Circulating extracellular vesicle isomiR signatures predict therapy response in patients with multiple myeloma

Abstract

Multiple myeloma (MM) is a plasma cell neoplasm characterized by high inter- and intra-patient clonal heterogeneity, leading to high variability in therapeutic responses. Minimally invasive biomarkers that predict response may help personalize treatment decisions. IsoSeek, a single-nucleotide resolution small RNA sequencing method can profile thousands of microRNAs (miRNAs) and their variants (isomiRs) from patient plasma-purified extracellular vesicles (EVs). Machine learning-generated miRNA/isomiR classifiers accurately predict therapeutic response in relapsed/refractory MM (RRMM) patients receiving daratumumab-containing regimens, achieving an area-under-the-curve of 0.98 (95% confidence interval [CI]:0.94–1.00). A classifier signature with the plasma cell-selective miR-148-3p, predicts durable response (≥6 months), progression-free (hazard ratio [HR]: 33.09, 95% CI: 4.2–262, p < 0.001), and overall survival (HR: 3.81, 95% CI: 1.05–13.99, p < 0.05). Targetome analysis connects the prognostic classifier to established MM drug targets BCL2 and MYC suggesting biological relevance. Thus, EV-isomiR sequencing in MM patients offers a tumor-naïve alternative to an invasive bone-marrow biopsy for predicting treatment outcome.