1
|
Nicolas A, Deplanche M, Commere PH, Diot A, Genthon C, Marques da Silva W, Azevedo V, Germon P, Jamme H, Guédon E, Le Loir Y, Laurent F, Bierne H, Berkova N. Transcriptome Architecture of Osteoblastic Cells Infected With Staphylococcus aureus Reveals Strong Inflammatory Responses and Signatures of Metabolic and Epigenetic Dysregulation. Front Cell Infect Microbiol 2022; 12:854242. [PMID: 35531332 PMCID: PMC9067450 DOI: 10.3389/fcimb.2022.854242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/03/2022] [Indexed: 11/21/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen that causes a range of devastating diseases including chronic osteomyelitis, which partially relies on the internalization and persistence of S. aureus in osteoblasts. The identification of the mechanisms of the osteoblast response to intracellular S. aureus is thus crucial to improve the knowledge of this infectious pathology. Since the signal from specifically infected bacteria-bearing cells is diluted and the results are confounded by bystander effects of uninfected cells, we developed a novel model of long-term infection. Using a flow cytometric approach we isolated only S. aureus-bearing cells from mixed populations that allows to identify signals specific to intracellular infection. Here we present an in-depth analysis of the effect of long-term S. aureus infection on the transcriptional program of human osteoblast-like cells. After RNA-seq and KEGG and Reactome pathway enrichment analysis, the remodeled transcriptomic profile of infected cells revealed exacerbated immune and inflammatory responses, as well as metabolic dysregulations that likely influence the intracellular life of bacteria. Numerous genes encoding epigenetic regulators were downregulated. The later included genes coding for components of chromatin-repressive complexes (e.g., NuRD, BAHD1 and PRC1) and epifactors involved in DNA methylation. Sets of genes encoding proteins of cell adhesion or neurotransmission were also deregulated. Our results suggest that intracellular S. aureus infection has a long-term impact on the genome and epigenome of host cells, which may exert patho-physiological dysfunctions additionally to the defense response during the infection process. Overall, these results not only improve our conceptual understanding of biological processes involved in the long-term S. aureus infections of osteoblast-like cells, but also provide an atlas of deregulated host genes and biological pathways and identify novel markers and potential candidates for prophylactic and therapeutic approaches.
Collapse
Affiliation(s)
- Aurélie Nicolas
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Institut Agro, Science et Technologie du Lait et de l’OEuf (STLO), Rennes, France
| | - Martine Deplanche
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Institut Agro, Science et Technologie du Lait et de l’OEuf (STLO), Rennes, France
| | - Pierre-Henri Commere
- Cytometry and Biomarkers Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, Paris, France
| | - Alan Diot
- Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 5308 (UMR5308), Ecole Normale Supérieure (ENS) de Lyon, Universit´ Claude Bernard Lyon 1 (UCBL1), Lyon, France
- Hospices Civils de Lyon, French National Reference Centre for Staphylococci, Lyon, France
| | - Clemence Genthon
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Unité Service 1426 (US1426), Transcriptome Plateforme Technologique (GeT-PlaGe), Genotoul, Castanet-Tolosan, France
| | - Wanderson Marques da Silva
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Institut Agro, Science et Technologie du Lait et de l’OEuf (STLO), Rennes, France
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Vasco Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Pierre Germon
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Université François Rabelais, Infectiologie et Santé Publique (ISP), Tours, France
| | - Hélène Jamme
- Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Biologie de la Reproduction, Environnement, Epigénétique et Développement (BREED), Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, Biologie de la Reproduction, Environnement, Epigénétique et Développement (BREED), Maisons-Alfort, France
| | - Eric Guédon
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Institut Agro, Science et Technologie du Lait et de l’OEuf (STLO), Rennes, France
| | - Yves Le Loir
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Institut Agro, Science et Technologie du Lait et de l’OEuf (STLO), Rennes, France
| | - Fréderic Laurent
- Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 5308 (UMR5308), Ecole Normale Supérieure (ENS) de Lyon, Universit´ Claude Bernard Lyon 1 (UCBL1), Lyon, France
- Hospices Civils de Lyon, French National Reference Centre for Staphylococci, Lyon, France
| | - Hélène Bierne
- Université Paris-Saclay, Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Nadia Berkova
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Institut Agro, Science et Technologie du Lait et de l’OEuf (STLO), Rennes, France
- *Correspondence: Nadia Berkova,
| |
Collapse
|
2
|
Tarashi S, Karimipoor M, Siadat SD, Fuso A. Epigenetic modifications in host-bacterial dialogues: more than meets the eye. Epigenomics 2021; 14:5-9. [PMID: 34676788 DOI: 10.2217/epi-2021-0375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Samira Tarashi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, 13169-43551, Iran.,Mycobacteriology & Pulmonary Research Department, Pasteur Institute of Iran, Tehran, 13169-43551, Iran
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, 13169-43551, Iran
| | - Seyed Davar Siadat
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, 13169-43551, Iran.,Mycobacteriology & Pulmonary Research Department, Pasteur Institute of Iran, Tehran, 13169-43551, Iran
| | - Andrea Fuso
- Department of Experimental Medicine, Sapienza University of Rome, 00161, Italy
| |
Collapse
|
3
|
|
4
|
El-Sayed A, Aleya L, Kamel M. The link among microbiota, epigenetics, and disease development. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:28926-28964. [PMID: 33860421 DOI: 10.1007/s11356-021-13862-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
The microbiome is a community of various microorganisms that inhabit or live on the skin of humans/animals, sharing the body space with their hosts. It is a sort of complex ecosystem of trillions of commensals, symbiotic, and pathogenic microorganisms, including trillions of bacteria, archaea, protozoa, fungi, and viruses. The microbiota plays a role in the health and disease status of the host. Their number, species dominance, and viability are dynamic. Their long-term disturbance is usually accompanied by serious diseases such as metabolic disorders, cardiovascular diseases, or even cancer. While epigenetics is a term that refers to different stimuli that induce modifications in gene expression patterns without structural changes in the inherited DNA sequence, these changes can be reversible or even persist for several generations. Epigenetics can be described as cell memory that stores experience against internal and external factors. Results from multiple institutions have contributed to the role and close interaction of both microbiota and epigenetics in disease induction. Understanding the mechanisms of both players enables a better understanding of disease induction and development and also opens the horizon to revolutionary therapeutic approaches. The present review illustrates the roles of diet, microbiome, and epigenetics in the induction of several chronic diseases. In addition, it discusses the application of epigenetic data to develop diagnostic biomarkers and therapeutics and evaluate their safety for patients. Understanding the interaction among all these elements enables the development of innovative preventive/therapeutic approaches for disease control.
Collapse
Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Lotfi Aleya
- Chrono-Environnement Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, F-25030, Besançon Cedex, France
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.
| |
Collapse
|
5
|
Bierne H, Hamon M. Targeting host epigenetic machinery: The Listeria paradigm. Cell Microbiol 2021; 22:e13169. [PMID: 32185898 DOI: 10.1111/cmi.13169] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 12/11/2022]
Abstract
By modifying the host cell transcription programme, pathogenic bacteria disrupt a wide range of cellular processes and take control of the host's immune system. Conversely, by mobilising a network of defence genes, the host cells trigger various responses that allow them to tolerate or eliminate invaders. The study of the molecular basis of this crosstalk is crucial to the understanding of infectious diseases. Although research has long focused on the targeting of eukaryotic DNA-binding transcription factors, more recently, another powerful way by which bacteria modify the expression of host genes has emerged: chromatin modifications in the cell nucleus. One of the most prolific bacterial models in this area has been Listeria monocytogenes, a facultative intracellular bacterium responsible for serious food-borne infections. Here, we aim to highlight the contribution of this model to the field of bacteria-mediated chromatin modifications. We will first recall the general principles of epigenetic regulation and then illustrate five mechanisms that mobilise the epigenetic machinery in response to Listeria factors, either through bacterial molecular patterns, a toxin, an invasion protein, or nucleomodulins. Strategies used by Listeria to control the expression of host genes at the chromatin level, by activation of cytosolic signalling pathways or direct targeting of epifactors in the nucleus, have contributed to the emergence of a new discipline combining cellular microbiology and epigenetics: "patho-epigenetics."
Collapse
Affiliation(s)
- Hélène Bierne
- Université Paris Saclay, INRAE, AgroParisTech, Micalis Institute, Epigenetics and Cellular Microbiology Team, Jouy-en-Josas, France
| | - Mélanie Hamon
- G5 Chromatin and Infection, Institut Pasteur, Paris, France
| |
Collapse
|
6
|
Fol M, Włodarczyk M, Druszczyńska M. Host Epigenetics in Intracellular Pathogen Infections. Int J Mol Sci 2020; 21:ijms21134573. [PMID: 32605029 PMCID: PMC7369821 DOI: 10.3390/ijms21134573] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 12/18/2022] Open
Abstract
Some intracellular pathogens are able to avoid the defense mechanisms contributing to host epigenetic modifications. These changes trigger alterations tothe chromatin structure and on the transcriptional level of genes involved in the pathogenesis of many bacterial diseases. In this way, pathogens manipulate the host cell for their own survival. The better understanding of epigenetic consequences in bacterial infection may open the door for designing new vaccine approaches and therapeutic implications. This article characterizes selected intracellular bacterial pathogens, including Mycobacterium spp., Listeria spp., Chlamydia spp., Mycoplasma spp., Rickettsia spp., Legionella spp. and Yersinia spp., which can modulate and reprogram of defense genes in host innate immune cells.
Collapse
Affiliation(s)
- Marek Fol
- Correspondence: ; Tel.: +48-42-635-44-72
| | | | | |
Collapse
|
7
|
Pourpre R, Naudon L, Meziane H, Lakisic G, Jouneau L, Varet H, Legendre R, Wendling O, Selloum M, Proux C, Coppée JY, Herault Y, Bierne H. BAHD1 haploinsufficiency results in anxiety-like phenotypes in male mice. PLoS One 2020; 15:e0232789. [PMID: 32407325 PMCID: PMC7224496 DOI: 10.1371/journal.pone.0232789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
BAHD1 is a heterochomatinization factor recently described as a component of a multiprotein complex associated with histone deacetylases HDAC1/2. The physiological and patho-physiological functions of BAHD1 are not yet well characterized. Here, we examined the consequences of BAHD1 deficiency in the brains of male mice. While Bahd1 knockout mice had no detectable defects in brain anatomy, RNA sequencing profiling revealed about 2500 deregulated genes in Bahd1-/- brains compared to Bahd1+/+ brains. A majority of these genes were involved in nervous system development and function, behavior, metabolism and immunity. Exploration of the Allen Brain Atlas and Dropviz databases, assessing gene expression in the brain, revealed that expression of the Bahd1 gene was limited to a few territories and cell subtypes, particularly in the hippocampal formation, the isocortex and the olfactory regions. The effect of partial BAHD1 deficiency on behavior was then evaluated on Bahd1 heterozygous male mice, which have no lethal or metabolic phenotypes. Bahd1+/- mice showed anxiety-like behavior and reduced prepulse inhibition (PPI) of the startle response. Altogether, these results suggest that BAHD1 plays a role in chromatin-dependent gene regulation in a subset of brain cells and support recent evidence linking genetic alteration of BAHD1 to psychiatric disorders in a human patient.
Collapse
Affiliation(s)
- Renaud Pourpre
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Laurent Naudon
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Micalis Institute, Université Paris-Saclay, CNRS, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Hamid Meziane
- Institut Clinique de la Souris-ICS, Université de Strasbourg, CNRS, INSERM, PHENOMIN, Illkirch, France
| | - Goran Lakisic
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Luc Jouneau
- Université Paris-Saclay, INRAE, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Hugo Varet
- Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
| | - Rachel Legendre
- Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
| | - Olivia Wendling
- Institut Clinique de la Souris-ICS, Université de Strasbourg, CNRS, INSERM, PHENOMIN, Illkirch, France
| | - Mohammed Selloum
- Institut Clinique de la Souris-ICS, Université de Strasbourg, CNRS, INSERM, PHENOMIN, Illkirch, France
| | - Caroline Proux
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
| | - Yann Herault
- Institut Clinique de la Souris-ICS, Université de Strasbourg, CNRS, INSERM, PHENOMIN, Illkirch, France
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique Biologie Moléculaire et Cellulaire (IGBMC), UMR7104, U1268, Illkirch, France
| | - Hélène Bierne
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| |
Collapse
|
8
|
Bacterial Factors Targeting the Nucleus: The Growing Family of Nucleomodulins. Toxins (Basel) 2020; 12:toxins12040220. [PMID: 32244550 PMCID: PMC7232420 DOI: 10.3390/toxins12040220] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/23/2020] [Accepted: 03/29/2020] [Indexed: 12/18/2022] Open
Abstract
Pathogenic bacteria secrete a variety of proteins that manipulate host cell function by targeting components of the plasma membrane, cytosol, or organelles. In the last decade, several studies identified bacterial factors acting within the nucleus on gene expression or other nuclear processes, which has led to the emergence of a new family of effectors called “nucleomodulins”. In human and animal pathogens, Listeria monocytogenes for Gram-positive bacteria and Anaplasma phagocytophilum, Ehrlichia chaffeensis, Chlamydia trachomatis, Legionella pneumophila, Shigella flexneri, and Escherichia coli for Gram-negative bacteria, have led to pioneering discoveries. In this review, we present these paradigms and detail various mechanisms and core elements (e.g., DNA, histones, epigenetic regulators, transcription or splicing factors, signaling proteins) targeted by nucleomodulins. We particularly focus on nucleomodulins interacting with epifactors, such as LntA of Listeria and ankyrin repeat- or tandem repeat-containing effectors of Rickettsiales, and nucleomodulins from various bacterial species acting as post-translational modification enzymes. The study of bacterial nucleomodulins not only generates important knowledge about the control of host responses by microbes but also creates new tools to decipher the dynamic regulations that occur in the nucleus. This research also has potential applications in the field of biotechnology. Finally, this raises questions about the epigenetic effects of infectious diseases.
Collapse
|
9
|
Abstract
In all domains of life, genomes contain epigenetic information superimposed over the nucleotide sequence. Epigenetic signals control DNA-protein interactions and can cause phenotypic change in the absence of mutation. A nearly universal mechanism of epigenetic signalling is DNA methylation. In bacteria, DNA methylation has roles in genome defence, chromosome replication and segregation, nucleoid organization, cell cycle control, DNA repair and regulation of transcription. In many bacterial species, DNA methylation controls reversible switching (phase variation) of gene expression, a phenomenon that generates phenotypic cell variants. The formation of epigenetic lineages enables the adaptation of bacterial populations to harsh or changing environments and modulates the interaction of pathogens with their eukaryotic hosts.
Collapse
|
10
|
Flores Saiffe Farías A, Mendizabal AP, Morales JA. An Ontology Systems Approach on Human Brain Expression and Metaproteomics. Front Microbiol 2018; 9:406. [PMID: 29568289 PMCID: PMC5852110 DOI: 10.3389/fmicb.2018.00406] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/21/2018] [Indexed: 12/21/2022] Open
Abstract
Research in the last decade has shown growing evidence of the gut microbiota influence on brain physiology. While many mechanisms of this influence have been proposed in animal models, most studies in humans are the result of a pathology–dysbiosis association and very few have related the presence of certain taxa with brain substructures or molecular pathways. In this paper, we associated the functional ontologies in the differential expression of brain substructures from the Allen Brain Atlas database, with those of the metaproteome from the Human Microbiome Project. Our results showed several coherent clustered ontologies where many taxa could influence brain expression and physiology. A detailed analysis of psychobiotics showed specific slim ontologies functionally associated with substructures in the basal ganglia and cerebellar cortex. Some of the most relevant slim ontology groups are related to Ion transport, Membrane potential, Synapse, DNA and RNA metabolism, and Antigen processing, while the most relevant neuropathology found was Parkinson disease. In some of these cases, new hypothetical gut microbiota-brain interaction pathways are proposed.
Collapse
|
11
|
Bierne H, Nielsen-LeRoux C. Is there a transgenerational inheritance of host resistance against pathogens? Lessons from the Galleria mellonella-Bacillus thuringiensis interaction model. Virulence 2017; 8:1471-1474. [PMID: 28758839 PMCID: PMC5810474 DOI: 10.1080/21505594.2017.1356538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 07/06/2017] [Indexed: 12/13/2022] Open
Affiliation(s)
- Hélène Bierne
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | | |
Collapse
|