method called CellAssign solves this problem by probabilistically assigning each cell to a given cell type — such as immune or stromal cells — automatically across large patient cohorts. Consequently, we can now routinely uncover the microenvironment composition from scRNA-seq samples, and we demonstrated this on data generated from both High Grade Serous Ovarian Cancer (HGSC) and Follicular Lymphomas.
View a commentary on CellAssign here.
You may read the article by Zhang et al. on Nature Methods.