Biphasic control of the B cell transcriptome by mTORC1 and GSK3

Dysregulated gene expression in germinal center (GC) B cells is associated with autoimmune disorders and lymphoma. To detect pivotal gene regulators and potential therapeutic targets, we fluorescently labeled 47 key B cell genes and performed genome-wide sgRNA screens in GC-lymphoma cells. We identified 4,440 regulators and 17,638 connections containing regulatory directions and strength. We developed the interactive data portal B-LEARN, to access, analyze and visualize the molecular network data. Mechanistic Target of Rapamycin (mTOR) signaling forms a regulator hub accounting for ~40% of regulators identified. Using reporter cell lines, we evaluated impact of rapamycin, a potent mTOR inhibitor, which repressed cell cycle genes early post-treatment but unexpectedly increased immune response genes later. Glycogen synthase kinase 3 (GSK3) counteracted mTOR for immune gene expression and cell cycle control but not translation. The matching set of reporter cell lines and interactive data portal will be a useful resource for future studies. Overall design: CRISPR screen, ChIPseq, mRNAseq