Germline mediated HR deficiency, alu element duplication, and immune pathway alterations define aggressive, drug-resistant multiple myeloma

Abstract

Abstract Background: Multiple Myeloma (MM) is a plasma cell malignancy characterized by genomic instability, often manifesting as chromothripsis. Although CNVs in DNA repair genes are recurrent in MM, the combined effect of germline defects and somatic alterations in driving aggressive, therapy-resistant disease remains incompletely understood. Methods: We performed whole-genome sequencing (WGS) on tumor DNA from a patient with newly diagnosed (NDMM), progressive, treatment-resistant multiple myeloma and CNV gains across multiple chromosomes. This patient was from the original cohort of 17 patients we reported where we detected a possible correlation of copy number gains in DDR genes and aggressive myeloma.1 Analysis included detection of SNVs, indels, CNVs, structural variants (SVs), HRD scoring, mutational signatures, and pathway enrichment. Results: Germline mutations were identified in key DDR genes (RAD50, BRCA1, CHD1, SEMA4D), resulting in an HR-deficient phenotype (high HRD score/ high Genomic Instability). Variants in CYP2B6, CYP2D6, CYP3A5 indicated impaired drug metabolism. Somatic mutations in TRAF3andARID5B affected immune signaling and transcription. The genome showed near-triploidy (ploidy score: 2.98), high SV burden, and dominant CNV signatures, associated with whole-genome duplication and chromothripsis (or, chromoplexy). Mutational signatures included SBS1, SBS5, and DBS17, indicating age-related processes, DNA repair defects, and oxidative stress. A high MATH score along with local hypermutation events reflected tumor heterogeneity. SV analysis revealed extensive deletions, duplications, and complex rearrangements, especially on chromosomes 1 and 11. Widespread Alu element duplications and Alu-mediated rearrangements suggest non-allelic homologous recombination and L1 retrotransposition events. Pathway analysis revealed:DNA repair: HRR and NHEJ dysfunction; BRCAness without BRCA1/2 biallelic inactivation.Cell cycle: Impaired G2/M checkpoints.Immune signaling: TRAF3 mutation disrupted cytokine and interferon pathways.Gene transcription: TP53 pathway dysregulation.Metabolism: CYP variants affected drug/xenobiotic metabolism.Signal transduction: CHD1 mutation impacted nuclear receptor signaling.Developmental biology: SEMA4D and BRCA1 affected migration and differentiation.Hemostasis: F5 mutation altered fibrin clot formation, suggesting thrombotic risk, which is a known feature of myeloma. Discussion: Thibaud et al.2 found pathogenic germline variants in BRCA1/2 contributing to hereditary risk in 10 percent myeloma cases. Nazaryan-Petersen et al.3 showed germline chromothripsis driven by L1-Mediated Retrotransposition and Alu/Alu Homologous Recombination. Aoki et al.4 found hypomethylation of LINE elements correlated with progression and poorer prognosis of myeloma. They detected an association between common breakpoint loci at commonly lost regions with increased LINE-1 densities. Our findings of widespread Alu duplications in this case suggests the possibility that chromoplexy in myeloma may be induced by retrotransposon activity. This case illustrates a “two-hit” MM pathogenesis model: germline mediated HRD creates a permissive genomic background for catastrophic somatic events, including chromothripsis (or, chromoplexy) and immune gene disruption. Similar “two-hit” model involving tumor suppressor genes and oncogenes has been reported by Rodrigues et al.5 These findings emphasize the value of integrated germline-somatic multimodal analysis to identify high-risk disease biology and guide therapeutic strategies. Pawlyn et al.6 have suggested using PARP inhibitors in HRD-LOH MM, which correlated with high-risk disease in the relapsed MM (RRMM) setting. Our case suggests that such high-risk presentation can occur in newly diagnosed myeloma (NDMM) too and begs the question: should PARP inhibitors be evaluated for upfront induction treatment of such cases? References: Raychaudhuri J et al. Abstract 507/Transplantation and Cellular Therapy 30 2S (2024) S370-S398 Thibaud et al. Blood Cancer Discovery (2024);5: 428–41 Nazaryan-Petersen L et al. Hum Mutat. (2016) Apr;37(4):385-95 Aoki et al. Genome Medicine (2012), 4:101 Rodrigues et al. iScience, (2025) 28, 111620, January 17, Pawlyn C et al. Leukemia (2018) 32:1561–1566