Myeloma cells with therapy-induced senescence-like phenotype are associated with resistance to CAR-T therapy

Background: Patients (pts) with myeloma (MM) receiving CAR-T therapy have usually been exposed to many prior therapies. Melphalan (HDM) and other chemotherapies can induce cellular senescence. It has recently been shown that MM cells can also exhibit features of therapy-induced senescence (TIS). TIS tumor cells are associated with resistance to therapy and relapse. To investigate the presence of TIS MM cells prior to CAR-T and association with response, we examined the transcriptome and phenotype of MM prior to CAR-T. Method: We used scRNA-seq data from bone marrow (BM) MM cells: Boiarsky, et al. (GSE193531, dbGaP: phs001323.v3.p1) newly diagnosed MM (NDMM) pts; Dhodapkar, et al. (GSE210079), pre- and post CAR-T; pts who received CAR-T at Mayo Clinic, pre- (N=10) and post- (N=2). To evaluate TIS, single-cell gene set enrichment analysis (scGSEA) for several gene sets (PMID: 40164720): SenUp (Senescence Upregulated), SenGA (Senescence Growth Arrest), and SCAPs (Senescent Cell Anti-apoptosis Pathways); and a Plasma Cell Senescence (PCSen) gene set (GSE5900, GSE47552). To assess TIS and myeloid phenotype, BM MM cells (CD138+) were stained for CD14, CD16, KLRG1 and GPNMB and analyzed by CytoFlex and Kaluza. Results: In the integrated dataset, scGSEA showed significantly higher enrichment of PCSen, SenUp, SenGA, and SCAPs in late-stage MM cells (both pre- and post-CAR-T) compared to NDMM and healthy donors (p<0.05, Kruskal-Wallis with Dunn's posttest). Conversely, the Normal gene set was significantly enriched in healthy plasma cells relative to MM (p<0.05). Expression of CDKN2A, which encodes the senescence marker p16, was also increased in late-stage MM relative to NDMM or healthy plasma cells. Notably, in our newly generated scRNA-seq samples collected within 6 months before CAR-T, a significant inverse correlation between senescence marker expression and progression free survival (PFS) post-CAR-T was seen, suggesting that MM cells exhibiting TIS may be more resistant to T cell mediated cytotoxicity. We found that 62.5% (25/40) of pts had >1% MM cells that were CD14+. Among them, the median CD14+ MM cells were 5.5% (1-71%); and median CD14+CD16+ MM cells were 2.14% (0.4-67%). Among 7 pts with available samples for KLRG1 and GPNMB assessment, 100% (7/7) had KLRG+ MM cells (median: 59% (24-99%)) and 57% (4/7) had GPNMB+ MM cells (median: 15% (3.9-30%)), and KLRG1+GPNMB+ MM cells (median: 9.6% (3.8-17%)). Conclusion: Our study shows that late-line MM cells exhibit transcriptional and phenotype profiles consistent with TIS. This senescent phenotype may contribute to resistance to immunotherapies, including CAR-T. Additional phenotype data is collected and will be presented. A phase II clinical trial is ongoing (NCT06940297) to assess for the combined treatment with senolytic drugs dasatinib and quercetin peri-CART to deepen clinical response.