Transcriptomic profiles and 5-year results from the randomized CLL14 study of venetoclax plus obinutuzumab versus chlorambucil plus obinutuzumab in chronic lymphocytic leukemia

Abstract

Data on long-term outcomes and biological drivers associated with depth of remission after BCL2 inhibition by venetoclax in the treatment of chronic lymphocytic leukemia (CLL) are limited. In this open-label parallel-group phase-3 study, 432 patients with previously untreated CLL were randomized (1:1) to receive either 1-year venetoclax-obinutuzumab (Ven-Obi, 216 patients) or chlorambucil-Obi (Clb-Obi, 216 patients) therapy (NCT02242942). The primary endpoint was investigator-assessed progression-free survival (PFS); secondary endpoints included minimal residual disease (MRD) and overall survival. RNA sequencing of CD19-enriched blood was conducted for exploratory post-hoc analyses. After a median follow-up of 65.4 months, PFS is significantly superior for Ven-Obi compared to Clb-Obi (Hazard ratio [HR] 0.35 [95% CI 0.26-0.46], p < 0.0001). At 5 years after randomization, the estimated PFS rate is 62.6% after Ven-Obi and 27.0% after Clb-Obi. In both arms, MRD status at the end of therapy is associated with longer PFS. MRD + ( ≥ 10^-4) status is associated with increased expression of multi-drug resistance gene ABCB1 (MDR1), whereas MRD6 (< 10^-6) is associated with BCL2L11 (BIM) expression. Inflammatory response pathways are enriched in MRD+ patient solely in the Ven-Obi arm. These data indicate sustained long-term efficacy of fixed-duration Ven-Obi in patients with previously untreated CLL. The distinct transcriptomic profile of MRD+ status suggests possible biological vulnerabilities.

Fig. 1. Progression-free survival (PFS) and overall survival (OS) analyses.

a PFS according to study arm, b PFS according to TP53 status, c PFS according to IGHV mutational status, d OS according to study arm, e multivariable analyses of PFS in Ven-Obi arm (n = 194) and f in Clb-Obi arm (n = 179); horizontal bars in e and f represent 95% confidence intervals of hazard ratios (indicated by squares) with the vertical lines representing a hazard ratio of 1.0.

Fig. 2. Minimal residual disease (MRD) status and outcomes.

a Longitudinal MRD assessments by NGS in peripheral blood in the Ven-Obi arm and b in the Clb-Obi arm, c landmark PFS according to MRD status in the Ven-Obi arm and d in the Clb-Obi arm, e landmark OS according to MRD status in the Ven-Obi arm and f in the Clb-Obi arm, g landmark PFS according to MRD status in the Ven-Obi arm and h in the Clb-Obi arm; ‘Not available’ indicates patients without an end of treatment MRD status, due to earlier withdrawal or missing/unevaluable samples.

Fig. 3. Differential gene expression according to minimal residual disease status and baseline versus relapse status.

a UMAP (Uniform Manifold Approximation and Projection) visualization of shared nearest neighbour (SNN) clustering before treatment, with MRD, IGHV, deletion 17p, TP53, deletion 13q, and trisomy 12 status overlaid. b Pre-treatment differential gene expression between MRD6 vs MRD +, gene previously associated with CLL pathology are highlighted; dashed lines indicate significance cut-offs. P-values from moderated two-sided t-test without adjusting for multiple testing. c Paired patient-level comparison of differentially expressed genes at baseline and relapse (‘progression’) according to Ven-Obi arm (upper row) and Clb-Obi arm (lower row), n = 44, p-values from two-sided Wilcoxon signed-rank test without adjusting for multiple testing. Source data of differential gene expression analyses are provided as Source Data file.

Fig. 4. Gene set enrichment analyses according to minimal residual disease status and baseline versus relapse status.

a Summarized pre-treatment gene set enrichment analysis of hallmark gene sets according to treatment arm and according to EOT MRD6 and MRD + status. Positive normalized enrichment scores (NES) indicates gene sets enriched in MRD + and negative NES indicates gene sets enriched in MRD6. b Patient-level gene set enrichment analysis of relapse versus baseline samples in both arms. Significantly enriched hallmark gene sets (adjusted p-value <0.05) are highlighted, positive NES indicate enrichment in relapsed samples. P-values derived from non-parametric permutation test and adjusted for multiple testing using the Benjamini-Hochberg procedure. c Leading edge analysis of baseline (left) versus relapse (right) samples based on ‘TNFa signalling via NFkB’, ‘G2M checkpoint’ and ‘MYC targets V1’ gene sets, which were significantly enriched at relapse. d Gene set variation analysis of selected inflammatory pathways before Ven-Obi (D, n = 29) or Clb-Obi (e, n = 15) treatment (baseline) and at relapse (progression); two-sided Wilcoxon signed-rank test, not adjusted for multiple testing. box plots represent lower quartile, median and upper quartile, whiskers extend to a maximum of 1.5 × IQR beyond the box, points indicate outliers. NES, normalized enrichment score; MRD, minimal residual disease, EOT, end of treatment. Source data of differential gene expression analyses are provided as Source Data file.