Genomic evolution and resistance to pirtobrutinib in covalent btk‐inhibitor pre‐treated chronic lymphocytic leukemia patients: results from the phase i/ii bruin study

Introduction: Pirtobrutinib, a highly selective, non-covalent (reversible) BTKi, demonstrated efficacy in patients (pts) with CLL resistant to cBTKi. Mechanisms of resistance to pirtobrutinib have not been systematically analyzed. Aim: To explore genomic evolution of pirtobrutinib resistance in cBTKi pre-treated CLL pts. Methods: Pts treated with pirtobrutinib monotherapy in phase 1/2 BRUIN trial (NCT03740529) who developed disease progression (PD) were included. Targeted NGS of all exons of 74 relevant genes was centrally performed on PBMCs. Somatic mutations were reported with a limit of detection (LoD) of 5% variant allele frequency (VAF). Manual inspection of BTK exons with LoD 1% was performed in selected cases. Results: As of 29 July 2022, 49 cBTKi pre-treated CLL pts who progressed on pirtobrutinib had paired NGS data at baseline and PD. The median age was 69 y (36–86), median number of prior lines was 4 (1–10) and 41 pts (84%) had discontinued prior cBTKi due to PD. Pts received one or more cBTKi: ibrutinib (n = 44, 90%), acalabrutinib (n = 10, 20%), or zanubrutinib (n = 1, 2%). ORR to pirtobrutinib (including PR-L) was 80%. Most common alterations at baseline were mutations in BTK (51%), TP53 (49%), ATM (27%), NOTCH1 (20%), SF3B1 (18%), PLCG2 (10%). Among 25 pts with ≥1 BTK mutation at baseline, mutations included C481S (n = 23), C481R (n = 4), C481Y (n = 2), C481F (n = 1), T474I (n = 1). BTK C481 VAF decrease/complete clearance was observed at PD in most pts (92%, 22/24, median VAF decrease=100%). At PD, 71% (35/49) of pts acquired ≥1 mutation, with 55% (27/49) acquiring ≥1 BTK mutation. Among these 27 pts, 36 acquired BTK mutations were identified; including gatekeeper mutations (T474I/F/L/Y, 17/49, 35%), kinase-impaired (L528W, 9/49, 18%), variants of unknown significance (VUS) proximal to the ATP-binding pocket (6/49, 12%; V416L (n = 2), A428D (n = 2), D539G/H (n = 1), Y545N (n = 1)) (Figure). Manual inspection for acquired BTK mutations at PD in baseline samples revealed 9 mutations (8 pts) pre-existed at baseline at low VAFs (1%–4%): 6 gatekeeper T474I/L, 2 kinase impaired L528W, 1 VUS A428D. These pts responded to pirtobrutinib (6/8, 75% ORR) and received prior ibrutinib (n = 5)/acalabrutinib (n = 4). Most commonly acquired non-BTK mutations were TP53 (7/49, 14%) and PLCG2 (4/49, 8%). Encore Abstract—previously submitted to EHA 2023 The research was funded by: Eli Lilly and Company Keyword: chronic lymphocytic leukemia (CLL) Conflicts of interests pertinent to the abstract K. Patel Consultant or advisory role: Abbvie, ADC Therapeutics, AstraZeneca, BeiGene, Bristol Myers Squibb, Caribou Biosciences, Celgene, Epizyme, Genentech/Roche, Kite, Loxo Oncology, MEI Pharma, Morphosys, Pharmacyclics/Janssen, TG Therapeutics, Trillium Therapeutics/Pfizer, Xencor Research funding: Adaptive Biotechnologies, Aptevo Therapeutics, AstraZeneca, Bristol Myers Squibb, CRISPR Therapeutics, Celgene, Curis, Inc, Epizyme, Fate Therapeutics, Genentech/Roche, Kite, Loxo Oncology, MEI Pharma, Nurix, Pharmacyclics/Janssen, Sunesis Pharmaceuticals, Trillium Therapeutics/Pfizer, Velos Bio, Xencor J. R. Brown Consultant or advisory role: Abbvie, Acerta/Astra-Zeneca, BeiGene, Bristol-Myers Squibb/Juno/Celgene, Catapult, Eli Lilly, Genentech/Roche, Hutchmed, iOnctura, Janssen, MEI Pharma, Pharmacyclics Research funding: BeiGene, Gilead, Loxo/Lilly, MEI Pharma, SecuraBio, Sun, TG Therapeutics B. Nguyen Employment or leadership position: [email protected] Stock ownership: [email protected] H. Won Employment or leadership position: [email protected] Stock ownership: [email protected] S. C. McNeely Employment or leadership position: Eli Lilly and Company Stock ownership: Eli Lilly and Company N. Marella Employment or leadership position: [email protected] Stock ownership: [email protected] K. Ebata Employment or leadership position: [email protected] Stock ownership: [email protected] J. A. Woyach Consultant or advisory role: Janssen, Pharmacyclics, Newave, MorphoSys, BeiGene, AstraZeneca, AbbVie, Genentech Research funding: Lox[email protected], Karyopharm Therapeutics, Schrodinger, MorphoSys, AbbVie C. S. Tam Honoraria: Janssen, AbbVie, Beigene, LOXO, AstraZeneca Research funding: Janssen, AbbVie, Beigene T. A. Eyre Consultant or advisory role: Roche, AstraZeneca, KITE Gilead, Loxo Oncology, Beigene, Incyte, Abbvie, Janssen, Secura Bio Honoraria: Roche, AstraZeneca, KITE Gilead, Loxo Oncology, Beigene, Incyte, Abbvie, Janssen Research funding: Astrazeneca, Beigene Other remuneration: Roche, AstraZeneca, Janssen, Abbive C. Y. Cheah Consultant or advisory role: Roche, Janssen, Gilead, AstraZenecca, Lilly, TG therapeutics, Beigene, Novartis, Menarini, Daizai, Abbvie, Genmab. BMS Honoraria: Roche, Janssen, Gilead, AstraZenecca, Lilly, TG therapeutics, Beigene, Novartis, Menarini, Daizai, Abbvie, Genmab. BMS Research funding: BMS, Roche, Abbvie; MSD, Lilly N. N. Shah Consultant or advisory role: Novartis, Lilly Oncology, Milentyi Biotec, Kite Pharma, BMS, TG therapeutics, Epizyme, Incyte Honoraria: Lilly Oncology Research funding: Miltenyi Biotec Other remuneration: Incyte P. Ghia Consultant or advisory role: AbbVie, AstraZeneca, BeiGene, BMS, Lilly/Loxo, Janssen, MSD, Roche Honoraria: AbbVie, AstraZeneca, BeiGene, BMS, Lilly/Loxo, Janssen, MSD, Roche Research funding: BMS, AbbVie, AstraZeneca, Janssen W. Jurczak Consultant or advisory role: Janssen, Astra Zeneca, Mei Pharma, Lilly, Takeda, Roche, Abbvie, Beigene Research funding: Abbvie, Bayer, Beigene, Celgene, Janssen, Roche, Takeda, TgTherapeutics,Astra Zeneca, Mei Pharma, Lilly M. Balbas Employment or leadership position: [email protected] Stock ownership: [email protected] B. Nair Employment or leadership position: [email protected] Stock ownership: [email protected] P. Abada Employment or leadership position: [email protected] Stock ownership: [email protected] C. Wang Employment or leadership position: Eli Lilly and Company Stock ownership: Eli Lilly and Company D. Wang Employment or leadership position: [email protected] Stock ownership: [email protected] A. R. Mato Honoraria: Adaptive Biotechnologies; AstraZeneca; AbbVie ; DTRM Biopharma ; Genentech ; Janssen ; BeiGene ; Octopharma ; TG Therapeutics , Inc ; Pharmacyclics , LLC ; LOXO ; Genmab ; Johnson & Johnson ; Curio ; Dava ; BMS ; Medscape ; PER, PerView Research funding: AstraZeneca; AbbVie ; DTRM Biopharma ; Genentech ; Janssen ; BeiGene ; Octopharma ; TG Therapeutics ; Nurix ; Pharmacyclics, LLC ; LOXO ; Genmab ; Johnson & Johnson ; Pfizer ; Acerta W. G. Wierda Other remuneration: GSK/Novartis, Abbvie, Genentech, Pharmacyclics LLC, AstraZeneca/Acerta Pharma, Gilead Sciences, Bristol Myers Squibb (Juno & Celgene), KITE Pharma, Sunesis, Miragen, Oncternal Therapeutics, Inc., Cyclacel, Loxo Oncology, Inc./Lilly, Janssen, Xencor