Acquired BTK and PLCG2 Mutations May Not Drive Progression After Zanubrutinib/Ibrutinib Treatment in Relapsed CLL

The majority of patients with relapsed chronic lymphocytic leukemia (CLL) treated with zanubrutinib (Brukinsa) or ibrutinib (Imbruvica) in the phase 3 ALPINE study (NCT03734016) did not acquire a BTK or PLCG2 mutation at the time of disease progression (PD), indicating that these mutations may not be the primary drivers of resistance and relapse in this population, according to findings from a genomic analysis presented at the 2023 ASH Annual Meeting.

Evaluation of BTK/PLCG2 mutations revealed that no patients with PD samples (n = 57) harbored BTK mutations at baseline, and 82.6% of patients included in the analysis (n = 52) did not acquire a BTK or PLCG2 mutation at the time of PD. Among those who experienced a PD during treatment, 5 patients treated with zanubrutinib displayed acquired BTK mutations, including L528W alone (n = 1), C481 alone (n = 2), L528W plus C481 (n = 1), and A428D plus C481 (n = 1). Two patients treated with ibrutinib displayed an acquired BTK mutation, and 1 patient who experienced a PD after treatment with ibrutinib displayed a single BTK mutation in PLCG2. Half of these patients experienced 2 or more BTK mutations, the majority of which were in C481 (77.8%). Of the 2 BTK L528 mutations observed at the time of progression, the variant allele frequency (VAF) was comparable to that of BTK C481 mutations.

The overall median duration of treatment was 17.0 months (range, 5.0-34.5); the median duration of treatment in patients with a BTK mutation at PD was 29.7 months (range, 18.4-34.2) in patients treated with zanubrutinib, and 30.8 months (range, 11.8-34.5) in patients who received ibrutinib. Notably, median treatment duration at PD in patients with wild-type BTK was 16.8 months with zanubrutinib (n = 19; range, 5.0-33.3; P < .01) and 15.9 months with ibrutinib (n = 25; 5.9-29.4; P = .21).

“Given the low incidence to date of non-C481 mutations in patients with PD in ALPINE, patients with CLL who have been treated with covalent BTK inhibitors are likely to remain sensitive to other BTK-targeting therapies,” lead author Jennifer Brown, MD, PhD, who is the director of Chronic Lymphocytic Leukemia at Dana-Farber Cancer Institute, stated in a poster presentation of the data.

Patients with CLL who receive covalent BTK inhibitors may develop drug resistance and subsequent disease progression. Although acquired resistance is often attributed to subclones with mutations at the BTK binding site, such as C481, resistance can also stem from less common mutations, such as T474 and L528. Moreover, prior characterizations of BTK resistance were based on limited or retrospective populations.

Accordingly, investigators sought to improve the mechanistic understanding of covalent BTK inhibitor resistance in CLL through a post-hoc biomarker analysis of a randomized cohort from the ALPINE study. ALPINE was a randomized, multinational phase 3 trial, in which 652 patients with relapsed/refractory CLL or small lymphocytic leukemia (SLL) who had received at least 1 prior systemic therapy were randomized assigned to receive either 160 mg zanubrutinib twice daily or 420 mg ibrutinib daily until disease progression or unacceptable toxicity.

The current analysis included patients who experienced disease progressionPD on treatment with zanubrutinib or ibrutinib, as determined by an independent review committee (n = 139) and/or investigators using previously established criteria (n = 132). Peripheral blood samples were collected at baseline, on or after PD, and before subsequent therapy to determine the final study population. The data cut off for the final analysis of PFS was August 8, 2022.

The high-sensitivity PredicineHEME panel was used to perform next-generation sequencing (NGS) on these samples. This panel covered 106 exons, including BTK, PLCG2, and 27 putative CLL driver genes. All BTK and PLCG2 mutations with a VAF of 0.25% or greater were reported, while pathogenic mutations with a VAF of 1% or higher were reported for all other genes. Fluorescence in situ hybridization was performed to detect chromosomal abnormalities;, cytogenetic analysis was performed to identify complex karyotype;, and NGS was also utilized to detect IGHV gene mutations.

A total of 57 patients had available samples collected at the time of disease collection; 26 of these patients had previously received zanubrutinib, and 31 had been exposed to ibrutinib. The median follow-up was 25.4 months (range, 10.6-40.5) in the zanubrutinib arm and 28.1 (range, 5.8-42.3) in the ibrutinib arm. The median duration of treatment was 19.9 months (range, 4.3-39.3) and 16.6 months (3.4-35.7), in these respective cohorts. Patients in both arms had received a median of 1 prior treatment (zanubrutinib range, 1-3; ibrutinib range, 1-7). In the zanubrutinib arm, 19.2% of patients harbored a 17p deletion and/or TP53 mutation, and 84.6% displayed unmutated IGHV; corresponding percentages in the ibrutinib arm were 19.4% and 83.9%.

The final study population consisted of 52 patients with paired baseline and PD samples who did not have Richter transformation at the time of PD, 24 of whom were in the zanubrutinib cohort and 28 of whom were in the ibrutinib cohort.

Additional analysis of drive gene mutations in this population identified 18 mutated driver genes among the 48 patients with baseline CLL driver gene mutations. The median number of driver genes mutated per patient was 3 (range, 1-5). The most common mutations seen at baseline occurred in NOTCH1 (n = 21), followed by BRAF (n = 10), SF3B1 (n = 8), and ATM (n = 8). One patient in the zanubrutinib arm displayed acquired drive gene mutations in TP53 and XPO1, while 5 patients in the ibrutinib arm displayed mutations in TP53 (n = 1), SETD2 (n = 1), SF3B1 (n = 1), and ASXL1 (n = 2). Driver gene mutations were not found to be associated with BTK mutational status, nor were baseline or PD driver mutations associated with 17p deletions, IGHV mutations, or complex karyotype status.

Most patients received subsequent therapy following discontinuation of study treatment. This included 69.2% of patients in the zanubrutinib arm and 67.7% in the ibrutinib arm, all of whom had acquired BTK and/or PLGCG2 mutations. Next lines of treatment included chemotherapy (1 in zanubrutinib arm; 0 in ibrutinib arm), chemoimmunotherapy (4;3), a covalent BTK inhibitor (2;5), a noncovalent BTK inhibitor (2;2), BCL2 inhibitor monotherapy (3:5), a BCL2 inhibitor plus a CD20 monoclonal antibody (3;2), a BCL2 inhibitor plus BTK inhibitor (0;3), a CD20 monoclonal antibody plus noncovalent BTK and BCL2 inhibitors (1;0), and other therapy (2;1).

Disclosures: Dr Brown reports receiving research funding from Gilead, BeiGene, MEI Pharma, Loxo/Lilly, iOnctura, SecuraBio, TG Therapeutics; she served as a consultant for Alloplex Biotherapeutics, Genentech/Roche, BeiGene, Abbvie, Acerta, AstraZeneca, Pharmacyclics, Pfizer, Numab Therapeutics, Merck, Loxo/Lilly, Kite, iOnctura, hutchmed, Grifols Worldwide Operations.

Reference

Brown JR, Li J, Eichhorst BF, et al. Acquired mutations in patients (pts) with relapsed/refractory (R/R) chronic lymphocytic leukemia (CLL) that progressed in the ALPINE study. Blood. 2023;142(suppl 1):1890. doi:10.1182/blood-2023-173547