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Feng D, Zhao H, Wang Q, Wu J, Ouyang L, Jia S, Lu Q, Zhao M. Aberrant H3K4me3 modification of immune response genes in CD4 + T cells of patients with systemic lupus erythematosus. Int Immunopharmacol 2024; 130:111748. [PMID: 38432146 DOI: 10.1016/j.intimp.2024.111748] [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: 08/22/2023] [Revised: 01/17/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Increasing evidence has highlighted the significant role of histone modifications in pathogenesis of systemic lupus erythematosus (SLE). However, few studies have comprehensively analyzed trimethylation of histone H3 lysine 4 (H3K4me3) features at specific immune gene loci in SLE patients. METHODS We conducted H3K4me3 chromatin immunoprecipitation sequencing (ChIP-seq) on CD4+ T cells from SLE patients and healthy controls (HC). Differential H3K4me3 peaks were identified, followed by enrichment analysis. We integrated online RNA-seq and DNA methylation datasets to explore the relationship between H3K4me3 modification, DNA methylation and gene expression. We validated several upregulated peak regions by ChIP-qPCR and confirmed their impact on gene expression using RT-qPCR. Finally, we investigated the impact of H3K4 methyltransferases KMT2A on the expression of immune response genes. RESULTS we identified 147 downregulated and 2701 upregulated H3K4me3 peaks in CD4+ T cells of SLE. The upregulated peaks primarily classified as gained peaks and enriched in immune response genes such as FCGR2A, C5AR1, SERPING1 and OASL. Genes with upregulated H3K4me3 and downregulated DNA methylations in the promoter were highly expressed in SLE patients. These genes, including OAS1, IFI27 and IFI44L, were enriched in immune response pathways. The IFI44L locus also showed increased H3K27ac modification, chromatin accessibility and chromatin interactions in SLE. Moreover, knockdown of KMT2A can downregulate the expression of immune response genes in T cells. CONCLUSION Our study uncovers dysregulated H3K4me3 modification patterns in immune response genes loci, which also exhibit downregulated DNA methylation and higher mRNA expression in CD4+ T cells of SLE patients.
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Affiliation(s)
- Delong Feng
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Hongjun Zhao
- Department of Rheumatology, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Qian Wang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jiali Wu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Lianlian Ouyang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Sujie Jia
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
| | - Qianjin Lu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China.
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Rao AM, Popper SJ, Gupta S, Davong V, Vaidya K, Chanthongthip A, Dittrich S, Robinson MT, Vongsouvath M, Mayxay M, Nawtaisong P, Karmacharya B, Thair SA, Bogoch I, Sweeney TE, Newton PN, Andrews JR, Relman DA, Khatri P. A robust host-response-based signature distinguishes bacterial and viral infections across diverse global populations. Cell Rep Med 2022; 3:100842. [PMID: 36543117 PMCID: PMC9797950 DOI: 10.1016/j.xcrm.2022.100842] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/12/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022]
Abstract
Limited sensitivity and specificity of current diagnostics lead to the erroneous prescription of antibiotics. Host-response-based diagnostics could address these challenges. However, using 4,200 samples across 69 blood transcriptome datasets from 20 countries from patients with bacterial or viral infections representing a broad spectrum of biological, clinical, and technical heterogeneity, we show current host-response-based gene signatures have lower accuracy to distinguish intracellular bacterial infections from viral infections than extracellular bacterial infections. Using these 69 datasets, we identify an 8-gene signature to distinguish intracellular or extracellular bacterial infections from viral infections with an area under the receiver operating characteristic curve (AUROC) > 0.91 (85.9% specificity and 90.2% sensitivity). In prospective cohorts from Nepal and Laos, the 8-gene classifier distinguished bacterial infections from viral infections with an AUROC of 0.94 (87.9% specificity and 91% sensitivity). The 8-gene signature meets the target product profile proposed by the World Health Organization and others for distinguishing bacterial and viral infections.
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Affiliation(s)
- Aditya M. Rao
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Immunology Graduate Program, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Stephen J. Popper
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Sanjana Gupta
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Viengmon Davong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Krista Vaidya
- Dhulikhel Hospital, Kathmandu University Hospital, Kavrepalanchok, Nepal
| | - Anisone Chanthongthip
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Sabine Dittrich
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew T. Robinson
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
| | - Pruksa Nawtaisong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Biraj Karmacharya
- Dhulikhel Hospital, Kathmandu University Hospital, Kavrepalanchok, Nepal
| | - Simone A. Thair
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Isaac Bogoch
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Paul N. Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jason R. Andrews
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - David A. Relman
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA,Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA,Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA,Corresponding author
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Strickland BA, Rajagopala SV, Kamali A, Shilts MH, Pakala SB, Boukhvalova MS, Yooseph S, Blanco JCG, Das SR. Species-specific transcriptomic changes upon respiratory syncytial virus infection in cotton rats. Sci Rep 2022; 12:16579. [PMID: 36195733 PMCID: PMC9531660 DOI: 10.1038/s41598-022-19810-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022] Open
Abstract
The cotton rat (Sigmodon) is the gold standard pre-clinical small animal model for respiratory viral pathogens, especially for respiratory syncytial virus (RSV). However, without a reference genome or a published transcriptome, studies requiring gene expression analysis in cotton rats are severely limited. The aims of this study were to generate a comprehensive transcriptome from multiple tissues of two species of cotton rats that are commonly used as animal models (Sigmodon fulviventer and Sigmodon hispidus), and to compare and contrast gene expression changes and immune responses to RSV infection between the two species. Transcriptomes were assembled from lung, spleen, kidney, heart, and intestines for each species with a contig N50 > 1600. Annotation of contigs generated nearly 120,000 gene annotations for each species. The transcriptomes of S. fulviventer and S. hispidus were then used to assess immune response to RSV infection. We identified 238 unique genes that are significantly differentially expressed, including several genes implicated in RSV infection (e.g., Mx2, I27L2, LY6E, Viperin, Keratin 6A, ISG15, CXCL10, CXCL11, IRF9) as well as novel genes that have not previously described in RSV research (LG3BP, SYWC, ABEC1, IIGP1, CREB1). This study presents two comprehensive transcriptome references as resources for future gene expression analysis studies in the cotton rat model, as well as provides gene sequences for mechanistic characterization of molecular pathways. Overall, our results provide generalizable insights into the effect of host genetics on host-virus interactions, as well as identify new host therapeutic targets for RSV treatment and prevention.
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Affiliation(s)
- Britton A Strickland
- Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Seesandra V Rajagopala
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, 1211 21st Avenue South, S2108 Medical Center North, Nashville, TN, 37232, USA
| | - Arash Kamali
- Sigmovir Biosystems Inc., 9610 Medical Center Drive, Suite 100, Rockville, MD, 20850, USA
| | - Meghan H Shilts
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, 1211 21st Avenue South, S2108 Medical Center North, Nashville, TN, 37232, USA
| | - Suman B Pakala
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, 1211 21st Avenue South, S2108 Medical Center North, Nashville, TN, 37232, USA
| | - Marina S Boukhvalova
- Sigmovir Biosystems Inc., 9610 Medical Center Drive, Suite 100, Rockville, MD, 20850, USA
| | - Shibu Yooseph
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, USA
| | - Jorge C G Blanco
- Sigmovir Biosystems Inc., 9610 Medical Center Drive, Suite 100, Rockville, MD, 20850, USA.
| | - Suman R Das
- Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, 1211 21st Avenue South, S2108 Medical Center North, Nashville, TN, 37232, USA.
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Feng Z, Xu L, Xie Z. Receptors for Respiratory Syncytial Virus Infection and Host Factors Regulating the Life Cycle of Respiratory Syncytial Virus. Front Cell Infect Microbiol 2022; 12:858629. [PMID: 35281439 PMCID: PMC8913501 DOI: 10.3389/fcimb.2022.858629] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 12/02/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a common cause of lower respiratory tract infections and responsible for a large proportion of mortality in children and the elderly. There are no licensed vaccines available to date. Prophylaxis and therapeutic RSV-specific antibodies are limited to populations at high risk owing to high cost and uncertain clinical value. Receptors and host factors are two determinants important for virus entry and establishment of infection in vivo. The identification and understanding of viral receptors and host factors can help us to gain insight into the pathogenesis of RSV infection. Herein, we reviewed receptors and host factors that have been reported thus far. RSV could bind to CX3C chemokine receptor 1 and heparan sulfate proteoglycans via the G protein, and to nucleolin, insulin-like growth factor-1 receptor, epidermal growth factor, and intercellular adhesion molecule-1 via the F protein. Seven host restriction factors and 13 host factors essential for RSV infection were reviewed. We characterized the functions and their roles in the life cycle of RSV, trying to provide an update on the information of RSV-related receptors and host factors.
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Affiliation(s)
- Ziheng Feng
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Lili Xu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Lili Xu,
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
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Gong L, Wu C, Lu M, Huang C, Chen Y, Li Z, Huang G, Liu D, Tang X. Analysis of Incidence and Clinical Characteristics of RSV Infection in Hospitalized Children: A Retrospective Study. Risk Manag Healthc Policy 2021; 14:1525-1531. [PMID: 33889036 PMCID: PMC8054821 DOI: 10.2147/rmhp.s305370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Objective To investigate the incidence and clinical characteristics of hospitalized children with respiratory syncytial virus (RSV) infection, and to provide evidence for the importance of preventive strategies and improvements in supportive care of RSV infection. Methods This retrospective study included children under 14 years who received throat swab test and were diagnosed with RSV infection from January 2019 to December 2020. Throat swabs and intravenous blood were the main sources of samples, which were obtained within 24 hours of hospitalization. Direct immunofluorescence assay was used to diagnose RSV infection. Results Among the 448 hospitalized children with RSV infection, males (71.9%) showed the highest proportion, the highest incidence was found in children<6 months old (45.3%), and 76.6% of them had pneumonia. Pharyngeal redness, cough, expectoration, and mental fatigue were the most common symptoms in hospitalized children of all ages. More than 60% of hospitalized children had increased lymphocyte count, aspartate aminotransferase, creatine kinase-MB form, lactate dehydrogenase, and α-HBDH levels. The rates of myocardial damage, respiratory failure, stay in the intensive care unit (ICU), use of mechanical ventilation, and absorption of oxygen were higher in children<6 months old. Except for children who were 37-60 months old, the percentage of length of hospital stay≥7 days in the other age groups was greater than 62.0%. Except for children who were 0-28 days old and>61 months old, the other age groups showed a re-hospitalization situation due to re-infection with RSV. In hospitalized children diagnosed with RSV infection from throat swabs, we also performed the RSV IgM test and found that 59.2% of them were positive, 8.0% of them were weakly positive, and 32.8% of them were negative. Conclusion This study analyzes the incidence and clinical characteristics of hospitalized children with RSV infection, which provides evidence for the importance of preventive strategies and improvements in supportive care of RSV infection.
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Affiliation(s)
- Ling Gong
- The First Clinical Medical College, Jinan University, Guangzhou, 510632, People's Republic of China.,Department of Respiratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, 563000, People's Republic of China
| | - Chunyan Wu
- Department of Respiratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, 563000, People's Republic of China
| | - Mingjie Lu
- Department of Respiratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, 563000, People's Republic of China
| | - Chengyan Huang
- Department of Respiratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, 563000, People's Republic of China
| | - Yongqian Chen
- Department of Respiratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, 563000, People's Republic of China
| | - Zhu Li
- Department of Respiratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, 563000, People's Republic of China
| | - Guichuan Huang
- Department of Respiratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, 563000, People's Republic of China
| | - Daishun Liu
- Department of Respiratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, 563000, People's Republic of China
| | - Xiaoping Tang
- The First Clinical Medical College, Jinan University, Guangzhou, 510632, People's Republic of China.,Infectious Disease Department, Guangzhou Eighth People's Hospital (the Affiliated Hospital ofGuangzhou Medical University), Guangzhou, 510060, People's Republic of China
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