Background

RAS signaling pathway mutations, mainly NRAS, KRAS, and/or PTPN11 variants, are common somatic events in de novo and MR-AML. BRAF mutations occur with lower frequency in AML and are reported to be associated with poor treatment outcome. However, no comprehensive analysis exists that firmly delineates clinical and molecular characteristics of BRAF-mutated AML, including insights into clonal architecture and co-occurring mutations.

Methods

We identified 42 patients (pts) with BRAF-mutated AML among pts with molecularly profiled disease in the setting of large comprehensive cancer centers [enriched for relapsed/refractory (R/R) and secondary AML] and cooperative group frontline trials (Cancer and Leukemia Group B/Alliance for Clinical Trials in Oncology, enriched for de novo AML). All pts had NGS-based targeted sequencing data, cytogenetic information, and detailed clinical annotations available. To fully evaluate the molecular landscape, 6 pts underwent integrated genomic profiling including paired tumor/normal whole exome sequencing and total transcriptome sequencing.

We also analyzed pt samples using simultaneous single-cell molecular profiling and cell surface protein expression (DNA+Protein) sequencing to assess cell states and clonal make-up at single-cell resolution in a subset of pts (n=8).

Results

The 42 pts with BRAF-mutated AML had a median age of 67 years (range, 19-84); 57% were male. BRAF mutations were most common in cases of MR-AML (as defined by WHO 5th edition), accounting for 32 (76%) pts. BRAF mutations were found in newly diagnosed (n=19, 45%), R/R (n=8, 19%) and secondary AML (n=15, 36%) pts. As detected by bulk NGS sequencing, BRAF mutations were found both as dominant clonal and subclonal events, present at variant allele fractions (VAF) of 1-83% ( Figure 1, BRAF VAF indicated via color scale). Most (n=30, 71%) pts had non-V600 BRAF mutations (including G469, n=12; D594, n=7 and other, n=12). The most frequent co-occurring mutations were in the TET2 (36%), ASXL1 (33%), NRAS (29%), KRAS (26%), RUNX1 (19%), DNMT3A, FLT3-ITD/TKD, NPM1 and SRSF2 (all 17%) genes. By whole exome sequencing, BRAF-mutated AML samples carried a median mutational burden of 15 non-synonymous coding variants (range, 9-30), including 6 RAS-pathway and 3 MR-AML mutations. In 2 pts with paired relapse material available, the BRAF mutation was either stable at relapse or lost and the pt instead acquired a IQGAP3 mutation, supporting the RAS-pathway “addiction” of this leukemia. Single-cell multi-omic sequencing studies uncovering unique genotype-immunophenotype relationships and confirming clonal hierarchies are ongoing and will be presented at the meeting. Clinically, the BRAF-mutated pts had extremely poor survival, regardless of therapy. Pts were treated with low intensity [LI, n=10 (29%); LI+venetoclax (VEN, n=10 (29%)], high-intensity [HI, n=12 (34%) or HI+VEN, n=3 (9%)] regimens. The overall composite remission (CR+CRi) rate was 39%. Median overall survival (OS) for the entire cohort was 7 months, with 31 (89%) of pts deceased at the time of last follow-up. There were no significant differences in OS based on treatment regimens ( Figure 2). Importantly, there was no impact of BRAF variant allele burden on OS, with pts wiith dominant clonal and those with subclonal mutations having similar outcomes. Given the enrichment of BRAF mutations in MR-AML, we assessed whether RAS pathway mutations generally represented poor outcome prognosticators in this subgroup. A comparison of a control cohort of MR-AML pts with (n=129) and without (n=403) RAS pathway mutations treated on cytarabine/daunorubicin-based frontline protocols, revealed no survival difference between RAS-mutated and wild-type pts, suggesting a negative survival impact specific to BRAF-carrying leukemic clones.

Conclusions

BRAF mutations are rare, but recurrent molecular alterations in AML that are enriched in MR-AML. They associate with distinctly poor prognosis regardless of their clonal burden, without significant therapeutic advantage of currently available treatment regimens. This suggests the need to assess the utility of BRAF inhibitors and/or RAS pathway-targeting regimens such as MEK inhibitors in pts with AML carrying BRAF mutations.

Support: U10CA180821, U10CA180882, U24CA196171; Clinicaltrials.gov: NCT00048958 (CALGB 8461), NCT00899223 (CALGB 9665), NCT00900224 (CALGB 20202)

Walker:Karyopharm Therapeutics Inc.: Consultancy, Current Employment, Current equity holder in publicly-traded company. DiNardo:Schrödinger: Consultancy; ImmuniOnc: Honoraria; Fogham: Honoraria; Astellas: Honoraria; Servier: Honoraria; Notable Labs: Honoraria; Novartis: Honoraria; BMS: Honoraria; AbbVie/Genentech: Honoraria; Takeda: Honoraria. Daver:Pfizer: Consultancy, Research Funding; AbbVie: Consultancy, Research Funding; Gilead: Consultancy, Research Funding; Syndax: Consultancy; Agios: Consultancy; Trovagene: Research Funding; ImmunoGen: Consultancy, Research Funding; Celgene: Consultancy; Jazz: Consultancy; Novartis: Consultancy; Novimmune: Research Funding; FATE: Research Funding; Trillium: Consultancy, Research Funding; Hanmi: Research Funding; Astellas: Consultancy, Research Funding; Bristol-Myers Squibb: Consultancy, Research Funding; Daiichi Sankyo: Consultancy, Research Funding; Genentech: Consultancy, Research Funding; Shattuck Labs: Consultancy; Servier: Consultancy, Research Funding; Glycomimetics: Research Funding; Kite, a Gilead company: Consultancy, Research Funding; AROG: Consultancy; Amgen: Consultancy, Research Funding; Kronos Bio: Research Funding. Kadia:AbbVie, Amgen, Inc, Ascentage Pharma Group, Astellas Pharma Global Development, Astex, AstraZeneca, BMS, Celgene, Cellenkos Inc, Cyclacel, Delta-Fly Pharma, Inc, Genentech, Inc., Genfleet, Glycomimetics, Iterion, Janssen Research and Development: Research Funding; Ascentage Pharma Group: Research Funding; Genentech: Consultancy, Research Funding; Pfizer: Consultancy, Research Funding; Cellenkos Inc.: Research Funding; Genzyme: Honoraria; Agios: Consultancy; Biologix, Cure, Hikma Pharmaceuticals: Speakers Bureau; Pulmotect, Inc.: Consultancy, Research Funding; Delta-Fly Pharma, Inc.: Research Funding; Liberum: Consultancy; Jazz Pharmaceuticals, Pfizer, Pulmotect, Inc, Regeneron Pharmaceuticals, SELLAS Life Sciences Group: Research Funding; Celgene: Research Funding; AstraZeneca: Research Funding; GenFleet Therapeutics: Research Funding; Iterion: Research Funding; Glycomimetics: Research Funding; Hikma Pharmaceuticals: Speakers Bureau; SELLAS Life Sciences Group: Research Funding; Novartis: Consultancy; Amgen, Inc.: Research Funding; Janssen Research and Development: Research Funding; Astellas Pharma Global Development: Research Funding; Sanofi-Aventis: Consultancy; Regeneron Pharmaceuticals: Research Funding; Cure: Speakers Bureau; Cyclacel: Research Funding; Daiichi Sankyo, Genentech, Inc., Genzyme, Jazz Pharmaceuticals, Liberum, Novartis, Pfizer, PinotBio, Inc, Pulmotect, Inc, Sanofi-Aventis, Servier: Consultancy; Servier: Consultancy; Pinotb-Bio: Consultancy; BMS: Consultancy, Research Funding; Astex: Honoraria. Borthakur:Astex Pharmaceuticals, Ryvu, PTC Therapeutics: Research Funding; Catamaran Bio, Abbvie, PPD Development, Protagonist Therapeutics, Janssen: Consultancy; Pacylex, Novartis, Cytomx, Bio Ascend:: Membership on an entity's Board of Directors or advisory committees. Ravandi:Astellas: Consultancy, Honoraria, Research Funding; Syros: Consultancy, Honoraria, Research Funding; Biomea fusion: Honoraria, Research Funding; Abbvie: Consultancy, Honoraria, Research Funding; Amgen: Honoraria, Research Funding; Celgene/BMS: Consultancy, Honoraria, Research Funding; Astex/taiho: Membership on an entity's Board of Directors or advisory committees, Research Funding; Xencor: Research Funding; Prelude: Research Funding. Baer:FORMA Therapeutics (Inst): Research Funding; Kite, a Gilead company (Inst): Research Funding; Kura Oncology (Inst): Research Funding; Takeda (Inst): Research Funding; Ascentage Pharma (Inst): Research Funding; Abbvie (Inst): Research Funding. Marcucci:Ostentus Therapeutics: Current equity holder in private company, Research Funding. Uy:Jazz: Other: Advisory Board. Stock:Newave: Honoraria; Kite: Consultancy; Kura: Research Funding; Servier: Other: Data Safety Monitoring Board/Advisory Board; Jazz Pharmaceuticals: Consultancy, Honoraria; Glaxo Smith Kline: Consultancy; Amgen: Honoraria. Stone:Rigel: Consultancy; Kura One: Consultancy; CTI Biopharma: Consultancy; Epizyme: Other: DSMB; Syntrix: Other: DSMB; Abbvie: Consultancy; Aptevo: Other: DSMB; Jazz: Consultancy; Cellularity: Consultancy; BerGenBio: Consultancy; AvenCell: Consultancy; Amgen: Consultancy; GSK: Consultancy; Takeda: Other: DSMB; Hermavant: Consultancy; Lava Therapeutics: Consultancy; Ligand Pharma: Consultancy. Byrd:Orange Grove Bio: Membership on an entity's Board of Directors or advisory committees; American Cancer: Membership on an entity's Board of Directors or advisory committees; AstraZeneca: Other: TRAVEL, ACCOMMODATIONS, EXPENSES; Eilean Therapeutics: Consultancy, Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees, Research Funding; Kurome: Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees; Vincerx: Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees; OSU Drug Devel. Inst.: Consultancy; Orbimed: Consultancy, Research Funding; Newave: Membership on an entity's Board of Directors or advisory committees, Research Funding. Blachly:Leukemia Diagnostic Device: Patents & Royalties: Being prosecuted; Epigenetic classification of leukemia: Patents & Royalties: PCT conversion filed; AbbVie: Consultancy; AstraZeneca: Consultancy; Astellas: Consultancy. Eisfeld:Karyopharm Therapeutics: Other: spouse employment; Astra Zeneca: Honoraria, Other: CEI Advisory Board; OncLive: Honoraria. Loghavi:Caris Diagnostics: Consultancy; Blueprint Medicine: Consultancy; Abbvie: Consultancy; Gerson Lehrman Group: Consultancy; QualWorld: Consultancy; Guidepoint: Consultancy; Recordati/ EUSA Pharma: Consultancy; Daiichi Sankyo: Consultancy; Astellas: Research Funding; Amgen: Research Funding; Abbvie: Current equity holder in publicly-traded company.

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2023
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