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Rashid F, Xie Z, Wei Y, Xie Z, Xie L, Li M, Luo S. Biological features of fowl adenovirus serotype-4. Front Cell Infect Microbiol 2024; 14:1370414. [PMID: 38915924 PMCID: PMC11194357 DOI: 10.3389/fcimb.2024.1370414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Fowl adenovirus serotype 4 (FAdV-4) is highly pathogenic to broilers aged 3 to 5 weeks and has caused considerable economic loss in the poultry industry worldwide. FAdV-4 is the causative agent of hydropericardium-hepatitis syndrome (HHS) or hydropericardium syndrome (HPS). The virus targets mainly the liver, and HPS symptoms are observed in infected chickens. This disease was first reported in Pakistan but has now spread worldwide, and over time, various deletions in the FAdV genome and mutations in its major structural proteins have been detected. This review provides detailed information about FAdV-4 genome organization, physiological features, epidemiology, coinfection with other viruses, and host immune suppression. Moreover, we investigated the role and functions of important structural proteins in FAdV-4 pathogenesis. Finally, the potential regulatory effects of FAdV-4 infection on ncRNAs are also discussed.
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Affiliation(s)
- Farooq Rashid
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
| | - Zhixun Xie
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
| | - You Wei
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
| | - Zhiqin Xie
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
| | - Liji Xie
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
| | - Meng Li
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
| | - Sisi Luo
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
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Hossain MI, Asha AT, Hossain MA, Mahmud S, Chowdhury K, Mohiuddin RB, Nahar N, Sarker S, Napis S, Hossain MS, Mohiuddin A. Investigating the role of hypothetical protein (AAB33144.1) in HIV-1 virus pathogenicity: A comparative study with FDA-Approved inhibitor compounds through In silico analysis and molecular docking. Heliyon 2024; 10:e23183. [PMID: 38163140 PMCID: PMC10755284 DOI: 10.1016/j.heliyon.2023.e23183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Aim and objective Due to the a lot of unexplored proteins in HIV-1, this research aimed to explore the functional roles of a hypothetical protein (AAB33144.1) that might play a key role in HIV-1 pathogenicity. Methods The homologous protein was identified along with building and validating the 3D structure by searching several bioinformatics tools. Results Retroviral aspartyl protease and retropepsin like functional domains and motifs, folding pattern (cupredoxins), and subcellular localization in cytoplasmic membrane were determined as biological activity. Besides, the functional annotation revealed that the chosen hypothetical protein possessed protease-like activity. To validate our generated protein 3D structure, molecular docking was performed with five compounds where nelfinavir showed (-8.2 kcal/mol) best binding affinity against HXB2 viral protease (PDB ID: 7SJX) and main protease (PDB ID: 4EYR) protein. Conclusions This study suggests that the annotated hypothetical protein related to protease action, which may be useful in viral genetics and drug discovery.
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Affiliation(s)
- Md. Imran Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Anika Tabassum Asha
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Md. Arju Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Shahin Mahmud
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Kamal Chowdhury
- Biology Department, Claflin University, 400 Magnolia St, Orangeburg, SC 29115, USA
| | - Ramisa Binti Mohiuddin
- Department of Pharmacy, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Nazneen Nahar
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Saborni Sarker
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Suhaimi Napis
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor D.E., Malaysia
| | - Md Sanower Hossain
- Centre for Sustainability of Mineral and Resource Recovery Technology (Pusat SMaRRT), Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan 26300, Malaysia
| | - A.K.M. Mohiuddin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
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Imamichi T, Chen Q, Sowrirajan B, Yang J, Laverdure S, Marquez M, Mele AR, Watkins C, Adelsberger JW, Higgins J, Sui H. Interleukin-27-induced HIV-resistant dendritic cells suppress reveres transcription following virus entry in an SPTBN1, autophagy, and YB-1 independent manner. PLoS One 2023; 18:e0287829. [PMID: 37910521 PMCID: PMC10619827 DOI: 10.1371/journal.pone.0287829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/03/2023] [Indexed: 11/03/2023] Open
Abstract
Interleukin (IL)-27, a member of the IL-12 family of cytokines, induces human immunodeficiency virus (HIV)-resistant monocyte-derived macrophages and T cells. This resistance is mediated via the downregulation of spectrin beta, non-erythrocytic 1 (SPTBN1), induction of autophagy, or suppression of the acetylation of Y-box binding protein-1 (YB-1); however, the role of IL-27 administration during the induction of immature monocyte-derived dendritic cells (iDC) is poorly investigated. In the current study, we investigated the function of IL-27-induced iDC (27DC) on HIV infection. 27DC inhibited HIV infection by 95 ± 3% without significant changes in the expression of CD4, CCR5, and SPTBN1 expression, autophagy induction and acetylation of YB-1 compared to iDC. An HIV proviral DNA copy number assay displayed that 27DC suppressed reverse transcriptase (RT) reaction without influencing the virus entry. A DNA microarray analysis was performed to identify the differentially expressed genes between 27DC and iDC. Compared to iDC, 51 genes were differentially expressed in 27DC, with more than 3-fold changes in four independent donors. Cross-reference analysis with the reported 2,214 HIV regulatory host genes identified nine genes as potential interests: Ankyrin repeat domain 22, Guanylate binding protein (GBP)-1, -2, -4, -5, Stabilin 1, Serpin family G member 1 (SERPING1), Interferon alpha inducible protein 6, and Interferon-induced protein with tetratricopeptide repeats 3. A knock-down study using si-RNA failed to determine a key factor associated with the anti-HIV activity due to the induction of robust amounts of off-target effects. Overexpression of each protein in cells had no impact on HIV infection. Thus, we could not define the mechanism of the anti-HIV effect in 27DC. However, our findings indicated that IL-27 differentiates monocytes into HIV-resistant DC, and the inhibitory mechanism differs from IL-27-induced HIV-resistant macrophages and T cells.
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Affiliation(s)
- Tomozumi Imamichi
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Qian Chen
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Bharatwaj Sowrirajan
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Jun Yang
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Sylvain Laverdure
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Mayra Marquez
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Anthony R. Mele
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Catherine Watkins
- AIDS monitoring Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Joseph W. Adelsberger
- AIDS monitoring Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Jeanette Higgins
- AIDS monitoring Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Hongyan Sui
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
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Lu X, Zhang Q, Xie Y. TCFL5 knockdown sensitizes DLBCL to doxorubicin treatment via regulation of GPX4. Cell Signal 2023; 110:110831. [PMID: 37516394 DOI: 10.1016/j.cellsig.2023.110831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/09/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
BACKGROUND Resistance to chemo-drug is a major cause of bad outcome in diffuse large B-cell lymphoma (DLBCL). It was reported that TCFL5 may be related to chemoresistance in childhood acute lymphoblastic leukemia. However, it is still unclear whether TCFL5 is involved in DLBCL drug-resistance. METHODS To explore the underlying mechanism of doxorubicin resistance, recombinant lentivirus was applied to control expression of TCFL5 in DLBCL cells. CCK-8 assay was perfomed to investigate the influence of doxorubicin on proliferation of TCFL5-overexpressed or sh-TCFL5 DLBCL cells. Correlation between TCFL5 and GPX4 was analyzed with bioinformatic methods, which was further confirmed by qPCR and western blot. TCFL5 overexpression conferred doxorubicin resistance via regulating GPX4 and was verified by TUNEL assay and western blot in vitro and mice model in vivo. RESULTS TCFL5 was enriched in DLBCL cells and conferred doxorubicin resistance through binding to GPX4. Inhibition of TCFL5 enhanced the sensitivity of DLBCL cells to doxorubicin. GPX4 knockdown reversed doxorubicin resistance in TCFL5-overexpressed DLBCL cells. CONCLUSION DLBCL cells overexpress TCFL5 that promotes chemoresistance by regulating GPX4. Targeting TCFL5 may provide a prospective therapeutic strategy for doxorubicin-resistant DLBCL.
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Affiliation(s)
- Xueying Lu
- Graduate School, Nanjing Medical University, Nanjing 210000, China
| | - Quan'e Zhang
- Department of Hematology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian 223300, China
| | - Yandong Xie
- Graduate School, Nanjing Medical University, Nanjing 210000, China.
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Geretz A, Ehrenberg PK, Clifford RJ, Laliberté A, Prelli Bozzo C, Eiser D, Kundu G, Yum LK, Apps R, Creegan M, Gunady M, Shangguan S, Sanders-Buell E, Sacdalan C, Phanuphak N, Tovanabutra S, Russell RM, Bibollet-Ruche F, Robb ML, Michael NL, Ake JA, Vasan S, Hsu DC, Hahn BH, Kirchhoff F, Thomas R. Single-cell transcriptomics identifies prothymosin α restriction of HIV-1 in vivo. Sci Transl Med 2023; 15:eadg0873. [PMID: 37531416 DOI: 10.1126/scitranslmed.adg0873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/21/2023] [Indexed: 08/04/2023]
Abstract
Host restriction factors play key roles in innate antiviral defense, but it remains poorly understood which of them restricts HIV-1 in vivo. Here, we used single-cell transcriptomic analysis to identify host factors associated with HIV-1 control during acute infection by correlating host gene expression with viral RNA abundance within individual cells. Wide sequencing of cells from one participant with the highest plasma viral load revealed that intracellular viral RNA transcription correlates inversely with expression of the gene PTMA, which encodes prothymosin α. This association was genome-wide significant (Padjusted < 0.05) and was validated in 28 additional participants from Thailand and the Americas with HIV-1 CRF01_AE and subtype B infections, respectively. Overexpression of prothymosin α in vitro confirmed that this cellular factor inhibits HIV-1 transcription and infectious virus production. Our results identify prothymosin α as a host factor that restricts HIV-1 infection in vivo, which has implications for viral transmission and cure strategies.
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Affiliation(s)
- Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Robert J Clifford
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Alexandre Laliberté
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | | | - Daina Eiser
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Gautam Kundu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Lauren K Yum
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Richard Apps
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Creegan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Mohamed Gunady
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Shida Shangguan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Carlo Sacdalan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Nittaya Phanuphak
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Ronnie M Russell
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederic Bibollet-Ruche
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Nelson L Michael
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Julie A Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Denise C Hsu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
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Imamichi T, Chen Q, Sowrirajan B, Yang J, Laverdure S, Mele AR, Watkins C, Adelsberger JW, Higgins J, Sui H. Interleukin-27-induced HIV-resistant dendritic cells suppress reveres transcription following virus entry in an SPTBN1, Autophagy, and YB-1 independent manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544550. [PMID: 37546823 PMCID: PMC10402176 DOI: 10.1101/2023.06.12.544550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Interleukin (IL)-27, a member of the IL-12 family of cytokines, induces human immunodeficiency virus (HIV)-resistant monocyte-derived macrophages and T cells. This resistance is mediated via the downregulation of spectrin beta, non-erythrocytic 1 (SPTBN1), induction of autophagy, or suppression of the acetylation of Y-box binding protein-1 (YB-1); however, the role of IL-27 administration during the induction of immature monocyte-derived dendritic cells (iDC) is poorly investigated. In the current study, we investigated the function of IL-27-induced iDC (27DC) on HIV infection. 27DC inhibited HIV infection by 95 ± 3 % without significant changes in the expression of CD4, CCR5, and SPTBN1 expression, autophagy induction and acetylation of YB-1 compared to iDC. An HIV proviral DNA copy number assay displayed that 27DC suppressed reverse transcriptase (RT) reaction without influencing the virus entry. A DNA microarray analysis was performed to identify the differentially expressed genes between 27DC and iDC. Compared to iDC, 51 genes were differentially expressed in 27DC, with more than 3-fold changes in four independent donors. Cross-reference analysis with the reported 2,214 HIV regulatory host genes identified nine genes as potential interests: Ankyrin repeat domain 22, Guanylate binding protein (GBP)-1, -2, -4, -5, Stabilin 1, Serpin family G member 1 (SERPING1), Interferon alpha inducible protein 6, and Interferon-induced protein with tetratricopeptide repeats 3. A knock-down study using si-RNA failed to determine a key factor associated with the anti-HIV activity due to the induction of robust amounts of off-target effects. Overexpression of each protein in cells had no impact on HIV infection. Thus, we could not define the mechanism of the anti-HIV effect in 27DC. However, our findings indicated that IL-27 differentiates monocytes into HIV-resistant DC, and the inhibitory mechanism differs from IL-27-induced HIV-resistant macrophages and T cells.
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Affiliation(s)
- Tomozumi Imamichi
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Qian Chen
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Bharatwaj Sowrirajan
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Jun Yang
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Sylvain Laverdure
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Anthony R. Mele
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Catherine Watkins
- AIDS monitoring Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Joseph W. Adelsberger
- AIDS monitoring Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Jeanette Higgins
- AIDS monitoring Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Hongyan Sui
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
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Parker E, Judge MA, Pastor L, Fuente-Soro L, Jairoce C, Carter KW, Anderson D, Mandomando I, Clifford HD, Naniche D, Le Souëf PN. Gene dysregulation in acute HIV-1 infection – early transcriptomic analysis reveals the crucial biological functions affected. Front Cell Infect Microbiol 2023; 13:1074847. [PMID: 37077524 PMCID: PMC10106835 DOI: 10.3389/fcimb.2023.1074847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
IntroductionTranscriptomic analyses from early human immunodeficiency virus (HIV) infection have the potential to reveal how HIV causes widespread and lasting damage to biological functions, especially in the immune system. Previous studies have been limited by difficulties in obtaining early specimens.MethodsA hospital symptom-based screening approach was applied in a rural Mozambican setting to enrol patients with suspected acute HIV infection (Fiebig stage I-IV). Blood samples were collected from all those recruited, so that acute cases and contemporaneously recruited, uninfected controls were included. PBMC were isolated and sequenced using RNA-seq. Sample cellular composition was estimated from gene expression data. Differential gene expression analysis was completed, and correlations were determined between viral load and differential gene expression. Biological implications were examined using Cytoscape, gene set enrichment analysis, and enrichment mapping.ResultsTwenty-nine HIV infected subjects one month from presentation and 46 uninfected controls were included in this study. Subjects with acute HIV infection demonstrated profound gene dysregulation, with 6131 (almost 13% of the genome mapped in this study) significantly differentially expressed. Viral load was correlated with 1.6% of dysregulated genes, in particular, highly upregulated genes involved in key cell cycle functions, were correlated with viremia. The most profoundly upregulated biological functions related to cell cycle regulation, in particular, CDCA7 may drive aberrant cell division, promoted by overexpressed E2F family proteins. Also upregulated were DNA repair and replication, microtubule and spindle organization, and immune activation and response. The interferome of acute HIV was characterized by broad activation of interferon-stimulated genes with antiviral functions, most notably IFI27 and OTOF. BCL2 downregulation alongside upregulation of several apoptotic trigger genes and downstream effectors may contribute to cycle arrest and apoptosis. Transmembrane protein 155 (TMEM155) was consistently highly overexpressed during acute infection, with roles hitherto unknown.DiscussionOur study contributes to a better understanding of the mechanisms of early HIV-induced immune damage. These findings have the potential to lead to new earlier interventions that improve outcomes.
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Affiliation(s)
- Erica Parker
- School of Medicine, University of Western Australia, Crawley, WA, Australia
| | - Melinda A. Judge
- School of Medicine, University of Western Australia, Crawley, WA, Australia
- *Correspondence: Melinda A. Judge,
| | - Lucia Pastor
- ISGlobal, Barcelona Institute for Global Health, Hospital Clinic–Universitat de Barcelona, Barcelona, Spain
- AIDS Research Institute-IrsiCaixa, Institut Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona, Spain
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | - Laura Fuente-Soro
- ISGlobal, Barcelona Institute for Global Health, Hospital Clinic–Universitat de Barcelona, Barcelona, Spain
| | - Chenjerai Jairoce
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | | | | | - Inácio Mandomando
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | | | - Denise Naniche
- ISGlobal, Barcelona Institute for Global Health, Hospital Clinic–Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | - Peter Neils Le Souëf
- School of Medicine, University of Western Australia, Crawley, WA, Australia
- Telethon Kids Institute, Perth, WA, Australia
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Xiong H, Chen Z, Lin B, Chen W, Li Q, Li Y, Fang M, Wang Y, Zhang H, Lu Y, Bi A, Wu S, Jia Y, Wang X. Comprehensive analysis of FKBP4/NR3C1/TMEM173 signaling pathway in triple-negative breast cancer cell and dendritic cell among tumor microenvironment. Mol Ther Oncolytics 2022; 24:371-384. [PMID: 35118194 PMCID: PMC8792076 DOI: 10.1016/j.omto.2021.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/31/2021] [Indexed: 11/17/2022] Open
Abstract
TMEM173 is a pattern recognition receptor detecting cytoplasmic nucleic acids and transmits cGAS related signals that activate host innate immune responses. It has also been found to be involved in tumor immunity and tumorigenesis. In this study, we first identified that the FKBP4/NR3C1 axis was a novel negative regulator of TMEM173 in human breast cancer (BC) cells. The effect of FKBP4 appeared to be at the transcriptional level of TMEM173, because it could suppress the promoter activity of TMEM173, thereby affecting TMEM173 at mRNA and protein levels. Past studies, our bioinformatics analysis, and in vitro experiments further implied that FKBP4 regulated TMEM173 via regulating nuclear translocation of NR3C1. We then demonstrated that the FKBP4/NR3C1/TMEM173 signaling pathway could regulate autophagy and proliferation of BC cells as well as dendritic cell (DC) abundance through exosome release. Our study found an unprecedented strategy used by BC to escape from TMEM173 mediated tumor suppression. Identification of the FKBP4/NR3C1 axis as a novel TMEM173 regulator would provide insights for novel anti-tumor strategy against BC among tumor microenvironment.
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Affiliation(s)
- Hanchu Xiong
- Department of Radiation Oncology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310000, China
| | - Zihan Chen
- Surgical Intensive Care Unit, First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310000, China
| | - Baihua Lin
- Department of Radiation Oncology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310000, China
| | - Weijun Chen
- Department of Radiation Oncology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310000, China
| | - Qiang Li
- Department of Radiation Oncology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310000, China
| | - Yucheng Li
- Department of Radiation Oncology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310000, China
| | - Min Fang
- Department of Radiation Oncology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310000, China
| | - Ying Wang
- Department of Radiation Oncology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310000, China
| | - Haibo Zhang
- Department of Radiation Oncology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310000, China
| | - Yanwei Lu
- Department of Radiation Oncology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310000, China
| | - Aihong Bi
- Department of Radiation Oncology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310000, China
| | - Shuqiang Wu
- Department of Radiation Oncology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310000, China
| | - Yongshi Jia
- Department of Radiation Oncology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310000, China
| | - Xiao Wang
- Department of Medical Oncology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310000, China
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Xiong H, Chen Z, Lin B, Xie B, Liu X, Chen C, Li Z, Jia Y, Wu Z, Yang M, Jia Y, Wang L, Zhou J, Meng X. Naringenin Regulates FKBP4/NR3C1/NRF2 Axis in Autophagy and Proliferation of Breast Cancer and Differentiation and Maturation of Dendritic Cell. Front Immunol 2022; 12:745111. [PMID: 35087512 PMCID: PMC8786807 DOI: 10.3389/fimmu.2021.745111] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/21/2021] [Indexed: 12/23/2022] Open
Abstract
NRF2 is an important regulatory transcription factor involved in tumor immunity and tumorigenesis. In this study, we firstly identified that FKBP4/NR3C1 axis was a novel negative regulator of NRF2 in human breast cancer (BC) cells. The effect of FKBP4 appeared to be at protein level of NRF2 since it could not suppress the expression of NRF2 at mRNA level. Bioinformatics analysis and in vitro experiments further demonstrated that FKBP4 regulated NRF2 via regulating nuclear translocation of NR3C1. We then reported that naringenin, a flavonoid, widely distributed in citrus and tomato, could suppress autophagy and proliferation of BC cells through FKBP4/NR3C1/NRF2 signaling pathway in vitro and in vivo. Naringenin was also found to promote dendritic cell (DC) differentiation and maturation through FKBP4/NR3C1/NRF2 axis. Therefore, our study found that naringenin could induce inhibition of autophagy and cell proliferation in BC cells and enhance DC differentiation and maturation, at least in part, though regulation of FKBP4/NR3C1/NRF2 signaling pathway. Identification of FKBP4/NR3C1/NRF2 axis would provide insights for novel anti-tumor strategy against BC among tumor microenvironment.
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Affiliation(s)
- Hanchu Xiong
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Zihan Chen
- Surgical Intensive Care Unit, First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Baihua Lin
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Bojian Xie
- Department of Breast and Thyroid Surgery, Taizhou Hospital of Zhejiang Province, Taizhou, China
| | - Xiaozhen Liu
- Cancer Center, Department of Breast Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Cong Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Zhaoqing Li
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Yunlu Jia
- Department of Medical Oncology, First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Zhuazhua Wu
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Min Yang
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Yongshi Jia
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Linbo Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jichun Zhou
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Xuli Meng
- Cancer Center, Department of Breast Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
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10
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Wu YH, Yeh IJ, Phan NN, Yen MC, Hung JH, Chiao CC, Chen CF, Sun Z, Hsu HP, Wang CY, Lai MD. Gene signatures and potential therapeutic targets of Middle East respiratory syndrome coronavirus (MERS-CoV)-infected human lung adenocarcinoma epithelial cells. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 54:845-857. [PMID: 34176764 PMCID: PMC7997684 DOI: 10.1016/j.jmii.2021.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/03/2020] [Accepted: 03/07/2021] [Indexed: 12/23/2022]
Abstract
Background Pathogenic coronaviruses include Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), and SARS-CoV-2. These viruses have induced outbreaks worldwide, and there are currently no effective medications against them. Therefore, there is an urgent need to develop potential drugs against coronaviruses. Methods High-throughput technology is widely used to explore differences in messenger (m)RNA and micro (mi)RNA expression profiles, especially to investigate protein–protein interactions and search for new therapeutic compounds. We integrated miRNA and mRNA expression profiles in MERS-CoV-infected cells and compared them to mock-infected controls from public databases. Results Through the bioinformatics analysis, there were 251 upregulated genes and eight highly differentiated miRNAs that overlapped in the two datasets. External validation verified that these genes had high expression in MERS-CoV-infected cells, including RC3H1, NF-κB, CD69, TNFAIP3, LEAP-2, DUSP10, CREB5, CXCL2, etc. We revealed that immune, olfactory or sensory system-related, and signal-transduction networks were discovered from upregulated mRNAs in MERS-CoV-infected cells. In total, 115 genes were predicted to be related to miRNAs, with the intersection of upregulated mRNAs and miRNA-targeting prediction genes such as TCF4, NR3C1, and POU2F2. Through the Connectivity Map (CMap) platform, we suggested potential compounds to use against MERS-CoV infection, including diethylcarbamazine, harpagoside, bumetanide, enalapril, and valproic acid. Conclusions The present study illustrates the crucial roles of miRNA-mRNA interacting networks in MERS-CoV-infected cells. The genes we identified are potential targets for treating MERS-CoV infection; however, these could possibly be extended to other coronavirus infections.
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Affiliation(s)
- Yen-Hung Wu
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - I-Jeng Yeh
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Nam Nhut Phan
- NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
| | - Meng-Chi Yen
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Jui-Hsiang Hung
- Department of Biotechnology, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan
| | - Chung-Chieh Chiao
- School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung 82445, Taiwan
| | - Chien-Fu Chen
- School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung 82445, Taiwan
| | - Zhengda Sun
- Kaiser Permanente, Northern California Regional Laboratories, The Permanente Medical Group, 1725 Eastshore Hwy, Berkeley, CA 94710, USA
| | - Hui-Ping Hsu
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN37232, USA.
| | - Chih-Yang Wang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan.
| | - Ming-Derg Lai
- Department of Biochemistry and Molecular Biology, National Cheng Kung University, Tainan 70101, Taiwan; Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan.
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11
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Judge M, Parker E, Naniche D, Le Souëf P. Gene Expression: the Key to Understanding HIV-1 Infection? Microbiol Mol Biol Rev 2020; 84:e00080-19. [PMID: 32404327 PMCID: PMC7233484 DOI: 10.1128/mmbr.00080-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Gene expression profiling of the host response to HIV infection has promised to fill the gaps in our knowledge and provide new insights toward vaccine and cure. However, despite 20 years of research, the biggest questions remained unanswered. A literature review identified 62 studies examining gene expression dysregulation in samples from individuals living with HIV. Changes in gene expression were dependent on cell/tissue type, stage of infection, viremia, and treatment status. Some cell types, notably CD4+ T cells, exhibit upregulation of cell cycle, interferon-related, and apoptosis genes consistent with depletion. Others, including CD8+ T cells and natural killer cells, exhibit perturbed function in the absence of direct infection with HIV. Dysregulation is greatest during acute infection. Differences in study design and data reporting limit comparability of existing research and do not as yet provide a coherent overview of gene expression in HIV. This review outlines the extraordinarily complex host response to HIV and offers recommendations to realize the full potential of HIV host transcriptomics.
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Affiliation(s)
- Melinda Judge
- Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Erica Parker
- Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Denise Naniche
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Centro de Investigação de Saúde de Manhiça (CISM), Manhiça, Mozambique
| | - Peter Le Souëf
- Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
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12
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Wu N, Yang B, Wen B, Wang T, Guo J, Qi X, Wang J. Interactions Among Expressed MicroRNAs and mRNAs in the Early Stages of Fowl Adenovirus Aerotype 4-Infected Leghorn Male Hepatocellular Cells. Front Microbiol 2020; 11:831. [PMID: 32508763 PMCID: PMC7248314 DOI: 10.3389/fmicb.2020.00831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/07/2020] [Indexed: 01/04/2023] Open
Abstract
Hydropericardium-hepatitis syndrome (HHS) is caused by some strains of fowl adenovirus serotype 4 (FAdV-4). However, the mechanism of FAdV-4 entry is not well understood. Therefore, to investigate the changes in host cellular response at the early stage of FAdV-4 infection, a conjoint analysis of miRNA-seq and mRNA-seq was utilized with leghorn male hepatocellular (LMH) cells at 30, 60, and 120 min after FAdV-4 infection. In total, we identified 785 differentially expressed (DE) miRNAs and 725 DE mRNAs in FAdV-4-infected LMH cells. Most miRNAs and mRNAs, including gga-miR-148a-3p, gga-miR-148a-5p, gga-miR-15c-3p, CRK, SOCS3, and EGR1, have not previously been reported to be associated with FAdV-4 infection. The conjoint analysis of the obtained data identified 856 miRNA–mRNA pairs at three time points. The interaction network analysis showed that gga-miR-128-2-5p, gga-miR-7475-5p, novel_miR205, and TCF7L1 were located in the core of the network. Furthermore, the relationship between gga-miR-128-2-5p and its target OBSL1 was confirmed using a dual-luciferase reporter system and a real-time quantitative polymerase chain reaction assay. In vitro experiments revealed that both gga-miR-128-2-5p overexpression and OBSL1 loss of function inhibited FAdV-4 entry. These results suggested that gga-miR-128-2-5p plays an important role in FAdV-4 entry by targeting OBSL1. To the best of our knowledge, the present study is the first to analyze host miRNA and mRNA expression at the early stage of FAdV-4 infection; furthermore, the results of this study help to elucidate the molecular mechanisms of FAdV-4 entry.
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Affiliation(s)
- Ning Wu
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Bo Yang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Bo Wen
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Ting Wang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Jiaona Guo
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Xuefeng Qi
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Jingyu Wang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
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13
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Byun S, Han S, Zheng Y, Planelles V, Lee Y. The landscape of alternative splicing in HIV-1 infected CD4 T-cells. BMC Med Genomics 2020; 13:38. [PMID: 32241262 PMCID: PMC7118826 DOI: 10.1186/s12920-020-0680-7] [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] [Indexed: 11/25/2022] Open
Abstract
Background Elucidating molecular mechanisms that are altered during HIV-1 infection may provide a better understanding of the HIV-1 life cycle and how it interacts with infected T-cells. One such mechanism is alternative splicing (AS), which has been studied for HIV-1 itself, but no systematic analysis has yet been performed on infected T-cells. We hypothesized that AS patterns in infected T-cells may illuminate the molecular mechanisms underlying HIV-1 infection and identify candidate molecular markers for specifically targeting infected T-cells. Methods We downloaded previously published raw RNA-seq data obtained from HIV-1 infected and non-infected T-cells. We estimated percent spliced in (PSI) levels for each AS exon, then identified differential AS events in the infected cells (FDR < 0.05, PSI difference > 0.1). We performed functional gene set enrichment analysis on the genes with differentially expressed AS exons to identify their functional roles. In addition, we used RT-PCR to validate differential alternative splicing events in cyclin T1 (CCNT1) as a case study. Results We identified 427 candidate genes with differentially expressed AS exons in infected T-cells, including 20 genes related to cell surface, 35 to kinases, and 121 to immune-related genes. In addition, protein-protein interaction analysis identified six essential subnetworks related to the viral life cycle, including Transcriptional regulation by TP53, Class I MHC mediated antigen, G2/M transition, and late phase of HIV life cycle. CCNT1 exon 7 was more frequently skipped in infected T-cells, leading to loss of the key Cyclin_N motif and affecting HIV-1 transcriptional elongation. Conclusions Our findings may provide new insight into systemic host AS regulation under HIV-1 infection and may provide useful initial candidates for the discovery of new markers for specifically targeting infected T-cells.
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Affiliation(s)
- Seyoun Byun
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Seonggyun Han
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Yue Zheng
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Vicente Planelles
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Younghee Lee
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA. .,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA.
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14
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Mtshali Z, Moodley J, Naicker T. An Insight into the Angiogenic and Lymphatic Interplay in Pre-eclampsia Comorbid with HIV Infection. Curr Hypertens Rep 2020; 22:35. [PMID: 32200445 DOI: 10.1007/s11906-020-01040-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW To provide insight on the imbalance of angiogenic and lymphangiogenic factors in pre-eclampsia, as well as highlight polymorphism in genes related to angiogenesis and lymphangiogenesis. RECENT FINDINGS The pregnancy-specific disorder pre-eclampsia is diagnosed by the presence of hypertension with/without proteinuria, after 20 weeks of gestation. The pathogenesis of pre-eclampsia remains ambiguous, but research over the years has identified an imbalance in maternal and foetal factors. Familial predisposition and gene variation are also linked to pre-eclampsia development. The sFlt-1/PIGF ratio has attracted great attention over the years; more recently several researchers have reported that a sFlt-1/PIGF ratio of ≤ 38 can be used to predict short-term absence of pre-eclampsia. This ratio has the potential to prevent adverse pregnancy outcomes and reduce healthcare costs significantly. Genome-wide studies have additionally identified variation in the foetal gene near Flt-1. The development of preeclampsia is not limited to the maternal interface, but foetal involvement as well as genetic interplay is associated with the disorder.
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Affiliation(s)
- Zamahlabangane Mtshali
- Optics and Imaging Centre, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.
| | - Jagidesa Moodley
- Department of Obstetrics and Gynaecology and Women's Health and HIV Research Group, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Thajasvarie Naicker
- Optics and Imaging Centre, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
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15
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Feng M, Xie T, Li Y, Zhang N, Lu Q, Zhou Y, Shi M, Sun J, Zhang X. A balanced game: chicken macrophage response to ALV-J infection. Vet Res 2019; 50:20. [PMID: 30841905 PMCID: PMC6404279 DOI: 10.1186/s13567-019-0638-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/09/2019] [Indexed: 12/13/2022] Open
Abstract
Avian leukosis virus subgroup J (ALV-J) infection can cause tumors and immunosuppression in infected chickens. Macrophages play a central role in host defense against invading pathogens. In this study, we discovered an interesting phenomenon: ALV-J replication is weakened from 3 hours post-infection (hpi) to 36 hpi, which was verified using Western blotting and RT-PCR. To further investigate the interaction between ALV-J and macrophages, transcriptome analysis was performed to analyze the host genes’ function in chicken primary monocyte-derived macrophages (MDM). Compared to the uninfected control, 624 up-regulated differentially expressed genes (DEG) and 341 down-regulated DEG at 3 hpi, and 174 up-regulated DEG and 87 down-regulated DEG at 36 hpi were identified in chicken MDM, respectively. ALV-J infection induced strong innate immune responses in chicken MDM at 3 hpi, instead of 36 hpi, according to the analysis results of Gene Ontology and KEGG pathway. Importantly, the host factors, such as up-regulated MIP-3α, IL-1β, iNOS, K60, IRG1, CH25H, NFKBIZ, lysozyme and OASL were involved in the host defense response during the course of ALV-J infection. On the contrary, up-regulated EX-FABP, IL4I1, COX-2, NFKBIA, TNFAIP3 and the Jak STAT pathway inhibitors including CISH, SOCS1 and SOCS3 are beneficial to ALV-J survival in chicken macrophages. We speculated that ALV-J tropism for macrophages helps to establish a latent infection in chicken MDM from 6 to 36 hpi. The present study provides a comprehensive view of the interactions between macrophages and ALV-J. It suggests the mechanisms of defense of chicken macrophages against ALV-J invasion and how ALV-J escape the host innate immune responses.
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Affiliation(s)
- Min Feng
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Tingting Xie
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Yuanfang Li
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Nan Zhang
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qiuyuan Lu
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yaohong Zhou
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Meiqing Shi
- Division of Immunology, Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China. .,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China.
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16
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Shang L, Smith AJ, Reilly CS, Duan L, Perkey KE, Wietgrefe S, Zupancic M, Southern PJ, Johnson RP, Carlis JV, Haase AT. Vaccine-modified NF-kB and GR signaling in cervicovaginal epithelium correlates with protection. Mucosal Immunol 2018; 11:512-522. [PMID: 28792003 PMCID: PMC5807226 DOI: 10.1038/mi.2017.69] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 06/19/2017] [Indexed: 02/04/2023]
Abstract
Cervicovaginal epithelium plays a critical role in determining the outcome of virus transmission in the female reproductive tract (FRT) by initiating or suppressing transmission-facilitating mucosal immune responses in naïve and SIVmac239Δnef-vaccinated animals, respectively. In this study, we examined the very early responses of cervical epithelium within 24 h after vaginal exposure to SIV in naive and SIVmac239Δnef-vaccinated rhesus macaques. Using both ex vivo and in vivo experimental systems, we found that vaginal exposure to SIV rapidly induces a broad spectrum of pro-inflammatory responses in the epithelium associated with a reciprocal regulation of NF-kB and glucocorticoid receptor (GR) signaling pathways. Conversely, maintenance of high-level GR expression and suppression of NF-kB expression in the epithelium were associated with an immunologically quiescent state in the FRT mucosa and protection against vaginal challenge in SIVmac239Δnef-vaccinated animals. We show that the immunologically quiescent state is induced by FCGR2B-immune complexes interactions that modify the reciprocal regulation of NF-kB and GR signaling pathways. Our results suggest that targeting the balance of NF-kB and GR signaling in early cervicovaginal epithelium responses could moderate mucosal inflammation and target cell availability after vaginal infection, thereby providing a complementary approach to current prevention strategies.
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Affiliation(s)
- L Shang
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - A J Smith
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - C S Reilly
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - L Duan
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - K E Perkey
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - S Wietgrefe
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - M Zupancic
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - P J Southern
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - R P Johnson
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - J V Carlis
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - A T Haase
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
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17
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Herpes simplex viruses activate phospholipid scramblase to redistribute phosphatidylserines and Akt to the outer leaflet of the plasma membrane and promote viral entry. PLoS Pathog 2018; 14:e1006766. [PMID: 29293671 PMCID: PMC5766253 DOI: 10.1371/journal.ppat.1006766] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/12/2018] [Accepted: 11/22/2017] [Indexed: 12/18/2022] Open
Abstract
Herpes simplex virus (HSV) entry is associated with Akt translocation to the outer leaflet of the plasma membrane to promote a complex signaling cascade. We hypothesized that phospholipid scramblase-1 (PLSCR1), a calcium responsive enzyme that flips phosphatidylserines between membrane leaflets, might redistribute Akt to the outside during entry. Confocal imaging, biotinylation of membrane proteins and flow cytometric analysis demonstrated that HSV activates PLSCR1 and flips phosphatidylserines and Akt to the outside shortly following HSV-1 or HSV-2 exposure. Translocation was blocked by addition of a cell permeable calcium chelator, pharmacological scramblase antagonist, or transfection with small interfering RNA targeting PLSCR1. Co-immunoprecipitation and proximity ligation studies demonstrated that PLSCR1 associated with glycoprotein L at the outer leaflet and studies with gL deletion viruses indicate that this interaction facilitates subsequent restoration of the plasma membrane architecture. Ionomycin, a calcium ionophore, also induced PLSCR1 activation resulting in Akt externalization, suggesting a previously unrecognized biological phenomenon. Defining the mechanisms by which herpes simplex viruses (HSV) enter cells will facilitate the development of new strategies to prevent or treat infections and provide insights into cell biology. We report the novel observation that HSV activates the enzyme, scramblase, which redistributes phosphatidylserines, the major component of the inner leaflet of the plasma membrane, and the associated protein, Akt, between the inner and outer leaflet of the plasma membrane, to promote viral entry.
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18
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Yang S, Pei Y, Zhao A. iTRAQ-based Proteomic Analysis of Porcine Kidney Epithelial PK15 cells Infected with Pseudorabies virus. Sci Rep 2017; 7:45922. [PMID: 28374783 PMCID: PMC5379687 DOI: 10.1038/srep45922] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/03/2017] [Indexed: 12/18/2022] Open
Abstract
Pseudorabies virus (PRV) is one of the most important pathogens of swine, resulting in severe economic losses to the pig industry. To improve our understanding of the host responses to PRV infection, we applied isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with liquid chromatography-tandem mass spectrometry to quantitatively identify the differentially expressed cellular proteins in PRV-infected PK15 cells. In total, relative quantitative data were identified for 4333 proteins in PRV and mock- infected PK15 cells, among which 466 cellular proteins were differentially expressed, including 234 upregulated proteins and 232 downregulated proteins. Bioinformatics analysis disclosed that most of these differentially expressed proteins were involved in metabolic processes, cellular growth and proliferation, endoplasmic reticulum (ER) stress response, cell adhesion and cytoskeleton. Moreover, expression levels of four representative proteins, beta-catenin, STAT1, GRB2 and PCNA, were further confirmed by western blot analysis. This is the first attempt to analyze the protein profile of PRV-infected PK15 cells using iTRAQ technology, and our findings may provide valuable information to help understand the host response to PRV infection.
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Affiliation(s)
- Songbai Yang
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Yue Pei
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Ayong Zhao
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
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19
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HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency. Sci Rep 2017; 7:45509. [PMID: 28358052 PMCID: PMC5371986 DOI: 10.1038/srep45509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/27/2017] [Indexed: 12/22/2022] Open
Abstract
Measuring the altered gene expression level and identifying differentially expressed genes/proteins during HIV infection, replication and latency is fundamental for broadening our understanding of the mechanisms of HIV infection and T-cell dysfunction. Such studies are crucial for developing effective strategies for virus eradication from the body. Inspired by the availability and enrichment of gene expression data during HIV infection, replication and latency, in this study, we proposed a novel compendium termed HIVed (HIV expression database; http://hivlatency.erc.monash.edu/) that harbours comprehensive functional annotations of proteins, whose genes have been shown to be dysregulated during HIV infection, replication and latency using different experimental designs and measurements. We manually curated a variety of third-party databases for structural and functional annotations of the protein entries in HIVed. With the goal of benefiting HIV related research, we collected a number of biological annotations for all the entries in HIVed besides their expression profile, including basic protein information, Gene Ontology terms, secondary structure, HIV-1 interaction and pathway information. We hope this comprehensive protein-centric knowledgebase can bridge the gap between the understanding of differentially expressed genes and the functions of their protein products, facilitating the generation of novel hypotheses and treatment strategies to fight against the HIV pandemic.
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20
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Shang L, Duan L, Perkey KE, Wietgrefe S, Zupancic M, Smith AJ, Southern PJ, Johnson RP, Haase AT. Epithelium-innate immune cell axis in mucosal responses to SIV. Mucosal Immunol 2017; 10:508-519. [PMID: 27435105 PMCID: PMC5250613 DOI: 10.1038/mi.2016.62] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 06/18/2016] [Indexed: 02/04/2023]
Abstract
In the SIV (simian immunodeficiency virus)-rhesus macaque model of HIV-1 (human immunodeficiency virus type I) transmission to women, one hallmark of the mucosal response to exposure to high doses of SIV is CD4 T-cell recruitment that fuels local virus expansion in early infection. In this study, we systematically analyzed the cellular events and chemoattractant profiles in cervical tissues that precede CD4 T-cell recruitment. We show that vaginal exposure to the SIV inoculum rapidly induces chemokine expression in cervical epithelium including CCL3, CCL20, and CXCL8. The chemokine expression is associated with early recruitment of macrophages and plasmacytoid dendritic cells that are co-clustered underneath the cervical epithelium. Production of chemokines CCL3 and CXCL8 by these cells in turn generates a chemokine gradient that is spatially correlated with the recruitment of CD4 T cells. We further show that the protection of SIVmac239Δnef vaccination against vaginal challenge is correlated with the absence of this epithelium-innate immune cell-CD4 T-cell axis response in the cervical mucosa. Our results reveal a critical role for cervical epithelium in initiating early mucosal responses to vaginal infection, highlight an important role for macrophages in target cell recruitment, and provide further evidence of a paradoxical dampening effect of a protective vaccine on these early mucosal responses.
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Affiliation(s)
- L Shang
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - L Duan
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - K E Perkey
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - S Wietgrefe
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - M Zupancic
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - A J Smith
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - P J Southern
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - R P Johnson
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - A T Haase
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
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21
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Afroz S, Giddaluru J, Abbas MM, Khan N. Transcriptome meta-analysis reveals a dysregulation in extra cellular matrix and cell junction associated gene signatures during Dengue virus infection. Sci Rep 2016; 6:33752. [PMID: 27651116 PMCID: PMC5030657 DOI: 10.1038/srep33752] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 09/02/2016] [Indexed: 12/28/2022] Open
Abstract
Dengue Viruses (DENVs) cause one of the most prevalent arthropod-borne viral diseases affecting millions of people worldwide. Identification of genes involved in DENV pathogenesis would help in deciphering molecular mechanisms responsible for the disease progression. Here, we carried out a meta-analysis of publicly available gene expression data of dengue patients and further validated the meta-profile using in-vitro infection in THP-1 cells. Our findings reveal that DENV infection modulates expression of several genes and signalling pathways including interferons, detoxification of ROS and viral assembly. Interestingly, we have identified novel gene signatures comprising of INADL/PATJ and CRTAP (Cartilage Associated Protein), which were significantly down-regulated across all patient data sets as well as in DENV infected THP-1 cells. PATJ and CRTAP genes are involved in maintaining cell junction integrity and collagen assembly (extracellular matrix component) respectively, which together play a crucial role in cell-cell adhesion. Our results categorically reveal that overexpression of CRTAP and PATJ genes restrict DENV infection, thereby suggesting a critical role of these genes in DENV pathogenesis. Conclusively, these findings emphasize the utility of meta-analysis approach in identifying novel gene signatures that might provide mechanistic insights into disease pathogenesis and possibly lead towards the development of better therapeutic interventions.
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Affiliation(s)
- Sumbul Afroz
- School of Life Sciences, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Jeevan Giddaluru
- School of Life Sciences, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Mohd Manzar Abbas
- School of Life Sciences, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Nooruddin Khan
- School of Life Sciences, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad-500046, Telangana, India
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22
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Tjernlund A, Burgener A, Lindvall JM, Peng T, Zhu J, Öhrmalm L, Picker LJ, Broliden K, McElrath MJ, Corey L. In Situ Staining and Laser Capture Microdissection of Lymph Node Residing SIV Gag-Specific CD8+ T cells--A Tool to Interrogate a Functional Immune Response Ex Vivo. PLoS One 2016; 11:e0149907. [PMID: 26986062 PMCID: PMC4795610 DOI: 10.1371/journal.pone.0149907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/05/2016] [Indexed: 11/18/2022] Open
Abstract
While a plethora of data describes the essential role of systemic CD8+ T cells in the control of SIV replication little is known about the local in situ CD8+ T cell immune responses against SIV at the intact tissue level, due to technical limitations. In situ staining, using GagCM9 Qdot 655 multimers, were here combined with laser capture microdissection to detect and collect SIV Gag CM9 specific CD8+ T cells in lymph node tissue from SIV infected rhesus macaques. CD8+ T cells from SIV infected and uninfected rhesus macaques were also collected and compared to the SIV GagCM9 specific CD8+ T cells. Illumina bead array and transcriptional analyses were used to assess the transcriptional profiles and the three different CD8+ T cell populations displayed unique transcriptional patterns. This pilot study demonstrates that rapid and specific immunostaining combined with laser capture microdissection in concert with transcriptional profiling may be used to elucidate phenotypic differences between CD8+ T cells in SIV infection. Such technologies may be useful to determine differences in functional activities of HIV/SIV specific T cells.
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Affiliation(s)
- Annelie Tjernlund
- Department of Medicine Solna, Unit of Infectious Diseases, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, L8:01, 17176 Stockholm, Sweden
- * E-mail:
| | - Adam Burgener
- Department of Medicine Solna, Unit of Infectious Diseases, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, L8:01, 17176 Stockholm, Sweden
- National Laboratory for HIV Immunology, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, 730 William Ave. Winnipeg, MB, Canada
| | - Jessica M. Lindvall
- Department of Biosciences and Nutrition, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Stockholm, Sweden
| | - Tao Peng
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - Jia Zhu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States of America
| | - Lars Öhrmalm
- Department of Medicine Solna, Unit of Infectious Diseases, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, L8:01, 17176 Stockholm, Sweden
| | - Louis J. Picker
- Department of Pathology, Vaccine and Gene Therapy Institute, and the Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, United States of America
| | - Kristina Broliden
- Department of Medicine Solna, Unit of Infectious Diseases, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, L8:01, 17176 Stockholm, Sweden
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States of America
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23
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Blazkova J, Boughorbel S, Presnell S, Quinn C, Chaussabel D. A curated transcriptome dataset collection to investigate the immunobiology of HIV infection. F1000Res 2016; 5:327. [PMID: 27134731 PMCID: PMC4838008 DOI: 10.12688/f1000research.8204.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/04/2016] [Indexed: 12/22/2022] Open
Abstract
Compendia of large-scale datasets available in public repositories provide an opportunity to identify and fill current gaps in biomedical knowledge. But first, these data need to be readily accessible to research investigators for interpretation. Here, we make available a collection of transcriptome datasets relevant to HIV infection. A total of 2717 unique transcriptional profiles distributed among 34 datasets were identified, retrieved from the NCBI Gene Expression Omnibus (GEO), and loaded in a custom web application, the Gene Expression Browser (GXB), designed for interactive query and visualization of integrated large-scale data. Multiple sample groupings and rank lists were created to facilitate dataset query and interpretation via this interface. Web links to customized graphical views can be generated by users and subsequently inserted in manuscripts reporting novel findings, such as discovery notes. The tool also enables browsing of a single gene across projects, which can provide new perspectives on the role of a given molecule across biological systems. This curated dataset collection is available at:
http://hiv.gxbsidra.org/dm3/geneBrowser/list.
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Affiliation(s)
| | | | - Scott Presnell
- Benaroya Research Institute, Research Technology, Seattle, WA, USA
| | - Charlie Quinn
- Benaroya Research Institute, Research Technology, Seattle, WA, USA
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24
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Sherrill-Mix S, Ocwieja KE, Bushman FD. Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats. Retrovirology 2015; 12:79. [PMID: 26377088 PMCID: PMC4574318 DOI: 10.1186/s12977-015-0205-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 08/28/2015] [Indexed: 02/07/2023] Open
Abstract
Background HIV infection has been reported to alter cellular gene activity, but published studies have commonly assayed transformed cell lines and lab-adapted HIV strains, yielding inconsistent results. Here we carried out a deep RNA-Seq analysis of primary human T cells infected with the low passage HIV isolate HIV89.6. Results Seventeen percent of cellular genes showed altered activity 48 h after infection. In a meta-analysis including four other studies, our data differed from studies of HIV infection in cell lines but showed more parallels with infections of primary cells. We found a global trend toward retention of introns after infection, suggestive of a novel cellular response to infection. HIV89.6 infection was also associated with activation of several human endogenous retroviruses (HERVs) and retrotransposons, of interest as possible novel antigens that could serve as vaccine targets. The most highly activated group of HERVs was a subset of the ERV-9. Analysis showed that activation was associated with a particular variant of ERV-9 long terminal repeats that contains an indel near the U3-R border. These data also allowed quantification of >70 splice forms of the HIV89.6 RNA and specified the main types of chimeric HIV89.6-host RNAs. Comparison to over 100,000 integration site sequences from the same infected cell populations allowed quantification of authentic versus artifactual chimeric reads, showing that 5′ read-in, splicing out of HIV89.6 from the D4 donor and 3′ read-through were the most common HIV89.6-host cell chimeric RNA forms. Conclusions Analysis of RNA abundance after infection of primary T cells with the low passage HIV89.6 isolate disclosed multiple novel features of HIV-host interactions, notably intron retention and induction of transcription of retrotransposons and endogenous retroviruses. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0205-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA.
| | - Karen E Ocwieja
- Children's Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA, 19104, USA.
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA.
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25
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Berard AR, Severini A, Coombs KM. Comparative proteomic analyses of two reovirus T3D subtypes and comparison to T1L identifies multiple novel proteins in key cellular pathogenic pathways. Proteomics 2015; 15:2113-35. [DOI: 10.1002/pmic.201400602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/23/2015] [Accepted: 04/16/2015] [Indexed: 01/14/2023]
Affiliation(s)
- Alicia R. Berard
- Department of Medical Microbiology; Faculty of Medicine; University of Manitoba; Winnipeg Canada R3E 0J9
- Manitoba Center for Proteomics and Systems Biology; Room 799 John Buhler Research Centre University of Manitoba; Winnipeg Canada R3E 3P4
| | - Alberto Severini
- Department of Medical Microbiology; Faculty of Medicine; University of Manitoba; Winnipeg Canada R3E 0J9
- National Microbiology Laboratory; Public Health Agency of Canada; 1015 Arlington St. Winnipeg Canada R3E 3R2
| | - Kevin M. Coombs
- Department of Medical Microbiology; Faculty of Medicine; University of Manitoba; Winnipeg Canada R3E 0J9
- Manitoba Center for Proteomics and Systems Biology; Room 799 John Buhler Research Centre University of Manitoba; Winnipeg Canada R3E 3P4
- Manitoba Institute of Child Health; Room 641 John Buhler Research Center; University of Manitoba; Winnipeg Canada R3E 3P4
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26
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Berard AR, Coombs KM, Severini A. Quantification of the host response proteome after herpes simplex virus type 1 infection. J Proteome Res 2015; 14:2121-42. [PMID: 25815715 DOI: 10.1021/pr5012284] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Viruses employ numerous host cell metabolic functions to propagate and manage to evade the host immune system. For herpes simplex virus type 1 (HSV1), a virus that has evolved to efficiently infect humans without seriously harming the host in most cases, the virus-host interaction is specifically interesting. This interaction can be best characterized by studying the proteomic changes that occur in the host during infection. Previous studies have been successful at identifying numerous host proteins that play important roles in HSV infection; however, there is still much that we do not know. This study identifies host metabolic functions and proteins that play roles in HSV infection, using global quantitative stable isotope labeling by amino acids in cell culture (SILAC) proteomic profiling of the host cell combined with LC-MS/MS. We showed differential proteins during early, mid and late infection, using both cytosolic and nuclear fractions. We identified hundreds of differentially regulated proteins involved in fundamental cellular functions, including gene expression, DNA replication, inflammatory response, cell movement, cell death, and RNA post-transcriptional modification. Novel differentially regulated proteins in HSV infections include some previously identified in other virus systems, as well as fusion protein, involved in malignant liposarcoma (FUS) and hypoxia up-regulated 1 protein precursor (HYOU1), which have not been identified previously in any virus infection.
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Affiliation(s)
- Alicia R Berard
- †Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9.,‡Manitoba Center for Proteomics and Systems Biology, University of Manitoba, Room 799 John Buhler Research Centre, Winnipeg, Manitoba, Canada R3E 3P4
| | - Kevin M Coombs
- †Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9.,‡Manitoba Center for Proteomics and Systems Biology, University of Manitoba, Room 799 John Buhler Research Centre, Winnipeg, Manitoba, Canada R3E 3P4.,§Manitoba Institute of Child Health, University of Manitoba, Room 641 John Buhler Research Centre, Winnipeg, Manitoba, Canada R3E 3P4
| | - Alberto Severini
- †Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9.,∥National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3P6
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27
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Tomasello E, Pollet E, Vu Manh TP, Uzé G, Dalod M. Harnessing Mechanistic Knowledge on Beneficial Versus Deleterious IFN-I Effects to Design Innovative Immunotherapies Targeting Cytokine Activity to Specific Cell Types. Front Immunol 2014; 5:526. [PMID: 25400632 PMCID: PMC4214202 DOI: 10.3389/fimmu.2014.00526] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 10/07/2014] [Indexed: 12/15/2022] Open
Abstract
Type I interferons (IFN-I) were identified over 50 years ago as cytokines critical for host defense against viral infections. IFN-I promote anti-viral defense through two main mechanisms. First, IFN-I directly reinforce or induce de novo in potentially all cells the expression of effector molecules of intrinsic anti-viral immunity. Second, IFN-I orchestrate innate and adaptive anti-viral immunity. However, IFN-I responses can be deleterious for the host in a number of circumstances, including secondary bacterial or fungal infections, several autoimmune diseases, and, paradoxically, certain chronic viral infections. We will review the proposed nature of protective versus deleterious IFN-I responses in selected diseases. Emphasis will be put on the potentially deleterious functions of IFN-I in human immunodeficiency virus type 1 (HIV-1) infection, and on the respective roles of IFN-I and IFN-III in promoting resolution of hepatitis C virus (HCV) infection. We will then discuss how the balance between beneficial versus deleterious IFN-I responses is modulated by several key parameters including (i) the subtypes and dose of IFN-I produced, (ii) the cell types affected by IFN-I, and (iii) the source and timing of IFN-I production. Finally, we will speculate how integration of this knowledge combined with advanced biochemical manipulation of the activity of the cytokines should allow designing innovative immunotherapeutic treatments in patients. Specifically, we will discuss how induction or blockade of specific IFN-I responses in targeted cell types could promote the beneficial functions of IFN-I and/or dampen their deleterious effects, in a manner adapted to each disease.
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Affiliation(s)
- Elena Tomasello
- UM2, Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University , Marseille , France ; U1104, Institut National de la Santé et de la Recherche Médicale (INSERM) , Marseille , France ; UMR7280, Centre National de la Recherche Scientifique (CNRS) , Marseille , France
| | - Emeline Pollet
- UM2, Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University , Marseille , France ; U1104, Institut National de la Santé et de la Recherche Médicale (INSERM) , Marseille , France ; UMR7280, Centre National de la Recherche Scientifique (CNRS) , Marseille , France
| | - Thien-Phong Vu Manh
- UM2, Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University , Marseille , France ; U1104, Institut National de la Santé et de la Recherche Médicale (INSERM) , Marseille , France ; UMR7280, Centre National de la Recherche Scientifique (CNRS) , Marseille , France
| | - Gilles Uzé
- UMR 5235, Centre National de la Recherche Scientifique (CNRS), University Montpellier II , Montpellier , France
| | - Marc Dalod
- UM2, Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University , Marseille , France ; U1104, Institut National de la Santé et de la Recherche Médicale (INSERM) , Marseille , France ; UMR7280, Centre National de la Recherche Scientifique (CNRS) , Marseille , France
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28
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Levovitz C, Chen D, Ivansson E, Gyllensten U, Finnigan JP, Alshawish S, Zhang W, Schadt EE, Posner MR, Genden EM, Boffetta P, Sikora AG. TGFβ receptor 1: an immune susceptibility gene in HPV-associated cancer. Cancer Res 2014; 74:6833-44. [PMID: 25273091 DOI: 10.1158/0008-5472.can-14-0602-t] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Only a minority of those exposed to human papillomavirus (HPV) develop HPV-related cervical and oropharyngeal cancer. Because host immunity affects infection and progression to cancer, we tested the hypothesis that genetic variation in immune-related genes is a determinant of susceptibility to oropharyngeal cancer and other HPV-associated cancers by performing a multitier integrative computational analysis with oropharyngeal cancer data from a head and neck cancer genome-wide association study (GWAS). Independent analyses, including single-gene, gene-interconnectivity, protein-protein interaction, gene expression, and pathway analysis, identified immune genes and pathways significantly associated with oropharyngeal cancer. TGFβR1, which intersected all tiers of analysis and thus selected for validation, replicated significantly in the head and neck cancer GWAS limited to HPV-seropositive cases and an independent cervical cancer GWAS. The TGFβR1 containing p38-MAPK pathway was significantly associated with oropharyngeal cancer and cervical cancer, and TGFβR1 was overexpressed in oropharyngeal cancer, cervical cancer, and HPV(+) head and neck cancer tumors. These concordant analyses implicate TGFβR1 signaling as a process dysregulated across HPV-related cancers. This study demonstrates that genetic variation in immune-related genes is associated with susceptibility to oropharyngeal cancer and implicates TGFβR1/TGFβ signaling in the development of both oropharyngeal cancer and cervical cancer. Better understanding of the immunogenetic basis of susceptibility to HPV-associated cancers may provide insight into host/virus interactions and immune processes dysregulated in the minority of HPV-exposed individuals who progress to cancer.
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Affiliation(s)
- Chaya Levovitz
- The Icahn School of Medicine at Mount Sinai, New York, New York. Department of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York. Institute for Translational Epidemiology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Dan Chen
- SciLifeLab Uppsala, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Emma Ivansson
- SciLifeLab Uppsala, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Ulf Gyllensten
- SciLifeLab Uppsala, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - John P Finnigan
- The Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sara Alshawish
- The Icahn School of Medicine at Mount Sinai, New York, New York
| | - Weijia Zhang
- Mount Sinai Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Eric E Schadt
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York. Mount Sinai Institute for Genomics and Multiscale Biology, New York, New York
| | - Marshal R Posner
- The Icahn School of Medicine at Mount Sinai, New York, New York. Department of Otolaryngology-Head and Neck Surgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Eric M Genden
- The Icahn School of Medicine at Mount Sinai, New York, New York. Department of Otolaryngology-Head and Neck Surgery, Icahn School of Medicine at Mount Sinai, New York, New York. Department of Immunology, Genetics and Pathology, Tisch Cancer Institute, New York, New York
| | - Paolo Boffetta
- The Icahn School of Medicine at Mount Sinai, New York, New York. Institute for Translational Epidemiology, Icahn School of Medicine at Mount Sinai, New York, New York. Department of Immunology, Genetics and Pathology, Tisch Cancer Institute, New York, New York
| | - Andrew G Sikora
- The Icahn School of Medicine at Mount Sinai, New York, New York. Department of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York. Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York. Department of Otolaryngology-Head and Neck Surgery, Icahn School of Medicine at Mount Sinai, New York, New York. Department of Immunology, Genetics and Pathology, Tisch Cancer Institute, New York, New York.
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29
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Smith AJ, Wietgrefe SW, Shang L, Reilly CS, Southern PJ, Perkey KE, Duan L, Kohler H, Müller S, Robinson J, Carlis JV, Li Q, Johnson RP, Haase AT. Live simian immunodeficiency virus vaccine correlate of protection: immune complex-inhibitory Fc receptor interactions that reduce target cell availability. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2014; 193:3126-33. [PMID: 25143442 PMCID: PMC4157094 DOI: 10.4049/jimmunol.1400822] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Principles to guide design of an effective vaccine against HIV are greatly needed, particularly to protect women in the pandemic's epicenter in Africa. We have been seeking these principles by identifying correlates of the robust protection associated with SIVmac239Δnef vaccination in the SIV-rhesus macaque animal model of HIV-1 transmission to women. We identified one correlate of SIVmac239Δnef protection against vaginal challenge as a resident mucosal system for SIV-gp41 trimer Ab production and neonatal FcR-mediated concentration of these Abs on the path of virus entry to inhibit establishment of infected founder populations at the portal of entry. In this study, we identify blocking CD4(+) T cell recruitment to thereby inhibit local expansion of infected founder populations as a second correlate of protection. Virus-specific immune complex interactions with the inhibitory FcγRIIb receptor in the epithelium lining the cervix initiate expression of genes that block recruitment of target cells to fuel local expansion. Immune complex-FcγRIIb receptor interactions at mucosal frontlines to dampen the innate immune response to vaginal challenge could be a potentially general mechanism for the mucosal immune system to sense and modulate the response to a previously encountered pathogen. Designing vaccines to provide protection without eliciting these transmission-promoting innate responses could contribute to developing an effective HIV-1 vaccine.
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Affiliation(s)
- Anthony J Smith
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455
| | - Stephen W Wietgrefe
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455
| | - Liang Shang
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455
| | - Cavan S Reilly
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455
| | - Peter J Southern
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455
| | - Katherine E Perkey
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455
| | - Lijie Duan
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455
| | - Heinz Kohler
- Department of Microbiology and Immunology and Molecular Genetics, University of Kentucky, Lexington, KY 40536
| | | | - James Robinson
- Department of Pediatrics, Center for Infectious Diseases, Tulane University, New Orleans, LA 70112
| | - John V Carlis
- Department of Computer Science and Engineering, College of Science and Engineering, University of Minnesota, Minneapolis, MN 55455
| | - Qingsheng Li
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska, Lincoln, NE 68583
| | - R Paul Johnson
- New England Primate Research Center, Harvard Medical School, Southborough Campus, Southborough, MA 01772; Ragon Institute of MGH, MIT and Harvard, Charlestown, MA 02129; and Infectious Disease Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115
| | - Ashley T Haase
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455;
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30
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Shang L, Smith AJ, Duan L, Perkey KE, Qu L, Wietgrefe S, Zupancic M, Southern PJ, Masek-Hammerman K, Reeves RK, Johnson RP, Haase AT. NK cell responses to simian immunodeficiency virus vaginal exposure in naive and vaccinated rhesus macaques. THE JOURNAL OF IMMUNOLOGY 2014; 193:277-84. [PMID: 24899503 DOI: 10.4049/jimmunol.1400417] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
NK cell responses to HIV/SIV infection have been well studied in acute and chronic infected patients/monkeys, but little is known about NK cells during viral transmission, particularly in mucosal tissues. In this article, we report a systematic study of NK cell responses to high-dose vaginal exposure to SIVmac251 in the rhesus macaque female reproductive tract (FRT). Small numbers of NK cells were recruited into the FRT mucosa following vaginal inoculation. The influx of mucosal NK cells preceded local virus replication and peaked at 1 wk and, thus, was in an appropriate time frame to control an expanding population of infected cells at the portal of entry. However, NK cells were greatly outnumbered by recruited target cells that fuel local virus expansion and were spatially dissociated from SIV RNA+ cells at the major site of expansion of infected founder populations in the transition zone and adjoining endocervix. The number of NK cells in the FRT mucosa decreased rapidly in the second week, while the number of SIV RNA+ cells in the FRT reached its peak. Mucosal NK cells produced IFN-γ and MIP-1α/CCL3 but lacked several markers of activation and cytotoxicity, and this was correlated with inoculum-induced upregulation of the inhibitory ligand HLA-E and downregulation of the activating receptor CD122/IL-2Rβ. Examination of SIVΔnef-vaccinated monkeys suggested that recruitment of NK cells to the genital mucosa was not involved in vaccine-induced protection from vaginal challenge. In summary, our results suggest that NK cells play, at most, a limited role in defenses in the FRT against vaginal challenge.
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Affiliation(s)
- Liang Shang
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455; and
| | - Anthony J Smith
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455; and
| | - Lijie Duan
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455; and
| | - Katherine E Perkey
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455; and
| | - Lucy Qu
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455; and
| | - Stephen Wietgrefe
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455; and
| | - Mary Zupancic
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455; and
| | - Peter J Southern
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455; and
| | | | - R Keith Reeves
- New England Primate Research Center, Harvard Medical School, Southborough, MA 01772
| | - R Paul Johnson
- New England Primate Research Center, Harvard Medical School, Southborough, MA 01772
| | - Ashley T Haase
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455; and
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31
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microRNA control of interferons and interferon induced anti-viral activity. Mol Immunol 2013; 56:781-93. [PMID: 23962477 DOI: 10.1016/j.molimm.2013.07.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Revised: 07/11/2013] [Accepted: 07/14/2013] [Indexed: 12/22/2022]
Abstract
Interferons (IFNs) are cytokines that are spontaneously produced in response to virus infection. They act by binding to IFN-receptors (IFN-R), which trigger JAK/STAT cell signalling and the subsequent induction of hundreds of IFN-inducible genes, including both protein-coding and microRNA genes. IFN-induced genes then act synergistically to prevent virus replication and create an anti-viral state. miRNA are therefore integral to the innate response to virus infection and are important components of IFN-mediated biology. On the other hand viruses also encode miRNAs that in some cases interfere directly with the IFN response to infection. This review summarizes the important roles of miRNAs in virus infection acting both as IFN-stimulated anti-viral molecules and as critical regulators of IFNs and IFN-stimulated genes. It also highlights how recent knowledge in RNA editing influence miRNA control of virus infection.
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32
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Breton G, Chomont N, Takata H, Fromentin R, Ahlers J, Filali-Mouhim A, Riou C, Boulassel MR, Routy JP, Yassine-Diab B, Sékaly RP. Programmed death-1 is a marker for abnormal distribution of naive/memory T cell subsets in HIV-1 infection. THE JOURNAL OF IMMUNOLOGY 2013; 191:2194-204. [PMID: 23918986 DOI: 10.4049/jimmunol.1200646] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Chronic activation of T cells is a hallmark of HIV-1 infection and plays an important role in disease progression. We previously showed that the engagement of the inhibitory receptor programmed death (PD)-1 on HIV-1-specific CD4(+) and CD8(+) T cells leads to their functional exhaustion in vitro. However, little is known about the impact of PD-1 expression on the turnover and maturation status of T cells during the course of the disease. In this study, we show that PD-1 is upregulated on all T cell subsets, including naive, central memory, and transitional memory T cells in HIV-1-infected subjects. PD-1 is expressed at similar levels on most CD4(+) T cells during the acute and the chronic phase of disease and identifies cells that have recently entered the cell cycle. In contrast, PD-1 expression is dramatically increased in CD8(+) T cells during the transition from acute to chronic infection, and this is associated with reduced levels of cell proliferation. The failure to downregulate expression of PD-1 in most T cells during chronic HIV-1 infection is associated with persistent alterations in the distribution of T cell subsets and is associated with impaired responses to IL-7. Our findings identify PD-1 as a marker for aberrant distribution of T cell subsets in HIV-1 infection.
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Affiliation(s)
- Gaëlle Breton
- Laboratoire d'Immunologie, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Saint-Luc, Montreal, Quebec H2X 1P1, Canada
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Xu WW, Han MJ, Chen D, Chen L, Guo Y, Willden A, Liu DQ, Zhang HT. Genome-wide search for the genes accountable for the induced resistance to HIV-1 infection in activated CD4+ T cells: apparent transcriptional signatures, co-expression networks and possible cellular processes. BMC Med Genomics 2013; 6:15. [PMID: 23635305 PMCID: PMC3655860 DOI: 10.1186/1755-8794-6-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 04/23/2013] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Upon co-stimulation with CD3/CD28 antibodies, activated CD4 + T cells were found to lose their susceptibility to HIV-1 infection, exhibiting an induced resistant phenotype. This rather unexpected phenomenon has been repeatedly confirmed but the underlying cell and molecular mechanisms are still unknown. METHODS We first replicated the reported system using the specified Dynal beads with PHA/IL-2-stimulated and un-stimulated cells as controls. Genome-wide expression and analysis were then performed by using Agilent whole genome microarrays and established bioinformatics tools. RESULTS We showed that following CD3/CD28 co-stimulation, a homogeneous population emerged with uniform expression of activation markers CD25 and CD69 as well as a memory marker CD45RO at high levels. These cells differentially expressed 7,824 genes when compared with the controls on microarrays. Series-Cluster analysis identified 6 distinct expression profiles containing 1,345 genes as the representative signatures in the permissive and resistant cells. Of them, 245 (101 potentially permissive and 144 potentially resistant) were significant in gene ontology categories related to immune response, cell adhesion and metabolism. Co-expression networks analysis identified 137 "key regulatory" genes (84 potentially permissive and 53 potentially resistant), holding hub positions in the gene interactions. By mapping these genes on KEGG pathways, the predominance of actin cytoskeleton functions, proteasomes, and cell cycle arrest in induced resistance emerged. We also revealed an entire set of previously unreported novel genes for further mining and functional validation. CONCLUSIONS This initial microarray study will stimulate renewed interest in exploring this system and open new avenues for research into HIV-1 susceptibility and its reversal in target cells, serving as a foundation for the development of novel therapeutic and clinical treatments.
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Affiliation(s)
- Wen-Wen Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Jiaochang East Road 32, Kunming, Yunnan Province, 650223 China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Miao-Jun Han
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Jiaochang East Road 32, Kunming, Yunnan Province, 650223 China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Dai Chen
- Novel Bioinformatics Co., Ltd, Shanghai, China
| | - Ling Chen
- Yunnan centers for disease control and prevention, Kunming, China
| | - Yan Guo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Jiaochang East Road 32, Kunming, Yunnan Province, 650223 China
| | - Andrew Willden
- Editorial Department, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Di-Qiu Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Jiaochang East Road 32, Kunming, Yunnan Province, 650223 China
| | - Hua-Tang Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Jiaochang East Road 32, Kunming, Yunnan Province, 650223 China
- Chongqing Center for Biomedical Research and Equipment Development, Chongqing Academy of Science and Technology, Chongqing, China
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Schweitzer CJ, Jagadish T, Haverland N, Ciborowski P, Belshan M. Proteomic analysis of early HIV-1 nucleoprotein complexes. J Proteome Res 2013; 12:559-72. [PMID: 23282062 PMCID: PMC3564510 DOI: 10.1021/pr300869h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
After entry into the cell, the early steps of the human immunodeficiency virus type 1 (HIV-1) replication cycle are mediated by two functionally distinct nucleoprotein complexes, the reverse transcription complex (RTC) and preintegration complex (PIC). These two unique viral complexes are responsible for the conversion of the single-stranded RNA genome into double-stranded DNA, transport of the DNA into the nucleus, and integration of the viral DNA into the host cell chromosome. Prior biochemical analyses suggest that these complexes are large and contain multiple undiscovered host cell factors. In this study, functional HIV-1 RTCs and PICs were partially purified by velocity gradient centrifugation and fractionation, concentrated, trypsin digested, and analyzed by LC-MS/MS. A total of seven parallel infected and control biological replicates were completed. Database searches were performed with Proteome Discoverer and a comparison of the HIV-1 samples to parallel uninfected control samples was used to identify unique cellular factors. The analysis produced a total data set of 11055 proteins. Several previously characterized HIV-1 factors were identified, including XRCC6, TFRC, and HSP70. The presence of XRCC6 was confirmed in infected fractions and shown to be associated with HIV-1 DNA by immunoprecipitation-PCR experiments. Overall, the analysis identified 94 proteins unique in the infected fractions and 121 proteins unique to the control fractions with ≥ 2 protein assignments. An additional 54 and 52 were classified as enriched in the infected and control samples, respectively, based on a 3-fold difference in total Proteome Discoverer probability score. The differential expression of several candidate proteins was validated by Western blot analysis. This study contributes additional novel candidate proteins to the growing published bioinformatic data sets of proteins that contribute to HIV-1 replication.
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MESH Headings
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Antigens, Nuclear/genetics
- Antigens, Nuclear/metabolism
- Cell Line
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Cell Nucleus/virology
- Centrifugation, Density Gradient
- Chromatography, Liquid
- DNA, Viral/genetics
- DNA, Viral/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Gene Expression Profiling
- HIV-1/genetics
- HIV-1/metabolism
- HSP70 Heat-Shock Proteins/genetics
- HSP70 Heat-Shock Proteins/metabolism
- Host-Pathogen Interactions
- Humans
- Ku Autoantigen
- Lymphocytes/metabolism
- Lymphocytes/virology
- Nucleoproteins/genetics
- Nucleoproteins/metabolism
- Protein Binding
- Proteome/genetics
- Proteome/metabolism
- Receptors, Transferrin/genetics
- Receptors, Transferrin/metabolism
- Reverse Transcription
- Tandem Mass Spectrometry
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Virus Integration
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Affiliation(s)
| | - Teena Jagadish
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE
| | - Nicole Haverland
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE
- The Nebraska Center for Virology, University of Nebraska, Lincoln, NE
| | - Michael Belshan
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE
- The Nebraska Center for Virology, University of Nebraska, Lincoln, NE
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35
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Sirois M, Robitaille L, Allary R, Shah M, Woelk CH, Estaquier J, Corbeil J. TRAF6 and IRF7 control HIV replication in macrophages. PLoS One 2011; 6:e28125. [PMID: 22140520 PMCID: PMC3225375 DOI: 10.1371/journal.pone.0028125] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 11/01/2011] [Indexed: 01/08/2023] Open
Abstract
The innate immune system recognizes virus infection and evokes antiviral responses which include producing type I interferons (IFNs). The induction of IFN provides a crucial mechanism of antiviral defense by upregulating interferon-stimulated genes (ISGs) that restrict viral replication. ISGs inhibit the replication of many viruses by acting at different steps of their viral cycle. Specifically, IFN treatment prior to in vitro human immunodeficiency virus (HIV) infection stops or significantly delays HIV-1 production indicating that potent inhibitory factors are generated. We report that HIV-1 infection of primary human macrophages decreases tumor necrosis factor receptor-associated factor 6 (TRAF6) and virus-induced signaling adaptor (VISA) expression, which are both components of the IFN signaling pathway controlling viral replication. Knocking down the expression of TRAF6 in macrophages increased HIV-1 replication and augmented the expression of IRF7 but not IRF3. Suppressing VISA had no impact on viral replication. Overexpression of IRF7 resulted in enhanced viral replication while knocking down IRF7 expression in macrophages significantly reduced viral output. These findings are the first demonstration that TRAF6 can regulate HIV-1 production and furthermore that expression of IRF7 promotes HIV-1 replication.
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Affiliation(s)
- Mélissa Sirois
- Department of Molecular Medicine, Infectious Disease Research Center, CHUL Research Center and Laval University, Québec, Québec, Canada
| | - Lynda Robitaille
- Department of Molecular Medicine, Infectious Disease Research Center, CHUL Research Center and Laval University, Québec, Québec, Canada
| | - Robin Allary
- Department of Molecular Medicine, Infectious Disease Research Center, CHUL Research Center and Laval University, Québec, Québec, Canada
| | - Mohak Shah
- Department of Electrical and Computer Engineering, Centre for Intelligent Machines, McGill University, Montreal, Québec, Canada
| | - Christopher H. Woelk
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Jérôme Estaquier
- Department of Molecular Medicine, Infectious Disease Research Center, CHUL Research Center and Laval University, Québec, Québec, Canada
- CNRS FRE3235, Université René Descartes Paris, Paris, France
| | - Jacques Corbeil
- Department of Molecular Medicine, Infectious Disease Research Center, CHUL Research Center and Laval University, Québec, Québec, Canada
- * E-mail:
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36
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Borjabad A, Morgello S, Chao W, Kim SY, Brooks AI, Murray J, Potash MJ, Volsky DJ. Significant effects of antiretroviral therapy on global gene expression in brain tissues of patients with HIV-1-associated neurocognitive disorders. PLoS Pathog 2011; 7:e1002213. [PMID: 21909266 PMCID: PMC3164642 DOI: 10.1371/journal.ppat.1002213] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 07/01/2011] [Indexed: 11/18/2022] Open
Abstract
Antiretroviral therapy (ART) has reduced morbidity and mortality in HIV-1 infection; however HIV-1-associated neurocognitive disorders (HAND) persist despite treatment. The reasons for the limited efficacy of ART in the brain are unknown. Here we used functional genomics to determine ART effectiveness in the brain and to identify molecular signatures of HAND under ART. We performed genome-wide microarray analysis using Affymetrix U133 Plus 2.0 Arrays, real-time PCR, and immunohistochemistry in brain tissues from seven treated and eight untreated HAND patients and six uninfected controls. We also determined brain virus burdens by real-time PCR. Treated and untreated HAND brains had distinct gene expression profiles with ART transcriptomes clustering with HIV-1-negative controls. The molecular disease profile of untreated HAND showed dysregulated expression of 1470 genes at p<0.05, with activation of antiviral and immune responses and suppression of synaptic transmission and neurogenesis. The overall brain transcriptome changes in these patients were independent of histological manifestation of HIV-1 encephalitis and brain virus burdens. Depending on treatment compliance, brain transcriptomes from patients on ART had 83% to 93% fewer dysregulated genes and significantly lower dysregulation of biological pathways compared to untreated patients, with particular improvement indicated for nervous system functions. However a core of about 100 genes remained similarly dysregulated in both treated and untreated patient brain tissues. These genes participate in adaptive immune responses, and in interferon, cell cycle, and myelin pathways. Fluctuations of cellular gene expression in the brain correlated in Pearson's formula analysis with plasma but not brain virus burden. Our results define for the first time an aberrant genome-wide brain transcriptome of untreated HAND and they suggest that antiretroviral treatment can be broadly effective in reducing pathophysiological changes in the brain associated with HAND. Aberrantly expressed transcripts common to untreated and treated HAND may contribute to neurocognitive changes defying ART.
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Affiliation(s)
- Alejandra Borjabad
- Molecular Virology Division, St. Luke's-Roosevelt Hospital Center and Columbia University, New York, New York, United States of America
| | - Susan Morgello
- Department of Pathology and Neuroscience, The Mount Sinai Medical Center, New York, New York, United States of America
| | - Wei Chao
- Molecular Virology Division, St. Luke's-Roosevelt Hospital Center and Columbia University, New York, New York, United States of America
| | - Seon-Young Kim
- Human Genomics Laboratory, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Andrew I. Brooks
- Department of Genetics, Environmental and Occupational Health Science Institute (EOHSI), Rutgers University, Piscataway, New Jersey, United States of America
| | - Jacinta Murray
- Department of Pathology and Neuroscience, The Mount Sinai Medical Center, New York, New York, United States of America
| | - Mary Jane Potash
- Molecular Virology Division, St. Luke's-Roosevelt Hospital Center and Columbia University, New York, New York, United States of America
| | - David J. Volsky
- Molecular Virology Division, St. Luke's-Roosevelt Hospital Center and Columbia University, New York, New York, United States of America
- * E-mail:
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37
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Innate antiviral response: role in HIV-1 infection. Viruses 2011; 3:1179-203. [PMID: 21994776 PMCID: PMC3185785 DOI: 10.3390/v3071179] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 06/28/2011] [Accepted: 06/29/2011] [Indexed: 12/14/2022] Open
Abstract
As an early response to infection, cells induce a profile of the early inflammatory proteins including antiviral cytokines and chemokines. Two families of transcriptional factors play a major role in the transcriptional activation of the early inflammatory genes: The well-characterized family of NFkB factors and the family of interferon regulatory factors (IRF). The IRFs play a critical role in the induction of type I interferon (IFN) and chemokine genes, as well as genes mediating antiviral, antibacterial, and inflammatory responses. Type I IFNs represent critical components of innate antiviral immunity. These proteins not only exert direct antiviral effects, but also induce maturation of dendritic cells (DC), and enhance functions of NK, T and B cells, and macrophages. This review will summarize the current knowledge of the mechanisms leading to the innate antiviral response with a focus on its role in the regulation of HIV-1 infection and pathogenicity. We would like this review to be both historical and a future perspective.
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38
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Rotger M, Dalmau J, Rauch A, McLaren P, Bosinger SE, Martinez R, Sandler NG, Roque A, Liebner J, Battegay M, Bernasconi E, Descombes P, Erkizia I, Fellay J, Hirschel B, Miró JM, Palou E, Hoffmann M, Massanella M, Blanco J, Woods M, Günthard HF, de Bakker P, Douek DC, Silvestri G, Martinez-Picado J, Telenti A. Comparative transcriptomics of extreme phenotypes of human HIV-1 infection and SIV infection in sooty mangabey and rhesus macaque. J Clin Invest 2011; 121:2391-400. [PMID: 21555857 DOI: 10.1172/jci45235] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 03/30/2011] [Indexed: 01/14/2023] Open
Abstract
High levels of HIV-1 replication during the chronic phase of infection usually correlate with rapid progression to severe immunodeficiency. However, a minority of highly viremic individuals remains asymptomatic and maintains high CD4⁺ T cell counts. This tolerant profile is poorly understood and reminiscent of the widely studied nonprogressive disease model of SIV infection in natural hosts. Here, we identify transcriptome differences between rapid progressors (RPs) and viremic nonprogressors (VNPs) and highlight several genes relevant for the understanding of HIV-1-induced immunosuppression. RPs were characterized by a specific transcriptome profile of CD4⁺ and CD8⁺ T cells similar to that observed in pathogenic SIV-infected rhesus macaques. In contrast, VNPs exhibited lower expression of interferon-stimulated genes and shared a common gene regulation profile with nonpathogenic SIV-infected sooty mangabeys. A short list of genes associated with VNP, including CASP1, CD38, LAG3, TNFSF13B, SOCS1, and EEF1D, showed significant correlation with time to disease progression when evaluated in an independent set of CD4⁺ T cell expression data. This work characterizes 2 minimally studied clinical patterns of progression to AIDS, whose analysis may inform our understanding of HIV pathogenesis.
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Affiliation(s)
- Margalida Rotger
- Institute of Microbiology, University Hospital and University of Lausanne, Lausanne, Switzerland
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39
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Smith AJ, Toledo CM, Wietgrefe SW, Duan L, Schacker TW, Reilly CS, Haase AT. The immunosuppressive role of IL-32 in lymphatic tissue during HIV-1 infection. THE JOURNAL OF IMMUNOLOGY 2011; 186:6576-84. [PMID: 21525393 DOI: 10.4049/jimmunol.1100277] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
One pathological hallmark of HIV-1 infection is chronic activation of the immune system, driven, in part, by increased expression of proinflammatory cytokines. The host attempts to counterbalance this prolonged immune activation through compensatory mediators of immune suppression. We recently identified a gene encoding the proinflammatory cytokine IL-32 in microarray studies of HIV-1 infection in lymphatic tissue (LT) and show in this study that increased expression of IL-32 in both gut and LT of HIV-1-infected individuals may have a heretofore unappreciated role as a mediator of immune suppression. We show that: 1) IL-32 expression is increased in CD4(+) T cells, B cells, macrophages, dendritic cells, and epithelial cells in vivo; 2) IL-32 induces the expression of immunosuppressive molecules IDO and Ig-like transcript 4 in immune cells in vitro; and 3) in vivo, IL-32-associated IDO/Ig-like transcript 4 expression in LT macrophages and gut epithelial cells decreases immune activation but also may impair host defenses, supporting productive viral replication, thereby accounting for the correlation between IL-32 levels and HIV-1 replication in LT. Thus, during HIV-1 infection, we propose that IL-32 moderates chronic immune activation to avert associated immunopathology but at the same time dampens the antiviral immune response and thus paradoxically supports HIV-1 replication and viral persistence.
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Affiliation(s)
- Anthony J Smith
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
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40
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Abstract
Until recently, progress in ex vivo gene therapy (GT) for human immunodeficiency virus-1 (HIV-1) treatment has been incremental. Long-term HIV-1 remission in a patient who received a heterologous stem cell transplant for acquired immunodeficiency syndrome-related lymphoma from a CCR5(-/-) donor, even after discontinuation of conventional therapy, has energized the field. We review the status of current approaches as well as future directions in the areas of therapeutic targets, combinatorial strategies, vector design, introduction of therapeutics into stem cells and enrichment/expansion of gene-modified cells. Finally, we discuss recent advances towards clinical application of HIV-1 GT.
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Affiliation(s)
- Lisa J Scherer
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
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Lever AML, Jeang KT. Insights into cellular factors that regulate HIV-1 replication in human cells. Biochemistry 2011; 50:920-31. [PMID: 21218853 DOI: 10.1021/bi101805f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Retroviruses integrate into the host cell's chromosome. Accordingly, many aspects of the life cycle of retroviruses like HIV-1 are intimately linked to the functions of cellular proteins and RNAs. In this review, we discuss in brief recent genomewide screens for the identification of cellular proteins that assist HIV-1 replication in human cells. We also review findings for other cellular moieties that help or restrict the viral life cycle.
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Affiliation(s)
- Andrew M L Lever
- Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, U.K
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