The follicular lymphoma and chronic lymphocytic leukemia proliferative microenvironment at single-cell resolution

Lymph nodes (LNs) are secondary lymphoid organs where lymphocytes interact with antigen presenting cells to initiate adaptive immune responses within microenvironments established by resident stromal cells. LNs are also the major site of growth of follicular lymphoma (FL) and chronic lymphocytic leukemia (CLL), B cell neoplasms that alter the stromal architecture of LNs in highly stereotypic ways. To characterize FL and CLL cells within the LN microenvironment, we developed a pipeline for single-cell RNA sequencing of all resident LN cells. We observed that proliferation of FL and CLL cells within specialized niches commences with transient upregulation of MYC, subsequent downregulation of which may act to limit the growth potential of these indolent neoplasms. Proliferating FL cells within neoplastic follicles co-localized with follicular dendritic cells, whereas proliferating CLL cells were spatially associated with a distinct set of fibroblasts expressing CCL19 that localized to proliferation centers. We used informatic analyses and microscopy to identify and validate interacting sets of ligand-receptor pairs between proliferating neoplastic B cells, immune cells and stromal fibroblasts, including interactions involving CD74-MIF, TNFRSF13C (BAFF receptor), immunomodulatory factors such as CD55 and Galectin-9 (Gal9), and adhesion molecules. Our analyses highlight common features of these two microenvironment-dependent neoplasms and provide a roadmap for identifying vulnerabilities and new therapeutic strategies. Key pointsO_LINodal FL and CLL cells have similar proliferative programs and predicted ligand-receptor interactions with immune and stromal cells. C_LIO_LIProliferation of FL and CLL cells occurs in distinct lymph node niches defined by different types of fibroblasts. C_LI