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Billant O, Friocourt G, Roux P, Voisset C. p53, A Victim of the Prion Fashion. Cancers (Basel) 2021; 13:E269. [PMID: 33450819 PMCID: PMC7828285 DOI: 10.3390/cancers13020269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/17/2022] Open
Abstract
Identified in the late 1970s as an oncogene, a driving force leading to tumor development, p53 turned out to be a key tumor suppressor gene. Now p53 is considered a master gene regulating the transcription of over 3000 target genes and controlling a remarkable number of cellular functions. The elevated prevalence of p53 mutations in human cancers has led to a recurring questioning about the roles of mutant p53 proteins and their functional consequences. Both mutants and isoforms of p53 have been attributed dominant-negative and gain of function properties among which is the ability to form amyloid aggregates and behave in a prion-like manner. This report challenges the ongoing "prion p53" hypothesis by reviewing evidence of p53 behavior in light of our current knowledge regarding amyloid proteins, prionoids and prions.
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Affiliation(s)
| | - Gaëlle Friocourt
- Inserm, Université de Bretagne Occidentale, EFS, UMR 1078, GGB, F-29200 Brest, France;
| | - Pierre Roux
- CRBM, CNRS, UMR5234, 34293 Montpellier, France;
| | - Cécile Voisset
- Inserm, Université de Bretagne Occidentale, EFS, UMR 1078, GGB, F-29200 Brest, France;
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2
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Leroy B, Ballinger ML, Baran-Marszak F, Bond GL, Braithwaite A, Concin N, Donehower LA, El-Deiry WS, Fenaux P, Gaidano G, Langerød A, Hellstrom-Lindberg E, Iggo R, Lehmann-Che J, Mai PL, Malkin D, Moll UM, Myers JN, Nichols KE, Pospisilova S, Ashton-Prolla P, Rossi D, Savage SA, Strong LC, Tonin PN, Zeillinger R, Zenz T, Fraumeni JF, Taschner PEM, Hainaut P, Soussi T. Recommended Guidelines for Validation, Quality Control, and Reporting of TP53 Variants in Clinical Practice. Cancer Res 2017; 77:1250-1260. [PMID: 28254861 DOI: 10.1158/0008-5472.can-16-2179] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 11/12/2016] [Accepted: 11/16/2016] [Indexed: 12/21/2022]
Abstract
Accurate assessment of TP53 gene status in sporadic tumors and in the germline of individuals at high risk of cancer due to Li-Fraumeni Syndrome (LFS) has important clinical implications for diagnosis, surveillance, and therapy. Genomic data from more than 20,000 cancer genomes provide a wealth of information on cancer gene alterations and have confirmed TP53 as the most commonly mutated gene in human cancer. Analysis of a database of 70,000 TP53 variants reveals that the two newly discovered exons of the gene, exons 9β and 9γ, generated by alternative splicing, are the targets of inactivating mutation events in breast, liver, and head and neck tumors. Furthermore, germline rearrange-ments in intron 1 of TP53 are associated with LFS and are frequently observed in sporadic osteosarcoma. In this context of constantly growing genomic data, we discuss how screening strategies must be improved when assessing TP53 status in clinical samples. Finally, we discuss how TP53 alterations should be described by using accurate nomenclature to avoid confusion in scientific and clinical reports. Cancer Res; 77(6); 1250-60. ©2017 AACR.
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Affiliation(s)
- Bernard Leroy
- Sorbonne Université, UPMC Univ Paris 06, Paris, France
| | - Mandy L Ballinger
- Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Fanny Baran-Marszak
- Hôpital Avicenne, Assistance Publique-Hôpitaux De Paris, Bobigny, Service D'H ematologie Biologique, France
| | - Gareth L Bond
- Ludwig Institute for Cancer Research, University of Oxford, Nuffield Department of Clinical Medicine, Old Road Campus Research Building, Oxford, United Kingdom
| | - Antony Braithwaite
- Dept of Pathology, School of Medicine, University of Otago, Dunedin, New Zealand.,Children's Medical Research Institute, University of Sydney, Westmead NSW, Australia
| | - Nicole Concin
- Department of Gynecology and Obstetrics, Innsbruck Medical University, Innsbruck, Austria
| | | | - Wafik S El-Deiry
- Department of Hematology/Oncology and Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Pierre Fenaux
- Service d'hématologie séniors, Hôpital St Louis/Université Paris 7, 1 avenue Claude Vellefaux, Paris, France
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Anita Langerød
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Eva Hellstrom-Lindberg
- Karolinska Institute, Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Iggo
- Bergonié Cancer Institute University of Bordeaux 229 cours de l'Argonne 33076 Bordeaux, France
| | | | - Phuong L Mai
- Cancer Genetics Program, Magee Womens Hospital, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - David Malkin
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Ute M Moll
- Department of Pathology, Stony Brook University, Stony Brook, New York
| | - Jeffrey N Myers
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kim E Nichols
- Department of Oncology, Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sarka Pospisilova
- Masaryk University, CEITEC - Molecular Medicine and University Hospital Brno, Department of Internal Medicine - Hematology and Oncology, Brno, Czech Republic
| | - Patricia Ashton-Prolla
- Universidade Federal do Rio Grande do Sul (UFRGS) e Serviço deGenética Médica-HCPA, Rua Ramiro Barcelos, Porto Alegre, Brasil
| | - Davide Rossi
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Louise C Strong
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University and Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Robert Zeillinger
- Molecular Oncology Group, Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
| | - Thorsten Zenz
- University of Heidelberg, Department of Medicine V, Heidelberg, Germany; Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center (dkfz), Heidelberg, Germany
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Peter E M Taschner
- Generade Centre of Expertise Genomics and University of Applied Sciences Leiden, Leiden, the Netherlands
| | - Pierre Hainaut
- Institut Albert Bonniot, Inserm 823, Université Grenoble Alpes, Rond Point de la Chantourne, La Tronche, France
| | - Thierry Soussi
- Sorbonne Université, UPMC Univ Paris 06, Paris, France. .,Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden.,INSERM, U1138, Centre de Recherche des Cordeliers, Paris, France
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3
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Abstract
Since its discovery in 1979, p53 has been on the forefront of cancer research. It is considered a master gene of cancer suppression and is found mutated in around 50% of all human tumors. In addition, the progressive identification of p53-related transcription factors p63 and p73 as well as their multiple isoforms have added further layers of complexity to an already dense network. Among the numerous models used to unravel the p53 family mysteries, S. cerevisiae has been particularly useful. This seemingly naive model allows the expression of a functional human p53 and thus the assessment of p53 intrinsic transcriptional activity. The aim of this article is to review the various contributions that the budding yeast has made to the understanding of p53, p63 and p73 biology and to envision new possible directions for yeast-based assays in the field of cancer as well as other p53-family-related diseases.
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4
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Gros A, Laharanne E, Vergier M, Prochazkova-Carlotti M, Pham-Ledard A, Bandres T, Poglio S, Berhouet S, Vergier B, Vial JP, Chevret E, Beylot-Barry M, Merlio JP. TP53 alterations in primary and secondary Sézary syndrome: A diagnostic tool for the assessment of malignancy in patients with erythroderma. PLoS One 2017; 12:e0173171. [PMID: 28301507 PMCID: PMC5354275 DOI: 10.1371/journal.pone.0173171] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 02/06/2017] [Indexed: 12/14/2022] Open
Abstract
Recent massive parallel sequencing data have evidenced the genetic diversity and complexity of Sézary syndrome mutational landscape with TP53 alterations being the most prevalent genetic abnormality. We analyzed a cohort of 35 patients with SS and a control group of 8 patients with chronic inflammatory dermatoses. TP53 status was analyzed at different clinical stages especially in 9 patients with a past-history of mycosis fungoides (MF), coined secondary SS. TP53 mutations were only detected in 10 patients with either primary or secondary SS (29%) corresponding to point mutations, small insertions and deletions which were unique in each case. Interestingly, TP53 mutations were both detected in sequential unselected blood mononuclear cells and in skin specimens. Cytogenetic analysis of blood specimens of 32 patients with SS showed a TP53 deletion in 27 cases (84%). Altogether 29 out of 35 cases exhibited TP53 mutation and/or deletion (83%). No difference in prognosis was observed according to TP53 status while patients with secondary SS had a worse prognosis than patients with primary SS. Interestingly, patients with TP53 alterations displayed a younger age and the presence of TP53 alteration at initial diagnosis stage supports a pivotal oncogenic role for TP53 mutation in SS as well as in erythrodermic MF making TP53 assessment an ancillary method for the diagnosis of patients with erythroderma as patients with inflammatory dermatoses did not display TP53 alteration.
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Affiliation(s)
- Audrey Gros
- INSERM U1053, Bordeaux Research in Translational Oncology University Bordeaux, Bordeaux, France.,Tumor Bank and Tumor Biology Laboratory, CHU de Bordeaux, Pessac, France
| | - Elodie Laharanne
- INSERM U1053, Bordeaux Research in Translational Oncology University Bordeaux, Bordeaux, France.,Tumor Bank and Tumor Biology Laboratory, CHU de Bordeaux, Pessac, France
| | - Marie Vergier
- Tumor Bank and Tumor Biology Laboratory, CHU de Bordeaux, Pessac, France
| | | | - Anne Pham-Ledard
- INSERM U1053, Bordeaux Research in Translational Oncology University Bordeaux, Bordeaux, France.,Dermatology Department, CHU de Bordeaux, Bordeaux, France
| | - Thomas Bandres
- Tumor Bank and Tumor Biology Laboratory, CHU de Bordeaux, Pessac, France
| | - Sandrine Poglio
- INSERM U1053, Bordeaux Research in Translational Oncology University Bordeaux, Bordeaux, France
| | - Sabine Berhouet
- Tumor Bank and Tumor Biology Laboratory, CHU de Bordeaux, Pessac, France
| | - Béatrice Vergier
- INSERM U1053, Bordeaux Research in Translational Oncology University Bordeaux, Bordeaux, France.,Pathology Department, CHU de Bordeaux, Pessac, France
| | | | - Edith Chevret
- INSERM U1053, Bordeaux Research in Translational Oncology University Bordeaux, Bordeaux, France
| | - Marie Beylot-Barry
- INSERM U1053, Bordeaux Research in Translational Oncology University Bordeaux, Bordeaux, France.,Dermatology Department, CHU de Bordeaux, Bordeaux, France
| | - Jean-Philippe Merlio
- INSERM U1053, Bordeaux Research in Translational Oncology University Bordeaux, Bordeaux, France.,Tumor Bank and Tumor Biology Laboratory, CHU de Bordeaux, Pessac, France
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5
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Rudewicz J, Soueidan H, Uricaru R, Bonnefoi H, Iggo R, Bergh J, Nikolski M. MICADo - Looking for Mutations in Targeted PacBio Cancer Data: An Alignment-Free Method. Front Genet 2016; 7:214. [PMID: 28008336 PMCID: PMC5143680 DOI: 10.3389/fgene.2016.00214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/23/2016] [Indexed: 12/11/2022] Open
Abstract
Targeted sequencing is commonly used in clinical application of NGS technology since it enables generation of sufficient sequencing depth in the targeted genes of interest and thus ensures the best possible downstream analysis. This notwithstanding, the accurate discovery and annotation of disease causing mutations remains a challenging problem even in such favorable context. The difficulty is particularly salient in the case of third generation sequencing technology, such as PacBio. We present MICADo, a de Bruijn graph based method, implemented in python, that makes possible to distinguish between patient specific mutations and other alterations for targeted sequencing of a cohort of patients. MICADo analyses NGS reads for each sample within the context of the data of the whole cohort in order to capture the differences between specificities of the sample with respect to the cohort. MICADo is particularly suitable for sequencing data from highly heterogeneous samples, especially when it involves high rates of non-uniform sequencing errors. It was validated on PacBio sequencing datasets from several cohorts of patients. The comparison with two widely used available tools, namely VarScan and GATK, shows that MICADo is more accurate, especially when true mutations have frequencies close to backgound noise. The source code is available at http://github.com/cbib/MICADo.
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Affiliation(s)
- Justine Rudewicz
- Centre de BioInformatique de Bordeaux, University of BordeauxBordeaux, France; Laboratoire Bordelais de Recherche en Informatique, Centre National de la Recherche Scientifique, University of BordeauxBordeaux, France; Bergonié Cancer Institute, Institut National de la Santé et de la Recherche Médicale U1218, University of BordeauxBordeaux, France
| | - Hayssam Soueidan
- Centre de BioInformatique de Bordeaux, University of BordeauxBordeaux, France; Laboratoire Bordelais de Recherche en Informatique, Centre National de la Recherche Scientifique, University of BordeauxBordeaux, France
| | - Raluca Uricaru
- Centre de BioInformatique de Bordeaux, University of BordeauxBordeaux, France; Laboratoire Bordelais de Recherche en Informatique, Centre National de la Recherche Scientifique, University of BordeauxBordeaux, France
| | - Hervé Bonnefoi
- Bergonié Cancer Institute, Institut National de la Santé et de la Recherche Médicale U1218, University of Bordeaux Bordeaux, France
| | - Richard Iggo
- Bergonié Cancer Institute, Institut National de la Santé et de la Recherche Médicale U1218, University of Bordeaux Bordeaux, France
| | - Jonas Bergh
- Karolinska Institute and University Hospital Stockholm, Sweden
| | - Macha Nikolski
- Centre de BioInformatique de Bordeaux, University of BordeauxBordeaux, France; Laboratoire Bordelais de Recherche en Informatique, Centre National de la Recherche Scientifique, University of BordeauxBordeaux, France
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6
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Hainaut P, Pfeifer GP. Somatic TP53 Mutations in the Era of Genome Sequencing. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026179. [PMID: 27503997 DOI: 10.1101/cshperspect.a026179] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Amid the complexity of genetic alterations in human cancer, TP53 mutation appears as an almost invariant component, representing by far the most frequent genetic alteration overall. Compared with previous targeted sequencing studies, recent integrated genomics studies offer a less biased view of TP53 mutation patterns, revealing that >20% of mutations occur outside the DNA-binding domain. Among the 12 mutations representing each at least 1% of all mutations, five occur at residues directly involved in specific DNA binding, four affect the tertiary fold of the DNA-binding domain, and three are nonsense mutations, two of them in the carboxyl terminus. Significant mutations also occur in introns, affecting alternative splicing events or generating rearrangements (e.g., in intron 1 in sporadic osteosarcoma). In aggressive cancers, mutation is so common that it may not have prognostic value (all these cancers have impaired p53 function caused by mutation or by other mechanisms). In several other cancers, however, mutation makes a clear difference for prognostication, as, for example, in HER2-enriched breast cancers and in lung adenocarcinoma with EGFR mutations. Thus, the clinical significance of TP53 mutation is dependent on tumor subtype and context. Understanding the clinical impact of mutation will require integrating mutation-specific information (type, frequency, and predicted impact) with data on haplotypes and on loss of heterozygosity.
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Affiliation(s)
- Pierre Hainaut
- University Grenoble Alpes, Institut Albert Bonniot, Institut National de la Santé et de la Recherche Médicale (INSERM), 823 Grenoble, France
| | - Gerd P Pfeifer
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan 49503
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7
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Sharma V, Monti P, Fronza G, Inga A. Human transcription factors in yeast: the fruitful examples of P53 and NF-кB. FEMS Yeast Res 2016; 16:fow083. [PMID: 27683095 DOI: 10.1093/femsyr/fow083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2016] [Indexed: 12/31/2022] Open
Abstract
The observation that human transcription factors (TFs) can function when expressed in yeast cells has stimulated the development of various functional assays to investigate (i) the role of binding site sequences (herein referred to as response elements, REs) in transactivation specificity, (ii) the impact of polymorphic nucleotide variants on transactivation potential, (iii) the functional consequences of mutations in TFs and (iv) the impact of cofactors or small molecules. These approaches have found applications in basic as well as applied research, including the identification and the characterisation of mutant TF alleles from clinical samples. The ease of genome editing of yeast cells and the availability of regulated systems for ectopic protein expression enabled the development of quantitative reporter systems, integrated at a chosen chromosomal locus in isogenic yeast strains that differ only at the level of a specific RE targeted by a TF or for the expression of distinct TF alleles. In many cases, these assays were proven predictive of results in higher eukaryotes. The potential to work in small volume formats and the availability of yeast strains with modified chemical uptake have enhanced the scalability of these approaches. Next to well-established one-, two-, three-hybrid assays, the functional assays with non-chimeric human TFs enrich the palette of opportunities for functional characterisation. We review ∼25 years of research on human sequence-specific TFs expressed in yeast, with an emphasis on the P53 and NF-кB family of proteins, highlighting outcomes, advantages, challenges and limitations of these heterologous assays.
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Affiliation(s)
- Vasundhara Sharma
- Centre for Integrative Biology, CIBIO, University of Trento, via Sommarive 9, 38123, Trento, Italy
| | - Paola Monti
- U.O.C. Mutagenesi, IRCCS AOU San Martino-IST, Largo R. Benzi, 10, 16132, Genova, Italy
| | - Gilberto Fronza
- U.O.C. Mutagenesi, IRCCS AOU San Martino-IST, Largo R. Benzi, 10, 16132, Genova, Italy
| | - Alberto Inga
- Centre for Integrative Biology, CIBIO, University of Trento, via Sommarive 9, 38123, Trento, Italy
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