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Lee SG, Furth PA, Hennighausen L, Lee HK. Variant- and vaccination-specific alternative splicing profiles in SARS-CoV-2 infections. iScience 2024; 27:109177. [PMID: 38414855 PMCID: PMC10897911 DOI: 10.1016/j.isci.2024.109177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/28/2023] [Accepted: 02/06/2024] [Indexed: 02/29/2024] Open
Abstract
The COVID-19 pandemic, driven by the SARS-CoV-2 virus and its variants, highlights the important role of understanding host-viral molecular interactions influencing infection outcomes. Alternative splicing post-infection can impact both host responses and viral replication. We analyzed RNA splicing patterns in immune cells across various SARS-CoV-2 variants, considering immunization status. Using a dataset of 190 RNA-seq samples from our prior studies, we observed a substantial deactivation of alternative splicing and RNA splicing-related genes in COVID-19 patients. The alterations varied significantly depending on the infecting variant and immunization history. Notably, Alpha or Beta-infected patients differed from controls, while Omicron-infected patients displayed a splicing profile closer to controls. Particularly, vaccinated Omicron-infected individuals showed a distinct dynamic in alternative splicing patterns not widely shared among other groups. Our findings underscore the intricate interplay between SARS-CoV-2 variants, vaccination-induced immunity, and alternative splicing, emphasizing the need for further investigations to deepen understanding and guide therapeutic development.
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Affiliation(s)
- Sung-Gwon Lee
- Section of Genetics and Physiology, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Priscilla A Furth
- Section of Genetics and Physiology, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Lothar Hennighausen
- Section of Genetics and Physiology, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Hye Kyung Lee
- Section of Genetics and Physiology, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
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2
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Villanueva-Martin G, Acosta-Herrera M, Carmona EG, Kerick M, Ortego-Centeno N, Callejas-Rubio JL, Mages N, Klages S, Börno S, Timmermann B, Bossini-Castillo L, Martin J. Non-classical circulating monocytes expressing high levels of microsomal prostaglandin E2 synthase-1 tag an aberrant IFN-response in systemic sclerosis. J Autoimmun 2023; 140:103097. [PMID: 37633117 DOI: 10.1016/j.jaut.2023.103097] [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: 05/18/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/28/2023]
Abstract
Systemic sclerosis (SSc) is a complex disease that affects the connective tissue, causing fibrosis. SSc patients show altered immune cell composition and activation in the peripheral blood (PB). PB monocytes (Mos) are recruited into tissues where they differentiate into macrophages, which are directly involved in fibrosis. To understand the role of CD14+ PB Mos in SSc, a single-cell transcriptome analysis (scRNA-seq) was conducted on 8 SSc patients and 8 controls. Using unsupervised clustering methods, CD14+ cells were assigned to 11 clusters, which added granularity to the known monocyte subsets: classical (cMos), intermediate (iMos) and non-classical Mos (ncMos) or type 2 dendritic cells. NcMos were significantly overrepresented in SSc patients and showed an active IFN-signature and increased expression levels of PTGES, in addition to monocyte motility and adhesion markers. We identified a SSc-related cluster of IRF7+ STAT1+ iMos with an aberrant IFN-response. Finally, a depletion of M2 polarised cMos in SSc was observed. Our results highlighted the potential of PB Mos as biomarkers for SSc and provided new possibilities for putative drug targets for modulating the innate immune response in SSc.
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Affiliation(s)
- Gonzalo Villanueva-Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Marialbert Acosta-Herrera
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain; Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Elio G Carmona
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain; Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Martin Kerick
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Norberto Ortego-Centeno
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain; Department of Medicine, University of Granada, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Jose Luis Callejas-Rubio
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Norbert Mages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Sven Klages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Stefan Börno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Lara Bossini-Castillo
- Department of Genetics and Biotechnology Institute, Biomedical Research Centre (CIBM), University of Granada, 18100, Granada, Spain; Advanced Therapies and Biomedical Technologies (TEC-14), Biosanitary Research Institute Ibs. GRANADA, 18016, Granada, Spain.
| | - Javier Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
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3
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Zhang Z, Sauerwald N, Cappuccio A, Ramos I, Nair VD, Nudelman G, Zaslavsky E, Ge Y, Gaitas A, Ren H, Brockman J, Geis J, Ramalingam N, King D, McClain MT, Woods CW, Henao R, Burke TW, Tsalik EL, Goforth CW, Lizewski RA, Lizewski SE, Weir DL, Letizia AG, Sealfon SC, Troyanskaya OG. Blood RNA alternative splicing events as diagnostic biomarkers for infectious disease. CELL REPORTS METHODS 2023; 3:100395. [PMID: 36936082 PMCID: PMC10014279 DOI: 10.1016/j.crmeth.2023.100395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/31/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Assays detecting blood transcriptome changes are studied for infectious disease diagnosis. Blood-based RNA alternative splicing (AS) events, which have not been well characterized in pathogen infection, have potential normalization and assay platform stability advantages over gene expression for diagnosis. Here, we present a computational framework for developing AS diagnostic biomarkers. Leveraging a large prospective cohort of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and whole-blood RNA sequencing (RNA-seq) data, we identify a major functional AS program switch upon viral infection. Using an independent cohort, we demonstrate the improved accuracy of AS biomarkers for SARS-CoV-2 diagnosis compared with six reported transcriptome signatures. We then optimize a subset of AS-based biomarkers to develop microfluidic PCR diagnostic assays. This assay achieves nearly perfect test accuracy (61/62 = 98.4%) using a naive principal component classifier, significantly more accurate than a gene expression PCR assay in the same cohort. Therefore, our RNA splicing computational framework enables a promising avenue for host-response diagnosis of infection.
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Affiliation(s)
- Zijun Zhang
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
- Division of Artificial Intelligence in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Natalie Sauerwald
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Antonio Cappuccio
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Venugopalan D. Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angelo Gaitas
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hui Ren
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Joel Brockman
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Jennifer Geis
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | | | - David King
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Micah T. McClain
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Christopher W. Woods
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas W. Burke
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ephraim L. Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | | | | | | | - Dawn L. Weir
- Naval Medical Research Center, Silver Spring, MD, USA
| | | | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Olga G. Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
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4
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Zhang J, Cheng S, Xie S, Xie Z, Zhang H, Wang F, Gao K, Jiang W. Significance of leukocyte-specific transcript 1 levels in nasal mucosal tissue to predict recurrence of nasal polyps. Braz J Otorhinolaryngol 2022; 89:321-328. [PMID: 36754676 PMCID: PMC10071535 DOI: 10.1016/j.bjorl.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/02/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Chronic Rhinosinusitis with Polyps (CRSwNP) is characterized by high heterogeneity and postoperative recurrence rate. This study aims to explore the clinical significance of tissue Leukocyte-Specific Transcript 1 (LST1) in predicting CRSwNP recurrence. METHODS We enrolled 62 CRSwNP patients including 30 primary CRSwNP and 32 recurrent CRSwNP patients, and 40 Healthy Controls (HC). Tissue samples were collected. Tissue LST1 expression was assessed by Reverse Transcription-Polymerase Chain Reaction (RT-PCR), Western Blotting (WB) and Immunofluorescence (IF) staining. The predictive values of LST1 expression for CRSwNP postoperative recurrence were assessed through the Receiver Operating Characteristic (ROC) curves. RESULTS The tissue levels of LST1 were significantly increased in the CRSwNP group than the HC group, especially in the recurrent group, and the elevated LST1 mRNA levels were positively correlated with the peripheral eosinophil percentages, tissue eosinophil counts and percentages. IF staining results showed that the LST1 protein levels were higher in CRSwNP patients, especially in the recurrent patients than in the HC group. ROC curves highlighted that tissue LST1 levels were associated with recurrent CRSwNP and exhibited a higher predictive ability for postoperative CRSwNP recurrence. CONCLUSION This was the first report suggesting that LST1 expression was upregulated and associated with mucosal eosinophil infiltration and CRSwNP recurrence. Tissue LST1 could be a promising biomarker for predicting postoperative recurrence in CRwNP patients. LEVEL OF EVIDENCE Level 5.
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Affiliation(s)
- Junyi Zhang
- Xiangya Hospital of Central South University, Department of Otolaryngology-Head and Neck Surgery, Changsha, Hunan, China
| | - Shenghao Cheng
- Xiangya Hospital of Central South University, Department of Otolaryngology-Head and Neck Surgery, Changsha, Hunan, China
| | - Shaobing Xie
- Xiangya Hospital of Central South University, Department of Otolaryngology-Head and Neck Surgery, Changsha, Hunan, China; Hunan Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China
| | - Zhihai Xie
- Xiangya Hospital of Central South University, Department of Otolaryngology-Head and Neck Surgery, Changsha, Hunan, China; Hunan Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China
| | - Hua Zhang
- Xiangya Hospital of Central South University, Department of Otolaryngology-Head and Neck Surgery, Changsha, Hunan, China; Hunan Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China
| | - Fengjun Wang
- Xiangya Hospital of Central South University, Department of Otolaryngology-Head and Neck Surgery, Changsha, Hunan, China; Hunan Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China
| | - Kelei Gao
- Xiangya Hospital of Central South University, Department of Otolaryngology-Head and Neck Surgery, Changsha, Hunan, China.
| | - Weihong Jiang
- Xiangya Hospital of Central South University, Department of Otolaryngology-Head and Neck Surgery, Changsha, Hunan, China.
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5
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Chen D, Wang W, Wu L, Liang L, Wang S, Cheng Y, Zhang T, Chai C, Luo Q, Sun C, Zhao W, Lv Z, Gao Y, Wu X, Sun N, Zhang Y, Zhang J, Chen Y, Tong J, Wang X, Bai Y, Sun C, Jin X, Niu J. Single-cell atlas of peripheral blood mononuclear cells from pregnant women. Clin Transl Med 2022; 12:e821. [PMID: 35522918 PMCID: PMC9076016 DOI: 10.1002/ctm2.821] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 03/09/2022] [Accepted: 03/31/2022] [Indexed: 11/29/2022] Open
Abstract
Background During pregnancy, mother–child interactions trigger a variety of subtle changes in the maternal body, which may be reflected in the status of peripheral blood mononuclear cells (PBMCs). Although these cells are easy to access and monitor, a PBMC atlas for pregnant women has not yet been constructed. Methods We applied single‐cell RNA sequencing (scRNA‐seq) to profile 198,356 PBMCs derived from 136 pregnant women (gestation weeks 6 to 40) and a control cohort. We also used scRNA‐seq data to establish a transcriptomic clock and thereby predicted the gestational age of normal pregnancy. Results We identified reconfiguration of the peripheral immune cell phenotype during pregnancy, including interferon‐stimulated gene upregulation, activation of RNA splicing‐related pathways and immune activity of cell subpopulations. We also developed a cell‐type‐specific model to predict gestational age of normal pregnancy. Conclusions We constructed a single‐cell atlas of PBMCs in pregnant women spanning the entire gestation period, which should help improve our understanding of PBMC composition turnover in pregnant women.
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Affiliation(s)
- Dongsheng Chen
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Linlin Wu
- Department of Obstetrics and Gynecology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Langchao Liang
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shiyou Wang
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yunfeng Cheng
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Fudan University Shanghai Medical College, Shanghai, China
| | | | - Chaochao Chai
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Chengcheng Sun
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wandong Zhao
- BGI-Shenzhen, Shenzhen, China.,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Zhiyuan Lv
- BGI-Shenzhen, Shenzhen, China.,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Engineering Laboratory for Birth Defects Screening, BGI-Shenzhen, Shenzhen, China
| | - Xiaoxia Wu
- Department of Obstetrics, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Ning Sun
- Department of Obstetrics, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Yiwei Zhang
- Department of Obstetrics, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Jing Zhang
- Department of Obstetrics, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Yixuan Chen
- Department of Obstetrics, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Jianing Tong
- Department of Obstetrics and Gynecology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xiangdong Wang
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Fudan University Shanghai Medical College, Shanghai, China.,Fudan University Shanghai Medical College, Shanghai, China
| | | | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, China.,School of Medicine, South China University of Technology, Guangzhou, China
| | - Jianmin Niu
- Department of Obstetrics and Gynecology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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6
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Wu W, Liang X, Li H, Huang X, Wan C, Xie Q, Liu Z. Landscape of T Cells in NK-AML(M4/M5) Revealed by Single-Cell Sequencing. J Leukoc Biol 2022; 112:745-758. [PMID: 35258858 DOI: 10.1002/jlb.5a0721-396rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 02/15/2022] [Indexed: 12/11/2022] Open
Abstract
Normal karyotype acute myeloid leukemia (NK-AML) is a highly heterogeneous malignancy that resides within a complex immune microenvironment, complicating efforts to reveal the interaction between leukemia cells and immune cells. Understanding tumor-infiltrating T cells is crucial to the advancement of immune therapies and the improvement of the prognosis for NK-AML patients. We performed single-cell RNA sequencing on bone marrow cells from 5 NK-AML (M4/M5) patients and 1 normal donor and paired single-cell T cell receptor (TCR) sequencing on single T cells. As a result, we identified 8 T cell clusters based on the gene expression characteristics of each subset in NK-AML and described their developmental trajectories. In NK-AML patients, specific clusters, such as mucosal-associated invariant T cells (MAITs), were preferentially enriched and potentially clonally expanded. These transcriptome and TCR data analyses provide valuable insights and rich resources for understanding the immune environment of NK-AML.
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Affiliation(s)
- Wenqi Wu
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaolin Liang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Huiqun Li
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaoke Huang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Chengyao Wan
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Qiongni Xie
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Zhenfang Liu
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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7
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Genome-wide analysis provides genetic evidence that ACE2 influences COVID-19 risk and yields risk scores associated with severe disease. Nat Genet 2022; 54:382-392. [PMID: 35241825 PMCID: PMC9005345 DOI: 10.1038/s41588-021-01006-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 12/17/2021] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters human host cells via angiotensin-converting enzyme 2 (ACE2) and causes coronavirus disease 2019 (COVID-19). Here, through a genome-wide association study, we identify a variant (rs190509934, minor allele frequency 0.2–2%) that downregulates ACE2 expression by 37% (P = 2.7 × 10−8) and reduces the risk of SARS-CoV-2 infection by 40% (odds ratio = 0.60, P = 4.5 × 10−13), providing human genetic evidence that ACE2 expression levels influence COVID-19 risk. We also replicate the associations of six previously reported risk variants, of which four were further associated with worse outcomes in individuals infected with the virus (in/near LZTFL1, MHC, DPP9 and IFNAR2). Lastly, we show that common variants define a risk score that is strongly associated with severe disease among cases and modestly improves the prediction of disease severity relative to demographic and clinical factors alone. Genome-wide meta-analysis of SARS-CoV-2 susceptibility and severity phenotypes in up to 756,646 samples identifies a rare protective variant proximal to ACE2. A 6-SNP genetic risk score provides additional predictive power when added to known risk factors.
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8
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Curson JE, Luo L, Liu L, Burgess BJ, Bokil NJ, Wall AA, Brdicka T, Kapetanovic R, Stow JL, Sweet MJ. An alternative downstream translation start site in the non-TIR adaptor Scimp enables selective amplification of CpG DNA responses in mouse macrophages. Immunol Cell Biol 2022; 100:267-284. [PMID: 35201640 PMCID: PMC9544816 DOI: 10.1111/imcb.12540] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 01/01/2023]
Abstract
Toll-like receptor (TLR) signaling relies on Toll/interleukin-1 receptor homology (TIR) domain-containing adaptor proteins that recruit downstream signaling molecules to generate tailored immune responses. In addition, the palmitoylated transmembrane adaptor protein family member Scimp acts as a non-TIR-containing adaptor protein in macrophages, scaffolding the Src family kinase Lyn to enable TLR phosphorylation and proinflammatory signaling responses. Here we report the existence of a smaller, naturally occurring translational variant of Scimp (Scimp TV1), which is generated through leaky scanning and translation at a downstream methionine. Scimp TV1 also scaffolds Lyn, but in contrast to full-length Scimp, it is basally rather than lipopolysaccharide (LPS)-inducibly phosphorylated. Macrophages from mice that selectively express Scimp TV1, but not full-length Scimp, have impaired sustained LPS-inducible cytokine responses. Furthermore, in granulocyte macrophage colony-stimulating factor-derived myeloid cells that express high levels of Scimp, selective overexpression of Scimp TV1 enhances CpG DNA-inducible cytokine production. Unlike full-length Scimp that localizes to the cell surface and filopodia, Scimp TV1 accumulates in intracellular compartments, particularly the Golgi. Moreover, this variant of Scimp is not inducibly phosphorylated in response to CpG DNA, suggesting that it may act via an indirect mechanism to enhance TLR9 responses. Our findings thus reveal the use of alternative translation start sites as a previously unrecognized mechanism for diversifying TLR responses in the innate immune system.
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Affiliation(s)
- James Eb Curson
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Lin Luo
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Liping Liu
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Belinda J Burgess
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Nilesh J Bokil
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Adam A Wall
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Tomas Brdicka
- Laboratory of Leukocyte Signaling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ronan Kapetanovic
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia.,Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jennifer L Stow
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience (IMB), IMB Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
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9
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Ho CH, Cheng CH, Huang TW, Peng SY, Lee KM, Cheng PC. Switched phenotypes of macrophages during the different stages of Schistosoma japonicum infection influenced the subsequent trends of immune responses. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 55:503-526. [PMID: 34330662 DOI: 10.1016/j.jmii.2021.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 05/28/2021] [Accepted: 06/24/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Macrophages play crucial roles in immune responses during the course of schistosomal infections. METHODS We currently investigated influence of immunocompetent changes in macrophages via microarray-based analysis, mRNA expression analysis, detection of serum cytokines, and subsequent evaluation of the immune phenotypes following the differentiation of infection-induced lymphocytes in a unique T1/T2 double-transgenic mouse model. RESULTS The gradual upregulation of genes encoding YM1, YM2, and interleukin (IL)-4/IL-13 receptors in infected mice indicated the role of type 2 alternatively activated macrophages (M2, AAMφs) in immune responses after Schistosoma japonicum egg production. FACS analysis showed that surface markers MHC class II (IA/IE) and CD8α+ of the macrophages also exhibited a dramatic change at the various time points before and after egg-production. The transgenic mouse experiments further demonstrated that the shifting of macrophage phenotypes influenced the percentage of helper T (Th)-2 cells, which was observed to be higher than that of Th1 cells, which increased only at 3 and 5 weeks post-infection. The differentiation of effector B cells showed a similar but more significant trend toward type-2 immunity. CONCLUSION These results suggest that the infection of mice with S. japonicum resulted in a final Th2- and Be2-skewed immune response. This may be due to phenotypic changes in the macrophages. The influence of alternatively activated macrophages was also activated by S. japonicum egg production. This study elucidated the existence of variations in immune mechanisms at the schistosome infection stages.
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Affiliation(s)
- Chen-Hsun Ho
- Division of Urology, Department of Surgery, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan; School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Chia-Hsiung Cheng
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tzu-Wen Huang
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Shih-Yi Peng
- Department of Biochemistry, College of Medicine, Tzu Chi University, Hualien, Taiwan.
| | - Kin-Mu Lee
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Po-Ching Cheng
- Department of Molecular Parasitology and Tropical Diseases, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Center for International Tropical Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
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10
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Horowitz JE, Kosmicki JA, Damask A, Sharma D, Roberts GHL, Justice AE, Banerjee N, Coignet MV, Yadav A, Leader JB, Marcketta A, Park DS, Lanche R, Maxwell E, Knight SC, Bai X, Guturu H, Sun D, Baltzell A, Kury FSP, Backman JD, Girshick AR, O'Dushlaine C, McCurdy SR, Partha R, Mansfield AJ, Turissini DA, Li AH, Zhang M, Mbatchou J, Watanabe K, Gurski L, McCarthy SE, Kang HM, Dobbyn L, Stahl E, Verma A, Sirugo G, Ritchie MD, Jones M, Balasubramanian S, Siminovitch K, Salerno WJ, Shuldiner AR, Rader DJ, Mirshahi T, Locke AE, Marchini J, Overton JD, Carey DJ, Habegger L, Cantor MN, Rand KA, Hong EL, Reid JG, Ball CA, Baras A, Abecasis GR, Ferreira MA. Genome-wide analysis in 756,646 individuals provides first genetic evidence that ACE2 expression influences COVID-19 risk and yields genetic risk scores predictive of severe disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 33619501 PMCID: PMC7899471 DOI: 10.1101/2020.12.14.20248176] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2 enters host cells by binding angiotensin-converting enzyme 2 (ACE2). Through a genome-wide association study, we show that a rare variant (MAF = 0.3%, odds ratio 0.60, P=4.5×10-13) that down-regulates ACE2 expression reduces risk of COVID-19 disease, providing human genetics support for the hypothesis that ACE2 levels influence COVID-19 risk. Further, we show that common genetic variants define a risk score that predicts severe disease among COVID-19 cases.
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Affiliation(s)
- J E Horowitz
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J A Kosmicki
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Damask
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D Sharma
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - G H L Roberts
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | | | - N Banerjee
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M V Coignet
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - A Yadav
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | | | - A Marcketta
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D S Park
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - R Lanche
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - E Maxwell
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S C Knight
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - X Bai
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - H Guturu
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - D Sun
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Baltzell
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - F S P Kury
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J D Backman
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A R Girshick
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - C O'Dushlaine
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S R McCurdy
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - R Partha
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - A J Mansfield
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D A Turissini
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - A H Li
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M Zhang
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - J Mbatchou
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - K Watanabe
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - L Gurski
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S E McCarthy
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - H M Kang
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - L Dobbyn
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - E Stahl
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - G Sirugo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - M D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - M Jones
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S Balasubramanian
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - K Siminovitch
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - W J Salerno
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A R Shuldiner
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - A E Locke
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J Marchini
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J D Overton
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | | | - L Habegger
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M N Cantor
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - K A Rand
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - E L Hong
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - J G Reid
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - C A Ball
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - A Baras
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - G R Abecasis
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M A Ferreira
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
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11
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Pan M, Yang P, Wang F, Luo X, Li B, Ding Y, Lu H, Dong Y, Zhang W, Xiu B, Liang A. Whole Transcriptome Data Analysis Reveals Prognostic Signature Genes for Overall Survival Prediction in Diffuse Large B Cell Lymphoma. Front Genet 2021; 12:648800. [PMID: 34178023 PMCID: PMC8220154 DOI: 10.3389/fgene.2021.648800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
Background With the improvement of clinical treatment outcomes in diffuse large B cell lymphoma (DLBCL), the high rate of relapse in DLBCL patients is still an established barrier, as the therapeutic strategy selection based on potential targets remains unsatisfactory. Therefore, there is an urgent need in further exploration of prognostic biomarkers so as to improve the prognosis of DLBCL. Methods The univariable and multivariable Cox regression models were employed to screen out gene signatures for DLBCL overall survival (OS) prediction. The differential expression analysis was used to identify representative genes in high-risk and low-risk groups, respectively, where student t test and fold change were implemented. The functional difference between the high-risk and low-risk groups was identified by the gene set enrichment analysis. Results We conducted a systematic data analysis to screen the candidate genes significantly associated with OS of DLBCL in three NCBI Gene Expression Omnibus (GEO) datasets. To construct a prognostic model, five genes (CEBPA, CYP27A1, LST1, MREG, and TARP) were then screened and tested using the multivariable Cox model and the stepwise regression method. Kaplan–Meier curve confirmed the good predictive performance of this five-gene Cox model. Thereafter, the prognostic model and the expression levels of the five genes were validated by means of an independent dataset. High expression levels of these five genes were significantly associated with favorable prognosis in DLBCL, both in training and validation datasets. Additionally, further analysis revealed the independent value and superiority of this prognostic model in risk prediction. Functional enrichment analysis revealed some vital pathways responsible for unfavorable outcome and potential therapeutic targets in DLBCL. Conclusion We developed a five-gene Cox model for the clinical outcome prediction of DLBCL patients. Meanwhile, potential drug selection using this model can help clinicians to improve the clinical practice for the benefit of patients.
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Affiliation(s)
- Mengmeng Pan
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pingping Yang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fangce Wang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiu Luo
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bing Li
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Ding
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huina Lu
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yan Dong
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wenjun Zhang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bing Xiu
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Aibin Liang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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12
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Fabisik M, Tureckova J, Pavliuchenko N, Kralova J, Balounova J, Vicikova K, Skopcova T, Spoutil F, Pokorna J, Angelisova P, Malissen B, Prochazka J, Sedlacek R, Brdicka T. Regulation of Inflammatory Response by Transmembrane Adaptor Protein LST1. Front Immunol 2021; 12:618332. [PMID: 33986741 PMCID: PMC8111073 DOI: 10.3389/fimmu.2021.618332] [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: 10/16/2020] [Accepted: 04/08/2021] [Indexed: 12/17/2022] Open
Abstract
LST1 is a small adaptor protein expressed in leukocytes of myeloid lineage. Due to the binding to protein tyrosine phosphatases SHP1 and SHP2 it was thought to have negative regulatory function in leukocyte signaling. It was also shown to be involved in cytoskeleton regulation and generation of tunneling nanotubes. LST1 gene is located in MHCIII locus close to many immunologically relevant genes. In addition, its expression increases under inflammatory conditions such as viral infection, rheumatoid arthritis and inflammatory bowel disease and its deficiency was shown to result in slightly increased sensitivity to influenza infection in mice. However, little else is known about its role in the immune system homeostasis and immune response. Here we show that similar to humans, LST1 is expressed in mice in the cells of the myeloid lineage. In vivo, its deficiency results in alterations in multiple leukocyte subset abundance in steady state and under inflammatory conditions. Moreover, LST1-deficient mice show significant level of resistance to dextran sodium sulphate (DSS) induced acute colitis, a model of inflammatory bowel disease. These data demonstrate that LST1 regulates leukocyte abundance in lymphoid organs and inflammatory response in the gut.
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Affiliation(s)
- Matej Fabisik
- Laboratory of Leukocyte Signalling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia.,Faculty of Science, Charles University, Prague, Czechia
| | - Jolana Tureckova
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia.,Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia
| | - Nataliia Pavliuchenko
- Laboratory of Leukocyte Signalling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia.,Faculty of Science, Charles University, Prague, Czechia
| | - Jarmila Kralova
- Laboratory of Leukocyte Signalling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Jana Balounova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia
| | - Kristina Vicikova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia
| | - Tereza Skopcova
- Laboratory of Leukocyte Signalling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Frantisek Spoutil
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia
| | - Jana Pokorna
- Laboratory of Leukocyte Signalling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Pavla Angelisova
- Laboratory of Leukocyte Signalling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Bernard Malissen
- Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Jan Prochazka
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia.,Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia.,Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia
| | - Tomas Brdicka
- Laboratory of Leukocyte Signalling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
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13
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Khurana N, Pulsipher A, Ghandehari H, Alt JA. Meta-analysis of global and high throughput public gene array data for robust vascular gene expression discovery in chronic rhinosinusitis: Implications in controlled release. J Control Release 2021; 330:878-888. [PMID: 33144181 PMCID: PMC7906912 DOI: 10.1016/j.jconrel.2020.10.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 01/21/2023]
Abstract
BACKGROUND Chronic inflammation is known to cause alterations in vascular homeostasis that directly affects blood vessel morphogenesis, angiogenesis, and tissue permeability. These phenomena have been investigated and exploited for targeted drug delivery applications in the context of cancers and other disease processes. Vascular pathophysiology and its associated genes and signaling pathways, however, have not been systematically investigated in patients with chronic rhinosinusitis (CRS). Understanding the interplay between key vascular signaling pathways and top biomarkers associated with CRS may facilitate the development of new targeted delivery strategies and treatment paradigms. Herein, we report findings from a gene meta-analysis to identify key vascular pathways and top genes involved in CRS. METHODS Proprietary software (Illumina BaseSpace Correlation Engine) and open-access data sets were used to perform a gene meta-analysis to systematically determine significant differences between key vascular biomarkers and vascular signaling pathways expressed in sinonasal tissue biopsies of controls and patients with CRS. RESULTS Thirteen studies were initially identified, and then reduced to five after applying exclusion principle algorithms. Genes associated with vasculature development and blood vessel morphogenesis signaling pathways were identified to be overexpressed among the top 15 signaling pathways. Out of many significantly upregulated genes, the levels of pro angiogenic genes such as early growth response (EGR3), platelet endothelial cell adhesion molecule (PECAM1) and L-selectin (SELL) were particularly significant in patients with CRS compared to controls. DISCUSSION Key vascular biomarkers and signaling pathways were significantly overexpressed in patients with CRS compared to controls, suggesting a contribution of vascular dysfunction in CRS pathophysiology. Vascular dysregulation and permeability may afford opportunities to develop drug delivery systems to improve efficacy and reduce toxicity of CRS treatment.
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Affiliation(s)
- Nitish Khurana
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT, 84112, USA; Utah Center for Nanomedicine, Nano Institute of Utah, University of Utah, Salt Lake City, UT, 84112, USA
| | - Abigail Pulsipher
- Utah Center for Nanomedicine, Nano Institute of Utah, University of Utah, Salt Lake City, UT, 84112, USA; Division of Otolaryngology, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Hamidreza Ghandehari
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT, 84112, USA; Utah Center for Nanomedicine, Nano Institute of Utah, University of Utah, Salt Lake City, UT, 84112, USA; Division of Otolaryngology, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA; Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Jeremiah A Alt
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT, 84112, USA; Utah Center for Nanomedicine, Nano Institute of Utah, University of Utah, Salt Lake City, UT, 84112, USA; Division of Otolaryngology, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA; Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, 84112, USA.
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14
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Marthong L, Ghosh S, Palodhi A, Imran M, Shunyu NB, Maitra A, Ghosh S. Whole Genome DNA Methylation and Gene Expression Profiling of Oropharyngeal Cancer Patients in North-Eastern India: Identification of Epigenetically Altered Gene Expression Reveals Potential Biomarkers. Front Genet 2020; 11:986. [PMID: 33133131 PMCID: PMC7578381 DOI: 10.3389/fgene.2020.00986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022] Open
Abstract
Oropharyngeal cancer is a subtype of head and neck squamous cell carcinoma that is associated with unique risk exposures like consumption of smokeless tobacco and areca nut and is highly prevalent in the northeastern region of India, especially Meghalaya. However, the underlying epigenetic and transcriptomic changes in this cancer type is yet to be delineated. We have undertaken a study on genome wide somatic alterations in the DNA methylation and transcriptome in oropharyngeal cancer patients from this region using genome wide techniques in paired tumors and adjacent normal tissues. By using integrative approaches, we have identified 194 epigenetically silenced and 241 epigenetically overexpressed genes in the tumor tissue of these patients. Pathways that are significantly enriched by these genes include the pathways of immune systems, such as the interleukin signaling pathways and Toll-like receptor signaling pathway. Also, osteoclast differentiation pathway was found to be epigenetically upregulated. The pathways enriched by the epigenetically downregulated genes were found to be predominantly those involved in xenobiotic metabolism and keratinization. Two major transcription factors - SPI1 and RUNX1 were identified as epigenetically dysregulated, which further modulates 129 downstream genes. Comparison of our observations with the head and neck cancer data from TCGA revealed distinct DNA methylation and gene expression landscapes which might be specific for oropharyngeal cancer. HPV DNA sequences were not detected in any of the tumor samples in RNA-Seq data. The results obtained in this study might provide improved understanding of the disease.
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Affiliation(s)
- Lastborn Marthong
- Department of Zoology, North Eastern Hill University (NEHU), Shillong, India
| | - Sahana Ghosh
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Arindam Palodhi
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Mohamed Imran
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Neizekhotuo Brian Shunyu
- Department of Otorhinolaryngology (ENT), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences (NEIGRIHMS), Shillong, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Srimoyee Ghosh
- Department of Zoology, North Eastern Hill University (NEHU), Shillong, India
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15
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Tubbs JD, Ding J, Baum L, Sham PC. Immune dysregulation in depression: Evidence from genome-wide association. Brain Behav Immun Health 2020; 7:100108. [PMID: 34589869 PMCID: PMC8474691 DOI: 10.1016/j.bbih.2020.100108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 07/12/2020] [Indexed: 12/15/2022] Open
Abstract
A strong body of evidence supports a role for immune dysregulation across many psychiatric disorders including depression, the leading cause of global disability. Recent progress in the search for genetic variants associated with depression provides the opportunity to strengthen our current understanding of etiological factors contributing to depression and generate novel hypotheses. Here, we provide an overview of the literature demonstrating a role for immune dysregulation in depression, followed by a detailed discussion of the immune-related genes identified by the most recent genome-wide meta-analysis of depression. These genes represent strong evidence-based targets for future basic and translational research which aims to understand the role of the immune system in depression pathology and identify novel points for therapeutic intervention.
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Affiliation(s)
- Justin D. Tubbs
- Department of Psychiatry, The University of Hong Kong, Hong Kong
| | - Jiahong Ding
- Department of Psychiatry, The University of Hong Kong, Hong Kong
| | - Larry Baum
- Department of Psychiatry, The University of Hong Kong, Hong Kong
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong
| | - Pak C. Sham
- Department of Psychiatry, The University of Hong Kong, Hong Kong
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong
- Centre for PanorOmic Sciences, The University of Hong Kong, Hong Kong
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16
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Zhang Y, Li Z, Kholodkevich S, Sharov A, Feng Y, Ren N, Sun K. Cadmium-induced oxidative stress, histopathology, and transcriptome changes in the hepatopancreas of freshwater crayfish (Procambarus clarkii). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 666:944-955. [PMID: 30970501 DOI: 10.1016/j.scitotenv.2019.02.159] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/01/2019] [Accepted: 02/10/2019] [Indexed: 05/06/2023]
Abstract
Cadmium (Cd) is a common contaminant in environment. Crayfish are considered suitable for indicating the impact of heavy metals on the environment. However, there is limited information on the mechanisms causing damage to the hepatopancreas of Procambarus clarkii exposed to Cd. We exposed adult male P. clarkii to 2.0, 5.0, and 10.0 mg/L Cd for 24, 48, and 72 h to explore Cd toxicity. Afterwards, we measured bioaccumulations in the hepatopancreas and determined malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT), and glutathione S-transferase (GST). Additionally, the hepatopancreas histopathology was analyzed and the transcriptome analysis of the P. clarkii hepatopancreas under Cd stress was conducted. The results revealed that hepatopancreas could accumulate Cd in a time- and dose-dependent manner. Cd induced significant changes in MDA content and antioxidant enzyme activity. Severe histological alterations were observed in crayfish hepatopancreas. After 72 h exposure to 2.0, 5.0, and 10.0 mg/L Cd, transcriptome analysis identified 1061, 747, and 1086 differentially expressed genes (DEGs), respectively. Exposure to 5.0 mg/L Cd inhibited heme binding, tetrapyrrole binding, iron ion binding and activity of oxidoreductase and sulfotransferase, while exposure to 10.0 mg/L Cd enhanced the export of matters from nucleus. In the hepatopancreas treated with 10.0 mg/L Cd, pathways related to diseases and immune system were significantly enriched. Meanwhile, 31, 31, 24, 7, and 12 identified DEGs were associated with the oxidation-reduction process, immune system, ion homeostasis, digestion and absorption, and ATPases, respectively. Our study provides comprehensive information for exploring the toxic mechanisms of Cd and candidate biomarkers for aquatic Cd risk evaluation.
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Affiliation(s)
- Yu Zhang
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zheyu Li
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Sergey Kholodkevich
- Institute of Earth Sciences, Saint-Petersburg State University, Saint-Petersburg 199034, Russia
| | - Andrey Sharov
- Institute of Earth Sciences, Saint-Petersburg State University, Saint-Petersburg 199034, Russia
| | - Yujie Feng
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nanqi Ren
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Kai Sun
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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17
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Zhou Y, Qiao H, Yin N, Chen L, Xie Y, Wu J, Du J, Lin X, Wang Y, Liu Y, Yi S, Zhang G, Sun M, He Z, Li H. Immune and cytokine/chemokine responses of PBMCs in rotavirus‐infected rhesus infants and their significance in viral pathogenesis. J Med Virol 2019; 91:1448-1469. [DOI: 10.1002/jmv.25460] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/17/2019] [Accepted: 02/01/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Yan Zhou
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Hongtu Qiao
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Na Yin
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Linlin Chen
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Yuping Xie
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Jinyuan Wu
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Jing Du
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Xiaochen Lin
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Yi Wang
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Yang Liu
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Shan Yi
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Guangming Zhang
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Maosheng Sun
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Zhanlong He
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Hongjun Li
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
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18
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Weidle UH, Rohwedder I, Birzele F, Weiss EH, Schiller C. LST1: A multifunctional gene encoded in the MHC class III region. Immunobiology 2018; 223:699-708. [PMID: 30055863 DOI: 10.1016/j.imbio.2018.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/14/2018] [Indexed: 12/11/2022]
Abstract
The LST1 gene is located in the MHC class III cluster between the MHC class I and II regions. While most genes in this cluster have been sufficiently characterised, a definitive function and expression pattern for LST1 still remains elusive. In the present review we describe its promotor, gene organisation, splice variants and expression in human tissues, cell lines and cancer. We focus on LST1 expression in inflammation and discuss known correlations with autoimmune diseases and cancer. Current data on LST1 polymorphisms and their known associations with pathologies are also discussed in detail. We summarize the potential functions that have been described for the full-length LST1 protein including its function as a transmembrane adaptor protein with inhibitory signal transduction and its role as a membrane scaffold facilitating the formation of tunnelling nanotubes. We also discuss further potential functions by compiling all known LST1-interacting proteins. Furthermore, we address knowledge gaps and conflictive issues regarding disease association, non-hematopoietic expression and the discrepancy between RNA and protein expression data.
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Affiliation(s)
- Ulrich H Weidle
- Zentrum Seniorenstudium, Ludwig-Maximilians-Universität München, Hohenstaufenstrasse 1, 80801 München, Germany
| | - Ina Rohwedder
- Department of Biology II, Ludwig-Maximilians-Universität München, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Fabian Birzele
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, Grenzacherstrasse 124, 4052 Basel, Switzerland
| | - Elisabeth H Weiss
- Zentrum Seniorenstudium, Ludwig-Maximilians-Universität München, Hohenstaufenstrasse 1, 80801 München, Germany; Department of Biology II, Ludwig-Maximilians-Universität München, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Christian Schiller
- Department of Biology II, Ludwig-Maximilians-Universität München, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany.
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19
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Yuan FF, Ye XP, Liu W, Xue LQ, Ma YR, Zhang LL, Zhang MM, Sun F, Wan YY, Zhang QY, Zhao SX, Song HD. Genetic study of early-onset Graves' disease in the Chinese Han population. Clin Genet 2017; 93:103-110. [PMID: 28598035 DOI: 10.1111/cge.13072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/31/2017] [Indexed: 01/19/2023]
Abstract
Graves' disease (GD) is a complex autoimmune disorder in which genetic and environmental factors are both involved in the pathogenesis. Early-onset patients have a shorter exposure time to environmental factors and are, therefore, good models to help understand the genetic architecture of GD. Based on previous studies of early-onset GD, 11 single nucleotide polymorphisms (SNPs) and their related SNPs (R2 > .6), SNPs located within a ±1-Mb region of the FOXP3 gene, and 20 validated GD-risk SNPs were selected and screened for genotyping in 3735 GD and 4893 control patients to investigate whether early-onset GD is a subtype of GD with distinct susceptibility genes. Ultimately, we did not confirm the reported genetic markers of early-onset GD in our Chinese Han population but found that a GD-risk SNP located in the human leukocyte antigen class I region-rs4947296-was more strongly correlated with early-onset GD than non-early-onset GD. In addition, heterogeneity analysis of GD patients suggests that it may be more reasonable to define early-onset GD as an onset age ≤20 years.
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Affiliation(s)
- F-F Yuan
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China.,Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - X-P Ye
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - W Liu
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China.,Department of Endocrinology, The Ninth People's Hospital (the north branch) Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - L-Q Xue
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Y-R Ma
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - L-L Zhang
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - M-M Zhang
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - F Sun
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Y-Y Wan
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Q-Y Zhang
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - S-X Zhao
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - H-D Song
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
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20
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Cai Q, Tu M, Xu-Monette ZY, Sun R, Manyam GC, Xu X, Tzankov A, Hsi ED, Møller MB, Medeiros LJ, Ok CY, Young KH. NF-κB p50 activation associated with immune dysregulation confers poorer survival for diffuse large B-cell lymphoma patients with wild-type p53. Mod Pathol 2017; 30:854-876. [PMID: 28281555 DOI: 10.1038/modpathol.2017.5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/29/2016] [Accepted: 12/29/2016] [Indexed: 12/12/2022]
Abstract
Dysregulated NF-κB signaling is critical for lymphomagenesis, however, the expression and clinical relevance of NF-κB subunit p50 in diffuse large B-cell lymphoma have not been evaluated. In this study, we analyzed the prognostic significance and gene expression signatures of p50 nuclear expression as a surrogate for p50 activation in 465 patients with de novo diffuse large B-cell lymphoma. We found that p50+ nuclear expression, observed in 34.6% of diffuse large B-cell lymphoma, predominantly composed of activated B-cell-like subtype, was an independent adverse prognostic factor in patients with activated B-cell-like diffuse large B-cell lymphoma. It was also an adverse prognostic factor in patients with wild-type TP53 independent of the activated B-cell-like and germinal center B-cell-like subtypes, even though p50 activation correlated with significantly lower levels of Myc, PI3K, phospho-AKT, and CXCR4 expression and less frequent BCL2 translocations. In contrast, in germinal center B-cell-like diffuse large B-cell lymphoma patients with TP53 mutations, p50+ nuclear expression correlated with significantly better clinical outcomes, and decreased p53, Bcl-2, and Myc expression. Gene expression profiling revealed multiple signaling pathways potentially upstream the p50 activation through either canonical or noncanonical NF-κB pathways, and suggested that immune suppression, including that by the immune checkpoint TIM-3 and that through leukocyte immunoglobulin-like receptors, but not antiapoptosis and proliferation, may underlie the observed poorer survival rates associated with p50+ nuclear expression in diffuse large B-cell lymphoma. In conclusion, these data show that p50 is important as a unique mechanism of R-CHOP-resistance in activated B-cell-like diffuse large B-cell lymphoma and in patients without TP53 mutations. The results also provide insights into the regulation and function of p50 in diffuse large B-cell lymphoma and its cross talk with the p53 pathway with important therapeutic implications.
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Affiliation(s)
- Qingqing Cai
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China.,Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Meifeng Tu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital &Institute, Beijing, China
| | - Zijun Y Xu-Monette
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruifang Sun
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ganiraju C Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaolu Xu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | | | - Eric D Hsi
- Department of Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Michael B Møller
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chi Young Ok
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ken H Young
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,The University of Texas School of Medicine, Graduate School of Biomedical Sciences, Houston, TX, USA
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21
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Yau AC, Tuncel J, Holmdahl R. The Major Histocompatibility Complex Class III Haplotype Ltab-Ncr3 Regulates Adjuvant-Induced but Not Antigen-Induced Autoimmunity. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:987-998. [DOI: 10.1016/j.ajpath.2016.12.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 12/23/2016] [Accepted: 12/27/2016] [Indexed: 12/12/2022]
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22
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Conserved 33-kb haplotype in the MHC class III region regulates chronic arthritis. Proc Natl Acad Sci U S A 2016; 113:E3716-24. [PMID: 27303036 DOI: 10.1073/pnas.1600567113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies have revealed many genetic loci associated with complex autoimmune diseases. In rheumatoid arthritis (RA), the MHC gene HLA-DRB1 is the strongest candidate predicting disease development. It has been suggested that other immune-regulating genes in the MHC contribute to the disease risk, but this contribution has been difficult to show because of the strong linkage disequilibrium within the MHC. We isolated genomic regions in the form of congenic fragments in rats to test whether there are additional susceptibility loci in the MHC. By both congenic mapping in inbred strains and SNP typing in wild rats, we identified a conserved, 33-kb large haplotype Ltab-Ncr3 in the MHC-III region, which regulates the onset, severity, and chronicity of arthritis. The Ltab-Ncr3 haplotype consists of five polymorphic immunoregulatory genes: Lta (lymphotoxin-α), Tnf, Ltb (lymphotoxin-β), Lst1 (leukocyte-specific transcript 1), and Ncr3 (natural cytotoxicity-triggering receptor 3). Significant correlation in the expression of the Ltab-Ncr3 genes suggests that interaction of these genes may be important in keeping these genes clustered together as a conserved haplotype. We studied the arthritis association and the spliceo-transcriptome of four different Ltab-Ncr3 haplotypes and showed that higher Ltb and Ncr3 expression, lower Lst1 expression, and the expression of a shorter splice variant of Lst1 correlate with reduced arthritis severity in rats. Interestingly, patients with mild RA also showed higher NCR3 expression and lower LST1 expression than patients with severe RA. These data demonstrate the importance of a conserved haplotype in the regulation of complex diseases such as arthritis.
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23
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Liu YZ, Maney P, Puri J, Zhou Y, Baddoo M, Strong M, Wang YP, Flemington E, Deng HW. RNA-sequencing study of peripheral blood monocytes in chronic periodontitis. Gene 2016; 581:152-60. [PMID: 26812355 DOI: 10.1016/j.gene.2016.01.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 11/25/2022]
Abstract
BACKGROUND Monocytes are an important cell type in chronic periodontitis (CP) by interacting with oral bacteria and mediating host immune response. The aim of this study was to reveal new functional genes and pathways for CP at monocyte transcriptomic level. METHODS We performed an RNA-sequencing (RNA-seq) study of peripheral blood monocytes (PBMs) in 5 non-smoking moderate to severe CP (case) individuals vs. 5 controls. We took advantage of a microarray study of periodontitis to support our findings. We also performed pathway-based analysis on the identified differentially expressed (DEx) transcripts/isoforms using DAVID (Database for Annotation, Visualization and Integrated Discovery). RESULTS Through differential expression analyses at both whole gene (or whole non-coding RNA) and isoform levels, we identified 380 DEx transcripts and 5955 DEx isoforms with a PPEE (posterior probability of equal expression) of <0.05. Pervasive up-regulation of transcripts at isoform level in CP vs. control individuals was observed, suggesting a more functionally active monocyte transcriptome for CP. By comparing with the microarray dataset, we identified several CP-associated novel genes (e.g., FACR and CUX1) that have functions to interact with invading microorganisms or enhance TNF production on lipopolysaccharide stimulation. DAVID analysis of both the RNA-seq and the microarray datasets leads to converging evidence supporting "endocytosis", "cytokine production" and "apoptosis" as significant biological processes in CP. CONCLUSIONS As the first RNA-seq study of PBMs for CP, this study provided novel findings at both gene (e.g., FCAR and CUX1) and biological process level. The findings will contribute to better understanding of CP disease mechanisms.
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Affiliation(s)
- Yao-Zhong Liu
- Center of Genomics and Bioinformatics, Dept. of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States.
| | - Pooja Maney
- Dept. of Periodontics, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, LA, United States.
| | - Jyoti Puri
- Dept. of Periodontics, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Yu Zhou
- Center of Genomics and Bioinformatics, Dept. of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Melody Baddoo
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, United States
| | - Michael Strong
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, United States
| | - Yu-Ping Wang
- Dept. of Biomedical Engineering, Tulane University School of Science and Engineering, United States
| | - Erik Flemington
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, United States
| | - Hong-Wen Deng
- Center of Genomics and Bioinformatics, Dept. of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
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24
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Schiller C, Nowak C, Diakopoulos KN, Weidle UH, Weiss EH. An upstream open reading frame regulates LST1 expression during monocyte differentiation. PLoS One 2014; 9:e96245. [PMID: 24816991 PMCID: PMC4015914 DOI: 10.1371/journal.pone.0096245] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 04/04/2014] [Indexed: 01/23/2023] Open
Abstract
The regulation of gene expression depends on the interplay of multiple factors at the transcriptional and translational level. Upstream open reading frames (uORFs) play an important role as translational repressors of main ORFs and their presence or usage in transcripts can be regulated by different mechanisms. The main objective of the present study was to assess whether uORFs regulate the expression of the MHC class III gene LST1. We report that expression of LST1 is tightly regulated by alternative transcription initiation and the presence of an uORF in the 5′-UTR of transcripts. Specifically, using EGFP reporter constructs in human HeLa and HEK-293T cells and flow cytometry as well as western blot analysis we found the uORF to reduce the expression of the main ORF by roughly two-thirds. Furthermore, we were able to correlate a previously detected increase in LST1 protein expression during monocyte differentiation with an increase of transcription initiation at an alternative exon that does not contain an uORF.
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Affiliation(s)
- Christian Schiller
- Department of Biology II, Ludwig-Maximilians-Universität München, Germany
| | - Carina Nowak
- Department of Biology II, Ludwig-Maximilians-Universität München, Germany
| | | | | | - Elisabeth H. Weiss
- Department of Biology II, Ludwig-Maximilians-Universität München, Germany
- * E-mail:
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25
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Heidemann J, Kebschull M, Tepasse PR, Bettenworth D. Regulated expression of leukocyte-specific transcript (LST) 1 in human intestinal inflammation. Inflamm Res 2014; 63:513-7. [PMID: 24682411 DOI: 10.1007/s00011-014-0732-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 03/09/2014] [Accepted: 03/21/2014] [Indexed: 01/24/2023] Open
Abstract
INTRODUCTION Leukocyte-specific transcript 1 (LST1) encoded peptides are involved in immunomodulation and nanotube-mediated cell-cell communication. The aim of this study was to assess the expression of LST1 in colonic epithelium and endothelium during intestinal inflammation. METHODS LST1 expression was evaluated by RT-PCR, FACS, western blot analysis, and immunohistochemistry in intestinal epithelial Caco-2 cells, human intestinal microvascular endothelial cells and in human histological specimens from inflammatory bowel disease (IBD) patients and non-IBD colitis patients. RESULTS LST1 expression was significantly increased upon proinflammatory stimulation in intestinal epithelial and endothelial cells. Furthermore, LST1 tissue expression was significantly enhanced in macroscopically inflamed colonic mucosal biopsies as compared to non-affected mucosal areas. CONCLUSIONS This is the first report demonstrating regulated LST1 expression in human intestinal epithelial and microvascular endothelial cells and in inflamed colonic tissue from IBD patients. Proinflammatory expression of LST1 occurs in the setting of human IBD and is not restricted to immune cell populations. Future studies are needed to further elucidate the role of soluble and membrane-expressed LST1 in the regulation of mucosal intestinal immunity and inflammation as well as to reveal possible therapeutic implications.
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Affiliation(s)
- Jan Heidemann
- Department of Internal Medicine B, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
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26
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Knetter SM, Bearson SMD, Huang TH, Kurkiewicz D, Schroyen M, Nettleton D, Berman D, Cohen V, Lunney JK, Ramer-Tait AE, Wannemuehler MJ, Tuggle CK. Salmonella enterica serovar Typhimurium-infected pigs with different shedding levels exhibit distinct clinical, peripheral cytokine and transcriptomic immune response phenotypes. Innate Immun 2014; 21:227-41. [PMID: 24632525 DOI: 10.1177/1753425914525812] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Foodborne salmonellosis costs the US $2.7 billion/year, including $100.0 million in annual losses to pork producers. Pigs colonized with Salmonella are usually asymptomatic with varied severity and duration of fecal shedding. Thus, understanding the responses that result in less shedding may provide a mechanism for control. Fifty-four pigs were inoculated with Salmonella enterica serovar Typhimurium (ST) and clinical signs, fecal ST shedding, growth performance, peripheral cytokines and whole blood gene expression were measured. Persistently shedding (PS) pigs had longer pyrexia and elevated serum IL-1β, TNF-α and IFN-γ compared with low shedding (LS) pigs, while LS pigs had brief pyrexia, less shedding that decreased more rapidly and greater serum CXCL8 than PS pigs. The PS pigs up-regulated genes involved with the STAT1, IFNB1 and IFN-γ networks on d 2, while up-regulation of genes involved in immune response regulation were only detected in LS pigs. This is the first study to examine host responses to ST infection at a clinical, performance, cytokine and transcriptomic level. The results indicated that pigs with different shedding outcomes developed distinct immune responses within the first 2 d of ST infection, and elucidated alternative mechanisms that could be targeted to reduce Salmonella shedding and spread.
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Affiliation(s)
- Susan M Knetter
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | | | - Ting-Hua Huang
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | | | - Martine Schroyen
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Daniel Berman
- Animal Parasitic Diseases Laboratory, USDA-ARS, Beltsville, MD, USA
| | - Valerie Cohen
- Animal Parasitic Diseases Laboratory, USDA-ARS, Beltsville, MD, USA
| | - Joan K Lunney
- Animal Parasitic Diseases Laboratory, USDA-ARS, Beltsville, MD, USA
| | - Amanda E Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Michael J Wannemuehler
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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27
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Palmitoylated transmembrane adaptor proteins in leukocyte signaling. Cell Signal 2014; 26:895-902. [PMID: 24440308 DOI: 10.1016/j.cellsig.2014.01.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/07/2014] [Accepted: 01/09/2014] [Indexed: 12/14/2022]
Abstract
Transmembrane adaptor proteins (TRAPs) are structurally related proteins that have no enzymatic function, but enable inducible recruitment of effector molecules to the plasma membrane, usually in a phosphorylation dependent manner. Numerous surface receptors employ TRAPs for either propagation or negative regulation of the signal transduction. Several TRAPs (LAT, NTAL, PAG, LIME, PRR7, SCIMP, LST1/A, and putatively GAPT) are known to be palmitoylated that could facilitate their localization in lipid rafts or tetraspanin enriched microdomains. This review summarizes expression patterns, binding partners, signaling pathways, and biological functions of particular palmitoylated TRAPs with an emphasis on the three most recently discovered members, PRR7, SCIMP, and LST1/A. Moreover, we discuss in silico methodology used for discovery of new family members, nature of their binding partners, and microdomain localization.
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28
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Abstract
Acute graft-versus-host disease (GVHD) afflicts as much as 80% of all patients who receive an unrelated donor hematopoietic cell transplant (HCT) for the treatment of blood disorders, even with optimal donor HLA matching and use of prophylactic immunosuppressive agents. Of patients who develop acute GVHD, many are at risk for chronic GVHD and bear the burden of considerable morbidity and lowered quality of life years after transplantation. The immunogenetic basis of GVHD has been the subject of intensive investigation, with the classic HLA genetic loci being the best-characterized determinants. Recent information on the major histocompatibility complex (MHC) region of chromosome 6 as an important source of untyped genetic variation has shed light on novel GVHD determinants. These data open new paradigms for understanding the genetic basis of GVHD.
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29
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Schiller C, Diakopoulos KN, Rohwedder I, Kremmer E, von Toerne C, Ueffing M, Weidle UH, Ohno H, Weiss EH. LST1 promotes the assembly of a molecular machinery responsible for tunneling nanotube formation. J Cell Sci 2012; 126:767-77. [PMID: 23239025 DOI: 10.1242/jcs.114033] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Carefully orchestrated intercellular communication is an essential prerequisite for the development of multicellular organisms. In recent years, tunneling nanotubes (TNT) have emerged as a novel and widespread mechanism of cell-cell communication. However, the molecular basis of their formation is still poorly understood. In the present study we report that the transmembrane MHC class III protein leukocyte specific transcript 1 (LST1) induces the formation of functional nanotubes and is required for endogenous nanotube generation. Mechanistically, we found that LST1 induces nanotube formation by recruiting the small GTPase RalA to the plasma membrane and promoting its interaction with the exocyst complex. Furthermore, we determined that LST1 recruits the actin-crosslinking protein filamin to the plasma membrane and interacts with M-Sec, myosin and myoferlin. These results allow us to suggest a molecular model for nanotube generation. In this proposal LST1 functions as a membrane scaffold mediating the assembly of a multimolecular complex, which controls the formation of functional nanotubes.
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Affiliation(s)
- Christian Schiller
- Department of Biology II, Ludwigs-Maximilians-Universität München, Großhadernerstr. 2, 82152 Planegg-Martinsried, Germany
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Schiller C, Huber JE, Diakopoulos KN, Weiss EH. Tunneling nanotubes enable intercellular transfer of MHC class I molecules. Hum Immunol 2012; 74:412-6. [PMID: 23228397 DOI: 10.1016/j.humimm.2012.11.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 10/04/2012] [Accepted: 11/28/2012] [Indexed: 10/27/2022]
Abstract
Carefully orchestrated intercellular communication is an essential prerequisite for an effective immune response. In recent years tunneling nanotubes (TNT) have emerged as a novel mechanism of cell-cell communication. These long membrane protrusions can establish cytoplasmic continuity between distant cells and enable the exchange of cellular components. In the present study we addressed the question whether these structures can facilitate the intercellular transfer of MHC class I molecules. We found a transmembrane HLA-A2-EGFP but not a soluble HLA-G1s-EGFP fusion protein to be effectively transferred between HeLa cells. Inhibition of actin polymerization significantly reduced the HLA-A2 transfer rate, indicating that transfer is dependent on tunneling nanotubes, whose de novo formation requires actin polymerization. Furthermore, overexpression of the nanotube-inducing protein LST1 promoted transfer of HLA-A2. Moreover, LST1 protein expression is enhanced in antigen presenting cells. Our results indicate that tunneling nanotubes can mediate transfer of MHC class I molecules between distant cells.
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Affiliation(s)
- Christian Schiller
- Department of Biology II, Ludwig-Maximilians-Universität München, Germany
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Wu H, Haag D, Muley T, Warth A, Zapatka M, Toedt G, Pscherer A, Hahn M, Rieker RJ, Wachter DL, Meister M, Schnabel P, Müller-Decker K, Rogers MA, Hoffmann H, Lichter P. Tumor-microenvironment interactions studied by zonal transcriptional profiling of squamous cell lung carcinoma. Genes Chromosomes Cancer 2012; 52:250-64. [PMID: 23074073 DOI: 10.1002/gcc.22025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 09/24/2012] [Accepted: 09/25/2012] [Indexed: 01/07/2023] Open
Abstract
Invasion is a critical step in lung tumor progression. The interaction between tumor cells and their surroundings may play an important role in tumor invasion and metastasis. To better understand the mechanisms of tumor invasion and tumor-microenvironment interactions in lung tumors, total RNA was isolated from the inner tumor, tumor invasion front, adjacent lung, and distant normal lung tissue from 17 patients with primary squamous cell lung carcinoma using punch-aided laser capture microdissection. Messenger RNA expression profiles were obtained by microarray analysis, and microRNA profiles were generated from eight of these samples using TaqMan Low Density Arrays. Statistical analysis of the expression data showed extensive changes in gene expression in the inner tumor and tumor front compared with the normal lung and adjacent lung tissue. Only a few genes were differentially expressed between tumor front and the inner tumor. Several genes were validated by immunohistochemistry. Evaluation of the microRNA data revealed zonal expression differences in nearly a fourth of the microRNAs analyzed. Validation of selected microRNAs by in situ hybridization demonstrated strong expression of hsa-miR-196a in the inner tumor; moderate expression of hsa-miR-224 in the inner tumor and tumor front, and strong expression of hsa-miR-650 in the adjacent lung tissue. Pathway analysis placed the majority of genes differentially expressed between tumor and nontumor cells in intrinsic processes associated with inflammation and extrinsic processes related to lymphocyte physiology. Genes differentially expressed between the inner tumor and the adjacent lung/normal lung tissue affected pathways of arachidonic acid metabolism and eicosanoid signaling.
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Affiliation(s)
- Hui Wu
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
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Draber P, Stepanek O, Hrdinka M, Drobek A, Chmatal L, Mala L, Ormsby T, Angelisova P, Horejsi V, Brdicka T. LST1/A is a myeloid leukocyte-specific transmembrane adaptor protein recruiting protein tyrosine phosphatases SHP-1 and SHP-2 to the plasma membrane. J Biol Chem 2012; 287:22812-21. [PMID: 22589543 DOI: 10.1074/jbc.m112.339143] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transmembrane adaptor proteins are membrane-anchored proteins consisting of a short extracellular part, a transmembrane domain, and a cytoplasmic part with various protein-protein interaction motifs but lacking any enzymatic activity. They participate in the regulation of various signaling pathways by recruiting other proteins to the proximity of cellular membranes where the signaling is often initiated and propagated. In this work, we show that LST1/A, an incompletely characterized protein encoded by MHCIII locus, is a palmitoylated transmembrane adaptor protein. It is expressed specifically in leukocytes of the myeloid lineage, where it localizes to the tetraspanin-enriched microdomains. In addition, it binds SHP-1 and SHP-2 phosphatases in a phosphotyrosine-dependent manner, facilitating their recruitment to the plasma membrane. These data suggest a role for LST1/A in negative regulation of signal propagation.
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Affiliation(s)
- Peter Draber
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic
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Bettens F, Passweg J, Schanz U, Chalandon Y, Heim D, Güngör T, Stussi G, Nicoloso G, Baldomero H, Gratwohl A, Tiercy JM. Impact of HLA-DPB1 haplotypes on outcome of 10/10 matched unrelated hematopoietic stem cell donor transplants depends on MHC-linked microsatellite polymorphisms. Biol Blood Marrow Transplant 2011; 18:608-16. [PMID: 21963878 DOI: 10.1016/j.bbmt.2011.09.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 09/26/2011] [Indexed: 10/17/2022]
Abstract
Hematopoietic stem cell transplantation (HSCT) with HLA-A, -B, -C, -DRB1, -DQB1 allele matched (10 of 10) unrelated donors is still associated with a significant rate of posttransplantation complications. In order to disclose additional immunogenetic factors, we analyzed the impact of HLA-DPB1 disparities and major histocompatibility complex (MHC)-resident microsatellite polymorphisms in 246 HLA 10 of 10 matched HSCT patients. First we showed that patients with more frequent/conserved HLA haplotypes had a higher 5-year survival (55% ± 18% versus 39% ± 18%, P = .021). In addition, DPB1 incompatibilities and 3 microsatellite alleles were associated with outcome. In a Cox regression model adjusting for European Blood and Marrow Transplant (EBMT) risk score, T cell depletion, and year of treatment, HSCT with a tumor necrosis factor d (TNFd) 4/d5-positive donor was associated with increased mortality (hazard ratio [HR] = 2.03; confidence interval [CI] 1.25-3.31; P = .004), whereas the D6S510-184 allele was protective (HR = 0.44; CI 0.22-0.87; P = .018). The 2 MHC-linked genetic donor factors, DPB1 mismatch (MM), and TNFd4/d5-positivity, acted in synergy with the EBMT risk score with an always lower survival (HR = 2.97; CI 1.27-6.92; P = .012). These data show that multiple MHC-linked genetic donor factors impact on outcome after unrelated donor HSCT. Their additive and potentially divergent effects could explain previous discrepant results, particularly with respect to the role of HLA-DPB1 disparities. We conclude that HLA-DPB1 typing combined with a simple TNFd microsatellite genotyping assay may significantly help in pretransplantation risk assessment for graft-versus-host disease and mortality, particularly for patients with several potential 10 of 10 matched donors.
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Affiliation(s)
- Florence Bettens
- National Reference Laboratory for Histocompatibility, Department of the Medical Specialties, University Hospital Geneva, Geneva, Switzerland
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Donos N, Hamlet S, Lang NP, Salvi GE, Huynh-Ba G, Bosshardt DD, Ivanovski S. Gene expression profile of osseointegration of a hydrophilic compared with a hydrophobic microrough implant surface. Clin Oral Implants Res 2011; 22:365-72. [DOI: 10.1111/j.1600-0501.2010.02113.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Novota P, Zinöcker S, Norden J, Wang XN, Sviland L, Opitz L, Salinas-Riester G, Rolstad B, Dickinson AM, Walter L, Dressel R. Expression profiling of major histocompatibility and natural killer complex genes reveals candidates for controlling risk of graft versus host disease. PLoS One 2011; 6:e16582. [PMID: 21305040 PMCID: PMC3030590 DOI: 10.1371/journal.pone.0016582] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 12/23/2010] [Indexed: 12/23/2022] Open
Abstract
Background The major histocompatibility complex (MHC) is the most important genomic region that contributes to the risk of graft versus host disease (GVHD) after haematopoietic stem cell transplantation. Matching of MHC class I and II genes is essential for the success of transplantation. However, the MHC contains additional genes that also contribute to the risk of developing acute GVHD. It is difficult to identify these genes by genetic association studies alone due to linkage disequilibrium in this region. Therefore, we aimed to identify MHC genes and other genes involved in the pathophysiology of GVHD by mRNA expression profiling. Methodology/Principal Findings To reduce the complexity of the task, we used genetically well-defined rat inbred strains and a rat skin explant assay, an in-vitro-model of the graft versus host reaction (GVHR), to analyze the expression of MHC, natural killer complex (NKC), and other genes in cutaneous GVHR. We observed a statistically significant and strong up or down regulation of 11 MHC, 6 NKC, and 168 genes encoded in other genomic regions, i.e. 4.9%, 14.0%, and 2.6% of the tested genes respectively. The regulation of 7 selected MHC and 3 NKC genes was confirmed by quantitative real-time PCR and in independent skin explant assays. In addition, similar regulations of most of the selected genes were observed in GVHD-affected skin lesions of transplanted rats and in human skin explant assays. Conclusions/Significance We identified rat and human MHC and NKC genes that are regulated during GVHR in skin explant assays and could therefore serve as biomarkers for GVHD. Several of the respective human genes, including HLA-DMB, C2, AIF1, SPR1, UBD, and OLR1, are polymorphic. These candidates may therefore contribute to the genetic risk of GVHD in patients.
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Affiliation(s)
- Peter Novota
- Department of Cellular and Molecular Immunology, University of Göttingen, Göttingen, Germany
| | - Severin Zinöcker
- Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jean Norden
- Haematological Sciences, Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Xiao Nong Wang
- Haematological Sciences, Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Lisbet Sviland
- Department of Pathology, Haukeland Sykehus, Section of Pathology, Gades Institute, University of Bergen, Bergen, Norway
| | - Lennart Opitz
- Transcriptome Analysis Laboratory, University of Göttingen, Göttingen, Germany
| | | | - Bent Rolstad
- Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Anne M. Dickinson
- Haematological Sciences, Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Lutz Walter
- Department of Primate Genetics, German Primate Center, Göttingen, Germany
| | - Ralf Dressel
- Department of Cellular and Molecular Immunology, University of Göttingen, Göttingen, Germany
- * E-mail:
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Ovsyannikova IG, Vierkant RA, Pankratz VS, Jacobson RM, Poland GA. Extended LTA, TNF, LST1 and HLA gene haplotypes and their association with rubella vaccine-induced immunity. PLoS One 2010; 5:e11806. [PMID: 20668555 PMCID: PMC2910726 DOI: 10.1371/journal.pone.0011806] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 06/28/2010] [Indexed: 12/31/2022] Open
Abstract
Background Recent studies have suggested the importance of HLA genes in determining immune responses following rubella vaccine. The telomeric class III region of the HLA complex harbors several genes, including lymphotoxin alpha (LTA), tumor necrosis factor (TNF) and leukocyte specific transcript -1 (LST1) genes, located between the class I B and class II DRB1 loci. Apart from HLA, little is known about the effect of this extended genetic region on HLA haplotypic backgrounds as applied to immune responses. Methodology/Principal Findings We examined the association between immune responses and extended class I-class II-class III haplotypes among 714 healthy children after two doses of rubella vaccination. These extended haplotypes were then compared to the HLA-only haplotypes. The most significant association was observed between haplotypes extending across the HLA class I region, ten-SNP haplotypes, and the HLA class II region (i.e. A-C-B-LTA-TNF-LST1-DRB1-DQA1-DQB1-DPA1-DPB1) and rubella-specific antibodies (global p-value of 0.03). Associations were found between both extended A*02-C*03-B*15-AAAACGGGGC-DRB1*04-DQA1*03-DQB1*03-DPA1*01-DPB1*04 (p = 0.002) and HLA-only A*02-C*03-B*15-DRB1*04-DQA1*03-DQB1*03-DPA1*01-DPB1*04 haplotypes (p = 0.009) and higher levels of rubella antibodies. The class II HLA-only haplotype DRB1*13-DQA1*01-DQB1*06-DPA1*01-DPB1*04 (p = 0.04) lacking LTA-TNF-LST1 SNPs was associated with lower rubella antibody responses. Similarly, the class I-class II HLA-only A*01-C*07-B*08-DRB1*03-DQA1*05-DQB1*02-DPA1*01-DPB1*04 haplotype was associated with increased TNF-α secretion levels (p = 0.009). In contrast, the extended AAAACGGGGC-DRB1*01-DQA1*01-DQB1*05-DPA1*01-DPB1*04 (p = 0.01) haplotype was found to trend with decreased rubella-specific IL-6 secretion levels. Conclusions/Significance These data suggest the importance of examining both HLA genes and genes in the class III region as part of the extended haplotypes useful in understanding genomic drivers regulating immune responses to rubella vaccine.
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Affiliation(s)
- Inna G. Ovsyannikova
- Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
- Program in Translational Immunovirology and Biodefense, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail: (GAP); (IGO)
| | - Robert A. Vierkant
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - V. Shane Pankratz
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Robert M. Jacobson
- Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Gregory A. Poland
- Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Program in Translational Immunovirology and Biodefense, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail: (GAP); (IGO)
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Varlet-Marie E, Audran M, Ashenden M, Sicart MT, Piquemal D. Modification of gene expression: help to detect doping with erythropoiesis-stimulating agents. Am J Hematol 2009; 84:755-9. [PMID: 19802893 DOI: 10.1002/ajh.21525] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Schiller C, Nitschké MJ, Seidl A, Kremmer E, Weiss EH. Rat Monoclonal Antibodies Specific for LST1 Proteins. Hybridoma (Larchmt) 2009; 28:281-6. [DOI: 10.1089/hyb.2009.0021] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Christian Schiller
- Department of Biology II, Ludwig-Maximilians-Universität München, Germany
- Institute of Molecular Immunology, Helmholtz Zentrum München, Germany
| | | | - Alexander Seidl
- Department of Biology II, Ludwig-Maximilians-Universität München, Germany
| | - Elisabeth Kremmer
- Institute of Molecular Immunology, Helmholtz Zentrum München, Germany
| | - Elisabeth H. Weiss
- Department of Biology II, Ludwig-Maximilians-Universität München, Germany
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Abstract
Major histocompatibility complex (MHC) variation is a key determinant of susceptibility and resistance to a large number of infectious, autoimmune and other diseases. Identification of the MHC variants conferring susceptibility to disease is problematic, due to high levels of variation and linkage disequilibrium. Recent cataloguing and analysis of variation over the complete MHC has facilitated localization of susceptibility loci for autoimmune diseases, and provided insight into the MHC's evolution. This review considers how the unusual genetic characteristics of the MHC impact on strategies to identify variants causing, or contributing to, disease phenotypes. It also considers the MHC in relation to novel mechanisms influencing gene function and regulation, such as epistasis, epigenetics and microRNAs. These developments, along with recent technological advances, shed light on genetic association in complex disease.
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Affiliation(s)
- J A Traherne
- Cambridge Institute for Medical Research, Addenbrookes Hospital, Wellcome Trust/MRC Building, Cambridge, UK.
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Macaulay IC, Tijssen MR, Thijssen-Timmer DC, Gusnanto A, Steward M, Burns P, Langford CF, Ellis PD, Dudbridge F, Zwaginga JJ, Watkins NA, van der Schoot CE, Ouwehand WH. Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins. Blood 2006; 109:3260-9. [PMID: 17192395 PMCID: PMC6485507 DOI: 10.1182/blood-2006-07-036269] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
To identify previously unknown platelet receptors we compared the transcriptomes of in vitro differentiated megakaryocytes (MKs) and erythroblasts (EBs). RNA was obtained from purified, biologically paired MK and EB cultures and compared using cDNA microarrays. Bioinformatical analysis of MK-up-regulated genes identified 151 transcripts encoding transmembrane domain-containing proteins. Although many of these were known platelet genes, a number of previously unidentified or poorly characterized transcripts were also detected. Many of these transcripts, including G6b, G6f, LRRC32, LAT2, and the G protein-coupled receptor SUCNR1, encode proteins with structural features or functions that suggest they may be involved in the modulation of platelet function. Immunoblotting on platelets confirmed the presence of the encoded proteins, and flow cytometric analysis confirmed the expression of G6b, G6f, and LRRC32 on the surface of platelets. Through comparative analysis of expression in platelets and other blood cells we demonstrated that G6b, G6f, and LRRC32 are restricted to the platelet lineage, whereas LAT2 and SUCNR1 were also detected in other blood cells. The identification of the succinate receptor SUCNR1 in platelets is of particular interest, because physiologically relevant concentrations of succinate were shown to potentiate the effect of low doses of a variety of platelet agonists.
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Affiliation(s)
- Iain C. Macaulay
- Department of Haematology, University of Cambridge, United Kingdom
- National Blood Service, Cambridge, United Kingdom
| | - Marloes R. Tijssen
- Department of Experimental Immunohaematology, Sanquin Research at Central Laboratory for the Blood Transfusion Service (CLB), Amsterdam, The Netherlands
- Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, The Netherlands
| | - Daphne C. Thijssen-Timmer
- Department of Experimental Immunohaematology, Sanquin Research at Central Laboratory for the Blood Transfusion Service (CLB), Amsterdam, The Netherlands
| | - Arief Gusnanto
- Medical Research Council (MRC) Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom
| | | | - Philippa Burns
- Department of Haematology, University of Cambridge, United Kingdom
- National Blood Service, Cambridge, United Kingdom
| | | | - Peter D. Ellis
- Microarray Facility, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Frank Dudbridge
- Medical Research Council (MRC) Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom
| | - Jaap-Jan Zwaginga
- Department of Experimental Immunohaematology, Sanquin Research at Central Laboratory for the Blood Transfusion Service (CLB), Amsterdam, The Netherlands
- Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, The Netherlands
- Department of Immunohematology–Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
| | - Nicholas A. Watkins
- Department of Haematology, University of Cambridge, United Kingdom
- National Blood Service, Cambridge, United Kingdom
| | - C. Ellen van der Schoot
- Department of Experimental Immunohaematology, Sanquin Research at Central Laboratory for the Blood Transfusion Service (CLB), Amsterdam, The Netherlands
- Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, The Netherlands
- Department of Hematology, Amsterdam Medical Centre, University of Amsterdam, The Netherlands
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge, United Kingdom
- National Blood Service, Cambridge, United Kingdom
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Deakin JE, Papenfuss AT, Belov K, Cross JGR, Coggill P, Palmer S, Sims S, Speed TP, Beck S, Graves JAM. Evolution and comparative analysis of the MHC Class III inflammatory region. BMC Genomics 2006; 7:281. [PMID: 17081307 PMCID: PMC1654159 DOI: 10.1186/1471-2164-7-281] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Accepted: 11/02/2006] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The Major Histocompatibility Complex (MHC) is essential for immune function. Historically, it has been subdivided into three regions (Class I, II, and III), but a cluster of functionally related genes within the Class III region has also been referred to as the Class IV region or "inflammatory region". This group of genes is involved in the inflammatory response, and includes members of the tumour necrosis family. Here we report the sequencing, annotation and comparative analysis of a tammar wallaby BAC containing the inflammatory region. We also discuss the extent of sequence conservation across the entire region and identify elements conserved in evolution. RESULTS Fourteen Class III genes from the tammar wallaby inflammatory region were characterised and compared to their orthologues in other vertebrates. The organisation and sequence of genes in the inflammatory region of both the wallaby and South American opossum are highly conserved compared to known genes from eutherian ("placental") mammals. Some minor differences separate the two marsupial species. Eight genes within the inflammatory region have remained tightly clustered for at least 360 million years, predating the divergence of the amphibian lineage. Analysis of sequence conservation identified 354 elements that are conserved. These range in size from 7 to 431 bases and cover 15.6% of the inflammatory region, representing approximately a 4-fold increase compared to the average for vertebrate genomes. About 5.5% of this conserved sequence is marsupial-specific, including three cases of marsupial-specific repeats. Highly Conserved Elements were also characterised. CONCLUSION Using comparative analysis, we show that a cluster of MHC genes involved in inflammation, including TNF, LTA (or its putative teleost homolog TNF-N), APOM, and BAT3 have remained together for over 450 million years, predating the divergence of mammals from fish. The observed enrichment in conserved sequences within the inflammatory region suggests conservation at the transcriptional regulatory level, in addition to the functional level.
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Affiliation(s)
- Janine E Deakin
- ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
| | - Katherine Belov
- Centre for Advanced Technologies in Animal Genetics and Reproduction, Faculty of Veterinary Science, The University of Sydney, NSW 2006, Australia
| | - Joseph GR Cross
- ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia
| | - Penny Coggill
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sophie Palmer
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sarah Sims
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Terence P Speed
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
| | - Stephan Beck
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jennifer A Marshall Graves
- ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia
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Mewar D, Marinou I, Lee ME, Timms JM, Kilding R, Teare MD, Read RC, Wilson AG. Haplotype-specific gene expression profiles in a telomeric major histocompatibility complex gene cluster and susceptibility to autoimmune diseases. Genes Immun 2006; 7:625-31. [PMID: 16971954 DOI: 10.1038/sj.gene.6364339] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The telomeric class III region of the major histocompatibility complex is gene dense, but apart from the three tumour necrosis factor (TNF) superfamily members (TNF, lymphotoxin alpha and lymphotoxin beta) little is known of the expression and function of the majority of the genes. Recent genetic studies in autoimmune diseases, particularly rheumatoid arthritis (RA), have suggested a human leukocyte antigen (HLA)-DR-independent disease effect in this region. To gain further insights into these associations, we used lipopolysaccharide-stimulated human macrophages to examine inducible mRNA expression and genotype-phenotype relationships for genes in this region. Following stimulation in addition to the expected induction of TNF mRNA, a 14-fold increase of ATP6V1G2 at 18 h (P<0.001) was seen, whereas B-associated transcript (BAT)2 (P<0.001) and leucocyte-specific transcript (LST)1 (P<0.001) were both downregulated. By genotyping single-nucleotide polymorphisms spanning a 70 kb interval centred on the TNF locus, we constructed haplotypes and determined associated expression profiles for 10 genes in the cluster using quantitative real-time polymerase chain reaction. Overexpression of BAT1 mRNA was associated with carriers of a haplotype containing the LST1 marker transmitted to RA cases in a family study and also DRB1(*)15 associated with susceptibility to nephritis in systemic lupus erythematosus. The implications of our findings for the understanding of genetic associations with disease susceptibility in this region are discussed.
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Affiliation(s)
- D Mewar
- School of Medicine and Biomedical Sciences, University of Sheffield, Sheffield, UK.
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Bettens F, Passweg J, Gratwohl A, Chalandon Y, Helg C, Chapuis B, Schanz U, Libura J, Roosnek E, Tiercy JM. Association of TNFd and IL-10 polymorphisms with mortality in unrelated hematopoietic stem cell transplantation. Transplantation 2006; 81:1261-7. [PMID: 16699452 DOI: 10.1097/01.tp.0000208591.70229.53] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Non-HLA immunogenetic polymorphisms may influence outcome of hematopoietic stem cell transplantation (HSCT). In this study, we have determined the role of TNFa, TNFd, IL-10, IL-1, IL-1Ra, and IL-4R polymorphisms in patients transplanted with HSC of an unrelated donor. METHODS The allelic variants of four SNPs (IL-10-1082, IL-1beta-511, IL-4R-3223, IL-4R-1902) and four microsatellites (TNFa, TNFd, IL-10-1064, IL-1Ra) were determined in 131 unrelated patient/donor pairs typed for HLA-A/B/C/DR/DQ (four digits). RESULTS The allelic distribution of the polymorphisms was similar to that previously reported in Caucasoid populations. Patient and donor TNFd and patient IL-10-1064 polymorphisms correlated with mortality in univariate analysis. Patients with TNFd1/d2/d3 genotypes had 3-year survival rates of 65%. A gradual decrease in survival rates was observed for patients with TNFd3/d3 genotypes (50%, p=n.s.), TNFd4 (46%, P=0.08), and TNFd5 (33%, P=0.03). A multivariate analysis of 10/10 matched patients revealed that the following patient genotypes correlated with lower survival: TNFd3/d3 (RR 4.08, P=0.026) TNFd4 (RR 3.78, P=0.032) and TNFd5 (RR 6.69, P=0.021) all compared to TNFd1/d2/d3 genotypes. Patient IL-10 (12, 14, 15) microsatellite alleles correlated with lower 3-year survival (28%) when compared to IL-10 (<12) (56%, P=0.052) and to Il-10 (13) alleles (60%, P=0.0023). In multivariate analysis this correlation remained significant only in recipients of HSCT of 10/10 HLA matched donors (RR=2.96, P=0.038). CONCLUSION The data demonstrate a significant correlation of the TNFd and IL-10-1064 microsatellite polymorphisms with mortality after unrelated HSCT. They support the hypothesis that simple genomic tests, in addition to precise HLA matching, may contribute to determine prognosis in patients undergoing unrelated HSCT.
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Affiliation(s)
- Florence Bettens
- Transplantation Immunology Unit/LNRH, University Hospital, Geneva, Switzerland
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Mulcahy H, O'Rourke KP, Adams C, Molloy MG, O'Gara F. LST1 and NCR3 expression in autoimmune inflammation and in response to IFN-gamma, LPS and microbial infection. Immunogenetics 2005; 57:893-903. [PMID: 16362817 DOI: 10.1007/s00251-005-0057-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Accepted: 10/01/2005] [Indexed: 10/25/2022]
Abstract
Many genes in the central region of the major histocompatibility complex (MHC) encode proteins involved in immune and inflammatory responses. In this study, we have further characterized two genes in the MHC class IV region, leucocyte-specific transcript (LST) 1 and natural cytotoxicity-triggering receptor 3 (NCR3) (also known as 1C7 and natural killer (NK)p30). The specific function of LST1 is not known, although expression analysis and functional data suggest an immunomodulatory role. The LST1 gene undergoes extensive alternative splicing, giving rise to both membrane-bound (encoded by exon 3) and soluble isoforms. The NCR3 protein is involved in NK-mediated cytotoxicity and plays a role in NK/dendritic cell crosstalk. Expression of these genes was examined, by real-time reverse transcriptase-polymerase chain reaction, in autoimmune-induced inflammation, specifically rheumatoid-arthritis-affected blood and synovium, and in response to stimulation with inflammatory mediators and bacterial agents. The expression of LST1, specifically splice variants encoding soluble isoforms and NCR3, was increased in rheumatoid-arthritis-affected blood and synovium and was associated with more severe inflammation in the synovium. Furthermore, both genes were significantly up-regulated in response to lipopolysaccharide, interferon (IFN)-gamma and bacterial infection. These findings suggest that NCR3 and soluble isoforms of LST1 may play a role in inflammatory and infectious diseases.
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Affiliation(s)
- H Mulcahy
- BIOMERIT Research Centre, Department of Microbiology, University College Cork, Cork, Ireland
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Kilding R, Wilson AG. Mapping of a novel susceptibility gene for rheumatoid arthritis in the telomeric MHC region. Cytokine 2005; 32:71-5. [PMID: 16199168 DOI: 10.1016/j.cyto.2005.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Rheumatoid arthritis (RA) is a complex heterogeneous disease with an estimated genetic contribution to of 30-50%. Approximately one third arises from the major histocompatibility complex (MHC) at 6p21.3. The contribution of specific DRB1 alleles encoding the shared epitope has been well described, however, several recent studies have suggested that additional telomeric genetic influences may exist. This region is difficult to study as a result of the presence of strong linkage disequilibrium (LD) within the MHC and high gene density particularly in the central class III region. In this article we review the current data supporting the existence of a non-DRB1 susceptibility gene for rheumatoid arthritis, in particular within the class III region.
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Affiliation(s)
- Rachael Kilding
- Division of Genomic Medicine, The University of Sheffield, Royal Hallamshire Hospital, Glossop Road, Sheffield S10 2JF, United Kingdom
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Lei H, Vorechovsky I. Identification of splicing silencers and enhancers in sense Alus: a role for pseudoacceptors in splice site repression. Mol Cell Biol 2005; 25:6912-20. [PMID: 16055705 PMCID: PMC1190243 DOI: 10.1128/mcb.25.16.6912-6920.2005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Auxiliary splicing signals in introns play an important role in splice site selection, but these elements are poorly understood. We show that a subset of serine/arginine (SR)-rich proteins activate a cryptic 3' splice site in a sense Alu repeat located in intron 4 of the human LST1 gene. Utilization of this cryptic splice site is controlled by juxtaposed Alu-derived splicing silencers and enhancers between closely linked short tandem repeats TNFd and TNFe. Systematic mutagenesis of these elements showed that AG dinucleotides that were not preceded by purine residues were critical for repressing exon inclusion of a chimeric splicing reporter. Since the splice acceptor-like sequences are present in excess in exonic splicing silencers, these signals may contribute to inhibition of a large number of pseudosites in primate genomes.
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Affiliation(s)
- Haixin Lei
- University of Southampton School of Medicine, Division of Human Genetics, Duthie Building, UK
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Ackerman HC, Ribas G, Jallow M, Mott R, Neville M, Sisay-Joof F, Pinder M, Campbell RD, Kwiatkowski DP. Complex haplotypic structure of the central MHC region flanking TNF in a West African population. Genes Immun 2004; 4:476-86. [PMID: 14551600 DOI: 10.1038/sj.gene.6364008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
TNF polymorphisms have been associated with susceptibility to malaria and other infectious and inflammatory conditions. We investigated a sample of 150 West African chromosomes to determine linkage disequilibrium (LD) between 25 SNP markers located in an 80 kb segment of the MHC Class III region encompassing TNF and eight neighbouring genes. We observed 45 haplotypes, and 22 of them comprise 80% of the sample. The pattern of LD is remarkably patchy, such that many markers show no LD with adjacent markers but high LD with markers that are much further away. We introduce a method of examining the implications of LD data for disease association studies based on sample size considerations: this shows that certain TNF polymorphisms would be likely to yield positive associations if the true disease allele resided in LTA or BAT1. We conclude that detailed marker maps are needed to resolve the causal origin of disease associations observed at the TNF locus.
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Affiliation(s)
- H C Ackerman
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, UK.
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Kilding R, Iles MM, Timms JM, Worthington J, Wilson AG. Additional genetic susceptibility for rheumatoid arthritis telomeric of the DRB1 locus. ACTA ACUST UNITED AC 2004; 50:763-9. [PMID: 15022317 DOI: 10.1002/art.20043] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Rheumatoid arthritis (RA) has an estimated genetic contribution of 30-50%, approximately one-third of which arises from the major histocompatibility complex on 6p21.3. Many studies have implicated alleles of DRB1 that encode a shared epitope. However, several recent studies have suggested that additional telomeric genetic influences may exist. In this study, we sought to investigate whether a separate non-DRB1 effect could be detected and to determine its likely location. METHODS We typed 13 single-nucleotide polymorphisms, located mainly in the telomeric class III region of the major histocompatibility complex, in 164 British Caucasian families with RA that had at least 1 affected offspring and used unconditioned and DRB1-conditioned transmission disequilibrium tests (TDTs). RESULTS Unconditioned TDTs revealed overtransmission of shared epitope alleles (P = 2.12 x 10(-5)) and an allele of the HLA-B-associated transcript 1 (BAT1) gene in the telomeric class III region (P = 0.009). Using a DRB1-conditioned TDT to assess whether an independent effect existed, we detected unequal transmission of alleles of lymphocyte-specific transcript 1 (P = 0.004), BAT1 (P = 0.003), and PG8 (P = 0.003). CONCLUSION At least 1 additional non-DRB1 susceptibility locus for RA exists in an interval that encompasses the junction of the class III and I regions. This is a genomic segment of high linkage disequilibrium containing a large number of poorly characterized immunomodulatory genes.
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Affiliation(s)
- Rachael Kilding
- The University of Sheffield, Royal Hallamshire Hospital, Sheffield, UK
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Xie T, Rowen L, Aguado B, Ahearn ME, Madan A, Qin S, Campbell RD, Hood L. Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. Genome Res 2004; 13:2621-36. [PMID: 14656967 PMCID: PMC403804 DOI: 10.1101/gr.1736803] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In mammals, the Major Histocompatibility Complex class I and II gene clusters are separated by an approximately 700-kb stretch of sequence called the MHC class III region, which has been associated with susceptibility to numerous diseases. To facilitate understanding of this medically important and architecturally interesting portion of the genome, we have sequenced and analyzed both the human and mouse class III regions. The cross-species comparison has facilitated the identification of 60 genes in human and 61 in mouse, including a potential RNA gene for which the introns are more conserved across species than the exons. Delineation of global organization, gene structure, alternative splice forms, protein similarities, and potential cis-regulatory elements leads to several conclusions: (1) The human MHC class III region is the most gene-dense region of the human genome: >14% of the sequence is coding, approximately 72% of the region is transcribed, and there is an average of 8.5 genes per 100 kb. (2) Gene sizes, number of exons, and intergenic distances are for the most part similar in both species, implying that interspersed repeats have had little impact in disrupting the tight organization of this densely packed set of genes. (3) The region contains a heterogeneous mixture of genes, only a few of which have a clearly defined and proven function. Although many of the genes are of ancient origin, some appear to exist only in mammals and fish, implying they might be specific to vertebrates. (4) Conserved noncoding sequences are found primarily in or near the 5'-UTR or the first intron of genes, and seldom in the intergenic regions. Many of these conserved blocks are likely to be cis-regulatory elements.
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Affiliation(s)
- Tao Xie
- Institute for Systems Biology, Seattle, Washington 98103, USA
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Barthel R, Goldfeld AE. T Cell-Specific Expression of the Human TNF-α Gene Involves a Functional and Highly Conserved Chromatin Signature in Intron 3. THE JOURNAL OF IMMUNOLOGY 2003; 171:3612-9. [PMID: 14500658 DOI: 10.4049/jimmunol.171.7.3612] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Using a phylogenetic approach, we identified highly conserved sequences within intron 3 of the human TNF-alpha gene. These sequences form cell type-specific DNase I hypersensitivity sites and display cell type-specific DNA-protein contacts in in vivo genomic footprints. Consistent with these results, intron 3 confers specific activity upon a TNF-alpha reporter gene in Jurkat T cells, but not THP-1 monocytic cells. Thus, using a combinatorial approach of phylogenetic analysis, DNase I hypersensitivity analysis, in vivo footprinting, and transfection analysis, we demonstrate that intronic regulatory elements are involved in the cell type-specific regulation of TNF-alpha gene expression.
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Affiliation(s)
- Robert Barthel
- Center for Blood Research and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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