Bone Marrow Stroma-Induced Transcriptome and Regulome Signatures of Multiple Myeloma

SIMPLE SUMMARY: The bone marrow (BM) microenvironment provides a protective sanctuary for multiple myeloma (MM) against therapeutic agents. MM cells interact with BM stromal cells (BMSCs) and the interaction is sufficient to confer de novo multi-drug resistance with epigenetic mechanisms as one of the contributors yet to be elucidated. We profiled genome-wide landscapes of gene expression (transcriptome) and chromatin accessibility (regulome) for MM cells interacting with BMSCs and characterized the induced signatures. We evaluated the contributions from soluble factors derived from BMSCs and compared these results to physical adhesion to the BMSC-induced changes in the transcriptome and regulome. The multi-omics approach further identified candidate transcription factors that regulate the BMSC-induced transcriptome through modulating the regulome, which may lead to promising novel therapeutic targets for the treatment of MM. ABSTRACT: Multiple myeloma (MM) is a hematological cancer with inevitable drug resistance. MM cells interacting with bone marrow stromal cells (BMSCs) undergo substantial changes in the transcriptome and develop de novo multi-drug resistance. As a critical component in transcriptional regulation, how the chromatin landscape is transformed in MM cells exposed to BMSCs and contributes to the transcriptional response to BMSCs remains elusive. We profiled the transcriptome and regulome for MM cells using a transwell coculture system with BMSCs. The transcriptome and regulome of MM cells from the upper transwell resembled MM cells that coexisted with BMSCs from the lower chamber but were distinctive to monoculture. BMSC-induced genes were enriched in the JAK2/STAT3 signaling pathway, unfolded protein stress, signatures of early plasma cells, and response to proteasome inhibitors. Genes with increasing accessibility at multiple regulatory sites were preferentially induced by BMSCs; these genes were enriched in functions linked to responses to drugs and unfavorable clinic outcomes. We proposed JUNB and ATF4::CEBPβ as candidate transcription factors (TFs) that modulate the BMSC-induced transformation of the regulome linked to the transcriptional response. Together, we characterized the BMSC-induced transcriptome and regulome signatures of MM cells to facilitate research on epigenetic mechanisms of BMSC-induced multi-drug resistance in MM.