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Udayasuryan B, Zhou Z, Ahmad RN, Sobol P, Deng C, Nguyen TTD, Kodikalla S, Morrison R, Goswami I, Slade DJ, Verbridge SS, Lu C. Fusobacterium nucleatum infection modulates the transcriptome and epigenome of HCT116 colorectal cancer cells in an oxygen-dependent manner. Commun Biol 2024; 7:551. [PMID: 38720110 PMCID: PMC11079022 DOI: 10.1038/s42003-024-06201-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Fusobacterium nucleatum, a gram-negative oral bacterium, has been consistently validated as a strong contributor to the progression of several types of cancer, including colorectal (CRC) and pancreatic cancer. While previous in vitro studies have shown that intracellular F. nucleatum enhances malignant phenotypes such as cell migration, the dependence of this regulation on features of the tumor microenvironment (TME) such as oxygen levels are wholly uncharacterized. Here we examine the influence of hypoxia in facilitating F. nucleatum invasion and its effects on host responses focusing on changes in the global epigenome and transcriptome. Using a multiomic approach, we analyze epigenomic alterations of H3K27ac and global transcriptomic alterations sustained within a hypoxia and normoxia conditioned CRC cell line HCT116 at 24 h following initial infection with F. nucleatum. Our findings reveal that intracellular F. nucleatum activates signaling pathways and biological processes in host cells similar to those induced upon hypoxia conditioning in the absence of infection. Furthermore, we show that a hypoxic TME favors F. nucleatum invasion and persistence and therefore infection under hypoxia may amplify malignant transformation by exacerbating the effects induced by hypoxia alone. These results motivate future studies to investigate host-microbe interactions in tumor tissue relevant conditions that more accurately define parameters for targeted cancer therapies.
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Affiliation(s)
- Barath Udayasuryan
- School of Biomedical Engineering and Sciences, Virginia Tech-Wake Forest University, Blacksburg, VA, USA
| | - Zirui Zhou
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Raffae N Ahmad
- School of Biomedical Engineering and Sciences, Virginia Tech-Wake Forest University, Blacksburg, VA, USA
| | - Polina Sobol
- School of Biomedical Engineering and Sciences, Virginia Tech-Wake Forest University, Blacksburg, VA, USA
| | - Chengyu Deng
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Tam T D Nguyen
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - Shivanie Kodikalla
- School of Biomedical Engineering and Sciences, Virginia Tech-Wake Forest University, Blacksburg, VA, USA
| | - Ryan Morrison
- School of Biomedical Engineering and Sciences, Virginia Tech-Wake Forest University, Blacksburg, VA, USA
| | - Ishan Goswami
- School of Biomedical Engineering and Sciences, Virginia Tech-Wake Forest University, Blacksburg, VA, USA
| | - Daniel J Slade
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - Scott S Verbridge
- School of Biomedical Engineering and Sciences, Virginia Tech-Wake Forest University, Blacksburg, VA, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA.
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2
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Sabat AJ, Durfee T, Baldwin S, Akkerboom V, Voss A, Friedrich AW, Bathoorn E. The complete genome sequence of unculturable Mycoplasma faucium obtained through clinical metagenomic next-generation sequencing. Front Cell Infect Microbiol 2024; 14:1368923. [PMID: 38694516 PMCID: PMC11062135 DOI: 10.3389/fcimb.2024.1368923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/25/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction Diagnosing Mycoplasma faucium poses challenges, and it's unclear if its rare isolation is due to infrequent occurrence or its fastidious nutritional requirements. Methods This study analyzes the complete genome sequence of M. faucium, obtained directly from the pus of a sternum infection in a lung transplant patient using metagenomic sequencing. Results Genome analysis revealed limited therapeutic options for the M. faucium infection, primarily susceptibility to tetracyclines. Three classes of mobile genetic elements were identified: two new insertion sequences, a new prophage (phiUMCG-1), and a species-specific variant of a mycoplasma integrative and conjugative element (MICE). Additionally, a Type I Restriction-Modification system was identified, featuring 5'-terminally truncated hsdS pseudogenes with overlapping repeats, indicating the potential for forming alternative hsdS variants through recombination. Conclusion This study represents the first-ever acquisition of a complete circularized bacterial genome directly from a patient sample obtained from invasive infection of a primary sterile site using culture-independent, PCR-free clinical metagenomics.
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Affiliation(s)
- Artur J. Sabat
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Tim Durfee
- DNASTAR, Inc., Madison, WI, United States
| | | | - Viktoria Akkerboom
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Andreas Voss
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | | | - Erik Bathoorn
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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Santana-da-Silva MN, Sena-dos-Santos C, Cáceres-Durán MÁ, de Souza FG, Gobbo AR, Pinto P, Salgado CG, dos Santos SEB. ncRNAs: an unexplored cellular defense mechanism in leprosy. Front Genet 2023; 14:1295586. [PMID: 38116294 PMCID: PMC10729009 DOI: 10.3389/fgene.2023.1295586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023] Open
Abstract
Leprosy is an infectious disease primarily caused by the obligate intracellular parasite Mycobacterium leprae. Although it has been considered eradicated in many countries, leprosy continues to be a health issue in developing nations. Besides the social stigma associated with it, individuals affected by leprosy may experience nerve damage leading to physical disabilities if the disease is not properly treated or early diagnosed. Leprosy is recognized as a complex disease wherein socioenvironmental factors, immune response, and host genetics interact to contribute to its development. Recently, a new field of study called epigenetics has emerged, revealing that the immune response and other mechanisms related to infectious diseases can be influenced by noncoding RNAs. This review aims to summarize the significant advancements concerning non-coding RNAs in leprosy, discussing the key perspectives on this novel approach to comprehending the pathophysiology of the disease and identifying molecular markers. In our view, investigations on non-coding RNAs in leprosy hold promise and warrant increased attention from researches in this field.
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Affiliation(s)
- Mayara Natália Santana-da-Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Imunologia, Seção de Virologia (SAVIR), Instituto Evandro Chagas, Ananindeua, Brazil
| | - Camille Sena-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Miguel Ángel Cáceres-Durán
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Felipe Gouvea de Souza
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Angelica Rita Gobbo
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Pablo Pinto
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Claudio Guedes Salgado
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Sidney Emanuel Batista dos Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
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4
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Mendes I, Vale N. How Can the Microbiome Induce Carcinogenesis and Modulate Drug Resistance in Cancer Therapy? Int J Mol Sci 2023; 24:11855. [PMID: 37511612 PMCID: PMC10380870 DOI: 10.3390/ijms241411855] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Over the years, cancer has been affecting the lives of many people globally and it has become one of the most studied diseases. Despite the efforts to understand the cell mechanisms behind this complex disease, not every patient seems to respond to targeted therapies or immunotherapies. Drug resistance in cancer is one of the limiting factors contributing to unsuccessful therapies; therefore, understanding how cancer cells acquire this resistance is essential to help cure individuals affected by cancer. Recently, the altered microbiome was observed to be an important hallmark of cancer and therefore it represents a promising topic of cancer research. Our review aims to provide a global perspective of some cancer hallmarks, for instance how genetic and epigenetic modifications may be caused by an altered human microbiome. We also provide information on how an altered human microbiome can lead to cancer development as well as how the microbiome can influence drug resistance and ultimately targeted therapies. This may be useful to develop alternatives for cancer treatment, i.e., future personalized medicine that can help in cases where traditional cancer treatment is unsuccessful.
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Affiliation(s)
- Inês Mendes
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal;
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- School of Life and Environmental Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Edifício de Geociências, 5000-801 Vila Real, Portugal
| | - Nuno Vale
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal;
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Community Medicine, Information and Health Decision Sciences (MEDCIDS), Faculty of Medicine, University of Porto, Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal
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5
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Stein RA, Thompson LM. Epigenetic changes induced by pathogenic Chlamydia spp. Pathog Dis 2023; 81:ftad034. [PMID: 38031337 DOI: 10.1093/femspd/ftad034] [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: 06/15/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023] Open
Abstract
Chlamydia trachomatis, C. pneumoniae, and C. psittaci, the three Chlamydia species known to cause human disease, have been collectively linked to several pathologies, including conjunctivitis, trachoma, respiratory disease, acute and chronic urogenital infections and their complications, and psittacosis. In vitro, animal, and human studies also established additional correlations, such as between C. pneumoniae and atherosclerosis and between C. trachomatis and ovarian cancer. As part of their survival and pathogenesis strategies as obligate intracellular bacteria, Chlamydia spp. modulate all three major types of epigenetic changes, which include deoxyribonucleic acid (DNA) methylation, histone post-translational modifications, and microRNA-mediated gene silencing. Some of these epigenetic changes may be implicated in key aspects of pathogenesis, such as the ability of the Chlamydia spp. to induce epithelial-to-mesenchymal transition, interfere with DNA damage repair, suppress cholesterol efflux from infected macrophages, act as a co-factor in human papillomavirus (HPV)-mediated cervical cancer, prevent apoptosis, and preserve the integrity of mitochondrial networks in infected host cells. A better understanding of the individual and collective contribution of epigenetic changes to pathogenesis will enhance our knowledge about the biology of Chlamydia spp. and facilitate the development of novel therapies and biomarkers. Pathogenic Chlamydia spp. contribute to epigenetically-mediated gene expression changes in host cells by multiple mechanisms.
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Affiliation(s)
- Richard A Stein
- NYU Tandon School of Engineering, Department of Chemical and Biomolecular Engineering, 6 MetroTech Center, Brooklyn, NY 11201, United States
| | - Lily M Thompson
- NYU Tandon School of Engineering, Department of Chemical and Biomolecular Engineering, 6 MetroTech Center, Brooklyn, NY 11201, United States
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6
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Gao Q, Lu S, Wang Y, He L, Wang M, Jia R, Chen S, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Mao S, Ou X, Sun D, Tian B, Cheng A. Bacterial DNA methyltransferase: A key to the epigenetic world with lessons learned from proteobacteria. Front Microbiol 2023; 14:1129437. [PMID: 37032876 PMCID: PMC10073500 DOI: 10.3389/fmicb.2023.1129437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/27/2023] [Indexed: 04/11/2023] Open
Abstract
Epigenetics modulates expression levels of various important genes in both prokaryotes and eukaryotes. These epigenetic traits are heritable without any change in genetic DNA sequences. DNA methylation is a universal mechanism of epigenetic regulation in all kingdoms of life. In bacteria, DNA methylation is the main form of epigenetic regulation and plays important roles in affecting clinically relevant phenotypes, such as virulence, host colonization, sporulation, biofilm formation et al. In this review, we survey bacterial epigenomic studies and focus on the recent developments in the structure, function, and mechanism of several highly conserved bacterial DNA methylases. These methyltransferases are relatively common in bacteria and participate in the regulation of gene expression and chromosomal DNA replication and repair control. Recent advances in sequencing techniques capable of detecting methylation signals have enabled the characterization of genome-wide epigenetic regulation. With their involvement in critical cellular processes, these highly conserved DNA methyltransferases may emerge as promising targets for developing novel epigenetic inhibitors for biomedical applications.
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Affiliation(s)
- Qun Gao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Shuwei Lu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuwei Wang
- Key Laboratory of Livestock and Poultry Provenance Disease Research in Mianyang, Sichuan, China
| | - Longgui He
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Sai Mao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
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7
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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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8
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Udayasuryan B, Nguyen TT, Slade DJ, Verbridge SS. Harnessing Tissue Engineering Tools to Interrogate Host-Microbiota Crosstalk in Cancer. iScience 2020; 23:101878. [PMID: 33344921 PMCID: PMC7736992 DOI: 10.1016/j.isci.2020.101878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Recent studies have begun to highlight the diverse and tumor-specific microbiomes across multiple cancer types. We believe this work raises the important question of whether the classical "Hallmarks of Cancer" should be expanded to include tumor microbiomes. To answer this question, the causal relationships and co-evolution of these microbiotic tumor ecosystems must be better understood. Because host-microbe interactions should be studied in a physiologically relevant context, animal models have been preferred. Yet these models are often poor mimics of human tumors and are difficult to interrogate at high spatiotemporal resolution. We believe that in vitro tissue engineered platforms could provide a powerful alternative approach that combines the high-resolution of in vitro studies with a high degree of physiological relevance. This review will focus on tissue engineered approaches to study host-microbe interactions and to establish their role as an emerging hallmark of cancer with potential as a therapeutic target.
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Affiliation(s)
- Barath Udayasuryan
- Virginia Tech – Wake Forest School of Biomedical Engineering and Sciences, Blacksburg, VA 24061, USA
| | - Tam T.D. Nguyen
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA
| | - Daniel J. Slade
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA
| | - Scott S. Verbridge
- Virginia Tech – Wake Forest School of Biomedical Engineering and Sciences, Blacksburg, VA 24061, USA
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9
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Besic V, Habibolahi F, Noël B, Rupp S, Genovesio A, Lebreton A. Coordination of transcriptional and translational regulations in human epithelial cells infected by Listeria monocytogenes. RNA Biol 2020; 17:1492-1507. [PMID: 32584699 PMCID: PMC7549700 DOI: 10.1080/15476286.2020.1777380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/04/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022] Open
Abstract
The invasion of mammalian cells by intracellular bacterial pathogens reshuffles their gene expression and functions; however, we lack dynamic insight into the distinct control levels that shape the host response. Here, we have addressed the respective contribution of transcriptional and translational regulations during a time-course of infection of human intestinal epithelial cells by an epidemic strain of Listeria monocytogenes, using transcriptome analysis paralleled with ribosome profiling. Upregulations were dominated by early transcriptional activation of pro-inflammatory genes, whereas translation inhibition appeared as the major driver of downregulations. Instead of a widespread but transient shutoff, translation inhibition affected specifically and durably transcripts encoding components of the translation machinery harbouring a 5'-terminal oligopyrimidine motif. Pre-silencing the most repressed target gene (PABPC1) slowed down the intracellular multiplication of Listeria monocytogenes, suggesting that the infected host cell can benefit from the repression of genes involved in protein synthesis and thereby better control infection.
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Affiliation(s)
- Vinko Besic
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Fatemeh Habibolahi
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- Computational Biology and Bioinformatics Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Benoît Noël
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- Computational Biology and Bioinformatics Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Sebastian Rupp
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Auguste Genovesio
- Computational Biology and Bioinformatics Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Alice Lebreton
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- INRAE, IBENS, Paris, France
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10
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Brooks D, Barr LC, Wiscombe S, McAuley DF, Simpson AJ, Rostron AJ. Human lipopolysaccharide models provide mechanistic and therapeutic insights into systemic and pulmonary inflammation. Eur Respir J 2020; 56:13993003.01298-2019. [PMID: 32299854 DOI: 10.1183/13993003.01298-2019] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 03/18/2020] [Indexed: 02/07/2023]
Abstract
Inflammation is a key feature in the pathogenesis of sepsis and acute respiratory distress syndrome (ARDS). Sepsis and ARDS continue to be associated with high mortality. A key contributory factor is the rudimentary understanding of the early events in pulmonary and systemic inflammation in humans, which are difficult to study in clinical practice, as they precede the patient's presentation to medical services. Lipopolysaccharide (LPS), a constituent of the outer membrane of Gram-negative bacteria, is a trigger of inflammation and the dysregulated host response in sepsis. Human LPS models deliver a small quantity of LPS to healthy volunteers, triggering an inflammatory response and providing a window to study early inflammation in humans. This allows biological/mechanistic insights to be made and new therapeutic strategies to be tested in a controlled, reproducible environment from a defined point in time. We review the use of human LPS models, focussing on the underlying mechanistic insights that have been gained by studying the response to intravenous and pulmonary LPS challenge. We discuss variables that may influence the response to LPS before considering factors that should be considered when designing future human LPS studies.
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Affiliation(s)
- Daniel Brooks
- Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, UK
| | - Laura C Barr
- Dept of Respiratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Sarah Wiscombe
- Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, UK
| | - Daniel F McAuley
- School of Medicine, Dentistry and Biomedical Sciences, Institute for Health Sciences, Wellcome-Wolfson Institute for Experimental Medicine, Belfast, UK
| | - A John Simpson
- Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, UK
| | - Anthony J Rostron
- Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, UK
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11
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Abstract
OBJECTIVE The majority of patients with colorectal cancer are diagnosed with locally advanced and/or disseminated disease, and treatment options include surgery in combination with cytotoxic chemotherapy regimens, biologics, and/or radiotherapy. Thus, colorectal cancer remains a heavy burden on society and health care systems.Mounting evidence show that driver gene mutations play only part of the role in carcinogenesis. Epigenetics are strongly implicated in initiation and progression of colorectal cancer along with major players such as intestinal microbiotic dysbiosis and chronic mucosal inflammation.To assess phenotypic changes in proteins and gene expression, multigene expression signatures based on sequencing techniques have been developed to hopefully improve predictors of the tumor profile, immune response, and therapeutic outcomes. Our objective was to review current advances in the field and to update surgeons and academics on driver gene mutations and epigenetics in colorectal cancer. BACKGROUND AND METHODS This is a narrative review studying relevant research published in the PUBMED database from 2012-2018. RESULTS AND CONCLUSION Increased understanding of the molecular biology will improve options to characterize colorectal cancer with regard to mutations and molecular pathways, including microsatellite instability, epigenetics, microbiota, and microenvironment. Research will inevitably improve risk group stratification and targeted treatment approaches.Epigenetic profiling and epigenetic modulating drugs will increase risk stratification, increase accessibility for DNA targeting chemotherapeutics and reduce cytotoxic drug resistance.New generation antibiotics such as biofilm inhibitors and quorum sensing inhibitors are being developed to target the carcinogenetic impact of colonic dysbiosis and inflammation.
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12
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Hall TJ, Vernimmen D, Browne JA, Mullen MP, Gordon SV, MacHugh DE, O’Doherty AM. Alveolar Macrophage Chromatin Is Modified to Orchestrate Host Response to Mycobacterium bovis Infection. Front Genet 2020; 10:1386. [PMID: 32117424 PMCID: PMC7020904 DOI: 10.3389/fgene.2019.01386] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/18/2019] [Indexed: 12/29/2022] Open
Abstract
Bovine tuberculosis is caused by infection with Mycobacterium bovis, which can also cause disease in a range of other mammals, including humans. Alveolar macrophages are the key immune effector cells that first encounter M. bovis and how the macrophage epigenome responds to mycobacterial pathogens is currently not well understood. Here, we have used chromatin immunoprecipitation sequencing (ChIP-seq), RNA-seq and miRNA-seq to examine the effect of M. bovis infection on the bovine alveolar macrophage (bAM) epigenome. We show that H3K4me3 is more prevalent, at a genome-wide level, in chromatin from M. bovis-infected bAM compared to control non-infected bAM; this was particularly evident at the transcriptional start sites of genes that determine programmed macrophage responses to mycobacterial infection (e.g. M1/M2 macrophage polarisation). This pattern was also supported by the distribution of RNA Polymerase II (Pol II) ChIP-seq results, which highlighted significantly increased transcriptional activity at genes demarcated by permissive chromatin. Identification of these genes enabled integration of high-density genome-wide association study (GWAS) data, which revealed genomic regions associated with resilience to infection with M. bovis in cattle. Through integration of these data, we show that bAM transcriptional reprogramming occurs through differential distribution of H3K4me3 and Pol II at key immune genes. Furthermore, this subset of genes can be used to prioritise genomic variants from a relevant GWAS data set.
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Affiliation(s)
- Thomas J. Hall
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College Dublin, Dublin, Ireland
| | - Douglas Vernimmen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - John A. Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College Dublin, Dublin, Ireland
| | - Michael P. Mullen
- Bioscience Research Institute, Athlone Institute of Technology, Athlone, Ireland
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - David E. MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Alan M. O’Doherty
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College Dublin, Dublin, Ireland
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13
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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.
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14
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Shi Q, Zhang Y, Liu W, Xiao H, Qi Y, Li J, Luo B. Latent membrane protein 2A inhibits expression level of Smad2 through regulating miR‐155‐5p in EBV‐associated gastric cancer cell lines. J Med Virol 2019; 92:96-106. [DOI: 10.1002/jmv.25579] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 08/27/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Qianzhu Shi
- Department of Pathogen Biology, School of Basic MedicineQingdao University Qingdao China
| | - Yan Zhang
- Department of Clinical LaboratoryCentral Hospital of Zibo Zibo China
| | - Wen Liu
- Department of Pathogen Biology, School of Basic MedicineQingdao University Qingdao China
| | - Hua Xiao
- Department of Pathogen Biology, School of Basic MedicineQingdao University Qingdao China
| | - Yifan Qi
- Department of Pathogen Biology, School of Basic MedicineQingdao University Qingdao China
| | - Jun Li
- Department of Pathogen Biology, School of Basic MedicineQingdao University Qingdao China
| | - Bing Luo
- Department of Pathogen Biology, School of Basic MedicineQingdao University Qingdao China
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15
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Constitutive activation of the canonical NF-κB signaling pathway in EBV-associated gastric carcinoma. Virology 2019; 532:1-10. [DOI: 10.1016/j.virol.2019.03.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/02/2019] [Accepted: 03/27/2019] [Indexed: 01/25/2023]
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16
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Zhang Y, Zhang W, Liu W, Liu H, Zhang Y, Luo B. Epstein–Barr virus miRNA-BART16 modulates cell proliferation by targeting LMP1. Virus Res 2018; 256:38-44. [DOI: 10.1016/j.virusres.2018.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/06/2018] [Accepted: 08/01/2018] [Indexed: 12/18/2022]
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17
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Abstract
PURPOSE OF REVIEW We wished to overview recent data on a subset of epigenetic changes elicited by intracellular bacteria in human cells. Reprogramming the gene expression pattern of various host cells may facilitate bacterial growth, survival, and spread. RECENT FINDINGS DNA-(cytosine C5)-methyltransferases of Mycoplasma hyorhinis targeting cytosine-phosphate-guanine (CpG) dinucleotides and a Mycobacterium tuberculosis methyltransferase targeting non-CpG sites methylated the host cell DNA and altered the pattern of gene expression. Gene silencing by CpG methylation and histone deacetylation, mediated by cellular enzymes, also occurred in M. tuberculosis-infected macrophages. M. tuberculosis elicited cell type-specific epigenetic changes: it caused increased DNA methylation in macrophages, but induced demethylation, deposition of euchromatic histone marks and activation of immune-related genes in dendritic cells. A secreted transposase of Acinetobacter baumannii silenced a cellular gene, whereas Mycobacterium leprae altered the epigenotype, phenotype, and fate of infected Schwann cells. The 'keystone pathogen' oral bacterium Porphyromonas gingivalis induced local DNA methylation and increased the level of histone acetylation in host cells. These epigenetic changes at the biofilm-gingiva interface may contribute to the development of periodontitis. SUMMARY Epigenetic regulators produced by intracellular bacteria alter the epigenotype and gene expression pattern of host cells and play an important role in pathogenesis.
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18
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Analysis of Epstein-Barr Virus Genomes and Expression Profiles in Gastric Adenocarcinoma. J Virol 2018; 92:JVI.01239-17. [PMID: 29093097 DOI: 10.1128/jvi.01239-17] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/05/2017] [Indexed: 01/10/2023] Open
Abstract
Epstein-Barr virus (EBV) is a causative agent of a variety of lymphomas, nasopharyngeal carcinoma (NPC), and ∼9% of gastric carcinomas (GCs). An important question is whether particular EBV variants are more oncogenic than others, but conclusions are currently hampered by the lack of sequenced EBV genomes. Here, we contribute to this question by mining whole-genome sequences of 201 GCs to identify 13 EBV-positive GCs and by assembling 13 new EBV genome sequences, almost doubling the number of available GC-derived EBV genome sequences and providing the first non-Asian EBV genome sequences from GC. Whole-genome sequence comparisons of all EBV isolates sequenced to date (85 from tumors and 57 from healthy individuals) showed that most GC and NPC EBV isolates were closely related although American Caucasian GC samples were more distant, suggesting a geographical component. However, EBV GC isolates were found to contain some consistent changes in protein sequences regardless of geographical origin. In addition, transcriptome data available for eight of the EBV-positive GCs were analyzed to determine which EBV genes are expressed in GC. In addition to the expected latency proteins (EBNA1, LMP1, and LMP2A), specific subsets of lytic genes were consistently expressed that did not reflect a typical lytic or abortive lytic infection, suggesting a novel mechanism of EBV gene regulation in the context of GC. These results are consistent with a model in which a combination of specific latent and lytic EBV proteins promotes tumorigenesis.IMPORTANCE Epstein-Barr virus (EBV) is a widespread virus that causes cancer, including gastric carcinoma (GC), in a small subset of individuals. An important question is whether particular EBV variants are more cancer associated than others, but more EBV sequences are required to address this question. Here, we have generated 13 new EBV genome sequences from GC, almost doubling the number of EBV sequences from GC isolates and providing the first EBV sequences from non-Asian GC. We further identify sequence changes in some EBV proteins common to GC isolates. In addition, gene expression analysis of eight of the EBV-positive GCs showed consistent expression of both the expected latency proteins and a subset of lytic proteins that was not consistent with typical lytic or abortive lytic expression. These results suggest that novel mechanisms activate expression of some EBV lytic proteins and that their expression may contribute to oncogenesis.
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19
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Foksinski M, Zarakowska E, Gackowski D, Skonieczna M, Gajda K, Hudy D, Szpila A, Bialkowski K, Starczak M, Labejszo A, Czyz J, Rzeszowska-Wolny J, Olinski R. Profiles of a broad spectrum of epigenetic DNA modifications in normal and malignant human cell lines: Proliferation rate is not the major factor responsible for the 5-hydroxymethyl-2'-deoxycytidine level in cultured cancerous cell lines. PLoS One 2017; 12:e0188856. [PMID: 29190698 PMCID: PMC5708640 DOI: 10.1371/journal.pone.0188856] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/14/2017] [Indexed: 12/20/2022] Open
Abstract
Active demethylation of 5-methylcytosine moiety in DNA occurs by its sequential oxidation to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine, catalysed by enzymes of the Ten-Eleven Translocation family proteins (TETs 1, 2 and 3). Here we analyzed for the first time all the intermediate products of DNA demethylation pathway in the form of deoxynucleosides (5-methyl-2′-deoxycytidine, 5-(hydroxymethyl)-2′-deoxycytidine, 5-formyl-2′-deoxycytidine and 5-carboxy-2′-deoxycytidine as well as 5-(hydroxymethyl)-2′-deoxyuridine) using automated isotope-dilution online two-dimensional ultra-performance liquid chromatography with tandem mass spectrometry. DNA was isolated from human malignant cell lines of colon adenocarcinoma (HCT 116), melanoma (Me45), myelogenous leukemia bone marrow blasts (K562), EBV-positive Burkitt’s lymphoma lymphoblasts (Raji), EBV-negative Burkitt’s lymphoma lymphoblasts (male-CA46 and female-ST486), as well as normal neonatal dermal fibroblasts (NHDF-Neo). The expression levels of TET1, TET2, TET3, SMUG1, and TDG genes were also assayed by RT-qPCR. Our results show a global erasure of 5-hydroxymethyl-2′-deoxycytidine and 5-carboxy-2′-deoxycytidine in DNA of cultured cells compared with DNA from primary malignant tissue. Moreover, malignant cells in culture have a quite different DNA epigenetic profile than cultured normal cells, and different types of malignant cells display different and characteristic profiles of DNA epigenetic marks. Similar analyses of a broader spectrum of epigenetic modifications, not restricted to 5-methyl-2′-deoxycytidine, could lead to better understanding of the mechanism(s) responsible for emergence of different types of cancer cells.
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Affiliation(s)
- Marek Foksinski
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Ewelina Zarakowska
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Magdalena Skonieczna
- Biosystems Group, Institute of Automatic Control, Faculty of Automatics, Electronics, and Informatics, Silesian University of Technology, Gliwice, Poland
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Karolina Gajda
- Biosystems Group, Institute of Automatic Control, Faculty of Automatics, Electronics, and Informatics, Silesian University of Technology, Gliwice, Poland
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Dorota Hudy
- Biosystems Group, Institute of Automatic Control, Faculty of Automatics, Electronics, and Informatics, Silesian University of Technology, Gliwice, Poland
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Anna Szpila
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Karol Bialkowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Marta Starczak
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Anna Labejszo
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Jaroslaw Czyz
- Department of Hematology, Faculty of Medicine, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Joanna Rzeszowska-Wolny
- Biosystems Group, Institute of Automatic Control, Faculty of Automatics, Electronics, and Informatics, Silesian University of Technology, Gliwice, Poland
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Ryszard Olinski
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
- * E-mail:
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20
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Grabiec AM, Potempa J. Epigenetic regulation in bacterial infections: targeting histone deacetylases. Crit Rev Microbiol 2017; 44:336-350. [PMID: 28971711 DOI: 10.1080/1040841x.2017.1373063] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Pathogens have developed sophisticated strategies to evade the immune response, among which manipulation of host cellular epigenetic mechanisms plays a prominent role. In the last decade, modulation of histone acetylation in host cells has emerged as an efficient strategy of bacterial immune evasion. Virulence factors and metabolic products of pathogenic microorganisms alter expression and activity of histone acetyltransferases (HATs) and histone deacetylases (HDACs) to suppress transcription of host defense genes through epigenetic changes in histone acetylation marks. This new avenue of pathogen-host interactions is particularly important in light of introduction of HDAC inhibitors into clinical practice. Considerable effort is currently being applied to better understand the effects of HDAC inhibitors on the quality of immune responses to pathogens and to characterize the therapeutic potential of these compounds in microbial infections. In this review, we will discuss the recently discovered mechanisms utilized by bacteria to facilitate their survival within infected hosts through subversion of the host acetylation system and the effects of acetylation modulators, including HDAC inhibitors and bromodomain-containing BET protein inhibitors, on innate immune responses against microbial pathogens. Integration of these two lines of experimental evidence provides critical information on the perspectives of epigenetic therapies targeting protein acetylation in infectious diseases.
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Affiliation(s)
- Aleksander M Grabiec
- a Department of Microbiology , Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Kraków , Poland
| | - Jan Potempa
- a Department of Microbiology , Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Kraków , Poland.,b Department of Oral Immunology and Infectious Diseases , University of Louisville School of Dentistry , Louisville , KY , USA
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21
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Conti P, Carinci F, Caraffa A, Ronconi G, Lessiani G, Theoharides TC. Link between mast cells and bacteria: Antimicrobial defense, function and regulation by cytokines. Med Hypotheses 2017; 106:10-14. [DOI: 10.1016/j.mehy.2017.06.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/04/2017] [Accepted: 06/25/2017] [Indexed: 01/12/2023]
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22
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Rajić J, Inic-Kanada A, Stein E, Dinić S, Schuerer N, Uskoković A, Ghasemian E, Mihailović M, Vidaković M, Grdović N, Barisani-Asenbauer T. Chlamydia trachomatis Infection Is Associated with E-Cadherin Promoter Methylation, Downregulation of E-Cadherin Expression, and Increased Expression of Fibronectin and α-SMA-Implications for Epithelial-Mesenchymal Transition. Front Cell Infect Microbiol 2017; 7:253. [PMID: 28660176 PMCID: PMC5469886 DOI: 10.3389/fcimb.2017.00253] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/31/2017] [Indexed: 12/21/2022] Open
Abstract
Chlamydia trachomatis (Ct) can induce scarring disease of the ocular mucosa, known as trachoma, the most common infectious cause of blindness worldwide. We hypothesized that epithelial-mesenchymal transition (EMT) contributes to the fibrotic process in trachomatous scarring. Infection of human conjunctival epithelial cells (HCjE) with Ct activated signaling pathways involved in EMT induction, which was correlated with decreased expression of E-cadherin, guardian of the epithelial phenotype. In addition, Ct infection was associated with increased expression of two mesenchymal cell markers: fibronectin and α-SMA. The DNA methylation statuses of selected regions of E-cadherin, fibronectin, and α-SMA genes revealed that Ct infection was accompanied with changes in DNA methylation of the E-cadherin promoter, while the expression of the two mesenchymal markers was not related with this epigenetic event. Our data suggest that Ct infection of conjunctival epithelial cells induces EMT-like changes that go along with modification of the methylation profile of the E-cadherin promoter and could, as one of the earliest events, contribute to processes triggering conjunctival scarring.
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Affiliation(s)
- Jovana Rajić
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković", University of BelgradeBelgrade, Serbia
| | - Aleksandra Inic-Kanada
- OCUVAC - Center of Ocular Inflammation and Infection, Laura Bassi Centres of Expertise; Center for Pathophysiology, Infectiology and Immunology; Medical University of ViennaVienna, Austria
| | - Elisabeth Stein
- OCUVAC - Center of Ocular Inflammation and Infection, Laura Bassi Centres of Expertise; Center for Pathophysiology, Infectiology and Immunology; Medical University of ViennaVienna, Austria
| | - Svetlana Dinić
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković", University of BelgradeBelgrade, Serbia
| | - Nadine Schuerer
- OCUVAC - Center of Ocular Inflammation and Infection, Laura Bassi Centres of Expertise; Center for Pathophysiology, Infectiology and Immunology; Medical University of ViennaVienna, Austria
| | - Aleksandra Uskoković
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković", University of BelgradeBelgrade, Serbia
| | - Ehsan Ghasemian
- OCUVAC - Center of Ocular Inflammation and Infection, Laura Bassi Centres of Expertise; Center for Pathophysiology, Infectiology and Immunology; Medical University of ViennaVienna, Austria
| | - Mirjana Mihailović
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković", University of BelgradeBelgrade, Serbia
| | - Melita Vidaković
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković", University of BelgradeBelgrade, Serbia
| | - Nevena Grdović
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković", University of BelgradeBelgrade, Serbia
| | - Talin Barisani-Asenbauer
- OCUVAC - Center of Ocular Inflammation and Infection, Laura Bassi Centres of Expertise; Center for Pathophysiology, Infectiology and Immunology; Medical University of ViennaVienna, Austria
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23
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Duval M, Cossart P, Lebreton A. Mammalian microRNAs and long noncoding RNAs in the host-bacterial pathogen crosstalk. Semin Cell Dev Biol 2017; 65:11-19. [PMID: 27381344 PMCID: PMC7089780 DOI: 10.1016/j.semcdb.2016.06.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 05/30/2016] [Accepted: 06/01/2016] [Indexed: 12/20/2022]
Abstract
Gene expression regulation is a critical question in host-pathogen interactions, and RNAs act as key players in this process. In this review, we focus on the mammalian RNA response to bacterial infection, with a special interest on microRNAs and long non-coding RNAs. We discuss the role of cellular miRNAs in immunity, the implication of circulating miRNAs as well as the influence of the microbiome on the miRNA response. We also review how pathogens counteract the host miRNA expression. Interestingly, bacterial non-coding RNAs regulate host gene expression and conversely eukaryotic miRNAs may regulate bacterial gene expression. Overall, the characterization of RNA regulatory networks represents an emerging theme in the field of host pathogen interactions.
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Affiliation(s)
- Mélodie Duval
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015 Paris, France; Inserm, U604, 75015 Paris, France; INRA, USC2020, 75015 Paris, France
| | - Pascale Cossart
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015 Paris, France; Inserm, U604, 75015 Paris, France; INRA, USC2020, 75015 Paris, France.
| | - Alice Lebreton
- École Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'École Normale Supérieure (IBENS), Équipe Infection et Devenir de l'ARN, 75005 Paris, France; INRA, IBENS, 75005 Paris, France.
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24
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How Our Other Genome Controls Our Epi-Genome. Trends Microbiol 2016; 24:777-787. [PMID: 27289569 DOI: 10.1016/j.tim.2016.05.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/03/2016] [Accepted: 05/18/2016] [Indexed: 12/12/2022]
Abstract
Eukaryotes and prokaryotes produce extracellular nanovescicles that contain RNAs and other molecules that they exploit to communicate. Recently, inter-kingdom crosstalk was demonstrated between humans and bacteria through fecal microRNAs. We suggest here how bacteria interact with humans via RNAs within membrane vesicles to alter our epigenome, thus filling the gap and closing the circle. At the same time, there are indications that there could be a wider inter-kingdom communication network that might encompass all known kingdoms. Now that the connection with our other genome has been established, we also should begin to explore the 'social' network that we have around us.
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