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Berkes-Bara E, Nemes A, Dudas B, Joo K, Murber A, Fekecs G, Urbancsek J, Fancsovits P. Successful pregnancy with intracytoplasmic sperm injection after bacterial contamination of embryo culture in in vitro fertilization: a case report. J Med Case Rep 2024; 18:247. [PMID: 38745332 PMCID: PMC11094885 DOI: 10.1186/s13256-024-04521-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/16/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Bacterial infection of embryo culture medium is rare but may be detrimental. The main source of embryo culture contamination is semen. Assisted reproduction centers currently lack consensus regarding the methods for preventing and managing embryo culture infection. In our recent case, a successful pregnancy was achieved with intracytoplasmic sperm injection after failed conventional in vitro fertilization owing to bacterial contamination. CASE PRESENTATION We present a case report of two consecutive in vitro fertilization-intracytoplasmic sperm injection cycles with photo and video documentation of the bacterial growth. A 36-year-old Hungarian woman and her 37-year-old Hungarian partner came to our department. They had two normal births followed by 2 years of infertility. The major causes of infertility were a closed fallopian tube and asthenozoospermia. Bacterial infection of the embryo culture medium was observed during in vitro fertilization and all oocytes degenerated. The source was found to be the semen. To prevent contamination, intracytoplasmic sperm injection was used for fertilization in the subsequent cycle. Intracytoplasmic bacterial proliferation was observed in one of the three fertilized eggs, but two good-quality embryos were successfully obtained. The transfer of one embryo resulted in a successful pregnancy and a healthy newborn was delivered. CONCLUSION Intracytoplasmic sperm injection may be offered to couples who fail conventional in vitro fertilization treatment owing to bacteriospermia, as it seems to prevent infection of the embryo culture. Even if bacterial contamination appears, our case encourages us to continue treatment. Nevertheless, the development of new management guidelines for the prevention and management of bacterial contamination is essential.
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Affiliation(s)
- Eva Berkes-Bara
- Division of Assisted Reproduction, Department of Obstetrics and Gynaecology, Semmelweis University, Baross U. 27., 1088, Budapest, Hungary.
| | - Annamaria Nemes
- Division of Assisted Reproduction, Department of Obstetrics and Gynaecology, Semmelweis University, Baross U. 27., 1088, Budapest, Hungary
| | - Beata Dudas
- Division of Assisted Reproduction, Department of Obstetrics and Gynaecology, Semmelweis University, Baross U. 27., 1088, Budapest, Hungary
| | - Kata Joo
- Division of Assisted Reproduction, Department of Obstetrics and Gynaecology, Semmelweis University, Baross U. 27., 1088, Budapest, Hungary
| | - Akos Murber
- Division of Assisted Reproduction, Department of Obstetrics and Gynaecology, Semmelweis University, Baross U. 27., 1088, Budapest, Hungary
| | - Gyorgyi Fekecs
- Division of Assisted Reproduction, Department of Obstetrics and Gynaecology, Semmelweis University, Baross U. 27., 1088, Budapest, Hungary
| | - Janos Urbancsek
- Division of Assisted Reproduction, Department of Obstetrics and Gynaecology, Semmelweis University, Baross U. 27., 1088, Budapest, Hungary
| | - Peter Fancsovits
- Division of Assisted Reproduction, Department of Obstetrics and Gynaecology, Semmelweis University, Baross U. 27., 1088, Budapest, Hungary
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Wazahat R, Zaidi R, Kumar P. Epigenetic regulations in Mycobacterium tuberculosis infection. Indian J Tuberc 2024; 71:204-212. [PMID: 38589125 DOI: 10.1016/j.ijtb.2023.06.011] [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: 04/06/2023] [Revised: 06/02/2023] [Accepted: 06/22/2023] [Indexed: 04/10/2024]
Abstract
Mycobacterium tuberculosis (Mtb) employs several sophisticated strategies to evade host immunity and facilitate its intracellular survival. One of them is the epigenetic manipulation of host chromatin by three strategies i.e., DNA methylation, histone modifications and miRNA involvement. A host-directed therapeutic can be an attractive approach that targets these host epigenetics or gene regulations and circumvent manipulation of host cell machinery by Mtb. Given the complexity of the nature of intracellular infection by Mtb, there are challenges in identifying the important host proteins, non-coding RNA or the secretory proteins of Mtb itself that directly or indirectly bring upon the epigenetic modifications in the host chromatin. Equally challenging is developing the methods of targeting these epigenetic factors through chemical or non-chemical approaches as host-directed therapeutics. The current review article briefly summarizes several of the epigenetic factors that serve to bring upon potential changes in the host transcriptional machinery and targets the immune system for immunosuppression and disease progression in Mtb infection.
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Affiliation(s)
- Rushna Wazahat
- Department of Biochemistry, Jamia Hamdard, New Delhi 110062, India.
| | - Rana Zaidi
- Department of Biochemistry, Jamia Hamdard, New Delhi 110062, India
| | - Pankaj Kumar
- Department of Biochemistry, Jamia Hamdard, New Delhi 110062, India.
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Frazer LC, Yamaguchi Y, Singh DK, Akopyants NS, Good M. DNA methylation in necrotizing enterocolitis. Expert Rev Mol Med 2024; 26:e16. [PMID: 38557638 PMCID: PMC11140546 DOI: 10.1017/erm.2024.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 03/05/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Epigenetic modifications, such as DNA methylation, are enzymatically regulated processes that directly impact gene expression patterns. In early life, they are central to developmental programming and have also been implicated in regulating inflammatory responses. Research into the role of epigenetics in neonatal health is limited, but there is a growing body of literature related to the role of DNA methylation patterns and diseases of prematurity, such as the intestinal disease necrotizing enterocolitis (NEC). NEC is a severe intestinal inflammatory disease, but the key factors that precede disease development remain to be determined. This knowledge gap has led to a failure to design effective targeted therapies and identify specific biomarkers of disease. Recent literature has identified altered DNA methylation patterns in the stool and intestinal tissue of neonates with NEC. These findings provide the foundation for a new avenue in NEC research. In this review, we will provide a general overview of DNA methylation and then specifically discuss the recent literature related to methylation patterns in neonates with NEC. We will also discuss how DNA methylation is used as a biomarker for other disease states and how, with further research, methylation patterns may serve as potential biomarkers for NEC.
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Affiliation(s)
- Lauren C. Frazer
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yukihiro Yamaguchi
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dhirendra K. Singh
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalia S. Akopyants
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Misty Good
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Rajabloo A, Karimi J, Mehrabadi M. Differential induction of NF-κB pathways by non-pathogenic and pathogenic bacteria in Helicoverpa armigera is critical for an efficient immune response and survival. J Invertebr Pathol 2024; 203:108049. [PMID: 38159795 DOI: 10.1016/j.jip.2023.108049] [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: 10/12/2023] [Revised: 12/05/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Following pathogen infection in a host, extensive changes occur in the host's gene expression pattern to suppress infection and increase the chance of host survival. Likewise, many pathogens have evolved to evade/suppress host immunity and increase their survival within the host. In this study, we assessed the NF-κB (Imd and Toll) essential gene expression response of Helicoverpa armigera to an entomopathogenic Serratia marcescens and non-pathogenic Escherichia coli. Bacterial cells of S. marcescens or E. coli were injected into the haemocoel of fifth-instar larvae of H. armigera, whereas distilled water was injected into control insects. Our results showed that the expression levels of the Imd and Toll pathway genes (i.e., Relish, imd, spätzle and dif) and the antimicrobial peptides (i.e., gloverin, transferin, gallerimycin, and galiomicin) were differentially expressed following the bacterial injections while control larvae showed no differences. The E. coli injection induced higher and longer-lasted gene expression than the S. marcescens injected larvae, in which the gene expressions were diminished from 24 h post injection. Transcript Knockdown of Relish increased the replication rates of S. marcescens and E. coli, and lowered the infected larvae survival rates. These results showed that H. armigera NF-κB immunity pathways (particularly Imd pathway) play a vital role in immunity against bacterial infections, and S. marcescens might modulate these pathways to survive and replicate in the host.
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Affiliation(s)
- Akram Rajabloo
- Department of Agricultural Biotechnology, Faculty of Agriculture, Shahed University, Tehran, Iran
| | - Jaber Karimi
- Department of Plant Protection, Faculty of Agriculture, Shahed University, Tehran, Iran.
| | - Mohammad Mehrabadi
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
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5
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Ashonibare VJ, Akorede BA, Ashonibare PJ, Akhigbe TM, Akhigbe RE. Gut microbiota-gonadal axis: the impact of gut microbiota on reproductive functions. Front Immunol 2024; 15:1346035. [PMID: 38482009 PMCID: PMC10933031 DOI: 10.3389/fimmu.2024.1346035] [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: 11/28/2023] [Accepted: 01/30/2024] [Indexed: 04/12/2024] Open
Abstract
The influence of gut microbiota on physiological processes is rapidly gaining attention globally. Despite being under-studied, there are available data demonstrating a gut microbiota-gonadal cross-talk, and the importance of this axis in reproduction. This study reviews the impacts of gut microbiota on reproduction. In addition, the possible mechanisms by which gut microbiota modulates male and female reproduction are presented. Databases, including Embase, Google scholar, Pubmed/Medline, Scopus, and Web of Science, were explored using relevant key words. Findings showed that gut microbiota promotes gonadal functions by modulating the circulating levels of steroid sex hormones, insulin sensitivity, immune system, and gonadal microbiota. Gut microbiota also alters ROS generation and the activation of cytokine accumulation. In conclusion, available data demonstrate the existence of a gut microbiota-gonadal axis, and role of this axis on gonadal functions. However, majority of the data were compelling evidences from animal studies with a great dearth of human data. Therefore, human studies validating the reports of experimental studies using animal models are important.
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Affiliation(s)
- Victory J. Ashonibare
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
| | - Bolaji A. Akorede
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
- Department of Biomedical Sciences, University of Wyoming, Laramie, WY, United States
| | - Precious J. Ashonibare
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Tunmise M. Akhigbe
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
- Breeding and Genetic Unit, Department of Agronomy, Osun State University, Ejigbo, Osun State, Nigeria
| | - Roland Eghoghosoa Akhigbe
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
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Peng Y, Xiao S, Zuo W, Xie Y, Xiao Y. Potential diagnostic value of miRNAs in sexually transmitted infections. Gene 2024; 895:147992. [PMID: 37977319 DOI: 10.1016/j.gene.2023.147992] [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: 09/21/2023] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
MiRNAs are small endogenous non-coding RNAs that have been demonstrated to be involved in post-transcriptional gene silencing, regulating a number of metabolic functions in the human body, including immune response, cellular physiology, organ development, angiogenesis, signaling, and other aspects. As popular molecules that have been studied in previous years, given their extensive regulatory functions, miRNAs hold considerable promise as non-invasive biomarkers. Sexually transmitted infections(STIs) are still widespread and have an adverse effect on individuals, communities, and society worldwide. miRNAs in the regulatory networks are generally involved in their molecular processes of formation and development. In this review, we discuss the value of miRNAs for the diagnosis of STIs.
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Affiliation(s)
- Yunchi Peng
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Shuangwen Xiao
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Wei Zuo
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yafeng Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yongjian Xiao
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China.
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7
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Barone S, Mateu B, Turco L, Pelliccia S, Lembo F, Summa V, Buommino E, Brindisi M. Unveiling the modulation of Pseudomonas aeruginosa virulence and biofilm formation by selective histone deacetylase 6 inhibitors. Front Microbiol 2024; 15:1340585. [PMID: 38371939 PMCID: PMC10869609 DOI: 10.3389/fmicb.2024.1340585] [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: 11/18/2023] [Accepted: 01/10/2024] [Indexed: 02/20/2024] Open
Abstract
Bacterial infections represent a key public health issue due to the occurrence of multidrug-resistant bacteria. Recently, the amount of data supporting the dynamic control of epigenetic pathways by environmental cues has triggered research efforts toward the clarification of their role in microbial infections. Among protein post-translational modifications, reversible acetylation is the most implicated in the feedback to environmental stimuli and in cellular homeostasis. Accordingly, the latest studies identified the histone deacetylase 6 (HDAC6) enzyme as a crucial player in the complex molecular machinery underlying bacterial clearance or killing. A very important milestone for the elucidation of the consequence of HDAC6 activity in bacterial infections is herein described, unveiling for the first time the role of a potent HDAC6 inhibitor in interfering with biofilm formation and modulating virulence factors of P. aeruginosa. We demonstrated that compound F2F-2020202 affected the production of some important virulence factors in P. aeruginosa, namely pyocyanin and rhamnolipids, clearly impairing its ability to form biofilm. Furthermore, evidence of possible QS involvement is supported by differential regulation of specific genes, namely RhlI, phAz1, and qsrO. The data herein obtained also complement and in part explain our previous results with selective HDAC6 inhibitors able to reduce inflammation and bacterial load in chronic infection models recapitulating the cystic fibrosis (CF) phenotype. This study fosters future in-depth investigation to allow the complete elucidation of the molecular mechanisms underlying HDAC6's role in bacterial infections.
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Affiliation(s)
- Simona Barone
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Baptiste Mateu
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Luigia Turco
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Sveva Pelliccia
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Francesca Lembo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Vincenzo Summa
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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8
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Abbott E, Loockerman C, Matz MV. Modifications to gene body methylation do not alter gene expression plasticity in a reef-building coral. Evol Appl 2024; 17:e13662. [PMID: 38390378 PMCID: PMC10883760 DOI: 10.1111/eva.13662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/17/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
As coral reefs continue to decline due to climate change, the role of coral epigenetics (specifically, gene body methylation, GBM) in coral acclimatization warrants investigation. The evidence is currently conflicting. In diverse animal phyla, the baseline GBM level is associated with gene function: continuously expressed "housekeeping" genes are typically highly methylated, while inducible context-dependent genes have low or no methylation at all. Some authors report an association between GBM and the environment and interpret this observation as evidence of the GBM's role in acclimatization. Yet, others argue that the correlation between GBM change and gene expression change is typically absent or negligible. Here, we used the reef-building coral, Acropora millepora, to test whether environmentally driven changes in GBM are associated with a gene's ability to respond to environmental changes (plasticity) rather than expression level. We analyzed two cases of modified gene expression plasticity observed in a 3-week-long heat acclimatization experiment. The first one was a group of heat-induced genes that failed to revert their expression after the coral was translocated back to the control tank. The second case involved genes that changed the magnitude of their response to the daily temperature fluctuations over the course of the experiment. In both cases, we found negligible or no association with GBM change. We conclude that although both gene expression plasticity and GBM can change during acclimatization, there is no direct association between the two. This adds to the increasing volume of evidence that the function of GBM in invertebrates is unrelated to acclimatization on physiological timescales.
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Affiliation(s)
- Evelyn Abbott
- Department of Integrative Biology University of Texas at Austin Austin Texas USA
| | - Coral Loockerman
- University of Hawai'i at Manoa Hawaii Institute of Marine Biology Kaneohe Kaneohe Hawai'i USA
| | - Mikhail V Matz
- Department of Integrative Biology University of Texas at Austin Austin Texas USA
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Cao Y, Xia H, Tan X, Shi C, Ma Y, Meng D, Zhou M, Lv Z, Wang S, Jin Y. Intratumoural microbiota: a new frontier in cancer development and therapy. Signal Transduct Target Ther 2024; 9:15. [PMID: 38195689 PMCID: PMC10776793 DOI: 10.1038/s41392-023-01693-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/20/2023] [Accepted: 10/24/2023] [Indexed: 01/11/2024] Open
Abstract
Human microorganisms, including bacteria, fungi, and viruses, play key roles in several physiological and pathological processes. Some studies discovered that tumour tissues once considered sterile actually host a variety of microorganisms, which have been confirmed to be closely related to oncogenesis. The concept of intratumoural microbiota was subsequently proposed. Microbiota could colonise tumour tissues through mucosal destruction, adjacent tissue migration, and hematogenic invasion and affect the biological behaviour of tumours as an important part of the tumour microenvironment. Mechanistic studies have demonstrated that intratumoural microbiota potentially promote the initiation and progression of tumours by inducing genomic instability and mutations, affecting epigenetic modifications, promoting inflammation response, avoiding immune destruction, regulating metabolism, and activating invasion and metastasis. Since more comprehensive and profound insights about intratumoral microbiota are continuously emerging, new methods for the early diagnosis and prognostic assessment of cancer patients have been under examination. In addition, interventions based on intratumoural microbiota show great potential to open a new chapter in antitumour therapy, especially immunotherapy, although there are some inevitable challenges. Here, we aim to provide an extensive review of the concept, development history, potential sources, heterogeneity, and carcinogenic mechanisms of intratumoural microorganisms, explore the potential role of microorganisms in tumour prognosis, and discuss current antitumour treatment regimens that target intratumoural microorganisms and the research prospects and limitations in this field.
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Affiliation(s)
- Yaqi Cao
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, Key Laboratory of Respiratory Diseases of National Health Commission, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Hui Xia
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, Key Laboratory of Respiratory Diseases of National Health Commission, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Xueyun Tan
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, Key Laboratory of Respiratory Diseases of National Health Commission, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Chunwei Shi
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Yanling Ma
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, Key Laboratory of Respiratory Diseases of National Health Commission, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Daquan Meng
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, Key Laboratory of Respiratory Diseases of National Health Commission, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Mengmeng Zhou
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, Key Laboratory of Respiratory Diseases of National Health Commission, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Zhilei Lv
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, Key Laboratory of Respiratory Diseases of National Health Commission, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Sufei Wang
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, Key Laboratory of Respiratory Diseases of National Health Commission, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China.
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China.
- Hubei Province Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China.
| | - Yang Jin
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, Key Laboratory of Respiratory Diseases of National Health Commission, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China.
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China.
- Hubei Province Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China.
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10
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Zhang M, Huang H, Wei M, Sun M, Deng G, Hu S, Wang H, Gong Y. Overexpression of BRD4 in Gastric Cancer and its Clinical Significance as a Novel Therapeutic Target. Curr Cancer Drug Targets 2024; 24:167-177. [PMID: 37282642 DOI: 10.2174/1568009623666230606164030] [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: 12/25/2022] [Revised: 04/24/2023] [Accepted: 05/09/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND BRD4 is a member of the bromodomain and extra terminal domain (BET) family of proteins, containing two bromodomains and one extra terminal domain, and is overexpressed in several human malignancies. However, its expression in gastric cancer has not yet been well illustrated. OBJECTIVE This study aimed to elucidate the overexpression of BRD4 in gastric cancer and its clinical significance as a novel therapeutic target. METHODS Fresh gastric cancer tissues and paraffin-embedded specimens of gastric cancer patients were collected, and the BRD4 expression was examined by Western Blot Analysis (WB) and Immunohistochemistry Analysis (IHC), respectively. The possible relationship between BRD4 expression and the clinicopathological features as well as survival in gastric cancer patients was analyzed. The effect of BRD4 silencing on human gastric cancer cell lines was investigated by MTT assay, WB, wound healing assay, and Transwell invasion. RESULTS The results showed that the expression level in tumor tissues and adjacent tissues was significantly higher than that in normal tissues, respectively (P < 0.01). BRD4 expression level in gastric cancer tissues was strongly correlated with the degree of tumor differentiated degree (P = 0.033), regional lymph nodes metastasis (P = 0.038), clinical staging (P = 0.002), and survival situation (P = 0.000), while the gender (P = 0.564), age (P = 0.926) and infiltrating depth (P = 0.619) of patients were not associated. Increased BRD4 expression resulted in poor overall survival (P = 0.003). In in vitro assays, BRD4 small interfering RNA resulted in significantly decreased BRD4 protein expression, therefore inhibiting proliferation, migration, and invasion of gastric cancer cells. CONCLUSION BRD4 might be a novel biomarker for the early diagnosis, prognosis, and therapeutic target in gastric cancer.
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Affiliation(s)
- Mengying Zhang
- Department of Pharmacy, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Hong Huang
- Department of Pharmacy, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Meijiao Wei
- Department of Pharmacy, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Mengjia Sun
- Department of Pharmacy, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Guojin Deng
- Department of Gastrointestinal Surgery, the People's Hospital of Jimo, Qingdao, China
| | - Shuiqing Hu
- Department of Gastrointestinal Surgery, the People's Hospital of Jimo, Qingdao, China
| | - Hongbo Wang
- Department of Gastrointestinal Surgery, the People's Hospital of Jimo, Qingdao, China
| | - Yanling Gong
- Department of Pharmacy, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, China
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11
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Singh PR, Dadireddy V, Udupa S, Kalladi SM, Shee S, Khosla S, Rajmani RS, Singh A, Ramakumar S, Nagaraja V. The Mycobacterium tuberculosis methyltransferase Rv2067c manipulates host epigenetic programming to promote its own survival. Nat Commun 2023; 14:8497. [PMID: 38129415 PMCID: PMC10739865 DOI: 10.1038/s41467-023-43940-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
Mycobacterium tuberculosis has evolved several mechanisms to counter host defense arsenals for its proliferation. Here we report that M. tuberculosis employs a multi-pronged approach to modify host epigenetic machinery for its survival. It secretes methyltransferase (MTase) Rv2067c into macrophages, trimethylating histone H3K79 in a non-nucleosomal context. Rv2067c downregulates host MTase DOT1L, decreasing DOT1L-mediated nucleosomally added H3K79me3 mark on pro-inflammatory response genes. Consequent inhibition of caspase-8-dependent apoptosis and enhancement of RIPK3-mediated necrosis results in increased pathogenesis. In parallel, Rv2067c enhances the expression of SESTRIN3, NLRC3, and TMTC1, enabling the pathogen to overcome host inflammatory and oxidative responses. We provide the structural basis for differential methylation of H3K79 by Rv2067c and DOT1L. The structures of Rv2067c and DOT1L explain how their action on H3K79 is spatially and temporally separated, enabling Rv2067c to effectively intercept the host epigenetic circuit and downstream signaling.
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Affiliation(s)
- Prakruti R Singh
- Department of Microbiology & Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
- Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | | | - Shubha Udupa
- Department of Microbiology & Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Shashwath Malli Kalladi
- Department of Microbiology & Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Somnath Shee
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Sanjeev Khosla
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh (CSIR -IMTech), Chandigarh, India
| | - Raju S Rajmani
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Amit Singh
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | | | - Valakunja Nagaraja
- Department of Microbiology & Cell Biology, Indian Institute of Science (IISc), Bengaluru, India.
- Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India.
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12
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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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13
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Barbachowska M, Arimondo PB. To target or not to target? The role of DNA and histone methylation in bacterial infections. Epigenetics 2023; 18:2242689. [PMID: 37731322 PMCID: PMC10515666 DOI: 10.1080/15592294.2023.2242689] [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: 12/16/2022] [Accepted: 07/25/2023] [Indexed: 09/22/2023] Open
Abstract
Epigenetics describes chemical modifications of the genome that do not alter DNA sequence but participate in the regulation of gene expression and cellular processes such as proliferation, division, and differentiation of eukaryotic cell. Disruption of the epigenome pattern in a human cell is associated with different diseases, including infectious diseases. During infection pathogens induce epigenetic modifications in the host cell. This can occur by controlling expression of genes involved in immune response. That enables bacterial survival and replication within the host and evasion of the immune response. Methylation is an example of epigenetic modification that occurs on DNA and histones. Reasoning that DNA and histone methylation of human host cells plays a crucial role during pathogenesis, these modifications are promising targets for the development of alternative treatment strategies in infectious diseases. Here, we discuss the role of DNA and histone methyltransferases in human host cell upon bacterial infections. We further hypothesize that compounds targeting methyltransferases are tools to study epigenetics in the context of host-pathogen interactions and can open new avenues for the treatment of bacterial infections.
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Affiliation(s)
- Magdalena Barbachowska
- Institut Pasteur, Université Paris Cité, CNRS UMR n°3523 Chem4Life, Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Paris, France
- Universite Paris Cité, Ecole Doctorale MTCI, Paris, France
- Institut Pasteur, Pasteur- Paris University (PPU)- Oxford International Doctoral Program, Paris, France
| | - Paola B. Arimondo
- Institut Pasteur, Université Paris Cité, CNRS UMR n°3523 Chem4Life, Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Paris, France
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14
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Shad NS, Shaikh NI, Cunningham SA. Migration Spurs Changes in the Human Microbiome: a Review. J Racial Ethn Health Disparities 2023:10.1007/s40615-023-01813-0. [PMID: 37843778 DOI: 10.1007/s40615-023-01813-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023]
Abstract
International migration often results in major changes in living environments and lifestyles, and these changes may lead to the observed increases in obesity and diabetes among foreign-born people after resettling in higher-income countries. A possible mechanism linking changes in living environments to the onset of health conditions may be changes in the microbiome. Previous research has shown that unfavorable changes in the composition of the microbiome can increase disposition to diseases such as diabetes, obesity, kidney disease, and inflammatory bowel disease. We investigated the relationship between human migration and microbiome composition through a review using microbiome- and migration-related search terms in PubMed and Web of Science. We included articles examining the gut, oral, or oropharyngeal microbiome in people who migrated internationally. Nine articles met eligibility criteria. All but one examined migration from a non-Western to a Western country. Four of these found a difference in the microbiome of migrants compared with non-migrating residents of their country of birth, seven found differences in the microbiome of migrants compared with the native-born population in the country of resettlement, and five found microbiome differences associated with duration of stay in the country of resettlement. Microbiome composition varies with country of birth, age at migration, time since immigration, and country of resettlement. The results suggest that migration may lead to changes in the microbiome; thus, microbiome characteristics are a plausible pathway to examine changes in health after resettlement in a new country.
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Affiliation(s)
| | - Nida I Shaikh
- Department of Nutrition, Georgia State University, Atlanta, GA, USA
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15
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Cossart P. Raising a Bacterium to the Rank of a Model System: The Listeria Paradigm. Annu Rev Microbiol 2023; 77:1-22. [PMID: 37713460 DOI: 10.1146/annurev-micro-110422-112841] [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] [Indexed: 09/17/2023]
Abstract
My scientific career has resulted from key decisions and reorientations, sometimes taken rapidly but not always, guided by discussions or collaborations with amazing individuals from whom I learnt a lot scientifically and humanly. I had never anticipated that I would accomplish so much in what appeared as terra incognita when I started to interrogate the mechanisms underlying the virulence of the bacterium Listeria monocytogenes. All this has been possible thanks to a number of talented team members who ultimately became friends.
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Affiliation(s)
- Pascale Cossart
- Department of Cell Biology and Infection, Institut Pasteur, Paris, France;
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16
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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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17
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Wrede D, Bordak M, Abraham Y, Mehedi M. Pulmonary Pathogen-Induced Epigenetic Modifications. EPIGENOMES 2023; 7:13. [PMID: 37489401 PMCID: PMC10366755 DOI: 10.3390/epigenomes7030013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/26/2023] Open
Abstract
Epigenetics generally involves genetic control by factors other than our own DNA sequence. Recent research has focused on delineating the mechanisms of two major epigenetic phenomena: DNA methylation and histone modification. As epigenetics involves many cellular processes, it is no surprise that it can also influence disease-associated gene expression. A direct link between respiratory infections, host cell epigenetic regulations, and chronic lung diseases is still unknown. Recent studies have revealed bacterium- or virus-induced epigenetic changes in the host cells. In this review, we focused on respiratory pathogens (viruses, bacteria, and fungi) induced epigenetic modulations (DNA methylation and histone modification) that may contribute to lung disease pathophysiology by promoting host defense or allowing pathogen persistence.
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Affiliation(s)
| | | | | | - Masfique Mehedi
- School of Medicine & Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (D.W.); (M.B.); (Y.A.)
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18
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Ogrodnik M, Gladyshev VN. The meaning of adaptation in aging: insights from cellular senescence, epigenetic clocks and stem cell alterations. NATURE AGING 2023; 3:766-775. [PMID: 37386259 DOI: 10.1038/s43587-023-00447-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 05/30/2023] [Indexed: 07/01/2023]
Abstract
With recent rapid progress in research on aging, there is increasing evidence that many features commonly considered to be mechanisms or drivers of aging in fact represent adaptations. Here, we examine several such features, including cellular senescence, epigenetic aging and stem cell alterations. We draw a distinction between the causes and consequences of aging and define short-term consequences as 'responses' and long-term ones as 'adaptations'. We also discuss 'damaging adaptations', which despite having beneficial effects in the short term, lead to exacerbation of the initial insult and acceleration of aging. Features commonly recognized as 'basic mechanisms of the aging process' are critically examined for the possibility of their adaptation-driven emergence from processes such as cell competition and the wound-like features of the aging body. Finally, we speculate on the meaning of these interactions for the aging process and their relevance for the development of antiaging interventions.
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Affiliation(s)
- Mikolaj Ogrodnik
- Ludwig Boltzmann Research Group Senescence and Healing of Wounds, Vienna, Austria.
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Austrian Workers' Compensation Board Research Center, Vienna, Austria.
- Austrian Cluster for Tissue Regeneration, Vienna, Austria.
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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19
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Chen X, Pacis A, Aracena KA, Gona S, Kwan T, Groza C, Lin YL, Sindeaux R, Yotova V, Pramatarova A, Simon MM, Pastinen T, Barreiro LB, Bourque G. Transposable elements are associated with the variable response to influenza infection. CELL GENOMICS 2023; 3:100292. [PMID: 37228757 PMCID: PMC10203045 DOI: 10.1016/j.xgen.2023.100292] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 11/15/2022] [Accepted: 03/06/2023] [Indexed: 05/27/2023]
Abstract
Influenza A virus (IAV) infections are frequent every year and result in a range of disease severity. Here, we wanted to explore the potential contribution of transposable elements (TEs) to the variable human immune response. Transcriptome profiling in monocyte-derived macrophages from 39 individuals following IAV infection revealed significant inter-individual variation in viral load post-infection. Using transposase-accessible chromatin using sequencing (ATAC-seq), we identified a set of TE families with either enhanced or reduced accessibility upon infection. Of the enhanced families, 15 showed high variability between individuals and had distinct epigenetic profiles. Motif analysis showed an association with known immune regulators (e.g., BATFs, FOSs/JUNs, IRFs, STATs, NFkBs, NFYs, and RELs) in stably enriched families and with other factors in variable families, including KRAB-ZNFs. We showed that TEs and host factors regulating TEs were predictive of viral load post-infection. Our findings shed light on the role TEs and KRAB-ZNFs may play in inter-individual variation in immunity.
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Affiliation(s)
- Xun Chen
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Alain Pacis
- Canadian Center for Computational Genomics, McGill University, Montréal, QC H3A 0G1, Canada
| | | | - Saideep Gona
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Tony Kwan
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC H3A 0G1, Canada
| | - Cristian Groza
- Quantitative Life Science, McGill University, Montréal, QC H3A 1E3, Canada
| | - Yen Lung Lin
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Renata Sindeaux
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Vania Yotova
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Albena Pramatarova
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC H3A 0G1, Canada
| | - Marie-Michelle Simon
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC H3A 0G1, Canada
| | - Tomi Pastinen
- Genomic Medicine Center, Children’s Mercy Hospital and Research Institute, Kansas City, MO 64108, USA
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Luis B. Barreiro
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Guillaume Bourque
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
- Canadian Center for Computational Genomics, McGill University, Montréal, QC H3A 0G1, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC H3A 0G1, Canada
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
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20
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Mohanty S, White JK, Brauner A. Epigenetic modifications influence urinary tract infection outcome. Nat Microbiol 2023; 8:764-766. [PMID: 37069403 DOI: 10.1038/s41564-023-01371-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Affiliation(s)
- Soumitra Mohanty
- Department of Microbiology, Tumor and Cell Biology, Division of Clinical Microbiology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - John Kerr White
- Department of Microbiology, Tumor and Cell Biology, Division of Clinical Microbiology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Annelie Brauner
- Department of Microbiology, Tumor and Cell Biology, Division of Clinical Microbiology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.
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21
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Debnath M, Berk M. Is paternal immune activation just as important as maternal immune activation? Time to rethink the bi-parental immune priming of neurodevelopmental model of schizophrenia. Med Hypotheses 2023. [DOI: 10.1016/j.mehy.2023.111059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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22
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Terletsky A, Akhmerova LG. Malignant human thyroid neoplasms associated with blood parasitic (haemosporidian) infection. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2023. [DOI: 10.15789/2220-7619-mht-1948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Investigation of archival cytological material obtained by cytologists during fine-needle aspiration biopsy in follicular, papillary, and medullary human thyroid cancers revealed haemosporidian (blood parasitic) infection. Haemosporidian infection was detected as exo- and intraerythrocytic stages of development in thyrocytes schizogony. The exoerythrocytic stage of development is represented as microschizonts in a thyroid needle biopsy specimen. Probably, blood parasitic infection is the common etiology for these pathologies. All biopsy material in medical laboratories was stained with RomanowskyGiemsa stain. To clarify the localization of nuclei (DNA) of thyrocytes and nuclei (DNA) of haemosporidian infection in cytological material following investigation of the entire set of smears, a selective series of original archival smears was stained (restained) with a Feulgen/Schiff reagent. Staining of smears with RomanowskyGiemsa stain is an adsorption method that enables re-use of the same smears for staining with a Feulgen/Schiff reagent where the fuchsin dye, after DNA hydrolysis by hydrochloric acid, is incorporated into DNA and stains it in redviolet (crimsonlilac) color. An intentionally unstained protoplasm of blood parasitic infection was present as a light band around erythrocyte nuclei. In follicular thyroid cancer, Feulgen staining of thyrocytes revealed nuclear DNA and parasitic DNA (haemosporidium nuclei) as point inclusions and rings and diffusely distributed in the thyrocyte cytoplasm. The thyrocyte cytoplasm and nuclei were vacuolated, with thyrocyte nuclei being deformed, flattened, and displaced to the cell periphery. The erythrocytes, which were initially stained with eosin (orange color), contained haemosporidian nuclei (DNA). In some cases, endoglobular inclusions in thyrocytes and erythrocytes were of the same size. In papillary thyroid cancer, we were able to localize the nuclear DNA of thyrocytes and the parasitic DNA as point inclusions and diffusely distributed in the thyrocyte cytoplasm. Two or more polymorphic nuclei may eccentrically occur in the hyperplastic cytoplasm. Haemosporidian microschizonts occurred circumnuclearly in thyrocytes and as an exoerythrocytic stage in the blood. The erythrocyte cytoplasm contained redviolet polymorphic haemosporidian nuclei (DNA). In medullary thyroid cancer, the hyperplastic cytoplasm of thyrocytes contained eccentrically located nuclei (DNA) of thyrocytes and small haemosporidian nuclei (DNA), which may occupy the whole thyrocyte. There were thyrocytes with vacuolated cytoplasm and pronounced nuclear polymorphism. The size of hyperplastic nuclei was several times larger than that of normal thyrocyte nuclei. The color of stained cytoplasmic and nuclear vacuoles of thyrocytes was less redviolet compared with that of surrounding tissues, which probably indicates the presence of parasitic DNA in them. The haemosporidian nuclear material in erythrocytes is represented by polymorphic nuclei, which may indicate the simultaneous presence of different pathogen species and/or generations in the blood. Intracellular parasitism of haemosporidian infection in thyrocytes (schizogony) associated with three thyroid cancers leads to pronounced cytoplasmic hyperplasia, cytoplasmic vacuolization, and nuclear vacuolization of the thyrocyte, followed by impaired secretory function. Multinucleated thyrocytes with incomplete cytokinesis appear. The absence of lytic death of the affected thyrocytes indicates that the contagium is able to control apoptosis and influence physiological functions of the cell. There is deformation of the nuclei, which leads to a decrease in their size, their flattening and displacement to the cell periphery, with high risk of DNA mutations and deletions in affected cells, reaching a neoplastic level.
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23
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Hulme J. Staphylococcus Infection: Relapsing Atopic Dermatitis and Microbial Restoration. Antibiotics (Basel) 2023; 12:antibiotics12020222. [PMID: 36830133 PMCID: PMC9952585 DOI: 10.3390/antibiotics12020222] [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: 12/15/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Atopic Dermatitis (AD) skin is susceptible to Staphylococcus aureus (SA) infection, potentially exposing it to a plethora of toxins and virulent determinants, including Panton-Valentine leukocidin (PVL) (α-hemolysin (Hla) and phenol-soluble modulins (PSMs)), and superantigens. Depending on the degree of infection (superficial or invasive), clinical treatments may encompass permanganate (aq) and bleach solutions coupled with intravenous/oral antibiotics such as amoxicillin, vancomycin, doxycycline, clindamycin, daptomycin, telavancin, linezolid, or tigecycline. However, when the skin is significantly traumatized (sheathing of epidermal sections), an SA infection can rapidly ensue, impairing the immune system, and inducing local and systemic AD presentations in susceptible areas. Furthermore, when AD presents systemically, desensitization can be long (years) and intertwined with periods of relapse. In such circumstances, the identification of triggers (stress or infection) and severity of the flare need careful monitoring (preferably in real-time) so that tailored treatments targeting the underlying pathological mechanisms (SA toxins, elevated immunoglobulins, impaired healing) can be modified, permitting rapid resolution of symptoms.
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Affiliation(s)
- John Hulme
- Gachon Bio-Nano Institute, Gachon University, Seongnam-si 461-701, Republic of Korea
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24
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Messman RD, Lemley CO. Bovine neonatal microbiome origins: a review of proposed microbial community presence from conception to colostrum. Transl Anim Sci 2023; 7:txad057. [PMID: 37334245 PMCID: PMC10276551 DOI: 10.1093/tas/txad057] [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: 03/20/2023] [Accepted: 05/24/2023] [Indexed: 06/20/2023] Open
Abstract
In recent years, there has been an influx of research evaluating the roles of the reproductive tract microbiota in modulating reproductive performance. These efforts have resulted in a breadth of research exploring the bovine reproductive tract microbiota. The female reproductive tract microbiota has been characterized during the estrus cycle, at timed artificial insemination, during gestation, and postpartum. Additionally, there are recently published studies investigating in-utero inoculation of the bovine fetus. However, critical review of the literature to understand how the microbial shifts during a dam's lifecycle could impact neonatal outcomes is limited. This review demonstrates a consistency at the phyla level throughout both the maternal, paternal, and neonatal microbiomes. Moreover, this review challenges the current gestational inoculation hypothesis and suggests instead a maturation of the resident uterine microbiota throughout gestation to parturition. Recent literature is indicative of microbial composition influencing metabolomic parameters that have developmental programming effects in feed utilization and metabolic performance later in life. Thus, this review enumerates the potential origins of neonatal microbial inoculation from conception, through gestation, parturition, and colostrum consumption while introducing clear paucities where future research is needed to better understand the ramifications of the reproductive microbiome on neonates.
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Affiliation(s)
- Riley D Messman
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS 39762, USA
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Moslehi Z, Derakhshan R, Chaichian S, Mehdizadeh Kashi A, Sabet B, Rokhgireh S. Correlation of High-Risk Human Papilloma Virus with Deep Endometriosis: A Cross-Sectional Study. BIOMED RESEARCH INTERNATIONAL 2023; 2023:6793898. [PMID: 37082187 PMCID: PMC10113060 DOI: 10.1155/2023/6793898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 02/05/2023] [Accepted: 02/08/2023] [Indexed: 04/22/2023]
Abstract
Background Recently, it has been suggested that microbial infections play a role in the pathogenesis of endometriosis. One of the most commonly suggested infections associated with the pathogenesis of endometriosis is human papillomavirus (HPV) infection. The present study is aimed at evaluating the prevalence, types, and risk factors for HPV infection in women with endometriosis and at investigating the association of upper and lower genital tract involvement with HPV and the severity of endometriosis. Methods This cross-sectional study was conducted on 81 patients with endometriosis, referred to Rasool Akram Medical Complex in Tehran, Iran, for laparoscopic surgery. The patients' demographic, clinical, and anthropometric data were extracted from their medical records, as well as interviews. The stage of disease was scored based on the revised American Society for Reproductive Medicine (rASRM) classification. The HPV-positive and HPV-negative cases were compared using the chi-square test for categorical variables and Student t-test for continuous variables. Results Twenty (24.69%) out of 81 women with endometriosis were infected with HPV (nine cases of pelvic HPV, nine cases of vaginal HPV, and two cases of both pelvic and vaginal HPV). The HPV-infected women had a significantly lower infertility rate (15% vs. 45.9%; P = 0.014). The VAS scores for dysmenorrhea and dyspareunia were relatively the same in the two groups (P > 0.05). HPV 6 and HPV 11 were the most common types of HPV, reported in 35% and 30% of endometriosis cases, respectively. Conclusion The prevalence of HPV was 24.69%, and low-risk genotypes were dominant. No significant association was found between HPV and the severity of endometriosis.
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Affiliation(s)
- Zohreh Moslehi
- Endometriosis Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Roya Derakhshan
- Endometriosis Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Shahla Chaichian
- Endometriosis Research Center, Iran University of Medical Sciences, Tehran, Iran
| | | | - Babak Sabet
- Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Smart University of Medical Sciences, Tehran, Iran
| | - Samaneh Rokhgireh
- Endometriosis Research Center, Iran University of Medical Sciences, Tehran, Iran
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Uzuner C, Mak J, El-Assaad F, Condous G. The bidirectional relationship between endometriosis and microbiome. Front Endocrinol (Lausanne) 2023; 14:1110824. [PMID: 36960395 PMCID: PMC10028178 DOI: 10.3389/fendo.2023.1110824] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/21/2023] [Indexed: 03/09/2023] Open
Abstract
Endometriosis has been described by many different theories of pathogenesis over the years. It is now also appreciated to be a state of chronic inflammation, and the role of immune dysfunction in its development has been proven. There is increasing evidence to support the role of the microbiome in the formation and progression of endometriosis via inflammatory pathways. The dysbiosis seen in endometriosis is thought to be both causative and a consequence of the pathogenesis. Gut, peritoneal fluid and female reproductive tract microbiota has been studied to understand if there are any microbiome signatures specific to endometriosis. New research on how to manipulate the microbiome for better detection and treatment of endometriosis is emerging.
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Affiliation(s)
- Cansu Uzuner
- Endometriosis Ultrasound and Advanced Endosurgery Unit, Sydney Medical School Nepean, University of Sydney, Nepean Hospital, Sydney, NSW, Australia
- *Correspondence: Cansu Uzuner,
| | - Jason Mak
- Endometriosis Ultrasound and Advanced Endosurgery Unit, Sydney Medical School Nepean, University of Sydney, Nepean Hospital, Sydney, NSW, Australia
| | - Fatima El-Assaad
- University of New South Wales Microbiome Research Centre, St. George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - George Condous
- Endometriosis Ultrasound and Advanced Endosurgery Unit, Sydney Medical School Nepean, University of Sydney, Nepean Hospital, Sydney, NSW, Australia
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Hamid Hassan K, Asaad Ebrahim A. Epigenetic effects on broiler exposure to magnetic field on progeny meat production traits. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.04.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
This experiment was conducted to determine the effect of the exposure of Ross 308 broiler breeders to a magnetic field on the meat production traits of progeny. The experimental flock consisted of 60 hens and ten cocks of Ross 308 broiler breeders at 36 weeks of age, divided randomly into four groups; each group applied for treatment with three replicates. The treatments were control (T1), storage of semen in an 803 gauss magnetic field for 24 h (T2), storage of fertilized eggs in a magnetic field of 250 gausses for 72 h before entering the incubator (T3), and exposing individual cages to 250 gausses of magnetic field for 8 Weeks (T4). The progeny result from the broiler breeders groups was recorded for body weight and feed intake, compared with the control (T1). The results showed no significant differences among progeny groups in body weight, weekly weight gain and weekly feed intake during the rearing period.
Keywords: Epigenetic, magnetic broiler breeders, broiler progeny performance
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Mahmoud Ali F, Hamid Hassan K. Epigenetic effects of selenium and vitamin E supplementation in broiler breeder diets on the performance of their progeny. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.04.47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nutritional supplements have been commonly used in the poultry industry last few years. The study aimed to investigate the epigenetic effects of adding vitamin E and organic selenium to the diet of broiler breeders Ross-308 on their progeny meat production performance. The treatments included the control group fed with a standard diet without supplementation (T1), T2 using a standard diet supplemented with 500 mg of vitamin E / kg, T3 using a standard diet supplemented with 0.5 mg of organic selenium (Availa powder) /kg, and T4 using a standard diet supplemented with a mixture of vitamin E and organic selenium in proportions 500 and 0.5 mg/kg respectively. The eggs were collected from each treatment to obtain the progeny reared for 35 periods, and measurements were recorded for meat production and carcass traits. The results showed that the treatments had significant epigenetic effects on body weight at hatching. Hence, T2 had a significantly heavier body weight than T1, while no significant differences were observed between T3 and T4. The result of T2 recorded extremely high feed intake compared with T3. On the other hand, T3 and T4 recorded a hefty weight of breast parts compared with T1 and T2.
In conclusion, organic selenium supplementation led to a significant increase in breast weight and a decrease in thigh part weight compared to the control group. In contrast, vitamin E supplementation led to an increase in chick weight at hatch, a reduction of total mortality and an improvement in feed conversion ratio compared to the control group. This refers to the epigenetic effects of organic selenium and vitamin E on progeny traits when added to the breeder diet.
Keywords: Epigenetics, broiler, selenium supplementation, meat production
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29
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Wang H, Hu J, Wu J, Ji P, Shang A, Li D. The Function and Molecular Mechanism of Commensal Microbiome in Promoting Malignant Progression of Lung Cancer. Cancers (Basel) 2022; 14:5394. [PMID: 36358812 PMCID: PMC9658664 DOI: 10.3390/cancers14215394] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/29/2022] [Accepted: 10/30/2022] [Indexed: 02/03/2024] Open
Abstract
The human commensal microbiome existing in an internal environment is relatively consistent with that of the host. The presence of bacterial dysbiosis, on the other hand, promptly results in the termination of this symbiotic association. The altered microbial structure in the lung may be responsible for the development of lung cancer by controlling the host's inflammatory response and influencing a variety of immunological pathways. More and more studies have pointed to the fact that the commensal microbiota plays a vital role in both the development of tumors and the body's response to lung cancer treatment. Microbiome dysbiosis, genotoxicity, virulence effect, and epigenetic dysregulations are some of the potential mechanisms that may lie behind the process of tumorigenesis that is mediated by microbiome. Other potential mechanisms include regulating host immune activity through a variety of pathogenic factors, dysregulating host metabolism as a result of microbiome alterations, and microbiome dysbiosis. In this historical overview, we go through some of the more recent mechanistic discoveries into the biological processes that are involved in lung cancer that are caused by bacteria. Without a question, obtaining a greater knowledge of the dynamic link between the lung microbiome and lung cancer has the potential to inspire the development of innovative early detection and customized treatment methods for lung cancer.
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Affiliation(s)
| | | | | | | | - Anquan Shang
- Department of Laboratory Medicine, Tongji Hospital of Tongji University School of Medicine, 389 Xincun Road, Shanghai 200065, China
| | - Dong Li
- Department of Laboratory Medicine, Tongji Hospital of Tongji University School of Medicine, 389 Xincun Road, Shanghai 200065, China
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30
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Khan FH, Bhat BA, Sheikh BA, Tariq L, Padmanabhan R, Verma JP, Shukla AC, Dowlati A, Abbas A. Microbiome dysbiosis and epigenetic modulations in lung cancer: From pathogenesis to therapy. Semin Cancer Biol 2022; 86:732-742. [PMID: 34273520 DOI: 10.1016/j.semcancer.2021.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/25/2021] [Accepted: 07/11/2021] [Indexed: 02/07/2023]
Abstract
The lung microbiome plays an essential role in maintaining healthy lung function, including host immune homeostasis. Lung microbial dysbiosis or disruption of the gut-lung axis can contribute to lung carcinogenesis by causing DNA damage, inducing genomic instability, or altering the host's susceptibility to carcinogenic insults. Thus far, most studies have reported the association of microbial composition in lung cancer. Mechanistic studies describing host-microbe interactions in promoting lung carcinogenesis are limited. Considering cancer as a multifaceted disease where epigenetic dysregulation plays a critical role, epigenetic modifying potentials of microbial metabolites and toxins and their roles in lung tumorigenesis are not well studied. The current review explains microbial dysbiosis and epigenetic aberrations in lung cancer and potential therapeutic opportunities.
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Affiliation(s)
- Faizan Haider Khan
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway, Galway, Ireland
| | | | | | - Lubna Tariq
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Roshan Padmanabhan
- Department of Medicine, Case Western Reserve University, and University Hospital, Cleveland, OH, 44106, USA
| | - Jay Prakash Verma
- Institute of Environment and Sustainable Development, Banaras Hindu University Varanasi, India
| | | | - Afshin Dowlati
- Division of Hematology and Oncology, Department of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA; University Hospitals Seidman Cancer Center, Cleveland, OH, 44106, USA; Developmental Therapeutics Program, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44116, USA
| | - Ata Abbas
- Division of Hematology and Oncology, Department of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA; Developmental Therapeutics Program, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44116, USA.
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Mukiibi R, Peñaloza C, Gutierrez A, Yáñez JM, Houston RD, Robledo D. The impact of Piscirickettsia salmonis infection on genome-wide DNA methylation profile in Atlantic Salmon. Genomics 2022; 114:110503. [PMID: 36244592 DOI: 10.1016/j.ygeno.2022.110503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 10/01/2022] [Accepted: 10/12/2022] [Indexed: 11/04/2022]
Abstract
Salmon rickettsial septicaemia (SRS), caused by the bacteria Piscirickettsia salmonis (P. salmonis), is responsible for significant mortality in farmed Atlantic salmon in Chile. Currently there are no effective treatments or preventive measures for this disease, although genetic selection or genome engineering to increase salmon resistance to SRS are promising strategies. The accuracy and efficiency of these strategies are usually influenced by the available biological background knowledge of the disease. The aim of this study was to investigate DNA methylation changes in response to P. salmonis infection in the head kidney and liver tissue of Atlantic salmon, and the interaction between gene expression and DNA methylation in the same tissues. The head kidney and liver methylomes of 66 juvenile salmon were profiled using reduced representation bisulphite sequencing (RRBS), and compared between P. salmonis infected animals (3 and 9 days post infection) and uninfected controls, and between SRS resistant and susceptible fish. Methylation was correlated with matching RNA-Seq data from the same animals, revealing that methylation in the first exon leads to an important repression of gene expression. Head kidney methylation showed a clear response to the infection, associated with immunological processes such as actin cytoskeleton regulation, phagocytosis, endocytosis and pathogen associated pattern receptor signaling. Our results contribute to the growing understanding of the role of methylation in regulation of gene expression and response to infectious diseases and could inform the incorporation of epigenetic markers into genomic selection for disease resistant and the design of diagnostic epigenetic markers to better manage fish health in salmon aquaculture.
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Affiliation(s)
- Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK
| | - Alejandro Gutierrez
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK; Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Chile
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK.
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK.
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Solodneva EV, Kuznetsov SB, Velieva AE, Stolpovsky YA. Molecular-Genetic Bases of Mammary Gland Development Using the Example of Cattle and Other Animal Species: I. Embryonic and Pubertal Developmental Stage. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422080087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Moreira JD, Iakhiaev A, Vankayalapati R, Jung BG, Samten B. Histone Deacetylase-2 Controls IL-1β Production through the Regulation of NLRP3 Expression and Activation in Tuberculosis Infection. iScience 2022; 25:104799. [PMID: 35982796 PMCID: PMC9379586 DOI: 10.1016/j.isci.2022.104799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/11/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022] Open
Abstract
Histone deacetylases (HDACs) are critical immune regulators. However, their roles in interleukin-1β (IL-1β) production remain unclear. By screening 11 zinc-dependent HDACs with chemical inhibitors, we found that HDAC1 inhibitor, 4-(dimethylamino)-N-[6-(hydroxyamino)-6-oxohexyl]-benzamide (DHOB), enhanced IL-1β production by macrophage and dendritic cells upon TLR4 stimulation or Mycobacterium tuberculosis infection through IL-1β maturation via elevated NLRP3 expression, increased cleaved caspase-1, and enhanced ASC oligomerization. DHOB rescued defective IL-1β production by dendritic cells infected with M. tuberculosis with ESAT-6 deletion, a virulence factor shown to activate NLRP3 inflammasome. DHOB increased IL-1β production and NLRP3 expression in a tuberculosis mouse model. Although DHOB inhibited HDAC activities of both HDAC1 and HDAC2 by direct binding, knockdown of HDAC2, but not HDAC1, increased IL-1β production and NLRP3 expression in M. tuberculosis-infected macrophages. These data suggest that HDAC2, but not HDAC1, controls IL-1β production through NLRP3 inflammasome activation, a mechanism with a significance in chronic inflammatory diseases including tuberculosis. HDAC1 inhibitor, DHOB, increased IL-1β production via NLRP3 inflammasome activation DHOB suppressed deacetylase activities of both HDAC1 and HDAC2 by direct interaction Deletion of HDAC2, but not HDAC1, increased IL-β production by increased NLRP3 expression DHOB increased IL-1β and NLRP3 expression in a mouse model of TB infection
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Affiliation(s)
- Jôsimar Dornelas Moreira
- Department of Pulmonary Immunology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Alexei Iakhiaev
- Division of Natural & Computational Sciences, Texas College, 2404 North Grand Avenue, Tyler, TX 75702, USA
| | - Ramakrishna Vankayalapati
- Department of Pulmonary Immunology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Bock-Gie Jung
- Department of Pulmonary Immunology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Buka Samten
- Department of Pulmonary Immunology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
- Corresponding author
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Sankar S, Maruthai K, Zachariah B, Bethou A. Global DNA hypomethylation and the expression profile of DNA methyltransferase genes in late-onset neonatal sepsis. Epigenomics 2022; 14:671-682. [PMID: 35587102 DOI: 10.2217/epi-2022-0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Infectious organisms tend to cause DNA methylation changes. Thus, this paper aims to study global DNA methylation and the expression of DNA methyltransferase (DNMT) genes in late-onset neonatal sepsis (LONS). Methods: Global and Alu DNA methylation and expression levels of DNMT were performed using 5mc ELISA, methylation-specific PCR and quantitative real-time-PCR, respectively for LONS and controls. Results: Significant hypomethylation of global DNA and Alu DNA methylation and lower expression of DNMT1 and DNMT3a were observed in LONS compared with controls. Receiver operating characteristic analysis of global and Alu DNA methylation showed good discrimination for the identification of LONS. Conclusion: The hypomethylation of global DNA and Alu elements is evident in neonates with LONS. This may be clinically useful for the prognosis of LONS.
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Affiliation(s)
- Saranya Sankar
- Department of Neonatology, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Puducherry, 605011, India
| | - Kathirvel Maruthai
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Puducherry, 605011, India.,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30605, USA
| | - Bobby Zachariah
- Department of Biochemistry, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Puducherry, 605011, India
| | - Adhisivam Bethou
- Department of Neonatology, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Puducherry, 605011, India
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Bordagaray MJ, Fernández A, Astorga J, Garrido M, Hernández P, Chaparro A, Lira MJ, Gebicke-Haerter P, Hernández M. CpG Single-Site Methylation Regulates TLR2 Expression in Proinflammatory PBMCs From Apical Periodontitis Individuals. Front Immunol 2022; 13:861665. [PMID: 35300329 PMCID: PMC8921253 DOI: 10.3389/fimmu.2022.861665] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/09/2022] [Indexed: 12/19/2022] Open
Abstract
Introduction Apical periodontitis (AP) is a common oral disease caused by the inflammatory destruction of the periapical tissues due to the infection of the root canal system of the tooth. It also contributes to systemic bacterial translocation, where peripheric mononuclear blood cells (PBMCs) can act as carriers. Toll-like receptor (TLR) 2 mediates the response to infection and activates inflammatory responses. DNA methylation can be induced by bacteria and contributes to the modulation of this response. Despite the evidence that supports the participation of PBMCs in immune-inflammatory disorders, the inflammatory profile and epigenetic regulatory mechanisms of PBMCs in AP individuals are unknown. Aim To determine TLR2 gene methylation and inflammatory profiles of PBMCs in AP. Methods Cross-sectional exploratory study. Otherwise, healthy individuals with AP (n=27) and controls (n=30) were included. PMBCs were isolated by a Ficoll gradient, cultured for 24 hours, and both RNA and DNA were extracted. DNA was bisulfite-treated, and specific sites at the promoter region of the TLR2 gene were amplified by qPCR using validated primers. To verify its amplification, agarose gels were performed. Then, the PCR product was sequenced. mRNA expression of TLR2 was determined by qPCR. The soluble levels of 105 inflammatory mediators were first explored with Proteome Profiler Human Cytokine Array Kit. Consequently, tumor necrosis factor (TNF)-α, interleukin (IL)-6, IL-10, IL-6Rα, IL-1β, and IL-12p70 levels were measured by Multiplex assay. Results PBMCs from individuals with AP demonstrated a proinflammatory profile showing higher soluble levels of TNF-α, IL-6, and IL-1β compared to controls (p<0.05). Higher TLR2 expression and higher global methylation pattern of the promoter region of the gene were found in AP compared to controls (p<0.05). The CpGs single-sites at positions -166 and -146 were completely methylated, while the site -102 was totally unmethylated, independently of the presence of AP. DNA methylation of CpG single-sites in positions -77 and +24 was positively associated with TLR2 expression. Conclusions PBMCs from AP subjects show a hyperinflammatory phenotype and TLR2 upregulation in association with single CpG-sites’ methylation from the TLR2 gene promoter, thereby contributing to a sustained systemic inflammatory load in individuals with periapical endodontic diseases.
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Affiliation(s)
- María José Bordagaray
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile.,Department of Conservative Dentistry, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - Alejandra Fernández
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile.,Faculty of Dentistry, Universidad Andres Bello, Santiago, Chile
| | - Jessica Astorga
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - Mauricio Garrido
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile.,Department of Conservative Dentistry, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - Patricia Hernández
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile.,Department of Conservative Dentistry, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - Alejandra Chaparro
- Department of Periodontology, Faculty of Dentistry, Centro de Investigación e Innovación Biomédica (CIIB), Universidad de Los Andes, Santiago, Chile
| | - María Jesús Lira
- Department of Orthopedic Surgery, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Peter Gebicke-Haerter
- Institute of Psychopharmacology, Central Institute of Mental Health, Faculty of Medicine, University of Heidelberg, Mannheim, Germany
| | - Marcela Hernández
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile.,Department of Pathology and Oral Medicine, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
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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.
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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,
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Barone S, Cassese E, Alfano AI, Brindisi M, Summa V. Chasing a Breath of Fresh Air in Cystic Fibrosis (CF): Therapeutic Potential of Selective HDAC6 Inhibitors to Tackle Multiple Pathways in CF Pathophysiology. J Med Chem 2022; 65:3080-3097. [PMID: 35148101 PMCID: PMC8883472 DOI: 10.1021/acs.jmedchem.1c02067] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
Compelling new support
has been provided for histone deacetylase
isoform 6 (HDAC6) as a common thread in the generation of the dysregulated
proinflammatory and fibrotic phenotype in cystic fibrosis (CF). HDAC6
also plays a crucial role in bacterial clearance or killing as a direct
consequence of its effects on CF immune responses. Inhibiting HDAC6
functions thus eventually represents an innovative and effective strategy
to tackle multiple aspects of CF-associated lung disease. In this
Perspective, we not only showcase the latest evidence linking HDAC(6)
activity and expression with CF phenotype but also track the new dawn
of HDAC(6) modulators in CF and explore potentialities and future
perspectives in the field.
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Affiliation(s)
- Simona Barone
- Department of Pharmacy, Department of Excellence 2018-2022, School of Medicine and Surgery, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
| | - Emilia Cassese
- Department of Pharmacy, Department of Excellence 2018-2022, School of Medicine and Surgery, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
| | - Antonella Ilenia Alfano
- Department of Pharmacy, Department of Excellence 2018-2022, School of Medicine and Surgery, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
| | - Margherita Brindisi
- Department of Pharmacy, Department of Excellence 2018-2022, School of Medicine and Surgery, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
| | - Vincenzo Summa
- Department of Pharmacy, Department of Excellence 2018-2022, School of Medicine and Surgery, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
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Capparelli R, Iannelli D. Epigenetics and Helicobacter pylori. Int J Mol Sci 2022; 23:ijms23031759. [PMID: 35163679 PMCID: PMC8836069 DOI: 10.3390/ijms23031759] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/21/2022] [Accepted: 02/01/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetics regulates gene expression, cell type development during differentiation, and the cell response to environmental stimuli. To survive, bacteria need to evade the host immune response. Bacteria, including Helicobacter pylori (Hp), reach this target epigenetically, altering the chromatin of the host cells, in addition to several more approaches, such as DNA mutation and recombination. This review shows that Hp prevalently silences the genes of the human gastric mucosa by DNA methylation. Epigenetics includes different mechanisms. However, DNA methylation persists after DNA replication and therefore is frequently associated with the inheritance of repressed genes. Chromatin modification can be transmitted to daughter cells leading to heritable changes in gene expression. Aberrant epigenetic alteration of the gastric mucosa DNA remains the principal cause of gastric cancer. Numerous methylated genes have been found in cancer as well as in precancerous lesions of Hp-infected patients. These methylated genes inactivate tumor-suppressor genes. It is time for us to complain about our genetic and epigenetic makeups for our diseases.
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Castro-Leyva V, Arenas-Huertero F, Espejel-Núñez A, Giono Cerezo S, Flores-Pliego A, Espino Y Sosa S, Reyes-Muñoz E, Vadillo-Ortega F, Borboa-Olivares H, Camacho-Arroyo I, Estrada-Gutierrez G. miR-21 differentially regulates IL-1β and IL-10 expression in human decidual cells infected with streptococcus B. Reprod Biol 2022; 22:100604. [PMID: 35033900 DOI: 10.1016/j.repbio.2022.100604] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 12/09/2021] [Accepted: 01/02/2022] [Indexed: 11/16/2022]
Abstract
Intrauterine infections caused by bacteria like group B streptococcus (GBS) and the subsequent activation of the maternal inflammatory response have been long suspected to be the underlying cause of preterm labor. The inflammatory network triggered by maternal decidua has been widely described and includes the secretion of pro- and anti-inflammatory cytokines as IL-1β and IL-10; however, the mechanisms that regulate their secretion have not been completely elucidated. MicroRNAs (miRNAs) are critical modulators of the inflammatory response by regulating cytokine expression in several cell types. Here, we explored the role of miR-21 in the expression of IL-1β and IL-10 in human decidual stromal cells (DSCs) exposed in vitro to GBS. We observed that IL1B and IL10 expression at the mRNA level was increased in DSCs after GBS infection. IL-10 but not IL-1β secretion was detected in the culture supernatants. We found a higher miR-21 expression (22-fold) in infected DSCs as compared with non-infected cells. miR-21 functional analysis revealed that DSCs transfected with an antagomiR vs. miR-21 significantly increased the secretion of IL-1β but decreased that of IL-10 in DSCs cells infected with GBS. Our results suggest that miR-21 participates in balancing the inflammatory response in infected decidua through at least IL-1β and IL-10 regulation. This is the first study attributing a functional role of miR-21 in the regulation of key molecules involved in the inflammatory response in infected DSCs, providing new insights into the epigenetic control of human decidual inflammation.
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Affiliation(s)
- Violeta Castro-Leyva
- Department of Immunobiochemistry, Instituto Nacional de Perinatología, Mexico City, Mexico; Posgrado en Ciencias Químico-Biológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, 11340, Mexico
| | - Francisco Arenas-Huertero
- Laboratorio de Investigación en Patología Experimental, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Aurora Espejel-Núñez
- Department of Immunobiochemistry, Instituto Nacional de Perinatología, Mexico City, Mexico
| | - Silvia Giono Cerezo
- Posgrado en Ciencias Químico-Biológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, 11340, Mexico
| | - Arturo Flores-Pliego
- Department of Immunobiochemistry, Instituto Nacional de Perinatología, Mexico City, Mexico
| | | | - Enrique Reyes-Muñoz
- Coordination of Gynecologic and Perinatal Endocrinology, Instituto Nacional de Perinatología, Mexico City, Mexico
| | - Felipe Vadillo-Ortega
- UNAM School of Medicine Branch, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Héctor Borboa-Olivares
- Community Interventions Research Branch, Instituto Nacional de Perinatología, Mexico City, Mexico
| | - Ignacio Camacho-Arroyo
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Destoumieux-Garzón D, Matthies-Wiesler F, Bierne N, Binot A, Boissier J, Devouge A, Garric J, Gruetzmacher K, Grunau C, Guégan JF, Hurtrez-Boussès S, Huss A, Morand S, Palmer C, Sarigiannis D, Vermeulen R, Barouki R. Getting out of crises: Environmental, social-ecological and evolutionary research is needed to avoid future risks of pandemics. ENVIRONMENT INTERNATIONAL 2022; 158:106915. [PMID: 34634622 PMCID: PMC8500703 DOI: 10.1016/j.envint.2021.106915] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 05/05/2023]
Abstract
The implementation of One Health/EcoHealth/Planetary Health approaches has been identified as key (i) to address the strong interconnections between risk for pandemics, climate change and biodiversity loss and (ii) to develop and implement solutions to these interlinked crises. As a response to the multiple calls from scientists on that subject, we have here proposed seven long-term research questions regarding COVID-19 and emerging infectious diseases (EIDs) that are based on effective integration of environmental, ecological, evolutionary, and social sciences to better anticipate and mitigate EIDs. Research needs cover the social ecology of infectious disease agents, their evolution, the determinants of susceptibility of humans and animals to infections, and the human and ecological factors accelerating infectious disease emergence. For comprehensive investigation, they include the development of nature-based solutions to interlinked global planetary crises, addressing ethical and philosophical questions regarding the relationship of humans to nature and regarding transformative changes to safeguard the environment and human health. In support of this research, we propose the implementation of innovative multidisciplinary facilities embedded in social ecosystems locally: ecological health observatories and living laboratories. This work was carried out in the frame of the European Community project HERA (www.HERAresearchEU.eu), which aims to set priorities for an environment, climate and health research agenda in the European Union by adopting a systemic approach in the face of global environmental change.
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Affiliation(s)
| | - Franziska Matthies-Wiesler
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Germany.
| | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Aurélie Binot
- Animals, health, Territories, Risks and Ecosystem (ASTRE), University of Montpellier, Agricultural Research for Development (CIRAD), National Research Institute for Agriculture, Food and the Environment (INRAE), Montpellier, France
| | - Jérôme Boissier
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | | | - Jeanne Garric
- Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), UR Riverly, F-69625 Villeurbanne, France
| | - Kim Gruetzmacher
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin Germany
| | - Christoph Grunau
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - Jean-François Guégan
- Animals, health, Territories, Risks and Ecosystem (ASTRE), University of Montpellier, Agricultural Research for Development (CIRAD), National Research Institute for Agriculture, Food and the Environment (INRAE), Montpellier, France; MIVEGEC, Univ Montpellier, IRD, CNRS, Montpellier, France
| | - Sylvie Hurtrez-Boussès
- MIVEGEC, Univ Montpellier, IRD, CNRS, Montpellier, France; Département de Biologie-Ecologie, Faculté des Sciences, Univ Montpellier, Montpellier, France
| | | | - Serge Morand
- Centre National de la Recherche Scientifique - UMR ASTRE, CIRAD, INRAE - Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Clare Palmer
- Department of Philosophy, YMCA Building, Texas A&M University, College Station, TX 77843, USA
| | - Denis Sarigiannis
- Aristotle University of Thessaloniki, Thessaloniki 54164, Greece; University School for Advanced Study IUSS, Pavia, Italy
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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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Lecoeur H, Prina E, Gutiérrez-Sanchez M, Späth GF. Going ballistic: Leishmania nuclear subversion of host cell plasticity. Trends Parasitol 2021; 38:205-216. [PMID: 34666937 DOI: 10.1016/j.pt.2021.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 12/16/2022]
Abstract
Intracellular parasites have evolved intricate strategies to subvert host cell functions for their own survival. These strategies are particularly damaging to the host if the infection involves immune cells, as illustrated by protozoan parasites of the genus Leishmania that thrive inside mononuclear phagocytic cells, causing devastating immunopathologies. While the impact of Leishmania infection on host cell phenotype and functions has been well documented, the regulatory mechanisms underlying host cell subversion were only recently investigated. Here we summarize the current knowledge on how Leishmania infection affects host nuclear activities and propose thought-provoking new concepts on the reciprocal relationship between epigenetic and transcriptional regulation in host cell phenotypic plasticity, its potential subversion by the intracellular parasite, and its relevance for host-directed therapy.
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Affiliation(s)
- Hervé Lecoeur
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | - Eric Prina
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | - Maria Gutiérrez-Sanchez
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France; UMR 8076 CNRS BioCIS, Université Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Gerald F Späth
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France.
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44
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Zhou J, Horton JR, Yu D, Ren R, Blumenthal RM, Zhang X, Cheng X. Repurposing epigenetic inhibitors to target the Clostridioides difficile-specific DNA adenine methyltransferase and sporulation regulator CamA. Epigenetics 2021; 17:970-981. [PMID: 34523387 PMCID: PMC9487755 DOI: 10.1080/15592294.2021.1976910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Epigenetically targeted therapeutic development, particularly for SAM-dependent methylations of DNA, mRNA and histones has been proceeding rapidly for cancer treatments over the past few years. However, this approach has barely begun to be exploited for developing new antibiotics, despite an overwhelming global need to counter antimicrobial resistance. Here, we explore whether SAM analogues, some of which are in (pre)clinical studies as inhibitors of human epigenetic enzymes, can also inhibit Clostridioides difficile-specific DNA adenine methyltransferase (CamA), a sporulation regulator present in all C. difficile genomes sequenced to date, but found in almost no other bacteria. We found that SGC0946 (an inhibitor of DOT1L), JNJ-64619178 (an inhibitor of PRMT5) and SGC8158 (an inhibitor of PRMT7) inhibit CamA enzymatic activity in vitro at low micromolar concentrations. Structural investigation of the ternary complexes of CamA-DNA in the presence of SGC0946 or SGC8158 revealed conformational rearrangements of the N-terminal arm, with no apparent disturbance of the active site. This N-terminal arm and its modulation of exchanges between SAM (the methyl donor) and SAH (the reaction product) during catalysis of methyl transfer are, to date, unique to CamA. Our work presents a substantial first step in generating potent and selective inhibitors of CamA that would serve in the near term as chemical probes to investigate the cellular mechanism(s) of CamA in controlling spore formation and colonization, and eventually as therapeutic antivirulence agents useful in treating C. difficile infection.
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Affiliation(s)
- Jujun Zhou
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dan Yu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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45
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Barno AR, Villela HDM, Aranda M, Thomas T, Peixoto RS. Host under epigenetic control: A novel perspective on the interaction between microorganisms and corals. Bioessays 2021; 43:e2100068. [PMID: 34463364 DOI: 10.1002/bies.202100068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022]
Abstract
Coral reefs have been challenged by the current rate and severity of environmental change that might outpace their ability to adapt and survive. Current research focuses on understanding how microbial communities and epigenetic changes separately affect phenotypes and gene expression of corals. Here, we provide the hypothesis that coral-associated microorganisms may directly or indirectly affect the coral's phenotypic response through the modulation of its epigenome. Homologs of ankyrin-repeat protein A and internalin B, which indirectly cause histone modifications in humans, as well as Rv1988 histone methyltransferase, and the DNA methyltransferases Rv2966c, Mhy1, Mhy2, and Mhy3 found in coral-associated bacteria indicate that there are potential host epigenome-modifying proteins in the coral microbiome. With the ideas presented here, we suggest that microbiome manipulation may be a means to alter a coral's epigenome, which could aid the current efforts to protect coral reefs. Also see the video abstract here: https://youtu.be/CW9GbChjKM4.
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Affiliation(s)
- Adam R Barno
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia
| | - Helena D M Villela
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia
| | - Manuel Aranda
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Australia
| | - Raquel S Peixoto
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia.,Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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Fatima S, Kumari A, Agarwal M, Pahuja I, Yadav V, Dwivedi VP, Bhaskar A. Epigenetic code during mycobacterial infections: therapeutic implications for tuberculosis. FEBS J 2021; 289:4172-4191. [PMID: 34453865 DOI: 10.1111/febs.16170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/23/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022]
Abstract
Epigenetics involves changing the gene function without any change in the sequence of the genes. In the case of tuberculosis (TB) infections, the bacilli, Mycobacterium tuberculosis (M.tb), uses epigenetics as a tool to protect itself from the host immune system. TB is a deadly disease-causing maximum death per year due to a single infectious agent. In the case of TB, there is an urgent need for novel host-directed therapies which can effectively target the survival and long-term persistence of the bacteria without developing drug resistance in the bacterial strains while also reducing the duration and toxicity associated with the mainstream anti-TB drugs. Recent studies have suggested that TB infection has a significant effect on the host epigenome thereby manipulating the host immune response in the favor of the pathogen. M.tb alters the activation status of key genes involved in the immune response against TB to promote its survival and subvert the antibacterial strategies of the host. These changes are reversible and can be exploited to design very efficient host-directed therapies to fight against TB. This review has been written with the purpose of discussing the role of epigenetic changes in TB pathogenesis and the therapeutic approaches involving epigenetics, which can be utilized for targeting the pathogen.
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Affiliation(s)
- Samreen Fatima
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Anjna Kumari
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Meetu Agarwal
- Department of Biosciences, Jamia Hamdard University, New Delhi, India
| | - Isha Pahuja
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Vinod Yadav
- Department of Microbiology, Central University of Haryana, Mahendragarh, India
| | - Ved Prakash Dwivedi
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashima Bhaskar
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Abo-Kadoum MA, Assad M, Ali MK, Uae M, Nzaou SAE, Gong Z, Moaaz A, Lambert N, Eltoukhy A, Xie J. Mycobacterium tuberculosis PE17 (Rv1646) promotes host cell apoptosis via host chromatin remodeling mediated by reduced H3K9me3 occupancy. Microb Pathog 2021; 159:105147. [PMID: 34400280 DOI: 10.1016/j.micpath.2021.105147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 03/20/2021] [Accepted: 08/12/2021] [Indexed: 01/03/2023]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis remains a serious global public health threat. M. tuberculosis PE and PPE proteins are closely involved in pathogen-host interaction. To explore the predicted function of the M. tuberculosis PE17 (Rv1646), we heterologously expressed PE17 in a non-pathogenic Mycobacterium smegmatis strain (Ms_PE17). PE17 can reduce the survival of M. smegmatis within macrophages associated with altering the transcription levels of inflammatory cytokines IL1β, IL6, TNFα, and IL10 in Ms_PE17 infected macrophages through JNK signaling. Furthermore, macrophages apoptosis was increased upon Ms_PE17 infection in a caspases-dependent manner, accompanied by the activation of the Endoplasmic Reticulum stress IRE1α/ASK1/JNK signaling pathway. This can be largely interpreted by the epigenetic changes through reduced H3K9me3 chromatin occupancy post Ms_PE17 infection. To our knowledge, this is the first report that PE17 altered the macrophages apoptosis via H3K9me3 mediated chromatin remodeling.
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Affiliation(s)
- M A Abo-Kadoum
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ecoenvironments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing, 400715, China; Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assuit Branch, 71524, Egypt
| | - Mohammed Assad
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ecoenvironments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing, 400715, China; Department of Biotechnology, Faculty of Science and Technology Omdurman Islamic University, Khartoum, Sudan
| | - Md Kaisar Ali
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ecoenvironments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing, 400715, China; College of Animal Science and Technology, Southwest University, Beibei, Chongqing, 400715, China
| | - Moure Uae
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ecoenvironments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing, 400715, China
| | - Stech A E Nzaou
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ecoenvironments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing, 400715, China
| | - Zhen Gong
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ecoenvironments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing, 400715, China
| | - Asmaa Moaaz
- The State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Nzungize Lambert
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ecoenvironments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing, 400715, China
| | - Adel Eltoukhy
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assuit Branch, 71524, Egypt; Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ecoenvironments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing, 400715, China.
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48
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Qin W, Scicluna BP, van der Poll T. The Role of Host Cell DNA Methylation in the Immune Response to Bacterial Infection. Front Immunol 2021; 12:696280. [PMID: 34394088 PMCID: PMC8358789 DOI: 10.3389/fimmu.2021.696280] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Host cells undergo complex transcriptional reprogramming upon infection. Epigenetic changes play a key role in the immune response to bacteria, among which DNA modifications that include methylation have received much attention in recent years. The extent of DNA methylation is well known to regulate gene expression. Whilst historically DNA methylation was considered to be a stable epigenetic modification, accumulating evidence indicates that DNA methylation patterns can be altered rapidly upon exposure of cells to changing environments and pathogens. Furthermore, the action of proteins regulating DNA methylation, particularly DNA methyltransferases and ten-eleven translocation methylcytosine dioxygenases, may be modulated, at least in part, by bacteria. This review discusses the principles of DNA methylation, and recent insights about the regulation of host DNA methylation during bacterial infection.
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Affiliation(s)
- Wanhai Qin
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Brendon P Scicluna
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Tom van der Poll
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Division of Infectious Diseases, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
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Zhou S, Zhang J, Xu J, Zhang F, Li P, He Y, Wu J, Wang C, Wang X, Zhang W, Ning K, Pan Y, Liu T, Zhao J, Yin L, Zhang R, Gao F, Zhao J, Dong L. An epigenome-wide DNA methylation study of patients with COVID-19. Ann Hum Genet 2021; 85:221-234. [PMID: 34185889 PMCID: PMC8441705 DOI: 10.1111/ahg.12440] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/05/2021] [Accepted: 06/15/2021] [Indexed: 01/08/2023]
Abstract
In the early 2000s, emerging SARS‐CoV‐2, which is highly pathogenic, posed a great threat to public health. During COVID‐19, epigenetic regulation is deemed to be an important part of the pathophysiology and illness severity. Using the Illumina Infinium Methylation EPIC BeadChip (850 K), we investigated genome‐wide differences in DNA methylation between healthy subjects and COVID‐19 patients with different disease severities. We conducted a combined analysis and selected 35 “marker” genes that could indicate a SARS‐CoV‐2 infection, including 12 (ATHL1, CHN2, CHST15, CPLX2, CRHR2, DCAKD, GNAI2, HECW1, HYAL1, MIR510, PDE11A, and SMG6) situated in the promoter region. The functions and pathways of differentially methylated genes were enriched in biological processes, signal transduction, and the immune system. In the “Severe versus Mild” group, differentially methylated genes, after eliminating duplicates, were used for PPI analyses. The four hub genes (GNG7, GNAS, PRKCZ, and PRKAG2) that had the highest degree of nodes were identified and among them, GNG7 and GNAS genes expressions were also downregulated in the severe group in sequencing results. Above all, the results suggest that GNG7 and GNAS may play a non‐ignorable role in the progression of COVID‐19. In conclusion, the identified key genes and related pathways in the current study can be used to study the molecular mechanisms of COVID‐19 and may provide possibilities for specific treatments.
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Affiliation(s)
- Shengyu Zhou
- Department of Respiratory and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Clinical Nursing Department, School of Nursing, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jintao Zhang
- Department of Respiratory, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jiawei Xu
- Department of Respiratory, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fayan Zhang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Peng Li
- Blood Center of Shandong Province, Jinan, China
| | - Yujie He
- Institute of Virology, Shandong Center for Diseases Prevention and Control, Jinan, China
| | - Julong Wu
- Institute of Virology, Shandong Center for Diseases Prevention and Control, Jinan, China
| | - Chunting Wang
- Department of Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ximing Wang
- Department of Radiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong University, Jinan, China
| | - Wei Zhang
- Department of Lung Disease, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Kang Ning
- Department of Respiratory, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yun Pan
- Department of Respiratory, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tian Liu
- Department of Respiratory and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jiping Zhao
- Department of Respiratory and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lixia Yin
- Department of Respiratory Medicine, Dezhou People's Hospital, Dezhou, China
| | - Rumin Zhang
- Department of Critical Care Medicine, Zibo Central Hospital, Zibo, China
| | - Feng Gao
- Department of Infectious Disease, Linyi People's Hospital, Linyi, China
| | - Jintong Zhao
- Department of Critical Care Medicine, Zibo Central Hospital, Zibo, China
| | - Liang Dong
- Department of Respiratory, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Respiratory, Shandong Provincial Qianfoshan Hospital, Shandong University, The First Affiliated Hospital of Shandong First Medical University, Shandong Institute of Respiratory Diseases, Jinan, China
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50
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Ram-Mohan N, Thair SA, Litzenburger UM, Cogill S, Andini N, Yang X, Chang HY, Yang S. Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection. Life Sci Alliance 2021; 4:4/8/e202000976. [PMID: 34145026 PMCID: PMC8321655 DOI: 10.26508/lsa.202000976] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
ATAC-seq reveals unique neutrophil chromatin architecture changes in response to different stimuli before transcriptional activation, possibly regulating downstream gene expression. Sepsis, sequela of bloodstream infections and dysregulated host responses, is a leading cause of death globally. Neutrophils tightly regulate responses to pathogens to prevent organ damage. Profiling early host epigenetic responses in neutrophils may aid in disease recognition. We performed assay for transposase-accessible chromatin (ATAC)-seq of human neutrophils challenged with six toll-like receptor ligands and two organisms; and RNA-seq after Escherichia coli exposure for 1 and 4 h along with ATAC-seq. ATAC-seq of neutrophils facilitates detection of pathogen DNA. In addition, despite similarities in genomic distribution of differential chromatin changes across challenges, only a fraction overlaps between the challenges. Ligands depict shared signatures, but majority are unique in position, function, and challenge. Epigenomic changes are plastic, only ∼120 are shared by E. coli challenges over time, resulting in varied differential genes and associated processes. We identify three classes of gene regulation, chromatin access changes in the promoter; changes in the promoter and distal enhancers; and controlling expression through changes solely in distal enhancers. These and transcription factor footprinting reveal timely and challenge specific mechanisms of transcriptional regulation in neutrophils.
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Affiliation(s)
- Nikhil Ram-Mohan
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Simone A Thair
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Steven Cogill
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nadya Andini
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Xi Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
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