Single-Cell RNA Sequencing before and after Light Chain Escape Reveals Intrapatient Multiple Myeloma Subpopulations with Divergent Osteolytic Gene Expression.

ABSTRACT

High-risk multiple myeloma is genomically unstable, comprising heterogeneous populations of tumor cells that evolve over time. Light chain escape (LCE) is a clinical phenomenon observed when light chains rise separately from M-spike values, which implies divergent tumor evolution. We sought to understand LCE by performing high-depth transcriptomic and phenotypic studies. We performed single-cell RNA-sequencing (scRNA-seq) and ex vivo drug sensitivity profiling on serial bone marrow biopsies from a patient with LCE at diagnosis, first relapse, and relapsed/refractory timepoints. scRNA-seq revealed distinct transcriptomic subpopulations with phenotypes that could be tracked separately by clinical serum light chain and M-spike values. Genes differentially expressed between subpopulations were assessed for generalizable effects on prognosis from the Multiple Myeloma Research Foundation CoMMpass and GSE24080 datasets. Notably, the LCE subpopulation exhibited gene expression profile featuring prominent LAMP5 overexpression, which was associated with risk for osteolytic bone lesions. Ex vivo drug sensitivity testing displayed differential sensitivity of the subpopulations. Copy number variant inference showed that the transcriptomic subpopulation underlying LCE was related to a genetic subclone that evolved over time. Our findings illustrate that malignant subpopulations underly LCE in multiple myeloma. These studies imply that LCE and LAMP5 gene overexpression portends for increased risk of osteolytic bone disease and adverse prognosis, findings that were confirmed in the subset of patients from the CoMMpass database with LCE.

SIGNIFICANCE

scRNA-seq was used to study a patient with high-risk multiple myeloma featuring LCE. LCE was rooted in a transcriptomic subpopulation that corresponded to a genetic subclone and established novel links between LCE and LAMP5 overexpression to osteolysis and prognosis, validated in RNA-seq databases.