RNA-Seq analysis of DLBCL cell lines

Diffuse large B cell lymphoma (DLBCL) is the most common B cell non-Hodgkin lymphoma and remains incurable in around 40% of patients. Efforts to sequence the coding genome identified several genes and pathways that are altered in this disease, including potential therapeutic targets. However, the non-coding genome of DLBCL remains largely unexplored. Here we show that active super-enhancers are highly and specifically hypermutated in 92% of samples from individuals with DLBCL, display signatures of activation-induced cytidine deaminase activity, and are linked to genes that encode B cell developmental regulators and oncogenes. As evidence of oncogenic relevance, we show that the hypermutated super-enhancers linked to the BCL6, BCL2 and CXCR4 proto-oncogenes prevent the binding and transcriptional downregulation of the corresponding target gene by transcriptional repressors, including BLIMP1 (targeting BCL6) and the steroid receptor NR3C1 (targeting BCL2 and CXCR4). Genetic correction of selected mutations restored repressor DNA binding, downregulated target gene expression and led to the counter-selection of cells containing corrected alleles, indicating an oncogenic dependency on the super-enhancer mutations. This pervasive super-enhancer mutational mechanism reveals a major set of genetic lesions deregulating gene expression, which expands the involvement of known oncogenes in DLBCL pathogenesis and identifies new deregulated gene targets of therapeutic relevance. Total RNA was extracted from cells in log phase of growth using the TRIzol reagent and assessed for quality and quantified using the Bioanalyzer 2100 (Agilent). Samples (all with RIN > 9) were used to generate RNA-seq libraries with the Illumina Stranded Total RNA Prep with Ribo-Zero Plus, followed by high throughput sequencing on the Illumina HiSeq 4000 (60 million reads, 2 × 100 bp mode) system. Please note that the following updates have been made on Oct 17, 2022: The processed data (linked to the Series records) and data processing description have been updated. The GSM6285354 sample title has been updated from (incorrectly named) HOCI-LY1 to HLY1. The (incorrectly-named) GSM6285354 raw files have been replaced with the (identical but correctly-named) files.