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Yang Y, Zhang H, Xiao X, Guo M. Identification of EPSTI1 as a new potential biomarker for SLE based on GEO database. Clin Rheumatol 2024; 43:1531-1540. [PMID: 38507132 DOI: 10.1007/s10067-024-06881-z] [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: 09/11/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 03/22/2024]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with highly heterogeneous. The aim of this study is to find the key genes in peripheral blood mononuclear cells (PBMCs) of SLE patients and to provide a new direction for the diagnosis and treatment of lupus. METHODS GSE121239, GSE50772, GSE81622, and GSE144390 mRNA expression profiles were obtained from the website of Gene Expression Omnibus (GEO), and differential expressed genes (DEGs) analysis was performed by R. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to elucidate signaling pathways for the DEGs. Real-time qPCR (RT-qPCR) was used to verify the key gene EPSTI1 in PBMCs of SLE patients. Finally, the correlation analysis and ROC curve analysis of EPSTI1 for SLE were performed. RESULTS A total of 12 upregulated DEGs were identified, including MMP8, MX1, IFI44, EPSTI1, OAS1, OAS3, HERC5, IFIT1, RSAD2, USP18, IFI44L, and IFI27. GO and KEGG pathway enrichment analysis showed that those DEGs were mainly concentrated in the response to virus and IFN signaling pathways. Real-time qPCR (RT-qPCR) revealed that EPSTI1 was increased in PBMCs of SLE. EPSTI1 was positively correlated with SLEDAI score in SLE patients. Besides, EPSTI1 was positively correlated with T cell activation- or differentiation-associated genes (BCL6 and RORC). Furthermore, ROC analyses proved EPSTI1 may have diagnostic value for SLE. CONCLUSION Together, EPSTI1 was found to be a potential biomarker for SLE, closely related to T cell immune imbalance. Key Points • EPSTI1 expression was significantly increased in PBMCs of SLE patients. • EPSTI1 was positively correlated with disease activity and T cell activation- or differentiation-associated genes in SLE patients. • EPSTI1 might have a good diagnostic value for SLE.
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Affiliation(s)
- Yiying Yang
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, Hunan, China
- Sepsis Translational Medicine Key Lab of Hunan Province, Changsha, Hunan, China
- Postdoctoral Research Station of Basic Medicine, School of Basic Medicine Science, Central South University, Changsha, Hunan, China
| | - Huali Zhang
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, Hunan, China
- Sepsis Translational Medicine Key Lab of Hunan Province, Changsha, Hunan, China
| | - Xiaoyu Xiao
- Department of Nutrition, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China.
| | - Muyao Guo
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China.
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China.
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2
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Cai T, Xu J, Fang Y, Wu Y, Qin Q, Zhang JA. Shared biomarkers of multi-tissue origin for primary Sjogren's syndrome and their importance in immune microenvironment alterations. Immunobiology 2023; 228:152726. [PMID: 37591179 DOI: 10.1016/j.imbio.2023.152726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/18/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023]
Abstract
With the recent advancement in omics and molecular techniques, a wealth of new molecular biomarkers have become available for the diagnosis and classification of primary Sjögren's syndrome (pSS) patients. However, whether these biomarkers are universal is of great interest to us. In this study, we used various methods to obtain shared biomarkers derived from multiple tissue in pSS patients and to explore their relationship with immune microenvironment alterations. First we identified differentially expressed genes (DEGs) between pSS and healthy controls utilizing nine mRNA microarray datasets obtained from the Gene Expression Omnibus (GEO). Then, shared biomarkers were filtered out using robust rank aggregation (RRA), data integration analysis, weighted gene co-expression network analysis (WGCNA), and least absolute selection and shrinkage operator (LASSO) regression; their roles in pSS and association with changes in the immune microenvironment were also analyzed. In addition, these biomarkers were further confirmed with both the testing set and immunohistochemistry (IHC). As a result, ten biomarkers, i.e., EPSTI1, IFI44, IFIT1, IFIT2, IFIT3, MX1, OAS1, PARP9, SAMD9L and TRIM22, were identified. Receiver operating characteristic (ROC) curves showed that the ten genes could discriminate pSS from controls. Gene set enrichment analysis (GSEA) showed that the enrichment of immune-related gene sets was significant in pSS patients with high expression of either biomarker. Furthermore, the association between some immunocytes and these biomarkers was identified. In the two distinct molecular patterns of pSS patients based on the expressions of these biomarkers, the proportions of immunocytes were significantly different. Our study identified shared biomarkers of multi-tissue origin and revealed their relationship with altered immune microenvironment in pSS patients. These markers not only have diagnostic implications but also provide potential immunotherapeutic targets for the clinical treatment of pSS patients.
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Affiliation(s)
- Tiantian Cai
- Graduate School, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China; Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, People's Republic of China
| | - Jianbin Xu
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, People's Republic of China
| | - Yudie Fang
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, People's Republic of China
| | - Yuqing Wu
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, People's Republic of China
| | - Qiu Qin
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, People's Republic of China.
| | - Jin-An Zhang
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, People's Republic of China; Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China.
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Zhou M, Tang Y, Xu W, Hao X, Li Y, Huang S, Xiang D, Wu J. Bacteria-based immunotherapy for cancer: a systematic review of preclinical studies. Front Immunol 2023; 14:1140463. [PMID: 37600773 PMCID: PMC10436994 DOI: 10.3389/fimmu.2023.1140463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/30/2023] [Indexed: 08/22/2023] Open
Abstract
Immunotherapy has been emerging as a powerful strategy for cancer management. Recently, accumulating evidence has demonstrated that bacteria-based immunotherapy including naive bacteria, bacterial components, and bacterial derivatives, can modulate immune response via various cellular and molecular pathways. The key mechanisms of bacterial antitumor immunity include inducing immune cells to kill tumor cells directly or reverse the immunosuppressive microenvironment. Currently, bacterial antigens synthesized as vaccine candidates by bioengineering technology are novel antitumor immunotherapy. Especially the combination therapy of bacterial vaccine with conventional therapies may further achieve enhanced therapeutic benefits against cancers. However, the clinical translation of bacteria-based immunotherapy is limited for biosafety concerns and non-uniform production standards. In this review, we aim to summarize immunotherapy strategies based on advanced bacterial therapeutics and discuss their potential for cancer management, we will also propose approaches for optimizing bacteria-based immunotherapy for facilitating clinical translation.
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Affiliation(s)
- Min Zhou
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, China
- Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Yucheng Tang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, China
- Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Wenjie Xu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, China
- Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Xinyan Hao
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, China
- Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Yongjiang Li
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, China
- Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Si Huang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, China
- Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Daxiong Xiang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, China
- Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Junyong Wu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, China
- Institute of Clinical Pharmacy, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
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Esteban-Cantos A, Rodríguez-Centeno J, Silla JC, Barruz P, Sánchez-Cabo F, Saiz-Medrano G, Nevado J, Mena-Garay B, Jiménez-González M, de Miguel R, Bernardino JI, Montejano R, Cadiñanos J, Marcelo C, Gutiérrez-García L, Martínez-Martín P, Wallet C, Raffi F, Rodés B, Arribas JR. Effect of HIV infection and antiretroviral therapy initiation on genome-wide DNA methylation patterns. EBioMedicine 2023; 88:104434. [PMID: 36640455 PMCID: PMC9842861 DOI: 10.1016/j.ebiom.2022.104434] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/09/2022] [Accepted: 12/22/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Previous epigenome-wide association studies have shown that HIV infection can disrupt the host DNA methylation landscape. However, it remains unclear how antiretroviral therapy (ART) affects the HIV-induced epigenetic modifications. METHODS 184 individuals with HIV from the NEAT001/ANRS143 clinical trial (with pre-ART and post-ART samples [96 weeks of follow-up]) and 44 age-and-sex matched individuals without HIV were included. We compared genome-wide DNA methylation profiles in whole blood between groups adjusting for age, sex, batch effects, and DNA methylation-based estimates of leucocyte composition. FINDINGS We identified 430 differentially methylated positions (DMPs) between HIV+ pre-ART individuals and HIV-uninfected controls. In participants with HIV, ART initiation modified the DNA methylation levels at 845 CpG positions and restored 49.3% of the changes found between HIV+ pre-ART and HIV-uninfected individuals. We only found 15 DMPs when comparing DNA methylation profiles between HIV+ post-ART individuals and participants without HIV. The Gene Ontology enrichment analysis of DMPs associated with untreated HIV infection revealed an enrichment in biological processes regulating the immune system and antiviral responses. In participants with untreated HIV infection, DNA methylation levels at top HIV-related DMPs were associated with CD4/CD8 ratios and viral loads. Changes in DNA methylation levels after ART initiation were weakly correlated with changes in CD4+ cell counts and the CD4/CD8 ratio. INTERPRETATION Control of HIV viraemia after 96 weeks of ART initiation partly restores the host DNA methylation changes that occurred before antiretroviral treatment of HIV infection. FUNDING NEAT-ID Foundation and Instituto de Salud Carlos III, co-funded by European Union.
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Affiliation(s)
- Andrés Esteban-Cantos
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Javier Rodríguez-Centeno
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Juan C Silla
- Bioinformatics Unit, Spanish National Centre for Cardiovascular Research (CNIC), Madrid, Spain
| | - Pilar Barruz
- Genomics Laboratory, Institute of Medical and Molecular Genetics, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Spanish National Centre for Cardiovascular Research (CNIC), Madrid, Spain
| | - Gabriel Saiz-Medrano
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Julián Nevado
- Genomics Laboratory, Institute of Medical and Molecular Genetics, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Beatriz Mena-Garay
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - María Jiménez-González
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Rosa de Miguel
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Jose I Bernardino
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Rocío Montejano
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Julen Cadiñanos
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Cristina Marcelo
- Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Lucía Gutiérrez-García
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Patricia Martínez-Martín
- Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Cédrick Wallet
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, CHU de Bordeaux, Bordeaux, France
| | - François Raffi
- Centre Hospitalier Universitaire de Nantes and CIC 1413 INSERM, Nantes, France
| | - Berta Rodés
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.
| | - José R Arribas
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.
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5
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Roberson ED, Carns M, Cao L, Aren K, Goldberg IA, Morales-Heil DJ, Korman BD, Atkinson JP, Varga J. Alterations of the Primary Cilia Gene SPAG17 and SOX9 Locus Noncoding RNAs Identified by RNA-Sequencing Analysis in Patients With Systemic Sclerosis. Arthritis Rheumatol 2023; 75:108-119. [PMID: 35762854 PMCID: PMC10445493 DOI: 10.1002/art.42281] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/12/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Systemic sclerosis (SSc) is characterized by immune activation, vasculopathy, and unresolving fibrosis in the skin, lungs, and other organs. We performed RNA-sequencing analysis on skin biopsy samples and peripheral blood mononuclear cells (PBMCs) from SSc patients and unaffected controls to better understand the pathogenesis of SSc. METHODS We analyzed these data 1) to test for case/control differences and 2) to identify genes whose expression levels correlate with SSc severity as measured by local skin score, modified Rodnan skin thickness score (MRSS), forced vital capacity (FVC), or diffusing capacity for carbon monoxide (DLco). RESULTS We found that PBMCs from SSc patients showed a strong type I interferon signature. This signal was found to be replicated in the skin, with additional signals for increased extracellular matrix (ECM) genes, classical complement pathway activation, and the presence of B cells. Notably, we observed a marked decrease in the expression of SPAG17, a cilia component, in SSc skin. We identified genes that correlated with the MRSS, DLco, and FVC in SSc PBMCs and skin using weighted gene coexpression network analysis. These genes were largely distinct from the case/control differentially expressed genes. In PBMCs, type I interferon signatures negatively correlated with the DLco. In SSc skin, ECM gene expression positively correlated with the MRSS. Network analysis of SSc skin genes that correlated with clinical features identified the noncoding RNAs SOX9-AS1 and ROCR, both near the SOX9 locus, as highly connected, "hub-like" genes in the network. CONCLUSION These results identify noncoding RNAs and SPAG17 as novel factors potentially implicated in the pathogenesis of SSc.
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Affiliation(s)
- Elisha D.O. Roberson
- Department of Medicine, Division of Rheumatology, Washington University, St. Louis, MO, USA
- Department of Genetics, Washington University, St. Louis, MO, USA
| | - Mary Carns
- Feinberg School of Medicine, Scleroderma Program, Northwestern University, Chicago, IL, USA
| | - Li Cao
- Department of Medicine, Division of Rheumatology, Washington University, St. Louis, MO, USA
| | - Kathleen Aren
- Feinberg School of Medicine, Scleroderma Program, Northwestern University, Chicago, IL, USA
| | - Isaac A. Goldberg
- Feinberg School of Medicine, Scleroderma Program, Northwestern University, Chicago, IL, USA
| | - David J. Morales-Heil
- Department of Medicine, Division of Rheumatology, Washington University, St. Louis, MO, USA
| | - Benjamin D. Korman
- Feinberg School of Medicine, Scleroderma Program, Northwestern University, Chicago, IL, USA
| | - John P. Atkinson
- Department of Medicine, Division of Rheumatology, Washington University, St. Louis, MO, USA
| | - John Varga
- Feinberg School of Medicine, Scleroderma Program, Northwestern University, Chicago, IL, USA
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, MI, USA
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Bei YR, Zhang SC, Song Y, Tang ML, Zhang KL, Jiang M, He RC, Wu SG, Liu XH, Wu LM, Dai XY, Hu YW. EPSTI1 promotes monocyte adhesion to endothelial cells in vitro via upregulating VCAM-1 and ICAM-1 expression. Acta Pharmacol Sin 2023; 44:71-80. [PMID: 35778487 DOI: 10.1038/s41401-022-00923-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/21/2022] [Indexed: 01/18/2023] Open
Abstract
Atherosclerosis is a chronic inflammatory disease of arterial wall, and circulating monocyte adhesion to endothelial cells is a crucial step in the pathogenesis of atherosclerosis. Epithelial-stromal interaction 1 (EPSTI1) is a novel gene, which is dramatically induced by epithelial-stromal interaction in human breast cancer. EPSTI1 expression is not only restricted to the breast but also in other normal tissues. In this study we investigated the role of EPSTI1 in monocyte-endothelial cell adhesion and its expression pattern in atherosclerotic plaques. We showed that EPSTI1 was dramatically upregulated in human and mouse atherosclerotic plaques when compared with normal arteries. In addition, the expression of EPSTI1 in endothelial cells of human and mouse atherosclerotic plaques is significantly higher than that of the normal arteries. Furthermore, we demonstrated that EPSTI1 promoted human monocytic THP-1 cell adhesion to human umbilical vein endothelial cells (HUVECs) via upregulating VCAM-1 and ICAM-1 expression in HUVECs. Treatment with LPS (100, 500, 1000 ng/mL) induced EPSTI1 expression in HUVECs at both mRNA and protein levels in a dose- and time-dependent manner. Knockdown of EPSTI1 significantly inhibited LPS-induced monocyte-endothelial cell adhesion via downregulation of VCAM-1 and ICAM-1. Moreover, we revealed that LPS induced EPSTI1 expression through p65 nuclear translocation. Thus, we conclude that EPSTI1 promotes THP-1 cell adhesion to endothelial cells by upregulating VCAM-1 and ICAM-1 expression, implying its potential role in the development of atherosclerosis.
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Affiliation(s)
- Yan-Rou Bei
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Shun-Chi Zhang
- Department of Clinical Laboratory, Guangzhou Twelfth People's Hospital, Guangzhou Medical University, Guangzhou, 510620, China
| | - Yu Song
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangzhou, 510620, China
| | - Mao-Lin Tang
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangzhou, 510620, China
| | - Ke-Lan Zhang
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangzhou, 510620, China
| | - Min Jiang
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangzhou, 510620, China
| | - Run-Chao He
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangzhou, 510620, China
| | - Shao-Guo Wu
- Department of Clinical Laboratory, Guangzhou Twelfth People's Hospital, Guangzhou Medical University, Guangzhou, 510620, China
| | - Xue-Hui Liu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Clinical Laboratory, Guangzhou Twelfth People's Hospital, Guangzhou Medical University, Guangzhou, 510620, China
| | - Li-Mei Wu
- Department of Clinical Laboratory, Guangzhou Twelfth People's Hospital, Guangzhou Medical University, Guangzhou, 510620, China
| | - Xiao-Yan Dai
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
| | - Yan-Wei Hu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangzhou, 510620, China.
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Systematic Analysis of Molecular Subtypes Based on the Expression Profile of Immune-Related Genes in Pancreatic Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3124122. [PMID: 36567857 PMCID: PMC9780013 DOI: 10.1155/2022/3124122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/07/2022] [Accepted: 09/14/2022] [Indexed: 12/23/2022]
Abstract
Immunotherapy has a good therapeutic effect and provides a new approach for cancer treatment. However, only limited studies have focused on the use of molecular typing to construct an immune characteristic index for gene expression in pancreatic adenocarcinoma (PAAD) and to assess the effectiveness of immunotherapy in patients with PAAD. Clinical follow-up data and gene expression profile of PAAD patients were retrieved from The Cancer Genome Atlas (TCGA) database. Based on 184 immune features, molecular subtypes of pancreatic cancer were found by the "ConsensusClusterPlus" package, and the association between clinical features and immune cell subtype distribution was analysed. In addition, the relationship between the proportion of immune subtypes and the expression of immune checkpoints was analysed. The CIBERSORT algorithm was introduced to evaluate the immune scores of different molecular subtypes. We used the tumor immune dysfunction and exclusion (TIDE) algorithm to assess the potential clinical effect of immunotherapy interventions on single-molecule subtypes. In addition, the oxidative stress index was constructed by linear discriminant analysis DNA (LDA), and weighted correlation network analysis was performed to identify the core module of the index and its characteristic genes. Expression of hub genes was verified by immunohistochemical analysis in an independent PAAD cohort. Pancreatic cancer is divided into three molecular subtypes (IS1, IS2, and IS3), with significant differences in prognosis between multiple cohorts. Expression of immune checkpoint-associated genes was significantly reduced in IS3 and higher in IS1 and IS2, suggesting that the three subgroups have different responsiveness to immunotherapy interventions. The results of the CIBERSORT analysis showed that IS1 exhibited the highest levels of immune infiltration, whereas the results of the TIDE analysis showed that the T-cell dysfunction score of IS1 was higher than that of IS2 and IS3. Furthermore, IS3 was found to be more sensitive to 5-FU and to have a higher immune signature index than IS1 and IS2. Based on WGCNA analysis, 10 potential gene markers were identified, and their expression at the protein level was verified by immunohistochemical analysis. Specific molecular expression patterns in pancreatic cancer can predict the efficacy of immunotherapy and influence the prognosis of patients.
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Dolinski AC, Homola JJ, Jankowski MD, Robinson JD, Owen JC. Host gene expression is associated with viral shedding magnitude in blue-winged teals (Spatula discors) infected with low-path avian influenza virus. Comp Immunol Microbiol Infect Dis 2022; 90-91:101909. [PMID: 36410069 PMCID: PMC10500253 DOI: 10.1016/j.cimid.2022.101909] [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: 08/01/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
Abstract
Intraspecific variation in host infectiousness affects disease transmission dynamics in human, domestic animal, and many wildlife host-pathogen systems including avian influenza virus (AIV); therefore, identifying host factors related to host infectiousness is important for understanding, controlling, and preventing future outbreaks. Toward this goal, we used RNA-seq data collected from low pathogenicity avian influenza virus (LPAIV)-infected blue-winged teal (Spatula discors) to determine the association between host gene expression and intraspecific variation in cloacal viral shedding magnitude, the transmissible fraction of virus. We found that host genes were differentially expressed between LPAIV-infected and uninfected birds early in the infection, host genes were differentially expressed between shed level groups at one-, three-, and five-days post-infection, host gene expression was associated with LPAIV infection patterns over time, and genes of the innate immune system had a positive linear relationship with cloacal viral shedding. This study provides important insights into host gene expression patterns associated with intraspecific LPAIV shedding variation and can serve as a foundation for future studies focused on the identification of host factors that drive or permit the emergence of high viral shedding individuals.
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Affiliation(s)
- Amanda C Dolinski
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Jared J Homola
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Mark D Jankowski
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA; US Environmental Protection Agency, Region 10, Seattle, WA 98101, USA
| | - John D Robinson
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Jennifer C Owen
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA; Michigan State University, Department of Large Animal Clinical Sciences, 736 Wilson Road, East Lansing, MI 48824, USA.
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9
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Wang X, Cheng W, Zeng X, Dou X, Zhou Z, Pei Q. EPSTI1 as an immune biomarker predicts the prognosis of patients with stage III colon cancer. Front Immunol 2022; 13:987394. [PMID: 36330510 PMCID: PMC9623419 DOI: 10.3389/fimmu.2022.987394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Objective The poor prognosis and heterogeneity of stage III colon cancer (CC) suggest the need for more prognostic biomarkers. The tumor microenvironment (TME) plays a crucial role in tumor progression. We aimed to explore novel immune infiltration-associated molecules that serve as potential prognostic and therapeutic targets. Methods TME immune scores were calculated using “TMEscore” algorithm. Differentially expressed genes between the high and low TME immune score groups were identified and further investigated through a protein-protein interaction network and the Molecular Complex Detection algorithm. Cox regression, meta-analysis and immunohistochemistry were applied to identify genes significantly correlated with relapse-free survival (RFS). We estimated immune infiltration using three different algorithms (TIMER 2.0, CIBERSORTx, and TIDE). Single-cell sequencing data were processed by Seurat software. Results Poor RFS was observed in the low TME immune score groups (log-rank P < 0.05). EPSTI1 was demonstrated to be significantly correlated with RFS (P < 0.05) in stage III CC. Meta-analysis comprising 547 patients revealed that EPSTI1 was a protective factor (HR = 0.79, 95% CI, 0.65-0. 96; P < 0.05)). More immune infiltrates were observed in the high EPSTI1 group, especially M1 macrophage and myeloid dendritic cell infiltration (P < 0.05). Conclusion The TME immune score is positively associated with better survival outcomes. EPSTI1 could serve as a novel immune prognostic biomarker for stage III CC.
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Affiliation(s)
- Xitao Wang
- Department of Hepatobiliary Surgery, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Cheng
- Department of Hepatobiliary Surgery, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Xingzhi Zeng
- Department of General Surgery, The First Affiliated Hospital of Shaoyang University, Shaoyang, China
| | - Xiaolin Dou
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhongyi Zhou
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Qian Pei
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Qian Pei,
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10
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Hsa_circ_0000479/Hsa-miR-149-5p/RIG-I, IL-6 Axis: A Potential Novel Pathway to Regulate Immune Response against COVID-19. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:2762582. [PMID: 36081604 PMCID: PMC9448594 DOI: 10.1155/2022/2762582] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 07/12/2022] [Accepted: 08/08/2022] [Indexed: 12/27/2022]
Abstract
Background. COVID-19, the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global pandemic and mortality of people around the world. Some circular RNAs (circRNAs), one of the new types of noncoding RNAs (ncRNAs), act as competing endogenous RNAs (ceRNAs) and compete with mRNAs for shared miRNAs, to regulate gene expression. In the present study, we aimed to evaluate the expression and roles of hsa_circ_0000479/hsa-miR-149-5p/RIG-I, IL-6 in COVID-19 infection. Materials and Methods. After extraction of total RNA from peripheral blood mononuclear cells (PBMC) of 50 patients with symptomatic COVID-19, 50 patients with nonsymptomatic COVID-19, and 50 normal controls, cDNA synthesis was performed. Online in silico tools were applied to evaluate the interaction between the genes in the hsa_circ_0000479/hsa-miR-149-5p/RIG-I, IL-6 axis, and its role in COVID-19-related pathways. Quantification of the expression of these genes and confirmation of their interaction was done using the quantitative real-time PCR (qRT-PCR) technique. Results. The expression levels of hsa_circ_0000479, RIG-I, and IL-6 were increased in COVID-19 patients compared to healthy controls, while hsa-miR-149-5p expression was decreased. Moreover, there was a significant negative correlation between hsa-miR-149-5p and hsa_circ_0000479, RIG-I, IL-6 expressions, and also a positive expression correlation between hsa_circ_0000479 and IL-6, RIG-I. Then, bioinformatics tools revealed the role of hsa_circ_0000479/hsa-miR-149-5p/RIG-I, IL-6 axis in PI3K-AKT and STAT3 signaling pathways. Conclusion. Upregulation of hsa_circ_0000479, RIG-I, and IL-6, and downregulation of hsa-miR-149-5p, along with correlation studies, indicate that hsa_circ_0000479/hsa-miR-149-5p/RIG-I, IL-6 axis could play a role in regulating the immune response against SARS-CoV-2. However, more studies are needed in this area.
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11
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Dong Z, Yan Q, Cao W, Liu Z, Wang X. Identification of key molecules in COVID-19 patients significantly correlated with clinical outcomes by analyzing transcriptomic data. Front Immunol 2022; 13:930866. [PMID: 36072597 PMCID: PMC9441550 DOI: 10.3389/fimmu.2022.930866] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/03/2022] [Indexed: 12/15/2022] Open
Abstract
Background Although several key molecules have been identified to modulate SARS-CoV-2 invasion of human host cells, the molecules correlated with outcomes in COVID-19 caused by SARS-CoV-2 infection remain insufficiently explored. Methods This study analyzed three RNA-Seq gene expression profiling datasets for COVID-19 and identified differentially expressed genes (DEGs) between COVID-19 patients and normal people, commonly in the three datasets. Furthermore, this study explored the correlation between the expression of these genes and clinical features in COVID-19 patients. Results This analysis identified 13 genes significantly upregulated in COVID-19 patients’ leukocyte and SARS-CoV-2-infected nasopharyngeal tissue compared to normal tissue. These genes included OAS1, OAS2, OAS3, OASL, HERC6, SERPING1, IFI6, IFI44, IFI44L, CMPK2, RSAD2, EPSTI1, and CXCL10, all of which are involved in antiviral immune regulation. We found that these genes’ downregulation was associated with worse clinical outcomes in COVID-19 patients, such as intensive care unit (ICU) admission, mechanical ventilatory support (MVS) requirement, elevated D-dimer levels, and increased viral loads. Furthermore, this analysis identified two COVID-19 clusters based on the expression profiles of the 13 genes, termed COV-C1 and COV-C2. Compared with COV-C1, COV-C2 more highly expressed the 13 genes, had stronger antiviral immune responses, were younger, and displayed more favorable clinical outcomes. Conclusions A strong antiviral immune response is essential in reducing severity of COVID-19.
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Affiliation(s)
- Zehua Dong
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, China
| | - Qiyu Yan
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, China
| | - Wenxiu Cao
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, China
| | - Zhixian Liu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Zhixian Liu, ; Xiaosheng Wang,
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, China
- *Correspondence: Zhixian Liu, ; Xiaosheng Wang,
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12
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Li X, Abdel-Moneim AME, Mesalam NM, Yang B. Effects of Lysophosphatidylcholine on Jejuna Morphology and Its Potential Mechanism. Front Vet Sci 2022; 9:911496. [PMID: 35795789 PMCID: PMC9252431 DOI: 10.3389/fvets.2022.911496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/10/2022] [Indexed: 01/13/2023] Open
Abstract
Lysophosphatidylcholine (LPC) plays a vital role in promoting jejuna morphology in broilers. However, the potential mechanism behind LPC improving the chicken jejuna morphology is unclear. Therefore, the present study was designed to reveal the important genes associated with LPC regulation in birds' jejuna. Thus, GSE94622, the gene expression microarray, was obtained from Gene Expression Omnibus (GEO). GSE94622 consists of 15 broiler jejuna samples from two LPC-treated (LPC500 and LPC1000) and the control groups. Totally 98 to 217 DEGs were identified by comparing LPC500 vs. control, LPC1000 vs. control, and LPC1000 vs. LPC500. Gene ontology (GO) analysis suggested that those DEGs were mainly involved in the one-carbon metabolic process, carbon dioxide transport, endodermal cell differentiation, the positive regulation of dipeptide transmembrane transport, cellular pH reduction, and synaptic transmission. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated the DEGs were enriched in NOD-like receptor (NLR), RIG-I-like receptor (RILR), Toll-like receptor (TLR), and necroptosis signaling pathway. Moreover, many genes, such as RSAD2, OASL, EPSTI1, CMPK2, IFIH1, IFIT5, USP18, MX1, and STAT1 might be involved in promoting the jejuna morphology of broilers. In conclusion, this study enhances our understanding of LPC regulation in jejuna morphology.
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Affiliation(s)
- Xiaofeng Li
- College of Animal Science, Anhui Science and Technology University, Huainan, China
| | | | - Noura M. Mesalam
- Department of Biological Applications, Nuclear Research Center, Egyptian Atomic Energy Authority, Abu-Zaabal, Egypt
| | - Bing Yang
- College of Animal Science, Anhui Science and Technology University, Huainan, China
- *Correspondence: Bing Yang
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13
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Li Z, Mei Z, Ding S, Chen L, Li H, Feng K, Huang T, Cai YD. Identifying Methylation Signatures and Rules for COVID-19 With Machine Learning Methods. Front Mol Biosci 2022; 9:908080. [PMID: 35620480 PMCID: PMC9127386 DOI: 10.3389/fmolb.2022.908080] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
The occurrence of coronavirus disease 2019 (COVID-19) has become a serious challenge to global public health. Definitive and effective treatments for COVID-19 are still lacking, and targeted antiviral drugs are not available. In addition, viruses can regulate host innate immunity and antiviral processes through the epigenome to promote viral self-replication and disease progression. In this study, we first analyzed the methylation dataset of COVID-19 using the Monte Carlo feature selection method to obtain a feature list. This feature list was subjected to the incremental feature selection method combined with a decision tree algorithm to extract key biomarkers, build effective classification models and classification rules that can remarkably distinguish patients with or without COVID-19. EPSTI1, NACAP1, SHROOM3, C19ORF35, and MX1 as the essential features play important roles in the infection and immune response to novel coronavirus. The six significant rules extracted from the optimal classifier quantitatively explained the expression pattern of COVID-19. Therefore, these findings validated that our method can distinguish COVID-19 at the methylation level and provide guidance for the diagnosis and treatment of COVID-19.
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Affiliation(s)
- Zhandong Li
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Zi Mei
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Shijian Ding
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Hao Li
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Tao Huang, ; Yu-Dong Cai,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Tao Huang, ; Yu-Dong Cai,
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14
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Di Lascio S, Fornasari D, Benfante R. The Human-Restricted Isoform of the α7 nAChR, CHRFAM7A: A Double-Edged Sword in Neurological and Inflammatory Disorders. Int J Mol Sci 2022; 23:ijms23073463. [PMID: 35408823 PMCID: PMC8998457 DOI: 10.3390/ijms23073463] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/13/2022] [Accepted: 03/21/2022] [Indexed: 12/13/2022] Open
Abstract
CHRFAM7A is a relatively recent and exclusively human gene arising from the partial duplication of exons 5 to 10 of the α7 neuronal nicotinic acetylcholine receptor subunit (α7 nAChR) encoding gene, CHRNA7. CHRNA7 is related to several disorders that involve cognitive deficits, including neuropsychiatric, neurodegenerative, and inflammatory disorders. In extra-neuronal tissues, α7nAChR plays an important role in proliferation, differentiation, migration, adhesion, cell contact, apoptosis, angiogenesis, and tumor progression, as well as in the modulation of the inflammatory response through the “cholinergic anti-inflammatory pathway”. CHRFAM7A translates the dupα7 protein in a multitude of cell lines and heterologous systems, while maintaining processing and trafficking that are very similar to the full-length form. It does not form functional ion channel receptors alone. In the presence of CHRNA7 gene products, dupα7 can assemble and form heteromeric receptors that, in order to be functional, should include at least two α7 subunits to form the agonist binding site. When incorporated into the receptor, in vitro and in vivo data showed that dupα7 negatively modulated α7 activity, probably due to a reduction in the number of ACh binding sites. Very recent data in the literature report that the presence of the duplicated gene may be responsible for the translational gap in several human diseases. Here, we will review the studies that have been conducted on CHRFAM7A in different pathologies, with the intent of providing evidence regarding when and how the expression of this duplicated gene may be beneficial or detrimental in the pathogenesis, and eventually in the therapeutic response, to CHRNA7-related neurological and non-neurological diseases.
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Affiliation(s)
- Simona Di Lascio
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, 20129 Milan, Italy; (S.D.L.); (D.F.)
| | - Diego Fornasari
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, 20129 Milan, Italy; (S.D.L.); (D.F.)
- CNR Institute of Neuroscience, 20845 Vedano al Lambro, Italy
| | - Roberta Benfante
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, 20129 Milan, Italy; (S.D.L.); (D.F.)
- CNR Institute of Neuroscience, 20845 Vedano al Lambro, Italy
- NeuroMi, Milan Center for Neuroscience, University of Milano Bicocca, 20126 Milan, Italy
- Correspondence:
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15
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Dolinski AC, Homola JJ, Jankowski MD, Robinson JD, Owen JC. Differential gene expression reveals host factors for viral shedding variation in mallards ( Anas platyrhynchos) infected with low-pathogenic avian influenza virus. J Gen Virol 2022; 103:10.1099/jgv.0.001724. [PMID: 35353676 PMCID: PMC10519146 DOI: 10.1099/jgv.0.001724] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Intraspecific variation in pathogen shedding impacts disease transmission dynamics; therefore, understanding the host factors associated with individual variation in pathogen shedding is key to controlling and preventing outbreaks. In this study, ileum and bursa of Fabricius tissues of wild-bred mallards (Anas platyrhynchos) infected with low-pathogenic avian influenza (LPAIV) were evaluated at various post-infection time points to determine genetic host factors associated with intraspecific variation in viral shedding. By analysing transcriptome sequencing data (RNA-seq), we found that LPAIV-infected wild-bred mallards do not exhibit differential gene expression compared to uninfected birds, but that gene expression was associated with cloacal viral shedding quantity early in the infection. In both tissues, immune gene expression was higher in high/moderate shedding birds compared to low shedding birds, and significant positive relationships with viral shedding were observed. In the ileum, expression for host genes involved in viral cell entry was lower in low shedders compared to moderate shedders at 1 day post-infection (DPI), and expression for host genes promoting viral replication was higher in high shedders compared to low shedders at 2 DPI. Our findings indicate that viral shedding is a key factor for gene expression differences in LPAIV-infected wild-bred mallards, and the genes identified in this study could be important for understanding the molecular mechanisms driving intraspecific variation in pathogen shedding.
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Affiliation(s)
- Amanda C. Dolinski
- Department of Fisheries and Wildlife, Michigan State
University, East Lansing, MI
| | - Jared J. Homola
- Department of Fisheries and Wildlife, Michigan State
University, East Lansing, MI
| | - Mark D. Jankowski
- Department of Fisheries and Wildlife, Michigan State
University, East Lansing, MI
- U.S. Environmental Protection Agency, Region 10, Seattle,
WA 98101
| | - John D. Robinson
- Department of Fisheries and Wildlife, Michigan State
University, East Lansing, MI
| | - Jennifer C. Owen
- Department of Fisheries and Wildlife, Michigan State
University, East Lansing, MI
- Department of Large Animal Clinical Sciences, Michigan
State University, East Lansing, MI, USA
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16
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Network Meta-Analysis of Chicken Microarray Data Following Avian Influenza Challenge—A Comparison of Highly and Lowly Pathogenic Strains. Genes (Basel) 2022; 13:genes13030435. [PMID: 35327988 PMCID: PMC8953847 DOI: 10.3390/genes13030435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 02/01/2023] Open
Abstract
The current bioinformatics study was undertaken to analyze the transcriptome of chicken (Gallus gallus) after influenza A virus challenge. A meta-analysis was carried out to explore the host expression response after challenge with lowly pathogenic avian influenza (LPAI) (H1N1, H2N3, H5N2, H5N3 and H9N2) and with highly pathogenic avian influenza (HPAI) H5N1 strains. To do so, ten microarray datasets obtained from the Gene Expression Omnibus (GEO) database were normalized and meta-analyzed for the LPAI and HPAI host response individually. Different undirected networks were constructed and their metrics determined e.g., degree centrality, closeness centrality, harmonic centrality, subgraph centrality and eigenvector centrality. The results showed that, based on criteria of centrality, the CMTR1, EPSTI1, RNF213, HERC4L, IFIT5 and LY96 genes were the most significant during HPAI challenge, with PARD6G, HMG20A, PEX14, RNF151 and TLK1L having the lowest values. However, for LPAI challenge, ZDHHC9, IMMP2L, COX7C, RBM18, DCTN3, and NDUFB1 genes had the largest values for aforementioned criteria, with GTF3C5, DROSHA, ATRX, RFWD2, MED23 and SEC23B genes having the lowest values. The results of this study can be used as a basis for future development of treatments/preventions of the effects of avian influenza in chicken.
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17
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Fan M, Arai M, Tawada A, Chiba T, Fukushima R, Uzawa K, Shiiba M, Kato N, Tanzawa H, Takiguchi Y. Contrasting functions of the epithelial‑stromal interaction 1 gene, in human oral and lung squamous cell cancers. Oncol Rep 2021; 47:5. [PMID: 34738627 PMCID: PMC8600417 DOI: 10.3892/or.2021.8216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/23/2020] [Indexed: 12/17/2022] Open
Abstract
The epithelial‑stromal interaction 1 gene (EPSTI1) is known to play multiple roles in the malignant progression of breast cancer and also in some aspects of the immune responses to the tumor. However, the relevance of the gene in the onset/progression of oral squamous cell carcinoma (OSCC) and lung squamous cell carcinoma (LSCC) is not yet known. The present study was aimed at revealing the roles of EPSTI1 in conferring malignant characteristics to OSCC and LSCC, and the underlying mechanisms. Quantitative real‑time polymerase chain reaction (PCR) and western blot analyses demonstrated significant upregulation of EPSTI1 in all four OSCC cell lines (HSC2, HSC3, HSC3‑M3 and HSC4), and significant downregulation of EPST11 in all three LSCC cell lines (LK‑2, EBC‑1 and H226) used in the present study, as compared to the expression levels in the corresponding control cell lines. Both knockdown of EPST11 in OSCC and overexpression of the gene in LSCC suppressed cell proliferation, and induced cell‑cycle arrest in the G1 phase, with upregulation of p21 and downregulation of CDK2 and cyclin D1. Furthermore, these alterations of EPST11 gene expression in the OSCC and LSCC cell lines suppressed the cell migration ability and reversed the EMT phenotype of the tumor cells. Collectively, while EPSTI1 appears to have oncogenic roles in OSCC, it appears to exert tumor‑suppressive roles in LSCC. PCR array analyses revealed some genes whose expression levels were altered along with the modified EPSTI1 expression in both the OSCC and LSCC cell lines. These findings suggest that EPSTI1 may be a therapeutic target for both OSCC and LSCC.
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Affiliation(s)
- Mengmeng Fan
- Department of Medical Oncology, Graduate School of Medicine, Chiba University, Chiba 260‑8670, Japan
| | - Makoto Arai
- Department of Medical Oncology, Graduate School of Medicine, Chiba University, Chiba 260‑8670, Japan
| | - Akinobu Tawada
- Department of Medical Oncology, Graduate School of Medicine, Chiba University, Chiba 260‑8670, Japan
| | - Tetsuhiro Chiba
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260‑8670, Japan
| | - Reo Fukushima
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba 260‑8670, Japan
| | - Katsuhiro Uzawa
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba 260‑8670, Japan
| | - Masashi Shiiba
- Department of Medical Oncology, Graduate School of Medicine, Chiba University, Chiba 260‑8670, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260‑8670, Japan
| | - Hideki Tanzawa
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba 260‑8670, Japan
| | - Yuichi Takiguchi
- Department of Medical Oncology, Graduate School of Medicine, Chiba University, Chiba 260‑8670, Japan
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18
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Mulvey CM, Breckels LM, Crook OM, Sanders DJ, Ribeiro ALR, Geladaki A, Christoforou A, Britovšek NK, Hurrell T, Deery MJ, Gatto L, Smith AM, Lilley KS. Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line. Nat Commun 2021; 12:5773. [PMID: 34599159 PMCID: PMC8486773 DOI: 10.1038/s41467-021-26000-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 09/07/2021] [Indexed: 02/07/2023] Open
Abstract
Protein localisation and translocation between intracellular compartments underlie almost all physiological processes. The hyperLOPIT proteomics platform combines mass spectrometry with state-of-the-art machine learning to map the subcellular location of thousands of proteins simultaneously. We combine global proteome analysis with hyperLOPIT in a fully Bayesian framework to elucidate spatiotemporal proteomic changes during a lipopolysaccharide (LPS)-induced inflammatory response. We report a highly dynamic proteome in terms of both protein abundance and subcellular localisation, with alterations in the interferon response, endo-lysosomal system, plasma membrane reorganisation and cell migration. Proteins not previously associated with an LPS response were found to relocalise upon stimulation, the functional consequences of which are still unclear. By quantifying proteome-wide uncertainty through Bayesian modelling, a necessary role for protein relocalisation and the importance of taking a holistic overview of the LPS-driven immune response has been revealed. The data are showcased as an interactive application freely available for the scientific community.
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Affiliation(s)
- Claire M Mulvey
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Oliver M Crook
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- MRC Biostatistics Unit, Cambridge Institute for Public Health, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
| | - David J Sanders
- Department of Microbial Diseases, Eastman Dental Institute, University College London, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK
| | - Andre L R Ribeiro
- Department of Microbial Diseases, Eastman Dental Institute, University College London, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK
| | - Aikaterini Geladaki
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | | | - Nina Kočevar Britovšek
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- Lek d.d., Kolodvorska 27, Mengeš, 1234, Slovenia
| | - Tracey Hurrell
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Michael J Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Laurent Gatto
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- de Duve Institute, UCLouvain, Avenue Hippocrate 75, Brussels, 1200, Belgium
| | - Andrew M Smith
- Department of Microbial Diseases, Eastman Dental Institute, University College London, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK.
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK.
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19
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Sarma A, Christenson SA, Byrne A, Mick E, Pisco AO, DeVoe C, Deiss T, Ghale R, Zha BS, Tsitsiklis A, Jauregui A, Moazed F, Detweiler AM, Spottiswoode N, Sinha P, Neff N, Tan M, Serpa PH, Willmore A, Ansel KM, Wilson JG, Leligdowicz A, Siegel ER, Sirota M, DeRisi JL, Matthay MA, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Calfee CS, Langelier CR. Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS. Nat Commun 2021; 12:5152. [PMID: 34446707 PMCID: PMC8390461 DOI: 10.1038/s41467-021-25040-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 07/13/2021] [Indexed: 12/15/2022] Open
Abstract
The immunological features that distinguish COVID-19-associated acute respiratory distress syndrome (ARDS) from other causes of ARDS are incompletely understood. Here, we report the results of comparative lower respiratory tract transcriptional profiling of tracheal aspirate from 52 critically ill patients with ARDS from COVID-19 or from other etiologies, as well as controls without ARDS. In contrast to a "cytokine storm," we observe reduced proinflammatory gene expression in COVID-19 ARDS when compared to ARDS due to other causes. COVID-19 ARDS is characterized by a dysregulated host response with increased PTEN signaling and elevated expression of genes with non-canonical roles in inflammation and immunity. In silico analysis of gene expression identifies several candidate drugs that may modulate gene expression in COVID-19 ARDS, including dexamethasone and granulocyte colony stimulating factor. Compared to ARDS due to other types of viral pneumonia, COVID-19 is characterized by impaired interferon-stimulated gene (ISG) expression. The relationship between SARS-CoV-2 viral load and expression of ISGs is decoupled in patients with COVID-19 ARDS when compared to patients with mild COVID-19. In summary, assessment of host gene expression in the lower airways of patients reveals distinct immunological features of COVID-19 ARDS.
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Affiliation(s)
- Aartik Sarma
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA
| | - Stephanie A. Christenson
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA
| | - Ashley Byrne
- grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA
| | - Eran Mick
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA ,grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Division of Infectious Diseases, University of California, San Francisco, CA USA
| | | | - Catherine DeVoe
- grid.266102.10000 0001 2297 6811Division of Infectious Diseases, University of California, San Francisco, CA USA
| | - Thomas Deiss
- grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA
| | - Rajani Ghale
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Division of Infectious Diseases, University of California, San Francisco, CA USA
| | - Beth Shoshana Zha
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA
| | - Alexandra Tsitsiklis
- grid.266102.10000 0001 2297 6811Division of Infectious Diseases, University of California, San Francisco, CA USA
| | - Alejandra Jauregui
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA
| | - Farzad Moazed
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA
| | - Angela M. Detweiler
- grid.266102.10000 0001 2297 6811Division of Infectious Diseases, University of California, San Francisco, CA USA
| | - Natasha Spottiswoode
- grid.266102.10000 0001 2297 6811Department of Medicine, University of California, San Francisco, CA USA
| | - Pratik Sinha
- grid.4367.60000 0001 2355 7002Department of Anesthesia, Washington University, Saint Louis, MO USA
| | - Norma Neff
- grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA
| | - Michelle Tan
- grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA
| | - Paula Hayakawa Serpa
- grid.266102.10000 0001 2297 6811Division of Infectious Diseases, University of California, San Francisco, CA USA
| | - Andrew Willmore
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA
| | - K. Mark Ansel
- grid.266102.10000 0001 2297 6811Department of Microbiology and Immunology, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Sandler Asthma Basic Research Center, University of California, San Francisco, CA USA
| | - Jennifer G. Wilson
- grid.168010.e0000000419368956Department of Emergency Medicine, Stanford University, Palo Alto, CA USA
| | - Aleksandra Leligdowicz
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA ,grid.17063.330000 0001 2157 2938Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, Ontario Canada ,grid.266102.10000 0001 2297 6811Cardiovascular Research Institute, University of California, San Francisco, CA USA
| | - Emily R. Siegel
- grid.266102.10000 0001 2297 6811School of Medicine, University of California, San Francisco, CA USA
| | - Marina Sirota
- grid.266102.10000 0001 2297 6811Division of Rheumatology, University of California, San Francisco, CA USA
| | - Joseph L. DeRisi
- grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Biochemistry and Biophysics, University of California, San Francisco, CA USA
| | - Michael A. Matthay
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Cardiovascular Research Institute, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Anesthesia, University of California, San Francisco, CA USA
| | | | - Carolyn M. Hendrickson
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA
| | - Kirsten N. Kangelaris
- grid.266102.10000 0001 2297 6811Department of Medicine, University of California, San Francisco, CA USA
| | - Matthew F. Krummel
- grid.266102.10000 0001 2297 6811Department of Pathology, University of California, San Francisco, CA USA
| | - Prescott G. Woodruff
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Sandler Asthma Basic Research Center, University of California, San Francisco, CA USA
| | - David J. Erle
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Medicine, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Lung Biology Center, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811UCSF CoLabs, University of California, San Francisco, CA USA
| | - Carolyn S. Calfee
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Cardiovascular Research Institute, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Anesthesia, University of California, San Francisco, CA USA
| | - Charles R. Langelier
- grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Division of Infectious Diseases, University of California, San Francisco, CA USA
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20
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Kron NS, Fieber LA. Co-expression analysis identifies neuro-inflammation as a driver of sensory neuron aging in Aplysia californica. PLoS One 2021; 16:e0252647. [PMID: 34116561 PMCID: PMC8195618 DOI: 10.1371/journal.pone.0252647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/20/2021] [Indexed: 01/08/2023] Open
Abstract
Aging of the nervous system is typified by depressed metabolism, compromised proteostasis, and increased inflammation that results in cognitive impairment. Differential expression analysis is a popular technique for exploring the molecular underpinnings of neural aging, but technical drawbacks of the methodology often obscure larger expression patterns. Co-expression analysis offers a robust alternative that allows for identification of networks of genes and their putative central regulators. In an effort to expand upon previous work exploring neural aging in the marine model Aplysia californica, we used weighted gene correlation network analysis to identify co-expression networks in a targeted set of aging sensory neurons in these animals. We identified twelve modules, six of which were strongly positively or negatively associated with aging. Kyoto Encyclopedia of Genes analysis and investigation of central module transcripts identified signatures of metabolic impairment, increased reactive oxygen species, compromised proteostasis, disrupted signaling, and increased inflammation. Although modules with immune character were identified, there was no correlation between genes in Aplysia that increased in expression with aging and the orthologous genes in oyster displaying long-term increases in expression after a virus-like challenge. This suggests anti-viral response is not a driver of Aplysia sensory neuron aging.
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Affiliation(s)
- N. S. Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
| | - L. A. Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
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21
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Gao X, Liu Y, Zou S, Liu P, Zhao J, Yang C, Liang M, Yang J. Genome-wide screening of SARS-CoV-2 infection-related genes based on the blood leukocytes sequencing data set of patients with COVID-19. J Med Virol 2021; 93:5544-5554. [PMID: 34009691 PMCID: PMC8242610 DOI: 10.1002/jmv.27093] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/23/2021] [Accepted: 05/15/2021] [Indexed: 12/14/2022]
Abstract
Coronavirus disease 2019 (COVID‐19) is a global epidemic disease caused by a novel virus, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), causing serious adverse effects on human health. In this study, we obtained a blood leukocytes sequencing data set of COVID‐19 patients from the GEO database and obtained differentially expressed genes (DEGs). We further analyzed these DEGs by protein–protein interaction analysis and Gene Ontology enrichment analysis and identified the DEGs closely related to SARS‐CoV‐2 infection. Then, we constructed a six‐gene model (comprising IFIT3, OASL, USP18, XAF1, IFI27, and EPSTI1) by logistic regression analysis and calculated the area under the ROC curve (AUC) for the diagnosis of COVID‐19. The AUC values of the training group, testing group, and entire group were 0.930, 0.914, and 0.921, respectively. The six genes were highly expressed in patients with COVID‐19 and positively correlated with the expression of SARS‐CoV‐2 invasion‐related genes (ACE2, TMPRSS2, CTSB, and CTSL). The risk score calculated by this model was also positively correlated with the expression of TMPRSS2, CTSB, and CTSL, indicating that the six genes were closely related to SARS‐CoV‐2 infection. In conclusion, we comprehensively analyzed the functions of DEGs in the blood leukocytes of patients with COVID‐19 and constructed a six‐gene model that may contribute to the development of new diagnostic and therapeutic ideas for COVID‐19. Moreover, these six genes may be therapeutic targets for COVID‐19. COVID‐19 is a global epidemic and poses a serious risk to human health. The differentially expressed genes related to SARS‐CoV‐2 infection in leukocytes of patients with COVD‐19 were screened. A 6‐gene model for COVID‐19 diagnosis and treatment was constructed by logistic regression analysis. The role and mechanism of these six genes (IFIT3, OASL, USP18, XAF1, IFI27, and EPSTI1) in COVID‐19 were preliminarily analyzed.
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Affiliation(s)
- Xin Gao
- Clinical Laboratory, The First People's Hospital of Huaihua, Huaihua, Hunan, China.,Clinical Laboratory, The Fourth Affiliated Hospital of Jishou University, Huaihua, Hunan, China
| | - Yuan Liu
- Clinical Laboratory, The First People's Hospital of Huaihua, Huaihua, Hunan, China.,Clinical Laboratory, The Fourth Affiliated Hospital of Jishou University, Huaihua, Hunan, China
| | - Shaohui Zou
- Clinical Laboratory, The First People's Hospital of Huaihua, Huaihua, Hunan, China.,Clinical Laboratory, The Fourth Affiliated Hospital of Jishou University, Huaihua, Hunan, China
| | - Pengqin Liu
- Department of Nuclear Medicine, The First People's Hospital of Huaihua, Huaihua, Hunan, China.,Department of Nuclear Medicine, The Fourth Affiliated Hospital of Jishou University, Huaihua, Hunan, China
| | - Jing Zhao
- Clinical Laboratory, The First People's Hospital of Huaihua, Huaihua, Hunan, China.,Clinical Laboratory, The Fourth Affiliated Hospital of Jishou University, Huaihua, Hunan, China
| | - Changshun Yang
- Clinical Laboratory, The First People's Hospital of Huaihua, Huaihua, Hunan, China.,Clinical Laboratory, The Fourth Affiliated Hospital of Jishou University, Huaihua, Hunan, China
| | - Mingxing Liang
- Clinical Laboratory, The First People's Hospital of Huaihua, Huaihua, Hunan, China.,Clinical Laboratory, The Fourth Affiliated Hospital of Jishou University, Huaihua, Hunan, China
| | - Jinlian Yang
- Clinical Laboratory, The First People's Hospital of Huaihua, Huaihua, Hunan, China.,Clinical Laboratory, The Fourth Affiliated Hospital of Jishou University, Huaihua, Hunan, China
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22
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Rao C, Frodyma DE, Southekal S, Svoboda RA, Black AR, Guda C, Mizutani T, Clevers H, Johnson KR, Fisher KW, Lewis RE. KSR1- and ERK-dependent translational regulation of the epithelial-to-mesenchymal transition. eLife 2021; 10:e66608. [PMID: 33970103 PMCID: PMC8195604 DOI: 10.7554/elife.66608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/09/2021] [Indexed: 01/06/2023] Open
Abstract
The epithelial-to-mesenchymal transition (EMT) is considered a transcriptional process that induces a switch in cells from a polarized state to a migratory phenotype. Here, we show that KSR1 and ERK promote EMT-like phenotype through the preferential translation of Epithelial-Stromal Interaction 1 (EPSTI1), which is required to induce the switch from E- to N-cadherin and coordinate migratory and invasive behavior. EPSTI1 is overexpressed in human colorectal cancer (CRC) cells. Disruption of KSR1 or EPSTI1 significantly impairs cell migration and invasion in vitro, and reverses EMT-like phenotype, in part, by decreasing the expression of N-cadherin and the transcriptional repressors of E-cadherin expression, ZEB1 and Slug. In CRC cells lacking KSR1, ectopic EPSTI1 expression restored the E- to N-cadherin switch, migration, invasion, and anchorage-independent growth. KSR1-dependent induction of EMT-like phenotype via selective translation of mRNAs reveals its underappreciated role in remodeling the translational landscape of CRC cells to promote their migratory and invasive behavior.
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Affiliation(s)
- Chaitra Rao
- Eppley Institute, University of Nebraska Medical CenterOmahaUnited States
| | - Danielle E Frodyma
- Eppley Institute, University of Nebraska Medical CenterOmahaUnited States
| | - Siddesh Southekal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical CenterOmahaUnited States
| | - Robert A Svoboda
- Department of Pathology and Microbiology, University of Nebraska Medical CenterOmahaUnited States
| | - Adrian R Black
- Eppley Institute, University of Nebraska Medical CenterOmahaUnited States
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical CenterOmahaUnited States
| | - Tomohiro Mizutani
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC UtrechtUtrechtNetherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC UtrechtUtrechtNetherlands
| | - Keith R Johnson
- Eppley Institute, University of Nebraska Medical CenterOmahaUnited States
- Department of Oral Biology, University of Nebraska Medical CenterOmahaUnited States
| | - Kurt W Fisher
- Department of Pathology and Microbiology, University of Nebraska Medical CenterOmahaUnited States
| | - Robert E Lewis
- Eppley Institute, University of Nebraska Medical CenterOmahaUnited States
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23
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Sarma A, Christenson SA, Mick E, DeVoe C, Deiss T, Pisco AO, Ghale R, Jauregui A, Byrne A, Moazed F, Spottiswoode N, Sinha P, Zha BS, Neff N, Tan M, Serpa PH, Ansel KM, Wilson JG, Leligdowicz A, Siegel ER, Sirota M, DeRisi JL, Matthay MA, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Calfee CS, Langelier CR. COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and is modified by dexamethasone. RESEARCH SQUARE 2021:rs.3.rs-141578. [PMID: 33469573 PMCID: PMC7814832 DOI: 10.21203/rs.3.rs-141578/v1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We performed comparative lower respiratory tract transcriptional profiling of 52 critically ill patients with the acute respiratory distress syndrome (ARDS) from COVID-19 or from other etiologies, as well as controls without ARDS. In contrast to a cytokine storm, we observed reduced proinflammatory gene expression in COVID-19 ARDS when compared to ARDS due to other causes. COVID-19 ARDS was characterized by a dysregulated host response with increased PTEN signaling and elevated expression of genes with non-canonical roles in inflammation and immunity that were predicted to be modulated by dexamethasone and granulocyte colony stimulating factor. Compared to ARDS due to other types of viral pneumonia, COVID-19 was characterized by impaired interferon-stimulated gene expression (ISG). We found that the relationship between SARS-CoV-2 viral load and expression of ISGs was decoupled in patients with COVID-19 ARDS when compared to patients with mild COVID-19. In summary, assessment of host gene expression in the lower airways of patients with COVID-19 ARDS did not demonstrate cytokine storm but instead revealed a unique and dysregulated host response predicted to be modified by dexamethasone.
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Affiliation(s)
- Aartik Sarma
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Stephanie A. Christenson
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Eran Mick
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Catherine DeVoe
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Thomas Deiss
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | - Rajani Ghale
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Alejandra Jauregui
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | - Farzad Moazed
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Pratik Sinha
- Department of Anesthesia, Washington University, Saint Louis, Missouri, MO, USA
| | - Beth Shoshana Zha
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Paula Hayakawa Serpa
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - K. Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, CA, USA
| | - Jennifer G. Wilson
- Department of Emergency Medicine, Stanford University, Palo Alto, CA, USA
| | | | - Emily R. Siegel
- School of Medicine, University of California, San Francisco, CA, USA
| | - Marina Sirota
- Division of Rheumatology, University of California, San Francisco, CA, USA
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Michael A. Matthay
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Carolyn M. Hendrickson
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Matthew F. Krummel
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Prescott G. Woodruff
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, CA, USA
| | - David J. Erle
- Department of Medicine, University of California, San Francisco, CA, USA
- Lung Biology Center, University of California, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, CA, USA
| | - Carolyn S. Calfee
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Charles R. Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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24
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Mavian C, Ramirez-Mata AS, Dollar JJ, Nolan DJ, Cash M, White K, Rich SN, Magalis BR, Marini S, Prosperi MCF, Amador DM, Riva A, Williams KC, Salemi M. Brain tissue transcriptomic analysis of SIV-infected macaques identifies several altered metabolic pathways linked to neuropathogenesis and poly (ADP-ribose) polymerases (PARPs) as potential therapeutic targets. J Neurovirol 2021; 27:101-115. [PMID: 33405206 PMCID: PMC7786889 DOI: 10.1007/s13365-020-00927-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/15/2020] [Accepted: 11/10/2020] [Indexed: 01/08/2023]
Abstract
Despite improvements in antiretroviral therapy, human immunodeficiency virus type 1 (HIV-1)-associated neurocognitive disorders (HAND) remain prevalent in subjects undergoing therapy. HAND significantly affects individuals' quality of life, as well as adherence to therapy, and, despite the increasing understanding of neuropathogenesis, no definitive diagnostic or prognostic marker has been identified. We investigated transcriptomic profiles in frontal cortex tissues of Simian immunodeficiency virus (SIV)-infected Rhesus macaques sacrificed at different stages of infection. Gene expression was compared among SIV-infected animals (n = 11), with or without CD8+ lymphocyte depletion, based on detectable (n = 6) or non-detectable (n = 5) presence of the virus in frontal cortex tissues. Significant enrichment in activation of monocyte and macrophage cellular pathways was found in animals with detectable brain infection, independently from CD8+ lymphocyte depletion. In addition, transcripts of four poly (ADP-ribose) polymerases (PARPs) were up-regulated in the frontal cortex, which was confirmed by real-time polymerase chain reaction. Our results shed light on involvement of PARPs in SIV infection of the brain and their role in SIV-associated neurodegenerative processes. Inhibition of PARPs may provide an effective novel therapeutic target for HIV-related neuropathology.
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Affiliation(s)
- Carla Mavian
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
| | - Andrea S Ramirez-Mata
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - James Jarad Dollar
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - David J Nolan
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Melanie Cash
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Kevin White
- Biology Department, Boston College, Boston, MD, USA
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
| | - Shannan N Rich
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Biology Department, Boston College, Boston, MD, USA
| | - Brittany Rife Magalis
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Simone Marini
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Biology Department, Boston College, Boston, MD, USA
| | - Mattia C F Prosperi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Biology Department, Boston College, Boston, MD, USA
| | - David Moraga Amador
- Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, FL, USA
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, FL, USA
| | - Kenneth C Williams
- Biology Department, Boston College, Boston, MD, USA
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
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25
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Song A, Wang J, Tong Y, Fang J, Zhang Y, Zhang H, Ruan H, Wang K, Liu Y. BKCa channels regulate the immunomodulatory properties of WJ-MSCs by affecting the exosome protein profiles during the inflammatory response. Stem Cell Res Ther 2020; 11:440. [PMID: 33059770 PMCID: PMC7560248 DOI: 10.1186/s13287-020-01952-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/24/2020] [Indexed: 12/13/2022] Open
Abstract
Background Wharton’s jelly-derived mesenchymal stem cells (WJ-MSCs) from the human umbilical cord have been studied extensively due to their immunomodulatory functions. Large-conductance Ca2+-activated K+ (BKCa channels) channels are involved in many inflammatory responses, but their involvement in the anti-inflammatory activity of WJ-MSCs is unknown. The underlying molecular mechanism, through which BKCa channels mediate the immunomodulation of WJ-MSC, which may include changes in exosomes proteomics, has not yet been clarified. Methods Alizarin staining, Oil Red O staining, and flow cytometry were used to identify WJ-MSCs, which were isolated from human umbilical cord Wharton’s jelly. BKCa channels were detected in WJ-MSCs using western blotting, real-time polymerase chain reaction (real-time PCR), and electrophysiology, and cytokine expression was examined using real-time PCR and enzyme-linked immunosorbent assays (ELISAs). Exosomes were characterized using transmission electron microscopy and nanoparticle tracking analysis. Proteomics analysis was performed to explore exosomal proteomic profiles. Results The cells derived from human umbilical cord Wharton’s jelly were identified as MSCs. BKCa channels were detected in the isolated WJ-MSCs, and the expression of these channels increased after lipopolysaccharide (LPS) stimulation. BKCa channels blockade in LPS-treated WJ-MSCs induced apoptosis and decreased interleukin-6 (IL-6) expression. Furthermore, THP-1 cells (human monocytic cell line) stimulated with LPS/interferon gamma (IFN-γ) produced more anti-inflammatory cytokines after treatment with exosomes derived from BKCa channel-knockdown WJ-MSCs (si-exo). We also observed altered expression of mitochondrial ATP synthase alpha subunit (ATP5A1), filamin B, and other proteins in si-exo, which might increase the anti-inflammatory activity of macrophages. Conclusions Our study described the functional expression of BKCa channels in WJ-MSCs, and BKCa channels regulated the immunomodulatory properties of WJ-MSCs by affecting the exosomal protein profiles during the inflammatory response.
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Affiliation(s)
- Ahui Song
- Department of Nephrology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, People's Republic of China
| | - Jingjing Wang
- Department of Nephrology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, People's Republic of China
| | - Yan Tong
- Department of Nephrology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, People's Republic of China
| | - Junyan Fang
- Department of Nephrology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, People's Republic of China
| | - Yi Zhang
- Shanghai Applied Protein Technology Co., Ltd.,Research & Development Center, 58 Yuanmei Road, Shanghai, People's Republic of China
| | - Huiping Zhang
- Shanghai Applied Protein Technology Co., Ltd.,Research & Development Center, 58 Yuanmei Road, Shanghai, People's Republic of China
| | - Hongqiang Ruan
- Shanghai Applied Protein Technology Co., Ltd.,Research & Development Center, 58 Yuanmei Road, Shanghai, People's Republic of China
| | - Kai Wang
- The Clinical and Translational Research Center Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Yingli Liu
- Department of Nephrology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, People's Republic of China.
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26
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Sol N, Leurs CE, Veld SGI', Strijbis EM, Vancura A, Schweiger MW, Teunissen CE, Mateen FJ, Tannous BA, Best MG, Würdinger T, Killestein J. Blood platelet RNA enables the detection of multiple sclerosis. Mult Scler J Exp Transl Clin 2020; 6:2055217320946784. [PMID: 32843989 PMCID: PMC7418262 DOI: 10.1177/2055217320946784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/05/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022] Open
Abstract
Background In multiple sclerosis (MS), clinical assessment, MRI and cerebrospinal fluid are important in the diagnostic process. However, no blood biomarker has been confirmed as a useful tool in the diagnostic work-up. Objectives Blood platelets contain a rich spliced mRNA repertoire that can alter during megakaryocyte development but also during platelet formation and platelet circulation. In this proof of concept study, we evaluate the diagnostic potential of spliced blood platelet RNA for the detection of MS. Methods We isolated and sequenced platelet RNA of blood samples obtained from 57 MS patients and 66 age- and gender-matched healthy controls (HCs). 60% was used to develop a particle swarm-optimized (PSO) support vector machine classification algorithm. The remaining 40% served as an independent validation series. Results In total, 1249 RNAs with differential spliced junction expression levels were identified between platelets of MS patients as compared to HCs, including EPSTI1, IFI6, and RPS6KA3, in line with reported inflammatory signatures in the blood of MS patients. The RNAs were subsequently used as input for a MS classifier, capable of detecting MS with 80% accuracy in the independent validation series. Conclusions Spliced platelet RNA may enable the blood-based diagnosis of MS, warranting large-scale validation.
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Affiliation(s)
- Nik Sol
- Department of Neurology, Neuroscience Amsterdam, VUmc MS Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands.,Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Cyra E Leurs
- Department of Neurology, Neuroscience Amsterdam, VUmc MS Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Sjors Gjg In 't Veld
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Eva M Strijbis
- Department of Neurology, Neuroscience Amsterdam, VUmc MS Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Adrienne Vancura
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Markus W Schweiger
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurology, Massachusetts General Hospital Harvard Medical School, Boston, MA, USA
| | - Charlotte E Teunissen
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Neuroscience Campus Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Farrah J Mateen
- Department of Neurology, Massachusetts General Hospital Harvard Medical School, Boston, MA, USA
| | - Bakhos A Tannous
- Department of Neurology, Massachusetts General Hospital Harvard Medical School, Boston, MA, USA
| | - Myron G Best
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Pathology, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Thomas Würdinger
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Joep Killestein
- Department of Neurology, Neuroscience Amsterdam, VUmc MS Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
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27
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Bush SJ, McCulloch MEB, Lisowski ZM, Muriuki C, Clark EL, Young R, Pridans C, Prendergast JGD, Summers KM, Hume DA. Species-Specificity of Transcriptional Regulation and the Response to Lipopolysaccharide in Mammalian Macrophages. Front Cell Dev Biol 2020; 8:661. [PMID: 32793601 PMCID: PMC7386301 DOI: 10.3389/fcell.2020.00661] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/01/2020] [Indexed: 02/02/2023] Open
Abstract
Mammalian macrophages differ in their basal gene expression profiles and response to the toll-like receptor 4 (TLR4) agonist, lipopolysaccharide (LPS). In human macrophages, LPS elicits a temporal cascade of transient gene expression including feed forward activators and feedback regulators that limit the response. Here we present a transcriptional network analysis of the response of sheep bone marrow-derived macrophages (BMDM) to LPS based upon RNA-seq at 0, 2, 4, 7, and 24 h post-stimulation. The analysis reveals a conserved transcription factor network with humans, and rapid induction of feedback regulators that constrain the response at every level. The gene expression profiles of sheep BMDM at 0 and 7 h post LPS addition were compared to similar data obtained from goat, cow, water buffalo, horse, pig, mouse and rat BMDM. This comparison was based upon identification of 8,200 genes annotated in all species and detected at >10TPM in at least one sample. Analysis of expression of transcription factors revealed a conserved transcriptional millieu associated with macrophage differentiation and LPS response. The largest co-expression clusters, including genes encoding cell surface receptors, endosome–lysosome components and secretory activity, were also expressed in all species and the combined dataset defines a macrophage functional transcriptome. All of the large animals differed from rodents in lacking inducible expression of genes involved in arginine metabolism and nitric oxide production. Instead, they expressed inducible transporters and enzymes of tryptophan and kynurenine metabolism. BMDM from all species expressed high levels of transcripts encoding transporters and enzymes involved in glutamine metabolism suggesting that glutamine is a major metabolic fuel. We identify and discuss transcripts that were uniquely expressed or regulated in rodents compared to large animals including ACOD1, CXC and CC chemokines, CD163, CLEC4E, CPM, CSF1, CSF2, CTSK, MARCO, MMP9, SLC2A3, SLC7A7, and SUCNR1. Conversely, the data confirm the conserved regulation of multiple transcripts for which there is limited functional data from mouse models and knockouts. The data provide a resource for functional annotation and interpretation of loci involved in susceptibility to infectious and inflammatory disease in humans and large animal species.
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Affiliation(s)
- Stephen J Bush
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Mary E B McCulloch
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Zofia M Lisowski
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Charity Muriuki
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Emily L Clark
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Rachel Young
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Clare Pridans
- Centre for Inflammation Research, The University of Edinburgh, Edinburgh, United Kingdom.,Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | | | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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28
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Sun JL, Zhang HZ, Liu SY, Lian CF, Chen ZL, Shao TH, Zhang S, Zhao LL, He CM, Wang M, Zhang W, Chen H, Zhang FC. Elevated EPSTI1 promote B cell hyperactivation through NF-κB signalling in patients with primary Sjögren's syndrome. Ann Rheum Dis 2020; 79:518-524. [PMID: 32114510 DOI: 10.1136/annrheumdis-2019-216428] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/18/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Primary Sjögren's syndrome (pSS) is a systemic autoimmune disease characterised by aberrant B cell hyperactivation, whose mechanism is partially understood. METHODS We performed whole transcriptome sequencing of B cells from three pSS patients and three matched healthy controls (HC). Differentially expression genes (DEGs) were confirmed with B cells from 40 pSS patients and 40 HC by quantitative PCR and western blot. We measured the proliferation potential and immunoglobulins production of siRNA-transfected or plasmid-transfected B cells stimulated with cytosine-phosphate-guanine (CpG) or anti-IgM. We also explored Toll-like receptor 9 (TLR9) signalling to reveal the potential mechanism of B cell hyperactivation in pSS. RESULTS We identified 77 upregulated and 32 downregulated DEGs in pSS B cells. We confirmed that epithelial stromal interaction (EPST1) expression in pSS B cells was significantly higher than that from HCs. EPSTI1-silencing B cells stimulated with CpG were less proliferated and produced lower level of IgG and IgM comparing with control B cells. EPSTI1-silencing B cells expressed lower level of p-p65 and higher level of IκBα, and B cells with overexpressed EPSTI1 showed higher level of p-p65 and lower level of IκBα. Finally, IκBα degradation inhibitor Dehydrocostus Lactone treatment attenuated p65 phosphorylation promoted by EPSTI1. CONCLUSION Elevated EPSTI1 expression in pSS B cells promoted TLR9 signalling activation and contributed to the abnormal B cell activation, which was promoted by facilitating p65 phosphorylation and activation of NF-κB signalling via promoting IκBα degradation. EPSTI1 might be implicated in pSS pathogenesis and was a potential therapeutic target of pSS.
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Affiliation(s)
- Jin-Lei Sun
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Hao-Ze Zhang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Su-Ying Liu
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Chao-Feng Lian
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Zhi-Lei Chen
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Ti-Hong Shao
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Shuo Zhang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Li-Ling Zhao
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Cheng-Mei He
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Mu Wang
- Department of Stomatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Wen Zhang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Hua Chen
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China .,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Feng-Chun Zhang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China .,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
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29
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Savage SA, Viard M, O'hUigin C, Zhou W, Yeager M, Li SA, Wang T, Ramsuran V, Vince N, Vogt A, Hicks B, Burdett L, Chung C, Dean M, de Andrade KC, Freedman ND, Berndt SI, Rothman N, Lan Q, Cerhan JR, Slager SL, Zhang Y, Teras LR, Haagenson M, Chanock SJ, Spellman SR, Wang Y, Willis A, Askar M, Lee SJ, Carrington M, Gadalla SM. Genome-wide Association Study Identifies HLA-DPB1 as a Significant Risk Factor for Severe Aplastic Anemia. Am J Hum Genet 2020; 106:264-271. [PMID: 32004448 PMCID: PMC7010969 DOI: 10.1016/j.ajhg.2020.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 01/07/2020] [Indexed: 12/20/2022] Open
Abstract
Severe aplastic anemia (SAA) is a rare disorder characterized by hypoplastic bone marrow and progressive pancytopenia. The etiology of acquired SAA is not understood but is likely related to abnormal immune responses and environmental exposures. We conducted a genome-wide association study of individuals with SAA genetically matched to healthy controls in discovery (359 cases, 1,396 controls) and validation sets (175 cases, 1,059 controls). Combined analyses identified linked SNPs in distinct blocks within the major histocompatibility complex on 6p21. The top SNP encodes p.Met76Val in the P4 binding pocket of the HLA class II gene HLA-DPB1 (rs1042151A>G, odds ratio [OR] 1.75, 95% confidence interval [CI] 1.50-2.03, p = 1.94 × 10-13) and was associated with HLA-DP cell surface expression in healthy individuals (p = 2.04 × 10-6). Phylogenetic analyses indicate that Val76 is not monophyletic and likely occurs in conjunction with different HLA-DP binding groove conformations. Imputation of HLA-DPB1 alleles revealed increased risk of SAA associated with Val76-encoding alleles DPB1∗03:01, (OR 1.66, p = 1.52 × 10-7), DPB1∗10:01 (OR 2.12, p = 0.0003), and DPB1∗01:01 (OR 1.60, p = 0.0008). A second SNP near HLA-B, rs28367832G>A, reached genome-wide significance (OR 1.49, 95% CI 1.22-1.78, p = 7.27 × 10-9) in combined analyses; the association remained significant after excluding cases with clonal copy-neutral loss-of-heterozygosity affecting class I HLA genes (8.6% of cases and 0% of controls). SNPs in the HLA class II gene HLA-DPB1 and possibly class I (HLA-B) are associated with SAA. The replacement of Met76 to Val76 in certain HLA-DPB1 alleles might influence risk of SAA through mechanisms involving DP peptide binding specificity, expression, and/or other factors affecting DP function.
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Affiliation(s)
- Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Colm O'hUigin
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Weiyin Zhou
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Meredith Yeager
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Shengchao Alfred Li
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Veron Ramsuran
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nicolas Vince
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Aurelie Vogt
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Belynda Hicks
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Laurie Burdett
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Charles Chung
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kelvin C de Andrade
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55902, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55902, USA
| | - Yawei Zhang
- Section of Surgical Outcomes and Epidemiology, Department of Surgery, Yale Medical School, New Haven, CT 06520, USA
| | - Lauren R Teras
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, 30303, USA
| | - Michael Haagenson
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Youjin Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Amanda Willis
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, TX 76798, USA
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, TX 76798, USA
| | - Stephanie J Lee
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Shahinaz M Gadalla
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
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30
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Chaly Y, Barr JY, Sullivan DA, Thomas HE, Brodnicki TC, Lieberman SM. Type I Interferon Signaling Is Required for Dacryoadenitis in the Nonobese Diabetic Mouse Model of Sjögren Syndrome. Int J Mol Sci 2018; 19:E3259. [PMID: 30347820 PMCID: PMC6214106 DOI: 10.3390/ijms19103259] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/01/2018] [Accepted: 10/13/2018] [Indexed: 12/26/2022] Open
Abstract
Nonobese diabetic (NOD) mice spontaneously develop lacrimal and salivary gland autoimmunity similar to human Sjögren syndrome. In both humans and NOD mice, the early immune response that drives T-cell infiltration into lacrimal and salivary glands is poorly understood. In NOD mice, lacrimal gland autoimmunity spontaneously occurs only in males with testosterone playing a role in promoting lacrimal gland inflammation, while female lacrimal glands are protected by regulatory T cells (Tregs). The mechanisms of this male-specific lacrimal gland autoimmunity are not known. Here, we studied the effects of Treg depletion in hormone-manipulated NOD mice and lacrimal gland gene expression to determine early signals required for lacrimal gland inflammation. While Treg-depletion was not sufficient to drive dacryoadenitis in castrated male NOD mice, chemokines (Cxcl9, Ccl19) and other potentially disease-relevant genes (Epsti1, Ubd) were upregulated in male lacrimal glands. Expression of Cxcl9 and Ccl19, in particular, remained significantly upregulated in the lacrimal glands of lymphocyte-deficient NOD-severe combined immunodeficiency (SCID) mice and their expression was modulated by type I interferon signaling. Notably, Ifnar1-deficient NOD mice did not develop dacryoadenitis. Together these data identify disease-relevant genes upregulated in the context of male-specific dacryoadenitis and demonstrate a requisite role for type I interferon signaling in lacrimal gland autoimmunity in NOD mice.
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Affiliation(s)
- Yury Chaly
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Jennifer Y Barr
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - David A Sullivan
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA.
| | - Helen E Thomas
- Department of Medicine, St. Vincent's Hospital, St. Vincent's Institute, The University of Melbourne, Fitzroy, Victoria 3065, Australia.
| | - Thomas C Brodnicki
- Department of Medicine, St. Vincent's Hospital, St. Vincent's Institute, The University of Melbourne, Fitzroy, Victoria 3065, Australia.
| | - Scott M Lieberman
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA 52242, USA.
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31
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Cervantes-Gracia K, Husi H. Integrative analysis of Multiple Sclerosis using a systems biology approach. Sci Rep 2018; 8:5633. [PMID: 29618802 PMCID: PMC5884799 DOI: 10.1038/s41598-018-24032-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 03/23/2018] [Indexed: 02/07/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune disorder characterized by inflammatory-demyelinating events in the central nervous system. Despite more than 40 years of MS research its aetiology remains unknown. This study aims to identify the most frequently reported and consistently regulated molecules in MS in order to generate molecular interaction networks and thereby leading to the identification of deregulated processes and pathways which could give an insight of the underlying molecular mechanisms of MS. Driven by an integrative systems biology approach, gene-expression profiling datasets were combined and stratified into "Non-treated" and "Treated" groups and additionally compared to other disease patterns. Molecular identifiers from dataset comparisons were matched to our Multiple Sclerosis database (MuScle; www.padb.org/muscle ). From 5079 statistically significant molecules, correlation analysis within groups identified a panel of 16 high-confidence genes unique to the naïve MS phenotype, whereas the "Treated" group reflected a common pattern associated with autoimmune disease. Pathway and gene-ontology clustering identified the Interferon gamma signalling pathway as the most relevant amongst all significant molecules, and viral infections as the most likely cause of all down-stream events observed. This hypothesis-free approach revealed the most significant molecular events amongst different MS phenotypes which can be used for further detailed studies.
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Affiliation(s)
| | - Holger Husi
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, G12 8TA, UK.
- Department of Diabetes and Cardiovascular Science, University of the Highlands and Islands, Centre for Health Science, Inverness, IV2 3JH, UK.
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