Identification of a CD138-negative therapy-resistant subpopulation in multiple myeloma with vulnerability to splicing factor inhibition

Abstract

The molecular basis of therapy resistance in multiple myeloma (MM) remains poorly understood. Here, we performed single-cell RNA sequencing coupled with VDJ-targeted sequencing of highly purified primary MM cells from patient bone marrow. This approach uncovered cellular heterogeneity and phenotypic plasticity along the CD138 axis, accompanied by drastic epigenetic alterations. Notably, therapy-resistant subpopulations were identified within a minor fraction of CD138- MM cells, and were shown via CRISPR/Cas9 screening to be vulnerable to splicing pathway inhibition. Consistently, this fraction of CD138- MM cells showed increased differential splicing associated with overexpression of SR protein family splicing factors. Among these splicing factors, RNA-binding protein 39 (RBM39) was specifically overexpressed in therapy-resistant cells and involved in aberrant splicing. Both genetic and pharmacological RBM39 inhibition exhibited a significant selective lethal effect on therapy-resistant CD138- MM cells. Collectively, our findings identify distinct therapy-resistant MM subpopulations and highlight the splicing pathway as a promising therapeutic target.