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Wang D, Booth JL, Wu W, Kiger N, Lettow M, Bates A, Pan C, Metcalf J, Schroeder SJ. Nanopore Direct RNA Sequencing Reveals Virus-Induced Changes in the Transcriptional Landscape in Human Bronchial Epithelial Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600852. [PMID: 38979243 PMCID: PMC11230378 DOI: 10.1101/2024.06.26.600852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Direct RNA nanopore sequencing reveals changes in gene expression, polyadenylation, splicing, m6A methylation, and pseudouridylation in response to influenza virus exposure in primary human bronchial epithelial cells. This study focuses on the epitranscriptomic profile of genes in the host immune response. In addition to polyadenylated noncoding RNA, we purified and sequenced nonpolyadenylated noncoding RNA and observed changes in expression, N6-methyl-adenosine (m6A), and pseudouridylation (Ψ) in these novel RNA. Two recently discovered lincRNA with roles in immune response, Chaserr and LEADR , became highly methylated in response to influenza exposure. Several H/ACA type snoRNAs that guide pseudouridylation are decreased in expression in response to influenza, and there is a corresponding decrease in the pseudouridylation of two novel lncRNA. Thus, novel epitranscriptomic changes revealed by direct RNA sequencing with nanopore technology provides unique insights into the host epitranscriptomic changes in epithelial gene networks that respond to influenza virus infection.
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Mai H, Yang X, Xie Y, Zhou J, Wei Y, Luo T, Yang J, Cui P, Ye L, Liang H, Huang J. Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension. Sci Rep 2024; 14:7048. [PMID: 38528047 DOI: 10.1038/s41598-024-55645-x] [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: 09/12/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024] Open
Abstract
The close link between HIV-1 infection and the occurrence of pulmonary arterial hypertension (PAH). However, the underlying molecular mechanisms of their interrelation remain unclear. The microarray data of HIV-1 and PAH were downloaded from GEO database. We utilized WGCNA to identify shared genes between HIV-1 and PAH, followed by conducting GO and pathway enrichment analyses. Subsequently, differentially genes analysis was performed using external validation datasets to further filter hub genes. Immunoinfiltration analysis was performed using CIBERSORT. Finally, hub gene expression was validated using scRNA-seq data. We identified 109 shared genes through WGCNA, primarily enriched in type I interferon (IFN) pathways. By taking the intersection of WGCNA important module genes and DEGs, ISG15 and IFI27 were identified as pivotal hub genes. Immunoinfiltration analysis and scRNA-seq results indicated the significant role of monocytes in the shared molecular mechanisms of HIV-1 and PAH. In summary, our study illustrated the possible mechanism of PAH secondary to HIV-1 and showed that the heightened IFN response in HIV-1 might be a crucial susceptibility factor for PAH, with monocytes being pivotal cells involved in the type I IFN response pathway. This provides potential new insights for further investigating the molecular mechanisms connecting HIV-1 and PAH.
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Affiliation(s)
- Huanzhuo Mai
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Xing Yang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
- Guangxi Academy of Medical Sciences, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Yulan Xie
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Jie Zhou
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Yiru Wei
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Tingyan Luo
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Jing Yang
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Ping Cui
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
- Life Science Institute, Guangxi Medical University, Nanning, 530021, China
| | - Li Ye
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Hao Liang
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
- Life Science Institute, Guangxi Medical University, Nanning, 530021, China
| | - Jiegang Huang
- School of Public Health, Guangxi Medical University, Nanning, 530021, China.
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China.
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, 530021, China.
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3
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Song S, Zhang JY, Liu FY, Zhang HY, Li XF, Zhang SX. B cell subsets-related biomarkers and molecular pathways for systemic lupus erythematosus by transcriptomics analyses. Int Immunopharmacol 2023; 124:110968. [PMID: 37741131 DOI: 10.1016/j.intimp.2023.110968] [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: 07/05/2023] [Revised: 09/07/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
BACKGROUND Systemic lupus erythematosus (SLE), an autoimmune disease, is characterised by B-cell abnormalities and a loss of tolerance that can produce autoantibody. However, the imperative genes and molecular pathways involved in the change of B cell populations remain unclear. METHODS The expression of B cell subsets between SLE and healthy controls (HCs) was detected based on micro-array transcriptome data. The Weighted Gene Co-Expression Network Analysis (WGCNA) further revealed the co-expression modules of naïve and memory B cells. Whereafter, we performed the functional enrichment analysis, Protein-protein interaction (PPI) networks construction and feature selection to screen hub genes. Ultimately, we recruited SLE patients and HCs from the Second Hospital of Shanxi Medical University and further verified these genes in transcriptome sequencing samples. RESULTS Total of 1087 SLE patients and 86 HCs constituted in the study. Compared to HCs, the levels of peripheral naïve B cells of SLE patients decreased, while memory B cells increased. WGCNA identified two modules with the highest correlation for the subsequent analysis. The purple module was primarily in connection with naïve B cells, and the GO analysis indicated that these genes were mainly abundant in B cell activation. The blue module relevant to memory B cells was most significantly enriched in the "defence response to virus" correlation pathway. Then we screened six hub genes by PPI and feature selection. Finally, four biomarkers (IFI27, IFITM1, MX2, IRF7) were identified by transcriptome sequencing verification. CONCLUSION Our study identified hub genes and key pathways associated with the naïve and memory B cells respectively, which may offer novel insights into the behaviours of B cells and the pathogenesis of SLE.
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Affiliation(s)
- Shan Song
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China; Ministry of Education Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Jing-Yuan Zhang
- Department of Pediatric Medicine, Shanxi Medical University, Taiyuan, China
| | - Fang-Yue Liu
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China; Ministry of Education Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - He-Yi Zhang
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China; Ministry of Education Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Xiao-Feng Li
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China; Ministry of Education Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Sheng-Xiao Zhang
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China; Ministry of Education Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China.
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4
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Kim GS, Harmon E, Gutierrez M, Stephenson J, Chauhan A, Banerjee A, Wise Z, Doan A, Wu T, Lee J, Jung JE, McCullough L, Wythe J, Marrelli S. Single-cell analysis identifies Ifi27l2a as a novel gene regulator of microglial inflammation in the context of aging and stroke. RESEARCH SQUARE 2023:rs.3.rs-2557290. [PMID: 36824976 PMCID: PMC9949241 DOI: 10.21203/rs.3.rs-2557290/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Microglia are key mediators of inflammatory responses within the brain, as they regulate pro-inflammatory responses while also limiting neuroinflammation via reparative phagocytosis. Thus, identifying genes that modulate microglial function may reveal novel therapeutic interventions for promoting better outcomes in diseases featuring extensive inflammation, such as stroke. To facilitate identification of potential mediators of inflammation, we performed single-cell RNA sequencing of aged mouse brains following stroke and found that Ifi27l2a was significantly up-regulated, particularly in microglia. The increased Ifi27l2a expression was further validated in microglial culture, stroke models with microglial depletion, and human autopsy samples. Ifi27l2a is known to be induced by interferons for viral host defense, however the role of Ifi27l2a in neurodegeneration is unknown. In vitro studies in cultured microglia demonstrated that Ifi27l2a overexpression causes neuroinflammation via reactive oxygen species. Interestingly, hemizygous deletion of Ifi27l2a significantly reduced gliosis in the thalamus following stroke, while also reducing neuroinflammation, indicating Ifi27l2a gene dosage is a critical mediator of neuroinflammation in ischemic stroke. Collectively, this study demonstrates that a novel gene, Ifi27l2a, regulates microglial function and neuroinflammation in the aged brain and following stroke. These findings suggest that Ifi27l2a may be a novel target for conferring cerebral protection post-stroke.
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Affiliation(s)
- Gab Seok Kim
- The University of Texas Health Science Center at Houston
| | | | | | | | | | | | - Zachary Wise
- The University of Texas Health Science Center at Houston
| | - Andrea Doan
- The University of Texas Health Science Center at Houston
| | - Ting Wu
- The University of Texas Health Science Center at Houston
| | - Juneyoung Lee
- The University of Texas Health Science Center at Houston
| | | | - Louise McCullough
- McGovern Medical School/University of Texas Health Science Center at Houston
| | | | - Sean Marrelli
- The University of Texas McGovern Medical School at Houston, 77030, TX
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5
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Liu H, Tian J, Lu K, Guan Z, Li Y, Cao X, Li X, Chang Z, Wang X, Sa X, Yang Z. Chicken ISG12(2) attenuates Newcastle disease virus and enhances the efficiency of Newcastle disease vaccine via activating immune pathways. Transbound Emerg Dis 2021; 69:2634-2648. [PMID: 34904395 DOI: 10.1111/tbed.14416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 10/31/2021] [Accepted: 11/30/2021] [Indexed: 11/30/2022]
Abstract
Low virulence and strong immunogenicity are quite important for Newcastle disease virus (NDV) producing Newcastle disease (ND) living-attenuated vaccine. However, immunogenicity of NDV positively correlates to its virulence. Usually, the velogenic NDV induces stronger immune responses of poultry than the lentogenic strain, but virulent NDV poses a risk for chicken. In this study, we identified the chicken interferon (IFN)-stimulated gene 12-2 (ISG12(2)) not only attenuated NDV, but also increased immunogenicity of ND vaccine strain. Firstly, we found that NDV infection or IFNs stimulation induced expression of chicken ISG12(2) that reinforced expression of IFNs. Overexpression or knockdown proved that chicken ISG12(2) inhibited NDV replication. Then, recombinant NDV LaSota strains (rLaSota/Fmut/ISG12(2) and rLaSota/ISG12(2)), expressing ISG12(2), were rescued. Pathogenicity tests showed that ISG12(2) expression attenuated NDV. RNA-seq or RT-qPCR demonstrated that, comparing to rLaSota/Fmut and rLaSota, rLaSota/Fmut/ISG12(2) and rLaSota/ISG12(2) induced hosts to produce cytokines enriching in innate and adaptive immune pathways in vitro and in vivo. Finally, we showed that rLaSota/ISG12(2) vaccination improved immune condition of chicken to quickly response NDV infection and then enhance protection. These results suggest that chicken ISG12(2) is a potential novel molecular adjuvant to regulate immune responses, which decrease virulence and increase immunogenicity of NDV. The chicken ISG12(2) may contribute to development of high efficient poultry vaccine. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Haijin Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jianxia Tian
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Kejia Lu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhao Guan
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yangyang Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xuhong Cao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoqin Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhengwu Chang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xinglong Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiao Sa
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zengqi Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
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6
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Adam BA, Murakami N, Reid G, Du K, Jasim R, Boils CL, Bu L, Hill PD, Murray AG, Renaudin K, Roufosse C, Weins A, Wen K, Riella LV, Mengel M. Gene Expression Profiling in Kidney Transplants with Immune Checkpoint Inhibitor-Associated Adverse Events. Clin J Am Soc Nephrol 2021; 16:1376-1386. [PMID: 34244334 PMCID: PMC8729568 DOI: 10.2215/cjn.00920121] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 07/03/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND OBJECTIVES Immune checkpoint inhibitors are increasingly used to treat various malignancies, but their application in patients with kidney transplants is complicated by high allograft rejection rates. Immune checkpoint inhibitor-associated rejection is a novel, poorly understood entity demonstrating overlapping histopathologic features with immune checkpoint inhibitor-associated acute interstitial nephritis, which poses a challenge for diagnosis and clinical management. We sought to improve the understanding of these entities through biopsy-based gene expression analysis. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS NanoString was used to measure and compare the expression of 725 immune-related genes in 75 archival kidney biopsies, including a 25-sample discovery cohort comprising pure T cell-mediated rejection and immune checkpoint inhibitor-associated acute interstitial nephritis and an independent 50-sample validation cohort comprising immune checkpoint inhibitor-associated acute interstitial nephritis, immune checkpoint inhibitor-associated T cell-mediated rejection, immune checkpoint inhibitor-associated crescentic GN, drug-induced acute interstitial nephritis, BK virus nephropathy, and normal biopsies. RESULTS Significant molecular overlap was observed between immune checkpoint inhibitor-associated acute interstitial nephritis and T cell-mediated rejection. Nevertheless, IFI27, an IFN-α-induced transcript, was identified and validated as a novel biomarker for differentiating immune checkpoint inhibitor-associated T cell-mediated rejection from immune checkpoint inhibitor-associated acute interstitial nephritis (validation cohort: P<0.001, area under the receiver operating characteristic curve =100%, accuracy =86%). Principal component analysis revealed heterogeneity in inflammatory gene expression patterns within sample groups; however, immune checkpoint inhibitor-associated T cell-mediated rejection and immune checkpoint inhibitor-associated acute interstitial nephritis both demonstrated relatively more molecular overlap with drug-induced acute interstitial nephritis than T cell-mediated rejection, suggesting potential dominance of hypersensitivity mechanisms in these entities. CONCLUSIONS These results indicate that, although there is significant molecular similarity between immune checkpoint inhibitor-associated rejection and acute interstitial nephritis, biopsy-based measurement of IFI27 gene expression represents a potential biomarker for differentiating these entities.
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Affiliation(s)
- Benjamin A. Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Naoka Murakami
- Renal Division, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Graeme Reid
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Katie Du
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Ruqaya Jasim
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Lihong Bu
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Peter D. Hill
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Allan G. Murray
- Division of Nephrology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Karine Renaudin
- Department of Pathology, Nantes University Hospital, Nantes, France
| | - Candice Roufosse
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Astrid Weins
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Kevin Wen
- Division of Nephrology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Leonardo V. Riella
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Michael Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
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7
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Phelan DE, Shigemura M, Aldhafiri S, Mota C, Hall TJ, Sznajder JI, Murphy EP, Crean D, Cummins EP. Transcriptional Profiling of Monocytes Deficient in Nuclear Orphan Receptors NR4A2 and NR4A3 Reveals Distinct Signalling Roles Related to Antigen Presentation and Viral Response. Front Immunol 2021; 12:676644. [PMID: 34248958 PMCID: PMC8267906 DOI: 10.3389/fimmu.2021.676644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/07/2021] [Indexed: 11/22/2022] Open
Abstract
The nuclear receptor sub-family 4 group A (NR4A) family are early response genes that encode proteins that are activated in several tissues/cells in response to a variety of stressors. The NR4A family comprises NR4A1, NR4A2 and NR4A3 of which NR4A2 and NR4A3 are under researched and less understood, particularly in the context of immune cells. NR4A expression is associated with multiple diseases e.g. arthritis and atherosclerosis and the development of NR4A-targetting molecules as therapeutics is a current focus in this research field. Here, we use a combination of RNA-sequencing coupled with strategic bioinformatic analysis to investigate the down-stream effects of NR4A2 and NR4A3 in monocytes and dissect their common and distinct signalling roles. Our data reveals that NR4A2 and NR4A3 depletion has a robust and broad-reaching effect on transcription in both the unstimulated state and in the presence of LPS. Interestingly, many of the genes affected were present in both the unstimulated and stimulated states revealing a previously unappreciated role for the NR4As in unstimulated cells. Strategic clustering and bioinformatic analysis identified both distinct and common transcriptional roles for NR4A2 and NR4A3 in monocytes. NR4A2 notably was linked by both bioinformatic clustering analysis and transcription factor interactome analysis to pathways associated with antigen presentation and regulation of MHC genes. NR4A3 in contrast was more closely linked to pathways associated with viral response. Functional studies further support our data analysis pointing towards preferential/selective roles for NR4A2 in the regulation of antigen processing with common roles for NR4A2 and NR4A3 evident with respect to cell migration. Taken together this study provides novel mechanistic insights into the role of the enigmatic nuclear receptors NR4A2 and NR4A3 in monocytes.
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Affiliation(s)
- David E Phelan
- School of Medicine, University College Dublin, Dublin, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Masahiko Shigemura
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Sarah Aldhafiri
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,Animal Genomics Laboratory, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Catarina Mota
- School of Medicine, University College Dublin, Dublin, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Thomas J Hall
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Jacob I Sznajder
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Evelyn P Murphy
- School of Medicine, University of Limerick, Limerick, Ireland
| | - Daniel Crean
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,Animal Genomics Laboratory, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Eoin P Cummins
- School of Medicine, University College Dublin, Dublin, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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8
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Hong J, Arneson D, Umar S, Ruffenach G, Cunningham CM, Ahn IS, Diamante G, Bhetraratana M, Park JF, Said E, Huynh C, Le T, Medzikovic L, Humbert M, Soubrier F, Montani D, Girerd B, Trégouët DA, Channick R, Saggar R, Eghbali M, Yang X. Single-Cell Study of Two Rat Models of Pulmonary Arterial Hypertension Reveals Connections to Human Pathobiology and Drug Repositioning. Am J Respir Crit Care Med 2021; 203:1006-1022. [PMID: 33021809 PMCID: PMC8048757 DOI: 10.1164/rccm.202006-2169oc] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
Rationale: The cellular and molecular landscape and translational value of commonly used models of pulmonary arterial hypertension (PAH) are poorly understood. Single-cell transcriptomics can enhance molecular understanding of preclinical models and facilitate their rational use and interpretation.Objectives: To determine and prioritize dysregulated genes, pathways, and cell types in lungs of PAH rat models to assess relevance to human PAH and identify drug repositioning candidates.Methods: Single-cell RNA sequencing was performed on the lungs of monocrotaline (MCT), Sugen-hypoxia (SuHx), and control rats to identify altered genes and cell types, followed by validation using flow-sorted cells, RNA in situ hybridization, and immunofluorescence. Relevance to human PAH was assessed by histology of lungs from patients and via integration with human PAH genetic loci and known disease genes. Candidate drugs were predicted using Connectivity Map.Measurements and Main Results: Distinct changes in genes and pathways in numerous cell types were identified in SuHx and MCT lungs. Widespread upregulation of NF-κB signaling and downregulation of IFN signaling was observed across cell types. SuHx nonclassical monocytes and MCT conventional dendritic cells showed particularly strong NF-κB pathway activation. Genes altered in SuHx nonclassical monocytes were significantly enriched for PAH-associated genes and genetic variants, and candidate drugs predicted to reverse the changes were identified. An open-access online platform was developed to share single-cell data and drug candidates (http://mergeomics.research.idre.ucla.edu/PVDSingleCell/).Conclusions: Our study revealed the distinct and shared dysregulation of genes and pathways in two commonly used PAH models for the first time at single-cell resolution and demonstrated their relevance to human PAH and utility for drug repositioning.
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Affiliation(s)
- Jason Hong
- Division of Pulmonary and Critical Care Medicine
| | | | - Soban Umar
- Department of Anesthesiology and Perioperative Medicine, and
| | | | | | - In Sook Ahn
- Department of Integrative Biology and Physiology
| | | | - May Bhetraratana
- Division of Cardiology, University of California Los Angeles, Los Angeles, California
| | - John F. Park
- Department of Anesthesiology and Perioperative Medicine, and
| | - Emma Said
- Department of Anesthesiology and Perioperative Medicine, and
| | | | - Trixie Le
- Department of Anesthesiology and Perioperative Medicine, and
| | | | - Marc Humbert
- Department of Respiratory and Intensive Care Medicine, Bicêtre Hospital, University of Paris-Saclay, National Institute of Health and Medical Research Joint Research Unit S 999, Public Assistance Hospitals of Paris, Le Kremlin-Bicêtre, France
| | - Florent Soubrier
- Institut Hospitalo–Universitaire Cardiométabolisme et Nutrition, Paris, France; and
| | - David Montani
- Department of Respiratory and Intensive Care Medicine, Bicêtre Hospital, University of Paris-Saclay, National Institute of Health and Medical Research Joint Research Unit S 999, Public Assistance Hospitals of Paris, Le Kremlin-Bicêtre, France
| | - Barbara Girerd
- Department of Respiratory and Intensive Care Medicine, Bicêtre Hospital, University of Paris-Saclay, National Institute of Health and Medical Research Joint Research Unit S 999, Public Assistance Hospitals of Paris, Le Kremlin-Bicêtre, France
| | - David-Alexandre Trégouët
- Bordeaux Population Health Research Center, University of Bordeaux, National Institute of Health and Medical Research Joint Research Unit 1219, Bordeaux, France
| | | | - Rajan Saggar
- Division of Pulmonary and Critical Care Medicine
| | | | - Xia Yang
- Department of Integrative Biology and Physiology
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9
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Xu L, Zu T, Li T, Li M, Mi J, Bai F, Liu G, Wen J, Li H, Brakebusch C, Wang X, Wu X. ATF3 downmodulates its new targets IFI6 and IFI27 to suppress the growth and migration of tongue squamous cell carcinoma cells. PLoS Genet 2021; 17:e1009283. [PMID: 33539340 PMCID: PMC7888615 DOI: 10.1371/journal.pgen.1009283] [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: 04/15/2020] [Revised: 02/17/2021] [Accepted: 11/18/2020] [Indexed: 01/16/2023] Open
Abstract
Activating transcription factor 3 (ATF3) is a key transcription factor involved in regulating cellular stress responses, with different expression levels and functions in different tissues. ATF3 has also been shown to play crucial roles in regulating tumor development and progression, however its potential role in oral squamous cell carcinomas has not been fully explored. In this study, we examined biopsies of tongue squamous cell carcinomas (TSCCs) and found that the nuclear expression level of ATF3 correlated negatively with the differentiation status of TSCCs, which was validated by analysis of the ATGC database. By using gain- or loss- of function analyses of ATF3 in four different TSCC cell lines, we demonstrated that ATF3 negatively regulates the growth and migration of human TSCC cells in vitro. RNA-seq analysis identified two new downstream targets of ATF3, interferon alpha inducible proteins 6 (IFI6) and 27 (IFI27), which were upregulated in ATF3-deleted cells and were downregulated in ATF3-overexpressing cells. Chromatin immunoprecipitation assays showed that ATF3 binds the promoter regions of the IFI6 and IFI27 genes. Both IFI6 and IFI27 were highly expressed in TSCC biopsies and knockdown of either IFI6 or IFI27 in TSCC cells blocked the cell growth and migration induced by the deletion of ATF3. Conversely, overexpression of either IFI6 or IFI27 counteracted the inhibition of TSCC cell growth and migration induced by the overexpression of ATF3. Finally, an in vivo study in mice confirmed those in vitro findings. Our study suggests that ATF3 plays an anti-tumor function in TSCCs through the negative regulation of its downstream targets, IFI6 and IFI27. Activating transcription factor 3 (ATF3), a stress response gene, has been shown to play either tumor promoting or tumor suppressing functions depending on the type of tumor cell and the stromal context. Here we discovered that ATF3 plays an anti-tumor role in tongue squamous cell carcinoma (TSCC) cells through the transcriptional suppression of its new downstream targets interferon alpha inducible proteins 6 (IFI6) and 27 (IFI27). This finding contributes to understanding how ATF3, a transcriptional repressor, can target specific downstream genes in different tumor cells to play anti-tumor or pro-tumor functions. A thorough understanding of ATF3 functions and its downstream signaling pathways provides a potential approach to develop new therapeutics for the treatment of tumors such as TSCCs.
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Affiliation(s)
- Lin Xu
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Shandong, China
- Department of Orthodontics, Liaocheng People’s Hospital, Liaocheng, Shandong, China
- Precision Biomedical Key Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Tingjian Zu
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
- School of Stomatology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai’an, Shandong, China
| | - Tao Li
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Shandong, China
| | - Min Li
- Precision Biomedical Key Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Jun Mi
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
| | - Fuxiang Bai
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
| | - Guanyi Liu
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
| | - Jie Wen
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
| | - Hui Li
- Department of Hematology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Cord Brakebusch
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, Denmark
| | - Xuxia Wang
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Shandong, China
- * E-mail: (XW); (XW)
| | - Xunwei Wu
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
- * E-mail: (XW); (XW)
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10
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Zhao X, Zhang L, Wang J, Zhang M, Song Z, Ni B, You Y. Identification of key biomarkers and immune infiltration in systemic lupus erythematosus by integrated bioinformatics analysis. J Transl Med 2021; 19:35. [PMID: 33468161 PMCID: PMC7814551 DOI: 10.1186/s12967-020-02698-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/31/2020] [Indexed: 02/07/2023] Open
Abstract
Background Systemic lupus erythematosus (SLE) is a multisystemic, chronic inflammatory disease characterized by destructive systemic organ involvement, which could cause the decreased functional capacity, increased morbidity and mortality. Previous studies show that SLE is characterized by autoimmune, inflammatory processes, and tissue destruction. Some seriously-ill patients could develop into lupus nephritis. However, the cause and underlying molecular events of SLE needs to be further resolved. Methods The expression profiles of GSE144390, GSE4588, GSE50772 and GSE81622 were downloaded from the Gene Expression Omnibus (GEO) database to obtain differentially expressed genes (DEGs) between SLE and healthy samples. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments of DEGs were performed by metascape etc. online analyses. The protein–protein interaction (PPI) networks of the DEGs were constructed by GENEMANIA software. We performed Gene Set Enrichment Analysis (GSEA) to further understand the functions of the hub gene, Weighted gene co‐expression network analysis (WGCNA) would be utilized to build a gene co‐expression network, and the most significant module and hub genes was identified. CIBERSORT tools have facilitated the analysis of immune cell infiltration patterns of diseases. The receiver operating characteristic (ROC) analyses were conducted to explore the value of DEGs for SLE diagnosis. Results In total, 6 DEGs (IFI27, IFI44, IFI44L, IFI6, EPSTI1 and OAS1) were screened, Biological functions analysis identified key related pathways, gene modules and co‐expression networks in SLE. IFI27 may be closely correlated with the occurrence of SLE. We found that an increased infiltration of moncytes, while NK cells resting infiltrated less may be related to the occurrence of SLE. Conclusion IFI27 may be closely related pathogenesis of SLE, and represents a new candidate molecular marker of the occurrence and progression of SLE. Moreover immune cell infiltration plays important role in the progession of SLE.
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Affiliation(s)
- Xingwang Zhao
- Department of Dermatology, Southwest Hospital, Army Medical University, (Third Military Medical University), Chongqing, 400038, China
| | - Longlong Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Juan Wang
- Department of Dermatology, Southwest Hospital, Army Medical University, (Third Military Medical University), Chongqing, 400038, China
| | - Min Zhang
- Department of Dermatology, Southwest Hospital, Army Medical University, (Third Military Medical University), Chongqing, 400038, China
| | - Zhiqiang Song
- Department of Dermatology, Southwest Hospital, Army Medical University, (Third Military Medical University), Chongqing, 400038, China
| | - Bing Ni
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, (Third Military Medical University), Chongqing, China.
| | - Yi You
- Department of Dermatology, Southwest Hospital, Army Medical University, (Third Military Medical University), Chongqing, 400038, China.
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11
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Gao J, Zhu X, Wu M, Jiang L, Wang F, He S. IFI27 may predict and evaluate the severity of respiratory syncytial virus infection in preterm infants. Hereditas 2021; 158:3. [PMID: 33388093 PMCID: PMC7778825 DOI: 10.1186/s41065-020-00167-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/06/2020] [Indexed: 02/06/2023] Open
Abstract
Background Preterm infants are a special population that vulnerable to respiratory syncytial virus (RSV) infection and the lower respiratory tract infections (LRTIs) caused by RSV could be severe and even life-threating. The purpose of the present study was to identify candidate genes of preterm infants who are susceptible to RSV infection and provide a new insight into the pathogenesis of RSV infection. Methods Three datasets (GSE77087, GSE69606 and GSE41374) containing 183 blood samples of RSV infected patients and 33 blood samples of healthy controls from Gene Expression Omnibus (GEO) database were downloaded and the differentially expressed genes (DEGs) were screened out. The function and pathway enrichments were analyzed through Database for Annotation, Visualization and Integrated Discovery (DAVID) website. The protein-protein interaction (PPI) network for DEGs was constructed through Search Tool for the Retrieval of Interacting Genes (STRING). The module analysis was performed by Cytoscape software and hub genes were identified. Clinical verification was employed to verify the expression level of top five hub genes among 72 infants including 50 RSV infected patients and 22 non-RSV-infected patients hospitalized in our center. Further, the RSV infected infants with high-expression IFI27 and those with low-expression IFI27 were compared (defined as higher or lower than the median mRNA level). Finally, the gene set enrichment analysis (GSEA) focusing on IFI27 was carried out. Results Totally, 4028 DEGs were screened out and among which, 131 most significant DEGs were selected. Subsequently, 13 hub genes were identified, and function and pathway enrichments of hub genes mainly were: response to virus, defense response to virus, regulation of viral genome replication and regulation of viral life cycle. Furthermore, IFI27 was confirmed to be the most significantly expressed in clinical verification. Gene sets associated with calcium signaling pathway, arachidonic acid metabolism, extracellular matrix receptor interaction and so on were significantly enriched when IFI27 was highly expressed. Moreover, high-expression IFI27 was associated with more severe cases (p = 0.041), more requirements of mechanical ventilation (p = 0.034), more frequent hospitalization (p < 0.001) and longer cumulative hospital stay (p = 0.012). Conclusion IFI27 might serve to predict RSV infection and evaluate the severity of RSV infection in preterm infants. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-020-00167-5.
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Affiliation(s)
- Junyan Gao
- Department of Pediatrics, Affiliated Hospital of Yangzhou University, NO.368 Hanjiang Middle Road, Yangzhou, 225000, Jiangsu, China
| | - Xueping Zhu
- Department of Neonatology, Children's Hospital of Soochow University, NO.92 Zhongnan Street, Industrial Park, Suzhou, 215025, Jiangsu, China
| | - Mingfu Wu
- Department of Pediatrics, Affiliated Hospital of Yangzhou University, NO.368 Hanjiang Middle Road, Yangzhou, 225000, Jiangsu, China
| | - Lijun Jiang
- Department of Pediatrics, Affiliated Hospital of Yangzhou University, NO.368 Hanjiang Middle Road, Yangzhou, 225000, Jiangsu, China
| | - Fudong Wang
- Department of Pediatrics, Affiliated Hospital of Yangzhou University, NO.368 Hanjiang Middle Road, Yangzhou, 225000, Jiangsu, China
| | - Shan He
- Department of Neonatology, Children's Hospital of Soochow University, NO.92 Zhongnan Street, Industrial Park, Suzhou, 215025, Jiangsu, China. .,Department of Pediatrics, The First People's Hospital of Yunnan Province, NO.152 Jinbi Road, Kunming, 650031, Yunnan, China.
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12
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Zhytnik L, Maasalu K, Reimann E, Märtson A, Kõks S. RNA sequencing analysis reveals increased expression of interferon signaling genes and dysregulation of bone metabolism affecting pathways in the whole blood of patients with osteogenesis imperfecta. BMC Med Genomics 2020; 13:177. [PMID: 33228694 PMCID: PMC7684725 DOI: 10.1186/s12920-020-00825-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/15/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Osteogenesis imperfecta (OI) is a rare genetic disorder in which the patients suffer from numerous fractures, skeletal deformities and bluish sclera. The disorder ranges from a mild form to severe and lethal cases. The main objective of this pilot study was to compare the blood transcriptional landscape of OI patients with COL1A1 pathogenic variants and their healthy relatives, in order to find out different gene expression and dysregulated molecular pathways in OI. METHODS We performed RNA sequencing analysis of whole blood in seven individuals affected with different OI severity and their five unaffected relatives from the three families. The data was analyzed using edgeR package of R Bioconductor. Functional profiling and pathway analysis of the identified differently expressed genes was performed with g:GOSt and MinePath web-based tools. RESULTS We identified 114 differently expressed genes. The expression of 79 genes was up-regulated, while 35 genes were down-regulated. The functional analysis identified a presence of dysregulated interferon signaling pathways (IFI27, IFITM3, RSAD12, GBP7). Additionally, the expressions of the genes related to extracellular matrix organization, Wnt signaling, vitamin D metabolism and MAPK-ERK 1/2 pathways were also altered. CONCLUSIONS The current pilot study successfully captured the differential expression of inflammation and bone metabolism pathways in OI patients. This work can contribute to future research of transcriptional bloodomics in OI. Transcriptional bloodomics has a strong potential to become a major contributor to the understanding of OI pathological mechanisms, the discovery of phenotype modifying factors, and the identification of new therapeutic targets. However, further studies in bigger cohorts of OI patients are needed to confirm the findings of the current work.
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Affiliation(s)
- Lidiia Zhytnik
- Clinic of Traumatology and Orthopedics, Tartu University Hospital, Puusepa 8, 51014, Tartu, Estonia.
| | - Katre Maasalu
- Clinic of Traumatology and Orthopedics, Tartu University Hospital, Puusepa 8, 51014, Tartu, Estonia
- Department of Traumatology and Orthopedics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Ene Reimann
- Estonian Genome Centre, University of Tartu, Tartu, Estonia
| | - Aare Märtson
- Clinic of Traumatology and Orthopedics, Tartu University Hospital, Puusepa 8, 51014, Tartu, Estonia
- Department of Traumatology and Orthopedics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
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13
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Jing F, Zhang SW, Zhang S. Prediction of enhancer-promoter interactions using the cross-cell type information and domain adversarial neural network. BMC Bioinformatics 2020; 21:507. [PMID: 33160328 PMCID: PMC7648314 DOI: 10.1186/s12859-020-03844-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/27/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Enhancer-promoter interactions (EPIs) play key roles in transcriptional regulation and disease progression. Although several computational methods have been developed to predict such interactions, their performances are not satisfactory when training and testing data from different cell lines. Currently, it is still unclear what extent a across cell line prediction can be made based on sequence-level information. RESULTS In this work, we present a novel Sequence-based method (called SEPT) to predict the enhancer-promoter interactions in new cell line by using the cross-cell information and Transfer learning. SEPT first learns the features of enhancer and promoter from DNA sequences with convolutional neural network (CNN), then designing the gradient reversal layer of transfer learning to reduce the cell line specific features meanwhile retaining the features associated with EPIs. When the locations of enhancers and promoters are provided in new cell line, SEPT can successfully recognize EPIs in this new cell line based on labeled data of other cell lines. The experiment results show that SEPT can effectively learn the latent import EPIs-related features between cell lines and achieves the best prediction performance in terms of AUC (the area under the receiver operating curves). CONCLUSIONS SEPT is an effective method for predicting the EPIs in new cell line. Domain adversarial architecture of transfer learning used in SEPT can learn the latent EPIs shared features among cell lines from all other existing labeled data. It can be expected that SEPT will be of interest to researchers concerned with biological interaction prediction.
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Affiliation(s)
- Fang Jing
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, 710072 Shaanxi China
| | - Shao-Wu Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, 710072 Shaanxi China
| | - Shihua Zhang
- NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 55 Zhongguancun East Road, Beijing, 10090 China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223 China
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14
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Cervantes-Badillo MG, Paredes-Villa A, Gómez-Romero V, Cervantes-Roldán R, Arias-Romero LE, Villamar-Cruz O, González-Montiel M, Barrios-García T, Cabrera-Quintero AJ, Rodríguez-Gómez G, Cancino-Villeda L, Zentella-Dehesa A, León-Del-Río A. IFI27/ISG12 Downregulates Estrogen Receptor α Transactivation by Facilitating Its Interaction With CRM1/XPO1 in Breast Cancer Cells. Front Endocrinol (Lausanne) 2020; 11:568375. [PMID: 33117284 PMCID: PMC7575815 DOI: 10.3389/fendo.2020.568375] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/16/2020] [Indexed: 11/13/2022] Open
Abstract
The estrogen receptor alpha (ERα) is a ligand-activated transcription factor whose activity is modulated by its interaction with multiple protein complexes. In this work, we have identified the protein interferon alpha inducible protein 27 (IFI27/ISG12) as a novel ERα-associated protein. IFI27/ISG12 transcription is regulated by interferon and estradiol and its overexpression is associated to reduced overall survival in ER+ breast cancer patients but its function in mammary gland tissue remains elusive. In this study we showed that overexpression of IFI27/ISG12 in breast cancer cells attenuates ERα transactivation activity and the expression of ERα-dependent genes. Our results demonstrated that IFI27/ISG12 overexpression in MCF-7 cells reduced their proliferation rate in 2-D and 3-D cell culture assays and impaired their ability to migrate in a wound-healing assay. We show that IFI27/ISG12 downregulation of ERα transactivation activity is mediated by its ability to facilitate the interaction between ERα and CRM1/XPO1 that mediates the nuclear export of large macromolecules to the cytoplasm. IFI27/ISG12 overexpression was shown to impair the estradiol-dependent proliferation and tamoxifen-induced apoptosis in breast cancer cells. Our results suggest that IFI27/ISG12 may be an important factor in regulating ERα activity in breast cancer cells by modifying its nuclear versus cytoplasmic protein levels. We propose that IFI27/ISG12 may be a potential target of future strategies to control the growth and proliferation of ERα-positive breast cancer tumors.
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Affiliation(s)
- Mayte Guadalupe Cervantes-Badillo
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alejandro Paredes-Villa
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Vania Gómez-Romero
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rafael Cervantes-Roldán
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Luis E. Arias-Romero
- Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores-Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Olga Villamar-Cruz
- Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores-Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Miroslava González-Montiel
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Tonatiuh Barrios-García
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alberto J. Cabrera-Quintero
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), Ciudad de México, Mexico
| | - Gabriel Rodríguez-Gómez
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Laura Cancino-Villeda
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alejandro Zentella-Dehesa
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), Ciudad de México, Mexico
| | - Alfonso León-Del-Río
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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15
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Fan H, He Z, Huang H, Zhuang H, Liu H, Liu X, Yang S, He P, Yang H, Feng D. Mitochondrial Quality Control in Cardiomyocytes: A Critical Role in the Progression of Cardiovascular Diseases. Front Physiol 2020; 11:252. [PMID: 32292354 PMCID: PMC7119225 DOI: 10.3389/fphys.2020.00252] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/05/2020] [Indexed: 12/11/2022] Open
Abstract
Mitochondria serve as an energy plant and participate in a variety of signaling pathways to regulate cellular metabolism, survival and immunity. Mitochondrial dysfunction, in particular in cardiomyocytes, is associated with the development and progression of cardiovascular disease, resulting in heart failure, cardiomyopathy, and cardiac ischemia/reperfusion injury. Therefore, mitochondrial quality control processes, including post-translational modifications of mitochondrial proteins, mitochondrial dynamics, mitophagy, and formation of mitochondrial-driven vesicles, play a critical role in maintenance of mitochondrial and even cellular homeostasis in physiological or pathological conditions. Accumulating evidence suggests that mitochondrial quality control in cardiomyocytes is able to improve cardiac function, rescue dying cardiomyocytes, and prevent the deterioration of cardiovascular disease upon external environmental stress. In this review, we discuss recent progress in understanding mitochondrial quality control in cardiomyocytes. We also evaluate potential targets to prevent or treat cardiovascular diseases, and highlight future research directions which will help uncover additional mechanisms underlying mitochondrial homeostasis in cardiomyocytes.
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Affiliation(s)
- Hualin Fan
- Guangdong Provincial People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China.,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Zhengjie He
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Haofeng Huang
- Institute of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Haixia Zhuang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Hao Liu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xiao Liu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Sijun Yang
- ABSL-Laboratory at the Center for Animal Experiment and Institute of Animal Model for Human Disease, Wuhan University School of Medicine, Wuhan, China
| | - Pengcheng He
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Huan Yang
- Department of Pulmonary and Critical Care Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Du Feng
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China.,The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou Medical University, Guangzhou, China
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16
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Intervention of Inflammatory Monocyte Activity Limits Dermal Fibrosis. J Invest Dermatol 2019; 139:2144-2153. [PMID: 31039360 DOI: 10.1016/j.jid.2019.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/12/2019] [Accepted: 04/17/2019] [Indexed: 11/20/2022]
Abstract
Monocytes and monocyte-derived cells are important players in the initiation, progression, and resolution of inflammatory skin reactions. As inflammation is a prerequisite for fibrosis development, we focused on the role of monocytes in cutaneous fibrosis, the clinical hallmark of patients suffering from systemic sclerosis. Investigating the function of monocytes in reactive oxygen species-induced dermal fibrosis, we observed that early monocyte depletion partially reduced disease severity. Low numbers of inflammatory Ly6Chigh monocytes, as well as inhibition of CCR2 and CCL2 in wild type animals by a specific L-RNA aptamer, mitigated disease parameters, indicating a pivotal role for CCR2+ inflammatory monocytes and the CCR2/CCL2 axis in fibrosis development. Of note, mice lacking splenic reservoirs failed to recruit monocytes to the skin and developed less fibrosis. Furthermore, enforced monocyte conversion into noninflammatory, patrolling Ly6Clow monocytes by a nuclear receptor Nur77-agonist also resulted in significantly impaired cutaneous inflammation and dermal fibrosis. Most evident, pronounced monocyte conversion in interferon stimulated gene 12-deficient mice with pronounced nuclear Nur77 signaling completely protected from dermal fibrosis. Our study shows that inflammatory monocytes that are recruited from splenic reservoirs play a key role in the development of skin fibrosis and can be therapeutically challenged by forced conversion via the Nur77/interferon stimulated gene 12 axis.
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17
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Liu N, Wu Z, Chen A, Chai D, Li L, Zhang L, Zheng J. ISG12a and its interaction partner NR4A1 are involved in TRAIL-induced apoptosis in hepatoma cells. J Cell Mol Med 2019; 23:3520-3529. [PMID: 30821058 PMCID: PMC6484314 DOI: 10.1111/jcmm.14251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/24/2018] [Accepted: 02/05/2019] [Indexed: 12/30/2022] Open
Abstract
Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) can induce apoptosis in cancer cells while sparing normal cells, thereby leading to the development of TRAIL receptor agonists for cancer treatment. However, these agonist-based therapeutics exhibit little clinical benefits due to the lack of biomarkers to predict whether patients are responsive to the treatment, as well as determine the resistance of cancer cells to TRAIL-based agonists. Our previous study has demonstrated that ISG12a enhances TRAIL-induced apoptosis and might serve as a biomarker to predict the TRAIL response. The downstream mechanism by which ISG12a augments TRAIL-induced apoptosis remains to be elucidated. In this study, we found that ISG12a was localized in the mitochondria and nucleus and augmented TRAIL-induced apoptosis through intrinsic apoptotic pathway. In addition, ISG12a interacted with NR4A1 and promoted its nuclear-to-cytoplasm translocation. Upon translocate to cytoplasm, NR4A1 targeted mitochondria and induced Bcl2 conformational change, thereby exposing its BH3 domain. Moreover, TRAIL treatment can induce NR4A1 expression through the activation of NF-κB in TRAIL-resistant Huh7 hepatoma cells. Knockdown of NR4A1 could overcome TRAIL resistance. However, in TRAIL-sensitive LH86 liver cancer cells, TRAIL activated the Jun N-terminal kinases signalling pathway. Overall, these results showed that both ISG12a and its interaction partner NR4A1 are involved in TRAIL-mediated apoptosis in hepatoma cells.
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Affiliation(s)
- Nianli Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhiyuan Wu
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Aoxing Chen
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Dafei Chai
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Liantao Li
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Longzhen Zhang
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Junnian Zheng
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
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18
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Tecalco-Cruz AC. Molecular pathways involved in the transport of nuclear receptors from the nucleus to cytoplasm. J Steroid Biochem Mol Biol 2018; 178:36-44. [PMID: 29107180 DOI: 10.1016/j.jsbmb.2017.10.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/18/2017] [Accepted: 10/25/2017] [Indexed: 12/30/2022]
Abstract
Nuclear receptors (NRs) are transcription regulators that direct the expression of many genes linked to cellular processes, such as proliferation, differentiation, and apoptosis. Additionally, some cellular events are also modulated by signaling pathways induced by NRs outside of the nucleus. Hence, the subcellular transport of NRs is dynamic and is modulated by several signals, protein-protein interactions, and posttranslational modifications. Particularly, the exit of NRs from the nucleus to cytoplasm and/or other compartments is transcendental, as it is this export event, which determines their abundance in the cells' compartments, the activation or attenuation of nuclear or extranuclear pathways, and the magnitude and duration of their effects inside or outside of the nucleus. Consequently, an adequate control of the distribution of NRs is critical for homeostasis, because a deregulation in the nucleo-cytoplasmic transport of NRs could be involved in diseases including cancer as well as metabolic and vascular alterations. In this review, we investigated the pathways and molecular and biological aspects that have been described for the nuclear export of NRs so far and their functional relevance in some diseases. This information suggests that the transport of NRs out of the nucleus is a key mechanism for the identification of new therapeutic targets for alterations associated with the deregulation of the function of NRs.
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Affiliation(s)
- Angeles C Tecalco-Cruz
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Apdo Postal, D.F. 04510, Mexico.
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Gytz H, Hansen MF, Skovbjerg S, Kristensen ACM, Hørlyck S, Jensen MB, Fredborg M, Markert LD, McMillan NA, Christensen EI, Martensen PM. Apoptotic properties of the type 1 interferon induced family of human mitochondrial membrane ISG12 proteins. Biol Cell 2016; 109:94-112. [DOI: 10.1111/boc.201600034] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Heidi Gytz
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
| | - Mariann F. Hansen
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
| | - Signe Skovbjerg
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
| | | | - Sofie Hørlyck
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
| | - Mette B. Jensen
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
| | - Marlene Fredborg
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
| | - Lotte D. Markert
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
| | - Nigel A. McMillan
- Centre of Immunological and Cancer Research; Queensland University; Brisbane Australia
| | | | - Pia M. Martensen
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
- Centre of Immunological and Cancer Research; Queensland University; Brisbane Australia
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20
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Luther N, Shahneh F, Brähler M, Krebs F, Jäckel S, Subramaniam S, Stanger C, Schönfelder T, Kleis-Fischer B, Reinhardt C, Probst HC, Wenzel P, Schäfer K, Becker C. Innate Effector-Memory T-Cell Activation Regulates Post-Thrombotic Vein Wall Inflammation and Thrombus Resolution. Circ Res 2016; 119:1286-1295. [PMID: 27707800 DOI: 10.1161/circresaha.116.309301] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/27/2016] [Accepted: 10/05/2016] [Indexed: 11/16/2022]
Abstract
RATIONALE Immune cells play an important role during the generation and resolution of thrombosis. T cells are powerful regulators of immune and nonimmune cell function, however, their role in sterile inflammation in venous thrombosis has not been systematically examined. OBJECTIVE This study investigated the recruitment, activation, and inflammatory activity of T cells in deep vein thrombosis and its consequences for venous thrombus resolution. METHODS AND RESULTS CD4+ and CD8+ T cells infiltrate the thrombus and vein wall rapidly on deep vein thrombosis induction and remain in the tissue throughout the thrombus resolution. In the vein wall, recruited T cells largely consist of effector-memory T (TEM) cells. Using T-cell receptor transgenic reporter mice, we demonstrate that deep vein thrombosis-recruited TEM receive an immediate antigen-independent activation and produce IFN-γ (interferon) in situ. Mapping inflammatory conditions in the thrombotic vein, we identify a set of deep vein thrombosis upregulated cytokines and chemokines that synergize to induce antigen-independent IFN-γ production in CD4+ and CD8+ TEM cells. Reducing the number of TEM cells through a depletion recovery procedure, we show that intravenous TEM activation determines neutrophil and monocyte recruitment and delays thrombus neovascularization and resolution. Examining T-cell recruitment in human venous stasis, we show that superficial varicose veins preferentially contain activated memory T cells. CONCLUSIONS TEM orchestrate the inflammatory response in venous thrombosis affecting thrombus resolution.
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Affiliation(s)
- Natascha Luther
- From the Department of Dermatology (N.L., F.S., M.B., F.K., C.S., B.K.-F., C.B.), Center for Thrombosis and Hemostasis (CTH) (S.J., S.S., T.S., C.R., P.W., C.B.), Institute for Immunology (H.C.P.), and Center for Cardiology, Cardiology I, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany (P.W., K.S.)
| | - Fatemeh Shahneh
- From the Department of Dermatology (N.L., F.S., M.B., F.K., C.S., B.K.-F., C.B.), Center for Thrombosis and Hemostasis (CTH) (S.J., S.S., T.S., C.R., P.W., C.B.), Institute for Immunology (H.C.P.), and Center for Cardiology, Cardiology I, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany (P.W., K.S.)
| | - Melanie Brähler
- From the Department of Dermatology (N.L., F.S., M.B., F.K., C.S., B.K.-F., C.B.), Center for Thrombosis and Hemostasis (CTH) (S.J., S.S., T.S., C.R., P.W., C.B.), Institute for Immunology (H.C.P.), and Center for Cardiology, Cardiology I, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany (P.W., K.S.)
| | - Franziska Krebs
- From the Department of Dermatology (N.L., F.S., M.B., F.K., C.S., B.K.-F., C.B.), Center for Thrombosis and Hemostasis (CTH) (S.J., S.S., T.S., C.R., P.W., C.B.), Institute for Immunology (H.C.P.), and Center for Cardiology, Cardiology I, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany (P.W., K.S.)
| | - Sven Jäckel
- From the Department of Dermatology (N.L., F.S., M.B., F.K., C.S., B.K.-F., C.B.), Center for Thrombosis and Hemostasis (CTH) (S.J., S.S., T.S., C.R., P.W., C.B.), Institute for Immunology (H.C.P.), and Center for Cardiology, Cardiology I, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany (P.W., K.S.)
| | - Saravanan Subramaniam
- From the Department of Dermatology (N.L., F.S., M.B., F.K., C.S., B.K.-F., C.B.), Center for Thrombosis and Hemostasis (CTH) (S.J., S.S., T.S., C.R., P.W., C.B.), Institute for Immunology (H.C.P.), and Center for Cardiology, Cardiology I, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany (P.W., K.S.)
| | - Christian Stanger
- From the Department of Dermatology (N.L., F.S., M.B., F.K., C.S., B.K.-F., C.B.), Center for Thrombosis and Hemostasis (CTH) (S.J., S.S., T.S., C.R., P.W., C.B.), Institute for Immunology (H.C.P.), and Center for Cardiology, Cardiology I, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany (P.W., K.S.)
| | - Tanja Schönfelder
- From the Department of Dermatology (N.L., F.S., M.B., F.K., C.S., B.K.-F., C.B.), Center for Thrombosis and Hemostasis (CTH) (S.J., S.S., T.S., C.R., P.W., C.B.), Institute for Immunology (H.C.P.), and Center for Cardiology, Cardiology I, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany (P.W., K.S.)
| | - Bettina Kleis-Fischer
- From the Department of Dermatology (N.L., F.S., M.B., F.K., C.S., B.K.-F., C.B.), Center for Thrombosis and Hemostasis (CTH) (S.J., S.S., T.S., C.R., P.W., C.B.), Institute for Immunology (H.C.P.), and Center for Cardiology, Cardiology I, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany (P.W., K.S.)
| | - Christoph Reinhardt
- From the Department of Dermatology (N.L., F.S., M.B., F.K., C.S., B.K.-F., C.B.), Center for Thrombosis and Hemostasis (CTH) (S.J., S.S., T.S., C.R., P.W., C.B.), Institute for Immunology (H.C.P.), and Center for Cardiology, Cardiology I, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany (P.W., K.S.)
| | - Hans Christian Probst
- From the Department of Dermatology (N.L., F.S., M.B., F.K., C.S., B.K.-F., C.B.), Center for Thrombosis and Hemostasis (CTH) (S.J., S.S., T.S., C.R., P.W., C.B.), Institute for Immunology (H.C.P.), and Center for Cardiology, Cardiology I, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany (P.W., K.S.)
| | - Philip Wenzel
- From the Department of Dermatology (N.L., F.S., M.B., F.K., C.S., B.K.-F., C.B.), Center for Thrombosis and Hemostasis (CTH) (S.J., S.S., T.S., C.R., P.W., C.B.), Institute for Immunology (H.C.P.), and Center for Cardiology, Cardiology I, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany (P.W., K.S.)
| | - Katrin Schäfer
- From the Department of Dermatology (N.L., F.S., M.B., F.K., C.S., B.K.-F., C.B.), Center for Thrombosis and Hemostasis (CTH) (S.J., S.S., T.S., C.R., P.W., C.B.), Institute for Immunology (H.C.P.), and Center for Cardiology, Cardiology I, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany (P.W., K.S.)
| | - Christian Becker
- From the Department of Dermatology (N.L., F.S., M.B., F.K., C.S., B.K.-F., C.B.), Center for Thrombosis and Hemostasis (CTH) (S.J., S.S., T.S., C.R., P.W., C.B.), Institute for Immunology (H.C.P.), and Center for Cardiology, Cardiology I, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany (P.W., K.S.).
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21
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ISG12a Restricts Hepatitis C Virus Infection through the Ubiquitination-Dependent Degradation Pathway. J Virol 2016; 90:6832-45. [PMID: 27194766 DOI: 10.1128/jvi.00352-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/11/2016] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED Interferons (IFNs) restrict various kinds of viral infection via induction of hundreds of IFN-stimulated genes (ISGs), while the functions of the majority of ISGs are broadly unclear. Here, we show that a high-IFN-inducible gene, ISG12a (also known as IFI27), exhibits a nonapoptotic antiviral effect on hepatitis C virus (HCV) infection. Viral NS5A protein is targeted specifically by ISG12a, which mediates NS5A degradation via a ubiquitination-dependent proteasomal pathway. K374R mutation in NS5A domain III abrogates ISG12a-induced ubiquitination and degradation of NS5A. S-phase kinase-associated protein 2 (SKP2) is identified as an ubiquitin E3 ligase for NS5A. ISG12a functions as a crucial adaptor that promotes SKP2 to interact with and degrade viral protein. Moreover, the antiviral effect of ISG12a is dependent on the E3 ligase activity of SKP2. These findings uncover an intriguing mechanism by which ISG12a restricts viral infection and provide clues for understanding the actions of innate immunity. IMPORTANCE Upon virus invasion, IFNs induce numerous ISGs to control viral spread, while the functions of the majority of ISGs are broadly unclear. The present study shows a novel antiviral mechanism of ISGs and elucidated that ISG12a recruits an E3 ligase, SKP2, for ubiquitination and degradation of viral protein and restricts viral infection. These findings provide important insights into exploring the working principles of innate immunity.
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22
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McDonald JU, Kaforou M, Clare S, Hale C, Ivanova M, Huntley D, Dorner M, Wright VJ, Levin M, Martinon-Torres F, Herberg JA, Tregoning JS. A Simple Screening Approach To Prioritize Genes for Functional Analysis Identifies a Role for Interferon Regulatory Factor 7 in the Control of Respiratory Syncytial Virus Disease. mSystems 2016; 1:e00051-16. [PMID: 27822537 PMCID: PMC5069771 DOI: 10.1128/msystems.00051-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 05/26/2016] [Indexed: 12/21/2022] Open
Abstract
Greater understanding of the functions of host gene products in response to infection is required. While many of these genes enable pathogen clearance, some enhance pathogen growth or contribute to disease symptoms. Many studies have profiled transcriptomic and proteomic responses to infection, generating large data sets, but selecting targets for further study is challenging. Here we propose a novel data-mining approach combining multiple heterogeneous data sets to prioritize genes for further study by using respiratory syncytial virus (RSV) infection as a model pathogen with a significant health care impact. The assumption was that the more frequently a gene is detected across multiple studies, the more important its role is. A literature search was performed to find data sets of genes and proteins that change after RSV infection. The data sets were standardized, collated into a single database, and then panned to determine which genes occurred in multiple data sets, generating a candidate gene list. This candidate gene list was validated by using both a clinical cohort and in vitro screening. We identified several genes that were frequently expressed following RSV infection with no assigned function in RSV control, including IFI27, IFIT3, IFI44L, GBP1, OAS3, IFI44, and IRF7. Drilling down into the function of these genes, we demonstrate a role in disease for the gene for interferon regulatory factor 7, which was highly ranked on the list, but not for IRF1, which was not. Thus, we have developed and validated an approach for collating published data sets into a manageable list of candidates, identifying novel targets for future analysis. IMPORTANCE Making the most of "big data" is one of the core challenges of current biology. There is a large array of heterogeneous data sets of host gene responses to infection, but these data sets do not inform us about gene function and require specialized skill sets and training for their utilization. Here we describe an approach that combines and simplifies these data sets, distilling this information into a single list of genes commonly upregulated in response to infection with RSV as a model pathogen. Many of the genes on the list have unknown functions in RSV disease. We validated the gene list with new clinical, in vitro, and in vivo data. This approach allows the rapid selection of genes of interest for further, more-detailed studies, thus reducing time and costs. Furthermore, the approach is simple to use and widely applicable to a range of diseases.
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Affiliation(s)
- Jacqueline U. McDonald
- Mucosal Infection and Immunity Group, Section of Virology, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatrics, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - Simon Clare
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Christine Hale
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Maria Ivanova
- Mucosal Infection and Immunity Group, Section of Virology, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - Derek Huntley
- Imperial College Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, United Kingdom
| | - Marcus Dorner
- Molecular Virology, Section of Virology, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - Victoria J. Wright
- Section of Paediatrics, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - Michael Levin
- Section of Paediatrics, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - Federico Martinon-Torres
- Department of Paediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Jethro A. Herberg
- Section of Paediatrics, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - John S. Tregoning
- Mucosal Infection and Immunity Group, Section of Virology, Imperial College London, St. Mary’s Campus, London, United Kingdom
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Raker VK, Becker C, Steinbrink K. The cAMP Pathway as Therapeutic Target in Autoimmune and Inflammatory Diseases. Front Immunol 2016; 7:123. [PMID: 27065076 PMCID: PMC4814577 DOI: 10.3389/fimmu.2016.00123] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/18/2016] [Indexed: 12/26/2022] Open
Abstract
Nucleotide signaling molecules contribute to the regulation of cellular pathways. In the immune system, cyclic adenosine monophosphate (cAMP) is well established as a potent regulator of innate and adaptive immune cell functions. Therapeutic strategies to interrupt or enhance cAMP generation or effects have immunoregulatory potential in autoimmune and inflammatory disorders. Here, we provide an overview of the cyclic AMP axis and its role as a regulator of immune functions and discuss the clinical and translational relevance of interventions with these processes.
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Affiliation(s)
- Verena Katharina Raker
- Department of Dermatology, University Medical Center Mainz, Johannes Gutenberg-University Mainz , Mainz , Germany
| | - Christian Becker
- Department of Dermatology, University Medical Center Mainz, Johannes Gutenberg-University Mainz , Mainz , Germany
| | - Kerstin Steinbrink
- Department of Dermatology, University Medical Center Mainz, Johannes Gutenberg-University Mainz , Mainz , Germany
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24
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Liu YJ, Lian ZY, Liu G, Zhou HY, Yang HJ. RNA sequencing reveals retinal transcriptome changes in STZ-induced diabetic rats. Mol Med Rep 2016; 13:2101-9. [PMID: 26781437 PMCID: PMC4768987 DOI: 10.3892/mmr.2016.4793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 12/11/2015] [Indexed: 02/05/2023] Open
Abstract
The present study aimed to investigate changes in retinal gene expression in streptozotocin (STZ)‑induced diabetic rats using next‑generation sequencing, utilize transcriptome signatures to investigate the molecular mechanisms of diabetic retinopathy (DR), and identify novel strategies for the treatment of DR. Diabetes was chemically induced in 10‑week‑old male Sprague‑Dawley rats using STZ. Flash‑electroretinography (F‑ERG) was performed to evaluate the visual function of the rats. The retinas of the rats were removed to perform high throughput RNA sequence (RNA‑seq) analysis. The a‑wave, b‑wave, oscillatory potential 1 (OP1), OP2 and ∑OP amplitudes were significantly reduced in the diabetic group, compared with those of the control group (P<0.05). Furthermore, the implicit b‑wave duration 16 weeks post‑STZ induction were significantly longer in the diabetic rats, compared with the control rats (P<0.001). A total of 868 genes were identified, of which 565 were upregulated and 303 were downregulated. Among the differentially expressed genes (DEGs), 94 apoptotic genes and apoptosis regulatory genes, and 19 inflammatory genes were detected. The results of the KEGG pathway significant enrichment analysis revealed enrichment in cell adhesion molecules, complement and coagulation cascades, and antigen processing and presentation. Diabetes alters several transcripts in the retina, and RNA‑seq provides novel insights into the molecular mechanisms underlying DR.
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Affiliation(s)
- Yuan-Jie Liu
- Department of Human Anatomy, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Zhi-Yun Lian
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Geng Liu
- Department of Human Anatomy, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Hong-Ying Zhou
- Department of Human Anatomy, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Hui-Jun Yang
- Department of Human Anatomy, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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25
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Lucas TM, Richner JM, Diamond MS. The Interferon-Stimulated Gene Ifi27l2a Restricts West Nile Virus Infection and Pathogenesis in a Cell-Type- and Region-Specific Manner. J Virol 2015; 90:2600-15. [PMID: 26699642 PMCID: PMC4810731 DOI: 10.1128/jvi.02463-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/15/2015] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED The mammalian host responds to viral infections by inducing expression of hundreds of interferon-stimulated genes (ISGs). While the functional significance of many ISGs has yet to be determined, their cell type and temporal nature of expression suggest unique activities against specific pathogens. Using a combination of ectopic expression and gene silencing approaches in cell culture, we previously identified Ifi27l2a as a candidate antiviral ISG within neuronal subsets of the central nervous system (CNS) that restricts infection by West Nile virus (WNV), an encephalitic flavivirus of global concern. To investigate the physiological relevance of Ifi27l2a in the context of viral infection, we generated Ifi27l2a(-/-) mice. Although adult mice lacking Ifi27l2a were more vulnerable to lethal WNV infection, the viral burden was greater only within the CNS, particularly in the brain stem, cerebellum, and spinal cord. Within neurons of the cerebellum and brain stem, in the context of WNV infection, a deficiency of Ifi27l2a was associated with less cell death, which likely contributed to sustained viral replication and higher titers in these regions. Infection studies in a primary cell culture revealed that Ifi27l2a(-/-) cerebellar granule cell neurons and macrophages but not cerebral cortical neurons, embryonic fibroblasts, or dendritic cells sustained higher levels of WNV infection than wild-type cells and that this difference was greater under conditions of beta interferon (IFN-β) pretreatment. Collectively, these findings suggest that Ifi27l2a has an antiviral phenotype in subsets of cells and that at least some ISGs have specific inhibitory functions in restricted tissues. IMPORTANCE The interferon-stimulated Ifi27l2a gene is expressed differentially within the central nervous system upon interferon stimulation or viral infection. Prior studies in cell culture suggested an antiviral role for Ifi27l2a during infection by West Nile virus (WNV). To characterize its antiviral activity in vivo, we generated mice with a targeted gene deletion of Ifi27l2a. Based on extensive virological analyses, we determined that Ifi27l2a protects mice from WNV-induced mortality by contributing to the control of infection of the hindbrain and spinal cord, possibly by regulating cell death of neurons. This antiviral activity was validated in granule cell neurons derived from the cerebellum and in macrophages but was not observed in other cell types. Collectively, these data suggest that Ifi27l2a contributes to innate immune restriction of WNV in a cell-type- and tissue-specific manner.
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Affiliation(s)
- Tiffany M Lucas
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Justin M Richner
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA The Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, Missouri, USA
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26
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Hounkpe BW, Fiusa MML, Colella MP, da Costa LNG, Benatti RDO, Saad STO, Costa FF, dos Santos MNN, De Paula EV. Role of innate immunity-triggered pathways in the pathogenesis of Sickle Cell Disease: a meta-analysis of gene expression studies. Sci Rep 2015; 5:17822. [PMID: 26648000 PMCID: PMC4673434 DOI: 10.1038/srep17822] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/06/2015] [Indexed: 12/19/2022] Open
Abstract
Despite the detailed characterization of the inflammatory and endothelial changes observed in Sickle Cell Disease (SCD), the hierarchical relationship between elements involved in the pathogenesis of this complex disease is yet to be described. Meta-analyses of gene expression studies from public repositories represent a novel strategy, capable to identify key mediators in complex diseases. We performed several meta-analyses of gene expression studies involving SCD, including studies with patient samples, as well as in-vitro models of the disease. Meta-analyses were performed with the Inmex bioinformatics tool, based on the RankProd package, using raw gene expression data. Functional gene set analysis was performed using more than 60 gene-set libraries. Our results demonstrate that the well-characterized association between innate immunity, hemostasis, angiogenesis and heme metabolism with SCD is also consistently observed at the transcriptomic level, across independent studies. The enrichment of genes and pathways associated with innate immunity and damage repair-associated pathways supports the model of erythroid danger-associated molecular patterns (DAMPs) as key mediators of the pathogenesis of SCD. Our study also generated a novel database of candidate genes, pathways and transcription factors not previously associated with the pathogenesis of SCD that warrant further investigation in models and patients of SCD.
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Affiliation(s)
| | - Maiara Marx Luz Fiusa
- Faculty of Medical Sciences, University of Campinas/Hematology and Hemotherapy Center, Campinas, SP, Brazil
| | - Marina Pereira Colella
- Faculty of Medical Sciences, University of Campinas/Hematology and Hemotherapy Center, Campinas, SP, Brazil
| | | | | | - Sara T Olalla Saad
- Faculty of Medical Sciences, University of Campinas/Hematology and Hemotherapy Center, Campinas, SP, Brazil
| | - Fernando Ferreira Costa
- Faculty of Medical Sciences, University of Campinas/Hematology and Hemotherapy Center, Campinas, SP, Brazil
| | | | - Erich Vinicius De Paula
- Faculty of Medical Sciences, University of Campinas/Hematology and Hemotherapy Center, Campinas, SP, Brazil
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RECEPTORES NUCLEARES: DEL NÚCLEO AL CITOPLASMA. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2015. [DOI: 10.1016/j.recqb.2015.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Wei X, Gao H, Zou J, Liu X, Chen D, Liao J, Xu Y, Ma L, Tang B, Zhang Z, Cai X, Jin K, Xia Y, Wang Q. Contra-directional Coupling of Nur77 and Nurr1 in Neurodegeneration: A Novel Mechanism for Memantine-Induced Anti-inflammation and Anti-mitochondrial Impairment. Mol Neurobiol 2015; 53:5876-5892. [PMID: 26497037 DOI: 10.1007/s12035-015-9477-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/06/2015] [Indexed: 01/05/2023]
Abstract
Recent evidence suggests that nerve growth factor IB (Nur77) and nuclear receptor related1 (Nurr1) are differentially involved in dopaminergic neurodegeneration. Since memantine has shown clinically relevant efficacy in Parkinson's disease (PD) and displayed a potent protective effect on dopaminergic neurons in experimental PD models, we asked if it exerts its neuroprotection by regulating Nur77 and Nurr1 signaling. We adopted a well-established in vitro PD model, 6-hydroxydopamine (OHDA)-lesioned PC12 cells, to test our hypothesis. Different concentrations of memantine were incubated with 6-OHDA-lesioned PC12 cells, and Nur77/Nurr1 and their related signaling molecules were examined by Western blot and immunocytochemistry. Nur77-deficient PC12 cells were used to verify the influences of Nur77 on neurodegeneration and memantine-mediated neuroprotection. We found that memantine reversed Nur77 upregulation and restored Nurr1 downregulation in 6-OHDA-lesioned PC12 cells. 6-OHDA incubation caused Nur77 translocation from the nucleus to cytosol and induced co-localization of Cyt c/HSP60/Nur77 in the cytosol. Memantine strongly reduced the sub-cellular translocations of Nur77/Cyt c/HSP60 under 6-OHDA-induced oxidative condition. Knockdown of Nur77 enhanced the viability of PC12 cells exposed to 6-OHDA, while memantine-induced neuroprotection was much less in the cells with Nur77 knockdown than in those without it. We conclude that Nur77 plays a crucial role in modulating mitochondrial impairment and contributes to neurodegeneration under the experimental PD condition. Memantine effectively suppresses such Nur77-mediated neurodegeneration and promotes survival signaling through post-translational modification of Nurr1. Nur77 and Nurr1 present a contra-directionally coupling interaction in memantine-mediated neuroprotection.
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Affiliation(s)
- Xiaobo Wei
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Tianhe Road 600, Guangzhou, Guangdong, 510630, China
| | - Huimin Gao
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Tianhe Road 600, Guangzhou, Guangdong, 510630, China
| | - Jing Zou
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Tianhe Road 600, Guangzhou, Guangdong, 510630, China
| | - Xu Liu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Tianhe Road 600, Guangzhou, Guangdong, 510630, China
| | - Dan Chen
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Tianhe Road 600, Guangzhou, Guangdong, 510630, China
| | - Jinchi Liao
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Tianhe Road 600, Guangzhou, Guangdong, 510630, China
| | - Yunqi Xu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Tianhe Road 600, Guangzhou, Guangdong, 510630, China
| | - Long Ma
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, 410078, China
| | - Beisha Tang
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, 410078, China
| | - Zhuohua Zhang
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, 410078, China
| | - Xiang Cai
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, 250# Changgang East Road, Guangzhou, 510260, China
| | - Kunling Jin
- Department of Pharmacology and Neuroscience, Institute for Aging and Alzheimer's Disease Research, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Ying Xia
- Department of Neurosurgery, The University of Texas Medical School at Houston, 6431 Fannin St. MSE R444, Houston, TX, 77030, USA.
| | - Qing Wang
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Tianhe Road 600, Guangzhou, Guangdong, 510630, China.
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HE KUN, DAI ZHUOYA, LI PEIZHI, ZHU XIWEN, GONG JIANPING. Association between liver X receptor-α and neuron-derived orphan nuclear receptor-1 in Kupffer cells of C57BL/6 mice during inflammation. Mol Med Rep 2015; 12:6098-104. [DOI: 10.3892/mmr.2015.4155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 06/15/2015] [Indexed: 11/05/2022] Open
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Nur77 deficiency leads to systemic inflammation in elderly mice. JOURNAL OF INFLAMMATION-LONDON 2015; 12:40. [PMID: 26113803 PMCID: PMC4480882 DOI: 10.1186/s12950-015-0085-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 06/18/2015] [Indexed: 01/18/2023]
Abstract
Background Nur77, an orphan member of the nuclear receptor superfamily, has been implicated in the regulation of inflammation. However, the in vivo function of Nur77 remains largely unexplored. In the current study, we investigated the role of Nur77 in inflammation and immunity in mice. Findings We found that elderly 8-month-old Nur77-deficient mice (Nur77−/−) developed systemic inflammation. Compared to wild-type (WT) mice (Nur77+/+), Nur77−/− mice showed splenomegaly, severe infiltration of inflammatory cells in several organs including liver, lung, spleen and kidney, increased hyperplasia of fibrous tissue in the lung and enlargement of kidney glomeruli. Additionally, Nur77−/− mice had increased production of pro-inflammatory cytokines and immunoglobulin, and elicited pro-inflammatory M1-like polarization in macrophages as revealed by increased expression of CXCL11 and INDO, and decreased expression of MRC1. Conclusions These in vivo observations provide evidence for a pivotal role for Nur77 in the regulation of systemic inflammation and emphasize the pathogenic significance of Nur77 in vivo. Electronic supplementary material The online version of this article (doi:10.1186/s12950-015-0085-0) contains supplementary material, which is available to authorized users.
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Tantawy MA, Hatesuer B, Wilk E, Dengler L, Kasnitz N, Weiß S, Schughart K. The interferon-induced gene Ifi27l2a is active in lung macrophages and lymphocytes after influenza A infection but deletion of Ifi27l2a in mice does not increase susceptibility to infection. PLoS One 2014; 9:e106392. [PMID: 25184786 PMCID: PMC4153650 DOI: 10.1371/journal.pone.0106392] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 08/06/2014] [Indexed: 12/20/2022] Open
Abstract
Interferons represent one of the first and essential host defense mechanisms after infection, and the activation of the IFN-pathway results in the transcriptional activation of hundreds of interferon-stimulated genes. The alpha-inducible protein 27 like 2A (Ifi27l2a) gene (human synonym: ISG12) is strongly up-regulated in the lung after influenza A infection in mice and has been shown in gene expression studies to be highly correlated to other activated genes. Therefore, we investigated the role of Ifi27l2a for the host defense to influenza A infections in more detail. RT-PCR analyses in non-infected mice demonstrated that Ifi27l2a was expressed in several tissues, including the lung. Detailed analyses of reporter gene expression in lungs from Ifi27l2a-LacZ mice revealed that Ifi27l2a was expressed in macrophages and lymphocytes but not in alveolar cells or bronchiolar epithelium cells. The number of macrophages and lymphocyte strongly increased in the lung after infection, but no significant increase in expression levels of the LacZ reporter gene was found within individual immune cells. Also, no reporter gene expression was found in bronchiolar epithelial cells, alveolar cells or infiltrating neutrophils after infection. Thus, up-regulation of Ifi27l2a in infected lungs is mainly due to the infiltration of macrophages and lymphocytes. Most surprisingly, deletion of Ifi27l2a in mouse knock-out lines did not result in increased susceptibility to infections with H1N1 or H7N7 influenza A virus compared to wild type C57BL/6N mice, suggesting a less important role of the gene for the host response to influenza infections than for bacterial infections.
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Affiliation(s)
- Mohamed A. Tantawy
- Department of Infection Genetics, Helmholtz Centre for Infection Research and University of Veterinary Medicine Hannover, Germany
| | - Bastian Hatesuer
- Department of Infection Genetics, Helmholtz Centre for Infection Research and University of Veterinary Medicine Hannover, Germany
| | - Esther Wilk
- Department of Infection Genetics, Helmholtz Centre for Infection Research and University of Veterinary Medicine Hannover, Germany
| | - Leonie Dengler
- Department of Infection Genetics, Helmholtz Centre for Infection Research and University of Veterinary Medicine Hannover, Germany
| | - Nadine Kasnitz
- Department of Molecular Immunology, Helmholtz Centre for Infection Research, Hannover, Germany
| | - Siegfried Weiß
- Department of Molecular Immunology, Helmholtz Centre for Infection Research, Hannover, Germany
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research and University of Veterinary Medicine Hannover, Germany
- University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- * E-mail:
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NR4A nuclear receptors are orphans but not lonesome. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:2543-2555. [PMID: 24975497 DOI: 10.1016/j.bbamcr.2014.06.010] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/13/2014] [Accepted: 06/17/2014] [Indexed: 01/23/2023]
Abstract
The NR4A subfamily of nuclear receptors consists of three mammalian members: Nur77, Nurr1, and NOR-1. The NR4A receptors are involved in essential physiological processes such as adaptive and innate immune cell differentiation, metabolism and brain function. They act as transcription factors that directly modulate gene expression, but can also form trans-repressive complexes with other transcription factors. In contrast to steroid hormone nuclear receptors such as the estrogen receptor or the glucocorticoid receptor, no ligands have been described for the NR4A receptors. This lack of known ligands might be explained by the structure of the ligand-binding domain of NR4A receptors, which shows an active conformation and a ligand-binding pocket that is filled with bulky amino acid side-chains. Other mechanisms, such as transcriptional control, post-translational modifications and protein-protein interactions therefore seem to be more important in regulating the activity of the NR4A receptors. For Nur77, over 80 interacting proteins (the interactome) have been identified so far, and roughly half of these interactions has been studied in more detail. Although the NR4As show some overlap in interacting proteins, less information is available on the interactome of Nurr1 and NOR-1. Therefore, the present review will describe the current knowledge on the interactomes of all three NR4A nuclear receptors with emphasis on Nur77.
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Makovitzki-Avraham E, Daniel-Carmi V, Alteber Z, Farago M, Tzehoval E, Eisenbach L. The human ISG12a gene is a novel caspase dependent and p53 independent pro-apoptotic gene, that is overexpressed in breast cancer. CELL BIOLOGY INTERNATIONAL REPORTS 2013. [DOI: 10.1002/cbi3.10009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | - Vered Daniel-Carmi
- Department of Immunology; The Weizmann Institute of Science; Rehovot 76100 Israel
| | - Zoya Alteber
- Department of Immunology; The Weizmann Institute of Science; Rehovot 76100 Israel
| | - Marganit Farago
- Department of Immunology; The Weizmann Institute of Science; Rehovot 76100 Israel
| | - Esther Tzehoval
- Department of Immunology; The Weizmann Institute of Science; Rehovot 76100 Israel
| | - Lea Eisenbach
- Department of Immunology; The Weizmann Institute of Science; Rehovot 76100 Israel
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Uhrin P, Perkmann T, Binder B, Schabbauer G. ISG12 is a critical modulator of innate immune responses in murine models of sepsis. Immunobiology 2013; 218:1207-16. [PMID: 23747037 PMCID: PMC3748340 DOI: 10.1016/j.imbio.2013.04.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 01/04/2023]
Abstract
Sepsis is still a major burden for our society with high incidence of morbidity and mortality each year. Molecular mechanisms underlying the systemic inflammatory response syndrome (SIRS) associated with sepsis are still ill defined and most therapies developed to target the acute inflammatory component of the disease are insufficient. Recently the role of nuclear receptors (NRs) became a major topic of interest in transcriptional regulation of inflammatory processes. Nuclear receptors, such as the peroxisome proliferators-activated receptors (PPARs), have been demonstrated to exert anti-inflammatory properties by interfering with the NFκB pathway. We identified the nuclear envelope protein, interferon stimulated gene 12 (ISG12), which directly interacts with NRs. ISG12 is a co-factor stimulating nuclear export of NRs, thereby reducing the anti-inflammatory potential of NRs such as NR4A1. To examine the role of ISG12 in acute inflammatory processes we used recently generated ISG12 deficient mice. We can clearly demonstrate that lack of ISG12 prolongs survival in experimental sepsis and endotoxemia. Furthermore we can show that several acute inflammatory parameters, such as systemic IL6 cytokine levels, are downregulated in septic ISG12-/- animals. Consistently, similar results were obtained in in vitro experiments in peritoneal macrophages derived from ISG12 deficient mice. In contrast, mice deficient for the nuclear receptor NR4A1 exhibited an exacerbated innate immune response, and showed a significantly higher mortality after lethal endotoxemic challenge. This dramatic phenotype could be restored in ISG12/NR4A1 double deficient mice. We conclude from our data in vitro and in vivo that ISG12 is a novel modulator of innate immune responses regulating anti-inflammatory nuclear receptors such as NR4A1.
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MESH Headings
- Animals
- Cell Line
- Disease Models, Animal
- Gene Expression Regulation/genetics
- Humans
- Immunity, Innate
- Immunomodulation
- Interleukin-6/genetics
- Interleukin-6/metabolism
- Lipopolysaccharides/immunology
- Macrophages, Peritoneal/immunology
- Mice
- Mice, Knockout
- Nuclear Receptor Subfamily 4, Group A, Member 1/genetics
- Nuclear Receptor Subfamily 4, Group A, Member 1/immunology
- Nuclear Receptor Subfamily 4, Group A, Member 1/metabolism
- Proteins/genetics
- Proteins/immunology
- Proteins/metabolism
- Sepsis/immunology
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Affiliation(s)
| | | | | | - G. Schabbauer
- Institute for Physiology, Center for Physiology and Pharmacology, Medical University of Vienna, Austria
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Circulation Research
Thematic Synopsis. Circ Res 2013. [DOI: 10.1161/circresaha.113.300982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Buga AM, Scholz CJ, Kumar S, Herndon JG, Alexandru D, Cojocaru GR, Dandekar T, Popa-Wagner A. Identification of new therapeutic targets by genome-wide analysis of gene expression in the ipsilateral cortex of aged rats after stroke. PLoS One 2012; 7:e50985. [PMID: 23251410 PMCID: PMC3521001 DOI: 10.1371/journal.pone.0050985] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 10/31/2012] [Indexed: 12/17/2022] Open
Abstract
Background Because most human stroke victims are elderly, studies of experimental stroke in the aged rather than the young rat model may be optimal for identifying clinically relevant cellular responses, as well for pinpointing beneficial interventions. Methodology/Principal Findings We employed the Affymetrix platform to analyze the whole-gene transcriptome following temporary ligation of the middle cerebral artery in aged and young rats. The correspondence, heat map, and dendrogram analyses independently suggest a differential, age-group-specific behaviour of major gene clusters after stroke. Overall, the pattern of gene expression strongly suggests that the response of the aged rat brain is qualitatively rather than quantitatively different from the young, i.e. the total number of regulated genes is comparable in the two age groups, but the aged rats had great difficulty in mounting a timely response to stroke. Our study indicates that four genes related to neuropathic syndrome, stress, anxiety disorders and depression (Acvr1c, Cort, Htr2b and Pnoc) may have impaired response to stroke in aged rats. New therapeutic options in aged rats may also include Calcrl, Cyp11b1, Prcp, Cebpa, Cfd, Gpnmb, Fcgr2b, Fcgr3a, Tnfrsf26, Adam 17 and Mmp14. An unexpected target is the enzyme 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 in aged rats, a key enzyme in the cholesterol synthesis pathway. Post-stroke axonal growth was compromised in both age groups. Conclusion/Significance We suggest that a multi-stage, multimodal treatment in aged animals may be more likely to produce positive results. Such a therapeutic approach should be focused on tissue restoration but should also address other aspects of patient post-stroke therapy such as neuropathic syndrome, stress, anxiety disorders, depression, neurotransmission and blood pressure.
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Affiliation(s)
- Ana-Maria Buga
- Department of Psychiatry, University of Medicine, Rostock, Germany
- Department of Functional Sciences, University of Medicine, Craiova, Romania
| | - Claus Jürgen Scholz
- Interdisciplinary Center for Clinical Research, Lab for Microarray Applications, University of Würzburg, Würzburg, Germany
| | - Senthil Kumar
- Department of Biomedical Sciences, College of Veterinary Medicine, Ames, Iowa, United States of America
| | - James G. Herndon
- Yerkes National Primate Research Center of Emory University, Atlanta, Georgia, United States of America
| | - Dragos Alexandru
- Department of Functional Sciences, University of Medicine, Craiova, Romania
| | | | - Thomas Dandekar
- Department of Bioinformatics, Biocenter Am Hubland, Würzburg, Germany
| | - Aurel Popa-Wagner
- Department of Psychiatry, University of Medicine, Rostock, Germany
- * E-mail:
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