Dissecting Pirtobrutinib Resistance in Mantle Cell Lymphoma Through Single-Cell Multi-Omics

Pirtobrutinib (PBN), a non-covalent BTK inhibitor, has been approved by the FDA for relapsed/refractory mantle cell lymphoma (MCL); however, resistance to PBN has been observed. To dissect the molecular dynamics driving PBN resistance, we performed integrative single-cell multi-omic profiling (scRNA-seq, scATAC-seq, and scDNA-seq) on longitudinal MCL patient samples. Our analyses revealed both genetic and non-genetic routes of resistance: In some patients, resistance involves sequential copy number gains (e.g., 1q, 2p, and 8q) accompanied by transcriptomic reprogramming and epigenetic alterations, whereas in others, resistance occurs through non-genetic mechanisms driven by transcriptional and epigenetic remodeling. Integration of scATAC-seq and scRNA-seq enabled gene regulatory network inference and in silico perturbation analysis, highlighting RAD21 and SMC3, core components of the cohesin complex, as chromatin regulators whose downregulation may re-sensitize cells to PBN. A stem-like malignant B cell population enriched in resistant samples exhibited features of metabolic reprogramming and epithelial-mesenchymal transition. Together, our findings highlight heterogeneous, multi-layered mechanisms of PBN resistance and suggest chromatin regulators as potential therapeutic targets to overcome PBN resistance in MCL.