Missense Mutations Located in Structural p53 DNA-Binding Motifs Are Associated With Extremely Poor Survival in Chronic Lymphocytic Leukemia

2011 ◽  
Vol 29 (19) ◽  
pp. 2703-2708 ◽  
Author(s):  
Martin Trbusek ◽  
Jana Smardova ◽  
Jitka Malcikova ◽  
Ludmila Sebejova ◽  
Petr Dobes ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Dna Binding ◽  
Response To Therapy ◽  
Lymphocytic Leukemia ◽  
Functional Assay ◽  
Missense Mutations ◽  
P53 Mutations ◽  
Binding Motifs ◽  
Dna Binding Motifs ◽  
The Impact

Purpose There is a distinct connection between TP53 defects and poor prognosis in chronic lymphocytic leukemia (CLL). It remains unclear whether patients harboring TP53 mutations represent a homogenous prognostic group. Patients and Methods We evaluated the survival of patients with CLL and p53 defects identified at our institution by p53 yeast functional assay and complementary interphase fluorescence in situ hybridization analysis detecting del(17p) from 2003 to 2010. Results A defect of the TP53 gene was identified in 100 of 550 patients. p53 mutations were strongly associated with the deletion of 17p and the unmutated IgVH locus (both P < .001). Survival assessed from the time of abnormality detection was significantly reduced in patients with both missense (P < .001) and nonmissense p53 mutations (P = .004). In addition, patients harboring missense mutation located in p53 DNA-binding motifs (DBMs), structurally well-defined parts of the DNA-binding domain, manifested a clearly shorter median survival (12 months) compared with patients having missense mutations outside DBMs (41 months; P = .002) or nonmissense alterations (36 months; P = .005). The difference in survival was similar in the analysis limited to patients harboring mutation accompanied by del(17p) and was also confirmed in a subgroup harboring TP53 defect at diagnosis. The patients with p53 DBMs mutation (at diagnosis) also manifested a short median time to first therapy (TTFT; 1 month). Conclusion The substantially worse survival and the short TTFT suggest a strong mutated p53 gain-of-function phenotype in patients with CLL with DBMs mutations. The impact of p53 DBMs mutations on prognosis and response to therapy should be analyzed in investigative clinical trials.

scholarly journals Clonal dynamics in chronic lymphocytic leukemia

Hematology ◽  
2019 ◽  
Vol 2019 (1) ◽  
pp. 466-475
Author(s):  
Catherine Gutierrez ◽  
Catherine J. Wu
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Large Scale ◽  
Growth Dynamics ◽  
Disease Recurrence ◽  
Response To Therapy ◽  
Lymphocytic Leukemia ◽  
Molecular Heterogeneity ◽  
Sequencing Studies ◽  
Dramatic Shift ◽  
The Impact

Abstract Chronic lymphocytic leukemia has a highly variable disease course across patients, thought to be driven by the vast inter- and intrapatient molecular heterogeneity described in several large-scale DNA-sequencing studies conducted over the past decade. Although the last 5 years have seen a dramatic shift in the therapeutic landscape for chronic lymphocytic leukemia, including the regulatory approval of several potent targeted agents (ie, idelalisib, ibrutinib, venetoclax), the vast majority of patients still inevitably experience disease recurrence or persistence. Recent genome-wide sequencing approaches have helped to identify subclonal populations within tumors that demonstrate a broad spectrum of somatic mutations, diverse levels of response to therapy, patterns of repopulation, and growth kinetics. Understanding the impact of genetic, epigenetic, and transcriptomic features on clonal growth dynamics and drug response will be an important step toward the selection and timing of therapy.

885 P53 Mutations Affecting DNA-binding Have Prominent Impact on Survival in Chronic Lymphocytic Leukemia

2012 ◽  
Vol 48 ◽  
pp. S214
Author(s):  
J. Malcikova ◽  
J. Smardova ◽  
L. Sebejova ◽  
V. Vranova ◽  
S. Pavlova ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Dna Binding ◽  
Lymphocytic Leukemia ◽  
P53 Mutations ◽  
Impact On Survival

p53 Pathway Alterations Influence Survival and Treatment Response In Chronic Lymphocytic Leukemia

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 2885-2885 ◽  
Author(s):  
Hun Ju Lee ◽  
Miguel Gallardo ◽  
Xiaorui Zhang ◽  
Alfonso Quintas-Cardama ◽  
Sean M. Post
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Treatment Response ◽  
Hot Spot ◽  
P53 Mutation ◽  
Lymphocytic Leukemia ◽  
Chromosome 17 ◽  
P53 Mutations ◽  
P53 Pathway ◽  
Ideal System ◽  
The Impact

Abstract Chronic lymphocytic leukemia (CLL) is a heterogeneous malignancy, with survival rates that range from months to decades. Numerous genetic markers have been identifying that predict for poor survival outcomes. One of the most significant prognostic risk factors is loss of integrity of the p53 pathway. It is well known that loss of the short arm of chromosome 17 (17p-), containing the p53 locus, is a major predictor poor outcome in CLL, however, there is a lack of clarity how specific p53 mutations influence cancer progression. It is our contention that understanding the impact of p53 mutations in CLL progression will facilitate the development of better treatments options. We are using a mouse model of B-CLL (Eµ-TCL1) that also carry a p53 hot-spot mutation p53R172H, corresponding to R175H in humans, to study the impact of p53 mutation on treatment response and survival. Cohorts of Eµ-TCL1 and Eµ-TCL1;p53R172H/+ were treated with fludarabine at 35mg/kg per day for 5 days each month. We have observed significant changes in survival and selective pressure on the p53 locus following fludarabine treatment, leading to a refractory population of clones. Mice in the Eu-TCL1 cohort received a median of 1 treatment cycle (Range; 1-3), while the mice in the Eµ-TCL1;p53R172H/+ cohort received a median of 3 treatment cycles (Range;1-4), suggesting that the mutant cohort are likely to benefit initially with treatment only to succumb to a refractory clone of CLL. Mice in the Eµ-TCL1 cohort had an overall survival of 373 days (range; 341-464 days) in comparison to 322 days (range; 270-382days) in the Eµ-TCL1;p53R172H/+ cohort, indicating a trend toward inferior survival in the Eµ-TCL1;p53R172H/+ cohort. Interestingly, mice in the Eµ-TCL1 cohort had significant splenomegaly (40%) as compared to the Eµ-TCL1;p53R172H/+ cohort (0%). However, we observed that all Eµ-TCL1;p53R172H/+ had extensive extranodal disease with mice having abdominal and/or cervical mass, which is suggestive of Richter’s transformation. Together, these data indicate that fludarabine based therapies may have a profound negative transformational impact on CLL progression when used as a treatment strategy in the context of p53 mutations. These results would suggest that less cytotoxic therapies may benefit patients harboring p53 mutations. To this end, we are evaluating the effect of Ibrutinib therapy in the context of p53 mutations. We are currently treating cohorts of Eµ-TCL1 and Eµ-TCL1;p53R172H/+ mice with Ibrutinib 25mg/kg/day. Our preliminary results suggest Ibrutinib’s innovative mechanism may lessen some of these selective pressures on the p53 pathway and may indicate Ibrutinib is a superior treatment option compared to fludarabine when p53 mutations are present. In conjunction with these mouse studies, we are also determining the impact of p53 mutation in human patients by examining changes in CLL patient samples and cell lines following fludaribine and Ibrutinib treatment. This dual mouse/human strategy represents an ideal system in which to study genetic anomalies in the p53 pathway and examine the dynamic molecular pressures exerted by both fludarabine and Ibrutinib in CLL. Disclosures: No relevant conflicts of interest to declare.

Rel A Is an Independent Biomarker of Clinical Outcome in Chronic Lymphocytic Leukemia

2009 ◽  
Vol 27 (5) ◽  
pp. 763-769 ◽  
Author(s):  
Saman Hewamana ◽  
Thet Thet Lin ◽  
Clare Rowntree ◽  
Kamaraj Karunanithi ◽  
Guy Pratt ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Dna Binding ◽  
Clinical Outcome ◽  
Prognostic Significance ◽  
Response To Therapy ◽  
Lymphocytic Leukemia ◽  
Enzyme Linked Immunosorbent Assay ◽  
Mutation Status ◽  
Binet Stage ◽  
Time To First Treatment

Purpose We recently demonstrated the biologic importance of the nuclear factor kappa B (NF-κB) subunit Rel A in chronic lymphocytic leukemia (CLL) and hypothesized that Rel A DNA binding would have prognostic significance in this disease. Patients and Methods Rel A DNA binding was quantified in nuclear extracts derived from 131 unselected CLL patient samples using a quantitative DNA-binding enzyme-linked immunosorbent assay–based method. We then investigated the ability of Rel A to predict for the requirement for treatment and survival and compared our findings with other established prognostic markers. Results Rel A DNA binding was strongly associated with advanced Binet stage (P < .0001) but did not correlate with immunoglobulin VH (IgVH) mutation status (P = .25), CD38 expression (P = .87), or zeta-chain–associated protein kinase 70 (ZAP-70) expression (P = .55). It was predictive of time to first treatment (P = .02) and time to subsequent treatment (P = .0001). In addition, Rel A was the most predictive marker of survival both from date of diagnosis (hazard ratio [HR], 9.1; P = .01) and date of entry into the study (HR, 3.9; P = .05) and retained prognostic significance in multivariate analysis for both time to first treatment and overall survival in the presence of Binet stage, IgVH mutation status, CD38, and ZAP-70. Conclusion Rel A is an independent prognostic marker of survival in CLL and seems to have the unique capacity to predict the duration of response to therapy. Prospective assessment of Rel A as a marker of clinical outcome and as a therapeutic target are now warranted.

Large Scale Screening for DNA Damage-Induced Transcription Factors as Potential Targets for Treatment of CLL with p53 Apoptotic Defect.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 3439-3439
Author(s):  
Victoria Weston ◽  
Paul Moss ◽  
A. Malcolm R Taylor ◽  
Tatjana Stankovic
Keyword(s):  
Dna Damage ◽  
Transcription Factors ◽  
Dna Binding ◽  
Aryl Hydrocarbon Receptor ◽  
P53 Pathway ◽  
Binding Motifs ◽  
Aryl Hydrocarbon ◽  
Dna Damaging Agents ◽  
Dna Binding Motifs ◽  
The Impact

Abstract Abstract 3439 Poster Board III-327 Chronic lymphocytic leukaemia (CLL) is a malignancy with a variable clinical course in which a proportion of patients exhibits rapid clinical progression despite treatment. One of the major causes of treatment resistance is alterations in the ATM/p53 pathway imposed by mutations in either the ATM or TP53 genes. Consequently, there is an urgent need to devise novel therapeutic approaches that will be able to counteract the p53 apoptotic defect in these tumours. We have previously shown that DNA damage induces a complex ATM-dependent network of pro-survival and pro-apoptotic transcriptional responses (both p53-dependent and -independent) and that the balance between these responses determines CLL cellular death. Therefore, it is plausible to expect that manipulation of ATM-dependent transcription to either reduce pro-survival or increase pro-apoptotic signals can sensitise ATM and TP53 mutant CLL tumours to DNA damaging agents. Individual transcription factors (TFs) that govern ATM-dependent transcription are largely unknown. In this study we aimed to identify those factors by employing a DNA/Protein Transcription Factor ComboArray (Panomics/Affymetrix) which includes 345 DNA binding motifs for a range of transcription factors, DNA binding proteins and response elements. We compared the ability of nuclear cell extracts from 3 combined ATM wildtype primary CLL samples and 3 combined ATM mutant primary CLL samples to bind to biotin-labelled DNA binding motifs prior to irradiation (IR)-induced DNA damage, 2h and 6h post-IR. Following hybridisation of nuclear protein-bound biotin-labelled probes to the array and HRP visualisation, we identified 49 binding motifs (several of which were detected more than once through alternative sequences) which, in response to DNA damage, exhibited reduced binding in ATM mutant compared to the ATM wildtype CLL nuclear extracts. The most prominent differentially bound DNA binding motifs included those for GATA1 and 2, Transcriptional enhancer factor 1 (TEF1), c-Rel, Aryl hydrocarbon receptor/aryl hydrocarbon receptor nuclear translocator binding element (AhR/Arnt), forkhead box I1 (HFH-3), Slow/Cardiac Troponin C (cTnC/CEF-2), E2A immunoglobulin enhancer binding factors (E12/E47), Pax-4, Wilms tumour 1 (WT1), antioxidant recognition element (ARE) and interferon-a stimulated response element (ISRE). We validated differential binding of individual TFs by electro-mobility shift analysis (EMSA) and selected six that were positively corroborated in an independent cohort of primary ATM mutant and ATM wildtype CLL tumour cells. We subsequently investigated the impact of altering the activity of the identified ATM-dependent TFs on the sensitivity of ATM mutant CLL tumours to DNA damage. Among the selected TFs, as a proof of principle, ARE demonstrated both ATM-dependent binding by EMSA as well as the capacity to modulate the DNA damage response in CLL cells: pharmacological activation of this TF by Dimethyl fumarate (DMF) sensitised ATM mutant cells to IR-induced DNA damage. In summary, we have identified a number of ATM-regulated transcription factors that could be directly or indirectly targeted to increase the sensitivity of CLL cells with a defective ATM/p53 pathway to DNA damaging agents. We also suggest that the DNA damage-dependent TF screen represents a feasible approach to identify novel molecular targets that may sensitise other subtypes of treatment-resistant CLL tumours. Disclosures No relevant conflicts of interest to declare.

scholarly journals Clonal dynamics in chronic lymphocytic leukemia

2019 ◽  
Vol 3 (22) ◽  
pp. 3759-3769 ◽  
Author(s):  
Catherine Gutierrez ◽  
Catherine J. Wu
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Large Scale ◽  
Growth Dynamics ◽  
Disease Recurrence ◽  
Response To Therapy ◽  
Lymphocytic Leukemia ◽  
Molecular Heterogeneity ◽  
Sequencing Studies ◽  
Dramatic Shift ◽  
The Impact

Abstract Chronic lymphocytic leukemia has a highly variable disease course across patients, thought to be driven by the vast inter- and intrapatient molecular heterogeneity described in several large-scale DNA-sequencing studies conducted over the past decade. Although the last 5 years have seen a dramatic shift in the therapeutic landscape for chronic lymphocytic leukemia, including the regulatory approval of several potent targeted agents (ie, idelalisib, ibrutinib, venetoclax), the vast majority of patients still inevitably experience disease recurrence or persistence. Recent genome-wide sequencing approaches have helped to identify subclonal populations within tumors that demonstrate a broad spectrum of somatic mutations, diverse levels of response to therapy, patterns of repopulation, and growth kinetics. Understanding the impact of genetic, epigenetic, and transcriptomic features on clonal growth dynamics and drug response will be an important step toward the selection and timing of therapy.

scholarly journals Rice protein-binding microarrays: a tool to detect cis-acting elements near promoter regions in rice

Planta ◽  
2021 ◽  
Vol 253 (2) ◽  
Author(s):  
Joung Sug Kim ◽  
SongHwa Chae ◽  
Kyong Mi Jun ◽  
Gang-Seob Lee ◽  
Jong-Seong Jeon ◽  
...  
Keyword(s):  
Dna Binding ◽  
Protein Binding ◽  
Gene Networks ◽  
Upstream Region ◽  
Transcriptional Level ◽  
Cis Elements ◽  
Promoter Regions ◽  
Entire Genome ◽  
Binding Motifs ◽  
Dna Binding Motifs

Abstract Main conclusion The present study showed that a rice (Oryza sativa)-specific protein-binding microarray (RPBM) can be applied to analyze DNA-binding motifs with a TF where binding is evaluated in extended natural promoter regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements. Abstract Transcription factors (TFs) regulate gene expression at the transcriptional level by binding a specific DNA sequence. Thus, predicting the DNA-binding motifs of TFs is one of the most important areas in the functional analysis of TFs in the postgenomic era. Although many methods have been developed to address this challenge, many TFs still have unknown DNA-binding motifs. In this study, we designed RPBM with 40-bp probes and 20-bp of overlap, yielding 49 probes spanning the 1-kb upstream region before the translation start site of each gene in the entire genome. To confirm the efficiency of RPBM technology, we selected two previously studied TFs, OsWOX13 and OsSMF1, and an uncharacterized TF, OsWRKY34. We identified the ATTGATTG and CCACGTCA DNA-binding sequences of OsWOX13 and OsSMF1, respectively. In total, 635 and 932 putative feature genes were identified for OsWOX13 and OsSMF1, respectively. We discovered the CGTTGACTTT DNA-binding sequence and 195 putative feature genes of OsWRKY34. RPBM could be applicable in the analysis of DNA-binding motifs for TFs where binding is evaluated in the promoter and 5′ upstream CDS regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements.

scholarly journals The Impact of Chlorambucil and Valproic Acid on Cell Viability, Apoptosis and Expression of p21, HDM2, BCL2 and MCL1 Genes in Chronic Lymphocytic Leukemia

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1088
Author(s):  
Katarzyna Lipska ◽  
Agata Filip ◽  
Anna Gumieniczek
Keyword(s):  
Valproic Acid ◽  
Chronic Lymphocytic Leukemia ◽  
Cell Viability ◽  
Antiepileptic Drug ◽  
Drug Combination ◽  
Target Genes ◽  
Histone Deacetylation ◽  
Lymphocytic Leukemia ◽  
Malignant Cells ◽  
The Impact

Malignant cells in chronic lymphocytic leukemia (CLL) show resistance to apoptosis, as well as to chemotherapy, which are related to deletions or mutations of TP53, high expression of MCL1 and BCL2 genes and other abnormalities. Thus, the main goal of the present study was to assess the impact of chlorambucil (CLB) combined with valproic acid (VPA), a known antiepileptic drug and histone deacetylation inhibitor, on apoptosis of the cells isolated from 17 patients with CLL. After incubation with CLB (17.5 µM) and VPA (0.5 mM), percentage of apoptosis, as well as expression of two TP53 target genes (p21 and HDM2) and two genes from Bcl-2 family (BCL2 and MCL1), were tested. As a result, an increased percentage of apoptosis was observed for CLL cells treated with CLB and VPA, and with CLB alone. Under the treatment with the drug combination, the expression of p21 gene was visibly higher than under the treatment with CLB alone. At the same time, the cultures under CLB treatment showed visibly higher expression of BCL2 than the cultures with VPA alone. Thus, the present study strongly suggests further investigations on the CLB and VPA combination in CLL treatment.

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