Researchers have identified the development of venetoclax resistance under therapeutic pressure in cancer cells of patients with chronic lymphocytic leukemia (CLL), according to a new study published in Nature Communications.
“Ongoing clonal evolution is sought to be a key mechanism for the development of treatment-resistant or -refractory CLL and is, therefore, limiting treatment success and duration,” wrote the authors, led by Carmen D. Herling, MD, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany.
The BCL2-inhibitor venetoclax has proven effective even in treating patients with high-risk relapse and chemotherapy-refractory CLL who exhibit alterations in TP53—a diagnosis that bodes especially poorly for patients. Unlike with ibrutinib, however, genetic mechanisms mediating venetoclax resistance have yet to be elucidated.
The researchers performed whole-exome sequencing and methylation profiling in serial CLL samples from eight patients before the patients started venetoclax treatment and when they evolved resistance secondary to BCL2 inhibition. Consequently, they deduced clonal evolution after venetoclax treatment and identified recurrent genome alterations in these cancer cells.
Blood, bone marrow, and tissue samples were obtained from eight patients with relapsed or refractory CLL who were receiving venetoclax treatment between February 2014 and February 2016. The team performed whole-exome sequencing and methylation profiling of serial CLL samples both before venetoclax treatment was started and at the point resistance took hold.
Specifically, the researchers drew baseline peripheral blood samples at a median of 12 days before venetoclax treatment. They also collected follow-up samples of peripheral blood, bone marrow, or tissue when subjects manifested signs of refractory or relapsing CLL disease and when excess material was available from diagnostic procedures.
All patients in the study exhibited significant clinical response to venetoclax before progression or recurrence occurred. The median time between the start of venetoclax treatment and clinical progression or relapse was 15.4 months. Time to progression took between 4 and 22 months. In total, six of eight patients exhibited partial remission as a best response. Furthermore, four of eight patients developed Richter’s transformation to diffuse large B-cell lymphoma during treatment.
The team inferred subclonal populations and reconstructed phylogenetic trees, thus observing variegate patterns of clonal dynamics on sequencing—including linear, convergent, and divergent evolution—after venetoclax treatment. They also saw signs of genomic instability, such as an expanding number of acquired copy number mutations.
Alterations in the cancer-related genes BRAF, CD274, NOTCH1, RB1, SF3B1, and TP53 evolved during treatment; however, alterations in BCL2 or BAX and BAK were not observed, contrary to expectations.
“We report recurrent mutations in BTG1 (2 patients) and homozygous deletions affecting CDKN2A/B (3 patients) that developed during treatment,” the researchers wrote, “as well as a mutation in BRAF and a high-level focal ampli?cation of CD274 (PD-L1) that might pinpoint molecular aberrations offering structures for further therapeutic interventions.”
Overexpression of BRAF in lymphoma cell lines resulted in lymphoma cells vs venetoclax resistance. Subsequent functional analyses, however, indicated the context-dependent interplay of genetically altered driver genes. The authors suspect that other molecular mechanisms are at play.
“Comprehensive molecular testing is a suitable methodology to decipher mechanisms of venetoclax resistance and should be incorporated into future protocols to create molecularly-targeted salvage strategies for CLL patients under venetoclax treatment,” the researchers concluded.
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