Molecular determinants of outcome in CLL patients treated on zanubrutinib registration trials

Abstract Background: Critical barriers to precision medicine in CLL include molecular heterogeneity of the disease and limited availability of large-scale, prospective patient cohorts with detailed prognostic data relevant to targeted therapy. Here, we analyzed genetic characteristics and their association with outcome using whole-exome sequencing (WES) data from 1,027 CLL patients treated in phase 3 registration trials testing zanubrutinib (NCT03336333 [SEQUOIA], NCT03734016 [ALPINE]). Methods: The frontline SEQUOIA study had four treatment arms: two randomized arms for patients without del(17p) (Arm A, zanubrutinib [Z] monotherapy vs. Arm B, bendamustine-rituximab), and two non-randomized arms enriched with patients with TP53 aberration (Arm C, Z in patients with del(17p) >7% by FISH; Arm D, zanubrutinib-venetoclax in patients with or without del(17p) and/or TP53 mutation [MUT]). The ALPINE study randomized patients with relapsed or refractory (R/R) CLL to Z or ibrutinib (I). WES was applied to DNAs from unsorted PBMCs collected at baseline, using established workflows at the Broad Institute for the detection of copy number changes and putative somatic single-nucleotide variants and indels. Matched germline samples were not available. Target coverage was 200x (observed average: 283x). All analytical work and statistical tests were performed using Python (version 3.13) and R (version 4.5). Results: Of 1,066 patients enrolled, 1,027 (96%) had WES data available. Median age was 69 (range 62-74). Median duration of follow-up was 47 months (range 27-54). Key clinical variables at baseline were well captured (rates of missing data: 0% FISH, 0% clinical stage, 1% lactate dehydrogenase, 3% IGHV, 10% beta-2 microglobulin, 24% karyotype). In the analysis of copy number (CN) data from WES, losses were more frequently detected than gains. Commonly detected CN changes were loss loss 11q22.3, 13q14.2-13.3, loss 17p13.1, and gain 12p13.32, corresponding to the regions included in the conventional CLL FISH panel. Other notable CN changes in the dataset were: gain 2p15 (XPO1 locus), gain 8q24.3 (MYC locus), loss 9p21.3 (CDKN2A/B locus), loss 14q11.2 (TCR locus), loss 14q42.33 (IGH locus), and loss 15q15.1 (MGA locus). Univariate analyses showed inferior PFS associated with gain 8q24.3 and gain 12p13.32 in TN patients treated with Z (p<0.05 for both tests). Common driver gene mutations (>10% of study population) in this dataset were TP53, NOTCH1, ATM, and SF3B1 mutations. TP53MUTand SF3B1MUT were more frequently found in R/R than TN CLL. As expected from the study design, TP53MUT was frequently detected in TN patients in SEQUOIA Arm C (34%) and Arm D (49%) (p<0.001). We observed inferior PFS associated with TP53MUT (hazard ratio: 2.4, p<0.01) in TN patients on Z, but not in R/R patients on Z. Further analyses revealed unique characteristics of TP53MUTin TN patients on Arm C. Specifically, patients in Arm C more frequently presented with “single-hit” TP53 lesions (Arm C vs. D: 65% vs. 11% with isolated del(17p), 34% vs. 41% with “two-hit” del(17p) and TP53MUT), lower burden of del(17p) on FISH (median 15% vs. 62%), and a higher proportion of patients with TP53MUT and mutated IGHV (TP53MUT/M-IGHV: 24% vs. 13%). Despite small numbers of patients in subgroup analyses, we observed excellent PFS associated with TP53MUT/M-IGHV compared to TP53MUT/U-IGHV in TN patients on Z (p=0.08). NOTCH1 MUT was found in similar frequencies across study arms (21-27%) and was consistently associated with inferior PFS in TN (HR 2.1, p<0.01) and R/R CLL (HR 1.5, p<0.01) treated with Z or I in univariate analyses. Results of the evaluation of other genetic lesions and multivariable analyses will be presented at the meeting. Conclusions: WES sensitively detected CN changes included in the conventional CLL FISH panel and identified additional lesions of prognostic relevance (gain 8q24.3, gain 12). While TP53MUT was associated with inferior PFS in TN CLL patients on Z, excellent PFS was observed in a subset of patients with concurrent TP53MUT/M-IGHV. NOTCH1MUT was associated with inferior PFS in TN and R/R patients treated with a BTK inhibitor.