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Cerapio JP, Marchio A, Cano L, López I, Fournié JJ, Régnault B, Casavilca-Zambrano S, Ruiz E, Dejean A, Bertani S, Pineau P. Global DNA hypermethylation pattern and unique gene expression signature in liver cancer from patients with Indigenous American ancestry. Oncotarget 2021; 12:475-492. [PMID: 33747361 PMCID: PMC7939527 DOI: 10.18632/oncotarget.27890] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/26/2021] [Indexed: 12/25/2022] Open
Abstract
Hepatocellular carcinoma (HCC) usually afflicts individuals in their maturity after a protracted liver disease. Contrasting with this pattern, the age structure of HCC in Andean people displays a bimodal distribution with half of the patients developing HCC in adolescence and early adulthood. To deepen our understanding of the molecular determinants of the disease in this population, we conducted an integrative analysis of gene expression and DNA methylation in HCC developed by 74 Peruvian patients, including 39 adolescents and young adults. While genome-wide hypomethylation is considered as a paradigm in human HCCs, our analysis revealed that Peruvian tumors are associated with a global DNA hypermethylation. Moreover, pathway enrichment analysis of transcriptome data characterized an original combination of signatures. Peruvian HCC forgoes canonical activations of IGF2, Notch, Ras/MAPK, and TGF-β signals to depend instead on Hippo/YAP1, MYC, and Wnt/β-catenin pathways. These signatures delineate a homogeneous subtype of liver tumors at the interface of the proliferative and non-proliferative classes of HCCs. Remarkably, the development of this HCC subtype occurs in patients with one of the four Native American mitochondrial haplogroups A-D. Finally, integrative characterization revealed that Peruvian HCC is apparently controlled by the PRC2 complex that mediates cell reprogramming with massive DNA methylation modulating gene expression and pinpointed retinoid signaling as a potential target for epigenetic therapy.
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Affiliation(s)
- Juan Pablo Cerapio
- Sorbonne Université, Institut Pasteur, Unité Organisation Nucléaire et Oncogenèse, INSERM, U 993, Paris, France.,Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, INSERM, UPS, UMR 1037, CNRS, ERL 5294, Toulouse, France
| | - Agnès Marchio
- Institut Pasteur, Unité Organisation Nucléaire et Oncogenèse, INSERM, U 993, Paris, France
| | - Luis Cano
- Université de Rennes 1, INSERM, CNRS, U 1241 NUMECAN, Rennes, France
| | - Ignacio López
- Institut Pasteur, Unité Organisation Nucléaire et Oncogenèse, INSERM, U 993, Paris, France
| | - Jean-Jacques Fournié
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, INSERM, UPS, UMR 1037, CNRS, ERL 5294, Toulouse, France
| | - Béatrice Régnault
- Institut Pasteur, Centre d'Innovation et Recherche Technologique, Plateforme de Génotypage des Eucaryotes, Paris, France
| | - Sandro Casavilca-Zambrano
- Instituto Nacional de Enfermedades Neoplásicas, Departamento de Patología, Banco de Tejidos Tumorales, Lima, Peru
| | - Eloy Ruiz
- Instituto Nacional de Enfermedades Neoplásicas, Departamento de Cirugía en Abdomen, Lima, Peru
| | - Anne Dejean
- Institut Pasteur, Unité Organisation Nucléaire et Oncogenèse, INSERM, U 993, Paris, France
| | - Stéphane Bertani
- Université de Toulouse, IRD, UPS, UMR 152 PHARMADEV, Toulouse, France.,These authors contributed equally to this work
| | - Pascal Pineau
- Institut Pasteur, Unité Organisation Nucléaire et Oncogenèse, INSERM, U 993, Paris, France.,These authors contributed equally to this work
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Mercati O, Huguet G, Danckaert A, André-Leroux G, Maruani A, Bellinzoni M, Rolland T, Gouder L, Mathieu A, Buratti J, Amsellem F, Benabou M, Van-Gils J, Beggiato A, Konyukh M, Bourgeois JP, Gazzellone MJ, Yuen RKC, Walker S, Delépine M, Boland A, Régnault B, Francois M, Van Den Abbeele T, Mosca-Boidron AL, Faivre L, Shimoda Y, Watanabe K, Bonneau D, Rastam M, Leboyer M, Scherer SW, Gillberg C, Delorme R, Cloëz-Tayarani I, Bourgeron T. CNTN6 mutations are risk factors for abnormal auditory sensory perception in autism spectrum disorders. Mol Psychiatry 2017; 22:625-633. [PMID: 27166760 PMCID: PMC5378808 DOI: 10.1038/mp.2016.61] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 02/12/2016] [Accepted: 02/17/2016] [Indexed: 12/11/2022]
Abstract
Contactin genes CNTN5 and CNTN6 code for neuronal cell adhesion molecules that promote neurite outgrowth in sensory-motor neuronal pathways. Mutations of CNTN5 and CNTN6 have previously been reported in individuals with autism spectrum disorders (ASDs), but very little is known on their prevalence and clinical impact. In this study, we identified CNTN5 and CNTN6 deleterious variants in individuals with ASD. Among the carriers, a girl with ASD and attention-deficit/hyperactivity disorder was carrying five copies of CNTN5. For CNTN6, both deletions (6/1534 ASD vs 1/8936 controls; P=0.00006) and private coding sequence variants (18/501 ASD vs 535/33480 controls; P=0.0005) were enriched in individuals with ASD. Among the rare CNTN6 variants, two deletions were transmitted by fathers diagnosed with ASD, one stop mutation CNTN6W923X was transmitted by a mother to her two sons with ASD and one variant CNTN6P770L was found de novo in a boy with ASD. Clinical investigations of the patients carrying CNTN5 or CNTN6 variants showed that they were hypersensitive to sounds (a condition called hyperacusis) and displayed changes in wave latency within the auditory pathway. These results reinforce the hypothesis of abnormal neuronal connectivity in the pathophysiology of ASD and shed new light on the genes that increase risk for abnormal sensory perception in ASD.
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Affiliation(s)
- O Mercati
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - G Huguet
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - A Danckaert
- Imagopole, Citech, Institut Pasteur, Paris, France
| | - G André-Leroux
- Institut Pasteur, Unité de Microbiologie Structurale, Paris, France
- CNRS UMR 3528, Paris, France
- INRA, Unité MaIAGE, UR1404, Jouy-en-Josas, France
| | - A Maruani
- Assistance Publique-Hôpitaux de Paris, Child and Adolescent Psychiatry Department, Robert Debré Hospital, Paris, France
| | - M Bellinzoni
- Institut Pasteur, Unité de Microbiologie Structurale, Paris, France
- CNRS UMR 3528, Paris, France
| | - T Rolland
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - L Gouder
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - A Mathieu
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - J Buratti
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - F Amsellem
- Assistance Publique-Hôpitaux de Paris, Child and Adolescent Psychiatry Department, Robert Debré Hospital, Paris, France
| | - M Benabou
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - J Van-Gils
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - A Beggiato
- Assistance Publique-Hôpitaux de Paris, Child and Adolescent Psychiatry Department, Robert Debré Hospital, Paris, France
| | - M Konyukh
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - J-P Bourgeois
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - M J Gazzellone
- Centre for Applied Genomics, Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - R K C Yuen
- Centre for Applied Genomics, Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - S Walker
- Centre for Applied Genomics, Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - M Delépine
- Centre National de Génotypage, Evry, France
| | - A Boland
- Centre National de Génotypage, Evry, France
| | - B Régnault
- Eukaryote Genotyping Platform, Genopole, Institut Pasteur, Paris, France
| | - M Francois
- Assistance Publique-Hôpitaux de Paris, ENT and Head and Neck Surgery Department, Robert Debré Hospital, Paris-VII University, Paris, France
| | - T Van Den Abbeele
- Assistance Publique-Hôpitaux de Paris, ENT and Head and Neck Surgery Department, Robert Debré Hospital, Paris-VII University, Paris, France
| | - A L Mosca-Boidron
- Département de Génétique, CHU Dijon et Université de Bourgogne, Dijon, France
| | - L Faivre
- Département de Génétique, CHU Dijon et Université de Bourgogne, Dijon, France
| | - Y Shimoda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - K Watanabe
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - D Bonneau
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, Angers, France
| | - M Rastam
- Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Gothenburg, Sweden
| | - M Leboyer
- INSERM U955, Psychiatrie Translationnelle, Créteil, France
- Université Paris Est, Faculté de Médecine, Créteil, France
- Assistance Publique-Hôpitaux de Paris, DHU Pe-PSY, H. Mondor Hospital, Department of Psychiatry, Créteil, France
- FondaMental Foundation, Créteil, France
| | - S W Scherer
- Centre for Applied Genomics, Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
- McLaughlin Centre, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - C Gillberg
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Gothenburg, Sweden
| | - R Delorme
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
- Assistance Publique-Hôpitaux de Paris, Child and Adolescent Psychiatry Department, Robert Debré Hospital, Paris, France
| | - I Cloëz-Tayarani
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - T Bourgeron
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Gothenburg, Sweden
- FondaMental Foundation, Créteil, France
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Hamon MA, Batsché E, Régnault B, Tham TN, Seveau S, Muchardt C, Cossart P. Histone modifications induced by a family of bacterial toxins. Proc Natl Acad Sci U S A 2007; 104:13467-72. [PMID: 17675409 PMCID: PMC1948930 DOI: 10.1073/pnas.0702729104] [Citation(s) in RCA: 214] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Upon infection, pathogens reprogram host gene expression. In eukaryotic cells, genetic reprogramming is induced by the concerted activation/repression of transcription factors and various histone modifications that control DNA accessibility in chromatin. We report here that the bacterial pathogen Listeria monocytogenes induces a dramatic dephosphorylation of histone H3 as well as a deacetylation of histone H4 during early phases of infection. This effect is mediated by the major listerial toxin listeriolysin O in a pore-forming-independent manner. Strikingly, a similar effect also is observed with other toxins of the same family, such as Clostridium perfringens perfringolysin and Streptococcus pneumoniae pneumolysin. The decreased levels of histone modifications correlate with a reduced transcriptional activity of a subset of host genes, including key immunity genes. Thus, control of epigenetic regulation emerges here as an unsuspected function shared by several bacterial toxins, highlighting a common strategy used by intracellular and extracellular pathogens to modulate the host response early during infection.
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Affiliation(s)
- Mélanie Anne Hamon
- *Unité des Interactions Bactéries–Cellules
- Unité 604, Institut National de la Santé et de la Recherche Médicale, F-75015 Paris, France; and
- Unité Externe sous Contrat 2020, Institut National de la Recherche Agronomique, F-75015 Paris, France
| | | | | | - To Nam Tham
- *Unité des Interactions Bactéries–Cellules
- Unité 604, Institut National de la Santé et de la Recherche Médicale, F-75015 Paris, France; and
- Unité Externe sous Contrat 2020, Institut National de la Recherche Agronomique, F-75015 Paris, France
| | - Stéphanie Seveau
- *Unité des Interactions Bactéries–Cellules
- Unité 604, Institut National de la Santé et de la Recherche Médicale, F-75015 Paris, France; and
- Unité Externe sous Contrat 2020, Institut National de la Recherche Agronomique, F-75015 Paris, France
| | | | - Pascale Cossart
- *Unité des Interactions Bactéries–Cellules
- Unité 604, Institut National de la Santé et de la Recherche Médicale, F-75015 Paris, France; and
- Unité Externe sous Contrat 2020, Institut National de la Recherche Agronomique, F-75015 Paris, France
- **To whom correspondence should be addressed. E-mail:
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