Dynamic transcriptional reprogramming leads to novel immunotherapeutic vulnerabilities in myeloma

While there is extensive evidence for genetic variation as a basis for treatment resistance, other sources of variation result from cellular plasticity. Using multiple myeloma as an example of an incurable lymphoid malignancy, we show how cancer cells modulate lineage restriction, adapt their enhancer usage and employ cell-intrinsic diversity for survival and treatment escape. By using single cell transcriptome and chromatin accessibility profiling, we show that distinct transcriptional states co-exist in individual cancer cells and that differential transcriptional regulon usage and enhancer rewiring underlie these alternate transcriptional states. We demonstrate that exposure to standard treatment further promotes transcriptional reprogramming and differential enhancer recruitment, while simultaneously reducing developmental potential. Importantly, treatment generates a novel complement of actionable immunotherapy targets, such as CXCR4, which can be exploited to overcome treatment resistance. Our studies therefore delineate how to transform the cellular plasticity that underlies drug resistance into novel immuno-oncologic therapeutic opportunities. Overall design: Single cell expression profiles of 9 patients with relapsed/refractory multiple myeloma and two normal donors. Note: to protect Patient's privacy we didn't upload raw data for scATAC and Smartseq_htseq Samples.