Integrated transcriptomic and immune profiling identifies determinants of deep remission with ibrutinib-venetoclax combination therapy in chronic lymphocytic leukemia
Authors
Varsha Gandhi, Gorkem Kismali, Evan N Cohen, Ganiraju Manyam, Mark Meerson, Anastasiia Shvyrkova, Ekaterina Postovalova, Nikita Kotlov, Alexander Bagaev, Nathan Fowler, William G Wierda, Nitin Jain
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- BostonGene Corporation, Waltham, MA, USA
Abstract
Background: B-cell receptor (BCR) signaling pathway and BCL-2 prosurvival proteins are established biomarkers in the pathophysiology of chronic lymphocytic leukemia (CLL). Ibrutinib, a covalent Bruton’s tyrosine kinase (BTK) inhibitor blunts BCR signaling while venetoclax neutralizes BCL-2 protein. Both these drugs are effective as monotherapy; however, their synergy was transformational when combined for patients with CLL. As monotherapy, these drugs rarely result in undetectable measurable residual disease (uMRD) status. In an investigator-initiated clinical trial, we demonstrated that combined ibrutinib and venetoclax (I+V) resulted in bone marrow uMRD4 (10-4 limit of detection) status in 60-66% of patients. This was observed in treatment-naïve (TN) disease (n=120 patients; Jain et al. NEJM 2019; Jain et al. JAMA Onc 2021) as well as relapsed-refractory (RR) CLL (n=79 patients; Swaminathan et al. Blood Cancer Discov 2026). I+V is approved in Europe based on the randomized GLOW trial (Kater et al. NEJM Evid 2022), with half of patients in the I+V arm attaining blood uMRD4 remission.
Aims:
To identify biologic and molecular mechanisms explaining the likelihood of achieving uMRD4 with I+V combination in CLL.
Methods:
In this trial, patients started with 3 cycles of ibrutinib monotherapy at 420 mg/d. On cycle 4 day 1, venetoclax (weekly ramp-up dosing reaching 400 mg/d) was added. Patients received 24 cycles of I+V. Blood samples were collected prior to therapy (C1D1), after 1 and 3 cycles of ibrutinib (C2D1 and C4D1) and after a week of I+V (C4D8). Transcriptomic data from these >200 samples (from 32 TN and 25 RR CLL patients) were analyzed. To perform differential gene expression analysis, reads were aligned using STAR (genome hg38), read counts were obtained by featurecounts, followed by limma. TPM-normalized expressions from Kallisto were used to predict cell composition using Kassandra (Zaitsev A et al. Cancer Cell 2022) algorithm.
Results: Compared to C1D1-TN and RR samples, there was a significant decline in BCR pathway molecules (BTK, CD79A and CD79B, LYN, CCL3 and CCL4) and MCL-1 transcript levels in C2D1 and C4D1 timepoints. This was confirmed by RT-PCR assay. Corresponding protein levels also decreased. Compared to baseline, CCL3 and CCL4 plasma levels were reduced in all patient samples. In the TN cohort, MRD+ patients at the end of 24 cycles of I+V had upregulated complement components (C1QA, C1QB, p<0.01), lactate dehydrogenase (LDH, p=0.02), and cell adhesion genes (JAM3, LRP5, p<0.01). Results from longitudinal comprehensive immune profiling using Kassandra deconvolution demonstrated consistent increases in total T (p=0.04) and NK (p=0.03) cell populations, including subpopulations of CD4 and CD8 effector T cells in patients who did not achieve uMRD4 status. Compared to RR-uMRD4 cohort, in the MRD+ group we noted upregulation of WNT signaling (WNT5A, WNT5B, p<0.01) and LPL-associated genes (AKAP12, KANK2, p<0.01). FAM167A, a key molecule involved in non-canonical NF-κB signaling, was upregulated in patients who failed to obtain uMRD4 across both TN/RR cohorts (p<0.01).
Summary/Conclusion: Differences in peripheral immune populations and gene expression in patients who failed to achieve deep remission suggest a common resistance mechanism in both TN/RR cohorts. Targeting these universally shared pathways, especially in high-risk disease could result in improved disease control. Updated data will be presented at the meeting.
Aims:
To identify biologic and molecular mechanisms explaining the likelihood of achieving uMRD4 with I+V combination in CLL.
Methods:
In this trial, patients started with 3 cycles of ibrutinib monotherapy at 420 mg/d. On cycle 4 day 1, venetoclax (weekly ramp-up dosing reaching 400 mg/d) was added. Patients received 24 cycles of I+V. Blood samples were collected prior to therapy (C1D1), after 1 and 3 cycles of ibrutinib (C2D1 and C4D1) and after a week of I+V (C4D8). Transcriptomic data from these >200 samples (from 32 TN and 25 RR CLL patients) were analyzed. To perform differential gene expression analysis, reads were aligned using STAR (genome hg38), read counts were obtained by featurecounts, followed by limma. TPM-normalized expressions from Kallisto were used to predict cell composition using Kassandra (Zaitsev A et al. Cancer Cell 2022) algorithm.
Results: Compared to C1D1-TN and RR samples, there was a significant decline in BCR pathway molecules (BTK, CD79A and CD79B, LYN, CCL3 and CCL4) and MCL-1 transcript levels in C2D1 and C4D1 timepoints. This was confirmed by RT-PCR assay. Corresponding protein levels also decreased. Compared to baseline, CCL3 and CCL4 plasma levels were reduced in all patient samples. In the TN cohort, MRD+ patients at the end of 24 cycles of I+V had upregulated complement components (C1QA, C1QB, p<0.01), lactate dehydrogenase (LDH, p=0.02), and cell adhesion genes (JAM3, LRP5, p<0.01). Results from longitudinal comprehensive immune profiling using Kassandra deconvolution demonstrated consistent increases in total T (p=0.04) and NK (p=0.03) cell populations, including subpopulations of CD4 and CD8 effector T cells in patients who did not achieve uMRD4 status. Compared to RR-uMRD4 cohort, in the MRD+ group we noted upregulation of WNT signaling (WNT5A, WNT5B, p<0.01) and LPL-associated genes (AKAP12, KANK2, p<0.01). FAM167A, a key molecule involved in non-canonical NF-κB signaling, was upregulated in patients who failed to obtain uMRD4 across both TN/RR cohorts (p<0.01).
Summary/Conclusion: Differences in peripheral immune populations and gene expression in patients who failed to achieve deep remission suggest a common resistance mechanism in both TN/RR cohorts. Targeting these universally shared pathways, especially in high-risk disease could result in improved disease control. Updated data will be presented at the meeting.
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