Recurrent Genomic Alterations in BCRi ‐Experienced CLL Patients Treated With Venetoclax: Extended Phase 2 Follow‐Up

First-generation covalent Bruton tyrosine kinase inhibitors (cBTKi; ie, ibrutinib) and second-generation cBTKis, acalabrutinib and zanubrutinib, disrupt aberrant B-cell receptor (BCR)-signaling via inhibition of BTK. BTKis, along with idelalisib, a phosphatidylinositol 3-kinase delta inhibitor that also inhibits BCR signaling, have transformed outcomes for patients with chronic lymphocytic leukemia (CLL) [1]. However, despite being in second-generation, these agents are not curative and adverse effects (albeit to a less extent) and susceptibility to resistance mechanisms remain [2, 3]. Venetoclax (ABT-199) is an oral selective small molecule BCL-2 inhibitor (BCL-2) approved as monotherapy or, in combination with an anti-CD20 antibody, as a fixed-duration regimen for adults with CLL, with high response rates observed in key pivotal trials in patients with relapsed or refractory CLL [4-6]. Unlike BTK or PI3K inhibitors, venetoclax acts independent of the BCR pathway [7]. In prior studies, objective response rates (ORR) with venetoclax following BTKi progression and/or intolerance ranged from 54%–65% with ibrutinib and 28%–67% with idelalisib [8, 9]; estimated 1-year progression-free survival (PFS) and overall survival (OS) ranged from 75%–79% and 91%–94%, respectively [8, 9]. This long-term follow-up report aims to better understand resistance mechanisms to these therapies, which may facilitate better treatment decisions for patients with CLL. To that end, this report provides updated data, with extended follow-up, on venetoclax monotherapy in patients with relapsed/refractory (R/R) CLL after prior BCRi treatment, including exploratory analyses looking at gene expression changes and mutational data. This was a Phase 2, open-label, single-agent, multicenter trial (NCT02141282) in adults previously treated with ibrutinib and/or idelalisib, whose disease relapsed on treatment or progressed after discontinuation due to toxicity of either agent. Patients with R/R CLL defined as per 2008 International Workshop for CLL National Cancer Institute–sponsored Working Group criteria were enrolled in two study arms based on most recent BCRi received (prior ibrutinib or prior idelalisib; Figure S1). Eligible patients received venetoclax 20 mg daily for 1 week, followed by weekly ramp-up to 400 mg target dose from Week 1 to Week 5 [8, 9]. Full study design was previously published [8, 9]. The trial was institutional review board approved and conducted in accordance with relevant ethical research standards. Patients provided written informed consent. The primary endpoint was ORR. Secondary endpoints included duration of response (DOR), time to progression (TTP), PFS, and OS. Undetectable minimal residual disease (uMRD) rate (threshold of 10−4, i.e., < 1 tumor cell/10 000 leukocytes in peripheral blood and/or bone marrow; assessed by central flow cytometry) was an exploratory endpoint. Safety assessments included monitoring treatment-emergent adverse events (TEAEs), serious AEs (SAEs), deaths, and changes in laboratory values and vital sign parameters. Post hoc genomic analyses were conducted on CD19+ cells pre- and post-venetoclax initiation. Detailed methods are available in the Supporting Information Appendix. In total, 127 patients with BCRi-R/R CLL were enrolled in the study (prior ibrutinib, n = 91 [including 13 with prior idelalisib at any time]; prior idelalisib, n = 36 [including 11 with prior ibrutinib at any time]). Demographic and baseline disease characteristics are reported in the Supporting Information Appendix (Tables S1 and S2). At data cutoff (December 22, 2021), patients in the prior ibrutinib arm had received ibrutinib before study entry for a median of 20.6 months (range, 1.0–60.8), while patients in the prior idelalisib arm had received idelalisib for 9.0 months (0.9–44.9). Median follow-up was 67.8 months (95% confidence interval [CI]: 66.0–72.1) overall, and 67.2 (65.4–71.1) and 71.2 months (64.6–75.6) in the prior-ibrutinib and -idelalisib groups, respectively. Overall median duration of venetoclax was 22.5 months (range, 0.1–83.1); 19.5 (0.1–83.1) and 35.5 months (1.3–82.3) in the prior-ibrutinib and idelalisib groups, respectively. In total, 39% of patients discontinued due to progressive disease (n = 13), AEs not related to progression (n = 13), and Richter's transformation (n = 7) (Figure S2). Sixty-three patients went on to receive at least one other line of therapy post study treatment. ORR was 66% (84/127) overall, 65% (59/91) with prior ibrutinib and 69% (25/36) with prior idelalisib (Figure 1A); response rates by subgroups are presented in Figure S3. Overall complete-remission/complete-remission-with-incomplete-bone-marrow-recovery rate was 13% (16/127); 11% (10/91) with prior ibrutinib and 17% (6/36) with prior idelalisib (Figure 1A). Median DOR (n = 84) was 43.6 months (95% CI: 28.6–55.4) overall; 35.1 months (95% CI: 19.4–50.5) and 55.4 (95% CI: 32.0–NE [not estimable]) months with prior-ibrutinib or idelalisib, respectively. Median TTP (n = 127) was 36.9 (95% CI: 23.4–53.0), 36.1 (95% CI: 21.9–49.0) and 43.4 months (95% CI: 20.1–NE) in the overall, prior-ibrutinib, and prior-idelalisib groups, respectively. Median PFS was 33.7 (95% CI: 21.8–46.2), 24.7 (95% CI: 19.2–40.9), and 43.4 months (95% CI: 20.1–NE) in the overall, prior-ibrutinib, and prior-idelalisib groups, respectively (Figure 1B). Of 127 patients, 72 (57%) were alive at study end (49/91 [54%] with prior ibrutinib, and 23/36 [64%] with prior idelalisib). Overall median OS was 70.6 months (95% CI: 62.2–NE); 69.6 months (51.3–NE) with prior ibrutinib and not reached (57.2–NE) with prior idelalisib (Figure 1C). Among evaluable patients (n = 77), 37/77 (48%) achieved uMRD (37/127 [29%] were undetectable by intention-to-treat principles). Of all patients with uMRD, 28/91 (31%) had prior ibrutinib and 9/36 (25%) had prior idelalisib. All patients experienced TEAEs. Most common grade 3/4 AEs (≥ 20%) were neutropenia/neutrophil count decreased (58%) and anemia (32%) with prior ibrutinib, and neutropenia/neutrophil count decreased (53%), anemia (22%), and thrombocytopenia (19%) with prior idelalisib (Table S3). A total of 55 (43%) patients died during the study; 10 (8%) experienced deaths ≤ 30 days after the last dose of venetoclax. TEAEs of tumor lysis syndrome (TLS) were reported in 2 (1.6%) patients; both were medium risk for TLS. Neither required venetoclax modification (Supplementary Results). Of 73 patients with a pretreatment specimen (n = 58 in prior ibrutinib, n = 15 in prior idelalisib cohorts), 34 had BTK C481 mutation at study entry; 43 patients had pre-existing TP53 mutation (59%; n = 35 with prior ibrutinib, n = 8 with prior idelalisib). Post hoc outcomes in participants with pre-existing BTK (C481) mutation are reported in Figure 1D,E and the Supporting Information Appendix (Figure S4), demonstrating similar efficacy to patients without pre-existing BTK mutation. Of available pre- and post-venetoclax samples, BCL-2 mutations were acquired in 13/68 patients (19%); 9 mutations detected at the time of relapse in patients with CLL progression and 4 in patients without progression (Figure 2A). The most common BCL-2 mutations post-venetoclax were G101V, R107-R110dup, D103E, D103Y, A113G, V156D, and D103V (Figure S5). The acquisition of a BCL-2 mutation did not appear to be associated with adverse outcomes compared with patients without these acquired mutations. That the BCL-2 mutations were observed at low variant allele frequency (VAF) (0.7%–34%) (Figure S5) and were detected in patients, regardless of whether their disease had progressed or was in remission at sample collection, suggests acquisition of BCL-2 mutation may be one of multiple co-occurring mechanisms associated with resistance to venetoclax therapy in vivo. Comparison of gene expression in pre- and post-venetoclax treatment samples (31 vs. 28) from patients whose disease progressed, delineated by prior BCRi, identified more than 2000 differentially expressed genes (false discovery rate < 0.05), with >90% upregulated post-venetoclax, including MCL1, BCL2L1, and BCL2A1 (Figure 2B,C). Pre- versus post-venetoclax sample comparisons (from patients whose disease did not progress; 27 vs. 18) at time of post-treatment sample collection identified over 10 000 differentially expressed genes, including MCL1, BCL2L1, and BCL2A1 upregulation at end of treatment (Figure 2D). The observation that the BCL-2 family genes change on Ven treatment independently of CLL progression suggests that additional alterations are needed for clinical relapse. In our study, uMRD in peripheral blood (29%) was similar to previous reports [7, 10], with slightly higher rates observed in patients who had prior ibrutinib versus prior idelalisib. There were 34/127 patients who had BTK C481 mutation at study entry; 20 of these had > 20% variant allele frequency (VAF) decrease after initiation of venetoclax, and BTK C481 was undetectable in 5 patients (3 at progression, 2 without progression) at final analysis (limit of quantitation: 0.7%) (Figure S4). Similar treatment efficacy was observed in patients with and without pre-existing BTKi mutations. Responses were early during treatment, indicating BTKi mutations do not impair venetoclax monotherapy efficacy [11, 12]. With extended follow-up, venetoclax monotherapy demonstrated deep and durable remissions in patients with CLL disease that progressed on BCRis, including achieving uMRD and disease stabilization in patients with high disease burden and poor prognostic features. Responses in these patients indicate a meaningful clinical benefit in a difficult-to-treat population. The safety profile of venetoclax monotherapy was similar to previous reports [13], with no new safety signals detected. This study further supports the utility of venetoclax-based therapy for management of R/R CLL post-progression on BCRis, particularly in patients who have discontinued BCRi monotherapy, and provides useful insights into potential mechanisms of resistance that are possibly extrapolatable to the combination-therapy setting. Although fixed-duration venetoclax combination therapy is generally favored for most patients, indefinite-duration monotherapy may yet be beneficial for patients who cannot tolerate anti-CD20 antibodies, those who have restrictive comorbidities, or who are heavily pre-treated. Data from the two study arms were published as two separate manuscripts: AbbVie and the authors wish to thank the participants and their families, as well as the study sites, investigators, coordinators, and support staff who participated in the NCT02141282 clinical trial. Medical writing support was provided by Vasileios Stamou, PhD, and Brandy Menges, PhD, of Avalere Health Ltd., and funded by AbbVie. As a special tribute, AbbVie and the authors would also like to acknowledge the significant contribution of Dr. Steven Coutre (Stanford Cancer Center, Stanford University School of Medicine, Stanford, CA, USA) to the design, conduction, and data interpretation of this study. Venetoclax is being developed in collaboration between AbbVie Inc. and Genentech. AbbVie Inc. is funding this study and participating in the study design, research, analysis, data collection, interpretation of data, reviewing, and approval of the publication. All authors had access to relevant data and participated in the drafting, reviewing for important intellectual content, and approval of this publication. No honoraria or payments were made for authorship. The trial was approved by the institutional review board and conducted in accordance with International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use guidelines and the ethical principles of the Declaration of Helsinki. All patients provided written informed consent. Jennifer A. Woyach provided consultancy for AbbVie, AstraZeneca, Beigene, Genentech, Janssen, Loxo, Newave, Merck, Pharmacyclics, and Schrodinger; and received research funding from AbbVie, Janssen, Morphosys, and Schrodinger. Michelle Boyer is an employee of Genentech Inc. and may hold stock or options. Jeffrey Jones is an employee of Celgene. Received honoraria from Janssen and Acerta has taken an advisory role for Pharmacyclics LLC, an AbbVie Company, Janssen, AbbVie, Morphosys, and Gilead and received research funding from Pharmacyclics LLC, an AbbVie Company, AbbVie, Janssen, Genentech, Gilead, and Acerta. Richard R. Furman provided consultancy for AbbVie, Alpine Immune Sciences, AstraZeneca, Beigene, Genentech, Ipsen, Janssen, Lilly, Pharmacyclics, Sanofi; has received research funding from Beigene, Janssen; has received speaker fees from Beigene and AstraZeneca. William Wierda received honoraria from Sanofi, Genentech/Roche, Pharmacyclics LLC, an AbbVie Company, Celgene, Gilead, GSK/Novartis, Genzyme, Merck, AbbVie, and Emergent; received research funding from GSK/Novartis, AbbVie, Genentech, Karyopharm, Pharmacyclics LLC, an AbbVie Company, Acerta, Gilead, Janssen, Emergent, Juno, and Kite; and taken an advisory role for Sanofi, Genentech/Roche, Pharmacyclics LLC, an AbbVie Company, Celgene, Gilead, GSK/Novartis, Genzyme, Merck, AbbVie, and Emergent. Jason Gotlib received honoraria from Incyte, Cogent Biosciences, and Blueprint Medicines; taken advisory role for Blueprint Medicines, Incyte, and Cogent Biosciences; received research funding from AbbVie (Inst), Blueprint Medicines (Inst), Incyte (Inst), CTI BioPharma Corp (Inst), Protagonist Therapeutics (Inst), BMS (Inst), Merck (Inst), and Telios (Inst); and received travel and accommodations expenses from Blueprint Medicines. Stephen J. Schuster received research funding from Celgene, Genentech/Roche, Incyte, Novartis, AbbVie, Adaptive Biotechnologies, DTRM, Juno Therapeutics, Merck, Pharmacyclics, TG Therapeutics; provided consultancy for Acerta, Beigene, Celgene, Genentech/Roche, Incyte, Janssen, Legend Biotech, Loxo, Morphosys, MustangBio, Nordic, Nanovector, Novartis, Regeneron; and served as an advisory board member for Regeneron and Caribou Biosciences. Relja Popovic, Emily L. Rossi, Sanjana Singh, Toshihiko Oki, Tanya S. Rosenberg, Chen Qian, Michael Moran, Zihuan Liu, Brenda Chyla are employees of AbbVie and may hold stock or options. Matthew S. Davids received grant support paid to his institution from Ascentage Pharma, MEI Pharma, Novartis; and received consulting fees from AbbVie, Adaptive Biotechnologies, Ascentage Pharma, AstraZeneca, BeiGene, BMS, Eli Lilly, Janssen, Galapagos, Genentech, Genmab, MEI Pharma, Merck, Nuvalent, and Schrödinger. 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For more information on the process or to submit a request, visit the following link: https://vivli.org/ourmember/abbvie/ then select “Home”. Figure S1: M14-032 trial enrollment scheme Table S1:. Demographic and baseline disease characteristics of all treated patents Table S2: Concordance table for pat ents with TP53 mutation Table S3: Summary of treatment-emergent adverse events and deaths during the study Figure S2: Patent disposition Figure S3: Summary of response rate for all treated pat ents (subgroup analysis) Figure S4: BTK mutations after venetoclax therapy by best responsea Figure S5: VAF of BCL-2 mutations at final visit by CLL progression status Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.