For patients with chronic lymphocytic leukemia (CLL) with disease progression while on venetoclax, several potential mechanisms of resistance to the BCL2 inhibitor were identified by whole-exome sequencing. This is according to results from a small study published in Blood, which could help guide the direction of combination treatments for patients with venetoclax-resistant CLL.
“The patients we studied all had relapsed or refractory disease and received continuous venetoclax,” explained corresponding author Jennifer R. Brown, MD, PhD, of Dana-Farber Cancer Institute in Boston. “In that context, our results do suggest multiple mechanisms of resistance, with the most prominent being the development of increased genomic complexity particularly focused on 8p deletion, along with upregulation of other BCL2 family members and NFKB and BCR [B-cell receptor] signaling leading to ERK activation.”
In patients with CLL who are heavily pretreated, the continuous use of venetoclax has shown a progression-free survival of longer than two years, but some patients’ disease fails to respond or relapses. Mutations of the venetoclax-binding site of BCL2 have been identified as late-occurring events, leading to venetoclax resistance. However, other mechanisms of acquired resistance are poorly understood.
In this study, Dr. Brown and colleagues analyzed longitudinal tumor samples from 11 patients with CLL and disease progression while on venetoclax. The patients had received a median of two prior therapies, including chemoimmunotherapy in eight patients and Bruton tyrosine kinase inhibitors in five patients. Samples were taken before venetoclax treatment initiation and at progression, which was the result of acquired resistance in 10 patients and primary refractory disease in one patient. The researchers used whole-exome sequencing and RNA sequencing on the samples to characterize the clonal evolution of venetoclax resistance. They performed in vitro validation of key findings using CLL cells collected from patients before and after disease progression.
All patients demonstrated in vitro resistance to venetoclax at the post-treatment time point. BCL2 G101V mutations were found in four patients, with two showing a very low variant allele fraction of 0.03% to 4.68%, suggesting that other mechanisms of venetoclax resistance existed. Whole-exome sequencing revealed acquired 8p loss in four patients, of which two also had 1q21.2-21.3 gain in the same cells affecting the MCL1 gene. Cells from patients with these genetic abnormalities — loss (8p) and gain (1q) — were more resistant to venetoclax than cells from patients without these genetic abnormalities. Moreover, treatment with an MCL1 inhibitor alone or combined with venetoclax decreased viability in progression cells from patients with gain (1q).
“Combining an MCL1 inhibitor with venetoclax might prevent the outgrowth of clones with this genetic abnormality. In addition, combination therapy may prevent the emergence of gain (1q), potentially delaying the onset of resistance in some patients,” the authors said.
Analyzing differential gene expression by comparing bulk RNA sequencing data obtained from patients at pretreatment and progression time points showed upregulation of proliferation, BCR, and NFKB gene sets, including MAPK genes. Compared with cells from before progression, those from the progression time point showed upregulation of surface immunoglobulin M and higher pERK levels. The authors noted that the upregulation of surface immunoglobulin M and MAPK signaling suggests the potential for treatment with MEK or ERK inhibitors in patients with venetoclax-resistant disease.
“The take-home messages for clinicians are that there are multiple mechanisms of resistance to venetoclax, and we hope that time-limited therapy used in earlier lines may reduce the development of these resistance mechanisms,” Dr. Brown said. “The results suggest several avenues to explore in clinical trials to overcome or avoid the development of resistance, such as inhibitors of other BCL2 family members or the use of ERK inhibitors.”
The authors did not discuss any limitations of the study.
Any conflicts of interest declared by the authors can be found in the original article.
Reference
Khalsa JK, Cha J, Utro F, et al. Genetic events associated with venetoclax resistance in CLL identified by whole-exome sequencing of patient samples. Blood. 2023;142(5):421-433.