RAS Pathway Mutations Are Associated with Progression after Hypomethylating Agent Therapy in Chronic Myelomonocytic Leukemia

Introduction: Hypomethylating agents (HMA) are the standard of care in chronic myelomonocytic leukemia (CMML), but responses remain transient with a subset of patients having high risk of progression with dismal prognosis. The mechanisms of resistance to HMA remain poorly understood and the genomic determinants of progression have not been fully elucidated. Identification of biological subsets with high risk of progression is paramount to develop novel therapeutic approaches.

Methods: We studied pts with CMML treated with HMA between 2018 and October 2021, whose bone marrow samples were analyzed by target next-generation sequencing. We performed chart review to obtain treatment responses and analyze correlations between clinical, cytogenetic and molecular characteristics and HMA failure. Primary objective was to determined risk factors associated with HMA failure and blast progression (BP). HMA failure was defined as lack of response after 4 cycles of therapy or relapse or progression after any number of cycles. Responses were evaluated following IWG 2006 response criteria. Blast progression was defined as presence of excess blasts at the time of failure including transformation to acute myeloid leukemia. Secondary objectives included to evaluate the clonal dynamic changes associated with blast progression.

Results: A total of 108 patients were identified including 50 (46.3%) patients with myeloproliferative CMML (MP-CMML) and 74 (68%) with either CMML-1 or CMML-2. Median age was 71 years (range 45-89). The most frequently identified mutations included ASXL1, TET2, SRSF2, RUNX1, NRAS, KRAS and CBL all present in more than 10% patients. After a median follow up of 19 months (95% confidence interval [CI] 15.8-23.9), 57 (53%) patients experienced HMA failure including 35 (32%) with blast progression at the time of failure of which 13 (12%) progressed to AML. Patients who experienced blast progression had significantly shorter survival compared to those without blast progression (median OS 18 months vs 50.2 months, HR 2.52 95% CI 1.34-4.74, p=0.004). By univariate analysis, none of the identified mutations was significantly associated with HMA failure. Development of a logistic regression model identified that patients with MP-CMML and those with SRSF2 mutations were more likely to experience HMA failure. We then evaluated if BP, among the types of HMA failure, was associated with specific genomic subsets of CMML. RAS pathway mutations (BRAF, CBL, KRAS, NF1, NRAS, and PTPN11) were significantly associated with BP (OR 3.35, 95% CI 1.46-7.70, P=0.004) (Fig. 1a) and shorter time to BP (HR 2.21, 95% CI 1.13-4.33, P=0.021). In addition to RAS pathway mutations, the WHO subtype (HR 1.73, 95% CI 1.08-2.76, p=0.022) and presence MP-CMML (HR 3.02, 95% CI 1.50-6.06, p=0.002) were also associated with shorter time to BP. Similar results were obtained when we developed a model using logistic regression analysis to evaluate the association between RAS pathway mutations and other clinical characteristics with the risk of BP (p=0.01158). To assess whether BP was associated with mutations not detected at disease initiation or with the clonal expansion of pre-existing mutations, we sequenced BM cells isolated at the time of HMA failure in 22 of the 35 patients with BP and compared their genomic landscape with that at baseline. Emergence of previously undetected mutations occurred in 17 (77%) of patients at time of blast progression (Fig. 1b). The most frequent acquired mutations involved genes in the RAS pathway (n=9) and ASXL1 (n=5). The expansion of pre-existing RAS pathway mutations was also observed in the BM of 2 patients (Fig. 1b).

Conclusions: Patients with CMML carrying pre-existing or emerging RAS pathway mutant clones alone or in combination with ASXL1 mutations have a higher risk of developing BP at the time of HMA therapy failure which is associated with shorter survival.

Kanagal-Shamanna:Amgen: Consultancy; Novartis: Consultancy; Aptitude Health: Speakers Bureau; Physicians Education Resource: Speakers Bureau. Kadia:Servier: Consultancy; Regeneron: Research Funding; Genentech: Consultancy, Research Funding; BMS: Consultancy, Research Funding; Novartis: Consultancy; Agios: Consultancy; Astex: Honoraria; cyclacel: Research Funding; Amgen: Research Funding; AstraZeneca: Research Funding; Delta-Fly: Research Funding; PinotBio: Consultancy; Iterion: Research Funding; Astellas: Research Funding; Genfleet: Research Funding; Ascentage: Research Funding; cellenkos: Research Funding; Glycomimetics: Research Funding; Pfizer: Research Funding; JAZZ: Consultancy, Research Funding; Abbvie: Consultancy, Research Funding. DiNardo:GenMab: Membership on an entity's Board of Directors or advisory committees; GlaxoSmithKline: Membership on an entity's Board of Directors or advisory committees; Kura: Honoraria, Membership on an entity's Board of Directors or advisory committees; Notable Labs: Current holder of stock options in a privately-held company, Membership on an entity's Board of Directors or advisory committees; AbbVie: Consultancy, Research Funding; Servier: Consultancy, Honoraria, Research Funding; Astellas: Honoraria; Bluebird Bio: Honoraria; Bristol Myers Squibb: Honoraria, Research Funding; Foghorn: Honoraria, Research Funding; ImmuneOnc: Honoraria, Research Funding; LOXO: Research Funding; Novartis: Honoraria; Takeda: Honoraria; Astex: Research Funding; Cleave: Research Funding; Forma: Research Funding; Jazz: Honoraria; Gilead: Honoraria. Daver:Agios, Celgene, SOBI and STAR Therapeutics: Consultancy, Membership on an entity's Board of Directors or advisory committees; Kartos and Jazz Pharmaceuticals: Other: Data monitoring committee member; Karyopham Therapeutics and Newave Pharmaceutical: Research Funding; Astellas, AbbVie, Genentech, Daiichi-Sankyo, Novartis, Jazz, Amgen, Servier, Karyopharm, Trovagene, Trillium, Syndax, Gilead, Pfizer, Bristol Myers Squibb, Kite, Actinium, Arog, Immunogen, Arcellx, and Shattuck: Consultancy, Other: Advisory Role; Astellas, AbbVie, Genentech, Daiichi-Sankyo, Gilead, Immunogen, Pfizer, Bristol Myers Squibb, Trovagene, Servier, Novimmune, Incyte, Hanmi, Fate, Amgen, Kite, Novartis, Astex, KAHR, Shattuck, Sobi, Glycomimetics, Trillium: Research Funding. Ravandi:Prelude: Research Funding; Biomea Fusion, Inc.: Research Funding; Xencor: Research Funding; AstraZeneca: Consultancy; Abbvie: Consultancy, Honoraria, Research Funding; Novartis: Consultancy; Syos: Consultancy, Honoraria, Research Funding; Astellas: Consultancy, Honoraria, Research Funding; Astex/Taiho: Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Honoraria, Research Funding; BMS/Celgene: Consultancy, Honoraria, Research Funding; Amgen: Honoraria, Research Funding. Jabbour:Amgen: Other: Advisory Role, Research Funding; Pfizer: Other: Advisory Role, Research Funding; Spectrum: Research Funding; Genentech: Other: Advisory Role, Research Funding; AbbVie: Other: Advisory Role, Research Funding; Adaptive Biotechnologies: Other: Advisory Role, Research Funding; Bristol Myers Squibb: Other: Advisory Role, Research Funding; Takeda: Other: Advisory Role, Research Funding. Pemmaraju:stemline: Consultancy; abbvie: Consultancy; immunogen: Consultancy; mustangbio: Research Funding; incyte: Consultancy; novartis: Research Funding; pacylex: Consultancy, Research Funding; samus: Research Funding; daiichi sankyo: Research Funding; cellectis: Research Funding; cellularity: Research Funding. Short:Astellas: Research Funding; Pfizer: Consultancy; Stemline Therapeutics: Research Funding; Amgen: Consultancy, Honoraria; Novartis: Consultancy; AstraZeneca: Consultancy; Takeda Oncology: Consultancy, Research Funding. Takahashi:Ostuka Pharmaceuticals: Honoraria; Agios: Consultancy; GSK: Consultancy; Illumina: Honoraria; Novartis: Consultancy; Mission Bio: Honoraria; Celgene/BMS: Consultancy; Symbio Pharmaceuticals: Consultancy. Kantarjian:Jazz Pharmaceuticals: Research Funding; AbbVie: Honoraria, Research Funding; Ascentage: Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Honoraria, Research Funding; Pfizer: Honoraria, Research Funding; ImmunoGen: Research Funding; Ipsen Pharmaceuticals: Honoraria, Membership on an entity's Board of Directors or advisory committees; KAHR Medical Ltd: Honoraria, Membership on an entity's Board of Directors or advisory committees; NOVA Research: Honoraria; Astellas Health: Honoraria, Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria, Research Funding; Daiichi-Sankyo: Consultancy, Research Funding; Takeda: Honoraria. Garcia-Manero:Aprea: Honoraria; Gilead Sciences: Research Funding; Astex: Consultancy, Honoraria, Research Funding; AbbVie: Honoraria, Research Funding; BMS: Consultancy, Honoraria, Research Funding; Acceleron Pharma: Consultancy; Novartis: Honoraria, Research Funding; Curis: Honoraria, Research Funding; Genentech: Honoraria, Research Funding.