Nuclear respiratory factor 1(NRF1) sustains the development, progression and resistance of Multiple Myeloma [ATAC-seq_patients_NRF1]
Multiple myeloma (MM) is a hematological malignancy characterized by the clonal proliferation of plasma cells within the bone marrow. Despite significant advancements in understanding the pathogenesis and the development of novel therapeutic approaches, MM remains incurable. Emerging evidence indicates aberrant epigenetic activity at cis-regulatory elements (CREs). However, the characterization of these events and the definition of relative impact with MM phenotype is only partially known. To address this gap, we comprehensively analyzed the epigenetic changes occurring during MM progression to identify the events and the key transcriptional regulators sustaining the disease.We profiled a cohort of 55 patient MM samples at diagnosis, post-therapy, and relapse and a cohort of 16 MGUS samples using ATAC-seq. Then, we used footprinting analysis to identify detailed changes in transcription factor engagement. We conducted experiments using in vitro and in vivo methods, including primary cell line models and a MM mouse model (vk-Myc). We employed high-throughput techniques such as ChIP-seq, RNA-seq, and RNA-Single Cell. Our results were confirmed using shRNA interference, dCas9-KRAB-Mediated interference, and the usage of an independent cohort.We stratified the pervasiveness of open chromatin loci in our MM cohort. Penetrant loci were enriched for the binding of the Nuclear Respiratory Factor 1 (NRF1) in MM but not in MGUS samples. These findings were validated using 144 published ATAC-seq profiles of MM. ChIP-seq analysis on 15 MM and 6 MGUS patients confirmed that NRF1 sustains the activity of promoters and enhancers exclusively in MM but not in MGUS. A distinctive NRF1-dependent transcriptional signature of 103 genes was identified, correlating with aggressive disease and bad prognosis (CoMMpass dataset). This signature defines a group of 195 patients with a significantly poorer prognosis (20 months overall survival gap). The gene signature is enriched for survival pathways and ubiquitination. Our experiments show that NRF1 drives the proteasome homeostatic mechanism by enhancing phosphorylation and ubiquitination. NRF1 levels increase during therapy with proteasome inhibitors in our models. We identified a strong MM-specific enhancer element producing eRNA, looping towards the NRF1 gene. Interference with this eRNA downregulated NRF1 expression. Lowering eRNA in the presence of bortezomib increased cell proliferation loss, suggesting potential clinical applications for eRNA interference as an adjuvant to proteasome inhibitors.Collectively, our research supports that MM cells exhibit an addiction to NRF1, providing a survival advantage and therapy escape mechanisms. NRF1 binding reflects higher proteotoxic stress in malignant plasma cells and is crucial for their adaptability. Interfering with NRF1 and its regulatory elements significantly impairs MM therapy escape potential, highlighting its therapeutic benefit in MM treatment strategies. Overall design: To detect accessible chromatin regions at the MM and MGUS stages, we performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) on CD138-positive plasma cells isolated from the bone marrow of patients at these stages.