Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition
Open accessAbstract
Resistance to the Bruton’s tyrosine kinase (BTK) inhibitor ibrutinib has been attributed solely to mutations in BTK and related pathway molecules. Using whole-exome and deep-targeted sequencing, we dissect evolution of ibrutinib resistance in serial samples from five chronic lymphocytic leukaemia patients. In two patients, we detect BTK-C481S mutation or multiple PLCG2 mutations. The other three patients exhibit an expansion of clones harbouring del (8p) with additional driver mutations ( EP300, MLL2 and EIF2A ), with one patient developing trans -differentiation into CD19-negative histiocytic sarcoma. Using droplet-microfluidic technology and growth kinetic analyses, we demonstrate the presence of ibrutinib-resistant subclones and estimate subclone size before treatment initiation. Haploinsufficiency of TRAIL-R, a consequence of del (8p), results in TRAIL insensitivity, which may contribute to ibrutinib resistance. These findings demonstrate that the ibrutinib therapy favours selection and expansion of rare subclones already present before ibrutinib treatment, and provide insight into the heterogeneity of genetic changes associated with ibrutinib resistance.
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Many mutations discovered in PLCγ2 have been linked to the development of complex immune disorders as well as resistance to ibrutinib treatment in chronic lymphocytic leukaemia.
“Furthermore, many mutations discovered in PLCγ2 have been linked to the development of complex immune disorders as well as resistance to ibrutinib treatment in chronic lymphocytic leukaemia.”
From Characterisation of molecular mechanisms for PLCγ2 disease-linked variants (2024) · cites this paper as Burger et al., 2016
The Results report four PLCG2 mutations emerging during ibrutinib treatment in a patient with CLL, supporting the resistance link. The References cite a study of one PLCG2 mutation causing an autoinflammatory disease with immunodeficiency, but this paper does not establish that many PLCG2 mutations are linked to complex immune disorders. (LLM, conf=0.87)
Experimental — accuracy not yet measuredIn published studies of disease progression during BTKi therapy, approximately 35% of patients were found to have a BTK mutation alone, an additional 10% had coexisting mutations in PLCG2, 5% had a PLCG2 mutation alone, and the remaining 50% were wild-type for BTK and PLCG2.
“In published studies of disease progression during BTKi therapy,approximately 35% of patients were found to have aBTK mutation alone, an additional 10% had a coexisting mutations in PLCG2, 5% of cases had a PLCG2mutation alone, and the remaining 50% were wild-type (WT) for BTK and PLCG2 (Figure 2)(12, 19, 21–31).”
From Resistance Mechanisms and Approach to Chronic Lymphocytic Leukemia after BTK Inhibitor Therapy (2025) · cites this paper as [23]
The Discussion reports BTK-C481S or PLCG2 mutations in two of five subjects, while the other three had different mutations associated with progression. The Results also report no BTK or PLCG2 mutations in Patients 2 and 3. These passages support the existence of mutation-positive and mutation-negative cases, but this paper does not report the cited 35%/10%/5%/50% distribution across published studies. (LLM, conf=0.86)
Experimental — accuracy not yet measuredAdditional genetic mechanisms of resistance to BTKi in CLL include PLCG2 mutations as well as chromosome 8p deletion (del [8p]).
“Additional genetic mechanisms of resistance to BTKi in CLL include,PLCG2 mutations as well as chromosome 8p deletion (del [8p])(23).”
From Resistance Mechanisms and Approach to Chronic Lymphocytic Leukemia after BTK Inhibitor Therapy (2025) · cites this paper as [23]
The Results report PLCG2 mutations expanding during ibrutinib treatment alongside CLL progression. They also identify del(8p) in relapse clones, but the Discussion calls its contribution a potential resistance mechanism and suggests that additional lesions may be needed to achieve ibrutinib resistance. The claim presents del(8p) more definitively than the paper does (page numbers unavailable in our copy). (LLM, conf=0.87)
Experimental — accuracy not yet measuredIbrutinib therapy of CLL patients favors selection and expansion of rare subclones already present before ibrutinib treatment, including subclones containing mutations in PLCG2.
“Very recent results suggest that ibrutinib therapy of CLL patients favors selection and expansion of rare subclones already present before ibrutinib treatment, including subclones containing mutations in PLCG2 (62).”
There has been a report of a single patient in whom a PLCG2 M1141R mutation was detected in 0.0002% of pre-treatment cells using ultra-sensitive droplet-digital amplification technology.
“Indeed, there has been a report ofa single patient in whom a PLCG2 M1141R mutation was detected in 0.0002% of pre-treatment cells using ultra-sensitive droplet-digital amplification technology(23).”
From Resistance Mechanisms and Approach to Chronic Lymphocytic Leukemia after BTK Inhibitor Therapy (2025) · cites this paper as [23]
In one longitudinal genomic study of 5 CLL patients who had disease progression on ibrutinib, del(8p) was observed in 3 patients with BTK and PLCG2 wild type CLL.
“In one longitudinal genomic study of 5 CLL patients who had disease progression on ibrutinib, del(8p) was observed in 3 patients withBTK and PLCG2 wild typeCLL(23).”
From Resistance Mechanisms and Approach to Chronic Lymphocytic Leukemia after BTK Inhibitor Therapy (2025) · cites this paper as [23]
Since these patients achieved partial remission on ibrutinib before PD and del(8p) was present in pre-treatment samples, del(8p) alone is likely insufficient to cause resistance to ibrutinib therapy.
“Since these patients achieved partial remission on ibrutinib before PD and del(8p) was present in pre-treatment samples, del(8p) alone is likely insufficient to cause resistance to ibrutinib therapy.”
From Resistance Mechanisms and Approach to Chronic Lymphocytic Leukemia after BTK Inhibitor Therapy (2025) · cites this paper as [23]
After Ibrutinib treatment, CLL progression favored the selection of rare subclones bearing PLCγ2 mutations.
“However, after Ibrutinib treatment, it was observed that CLL progression favored the selection of rare subclones bearing PLCγ2 mutations (129, 130).”
From The role of PLCγ2 in immunological disorders, cancer, and neurodegeneration (2021) · cites this paper as [130]
Co-occurrence of BTK mutations within the same cell has not been demonstrated in patient samples.
“However, co-occurrence of BTK mutations within the same cell has not been demonstrated in patient samples(12, 23).”
From Resistance Mechanisms and Approach to Chronic Lymphocytic Leukemia after BTK Inhibitor Therapy (2025) · cites this paper as [23]
The Results section reports BTK-C481S in Patient 4 and uses single-cell testing to distinguish PLCG2-mutated subclones in Patient 1. It does not state whether co-occurring BTK mutations have been demonstrated within the same cell in patient samples. Searches for multiple BTK mutations and their single-cell co-occurrence found no passage addressing that claim; page numbers were not available in our copy. (LLM, conf=0.72)
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- Authors
- Burger, J. A., Landau, D. A., Taylor-Weiner, A., Bozic, I., Zhang, H., Sarosiek, K., Wang, L., Stewart, C., Fan, J., Hoellenriegel, J., Sivina, M., Dubuc, A. M., Fraser, C., Han, Y., Li, S., Livak, K. J., Zou, L., Wan, Y., Konoplev, S., Sougnez, C., Brown, J. R., Abruzzo, L. V., Carter, S. L., Keating, M. J., Davids, M. S., Wierda, W. G., Cibulskis, K., Zenz, T., Werner, L., Cin, P. D., Kharchencko, P., Neuberg, D., Kantarjian, H., Lander, E., Gabriel, S., O’Brien, S., Letai, A., Weitz, D. A., Nowak, M. A., Getz, G., & Wu, C. J.
- Affiliations
- The University of Texas MD Anderson Cancer Center (US)
- Broad Institute (US)
- Harvard University (US)
- Dana-Farber Cancer Institute (US)
- Brigham and Women's Hospital (US)
- Xi'an Jiaotong University (CN)
- Standard BioTools (United States) (US)
- German Cancer Research Center (DE)
- Corresponding author
- Burger, Jan A.
- Wu, Catherine J.
- ORCID
- Burger, Jan A.
- Landau, Dan A.
- Taylor-Weiner, Amaro
- Zhang, Huidan
- Sarosiek, Kristopher
- Wang, Lili
- Stewart, Chip
- Fan, Jean
- Sivina, Mariela
- Dubuc, Adrian M.
- Fraser, Cameron
- Han, Yulong
- Li, Shuqiang
- Livak, Kenneth J.
- Zou, Lihua
- Wan, Youzhong
- Konoplev, Sergej
- Brown, Jennifer R.
- Abruzzo, Lynne V.
- Carter, Scott L.
- Keating, Michael J.
- Davids, Matthew S.
- Wierda, William G.
- Cibulskis, Kristian
- Zenz, Thorsten
- Werner, Lillian
- Cin, Paola Dal
- Neuberg, Donna
- Kantarjian, Hagop
- Lander, Eric
- Gabriel, Stacey
- Letai, Anthony
- Weitz, David A.
- Nowak, Martin A.
- Getz, Gad
- Wu, Catherine J.
- Venue
- Nature Communications
- Published
- 2016-05-20
- Volume
- 7
- Issue
- 1
- Pages
- 11589-11589
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC4876453
- OpenAlex
- W2408036343
- Cited by
- 345
- References
- 46
- Citations by year
- 2026: 13 · 2025: 18 · 2024: 20 · 2023: 29 · 2022: 20 · 2021: 42 · 2020: 44 · 2019: 51 · 2018: 39 · 2017: 51 · 2016: 10 · 2015: 3 · 2014: 3
- FWCI
- 36.76
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Nature
- Funders
- National Science Foundation (ECS- 03-35765, 1310266, 0335765, 1144152, 1420570)
- John Templeton Foundation
- Harvard University (ECS-0335765, DMR-1420570)
- Deutsches Krebsforschungszentrum
- National Natural Science Foundation of China (81372496)
- University of Texas MD Anderson Cancer Center ((CA016672), grant CA016672)
- Stand Up To Cancer
- Materials Research Science and Engineering Center, Harvard University (DMR- 1420570, 1420570, DMR-1310266)
- National Heart, Lung, and Blood Institute (R01HL116452, R01HL131768)
- National Human Genome Research Institute (U54HG003067)
- National Cancer Institute (Grant CA016672, CA 016672, U10CA180861, R01CA184922, P01CA206978, R01CA155010, P30CA016672)
- Division of Materials Research (DMR 14–20570, DMR-1310266, 1420570, DGE1144152, 1310266)
- Topics
- Health Sciences › Medicine › Genetics › Chronic Lymphocytic Leukemia Research
- Health Sciences › Medicine › Pathology and Forensic Medicine › Lymphoma Diagnosis and Treatment
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Acute Lymphoblastic Leukemia research
- Keywords
- chronic lymphocytic leukemia, ibrutinib resistance, BTK inhibitors, clonal evolution, BTK C481S mutation, PLCG2 mutations, histiocytic sarcoma, subclonal selection, drug resistance, clonal heterogeneity
- MeSH terms
- Agammaglobulinaemia Tyrosine Kinase, Adenine, Adult, Aged, 80 and over, Female, Humans, Male, Middle Aged, Mutation, Neoplasm Recurrence, Local, Piperidines, Protein-Tyrosine Kinases, Pyrazoles, Pyrimidines, Selection, Genetic, Leukemia, Lymphocytic, Chronic, B-Cell, Apoptosis, Drug Resistance, Neoplasm, Cell Transdifferentiation, Histiocytic Sarcoma, Clonal Evolution
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