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Guo C, Ji W, Yang W, Deng Q, Zheng T, Wang Z, Sui W, Zhai C, Yu F, Xi B, Yu X, Xu F, Zhang Q, Zhang W, Kong J, Zhang M, Zhang C. NKRF in Cardiac Fibroblasts Protects against Cardiac Remodeling Post-Myocardial Infarction via Human Antigen R. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303283. [PMID: 37667861 PMCID: PMC10602562 DOI: 10.1002/advs.202303283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/09/2023] [Indexed: 09/06/2023]
Abstract
Myocardial infarction (MI) remains the leading cause of death worldwide. Cardiac fibroblasts (CFs) are abundant in the heart and are responsible for cardiac repair post-MI. NF-κB-repressing factor (NKRF) plays a significant role in the transcriptional inhibition of various specific genes. However, the NKRF action mechanism in CFs remains unclear in cardiac repair post-MI. This study investigates the NKRF mechanism in cardiac remodeling and dysfunction post-MI by establishing a CF-specific NKRF-knockout (NKRF-CKO) mouse model. NKRF expression is downregulated in CFs in response to pathological cardiac remodeling in vivo and TNF-α in vitro. NKRF-CKO mice demonstrate worse cardiac function and survival and increased infarct size, heart weight, and MMP2 and MMP9 expression post-MI compared with littermates. NKRF inhibits CF migration and invasion in vitro by downregulating MMP2 and MMP9 expression. Mechanistically, NKRF inhibits human antigen R (HuR) transcription by binding to the classical negative regulatory element within the HuR promoter via an NF-κB-dependent mechanism. This decreases HuR-targeted Mmp2 and Mmp9 mRNA stability. This study suggests that NKRF is a therapeutic target for pathological cardiac remodeling.
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Affiliation(s)
- Chenghu Guo
- National Key Laboratory for Innovation and Transformation of Luobing TheoryThe Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of EducationChinese National Health Commission and Chinese Academy of Medical SciencesDepartment of CardiologyQilu Hospital of Shandong UniversityJinan250012China
| | - Wei Ji
- Department of UltrasonographyAffiliated Hospital of Shandong University of Traditional Chinese MedicineJinan250014China
| | - Wei Yang
- National Key Laboratory for Innovation and Transformation of Luobing TheoryThe Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of EducationChinese National Health Commission and Chinese Academy of Medical SciencesDepartment of CardiologyQilu Hospital of Shandong UniversityJinan250012China
| | - Qiming Deng
- National Key Laboratory for Innovation and Transformation of Luobing TheoryThe Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of EducationChinese National Health Commission and Chinese Academy of Medical SciencesDepartment of CardiologyQilu Hospital of Shandong UniversityJinan250012China
| | - Tengfei Zheng
- National Key Laboratory for Innovation and Transformation of Luobing TheoryThe Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of EducationChinese National Health Commission and Chinese Academy of Medical SciencesDepartment of CardiologyQilu Hospital of Shandong UniversityJinan250012China
| | - Zunzhe Wang
- Department of Geriatric CardiologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan250021China
| | - Wenhai Sui
- National Key Laboratory for Innovation and Transformation of Luobing TheoryThe Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of EducationChinese National Health Commission and Chinese Academy of Medical SciencesDepartment of CardiologyQilu Hospital of Shandong UniversityJinan250012China
| | - Chungang Zhai
- National Key Laboratory for Innovation and Transformation of Luobing TheoryThe Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of EducationChinese National Health Commission and Chinese Academy of Medical SciencesDepartment of CardiologyQilu Hospital of Shandong UniversityJinan250012China
| | - Fangpu Yu
- National Key Laboratory for Innovation and Transformation of Luobing TheoryThe Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of EducationChinese National Health Commission and Chinese Academy of Medical SciencesDepartment of CardiologyQilu Hospital of Shandong UniversityJinan250012China
| | - Bo Xi
- Department of EpidemiologySchool of Public HealthCheeloo College of MedicineShandong UniversityJinan250012China
| | - Xiao Yu
- Key Laboratory Experimental Teratology of the Ministry of EducationDepartment of PhysiologySchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinan250012China
| | - Feng Xu
- Department of Emergency MedicineChest Pain CenterShandong Provincial Clinical Research Center for Emergency and Critical Care MedicineQilu HospitalShandong UniversityJinan250012China
| | - Qunye Zhang
- National Key Laboratory for Innovation and Transformation of Luobing TheoryThe Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of EducationChinese National Health Commission and Chinese Academy of Medical SciencesDepartment of CardiologyQilu Hospital of Shandong UniversityJinan250012China
| | - Wencheng Zhang
- National Key Laboratory for Innovation and Transformation of Luobing TheoryThe Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of EducationChinese National Health Commission and Chinese Academy of Medical SciencesDepartment of CardiologyQilu Hospital of Shandong UniversityJinan250012China
| | - Jing Kong
- National Key Laboratory for Innovation and Transformation of Luobing TheoryThe Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of EducationChinese National Health Commission and Chinese Academy of Medical SciencesDepartment of CardiologyQilu Hospital of Shandong UniversityJinan250012China
| | - Meng Zhang
- National Key Laboratory for Innovation and Transformation of Luobing TheoryThe Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of EducationChinese National Health Commission and Chinese Academy of Medical SciencesDepartment of CardiologyQilu Hospital of Shandong UniversityJinan250012China
- Cardiovascular Disease Research Center of Shandong First Medical UniversityCentral Hospital Affiliated to Shandong First Medical UniversityJinan250013China
| | - Cheng Zhang
- National Key Laboratory for Innovation and Transformation of Luobing TheoryThe Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of EducationChinese National Health Commission and Chinese Academy of Medical SciencesDepartment of CardiologyQilu Hospital of Shandong UniversityJinan250012China
- Cardiovascular Disease Research Center of Shandong First Medical UniversityCentral Hospital Affiliated to Shandong First Medical UniversityJinan250013China
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2
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Hay M, Kumar V, Ricaño-Ponce I. The role of the X chromosome in infectious diseases. Brief Funct Genomics 2021; 21:143-158. [PMID: 34651167 DOI: 10.1093/bfgp/elab039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 02/07/2023] Open
Abstract
Many infectious diseases in humans present with a sex bias. This bias arises from a combination of environmental factors, hormones and genetics. In this study, we review the contribution of the X chromosome to the genetic factor associated with infectious diseases. First, we give an overview of the X-linked genes that have been described in the context of infectious diseases and group them in four main pathways that seem to be dysregulated in infectious diseases: nuclear factor kappa-B, interleukin 2 and interferon γ cascade, toll-like receptors and programmed death ligand 1. Then, we review the infectious disease associations in existing genome-wide association studies (GWAS) from the GWAS Catalog and the Pan-UK Biobank, describing the main associations and their possible implications for the disease. Finally, we highlight the importance of including the X chromosome in GWAS analysis and the importance of sex-specific analysis.
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3
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Vergara C, Valencia A, Thio CL, Goedert JJ, Mangia A, Piazzolla V, Johnson E, Kral AH, O’Brien TR, Mehta SH, Kirk GD, Kim AY, Lauer GM, Chung RT, Cox AL, Peters MG, Khakoo SI, Alric L, Cramp ME, Donfield SM, Edlin BR, Busch MP, Alexander G, Rosen HR, Murphy EL, Wojcik GL, Taub MA, Thomas DL, Duggal P. A Multiancestry Sex-Stratified Genome-Wide Association Study of Spontaneous Clearance of Hepatitis C Virus. J Infect Dis 2021; 223:2090-2098. [PMID: 33119750 PMCID: PMC8205624 DOI: 10.1093/infdis/jiaa677] [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: 07/27/2020] [Accepted: 10/28/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Spontaneous clearance of acute hepatitis C virus (HCV) infection is more common in women than in men, independent of known risk factors. METHODS To identify sex-specific genetic loci, we studied 4423 HCV-infected individuals (2903 male, 1520 female) of European, African, and Hispanic ancestry. We performed autosomal, and X chromosome sex-stratified and combined association analyses in each ancestry group. RESULTS A male-specific region near the adenosine diphosphate-ribosylation factor-like 5B (ARL5B) gene was identified. Individuals with the C allele of rs76398191 were about 30% more likely to have chronic HCV infection than individuals with the T allele (OR, 0.69; P = 1.98 × 10-07), and this was not seen in females. The ARL5B gene encodes an interferon-stimulated gene that inhibits immune response to double-stranded RNA viruses. We also identified suggestive associations near septin 6 and ribosomal protein L39 genes on the X chromosome. In box sexes, allele G of rs12852885 was associated with a 40% increase in HCV clearance compared with the A allele (OR, 1.4; P = 2.46 × 10-06). Septin 6 facilitates HCV replication via interaction with the HCV NS5b protein, and ribosomal protein L39 acts as an HCV core interactor. CONCLUSIONS These novel gene associations support differential mechanisms of HCV clearance between the sexes and provide biological targets for treatment or vaccine development.
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Affiliation(s)
- Candelaria Vergara
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Ana Valencia
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
- Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Chloe L Thio
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Alessandra Mangia
- Liver Unit IRCCS “Casa Sollievo della Sofferenza,” San Giovanni Rotondo, Italy
| | - Valeria Piazzolla
- Liver Unit IRCCS “Casa Sollievo della Sofferenza,” San Giovanni Rotondo, Italy
| | - Eric Johnson
- RTI International, Research Triangle Park, North Carolina, USA
| | - Alex H Kral
- RTI International, Research Triangle Park, North Carolina, USA
| | - Thomas R O’Brien
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Shruti H Mehta
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Gregory D Kirk
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Arthur Y Kim
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Georg M Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea L Cox
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Marion G Peters
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California, San Francisco, California, USA
| | - Salim I Khakoo
- University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Laurent Alric
- Department of Internal Medicine and Digestive Diseases, CHU Rangueil, UMR 152 IRD, Toulouse 3 University, France
| | | | | | - Brian R Edlin
- SUNY Downstate College of Medicine, Brooklyn, New York, USA
| | - Michael P Busch
- University of California and Vitalant Research Institute, San Francisco, California, USA
| | - Graeme Alexander
- UCL Institute for Liver and Digestive Health, Royal Free Hospital, Hampstead, London, United Kingdom
| | | | - Edward L Murphy
- University of California and Vitalant Research Institute, San Francisco, California, USA
| | - Genevieve L Wojcik
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Margaret A Taub
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - David L Thomas
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Priya Duggal
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
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4
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Smita S, Ghosh A, Biswas VK, Ahad A, Podder S, Jha A, Sen K, Acha-Orbea H, Raghav SK. Zbtb10 transcription factor is crucial for murine cDC1 activation and cytokine secretion. Eur J Immunol 2021; 51:1126-1142. [PMID: 33527393 DOI: 10.1002/eji.202048933] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/14/2020] [Accepted: 01/28/2021] [Indexed: 12/14/2022]
Abstract
Dendritic cell (DC) activation and cytokine production is tightly regulated. In this study, we found that Zbtb10 expression is activation dependent and it is essential for the immunogenic function of cDC1. Zbtb10 knockdown (KD) significantly reduced the expression of co-stimulatory genes CD80 and CD86 along with cytokines including IL-12, IL-6, and IL-10, in activated cDC1 Mutu-DC line. Consequently, the clonal expansion of CD44+ effector T cells in co-cultured CD4+ T cells was drastically reduced owing to significantly reduced IL-2. At the same time, these CD44+ effector T cells were unable to differentiate toward Tbet+ IFNγ+ Th1 subtype. Instead, an increased frequency of Th2 cells expressing GATA3+ and IL-13+ was observed. Interestingly, in Zbtb10 KD condition the co-cultured T cells depicted increased expression of PD1 and LAG3, the T-cell anergic markers. Moreover, the global transcriptome analysis identified that Zbtb10 is pertinent for DC activation and its depletion in cDC1 completely shuts down their immune responses. Mechanistic analysis revealed that Zbtb10 KD enhanced the expression of NKRF (NF-κB repressing factor) leading to drastic suppression of NF-κB related genes. Zbtb10 KD abrogated p65 and RelB nuclear translocation, thereby controlling the activation and maturation of cDC1 and the ensuing adaptive T cell responses.
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Affiliation(s)
- Shuchi Smita
- Immuno-genomics & Systems Biology group, Institute of Life Sciences, Bhubaneswar, India.,Department of Biotechnology, Manipal Academy of Higher Education, Manipal, India
| | - Arup Ghosh
- Immuno-genomics & Systems Biology group, Institute of Life Sciences, Bhubaneswar, India.,Department of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Viplov Kumar Biswas
- Immuno-genomics & Systems Biology group, Institute of Life Sciences, Bhubaneswar, India.,Department of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Abdul Ahad
- Immuno-genomics & Systems Biology group, Institute of Life Sciences, Bhubaneswar, India.,Department of Biotechnology, Manipal Academy of Higher Education, Manipal, India
| | - Sreeparna Podder
- Immuno-genomics & Systems Biology group, Institute of Life Sciences, Bhubaneswar, India.,Department of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Atimukta Jha
- Immuno-genomics & Systems Biology group, Institute of Life Sciences, Bhubaneswar, India.,Department of Biotechnology, Manipal Academy of Higher Education, Manipal, India
| | - Kaushik Sen
- Immuno-genomics & Systems Biology group, Institute of Life Sciences, Bhubaneswar, India.,Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Hans Acha-Orbea
- Department of Biochemistry CIIL, University of Lausanne (UNIL), Epalinges, Switzerland
| | - Sunil K Raghav
- Immuno-genomics & Systems Biology group, Institute of Life Sciences, Bhubaneswar, India.,Department of Biotechnology, Manipal Academy of Higher Education, Manipal, India.,Department of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
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5
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Li J, Guo M, Tian X, Wang X, Yang X, Wu P, Liu C, Xiao Z, Qu Y, Yin Y, Wang C, Zhang Y, Zhu Z, Liu Z, Peng C, Zhu T, Liang Q. Virus-Host Interactome and Proteomic Survey Reveal Potential Virulence Factors Influencing SARS-CoV-2 Pathogenesis. MED 2021. [PMID: 32838362 DOI: 10.1101/2020.03.31.019216] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
BACKGROUND The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a global public health concern due to relatively easy person-to-person transmission and the current lack of effective antiviral therapy. However, the exact molecular mechanisms of SARS-CoV-2 pathogenesis remain largely unknown. METHODS Genome-wide screening was used to establish intraviral and viral-host interactomes. Quantitative proteomics was used to investigate the peripheral blood mononuclear cell (PBMC) proteome signature in COVID-19. FINDINGS We elucidated 286 host proteins targeted by SARS-CoV-2 and >350 host proteins that are significantly perturbed in COVID-19-derived PBMCs. This signature in severe COVID-19 PBMCs reveals a significant upregulation of cellular proteins related to neutrophil activation and blood coagulation, as well as a downregulation of proteins mediating T cell receptor signaling. From the interactome, we further identified that non-structural protein 10 interacts with NF-κB-repressing factor (NKRF) to facilitate interleukin-8 (IL-8) induction, which potentially contributes to IL-8-mediated chemotaxis of neutrophils and the overexuberant host inflammatory response observed in COVID-19 patients. CONCLUSIONS Our study not only presents a systematic examination of SARS-CoV-2-induced perturbation of host targets and cellular networks but it also reveals insights into the mechanisms by which SARS-CoV-2 triggers cytokine storms, representing a powerful resource in the pursuit of therapeutic interventions. FUNDING National Key Research and Development Project of China, National Natural Science Foundation of China, National Science and Technology Major Project, Program for Professor of Special Appointment (Eastern Scholar) at Shanghai Institutions of Higher Learning, Shanghai Science and Technology Commission, Shanghai Municipal Health Commission, Shanghai Municipal Key Clinical Specialty, Innovative Research Team of High-level Local Universities in Shanghai, Interdisciplinary Program of Shanghai Jiao Tong University, SII Challenge Fund for COVID-19 Research, Chinese Academy of Sciences (CAS) Large Research Infrastructure of Maintenance and Remolding Project, and Chinese Academy of Sciences Key Technology Talent Program.
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Affiliation(s)
- Jingjiao Li
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mingquan Guo
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Xiaoxu Tian
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Xin Wang
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xing Yang
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ping Wu
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Chengrong Liu
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zixuan Xiao
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Yafei Qu
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Chunxia Wang
- Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Yucai Zhang
- Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Zhaoqin Zhu
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Zhenshan Liu
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Tongyu Zhu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qiming Liang
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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6
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Ahluwalia P, Ahluwalia M, Vaibhav K, Mondal A, Sahajpal N, Islam S, Fulzele S, Kota V, Dhandapani K, Baban B, Rojiani AM, Kolhe R. Infections of the lung: a predictive, preventive and personalized perspective through the lens of evolution, the emergence of SARS-CoV-2 and its pathogenesis. EPMA J 2020; 11:581-601. [PMID: 33204369 PMCID: PMC7661834 DOI: 10.1007/s13167-020-00230-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022]
Abstract
The long evolutionary battle between humans and pathogens has played an important role in shaping the current network of host-pathogen interactions. Each organ brings new challenges from the perspective of a pathogen to establish a suitable niche for survival while subverting the protective mechanisms of the host. Lungs, the organ for oxygen exchange, have been an easy target for pathogens due to its accessibility. The organ has evolved diverse capabilities to provide the flexibility required for an organism's health and at the same time maintain protective functionality to prevent and resolve assault by pathogens. The pathogenic invasions are strongly challenged by healthy lung architecture which includes the presence and activity of the epithelium, mucous, antimicrobial proteins, surfactants, and immune cells. Competitively, the pathogens in the form of viruses, bacteria, and fungi have evolved an arsenal of strategies that can over-ride the host's protective mechanisms. While bacteria such as Mycobacterium tuberculosis (M. tuberculosis) can survive in dormant form for years before getting active in humans, novel pathogens can wreak havoc as they pose a high risk of morbidity and mortality in a very short duration of time. Recently, a coronavirus strain SARS-CoV-2 has caused a pandemic which provides us an opportunity to look at the host manipulative strategies used by respiratory pathogens. Their ability to hide, modify, evade, and exploit cell's processes are key to their survival. While pathogens like M. tuberculosis have been infecting humans for thousands of years, SARS-CoV-2 has been the cause of the recent pandemic. Molecular understanding of the strategies used by these pathogens could greatly serve in design of predictive, preventive, personalized medicine (PPPM). In this article, we have emphasized on the clinically relevant evasive strategies of the pathogens in the lungs with emphasis on M. tuberculosis and SARS-CoV-2. The molecular basis of these evasive strategies illuminated through advances in genomics, cell, and structural biology can assist in the mapping of vulnerable molecular networks which can be exploited translationally. These evolutionary approaches can further assist in generating screening and therapeutic options for susceptible populations and could be a promising approach for the prediction, prevention of disease, and the development of personalized medicines. Further, tailoring the clinical data of COVID-19 patients with their physiological responses in light of known host-respiratory pathogen interactions can provide opportunities to improve patient profiling and stratification according to identified therapeutic targets.
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Affiliation(s)
- Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Meenakshi Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Kumar Vaibhav
- Department of Neurosurgery, Medical College of Georgia, Augusta University, Augusta, GA USA
- Department of Oral Biology, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Ashis Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Nikhil Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Shaheen Islam
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Sadanand Fulzele
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Vamsi Kota
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Krishnan Dhandapani
- Department of Neurosurgery, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Babak Baban
- Department of Oral Biology, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Amyn M. Rojiani
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA USA
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7
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Li J, Guo M, Tian X, Wang X, Yang X, Wu P, Liu C, Xiao Z, Qu Y, Yin Y, Wang C, Zhang Y, Zhu Z, Liu Z, Peng C, Zhu T, Liang Q. Virus-Host Interactome and Proteomic Survey Reveal Potential Virulence Factors Influencing SARS-CoV-2 Pathogenesis. MED 2020; 2:99-112.e7. [PMID: 32838362 PMCID: PMC7373048 DOI: 10.1016/j.medj.2020.07.002] [Citation(s) in RCA: 216] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/27/2020] [Accepted: 07/15/2020] [Indexed: 02/05/2023]
Abstract
Background The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a global public health concern due to relatively easy person-to-person transmission and the current lack of effective antiviral therapy. However, the exact molecular mechanisms of SARS-CoV-2 pathogenesis remain largely unknown. Methods Genome-wide screening was used to establish intraviral and viral-host interactomes. Quantitative proteomics was used to investigate the peripheral blood mononuclear cell (PBMC) proteome signature in COVID-19. Findings We elucidated 286 host proteins targeted by SARS-CoV-2 and >350 host proteins that are significantly perturbed in COVID-19-derived PBMCs. This signature in severe COVID-19 PBMCs reveals a significant upregulation of cellular proteins related to neutrophil activation and blood coagulation, as well as a downregulation of proteins mediating T cell receptor signaling. From the interactome, we further identified that non-structural protein 10 interacts with NF-κB-repressing factor (NKRF) to facilitate interleukin-8 (IL-8) induction, which potentially contributes to IL-8-mediated chemotaxis of neutrophils and the overexuberant host inflammatory response observed in COVID-19 patients. Conclusions Our study not only presents a systematic examination of SARS-CoV-2-induced perturbation of host targets and cellular networks but it also reveals insights into the mechanisms by which SARS-CoV-2 triggers cytokine storms, representing a powerful resource in the pursuit of therapeutic interventions. Funding National Key Research and Development Project of China, National Natural Science Foundation of China, National Science and Technology Major Project, Program for Professor of Special Appointment (Eastern Scholar) at Shanghai Institutions of Higher Learning, Shanghai Science and Technology Commission, Shanghai Municipal Health Commission, Shanghai Municipal Key Clinical Specialty, Innovative Research Team of High-level Local Universities in Shanghai, Interdisciplinary Program of Shanghai Jiao Tong University, SII Challenge Fund for COVID-19 Research, Chinese Academy of Sciences (CAS) Large Research Infrastructure of Maintenance and Remolding Project, and Chinese Academy of Sciences Key Technology Talent Program. Genome-wide screens identify 58 binary interactions between 29 SARS-CoV-2 proteins Virus-host interactome identifies 286 host targets for SARS-CoV-2 proteins Quantitative analysis depicts the overall proteome signature in COVID-19 PBMCs Nsp10 targets NKRF to facilitate IL-8 induction
The COVID-19 pandemic is caused by SARS-CoV-2, but little is known about the functions of its viral proteins. The authors characterized the SARS-CoV-2 intraviral and virus-host interaction networks in human cells and identified 286 potential host targets. Quantitative proteomic analysis revealed elevated levels of IL-6 and IL-8 in PBMCs collected from severe COVID-19 patients compared with mild ones, and the functional annotation of differentially expressed proteins implicate pathways involved in neutrophil activation, T cell receptor signaling, and the coagulation cascade. Combining virus-host interactome with COVID-19 proteomic analysis, the authors found that nsp10 interacts with NKRF to mediate IL-8 expression, providing a potential molecular mechanism for SARS-CoV-2-induced cytokine storm and marking it as a possible emerging therapeutic target.
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Affiliation(s)
- Jingjiao Li
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mingquan Guo
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Xiaoxu Tian
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Xin Wang
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xing Yang
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ping Wu
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Chengrong Liu
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zixuan Xiao
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Yafei Qu
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Chunxia Wang
- Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Yucai Zhang
- Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Zhaoqin Zhu
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Zhenshan Liu
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Tongyu Zhu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qiming Liang
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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8
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Interleukin 8 and Pentaxin (C-Reactive Protein) as Potential New Biomarkers of Bovine Tuberculosis. J Clin Microbiol 2019; 57:JCM.00274-19. [PMID: 31340991 PMCID: PMC6760949 DOI: 10.1128/jcm.00274-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/03/2019] [Indexed: 12/15/2022] Open
Abstract
Bovine tuberculosis (bTB) is caused by Mycobacterium bovis. During the early stage of infection, greater than 15% of M. bovis-infected cattle shed mycobacteria through nasal secretions, which can be detected by nested PCR. Bovine tuberculosis (bTB) is caused by Mycobacterium bovis. During the early stage of infection, greater than 15% of M. bovis-infected cattle shed mycobacteria through nasal secretions, which can be detected by nested PCR. To compare the differences in the protein profiles of M. bovis-infected cattle that were nested PCR positive (bTBPCR-P) and M. bovis-infected cattle that were nested PCR negative (bTBPCR-N) and to screen for biomarkers that will facilitate the early and accurate detection of bTB, we investigated the protein expression profiles of serum and bovine purified protein derivative (PPD-B)-stimulated plasma among bTBPCR-P (n = 20), bTBPCR-N (n = 20), and uninfected cattle (NC; n = 20) by iTRAQ labeling coupled with two-dimensional liquid chromatography-tandem mass spectrometry (iTRAQ-2D LC-MS/MS). After comprehensive analysis, we selected 15 putative differentially expressed serum proteins and 15 plasma proteins for validation by parallel reaction monitoring (PRM) with the same cohort used in the iTRAQ analysis. Four serum and five PPD-B-stimulated proteins were confirmed in follow-up enzyme-linked immunosorbent assays. PPD-B-stimulated interleukin 8 (IL-8) displayed the potential to differentiate M. bovis-infected cattle from NC, with an area under the curve (AUC) value of 0.9662, while PPD-B-stimulated C-reactive protein (CRP) displayed the potential to differentiate bTBPCR-P from bTBPCR-N, with an AUC value of 1.00. Finally, double-blind testing with 244 cattle indicated that the PPD-B-stimulated IL-8 test exhibited good agreement with traditional tests (κ > 0.877) with a >90% relative sensitivity and a >98% relative specificity; the PPD-B-stimulated CRP test displayed good agreement with nested PCR (κ = 0.9117), with an observed 94% relative sensitivity and 97% relative specificity. Therefore, the PPD-B-stimulated IL-8 and CRP tests could be used to detect bTB and to differentiate bTBPCR-P from bTBPCR-N.
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9
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Perčulija V, Ouyang S. Diverse Roles of DEAD/DEAH-Box Helicases in Innate Immunity and Diseases. HELICASES FROM ALL DOMAINS OF LIFE 2019. [PMCID: PMC7158350 DOI: 10.1016/b978-0-12-814685-9.00009-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
DEAD/DEAH-box helicases are enzymes that belong to the DEAD/H-box family of SF2 helicase superfamily. These enzymes are essential in RNA metabolism, where they are involved in a number of processes that require manipulation of RNA structure. Recent studies have found that some DEAD/DEAH-box helicases play important roles in innate immunity, where they act as sensors of cytosolic DNA/RNA, as adaptor proteins, or as regulators of signaling and gene expression. In spite of their function in immunity, DEAD/DEAH-box helicases can also be hijacked and exploited by viruses to circumvent detection and aid in viral replication. These findings not only imply that DEAD/DEAH-box helicases have a broader function than previously thought, but also give us a much better understanding of immune mechanisms and diseases that arise due to the dysregulation or evasion thereof. In this chapter, we demonstrate the known scope of activities of human DEAD/DEAH-box helicases in innate immunity and interaction with viruses or other pathogens. Additionally, we give an outline of diseases in which they are, or may be, involved in the context of immunity.
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10
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Antibacterial Activity of Leukocyte- and Platelet-Rich Plasma: An In Vitro Study. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9471723. [PMID: 30050949 PMCID: PMC6040244 DOI: 10.1155/2018/9471723] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 05/26/2018] [Indexed: 02/06/2023]
Abstract
The aim of the study was to investigate the leukocyte- and platelet-rich plasma (L-PRP) antimicrobial activity. The studied sample comprised 20 healthy males. The L-PRP gel, liquid L-PRP, and thrombin samples were tested in vitro for their antibacterial properties against selected bacterial strains using the Kirby-Bauer disc diffusion method. Two types of thrombin were used (autologous and bovine). Zones of inhibition produced by L-PRP ranged between 6 and 18 mm in diameter. L-PRP inhibited the growth of Staphylococcus aureus (MRSA and MSSA strains) and was also active against Enterococcus faecalis and Pseudomonas aeruginosa. There was no activity against Escherichia coli and Klebsiella pneumoniae. The statistically significant increase of L-PRP antimicrobial effect was noted with the use of major volume of thrombin as an activator. Additionally, in groups where a bovine thrombin mixture was added to L-PRP the zones of inhibition concerning MRSA, Enterococcus faecalis, and Pseudomonas aeruginosa were larger than in the groups with autologous thrombin. Based on the conducted studies, it can be determined that L-PRP can evoke in vitro antimicrobial effects and might be used to treat selected infections in the clinical field. The major volume of thrombin as an activator increases the strength of the L-PRP antimicrobial effect.
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11
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Bradburn S, McPhee J, Bagley L, Carroll M, Slevin M, Al-Shanti N, Barnouin Y, Hogrel JY, Pääsuke M, Gapeyeva H, Maier A, Sipilä S, Narici M, Robinson A, Mann D, Payton A, Pendleton N, Butler-Browne G, Murgatroyd C. Dysregulation of C-X-C motif ligand 10 during aging and association with cognitive performance. Neurobiol Aging 2017; 63:54-64. [PMID: 29223680 PMCID: PMC5805841 DOI: 10.1016/j.neurobiolaging.2017.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/04/2017] [Accepted: 11/17/2017] [Indexed: 01/20/2023]
Abstract
Chronic low-grade inflammation during aging (inflammaging) is associated with cognitive decline and neurodegeneration; however, the mechanisms underlying inflammaging are unclear. We studied a population (n = 361) of healthy young and old adults from the MyoAge cohort. Peripheral levels of C-X-C motif chemokine ligand 10 (CXCL10) was found to be higher in older adults, compared with young, and negatively associated with working memory performance. This coincided with an age-related reduction in blood DNA methylation at specific CpGs within the CXCL10 gene promoter. In vitro analysis supported the role of DNA methylation in regulating CXCL10 transcription. A polymorphism (rs56061981) that altered methylation at one of these CpG sites further associated with working memory performance in 2 independent aging cohorts. Studying prefrontal cortex samples, we found higher CXCL10 protein levels in those with Alzheimer's disease, compared with aged controls. These findings support the association of peripheral inflammation, as demonstrated by CXCL10, in aging and cognitive decline. We reveal age-related epigenetic and genetic factors which contribute to the dysregulation of CXCL10.
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Affiliation(s)
- Steven Bradburn
- School of Healthcare Science, Manchester Metropolitan University, Manchester, UK
| | - Jamie McPhee
- School of Healthcare Science, Manchester Metropolitan University, Manchester, UK
| | - Liam Bagley
- School of Healthcare Science, Manchester Metropolitan University, Manchester, UK
| | - Michael Carroll
- School of Healthcare Science, Manchester Metropolitan University, Manchester, UK
| | - Mark Slevin
- School of Healthcare Science, Manchester Metropolitan University, Manchester, UK
| | - Nasser Al-Shanti
- School of Healthcare Science, Manchester Metropolitan University, Manchester, UK
| | - Yoann Barnouin
- Institut de Myologie, UPMC UM 76, INSERM U 974, CNRS UMR, Paris, France
| | - Jean-Yves Hogrel
- Institut de Myologie, UPMC UM 76, INSERM U 974, CNRS UMR, Paris, France
| | - Mati Pääsuke
- Institute of Sport Sciences and Physiotherapy, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Helena Gapeyeva
- Institute of Sport Sciences and Physiotherapy, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Andrea Maier
- Department of Human Movement Sciences, MOVE Research Institute, VU University Medical Center, Amsterdam, the Netherlands; Department of Medicine and Aged Care, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Sarianna Sipilä
- Gerontology Research Center, Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Marco Narici
- Faculty of Medicine and Health Sciences, University of Nottingham, Derby, UK
| | - Andrew Robinson
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - David Mann
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Antony Payton
- Centre for Epidemiology, Division of Population Health, Health Services Research & Primary Care, School of Health Sciences, The University of Manchester, Manchester, UK
| | - Neil Pendleton
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, The University of Manchester, Manchester, UK
| | | | - Chris Murgatroyd
- School of Healthcare Science, Manchester Metropolitan University, Manchester, UK.
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12
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Effects of α-conotoxin ImI on TNF-α, IL-8 and TGF-β expression by human macrophage-like cells derived from THP-1 pre-monocytic leukemic cells. Sci Rep 2017; 7:12742. [PMID: 28986583 PMCID: PMC5630575 DOI: 10.1038/s41598-017-11586-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 08/25/2017] [Indexed: 12/16/2022] Open
Abstract
α7 nicotinic acetylcholine receptors (nAChRs) are ubiquitous in the nervous system and ensure important neurophysiological functionality for many processes. However, they are also found in cells of the immune system, where their role has been less studied. Here we report the pro-inflammatory effect of ImI, a well characterized conotoxin that inhibits α7 nAChRs, on differentiated THP-1 pre-monocyte macrophages (MDM) obtained by phorbol 12-myristate 13 acetate (PMA) treatment. Enzyme-linked immunosorbent assay (ELISA) performed on supernatant fluids of LPS challenged MDM showed ImI-mediated upregulation of pro-inflammatory cytokine TNF-α in an ImI concentration-dependent manner from 0.5 to 5.0 µmol/L and for IL-8 up to 1.0 µmol/L. Levels of anti-inflammatory cytokine TGF-β remained practically unaffected in ImI treated MDMs. Nicotine at 10 µmol/L significantly downregulated the release of TNF-α, but showed a lesser effect on IL-8 secretion and no effect on TGF-β. Fluorescent competitive assays involving ImI, α-bungarotoxin and nicotine using MDM and the murine macrophage RAW 264.7 suggest a common binding site in the α7 receptor. This work extends the application of conotoxins as molecular probes to non-excitatory cells, such as macrophages and supports the involvement of the α7 nAChR in regulating the inflammatory response via the cholinergic anti-inflammatory pathway (CAP).
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13
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Memet I, Doebele C, Sloan KE, Bohnsack MT. The G-patch protein NF-κB-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis. Nucleic Acids Res 2017; 45:5359-5374. [PMID: 28115624 PMCID: PMC5435916 DOI: 10.1093/nar/gkx013] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/04/2017] [Indexed: 01/05/2023] Open
Abstract
In eukaryotes, the synthesis of ribosomal subunits, which involves the maturation of the ribosomal (r)RNAs and assembly of ribosomal proteins, requires the co-ordinated action of a plethora of ribosome biogenesis factors. Many of these cofactors remain to be characterized in human cells. Here, we demonstrate that the human G-patch protein NF-κB-repressing factor (NKRF) forms a pre-ribosomal subcomplex with the DEAH-box RNA helicase DHX15 and the 5΄-3΄ exonuclease XRN2. Using UV crosslinking and analysis of cDNA (CRAC), we reveal that NKRF binds to the transcribed spacer regions of the pre-rRNA transcript. Consistent with this, we find that depletion of NKRF, XRN2 or DHX15 impairs an early pre-rRNA cleavage step (A’). The catalytic activity of DHX15, which we demonstrate is stimulated by NKRF functioning as a cofactor, is required for efficient A’ cleavage, suggesting that a structural remodelling event may facilitate processing at this site. In addition, we show that depletion of NKRF or XRN2 also leads to the accumulation of excised pre-rRNA spacer fragments and that NKRF is essential for recruitment of the exonuclease to nucleolar pre-ribosomal complexes. Our findings therefore reveal a novel pre-ribosomal subcomplex that plays distinct roles in the processing of pre-rRNAs and the turnover of excised spacer fragments.
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Affiliation(s)
- Indira Memet
- Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University, 37073 Göttingen, Germany
| | - Carmen Doebele
- Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University, 37073 Göttingen, Germany
| | - Katherine E Sloan
- Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University, 37073 Göttingen, Germany.,Göttingen Centre for Molecular Biosciences, Georg-August-University, 37073 Göttingen, Germany
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14
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Tientcheu LD, Haks MC, Agbla SC, Sutherland JS, Adetifa IM, Donkor S, Quinten E, Daramy M, Antonio M, Kampmann B, Ottenhoff THM, Dockrell HM, Ota MO. Host Immune Responses Differ between M. africanum- and M. tuberculosis-Infected Patients following Standard Anti-tuberculosis Treatment. PLoS Negl Trop Dis 2016; 10:e0004701. [PMID: 27192147 PMCID: PMC4871581 DOI: 10.1371/journal.pntd.0004701] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/19/2016] [Indexed: 11/19/2022] Open
Abstract
Epidemiological differences exist between Mycobacterium africanum (Maf)- and Mycobacterium tuberculosis (Mtb)-infected patients, but to date, contributing host factors have not been characterised. We analysed clinical outcomes, as well as soluble markers and gene expression profiles in unstimulated, and ESAT6/CFP-10-, whole-Maf- and Mtb-stimulated blood samples of 26 Maf- and 49 Mtb-HIV-negative tuberculosis patients before, and after 2 and 6 months of anti-tuberculosis therapy. Before treatment, both groups had similar clinical parameters, but differed in few cytokines concentration and gene expression profiles. Following treatment the body mass index, skinfold thickness and chest X-ray scores showed greater improvement in the Mtb- compared to Maf-infected patients, after adjusting for age, sex and ethnicity (p = 0.02; 0.04 and 0.007, respectively). In addition, in unstimulated blood, IL-12p70, IL12A and TLR9 were significantly higher in Maf-infected patients, while IL-15, IL-8 and MIP-1α were higher in Mtb-infected patients. Overnight stimulation with ESAT-6/CFP-10 induced significantly higher levels of IFN-γ and TNF-α production, as well as gene expression of CCL4, IL1B and TLR4 in Mtb- compared to Maf-infected patients. Our study confirms differences in clinical features and immune genes expression and concentration of proteins associated with inflammatory processes between Mtb- and Maf-infected patients following anti-tuberculosis treatment These findings have public health implications for treatment regimens, and biomarkers for tuberculosis diagnosis and susceptibility.
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Affiliation(s)
- Leopold D. Tientcheu
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
- Department of Immunology and Infection, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Biochemistry, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
- * E-mail: ;
| | - Mariëlle C. Haks
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Schadrac C. Agbla
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
- Department of Medical Statistics, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jayne S. Sutherland
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
| | - Ifedayo M. Adetifa
- Disease Control and Elimination Theme, Medical Research Council Unit, The Gambia, Fajara, The Gambia
- Department of Infectious Diseases Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Simon Donkor
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
| | - Edwin Quinten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Mohammed Daramy
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
| | - Tom H. M. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Hazel M. Dockrell
- Department of Immunology and Infection, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Martin O. Ota
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
- World Health Organization Regional Office for Africa, Brazzaville, Congo
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15
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Yamaguchi R, Yamamoto T, Sakamoto A, Ishimaru Y, Narahara S, Sugiuchi H, Yamaguchi Y. Chemokine profiles of human visceral adipocytes from cryopreserved preadipocytes: Neutrophil activation and induction of nuclear factor-kappa B repressing factor. Life Sci 2015; 143:225-30. [DOI: 10.1016/j.lfs.2015.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/18/2015] [Accepted: 11/11/2015] [Indexed: 12/31/2022]
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16
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Rother S, Bartels M, Schweda AT, Resch K, Pallua N, Nourbakhsh M. NF‐κB‐repressing factor phosphorylation regulates transcription elongation
via
its interactions with 5'→3' exoribonuclease 2 and negative elongation factor. FASEB J 2015; 30:174-85. [DOI: 10.1096/fj.15-270256] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/31/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Sascha Rother
- Institute of Pharmacology, Hannover Medical SchoolHannoverGermany
| | - Myriam Bartels
- Institute of Pharmacology, Hannover Medical SchoolHannoverGermany
| | | | - Klaus Resch
- Institute of Pharmacology, Hannover Medical SchoolHannoverGermany
| | - Norbert Pallua
- Department of Plastic and Reconstructive Surgery, Hand Surgery and Burn CenterRheinisch‐Westfälische Technische Hochschule (RWTH) Aachen University HospitalAachenGermany
| | - Mahtab Nourbakhsh
- Department of Plastic and Reconstructive Surgery, Hand Surgery and Burn CenterRheinisch‐Westfälische Technische Hochschule (RWTH) Aachen University HospitalAachenGermany
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17
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Diner BA, Lum KK, Javitt A, Cristea IM. Interactions of the Antiviral Factor Interferon Gamma-Inducible Protein 16 (IFI16) Mediate Immune Signaling and Herpes Simplex Virus-1 Immunosuppression. Mol Cell Proteomics 2015; 14:2341-56. [PMID: 25693804 DOI: 10.1074/mcp.m114.047068] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Indexed: 12/19/2022] Open
Abstract
The interferon-inducible protein IFI16 has emerged as a critical antiviral factor and sensor of viral DNA. IFI16 binds nuclear viral DNA, triggering expression of antiviral cytokines during infection with herpesviruses. The knowledge of the mechanisms and protein interactions through which IFI16 exerts its antiviral functions remains limited. Here, we provide the first characterization of endogenous IFI16 interactions following infection with the prominent human pathogen herpes simplex virus 1 (HSV-1). By integrating proteomics and virology approaches, we identified and validated IFI16 interactions with both viral and host proteins that are involved in HSV-1 immunosuppressive mechanisms and host antiviral responses. We discover that during early HSV-1 infection, IFI16 is recruited to sub-nuclear puncta and subsequently targeted for degradation. We observed that the HSV-1 E3 ubiquitin ligase ICP0 is necessary, but not sufficient, for the proteasom e-mediated degradation of IFI16 following infection. We substantiate that this ICP0-mediated mechanism suppresses IFI16-dependent immune responses. Utilizing an HSV-1 strain that lacks ICP0 ubiquitin ligase activity provided a system for studying IFI16-dependent cytokine responses to HSV-1, as IFI16 levels were maintained throughout infection. We next defined temporal IFI16 interactions during this immune signaling response. We discovered and validated interactions with the viral protein ICP8 and cellular ND10 nuclear body components, sites at which HSV-1 DNA is present during infection. These interactions may be critical for IFI16 to bind to nuclear viral DNA. Altogether, our results provide critical insights into both viral inhibition of IFI16 and interactions that can contribute to IFI16 antiviral functions.
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Affiliation(s)
- Benjamin A Diner
- From the Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Krystal K Lum
- From the Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Aaron Javitt
- From the Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Ileana M Cristea
- From the Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
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18
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Petersen C, DeMuro P. Legal and regulatory considerations associated with use of patient-generated health data from social media and mobile health (mHealth) devices. Appl Clin Inform 2015; 6:16-26. [PMID: 25848410 DOI: 10.4338/aci-2014-09-r-0082] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 12/14/2014] [Indexed: 11/23/2022] Open
Abstract
Patient-generated health data are coming into broader use across the health care spectrum and hold great promise as a means to improve care and health outcomes. At the same time, rapid evolution in the social media and mobile health (mHealth) market has promoted an environment in which creation and transmission of personal health information is easy, quick, and appealing to patients. However, adoption of social media and mHealth by providers is hampered by legal and regulatory concerns with regard to data ownership and data use. This article defines common forms of patient-generated health data (PGHD) and describes how PGHD is used in clinical settings. It explores issues related to protection of personal health information, including that of children and adolescents, data security, and other potential barriers such as physician licensure. It also discusses regulatory and legal considerations providers and patients should consider before using social media and mobile health apps.
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Affiliation(s)
| | - P DeMuro
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University , Portland, Oregon, USA ; Schwabe, Williamson & Wyatt , Seattle, Washington, USA
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