To the Editor
Disruption of the TP53 gene, either by deletion at chromosome 17p13.1 (del17p) or mutations, is the most important prognostic/predictive biomarker in chronic lymphocytic leukemia (CLL), also in the context of the novel target therapies including ibrutinib [1,2,3,4]. Although TP53 deletion and mutations mostly co-occur and are considered as equal prognosticators, the prognostic value of isolated or concomitant mutations and deletions remains unclear [2, 3]. Here we applied an ultra-deep next-generation sequencing (NGS) approach in CLL patients treated with ibrutinib, to investigate the clinical impact of TP53 mutations and del17p, either concomitant or isolated, or in relation to their disruption burden.
This study, generated in the framework of an institutional Italian multicenter working group on CLL (“Campus CLL”), is a retrospective/multicenter analysis of 229 CLL patients treated with ibrutinib in the current clinical practice. All cases have been either referred to a single institution for molecular and cytogenetic analyses (February 2014–February 2021), or retrospectively referred by delivering frozen cell samples taken prior to starting ibrutinib treatment. Clinical outcome data were updated as of October 2021. Eighty patients, included in a previous study [3], are presented here with an updated median follow-up (24.7 months). As a stringent criterion, only patients assayed for TP53 mutation and 17p deletion in the same blood sample taken within 6 months prior to the start of ibrutinib were included. Median follow-up from ibrutinib treatment was 36.3 months (95% CI 29.5–41.5 months); 51 patients were treatment naïve (TN) and, 178 refractory/relapsed (RR). In accordance with the ERIC recommendations for TP53 disruption [5], mutation analyses were always carried out on samples containing >80% tumor cells; when lower than the 80% cutoff, CD19 positive CLL cells were purified by cell sorting. Briefly, analysis of TP53 mutations was performed with an amplicon-based strategy, covering exons 2–11, as previously reported [4]. A minimum coverage of 2,000X was obtained for each sequence in 100% of the analyzed positions, with a limit of detection of 0.3% VAF; TP53 mutated cases with less than 2% VAF were all confirmed by a second independent NGS run starting from DNA [4]. Moreover, selected low-VAF TP53 mutations were verified by a different experimental approach (digital droplet PCR, ddPCR). BTK and PLCG2 mutations related to ibrutinib resistance were studied by NGS. Interphase FISH was performed to detect del17p and 11q22.3 deletion (del11q) [4]. Further methodological details are provided in Supplementary Information. The clinical and biological baseline characteristics of patients [6] are detailed in Supplementry Table S1. All statistical analyses were performed by using standard methods. Overall survival (OS) and progression free survival (PFS) were computed from date of ibrutinib treatment to date of death or progression/suspension (events), respectively, or last follow-up (censoring). Molecular studies were blinded to the study end points.
Among 229 patients, 68 died and 57 progressed after median follow-up of 15.6 months (95% CI 11.9–20.5 months) and 24 months (95% CI 16.0–32.7 months) from ibrutinib starting, respectively. As in previous reports [7,8,9], Rai stage, the number of previous treatments (0/1 versus >1), anemia and abnormal LDH values were found to associate with shorter PFS and/or OS by univariable analyses (Table 1 and Supplementry Fig. S1).
CLL bearing del17p (n = 74; Supplementry Table S1) showed inferior OS and PFS compared to non-del17p cases (Fig. 1A and Supplementry Table S2), as previously reported [10]. Consistently, del17p was independent predictor in multivariable models for OS/PFS (P = 0.0209, OS; P = 0.0057, PFS; Model 1 Supplementry Table S2). At baseline, before ibrutinib treatment, we identified a total of 296 TP53 mutations in 126 patients (median mutations per patient: 1; range of mutations/patient: 1–11; Supplementry Table S3). The relative high proportion of cases (126/229, 55%) with TP53 mutations can be explained by the use of an ultra-deep NGS strategy that allows the detection of very small mutated clone (see also Supplementry Table S4 and Supplementry Fig. S2 for ddPCR validation of selected mutations) [4, 5]. By classifying TP53-mutated patients according to the VAF of the most prevalent TP53 mutation, VAF range for TP53-mutated cases was 0.53–95.24% (Supplementry Table S3). As in the chemo-immuno therapy setting [4], also in the ibrutinib setting, patients bearing TP53 mutations with low (<10%) and high (≥10%) VAF had shorter OS than TP53wt cases, either kept separate (Fig. 1B), or when low-VAF and high-VAF cases were combined (Supplementry Fig. S3). These results suggest that even low burden TP53 alterations confer a negative impact on outcomes, widening previous findings [11]. Accordingly, TP53 mutations were associated with shorter OS/PFS intervals in univariable analyses (Supplementry Table S2), as well as in an OS multivariable model (P = 0.0217; Model 2, Supplementry Table S2). Here, we expanded to low-VAF TP53-mutated patients previous observations on the clinical impact of TP53 disruption upon ibrutinib, as they emerged in the context of clinical trials [7], or in real-life [3, 6, 8], where TP53 disrupted patients were identified according to the current standard criteria (i.e. VAF ≥ 10%).
The combination of del17p with TP53 mutation data identified 95 cases without any TP53 aberrations (non-del17p/non-TP53mut), 8 del17p only cases, 60 TP53-mutated only cases (28 low-VAF), and 66 cases bearing both del17p deletion and TP53 mutations (7 low-VAF). Only patients with concomitant TP53 mutations and del17p showed significantly shorter OS/PFS intervals compared to non-del17p/non-TP53mut cases, while no difference in OS/PFS was found in patients presenting single aberration (Fig. 1C, D). The simultaneous presence of TP53 mutations and del17p confirmed its detrimental clinical impact by univariable analysis and remained independent predictor for short OS/PFS by multivariable analyses together with the number of previous lines of therapy and anemia; consistently, these variables were the most frequently selected by internal bootstrap validation (Table 1). Given the low number of patients of some subgroups (e.g. 8 del17p alone cases), these results need to be confirmed in larger cohorts.
At variance from chemo-immunotherapy where the presence of a single TP53 mutation, even with a low-VAF, is associated with a worse outcome [4, 12], in the ibrutinib setting only cases presenting a more complex disruption of the TP53 function, due to the concomitant presence of mutations and deletions, fail to have the best benefit from therapy. Our results are in keeping with recent findings suggesting that only double-hit aberrations (i.e. more than one TP53 mutation or TP53 mutation and del17p) are independently associated with a shorter outcome in ibrutinib-treated patients, single-hit aberrations (a single TP53 mutation or del17p only) having an outcome comparable to that of TP53wt patients [2]. Differently from Brieghel et al. [2], however, in our cohort, TP53 mutated patients with more than one mutations but without del17p failed to experience a significantly worse prognosis respect to patients without any aberrations (data not shown). In the present series, 52/66 cases concomitantly bearing del17p and TP53 mutations (79%) bore TP53 mutations and/or 17p deletion in most of the neoplastic clone (Supplementry Table S3). We could, therefore, speculate that the genetic instability fostered by such a massive TP53 disruption might eventually lead to the development of more complex genetic lesions, known to correlate with dismal outcomes in the ibrutinib setting [11, 13]. Our finding may help to explain previous reports of ibrutinib-treated CLL in which TP53 mutations failed to have a prognostic impact [12], and in which the simultaneous presence of TP53 mutations and deletion was not investigated.
The evolution of TP53 mutated clones was assessed in 38 patients by longitudinal NGS analysis of paired samples collected at pre-treatment (median time, −0.9 month; range −6.0–0.0) and during (non-relapsed cases; n = 22) or after (relapsed cases; n = 16) ibrutinib treatment (median time interval, 31.8 months, range 3.0–76.9). For relapsed cases, the second time point was collected in close proximity of progression (median time, −0.7 months, range −3.0–1.0 months). No significant differences were observed between relapsed and non-relapsed cases in relation to the timing of the second sampling (P = 0.74). Of a total of 127 TP53 mutations, 92 were present before and 106 after treatment; among these, 21 mutations (median VAF, 1.7%, range 0.4–52.3%) disappeared during the course of treatment, while 35 were newly identified (median VAF, 1.0%, range 0.4–95.2%; Supplementry Table S5). Among relapsed cases, 15/16 showed either a prominent expansion (i.e. a VAF increase greater than 20%) or stability (i.e. VAF variations within the range of 20% VAF variation) over time of the TP53 mutated clone(s) (Fig. 1E). Conversely, in the context of non-relapsed patients, 3 cases presented a VAF increase of the TP53 mutated clones, 13 remained stable, and 6 showed a VAF reduction (Fig. 1F). These data support the idea of a general stability of TP53 subclones under ibrutinib [14], although a positive selection of TP53 mutations over time was slightly over-represented in relapsed cases (P = 0.04, χ2 test), suggesting the occurrence of other genetic events complementing the clonal advantage due to TP53 disruption [11, 14, 15]. Considering the 127 TP53 mutations identified across the different time-points, 8 mutations were shared by ≥3 cases (Supplementry Table S5). Among them, G245S and R175H were found expanded (>20% VAF increase) in 3/4 and 2/3 cases, respectively (Supplementry Table S5), suggesting their possible role in ibrutinib resistance. BTK and PLCG2 mutations, were retrieved in 3/7 relapsed cases presenting a positive selection for TP53 mutations at the relapse time (Supplementry Table S5). Overall, BTK and PLCG2 mutations were discovered in 9/16 (56%) relapsed cases versus 3/22 (14%) patients under ibrutinib treatment (P = 0.006, χ2 test; Supplementry Table S5).
In conclusion, here we provided evidence that only the co-presence of TP53 deletion and mutations, the latter even with a low-VAF representation, and not the single aberrations have a negative prognostic impact in CLL patients under ibrutinib treatment. In practice, this finding points toward the need of a complete assessment of TP53 aberrations to be performed in all CLL patients prior to start ibrutinib treatment. A lower threshold for reporting TP53 mutations (e.g. VAF < 10%) must be evaluated in prospective clinical trial cohorts before it can be accepted as standard for routine practice. Moreover, low-VAF TP53 mutations should be always confirmed by orthogonal assays (e.g. ddPCR) or by repetition [4].
Data availability
The data that support the findings of this study are available from the corresponding author upon request.
References
Campo E, Cymbalista F, Ghia P, Jäger U, Pospisilova S, Rosenquist R, et al. TP53 aberrations in chronic lymphocytic leukemia: An overview of the clinical implications of improved diagnostics. Haematologica. 2018;103:1956–68.
Brieghel C, Aarup K, Torp MH, Andersen MA, Yde CW, Tian X, et al. Clinical outcomes in patients with multi-hit TP53 chronic lymphocytic leukemia treated with ibrutinib. Clin Cancer Res. 2021;27:4531–8.
Morabito F, Del Poeta G, Mauro FR, Reda G, Sportoletti P, Laurenti L, et al. TP53 disruption as a risk factor in the era of targeted therapies: a multicenter retrospective study of 525 chronic lymphocytic leukemia cases. Am J Hematol. 2021;96:E306–10.
Bomben R, Rossi FM, Vit F, Bittolo T, D’Agaro T, Zucchetto A, et al. TP53 mutations with low variant allele frequency predict short survival in Chronic Lymphocytic Leukemia. Clin Cancer Res. 2021;27:5566–76.
Malcikova J, Tausch E, Rossi D, Sutton LA, Soussi T, Zenz T, et al. ERIC recommendations for TP53 mutation analysis in chronic lymphocytic leukemia - Update on methodological approaches and results interpretation. Leukemia. 2018;32:1070–80.
Tissino E, Benedetti D, Herman SEM, ten Hacken E, Ahn IE, Chaffee KG, et al. Functional and clinical relevance of VLA-4 (CD49d/CD29) in ibrutinib-treated chronic lymphocytic leukemia. J Exp Med. 2018;215:681–97.
Ahn IE, Tian X, Ipe D, Cheng M, Albitar M, Tsao LC, et al. Prediction of outcome in patients with chronic lymphocytic leukemia treated with ibrutinib: development and validation of a four-factor prognostic model. J Clin Oncol. 2021;39:576–85.
Morabito F, Tripepi G, Del Poeta G, Mauro FR, Reda G, Sportoletti P, et al. Assessment of the 4-factor score: retrospective analysis of 586 CLL patients receiving ibrutinib. A campus CLL study. Am J Hematol. 2021;96:168–71.
Gentile M, Martino EA, Visentin A, Coscia M, Reda G, Sportoletti P, et al. Validation of a survival-risk score (SRS) in relapsed/refractory CLL patients treated with idelalisib–rituximab. Blood. Cancer J. 2020;10:0–2.
Mato AR, Tang B, Azmi S, Yang K, Zhang X, Stern JC, et al. A clinical practice comparison of patients with chronic lymphocytic leukemia with and without deletion 17p receiving first-line treatment with ibrutinib. Haematologica 2022;107:2630–40.
Cherng HJ, Khwaja R, Kanagal-Shamanna R, Tang G, Burger J, Thompson P, et al. TP53-altered chronic lymphocytic leukemia treated with firstline Bruton’s tyrosine kinase inhibitor-based therapy: a retrospective analysis. Am J Hematol. 2022;97:1005–12.
Malcikova J, Pavlova S, Kunt Vonkova B, Radova L, Plevova K, Kotaskova J, et al. Low-burden TP53 mutations in CLL: clinical impact and clonal evolution within the context of different treatment options. Blood. 2021;138:2670–85.
Kittai AS, Miller C, Goldstein D, Huang Y, Abruzzo LV, Beckwith K, et al. The impact of increasing karyotypic complexity and evolution on survival in patients with CLL treated with ibrutinib. Blood. 2021;138:2372–82.
Cafforio L, Raponi S, Cappelli LV, Ilari C, Soscia R, De Propris MS, et al. Treatment with ibrutinib does not induce a TP53 clonal evolution in chronic lymphocytic leukemia. Haematologica. 2022;107:334–7.
Kadri S, Lee J, Fitzpatrick C, Galanina N, Sukhanova M, Venkataraman G, et al. Clonal evolution underlying leukemia progression and Richter transformation in patients with ibrutinib-relapsed CLL. Blood Adv. 2017;1:715–27.
Funding
The present study is supported in part by: Progetto Ricerca Finalizzata PE-2016-02362756, and RF-2018-12365790, Italian Ministry of Health, Rome, Italy; Associazione Italiana Ricerca Cancro (AIRC), Investigator Grant IG-21687; Associazione Italiana contro le Leucemie, linfomi e mielomi (AIL), Venezia Section, Pramaggiore/Veneto Orientale Group, Italy; Fundaciò La Maratò de TV3 (Spain); Linfo-check - Bando ricerca - contributo art. 15, comma 2, lett b) LR 17/2014; “5 × 1000 Intramural Program”, Centro di Riferimento Oncologico, Aviano, Italy; Italian Ministry of Health 5 × 1000 funds 2013, 2015, 2016; Current Research 2016; Compagnia S. Paolo Turin Italy project 2017.0526.
Author information
Authors and Affiliations
Contributions
RB, designed the study, interpreted data, and wrote the manuscript; FMR, FV, TB, AZ, RP, ET, FP, MD, GF, performed and interpreted molecular studies, and contributed to data interpretation; FV, JP, and RB generated the bioinformatics pipeline of analysis, and performed statistical analyses; PB, RM, GR, LL, JO, AC, RL, MP, MIDP, AC, MG, FM, AT, FZ, RF, FDR, GDP collected clinical data and contributed to data interpretation; VG designed the study, interpreted data, and wrote the manuscript. All the Authors agreed on the final form of the manuscript with the only exclusion of GDP (deceased).
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
About this article
Cite this article
Bomben, R., Rossi, F.M., Vit, F. et al. Clinical impact of TP53 disruption in chronic lymphocytic leukemia patients treated with ibrutinib: a campus CLL study. Leukemia 37, 914–918 (2023). https://doi.org/10.1038/s41375-023-01845-9
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41375-023-01845-9