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Landscape of TP53 Alterations in Chronic Lymphocytic Leukemia via Data Mining Mutation Databases

Soussi, Thierry, Baliakas, Panagiotis·2022·Frontiers in Oncology

Abstract

Locus-specific databases are invaluable tools for both basic and clinical research. The extensive information they contain is gathered from the literature and manually curated by experts. Cancer genome sequencing projects generate an immense amount of data, which are stored directly in large repositories (cancer genome databases). The presence of a TP53 defect (17p deletion and/or TP53 mutations) is an independent prognostic factor in chronic lymphocytic leukemia (CLL) and TP53 status analysis has been adopted in routine clinical practice. For that reason, TP53 mutation databases have become essential for the validation of the plethora of TP53 variants detected in tumor samples. TP53 profiles in CLL are characterized by a great number of subclonal TP53 mutations with low variant allelic frequencies and the presence of multiple minor subclones harboring different TP53 mutations. In this review, we describe the various characteristics of the multiple levels of heterogeneity of TP53 variants in CLL through the analysis of TP53 mutation databases and the utility of their diagnosis in the clinic.

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Research works printed but not linked: 67

  1. Collins, 1995, Positional Cloning Moves From Perditional to Traditional, Nat Genet, 9, 10.1038/ng0495-347 · DOI · Paper page
  2. Horaitis, 2004, The Challenge of Documenting Mutation Across the Genome: The Human Genome Variation Society Approach, Hum Mutat, 23, 10.1002/humu.20038 · DOI
  3. Auerbach, 2011, Mutation (Variation) Databases and Registries: A Rationale for Coordination of Efforts, Nat Rev Genet, 12, 881; discussion 881, 10.1038/nrg3011-c1 · doi:10.1038/nrg3011-c1
  4. Dalgleish, 2016, LSDBs and How They Have Evolved, Hum Mutat, 37, 10.1002/humu.22979 · DOI
  5. Soussi, 2014, Locus-Specific Databases in Cancer: What Future in a Post-Genomic Era? The TP53 LSDB Paradigm, Hum Mutat, 35, 10.1002/humu.22518 · DOI
  6. Pinard, 2016, Actionable Genes, Core Databases, and Locus-Specific Databases, Hum Mutat, 37, 10.1002/humu.23112 · DOI
  7. Zhang, 2011, International Cancer Genome Consortium Data Portal–A One-Stop Shop for Cancer Genomics Data, Database (Oxford), 2011, 10.1093/database/bar026 · DOI · Paper page
  8. Tate, 2018, COSMIC: The Catalogue Of Somatic Mutations In Cancer, Nucleic Acids Res, 47, 10.1093/nar/gky1015 · DOI · Paper page
  9. Network, 2013, The Cancer Genome Atlas Pan-Cancer Analysis Project, Nat Genet, 45, 10.1038/ng.2764 · DOI · Paper page
  10. Bouaoun, 2016, TP53 Variations in Human Cancers: New Lessons From the IARC TP53 Database and Genomics Data, Hum Mutat, 37, 10.1002/humu.23035 · DOI · Paper page
  11. Leroy, 2017, Recommended Guidelines for Validation, Quality Control, and Reporting of TP53 Variants in Clinical Practice, Cancer Res, 77, 10.1158/0008-5472.CAN-16-2179 · DOI
  12. Tikkanen, 2018, Seshat: A Web Service for Accurate Annotation, Validation, and Analysis of TP53 Variants Generated by Conventional and Next-Generation Sequencing, Hum Mutat, 39, 10.1002/humu.23543 · DOI
  13. Soussi, 2005, Reassessment of the TP53 Mutation Database in Human Disease by Data Mining With a Library of TP53 Missense Mutations, Hum Mutat, 25, 6, 10.1002/humu.20114 · DOI
  14. Soussi, 2006, Meta-Analysis of the P53 Mutation Database for Mutant P53 Biological Activity Reveals a Methodologic Bias in Mutation Detection, Clin Cancer Res, 12, 10.1158/1078-0432.CCR-05-0413 · DOI
  15. Kotler, 2018, A Systematic P53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation, Mol Cell, 71, 178, 10.1016/j.molcel.2018.06.012 · DOI · Paper page
  16. Carbonnier, 2020, Comprehensive Assessment of TP53 Loss of Function Using Multiple Combinatorial Mutagenesis Libraries, Sci Rep, 10, 20368, 10.1038/s41598-020-74892-2 · DOI
  17. Li, 2005, The Codon 47 Polymorphism in P53 Is Functionally Significant, J Biol Chem, 280, 10.1074/jbc.M414637200 · DOI
  18. Doffe, 2021, Identification and Functional Characterization of New Missense SNPs in the Coding Region of the TP53 Gene, Cell Death Differ, 28, 10.1038/s41418-020-00672-0 · DOI
  19. Donehower, 2019, Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas, Cell Rep, 28, 10.1016/j.celrep.2019.07.001 · DOI · Paper page
  20. Soussi, 2015, TP53: An Oncogene in Disguise, Cell Death Differ, 22, 10.1038/cdd.2015.53 · DOI · Paper page
  21. Leroy, 2014, TP53 Mutations in Human Cancer: Database Reassessment and Prospects for the Next Decade, Hum Mutat, 35, 10.1002/humu.22552 · DOI · Paper page
  22. Lazarian, 2017, Clinical Implications of Novel Genomic Discoveries in Chronic Lymphocytic Leukemia, J Clin Oncol, 35, 10.1200/JCO.2016.71.0822 · DOI
  23. Fabbri, 2016, The Molecular Pathogenesis of Chronic Lymphocytic Leukaemia, Nat Rev Cancer, 16, 10.1038/nrc.2016.8 · DOI · Paper page
  24. Rossi, 2014, Clinical Impact of Small TP53 Mutated Subclones in Chronic Lymphocytic Leukemia, Blood, 123, 10.1182/blood-2013-11-539726 · DOI · Paper page
  25. Bomben, 2021, TP53 Mutations With Low Variant Allele Frequency Predict Short Survival in Chronic Lymphocytic Leukemia, Clin Cancer Res, 27, 10.1158/1078-0432.CCR-21-0701 · DOI
  26. Nadeu, 2016, Clinical Impact of Clonal and Subclonal TP53, SF3B1, BIRC3, NOTCH1, and ATM Mutations in Chronic Lymphocytic Leukemia, Blood, 127, 10.1182/blood-2015-07-659144 · DOI · Paper page
  27. Brieghel, 2019, Deep Targeted Sequencing of TP53 in Chronic Lymphocytic Leukemia: Clinical Impact at Diagnosis and at Time of Treatment, Haematologica, 104, 10.3324/haematol.2018.195818 · DOI
  28. Stengel, 2017, The Impact of TP53 Mutations and TP53 Deletions on Survival Varies Between AML, ALL, MDS and CLL: An Analysis of 3307 Cases, Leukemia, 31, 10.1038/leu.2016.263 · DOI · Paper page
  29. Blakemore, 2020, Clinical Significance of TP53, BIRC3, ATM and MAPK-ERK Genes in Chronic Lymphocytic Leukaemia: Data From the Randomised UK LRF CLL4 Trial, Leukemia, 34, 10.1038/s41375-020-0723-2 · DOI
  30. Malcikova, 2015, Detailed Analysis of Therapy-Driven Clonal Evolution of TP53 Mutations in Chronic Lymphocytic Leukemia, Leukemia, 29, 10.1038/leu.2014.297 · DOI
  31. Kumar, 2009, Predicting the Effects of Coding non-Synonymous Variants on Protein Function Using the SIFT Algorithm, Nat Protoc, 4, 10.1038/nprot.2009.86 · DOI · Paper page
  32. Ng, 2001, Predicting Deleterious Amino Acid Substitutions, Genome Res, 11, 10.1101/gr.176601 · DOI · Paper page
  33. Adzhubei, 2010, A Method and Server for Predicting Damaging Missense Mutations, Nat Methods, 7, 10.1038/nmeth0410-248 · DOI · Paper page
  34. González-Pérez, 2011, Improving the Assessment of the Outcome of Nonsynonymous SNVs With a Consensus Deleteriousness Score, Condel, Am J Hum Genet, 88, 10.1016/j.ajhg.2011.03.004 · DOI · Paper page
  35. Kircher, 2014, A General Framework for Estimating the Relative Pathogenicity of Human Genetic Variants, Nat Genet, 46, 10.1038/ng.2892 · DOI · Paper page
  36. Shihab, 2015, An Integrative Approach to Predicting the Functional Effects of Non-Coding and Coding Sequence Variation, Bioinformatics, 31, 10.1093/bioinformatics/btv009 · DOI · Paper page
  37. Schwarz, 2010, MutationTaster Evaluates Disease-Causing Potential of Sequence Alterations, Nat Methods, 7, 10.1038/nmeth0810-575 · DOI · Paper page
  38. Reva, 2011, Predicting the Functional Impact of Protein Mutations: Application to Cancer Genomics, Nucleic Acids Res, 39, e118, 10.1093/nar/gkr407 · DOI · Paper page
  39. Khurana, 2015, GESPA: Classifying nsSNPs to Predict Disease Association, BMC Bioinf, 16, 228, 10.1186/s12859-015-0673-2 · DOI
  40. Ioannidis, 2016, REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants, Am J Hum Genet, 99, 10.1016/j.ajhg.2016.08.016 · DOI · Paper page
  41. Gray, 2018, Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data, Cell Syst, 6, 116, 10.1016/j.cels.2017.11.003 · DOI · Paper page
  42. Li, 2017, Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists, J Mol Diagn, 19, 4, 10.1016/j.jmoldx.2016.10.002 · DOI · Paper page
  43. Kato, 2003, Understanding the Function-Structure and Function-Mutation Relationships of P53 Tumor Suppressor Protein by High-Resolution Missense Mutation Analysis, Proc Natl Acad Sci USA, 100, 10.1073/pnas.1431692100 · DOI · Paper page
  44. Gaidano, 1991, P53 Mutations in Human Lymphoid Malignancies: Association With Burkitt Lymphoma and Chronic Lymphocytic Leukemia, Proc Natl Acad Sci USA, 88, 10.1073/pnas.88.12.5413 · DOI · Paper page
  45. Fenaux, 1992, Mutations of the P53 Gene in B-Cell Chronic Lymphocytic Leukemia: A Report on 39 Cases With Cytogenetic Analysis, Leukemia, 6
  46. el Rouby, 1993, P53 Gene Mutation in B-Cell Chronic Lymphocytic Leukemia Is Associated With Drug Resistance and is Independent of MDR1/MDR3 Gene Expression, Blood, 82, 10.1182/blood.V82.11.3452.3452 · DOI · Paper page
  47. Dohner, 1995, P53 Gene Deletion Predicts for Poor Survival and Non-Response to Therapy With Purine Analogs in Chronic B-Cell Leukemias, Blood, 85, 10.1182/blood.V85.6.1580.bloodjournal8561580 · DOI · Paper page
  48. Wattel, 1994, P53 Mutations Are Associated With Resistance to Chemotherapy and Short Survival in Hematologic Malignancies, Blood, 84, 10.1182/blood.V84.9.3148.3148 · DOI · Paper page
  49. Döhner, 2000, Genomic Aberrations and Survival in Chronic Lymphocytic Leukemia, N Engl J Med, 343, 10.1056/NEJM200012283432602 · DOI · Paper page
  50. Burger, 2020, Treatment of Chronic Lymphocytic Leukemia, N Engl J Med, 383, 10.1056/NEJMra1908213 · DOI · Paper page
  51. Ding, 2021, The Ongoing Unmet Needs in Chronic Lymphocytic Leukemia: TP53 Disruption, Richter, and Beyond, Hematol Oncol Clin North Am, 35, 10.1016/j.hoc.2021.04.001 · DOI
  52. Stilgenbauer, 2018, Venetoclax for Patients With Chronic Lymphocytic Leukemia With 17p Deletion: Results From the Full Population of a Phase II Pivotal Trial, J Clin Oncol, 36, 10.1200/JCO.2017.76.6840 · DOI · Paper page
  53. Stilgenbauer, 2016, Venetoclax in Relapsed or Refractory Chronic Lymphocytic Leukaemia With 17p Deletion: A Multicentre, Open-Label, Phase 2 Study, Lancet Oncol, 17, 10.1016/S1470-2045(16)30019-5 · DOI · Paper page
  54. Brown, 2018, Extended Follow-Up and Impact of High-Risk Prognostic Factors From the Phase 3 RESONATE Study in Patients With Previously Treated CLL/SLL, Leukemia, 32, 83, 10.1038/leu.2017.175 · DOI · Paper page
  55. Byrd, 2013, Targeting BTK With Ibrutinib in Relapsed Chronic Lymphocytic Leukemia, N Engl J Med, 369, 32, 10.1056/NEJMoa1215637 · DOI · Paper page
  56. Byrd, 2020, Ibrutinib Treatment for First-Line and Relapsed/Refractory Chronic Lymphocytic Leukemia: Final Analysis of the Pivotal Phase Ib/II PCYC-1102 Study, Clin Cancer Res, 26, 10.1158/1078-0432.CCR-19-2856 · DOI · Paper page
  57. Fischer, 2019, Venetoclax and Obinutuzumab in Patients With CLL and Coexisting Conditions, N Engl J Med, 380, 10.1056/NEJMoa1815281 · DOI · Paper page
  58. Burger, 2019, Randomized Trial of Ibrutinib vs Ibrutinib Plus Rituximab in Patients With Chronic Lymphocytic Leukemia, Blood, 133, 10.1182/blood-2018-10-879429 · DOI · Paper page
  59. Roberts, 2016, Targeting BCL2 With Venetoclax in Relapsed Chronic Lymphocytic Leukemia, N Engl J Med, 374, 10.1056/NEJMoa1513257 · DOI · Paper page
  60. Baliakas, 2019, Cytogenetic Complexity in Chronic Lymphocytic Leukemia: Definitions, Associations, and Clinical Impact, Blood, 133, 10.1182/blood-2018-09-873083 · DOI · Paper page
  61. Leeksma, 2021, Genomic Arrays Identify High-Risk Chronic Lymphocytic Leukemia With Genomic Complexity: A Multi-Center Study, Haematologica, 106, 87, 10.3324/haematol.2019.239947 · DOI
  62. Baliakas, 2019, Tailored Approaches Grounded on Immunogenetic Features for Refined Prognostication in Chronic Lymphocytic Leukemia, Haematologica, 104, 10.3324/haematol.2018.195032 · DOI
  63. Sutton, 2017, Immunoglobulin Genes in Chronic Lymphocytic Leukemia: Key to Understanding the Disease and Improving Risk Stratification, Haematologica, 102, 10.3324/haematol.2017.165605 · doi:10.3324/haematol.2017.165605
  64. Ljungström, 2016, Whole-Exome Sequencing in Relapsing Chronic Lymphocytic Leukemia: Clinical Impact of Recurrent RPS15 Mutations, Blood, 127, 10.1182/blood-2015-10-674572 · DOI
  65. Yu, 2017, Survival of Del17p CLL Depends on Genomic Complexity and Somatic Mutation, Clin Cancer Res, 23, 10.1158/1078-0432.CCR-16-0594 · DOI
  66. Malcikova, 2018, ERIC Recommendations for TP53 Mutation Analysis in Chronic Lymphocytic Leukemia-Update on Methodological Approaches and Results Interpretation, Leukemia, 32, 10.1038/s41375-017-0007-7 · DOI · Paper page
  67. Pospisilova, 2012, ERIC Recommendations on TP53 Mutation Analysis in Chronic Lymphocytic Leukemia, Leukemia, 26, 10.1038/leu.2012.25 · DOI · Paper page

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Metadata

Authors
Soussi, T., & Baliakas, P.
Venue
Frontiers in Oncology
Published
2022-02-16
Volume
12
ISSN
2234-943X
Cited by
17
References
7

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Soussi, T., & Baliakas, P. (2022). Landscape of TP53 Alterations in Chronic Lymphocytic Leukemia via Data Mining Mutation Databases. Frontiers in Oncology. https://doi.org/10.3389/fonc.2022.808886

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