Convergent Evolution Towards CD38 Biallelic Loss Is a Recurrent Mechanism of Resistance to Anti-CD38 Antibodies in Multiple Myeloma
Authors: Diamond Benjamin , Baughn Linda B. , Poorebrahim Mansour , Poos Alexandra Maria , Lee Holly , Kaddoura Marcella , Wiedmeier-Nutor J Erin , Durante Michael , Otteson Gregory , Jevremovic Dragan , Tang Hongwei , Frohling Stefan , Papadimitriou Marios , Ziccheddu Bachisio , Jelinek Tomas , Landgren Ola , Neri Paola , Bergsagel P. Leif , Braggio Esteban , Kumar Shaji , Raab Marc S. , Fonseca Rafael , Bahlis Nizar J. , Weinhold Niels , Maura Francesco 
Published: December 2024

Introduction
Monoclonal antibodies (MoAbs) directed against CD38 are a mainstay in multiple myeloma (MM). Downregulation of CD38 expression is a resistance mechanism of antigenic escape, however, cell surface expression may return. While this tumor cell plasticity is likely driven by epigenetic mechanisms, it is unknown if MM cells can develop permanent resistance to anti-CD38 MoAb by acquiring genomic events leading to biallelic disruption of CD38 thus precluding re-treatment. Here, we report biallelic loss of CD38 as a recurrent mechanism of resistance, often via convergent evolution where distinct subclones are advantaged towards the same selective pressure.
Methods
We interrogated two sets of patients (Mayo Clinic; n = 31, Calgary University; n =19) with relapse following anti-CD38 MoAbs. Two additional cases of interest were selected from Heidelberg University. Whole genome sequencing (WGS, 60-100x) or whole exome sequencing (WXS), flow cytometry (flow), and bulk RNAseq were used to validate the effect of genomic events on CD38. Missense mutations predicted to affect CD38 MoAb binding were validated with site-directed mutagenesis of a CD38 plasmid, transduction into K562 MM cells, and CD38 MoAb binding assays.
Results
The prevalence of biallelic inactivation of CD38 at anti-CD38 MoAb relapse was 6% (3/50). An additional selected biallelic event was noted in the Heidelberg set. Each case is described in detail: MM-19 (Calgary) received daratumumab (Dara), lenalidomide, and dexamethasone (Dex), and then had a second exposure to Dara, following relapse. At this second relapse, WGS was performed on two independent extramedullary disease localizations in the liver. Both samples had unique, large deletions (&gt;3 Mb) on chromosome 4 coupled with additional unique focal deletions involving CD38. Flow confirmed the presence of CD138+/CD38- plasma cell populations in both sites.
A second case of convergent evolution was seen in a patient (Mayo) after seventh-line Dara/Len/Dex. WGS revealed a common deletion encompassing CD38. On the remaining allele, one subclone had a structural variation-mediated loss of CD38(cancer cell fraction; CCF 40%) while another harbored an L153H missense mutation (CCF 60%). Flow confirmed presence of two CD138+ clones; one with diminished CD38 expression. L153H was functionally validated to abrogate Dara binding, while maintaining CD38 expression. The third sample was collected after fifth-line Dara and sixth-line Dara/Bortezomib/Dex (Heidelberg) and represents another case of convergent evolution with a common loss of chromosome 4 and two subclones detected by WGS (P98Lfs*12, CCF 39% resulting in biallelic inactivation; R140G, CCF 61%). Bulk RNAseq revealed, in comparison to NDMM from CoMMpass, CD38 expression below the first decile. Notably, the R140G variant reduced binding affinity to Dara but not to Isatuximab (Isa).
A fourth case (Mayo) relapsing after 6 months of Dara-based therapy similarly had a focal deletion of CD38 with an L18Sfs*16 frameshift deletion on the remaining allele associated with a 4.35-fold reduction in CD38 expression by RNAseq compared to pre-treatment.
Interestingly, in 3/4 cases the CD38-negative clone emerged after a second exposure to anti-CD38 MoAb, suggesting emergence with the first exposure and then selection during the second. One other monoallelic event (C275Y; Heidelberg) was detected post-Isa. Copy number of the alternate allele is not known given targeted sequencing methodology, but the variant was seen to reduce binding affinity to both Dara and Isa. The prevalence of monoallelic loss of CD38 in newly diagnosed MM from MMRF CoMMpass was 7% (50/701) and two patients had mutations in CD38, but there were no cases of biallelic loss suggesting these events are driven by treatment pressure.
Conclusion
Distinction of the mode of CD38 loss is valuable for predicting outcome of re-challenge to anti-CD38 MoAbs. We see here an estimated 5-10% of anti-CD38 MoAb relapses are characterized by genomic antigen escape. Results here are in line with antigen escape to BCMA- and GPRC5D-directed immunotherapies (Lee et al, Nat Med 2023), suggesting that acquired antigen escape resulting from prolonged exposure to the selective pressures of immunotherapy is a recurrent mechanism of resistance in MM. Moreover, in select cases, non-overlapping resistance mutations provide rationale for switching agents at second exposure.