Biallelic Loss of BCMA Triggers Resistance to Anti-BCMA CAR T Cell Therapy in Multiple Myeloma

Chimeric antigen receptor (CAR) T-cell therapy targeting B cell maturation antigen (BCMA) has provided deep (73% - 100%) responses in relapsed/refractory multiple myeloma (MM). However, median PFS has been less than 12 months, and amongst the small number of patients retreated at the time of progression with the same CAR T product, responses have been infrequent. This highlights development of resistance that may preclude effectiveness of the 2^ndinfusion, and may also underly relapse following response to the initial CAR-T cell therapy. Here, we have investigated one of the resistance mechanisms using longitudinal single cell transcriptomic and bulk genomic analysis. This patient had relapsed/refractory IgG lambda MM with hypodiploidy and a complex karyotype with t(8;12) (q24;q14), clonal t(11;14) (q13;q32), and clonal deletion 13. Patient received 150x10⁶CAR+ T cells (ide-cel) and achieved partial response, with duration of response of 8 months. The patient was retreated with 450 x10⁶CAR+ T cells at relapse, but with no response.

To delineate the resistance mechanism, we evaluated the bone marrow (BM) niche using 37658 cells from eight time points from before 1st CAR T cell infusion to 2 months after 2nd CAR T cell infusion, and identified 13 clusters consisting of hematopoietic cells and MM/plasma cells. Using RT-PCR based detection, we observed engineered CAR T cells only at 2 weeks after first infusion, when maximal CAR T cell expansion was observed. We did not observe infused CAR T cells with single cell RNAseq after 2^ndinfusion, but a limited expansion was confirmed using RT-PCR.Re-clustering of the T cell cluster showed an increased proportion of CD4+ helper and T regulatory cells (Treg) 2 weeks after 1st infusion. In contrast, TREG proportion remained constant at the 2nd infusion, suggesting other causes for lack of expansion of CAR-T cells. We also did not identify any significant increase in the proportion of cells expressing immune check point inhibitory markers or in accessory cell types with immune inhibitory function in MM BM.

Since we did not delinate a role of the BM milieu mediating suppression of CAR-T cell expansion and function following 2^ndinfusion, we next explored tumor intrinsic factors. Soluble BCMA level (produced predominantly by MM cells) was high before the first CAR T cell infusion and dropped significantly to a very low level coinciding with the clinical response; however, it remained low even at the time of relapse with increase burden of MM, indicating a lack of BCMA production by MM cells. We therefore investigated genomic changes in MM cells at the time of relapse. Our single cell analysis of BM samples identified 3 samples (at the time of relapse and post 2^ndCAR T cell infusion) with significant numbers of MM cells, evidenced by expression of CD138 and XBP1 (marker of plasma cells), CCND1 (upregulated in this patient with t(11;14)) and lack of RB1 (downregulated in this patient with del13). Imputation of copy number alterations scRNAseq showed that the majority of MM cells had a deletion of 16p, including the BCMA locus located on 16p13.13. We further validated these findings using deep whole exome sequencing (WES) of purified CD138+ cells collected after the second CAR T infusion. Before first CAR T cell infusion, 4% MM cells showed deletion 17p, while after second infusion both WES and scRNAseq prediction showed that del17p and del16p were clonal, and longitudinal scRNAseq analysis indicated that del17p and del16p co-occurred in the same clone. Moreover, WES identified a subclonal nonsense mutation (p.Q38*) in BCMA that creates an early stop codon in the BCMA gene. This biallelic BCMA deletion, acquired with one copy loss and a 2^ndloss-of-function mutation, provides the molecular basis for lack of BCMA expression in MM cells at the time of relapse. Our data showed that both TP53 and BCMA had deletion in one allele and mutation in the second allele.

These results identify biallelic loss of BCMA locus as a potential resistance mechanism to BCMA targeting therapy. Our results highlight the need to investigate sBCMA as a potential indicator of BCMA loss at relapse, and to carry out detailed transcriptomic or genomic analysis to confirm mutations. Moreover, these data also demonstrate the ability of MM cells to survive without BCMA expression. With the growing number of BCMA targeting therapeutic modalities under development, we would expect to see such occurrences more commonly in the future.