Genomic Determinants of Resistance in Newly Diagnosed Multiple Myeloma Treated with Targeted-Immunotherapy

INTRODUCTION: Targeted immunotherapy combinations including anti-CD38 monoclonal antibody daratumumab have significantly increased the depth of response and clinical outcome in newly diagnosed multiple myeloma (NDMM). Despite this improvement, 30-40% of patients still progress and fail to achieve sustained minimal residual disease negativity (MRD-neg) through largely unknown resistance mechanisms. Here, we investigate the molecular variants associated with resistance to a quadruplet treatment combination.

METHODS: Whole genome sequencing (WGS) was performed on BM malignant plasma cells isolated using CD138+ magnetic- or flowcytometry (CD38, CD138, and CD45) from 58 NDMM patients treated with carfilzomib, lenalidomide, and dexamethasone with (DKRd, n=44; MANHATTAN trial) or without daratumumab (KRd, n=14; NCT01402284). Sustained MRD-neg was defined as two MRD-neg results, the first at the end of induction and the subsequent tested after at least 10 months. In the DKRd group, 42/44 (95%) received a total of 8 cyles; of 14 WGS who got KRd 11 either got 12 cycles, or 2 additional cycles after achieving MRD-neg CR (i.e., completed the protocol). Twelve (20.7%) patients received autologous stem cell transplantation. At the most updated follow up (median 3.7 years), 38 (66%) patients achieved MRD-neg; 27 (47%) were sustained, while 16 (28%) progressed. No difference in outcome or rate of MRD-neg was observed between KRd or DKRd), ISS, FISH or key clinical features including age, race, sex or ECOG). WGS gave us the resolution to accurately study 68 recurrent structural variants (SV), complex SV, 152 recurrent aneuploidies defined by GISTIC2.0), mutational signatures, and mutations in 80 driver genes (Rustad et al. Blood Cancer Discovery 2021).

RESULTS: With a median coverage of 75x (range 66-94), the median mutational burden was 6028 (range 1268-16745). Neither the clinical outcome nor the proportion of sustained MRD-neg were affected by this variable. Running mutational signatures analysis, high APOBEC single base substation signatures (SBS2 and SBS13) were associated with significantly shorter progression free survival (p=0.002).

We identified known features associated with poor prognosis including, del1p22 (RPL5), del1p12 (FAM46c), gain1q, del16q12 (CYLD) and del22q12 (XBP1). We validated these findings, in scRNA data from the KyDaR study (Cohen et al. Nat Med 2020) where 24 patients were treated with DKRd. Interestingly, we noted a significant correlation between non-responders and low expression of XBP1, FAM46c, and CYLD (p=0.04, p=0.03, p=0.009 respectively), in line with what observed in our WGS data. XBP1 loss was particularly interesting because of its inverse correlation with CD38 expression that could explain resistance to daratumumab. Focal loss of 17q12 (IKZF3) was seen in 4 cases, all of which progressed after DKRd. We validated the role of this deletion in resistance to lenalidomide-based treatment using CoMMpass (n=752). In this analysis, 13 out of 752 (1.7%) of NDMM cases had focal IKZF3 loss, with 61% having early progression (p=0.01).

We identified two novel gain of function SV hotspots associated with poor outcome after DKRd. The first involving 19p13.11 (the site of KLF2; p=0.00019), where the association between KLF2 over expression and poor prognosis was also seen in the KyDaR study (p=0.03). The second involved MYC (i.e., events on NSMCE2 and PVT1; p=0.017). Furthermore, we identified 4 novel regions of large chromosomal gain associated with early progression: 18q, 4q, 8q and 17q. We validated the prognostic and biological impact of these events in KyDaR and CoMMpass studies, respectively, focusing on the potential role played by these large chromosomal events affecting multiple genes. In these pathway-based analyses we show that KyDaR non-responders and gain 8q patients are significantly enriched for E2F and G2M pathway deregulation with significant down-regulation of IFN pathway genes. MYC targets pathway was also enriched in all the 4 gains, as well as in the KyDaR non-responders. Overall, all these genomic association were also confirmed after restricting our analysis to the patients treated with DKRd (N=44).

CONCLUSION: In this study, we have defined a comprehensive catalogue of genomic determinants of response to DKRd in NDMM identifying a number of new genomic alterations that explain resistance to the agents currently used in quadruplet combinations.

Hoffman:Bristol-Myers Squibb: Honoraria; Celgene: Honoraria; Seagen Inc.: Research Funding. Kazandjian:MMRF: Honoraria; Curio Science: Honoraria; Aptitude Health: Honoraria; Arcellx: Membership on an entity's Board of Directors or advisory committees; SINTOMA: Honoraria; Sanofi: Membership on an entity's Board of Directors or advisory committees; Plexus Communications: Honoraria; BMS: Membership on an entity's Board of Directors or advisory committees; CURE: Honoraria. Hassoun:Celgene: Research Funding; Takeda: Research Funding; Janssen Pharmaceuticals: Research Funding. Mailankody:Evicore: Consultancy; Janssen Oncology: Consultancy, Research Funding; BioAscend: Consultancy; Optum Oncology: Consultancy; Allogene Therapeutics: Research Funding; Takeda Oncology: Research Funding; Juno Therapeutics: Research Funding; Bristol Myers Squibb: Research Funding; Fate Therapeutics: Research Funding; Plexus Communication: Honoraria; OncLive: Honoraria; Physician Education Resource: Honoraria; Legend Biotech: Consultancy; Memorial Sloan Kettering Cancer Center: Current Employment. Shah:Bristol Myers Squibb: Consultancy, Research Funding; ACCC: Honoraria; Janssen: Consultancy, Research Funding; MashUpMD: Honoraria; MJH Lifesciences: Consultancy, Honoraria; Sanofi: Consultancy. Tan:Janssen: Honoraria, Research Funding. Hultcrantz:GSK: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Intellisphere LLC: Consultancy; Curio Science LLC: Consultancy; Bristol-Myers Squibb: Membership on an entity's Board of Directors or advisory committees; Amgen, Daichii Sankyo, Cosette, GSK: Research Funding. Scordo:McKinsey & Company: Consultancy; i3Health (CME): Honoraria; Kite - A Gilead Company: Other: Ad-hoc advisory board (past); Angiocrine Bioscience, Inc.: Consultancy, Research Funding; Amgen, Inc.: Research Funding; Omeros Corporation: Consultancy, Research Funding; Medscape, LCC (CME): Honoraria. Shah:Beyond Spring: Research Funding; Amgen: Research Funding; Janssen: Research Funding. Landau:Celgene: Consultancy; Janssen Scientific Affairs, LLC: Other: grants/pending grants; Memorial Sloan Kettering Cancer Center: Current Employment; Karyopharm: Consultancy; Pfizer: Consultancy; Caelum Biosciences: Consultancy; Legend Biotech USA Inc: Consultancy; Takeda Pharmaceuticals: Consultancy, Other: grants/pending grants; Janssen: Consultancy; Alexion: Other: grants/pending grants; Juno: Consultancy; Prothena: Honoraria. Giralt:Kite: Membership on an entity's Board of Directors or advisory committees; Novartis: Membership on an entity's Board of Directors or advisory committees; MILTENYI: Research Funding; TAKEDA: Membership on an entity's Board of Directors or advisory committees, Research Funding; OMEROS: Research Funding; SPECTRUM Pharma: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; Actinuum: Membership on an entity's Board of Directors or advisory committees, Research Funding; Jazz Pharmaceutical: Membership on an entity's Board of Directors or advisory committees; Johnson & Johnson: Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding. Dogan:EUSA Pharma: Consultancy; Peer View: Honoraria; Takeda: Other: Research Funding; Roche: Other: Research Funding; Physicians' Education Resource: Consultancy, Honoraria; Seattle Genetics: Consultancy; Incyte: Consultancy; Loxo: Consultancy. Lesokhin:Pfizer, Genmab, Sanofi, Iteos, BMS, Janssen: Consultancy; Memorial Sloan Kettering Cancer Center: Current Employment; Janssen, Pfizer, Iteos, Sanofi, Genmab: Honoraria; Janssen, Pfizer, BMS, Genentech/Roche: Research Funding; Serametrix, inc: Patents & Royalties; Trillium Therapeutics: Consultancy, Research Funding; Amgen: Honoraria; Sanofi: Research Funding; BMS: Honoraria. Davies:Takeda, Abbvie, Amgen, BMS/Celgene, Sanofi, GSK, Janssen: Membership on an entity's Board of Directors or advisory committees. Usmani:Amgen, BMS, Janssen, Sanofi: Speakers Bureau; Abbvie, Amgen, BMS, Celgene, EdoPharma, Genentech, Gilead, GSK, Janssen,Oncopeptides, Sanofi, Seattle Genetics, SecuraBio, SkylineDX, Takeda, TeneoBio: Consultancy; Amgen, Array Biopharma, BMS, Celgene, GSK, Janssen, Merck, Pharmacyclics, Sanofi, Seattle Genetics, SkylineDX, Takeda: Research Funding. Landgren:Janssen: Honoraria, Other: Independent Data Monitoring Committee (IDMC) member for clinical trials, Research Funding; Aptitude Health: Honoraria; Pfizer Inc: Consultancy; Theradex: Other: Independent Data Monitoring Committee (IDMC) member for clinical trials; NCI/NIH: Research Funding; Riney Foundation: Research Funding; Tow Foundation: Research Funding; Rising Tide Foundation: Research Funding; Leukemia & Lymphoma Society: Research Funding; MMRF: Honoraria; Merck & Co., Inc.: Other: Independent Data Monitoring Committee (IDMC) member for clinical trials; Amgen: Honoraria, Research Funding.