SF3B1 Mutations in CLL Are Equivalent to p53/ATM Dysfunction and Cause Defective Puma Upregulation in Response to Chemotherapy

Raa, Doreen te; Derks, Ingrid A. M.; Luijks, Dieuwertje M.; Laar, Jacoline van; Monsuur, Hanneke N.; Oldreive, Ceri; Jethwa, Alexander; Hüllein, Jennifer; Stanković, Tatjana; Zenz, Thorsten; Oers, Marinus H. J. van; Kater, Arnon P.; Eldering, Eric

doi:10.1182/blood.v120.21.711.711

Cited by 6 publications

(5 citation statements)

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“… 26 An alternative assay, based on measuring CDKN1A levels by RT-PCR following fludarabine and doxorubicin treatment, was primarily designed for ATM function testing and can also distinguish between TP53 and ATM defects. 11 As we have previously published, also cell death following DNA-damaging agents can distinguish a group of functional WT samples from a group of ATM -mutated and a group of TP53 -mutated samples; 22 however, this method seems less suitable to functionally test samples at the individual level to predict (dys)functionality, as exemplified in Figure 3a showing that two out of seven WT samples showed small percentages of cell death following irradiation, comparable with the percentage of cell death seen in dysfunctional patients. Finally, promising results were shown for the detection of ATM defects by measuring the percentage of mitotic cells with p53 localization at the centrosome.…”

Section: Discussionmentioning

confidence: 92%

“…This is corroborated by the fact that apoptotic responses to various DNA-damaging agents were affected in the four cases that were further evaluated. Mutational analysis to uncover an underlying mechanism that could be involved in the observed defective DNA-damage-induced responses showed that two cases carried an SF3B1 mutation, 22 whereas the underlying defects in the other two samples remains elusive. These cases underscore the clinically highly relevant divergence between determination of ATM/p53 status by functional testing and by mutational analysis.…”

Section: Discussionmentioning

confidence: 99%

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Assessment of p53 and ATM functionality in chronic lymphocytic leukemia by multiplex ligation-dependent probe amplification

et al. 2015

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The ATM-p53 DNA-damage response (DDR) pathway has a crucial role in chemoresistance in CLL, as indicated by the adverse prognostic impact of genetic aberrations of TP53 and ATM. Identifying and distinguishing TP53 and ATM functional defects has become relevant as epigenetic and posttranscriptional dysregulation of the ATM/p53 axis is increasingly being recognized as the underlying cause of chemoresistance. Also, specific treatments sensitizing TP53- or ATM-deficient CLL cells are emerging. We therefore developed a new ATM-p53 functional assay with the aim to (i) identify and (ii) distinguish abnormalities of TP53 versus ATM and (iii) enable the identification of additional defects in the ATM-p53 pathway. Reversed transcriptase multiplex ligation-dependent probe amplification (RT-MLPA) was used to measure ATM and/or p53-dependent genes at the RNA level following DNA damage using irradiation. Here, we showed that this assay is able to identify and distinguish three subgroups of CLL tumors (i.e., TP53-defective, ATM-defective and WT) and is also able to detect additional samples with a defective DDR, without molecular aberrations in TP53 and/or ATM. These findings make the ATM-p53 RT-MLPA functional assay a promising prognostic tool for predicting treatment responses in CLL.

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Section: Discussionmentioning

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Assessment of p53 and ATM functionality in chronic lymphocytic leukemia by multiplex ligation-dependent probe amplification

et al. 2015

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“…This is corroborated by the fact that apoptotic responses to various DNA-damaging agents were affected in the four cases that were further evaluated. Mutational analysis to uncover an underlying mechanism that could be involved in the observed defective DNA-damageinduced responses showed that two cases carried an SF3B1 mutation, 22 whereas the underlying defects in the other two samples remains elusive. These cases underscore the clinically highly relevant divergence between determination of ATM/p53 status by functional testing and by mutational analysis.…”

Section: Discussionmentioning

confidence: 99%

Assessment of p53 and ATM Functionality in Chronic Lymphocytic Leukemia By Multiplex Ligation-Dependent Probe Amplification

Raa

Moerland

Leeksma

et al. 2015

Blood

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The ATM-p53 DNA damage response pathway plays a crucial role in chemoresistance in CLL, as indicated by the adverse prognostic impact of genetic aberrations of TP53 and ATM. Identifying and distinguishing TP53 and ATM functional defects has become relevant as epigenetic and posttranscriptional dysregulation of the ATM/p53 axis is increasingly being recognized as underlying cause of chemoresistance. Also, specific treatments sensitizing TP53-or ATM-deficient CLL cells are emerging. We therefore developed a new ATM-p53 functional assay with the aim to (i) identify and (ii) distinguish abnormalities of TP53 versus ATM and (iii) enable the identification of additional defects in the ATM-p53 pathway. Previously we showed that a reverse transcriptase multiplex ligation-dependent probe amplification (RT-MLPA) procedure which quantifies expression levels of the p53-targets, CDKN1A, BBC3 and Bax, in CLL cells following irradiation is able to determine p53 functionality. With the aim of identifying and distinguishing abnormalities of TP53 versus ATM and enabling the identification of additional defects in the DDR, we developed a new RT-MLPA based functional assay. Reversed transcriptase multiplex ligation-dependent probe amplification (RT-MLPA) was used to measure ATM and/or p53-dependent genes at the RNA level following DNA-damage using irradiation. A new RT-MLPA probe set (R016-X2, MRC-Holland), which included several p53 and ATM target genes was designed. Genes were selected based on the results of an earlier microarray study [Stankovic et al. Blood 2004;103:291-300]. A cohort of 30 CLL patients was utilized to set-up the RT-MLPA functional assay (training cohort) and an independent second cohort including 67 CLL patients included in the HOVON68 clinical trial was used as a validation cohort. From all these patients genetic analysis of ATM and TP53 was available using FISH and sequencing. First, the assay was performed on the training cohort and was able to identify and distinguish three subgroups of CLL tumors (i.e. TP53-defective, ATM-defective and WT). Next, based on the fold induction factors (i.e. gene expression upon irradiation versus non-irradiation) of 10 selected genes, a support vector machine (SVM) classifier was constructed to enable the classification of CLL samples into 3 different types of response, i.e. ATM/p53 functional, p53-dysfunctional, or ATM-dysfunctional. The RT-MLPA assay and SVM classifier were validated in a separate validation cohort. CLL samples with clear genotypic characteristics (i.e. biallelic defects) were assigned with a high degree of confidence to one of the three categories with sensitivities of 93%, 100% and 78% for TP53/ATM WT, biallelic TP53-defective and biallelic ATM-defective samples, respectively. Interestingly the assay was also able to detect additional samples with a defective DNA-damage response, without molecular aberrations in TP53 and/or ATM (22%; 6 out of 27 WT patients). Additional analysis of these samples showed significantly reduced apoptosis to fludarabine, doxorubicin and irradiation in comparison to the ATM/p53 functional samples, indicating that defects in the DNA-damage response other than TP53/ATM aberrations are indeed present and probably responsible for the observed defective DNA-damage induced apoptotic responses. In conclusion, the newly designed ATM-p53 RT-MLPA assay is able to distinguish three subgroups of CLL tumors (i.e. TP53-defective, ATM-defective and WT) and was also able to detect additional samples with a functional defective DNA-damage response, without molecular defects of TP53 and/or ATM. This indicates that the ATM-p53 RT-MLPA might not only be of additional clinical value over FISH to screen for mutations of TP53 and ATM instead of sequencing, but might also be useful for screening of other defects in the DNA-damage response pathway in addition to ATM and/or TP53 aberrations. These findings make the ATM-p53 RT-MLPA functional assay a promising prognostic tool for predicting treatment responses in CLL. Disclosures Hoogendoorn: Novartis: Consultancy; Gilead: Consultancy.

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“…Mutations in SF3B1 and TP53 were not mutually exclusive (Table 1), as found in some patient cohorts in the literature [31,32]. To understand the sole effect of SF3B1 mutations, we separated sole SF3B1 mutated cases from patients displaying del17p and/or TP53 mutations.…”

Section: Sf3b1 Mutations In Cll Samples Predict Poor Overall Patient ...mentioning

confidence: 97%

SF3B1 Mutations Are Associated with Resistance to Non-Genotoxic MDM2 Inhibition in Chronic Lymphocytic Leukemia

Aptullahoglu

Wallis

Marr

et al. 2023

IJMS

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Chronic lymphocytic leukemia (CLL) is a genetically and clinically heterogeneous malignancy affecting older individuals. There are a number of current treatment options for CLL, including monoclonal antibodies, targeted drugs, chemotherapy, and different combinations of these. However, for those patients who are intrinsically treatment resistant, or relapse following initial responses, novel targeted therapies are still needed. Targeting the mouse double-minute-2 human homolog (MDM2), a primary negative regulator of p53, is an appealing therapeutic strategy for non-genotoxic reactivation of p53, since the TP53 gene is in its wild-type state at diagnosis in approximately 90% of patients. Mutated SF3B1 and TP53 are both associated with more aggressive disease, resistance to therapies and poorer overall survival for CLL. In this study, we performed a screen for SF3B1 and TP53 mutations and tested RG7388 (idasanutlin), a second-generation MDM2 inhibitor, in a cohort of CLL primary patient samples. SF3B1 mutations were detected in 24 of 195 cases (12.3%) and found associated with poor overall survival (hazard ratio [HR] 2.12, p = 0.032) and high CD38 expression (median CD38 (%) 32 vs. 5; p = 0.0087). The novel striking finding of this study was an independent link between SF3B1 mutational status and poor response to RG7388. Overall, SF3B1 mutations in CLL patient samples were associated with resistance to treatment with RG7388 ex vivo, and patients with the wild type for both SF3B1 and TP53 are more likely to benefit from treatment with MDM2 inhibitors.

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SF3B1 Mutations in CLL Are Equivalent to p53/ATM Dysfunction and Cause Defective Puma Upregulation in Response to Chemotherapy

Cited by 6 publications

References 0 publications

Assessment of p53 and ATM functionality in chronic lymphocytic leukemia by multiplex ligation-dependent probe amplification

Assessment of p53 and ATM functionality in chronic lymphocytic leukemia by multiplex ligation-dependent probe amplification

Assessment of p53 and ATM Functionality in Chronic Lymphocytic Leukemia By Multiplex Ligation-Dependent Probe Amplification

SF3B1 Mutations Are Associated with Resistance to Non-Genotoxic MDM2 Inhibition in Chronic Lymphocytic Leukemia

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