Single-cell sequencing demonstrates complex resistance landscape in CLL and MCL treated with BTK and BCL2 inhibitors

Area of Science:

• Hematology
• Genomics
• Oncology

Background:

• Targeted agents (TAs) like Bruton tyrosine kinase (BTK) and B-cell lymphoma 2 (BCL2) inhibitors are crucial in treating chronic lymphocytic leukemia (CLL).
• Acquired resistance to these TAs can be complex and heterogeneous within patients.
• Understanding the clonal architecture of resistance is vital for optimizing treatment strategies.

Purpose of the Study:

• To investigate the clonal architecture of acquired genomic resistance to BTK and BCL2 inhibitors in CLL.
• To analyze resistance mechanisms in patients with multiple resistance mutations.
• To identify BCL2 resistance mechanisms in mantle cell lymphoma (MCL).

Main Methods:

• Targeted single-cell DNA sequencing was performed on 8 patients with progressive disease (PD) on TAs.
• Analysis focused on identifying resistance mutations and their clonal co-occurrence.
• Genomic analysis was also conducted on a patient with MCL and PD on sequential monotherapy.

Main Results:

• Single-cell analysis revealed mutual exclusivity of resistance mutations within the same TA class.
• Variable clonal co-occurrence of mutations affecting different TAs was observed in patients exposed to both inhibitor classes.
• Identical nucleotide changes conferring resistance emerged independently across multiple clones.
• Established BCL2 resistance mutations were identified in an MCL patient, suggesting a venetoclax resistance mechanism.

Conclusions:

• The genomic landscape of TA resistance in CLL is characterized by significant clonal complexity at the nucleotide level.
• Multiple, clonally independent resistance mechanisms operate within individual CLL and MCL cases.
• These findings highlight the intricate nature of acquired resistance to targeted therapies in hematologic malignancies.