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Siegler BH, Thon JN, Altvater M, Schenz J, Larmann J, Weigand MA, Weiterer S. Abdominal surgery induces long-lasting changes in expression and binding of CTCF with impact on Major Histocompatibility Complex II transcription in circulating human monocytes. PLoS One 2023; 18:e0293347. [PMID: 37878653 PMCID: PMC10599505 DOI: 10.1371/journal.pone.0293347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/11/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Postoperative immunosuppression has been recognized as an important driver of surgery-related morbidity and mortality. It is characterized by lymphocyte depression and impaired monocyte capability to present foreign antigens to T-cells via Major Histocompatibility Complex, Class II (MHC-II) molecules. In patients with postoperative abdominal sepsis, we previously detected a persisting differential binding of the CCCTC-Binding Factor (CTCF), a superordinate regulator of transcription, inside the MHC-II region with specific impact on human leucocyte antigen (HLA) gene expression. In this prospective exploratory study, we investigated to which extent major surgery affects the MHC-II region of circulating CD14+-monocytes. RESULTS In non-immunocompromised patients undergoing elective major abdominal surgery, a postoperative loss of monocyte HLA-DR surface receptor density was accompanied by a decline in the transcription levels of the classical MHC-II genes HLA-DRA, HLA-DRB1, HLA-DPA1 and HLA-DPB1. The surgical event decreased the expression of the transcriptional MHC-II regulators CIITA and CTCF and led to a lower CTCF enrichment at an intergenic sequence within the HLA-DR subregion. During the observation period, we found a slow and only incomplete restoration of monocyte HLA-DR surface receptor density as well as a partial recovery of CIITA, HLA-DRA and HLA-DRB1 expression. In contrast, transcription of HLA-DPA1, HLA-DPB1, CTCF and binding of CTCF within the MHC-II remained altered. CONCLUSION In circulating monocytes, major surgery does not globally affect MHC-II transcription but rather induces specific changes in the expression of selected HLA genes, followed by differential recovery patterns and accompanied by a prolonged reduction of CTCF expression and binding within the MHC-II region. Our results hint toward a long-lasting impact of a major surgical intervention on monocyte functionality, possibly mediated by epigenetic changes that endure the life span of the individual cell.
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Affiliation(s)
- Benedikt Hermann Siegler
- Medical Faculty Heidelberg, Department of Anesthesiology, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Jan Niklas Thon
- Medical Faculty Heidelberg, Department of Anesthesiology, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Marc Altvater
- Medical Faculty Heidelberg, Department of Anesthesiology, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Judith Schenz
- Medical Faculty Heidelberg, Department of Anesthesiology, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Jan Larmann
- Medical Faculty Heidelberg, Department of Anesthesiology, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Markus Alexander Weigand
- Medical Faculty Heidelberg, Department of Anesthesiology, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Sebastian Weiterer
- Medical Faculty Heidelberg, Department of Anesthesiology, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
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Liao SY, Jacobson S, Hamzeh NY, Culver DA, Barkes BQ, Mroz M, Macphail K, Pacheco K, Patel DC, Wasfi YS, Koth LL, Langefeld CD, Leach SM, White E, Montgomery C, Maier LA, Fingerlin TE. Genome-wide association study identifies multiple HLA loci for sarcoidosis susceptibility. Hum Mol Genet 2023; 32:2669-2678. [PMID: 37399103 PMCID: PMC10407706 DOI: 10.1093/hmg/ddad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/30/2023] [Accepted: 04/19/2023] [Indexed: 07/05/2023] Open
Abstract
Sarcoidosis is a complex systemic disease. Our study aimed to (1) identify novel alleles associated with sarcoidosis susceptibility; (2) provide an in-depth evaluation of HLA alleles and sarcoidosis susceptibility and (3) integrate genetic and transcription data to identify risk loci that may more directly impact disease pathogenesis. We report a genome-wide association study of 1335 sarcoidosis cases and 1264 controls of European descent (EA) and investigate associated alleles in a study of African Americans (AA: 1487 cases and 1504 controls). The EA and AA cohort was recruited from multiple United States sites. HLA alleles were imputed and tested for association with sarcoidosis susceptibility. Expression quantitative locus and colocalization analysis were performed using a subset of subjects with transcriptome data. Forty-nine SNPs in the HLA region in HLA-DRA, -DRB9, -DRB5, -DQA1 and BRD2 genes were significantly associated with sarcoidosis susceptibility in EA, rs3129888 was also a risk variant for sarcoidosis in AA. Classical HLA alleles DRB1*0101, DQA1*0101 and DQB1*0501, which are highly correlated, were also associated with sarcoidosis. rs3135287 near HLA-DRA was associated with HLA-DRA expression in peripheral blood mononuclear cells and bronchoalveolar lavage from subjects and lung tissue and whole blood from GTEx. We identified six novel SNPs (out of the seven SNPs representing the 49 significant SNPs) and nine HLA alleles associated with sarcoidosis susceptibility in the largest EA population. We also replicated our findings in an AA population. Our study reiterates the potential role of antigen recognition and/or presentation HLA class II genes in sarcoidosis pathogenesis.
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Affiliation(s)
- Shu-Yi Liao
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado School of Public Health, University of Colorado Denver–Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sean Jacobson
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Nabeel Y Hamzeh
- Department of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Daniel A Culver
- Department of Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Briana Q Barkes
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Margarita Mroz
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Kristyn Macphail
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Karin Pacheco
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado School of Public Health, University of Colorado Denver–Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Divya C Patel
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Gainesville, FL 32610, USA
| | | | - Laura L Koth
- Department of Medicine, University of California-San Fransisco, San Fransisco, CA 94143, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
- Wake Forest University School of Medicine, Center for Precision Medicine, Winston-Salem, NC 27101, USA
| | - Sonia M Leach
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Elizabeth White
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | | | - Lisa A Maier
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado School of Public Health, University of Colorado Denver–Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tasha E Fingerlin
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado School of Public Health, University of Colorado Denver–Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA
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Chan KR, Koh CWT, Ng DHL, Qin S, Ooi JSG, Ong EZ, Zhang SLX, Sam H, Kalimuddin S, Low JGH, Ooi EE. Early peripheral blood MCEMP1 and HLA-DRA expression predicts COVID-19 prognosis. EBioMedicine 2023; 89:104472. [PMID: 36801619 PMCID: PMC9934388 DOI: 10.1016/j.ebiom.2023.104472] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Mass vaccination has dramatically reduced the incidence of severe COVID-19, with most cases now presenting as self-limiting upper respiratory tract infections. However, those with co-morbidities, the elderly and immunocompromised, as well as the unvaccinated, remain disproportionately vulnerable to severe COVID-19 and its sequelae. Furthermore, as the effectiveness of vaccination wanes with time, immune escape SARS-CoV-2 variants could emerge to cause severe COVID-19. Reliable prognostic biomarkers for severe disease could be used as early indicator of re-emergence of severe COVID-19 as well as for triaging of patients for antiviral therapy. METHODS We performed a systematic review and re-analysis of 7 publicly available datasets, analysing a total of 140 severe and 181 mild COVID-19 patients, to determine the most consistent differentially regulated genes in peripheral blood of severe COVID-19 patients. In addition, we included an independent cohort where blood transcriptomics of COVID-19 patients were prospectively and longitudinally monitored previously, to track the time in which these gene expression changes occur before nadir of respiratory function. Single cell RNA-sequencing of peripheral blood mononuclear cells from publicly available datasets was then used to determine the immune cell subsets involved. FINDINGS The most consistent differentially regulated genes in peripheral blood of severe COVID-19 patients were MCEMP1, HLA-DRA and ETS1 across the 7 transcriptomics datasets. Moreover, we found significantly heightened MCEMP1 and reduced HLA-DRA expression as early as four days before the nadir of respiratory function, and the differential expression of MCEMP1 and HLA-DRA occurred predominantly in CD14+ cells. The online platform which we developed is publicly available at https://kuanrongchan-covid19-severity-app-t7l38g.streamlitapp.com/, for users to query gene expression differences between severe and mild COVID-19 patients in these datasets. INTERPRETATION Elevated MCEMP1 and reduced HLA-DRA gene expression in CD14+ cells during the early phase of disease are prognostic of severe COVID-19. FUNDING K.R.C is funded by the National Medical Research Council (NMRC) of Singapore under the Open Fund Individual Research Grant (MOH-000610). E.E.O. is funded by the NMRC Senior Clinician-Scientist Award (MOH-000135-00). J.G.H.L. is funded by the NMRC under the Clinician-Scientist Award (NMRC/CSAINV/013/2016-01). S.K. is funded by the NMRC under the Transition Award. This study was sponsored in part by a generous gift from The Hour Glass.
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Affiliation(s)
- Kuan Rong Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.
| | - Clara W T Koh
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Dorothy H L Ng
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Shijie Qin
- Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Justin S G Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Eugenia Z Ong
- Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Summer L X Zhang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Huizhen Sam
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Shirin Kalimuddin
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Jenny G H Low
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore; Department of Infectious Diseases, Singapore General Hospital, Singapore; Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Eng Eong Ooi
- Department of Infectious Diseases, Singapore General Hospital, Singapore; Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore
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Yang Z, Li S, Liu H, Su Q, Li X, Qiu Y, Mo W. Identification of key genes and pathways associated with diabetes of the exocrine pancreas. Medicine (Baltimore) 2022; 101:e29781. [PMID: 36042664 PMCID: PMC9410602 DOI: 10.1097/md.0000000000029781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
This study aimed to identify potential essential genes and pathways in diabetes of the exocrine pancreas (DEP) and explore possible molecular mechanisms. The array dataset GSE76895 was downloaded from the Gene Expression Omnibus database. Pancreatic tissue samples from 20 Diabetes of the exocrine pancreas and 32 nondiabetic individuals were selected for analysis. GEO2R analyzed differentially expressed genes (DEGs) in the 2 groups. Gene ontology annotation, Kyoto Encyclopedia of Genes Genomes and Reactome pathway enrichment analyses and Gene Set Enrichment Analysis were performed in this study. Protein-protein interaction (PPI) networks were constructed using Cytoscape software, and core networks were identified using MCODE plugins. A total of 62 genes, including 59 up-regulated and 3 down-regulated genes, were differentially expressed in DEP samples compared with nondiabetic patients. PPI network with 53 nodes and 138 edges was established. HLA-DRA is identified as the central gene of the PPI network and maybe a marker gene for DEP. Furthermore, up-regulated DEGs are mainly enriched in pathways related to the immune system and infection. The results of this study suggest that HLA-DRA and immune system pathways may play essential roles in DEP.
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Affiliation(s)
- Zheng Yang
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Shengqi Li
- Department of Medicine, Guangxi Medical College, Nanning, Guangxi, China
| | - Huaying Liu
- Department of Medicine, Guangxi Medical College, Nanning, Guangxi, China
| | - Qisheng Su
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaohong Li
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yulin Qiu
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Wuning Mo
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- *Correspondence: Wuning Mo, Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Province, China (e-mail: )
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Liu D, Hofman P. Expression of NOTCH1, NOTCH4, HLA-DMA and HLA-DRA is synergistically associated with T cell exclusion, immune checkpoint blockade efficacy and recurrence risk in ER-negative breast cancer. Cell Oncol (Dordr) 2022; 45:463-477. [PMID: 35543859 DOI: 10.1007/s13402-022-00677-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2022] [Indexed: 11/26/2022] Open
Abstract
PURPOSE Reliable biomarkers to predict the outcome and treatment response of estrogen receptor (ER)-negative breast cancer (BC) are urgently needed. Since immune-related signaling plays an important role in the tumorigenesis of ER-negative BC, we asked whether Notch genes, alone or in combination with other immune genes, can be used to predict the clinical outcome and immune checkpoint blockade (ICB) for this type of cancer. METHODS We analyzed transcriptome data of 6918 BC samples from five independent cohorts, 81 xenograft triple-negative BC tumors that respond differently to ICB treatment and 754 samples of different cancer types from patients treated with ICB agents. RESULTS We found that among four Notch genes, the expression levels of NOTCH1 and NOTCH4 were positively associated with recurrence of ER-negative BC, and that combined expression of these two genes (named Notch14) further enhanced this association, which was comparable with that of the Notch pathway signature. Analysis of 1182 immune-related genes revealed that the expression levels of most HLA genes, particularly HLA-DMA and -DRA, were reversely associated with recurrence in ER-negative BC with low, but not high Notch14 expression. A combined expression signature of NOTCH1, NOTCH4, HLA-DMA and HLA-DRA was more prognostic for ER-negative and triple-negative BCs than previously reported immune-related signatures. Furthermore, we found that the expression levels of these four genes were also synergistically associated with T cell exclusion score, infiltration of specific T cells and ICB efficacy in ER-negative BC, thereby providing a potential molecular mechanism for the synergistic effect of these genes on BC. CONCLUSIONS Our data indicate that a gene signature composed of NOTCH1, NOTCH4, HLA-DMA and HLA-DRA may serve as a potential promising biomarker for predicting ICB therapy efficacy and recurrence in ER-negative/triple-negative BCs.
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Affiliation(s)
- Dingxie Liu
- Bluewater Biotech LLC, PO Box 1010, New Providence, NJ, 07974, USA.
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, CHU Nice, FHU OncoAge, University Côte d'Azur, 06100, Nice, France.
- Team 4, IRCAN, UMR 7284 U10181, FHU OncoAge, Centre Antoine Lacassagne University Côte d'Azur, 06107, Nice, France.
- Hospital-Integrated Biobank (BB-0033-00025), CHU Nice, FHU OncoAge, University Côte d'Azur, 06100, Nice, France.
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Balakrishnan CK, Tye GJ, Balasubramaniam SD, Kaur G. CD74 and HLA-DRA in Cervical Carcinogenesis: Potential Targets for Antitumour Therapy. Medicina (B Aires) 2022; 58:medicina58020190. [PMID: 35208514 PMCID: PMC8877221 DOI: 10.3390/medicina58020190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 11/21/2022] Open
Abstract
Background and Objectives: Abnormal expressions of CD74 and human leukocyte antigen-DR alpha (HLA-DRA) have been reported in various cancers, though their roles in cervical cancer remain unclear. This study aimed to evaluate the gene and protein expressions of CD74 and HLA-DRA in the progression from normal cervix to precancerous cervical intraepithelial neoplasia (CIN) and finally to squamous cell carcinoma (SCC). Materials and Methods: The gene expression profiles of CD74 and HLA-DRA were determined in formalin-fixed paraffin-embedded tissues, with three samples each from normal cervixes, human papillomavirus type 16/18-positive, low-grade CIN (LGCIN), high-grade CIN (HGCIN), and squamous cell carcinoma (SCC) using Human Transcriptome Array 2.0. Immunohistochemical expression of the proteins was semi-quantitatively assessed in another cohort of tissue microarray samples comprising 7 normal cervix cases, 10 LGCIN, 10 HGCIN, and 95 SCC. Results: The transcriptomics profile and proteins’ expression demonstrated similar trends of upregulation of CD74 and HLA-DRA from normal cervix to CIN and highest in SCC. There was a significant difference in both proteins’ expression between the histological groups (p = 0.0001). CD74 and HLA-DRA expressions were significantly associated with CIN grade (p = 0.001 and p = 0.030, respectively) but not with the subjects’ age or SCC stage. Further analysis revealed a positive correlation between CD74 and HLA-DRA proteins. Conclusions: CD74 appears to promote cervical carcinogenesis via oncogenic signalling mechanisms and may serve as a potential antitumour target. Additionally, the upregulation of HLA-DRA, often associated with stronger immunogenicity, could be a promising biomarker for developing immunotherapies.
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Affiliation(s)
- Carol K. Balakrishnan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden 11800, Pulau Pinang, Malaysia; (C.K.B.); (G.J.T.); (S.D.B.)
| | - Gee Jun Tye
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden 11800, Pulau Pinang, Malaysia; (C.K.B.); (G.J.T.); (S.D.B.)
| | - Shandra Devi Balasubramaniam
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden 11800, Pulau Pinang, Malaysia; (C.K.B.); (G.J.T.); (S.D.B.)
- Unit of Microbiology, Faculty of Medicine, AIMST University, Bedong 08100, Semeling, Malaysia
| | - Gurjeet Kaur
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden 11800, Pulau Pinang, Malaysia; (C.K.B.); (G.J.T.); (S.D.B.)
- Correspondence: ; Tel.: +604-6534865
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Tang H, Harte M. Investigating Markers of the NLRP3 Inflammasome Pathway in Alzheimer's Disease: A Human Post-Mortem Study. Genes (Basel) 2021; 12:genes12111753. [PMID: 34828359 PMCID: PMC8622528 DOI: 10.3390/genes12111753] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
Neuroinflammatory mechanisms with glial cell activation have been implicated in the pathogenic process of Alzheimer’s disease (AD). Activation of the NLRP3 inflammasome is an essential component of the neuroinflammatory response. A role for NLRP3 activation in AD is supported by both in vitro and in vivo preclinical studies with little direct investigation of AD brain tissue. RNA expression of genes of three glial cell markers, HLA-DRA, AIF-1 and GFAP; the components of the NLRP3 inflammasome NLRP3, ASC, and caspase-1; and downstream pre-inflammatory cytokines IL-1 β and IL-18, were investigated in the temporal cortex of AD patients and age- and sex-matched controls. Protein expression of GFAP was also assessed. Increases in both mRNA and protein expression were observed for GFAP in AD. There were no significant changes in other NLRP3 activation markers between groups. Our results indicate the involvement of astrocyte activation in AD, particularly in more severe patients. We found no evidence for the specific involvement of the NLRP3 inflammasome.
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Affiliation(s)
- Hao Tang
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
- Department of Neurology, The First People’s Hospital of Yunnan Province, Kunming 650032, China
| | - Michael Harte
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
- Correspondence:
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Heesters BA, van Megesen K, Tomris I, de Vries RP, Magri G, Spits H. Characterization of human FDCs reveals regulation of T cells and antigen presentation to B cells. J Exp Med 2021; 218:e20210790. [PMID: 34424268 PMCID: PMC8404474 DOI: 10.1084/jem.20210790] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/02/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Stromal-derived follicular dendritic cells (FDCs) are essential for germinal centers (GCs), the site where B cells maturate their antibodies. FDCs present native antigen to B cells and maintain a CXCL13 gradient to form the B cell follicle. Yet despite their essential role, the transcriptome of human FDCs remains undefined. Using single-cell RNA sequencing and microarray, we provided the transcriptome of these enigmatic cells as a comprehensive resource. Key genes were validated by flow cytometry and microscopy. Surprisingly, marginal reticular cells (MRCs) rather than FDCs expressed B cell activating factor (BAFF). Furthermore, we found that human FDCs expressed TLR4 and can alter antigen availability in response to pathogen-associated molecular patterns (PAMPs). High expression of PD-L1 and PD-L2 on FDCs activated PD1 on T cells. In addition, we found expression of genes related to T cell regulation, such as HLA-DRA, CD40, and others. These data suggest intimate contact between human FDCs and T cells.
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Affiliation(s)
- Balthasar A. Heesters
- Amsterdam University Medical Centers, University of Amsterdam, Department of Experimental Immunology, Amsterdam institute for Infection and Immunity, Amsterdam, Netherlands
| | - Kyah van Megesen
- Amsterdam University Medical Centers, University of Amsterdam, Department of Experimental Immunology, Amsterdam institute for Infection and Immunity, Amsterdam, Netherlands
| | - Ilhan Tomris
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Robert P. de Vries
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Giuliana Magri
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain
| | - Hergen Spits
- Amsterdam University Medical Centers, University of Amsterdam, Department of Experimental Immunology, Amsterdam institute for Infection and Immunity, Amsterdam, Netherlands
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Abstract
Genome-wide association studies (GWAS) have identified several susceptibility loci of Alzheimer's disease (AD), which were mainly located in noncoding regions of the genome. Meanwhile, the putative biological mechanisms underlying AD susceptibility loci were still unclear. At present, identifying the functional variants of AD pathogenesis remains a major challenge. Herein, we first used summary data-based Mendelian randomization (SMR) with AD GWAS summary and expression quantitative trait loci (eQTL) data to identify variants who affects expression levels of nearby genes and contributed to the risk of AD. Using the SMR integrative analysis, we totally identified 14 SNPs significantly affected the expression level of 16 nearby genes in blood or brain tissues and contributed to the AD risk. Then, to confirm the results, we replicated the GWAS and eQTL results across multiple samples. Totally, four risk SNP (rs11682128, rs601945, rs3935067, and rs679515) were validated to be associated with AD and affected the expression level of nearby genes (BIN1, HLA-DRA, EPHA1-AS1, and CR1). Besides, our differential expression analysis showed that the BIN1 gene was significantly downregulated in the hippocampus (P = 2.0 × 10-3) and survived after multiple comparisons. These convergent lines of evidence suggest that the BIN1 gene identified by SMR has potential roles in the pathogenesis of AD. Further investigation of the roles of the BIN1 gene in the pathogenesis of AD is warranted.
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Affiliation(s)
- Jin Zhu
- Department of Psychiatry, Jining Medical University, 133 He Hua Road, Jining, 272067 Shandong China
| | - Xia Liu
- Department of Psychiatry, Jining Psychiatric Hospital, Jining, 272051 Shandong China
| | - Hongtao Yin
- Department of Neurology, Zibo Central Hospital, 54 Gongqingtuan Xi Road, Zibo, 255036 China
| | - Yan Gao
- Department of Psychiatry, Jining Medical University, 133 He Hua Road, Jining, 272067 Shandong China
| | - Hao Yu
- Department of Psychiatry, Jining Medical University, 133 He Hua Road, Jining, 272067 Shandong China
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Affiliation(s)
- Arthur A Vandenbark
- Neuroimmunology Research, R&D-31, VA Portland Health Care System, 3710 SW U.S. Veterans Hospital Rd., Portland, OR 97239, USA; Department of Neurology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA; Department of Molecular Microbiology & Immunology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA.
| | - Roberto Meza-Romero
- Neuroimmunology Research, R&D-31, VA Portland Health Care System, 3710 SW U.S. Veterans Hospital Rd., Portland, OR 97239, USA; Department of Neurology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - Halina Offner
- Neuroimmunology Research, R&D-31, VA Portland Health Care System, 3710 SW U.S. Veterans Hospital Rd., Portland, OR 97239, USA; Department of Neurology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA; Department of Anesthesiology and Perioperative Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
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Aydemir Ö, Noble JA, Bailey JA, Lernmark Å, Marsh P, Andersson Svärd A, Bearoff F, Blankenhorn EP, Mordes JP. Genetic Variation Within the HLA-DRA1 Gene Modulates Susceptibility to Type 1 Diabetes in HLA-DR3 Homozygotes. Diabetes 2019; 68:1523-1527. [PMID: 30962219 PMCID: PMC6609989 DOI: 10.2337/db18-1128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/28/2019] [Indexed: 01/22/2023]
Abstract
Type 1 diabetes (T1D) involves the interaction of multiple gene variants, environmental factors, and immunoregulatory dysfunction. Major T1D genetic risk loci encode HLA-DR and -DQ. Genetic heterogeneity and linkage disequilibrium in the highly polymorphic HLA region confound attempts to identify additional T1D susceptibility loci. To minimize HLA heterogeneity, T1D patients (N = 365) and control subjects (N = 668) homozygous for the HLA-DR3 high-risk haplotype were selected from multiple large T1D studies and examined to identify new T1D susceptibility loci using molecular inversion probe sequencing technology. We report that risk for T1D in HLA-DR3 homozygotes is increased significantly by a previously unreported haplotype of three single nucleotide polymorphisms (SNPs) within the first intron of HLA-DRA1. The homozygous risk haplotype has an odds ratio of 4.65 relative to the protective homozygous haplotype in our sample. Individually, these SNPs reportedly function as "expression quantitative trait loci," modulating HLA-DR and -DQ expression. From our analysis of available data, we conclude that the tri-SNP haplotype within HLA-DRA1 may modulate class II expression, suggesting that increased T1D risk could be attributable to regulated expression of class II genes. These findings could help clarify the role of HLA in T1D susceptibility and improve diabetes risk assessment, particularly in high-risk HLA-DR3 homozygous individuals.
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Affiliation(s)
- Özkan Aydemir
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | | | - Jeffrey A Bailey
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, Malmö, Sweden
| | - Patrick Marsh
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Agnes Andersson Svärd
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, Malmö, Sweden
| | - Frank Bearoff
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA
| | - Elizabeth P Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA
| | - John P Mordes
- Division of Endocrinology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
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Minchenko OH, Tsymbal DO, Minchenko DO, Prylutska SV, Hnatiuk OS, Prylutskyy YI, Tsierkezos NG, Ritter U. Single-walled carbon nanotubes affect the expression of genes associated with immune response in normal human astrocytes. Toxicol In Vitro 2018; 52:122-130. [PMID: 29906516 DOI: 10.1016/j.tiv.2018.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 06/02/2018] [Accepted: 06/08/2018] [Indexed: 12/11/2022]
Abstract
The effect of single-walled carbon nanotubes (SWCNTs) on the expression of a subset of immune response, apoptosis and cell proliferation -associated genes was studied in normal human astrocytes (line NHA/TS). In the cells treated with SWCNTs (2, 10 and 50 ng/ml of medium for 24 h) we observed a strong dose-dependent down-regulation of the expression of a cell surface glycoproteins HLA-DRA (major histocompatibility complex, class II, DR alpha) and HLA-DRB1. At the same time, the expression of HLA-F (major histocompatibility complex, class I, F), LMNB1 (lamin B1), and HTRA1 (high temperature requirement A1) genes as well as the level of miR-190b and miR-7 was up-regulated in NHA/TS subjected to different concentrations of SWCNTs. After 24 h of treatment with SWCNTs we detected a dose-dependent suppression of PHLDA2 (pleckstrin homology-like domain, family A, member 2) gene expression in these cells. Obtained data show that SWCNTs may affect an immune response, in particular through suppression of HLA-DRA and HLA-DRB1 gene expressions and that miR-190b and miR-7 possibly participated in this suppression. Deregulation of lamin B1 expression indicates the possibility of alterations in genome stability following treatment of astrocytes with SWCNTs. Thus, more caution is needed in biomedical application of SWCNTs.
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Affiliation(s)
- Oleksandr H Minchenko
- Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, 9 Leontovycha Str, Kyiv 01601, Ukraine.
| | - Dariia O Tsymbal
- Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, 9 Leontovycha Str, Kyiv 01601, Ukraine
| | - Dmytro O Minchenko
- Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, 9 Leontovycha Str, Kyiv 01601, Ukraine; Department of Pediatrics, Bohomolets National Medical University, 13 Taras Shevchenko Blvd., Kyiv 01601, Ukraine
| | - Svitlana V Prylutska
- Taras Shevchenko National University of Kyiv, 64 Volodymyrska Str, 01601 Kyiv, Ukraine
| | - Oksana S Hnatiuk
- Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, 9 Leontovycha Str, Kyiv 01601, Ukraine
| | - Yuriy I Prylutskyy
- Taras Shevchenko National University of Kyiv, 64 Volodymyrska Str, 01601 Kyiv, Ukraine
| | - Nikos G Tsierkezos
- Technische Universität Ilmenau, Institut für Chemie und Biotechnik, 25 Weimarer Str., 98693 Ilmenau, Germany.
| | - Uwe Ritter
- Technische Universität Ilmenau, Institut für Chemie und Biotechnik, 25 Weimarer Str., 98693 Ilmenau, Germany
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Woo YR, Lim JH, Cho DH, Park HJ. Rosacea: Molecular Mechanisms and Management of a Chronic Cutaneous Inflammatory Condition. Int J Mol Sci 2016; 17:ijms17091562. [PMID: 27649161 PMCID: PMC5037831 DOI: 10.3390/ijms17091562] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/23/2016] [Accepted: 09/07/2016] [Indexed: 01/21/2023] Open
Abstract
Rosacea is a chronic cutaneous inflammatory disease that affects the facial skin. Clinically, rosacea can be categorized into papulopustular, erythematotelangiectatic, ocular, and phymatous rosacea. However, the phenotypic presentations of rosacea are more heterogeneous. Although the pathophysiology of rosacea remains to be elucidated, immunologic alterations and neurovascular dysregulation are thought to have important roles in initiating and strengthening the clinical manifestations of rosacea. In this article, we present the possible molecular mechanisms of rosacea based on recent laboratory and clinical studies. We describe the genetic predisposition for rosacea along with its associated diseases, triggering factors, and suggested management options in detail based on the underlying molecular biology. Understanding the molecular pathomechanisms of rosacea will likely aid toward better comprehending its complex pathogenesis.
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Affiliation(s)
- Yu Ri Woo
- Department of Dermatology, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 07345, Korea.
| | - Ji Hong Lim
- Department of Dermatology, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 07345, Korea.
| | - Dae Ho Cho
- Department of Life Science, Sookmyung Women's University, Seoul 04310, Korea.
| | - Hyun Jeong Park
- Department of Dermatology, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 07345, Korea.
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Cajander S, Tina E, Bäckman A, Magnuson A, Strålin K, Söderquist B, Källman J. Quantitative Real-Time Polymerase Chain Reaction Measurement of HLA-DRA Gene Expression in Whole Blood Is Highly Reproducible and Shows Changes That Reflect Dynamic Shifts in Monocyte Surface HLA-DR Expression during the Course of Sepsis. PLoS One 2016; 11:e0154690. [PMID: 27144640 PMCID: PMC4856385 DOI: 10.1371/journal.pone.0154690] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 04/18/2016] [Indexed: 12/21/2022] Open
Abstract
Introduction A decrease in the expression of monocyte surface protein HLA-DR (mHLA-DR), measured by flow cytometry (FCM), has been suggested as a marker of immunosuppression and negative outcome in severe sepsis. However, FCM is not always available due to sample preparation that limits its use to laboratory operational hours. In this prospective study we evaluated dynamic changes in mHLA-DR expression during sepsis in relation to changes in HLA-DRA gene expression and Class II transactivator (CIITA), measured by quantitative Real-Time Polymerase Chain Reaction (qRT-PCR). Aims The aims of this study were: 1. to validate the robustness of qRT-PCR measurement of HLA-DRA- and CIITA–mRNA expression, in terms of reproducibility; and 2. to see if changes in expression of these genes reflect changes in mHLA-DR expression during the course of severe and non-severe bacteraemic sepsis. Methods and Findings Blood samples were collected from 60 patients with bacteraemic sepsis on up to five occasions during Days 1–28 after hospital admission. We found the reproducibility of the qRT-PCR method to be high by demonstrating low threshold variations (<0.11 standard deviation (SD)) of the qRT-PCR system, low intra-assay variation of Ct-values within triplicates (≤0.15 SD) and low inter-assay variations (12%) of the calculated target gene ratios. Our results also revealed dynamic HLA-DRA expression patterns during the course of sepsis that reflected those of mHLA-DR measured by FCM. Furthermore, HLA-DRA and mHLA-DR recovery slopes in patients with non-severe sepsis differed from those in patients with severe sepsis, shown by mixed model for repeated measurements (p<0.05). However, during the first seven days of sepsis, PCR-measurements showed a higher magnitude of difference between the two sepsis groups. Mean differences (95% CI) between severe sepsis (n = 20) and non-severe sepsis (n = 40) were; on day 1–2, HLA-DRA 0.40 (0.28–0.59) p<0.001, CIITA 0.48 (0.32–0.72) p = 0.005, mHLA-DR 0.63 (0.45–1.00) p = 0.04, day 7 HLA-DRA 0.59 (0.46–0.77) p<0.001, CIITA 0.56 (0.41–0.76) p<0.001, mHLA-DR 0.81 (0.66–1.00) p = 0.28. Conclusion We conclude that qRT-PCR measurement of HLA-DRA expression is robust, and that this method appears to be preferable to FCM in identifying patients with severe sepsis that may benefit from immunostimulation.
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Affiliation(s)
- Sara Cajander
- Department of Infectious Diseases, Faculty of Medicine and Health, Örebro University, SE 70182 Örebro, Sweden
- * E-mail:
| | - Elisabet Tina
- Department of Clinical Research Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Anders Bäckman
- Department of Clinical Research Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Anders Magnuson
- Clinical Epidemiology and Biostatistics, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Kristoffer Strålin
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Bo Söderquist
- Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jan Källman
- Department of Infectious Diseases, Faculty of Medicine and Health, Örebro University, SE 70182 Örebro, Sweden
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Beaulieu YB, Leon Machado JA, Ethier S, Gaudreau L, Steimle V. Degradation, Promoter Recruitment and Transactivation Mediated by the Extreme N-Terminus of MHC Class II Transactivator CIITA Isoform III. PLoS One 2016; 11:e0148753. [PMID: 26871568 PMCID: PMC4752451 DOI: 10.1371/journal.pone.0148753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 01/22/2016] [Indexed: 12/17/2022] Open
Abstract
Multiple relationships between ubiquitin-proteasome mediated protein turnover and transcriptional activation have been well documented, but the underlying mechanisms are still poorly understood. One way to induce degradation is via ubiquitination of the N-terminal α-amino group of proteins. The major histocompatibility complex (MHC) class II transactivator CIITA is the master regulator of MHC class II gene expression and we found earlier that CIITA is a short-lived protein. Using stable and transient transfections of different CIITA constructs into HEK-293 and HeLa cell lines, we show here that the extreme N-terminal end of CIITA isoform III induces both rapid degradation and transactivation. It is essential that this sequence resides at the N-terminal end of the protein since blocking of the N-terminal end with an epitope-tag stabilizes the protein and reduces transactivation potential. The first ten amino acids of CIITA isoform III act as a portable degron and transactivation sequence when transferred as N-terminal extension to truncated CIITA constructs and are also able to destabilize a heterologous protein. The same is observed with the N-terminal ends of several known N-terminal ubiquitination substrates, such as Id2, Cdt1 and MyoD. Arginine and proline residues within the N-terminal ends contribute to rapid turnover. The N-terminal end of CIITA isoform III is responsible for efficient in vivo recruitment to the HLA-DRA promoter and increased interaction with components of the transcription machinery, such as TBP, p300, p400/Domino, the 19S ATPase S8, and the MHC-II promoter binding complex RFX. These experiments reveal a novel function of free N-terminal ends of proteins in degradation-dependent transcriptional activation.
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Affiliation(s)
- Yves B. Beaulieu
- Département de biologie, Université de Sherbrooke, Sherbrooke, Qc, Canada
| | | | - Sylvain Ethier
- Département de biologie, Université de Sherbrooke, Sherbrooke, Qc, Canada
| | - Luc Gaudreau
- Département de biologie, Université de Sherbrooke, Sherbrooke, Qc, Canada
| | - Viktor Steimle
- Département de biologie, Université de Sherbrooke, Sherbrooke, Qc, Canada
- * E-mail:
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16
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Zhu RL, Lu XC, Tang LJ, Huang BS, Yu W, Li S, Li LX. Association between HLA rs3129882 polymorphism and Parkinson's disease: a meta-analysis. Eur Rev Med Pharmacol Sci 2015; 19:423-432. [PMID: 25720714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
OBJECTIVE As one of potential candidate genes for the risk of Parkinson's disease (PD), the HLA-DRA/PARK18 (rs3129882, A > G) gene has been studied extensively. However, direct evidence for the genetic association studies between PD and rs3129882 remains inconclusive. The aim of our meta-analysis was to determine a more reliable association between the rs3129882 and PD. MATERIALS AND METHODS Comprehensive search strategy was used for electronic searches through PubMed, Elsevier, Springer Link, CNKI (Chinese National Knowledge Infrastructure) and WanFang (Chinese) databases to evaluate the association between rs3129882 and PD risk. Data were extracted and the odd ratios (ORs) and 95% confidence intervals (95% CIs) were calculated. Finally, we performed a meta-analysis of 13 appropriate papers by using a total of 11951 patients and 11902 controls. RESULTS The meta-analysis showed no significant association between rs3129882 and PD risk in all four models (the allele model, dominant model, homozygote model and the recessive model). In allele model, the result was OR = 1.043 (95% CI = 0.978, 1.113). Moreover, this association remained no significant in the subgroup analysis stratified by ethnicity. CONCLUSIONS In current meta-analysis, no significant association was found for rs3129882 and PD risk. And more well-designed primary researches will be needed to further evaluate the interaction of rs3129882 polymorphism and the susceptibility of PD.
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Affiliation(s)
- R-L Zhu
- Department of Neurosurgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
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17
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Maetzler W, Apel A, Langkamp M, Deuschle C, Dilger SS, Stirnkorb JG, Schulte C, Schleicher E, Gasser T, Berg D. Comparable autoantibody serum levels against amyloid- and inflammation-associated proteins in Parkinson's disease patients and controls. PLoS One 2014; 9:e88604. [PMID: 24586351 PMCID: PMC3931625 DOI: 10.1371/journal.pone.0088604] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 01/10/2014] [Indexed: 11/21/2022] Open
Abstract
Naturally occurring autoantibodies (NAbs) against a number of potentially disease-associated cellular proteins, including Amyloid-beta1–42 (Abeta1–42), Alpha-synuclein (Asyn), myelin basic protein (MBP), myelin oligodendrocyte glycoprotein (MOG), and S100 calcium binding protein B (S100B) have been suggested to be associated with neurodegenerative disorders, in particular Alzheimer’s (AD) and Parkinson’s disease (PD). Whereas the (reduced) occurrence of specific NAbs in AD is widely accepted, previous literature examining the relation of these NAb titres between PD patients and controls, as well as comparing these levels with demographic and clinical parameters in PD patients have produced inconsistent findings. We therefore aimed, in a cross-sectional approach, to determine serum titres of the above NAbs in a cohort of 93 PD patients (31 of them demented) and 194 controls. Levels were correlated with demographic and clinical variables, cerebrospinal fluid Abeta1–42, total tau and phospho-tau levels, as well as with single nucleotide polymorphisms (SNPs) of genes which either have been reported to influence the immune system, the amyloid cascade or the occurrence of PD (ApoE, GSK3B, HLA-DRA, HSPA5, SNCA, and STK39). The investigated NAb titres were neither significantly associated with the occurrence of PD, nor with demographic and clinical parameters, neurodegenerative markers or genetic variables. These results argue against a major potential of blood-borne parameters of the adaptive immune system to serve as trait or state markers in PD.
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Affiliation(s)
- Walter Maetzler
- Center of Neurology, Department of Neurodegeneration and Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
- * E-mail:
| | - Anja Apel
- Center of Neurology, Department of Neurodegeneration and Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | | | - Christian Deuschle
- Center of Neurology, Department of Neurodegeneration and Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | - Sarah Selina Dilger
- Center of Neurology, Department of Neurodegeneration and Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | - Johannes Georg Stirnkorb
- Center of Neurology, Department of Neurodegeneration and Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | - Claudia Schulte
- Center of Neurology, Department of Neurodegeneration and Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | - Erwin Schleicher
- Department of Internal Medicine IV, University Hospital Tuebingen, Tuebingen, Germany
| | - Thomas Gasser
- Center of Neurology, Department of Neurodegeneration and Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | - Daniela Berg
- Center of Neurology, Department of Neurodegeneration and Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
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18
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Temme S, Zacharias M, Neumann J, Wohlfromm S, König A, Temme N, Springer S, Trowsdale J, Koch N. A novel family of human leukocyte antigen class II receptors may have its origin in archaic human species. J Biol Chem 2014; 289:639-53. [PMID: 24214983 PMCID: PMC3887193 DOI: 10.1074/jbc.m113.515767] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/08/2013] [Indexed: 01/10/2023] Open
Abstract
HLA class II α and β chains form receptors for antigen presentation to CD4(+) T cells. Numerous pairings of class II α and β subunits from the wide range of haplotypes and isotypes may form, but most of these combinations, in particular those produced by isotype mixing, yielded mismatched dimers. It is unclear how selection of functional receptors is achieved. At the atomic level, it is not known which interactions of class II residues regulate selection of matched αβ heterodimers and the evolutionary origin of matched isotype mixed dimer formation. In this study we investigated assembly of isotype-mixed HLA class II α and β heterodimers. Assembly and carbohydrate maturation of various HLA-class II isotype-mixed α and β subunits was dependent on the groove binding section of the invariant chain (Ii). By mutation of polymorphic DPβ sequences, we identified two motifs, Lys-69 and GGPM-(84-87), that are engaged in Ii-dependent assembly of DPβ with DRα. We identified five members of a family of DPβ chains containing Lys-69 and GGPM 84-87, which assemble with DRα. The Lys/GGPM motif is present in the DPβ sequence of the Neanderthal genome, and this ancient sequence is related to the human allele DPB1*0401. By site-directed mutagenesis, we inspected Neanderthal amino acid residues that differ from the DPB1*0401 allele and aimed to determine whether matched heterodimers are formed by assembly of DPβ mutants with DRα. Because the *0401 allele is rare in the sub-Saharan population but frequent in the European population, it may have arisen in modern humans by admixture with Neanderthals in Europe.
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Affiliation(s)
- Sebastian Temme
- From the Section of Immunobiology, Institute of Genetics, University of Bonn, 53115 Bonn, Germany
- Department of Molecular Cardiology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Martin Zacharias
- Physics Department, Technical University Munich, 85747 Garching, Germany
| | - Jürgen Neumann
- From the Section of Immunobiology, Institute of Genetics, University of Bonn, 53115 Bonn, Germany
| | - Sebastian Wohlfromm
- Biologisch-Medizinisches Forschungszentrum, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Angelika König
- From the Section of Immunobiology, Institute of Genetics, University of Bonn, 53115 Bonn, Germany
| | - Nadine Temme
- From the Section of Immunobiology, Institute of Genetics, University of Bonn, 53115 Bonn, Germany
- Forschungszentrum Caesar, 53175 Bonn, Germany
| | | | - John Trowsdale
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kindgom
| | - Norbert Koch
- From the Section of Immunobiology, Institute of Genetics, University of Bonn, 53115 Bonn, Germany
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He S, Tan W, Wang S, Wu C, Wang P, Wang B, Su X, Zhao J, Guo X, Xiang Y. Genome-wide study reveals an important role of spontaneous autoimmunity, cardiomyocyte differentiation defect and anti-angiogenic activities in gender-specific gene expression in Keshan disease. Chin Med J (Engl) 2014; 127:72-78. [PMID: 24384427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Keshan disease (KD) is an endemic cardiomyopathy in China. The etiology of KD is still under debate and there is no effective approach to preventing and curing this disease. Young women of child-bearing age are the most frequent victims in rural areas. The aim of this study was to determine the differences between molecular pathogenic mechanisms in male and female KD sufferers. METHODS We extracted RNA from the peripheral blood mononuclear cells of KD patients (12 women and 4 men) and controls (12 women and 4 men). Then the isolated RNA was amplified, labeled and hybridized to Agilent human 4×44k whole genome microarrays. Gene expression was examined using oligonucleotide microarray analysis. A quantitative polymerase chain reaction assay was also performed to validate our microarray results. RESULTS Among the genes differentially expressed in female KD patients we identified: HLA-DOA, HLA-DRA, and HLA-DQA1 associated with spontaneous autoimmunity; BMP5 and BMP7, involved in cardiomyocyte differentiation defect; and ADAMTS 8, CCL23, and TNFSF15, implicated in anti-angiogenic activities. These genes are involved in the canonical pathways and networks recognized for the female KD sufferers and might be related to the pathogenic mechanism of KD. CONCLUSION Our results might help to explain the higher susceptibility of women to this disease.
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Affiliation(s)
- Shulan He
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Wuhong Tan
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Sen Wang
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Cuiyan Wu
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Pan Wang
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Bin Wang
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Xiaohui Su
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Junjie Zhao
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Xiong Guo
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China. )
| | - Youzhang Xiang
- Shandong Institute for Prevention & Treatment of Endemic Disease, Jinan, Shandong 250014, China
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20
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Lin CH, Chen ML, Tai YC, Yu CY, Wu RM. Reaffirmation of GAK, but not HLA-DRA, as a Parkinson's disease susceptibility gene in a Taiwanese population. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:841-6. [PMID: 24039160 DOI: 10.1002/ajmg.b.32188] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 06/26/2013] [Indexed: 12/22/2022]
Abstract
Recent genome-wide association studies of Parkinson's disease (PD) in Caucasian populations have identified two new susceptibility loci, GAK and HLA-DRA; however, only limited information exists regarding the involvement of these genes in PD risk in other ethnic groups. Here, we examined whether these genetic effects were consistent in a Taiwanese PD population. In a total 900 participants, including 448 PD patients and 452 control subjects, we genotyped the rs11248051 and rs1564282 variants of GAK, and the rs3129882 variant of HLA-DRA. Logistic regression analysis was used to test for associations between genotype and PD under an additive model, adjusting for age and gender. Subjects with CT/TT genotypes of GAK rs11248051 had a modestly increased association with PD compared to those with CC genotype (OR = 1.37; 95% CI = 1.09, 1.87; P = 0.03). Carriers and non-carriers exhibited indistinguishable phenotypes in regards to clinical presentation and onset age. We observed no association between PD risk and GAK rs1564282 or HLA-DRA rs3129882 variant. The different genetic effects between Taiwanese and Caucasian populations may come from differences in population structure and geographic region-specific genetic-environmental interactions. In conclusion, our results supported the association between the rs11248051 variant in GAK and PD risk in a Taiwanese population. Future functional studies of GAK in neuronal degeneration are warranted to unravel its role in the pathogenetic mechanism of PD.
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Affiliation(s)
- Chin-Hsien Lin
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
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Allantaz-Frager F, Turrel-Davin F, Venet F, Monnin C, De Saint Jean A, Barbalat V, Cerrato E, Pachot A, Lepape A, Monneret G. Identification of biomarkers of response to IFNg during endotoxin tolerance: application to septic shock. PLoS One 2013; 8:e68218. [PMID: 23874546 PMCID: PMC3708924 DOI: 10.1371/journal.pone.0068218] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/28/2013] [Indexed: 11/27/2022] Open
Abstract
The rapid development in septic patients of features of marked immunosuppression associated with increased risk of nosocomial infections and mortality represents the rational for the initiation of immune targeted treatments in sepsis. However, as there is no clinical sign of immune dysfunctions, the current challenge is to develop biomarkers that will help clinicians identify the patients that would benefit from immunotherapy and monitor its efficacy. Using an in vitro model of endotoxin tolerance (ET), a pivotal feature of sepsis-induced immunosuppression in monocytes, we identified using gene expression profiling by microarray a panel of transcripts associated with the development of ET which expression was restored after immunostimulation with interferon-gamma (IFN-γ). These results were confirmed by qRT-PCR. Importantly, this short-list of markers was further evaluated in patients. Of these transcripts, six (TNFAIP6, FCN1, CXCL10, GBP1, CXCL5 and PID1) were differentially expressed in septic patients’ blood compared to healthy blood upon ex vivo LPS stimulation and were restored by IFN-γ. In this study, by combining a microarray approach in an in vitro model and a validation in clinical samples, we identified a panel of six new transcripts that could be used for the identification of septic patients eligible for IFNg therapy. Along with the previously identified markers TNFa, IL10 and HLA-DRA, the potential value of these markers should now be evaluated in a larger cohort of patients. Upon favorable results, they could serve as stratification tools prior to immunostimulatory treatment and to monitor drug efficacy.
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Affiliation(s)
- Florence Allantaz-Frager
- Joint Unit Hospices Civils de Lyon-Biomérieux « sepsis », Hôpital Edouard Herriot, Lyon, France.
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22
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Pillai S, Szekeres K, Lawrence NJ, Chellappan SP, Blanck G. Regulation of interlocking gene regulatory network subcircuits by a small molecule inhibitor of retinoblastoma protein (RB) phosphorylation: cancer cell expression of HLA-DR. Gene 2012; 512:403-7. [PMID: 23041127 DOI: 10.1016/j.gene.2012.09.092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 08/28/2012] [Accepted: 09/23/2012] [Indexed: 11/17/2022]
Abstract
The induction of the major histocompatibility (MHC), antigen-presenting class II molecules by interferon-gamma, in solid tumor cells, requires the retinoblastoma tumor suppressor protein (Rb). In the absence of Rb, a repressosome blocks the access of positive-acting, promoter binding proteins to the MHC class II promoter. However, a complete molecular linkage between Rb expression and the disassembly of the MHC class II repressosome has been lacking. By treating A549 lung carcinoma cells with a novel small molecule that prevents phosphorylation-mediated, Rb inactivation, we demonstrate that Rb represses the synthesis of an MHC class II repressosome component, YY1. The reduction in YY1 synthesis correlates with the advent of MHC class II inducibility; with loss of YY1 binding to the promoter of the HLA-DRA gene, the canonical human MHC class II gene; and with increased Rb binding to the YY1 promoter. These results support the concept that the Rb gene regulatory network (GRN) subcircuit that regulates cell proliferation is linked to a GRN subcircuit regulating a tumor cell immune function.
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Affiliation(s)
- Smitha Pillai
- Drug Discovery Program, Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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Yang X, Sun J, Gao Y, Tan A, Zhang H, Hu Y, Feng J, Qin X, Tao S, Chen Z, Kim ST, Peng T, Liao M, Lin X, Zhang Z, Tang M, Li L, Mo L, Liang Z, Shi D, Huang Z, Huang X, Liu M, Liu Q, Zhang S, Trent JM, Zheng SL, Xu J, Mo Z. Genome-wide association study for serum complement C3 and C4 levels in healthy Chinese subjects. PLoS Genet 2012; 8:e1002916. [PMID: 23028341 PMCID: PMC3441730 DOI: 10.1371/journal.pgen.1002916] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 07/06/2012] [Indexed: 12/26/2022] Open
Abstract
Complement C3 and C4 play key roles in the main physiological activities of complement system, and their deficiencies or over-expression are associated with many clinical infectious or immunity diseases. A two-stage genome-wide association study (GWAS) was performed for serum levels of C3 and C4. The first stage was conducted in 1,999 healthy Chinese men, and the second stage was performed in an additional 1,496 subjects. We identified two SNPs, rs3753394 in CFH gene and rs3745567 in C3 gene, that are significantly associated with serum C3 levels at a genome-wide significance level (P = 7.33×10−11 and P = 1.83×10−9, respectively). For C4, one large genomic region on chromosome 6p21.3 is significantly associated with serum C4 levels. Two SNPs (rs1052693 and rs11575839) were located in the MHC class I area that include HLA-A, HLA-C, and HLA-B genes. Two SNPs (rs2075799 and rs2857009) were located 5′ and 3′ of C4 gene. The other four SNPs, rs2071278, rs3763317, rs9276606, and rs241428, were located in the MHC class II region that includes HLA-DRA, HLA-DRB, and HLA-DQB genes. The combined P-values for those eight SNPs ranged from 3.19×10−22 to 5.62×10−97. HBsAg-positive subjects have significantly lower C3 and C4 protein concentrations compared with HBsAg-negative subjects (P<0.05). Our study is the first GWAS report which shows genetic components influence the levels of complement C3 and C4. Our significant findings provide novel insights of their related autoimmune, infectious diseases, and molecular mechanisms. The complement system plays important roles in the innate and adaptive immune functions. C3 and C4 participate in almost all physiological activities and activated pathways as key complement members and host defense proteins. Identifying the genes that influence serum levels of C3 and C4 may help to elucidate the factors and mechanisms underlying the complement system. The genome-wide association studies (GWAS) have shown great success in revealing robust associations in both quantitative and qualitative traits. In this study, we performed a two-stage GWAS in a large cohort from the Chinese male population to examine the roles of common genetic variants on serum C3 and C4 levels. Our research identified genetic determinants associated with the quantitative levels of C3 and C4. Overall, our study highlights an intricate regulation of complement levels and potentially reveals novel mechanisms that may be followed up with additional functional studies.
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Affiliation(s)
- Xiaobo Yang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Jielin Sun
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Yong Gao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Fudan-VARI Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Aihua Tan
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Haiying Zhang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Yanling Hu
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi, China
| | - Junjie Feng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Xue Qin
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Sha Tao
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Zhuo Chen
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Seong-Tae Kim
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Laboratory of Genomic Diversity, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
| | - Ming Liao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaoling Lin
- Fudan-VARI Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Zengfeng Zhang
- Department of Microbiology, School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Minzhong Tang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Li Li
- Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi, China
| | - Linjian Mo
- Institute of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Zhengjia Liang
- Medical Examination Center, Fangchenggang First People's Hospital, Fangchenggang, Guangxi, China
| | - Deyi Shi
- Medical Examination Center, Fangchenggang First People's Hospital, Fangchenggang, Guangxi, China
| | - Zhang Huang
- Medical Examination Center, Fangchenggang First People's Hospital, Fangchenggang, Guangxi, China
| | - Xianghua Huang
- Medical Examination Center, Guigang People's Hospital, Guigang, Guangxi, China
| | - Ming Liu
- Medical Examination Center, Yulin First People's Hospital, Yulin, Guangxi, China
| | - Qian Liu
- Institute of Cardiovascular Diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Shijun Zhang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Jeffrey M. Trent
- Center for Genetic Epidemiology, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
| | - S. Lilly Zheng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Jianfeng Xu
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
- Fudan-VARI Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
- Center for Genetic Epidemiology, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
- Fudan University Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Institute of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- * E-mail:
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Jahnke M, Trowsdale J, Kelly AP. Structural requirements for recognition of major histocompatibility complex class II by membrane-associated RING-CH (MARCH) protein E3 ligases. J Biol Chem 2012; 287:28779-89. [PMID: 22761441 PMCID: PMC3436574 DOI: 10.1074/jbc.m112.381541] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 06/26/2012] [Indexed: 01/12/2023] Open
Abstract
MARCH E3 ligases play a key role in controlling MHC class II surface expression by regulated ubiquitination of a lysine residue in the β-chain. Little is known concerning how these enzymes target their specific substrates. Here we show that recognition of HLA-DR by MARCH proteins is complex. Several features associated with the transmembrane domain and bordering regions influence the overall efficiency of receptor internalization. A cluster of residues at the interface of the lipid bilayer and the cytosol plays the most important role in MARCH8 recognition of HLA-DRβ. Variation in this sequence also determines specificity of MARCH9 for HLA-DQ. Residues located in helical face four of HLA-DRβ together with a charged residue at the boundary with the stalk region also contribute significantly to recognition. Truncation analysis suggested that a dileucine-like motif in the DRβ cytoplasmic tail influences the efficiency of co-localization of HLA-DR with MARCH8. The DRβ-encoded acceptor lysine functioned optimally when placed in its natural location relative to the bilayer. In the DRα/DRβ dimer most other amino acids in the cytoplasmic tail could be substituted for alanine with minimal influence on function. Our data support a model whereby multiple features of HLA-DR are involved in substrate recognition by MARCH8. The single most important region is located at the interface between the transmembrane domain and the cytosol. Variation in sequence in this location between different class II isotypes controls efficiency of recognition by different MARCH E3 ligases.
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Affiliation(s)
- Martin Jahnke
- From the Division of Immunology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - John Trowsdale
- From the Division of Immunology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Adrian P. Kelly
- From the Division of Immunology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
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Abstract
Major histocompatibility complex class II (MHC-II) genes are fundamental components that contribute to adaptive immune responses. While characterization of the chromatin features at the core promoter region of these genes has been studied, the scope of histone modifications and the modifying factors responsible for activation of these genes are less well defined. Using the MHC-II gene HLA-DRA as a model, the extent and distribution of major histone modifications associated with active expression were defined in interferon-γ induced epithelial cells, B cells, and B-cell mutants for MHC-II expression. With active transcription, nucleosome density around the proximal regulatory region was diminished and histone acetylation and methylation modifications were distributed throughout the gene in distinct patterns that were dependent on the modification examined. Irrespective of the location, the majority of these modifications were dependent on the binding of either the X-box binding factor RFX or the class II transactivator (CIITA) to the proximal regulatory region. Importantly, once established, the modifications were stable through multiple cell divisions after the activating stimulus was removed, suggesting that activation of this system resulted in an epigenetic state. A dual crosslinking chromatin immunoprecipitation method was used to detect histone modifying protein components that interacted across the gene. Components of the MLL methyltransferase and GCN5 acetyltransferase complexes were identified. Some MLL complex components were found to be CIITA independent, including MLL1, ASH2L and RbBP5. Likewise, GCN5 containing acetyltransferase complex components belonging to the ATAC and STAGA complexes were also identified. These results suggest that multiple complexes are either used or are assembled as the gene is activated for expression. Together the results define and illustrate a complex network of histone modifying proteins and multisubunit complexes participating in MHC-II transcription.
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Affiliation(s)
- Nancy M. Choi
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Jeremy M. Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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Truax AD, Thakkar M, Greer SF. Dysregulated recruitment of the histone methyltransferase EZH2 to the class II transactivator (CIITA) promoter IV in breast cancer cells. PLoS One 2012; 7:e36013. [PMID: 22563434 PMCID: PMC3338556 DOI: 10.1371/journal.pone.0036013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 03/27/2012] [Indexed: 11/19/2022] Open
Abstract
One mechanism frequently utilized by tumor cells to escape immune system recognition and elimination is suppression of cell surface expression of Major Histocompatibility Class II (MHC II) molecules. Expression of MHC II is regulated primarily at the level of transcription by the Class II Transactivator, CIITA, and decreased CIITA expression is observed in multiple tumor types. We investigate here contributions of epigenetic modifications to transcriptional silencing of CIITA in variants of the human breast cancer cell line MDA MB 435. Significant increases in histone H3 lysine 27 trimethylation upon IFN-γ stimulation correlate with reductions in transcription factor recruitment to the interferon-γ inducible CIITA promoter, CIITApIV, and with significantly increased CIITApIV occupancy by the histone methyltransferase enhancer of zeste homolog 2 (EZH2). Most compelling is evidence that decreased expression of EZH2 in MDA MB 435 variants results in significant increases in CIITA and HLA-DRA mRNA expression, even in the absence of interferon-γ stimulation, as well as increased cell surface expression of MHC II. Together, these data add mechanistic insight to prior observations of increased EZH2 expression and decreased CIITA expression in multiple tumor types.
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Affiliation(s)
- Agnieszka D. Truax
- Division of Cellular and Molecular Biology and Physiology, Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - Meghna Thakkar
- Division of Cellular and Molecular Biology and Physiology, Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - Susanna F. Greer
- Division of Cellular and Molecular Biology and Physiology, Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
- * E-mail:
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Hill-Burns EM, Factor SA, Zabetian CP, Thomson G, Payami H. Evidence for more than one Parkinson's disease-associated variant within the HLA region. PLoS One 2011; 6:e27109. [PMID: 22096524 PMCID: PMC3212531 DOI: 10.1371/journal.pone.0027109] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 10/10/2011] [Indexed: 11/18/2022] Open
Abstract
Parkinson's disease (PD) was recently found to be associated with HLA in a genome-wide association study (GWAS). Follow-up GWAS's replicated the PD-HLA association but their top hits differ. Do the different hits tag the same locus or is there more than one PD-associated variant within HLA? We show that the top GWAS hits are not correlated with each other (0.00≤r(2)≤0.15). Using our GWAS (2000 cases, 1986 controls) we conducted step-wise conditional analysis on 107 SNPs with P<10(-3) for PD-association; 103 dropped-out, four remained significant. Each SNP, when conditioned on the other three, yielded P(SNP1) = 5×10(-4), P(SNP2) = 5×10(-4), P(SNP3) = 4×10(-3) and P(SNP4) = 0.025. The four SNPs were not correlated (0.01≤r(2)≤0.20). Haplotype analysis (excluding rare SNP2) revealed increasing PD risk with increasing risk alleles from OR = 1.27, P = 5×10(-3) for one risk allele to OR = 1.65, P = 4×10(-8) for three. Using additional 843 cases and 856 controls we replicated the independent effects of SNP1 (P(conditioned-on-SNP4) = 0.04) and SNP4 (P(conditioned-on-SNP1) = 0.04); SNP2 and SNP3 could not be replicated. In pooled GWAS and replication, SNP1 had OR(conditioned-on-SNP4) = 1.23, P(conditioned-on-SNP4) = 6×10(-7); SNP4 had OR(conditioned-on-SNP1) = 1.18, P(conditioned-on-SNP1) = 3×10(-3); and the haplotype with both risk alleles had OR = 1.48, P = 2×10(-12). Genotypic OR increased with the number of risk alleles an individual possessed up to OR = 1.94, P = 2×10(-11) for individuals who were homozygous for the risk allele at both SNP1 and SNP4. SNP1 is a variant in HLA-DRA and is associated with HLA-DRA, DRB5 and DQA2 gene expression. SNP4 is correlated (r(2) = 0.95) with variants that are associated with HLA-DQA2 expression, and with the top HLA SNP from the IPDGC GWAS (r(2) = 0.60). Our findings suggest more than one PD-HLA association; either different alleles of the same gene, or separate loci.
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Affiliation(s)
- Erin M. Hill-Burns
- New York State Department of Health Wadsworth Center, Albany, New York, United States of America
| | - Stewart A. Factor
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Cyrus P. Zabetian
- Veteran's Affairs Puget Sound Health Care System and Department of Neurology, University of Washington, Seattle, Washington, United States of America
| | - Glenys Thomson
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Haydeh Payami
- New York State Department of Health Wadsworth Center, Albany, New York, United States of America
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