Despite the well-established adverse impact of del(11q) in chronic lymphocytic leukemia (CLL), the prognostic significance of somatic ATM mutations remains uncertain. We evaluated the effects of ATM aberrations (del(11q) and/or ATM mutations) on time-to-first-treatment (TTFT) in 3631 untreated patients with CLL, in the context of IGHV gene mutational status and mutations in nine CLL-related genes. ATM mutations were present in 246 cases (6.8%), frequently co-occurring with del(11q) (112/246 cases, 45.5%). ATM-mutated patients displayed a different spectrum of genetic abnormalities when comparing IGHV-mutated (M-CLL) and unmutated (U-CLL) cases: M-CLL was enriched for SF3B1 and NFKBIE mutations, whereas U-CLL showed mutual exclusivity with trisomy 12 and TP53 mutations. Isolated ATM mutations were rare, affecting 1.2% of Binet A patients and <1% of M-CLL cases. While univariable analysis revealed shorter TTFT for Binet A patients with any ATM aberration compared to ATM-wildtype, multivariable analysis identified only del(11q), trisomy 12, SF3B1, and EGR2 mutations as independent prognosticators of shorter TTFT among Binet A patients and within M-CLL and U-CLL subgroups. These findings highlight del(11q), and not ATM mutations, as a key biomarker of increased risk of early progression and need for therapy, particularly in otherwise indolent M-CLL, providing insights into risk-stratification and therapeutic decision-making.

• MeSH
• Ataxia Telangiectasia Mutated Proteins * genetics   MeSH
• Chromosome Deletion * MeSH
• Leukemia, Lymphocytic, Chronic, B-Cell * genetics   mortality   pathology   MeSH
• Adult MeSH
• Middle Aged MeSH
• Humans MeSH
• Chromosomes, Human, Pair 11 * genetics   MeSH
• Mutation * MeSH
• Biomarkers, Tumor * genetics   MeSH
• Prognosis MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• Check Tag
• Adult MeSH
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• ATM protein, human MeSH Browser
• Ataxia Telangiectasia Mutated Proteins * MeSH
• Biomarkers, Tumor * MeSH

TP53 gene abnormalities represent the most important biomarker in chronic lymphocytic leukemia (CLL). Altered protein modifications could also influence p53 function, even in the wild-type protein. We assessed the impact of p53 protein phosphorylations on p53 functions as an alternative inactivation mechanism. We studied p53 phospho-profiles induced by DNA-damaging agents (fludarabine, doxorubicin) in 71 TP53-intact primary CLL samples. Doxorubicin induced two distinct phospho-profiles: profile I (heavily phosphorylated) and profile II (hypophosphorylated). Profile II samples were less capable of activating p53 target genes upon doxorubicin exposure, resembling TP53-mutant samples at the transcriptomic level, whereas standard p53 signaling was triggered in profile I. ATM locus defects were more common in profile II. The samples also differed in the basal activity of the hypoxia pathway: the highest level was detected in TP53-mutant samples, followed by profile II and profile I. Our study suggests that wild-type TP53 CLL cells with less phosphorylated p53 show TP53-mutant-like behavior after DNA damage. p53 hypophosphorylation and the related lower ability to respond to DNA damage are linked to ATM locus defects and the higher basal activity of the hypoxia pathway.

• Keywords
• CLL, p53, phosphorylation,
• MeSH
• Ataxia Telangiectasia Mutated Proteins genetics   metabolism   MeSH
• Leukemia, Lymphocytic, Chronic, B-Cell * genetics   MeSH
• Doxorubicin pharmacology   MeSH
• Phosphorylation MeSH
• Genes, p53 MeSH
• Hypoxia genetics   MeSH
• Humans MeSH
• Tumor Suppressor Protein p53 * metabolism   MeSH
• DNA Damage MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Ataxia Telangiectasia Mutated Proteins MeSH
• Doxorubicin MeSH
• Tumor Suppressor Protein p53 * MeSH

Recurrent mutations within EGR2 were recently reported in advanced-stage chronic lymphocytic leukemia (CLL) patients and associated with a worse outcome. To study their prognostic impact, 2403 CLL patients were examined for mutations in the EGR2 hotspot region including a screening (n=1283) and two validation cohorts (UK CLL4 trial patients, n=366; CLL Research Consortium (CRC) patients, n=490). Targeted deep-sequencing of 27 known/postulated CLL driver genes was also performed in 38 EGR2-mutated patients to assess concurrent mutations. EGR2 mutations were detected in 91/2403 (3.8%) investigated cases, and associated with younger age at diagnosis, advanced clinical stage, high CD38 expression and unmutated IGHV genes. EGR2-mutated patients frequently carried ATM lesions (42%), TP53 aberrations (18%) and NOTCH1/FBXW7 mutations (16%). EGR2 mutations independently predicted shorter time-to-first-treatment (TTFT) and overall survival (OS) in the screening cohort; they were confirmed associated with reduced TTFT and OS in the CRC cohort and independently predicted short OS from randomization in the UK CLL4 cohort. A particularly dismal outcome was observed among EGR2-mutated patients who also carried TP53 aberrations. In summary, EGR2 mutations were independently associated with an unfavorable prognosis, comparable to CLL patients carrying TP53 aberrations, suggesting that EGR2-mutated patients represent a new patient subgroup with very poor outcome.

• MeSH
• Leukemia, Lymphocytic, Chronic, B-Cell classification   drug therapy   genetics   mortality   MeSH
• Adult MeSH
• Genes, p53 MeSH
• Middle Aged MeSH
• Humans MeSH
• Mutation * MeSH
• Proportional Hazards Models MeSH
• Early Growth Response Protein 2 genetics   MeSH
• Aged MeSH
• Check Tag
• Adult MeSH
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• EGR2 protein, human MeSH Browser
• Early Growth Response Protein 2 MeSH

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.

• MeSH
• Ataxia Telangiectasia Mutated Proteins genetics   metabolism   MeSH
• Biological Assay MeSH
• Drug Resistance, Neoplasm genetics   MeSH
• Leukemia, Lymphocytic, Chronic, B-Cell drug therapy   genetics   metabolism   pathology   MeSH
• Doxorubicin pharmacology   MeSH
• Epigenesis, Genetic MeSH
• Humans MeSH
• Multiplex Polymerase Chain Reaction methods   MeSH
• Mutation * MeSH
• Tumor Suppressor Protein p53 genetics   metabolism   MeSH
• Reverse Transcriptase Polymerase Chain Reaction methods   MeSH
• DNA Damage MeSH
• Antineoplastic Agents pharmacology   MeSH
• Gene Expression Regulation, Leukemic * MeSH
• RNA, Neoplasm genetics   MeSH
• Sensitivity and Specificity MeSH
• Vidarabine analogs & derivatives   pharmacology   MeSH
• Gamma Rays MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• ATM protein, human MeSH Browser
• Ataxia Telangiectasia Mutated Proteins MeSH
• Doxorubicin MeSH
• fludarabine MeSH Browser
• Tumor Suppressor Protein p53 MeSH
• Antineoplastic Agents MeSH
• RNA, Neoplasm MeSH
• Vidarabine MeSH

• MeSH
• Ataxia Telangiectasia Mutated Proteins deficiency   genetics   metabolism   MeSH
• Leukemia, Lymphocytic, Chronic, B-Cell drug therapy   genetics   metabolism   MeSH
• Molecular Targeted Therapy MeSH
• Epistasis, Genetic MeSH
• Humans MeSH
• Cell Transformation, Neoplastic genetics   metabolism   MeSH
• Oxidative Stress * drug effects   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Research Support, Non-U.S. Gov't MeSH
• Editorial MeSH
• Names of Substances
• Ataxia Telangiectasia Mutated Proteins MeSH

Mutations or deletions in TP53 or ATM are well-known determinants of poor prognosis in chronic lymphocytic leukemia (CLL), but only account for approximately 40% of chemo-resistant patients. Genome-wide sequencing has uncovered novel mutations in the splicing factor sf3b1, that were in part associated with ATM aberrations, suggesting functional synergy. We first performed detailed genetic analyses in a CLL cohort (n=110) containing ATM, SF3B1 and TP53 gene defects. Next, we applied a newly developed multiplex assay for p53/ATM target gene induction and measured apoptotic responses to DNA damage. Interestingly, SF3B1 mutated samples without concurrent ATM and TP53 aberrations (sole SF3B1) displayed partially defective ATM/p53 transcriptional and apoptotic responses to various DNA-damaging regimens. In contrast, NOTCH1 or K/N-RAS mutated CLL displayed normal responses in p53/ATM target gene induction and apoptosis. In sole SF3B1 mutated cases, ATM kinase function remained intact, and γH2AX formation, a marker for DNA damage, was increased at baseline and upon irradiation. Our data demonstrate that single mutations in sf3b1 are associated with increased DNA damage and/or an aberrant response to DNA damage. Together, our observations may offer an explanation for the poor prognosis associated with SF3B1 mutations.

• MeSH
• Apoptosis MeSH
• Ataxia Telangiectasia Mutated Proteins metabolism   MeSH
• Leukemia, Lymphocytic, Chronic, B-Cell genetics   MeSH
• Gene Deletion MeSH
• Doxorubicin pharmacology   MeSH
• Phosphoproteins genetics   MeSH
• Genome, Human MeSH
• Histones metabolism   MeSH
• Imidazoles pharmacology   MeSH
• Cohort Studies MeSH
• Humans MeSH
• Ribonucleoprotein, U2 Small Nuclear genetics   MeSH
• Mutation * MeSH
• DNA Mutational Analysis MeSH
• Tumor Suppressor Protein p53 genetics   MeSH
• Piperazines pharmacology   MeSH
• DNA Damage MeSH
• Prognosis MeSH
• Flow Cytometry MeSH
• Receptor, Notch1 genetics   MeSH
• Gene Expression Regulation, Leukemic * MeSH
• RNA Splicing Factors MeSH
• Vidarabine analogs & derivatives   pharmacology   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• ATM protein, human MeSH Browser
• Ataxia Telangiectasia Mutated Proteins MeSH
• Doxorubicin MeSH
• fludarabine MeSH Browser
• Phosphoproteins MeSH
• H2AX protein, human MeSH Browser
• Histones MeSH
• Imidazoles MeSH
• Ribonucleoprotein, U2 Small Nuclear MeSH
• Tumor Suppressor Protein p53 MeSH
• NOTCH1 protein, human MeSH Browser
• nutlin 3 MeSH Browser
• Piperazines MeSH
• Receptor, Notch1 MeSH
• RNA Splicing Factors MeSH
• SF3B1 protein, human MeSH Browser
• TP53 protein, human MeSH Browser
• Vidarabine MeSH