Deep characterization of tumor microenvironments using single cell multi-omics analysis

Abstract Understanding the complexity of cell interactions in the tumor microenvironment (TME) requires the ability to distinguish each cell type, and is a prerequisite of personalized cancer treatments. Here, we use a fully integrated system for single cell RNA sequencing, to simultaneously profile the transcriptome, cell surface proteins and immune repertoire of cells from primary colorectal cancer (CRC), non-small cell lung cancer (NSCLC), and mucosa-associated lymphoid tissue (MALT) lymphoma. Each tumor varied in type and proportion of its cellular components, and in particular in the proportion of immune cells. The CRC tumor consisted of T (3% CD4+, 3% CD8+), B lymphocytes (5% CD79A+) and plasma B cells (11% IGH high). Repertoire sequencing identified a clonal expansion (>4% of B cell clonotypes) suggesting a strong B cell response in this tumor. The NSCLC tumor displayed a marked immune cell infiltration containing predominantly B cells (30% CD79A+ and 8% IGH high plasma B) with a very limited clonal expansion. The MALT lymphoma consisted of only T and B lymphocytes (31% CD4+, 8% CD8+, 57% CD79A+). In addition to the activated CD4+ and CD8+ T cells, Tfh and Treg cells were clearly identified as well as two distinct large B cell populations showing plasmacytic differentiation. Analysis of the B cell repertoire revealed a large expanded clone bearing an IGHV segment associated with parotid MALT lymphoma. These findings emphasize the importance of combining repertoire and gene expression sequencing data to determine the nature and clonality of an immune response. This method enables full characterization of tumor heterogeneity and the adaptive immune response to the TME and will be key in the development of successful immunotherapies.