16p Deletion Involving BCMA Locus Is Frequent and Predominantly Observed with del17p

New generation immunotherapies in Multiple Myeloma (MM) targeting BCMA, have shown remarkable clinical benefits. However relapse still occurs due to tumor intrinsic and extrisic resistance mechanisms including antigen loss related to mutation, deletion and splicing pattern changes. Two recent case reports including ours highlighted biallelic loss of BCMA as a cause for resistance to anti-BCMA targeting therapy. In both studies BCMA locus at 16p was deleted bringing in focus importance of del16p. Here, we have evaluated 2883 MM patients at diagnosis and relapse to understand frequency characteristics of somatic events targeting BCMA.

We first evaluated the frequency of deletion involving the BCMA locus (16p13.13) in MM patients from multiple studies using WGS sequencing data as well as using Affymetrix Cytoscan HD and SNP 6.0 arrays. We observed del16p in 8.58 % (7.6% to 14.6% in individual studies) of newly-diagnosed patients (n=2458). Similar frequency was observed in relapsed MM patients not previously exposed to BCMA targeting therapy. Next, we evaluated genome wide copy number alterations (CNAs) in all patients with loss of BCMA locus and observed similar frequency of loss in both hyperdiploid MM (HMM) and non-HMM suggesting its independence from cytogentic subtypes of MM. Overall copy number loss was significantly higher in patients with BCMA loss compared to rest of the MM patients. Patients with loss of BCMA locus have increased mutational load (8202 with 95% HDI 6921 and 9535) compared to those without BCMA locus loss (6975 with 95% HDI 6626 - 7343); probability of difference greater than 0 was 96.8% and difference of the means were 1222 [95% CI -112 - 2589]

We next evaluated co-occurrence of BCMA loss with other high risk events and observed del1p and del17p as being significantly associated with loss of BCMA locus [Odds ratio 19.37 (13.13-25.80), FDR = 1.57e-65; and 8.8 (6.39-12.15), FDR = 5.57E-39, respectively)]. Furthermore, we observed that when both BCMA and TP53 loss are present, they have same log ratio (sequencing) or smoothed copy numbers (SNP array). Similarly, we used CDKN2C as a proxy to chromosome 1p loss and observed that when both BCMA and CKDN2C loss are present in the same patient they tend to show similar copy number values. These data suggested a possibility of co-occurrence of these events in the same cell.

To further investigate this observation, we used single cell DNA sequencing data from patients with sub clonal and clonal BCMA locus loss. scDNA sequencing showed that almost all cells with BCMA deletion also had TP53 deletion (95%). Interestingly, almost all cells with BCMA loss also had p53 loss, while not all cells with p53 loss had BCMA loss suggesting that the chronology of this copy number alternation may suggest first p53 loss followed by BCMA loss. We further investigated whether a bi-allelic BCMA loss was observed after anti-BCMA targeted CAR-T cell therapy by imputing the copy number alterations using single cell RNA sequencing data. Our data from this case also indicated that BCMA loss tend to co-occur with TP53 deletions (OR=5.67 [95% CI 4.12-7.84], p value < 0.0001). Moreover, TP53 mutations were also more frequent in patients with del16p and del17p, compared to patients who only had del16p or del17p.

In summary, our data from large scale copy number profiles at the diagnosis and relapse showed that monoallelic BCMA deletions are frequent events, patients with these events show increased aneuploidy, mostly deletions, potentially making these cells vulnerable for biallelic loss of genes, especially under the pressure of targeted therapy. Our results also highlight that BCMA expressions in bulk sample may not detect the presence or absence of cells with target loss and therefore combining strategies at bulk and single cell level are necessary to understand the disease status. These results suggest the need to study del16p in patients being targeted for BCMA-directed therapy and its association with other risk factors in MM.