Evolution of tumor subclones and T-cell dynamics underlie variable ibrutinib responses in Waldenström macroglobulinemia

Clinical Snapshot

Key Findings

• P Value: Not reported in abstract

• Effect Size: Evolution pattern strongly associated with disease progression; devolution pattern correlated with durable clinical response

• Primary Outcome: Three distinct clonal evolution patterns identified: evolution (associated with progression), devolution (associated with durable response), and no evolution (stable architecture)

• Nnt Or Sensitivity: WIP score developed for baseline prediction of treatment response; LYN knockdown increased WM cell sensitivity to ibrutinib

• Confidence Interval: Not reported in abstract

Clinical Application

Single-cell analysis currently research-based; WIP score could be clinically feasible if validated and simplified Ibrutinib is PBS-listed for WM in Australia; WIP score could inform treatment selection if validated, potentially improving cost-effectiveness of targeted therapy Treatment-naïve patients with Waldenström macroglobulinemia considering ibrutinib therapy

Abstract

To elucidate the molecular basis underlying differential responses and resistance to ibrutinib in Waldenström macroglobulinemia (WM), we conducted a prospective phase 2 trial of ibrutinib monotherapy in treatment-naïve patients. A total of 74 sequential bone marrow (BM) aspirates from 17 patients, collected from baseline through 48 treatment cycles, were profiled using single-cell multiomics. BM cells were segregated primarily into B-cell/plasma cell and T-cell compartments. Longitudinal clonal tracking of malignant B cells/plasma cells identified 3 distinct evolutionary patterns: evolution (early clone contraction with late clone expansion and increasing genomic complexity), devolution (early clone expansion with late clone contraction and genomic simplification), and no evolution (stable clonal architecture). The evolution pattern was strongly associated with disease progression, whereas devolution correlated with durable clinical response. Transcriptomic profiling of resistant clones enabled development and validation of the Waldenström ibrutinib prediction (WIP) score, which predicted treatment response at baseline. Within the WIP signature, LYN emerged as a key regulator; LYN knockdown or inhibition significantly increased WM cell sensitivity to ibrutinib, suggesting a rational combination strategy. In parallel, GZMB+ CD8+ effector-memory T cells expanded after treatment in patients with progressive disease and coexisted with tumor evolution. These cells exhibited persistently impaired cytotoxic programs (eg, GNLY), a dedifferentiated memory-like state, elevated PDCD1 expression, and reduced T-cell receptor diversity. Together, this study provides, to our knowledge, the first single-cell framework of tumor clonal evolution and T-cell dysfunction under ibrutinib in WM, introduces the WIP score as a predictive biomarker for treatment response, and identifies actionable tumor-intrinsic and immune mechanisms driving resistance. This trial was registered at www.ClinicalTrials.gov as NCT02604511.

References

1. 1.Sun, H., Sklavenitis-Pistofidis, R., Liu, S., Liu, X., Tsakmaklis, N., Hatcher, J. M., Guerrera, M. L., Kofides, A., Ramirez-Gamero, A., Peachey, A. L., Li, S., Keskin, D. B., Chea, V., Kim, N., Lyu, H., Lu, W., Livak, K. J., Meid, K., Guijosa, A., Flynn, C. A., Pizzarella, D., Patterson, C. J., Hao, M., Yi, S., Yuan, W., Branagan, A. R., Wu, C. J., Ghobrial, I. M., Qiu, L., Sarosiek, S. R., Castillo, J. J., Hunter, Z. R., & Treon, S. P. (2026). Evolution of tumor subclones and T-cell dynamics underlie variable ibrutinib responses in Waldenström macroglobulinemia. Blood. https://doi.org/10.1182/blood.2025032268