Convergent Evolution Towards CD38 Biallelic Loss Is a Recurrent Mechanism of Resistance to Anti-CD38 Antibodies in Multiple Myeloma

• Published in: Blood 2024-11, Vol.144 (Supplement 1), p.592-592
• Main 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
• Format: Article
• Language: English
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood-2024-201056

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 (>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 (