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Rana S, Maurya S, Mohapatra G, Singh S, Babar R, Chandrasekhar H, Chamoli G, Rathore D, Kshetrapal P, Srikanth CV. Activation of epigenetic regulator KDM6B by Salmonella Typhimurium enables chronic infections. Gut Microbes 2022; 13:1986665. [PMID: 34696686 PMCID: PMC8555538 DOI: 10.1080/19490976.2021.1986665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Non-typhoidal Salmonella (NTS) infections result in self limiting gastroenteritis except in rare cases wherein manifestations of chronic infections can occur. Strategies employed by Salmonella to thrive in hostile environments of host during chronic infections are complex and multifaceted. In chronic state, a coordinated action of bacterial effectors allows reprogramming of macrophages to M2 subtype and thereby creating a permissible replicative niche. The mechanistic details of these processes are not fully known. In the current study we identified, histone H3-lysine 27 trimethylation (H3K27me3)-specific demethylase, KDM6B to be upregulated in both cell culture and in murine model of Salmonella infection. KDM6B recruitment upon infection exhibited an associated loss of overall H3K27me3 in host cells and was Salmonella SPI1 effectors coordinated. ChIP-qRT-PCR array analysis revealed several new gene promoter targets of KDM6B demethylase activity including PPARδ, a crucial regulator of fatty acid oxidation pathway and Salmonella-persistent infections. Furthermore, pharmacological inhibition of KDM6B demethylase activity with GSKJ4 in chronic Salmonella infection mice model led to a significant reduction in pathogen load and M2 macrophage polarization in peripheral lymphoid organs. The following work thus reveals Salmonella effector-mediated epigenetic reprogramming of macrophages responsible for its long-term survival and chronic carriage.
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Affiliation(s)
- Sarika Rana
- Laboratory of Gut Infection and Inflammation Biology, Regional Centre for Biotechnology, Faridabad, India,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sonalika Maurya
- Laboratory of Gut Infection and Inflammation Biology, Regional Centre for Biotechnology, Faridabad, India
| | - Gayatree Mohapatra
- Laboratory of Gut Infection and Inflammation Biology, Regional Centre for Biotechnology, Faridabad, India
| | - Savita Singh
- Maternal and Child Health, Translational Health Science and Technology Institute, Faridabad, India
| | - Rohan Babar
- Laboratory of Gut Infection and Inflammation Biology, Regional Centre for Biotechnology, Faridabad, India
| | - Hridya Chandrasekhar
- Laboratory of Gut Infection and Inflammation Biology, Regional Centre for Biotechnology, Faridabad, India
| | - Garima Chamoli
- Laboratory of Gut Infection and Inflammation Biology, Regional Centre for Biotechnology, Faridabad, India
| | - Deepak Rathore
- Maternal and Child Health, Translational Health Science and Technology Institute, Faridabad, India
| | - Pallavi Kshetrapal
- Maternal and Child Health, Translational Health Science and Technology Institute, Faridabad, India
| | - C. V. Srikanth
- Laboratory of Gut Infection and Inflammation Biology, Regional Centre for Biotechnology, Faridabad, India,CONTACT C. V. Srikanth Regional Centre for Biotechnology, 3rd Milestone Gurgaon Faridabad Expressway, Faridabad, India
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Bekere I, Huang J, Schnapp M, Rudolph M, Berneking L, Ruckdeschel K, Grundhoff A, Günther T, Fischer N, Aepfelbacher M. Yersinia remodels epigenetic histone modifications in human macrophages. PLoS Pathog 2021; 17:e1010074. [PMID: 34793580 PMCID: PMC8639070 DOI: 10.1371/journal.ppat.1010074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/02/2021] [Accepted: 10/28/2021] [Indexed: 01/10/2023] Open
Abstract
Various pathogens systematically reprogram gene expression in macrophages, but the underlying mechanisms are largely unknown. We investigated whether the enteropathogen Yersinia enterocolitica alters chromatin states to reprogram gene expression in primary human macrophages. Genome-wide chromatin immunoprecipitation (ChIP) seq analyses showed that pathogen-associated molecular patterns (PAMPs) induced up- or down-regulation of histone modifications (HMod) at approximately 14500 loci in promoters and enhancers. Effectors of Y. enterocolitica reorganized about half of these dynamic HMod, with the effector YopP being responsible for about half of these modulatory activities. The reorganized HMod were associated with genes involved in immune response and metabolism. Remarkably, the altered HMod also associated with 61% of all 534 known Rho GTPase pathway genes, revealing a new level in Rho GTPase regulation and a new aspect of bacterial pathogenicity. Changes in HMod were associated to varying degrees with corresponding gene expression, e. g. depending on chromatin localization and cooperation of the HMod. In summary, infection with Y. enterocolitica remodels HMod in human macrophages to modulate key gene expression programs of the innate immune response. Human pathogenic bacteria can affect epigenetic histone modifications to modulate gene expression in host cells. However, a systems biology analysis of this bacterial virulence mechanism in immune cells has not been performed. Here we analyzed genome-wide epigenetic histone modifications and associated gene expression changes in primary human macrophages infected with enteropathogenic Yersinia enterocolitica. We demonstrate that Yersinia virulence factors extensively modulate histone modifications and associated gene expression triggered by the pathogen-associated molecular patterns (PAMPs) of the bacteria. The epigenetically modulated genes are involved in several key pathways of the macrophage immune response, including the Rho GTPase pathway, revealing a novel level of Rho GTPase regulation by a bacterial pathogen. Overall, our findings provide an in-depth view of epigenetic and gene expression changes during host-pathogen interaction and might have further implications for understanding of the innate immune memory in macrophages.
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Affiliation(s)
- Indra Bekere
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- * E-mail: (IB); (MA)
| | - Jiabin Huang
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Marie Schnapp
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Maren Rudolph
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Laura Berneking
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Klaus Ruckdeschel
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Adam Grundhoff
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Thomas Günther
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- * E-mail: (IB); (MA)
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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."
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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
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