Dissection of subclonal evolution by temporal mutation profiling in chronic lymphocytic leukemia patients treated with ibrutinib
Open accessAbstract
The Bruton's tyrosine kinase (BTK) inhibitor ibrutinib is inducing durable responses in chronic lymphocytic leukemia (CLL) patients with refractory/relapsed disease or with TP53 defect, with BTK and phospholipase C gamma 2 (PLCG2) mutations representing the predominant mechanisms conferring secondary ibrutinib resistance. To understand the landscape of genomic changes and the dynamics of subclonal architecture associated with ibrutinib treatment, an ultra-deep next-generation sequencing analysis of 30 recurrently mutated genes was performed on sequential samples of 20 patients, collected before and during single-agent ibrutinib treatment. Mutations in the SF3B1, MGAand BIRC3 genes were enriched during ibrutinib treatment, while aberrations in the BTK, PLCG2, RIPK1, NFKBIE and XPO1 genes were exclusively detected in posttreatment samples. Besides the canonical mutations, four novel BTK mutations and three previously unreported PLCG2 variants were identified. BTK and PLCG2 mutations were backtracked in five patients using digital droplet PCR and were detectable on average 10.5 months before clinical relapse. With a median follow-up time of 36.5 months, 7/9 patients harboring BTK mutations showed disease progression based on clinical and/or laboratory features. In conclusion, subclonal heterogeneity, dynamic clonal selection and various patterns of clonal variegation were identified with novel resistance-associated BTK mutations in individual patients treated with ibrutinib.
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In 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 [25]
The Subclonal dynamics section reports BTK and PLCG2 mutations, including co-occurrence, in a 20-patient ibrutinib cohort. It does not establish the quoted four-part distribution among patients whose disease progressed, or present those percentages as a summary of published studies. The Clinical outcome section also says the patient with a PLCG2-only variant died without CLL progression. (LLM, conf=0.84)
Experimental — accuracy not yet measuredMutations in PLCγ2 and/or Btk have been reported in 11 to 90% of cases of Ibrutinib-refractory CLL.
“Mutations in PLCγ2 and/or Btk have been reported in 11 to 90% cases of Ibrutinib-refractory CLL, further underscoring the importance of better understanding the process by which the partnership of Btk and PLCγ2 drives CLL disease progression (122, 123, 124, 125, 126).”
From The role of PLCγ2 in immunological disorders, cancer, and neurodegeneration (2021) · cites this paper as [123]
The Introduction (page unavailable) says BTK and PLCG2 mutations are predominant mechanisms of secondary ibrutinib resistance, supporting the association. The Discussion reports that 7 of 20 patients in this cohort relapsed with a BTK or PLCG2 mutation, but our copy does not give the claimed 11–90% range for ibrutinib-refractory CLL cases. (LLM, conf=0.84)
Experimental — accuracy not yet measuredA subset of patients with CLL become refractory to Ibrutinib treatment over time and relapse, with PLCγ2 as a primary driver of the recurrent disease.
“However, a subset of patients become refractory to this treatment over time and relapse, with PLCγ2 as a primary driver of the recurrent disease (122, 123).”
From The role of PLCγ2 in immunological disorders, cancer, and neurodegeneration (2021) · cites this paper as [123]
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Genomics of Resistance to Targeted Therapies
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- Authors
- Gángó, A., Alpár, D., Galik, B., Marosvári, D., Kiss, R., Fésüs, V., Aczél, D., Eyüpoglu, E., Nagy, N., Nagy, Á., Krizsán, S., Reiniger, L., Farkas, P., Kozma, A., Ádám, E., Tasnády, S., Réti, M., Matolcsy, A., Gyenesei, A., Mátrai, Z., & Bödör, C.
- Affiliations
- Semmelweis University (HU)
- Bioinformatics Research Group, Bioinformatics and Sequencing Core Facilities, Szentágothai Research Centre University of Pécs Pécs Hungary
- Unified Szent István and Szent László Hospital (HU)
- Medical University of Białystok (PL)
- Corresponding author
- Bödör, Csaba
- ORCID
- Venue
- International Journal of Cancer
- Publisher
- Wiley
- Published
- 2019-06-25
- Volume
- 146
- Issue
- 1
- Pages
- 85-93
- ISSN
- 0020-7136 (ISSN-L)
- 1097-0215
- OpenAlex
- W2950767934
- Cited by
- 54
- References
- 32
- Citations by year
- 2026: 2 · 2025: 4 · 2024: 11 · 2023: 9 · 2022: 8 · 2021: 11 · 2020: 8 · 2019: 1
- FWCI
- 3.84
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- International Journal of Cancer (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Repository of the Academy's Library (Library of the Hungarian Academy of Sciences) (acceptedVersion)
- Funders
- Emberi Eroforrások Minisztériuma (EFOP‐3.6.3‐VEKOP‐16‐2017‐00009, ÚNKP‐18‐3‐I‐SE‐48, ÚNKP‐18‐4‐SE‐62)
- Magyar Tudományos Akadémia (János Bolyai Research Scholarship Program (BO/00320/18/5), LP‐95021)
- 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, BTK inhibitors, drug resistance, BTK mutations, PLCG2 mutations, subclonal evolution, clonal heterogeneity, clonal selection, SF3B1, MGA, cIAP2, RIPK1, NFKBIE, CRM1, relapse
- MeSH terms
- Adenine, Female, Humans, Male, Middle Aged, Mutation, Piperidines, Pyrazoles, Pyrimidines, Cohort Studies, Leukemia, Lymphocytic, Chronic, B-Cell, Gene Expression Profiling, Protein Kinase Inhibitors, High-Throughput Nucleotide Sequencing
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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