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Jude MS, Yang CX, Filho FSL, Hernandez Cordero AI, Yang J, Shaipanich T, Li X, Lin D, MacIsaac J, Kobor MS, Sinha S, Nislow C, Singh A, Lam W, Lam S, Guillemi S, Harris M, Montaner J, Ng RT, Carlsten C, Paul Man SF, Sin DD, Leung JM. Microbial dysbiosis and the host airway epithelial response: insights into HIV-associated COPD using multi'omics profiling. Respir Res 2023; 24:124. [PMID: 37143066 PMCID: PMC10161506 DOI: 10.1186/s12931-023-02431-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 04/21/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND People living with HIV (PLWH) are at increased risk of developing Chronic Obstructive Pulmonary Disease (COPD) independent of cigarette smoking. We hypothesized that dysbiosis in PLWH is associated with epigenetic and transcriptomic disruptions in the airway epithelium. METHODS Airway epithelial brushings were collected from 18 COPD + HIV + , 16 COPD - HIV + , 22 COPD + HIV - and 20 COPD - HIV - subjects. The microbiome, methylome, and transcriptome were profiled using 16S sequencing, Illumina Infinium Methylation EPIC chip, and RNA sequencing, respectively. Multi 'omic integration was performed using Data Integration Analysis for Biomarker discovery using Latent cOmponents. A correlation > 0.7 was used to identify key interactions between the 'omes. RESULTS The COPD + HIV -, COPD -HIV + , and COPD + HIV + groups had reduced Shannon Diversity (p = 0.004, p = 0.023, and p = 5.5e-06, respectively) compared to individuals with neither COPD nor HIV, with the COPD + HIV + group demonstrating the most reduced diversity. Microbial communities were significantly different between the four groups (p = 0.001). Multi 'omic integration identified correlations between Bacteroidetes Prevotella, genes FUZ, FASTKD3, and ACVR1B, and epigenetic features CpG-FUZ and CpG-PHLDB3. CONCLUSION PLWH with COPD manifest decreased diversity and altered microbial communities in their airway epithelial microbiome. The reduction in Prevotella in this group was linked with epigenetic and transcriptomic disruptions in host genes including FUZ, FASTKD3, and ACVR1B.
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Affiliation(s)
- Marcia Smiti Jude
- Centre for Heart Lung Innovation, St. Paul's Hospital, Centre for Heart Lung Innovation, University of British Columbia, Room 166-1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, St. Paul's Hospital, Centre for Heart Lung Innovation, University of British Columbia, Room 166-1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada
| | - Fernando Studart Leitao Filho
- Centre for Heart Lung Innovation, St. Paul's Hospital, Centre for Heart Lung Innovation, University of British Columbia, Room 166-1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada
| | - Ana I Hernandez Cordero
- Centre for Heart Lung Innovation, St. Paul's Hospital, Centre for Heart Lung Innovation, University of British Columbia, Room 166-1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada
| | - Julia Yang
- Centre for Heart Lung Innovation, St. Paul's Hospital, Centre for Heart Lung Innovation, University of British Columbia, Room 166-1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada
| | - Tawimas Shaipanich
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Xuan Li
- Centre for Heart Lung Innovation, St. Paul's Hospital, Centre for Heart Lung Innovation, University of British Columbia, Room 166-1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada
| | - David Lin
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Julie MacIsaac
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Sunita Sinha
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Amrit Singh
- Centre for Heart Lung Innovation, St. Paul's Hospital, Centre for Heart Lung Innovation, University of British Columbia, Room 166-1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada
| | - Wan Lam
- British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Stephen Lam
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Silvia Guillemi
- British Columbia Centre for Excellence in HIV/AIDS, Providence Health Care, Vancouver, BC, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Providence Health Care, Vancouver, BC, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Julio Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Providence Health Care, Vancouver, BC, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Raymond T Ng
- Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
| | - Christopher Carlsten
- Centre for Heart Lung Innovation, St. Paul's Hospital, Centre for Heart Lung Innovation, University of British Columbia, Room 166-1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - S F Paul Man
- Centre for Heart Lung Innovation, St. Paul's Hospital, Centre for Heart Lung Innovation, University of British Columbia, Room 166-1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital, Centre for Heart Lung Innovation, University of British Columbia, Room 166-1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Janice M Leung
- Centre for Heart Lung Innovation, St. Paul's Hospital, Centre for Heart Lung Innovation, University of British Columbia, Room 166-1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada.
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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2
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Zhang Y, Zhu Y, Cao X, Zhang G, Liu S. Cell adhesion function was altered during the seasonal regression of the seminiferous epithelium in the mink species Neovison vison. J Anim Sci 2023; 101:skad190. [PMID: 37282598 PMCID: PMC10276646 DOI: 10.1093/jas/skad190] [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: 02/07/2023] [Accepted: 06/06/2023] [Indexed: 06/08/2023] Open
Abstract
Minks are seasonal breeders whose seminiferous epithelium undergoes regression through massive germ cell death, leaving only Sertoli cells and spermatogonial cells in the tubules. However, the molecular mechanisms that control this biological process remain largely unknown. This study describes a transcriptomic analysis of mink testes at various reproductive stages (active, regressing, and inactive). A comparison of seminiferous epithelium at different stages of reproduction shows that cell adhesion is altered during regression. In addition, genes and proteins involved in forming the blood-testis barrier (BTB) were examined in sexually active and inactive minks. The seminiferous epithelium in the testes of sexually inactive minks expressed occludin, but this expression was not discernibly observed in the testes of sexually active minks. There was no discernible expression of CX43 in the seminiferous epithelium in the testes of sexually inactive minks, but CX43 was expressed in the testes of sexually active minks. During the regression process, we observed a remarkable increase in the expression levels of Claudin-11, which is associated with Sertoli-germ cell junctions. In conclusion, these findings suggest a loss of Sertoli-germ cell adhesion, which may regulate postmeiotic cell shedding during testicular regression in mink.
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Affiliation(s)
- Yufei Zhang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Zhao Wu Da Road No. 306, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Hohhot 010018, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture, Hohhot 010018, China
| | - Yanzhu Zhu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xiaodong Cao
- School of pharmacy, Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonmous Region, China
- School of pharmacy New Drug Safety Evaluation Research Center, Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonmous Region, China
| | - Guanhua Zhang
- Agriculture and Animal Husbandry Comprehensive Inspection and Testing Center of chifeng, Inner Mongolia, China
| | - Shuying Liu
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Zhao Wu Da Road No. 306, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Hohhot 010018, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture, Hohhot 010018, China
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3
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De La Torre-Tarazona E, Ayala-Suárez R, Díez-Fuertes F, Alcamí J. Omic Technologies in HIV: Searching Transcriptional Signatures Involved in Long-Term Non-Progressor and HIV Controller Phenotypes. Front Immunol 2022; 13:926499. [PMID: 35844607 PMCID: PMC9284212 DOI: 10.3389/fimmu.2022.926499] [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: 04/22/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
This article reviews the main discoveries achieved by transcriptomic approaches on HIV controller (HIC) and long-term non-progressor (LTNP) individuals, who are able to suppress HIV replication and maintain high CD4+ T cell levels, respectively, in the absence of antiretroviral therapy. Different studies using high throughput techniques have elucidated multifactorial causes implied in natural control of HIV infection. Genes related to IFN response, calcium metabolism, ribosome biogenesis, among others, are commonly differentially expressed in LTNP/HIC individuals. Additionally, pathways related with activation, survival, proliferation, apoptosis and inflammation, can be deregulated in these individuals. Likewise, recent transcriptomic studies include high-throughput sequencing in specific immune cell subpopulations, finding additional gene expression patterns associated to viral control and/or non-progression in immune cell subsets. Herein, we provide an overview of the main differentially expressed genes and biological routes commonly observed on immune cells involved in HIV infection from HIC and LTNP individuals, analyzing also different technical aspects that could affect the data analysis and the future perspectives and gaps to be addressed in this field.
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Affiliation(s)
- Erick De La Torre-Tarazona
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Rubén Ayala-Suárez
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Francisco Díez-Fuertes
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- *Correspondence: Francisco Díez-Fuertes,
| | - José Alcamí
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Human Immunodeficiency Virus (HIV) Unit, Hospital Clínic de Barcelona, Barcelona, Spain
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4
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Li C, Zhu J, Shi H, Luo J, Zhao W, Shi H, Xu H, Wang H, Loor JJ. Comprehensive Transcriptome Profiling of Dairy Goat Mammary Gland Identifies Genes and Networks Crucial for Lactation and Fatty Acid Metabolism. Front Genet 2020; 11:878. [PMID: 33101357 PMCID: PMC7545057 DOI: 10.3389/fgene.2020.00878] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/17/2020] [Indexed: 11/17/2022] Open
Abstract
Milk fatty acids secreted by the mammary gland are one of the most important determinants of the nutritional value of goat milk. Unlike cow milk, limited data are available on the transcriptome-wide changes across stages of lactation in dairy goats. In this study, goat mammary gland tissue collected at peak lactation, cessation of milking, and involution were analyzed with digital gene expression (DGE) sequencing to generate longitudinal transcript profiles. A total of 51,299 unigenes were identified and further annotated to 12,763 genes, of which 9,131 were differentially expressed across various stages of lactation. Most abundant genes and differentially expressed genes (DEGs) were functionally classified through clusters of euKaryotic Orthologous Groups (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A total of 16 possible expression patterns were uncovered, and 13 genes were deemed novel candidates for regulation of lactation in the goat: POLG, SPTA1, KLC, GIT2, COPS3, PDP, CD31, USP16/29/37, TLL1, NCAPH, ABI2, DNAJC4, and MAPK8IP3. In addition, PLA2, CPT1, PLD, GGA, SRPRB, and AP4S1 are proposed as novel and promising candidates regulating mammary fatty acid metabolism. “Butirosin and neomycin biosynthesis” and “Glyoxylate and dicarboxylate metabolism” were the most impacted pathways, and revealed novel metabolic alterations in lipid metabolism as lactation progressed. Overall, the present study provides new insights into the synthesis and metabolism of fatty acids and lipid species in the mammary gland along with more detailed information on molecular regulation of lactogenesis. The major findings will benefit efforts to further improve milk quality in dairy goats.
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Affiliation(s)
- Cong Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Jiangjiang Zhu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Hengbo Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China.,College of Animal Science, Zhejiang University, Hangzhou, China
| | - Jun Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Wangsheng Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Huaiping Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Huifen Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Hui Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Juan J Loor
- Mammalian NutriPhysioGenomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
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5
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Ivanov S, Lagunin A, Filimonov D, Tarasova O. Network-Based Analysis of OMICs Data to Understand the HIV-Host Interaction. Front Microbiol 2020; 11:1314. [PMID: 32625189 PMCID: PMC7311653 DOI: 10.3389/fmicb.2020.01314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/25/2020] [Indexed: 12/22/2022] Open
Abstract
The interaction of human immunodeficiency virus with human cells is responsible for all stages of the viral life cycle, from the infection of CD4+ cells to reverse transcription, integration, and the assembly of new viral particles. To date, a large amount of OMICs data as well as information from functional genomics screenings regarding the HIV–host interaction has been accumulated in the literature and in public databases. We processed databases containing HIV–host interactions and found 2910 HIV-1-human protein-protein interactions, mostly related to viral group M subtype B, 137 interactions between human and HIV-1 coding and non-coding RNAs, essential for viral lifecycle and cell defense mechanisms, 232 transcriptomics, 27 proteomics, and 34 epigenomics HIV-related experiments. Numerous studies regarding network-based analysis of corresponding OMICs data have been published in recent years. We overview various types of molecular networks, which can be created using OMICs data, including HIV–human protein–protein interaction networks, co-expression networks, gene regulatory and signaling networks, and approaches for the analysis of their topology and dynamics. The network-based analysis can be used to determine the critical pathways and key proteins involved in the HIV life cycle, cellular and immune responses to infection, viral escape from host defense mechanisms, and mechanisms mediating different susceptibility of humans to infection. The proteins and pathways identified in these studies represent a basis for developing new anti-HIV therapeutic strategies such as new drugs preventing infection of CD4+ cells and viral replication, effective vaccines, “shock and kill” and “block and lock” approaches to cure latent infection.
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Affiliation(s)
- Sergey Ivanov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia.,Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexey Lagunin
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia.,Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry Filimonov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Olga Tarasova
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
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6
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Le Clerc S, Limou S, Zagury JF. Large-Scale "OMICS" Studies to Explore the Physiopatholgy of HIV-1 Infection. Front Genet 2019; 10:799. [PMID: 31572435 PMCID: PMC6754074 DOI: 10.3389/fgene.2019.00799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
In this review, we present the main large-scale experimental studies that have been performed in the HIV/AIDS field. These “omics” studies are based on several technologies including genotyping, RNA interference, and transcriptome or epigenome analysis. Due to the direct connection with disease evolution, there has been a large focus on genotyping cohorts of well-characterized patients through genome-wide association studies (GWASs), but there have also been several invitro studies such as small interfering RNA (siRNA) interference or transcriptome analyses of HIV-1–infected cells. After describing the major results obtained with these omics technologies—including some with a high relevance for HIV-1 treatment—we discuss the next steps that the community needs to embrace in order to derive new actionable therapeutic or diagnostic targets. Only integrative approaches that combine all big data results and consider their complex interactions will allow us to capture the global picture of HIV molecular pathogenesis. This novel challenge will require large collaborative efforts and represents a huge open field for innovative bioinformatics approaches.
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Affiliation(s)
- Sigrid Le Clerc
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation en Urologie et Néphrologie (ITUN), CHU de Nantes, Nantes, France.,Computer Sciences and Mathematics Department, Ecole Centrale de Nantes, Nantes, France
| | - Jean-François Zagury
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
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7
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Gonzalo-Gil E, Rapuano PB, Ikediobi U, Leibowitz R, Mehta S, Coskun AK, Porterfield JZ, Lampkin TD, Marconi VC, Rimland D, Walker BD, Deeks S, Sutton RE. Transcriptional down-regulation of ccr5 in a subset of HIV+ controllers and their family members. eLife 2019; 8:e44360. [PMID: 30964004 PMCID: PMC6456299 DOI: 10.7554/elife.44360] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/01/2019] [Indexed: 11/13/2022] Open
Abstract
HIV +Elite and Viremic controllers (EC/VCs) are able to control virus infection, perhaps because of host genetic determinants. We identified 16% (21 of 131) EC/VCs with CD4 +T cells with resistance specific to R5-tropic HIV, reversed after introduction of ccr5. R5 resistance was not observed in macrophages and depended upon the method of T cell activation. CD4 +T cells of these EC/VCs had lower ccr2 and ccr5 RNA levels, reduced CCR2 and CCR5 cell-surface expression, and decreased levels of secreted chemokines. T cells had no changes in chemokine receptor mRNA half-life but instead had lower levels of active transcription of ccr2 and ccr5, despite having more accessible chromatin by ATAC-seq. Other nearby genes were also down-regulated, over a region of ~500 kb on chromosome 3p21. This same R5 resistance phenotype was observed in family members of an index VC, also associated with ccr2/ccr5 down-regulation, suggesting that the phenotype is heritable.
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Affiliation(s)
- Elena Gonzalo-Gil
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Patrick B Rapuano
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Uchenna Ikediobi
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Rebecca Leibowitz
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Sameet Mehta
- Yale Center for Genome Analysis Bioinformatics groupYale University School of MedicineNew HavenUnited States
| | - Ayse K Coskun
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - J Zachary Porterfield
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Teagan D Lampkin
- Infectious Diseases SectionDallas VA Medical CenterDallasUnited States
| | - Vincent C Marconi
- Atlanta VA Medical Center, Emory University School of MedicineAtlantaUnited States
| | - David Rimland
- Atlanta VA Medical Center, Emory University School of MedicineAtlantaUnited States
| | - Bruce D Walker
- Ragon Institute of MGHMIT and Harvard UniversityCambridgeUnited States
| | - Steven Deeks
- Department of MedicineUniversity of California San FranciscoSan FranciscoUnited States
- Department of Epidemiology and BiostatisticsUniversity of California San FranciscoSan FranciscoUnited States
| | - Richard E Sutton
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
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8
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Boucau J, Madouasse J, Kourjian G, Carlin CS, Wambua D, Berberich MJ, Le Gall S. The Activation State of CD4 T Cells Alters Cellular Peptidase Activities, HIV Antigen Processing, and MHC Class I Presentation in a Sequence-Dependent Manner. THE JOURNAL OF IMMUNOLOGY 2019; 202:2856-2872. [PMID: 30936293 DOI: 10.4049/jimmunol.1700950] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 03/08/2019] [Indexed: 12/19/2022]
Abstract
CD4 T cell activation is critical to the initiation of adaptive immunity. CD4 T cells are also the main targets of HIV infection, and their activation status contributes to the maintenance and outcome of infection. Although the role of activation in the differentiation and proliferation of CD4 T cells is well studied, its impact on the processing and MHC class I (MHC-I) presentation of epitopes and immune recognition by CD8 T cells are not investigated. In this study, we show that the expression and hydrolytic activities of cellular peptidases are increased upon TCR-dependent and MHC-peptide activation of primary CD4 T cells from healthy or HIV-infected persons. Changes in peptidase activities altered the degradation patterns of HIV Ags analyzed by mass spectrometry, modifying the amount of MHC-I epitopes produced, the antigenicity of the degradation products, and the coverage of Ags by degradation peptides presentable by MHC-I. The computational analysis of 2237 degradation peptides generated during the degradation of various HIV-antigenic fragments in CD4 T cells identified cleavage sites that were predictably enhanced, reduced, or unchanged upon cellular activation. Epitope processing and presentation by CD4 T cells may be modulated by the activation state of cells in a sequence-dependent manner. Accordingly, cellular activation modified endogenous Ag processing and presentation and killing of HIV-infected CD4 T cells by CD8 T cells in a way that mirrored differences in in vitro epitope processing. The clearance of HIV-infected cells may rely on different immune responses according to activation state during HIV infection.
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Affiliation(s)
- Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | | | | | | | - Daniel Wambua
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | | | - Sylvie Le Gall
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
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9
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Gong X, Hu A, Li X, He J, Wu Z, Zuo X, Ning P. Coordinated expression of vascular endothelial growth factor A and urokinase-type plasminogen activator contributes to classical swine fever virus Shimen infection in macrophages. BMC Vet Res 2019; 15:82. [PMID: 30849965 PMCID: PMC6407193 DOI: 10.1186/s12917-019-1826-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 02/27/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Shimen strain of classical swine fever (CSF) virus (CSFV) causes CSF, which is mainly characterised by disseminated intravascular haemorrhage. Macrophages are an essential component of innate immunity against pathogenic microorganisms; however, the role of macrophages in CSF pathogenesis remains unclear. To illuminate the infective mechanism of CSFV, we used gene co-expression networks derived from macrophages infected with CSFV Shimen and CSFV C as well as uninfected macrophages to screen key regulatory genes, and their contributions to the pathogenesis of CSF were discussed. RESULTS Vascular endothelial growth factor A (VEGFA) and plasminogen activator, urokinase (PLAU, which encodes urokinase-type plasminogen activator [uPA]) were identified as coordinated genes expressed in macrophages by gene co-expression networks. Quantitative polymerase chain reaction and western blot analysis confirmed that VEGFA and PLAU were significantly up-regulated at both the transcription and translation levels after infection. Further, confocal microscopy analysis proposed that the VEGFA and uPA proteins were temporally co-localised with the CSFV protein E2. CONCLUSIONS Our findings suggest that co-expression of VEGFA and PLAU in macrophages contributes to CSFV Shimen infection and serves as a significant avenue for the strain to form an inflammatory microenvironment, providing new insight into the mechanisms of CSF caused by a virulent strain.
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Affiliation(s)
- Xiaocheng Gong
- School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710071, People's Republic of China
| | - Aoxue Hu
- School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710071, People's Republic of China
| | - Xuepeng Li
- School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710071, People's Republic of China
| | - Jun He
- School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710071, People's Republic of China
| | - Zhongxing Wu
- School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710071, People's Republic of China
| | - Xi Zuo
- School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710071, People's Republic of China
| | - Pengbo Ning
- School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710071, People's Republic of China. .,Engineering Research Center of Molecular and Neuro Imaging Ministry of Education, Xi'an, Shaanxi, 710071, People's Republic of China.
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10
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Guo K, Xu L, Wu M, Hou Y, Jiang Y, Lv J, Xu P, Fan Z, Zhang R, Xing F, Zhang Y. A Host Factor GPNMB Restricts Porcine Circovirus Type 2 (PCV2) Replication and Interacts With PCV2 ORF5 Protein. Front Microbiol 2019; 9:3295. [PMID: 30671053 PMCID: PMC6331448 DOI: 10.3389/fmicb.2018.03295] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022] Open
Abstract
Porcine circovirus type 2 (PCV2) is the infectious agent of postweaning multisystemic wasting syndrome (PMWS). The recently discovered open reading frame 5 (ORF5) in PCV2 genome encodes a non-structural protein. Previous study revealed that ORF5 protein inhibits cell proliferation and may interact with host transmembrane glycoprotein NMB (GPNMB). However, whether the GPNMB affects PCV2 replication and the underlying molecular mechanisms are still unknown. In this study, the transcriptome maps of PCV2-infected and ORF5-transfected porcine alveolar macrophages 3D4/2 (PAM) cells were profiled. The GPNMB gene was down-regulated in PCV2-infected and ORF5-transfected PAMs. By using glutathione S-transferase (GST) pull-down, co-immunoprecipitation (co-IP) and confocal microscopy approaches, we convincingly showed that PCV2 ORF5 protein interacts with GPNMB. Furthermore, by utilizing lentivirus mediated overexpression or knockdown approach, we showed that the cellular GPNMB significantly inhibits PCV2 replication and ORF5 expression. Moreover, GPNMB overexpressing leads to an increased Cyclin A expression and a reduced S phase, whereas GPNMB knockdown causes a decreased Cyclin A expression and a prolonged S phase. In conclusion, we identified a novel host factor GPNMB that interacts with PCV2 ORF5 protein and restricts PCV2 replication.
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Affiliation(s)
- Kangkang Guo
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Lei Xu
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Mengmeng Wu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yufeng Hou
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yanfen Jiang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jiangman Lv
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Panpan Xu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Zhixin Fan
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Ruiqi Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Fushan Xing
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yanming Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
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11
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Identification of differentially expressed genes through RNA sequencing in goats (Capra hircus) at different postnatal stages. PLoS One 2017; 12:e0182602. [PMID: 28800357 PMCID: PMC5553645 DOI: 10.1371/journal.pone.0182602] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/23/2017] [Indexed: 11/24/2022] Open
Abstract
Intramuscular fat (IMF) content and fatty acid composition of longissimus dorsi muscle (LM) change with growth, which partially determines the flavor and nutritional value of goat (Capra hircus) meat. However, unlike cattle, little information is available on the transcriptome-wide changes during different postnatal stages in small ruminants, especially goats. In this study, the sequencing reads of goat LM tissues collected from kid, youth, and adult period were mapped to the goat genome. Results showed that out of total 24 689 Unigenes, 20 435 Unigenes were annotated. Based on expected number of fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM), 111 annotated differentially expressed genes (DEGs) were identified among different postnatal stages, which were subsequently assigned to 16 possible expression patterns by series-cluster analysis. Functional classification by Gene Ontology (GO) analysis was used for selecting the genes showing highest expression related to lipid metabolism. Finally, we identified the node genes for lipid metabolism regulation using co-expression analysis. In conclusion, these data may uncover candidate genes having functional roles in regulation of goat muscle development and lipid metabolism during the various growth stages in goats.
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12
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Dong K, Chang S, Xie Q, Black-Pyrkosz A, Zhang H. Comparative transcriptomics of genetically divergent lines of chickens in response to Marek's disease virus challenge at cytolytic phase. PLoS One 2017; 12:e0178923. [PMID: 28591220 PMCID: PMC5462384 DOI: 10.1371/journal.pone.0178923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/22/2017] [Indexed: 11/30/2022] Open
Abstract
Marek's disease (MD), caused by Marek's disease virus (MDV), remains an economically significant threat to the poultry industry worldwide. Genetic resistance to MD is a promising alternative strategy to augment current control measures (vaccination and management). However, only a few functional genes reportedly conferring MD resistance have been identified. Here, we performed a comparative transcriptomics analysis of two highly inbred yet genetically divergent lines of chickens (line 63 and 72) that are resistant and susceptible to MD, respectively, in response to a very virulent plus strain of MDV (vv+MDV) challenge at cytolytic phase. A total of 203 DEGs in response to MDV challenge were identified in the two lines. Of these, 96 DEGs were in common for both lines, in addition to 36 and 71 DEGs that were specific for line 63 and 72, respectively. Functional enrichment analysis results showed the DEGs were significantly enriched in GO terms and pathways associated with immune response. Especially, the four DEGs, FGA, ALB, FN1, and F13A1 that reportedly facilitate virus invasion or immunosuppression, were found to be significantly up-regulated in the susceptible line 72 but down-regulated in the resistant line 63 birds. These results provide new resources for future studies to further elucidate the genetic mechanism conferring MD resistance.
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Affiliation(s)
- Kunzhe Dong
- USDA, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, Michigan, United States of America
- ORISE Fellow, USDA, Agriculture Research Service, Avian Disease and Oncology Laboratory, East Lansing, Michigan, United States of America
| | - Shuang Chang
- College of Veterinary Medicine, Shandong Agricultural University, Tai’an, Shandong, China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Alexis Black-Pyrkosz
- USDA, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, Michigan, United States of America
| | - Huanmin Zhang
- USDA, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, Michigan, United States of America
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13
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Expression profiling-based clustering of healthy subjects recapitulates classifications defined by clinical observation in Chinese medicine. J Genet Genomics 2017; 44:191-197. [DOI: 10.1016/j.jgg.2017.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 01/10/2017] [Accepted: 01/13/2017] [Indexed: 01/30/2023]
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14
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Liu S, Chen Y, Xie S, Xu Q, Chen J, Wang C, Wang Z, Ma S, Wu X, Zhang N. Gene Expression Profiles of HIV/AIDS Patients with Qi-Yin Deficiency and Dampness-Heat Retention. J Altern Complement Med 2016; 22:865-879. [PMID: 27759429 PMCID: PMC5116685 DOI: 10.1089/acm.2015.0350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Objectives: Traditional Chinese Medicine (TCM) applied in the clinic as a complementary and alternative therapy has helped improve immunity and reduce side effects and symptomatic treatment in patients with HIV/AIDS. However, the mechanisms of TCM syndromes are not clear. Transcriptomics enables the study of such TCM syndromes. Design: This study compared the messenger RNA (mRNA) expressions of healthy persons and patients with HIV/AIDS who had two common TCM syndromes, qi-yin deficiency and dampness-heat retention, to find the difference in HIV/AIDS with TCM syndromes. Results: Comparison with healthy persons identified 113 mRNAs—41 enhanced and 72 decreased—in the qi-yin deficiency group. Additionally, 76 mRNAs were found in the dampness-heat retention group: 14 increased and 62 decreased. Functional genetic analysis of the mRNAs indicated that two TCM syndromes were correlated with cell apoptosis, immunoinflammatory responses, and lymphocyte activation. Differentially expressed mRNAs in the qi-yin deficiency group were obviously associated with cellular activity, communication, protein localization, cellular ion homeostasis, and regulation of cell motion, whereas mRNAs in the dampness-heat retention group were associated with sequence-specific DNA binding, cellular response to stress, and hemopoietic or lymphoid organ development. Conclusions: These results suggest that the formation of different TCM syndromes in patients with HIV/AIDS were founded on biological transcriptomics, which reveal mechanisms of the formation of these syndromes in HIV/AIDS. Differentially expressed mRNAs in two TCM syndrome groups tended to normalize after TCM intervention, which indicates that TCM might remit symptoms by changing genetic expression.
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Affiliation(s)
- Sa Liu
- 1 Department of Clinical Foundation of TCM, Henan University of TCM , Zhengzhou, China
| | - Yulong Chen
- 2 Department of Molecular Biology, Henan University of TCM , Zhengzhou, China
| | - Shiping Xie
- 1 Department of Clinical Foundation of TCM, Henan University of TCM , Zhengzhou, China
| | - Qianlei Xu
- 3 Department of Infection Epidemiology, The First Affiliated Hospital of Henan, University of TCM , Zhengzhou, China
| | - Jianshe Chen
- 4 Andrology of Henan, Chinese Medicine Hospital , Zhengzhou, China
| | - Changhai Wang
- 5 Department of Diagnostics, Traditional Chinese Medicine, Henan University of TCM , Zhengzhou, China
| | - Zhao Wang
- 6 College of Life Science, Tsinghua University , Beijing, China
| | - Suna Ma
- 7 AIDS Institute of Henan University of TCM, Henan University of TCM , Zhengzhou, China
| | - Xingwei Wu
- 7 AIDS Institute of Henan University of TCM, Henan University of TCM , Zhengzhou, China
| | - Ning Zhang
- 8 Department of Internal Medicine of TCM, People's Hospital of Zhongmou County , Zhongmou, China
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15
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Ning P, Zhou Y, Liang W, Zhang Y. Different RNA splicing mechanisms contribute to diverse infective outcome of classical swine fever viruses of differing virulence: insights from the deep sequencing data in swine umbilical vein endothelial cells. PeerJ 2016; 4:e2113. [PMID: 27330868 PMCID: PMC4906664 DOI: 10.7717/peerj.2113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/17/2016] [Indexed: 11/20/2022] Open
Abstract
Molecular mechanisms underlying RNA splicing regulation in response to viral infection are poorly understood. Classical swine fever (CSF), one of the most economically important and highly contagious swine diseases worldwide, is caused by classical swine fever virus (CSFV). Here, we used high-throughput sequencing to obtain the digital gene expression (DGE) profile in swine umbilical vein endothelial cells (SUVEC) to identify different response genes for CSFV by using both Shimen and C strains. The numbers of clean tags obtained from the libraries of the control and both CSFV-infected libraries were 3,473,370, 3,498,355, and 3,327,493 respectively. In the comparison among the control, CSFV-C, and CSFV-Shimen groups, 644, 158, and 677 differentially expressed genes (DEGs) were confirmed in the three groups. Pathway enrichment analysis showed that many of these DEGs were enriched in spliceosome, ribosome, proteasome, ubiquitin-mediated proteolysis, cell cycle, focal adhesion, Wnt signalling pathway, etc., where the processes differ between CSFV strains of differing virulence. To further elucidate important mechanisms related to the differential infection by the CSFV Shimen and C strains, we identified four possible profiles to assess the significantly expressed genes only by CSFV Shimen or CSFV C strain. GO analysis showed that infection with CSFV Shimen and C strains disturbed ‘RNA splicing’ of SUVEC, resulting in differential ‘gene expression’ in SUVEC. Mammalian target of rapamycin (mTOR) was identified as a significant response regulator contributed to impact on SUVEC function for CSFV Shimen. This computational study suggests that CSFV of differing virulence could induce alterations in RNA splicing regulation in the host cell to change cell metabolism, resulting in acute haemorrhage and pathological damage or infectious tolerance.
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Affiliation(s)
- Pengbo Ning
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi; School of Life Science and Technology, Xidian University, Xi'an, China
| | - Yulu Zhou
- College of Science, Northwest A&F University , Yangling , China
| | - Wulong Liang
- College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi
| | - Yanming Zhang
- College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi
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16
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Devadas K, Biswas S, Haleyurgirisetty M, Wood O, Ragupathy V, Lee S, Hewlett I. Analysis of Host Gene Expression Profile in HIV-1 and HIV-2 Infected T-Cells. PLoS One 2016; 11:e0147421. [PMID: 26821323 PMCID: PMC4731573 DOI: 10.1371/journal.pone.0147421] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 01/04/2016] [Indexed: 01/09/2023] Open
Abstract
HIV replication is closely regulated by a complex pathway of host factors, many of them being determinants of cell tropism and host susceptibility to HIV infection. These host factors are known to exert a positive or negative influence on the replication of the two major types of HIV, HIV-1 and HIV-2, thereby modulating virus infectivity, host response to infection and ultimately disease progression profiles characteristic of these two types. Understanding the differential regulation of host cellular factors in response to HIV-1 and HIV-2 infections will help us to understand the apparent differences in rates of disease progression and pathogenesis. This knowledge would aid in the discovery of new biomarkers that may serve as novel targets for therapy and diagnosis. The objective of this study was to determine the differential expression of host genes in response to HIV-1/HIV-2 infection. To achieve this, we analyzed the effects of HIV-1 (MN) and HIV-2 (ROD) infection on the expression of host factors in PBMC at the RNA level using the Agilent Whole Human Genome Oligo Microarray. Differentially expressed genes were identified and their biological functions determined. Host gene expression profiles were significantly changed. Gene expression profiling analysis identified a subset of differentially expressed genes in HIV-1 and HIV-2 infected cells. Genes involved in cellular metabolism, apoptosis, immune cell proliferation and activation, cytokines, chemokines, and transcription factors were differentially expressed in HIV-1 infected cells. Relatively few genes were differentially expressed in cells infected with HIV-2.
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Affiliation(s)
- Krishnakumar Devadas
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, Maryland, 20993–0002, United States of America
- * E-mail: (KD); (IKH)
| | - Santanu Biswas
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, Maryland, 20993–0002, United States of America
| | - Mohan Haleyurgirisetty
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, Maryland, 20993–0002, United States of America
| | - Owen Wood
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, Maryland, 20993–0002, United States of America
| | - Viswanath Ragupathy
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, Maryland, 20993–0002, United States of America
| | - Sherwin Lee
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, Maryland, 20993–0002, United States of America
| | - Indira Hewlett
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, Maryland, 20993–0002, United States of America
- * E-mail: (KD); (IKH)
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17
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Bobbin ML, Burnett JC, Rossi JJ. RNA interference approaches for treatment of HIV-1 infection. Genome Med 2015; 7:50. [PMID: 26019725 PMCID: PMC4445287 DOI: 10.1186/s13073-015-0174-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/13/2015] [Indexed: 01/05/2023] Open
Abstract
HIV/AIDS is a chronic and debilitating disease that cannot be cured with current antiretroviral drugs. While combinatorial antiretroviral therapy (cART) can potently suppress HIV-1 replication and delay the onset of AIDS, viral mutagenesis often leads to viral escape from multiple drugs. In addition to the pharmacological agents that comprise cART drug cocktails, new biological therapeutics are reaching the clinic. These include gene-based therapies that utilize RNA interference (RNAi) to silence the expression of viral or host mRNA targets that are required for HIV-1 infection and/or replication. RNAi allows sequence-specific design to compensate for viral mutants and natural variants, thereby drastically expanding the number of therapeutic targets beyond the capabilities of cART. Recent advances in clinical and preclinical studies have demonstrated the promise of RNAi therapeutics, reinforcing the concept that RNAi-based agents might offer a safe, effective, and more durable approach for the treatment of HIV/AIDS. Nevertheless, there are challenges that must be overcome in order for RNAi therapeutics to reach their clinical potential. These include the refinement of strategies for delivery and to reduce the risk of mutational escape. In this review, we provide an overview of RNAi-based therapies for HIV-1, examine a variety of combinatorial RNAi strategies, and discuss approaches for ex vivo delivery and in vivo delivery.
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Affiliation(s)
- Maggie L Bobbin
- Irell & Manella School of Biological Sciences, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 91010 USA
| | - John C Burnett
- Irell & Manella School of Biological Sciences, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 91010 USA ; Department of Molecular and Cell Biology, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 9101 USA
| | - John J Rossi
- Irell & Manella School of Biological Sciences, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 91010 USA ; Department of Molecular and Cell Biology, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 9101 USA
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Chen SK, Chung CA, Cheng YC, Huang CJ, Chen WY, Ruaan RC, Li C, Tsao CW, Hu WW, Chien CC. Toll-like receptor 6 and connective tissue growth factor are significantly upregulated in mitomycin-C-treated urothelial carcinoma cells under hydrostatic pressure stimulation. Genet Test Mol Biomarkers 2014; 18:410-6. [PMID: 24689870 DOI: 10.1089/gtmb.2013.0443] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Urothelial carcinoma (UC) is the most common histologic subtype of bladder cancer. The administration of mitomycin C (MMC) into the bladder after transurethral resection of the bladder tumor (TURBT) is a common treatment strategy for preventing recurrence after surgery. We previously applied hydrostatic pressure combined with MMC in UC cells and found that hydrostatic pressure synergistically enhanced MMC-induced UC cell apoptosis through the Fas/FasL pathways. To understand the alteration of gene expressions in UC cells caused by hydrostatic pressure and MMC, oligonucleotide microarray was used to explore all the differentially expressed genes. RESULTS After bioinformatics analysis and gene annotation, Toll-like receptor 6 (TLR6) and connective tissue growth factor (CTGF) showed significant upregulation among altered genes, and their gene and protein expressions with each treatment of UC cells were validated by quantitative real-time PCR and immunoblotting. CONCLUSION Under treatment with MMC and hydrostatic pressure, UC cells showed increasing apoptosis using extrinsic pathways through upregulation of TLR6 and CTGF.
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Affiliation(s)
- Shao-Kuan Chen
- 1 Department of Urology, Sijhih Cathay General Hospital , New Taipei City, Taiwan
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Guo H, Sun F, Huang W, Liu Z, Zhang S, Zhou Q, Liang C. The effect of rhG-CSF on spleen transcriptome in mouse leukopenia model induced by cyclophosphamide. Immunopharmacol Immunotoxicol 2014; 36:114-23. [PMID: 24611752 DOI: 10.3109/08923973.2013.869696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
CONTEXT RhG-CSF significantly elevates the otherwise reduced numbers of leukocytes following chemotherapy. However, prior work has predominantly focused on the effect of rhG-CSF on the hematopoietic system, and few studies have focused on the immune system. OBJECTIVE We aimed to investigate the effect of rhG-CSF on the immune system transcriptome in a mouse leukopenia model that was induced by cyclophosphamide. MATERIALS AND METHODS A cyclophosphamide leukopenia model was established in C57BL/6 mice, which were randomly divided into a normal control group (CK), a cyclophosphamide model group (CY) and a rhG-CSF treatment group (rhG-CSF). After 3 d of rhG-CSF treatment, a mouse gene expression microarray enabled evaluation of changes in the transcriptome in the mouse spleen. RESULTS About 3552 differentially expressed genes occurred among the three experimental groups, of which 74.9% (2659) concentrated on three gene expression patterns. Gene ontology and pathway analysis of 2659 differential genes showed that early in treatment when leukocyte counts remained low, rhG-CSF recovered the transcription of genes that were related to DNA damage repair and metabolism of nucleotides and amino acids. By contrast, rhG-CSF inhibited the transcription of genes involved in transendothelial migration and endocytosis, and dampened the transcription of genes associated with cell proliferation as compared with the CY group. CONCLUSIONS Our study suggests that rhG-CSF recovered metabolism in immune cells, suppressed in vivo immune defense, and attenuated immune cell proliferation in a cyclophosphamide induced leukopenia model. Use of gene expression microarrays can macroscopically and systematically inform the mechanism of rhG-CSF on immune cells.
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Affiliation(s)
- He Guo
- Department of Cytobiology, Institute of Frontier Medical Sciences, Jilin University , Changchun , China
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