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Németh E, Szüts D. The mutagenic consequences of defective DNA repair. DNA Repair (Amst) 2024; 139:103694. [PMID: 38788323 DOI: 10.1016/j.dnarep.2024.103694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Multiple separate repair mechanisms safeguard the genome against various types of DNA damage, and their failure can increase the rate of spontaneous mutagenesis. The malfunction of distinct repair mechanisms leads to genomic instability through different mutagenic processes. For example, defective mismatch repair causes high base substitution rates and microsatellite instability, whereas homologous recombination deficiency is characteristically associated with deletions and chromosome instability. This review presents a comprehensive collection of all mutagenic phenotypes associated with the loss of each DNA repair mechanism, drawing on data from a variety of model organisms and mutagenesis assays, and placing greatest emphasis on systematic analyses of human cancer datasets. We describe the latest theories on the mechanism of each mutagenic process, often explained by reliance on an alternative repair pathway or the error-prone replication of unrepaired, damaged DNA. Aided by the concept of mutational signatures, the genomic phenotypes can be used in cancer diagnosis to identify defective DNA repair pathways.
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Affiliation(s)
- Eszter Németh
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Dávid Szüts
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
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2
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Laughter MR, Tegla CA, Pawar S, Moshiri AS, Orlow SJ. Diffuse large B-cell lymphoma with cutaneous involvement in a patient with xeroderma pigmentosum type C. JAAD Case Rep 2024; 49:28-31. [PMID: 38883169 PMCID: PMC11179172 DOI: 10.1016/j.jdcr.2024.04.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024] Open
Affiliation(s)
- Melissa R Laughter
- Ronald O Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, New York
| | - Cosmin A Tegla
- Division of Hematology and Medical Oncology, NYU Langone Health, New York, New York
| | - Shashi Pawar
- Department of Pathology, NYU Grossman School of Medicine, New York, New York
| | - Ata S Moshiri
- Ronald O Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, New York
| | - Seth J Orlow
- Ronald O Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, New York
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3
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Liu MH, Costa BM, Bianchini EC, Choi U, Bandler RC, Lassen E, Grońska-Pęski M, Schwing A, Murphy ZR, Rosenkjær D, Picciotto S, Bianchi V, Stengs L, Edwards M, Nunes NM, Loh CA, Truong TK, Brand RE, Pastinen T, Wagner JR, Skytte AB, Tabori U, Shoag JE, Evrony GD. DNA mismatch and damage patterns revealed by single-molecule sequencing. Nature 2024; 630:752-761. [PMID: 38867045 PMCID: PMC11216816 DOI: 10.1038/s41586-024-07532-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Mutations accumulate in the genome of every cell of the body throughout life, causing cancer and other diseases1,2. Most mutations begin as nucleotide mismatches or damage in one of the two strands of the DNA before becoming double-strand mutations if unrepaired or misrepaired3,4. However, current DNA-sequencing technologies cannot accurately resolve these initial single-strand events. Here we develop a single-molecule, long-read sequencing method (Hairpin Duplex Enhanced Fidelity sequencing (HiDEF-seq)) that achieves single-molecule fidelity for base substitutions when present in either one or both DNA strands. HiDEF-seq also detects cytosine deamination-a common type of DNA damage-with single-molecule fidelity. We profiled 134 samples from diverse tissues, including from individuals with cancer predisposition syndromes, and derive from them single-strand mismatch and damage signatures. We find correspondences between these single-strand signatures and known double-strand mutational signatures, which resolves the identity of the initiating lesions. Tumours deficient in both mismatch repair and replicative polymerase proofreading show distinct single-strand mismatch patterns compared to samples that are deficient in only polymerase proofreading. We also define a single-strand damage signature for APOBEC3A. In the mitochondrial genome, our findings support a mutagenic mechanism occurring primarily during replication. As double-strand DNA mutations are only the end point of the mutation process, our approach to detect the initiating single-strand events at single-molecule resolution will enable studies of how mutations arise in a variety of contexts, especially in cancer and ageing.
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Affiliation(s)
- Mei Hong Liu
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Benjamin M Costa
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Emilia C Bianchini
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Una Choi
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Rachel C Bandler
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
| | - Emilie Lassen
- Cryos International Sperm and Egg Bank, Aarhus, Denmark
| | - Marta Grońska-Pęski
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Adam Schwing
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Zachary R Murphy
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | | | - Shany Picciotto
- Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Vanessa Bianchi
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lucie Stengs
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Melissa Edwards
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nuno Miguel Nunes
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Caitlin A Loh
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Tina K Truong
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Randall E Brand
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - J Richard Wagner
- Department of Nuclear Medicine and Radiobiology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | | | - Uri Tabori
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Haematology/Oncology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jonathan E Shoag
- Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Gilad D Evrony
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA.
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA.
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Chen R, Lo HH, Yang C, Law BYK, Chen X, Lam CCI, Ho C, Cheong HL, Li Q, Zhong C, Ng JPL, Peter CKF, Wong VKW. Natural small-molecules reverse Xeroderma Pigmentosum Complementation Group C (XPC) deficient-mediated drug-resistance in renal cell carcinoma. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 124:155310. [PMID: 38215574 DOI: 10.1016/j.phymed.2023.155310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/14/2024]
Abstract
BACKGROUND Renal cancer is insensitive to radiotherapy or most chemotherapies. While the loss of the XPC gene was correlated with drug resistance in colon cancer, the expression of XPC and its role in the drug resistance of renal cancer have not yet been elucidated. With the fact that natural small-molecules have been adopted in combinational therapy with classical chemotherapeutic agents to increase the drug sensitivity and reduce adverse effects, the use of herbal compounds to tackle drug-resistance in renal cancer is advocated. PURPOSE To correlate the role of XPC gene deficiency to drug-resistance in renal cancer, and to identify natural small-molecules that can reverse drug-resistance in renal cancer via up-regulation of XPC. METHODS IHC was adopted to analyze the XPC expression in human tumor and adjacent tissues. Clinical data extracted from The Cancer Genome Atlas (TCGA) database were further analysed to determine the relationship between XPC gene expression and tumor staging of renal cancer. Two types of XPC-KD renal cancer cell models were established to investigate the drug-resistant phenotype and screen XPC gene enhancers from 134 natural small-molecules derived from herbal plants. Furthermore, the identified XPC enhancers were verified in single or in combination with FDA-approved chemotherapy drugs for reversing drug-resistance in renal cancer using MTT cytotoxicity assay. Drug resistance gene profiling, ROS detection assay, immunocytochemistry and cell live-dead imaging assay were adopted to characterize the XPC-related drug resistant mechanism. RESULTS XPC gene expression was significantly reduced in renal cancer tissue compared with its adjacent tissue. Clinical analysis of TCGA database also identified the downregulated level of XPC gene in renal tumor tissue of stage IV patients with cancer metastasis, which was also correlated with their lower survival rate. 6 natural small-molecules derived from herbal plants including tectorigenin, pinostilbene, d-pinitol, polygalasaponin F, atractylenolide III and astragaloside II significantly enhanced XPC expression in two renal cancer cell types. Combinational treatment of the identified natural compound with the treatment of FDA-approved drug, further confirmed the up-regulation of XPC gene expression can sensitize the two types of XPC-KD drug-resistant renal cancer cells towards the FDA-approved drugs. Mechanistic study confirmed that GSTP1/ROS axis was activated in drug resistant XPC-KD renal cancer cells. CONCLUSION XPC gene deficiency was identified in patient renal tumor samples, and knockdown of the XPC gene was correlated with a drug-resistant phenotype in renal cancer cells via activation of the GSTP1/ROS axis. The 6 identified natural small molecules were confirmed to have drug sensitizing effects via upregulation of the XPC gene. Therefore, the identified active natural small molecules may work as an adjuvant therapy for circumventing the drug-resistant phenotype in renal cancer via enhancement of XPC expression.
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Affiliation(s)
- Ruihong Chen
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China; Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Hang Hong Lo
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Chenxu Yang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Betty Yuen Kwan Law
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Xi Chen
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Calista Chi In Lam
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Charles Ho
- University Hospital, Macau University of Science and Technology, Macao, China
| | - Hio Lam Cheong
- University Hospital, Macau University of Science and Technology, Macao, China
| | - Qianzi Li
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Chenyu Zhong
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Jerome Pak Lam Ng
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | | | - Vincent Kam Wai Wong
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China.
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Corradi C, Vilar JB, Buzatto VC, de Souza TA, Castro LP, Munford V, De Vecchi R, Galante PAF, Orpinelli F, Miller TLA, Buzzo JL, Sotto MN, Saldiva P, de Oliveira JW, Chaibub SCW, Sarasin A, Menck CFM. Mutational signatures and increased retrotransposon insertions in xeroderma pigmentosum variant skin tumors. Carcinogenesis 2023; 44:511-524. [PMID: 37195263 DOI: 10.1093/carcin/bgad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/06/2023] [Accepted: 05/05/2023] [Indexed: 05/18/2023] Open
Abstract
Xeroderma pigmentosum variant (XP-V) is an autosomal recessive disease with an increased risk of developing cutaneous neoplasms in sunlight-exposed regions. These cells are deficient in the translesion synthesis (TLS) DNA polymerase eta, responsible for bypassing different types of DNA lesions. From the exome sequencing of 11 skin tumors of a genetic XP-V patients' cluster, classical mutational signatures related to sunlight exposure, such as C>T transitions targeted to pyrimidine dimers, were identified. However, basal cell carcinomas also showed distinct C>A mutation spectra reflecting a mutational signature possibly related to sunlight-induced oxidative stress. Moreover, four samples carry different mutational signatures, with C>A mutations associated with tobacco chewing or smoking usage. Thus, XP-V patients should be warned of the risk of these habits. Surprisingly, higher levels of retrotransposon somatic insertions were also detected when the tumors were compared with non-XP skin tumors, revealing other possible causes for XP-V tumors and novel functions for the TLS polymerase eta in suppressing retrotransposition. Finally, the expected high mutation burden found in most of these tumors renders these XP patients good candidates for checkpoint blockade immunotherapy.
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Affiliation(s)
- Camila Corradi
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Juliana B Vilar
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Vanessa C Buzatto
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Tiago A de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
- Tau GC Bioinformatics, Cotia, SP 06711-020, Brazil
| | - Ligia P Castro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Veridiana Munford
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | | | - Pedro A F Galante
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Fernanda Orpinelli
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Thiago L A Miller
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, SP 05508-000, Brazil
| | - José L Buzzo
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Mirian N Sotto
- Medical School, University of Sao Paulo, Sao Paulo, SP 01246-903, Brazil
| | - Paulo Saldiva
- Medical School, University of Sao Paulo, Sao Paulo, SP 01246-903, Brazil
| | - Jocelânio W de Oliveira
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, SP 05508-090, Brazil
| | | | - Alain Sarasin
- Laboratory of Genetic Instability and Oncogenesis, UMR8200 CNRS, Gustave Roussy, Université Paris-Sud, Villejuif, France
| | - Carlos F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
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Yurchenko AA, Fresneau B, Borghese B, Rajabi F, Tata Z, Genestie C, Sarasin A, Nikolaev SI. Early-onset gynecological tumors in DNA repair-deficient xeroderma pigmentosum group C patients: a case series. COMMUNICATIONS MEDICINE 2023; 3:109. [PMID: 37567969 PMCID: PMC10421935 DOI: 10.1038/s43856-023-00341-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Xeroderma pigmentosum (XP) is a group of rare hereditary disorders with highly increased risk of skin tumors due to defective DNA repair. Recently we reported 34-fold increased risk of internal tumors in XP patients in comparison with general population. The molecular data and clinical practice on the internal tumors treatment in XP patients is limited and scarcely represented in the medical literature. In this work, we describe young patients with constitutive biallelic deactivation of the XPC gene developing gynecological tumors with somatic DICER1 mutations. METHODS Whole genome sequencing was used to analyze in detail somatic mutational landscape and driver events of these rare tumors. RESULTS We describe five early-onset gynecological tumors in four xeroderma pigmentosum group C (XP-C) young patients (11 to 19 years old) including vaginal embryonal rhabdomyosarcomas in monozygotic twin sisters, juvenile granulosa-cell tumor of the ovary and poorly differentiated stage IA Sertoli-Leydig cell tumor in 19-years old patient, and FIGO stage IC1 tumor of ovary in 13-years old patient. XP-C ovarian tumors harbor 4.4 times more single base substitutions than sporadic tissue-matched cancers and demonstrate XP-C specific mutation signature with strong transcriptional bias indicating inability of the cells to repair bulky DNA lesions of unknown etiology. A special mode of treatment was applied to avoid usage of chemotherapy which is toxic for XP patients. CONCLUSIONS XP-C status should be accounted for prevention and specific treatment of gynecological tumors in young DNA repair-deficient XP patients.
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Affiliation(s)
- Andrey A Yurchenko
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Brice Fresneau
- Department of Children and Adolescents Oncology, Gustave Roussy, Villejuif, France
- Université Paris-Saclay, UVSQ, Inserm, CESP, Villejuif, France
| | - Bruno Borghese
- Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris Cité, INSERM, Paris, France
- Université de Paris Cité, Paris, France
- Institut du Cancer Paris CARPEM, AP-HP, APHP Centre, Department of Gynecological Surgery, Hôpital Cochin, Paris, France
| | - Fatemeh Rajabi
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Zora Tata
- Liberal Endocrinologist, Algiers, Algeria
| | | | - Alain Sarasin
- CNRS UMR9019 Genome Integrity and Cancers, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Sergey I Nikolaev
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France.
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Sarasin A. The French Cohort of DNA Repair-Deficient Xeroderma Pigmentosum Patients: Risk of Hematological Malignancies. Cancers (Basel) 2023; 15:2706. [PMID: 37345043 DOI: 10.3390/cancers15102706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND Xeroderma pigmentosum (XP) is a rare genetic disorder characterized by a high incidence of skin cancers. These patients are deficient in nucleotide excision repair caused by mutations in one of the 7 XP genes. METHODS We diagnosed 181 XP patients using UV-induced DNA repair measurements and/or DNA sequencing from 1982 to 2022 in France. RESULTS As all XP patients, the French ones are very sensitive to UV exposure but since they are usually very well protected, they develop relatively few skin cancers. A majority of French XP patients originate from North Africa and bear a founder mutation on the XPC gene. The striking discovery is that these patients are at a very high risk to develop aggressive and lethal internal tumors such as hematological malignancies (more than a 100-fold risk compared to the general population for myelodysplasia/leukemia) with a median age of death of 25 years, and brain, gynecological, and thyroid tumors with even lower median ages of death. The high mutation rates found in XP-C internal tumors allow us to think that these XP patients could be successfully treated by immunotherapies. A full analysis of the molecular origins of these DNA repair-deficient tumors is discussed. Several explanations for this high predisposition risk are proposed. CONCLUSIONS As the age of the XP population is increasing due to better photo-protection, the risk of lethal internal tumors is a new Damocles sword that hangs over XP-C patients. This review of the French cohort is of particular importance for alerting physicians and families to the prevention and early detection of aggressive internal tumors in XP patients.
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Affiliation(s)
- Alain Sarasin
- Unité Mixte de Recherche UMR9019 Centre National de la Recherche Scientifique, 94805 Villejuif, France
- Gustave Roussy Institute, 94805 Villejuif, France
- Université Paris-Saclay, 91400 Saclay, France
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8
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Yurchenko AA, Rajabi F, Braz-Petta T, Fassihi H, Lehmann A, Nishigori C, Wang J, Padioleau I, Gunbin K, Panunzi L, Morice-Picard F, Laplante P, Robert C, Kannouche PL, Menck CFM, Sarasin A, Nikolaev SI. Genomic mutation landscape of skin cancers from DNA repair-deficient xeroderma pigmentosum patients. Nat Commun 2023; 14:2561. [PMID: 37142601 PMCID: PMC10160032 DOI: 10.1038/s41467-023-38311-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
Xeroderma pigmentosum (XP) is a genetic disorder caused by mutations in genes of the Nucleotide Excision Repair (NER) pathway (groups A-G) or in Translesion Synthesis DNA polymerase η (V). XP is associated with an increased skin cancer risk, reaching, for some groups, several thousand-fold compared to the general population. Here, we analyze 38 skin cancer genomes from five XP groups. We find that the activity of NER determines heterogeneity of the mutation rates across skin cancer genomes and that transcription-coupled NER extends beyond the gene boundaries reducing the intergenic mutation rate. Mutational profile in XP-V tumors and experiments with POLH knockout cell line reveal the role of polymerase η in the error-free bypass of (i) rare TpG and TpA DNA lesions, (ii) 3' nucleotides in pyrimidine dimers, and (iii) TpT photodimers. Our study unravels the genetic basis of skin cancer risk in XP and provides insights into the mechanisms reducing UV-induced mutagenesis in the general population.
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Affiliation(s)
- Andrey A Yurchenko
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Fatemeh Rajabi
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Tirzah Braz-Petta
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Av. Senador Salgado Filho, s/n, Natal, 59078-970, Brazil
| | - Hiva Fassihi
- National Xeroderma Pigmentosum Service, Department of Photodermatology, St John's Institute of Dermatology, Guy's and St Thomas' Foundation Trust, London, SE1 7EH, UK
| | - Alan Lehmann
- National Xeroderma Pigmentosum Service, Department of Photodermatology, St John's Institute of Dermatology, Guy's and St Thomas' Foundation Trust, London, SE1 7EH, UK
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Chikako Nishigori
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Jinxin Wang
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Ismael Padioleau
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Konstantin Gunbin
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Leonardo Panunzi
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | | | - Pierre Laplante
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
- Department of Medical Oncology, Gustave Roussy and Paris-Saclay University, Villejuif, France
| | - Patricia L Kannouche
- CNRS UMR9019 Genome Integrity and Cancers, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Carlos F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Alain Sarasin
- CNRS UMR9019 Genome Integrity and Cancers, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Sergey I Nikolaev
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France.
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Garaycoechea JI, Quinlan C, Luijsterburg MS. Pathological consequences of DNA damage in the kidney. Nat Rev Nephrol 2023; 19:229-243. [PMID: 36702905 DOI: 10.1038/s41581-022-00671-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2022] [Indexed: 01/27/2023]
Abstract
DNA lesions that evade repair can lead to mutations that drive the development of cancer, and cellular responses to DNA damage can trigger senescence and cell death, which are associated with ageing. In the kidney, DNA damage has been implicated in both acute and chronic kidney injury, and in renal cell carcinoma. The susceptibility of the kidney to chemotherapeutic agents that damage DNA is well established, but an unexpected link between kidney ciliopathies and the DNA damage response has also been reported. In addition, human genetic deficiencies in DNA repair have highlighted DNA crosslinks, DNA breaks and transcription-blocking damage as lesions that are particularly toxic to the kidney. Genetic tools in mice, as well as advances in kidney organoid and single-cell RNA sequencing technologies, have provided important insights into how specific kidney cell types respond to DNA damage. The emerging view is that in the kidney, DNA damage affects the local microenvironment by triggering a damage response and cell proliferation to replenish injured cells, as well as inducing systemic responses aimed at reducing exposure to genotoxic stress. The pathological consequences of DNA damage are therefore key to the nephrotoxicity of DNA-damaging agents and the kidney phenotypes observed in human DNA repair-deficiency disorders.
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Affiliation(s)
- Juan I Garaycoechea
- Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Catherine Quinlan
- Department of Paediatrics, University of Melbourne, Parkville, Australia
- Department of Nephrology, Royal Children's Hospital, Melbourne, Australia
- Department of Kidney Regeneration, Murdoch Children's Research Institute, Melbourne, Australia
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
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10
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Liu MH, Costa B, Choi U, Bandler RC, Lassen E, Grońska-Pęski M, Schwing A, Murphy ZR, Rosenkjær D, Picciotto S, Bianchi V, Stengs L, Edwards M, Loh CA, Truong TK, Brand RE, Pastinen T, Wagner JR, Skytte AB, Tabori U, Shoag JE, Evrony GD. Single-strand mismatch and damage patterns revealed by single-molecule DNA sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.19.526140. [PMID: 36824744 PMCID: PMC9949150 DOI: 10.1101/2023.02.19.526140] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Mutations accumulate in the genome of every cell of the body throughout life, causing cancer and other genetic diseases1-4. Almost all of these mosaic mutations begin as nucleotide mismatches or damage in only one of the two strands of the DNA prior to becoming double-strand mutations if unrepaired or misrepaired5. However, current DNA sequencing technologies cannot resolve these initial single-strand events. Here, we developed a single-molecule, long-read sequencing method that achieves single-molecule fidelity for single-base substitutions when present in either one or both strands of the DNA. It also detects single-strand cytosine deamination events, a common type of DNA damage. We profiled 110 samples from diverse tissues, including from individuals with cancer-predisposition syndromes, and define the first single-strand mismatch and damage signatures. We find correspondences between these single-strand signatures and known double-strand mutational signatures, which resolves the identity of the initiating lesions. Tumors deficient in both mismatch repair and replicative polymerase proofreading show distinct single-strand mismatch patterns compared to samples deficient in only polymerase proofreading. In the mitochondrial genome, our findings support a mutagenic mechanism occurring primarily during replication. Since the double-strand DNA mutations interrogated by prior studies are only the endpoint of the mutation process, our approach to detect the initiating single-strand events at single-molecule resolution will enable new studies of how mutations arise in a variety of contexts, especially in cancer and aging.
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Affiliation(s)
- Mei Hong Liu
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Benjamin Costa
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Una Choi
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Rachel C. Bandler
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
| | | | - Marta Grońska-Pęski
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Adam Schwing
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Zachary R. Murphy
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | | | - Shany Picciotto
- Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, USA
| | - Vanessa Bianchi
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Canada
| | - Lucie Stengs
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Canada
| | - Melissa Edwards
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Canada
| | - Caitlin A. Loh
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Tina K. Truong
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Randall E. Brand
- Department of Medicine, University of Pittsburgh School of Medicine, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children’s Mercy Kansas City, USA
| | - J. Richard Wagner
- Department of Nuclear Medicine and Radiobiology, Université de Sherbrooke, Canada
| | | | - Uri Tabori
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Canada
- Division of Haematology/Oncology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Canada
| | - Jonathan E. Shoag
- Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, USA
| | - Gilad D. Evrony
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
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11
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Sebert M, Gachet S, Leblanc T, Rousseau A, Bluteau O, Kim R, Ben Abdelali R, Sicre de Fontbrune F, Maillard L, Fedronie C, Murigneux V, Bellenger L, Naouar N, Quentin S, Hernandez L, Vasquez N, Da Costa M, Prata PH, Larcher L, de Tersant M, Duchmann M, Raimbault A, Trimoreau F, Fenneteau O, Cuccuini W, Gachard N, Auger N, Tueur G, Blanluet M, Gazin C, Souyri M, Langa Vives F, Mendez-Bermudez A, Lapillonne H, Lengline E, Raffoux E, Fenaux P, Adès L, Forcade E, Jubert C, Domenech C, Strullu M, Bruno B, Buchbinder N, Thomas C, Petit A, Leverger G, Michel G, Cavazzana M, Gluckman E, Bertrand Y, Boissel N, Baruchel A, Dalle JH, Clappier E, Gilson E, Deriano L, Chevret S, Sigaux F, Socié G, Stoppa-Lyonnet D, de Thé H, Antoniewski C, Bluteau D, Peffault de Latour R, Soulier J. Clonal hematopoiesis driven by chromosome 1q/MDM4 trisomy defines a canonical route toward leukemia in Fanconi anemia. Cell Stem Cell 2023; 30:153-170.e9. [PMID: 36736290 DOI: 10.1016/j.stem.2023.01.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 12/02/2022] [Accepted: 01/13/2023] [Indexed: 02/05/2023]
Abstract
Fanconi anemia (FA) patients experience chromosome instability, yielding hematopoietic stem/progenitor cell (HSPC) exhaustion and predisposition to poor-prognosis myeloid leukemia. Based on a longitudinal cohort of 335 patients, we performed clinical, genomic, and functional studies in 62 patients with clonal evolution. We found a unique pattern of somatic structural variants and mutations that shares features of BRCA-related cancers, the FA-hallmark being unbalanced, microhomology-mediated translocations driving copy-number alterations. Half the patients developed chromosome 1q gain, driving clonal hematopoiesis through MDM4 trisomy downmodulating p53 signaling later followed by secondary acute myeloid lukemia genomic alterations. Functionally, MDM4 triplication conferred greater fitness to murine and human primary FA HSPCs, rescued inflammation-mediated bone marrow failure, and drove clonal dominance in FA mouse models, while targeting MDM4 impaired leukemia cells in vitro and in vivo. Our results identify a linear route toward secondary leukemogenesis whereby early MDM4-driven downregulation of basal p53 activation plays a pivotal role, opening monitoring and therapeutic prospects.
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Affiliation(s)
- Marie Sebert
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France; INSERM U944/CNRS UMR7212, Paris, France
| | - Stéphanie Gachet
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France
| | - Thierry Leblanc
- Robert Debré Hospital, Department of Pediatric Hematology, Paris, France; EA 3518, IRSL, Paris, France; Centre de Référence Maladies Rares "Aplasie Médullaire", Saint-Louis and Robert Debré Hospitals, Paris, France
| | - Alix Rousseau
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France
| | - Olivier Bluteau
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France
| | - Rathana Kim
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France
| | - Raouf Ben Abdelali
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France
| | - Flore Sicre de Fontbrune
- Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France; EA 3518, IRSL, Paris, France; Centre de Référence Maladies Rares "Aplasie Médullaire", Saint-Louis and Robert Debré Hospitals, Paris, France
| | - Loïc Maillard
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France
| | - Carèle Fedronie
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France
| | - Valentine Murigneux
- Genome Integrity, Immunity and Cancer Unit, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Institut Pasteur, Paris, France
| | - Léa Bellenger
- Sorbonne Université, CNRS FR3631, INSERM US037, Institut de Biologie Paris Seine (IBPS), ARTbio Bioinformatics Analysis Facility, Institut Français de Bioinformatique (IFB), Paris, France
| | - Naira Naouar
- Sorbonne Université, CNRS FR3631, INSERM US037, Institut de Biologie Paris Seine (IBPS), ARTbio Bioinformatics Analysis Facility, Institut Français de Bioinformatique (IFB), Paris, France
| | - Samuel Quentin
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France
| | - Lucie Hernandez
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France
| | - Nadia Vasquez
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France; Centre de Référence Maladies Rares "Aplasie Médullaire", Saint-Louis and Robert Debré Hospitals, Paris, France
| | - Mélanie Da Costa
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France; Centre de Référence Maladies Rares "Aplasie Médullaire", Saint-Louis and Robert Debré Hospitals, Paris, France
| | - Pedro H Prata
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France
| | - Lise Larcher
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France; Centre de Référence Maladies Rares "Aplasie Médullaire", Saint-Louis and Robert Debré Hospitals, Paris, France
| | - Marie de Tersant
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France
| | - Matthieu Duchmann
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France
| | - Anna Raimbault
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France
| | - Franck Trimoreau
- Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France; Hematology Laboratory, CHU Limoges, Limoges, France
| | | | - Wendy Cuccuini
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France
| | - Nathalie Gachard
- Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France; Hematology Laboratory, CHU Limoges, Limoges, France
| | - Nathalie Auger
- Département de Biologie et Pathologie Médicales, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Giulia Tueur
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France
| | - Maud Blanluet
- Department of Genetics, Institut Curie, Université de Paris, INSERM U830, Paris, France
| | - Claude Gazin
- INSERM U944/CNRS UMR7212, Paris, France; Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Evry, France
| | - Michèle Souyri
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM UMR S1131, Hôpital Saint Louis, Paris, France
| | | | - Aaron Mendez-Bermudez
- Université Côte d'Azur, CNRS, Inserm, Institute for Research on Cancer and Aging, Nice (IRCAN), France; Department of Medical Genetics, CHU, Nice, France
| | | | - Etienne Lengline
- Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Emmanuel Raffoux
- Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Pierre Fenaux
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France; INSERM U944/CNRS UMR7212, Paris, France
| | - Lionel Adès
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France; INSERM U944/CNRS UMR7212, Paris, France
| | - Edouard Forcade
- CHU Bordeaux, Service d'Hématologie et Thérapie Cellulaire et Unité d'Hématologie Oncologie Pédiatrique, 33000 Bordeaux, France
| | - Charlotte Jubert
- CHU Bordeaux, Service d'Hématologie et Thérapie Cellulaire et Unité d'Hématologie Oncologie Pédiatrique, 33000 Bordeaux, France
| | - Carine Domenech
- Institut of Hematology and Pediatric Oncology (IHOP), Hospices Civils de Lyon, France; Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard, Université Lyon 1, Lyon, France
| | - Marion Strullu
- Robert Debré Hospital, Department of Pediatric Hematology, Paris, France; EA 3518, IRSL, Paris, France
| | | | - Nimrod Buchbinder
- Centre Pédiatrique de Transplantation de Cellules Souches Hématopoïétiques, CHU de Rouen, Rouen, France
| | - Caroline Thomas
- Service d'Oncologie-Hématologie et Immunologie Pédiatrique, CHU de Nantes, Nantes, France
| | - Arnaud Petit
- Pediatric Hematology-Oncology, Trousseau Hospital and HUEP, Paris, France
| | - Guy Leverger
- Pediatric Hematology-Oncology, Trousseau Hospital and HUEP, Paris, France
| | - Gérard Michel
- Timone Enfants Hospital, Department of Pediatric Hematology and Oncology, Aix-Marseille University, EA 3279, Marseille, France
| | - Marina Cavazzana
- Biotherapy Department, Necker Children's Hospital, APHP Centre, Biotherapy Clinical Investigation Center, Inserm U1416, University of Paris, Imagine Institute, Paris, France
| | - Eliane Gluckman
- Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France; Eurocord, Department of Hematology, Saint-Louis Hospital, Paris, France
| | - Yves Bertrand
- Institut of Hematology and Pediatric Oncology (IHOP), Hospices Civils de Lyon, France; Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard, Université Lyon 1, Lyon, France
| | - Nicolas Boissel
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France; EA 3518, IRSL, Paris, France
| | - André Baruchel
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; Robert Debré Hospital, Department of Pediatric Hematology, Paris, France; EA 3518, IRSL, Paris, France; Centre de Référence Maladies Rares "Aplasie Médullaire", Saint-Louis and Robert Debré Hospitals, Paris, France
| | - Jean-Hugues Dalle
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; Robert Debré Hospital, Department of Pediatric Hematology, Paris, France; EA 3518, IRSL, Paris, France; Centre de Référence Maladies Rares "Aplasie Médullaire", Saint-Louis and Robert Debré Hospitals, Paris, France
| | - Emmanuelle Clappier
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, Inserm, Institute for Research on Cancer and Aging, Nice (IRCAN), France; Department of Medical Genetics, CHU, Nice, France
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Institut Pasteur, Paris, France
| | - Sylvie Chevret
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; Division of Biostatistics, Saint-Louis Hospital, APHP, Paris, France
| | - François Sigaux
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France
| | - Gérard Socié
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France; INSERM UMR-976, Saint-Louis Hospital, Paris, France; Centre de Référence Maladies Rares "Aplasie Médullaire", Saint-Louis and Robert Debré Hospitals, Paris, France
| | | | - Hugues de Thé
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France; Collège de France, Paris, France
| | - Christophe Antoniewski
- Sorbonne Université, CNRS FR3631, INSERM US037, Institut de Biologie Paris Seine (IBPS), ARTbio Bioinformatics Analysis Facility, Institut Français de Bioinformatique (IFB), Paris, France
| | - Dominique Bluteau
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; EPHE, PSL University, Paris, France.
| | - Régis Peffault de Latour
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France; EA 3518, IRSL, Paris, France; Centre de Référence Maladies Rares "Aplasie Médullaire", Saint-Louis and Robert Debré Hospitals, Paris, France
| | - Jean Soulier
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010 Paris, France; INSERM U944/CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, APHP, Paris, France; Centre de Référence Maladies Rares "Aplasie Médullaire", Saint-Louis and Robert Debré Hospitals, Paris, France.
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12
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Nasrallah NA, Wiese BM, Sears CR. Xeroderma Pigmentosum Complementation Group C (XPC): Emerging Roles in Non-Dermatologic Malignancies. Front Oncol 2022; 12:846965. [PMID: 35530314 PMCID: PMC9069926 DOI: 10.3389/fonc.2022.846965] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
Xeroderma pigmentosum complementation group C (XPC) is a DNA damage recognition protein essential for initiation of global-genomic nucleotide excision repair (GG-NER). Humans carrying germline mutations in the XPC gene exhibit strong susceptibility to skin cancer due to defective removal via GG-NER of genotoxic, solar UV-induced dipyrimidine photoproducts. However, XPC is increasingly recognized as important for protection against non-dermatologic cancers, not only through its role in GG-NER, but also by participating in other DNA repair pathways, in the DNA damage response and in transcriptional regulation. Additionally, XPC expression levels and polymorphisms likely impact development and may serve as predictive and therapeutic biomarkers in a number of these non-dermatologic cancers. Here we review the existing literature, focusing on the role of XPC in non-dermatologic cancer development, progression, and treatment response, and highlight possible future applications of XPC as a prognostic and therapeutic biomarker.
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Affiliation(s)
- Nawar Al Nasrallah
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Benjamin M. Wiese
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Catherine R. Sears
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
- Division of Pulmonary Medicine, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN, United States
- *Correspondence: Catherine R. Sears,
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13
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Increased risk of internal tumors in DNA repair-deficient xeroderma pigmentosum patients: analysis of four international cohorts. Orphanet J Rare Dis 2022; 17:104. [PMID: 35246173 PMCID: PMC8896305 DOI: 10.1186/s13023-022-02203-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/30/2022] [Indexed: 12/26/2022] Open
Abstract
Background Xeroderma pigmentosum (XP) is a rare, autosomal, recessive DNA repair-deficiency disorder with a frequency of 1–3 per million livebirths in Europe and USA but with higher frequencies in isolated islands or in countries with a high level of consanguinity. XP is characterized by high incidence of skin cancers on sun-exposed sites. Recent improvement in life expectancy of XP patients suggests an increased risk of frequently aggressive and lethal internal tumors. Our purpose was to quantify relative risks of internal tumor development for XP patients by tumor type, XP-subtype, patients’ ages and ethnicity through comparison with the US general population. Methods We analyzed four independent international well-characterized XP cohorts (from USA, UK, France and Brazil) with a total of 434 patients, where 11.3% developed internal tumors and compared them to the American general population. We also compiled, through PubMed/Medline, a dataset of 89 internal tumors in XP patients published between 1958 and 2020. Results In the combined 4-XP cohort, relative risk of internal tumors was 34 (95% confidence interval (CI) 25–47) times higher than in the general population (p-value = 1.0E−47) and tumor arose 50 years earlier. The XP-C group was at the highest risk for the 0–20 years old-patients (OR = 665; 95% CI 368–1200; p-value = 4.3E−30). The highest risks were observed for tumors of central nervous system (OR = 331; 95% CI 171–641; p-value = 2.4E−20), hematological malignancies (OR = 120; 95% CI 77–186; p-value = 3.7E−36), thyroid (OR = 74; 95% CI 31–179; p-value = 1.2E−8) and gynecological tumors (OR = 91; 95% CI 42–193; p-value = 3.5E−12). The type of mutation on the XPC gene is associated with different classes of internal tumors. The majority of French XP-C patients (80%) are originated from North Africa and carried the XPC delTG founder mutation specific from the South Mediterranean area. The OR is extremely high for young (0–20 years) patients with more than 1300-fold increase for the French XPs carrying the founder mutation. Conclusion Because the age of XP population is increasing due to better sun-protection and knowledge of the disease, these results are of particular importance for the physicians to help in early prevention and detection of internal tumors in their XP patients. Few preventive blood analyses or simple medical imaging may help to better detect early cancer appearance in this population. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02203-1.
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Manders F, Brandsma AM, de Kanter J, Verheul M, Oka R, van Roosmalen MJ, van der Roest B, van Hoeck A, Cuppen E, van Boxtel R. MutationalPatterns: the one stop shop for the analysis of mutational processes. BMC Genomics 2022; 23:134. [PMID: 35168570 PMCID: PMC8845394 DOI: 10.1186/s12864-022-08357-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/01/2022] [Indexed: 01/01/2023] Open
Abstract
Background The collective of somatic mutations in a genome represents a record of mutational processes that have been operative in a cell. These processes can be investigated by extracting relevant mutational patterns from sequencing data. Results Here, we present the next version of MutationalPatterns, an R/Bioconductor package, which allows in-depth mutational analysis of catalogues of single and double base substitutions as well as small insertions and deletions. Major features of the package include the possibility to perform regional mutation spectra analyses and the possibility to detect strand asymmetry phenomena, such as lesion segregation. On top of this, the package also contains functions to determine how likely it is that a signature can cause damaging mutations (i.e., mutations that affect protein function). This updated package supports stricter signature refitting on known signatures in order to prevent overfitting. Using simulated mutation matrices containing varied signature contributions, we showed that reliable refitting can be achieved even when only 50 mutations are present per signature. Additionally, we incorporated bootstrapped signature refitting to assess the robustness of the signature analyses. Finally, we applied the package on genome mutation data of cell lines in which we deleted specific DNA repair processes and on large cancer datasets, to show how the package can be used to generate novel biological insights. Conclusions This novel version of MutationalPatterns allows for more comprehensive analyses and visualization of mutational patterns in order to study the underlying processes. Ultimately, in-depth mutational analyses may contribute to improved biological insights in mechanisms of mutation accumulation as well as aid cancer diagnostics. MutationalPatterns is freely available at http://bioconductor.org/packages/MutationalPatterns. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08357-3.
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Affiliation(s)
- Freek Manders
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.,Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Arianne M Brandsma
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.,Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Jurrian de Kanter
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.,Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.,Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Rurika Oka
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.,Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Markus J van Roosmalen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.,Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Bastiaan van der Roest
- Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Arne van Hoeck
- Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Edwin Cuppen
- Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands. .,Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands.
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Zebian A, El-Dor M, Shaito A, Mazurier F, Rezvani HR, Zibara K. XPC multifaceted roles beyond DNA damage repair: p53-dependent and p53-independent functions of XPC in cell fate decisions. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108400. [PMID: 35690409 DOI: 10.1016/j.mrrev.2021.108400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 06/15/2023]
Abstract
Xeroderma pigmentosum group C protein (XPC) acts as a DNA damage recognition factor for bulky adducts and as an initiator of global genome nucleotide excision repair (GG-NER). Novel insights have shown that the role of XPC is not limited to NER, but is also implicated in DNA damage response (DDR), as well as in cell fate decisions upon stress. Moreover, XPC has a proteolytic role through its interaction with p53 and casp-2S. XPC is also able to determine cellular outcomes through its interaction with downstream proteins, such as p21, ARF, and p16. XPC interactions with effector proteins may drive cells to various fates such as apoptosis, senescence, or tumorigenesis. In this review, we explore XPC's involvement in different molecular pathways in the cell and suggest that XPC can be considered not only as a genomic caretaker and gatekeeper but also as a tumor suppressor and cellular-fate decision maker. These findings envisage that resistance to cell death, induced by DNA-damaging therapeutics, in highly prevalent P53-deficent tumors might be overcome through new therapeutic approaches that aim to activate XPC in these tumors. Moreover, this review encourages care providers to consider XPC status in cancer patients before chemotherapy in order to improve the chances of successful treatment and enhance patients' survival.
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Affiliation(s)
- Abir Zebian
- University of Bordeaux, INSERM U1035, BMGIC, Bordeaux, France; PRASE, Lebanese University, Beirut, Lebanon
| | | | - Abdullah Shaito
- Biomedical Research Center, Qatar University, P.O. Box 2713, Doha, Qatar
| | | | | | - Kazem Zibara
- PRASE, Lebanese University, Beirut, Lebanon; Biology Department, Faculty of Sciences - I, Lebanese University, Beirut, Lebanon.
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Duchmann M, Laplane L, Itzykson R. Clonal Architecture and Evolutionary Dynamics in Acute Myeloid Leukemias. Cancers (Basel) 2021; 13:4887. [PMID: 34638371 PMCID: PMC8507870 DOI: 10.3390/cancers13194887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/19/2022] Open
Abstract
Acute myeloid leukemias (AML) results from the accumulation of genetic and epigenetic alterations, often in the context of an aging hematopoietic environment. The development of high-throughput sequencing-and more recently, of single-cell technologies-has shed light on the intratumoral diversity of leukemic cells. Taking AML as a model disease, we review the multiple sources of genetic, epigenetic, and functional heterogeneity of leukemic cells and discuss the definition of a leukemic clone extending its definition beyond genetics. After introducing the two dimensions contributing to clonal diversity, namely, richness (number of leukemic clones) and evenness (distribution of clone sizes), we discuss the mechanisms at the origin of clonal emergence (mutation rate, number of generations, and effective size of the leukemic population) and the causes of clonal dynamics. We discuss the possible role of neutral drift, but also of cell-intrinsic and -extrinsic influences on clonal fitness. After reviewing available data on the prognostic role of genetic and epigenetic diversity of leukemic cells on patients' outcome, we discuss how a better understanding of AML as an evolutionary process could lead to the design of novel therapeutic strategies in this disease.
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Affiliation(s)
- Matthieu Duchmann
- Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Université de Paris, 75010 Paris, France;
- Laboratoire d’Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 75010 Paris, France
| | - Lucie Laplane
- Institut d’Histoire et Philosophie des Sciences et des Techniques UMR 8590, CNRS, Université Paris 1 Panthéon-Sorbonne, 75010 Paris, France;
- Gustave Roussy Cancer Center, UMR1287, 94805 Villejuif, France
| | - Raphael Itzykson
- Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Université de Paris, 75010 Paris, France;
- Département Hématologie et Immunologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 75010 Paris, France
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