Single cell RNA-seq of relapsed and refractory multiple myeloma patients defines new resistance pathways and targeted treatments

Multiple myeloma (MM) is a neoplastic plasma cell (PC) disorder, characterized by clonal proliferation of malignant PC. Despite extensive research, disease heterogeneity within and between treatment resistant patients is poorly characterized. Here, we conduct a prospective multi-center single-arm clinical trial (NCT04065789), combined with longitudinal single cell RNA-seq to study the molecular dynamics of MM resistance mechanisms. Forty-one newly diagnosed MM patients who either failed to respond or experienced early relapse after a bortezomib-containing induction regimen, were enrolled to evaluate the safety and efficacy of a daratumumab/carfilzomib/lenalidomide/dexamethasone combination. Primary clinical endpoint was safety and tolerability. Secondary endpoints included overall response rate; progression free survival, and overall survival. Treatment was safe and well-tolerated, deep and durable responses were achieved. In prespecified exploratory analyses, comparison of 41 primary-refractory and early-relapsed patients with 11 healthy subjects and 15 newly diagnosed MM patients revealed new MM molecular pathways of resistance, including hypoxia tolerance, protein folding, and mitochondria respiration, that generalized to larger clinical cohorts (CoMMpass). We found peptidylprolyl isomerase A (PPIA), a central gene in the protein-folding response pathway, as a potential new target for resistant MM. CRISPR/Cas9 deletion of PPIA or inhibition of PPIA with cyclosporin A significantly sensitizes MM tumor cells to proteasome inhibitors. Together, our study defines a roadmap for integrating scRNA-seq in clinical trials, identifies a signature of highly resistant MM patients and discovers PPIA as a potent therapeutic target for these tumors. To better understand early resistance mechanisms of PRMM patients, we designed an open-label single arm prospective clinical and translational trial combined with comprehensive scRNA-seq. We recruited patients with MM who received a bortezomib-based induction and either failed to achieve a timely response (<4 months/ cohort A) or progressed early (<18 months/ cohort B). The designed therapeutic treatment includes a quadruple regimen comprised of Daratumumab, Carfilzomib, Lenalidomide and Dexamethasone (DARA-KRD) (Methods; KYDAR Clinical Trial). We sequenced bone marrow PC from a total of 41 KYDAR patients: 34 baseline, 27 cycle-4 (3 months -marked post), and 10 cycle-10 (9 months -marked post2). In addition, we also characterized BM PC using MARS-seq from 15 newly diagnosed MM (NDMM) patients and 11 healthy aged control group undergoing hip replacement surgery as previously described.