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Wei Y, Song J, Zhang J, Chen S, Yu Z, He L, Chen J. Exploring TRIM proteins' role in antiviral defense against influenza A virus and respiratory coronaviruses. Front Cell Infect Microbiol 2024; 14:1420854. [PMID: 39077432 PMCID: PMC11284085 DOI: 10.3389/fcimb.2024.1420854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 06/19/2024] [Indexed: 07/31/2024] Open
Abstract
Numerous tripartite motif (TRIM) proteins, identified as E3 ubiquitin ligases, participate in various viral infections through ubiquitylation, ISGylation, and SUMOylation processes. Respiratory viruses, particularly influenza A virus (IAV) and respiratory coronaviruses (CoVs), have severely threatened public health with high morbidity and mortality, causing incalculable losses. Research on the regulation of TRIM proteins in respiratory virus infections is crucial for disease prevention and control. This review introduces TRIM proteins, summarizes recent discoveries regarding their roles and molecular mechanisms in IAV and CoVs infections, discusses current research gaps, and explores potential future trends in this rapidly developing field. It aims to enhance understanding of virus-host interactions and inform the development of new molecularly targeted therapies.
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Affiliation(s)
- Ying Wei
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, China
- The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, China
| | - Junzhu Song
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, China
- The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, China
| | - Jingyu Zhang
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, China
- The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, China
| | - Songbiao Chen
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, China
- The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, China
| | - Zuhua Yu
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, China
- The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, China
| | - Lei He
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, China
- The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, China
| | - Jian Chen
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, China
- The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, China
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Hernández-Sarmiento LJ, Tamayo-Molina YS, Valdés-López JF, Urcuqui-Inchima S. Interleukin 27, Similar to Interferons, Modulates Gene Expression of Tripartite Motif (TRIM) Family Members and Interferes with Mayaro Virus Replication in Human Macrophages. Viruses 2024; 16:996. [PMID: 38932287 PMCID: PMC11209095 DOI: 10.3390/v16060996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The Tripartite motif (TRIM) family includes more than 80 distinct human genes. Their function has been implicated in regulating important cellular processes, including intracellular signaling, transcription, autophagy, and innate immunity. During viral infections, macrophages are key components of innate immunity that produce interferons (IFNs) and IL27. We recently published that IL27 and IFNs induce transcriptional changes in various genes, including those involved in JAK-STAT signaling. Furthermore, IL27 and IFNs share proinflammatory and antiviral pathways in monocyte-derived macrophages (MDMs), resulting in both common and unique expression of inflammatory factors and IFN-stimulated genes (ISGs) encoding antiviral proteins. Interestingly, many TRIM proteins have been recognized as ISGs in recent years. Although it is already very well described that TRIM expression is induced by IFNs, it is not fully understood whether TRIM genes are induced in macrophages by IL27. Therefore, in this study, we examined the effect of stimulation with IL27 and type I, II, and III IFNs on the mRNA expression profiles of TRIM genes in MDMs. METHODS We used bulk RNA-seq to examine the TRIM expression profile of MDMs treated with IFNs or IL27. Initially, we characterized the expression patterns of different TRIM subfamilies using a heatmap. Subsequently, a volcano plot was employed to identify commonly differentially expressed TRIM genes. Additionally, we conducted gene ontology analysis with ClueGO to explore the biological processes of the regulated TRIMs, created a gene-gene interaction network using GeneMANIA, and examined protein-protein interactions with the STRING database. Finally, RNA-seq data was validated using RT-qPCR. Furthermore, the effect of IL27 on Mayaro virus replication was also evaluated. RESULTS We found that IL27, similar to IFNs, upregulates several TRIM genes' expression in human macrophages. Specifically, we identified three common TRIM genes (TRIM19, 21, and 22) induced by IL27 and all types of human IFNs. Additionally, we performed the first report of transcriptional regulation of TRIM19, 21, 22, and 69 genes in response to IL27. The TRIMs involved a broad range of biological processes, including defense response to viruses, viral life cycle regulation, and negative regulation of viral processes. In addition, we observed a decrease in Mayaro virus replication in MDMs previously treated with IL27. CONCLUSIONS Our results show that IL27, like IFNs, modulates the transcriptional expression of different TRIM-family members involved in the induction of innate immunity and an antiviral response. In addition, the functional analysis demonstrated that, like IFN, IL27 reduced Mayaro virus replication in MDMs. This implies that IL27 and IFNs share many similarities at a functional level. Moreover, identifying distinct TRIM groups and their differential expressions in response to IL27 provides new insights into the regulatory mechanisms underlying the antiviral response in human macrophages.
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Affiliation(s)
| | | | | | - Silvio Urcuqui-Inchima
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050001, Colombia; (L.J.H.-S.); (Y.S.T.-M.); (J.F.V.-L.)
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Heo H, Park H, Lee MS, Kim J, Kim J, Jung SY, Kim SK, Lee S, Chang J. TRIM22 facilitates autophagosome-lysosome fusion by mediating the association of GABARAPs and PLEKHM1. Autophagy 2024; 20:1098-1113. [PMID: 38009729 PMCID: PMC11135824 DOI: 10.1080/15548627.2023.2287925] [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: 01/18/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023] Open
Abstract
Tripartite motif (TRIM) proteins are a large family of E3 ubiquitin ligases implicated in antiviral defense systems, tumorigenesis, and protein quality control. TRIM proteins contribute to protein quality control by regulating the ubiquitin-proteasome system, endoplasmic reticulum-associated degradation, and macroautophagy/autophagy. However, the detailed mechanisms through which various TRIM proteins regulate downstream events have not yet been fully elucidated. Herein, we identified a novel function of TRIM22 in the regulation of autophagy. TRIM22 promotes autophagosome-lysosome fusion by mediating the association of GABARAP family proteins with PLEKHM1, thereby inducing the autophagic clearance of protein aggregates, independent of its E3 ubiquitin ligase activity. Furthermore, a TRIM22 variant associated with early-onset familial Alzheimer disease interferes with autophagosome-lysosome fusion and autophagic clearance. These findings suggest TRIM22 as a critical autophagic regulator that orchestrates autophagosome-lysosome fusion by scaffolding autophagy-related proteins, thus representing a potential therapeutic target in neurodegenerative diseases.Abbreviations: AD: Alzheimer disease; ADAOO: AD age of onset; AICD: APP intracellular domain; APP: amyloid beta precursor protein; BSA: bovine serum albumin; cDNAs: complementary DNAs; CQ: chloroquine; CTF: carboxyl-terminal fragment; EBSS: Earle's balanced salt solution; GABARAP: GABA type A receptor-associated protein; GST: glutathione S-transferase; HA: hemagglutinin; HOPS: homotypic fusion and protein sorting; IFN: interferon; IL1A/IL-1α: interleukin 1 alpha; KO: knockout; MTORC1: mechanistic target of rapamycin kinase complex 1; NFKBIA/IκBα: NFKB inhibitor alpha; NFE2L2/NRF2: NFE2 like bZIP transcription factor; PBS: phosphate-buffered saline; PI3K: class I phosphoinositide 3-kinase; PLA: proximity ligation assay; PLEKHM1: pleckstrin homology and RUN domain containing M1; PSEN1: presenilin 1; SEM: standard errors of the means; SNAREs: soluble N-ethylmaleimide-sensitive factor attachment protein receptors; SNCA: synuclein alpha; SNP: single nucleotide polymorphism; TBS: tris-buffered saline; TNF/TNF-α: tumor necrosis factor; TRIM: tripartite motif; ULK1: unc-51 like autophagy activating kinase 1; WT: wild-type.
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Affiliation(s)
- Hansol Heo
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Hyungsun Park
- Department of Anatomy, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
| | - Myung Shin Lee
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jongyoon Kim
- Department of Anatomy, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
| | - Juyeong Kim
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Soon-Young Jung
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Sun Kyeon Kim
- Department of Anatomy, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
| | - Seongju Lee
- Department of Anatomy, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
| | - Jaerak Chang
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Brain Science, Ajou University School of Medicine, Suwon, Republic of Korea
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Zhang J, Zhang Y, Ren Z, Yan D, Li G. The role of TRIM family in metabolic associated fatty liver disease. Front Endocrinol (Lausanne) 2023; 14:1210330. [PMID: 37867509 PMCID: PMC10585262 DOI: 10.3389/fendo.2023.1210330] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/20/2023] [Indexed: 10/24/2023] Open
Abstract
Metabolic associated fatty liver disease (MAFLD) ranks among the most prevalent chronic liver conditions globally. At present, the mechanism of MAFLD has not been fully elucidated. Tripartite motif (TRIM) protein is a kind of protein with E3 ubiquitin ligase activity, which participates in highly diversified cell activities and processes. It not only plays an important role in innate immunity, but also participates in liver steatosis, insulin resistance and other processes. In this review, we focused on the role of TRIM family in metabolic associated fatty liver disease. We also introduced the structure and functions of TRIM proteins. We summarized the TRIM family's regulation involved in the occurrence and development of metabolic associated fatty liver disease, as well as insulin resistance. We deeply discussed the potential of TRIM proteins as targets for the treatment of metabolic associated fatty liver disease.
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Affiliation(s)
- Jingyue Zhang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Yingming Zhang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Ze Ren
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Dongmei Yan
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Guiying Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
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Müller M, Sauter D. The more the merrier? Gene duplications in the coevolution of primate lentiviruses with their hosts. Curr Opin Virol 2023; 62:101350. [PMID: 37651832 DOI: 10.1016/j.coviro.2023.101350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/20/2023] [Accepted: 07/29/2023] [Indexed: 09/02/2023]
Abstract
Gene duplications are a major source of genetic diversity and evolutionary innovation. Newly formed, duplicated genes can provide a selection advantage in constantly changing environments. One such example is the arms race of HIV and related lentiviruses with innate immune responses of their hosts. In recent years, it has become clear that both sides have benefited from multiple gene duplications. For example, amplifications of antiretroviral factors such as apolipoprotein-B mRNA-editing enzyme catalytic polypeptide-3 (APOBEC3), interferon-induced transmembrane protein (IFITM), and tripartite motif-containing (TRIM) proteins have expanded the repertoire of cell-intrinsic defense mechanisms and increased the barriers to retroviral replication and cross-species transmission. Conversely, recent studies have also shed light on how duplications of accessory lentiviral genes and Long terminal repeat (LTR) elements can provide a selection advantage in the coevolution with antiviral host proteins.
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Affiliation(s)
- Martin Müller
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Elfriede-Aulhorn-Straße 6, 72076 Tübingen, Germany
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Elfriede-Aulhorn-Straße 6, 72076 Tübingen, Germany.
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Campbell LK, Peery RM, Magor KE. Evolution and expression of the duck TRIM gene repertoire. Front Immunol 2023; 14:1220081. [PMID: 37622121 PMCID: PMC10445537 DOI: 10.3389/fimmu.2023.1220081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/05/2023] [Indexed: 08/26/2023] Open
Abstract
Tripartite motif (TRIM) proteins are involved in development, innate immunity, and viral restriction. TRIM gene repertoires vary between species, likely due to diversification caused by selective pressures from pathogens; however, this has not been explored in birds. We mined a de novo assembled transcriptome for the TRIM gene repertoire of the domestic mallard duck (Anas platyrhynchos), a reservoir host of influenza A viruses. We found 57 TRIM genes in the duck, which represent all 12 subfamilies based on their C-terminal domains. Members of the C-IV subfamily with C-terminal PRY-SPRY domains are known to augment immune responses in mammals. We compared C-IV TRIM proteins between reptiles, birds, and mammals and show that many C-IV subfamily members have arisen independently in these lineages. A comparison of the MHC-linked C-IV TRIM genes reveals expansions in birds and reptiles. The TRIM25 locus with related innate receptor modifiers is adjacent to the MHC in reptile and marsupial genomes, suggesting the ancestral organization. Within the avian lineage, both the MHC and TRIM25 loci have undergone significant TRIM gene reorganizations and divergence, both hallmarks of pathogen-driven selection. To assess the expression of TRIM genes, we aligned RNA-seq reads from duck tissues. C-IV TRIMs had high relative expression in immune relevant sites such as the lung, spleen, kidney, and intestine, and low expression in immune privileged sites such as in the brain or gonads. Gene loss and gain in the evolution of the TRIM repertoire in birds suggests candidate immune genes and potential targets of viral subversion.
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Affiliation(s)
- Lee K. Campbell
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Rhiannon M. Peery
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Katharine E. Magor
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
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Bauer A, Lindemuth E, Marino FE, Krause R, Joy J, Docken SS, Mallick S, McCormick K, Holt C, Georgiev I, Felber B, Keele BF, Veazey R, Davenport MP, Li H, Shaw GM, Bar KJ. Adaptation of a transmitted/founder simian-human immunodeficiency virus for enhanced replication in rhesus macaques. PLoS Pathog 2023; 19:e1011059. [PMID: 37399208 PMCID: PMC10348547 DOI: 10.1371/journal.ppat.1011059] [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: 12/10/2022] [Revised: 07/14/2023] [Accepted: 06/21/2023] [Indexed: 07/05/2023] Open
Abstract
Transmitted/founder (TF) simian-human immunodeficiency viruses (SHIVs) express HIV-1 envelopes modified at position 375 to efficiently infect rhesus macaques while preserving authentic HIV-1 Env biology. SHIV.C.CH505 is an extensively characterized virus encoding the TF HIV-1 Env CH505 mutated at position 375 shown to recapitulate key features of HIV-1 immunobiology, including CCR5-tropism, a tier 2 neutralization profile, reproducible early viral kinetics, and authentic immune responses. SHIV.C.CH505 is used frequently in nonhuman primate studies of HIV, but viral loads after months of infection are variable and typically lower than those in people living with HIV. We hypothesized that additional mutations besides Δ375 might further enhance virus fitness without compromising essential components of CH505 Env biology. From sequence analysis of SHIV.C.CH505-infected macaques across multiple experiments, we identified a signature of envelope mutations associated with higher viremia. We then used short-term in vivo mutational selection and competition to identify a minimally adapted SHIV.C.CH505 with just five amino acid changes that substantially improve virus replication fitness in macaques. Next, we validated the performance of the adapted SHIV in vitro and in vivo and identified the mechanistic contributions of selected mutations. In vitro, the adapted SHIV shows improved virus entry, enhanced replication on primary rhesus cells, and preserved neutralization profiles. In vivo, the minimally adapted virus rapidly outcompetes the parental SHIV with an estimated growth advantage of 0.14 days-1 and persists through suppressive antiretroviral therapy to rebound at treatment interruption. Here, we report the successful generation of a well-characterized, minimally adapted virus, termed SHIV.C.CH505.v2, with enhanced replication fitness and preserved native Env properties that can serve as a new reagent for NHP studies of HIV-1 transmission, pathogenesis, and cure.
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Affiliation(s)
- Anya Bauer
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Emily Lindemuth
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Francesco Elia Marino
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ryan Krause
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jaimy Joy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Suvadip Mallick
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kevin McCormick
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Clinton Holt
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ivelin Georgiev
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Barbara Felber
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Maryland, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Ronald Veazey
- Department of Pathology and Laboratory Medicine, Tulane School of Medicine, New Orleans, Louisiana, United States of America
| | | | - Hui Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Departments of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - George M. Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Departments of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katharine J. Bar
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Itell HL, Humes D, Overbaugh J. Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4 + T cells. Cell Rep 2023; 42:112556. [PMID: 37227817 PMCID: PMC10592456 DOI: 10.1016/j.celrep.2023.112556] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/30/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
Type I interferon (IFN) upregulates proteins that inhibit HIV within infected cells. Prior studies have identified IFN-stimulated genes (ISGs) that impede lab-adapted HIV in cell lines, yet the ISG(s) that mediate IFN restriction in HIV target cells, primary CD4+ T cells, are unknown. Here, we interrogate ISG restriction of primary HIV in CD4+ T cells by performing CRISPR-knockout screens with a custom library that specifically targets ISGs expressed in CD4+ T cells. Our investigation identifies previously undescribed HIV-restricting ISGs (HM13, IGFBP2, LAP3) and finds that two factors characterized in other HIV infection models (IFI16 and UBE2L6) mediate IFN restriction in T cells. Inactivation of these five ISGs in combination further diminishes IFN's protective effect against diverse HIV strains. This work demonstrates that IFN restriction of HIV is multifaceted, resulting from several effectors functioning collectively, and establishes a primary cell ISG screening model to identify both single and combinations of HIV-restricting ISGs.
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Affiliation(s)
- Hannah L Itell
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA 98195, USA; Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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Xie J, Tan B, Zhang Y. Positive Selection and Duplication of Bat TRIM Family Proteins. Viruses 2023; 15:v15040875. [PMID: 37112854 PMCID: PMC10145180 DOI: 10.3390/v15040875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Bats have received increasing attention because of some unique biological features they possess. TRIM is a large family of proteins that participate in diverse cellular functions, such as antiviral immunity, DNA damage repair, tumor suppression, and aging. These functional areas appear to be highly consistent with the special characteristics of bats, such as tolerance to viruses and DNA damage generated in flight, low cancer incidence, and longevity. However, there is still a lack of systematic study of the TRIM family in bats. Here, we explored the TRIM family of bats using the genomes of 16 representative species. The results showed that the bat TRIM family contains 70 members, with 24 under positive selection and 7 duplicated. Additional transcriptomic analysis revealed the tissue-specific expressions of TRIM9, 46, 54, 55, 63, and 72. Additionally, following interferon or viral stimulation, TRIM orthologs associated with antiviral immunity reported in humans were also upregulated in bat cells. The present study systematically analyzed the composition, evolution, and expression of bat TRIM genes. It may provide a theoretical basis for studies of bat TRIM in the fields of antiviral immunity, longevity, and tolerance to DNA damage.
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Affiliation(s)
- Jiazheng Xie
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Bowen Tan
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Yi Zhang
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
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Itell HL, Humes D, Overbaugh J. Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4 + T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527545. [PMID: 36798236 PMCID: PMC9934674 DOI: 10.1101/2023.02.07.527545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Type I interferon (IFN) upregulates proteins that inhibit HIV within infected cells. Prior studies have identified IFN-stimulated genes (ISGs) that impede lab-adapted HIV in cell lines, yet the ISG(s) that mediate IFN restriction in HIV target cells, primary CD4 + T cells, are unknown. Here, we interrogate ISG restriction of primary HIV in CD4 + T cells. We performed CRISPR-knockout screens using a custom library that specifically targets ISGs expressed in CD4 + T cells and validated top hits. Our investigation identified new HIV-restricting ISGs (HM13, IGFBP2, LAP3) and found that two previously studied factors (IFI16, UBE2L6) are IFN effectors in T cells. Inactivation of these five ISGs in combination further diminished IFN’s protective effect against six diverse HIV strains. This work demonstrates that IFN restriction of HIV is multifaceted, resulting from several effectors functioning collectively, and establishes a primary cell ISG screening model to identify both single and combinations of HIV-restricting ISGs.
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Affiliation(s)
- Hannah L. Itell
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA, 98109, USA
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Present address: Tr1X Inc, La Jolla, CA, 92037, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
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Rashid F, Zaongo SD, Song F, Chen Y. The diverse roles of miRNAs in HIV pathogenesis: Current understanding and future perspectives. Front Immunol 2023; 13:1091543. [PMID: 36685589 PMCID: PMC9849909 DOI: 10.3389/fimmu.2022.1091543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/14/2022] [Indexed: 01/07/2023] Open
Abstract
Despite noteworthy progress made in the management and treatment of HIV/AIDS-related disease, including the introduction of the now almost ubiquitous HAART, there remains much to understand with respect to HIV infection. Although some roles that miRNAs play in some diseases have become more obvious of late, the roles of miRNAs in the context of HIV pathogenesis have not, as yet, been elucidated, and require further investigations. miRNAs can either be beneficial or harmful to the host, depending upon the genes they target. Some miRNAs target the 3' UTR of viral mRNAs to accomplish restriction of viral infection. However, upon HIV-1 infection, there are several dysregulated host miRNAs which target their respective host factors to either facilitate or abrogate viral infection. In this review, we discuss the miRNAs which play roles in various aspects of viral pathogenesis. We describe in detail the various mechanisms thereby miRNAs either directly or indirectly regulate HIV-1 infection. Moreover, the predictive roles of miRNAs in various aspects of the HIV viral life cycle are also discussed. Contemporary antiretroviral therapeutic drugs have received much attention recently, due to their success in the treatment of HIV/AIDS; therefore, miRNA involvement in various aspects of antiretroviral therapeutics are also elaborated upon herein. The therapeutic potential of miRNAs are discussed, and we also propose herein that the therapeutic potential of one specific miRNA, miR-34a, warrants further exploration, as this miRNA is known to target three host proteins to promote HIV-1 pathogenesis. Finally, future perspectives and some controversy around the expression of miRNAs by HIV-1 are also discussed.
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Affiliation(s)
- Farooq Rashid
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Silvere D. Zaongo
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Fangzhou Song
- Basic Medicine College, Chongqing Medical University, Chongqing, China
| | - Yaokai Chen
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China,*Correspondence: Yaokai Chen,
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Chen WY, Gong YQ, Zhou XR, Zhang RD, Liu SH, Lu W, Ren Q, Huang Y. Eight TRIM32 isoforms from oriental river prawn Macrobrachium nipponense are involved in innate immunity during white spot syndrome virus infection. FISH & SHELLFISH IMMUNOLOGY 2022; 131:368-380. [PMID: 36243272 DOI: 10.1016/j.fsi.2022.10.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Tripartite motif (TRIM) proteins comprise a large family of RING-type ubiquitin E3 ligases that regulate important biological processes. In this study, full-length MnTRIM32 cDNA was obtained from oriental river prawn Macrobrachium nipponense, and eight MnTRIM32 isoforms generated by alternative splicing were identified. The open reading frames of the eight MnTRIM32 isoforms were predicted to be separately composed of 402, 346, 347, 346, 414, 358, 359, and 358 amino acid residues. Protein structural analysis revealed that all MnTRIM32 isoforms contained a RING domain and a coiled coil region. MnTRIM32 was ubiquitously expressed in all tissues tested, with the highest expression in the hepatopancreas. The mRNA levels of MnTRIM32 in the gills, stomach, and intestine of prawns were found to undergo time-dependent enhancement following white spot syndrome virus (WSSV) stimulation. Double-stranded RNA interference studies revealed that MnTRIM32 silencing significantly downregulated the expression levels of interferon (IFN) regulatory factor MnIRF, IFN-like factor MnVago4, and tumor necrosis factor MnTNF. Furthermore, knockdown of MnTRIM32 in WSSV-challenged prawns increased the expression of VP28 and the number of WSSV copies, suggesting that MnTRIM32 plays a positive role in limiting WSSV infection. These findings provided strong evidence for the important role of MnTRIM32 in the antiviral innate immunity of M. nipponense.
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Affiliation(s)
- Wei-Yu Chen
- College of Water Conservancy and Hydropower Engineering, Hohai University, 1 Xikang Road, Nanjing, Jiangsu, 210098, China
| | - Yi-Qing Gong
- Institute of Water Science and Technology, Hohai University, 1 Xikang Road, Nanjing, Jiangsu, 210098, China
| | - Xu-Ri Zhou
- Jiangsu Power Transmission and Transformation Company Limited, 280 Heyan Road, Nanjing, Jiangsu, 210038, China
| | - Rui-Dong Zhang
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu, 210023, China
| | - Song-Hai Liu
- Jiangsu Power Transmission and Transformation Company Limited, 280 Heyan Road, Nanjing, Jiangsu, 210038, China
| | - Wei Lu
- Jiangsu Power Transmission and Transformation Company Limited, 280 Heyan Road, Nanjing, Jiangsu, 210038, China
| | - Qian Ren
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu, 210023, China
| | - Ying Huang
- College of Oceanography, Hohai University, 1 Xikang Road, Nanjing, Jiangsu, 210098, China.
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13
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Qu ZL, Li YL, Gong XY, Zhao X, Sun HY, Dan C, Gui JF, Zhang YB. A finTRIM Family Protein Acquires RNA-Binding Activity and E3 Ligase Activity to Shape the IFN Response in Fish. THE JOURNAL OF IMMUNOLOGY 2022; 209:1335-1347. [DOI: 10.4049/jimmunol.2200343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/25/2022] [Indexed: 01/04/2023]
Abstract
Abstract
Tripartite motif (TRIM) family proteins have come forth as important modulators of innate signaling dependent on of E3 ligase activity. Recently, several human TRIM proteins have been identified as unorthodox RNA-binding proteins by RNA interactome analyses; however, their targets and functions remain largely unknown. FTRCA1 is a crucian carp (Carassius auratus)–specific finTRIM (fish novel TRIM) member and negatively regulates the IFN antiviral response by targeting two retinoic acid–inducible gene-I (RIG-I)–like receptor (RLR) pathway molecules, that is, TANK-binding kinase 1 (TBK1) and IFN regulatory factor 7 (IRF7). In this study, we identify FTRCA1 as an RNA-binding E3 ligase and characterize the contribution of its RNA-binding activity and E3 ligase activity to fish IFN response. Besides targeting TBK1 and IRF7, FTRCA1 downregulates fish IFN response also by targeting stimulator of IFN response cGAMP interactor 1 (STING1). E3 ligase activity is required for full inhibition on the TBK1- and IRF7-mediated IFN response, but partial inhibition on the STING1-mediated IFN response. However, FTRCA1 has a general binding potential to mRNAs in vitro, it selectively binds STING1 and IRF7 mRNAs in vivo to attenuate mRNA levels, and it directly interacts with TBK1 protein to target protein degradation for downregulating the IFN response. Our results present an interesting example of a fish species–specific finTRIM protein that has acquired RNA-binding activity and E3 ligase activity to fine-tune fish IFN response.
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Affiliation(s)
- Zi-Ling Qu
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
| | - Yi-Lin Li
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
| | - Xiu-Ying Gong
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
| | - Xiang Zhao
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
| | - Hao-Yu Sun
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
| | - Cheng Dan
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
| | - Jian-Fang Gui
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
- ‡The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Yi-Bing Zhang
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
- ‡The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
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Inoue A, Watanabe M, Kondo T, Hirano S, Hatakeyama S. TRIM22 negatively regulates MHC-II expression. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119318. [PMID: 35777501 DOI: 10.1016/j.bbamcr.2022.119318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/01/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
The development of cancer treatment has recently achieved a remarkable breakthrough, and checkpoint blockade immunotherapy has received much attention. To enhance the therapeutic efficacy of checkpoint blockade immunotherapy, recent studies have revealed the importance of activation of CD4+ T cells via an increase in major histocompatibility complex (MHC) class II molecules in cancer cells. Here, we demonstrate that tripartite motif-containing (TRIM) 22, negatively regulates MHC-II expression. Gene knockout of TRIM22 using Cas9-sgRNAs led to an increase of MHC-II proteins, while TRIM22 overexpression remarkably decreased MHC-II proteins. mRNA levels of MHC-II and class II transactivator (CIITA), which plays an essential role in the regulation of MHC-II transcription, were not affected by TRIM22. Furthermore, TRIM22 knockout did not suppress the degradation of MHC-II protein but rather promoted it. These results suggest that TRIM22 decreases MHC-II protein levels through a combination of multiple mechanisms other than transcription or degradation. We showed that inhibition of TRIM22 can increase the amount of MHC-II expression in cancer cells, suggesting a possibility of providing the biological basis for a possible therapeutic target to potentiate checkpoint blockade immunotherapy.
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Affiliation(s)
- Ayano Inoue
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan; Department of Gastroenterological Surgery II, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Masashi Watanabe
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Takeshi Kondo
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Satoshi Hirano
- Department of Gastroenterological Surgery II, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Shigetsugu Hatakeyama
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan.
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15
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Zu S, Li C, Li L, Deng YQ, Chen X, Luo D, Ye Q, Huang YJ, Li XF, Zhang RR, Sun N, Zhang X, Aliyari SR, Nielsen-Saines K, Jung JU, Yang H, Qin CF, Cheng G. TRIM22 suppresses Zika virus replication by targeting NS1 and NS3 for proteasomal degradation. Cell Biosci 2022; 12:139. [PMID: 36042495 PMCID: PMC9429444 DOI: 10.1186/s13578-022-00872-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/03/2022] [Indexed: 12/03/2022] Open
Abstract
Background Recognition of viral invasion by innate antiviral immune system triggers activation of the type I interferon (IFN-I) and proinflammatory signaling pathways. Subsequently, IFN-I induction regulates expression of a group of genes known as IFN-I-stimulated genes (ISGs) to block viral infection. The tripartite motif containing 22 (TRIM22) is an ISG with strong antiviral functions. Results Here we have shown that the TRIM22 has been strongly upregulated both transcriptionally and translationally upon Zika virus (ZIKV) infection. ZIKV infection is associated with a wide range of clinical manifestations in human from mild to severe symptoms including abnormal fetal brain development. We found that the antiviral function of TRIM22 plays a crucial role in counterattacking ZIKV infection. Overexpression of TRIM22 protein inhibited ZIKV growth whereas deletion of TRIM22 in host cells increased ZIKV infectivity. Mechanistically, TRIM22, as a functional E3 ubiquitin ligase, promoted the ubiquitination and degradation of ZIKV nonstructural protein 1 (NS1) and nonstructural protein 3 (NS3). Further studies showed that the SPRY domain and Ring domain of TRIM22 played important roles in protein interaction and degradation, respectively. In addition, we found that TRIM22 also inhibited other flaviviruses infection including dengue virus (DENV) and yellow fever virus (YFV). Conclusion Thus, TRIM22 is an ISG with important role in host defense against flaviviruses through binding and degradation of the NS1 and NS3 proteins. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00872-w.
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16
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Raheem Juhi Al-Kaabi N, Khameneh SC, Montazeri M, Mardasi M, Amroabadi JM, Sakhaee F, Fateh A. On the relationship between tripartite motif-containing 22 single-nucleotide polymorphisms and COVID-19 infection severity. Hum Genomics 2022; 16:33. [PMID: 36028902 PMCID: PMC9412778 DOI: 10.1186/s40246-022-00394-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background The tripartite motif containing (TRIM)-22 participates in innate immune responses and exhibits antiviral activities. The present study aimed to assess of the relationship between TRIM22 single-nucleotide polymorphisms and clinical parameters with the coronavirus disease 2019 (COVID-19) infection severity.
Methods TRIM22 polymorphisms (rs7113258, rs7935564, and rs1063303) were genotyped using TaqMan polymerase chain reaction (PCR) assay in 495 dead and 497 improved severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive patients.
Results In this study, the frequencies of TRIM22 rs1063303 GG, rs7935564 GG, and rs7113258 TT were significantly higher in dead patients than in improved patients, and higher viral load with low PCR Ct value was noticed in dead patients. The multivariate logistic regression analysis revealed that the lower levels of low-density lipoprotein (LDL), cholesterol, PCR Ct value, and lower 25-hydroxyvitamin D, and also higher levels of erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and TRIM22 rs1063303 GG, rs7113258 TT, and rs3824949 GG genotypes were related to the COVID-19 infection severity.
Conclusion Our finding proved the probable relationship between the COVID-19 infection severity with the genotypes of TRIM22 SNPs and clinical parameters. More research is required worldwide to show the association between the COVID-19 infection severity and host genetic factors.
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Affiliation(s)
| | | | - Mohadeseh Montazeri
- Tissue Engineering and Biomaterials Research Center, National Institute of Genetic, Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Mahsa Mardasi
- Department of Plant Science and Biotechnology, Faculty of Life Science and Biotechnology, Shahid Beheshti University G.C, Evin, Tehran, Iran
| | | | - Fatemeh Sakhaee
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran. .,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Chilunda V, Weiselberg J, Martinez-Meza S, Mhamilawa LE, Cheney L, Berman JW. Methamphetamine induces transcriptional changes in cultured HIV-infected mature monocytes that may contribute to HIV neuropathogenesis. Front Immunol 2022; 13:952183. [PMID: 36059515 PMCID: PMC9433802 DOI: 10.3389/fimmu.2022.952183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
HIV-associated neurocognitive impairment (HIV-NCI) persists in 15-40% of people with HIV (PWH) despite effective antiretroviral therapy. HIV-NCI significantly impacts quality of life, and there is currently no effective treatment for it. The development of HIV-NCI is complex and is mediated, in part, by the entry of HIV-infected mature monocytes into the central nervous system (CNS). Once in the CNS, these cells release inflammatory mediators that lead to neuroinflammation, and subsequent neuronal damage. Infected monocytes may infect other CNS cells as well as differentiate into macrophages, thus contributing to viral reservoirs and chronic neuroinflammation. Substance use disorders in PWH, including the use of methamphetamine (meth), can exacerbate HIV neuropathogenesis. We characterized the effects of meth on the transcriptional profile of HIV-infected mature monocytes using RNA-sequencing. We found that meth mediated an upregulation of gene transcripts related to viral infection, cell adhesion, cytoskeletal arrangement, and extracellular matrix remodeling. We also identified downregulation of several gene transcripts involved in pathogen recognition, antigen presentation, and oxidative phosphorylation pathways. These transcriptomic changes suggest that meth increases the infiltration of mature monocytes that have a migratory phenotype into the CNS, contributing to dysregulated inflammatory responses and viral reservoir establishment and persistence, both of which contribute to neuronal damage. Overall, our results highlight potential molecules that may be targeted for therapy to limit the effects of meth on HIV neuropathogenesis.
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Affiliation(s)
- Vanessa Chilunda
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Jessica Weiselberg
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Samuel Martinez-Meza
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Lwidiko E. Mhamilawa
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Women’s and Children’s Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden
| | - Laura Cheney
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Medicine, Division of Infectious Diseases, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY, United States
| | - Joan W. Berman
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- *Correspondence: Joan W. Berman,
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18
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Identification of hub biomarkers and immune cell infiltration in polymyositis and dermatomyositis. Aging (Albany NY) 2022; 14:4530-4555. [PMID: 35609018 PMCID: PMC9186768 DOI: 10.18632/aging.204098] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/12/2022] [Indexed: 12/03/2022]
Abstract
Objective: Polymyositis (PM) and dermatomyositis (DM) are heterogeneous disorders. However, the etiology of PM/DM development has not been thoroughly clarified. Methods: Gene expression data of PM/DM were obtained from Gene Expression Omnibus. We used robust rank aggregation (RRA) to identify differentially expressed genes (DEGs). Gene Ontology functional enrichment and pathway analyses were used to investigate potential functions of the DEGs. Weighted gene co-expression network analysis (WGCNA) was used to establish a gene co-expression network. CIBERSORT was utilized to analyze the pattern of immune cell infiltration in PM/DM. Protein–protein interaction (PPI) network, Venn, and association analyses between core genes and muscle injury were performed to identify hub genes. Receiver operating characteristic analyses were executed to investigate the value of hub genes in the diagnosis of PM/DM, and the results were verified using the microarray dataset GSE48280. Results: Five datasets were included. The RRA integrated analysis identified 82 significant DEGs. Functional enrichment analysis revealed that immune function and the interferon signaling pathway were enriched in PM/DM. WGCNA outcomes identified MEblue and MEturquoise as key target modules in PM/DM. Immune cell infiltration analysis revealed greater macrophage infiltration and lower regulatory T-cell infiltration in PM/DM patients than in healthy controls. PPI network, Venn, and association analyses of muscle injury identified five putative hub genes: TRIM22, IFI6, IFITM1, IFI35, and IRF9. Conclusions: Our bioinformatics analysis identified new genetic biomarkers of the pathogenesis of PM/DM. We demonstrated that immune cell infiltration plays a pivotal part in the occurrence of PM/DM.
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Chinniah R, Adimulam T, Nandlal L, Arumugam T, Ramsuran V. The Effect of miRNA Gene Regulation on HIV Disease. Front Genet 2022; 13:862642. [PMID: 35601502 PMCID: PMC9117004 DOI: 10.3389/fgene.2022.862642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/13/2022] [Indexed: 12/24/2022] Open
Abstract
Over many years, research on HIV/AIDS has advanced with the introduction of HAART. Despite these advancements, significant gaps remain with respect to aspects in HIV life cycle, with specific attention to virus-host interactions. Investigating virus-host interactions may lead to the implementation of novel therapeutic strategies against HIV/AIDS. Notably, host gene silencing can be facilitated by cellular small non-coding RNAs such as microRNAs paving the way for epigenetic anti-viral therapies. Numerous studies have elucidated the importance of microRNAs in HIV pathogenesis. Some microRNAs can either promote viral infection, while others can be detrimental to viral replication. This is accomplished by targeting the HIV-proviral genome or by regulating host genes required for viral replication and immune responses. In this review, we report on 1) the direct association of microRNAs with HIV infection; 2) the indirect association of known human genetic factors with HIV infection; 3) the regulation of human genes by microRNAs in other diseases that can be explored experimentally to determine their effect on HIV-1 infection; and 4) therapeutic interactions of microRNA against HIV infection.
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Affiliation(s)
- Romona Chinniah
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Theolan Adimulam
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Louansha Nandlal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Veron Ramsuran
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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20
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Bagga T, Tulsian NK, Mok YK, Kini RM, Sivaraman J. Mapping of molecular interactions between human E3 ligase TRIM69 and Dengue virus NS3 protease using hydrogen-deuterium exchange mass spectrometry. Cell Mol Life Sci 2022; 79:233. [PMID: 35397701 PMCID: PMC11072344 DOI: 10.1007/s00018-022-04245-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 11/03/2022]
Abstract
Tripartite motif (TRIM) E3 ligases target specific substrates, including viral proteins, for proteasomal degradation, and are thus essential regulators of the innate antiviral response. TRIM69 ubiquitinates the non-structural NS3 protein of Dengue virus for its degradation by the host machinery. This antiviral strategy abrogates the immunosuppression mediated by the NS2B-NS3 protease complex. To understand how this host-driven antiviral response against Dengue virus, we sought to define the mode of interaction between human TRIM69 and Dengue NS2B-NS3 and the subsequent polyubiquitination of the protease by the E3 ligase. We show that NS2B-NS3Δpro is sufficient as a substrate for ubiquitination by TRIM69 using ELISA and in vitro assays. Using hydrogen-deuterium exchange mass spectrometry (HDXMS), we mapped the interface of the interaction between TRIM69 and NS2B-NS3Δpro, and propose a rationale for the binding and subsequent ubiquitination process. Furthermore, through sequence analysis, we showed that the regions targeted by TRIM69 on the DENV-2 NS3 protease (NS3Δpro) are well conserved across DENV serotypes and other flaviviruses, including Zika virus, West Nile virus, and Japanese encephalitis virus. Our results show the direct interactions of TRIM69 with viral proteins, provide mechanistic insights at a molecular level, and highlight the functional relevance of TRIM69 interacting with the Dengue viral protein. Collectively, our findings suggest that TRIM69 may act as a pan-antiflaviviral restriction factor.
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Affiliation(s)
- Tanaya Bagga
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Nikhil Kumar Tulsian
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
- Department of Biochemistry, National University of Singapore, 28 Medical Drive, Singapore, 117546, Singapore.
| | - Yu Keung Mok
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - R Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 16 Medical Drive, Singapore, 117600, Singapore
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, 1101 E Marshall Street, Richmond, VA, 23298, USA
| | - J Sivaraman
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
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21
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Liang G, He Y, Zhao L, Ouyang J, Geng W, Zhang X, Han X, Jiang Y, Ding H, Xiong Y, Dong J, Liu M, Shang H. CTNNBL1 restricts HIV-1 replication by suppressing viral DNA integration into the cell genome. Cell Rep 2022; 38:110533. [PMID: 35294870 DOI: 10.1016/j.celrep.2022.110533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 10/17/2021] [Accepted: 02/25/2022] [Indexed: 11/03/2022] Open
Abstract
Retroviral integration is mediated by a unique enzymatic process shared by all retroviruses and retrotransposons. During integration, double-stranded linear viral DNA is inserted into the host genome in a process catalyzed by viral-encoded integrase (IN). However, host cell defenses against HIV-1 integration are not clear. This study identifies β-catenin-like protein 1 (CTNNBL1) as a potent inhibitor of HIV-1 integration via association with viral-encoded integrase (IN) and its cofactor, lens epithelium-derived growth factor/p75. CTNNBL1 overexpression blocks HIV-1 integration and inhibits viral replication, whereas CTNNBL1 depletion significantly upregulates HIV-1 integration into the genome of various target cells. Further, CTNNBL1 expression is downregulated in CD4+ T cells by activation, and CTNNBL1 depletion also facilitates HIV-1 integration in resting CD4+ T cells. Thus, host cells may employ CTNNBL1 to inhibit HIV-1 integration into the genome. This finding suggests a strategy for the treatment of HIV infections.
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Affiliation(s)
- Guoxin Liang
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China; National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China; Research Institute for Cancer Therapy, The First Affiliated Hospital of China Medical University, Shenyang, China.
| | - Yang He
- Research Institute for Cancer Therapy, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Li Zhao
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China; National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Jiayue Ouyang
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China; National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Wenqing Geng
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China; National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiaowei Zhang
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China; National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiaoxu Han
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China; National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yongjun Jiang
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China; National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Haibo Ding
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China; National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ying Xiong
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China; National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Jinxiu Dong
- National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Mei Liu
- National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Hong Shang
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China; National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China; Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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22
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Chai H, Gu Q, Hughes J, Robertson DL. In silico prediction of HIV-1-host molecular interactions and their directionality. PLoS Comput Biol 2022; 18:e1009720. [PMID: 35134057 PMCID: PMC8856524 DOI: 10.1371/journal.pcbi.1009720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 02/18/2022] [Accepted: 12/03/2021] [Indexed: 11/18/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) continues to be a major cause of disease and premature death. As with all viruses, HIV-1 exploits a host cell to replicate. Improving our understanding of the molecular interactions between virus and human host proteins is crucial for a mechanistic understanding of virus biology, infection and host antiviral activities. This knowledge will potentially permit the identification of host molecules for targeting by drugs with antiviral properties. Here, we propose a data-driven approach for the analysis and prediction of the HIV-1 interacting proteins (VIPs) with a focus on the directionality of the interaction: host-dependency versus antiviral factors. Using support vector machine learning models and features encompassing genetic, proteomic and network properties, our results reveal some significant differences between the VIPs and non-HIV-1 interacting human proteins (non-VIPs). As assessed by comparison with the HIV-1 infection pathway data in the Reactome database (sensitivity > 90%, threshold = 0.5), we demonstrate these models have good generalization properties. We find that the ‘direction’ of the HIV-1-host molecular interactions is also predictable due to different characteristics of ‘forward’/pro-viral versus ‘backward’/pro-host proteins. Additionally, we infer the previously unknown direction of the interactions between HIV-1 and 1351 human host proteins. A web server for performing predictions is available at http://hivpre.cvr.gla.ac.uk/.
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Affiliation(s)
- Haiting Chai
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- * E-mail:
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23
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Boswell MT, Yindom LM, Hameiri-Bowen D, McHugh G, Dauya E, Bandason T, Mujuru H, Esbjörnsson J, Ferrand RA, Rowland-Jones S. TRIM22 genotype is not associated with markers of disease progression in children with HIV-1 infection. AIDS 2021; 35:2445-2450. [PMID: 34870928 PMCID: PMC7614957 DOI: 10.1097/qad.0000000000003053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Untreated perinatal HIV-1 infection is often associated with rapid disease progression in children with HIV (CWH), characterized by high viral loads and early mortality. TRIM22 is a host restriction factor, which directly inhibits HIV-1 transcription, and its genotype variation is associated with disease progression in adults. We tested the hypothesis that TRIM22 genotype is associated with disease progression in CWH. DESIGN ART-naive CWH, aged 6-16 years, were recruited from primary care clinics in Harare, Zimbabwe. We performed a candidate gene association study of TRIM22 genotype and haplotypes with markers of disease progression and indicators of advanced disease. METHODS TRIM22 exons three and four were sequenced by Sanger sequencing and single nucleotide polymorphisms were associated with markers of disease progression (CD4+ T-cell count and HIV viral load) and clinical indicators of advanced HIV disease (presence of stunting and chronic diarrhoea). Associations were tested using multivariate linear and logistic regression models. RESULTS A total of 241 children, median age 11.4 years, 50% female, were included. Stunting was present in 16% of participants. Five SNPs were analyzed including rs7935564, rs2291842, rs78484876, rs1063303 and rs61735273. The median CD4+ count was 342 (IQR: 195-533) cells/μl and median HIV-1 viral load 34 199 (IQR: 8211-90 662) IU/ml. TRIM22 genotype and haplotypes were not associated with CD4+ T-cell count, HIV-1 viral load, stunting or chronic diarrhoea. CONCLUSION TRIM22 genotype was not associated with markers of HIV disease progression markers or advanced disease in CWH.
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Affiliation(s)
| | | | | | - Grace McHugh
- Biomedical Research and Training Institute, Zimbabwe
| | - Ethel Dauya
- Biomedical Research and Training Institute, Zimbabwe
| | | | - Hilda Mujuru
- Department of Paediatrics, University of Zimbabwe, Zimbabwe
| | - Joakim Esbjörnsson
- Nuffield Department of Medicine, Oxford University, UK
- Department of Translational Medicine, Lund University, Sweden
| | - Rashida A Ferrand
- Biomedical Research and Training Institute, Zimbabwe
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, United Kingdom
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24
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Charman M, McFarlane S, Wojtus JK, Sloan E, Dewar R, Leeming G, Al-Saadi M, Hunter L, Carroll MW, Stewart JP, Digard P, Hutchinson E, Boutell C. Constitutive TRIM22 Expression in the Respiratory Tract Confers a Pre-Existing Defence Against Influenza A Virus Infection. Front Cell Infect Microbiol 2021; 11:689707. [PMID: 34621686 PMCID: PMC8490869 DOI: 10.3389/fcimb.2021.689707] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/26/2021] [Indexed: 12/19/2022] Open
Abstract
The induction of antiviral effector proteins as part of a homeostatically controlled innate immune response to infection plays a critical role in limiting the propagation and transmission of respiratory pathogens. However, the prolonged induction of this immune response can lead to lung hyperinflammation, tissue damage, and respiratory failure. We hypothesized that tissues exposed to the constant threat of infection may constitutively express higher levels of antiviral effector proteins to reduce the need to activate potentially harmful innate immune defences. By analysing transcriptomic data derived from a range of human tissues, we identify lung tissue to express constitutively higher levels of antiviral effector genes relative to that of other mucosal and non-mucosal tissues. By using primary cell lines and the airways of rhesus macaques, we show the interferon-stimulated antiviral effector protein TRIM22 (TRIpartite Motif 22) to be constitutively expressed in the lung independently of viral infection or innate immune stimulation. These findings contrast with previous reports that have shown TRIM22 expression in laboratory-adapted cell lines to require interferon stimulation. We demonstrate that constitutive levels of TRIM22 are sufficient to inhibit the onset of human and avian influenza A virus (IAV) infection by restricting the onset of viral transcription independently of interferon-mediated innate immune defences. Thus, we identify TRIM22 to confer a pre-existing (intrinsic) intracellular defence against IAV infection in cells derived from the respiratory tract. Our data highlight the importance of tissue-specific and cell-type dependent patterns of pre-existing immune gene expression in the intracellular restriction of IAV from the outset of infection.
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Affiliation(s)
- Matthew Charman
- MRC - University of Glasgow Centre for Virus Research, Glasgow, United Kingdom.,Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Steven McFarlane
- MRC - University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Joanna K Wojtus
- MRC - University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Elizabeth Sloan
- MRC - University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Rebecca Dewar
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Gail Leeming
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Mohammed Al-Saadi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.,Department of Animal Production, University of Al-Qadisiyah, Al-Diwaniyah, Iraq
| | - Laura Hunter
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Miles W Carroll
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - James P Stewart
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Paul Digard
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Edward Hutchinson
- MRC - University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Chris Boutell
- MRC - University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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25
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Peng C, Zhao C, Wang PF, Yan LL, Fan SG, Qiu LH. Identification of a TRIM32 from Penaeus monodon is involved in autophagy and innate immunity during white spot syndrome virus infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 123:104169. [PMID: 34118280 DOI: 10.1016/j.dci.2021.104169] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/02/2021] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
Many tripartite motif (TRIM) family proteins played an important role in regulating innate immune and autophagy pathway and were important for host defenses against viral pathogens. However, the role of TRIM proteins in autophagy and innate immunity during virus infection was seldom studied in crustaceans. In this study, a novel TRIM32 homolog was identified from Penaeus monodon (named PmTRIM32). PmTRIM32 was significantly upregulated by rapamycin stimulation and WSSV infection. RNA interference experiments showed that PmTRIM32 could restrict WSSV replication and lead P. monodon more resistance to WSSV challenge. Autophagy could be induced by WSSV or rapamycin challenge and has been proved to play a positive role in restricting WSSV replication in P. monodon. The autophagy activity induced by WSSV or rapamycin challenge could be obviously inhibited by silence of PmTRIM32 in P. monodon. Further studies revealed that PmTRIM32 positively regulated the expression of nuclear transcription factor (NF-κB) and it mediated antimicrobial peptides. Moreover, Pull-down and in vitro ubiquitination assay demonstrated that PmTRIM32 could interact with WSSV envelope protein and target it for ubiquitination in vitro. Collectively, this study demonstrated that PmTRIM32 restricted WSSV replication and was involved in positively regulating autophagy and NF-κB pathway during WSSV infection in P. monodon.
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Affiliation(s)
- Chao Peng
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Key Laboratory of Exploration and Utilization of Aquatic Resources, Ministry of Education; National Demonstration Center for Experimental Fisheries Science Education; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Chao Zhao
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China
| | - Peng-Fei Wang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China
| | - Lu-Lu Yan
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China
| | - Si-Gang Fan
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China
| | - Li-Hua Qiu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China; Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Chinese Academy of Fishery Science, Guangzhou, Guangdong Province, China.
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26
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Peng T, Phasouk K, Sodroski CN, Sun S, Hwangbo Y, Layton ED, Jin L, Klock A, Diem K, Magaret AS, Jing L, Laing K, Li A, Huang ML, Mertens M, Johnston C, Jerome KR, Koelle DM, Wald A, Knipe DM, Corey L, Zhu J. Tissue-Resident-Memory CD8 + T Cells Bridge Innate Immune Responses in Neighboring Epithelial Cells to Control Human Genital Herpes. Front Immunol 2021; 12:735643. [PMID: 34552595 PMCID: PMC8450389 DOI: 10.3389/fimmu.2021.735643] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/11/2021] [Indexed: 12/02/2022] Open
Abstract
Tissue-resident-memory T cells (TRM) populate the body's barrier surfaces, functioning as frontline responders against reencountered pathogens. Understanding of the mechanisms by which CD8TRM achieve effective immune protection remains incomplete in a naturally recurring human disease. Using laser capture microdissection and transcriptional profiling, we investigate the impact of CD8TRM on the tissue microenvironment in skin biopsies sequentially obtained from a clinical cohort of diverse disease expression during herpes simplex virus 2 (HSV-2) reactivation. Epithelial cells neighboring CD8TRM display elevated and widespread innate and cell-intrinsic antiviral signature expression, largely related to IFNG expression. Detailed evaluation via T-cell receptor reconstruction confirms that CD8TRM recognize viral-infected cells at the specific HSV-2 peptide/HLA level. The hierarchical pattern of core IFN-γ signature expression is well-conserved in normal human skin across various anatomic sites, while elevation of IFI16, TRIM 22, IFITM2, IFITM3, MX1, MX2, STAT1, IRF7, ISG15, IFI44, CXCL10 and CCL5 expression is associated with HSV-2-affected asymptomatic tissue. In primary human cells, IFN-γ pretreatment reduces gene transcription at the immediate-early stage of virus lifecycle, enhances IFI16 restriction of wild-type HSV-2 replication and renders favorable kinetics for host protection. Thus, the adaptive immune response through antigen-specific recognition instructs innate and cell-intrinsic antiviral machinery to control herpes reactivation, a reversal of the canonical thinking of innate activating adaptive immunity in primary infection. Communication from CD8TRM to surrounding epithelial cells to activate broad innate resistance might be critical in restraining various viral diseases.
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Affiliation(s)
- Tao Peng
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Khamsone Phasouk
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Catherine N. Sodroski
- Department of Microbiology and Virology Program, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Sijie Sun
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Yon Hwangbo
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Erik D. Layton
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Lei Jin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Alexis Klock
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Kurt Diem
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Amalia S. Magaret
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Lichen Jing
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Kerry Laing
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Alvason Li
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Meei-Li Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Max Mertens
- Department of Microbiology and Virology Program, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Christine Johnston
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - David M. Koelle
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Global Health, University of Washington School of Medicine, Seattle, WA, United States
- Benaroya Research Institute, Seattle, WA, United States
| | - Anna Wald
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - David M. Knipe
- Department of Microbiology and Virology Program, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Lawrence Corey
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Global Health, University of Washington School of Medicine, Seattle, WA, United States
| | - Jia Zhu
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, United States
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27
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Wang Y, Fan Y, Huang Y, Du T, Liu Z, Huang D, Wang Y, Wang N, Zhang P. TRIM28 regulates SARS-CoV-2 cell entry by targeting ACE2. Cell Signal 2021; 85:110064. [PMID: 34146659 PMCID: PMC8213541 DOI: 10.1016/j.cellsig.2021.110064] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 01/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019, it binds to angiotensin-converting enzyme 2 (ACE2) to enter into human cells. The expression level of ACE2 potentially determine the susceptibility and severity of COVID-19, it is thus of importance to understand the regulatory mechanism of ACE2 expression. Tripartite motif containing 28 (TRIM28) is known to be involved in multiple processes including antiviral restriction, endogenous retrovirus latency and immune response, it is recently reported to be co-expressed with SARS-CoV-2 receptor in type II pneumocytes; however, the roles of TRIM28 in ACE2 expression and SARS-CoV-2 cell entry remain unclear. This study showed that knockdown of TRIM28 induces ACE2 expression and increases pseudotyped SARS-CoV-2 cell entry of A549 cells and primary pulmonary alveolar epithelial cells (PAEpiCs). In a co-culture model of NK cells and lung epithelial cells, our results demonstrated that NK cells inhibit TRIM28 and promote ACE2 expression in lung epithelial cells, which was partially reversed by depletion of interleukin-2 and blocking of granzyme B in the co-culture medium. Furthermore, TRIM28 knockdown enhanced interferon-γ (IFN-γ)- induced ACE2 expression through a mechanism involving upregulating IFN-γ receptor 2 (IFNGR2) in both A549 and PAEpiCs. The upregulated ACE2 induced by TRIM28 knockdown and co-culture of NK cells was partially reversed by dexamethasone in A549 cells. Our study identified TRIM28 as a novel regulator of ACE2 expression and SARS-CoV-2 cell entry.
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Affiliation(s)
- Yinfang Wang
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China,Institute of Translational Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China,Department of Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China
| | - Yingzhe Fan
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China
| | - Yitong Huang
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China,Institute of Translational Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China
| | - Tao Du
- Department of Gastrointestinal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Zongjun Liu
- Institute of Translational Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China,Department of Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China
| | - Dekui Huang
- Institute of Translational Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China,Department of Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China
| | - Ying Wang
- Department of Biochemistry and Molecular Biology, College of Medicine and Science, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Nanping Wang
- The Advanced Institute for Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Peng Zhang
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China,Institute of Translational Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China,Department of Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China,Corresponding author at: Central Laboratory, Institute of Experimental and Translational Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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28
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Pagani I, Poli G, Vicenzi E. TRIM22. A Multitasking Antiviral Factor. Cells 2021; 10:cells10081864. [PMID: 34440633 PMCID: PMC8391480 DOI: 10.3390/cells10081864] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/03/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
Viral invasion of target cells triggers an immediate intracellular host defense system aimed at preventing further propagation of the virus. Viral genomes or early products of viral replication are sensed by a number of pattern recognition receptors, leading to the synthesis and production of type I interferons (IFNs) that, in turn, activate a cascade of IFN-stimulated genes (ISGs) with antiviral functions. Among these, several members of the tripartite motif (TRIM) family are antiviral executors. This article will focus, in particular, on TRIM22 as an example of a multitarget antiviral member of the TRIM family. The antiviral activities of TRIM22 against different DNA and RNA viruses, particularly human immunodeficiency virus type 1 (HIV-1) and influenza A virus (IAV), will be discussed. TRIM22 restriction of virus replication can involve either direct interaction of TRIM22 E3 ubiquitin ligase activity with viral proteins, or indirect protein–protein interactions resulting in control of viral gene transcription, but also epigenetic effects exerted at the chromatin level.
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Affiliation(s)
- Isabel Pagani
- Viral Pathogenesis and Biosafety Unit, IRCCS-Ospedale San Raffaele, 20132 Milan, Italy;
| | - Guido Poli
- Human Immuno-Virology Unit, IRCCS-Ospedale San Raffaele, 20132 Milan, Italy;
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, IRCCS-Ospedale San Raffaele, 20132 Milan, Italy;
- Correspondence:
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29
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Wei Y, Zeng S, Zou C, Zhang H, Peng O, Xue C, Cao Y. Porcine TRIM21 RING-finger E3 ubiquitin ligase is essential for anti-PRRSV activity. Vet Microbiol 2021; 256:109043. [PMID: 33780804 DOI: 10.1016/j.vetmic.2021.109043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/19/2021] [Indexed: 12/15/2022]
Abstract
Porcine reproductive and respiratory syndrome (PRRS) causes substantial economic losses to the global pig industry. Members of the tripartite motif (TRIM) family are the important effectors of the innate immune response against viral infections. We have previously characterized the entire porcine TRIM (pTRIM) family, and predicted pTRIM5, 14, 21, 25 and 38 as host restriction factors against PRRSV infection. However, little is known about whether and how pTRIMs restrict the infection of PRRSV. In this study, we firstly performed the amino acid alignments of the RING domain of pTRIM5, 21, 25 and 38, and found that pTRIM proteins contained the characteristic consensus C3HC4 type zinc-binding motif which is important for the ubiquitination function. Then we detected the mRNA changes of pTRIMs in porcine alveolar macrophages (PAMs) by transcriptome sequencing after PRRSV infection in piglets. Transcriptional profiles showed that the expression of pTRIM5, 21 and 26 was significantly (P < 0.05) up-regulated, consistent with their expression in vitro. Finally, as the most up-regulated gene after PRRSV infection both in vivo and in vitro, pTRIM21 was investigated for its anti-PRRSV activity in immortalized PAMs (iPAMs) in two aspects: knockdown and overexpression of pTRIM21. Knockdown of endogenic pTRIM21 could significantly promote PRRSV replication at 12 and 24 h post infection in iPAMs. Meanwhile, overexpression of pTRIM21 could significantly suppress PRRSV replication but not affect its attachment and endocytosis. Moreover, pTRIM21 RING-finger E3 ubiquitin ligase was essential for anti-PRRSV activity. Our data enhance our understanding of the pTRIMs against PRRSV infection, which may help us develop novel therapeutic tools to control PRRSV.
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Affiliation(s)
- Ying Wei
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China; College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023, China
| | - Siying Zeng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Chuangchao Zou
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Hao Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ouyang Peng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Chunyi Xue
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Yongchang Cao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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30
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Singh K, Chen YC, Hassanzadeh S, Han K, Judy JT, Seifuddin F, Tunc I, Sack MN, Pirooznia M. Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection. Front Genet 2021; 12:599261. [PMID: 33796130 PMCID: PMC8008150 DOI: 10.3389/fgene.2021.599261] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/15/2021] [Indexed: 01/08/2023] Open
Abstract
Analyzing host cells' transcriptional response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection will help delineate biological processes underlying viral pathogenesis. First, analysis of expression profiles of lung cell lines A549 and Calu3 revealed upregulation of antiviral interferon signaling genes in response to all three SARS-CoV-2, MERS-CoV, or influenza A virus (IAV) infections. However, perturbations in expression of genes involved in inflammatory, mitochondrial, and autophagy processes were specifically observed in SARS-CoV-2-infected cells. Next, a validation study in infected human nasopharyngeal samples also revealed perturbations in autophagy and mitochondrial processes. Specifically, mTOR expression, mitochondrial ribosomal, mitochondrial complex I, lysosome acidification, and mitochondrial fission promoting genes were concurrently downregulated in both infected cell lines and human samples. SARS-CoV-2 infection impeded autophagic flux either by upregulating GSK3B in lung cell lines or by downregulating autophagy genes, SNAP29, and lysosome acidification genes in human samples, contributing to increased viral replication. Therefore, drugs targeting lysosome acidification or autophagic flux could be tested as intervention strategies. Finally, age-stratified SARS-CoV-2-positive human data revealed impaired upregulation of chemokines, interferon-stimulated genes, and tripartite motif genes that are critical for antiviral signaling. Together, this analysis has revealed specific aspects of autophagic and mitochondrial function that are uniquely perturbed in SARS-CoV-2-infected host cells.
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Affiliation(s)
- Komudi Singh
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Yun-Ching Chen
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Shahin Hassanzadeh
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Kim Han
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jennifer T. Judy
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Fayaz Seifuddin
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Ilker Tunc
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Michael N. Sack
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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31
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Peng C, Zhao C, Wang P, Yan L, Fan S, Qiu L. TRIM9 is involved in facilitating Vibrio parahaemolyticus infection by inhibition of relish pathway in Penaeus monodon. Mol Immunol 2021; 133:77-85. [PMID: 33636432 DOI: 10.1016/j.molimm.2021.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/26/2021] [Accepted: 02/04/2021] [Indexed: 12/23/2022]
Abstract
Tripartite motif-containing 9 (TRIM9) has been demonstrated to exert important roles in regulation of innate immune signaling. In this study, a novel TRIM9 homolog was identified from Penaeus monodon (named PmTRIM9). The open reading frame (ORF) of PmTRIM9 was 2064 bp, which encoding a 687-amino-acid polypeptide. Following Vibrio parahaemolyticus challenge, the expression levels of PmTRIM9 mRNA were significantly down-regulated in tested tissues. RNA interference and recombinant protein injection experiments were performed to explore the function of PmTRIM9, and the results showed it could facilitate V. parahaemolyticus replication and lead P. monodon more vulnerable to V. parahaemolyticus challenge. The dual-luciferase reporter assay showed that PmTRIM9 possessed the ability to inhibit the promoter activity in HEK293 T cells. Silencing of PmTRIM9 could increase the expression of the major NF-κB transcription factor, PmRelish. Further studies showed that knockdown of PmRelish promoted the V. parahaemolyticus infection and decreased the expression of specific antimicrobial peptides (AMPs), including PmCRU5, PmCRU7, PmALF6, PmALF3, PmLYZ and PmPEN5. However, knockdown of PmTRIM9 increased expression levels of the same AMPs, but except for PmCRU5, indicating that PmTRIM9 may negatively regulate the PmRelish-mediated expression of AMPs. All these results suggest that PmTRIM9 was involved in facilitating V. parahaemolyticus infection by inhibition of Relish pathway in P. monodon.
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Affiliation(s)
- Chao Peng
- Key Laboratory of Exploration and Utilization of Aquatic Resources, Ministry of Education, National Demonstration Center for Experimental Fisheries Science Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China
| | - Chao Zhao
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China
| | - Pengfei Wang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China
| | - Lulu Yan
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China
| | - Sigang Fan
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China
| | - Lihua Qiu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China; Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Chinese Academy of Fishery Science, China.
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32
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Zohra Smaili F, Tian S, Roy A, Alazmi M, Arold ST, Mukherjee S, Scott Hefty P, Chen W, Gao X. QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:998-1011. [PMID: 33631427 PMCID: PMC9403031 DOI: 10.1016/j.gpb.2021.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 04/03/2019] [Accepted: 05/17/2019] [Indexed: 11/25/2022]
Abstract
The number of available protein sequences in public databases is increasing exponentially. However, a significant percentage of these sequences lack functional annotation, which is essential for the understanding of how biological systems operate. Here, we propose a novel method, Quantitative Annotation of Unknown STructure (QAUST), to infer protein functions, specifically Gene Ontology (GO) terms and Enzyme Commission (EC) numbers. QAUST uses three sources of information: structure information encoded by global and local structure similarity search, biological network information inferred by protein–protein interaction data, and sequence information extracted from functionally discriminative sequence motifs. These three pieces of information are combined by consensus averaging to make the final prediction. Our approach has been tested on 500 protein targets from the Critical Assessment of Functional Annotation (CAFA) benchmark set. The results show that our method provides accurate functional annotation and outperforms other prediction methods based on sequence similarity search or threading. We further demonstrate that a previously unknown function of human tripartite motif-containing 22 (TRIM22) protein predicted by QAUST can be experimentally validated.
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Affiliation(s)
- Fatima Zohra Smaili
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Shuye Tian
- Department of Biology, Southern University of Science and Technology of China (SUSTC), Shenzhen 518055, China
| | - Ambrish Roy
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Meshari Alazmi
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; College of Computer Science and Engineering, University of Hail, Hail 55476, Saudi Arabia
| | - Stefan T Arold
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Srayanta Mukherjee
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - P Scott Hefty
- Department of Molecular Bioscience, University of Kansas, Lawrence, KS 66047, USA
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology of China (SUSTC), Shenzhen 518055, China.
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia.
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33
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Human TRIM5α: Autophagy Connects Cell-Intrinsic HIV-1 Restriction and Innate Immune Sensor Functioning. Viruses 2021; 13:v13020320. [PMID: 33669846 PMCID: PMC7923229 DOI: 10.3390/v13020320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 12/12/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) persists as a global health concern, with an incidence rate of approximately 2 million, and estimated global prevalence of over 35 million. Combination antiretroviral treatment is highly effective, but HIV-1 patients that have been treated still suffer from chronic inflammation and residual viral replication. It is therefore paramount to identify therapeutically efficacious strategies to eradicate viral reservoirs and ultimately develop a cure for HIV-1. It has been long accepted that the restriction factor tripartite motif protein 5 isoform alpha (TRIM5α) restricts HIV-1 infection in a species-specific manner, with rhesus macaque TRIM5α strongly restricting HIV-1, and human TRIM5α having a minimal restriction capacity. However, several recent studies underscore human TRIM5α as a cell-dependent HIV-1 restriction factor. Here, we present an overview of the latest research on human TRIM5α and propose a novel conceptualization of TRIM5α as a restriction factor with a varied portfolio of antiviral functions, including mediating HIV-1 degradation through autophagy- and proteasome-mediated mechanisms, and acting as a viral sensor and effector of antiviral signaling. We have also expanded on the protective antiviral roles of autophagy and outline the therapeutic potential of autophagy modulation to intervene in chronic HIV-1 infection.
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34
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Recent Progress on Exosomes in RNA Virus Infection. Viruses 2021; 13:v13020256. [PMID: 33567490 PMCID: PMC7915723 DOI: 10.3390/v13020256] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 12/16/2022] Open
Abstract
Recent research indicates that most tissue and cell types can secrete and release membrane-enclosed small vesicles, known as exosomes, whose content reflects the physiological/pathological state of the cells from which they originate. These exosomes participate in the communication and cell-to-cell transfer of biologically active proteins, lipids, and nucleic acids. Studies of RNA viruses have demonstrated that exosomes release regulatory factors from infected cells and deliver other functional host genetic elements to neighboring cells, and these functions are involved in the infection process and modulate the cellular responses. This review provides an overview of the biogenesis, composition, and some of the most striking functions of exosome secretion and identifies physiological/pathological areas in need of further research. While initial indications suggest that exosome-mediated pathways operate in vivo, the exosome mechanisms involved in the related effects still need to be clarified. The current review focuses on the role of exosomes in RNA virus infections, with an emphasis on the potential contributions of exosomes to pathogenesis.
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35
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Reddi TS, Merkl PE, Lim SY, Letvin NL, Knipe DM. Tripartite Motif 22 (TRIM22) protein restricts herpes simplex virus 1 by epigenetic silencing of viral immediate-early genes. PLoS Pathog 2021; 17:e1009281. [PMID: 33524065 PMCID: PMC7877759 DOI: 10.1371/journal.ppat.1009281] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 02/11/2021] [Accepted: 01/04/2021] [Indexed: 12/11/2022] Open
Abstract
Intrinsic resistance is a crucial line of defense against virus infections, and members of the Tripartite Ring Interaction Motif (TRIM) family of proteins are major players in this system, such as cytoplasmic TRIM5α or nuclear promyelocytic leukemia (PML/TRIM19) protein. Previous reports on the antiviral function of another TRIM protein, TRIM22, emphasized its innate immune role as a Type I and Type II interferon-stimulated gene against RNA viruses. This study shows that TRIM22 has an additional intrinsic role against DNA viruses. Here, we report that TRIM22 is a novel restriction factor of HSV-1 and limits ICP0-null virus replication by increasing histone occupancy and heterochromatin, thereby reducing immediate-early viral gene expression. The corresponding wild-type equivalent of the virus evades the TRIM22-specific restriction by a mechanism independent of ICP0-mediated degradation. We also demonstrate that TRIM22 inhibits other DNA viruses, including representative members of the β- and γ- herpesviruses. Allelic variants in TRIM22 showed different degrees of anti-herpesviral activity; thus, TRIM22 genetic variability may contribute to the varying susceptibility to HSV-1 infection in humans. Collectively, these results argue that TRIM22 is a novel restriction factor and expand the list of restriction factors functioning in the infected cell nucleus to counter DNA virus infection. The host immune response to herpesviruses includes intrinsic immunity, which is a constitutively active line of defense. Members of the Tripartite Motif (TRIM) superfamily of proteins, such as cytoplasmic TRIM5α and nuclear TRIM19, are examples of such restriction factors against the prototypical α-herpesvirus, herpes simplex virus-1 (HSV-1). Previous reports on the antiviral function of the protein encoded by TRIM22, a gene closely related to the TRIM5 gene, emphasized its antiretroviral role. We show that TRIM22 has an additional role as a restriction factor against herpesviruses. We found that TRIM22 inhibits a mutant form of HSV-1, by promoting chromatin compaction of the viral DNA encoding immediate-early viral genes–this consequently inhibits viral replication and reduces virus yields. Unlike other restriction factors that are degraded by the viral infected cell polypeptide 0 (ICP0), TRIM22 is not degraded by ICP0. We also show that TRIM22 inhibits representative members of the β-herpesvirus (cytomegalovirus) and γ- herpesviruses (Epstein-Barr virus). In addition, different TRIM22 genetic variants show differing levels of HSV-1 inhibition. Together, these results argue for the importance of the TRIM22 gene as a restriction factor against herpesviruses, and offer a novel avenue for further investigation on the role of TRIM genes in host genetic variation in herpesviral susceptibility.
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Affiliation(s)
- Tejaswini S. Reddi
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Philipp E. Merkl
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - So-Yon Lim
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Norman L. Letvin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David M. Knipe
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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36
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Genetic Exchange of Lung-Derived Exosome to Brain Causing Neuronal Changes on COVID-19 Infection. Mol Neurobiol 2021; 58:5356-5368. [PMID: 34312772 PMCID: PMC8313419 DOI: 10.1007/s12035-021-02485-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023]
Abstract
The pandemic of novel coronavirus 2 (SARS-CoV-2) has made global chaos for normal human living. Despite common COVID-19 symptoms, variability in clinical phenotypes was reported worldwide. Reports on SARS-CoV-2 suggest causing neurological manifestation. In addition, the susceptibility of SARS-CoV-2 in patients with neurodegenerative diseases and its complexity are largely unclear. Here, we aimed to demonstrate the possible transport of exosome from SARS-CoV-2-infected lungs to the brain regions associated with neurodegenerative diseases using multiple transcriptome datasets of SARS-CoV-2-infected lungs, RNA profiles from lung exosome, and gene expression profiles of the human brain. Upon transport, the transcription factors localized in the exosome regulate genes at lateral substantia nigra, medial substantia nigra, and superior frontal gyrus regions of Parkinson's disease (PD) and frontal cortex, hippocampus, and temporal cortex of Alzheimer's disease (AD). On SARS-CoV-2 infection, BCL3, JUND, MXD1, IRF2, IRF9, and STAT1 transcription factors in the exosomes influence the neuronal gene regulatory network and accelerate neurodegeneration. STAT1 transcription factor regulates 64 PD genes at lateral substantia nigra, 65 at superior frontal gyrus, and 19 at medial substantia nigra. Similarly, in AD, STAT1 regulates 74 AD genes at the temporal cortex, 40 genes at the hippocampus, and 16 genes at the frontal cortex. We further demonstrate that dysregulated neuronal genes showed involvement in immune response, signal transduction, apoptosis, and stress response process. In conclusion, SARS-CoV-2 may dysregulate neuronal gene regulatory network through exosomes that attenuate disease severity of neurodegeneration.
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Abstract
The innate immune system is comprised of both cellular and humoral players that recognise and eradicate invading pathogens. Therefore, the interplay between retroviruses and innate immunity has emerged as an important component of viral pathogenesis. HIV-1 infection in humans that results in hematologic abnormalities and immune suppression is well represented by changes in the CD4/CD8 T cell ratio and consequent cell death causing CD4 lymphopenia. The innate immune responses by mucosal barriers such as complement, DCs, macrophages, and NK cells as well as cytokine/chemokine profiles attain great importance in acute HIV-1 infection, and thus, prevent mucosal capture and transmission of HIV-1. Conversely, HIV-1 has evolved to overcome innate immune responses through RNA-mediated rapid mutations, pathogen-associated molecular patterns (PAMPs) modification, down-regulation of NK cell activity and complement receptors, resulting in increased secretion of inflammatory factors. Consequently, epithelial tissues lining up female reproductive tract express innate immune sensors including anti-microbial peptides responsible for forming primary barriers and have displayed an effective potent anti-HIV activity during phase I/II clinical trials.
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38
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Li L, Zhuang P, Cheng Z, Yang J, Bi J, Wang G. Avian leukosis virus subgroup J and reticuloendotheliosis virus coinfection induced TRIM62 regulation of the actin cytoskeleton. J Vet Sci 2020; 21:e49. [PMID: 32476322 PMCID: PMC7263916 DOI: 10.4142/jvs.2020.21.e49] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/26/2020] [Accepted: 03/12/2020] [Indexed: 11/20/2022] Open
Abstract
Background Coinfection with avian leukosis virus subgroup J (ALV-J) and reticuloendotheliosis virus (REV) is common in chickens, and the molecular mechanism of the synergistic pathogenic effects of the coinfection is not clear. Exosomes have been identified as new players in the pathogenesis of retroviruses. The different functions of exosomes depend on their cargo components. Objectives The aim of this study was to investigate the function of co-regulation differentially expressed proteins in exosomes on coinfection of ALV-J and REV. Methods Here, viral replication in CEF cells infected with ALV-J, REV or both was detected by immunofluorescence microscopy. Then, we analyzed the exosomes isolated from supernatants of chicken embryo fibroblast (CEF) cells single infected and coinfected with ALV-J and REV by mass spectrometry. KEGG pathway enrichment analyzed the co-regulation differentially expressed proteins in exosomes. Next, we silenced and overexpressed tripartite motif containing 62 (TRIM62) to evaluate the effects of TRIM62 on viral replication and the expression levels of NCK-association proteins 1 (NCKAP1) and actin-related 2/3 complex subunit 5 (ARPC5) determined by quantitative reverse transcription polymerase chain reaction. Results The results showed that coinfection of ALV-J and REV promoted the replication of each other. Thirty proteins, including TRIM62, NCK-association proteins 1 (NCKAP1, also known as Nap125), and Arp2/3-5, ARPC5, were identified. NCKAP1 and ARPC5 were involved in the actin cytoskeleton pathway. TRIM62 negatively regulated viral replication and that the inhibition of REV was more significant than that on ALV-J in CEF cells coinfected with TRIM62. In addition, TRIM62 decreased the expression of NCKAP1 and increased the expression of ARPC5 in coinfected CEF cells. Conclusions Collectively, our results indicated that coinfection with ALV-J and REV competitively promoted each other's replication, the actin cytoskeleton played an important role in the coinfection mechanism, and TRIM62 regulated the actin cytoskeleton.
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Affiliation(s)
- Ling Li
- Department of Fundamental Veterinary, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Pingping Zhuang
- Department of Fundamental Veterinary, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Ziqiang Cheng
- Department of Fundamental Veterinary, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Jie Yang
- Department of Fundamental Veterinary, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Jianmin Bi
- China Animal Husbandry Industry Co. Ltd., Beijing 10070, China
| | - Guihua Wang
- Department of Fundamental Veterinary, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China.
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39
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Planas D, Fert A, Zhang Y, Goulet JP, Richard J, Finzi A, Ruiz MJ, Marchand LR, Chatterjee D, Chen H, Wiche Salinas TR, Gosselin A, Cohen EA, Routy JP, Chomont N, Ancuta P. Pharmacological Inhibition of PPARy Boosts HIV Reactivation and Th17 Effector Functions, While Preventing Progeny Virion Release and de novo Infection. Pathog Immun 2020; 5:177-239. [PMID: 33089034 PMCID: PMC7556414 DOI: 10.20411/pai.v5i1.348] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/04/2020] [Indexed: 01/02/2023] Open
Abstract
The frequency and functions of Th17-polarized
CCR6+RORyt+CD4+ T cells are rapidly
compromised upon HIV infection and are not restored with long-term viral
suppressive antiretroviral therapy (ART). In line with this, Th17 cells
represent selective HIV-1 infection targets mainly at mucosal sites, with
long-lived Th17 subsets carrying replication-competent HIV-DNA during ART.
Therefore, novel Th17-specific therapeutic interventions are needed as a
supplement of ART to reach the goal of HIV remission/cure. Th17 cells express
high levels of peroxisome proliferator-activated receptor gamma
(PPARy), which acts as a transcriptional repressor of the HIV provirus and the
rorc gene, which encodes for the Th17-specific master
regulator RORyt. Thus, we hypothesized that the pharmacological inhibition of
PPARy will facilitate HIV reservoir reactivation while enhancing Th17 effector
functions. Consistent with this prediction, the PPARy antagonist T0070907
significantly increased HIV transcription (cell-associated HIV-RNA) and
RORyt-mediated Th17 effector functions (IL-17A). Unexpectedly, the PPARy
antagonism limited HIV outgrowth from cells of ART-treated people living with
HIV (PLWH), as well as HIV replication in vitro.
Mechanistically, PPARy inhibition in CCR6+CD4+ T cells
induced the upregulation of transcripts linked to Th17-polarisation (RORyt,
STAT3, BCL6 IL-17A/F, IL-21) and HIV transcription (NCOA1-3, CDK9, HTATIP2).
Interestingly, several transcripts involved in HIV-restriction were upregulated
(Caveolin-1, TRIM22, TRIM5α, BST2, miR-29), whereas HIV permissiveness
transcripts were downregulated (CCR5, furin), consistent with the decrease in
HIV outgrowth/replication. Finally, PPARy inhibition increased intracellular
HIV-p24 expression and prevented BST-2 downregulation on infected T cells,
suggesting that progeny virion release is restricted by BST-2-dependent
mechanisms. These results provide a strong rationale for considering PPARy
antagonism as a novel strategy for HIV-reservoir purging and restoring
Th17-mediated mucosal immunity in ART-treated PLWH.
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Affiliation(s)
- Delphine Planas
- Département de microbiologie, infectiologie et immunologie; Faculté de médecine; Université de Montréal; Montréal, Québec, Canada.,Centre de recherche du CHUM; Montréal, Québec, Canada
| | - Augustine Fert
- Département de microbiologie, infectiologie et immunologie; Faculté de médecine; Université de Montréal; Montréal, Québec, Canada.,Centre de recherche du CHUM; Montréal, Québec, Canada
| | - Yuwei Zhang
- Département de microbiologie, infectiologie et immunologie; Faculté de médecine; Université de Montréal; Montréal, Québec, Canada.,Centre de recherche du CHUM; Montréal, Québec, Canada
| | | | - Jonathan Richard
- Département de microbiologie, infectiologie et immunologie; Faculté de médecine; Université de Montréal; Montréal, Québec, Canada.,Centre de recherche du CHUM; Montréal, Québec, Canada
| | - Andrés Finzi
- Département de microbiologie, infectiologie et immunologie; Faculté de médecine; Université de Montréal; Montréal, Québec, Canada.,Centre de recherche du CHUM; Montréal, Québec, Canada
| | - Maria Julia Ruiz
- Département de microbiologie, infectiologie et immunologie; Faculté de médecine; Université de Montréal; Montréal, Québec, Canada.,Centre de recherche du CHUM; Montréal, Québec, Canada
| | | | - Debashree Chatterjee
- Département de microbiologie, infectiologie et immunologie; Faculté de médecine; Université de Montréal; Montréal, Québec, Canada.,Centre de recherche du CHUM; Montréal, Québec, Canada
| | - Huicheng Chen
- Département de microbiologie, infectiologie et immunologie; Faculté de médecine; Université de Montréal; Montréal, Québec, Canada.,Centre de recherche du CHUM; Montréal, Québec, Canada
| | - Tomas Raul Wiche Salinas
- Département de microbiologie, infectiologie et immunologie; Faculté de médecine; Université de Montréal; Montréal, Québec, Canada.,Centre de recherche du CHUM; Montréal, Québec, Canada
| | - Annie Gosselin
- Département de microbiologie, infectiologie et immunologie; Faculté de médecine; Université de Montréal; Montréal, Québec, Canada.,Centre de recherche du CHUM; Montréal, Québec, Canada
| | - Eric A Cohen
- Institut de recherches cliniques de Montréal; Montréal, Québec, Canada
| | - Jean-Pierre Routy
- Chronic Viral Illness Service; Division of Hematology; McGill University Health Centre-Glen site; Montreal, Québec, Canada
| | - Nicolas Chomont
- Département de microbiologie, infectiologie et immunologie; Faculté de médecine; Université de Montréal; Montréal, Québec, Canada.,Centre de recherche du CHUM; Montréal, Québec, Canada
| | - Petronela Ancuta
- Département de microbiologie, infectiologie et immunologie; Faculté de médecine; Université de Montréal; Montréal, Québec, Canada.,Centre de recherche du CHUM; Montréal, Québec, Canada
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40
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Aljabban J, Syed S, Syed S, Rohr M, Weisleder N, McElhanon KE, Hasan L, Safeer L, Hoffman K, Aljabban N, Mukhtar M, Adapa N, Allarakhia Z, Panahiazar M, Neuhaus I, Kim S, Hadley D, Jarjour W. Investigating genetic drivers of dermatomyositis pathogenesis using meta-analysis. Heliyon 2020; 6:e04866. [PMID: 33015383 PMCID: PMC7522761 DOI: 10.1016/j.heliyon.2020.e04866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/17/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022] Open
Abstract
AIMS Dermatomyositis (DM) is a progressive, idiopathic inflammatory myopathy with poorly understood pathogenesis. A hallmark of DM is an increased risk for developing breast, ovarian, and lung cancer. Since autoantibodies against anti-TIF-1-γ, a member of the tripartite motif (TRIM) proteins, has a strong association with malignancy, we examined expression of the TRIM gene family to identify pathways that may be contributing to DM pathogenesis. MATERIALS AND METHODS We employed the Search Tag Analyze Resource for GEO platform to search the NCBI Gene Expression Omnibus to elucidate TRIM family gene expression as well as oncogenic drivers in DM pathology. We conducted meta-analysis of the data from human skin (60 DM vs 34 healthy) and muscle (71 DM vs 22 healthy). KEY FINDINGS We identified genes involved in innate immunity, antigen presentation, metabolism, and other cellular processes as facilitators of DM disease activity and confirmed previous observations regarding the presence of a robust interferon signature. Moreover, analysis of DM muscle samples revealed upregulation of TRIM14, TRIM22, TRIM25, TRIM27, and TRIM38. Likewise, analysis of DM skin samples showed upregulation of TRIM5, TRIM6, TRIM 14, TRIM21, TRIM34, and TRIM38 and downregulation of TRIM73. Additionally, we noted upregulation of oncogenes IGLC1, IFI44, POSTN, MYC, NPM1, and IDO1 and related this change to interferon signaling. While the clinical data associated with genetic data that was analyzed did not contain clinical data regarding malignancy in these cohorts, the observed genetic changes may be associated with homeostatic and signaling changes that relate to the increased risk in malignancy in DM. SIGNIFICANCE Our results implicate previously unknown genes as potential drivers of DM pathology and suggest certain TRIM family members may have disease-specific roles with potential diagnostic and therapeutic implications.
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Affiliation(s)
- Jihad Aljabban
- University of Wisconsin Hospital and Clinics, Madison, WI, USA
| | - Saad Syed
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sharjeel Syed
- University of Chicago Medical Center, Chicago, IL, USA
| | - Michael Rohr
- University of Central Florida College of Medicine, Orlando, FL, USA
| | - Noah Weisleder
- The Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Laith Hasan
- Tulane School of Medicine, New Orleans, LA, USA
| | | | - Kalyn Hoffman
- The Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Mohamed Mukhtar
- Michigan State University College of Human Medicine, Lansing, MI, USA
| | | | - Zahir Allarakhia
- The Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Isaac Neuhaus
- University of California San Francisco, San Francisco, CA, USA
| | - Susan Kim
- University of California San Francisco, San Francisco, CA, USA
| | - Dexter Hadley
- University of Central Florida College of Medicine, Orlando, FL, USA
| | - Wael Jarjour
- The Ohio State University College of Medicine, Columbus, OH, USA
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41
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Ji J, Ding K, Luo T, Zhang X, Chen A, Zhang D, Li G, Thorsen F, Huang B, Li X, Wang J. TRIM22 activates NF-κB signaling in glioblastoma by accelerating the degradation of IκBα. Cell Death Differ 2020; 28:367-381. [PMID: 32814880 PMCID: PMC7853150 DOI: 10.1038/s41418-020-00606-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 07/29/2020] [Accepted: 08/06/2020] [Indexed: 01/16/2023] Open
Abstract
NF-κB signaling plays a critical role in tumor growth and treatment resistance in GBM as in many other cancers. However, the molecular mechanisms underlying high, constitutive NF-κB activity in GBM remains to be elucidated. Here, we screened a panel of tripartite motif (TRIM) family proteins and identified TRIM22 as a potential activator of NF-κB using an NF-κB driven luciferase reporter construct in GBM cell lines. Knockout of TRIM22 using Cas9-sgRNAs led to reduced GBM cell proliferation, while TRIM22 overexpression enhanced proliferation of cell populations, in vitro and in an orthotopic xenograft model. However, two TRIM22 mutants, one with a critical RING-finger domain deletion and the other with amino acid changes at two active sites of RING E3 ligase (C15/18A), were both unable to promote GBM cell proliferation over controls, thus implicating E3 ligase activity in the growth-promoting properties of TRIM22. Co-immunoprecipitations demonstrated that TRIM22 bound a negative regulator of NF-κB, NF-κB inhibitor alpha (IκBα), and accelerated its degradation by inducing K48-linked ubiquitination. TRIM22 also formed a complex with the NF-κB upstream regulator IKKγ and promoted K63-linked ubiquitination, which led to the phosphorylation of both IKKα/β and IκBα. Expression of a non-phosphorylation mutant, srIκBα, inhibited the growth-promoting properties of TRIM22 in GBM cell lines. Finally, TRIM22 was increased in a cohort of primary GBM samples on a tissue microarray, and high expression of TRIM22 correlated with other clinical parameters associated with progressive gliomas, such as wild-type IDH1 status. In summary, our study revealed that TRIM22 activated NF-κB signaling through posttranslational modification of two critical regulators of NF-κB signaling in GBM cells.
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Affiliation(s)
- Jianxiong Ji
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Kaikai Ding
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Tao Luo
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Xin Zhang
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Anjing Chen
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Di Zhang
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Frits Thorsen
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009, Bergen, Norway.,Molecular Imaging Center, University of Bergen, Jonas Lies vei 91, 5009, Bergen, Norway
| | - Bin Huang
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, China. .,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China.
| | - Xingang Li
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, China. .,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China.
| | - Jian Wang
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, China. .,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China. .,Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009, Bergen, Norway.
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42
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Huo S, Jiao H, Chen B, Kuang M, Li Q, Lu Y, Liu X. FTR67, a member of the fish-specific finTRIM family, triggers IFN pathway and against spring viremia of carp virus. FISH & SHELLFISH IMMUNOLOGY 2020; 103:1-8. [PMID: 32334126 DOI: 10.1016/j.fsi.2020.04.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/14/2020] [Accepted: 04/18/2020] [Indexed: 06/11/2023]
Abstract
Tripartite motif (TRIM) proteins have attracted particular research interest because of their multiple functions in the antiviral innate immune response. TRIM proteins perform different functions during virus infection, some play a role in inhibiting while others play a role in promoting. In this study, we described a species-specific TRIM gene named ftr67. Analysis of tissue distribution showed that ftr67 was mainly expressed in the gill and liver in five examined tissues of zebrafish. The phylogenic analysis showed that ftr67 was closest to the grass carp TRIM67. Overexpression of ftr67 resulted in a significantly decreased SVCV entry and impaired SVCV replication in FHM cells. Furthermore, overexpression of ftr67 could significantly induce the upregulation of molecular sensor RIG-I, IRF3/7, IFN and ISGs. In addition, RING domain of ftr67 was a required part essential for the antiviral effect. In summary, our results demonstrated that the important role of ftr67 in regulating SVCV infection, which offers a potential target for development of anti-SVCV therapies.
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Affiliation(s)
- Shitian Huo
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Houqi Jiao
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Bo Chen
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Ming Kuang
- Institute of Systems Biomedicine, Department of Immunology, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Qing Li
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Yuanan Lu
- Department of Public Health Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, 96822, USA
| | - Xueqin Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China.
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43
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Singh K, Chen YC, Judy JT, Seifuddin F, Tunc I, Pirooznia M. Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.05.13.092536. [PMID: 32511341 PMCID: PMC7241104 DOI: 10.1101/2020.05.13.092536] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Analyzing host transcriptional changes in response to SARS-CoV-2 infection will help delineate biological processes underlying viral pathogenesis. Comparison of expression profiles of lung cell lines A549 (infected with either SARS-CoV-2 (with ACE2 expression)) or Influenza A virus (IAV)) and Calu3 (infected with SARS-CoV-2 or MERS-CoV) revealed upregulation of the antiviral interferon signaling in all three viral infections. However, perturbations in inflammatory, mitochondrial, and autophagy processes were specifically observed in SARS-CoV-2 infected cells. Validation of findings from cell line data revealed perturbations in autophagy and mitochondrial processes in the infected human nasopharyngeal samples. Specifically, downregulation of mTOR expression, mitochondrial ribosomal, mitochondrial complex I, and lysosome acidification genes were concurrently observed in both infected cell lines and human datasets. Furthermore, SARS-CoV-2 infection impedes autophagic flux by upregulating GSK3B in lung cell lines, or by downregulating autophagy genes, SNAP29 and lysosome acidification genes in human samples, contributing to increased viral replication. Therefore, drugs targeting lysosome acidification or autophagic flux could be tested as intervention strategies. Additionally, downregulation of MTFP1 (in cell lines) or SOCS6 (in human samples) results in hyperfused mitochondria and impede proper interferon response. Coexpression networks analysis identifies correlated clusters of genes annotated to inflammation and mitochondrial processes that are misregulated in SARS-CoV-2 infected cells. Finally, comparison of age stratified human gene expression data revealed impaired upregulation of chemokines, interferon stimulated and tripartite motif genes that are critical for antiviral signaling. Together, this analysis has revealed specific aspects of autophagic and mitochondrial function that are uniquely perturbed in SARS-CoV-2 infection.
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Affiliation(s)
- Komudi Singh
- Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yun-Ching Chen
- Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer T Judy
- Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fayaz Seifuddin
- Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ilker Tunc
- Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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44
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Characterization of the primate TRIM gene family reveals the recent evolution in primates. Mol Genet Genomics 2020; 295:1281-1294. [PMID: 32564135 DOI: 10.1007/s00438-020-01698-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 06/09/2020] [Indexed: 10/24/2022]
Abstract
The tripartite motif (TRIM) gene family encodes diverse distinct proteins that play important roles in many biological processes. However, the molecular evolution and phylogenetic relationships of TRIM genes in primates are still elusive. We performed a genomic approach to identify and characterize TRIM genes in human and other six primate genomes. In total, 537 putative functional TRIM genes were identified and TRIM members varied among primates. A neighbor joining (NJ) tree based on the protein sequences of 82 human TRIM genes indicates seven TRIM groups, which is consistent with the results based on the architectural motifs. Many TRIM gene duplication events were identified, indicating a recent expansion of TRIM family in primate lineages. Interestingly, the chimpanzee genome shows the greatest TRIM gene expansion among the primates; however, its congeneric species, bonobo, has the least number of TRIM genes and no duplication event. Moreover, we identified a ~ 200 kb deletion on chromosome 11 of bonobos that results in a loss of cluster3 TRIM genes. The loss of TRIM genes might have occurred within the last 2 mys. Analysis of positive selection recovered 9 previously reported and 21 newly identified positively selected TRIM genes. In particular, most positive selected sites are located in the B30.2 domains. Our results have provided new insight into the evolution of primate TRIM genes and will broaden our understanding on the functions of the TRIM family.
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45
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Shedding Light on the Role of Extracellular Vesicles in HIV Infection and Wound Healing. Viruses 2020; 12:v12060584. [PMID: 32471020 PMCID: PMC7354510 DOI: 10.3390/v12060584] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/19/2020] [Accepted: 05/25/2020] [Indexed: 12/18/2022] Open
Abstract
Extracellular vesicles (EVs) play an important role in intercellular communication. They are naturally released from cells into the extracellular environment. Based on their biogenesis, release pathways, size, content, and function, EVs are classified into exosomes, microvesicles (MVs), and apoptotic bodies (ApoBDs). Previous research has documented that EVs, specifically exosomes and MVs, play an important role in HIV infection, either by promoting HIV infection and pathogenesis or by inhibiting HIV-1 to a certain extent. We have also previously reported that EVs (particularly exosomes) from vaginal fluids inhibit HIV at the post-entry step (i.e., reverse transcription, integration). Besides the role that EVs play in HIV, they are also known to regulate the process of wound healing by regulating both the immune and inflammatory responses. It is noted that during the advanced stages of HIV infection, patients are at greater risk of wound-healing and wound-related complications. Despite ongoing research, the data on the actual effects of EVs in HIV infection and wound healing are still premature. This review aimed to update the current knowledge about the roles of EVs in regulating HIV pathogenesis and wound healing. Additionally, we highlighted several avenues of EV involvement in the process of wound healing, including coagulation, inflammation, proliferation, and extracellular matrix remodeling. Understanding the role of EVs in HIV infection and wound healing could significantly contribute to the development of new and potent antiviral therapeutic strategies and approaches to resolve impaired wounds in HIV patients.
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46
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Naveed M, Ali A, Sheikh N, Rafique S, Idrees M. Expression of TRIM22 mRNA in chronic hepatitis C patients treated with direct-acting antiviral drugs. APMIS 2020; 128:326-334. [PMID: 31863490 DOI: 10.1111/apm.13024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 12/17/2019] [Indexed: 12/20/2022]
Abstract
Hepatitis C is a global public health problem, and Pakistan is the second largest country in the globe with highest prevalence rate of hepatitis C virus (HCV). Until 2014, pegylated interferon (PEG-IFN) plus ribavirin (RBV) has been the standard therapy for HCV, however, owing to its adverse side effects and very low sustained virologic response (SVR) rates therapeutics trend is shifted toward direct-acting antivirals. Tripartite motif containing 22 (TRIM22) is a dynamic antiviral protein that can inhibit multiple viruses in vivo. Expression of TRIM22 mRNA has been linked to outcome of PEG-IFN and ribavirin therapy, where its higher expression leads to rapid virus clearance. However, in terms of therapy with direct-acting antiviral (DAA) or double DAA, impact of TRIM22 expression is largely unknown. These new drugs show more than 90% of SVR rates and lesser side effects and have proven to be better than IFN therapy. Endogenous IFN system suppresses various pathogens through the induction of antiviral effectors termed as interferon-stimulating genes (ISGs). We have studied the expression levels of one of these antiviral effectors, TRIM22 in response to sofosbuvir (SOF) and daclatasvir (DAC) in combination with RBV, using quantitative PCR in the peripheral blood mononuclear cells (PBMCs) of HCV-infected patients. We have observed sustained virus clearance in more than 90% of patients treated with DAA and double DAA and have seen the expression of TRIM22 to be higher in patients who attained SVR as compared to the untreated patients. We have also observed downregulation of TRIM22 in patients who failed to attain rapid virus clearance, and upregulation in those who achieved rapid clearance of virus. Genetic factors that determine the lower TRIM22 expression in these patients are needed to be explored that may also play a role in lower response to anti-HCV therapy. Endogenous IFN system and effects of antiviral proteins in response to DAA therapy is needed to be studied in order to better understand the host response toward these drugs to make them more effective.
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Affiliation(s)
- Mariam Naveed
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Amjad Ali
- Department of Genetics, Hazara University, Mansehra, Pakistan
| | - Nadeem Sheikh
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Shazia Rafique
- Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Muhammad Idrees
- Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
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47
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Sarker N, Tarlinton R, Owen H, David Emes R, Seddon J, Simmons G, Meers J. Novel insights into viral infection and oncogenesis from koala retrovirus (KoRV) infection of HEK293T cells. Gene 2020; 733:144366. [PMID: 31972306 DOI: 10.1016/j.gene.2020.144366] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/22/2019] [Accepted: 01/12/2020] [Indexed: 01/11/2023]
Abstract
Koala retrovirus is thought to be an underlying cause of high levels of neoplasia and immunosuppression in koalas. While epidemiology studies suggest a strong link between KoRV and disease it has been difficult to prove causality because of the complex nature of the virus, which exists in both endogenous and exogenous forms. It has been difficult to identify koalas completely free of KoRV, and infection studies in koalas or koala cells are fraught with ethical and technical difficulties, respectively. This study uses KoRV infection of the susceptible human cell line HEK293T and RNAseq to demonstrate gene networks differentially regulated upon KoRV infection. Many of the pathways identified are those associated with viral infection, such as cytokine receptor interactions and interferon signalling pathways, as well as viral oncogenesis pathways. This study provides strong evidence that KoRV does indeed behave similarly to infectious retroviruses in stimulating antiviral and oncogenic cellular responses. In addition, it provides novel insights into KoRV oncogenesis with the identification of a group of histone family genes that are part of several oncogenic pathways as upregulated in KoRV infection.
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Affiliation(s)
- Nishat Sarker
- School of Veterinary Science, The University of Queensland, Australia; Laboratory of Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh
| | - Rachael Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, United Kingdom
| | - Helen Owen
- School of Veterinary Science, The University of Queensland, Australia
| | - Richard David Emes
- School of Veterinary Medicine and Science, University of Nottingham, United Kingdom; Advanced Data Analysis Centre (ADAC), University of Nottingham, United Kingdom
| | - Jennifer Seddon
- School of Veterinary Science, The University of Queensland, Australia
| | - Greg Simmons
- School of Veterinary Science, The University of Queensland, Australia
| | - Joanne Meers
- School of Veterinary Science, The University of Queensland, Australia.
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48
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Li L, Feng W, Cheng Z, Yang J, Bi J, Wang X, Wang G. TRIM62-mediated restriction of avian leukosis virus subgroup J replication is dependent on the SPRY domain. Poult Sci 2020; 98:6019-6025. [PMID: 31309233 DOI: 10.3382/ps/pez408] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/20/2019] [Indexed: 12/17/2022] Open
Abstract
Emerging evidence suggests that some members of the tripartite motif (TRIM) family play a crucial role in antiretroviral. However, the chicken TRIM62 antiretroviral activity is unknown. Avian leukosis virus subgroup J (ALV-J) is an avian retrovirus mainly inducing tumor formation and immunosuppression. The purpose of the study was to explore chicken TRIM62's role in ALV-J replication. In this study, we first tested the RNA expression of ALV-J and TRIM62 in chicken embryo fibroblasts (CEFs) cells infected with ALV-J by qRT-PCR. The result showed that ALV-J infection affected TRIM62 RNA expression, first upregulation and then downregulation, with the time course infection of ALV-J. Then, we silenced and overexpressed the TRIM62 to evaluate the effect of TRIM62 on ALV-J replication by qRT-PCR. We found that the knockdown of TRIM62 in CEF cells with shRNA targeting SPRY domain enhanced the viral replication more significantly than that with shRNA targeting coiled coil/unstructured domain, and overexpression of TRIM62 inhibited the viral replication. Further, we detected the effect of the domain deletion on TRIM62's antiviral activity. The result demonstrated that deletion of RING, B-box, coiled-coil domains partially abolished TRIM62's antiviral activity, while SPRY domain deletion resulted in the disappearance of antiviral activity of TRIM62. Taken together, our findings strongly suggested that TRIM62 plays an important role in the restriction of ALV-J replication, and SPRY domain is a prerequisite for the antiviral activity of TRIM62.
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Affiliation(s)
- Ling Li
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China
| | - Weiguo Feng
- College of Bioscience and Technology, Weifang Medical University, Weifang 261053, China
| | - Ziqiang Cheng
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China
| | - Jie Yang
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China
| | - Jianmin Bi
- China Animal Husbandry Industry Co. Ltd., Beijing 10070, China
| | - Xiaoman Wang
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China
| | - Guihua Wang
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China
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Effects of Pseudomonas aeruginosa on Microglial-Derived Extracellular Vesicle Biogenesis and Composition. Pathogens 2019; 8:pathogens8040297. [PMID: 31847332 PMCID: PMC6963293 DOI: 10.3390/pathogens8040297] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/29/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022] Open
Abstract
The packaging of molecular constituents inside extracellular vesicles (EVs) allows them to participate in intercellular communication and the transfer of biological molecules, however the role of EVs during bacterial infection is poorly understood. The goal of this study was to examine the effects of Pseudomonas aeruginosa (P. aeruginosa) infection on the biogenesis and composition of EVs derived from the mouse microglia cell line, BV-2. BV-2 cells were cultured in exosome-free media and infected with 0, 1.3 × 104, or 2.6 × 104 colony forming units per milliliter P. aeruginosa for 72 h. The results indicated that compared with the control group, BV-2 cell viability significantly decreased after P. aeruginosa infection and BV-2-derived EVs concentration decreased significantly in the P. aeruginosa-infected group. P. aeruginosa infection significantly decreased chemokine ligand 4 messenger RNA in BV-2-derived infected EVs, compared with the control group (p ≤ 0.05). This study also revealed that heat shock protein 70 (p ≤ 0.05) and heat shock protein 90β (p ≤ 0.001) levels of expression within EVs increased after P. aeruginosa infection. EV treatment with EVs derived from P. aeruginosa infection reduced cell viability of BV-2 cells. P. aeruginosa infection alters the expression of specific proteins and mRNA in EVs. Our study suggests that P. aeruginosa infection modulates EV biogenesis and composition, which may influence bacterial pathogenesis and infection.
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50
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Forlani G, Shallak M, Ramia E, Tedeschi A, Accolla RS. Restriction factors in human retrovirus infections and the unprecedented case of CIITA as link of intrinsic and adaptive immunity against HTLV-1. Retrovirology 2019; 16:34. [PMID: 31783769 PMCID: PMC6884849 DOI: 10.1186/s12977-019-0498-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/23/2019] [Indexed: 12/17/2022] Open
Abstract
Background Immunity against pathogens evolved through complex mechanisms that only for sake of simplicity are defined as innate immunity and adaptive immunity. Indeed innate and adaptive immunity are strongly intertwined each other during evolution. The complexity is further increased by intrinsic mechanisms of immunity that rely on the action of intracellular molecules defined as restriction factors (RFs) that, particularly in virus infections, counteract the action of pathogen gene products acting at different steps of virus life cycle. Main body and conclusion Here we provide an overview on the nature and the mode of action of restriction factors involved in retrovirus infection, particularly Human T Leukemia/Lymphoma Virus 1 (HTLV-1) infection. As it has been extensively studied by our group, special emphasis is given to the involvement of the MHC class II transactivator CIITA discovered in our laboratory as regulator of adaptive immunity and subsequently as restriction factor against HIV-1 and HTLV-1, a unique example of dual function linking adaptive and intrinsic immunity during evolution. We describe the multiple molecular mechanisms through which CIITA exerts its restriction on retroviruses. Of relevance, we review the unprecedented findings pointing to a concerted action of several restriction factors such as CIITA, TRIM22 and TRIM19/PML in synergizing against retroviral replication. Finally, as CIITA profoundly affects HTLV-1 replication by interacting and inhibiting the function of HTLV-1 Tax-1 molecule, the major viral product associated to the virus oncogenicity, we also put forward the hypothesis of CIITA as counteractor of HTLV-1-mediated cancer initiation.
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Affiliation(s)
- Greta Forlani
- Laboratories of General Pathology and Immunology "Giovanna Tosi", Department of Medicine and Surgery, School of Medicine, University of Insubria, Via Ottorino Rossi 9, 21100, Varese, Italy
| | - Mariam Shallak
- Laboratories of General Pathology and Immunology "Giovanna Tosi", Department of Medicine and Surgery, School of Medicine, University of Insubria, Via Ottorino Rossi 9, 21100, Varese, Italy
| | - Elise Ramia
- Laboratories of General Pathology and Immunology "Giovanna Tosi", Department of Medicine and Surgery, School of Medicine, University of Insubria, Via Ottorino Rossi 9, 21100, Varese, Italy
| | - Alessandra Tedeschi
- Laboratories of General Pathology and Immunology "Giovanna Tosi", Department of Medicine and Surgery, School of Medicine, University of Insubria, Via Ottorino Rossi 9, 21100, Varese, Italy
| | - Roberto S Accolla
- Laboratories of General Pathology and Immunology "Giovanna Tosi", Department of Medicine and Surgery, School of Medicine, University of Insubria, Via Ottorino Rossi 9, 21100, Varese, Italy.
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