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Thimmappa PY, Nair AS, D'silva S, Aravind A, Mallya S, Soman SP, Guruprasad KP, Shastry S, Raju R, Prasad TSK, Joshi MB. Neutrophils display distinct post-translational modifications in response to varied pathological stimuli. Int Immunopharmacol 2024; 132:111950. [PMID: 38579564 DOI: 10.1016/j.intimp.2024.111950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/08/2024] [Accepted: 03/26/2024] [Indexed: 04/07/2024]
Abstract
Neutrophils play a vital role in the innate immunity by perform effector functions through phagocytosis, degranulation, and forming extracellular traps. However, over-functioning of neutrophils has been associated with sterile inflammation such as Type 2 Diabetes, atherosclerosis, cancer and autoimmune disorders. Neutrophils exhibiting phenotypical and functional heterogeneity in both homeostatic and pathological conditions suggests distinct signaling pathways are activated in disease-specific stimuli and alter neutrophil functions. Hence, we examined mass spectrometry based post-translational modifications (PTM) of neutrophil proteins in response to pathologically significant stimuli, including high glucose, homocysteine and bacterial lipopolysaccharides representing diabetes-indicator, an activator of thrombosis and pathogen-associated molecule, respectively. Our data revealed that these aforesaid stimulators differentially deamidate, citrullinate, acetylate and methylate neutrophil proteins and align to distinct biological functions associated with degranulation, platelet activation, innate immune responses and metabolic alterations. The PTM patterns in response to high glucose showed an association with neutrophils extracellular traps (NETs) formation, homocysteine induced proteins PTM associated with signaling of systemic lupus erythematosus and lipopolysaccharides induced PTMs were involved in pathways related to cardiomyopathies. Our study provides novel insights into neutrophil PTM patterns and functions in response to varied pathological stimuli, which may serve as a resource to design therapeutic strategies for the management of neutrophil-centred diseases.
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Affiliation(s)
- Pooja Yedehalli Thimmappa
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Aswathy S Nair
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Sian D'silva
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Anjana Aravind
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Sandeep Mallya
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Sreelakshmi Pathappillil Soman
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Kanive Parashiva Guruprasad
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Shamee Shastry
- Department of Immunohematology and Blood Transfusion, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | | | - Manjunath B Joshi
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India.
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Li XY, Yu JT, Dong YH, Shen XY, Hou R, Xie MM, Wei J, Hu XW, Dong ZH, Shan RR, Jin J, Shao W, Meng XM. Protein acetylation and related potential therapeutic strategies in kidney disease. Pharmacol Res 2023; 197:106950. [PMID: 37820854 DOI: 10.1016/j.phrs.2023.106950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/16/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023]
Abstract
Kidney disease can be caused by various internal and external factors that have led to a continual increase in global deaths. Current treatment methods can alleviate but do not markedly prevent disease development. Further research on kidney disease has revealed the crucial function of epigenetics, especially acetylation, in the pathology and physiology of the kidney. Histone acetyltransferases (HATs), histone deacetylases (HDACs), and acetyllysine readers jointly regulate acetylation, thus affecting kidney physiological homoeostasis. Recent studies have shown that acetylation improves mechanisms and pathways involved in various types of nephropathy. The discovery and application of novel inhibitors and activators have further confirmed the important role of acetylation. In this review, we provide insights into the physiological process of acetylation and summarise its specific mechanisms and potential therapeutic effects on renal pathology.
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Affiliation(s)
- Xiang-Yu Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Ju-Tao Yu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Yu-Hang Dong
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Xiao-Yu Shen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Rui Hou
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Man-Man Xie
- School of Life Sciences, Anhui Medical University, Hefei 230032, China
| | - Jie Wei
- Department of Nephrology, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei 230601, Anhui, China
| | - Xiao-Wei Hu
- Department of Clinical Pharmacy, Anhui Provincial Children's Hospital, Hefei 230051, China
| | - Ze-Hui Dong
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Run-Run Shan
- School of Life Sciences, Anhui Medical University, Hefei 230032, China
| | - Juan Jin
- Research Center for Translational Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China
| | - Wei Shao
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China.
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China.
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3
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Crescioli S, Correa I, Ng J, Willsmore ZN, Laddach R, Chenoweth A, Chauhan J, Di Meo A, Stewart A, Kalliolia E, Alberts E, Adams R, Harris RJ, Mele S, Pellizzari G, Black ABM, Bax HJ, Cheung A, Nakamura M, Hoffmann RM, Terranova-Barberio M, Ali N, Batruch I, Soosaipillai A, Prassas I, Ulndreaj A, Chatanaka MK, Nuamah R, Kannambath S, Dhami P, Geh JLC, MacKenzie Ross AD, Healy C, Grigoriadis A, Kipling D, Karagiannis P, Dunn-Walters DK, Diamandis EP, Tsoka S, Spicer J, Lacy KE, Fraternali F, Karagiannis SN. B cell profiles, antibody repertoire and reactivity reveal dysregulated responses with autoimmune features in melanoma. Nat Commun 2023; 14:3378. [PMID: 37291228 PMCID: PMC10249578 DOI: 10.1038/s41467-023-39042-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
B cells are known to contribute to the anti-tumor immune response, especially in immunogenic tumors such as melanoma, yet humoral immunity has not been characterized in these cancers to detail. Here we show comprehensive phenotyping in samples of circulating and tumor-resident B cells as well as serum antibodies in melanoma patients. Memory B cells are enriched in tumors compared to blood in paired samples and feature distinct antibody repertoires, linked to specific isotypes. Tumor-associated B cells undergo clonal expansion, class switch recombination, somatic hypermutation and receptor revision. Compared with blood, tumor-associated B cells produce antibodies with proportionally higher levels of unproductive sequences and distinct complementarity determining region 3 properties. The observed features are signs of affinity maturation and polyreactivity and suggest an active and aberrant autoimmune-like reaction in the tumor microenvironment. Consistent with this, tumor-derived antibodies are polyreactive and characterized by autoantigen recognition. Serum antibodies show reactivity to antigens attributed to autoimmune diseases and cancer, and their levels are higher in patients with active disease compared to post-resection state. Our findings thus reveal B cell lineage dysregulation with distinct antibody repertoire and specificity, alongside clonally-expanded tumor-infiltrating B cells with autoimmune-like features, shaping the humoral immune response in melanoma.
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Affiliation(s)
- Silvia Crescioli
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Isabel Correa
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Joseph Ng
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
- Research Department of Structural and Molecular Biology, University College London, London, UK
| | - Zena N Willsmore
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Roman Laddach
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- Department of Informatics, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, London, UK
| | - Alicia Chenoweth
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - Jitesh Chauhan
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Ashley Di Meo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Alexander Stewart
- School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Eleni Kalliolia
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Elena Alberts
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - Rebecca Adams
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Robert J Harris
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Silvia Mele
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Giulia Pellizzari
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Anna B M Black
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Heather J Bax
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Anthony Cheung
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - Mano Nakamura
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Ricarda M Hoffmann
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Manuela Terranova-Barberio
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Niwa Ali
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
- Centre for Gene Therapy and Regenerative Medicine, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Ihor Batruch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | | | - Ioannis Prassas
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Antigona Ulndreaj
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Miyo K Chatanaka
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Rosamund Nuamah
- Biomedical Research Centre, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Shichina Kannambath
- Biomedical Research Centre, Guy's and St. Thomas' NHS Foundation Trust, London, UK
- Genomics Facility, Institute of Cancer Research, London, UK
| | - Pawan Dhami
- Biomedical Research Centre, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Jenny L C Geh
- St John's Institute of Dermatology, Guy's, King's, and St. Thomas' Hospitals NHS Foundation Trust, London, UK
- Department of Plastic Surgery at Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | | | - Ciaran Healy
- Department of Plastic Surgery at Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Anita Grigoriadis
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - David Kipling
- School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Panagiotis Karagiannis
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Eleftherios P Diamandis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
| | - Sophia Tsoka
- Department of Informatics, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, London, UK
| | - James Spicer
- School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - Katie E Lacy
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
- Research Department of Structural and Molecular Biology, University College London, London, UK
| | - Sophia N Karagiannis
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK.
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK.
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4
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Santambrogio L. Autoimmunity to the modified self. Science 2023; 379:1092-1093. [PMID: 36927028 DOI: 10.1126/science.adg3925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Protein posttranslational modifications can break tolerance to the self-proteome.
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Affiliation(s)
- Laura Santambrogio
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA
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5
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Lee AYS, McDonald D, Lin MW. Comparison of two anti-histones antibodies commercial assays in an immunology laboratory and systemic lupus erythematosus. J Immunol Methods 2023; 512:113401. [PMID: 36473536 DOI: 10.1016/j.jim.2022.113401] [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: 07/21/2022] [Revised: 11/15/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Anti-histones antibodies (AHAs) are antibodies directed against histone proteins - structural proteins that provides scaffolding for DNA to be wrapped around. AHAs, measured in the serum, are diagnostically helpful in cases of systemic lupus erythematosus (SLE) and drug-induced lupus erythematosus (DILE). In the diagnostic laboratory, they may be measured by enzyme-linked immune-sorbent assay (ELISA) or line immunoassays (LIA); however, the performance of these have never been directly compared in the literature. METHODS We evaluated a commonly used commercial ELISA and LIA to compare the performance in our immunology laboratory. Retrospective and prospective analyses were undertaken over a 5.5-year period. We also examined their performance in the model disease of SLE and compared their performance to disease activity and the main clinical features. RESULTS One hundred and thirty-five patients were evaluated including 65 SLE patients. Based on the quantitative cut-offs, there was only moderate agreement between the two assays (κ = 0.444). Both assays only had modest agreement with the clinical situation of the evaluated patients. When considered within the SLE context, both assays were moderately correlated with disease activity. Positive AHAs by ELISA were associated with SLE cytopaenias, and both ELISA and LIA correlated with positive anti-double stranded DNA. CONCLUSIONS Moderate agreement analytically were seen between ELISA and LIA methods in a general laboratory cohort. Both assays were comparable in their diagnostic performance. ELISA detection of AHAs appears to have some clinical use in our cohort of SLE patients. Future studies are required to explore the clinical utility of AHAs in SLE and other disorders.
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Affiliation(s)
- Adrian Y S Lee
- Department of Immunopathology, ICPMR, Westmead Hospital, Westmead, NSW, Australia; Department of Clinical Immunology & Allergy, Westmead Hospital, Westmead, NSW, Australia; Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia.
| | - David McDonald
- Department of Immunopathology, ICPMR, Westmead Hospital, Westmead, NSW, Australia
| | - Ming-Wei Lin
- Department of Immunopathology, ICPMR, Westmead Hospital, Westmead, NSW, Australia; Department of Clinical Immunology & Allergy, Westmead Hospital, Westmead, NSW, Australia; Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia
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6
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Santambrogio L, Franco A. The yin/yang balance of the MHC-self -immunopeptidome. Front Immunol 2022; 13:1035363. [PMID: 36405763 PMCID: PMC9666884 DOI: 10.3389/fimmu.2022.1035363] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/07/2022] [Indexed: 07/22/2023] Open
Abstract
The MHC-self immunopeptidome of professional antigen presenting cells is a cognate ligand for the TCRs expressed on both conventional and thymic-derived natural regulatory T cells. In regulatory T cells, the TCR signaling associated with MHC-peptide recognition induces antigen specific as well as bystander immunosuppression. On the other hand, TCR activation of conventional T cells is associated with protective immunity. As such the peripheral T cell repertoire is populated by a number of T cells with different phenotypes and different TCRs, which can recognize the same MHC-self-peptide complex, resulting in opposite immunological outcomes. This article summarizes what is known about regulatory and conventional T cell recognition of the MHC-self-immunopeptidome at steady state and in inflammatory conditions associated with increased T and B cell self-reactivity, discussing how changes in the MHC-ligandome including epitope copy number and post-translational modifications can tilt the balance toward the expansion of pro-inflammatory or regulatory T cells.
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Affiliation(s)
- Laura Santambrogio
- Department of Radiation Oncology, Physiology and Biophysics, Englander Institute of Precision Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Alessandra Franco
- University of California San Diego School of Medicine, Department of Pediatrics, La Jolla, CA, United States
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Magalingam KB, Somanath SD, Ramdas P, Haleagrahara N, Radhakrishnan AK. 6-Hydroxydopamine Induces Neurodegeneration in Terminally Differentiated SH-SY5Y Neuroblastoma Cells via Enrichment of the Nucleosomal Degradation Pathway: a Global Proteomics Approach. J Mol Neurosci 2022; 72:1026-1046. [PMID: 35258800 PMCID: PMC9064865 DOI: 10.1007/s12031-021-01962-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 12/22/2021] [Indexed: 01/07/2023]
Abstract
The SH-SY5Y human neuroblastoma cells have been used for decades as a cell-based model of dopaminergic neurons to explore the underlying science of cellular and molecular mechanisms of neurodegeneration in Parkinson’s disease (PD). However, data revealing the protein expression changes in 6-OHDA induced cytotoxicity in differentiated SH-SY5Y cells remain void. Therefore, we investigated the differentially regulated proteins expressed in terminally differentiated SH-SY5Y cells (differ-SH-SY5Y neural cells) exposed to 6-hydroxydopamine (6-OHDA) using the LC–MS/MS technology and construed the data using the online bioinformatics databases such as PANTHER, STRING, and KEGG. Our studies demonstrated that the neuronal development in differ-SH-SY5Y neural cells was indicated by the overexpression of proteins responsible for neurite formations such as calnexin (CANX) and calreticulin (CALR) besides significant downregulation of ribosomal proteins. The enrichment of the KEGG ribosome pathway was detected with significant downregulation (p < 0.05) of all the 21 ribosomal proteins in differ-SH-SY5Y neural cells compared with undifferentiated cells. Whereas in the PD model, the pathological changes induced by 6-OHDA were indicated by the presence of unfolded and misfolded proteins, which triggered the response of 10 kDa heat shock proteins (HSP), namely HSPE1 and HSPA9. Moreover, the 6-OHDA-induced neurodegeneration in differ-SH-SY5Y neural cells also upregulated the voltage-dependent anion-selective channel protein 1 (VDAC1) protein and enriched the KEGG systemic lupus erythematosus (SLE) pathway that was regulated by 17 histone proteins (p < 0.05) in differ-SH-SY5Y neural cells. These results suggest that the nucleosomal degradation pathway may have regulated the 6-OHDA induced neurodegeneration in PD cell-based model, which is reflected by increased apoptosis and histone release in differ-SH-SY5Y neural cells.
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Affiliation(s)
- Kasthuri Bai Magalingam
- School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Malaysia, Bandar Sunway, Malaysia
| | - Sushela Devi Somanath
- Pathology Division, School of Medicine, International Medical University, Kuala Lumpur, Malaysia
| | - Premdass Ramdas
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, Kuala Lumpur, Malaysia
| | - Nagaraja Haleagrahara
- College of Public Health, Medicine and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - Ammu Kutty Radhakrishnan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Malaysia, Bandar Sunway, Malaysia.
- Monash-Industry Palm Oil Education and Research Platform (MIPO), Monash University Malaysia, Bandar Sunway, Selangor, Malaysia.
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8
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Tan G, Baby B, Zhou Y, Wu T. Emerging Molecular Markers Towards Potential Diagnostic Panels for Lupus. Front Immunol 2022; 12:808839. [PMID: 35095896 PMCID: PMC8792845 DOI: 10.3389/fimmu.2021.808839] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a multifactorial autoimmune disease which can affect various tissues and organs, posing significant challenges for clinical diagnosis and treatment. The etiology of SLE is highly complex with contributions from environmental factors, stochastic factors as well as genetic susceptibility. The current criteria for diagnosing SLE is based primarily on a combination of clinical presentations and traditional lab testing. However, these tests have suboptimal sensitivity and specificity. They are unable to indicate disease cause or guide physicians in decision-making for treatment. Therefore, there is an urgent need to develop a more accurate and robust tool for effective clinical management and drug development in lupus patients. It is fortunate that the emerging Omics have empowered scientists in the discovery and identification of potential novel biomarkers of SLE, especially the markers from blood, urine, cerebrospinal fluids (CSF), and other bodily fluids. However, many of these markers have not been carefully validated for clinical use. In addition, it is apparent that individual biomarkers lack sensitivity or specificity. This review summarizes the sensitivity, specificity and diagnostic value of emerging biomarkers from recent studies, and discusses the potential of these markers in the development of biomarker panel based diagnostics or disease monitoring system in SLE.
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Affiliation(s)
- Gongjun Tan
- Department of Clinical Laboratory, Zhuhai Maternal and Child Healthcare Hospital, Zhuhai, China
| | - Binila Baby
- Department of Biomedical Engineering, University of Houston, Houston, TX, United States
| | - Yuqiu Zhou
- Department of Clinical Laboratory, Zhuhai Maternal and Child Healthcare Hospital, Zhuhai, China
| | - Tianfu Wu
- Department of Biomedical Engineering, University of Houston, Houston, TX, United States
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9
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Rekvig OP. The Anti-DNA Antibodies: Their Specificities for Unique DNA Structures and Their Unresolved Clinical Impact-A System Criticism and a Hypothesis. Front Immunol 2022; 12:808008. [PMID: 35087528 PMCID: PMC8786728 DOI: 10.3389/fimmu.2021.808008] [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: 11/02/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is diagnosed and classified by criteria, or by experience, intuition and traditions, and not by scientifically well-defined etiology(ies) or pathogenicity(ies). One central criterion and diagnostic factor is founded on theoretical and analytical approaches based on our imperfect definition of the term “The anti-dsDNA antibody”. “The anti-dsDNA antibody” holds an archaic position in SLE as a unique classification criterium and pathogenic factor. In a wider sense, antibodies to unique transcriptionally active or silent DNA structures and chromatin components may have individual and profound nephritogenic impact although not considered yet – not in theoretical nor in descriptive or experimental contexts. This hypothesis is contemplated here. In this analysis, our state-of-the-art conception of these antibodies is probed and found too deficient with respect to their origin, structural DNA specificities and clinical/pathogenic impact. Discoveries of DNA structures and functions started with Miescher’s Nuclein (1871), via Chargaff, Franklin, Watson and Crick, and continues today. The discoveries have left us with a DNA helix that presents distinct structures expressing unique operations of DNA. All structures are proven immunogenic! Unique autoimmune antibodies are described against e.g. ssDNA, elongated B DNA, bent B DNA, Z DNA, cruciform DNA, or individual components of chromatin. In light of the massive scientific interest in anti-DNA antibodies over decades, it is an unexpected observation that the spectrum of DNA structures has been known for decades without being implemented in clinical immunology. This leads consequently to a critical analysis of historical and contemporary evidence-based data and of ignored and one-dimensional contexts and hypotheses: i.e. “one antibody - one disease”. In this study radical viewpoints on the impact of DNA and chromatin immunity/autoimmunity are considered and discussed in context of the pathogenesis of lupus nephritis.
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Affiliation(s)
- Ole Petter Rekvig
- Section of Autoimmunity, Fürst Medical Laboratory, Oslo, Norway.,Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
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10
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Chamardani TM, Amiritavassoli S. Inhibition of NETosis for treatment purposes: friend or foe? Mol Cell Biochem 2022; 477:673-688. [PMID: 34993747 PMCID: PMC8736330 DOI: 10.1007/s11010-021-04315-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/25/2021] [Indexed: 12/29/2022]
Abstract
Active neutrophils participate in innate and adaptive immune responses through various mechanisms, one of the most important of which is the formation and release of neutrophil extracellular traps (NETs). The NETs are composed of network-like structures made of histone proteins, DNA and other released antibacterial proteins by activated neutrophils, and evidence suggests that in addition to the innate defense against infections, NETosis plays an important role in the pathogenesis of several other non-infectious pathological states, such as autoimmune diseases and even cancer. Therefore, targeting NET has become one of the important therapeutic approaches and has been considered by researchers. NET inhibitors or other molecules involved in the NET formation, such as the protein arginine deiminase 4 (PAD4) enzyme, an arginine-to-citrulline converter, participate in chromatin condensation and NET formation, is the basis of this therapeutic approach. The important point is whether complete inhibition of NETosis can be helpful because by inhibiting this mechanism, the activity of neutrophils is suppressed. In this review, the biology of NETosis and its role in the pathogenesis of some important diseases have been summarized, and the consequences of treatment based on inhibition of NET formation have been discussed.
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11
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The Complex Role of C-Reactive Protein in Systemic Lupus Erythematosus. J Clin Med 2021; 10:jcm10245837. [PMID: 34945133 PMCID: PMC8708507 DOI: 10.3390/jcm10245837] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/29/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022] Open
Abstract
C-reactive protein (CRP) is well-known as a sensitive albeit unspecific biomarker of inflammation. In most rheumatic conditions, the level of this evolutionarily highly conserved pattern recognition molecule conveys reliable information regarding the degree of ongoing inflammation, driven mainly by interleukin-6. However, the underlying causes of increased CRP levels are numerous, including both infections and malignancies. In addition, low to moderate increases in CRP predict subsequent cardiovascular events, often occurring years later, in patients with angina and in healthy individuals. However, autoimmune diseases characterized by the Type I interferon gene signature (e.g., systemic lupus erythematosus, primary Sjögren’s syndrome and inflammatory myopathies) represent exceptions to the general rule that the concentrations of CRP correlate with the extent and severity of inflammation. In fact, adequate levels of CRP can be beneficial in autoimmune conditions, in that they contribute to efficient clearance of cell remnants and immune complexes through complement activation/modulation, opsonization and phagocytosis. Furthermore, emerging data indicate that CRP constitutes an autoantigen in systemic lupus erythematosus. At the same time, the increased risks of cardiovascular and cerebrovascular diseases in patients diagnosed with systemic lupus erythematosus and rheumatoid arthritis are well-established, with significant impacts on quality of life, accrual of organ damage, and premature mortality. This review describes CRP-mediated biological effects and the regulation of CRP release in relation to aspects of cardiovascular disease and mechanisms of autoimmunity, with particular focus on systemic lupus erythematosus.
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12
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Sjöwall J, Azharuddin M, Frodlund M, Zhang Y, Sandner L, Dahle C, Hinkula J, Sjöwall C. SARS-CoV-2 Antibody Isotypes in Systemic Lupus Erythematosus Patients Prior to Vaccination: Associations With Disease Activity, Antinuclear Antibodies, and Immunomodulatory Drugs During the First Year of the Pandemic. Front Immunol 2021; 12:724047. [PMID: 34512651 PMCID: PMC8430325 DOI: 10.3389/fimmu.2021.724047] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/04/2021] [Indexed: 12/23/2022] Open
Abstract
Objectives Impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic on individuals with arthritis has been highlighted whereas data on other rheumatic diseases, e.g., systemic lupus erythematosus (SLE), are scarce. Similarly to SLE, severe SARS-CoV-2 infection includes risks for thromboembolism, an unbalanced type I interferon response, and complement activation. Herein, SARS-CoV-2 antibodies in longitudinal samples collected prior to vaccination were analyzed and compared with SLE progression and antinuclear antibody (ANA) levels. Methods One hundred patients (83 women) with established SLE and a regular visit to the rheumatologist (March 2020 to January 2021) were included. All subjects donated blood and had done likewise prior to the pandemic. SARS-CoV-2 antibody isotypes (IgG, IgA, IgM) to the cell receptor-binding S1-spike outer envelope protein were detected by ELISA, and their neutralizing capacity was investigated. IgG-ANA were measured by multiplex technology. Results During the pandemic, 4% had PCR-confirmed infection but 36% showed SARS-CoV-2 antibodies of ≥1 isotype; IgA was the most common (30%), followed by IgM (9%) and IgG (8%). The antibodies had low neutralizing capacity and were detected also in prepandemic samples. Plasma albumin (p = 0.04) and anti-dsDNA (p = 0.003) levels were lower in patients with SARS-CoV-2 antibodies. Blood group, BMI, smoking habits, complement proteins, daily glucocorticoid dose, use of hydroxychloroquine, or self-reported coronavirus disease 2019 (COVID-19) symptoms (except fever, >38.5°C) did not associate with SARS-CoV-2 antibodies. Conclusion Our data from early 2021 indicate that a large proportion of Swedish SLE patients had serological signs of exposure to SARS-CoV-2 but apparently with a minor impact on the SLE course. Use of steroids and hydroxychloroquine showed no distinct effects, and self-reported COVID-19-related symptoms correlated poorly with all antibody isotypes.
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Affiliation(s)
- Johanna Sjöwall
- Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection/Infectious Diseases, Linköping University, Linköping, Sweden
| | - Mohammad Azharuddin
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Linköping University, Linköping, Sweden
| | - Martina Frodlund
- Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection/Rheumatology, Linköping University, Linköping, Sweden
| | - Yuming Zhang
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Linköping University, Linköping, Sweden
| | - Laura Sandner
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Linköping University, Linköping, Sweden
| | - Charlotte Dahle
- Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection/Clinical Immunology & Transfusion Medicine, Linköping University, Linköping, Sweden
| | - Jorma Hinkula
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Linköping University, Linköping, Sweden
| | - Christopher Sjöwall
- Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection/Rheumatology, Linköping University, Linköping, Sweden
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13
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Wang JY, Roehrl MW, Roehrl VB, Roehrl MH. A Master Autoantigen-ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.07.30.454526. [PMID: 34373855 PMCID: PMC8351778 DOI: 10.1101/2021.07.30.454526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chronic and debilitating autoimmune sequelae pose a grave concern for the post-COVID-19 pandemic era. Based on our discovery that the glycosaminoglycan dermatan sulfate (DS) displays peculiar affinity to apoptotic cells and autoantigens (autoAgs) and that DS-autoAg complexes cooperatively stimulate autoreactive B1 cell responses, we compiled a database of 751 candidate autoAgs from six human cell types. At least 657 of these have been found to be affected by SARS-CoV-2 infection based on currently available multi-omic COVID data, and at least 400 are confirmed targets of autoantibodies in a wide array of autoimmune diseases and cancer. The autoantigen-ome is significantly associated with various processes in viral infections, such as translation, protein processing, and vesicle transport. Interestingly, the coding genes of autoAgs predominantly contain multiple exons with many possible alternative splicing variants, short transcripts, and short UTR lengths. These observations and the finding that numerous autoAgs involved in RNA-splicing showed altered expression in viral infections suggest that viruses exploit alternative splicing to reprogram host cell machinery to ensure viral replication and survival. While each cell type gives rise to a unique pool of autoAgs, 39 common autoAgs associated with cell stress and apoptosis were identified from all six cell types, with several being known markers of systemic autoimmune diseases. In particular, the common autoAg UBA1 that catalyzes the first step in ubiquitination is encoded by an X-chromosome escape gene. Given its essential function in apoptotic cell clearance and that X-inactivation escape tends to increase with aging, UBA1 dysfunction can therefore predispose aging women to autoimmune disorders. In summary, we propose a model of how viral infections lead to extensive molecular alterations and host cell death, autoimmune responses facilitated by autoAg-DS complexes, and ultimately autoimmune diseases. Overall, this master autoantigen-ome provides a molecular guide for investigating the myriad of autoimmune sequalae to COVID-19 and clues to the rare but reported adverse effects of the currently available COVID vaccines.
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Affiliation(s)
| | | | | | - Michael H. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
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14
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Wang JY, Zhang W, Roehrl MW, Roehrl VB, Roehrl MH. An Autoantigen Profile from Jurkat T-Lymphoblasts Provides a Molecular Guide for Investigating Autoimmune Sequelae of COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.07.05.451199. [PMID: 34729561 PMCID: PMC8562547 DOI: 10.1101/2021.07.05.451199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In order to understand autoimmune phenomena contributing to the pathophysiology of COVID-19 and post-COVID syndrome, we have been profiling autoantigens (autoAgs) from various cell types. Although cells share numerous autoAgs, each cell type gives rise to unique COVID-altered autoAg candidates, which may explain the wide range of symptoms experienced by patients with autoimmune sequelae of SARS-CoV-2 infection. Based on the unifying property of affinity between autoantigens (autoAgs) and the glycosaminoglycan dermatan sulfate (DS), this paper reports 140 candidate autoAgs identified from proteome extracts of human Jurkat T-cells, of which at least 105 (75%) are known targets of autoantibodies. Comparison with currently available multi-omic COVID-19 data shows that 125 (89%) of DS-affinity proteins are altered at protein and/or RNA levels in SARS-CoV-2-infected cells or patients, with at least 94 being known autoAgs in a wide spectrum of autoimmune diseases and cancer. Protein alterations by ubiquitination and phosphorylation in the viral infection are major contributors of autoAgs. The autoAg protein network is significantly associated with cellular response to stress, apoptosis, RNA metabolism, mRNA processing and translation, protein folding and processing, chromosome organization, cell cycle, and muscle contraction. The autoAgs include clusters of histones, CCT/TriC chaperonin, DNA replication licensing factors, proteasome and ribosome proteins, heat shock proteins, serine/arginine-rich splicing factors, 14-3-3 proteins, and cytoskeletal proteins. AutoAgs such as LCP1 and NACA that are altered in the T cells of COVID patients may provide insight into T-cell responses in the viral infection and merit further study. The autoantigen-ome from this study contributes to a comprehensive molecular map for investigating acute, subacute, and chronic autoimmune disorders caused by SARS-CoV-2.
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Affiliation(s)
| | - Wei Zhang
- Department of Gastroenterology, Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | | | | | - Michael H. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
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15
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Immune-Related Urine Biomarkers for the Diagnosis of Lupus Nephritis. Int J Mol Sci 2021; 22:ijms22137143. [PMID: 34281193 PMCID: PMC8267641 DOI: 10.3390/ijms22137143] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 12/17/2022] Open
Abstract
The kidney is one of the main organs affected by the autoimmune disease systemic lupus erythematosus. Lupus nephritis (LN) concerns 30-60% of adult SLE patients and it is significantly associated with an increase in the morbidity and mortality. The definitive diagnosis of LN can only be achieved by histological analysis of renal biopsies, but the invasiveness of this technique is an obstacle for early diagnosis of renal involvement and a proper follow-up of LN patients under treatment. The use of urine for the discovery of non-invasive biomarkers for renal disease in SLE patients is an attractive alternative to repeated renal biopsies, as several studies have described surrogate urinary cells or analytes reflecting the inflammatory state of the kidney, and/or the severity of the disease. Herein, we review the main findings in the field of urine immune-related biomarkers for LN patients, and discuss their prognostic and diagnostic value. This manuscript is focused on the complement system, antibodies and autoantibodies, chemokines, cytokines, and leukocytes, as they are the main effectors of LN pathogenesis.
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16
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Grönwall C, Liljefors L, Bang H, Hensvold AH, Hansson M, Mathsson-Alm L, Israelsson L, Joshua V, Svärd A, Stålesen R, Titcombe PJ, Steen J, Piccoli L, Sherina N, Clavel C, Svenungsson E, Gunnarsson I, Saevarsdottir S, Kastbom A, Serre G, Alfredsson L, Malmström V, Rönnelid J, Catrina AI, Lundberg K, Klareskog L. A Comprehensive Evaluation of the Relationship Between Different IgG and IgA Anti-Modified Protein Autoantibodies in Rheumatoid Arthritis. Front Immunol 2021; 12:627986. [PMID: 34093522 PMCID: PMC8173192 DOI: 10.3389/fimmu.2021.627986] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/26/2021] [Indexed: 12/25/2022] Open
Abstract
Seropositive rheumatoid arthritis (RA) is characterized by the presence of rheumatoid factor (RF) and anti-citrullinated protein autoantibodies (ACPA) with different fine-specificities. Yet, other serum anti-modified protein autoantibodies (AMPA), e.g. anti-carbamylated (Carb), -acetylated (KAc), and malondialdehyde acetaldehyde (MAA) modified protein antibodies, have been described. In this comprehensive study, we analyze 30 different IgG and IgA AMPA reactivities to Cit, Carb, KAc, and MAA antigens detected by ELISA and autoantigen arrays in N=1985 newly diagnosed RA patients. Association with patient characteristics such as smoking and disease activity were explored. Carb and KAc reactivities by different assays were primarily seen in patients also positive for anti-citrulline reactivity. Modified vimentin (mod-Vim) peptides were used for direct comparison of different AMPA reactivities, revealing that IgA AMPA recognizing mod-Vim was mainly detected in subsets of patients with high IgG anti-Cit-Vim levels and a history of smoking. IgG reactivity to acetylation was mainly detected in a subset of patients with Cit and Carb reactivity. Anti-acetylated histone reactivity was RA-specific and associated with high anti-CCP2 IgG levels, multiple ACPA fine-specificities, and smoking status. This reactivity was also found to be present in CCP2+ RA-risk individuals without arthritis. Our data further demonstrate that IgG autoreactivity to MAA was increased in RA compared to controls with highest levels in CCP2+ RA, but was not RA-specific, and showed low correlation with other AMPA. Anti-MAA was instead associated with disease activity and was not significantly increased in CCP2+ individuals at risk of RA. Notably, RA patients could be subdivided into four different subsets based on their AMPA IgG and IgA reactivity profiles. Our serology results were complemented by screening of monoclonal antibodies derived from single B cells from RA patients for the same antigens as the RA cohort. Certain CCP2+ clones had Carb or Carb+KAc+ multireactivity, while such reactivities were not found in CCP2- clones. We conclude that autoantibodies exhibiting different patterns of ACPA fine-specificities as well as Carb and KAc reactivity are present in RA and may be derived from multireactive B-cell clones. Carb and KAc could be considered reactivities within the “Cit-umbrella” similar to ACPA fine-specificities, while MAA reactivity is distinctly different.
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Affiliation(s)
- Caroline Grönwall
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lisa Liljefors
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Aase H Hensvold
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Center for Rheumatology, Academic Specialist Center, Stockholm Health Region, Stockholm, Sweden.,Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Monika Hansson
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Linda Mathsson-Alm
- Thermo Fisher Scientific, Immuno Diagnostics Division, Uppsala, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lena Israelsson
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Vijay Joshua
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Svärd
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.,Center for Clinical Research Dalarna, Uppsala University, Uppsala, Sweden
| | - Ragnhild Stålesen
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Philip J Titcombe
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,The Center for Immunology and Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Johanna Steen
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Luca Piccoli
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Natalia Sherina
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Cyril Clavel
- Unité Différenciation Épithéliale et Autoimmunité Rhumatoïde, INSERM - Université de Toulouse, Toulouse, France
| | - Elisabet Svenungsson
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Gunnarsson
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Saedis Saevarsdottir
- Department of Medicine Solna, Division of Clinical Epidemiology, Karolinska Institutet, Stockholm, Sweden.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Alf Kastbom
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Guy Serre
- Unité Différenciation Épithéliale et Autoimmunité Rhumatoïde, INSERM - Université de Toulouse, Toulouse, France
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm Health Region, Stockholm, Sweden
| | - Vivianne Malmström
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Rönnelid
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anca I Catrina
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Center for Rheumatology, Academic Specialist Center, Stockholm Health Region, Stockholm, Sweden.,Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Lundberg
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lars Klareskog
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Center for Rheumatology, Academic Specialist Center, Stockholm Health Region, Stockholm, Sweden.,Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
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17
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Shmueli MD, Sheban D, Eisenberg-Lerner A, Merbl Y. Histone degradation by the proteasome regulates chromatin and cellular plasticity. FEBS J 2021; 289:3304-3316. [PMID: 33914417 PMCID: PMC9292675 DOI: 10.1111/febs.15903] [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: 01/19/2021] [Revised: 04/07/2021] [Accepted: 04/26/2021] [Indexed: 11/27/2022]
Abstract
Histones constitute the primary protein building blocks of the chromatin and play key roles in the dynamic control of chromatin compaction and epigenetic regulation. Histones are regulated by intricate mechanisms that alter their functionality and stability, thereby expanding the regulation of chromatin‐transacting processes. As such, histone degradation is tightly regulated to provide spatiotemporal control of cellular histone abundance. While several mechanisms have been implicated in controlling histone stability, here, we discuss proteasome‐dependent degradation of histones and the protein modifications that are associated with it. We then highlight specific cellular and physiological states that are associated with altered histone degradation by cellular proteasomes.
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Affiliation(s)
- Merav D Shmueli
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Daoud Sheban
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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18
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Datta SK. Harnessing Tolerogenic Histone Peptide Epitopes From Nucleosomes for Selective Down-Regulation of Pathogenic Autoimmune Response in Lupus (Past, Present, and Future). Front Immunol 2021; 12:629807. [PMID: 33936042 PMCID: PMC8080879 DOI: 10.3389/fimmu.2021.629807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/23/2021] [Indexed: 12/11/2022] Open
Abstract
Autoantigen-directed tolerance can be induced by certain nucleosomal histone peptide epitope/s in nanomolar dosage leading to sustained remission of disease in mice with spontaneous SLE. By contrast, lupus is accelerated by administration of intact (whole) histones, or whole nucleosomes in microparticles from apoptotic cells, or by post-translationally acetylated histone-peptides. Low-dose therapy with the histone-peptide epitopes simultaneously induces TGFβ and inhibits IL-6 production by DC in vivo, especially pDC, which then induce CD4+CD25+ Treg and CD8+ Treg cells that suppress pathogenic autoimmune response. Both types of induced Treg cells are FoxP3+ and act by producing TGFβ at close cell-to-cell range. No anaphylactic adverse reactions, or generalized immunosuppression have been detected in mice injected with the peptides, because the epitopes are derived from evolutionarily conserved histones in the chromatin; and the peptides are expressed in the thymus during ontogeny, and their native sequences have not been altered. The peptide-induced Treg cells can block severe lupus on adoptive transfer reducing inflammatory cell reaction and infiltration in the kidney. In Humans, similar potent Treg cells are generated by the histone peptide epitopes in vitro in lupus patients’ PBMC, inhibiting anti-dsDNA autoantibody and interferon production. Furthermore, the same types of Treg cells are generated in lupus patients who are in very long-term remission (2-8 years) after undergoing autologous hematopoietic stem cell transplantation. These Treg cells are not found in lupus patients treated conventionally into clinical remission (SLEDAI of 0); and consequently they still harbor pathogenic autoimmune cells, causing subclinical damage. Although antigen-specific therapy with pinpoint accuracy is suitable for straight-forward organ-specific autoimmune diseases, Systemic Lupus is much more complex. The histone peptide epitopes have unique tolerogenic properties for inhibiting Innate immune cells (DC), T cells and B cell populations that are both antigen-specifically and cross-reactively involved in the pathogenic autoimmune response in lupus. The histone peptide tolerance is a natural and non-toxic therapy suitable for treating early lupus, and also maintaining lupus patients after toxic drug therapy. The experimental steps, challenges and possible solutions for successful therapy with these peptide epitopes are discussed in this highly focused review on Systemic Lupus.
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Affiliation(s)
- Syamal K Datta
- Department of Medicine, Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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19
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Fresneda Alarcon M, McLaren Z, Wright HL. Neutrophils in the Pathogenesis of Rheumatoid Arthritis and Systemic Lupus Erythematosus: Same Foe Different M.O. Front Immunol 2021; 12:649693. [PMID: 33746988 PMCID: PMC7969658 DOI: 10.3389/fimmu.2021.649693] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/12/2021] [Indexed: 12/14/2022] Open
Abstract
Dysregulated neutrophil activation contributes to the pathogenesis of autoimmune diseases including rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). Neutrophil-derived reactive oxygen species (ROS) and granule proteases are implicated in damage to and destruction of host tissues in both conditions (cartilage in RA, vascular tissue in SLE) and also in the pathogenic post-translational modification of DNA and proteins. Neutrophil-derived cytokines and chemokines regulate both the innate and adaptive immune responses in RA and SLE, and neutrophil extracellular traps (NETs) expose nuclear neoepitopes (citrullinated proteins in RA, double-stranded DNA and nuclear proteins in SLE) to the immune system, initiating the production of auto-antibodies (ACPA in RA, anti-dsDNA and anti-acetylated/methylated histones in SLE). Neutrophil apoptosis is dysregulated in both conditions: in RA, delayed apoptosis within synovial joints contributes to chronic inflammation, immune cell recruitment and prolonged release of proteolytic enzymes, whereas in SLE enhanced apoptosis leads to increased apoptotic burden associated with development of anti-nuclear auto-antibodies. An unbalanced energy metabolism in SLE and RA neutrophils contributes to the pathology of both diseases; increased hypoxia and glycolysis in RA drives neutrophil activation and NET production, whereas decreased redox capacity increases ROS-mediated damage in SLE. Neutrophil low-density granulocytes (LDGs), present in high numbers in the blood of both RA and SLE patients, have opposing phenotypes contributing to clinical manifestations of each disease. In this review we will describe the complex and contrasting phenotype of neutrophils and LDGs in RA and SLE and discuss their discrete roles in the pathogenesis of each condition. We will also review our current understanding of transcriptomic and metabolomic regulation of neutrophil phenotype in RA and SLE and discuss opportunities for therapeutic targeting of neutrophil activation in inflammatory auto-immune disease.
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Affiliation(s)
- Michele Fresneda Alarcon
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Zoe McLaren
- Liverpool University Hospitals National Health Service (NHS) Foundation Trust, Liverpool, United Kingdom
| | - Helen Louise Wright
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
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20
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Elsayed SA, Mohafez OMM. Autoantibodies spectrum in lupus nephritis in a cohort of Egyptian patients: relation to disease activity and prognostic value. EGYPTIAN RHEUMATOLOGY AND REHABILITATION 2020. [DOI: 10.1186/s43166-020-00039-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Specific autoantibodies are considered as an important marker in autoimmune rheumatic diseases and are of great value for the diagnosis and prognosis of systemic lupus erythematosus (SLE) patients. A total of eighteen autoantibodies were analyzed for their positivity in SLE patients and we evaluated the clinical relevance of the five most frequent autoantibodies: anti-dsDNA, anti-nucleosome, anti-histone, anti-Ro60, and anti-Ro52 on disease activity and renal affection in SLE Egyptian patients.
Results
Immunological profile and correlation of the five autoantibodies with disease activity and histopathological pattern of renal involvement were analyzed for 190 SLE patients. Lupus nephritis (LN) patients showed much worse constitutional and mucocutaneous manifestations than patients without nephritis. Autoantibody profile showed a significant increased frequency of anti-dsDNA, anti-nucleosome, anti-histone, anti-Ro-60, and anti-Ro52 antibodies in LN patients. The impact of the co-positivity of the autoantibodies on the renal function was obvious. Moreover, the disease activity increased by the increased frequency of autoantibodies positivity in LN patients. ROC curve analysis showed that anti-nucleosome had the highest sensitivity; 93% followed by anti-dsDNA 83.3% then anti-histone 73.8%, but anti-Ro60 and anti-Ro52 showed a humble sensitivity. Furthermore, the highest frequency of positivity for the five autoantibodies was found in class-III and class-IV LN patients.
Conclusion
Detection of anti-dsDNA, anti-nucleosome, anti-histone, and anti-Ro60 in SLE patients may be important for predicting disease progression and kidney affection. Moreover, anti-nucleosome and anti-dsDNA show high sensitivity and specificity for lupus nephritis, thus patients with four to five positive autoantibody panels should be kept under close monitoring as they may warrant considering aggressive therapy to control their disease and prevent renal damage.
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Guo C, Qi Y, Qu J, Gai L, Shi Y, Yuan C. Pathophysiological Functions of the lncRNA TUG1. Curr Pharm Des 2020; 26:688-700. [PMID: 31880241 DOI: 10.2174/1381612826666191227154009] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 12/23/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) with little or no coding capacity are associated with a plethora of cellular functions, participating in various biological processes. Cumulative study of lncRNA provides explanations to the physiological and pathological processes and new perspectives to the diagnosis, prevention, and treatment of some clinical diseases. Long non-coding RNA taurine-upregulated gene 1(TUG1) is one of the first identified lncRNAs associated with human disease, which actively involved in various physiological processes, including regulating genes at epigenetics, transcription, post-transcription, translation, and posttranslation. The aim of this review was to explore the molecular mechanism of TUG1 in various types of human diseases. METHODS In this review, we summarized and analyzed the latest findings related to the physiologic and pathophysiological processes of TUG1 in human diseases. The related studies were retrieved and selected the last six years of research articles in PubMed with lncRNA and TUG1 as keywords. RESULTS TUG1 is a valuable lncRNA that its dysregulated expression and regulating the biological processes were found in a variety of human diseases. TUG1 is found to exhibit aberrant expression in a variety of malignancies. Dysregulation of TUG1 has been shown to contribute to proliferation, migration, cell cycle changes, inhibited apoptosis, and drug resistance of cancer cells, which revealed an oncogenic role for this lncRNA, but some reports have shown downregulation of TUG1 in lung cancer samples compared with noncancerous samples. In addition, the molecular and biological functions of TUG1 in physiology and disease (relevant to endocrinology, metabolism, immunology, neurobiology) have also been highlighted. Finally, we discuss the limitations and tremendous diagnostic/therapeutic potential of TUG1 in cancer and other diseases. CONCLUSION Long non-coding RNA-TUG1 likely served as useful disease biomarkers or therapy targets and effectively applied in different kinds of diseases, such as human cancer and cardiovascular diseases.
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Affiliation(s)
- Chong Guo
- Department of Biochemistry, China Three Gorges University, Yichang City Hubei Province, China
| | - Yuying Qi
- Department of Biochemistry, China Three Gorges University, Yichang City Hubei Province, China
| | - Jiayuan Qu
- Department of Biochemistry, China Three Gorges University, Yichang City Hubei Province, China
| | - Liyue Gai
- Department of Biochemistry, China Three Gorges University, Yichang City Hubei Province, China
| | - Yue Shi
- Department of Biochemistry, China Three Gorges University, Yichang City Hubei Province, China
| | - Chengfu Yuan
- Department of Biochemistry, China Three Gorges University, Yichang City Hubei Province, China.,Tumor Microenvironment and Immunotherapy Key Laboratory of Hubei province in China, Yichang City, China
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22
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Wang JY, Zhang W, Rho JH, Roehrl MW, Roehrl MH. A proteomic repertoire of autoantigens identified from the classic autoantibody clinical test substrate HEp-2 cells. Clin Proteomics 2020; 17:35. [PMID: 32973414 PMCID: PMC7507713 DOI: 10.1186/s12014-020-09298-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Autoantibodies are a hallmark of autoimmune diseases. Autoantibody screening by indirect immunofluorescence staining of HEp-2 cells with patient sera is a current standard in clinical practice. Differential diagnosis of autoimmune disorders is based on commonly recognizable nuclear and cytoplasmic staining patterns. In this study, we attempted to identify as many autoantigens as possible from HEp-2 cells using a unique proteomic DS-affinity enrichment strategy. METHODS HEp-2 cells were cultured and lysed. Total proteins were extracted from cell lysate and fractionated with DS-Sepharose resins. Proteins were eluted with salt gradients, and fractions with low to high affinity were collected and sequenced by mass spectrometry. Literature text mining was conducted to verify the autoantigenicity of each protein. Protein interaction network and pathway analyses were performed on all identified proteins. RESULTS This study identified 107 proteins from fractions with low to high DS-affinity. Of these, 78 are verified autoantigens with previous reports as targets of autoantibodies, whereas 29 might be potential autoantigens yet to be verified. Among the 107 proteins, 82 can be located to nucleus and 15 to the mitotic cell cycle, which may correspond to the dominance of nuclear and mitotic staining patterns in HEp-2 test. There are 55 vesicle-associated proteins and 12 ribonucleoprotein granule proteins, which may contribute to the diverse speckled patterns in HEp-2 stains. There are also 32 proteins related to the cytoskeleton. Protein network analysis indicates that these proteins have significantly more interactions among themselves than would be expected of a random set, with the top 3 networks being mRNA metabolic process regulation, apoptosis, and DNA conformation change. CONCLUSIONS This study provides a proteomic repertoire of confirmed and potential autoantigens for future studies, and the findings are consistent with a mechanism for autoantigenicity: how self-molecules may form molecular complexes with DS to elicit autoimmunity. Our data contribute to the molecular etiology of autoimmunity and may deepen our understanding of autoimmune diseases.
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Affiliation(s)
| | - Wei Zhang
- Department of Gastroenterology, Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Jung-hyun Rho
- MP Biomedicals New Zealand Limited, Auckland, New Zealand
| | | | - Michael H. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
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23
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Funes SC, Ríos M, Gómez‐Santander F, Fernández‐Fierro A, Altamirano‐Lagos MJ, Rivera‐Perez D, Pulgar‐Sepúlveda R, Jara EL, Rebolledo‐Zelada D, Villarroel A, Roa JC, Mackern‐Oberti JP, Kalergis AM. Tolerogenic dendritic cell transfer ameliorates systemic lupus erythematosus in mice. Immunology 2019; 158:322-339. [PMID: 31509246 PMCID: PMC6856940 DOI: 10.1111/imm.13119] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 08/28/2019] [Accepted: 09/05/2019] [Indexed: 12/11/2022] Open
Abstract
Current treatments for systemic autoimmune diseases partially improve the health of patients displaying low pharmacological efficacy and systemic immunosuppression. Here, the therapeutic potential of transferring tolerogenic dendritic cells (tolDCs) generated with heme-oxygenase inductor cobalt (III) protoporphyrin IX (CoPP), dexamethasone and rosiglitazone for the treatment of systemic autoimmunity was evaluated in two murine models of systemic lupus erythematosus (SLE), MRL-Faslpr and NZM2410 mice. Dendritic cells treated ex vivo with these drugs showed a stable tolerogenic profile after lipopolysaccharide stimulation. Regular doses of tolDCs were administered to anti-nuclear antibody-positive mice throughout 60-70 days, and the clinical score was evaluated. Long-term treatment with these tolDCs was well tolerated and effective to improve the clinical score on MRL-Faslpr lupus-prone mice. Additionally, decreased levels of anti-nuclear antibodies in NZM2410 mice were observed. Although tolDC treatment increased regulatory T cells, no significant reduction of renal damage or glomerulonephritis could be found. In conclusion, these results suggest that the transfer of histone-loaded tolDCs could improve only some SLE symptoms and reduced anti-nuclear antibodies. This is the first study to evaluate antigen-specific tolDC administration to treat SLE. Our report strengthens the clinical relevance of tolDC generation with CoPP, dexamethasone and rosiglitazone and the use of these modified cells as a therapy for systemic autoimmunity.
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Affiliation(s)
- Samanta C. Funes
- Millennium Institute on Immunology and ImmunotherapyDepartamento de Genética Molecular y MicrobiologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
| | - Mariana Ríos
- Millennium Institute on Immunology and ImmunotherapyDepartamento de Genética Molecular y MicrobiologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
| | - Felipe Gómez‐Santander
- Millennium Institute on Immunology and ImmunotherapyDepartamento de Genética Molecular y MicrobiologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
| | - Ayleen Fernández‐Fierro
- Millennium Institute on Immunology and ImmunotherapyDepartamento de Genética Molecular y MicrobiologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
| | - María J. Altamirano‐Lagos
- Millennium Institute on Immunology and ImmunotherapyDepartamento de Genética Molecular y MicrobiologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
| | - Daniela Rivera‐Perez
- Millennium Institute on Immunology and ImmunotherapyDepartamento de Genética Molecular y MicrobiologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
| | - Raul Pulgar‐Sepúlveda
- Millennium Institute on Immunology and ImmunotherapyDepartamento de Genética Molecular y MicrobiologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
| | - Evelyn L. Jara
- Millennium Institute on Immunology and ImmunotherapyDepartamento de Genética Molecular y MicrobiologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
- Present address:
Facultad de CienciasDepartamento de Ciencias BásicasUniversidad Santo TomásTemucoChile
| | - Diego Rebolledo‐Zelada
- Millennium Institute on Immunology and ImmunotherapyDepartamento de Genética Molecular y MicrobiologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
| | - Alejandra Villarroel
- Departamento de Anatomía PatológicaFacultad de MedicinaPontificia Universidad Católica de ChileSantiagoChile
| | - Juan C. Roa
- Departamento de Anatomía PatológicaFacultad de MedicinaPontificia Universidad Católica de ChileSantiagoChile
| | - Juan P. Mackern‐Oberti
- Instituto de Medicina y Biología Experimental de CuyoIMBECU CCT Mendoza‐ CONICETMendozaArgentina
- Instituto de FisiologíaFacultad de Ciencias MédicasUniversidad Nacional de CuyoMendozaArgentina
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and ImmunotherapyDepartamento de Genética Molecular y MicrobiologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
- Departamento de EndocrinologíaEscuela de Medicina, Facultad de MedicinaPontificia Universidad Católica de ChileSantiagoChile
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Javitt A, Merbl Y. Global views of proteasome-mediated degradation by mass spectrometry. Expert Rev Proteomics 2019; 16:711-716. [PMID: 31387416 DOI: 10.1080/14789450.2019.1651979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Introduction: Degradation of proteins by cellular proteasomes is critical for the fidelity of protein homeostasis and proper cell function. Indeed, perturbations in proteasome function, as well as the degradation of specific substrates, are associated with a variety of human diseases. Yet, monitoring and analyzing protein degradation in a high throughput manner in physiology and pathology remains limited. Areas covered: Here we discuss several of the recently developed mass spectrometry-based methods for studying proteasome-mediated cellular degradation and discuss their advantages and limitations. We highlight Mass Spectrometry Analysis of Proteolytic Peptides (MAPP), a method designed to purify and identify proteasome-cleaved cellular proteins as a novel approach in molecular and clinical profiling of human disease. Expert opinion: The recent improvement of proteomics technologies now offers an unprecedented ability to study disease in clinical settings. Expanding clinical studies to include the degradation landscape will provide a new resolution to complement the cellular proteome. In turn, this holds promise to provide both new disease targets and novel peptide biomarkers which will further enhance personalized proteomics.
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Affiliation(s)
- Aaron Javitt
- Department of Immunology, Weizmann Institute of Science , Rehovot , Israel
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science , Rehovot , Israel
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25
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Zhang W, Rho JH, Roehrl MH, Wang JY. A comprehensive autoantigen-ome of autoimmune liver diseases identified from dermatan sulfate affinity enrichment of liver tissue proteins. BMC Immunol 2019; 20:21. [PMID: 31242852 PMCID: PMC6595630 DOI: 10.1186/s12865-019-0304-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/19/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Autoimmune diseases result from aberrant immune attacks by the body itself. It is mysterious how autoantigens, a large cohort of seemingly unconnected molecules expressed in different parts of the body, can induce similar autoimmune responses. We have previously found that dermatan sulfate (DS) can form complexes with molecules of apoptotic cells and stimulate autoreactive CD5+ B cells to produce autoantibodies. Hence, autoantigenic molecules share a unique biochemical property in their affinity to DS. This study sought to further test this uniform principle of autoantigenicity. RESULTS Proteomes were extracted from freshly collected mouse livers. They were loaded onto columns packed with DS-Sepharose resins. Proteins were eluted with step gradients of increasing salt strength. Proteins that bound to DS with weak, moderate, or strong affinity were eluted with 0.4, 0.6, and 1.0 M NaCl, respectively. After desalting, trypsin digestion, and gel electrophoresis, proteins were sequenced by mass spectrometry. To validate whether these proteins have been previously identified as autoantigens, an extensive literature search was conducted using the protein name or its alternative names as keywords. Of the 41 proteins identified from the strong DS-affinity fraction, 33 (80%) were verified autoantigens. Of the 46 proteins with moderate DS-affinity, 27 (59%) were verified autoantigens. Of the 125 proteins with weak DS-affinity, 44 (35%) were known autoantigens. Strikingly, these autoantigens fell into the classical autoantibody categories of autoimmune liver diseases: ANA (anti-nuclear autoantibodies), SMA (anti-smooth muscle autoantibodies), AMA (anti-mitochondrial autoantibodies), and LKM (liver-kidney microsomal autoantigens). CONCLUSIONS This study of DS-affinity enrichment of liver proteins establishes a comprehensive autoantigen-ome for autoimmune liver diseases, yielding 104 verified and 108 potential autoantigens. The liver autoantigen-ome sheds light on the molecular origins of autoimmune liver diseases and further supports the notion of a unifying biochemical principle of autoantigenicity.
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Affiliation(s)
- Wei Zhang
- Department of Gastroenterology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | | | - Michael H Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
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26
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Zhang W, Rho JH, Roehrl MW, Roehrl MH, Wang JY. A repertoire of 124 potential autoantigens for autoimmune kidney diseases identified by dermatan sulfate affinity enrichment of kidney tissue proteins. PLoS One 2019; 14:e0219018. [PMID: 31237920 PMCID: PMC6592568 DOI: 10.1371/journal.pone.0219018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/13/2019] [Indexed: 12/30/2022] Open
Abstract
Autoantigens are the molecular targets in autoimmune diseases. They are a cohort of seemingly unrelated self-molecules present in different parts of the body, yet they can trigger a similar chain of autoimmune responses such as autoantibody production. We previously reported that dermatan sulfate (DS) can bind self-molecules of dying cells to stimulate autoreactive CD5+ B cells to produce autoantibodies. The formation of autoantigen-DS complexes converts the normally non-antigenic self-molecules to none-self antigens, and thus DS-affinity represents a common underlying biochemical property for autoantigens. This study sought to apply this property to identify potential autoantigens in the kidney. Total proteins were extracted from mouse kidney tissues and loaded onto DS-Sepharose resins. Proteins without affinity were washed off the resins, whereas those with increasing DS-affinity were eluted with step gradients of increasing salt strength. Fractions with strong and moderate DS-affinity were sequenced by mass spectrometry and yielded 25 and 99 proteins, respectively. An extensive literature search was conducted to validate whether these had been previously reported as autoantigens. Of the 124 proteins, 79 were reported autoantigens, and 19 out of 25 of the strong-DS-binding ones were well-known autoantigens. Moreover, these proteins largely fell into the two most common autoantibody categories in autoimmune kidney diseases, including 40 ANA (anti-nuclear autoantibodies) and 25 GBM (glomerular basement membrane) autoantigens. In summary, this study compiles a large repertoire of potential autoantigens for autoimmune kidney diseases. This autoantigen-ome sheds light on the molecular etiology of autoimmunity and further supports our hypothesis DS-autoantigen complexes as a unifying principle of autoantigenicity.
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Affiliation(s)
- Wei Zhang
- Department of Gastroenterology, Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | | | | | - Michael H. Roehrl
- Department of Pathology and Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York City, New York, United States of America
- * E-mail: (JYW); (MHR)
| | - Julia Y. Wang
- Curandis, Scarsdale, New York, United States of America
- * E-mail: (JYW); (MHR)
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27
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Rekvig OP. The dsDNA, Anti-dsDNA Antibody, and Lupus Nephritis: What We Agree on, What Must Be Done, and What the Best Strategy Forward Could Be. Front Immunol 2019; 10:1104. [PMID: 31156647 PMCID: PMC6529578 DOI: 10.3389/fimmu.2019.01104] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/30/2019] [Indexed: 12/19/2022] Open
Abstract
This study aims to understand what lupus nephritis is, its origin, clinical context, and its pathogenesis. Truly, we encounter many conceptual and immanent tribulations in our attempts to search for the pathogenesis of this disease—and how to explain its assumed link to SLE. Central in the present landscape stay a short history of the early studies that substantiated the structures of isolated or chromatin-assembled mammalian dsDNA, and its assumed, highly controversial role in induction of anti-dsDNA antibodies. Arguments discussed here may provoke the view that anti-dsDNA antibodies are not what we think they are, as they may be antibodies operational in quite different biological contexts, although they bind dsDNA by chance. This may not mean that these antibodies are not pathogenic but they do not inform how they are so. This theoretical study centers the content around the origin and impact of extra-cellular DNA, and if dsDNA has an effect on the adaptive immune system. The pathogenic potential of chromatin-anti-dsDNA antibody interactions is limited to incite lupus nephritis and dermatitis which may be linked in a common pathogenic process. These are major criteria in SLE classification systems but are not shared with other defined manifestations in SLE, which may mean that they are their own disease entities, and not integrated in SLE. Today, the models thought to explain lupus nephritis are divergent and inconsistent. We miss a comprehensive perspective to try the different models against each other. To do this, we need to take all elements of the syndrome SLE into account. This can only be achieved by concentrating on the interactions between autoimmunity, immunopathology, deviant cell death and necrotic chromatin in context of elements of system science. System science provides a framework where data generated by experts can be compared, and tested against each other. This approach open for consensus on central elements making up “lupus nephritis” to separate what we agree on and how to understand the basis for conflicting models. This has not been done yet in a systematic context.
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Affiliation(s)
- Ole Petter Rekvig
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
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28
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Tsai KL, Liao CC, Chang YS, Huang CW, Huang YC, Chen JH, Lin SH, Tai CC, Lin YF, Lin CY. Low Levels of IgM and IgA Recognizing Acetylated C1-Inhibitor Peptides Are Associated with Systemic Lupus Erythematosus in Taiwanese Women. Molecules 2019; 24:molecules24091645. [PMID: 31027344 PMCID: PMC6539680 DOI: 10.3390/molecules24091645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/20/2019] [Accepted: 04/24/2019] [Indexed: 11/16/2022] Open
Abstract
The objective of this study was to identify novel acetylation (Ac) modifications of the C1-inhibitor (C1-INH) and explain the association of the levels of autoantibodies against acetylated C1-INH peptides with the risk of developing systemic lupus erythematosus (SLE). Ac modifications of the C1-INH were identified and validated through in-gel digestion, nano-liquid chromatography-tandem mass spectrometry, immunoprecipitation, and Western blotting by using serum protein samples obtained from patients with SLE and age-matched healthy controls (HCs). In addition, the levels of serum C1-INH, Ac-protein adducts, and autoantibodies against unmodified and acetylated C1-INH peptides were measured. C1-INH levels in patients with SLE were significantly lower than those in HCs by 1.53-fold (p = 0.0008); however, Ac-protein adduct concentrations in patients with SLE were significantly higher than those in HCs by 1.35-fold (p = 0.0009). Moreover, immunoglobulin M (IgM) anti-C1-INH367-385 Ac and IgA anti-C1-INH367-385 Ac levels in patients with SLE were significantly lower than those in HCs. The low levels of IgM anti-C1-INH367-385 (odds ratio [OR] = 4.725, p < 0.001), IgM anti-C1-INH367-385 Ac (OR = 4.089, p = 0.001), and IgA anti-C1-INH367-385 Ac (OR = 5.566, p < 0.001) indicated increased risks for the development of SLE compared with HCs.
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Affiliation(s)
- Kai-Leun Tsai
- Division of Allergy, Immunology, and Rheumatology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan.
- Division of Allergy, Immunology, and Rheumatology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan.
| | - Chen-Chung Liao
- Proteomics Research Center, National Yang-Ming University, Taipei 112, Taiwan.
| | - Yu-Sheng Chang
- Division of Allergy, Immunology, and Rheumatology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan.
- Division of Allergy, Immunology, and Rheumatology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan.
| | - Ching-Wen Huang
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan.
| | - Yu-Chu Huang
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan.
| | - Jin-Hua Chen
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei 11031, Taiwan.
- Research Center of Biostatistics, College of Management, Taipei Medical University, Taipei 11031, Taiwan.
| | - Sheng-Hong Lin
- Division of Allergy, Immunology, and Rheumatology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan.
| | - Chih-Chun Tai
- Department of Laboratory Medicine, Taipei Medical University-Shuang-Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan.
| | - Yi-Fang Lin
- Department of Laboratory Medicine, Taipei Medical University-Shuang-Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan.
| | - Ching-Yu Lin
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan.
- Department of Biotechnology and Animal Science, National Ilan University, Ilan 26047, Taiwan.
- PhD Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan.
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29
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Chapman EA, Lyon M, Simpson D, Mason D, Beynon RJ, Moots RJ, Wright HL. Caught in a Trap? Proteomic Analysis of Neutrophil Extracellular Traps in Rheumatoid Arthritis and Systemic Lupus Erythematosus. Front Immunol 2019; 10:423. [PMID: 30915077 PMCID: PMC6421309 DOI: 10.3389/fimmu.2019.00423] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/18/2019] [Indexed: 12/22/2022] Open
Abstract
Neutrophil Extracellular Traps (NETs) are implicated in the development of auto-immunity in diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) through the externalization of intracellular neoepitopes e.g., dsDNA and nuclear proteins in SLE and citrullinated peptides in RA. The aim of this work was to use quantitative proteomics to identify and measure NET proteins produced by neutrophils from healthy controls, and from patients with RA and SLE to determine if NETs can be differentially-generated to expose different sets of neoepitopes. Ultra-pure neutrophils (>99%) from healthy individuals (n = 3) and patients with RA or SLE (n = 6 each) were incubated ± PMA (50 nM, PKC super-activator) or A23187 (3.8 μM, calcium ionophore) for 4 h. NETs were liberated by nuclease digestion and concentrated onto Strataclean beads prior to on-bead digestion with trypsin. Data-dependent LC-MS/MS analyses were conducted on a QExactive HF quadrupole-Orbitrap mass spectrometer, and label-free protein quantification was carried out using Progenesis QI. PMA-induced NETs were decorated with annexins, azurocidin and histone H3, whereas A23187-induced NETs were decorated with granule proteins including CAMP/LL37, CRISP3, lipocalin and MMP8, histones H1.0, H1.4, and H1.5, interleukin-8, protein-arginine deiminase-4 (PADI4), and α-enolase. Four proteins were significantly different between PMA-NETs from RA and SLE neutrophils (p < 0.05): RNASE2 was higher in RA, whereas MPO, leukocyte elastase inhibitor and thymidine phosphorylase were higher in SLE. For A23187-NETs, six NET proteins were higher in RA (p < 0.05), including CAMP/LL37, CRISP3, interleukin-8, MMP8; Thirteen proteins were higher in SLE, including histones H1.0, H2B, and H4. This work provides the first, direct comparison of NOX2-dependent (PMA) and NOX2-independent (A23187) NETs using quantitative proteomics, and the first direct comparison of RA and SLE NETs using quantitative proteomics. We show that it is the nature of the stimulant rather than neutrophil physiology that determines NET protein profiles in disease, since stimulation of NETosis in either a NOX2-dependent or a NOX2-independent manner generates broadly similar NET proteins irrespective of the disease background. We also use our proteomics pipeline to identify an extensive range of post-translationally modified proteins in RA and SLE, including histones and granule proteins, many of which are known targets of auto-antibodies in each disease.
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Affiliation(s)
- Elinor A Chapman
- Department of Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Max Lyon
- Department of Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Deborah Simpson
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,Centre for Proteome Research, University of Liverpool, Liverpool, United Kingdom
| | - David Mason
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,Centre for Cell Imaging, University of Liverpool, Liverpool, United Kingdom
| | - Robert J Beynon
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,Centre for Proteome Research, University of Liverpool, Liverpool, United Kingdom
| | - Robert J Moots
- Department of Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom.,University of Liverpool and Aintree University Hospital, Members of Liverpool Health Partners, Liverpool, United Kingdom
| | - Helen L Wright
- Department of Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
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Lloyd KA, Wigerblad G, Sahlström P, Garimella MG, Chemin K, Steen J, Titcombe PJ, Marklein B, Zhou D, Stålesen R, Ossipova E, Lundqvist C, Ekwall O, Rönnelid J, Mueller DL, Karlsson MCI, Kaplan MJ, Skriner K, Klareskog L, Wermeling F, Malmström V, Grönwall C. Differential ACPA Binding to Nuclear Antigens Reveals a PAD-Independent Pathway and a Distinct Subset of Acetylation Cross-Reactive Autoantibodies in Rheumatoid Arthritis. Front Immunol 2019; 9:3033. [PMID: 30662440 PMCID: PMC6328449 DOI: 10.3389/fimmu.2018.03033] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/07/2018] [Indexed: 12/17/2022] Open
Abstract
Rheumatoid arthritis (RA) associated anti-citrullinated protein autoantibodies (ACPA) target a wide range of modified proteins. Citrullination occurs during physiological processes such as apoptosis, yet little is known about the interaction of ACPA with nuclear antigens or apoptotic cells. Since uncleared apoptotic cells and neutrophil extracellular trap (NET) products have been postulated to be central sources of autoantigen and immunostimulation in autoimmune disease, we sought to characterize the anti-nuclear and anti-neutrophil reactivities of ACPA. Serology showed that a subset of anti-CCP2 seropositive RA patients had high reactivity to full-length citrullinated histones. In contrast, seronegative RA patients displayed elevated IgG reactivity to native histone compared to controls, but no citrulline-specific reactivity. Screening of 10 single B-cell derived monoclonal ACPA from RA patients revealed that four ACPA exhibited strong binding to apoptotic cells and three of these had anti-nuclear (ANA) autoantibody reactivity. Modified histones were confirmed to be the primary targets of this anti-nuclear ACPA subset following immunoprecipitation from apoptotic cell lysates. Monoclonal ACPA were also screened for reactivities against stimulated murine and human neutrophils, and all the nuclear-reactive monoclonal ACPA bound to NETs. Intriguingly, one ACPA mAb displayed a contrasting cytoplasmic perinuclear neutrophil binding and may represent a different NET-reactive ACPA subset. Notably, studies of CRISPR-Cas9 PAD4 KO cells and cells from PAD KO mice showed that the cytoplasmic NET-binding was fully dependent on PAD4, whilst nuclear- and histone-mediated NET reactivity was largely PAD-independent. Our further analysis revealed that the nuclear binding could be explained by consensus-motif driven ACPA cross-reactivity to acetylated histones. Specific acetylated histone peptides targeted by the monoclonal antibodies were identified and the anti-modified protein autoantibody (AMPA) profile of the ACPA was found to correlate with the functional activity of the antibodies. In conclusion, when investigating monoclonal ACPA, we could group ACPA into distinct subsets based on their nuclear binding-patterns and acetylation-mediated binding to apoptotic cells, neutrophils, and NETs. Differential anti-modified protein reactivities of RA-autoantibody subsets could have an important functional impact and provide insights in RA pathogenesis.
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Affiliation(s)
- Katy A. Lloyd
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gustaf Wigerblad
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Systemic Autoimmunity Branch, Intramural Research Program, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Peter Sahlström
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine, Charité University Hospital, Berlin, Germany
| | - Manasa G. Garimella
- Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Karine Chemin
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Johanna Steen
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Philip J. Titcombe
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- The Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Bianka Marklein
- Systemic Autoimmunity Branch, Intramural Research Program, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Diana Zhou
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ragnhild Stålesen
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Elena Ossipova
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Christina Lundqvist
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Olov Ekwall
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johan Rönnelid
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Daniel L. Mueller
- The Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Mikael C. I. Karlsson
- Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Mariana J. Kaplan
- Systemic Autoimmunity Branch, Intramural Research Program, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Karl Skriner
- Department of Medicine, Charité University Hospital, Berlin, Germany
| | - Lars Klareskog
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Wermeling
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Vivianne Malmström
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Grönwall
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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van Dam LS, Rabelink TJ, van Kooten C, Teng YKO. Clinical Implications of Excessive Neutrophil Extracellular Trap Formation in Renal Autoimmune Diseases. Kidney Int Rep 2018; 4:196-211. [PMID: 30775617 PMCID: PMC6365354 DOI: 10.1016/j.ekir.2018.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/02/2018] [Accepted: 11/12/2018] [Indexed: 12/20/2022] Open
Abstract
Neutrophil extracellular traps (NETs) are extracellular DNA structures covered with antimicrobial peptides, danger molecules, and autoantigens that can be released by neutrophils. NETs are an important first-line defense mechanism against bacterial, viral, fungal, and parasitic infections, but they can also play a role in autoimmune diseases. NETs are immunogenic and toxic structures that are recognized by the autoantibodies of patients with antineutrophil cytoplasmic antibodies−associated vasculitis (AAV) (i.e., against myeloperoxidase or proteinase-3) and systemic lupus erythematosus (SLE) (i.e., against double-stranded DNA, histones, or nucleosomes). There is cumulating preclinical and clinical evidence that both excessive formation and impaired degradation of NETs are involved in the pathophysiology of AAV and SLE. These autoimmune diseases give rise to 2 clinically and pathologically distinct forms of glomerulonephritis (GN), respectively, crescentic pauci-immune GN and immune complex−mediated GN. Therefore, it is relevant to understand the different roles NET formation can play in the pathophysiology of these most prevalent renal autoimmune diseases. This review summarizes the current concepts on the role of NET formation in the pathophysiology of AAV and SLE, and provides a translational perspective on the clinical implications of NETs, such as potential therapeutic approaches that target NET formation in these renal autoimmune diseases.
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Affiliation(s)
- Laura S van Dam
- Department of Nephrology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Ton J Rabelink
- Department of Nephrology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Cees van Kooten
- Department of Nephrology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Y K Onno Teng
- Department of Nephrology, Leiden University Medical Centre, Leiden, The Netherlands
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Xu Y, Deng W, Zhang W. Long non-coding RNA TUG1 protects renal tubular epithelial cells against injury induced by lipopolysaccharide via regulating microRNA-223. Biomed Pharmacother 2018; 104:509-519. [PMID: 29800915 DOI: 10.1016/j.biopha.2018.05.069] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lupus nephritis (LN) is a serious complication of systemic lupus erythematosus (SLE). Long non-coding RNA taurine upregulated gene 1 (lncRNA TUG1) exerted critical regulatory effects on inhibiting cell injury and inflammation. However, its role in LN is still unclear. METHODS HK-2 cells were treated with lipopolysaccharide (LPS) to simulate cell inflammatory injury. Cell viability and apoptosis, as well as pro-inflammatory factors expression were measured, respectively. Then, HK-2 cells were transfected with pEX-TUG1 or sh-TUG1 to explore the effects of TUG1 on LPS-induced cell injury. Potential binding effects between TUG1 and microRNA-223 (miR-223), as well as between miR-223 and Sirtuin 1 (Sirt1) were verified. miR-223 mimic or miR-223 inhibitor was transfected to assess the effects of miR-223 on cell injury. Finally, the roles of Sirt1 in LPS-induced HK-2 cell injury and activation of phosphatidylinositol 3-kinase/protein kinase 3 (PI3K/AKT) and nuclear factor kappa B (NF-κB) pathways were explored. RESULTS LPS administration inhibited HK-2 cell viability and proliferation, increased expression of pro-inflammatory factors, and promoted cell apoptosis. TUG1 overexpression protected HK-2 cells against LPS-induced injury via negatively regulating miR-223 expression. TUG1 suppression had opposite effects. Sirt1 was a direct target gene of miR-223 in HK-2 cells, which participated in the effects of miR-223 on HK-2 cells and was related with the activation of PI3K/AKT and NF-κB pathways. CONCLUSION TUG1 protected HK-2 cells against LPS-induced inflammatory injury by regulating miR-223 and Sirt1 expression, and then activating PI3K/AKT and inactivating NF-κB pathways. TUG1 might be a potential therapeutic target for LN treatment.
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Affiliation(s)
- Yan Xu
- Department of Nephrology, Jining No. 1 People's Hospital, Jining, 272011, Shandong, China
| | - Wenyan Deng
- Department of Nephrology, Jining No. 1 People's Hospital, Jining, 272011, Shandong, China
| | - Wei Zhang
- Department of Nephrology, Jining No. 1 People's Hospital, Jining, 272011, Shandong, China.
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Biermann MHC, Boeltz S, Pieterse E, Knopf J, Rech J, Bilyy R, van der Vlag J, Tincani A, Distler JHW, Krönke G, Schett GA, Herrmann M, Muñoz LE. Autoantibodies Recognizing Secondary NEcrotic Cells Promote Neutrophilic Phagocytosis and Identify Patients With Systemic Lupus Erythematosus. Front Immunol 2018; 9:989. [PMID: 29867966 PMCID: PMC5949357 DOI: 10.3389/fimmu.2018.00989] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/20/2018] [Indexed: 12/15/2022] Open
Abstract
Deficient clearance of apoptotic cells reportedly contributes to the etiopathogenesis of the autoimmune disease systemic lupus erythematosus (SLE). Based on this knowledge, we developed a highly specific and sensitive test for the detection of SLE autoantibodies (AAb) utilizing secondary NEcrotic cell (SNEC)-derived material as a substrate. The goal of the present study was to validate the use of SNEC as an appropriate antigen for the diagnosis of SLE in large cohort of patients. We confirmed the presence of apoptotically modified autoantigens on SNEC (dsDNA, high mobility group box 1 protein, apoptosis-associated chromatin modifications, e.g., histones H3-K27-me3; H2A/H4 AcK8,12,16; and H2B-AcK12). Anti-SNEC AAb were measured in the serum of 155 patients with SLE, 89 normal healthy donors (NHD), and 169 patients with other autoimmune connective tissue diseases employing SNEC-based indirect enzyme-linked immunosorbent assay (SNEC ELISA). We compared the test performance of SNEC ELISA with the routine diagnostic tests dsDNA Farr radioimmunoassay (RIA) and nucleosome-based ELISA (anti-dsDNA-NcX-ELISA). SNEC ELISA distinguished patients with SLE with a specificity of 98.9% and a sensitivity of 70.6% from NHD clearly surpassing RIA and anti-dsDNA-NcX-ELISA. In contrast to the other tests, SNEC ELISA significantly discriminated patients with SLE from patients with rheumatoid arthritis, primary anti-phospholipid syndrome, spondyloarthropathy, psoriatic arthritis, and systemic sclerosis. A positive test result in SNEC ELISA significantly correlated with serological variables and reflected the uptake of opsonized SNEC by neutrophils. This stresses the relevance of SNECs in the pathogenesis of SLE. We conclude that SNEC ELISA allows for the sensitive detection of pathologically relevant AAb, enabling its diagnostic usage. A positive SNEC test reflects the opsonization of cell remnants by AAb, the neutrophil recruitment to tissues, and the enhancement of local and systemic inflammatory responses.
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Affiliation(s)
- Mona H C Biermann
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Sebastian Boeltz
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Elmar Pieterse
- Department of Nephrology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Jasmin Knopf
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Jürgen Rech
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Rostyslav Bilyy
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany.,Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - Johan van der Vlag
- Department of Nephrology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Angela Tincani
- Division of Rheumatology and Clinical Immunology, Department of Clinical and Experimental Sciences, Spedali Civili and University of Brescia, Brescia, Italy
| | - Jörg H W Distler
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Gerhard Krönke
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Georg Andreas Schett
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Martin Herrmann
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Luis E Muñoz
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
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Brahma R, Gurumayum S, Naorem LD, Muthaiyan M, Gopal J, Venkatesan A. Identification of Hub Genes and Pathways in Zika Virus Infection Using RNA-Seq Data: A Network-Based Computational Approach. Viral Immunol 2018; 31:321-332. [PMID: 29608426 DOI: 10.1089/vim.2017.0116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Zika virus (ZIKV), a single-strand RNA flavivirus, is transmitted primarily through Aedes aegypti. The recent outbreaks in America and unexpected association between ZIKV infection and birth defects have triggered the global attention. This vouches to understand the molecular mechanisms of ZIKV infection to develop effective drug therapy. A systems-level understanding of biological process affected by ZIKV infection in fetal brain sample led us to identify the candidate genes for pharmaceutical intervention and potential biomarkers for diagnosis. To identify the key genes, transcriptomics data (RNA-Seq) with GSE93385 of ZIKV (Strain: MR766) infected human fetal neural stem cell are analyzed. In total, 1,084 differentially expressed genes (DEGs) are identified, that is, 471 upregulated and 613 downregulated genes. Further analysis such as the gene ontology term suggested that the downregulated genes are mostly enriched in defense response to virus, receptor binding, laminin binding, extracellular matrix, endoplasmic reticulum, and for upregulated DEGs: translation initiation, RNA binding, cytosol, and nucleosome are enriched. And through pathway analysis, systemic lupus erythematosus (SLE) is found to be the most enriched pathway. Protein-protein interaction (PPI) network is constructed to find the hub genes using STRING database. The seven key genes namely cyclin-dependent kinase 1 (CDK1), cyclin B1 (CCNB1), histone cluster 1 H2B family member K, (HIST1H2BK) histone cluster 1 H2B family member O (HIST1H2BO), and histone cluster 1 H2B family member B (HIST1H2BB), polo-like kinase 1 (PLK1), and cell division cycle 20 (CDC20) with highest degree are found to be hub genes using Centiscape, a Cytoscape plugin. The modules of PPI network using Molecular Complex Detection plugin are found significant in structural constituent of ribosome, defense response to virus, nucleosome, SLE, extracellular region, and regulation of gene silencing. Thus, identified key hub genes and pathways shed light on molecular mechanism that may contribute to the discovery of novel therapeutic targets and development of new strategies for the intervention of ZIKV disease.
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Affiliation(s)
- Rahul Brahma
- 1 Centre for Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry, India
| | - Sanathoi Gurumayum
- 1 Centre for Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry, India
| | - Leimarembi Devi Naorem
- 1 Centre for Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry, India
| | - Mathavan Muthaiyan
- 1 Centre for Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry, India
| | - Jeyakodi Gopal
- 2 Biomedical Informatics Centre, Vector Control Research Centre , Puducherry, India
| | - Amouda Venkatesan
- 1 Centre for Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry, India
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Abstract
Background Patients with systemic lupus erythematosus (SLE) may form clusters with clinical manifestations and autoantibodies. Objective The objective of this report is to study whether SLE patients with positive rheumatoid factor (RF) have a special clinical and/or serological profile. Methods A retrospective study of 467 SLE patients seen at a single rheumatology unit was conducted. Epidemiological data (age, gender, age at disease onset, ethnic background and tobacco use), clinical data (malar rash, photosensitivity, oral ulcers, discoid lesions, serositis, glomerulonephritis, convulsions, psychosis, hemolytic anemia, leukopenia, lymphocytopenia, arthritis and hypothyroidism) and serological profile (anti-dsDNA, anti-Ro/SS-A, anti-La/SS-B, anti-RNP, anti-Sm, IgG aCL, IgM aCL, lupus anticoagulant, direct Coombs and RF) were collected. Patients with positive and negative RF were compared. Results RF was found in 24.9% of the sample. In univariate analysis, RF was positively associated with butterfly rash ( p = 0.04), anti-Ro ( p = 0.03), anti-Sm antibodies ( p = 0.01) and hypothyroidism ( p = 0.01) and negatively associated with glomerulonephritis ( p = 0.003). Logistic regression showed that only glomerulonephritis ( p = 0.03; OR = 0.45; 95% CI = 0.21-0.93) and anti-Ro ( p = 0.009; OR = 2.3; 95% CI = 1.24-4.57) were independent associations. Conclusion In our sample RF was associated with protection from glomerulonephritis and with higher prevalence of anti-Ro antibodies.
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Affiliation(s)
- A Fedrigo
- 1 Rheumatology Service, Evangelical University Hospital of Curitiba, Curitiba, Brazil
| | - T A F G Dos Santos
- 1 Rheumatology Service, Evangelical University Hospital of Curitiba, Curitiba, Brazil
| | - R Nisihara
- 1 Rheumatology Service, Evangelical University Hospital of Curitiba, Curitiba, Brazil
- 2 Department of Medicine, Positivo University, Curitiba, Brazil
| | - T Skare
- 1 Rheumatology Service, Evangelical University Hospital of Curitiba, Curitiba, Brazil
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Keragala CB, Draxler DF, McQuilten ZK, Medcalf RL. Haemostasis and innate immunity - a complementary relationship: A review of the intricate relationship between coagulation and complement pathways. Br J Haematol 2017; 180:782-798. [PMID: 29265338 DOI: 10.1111/bjh.15062] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Coagulation and innate immunity are linked evolutionary processes that orchestrate the host defence against invading pathogens and injury. The complement system is integral to innate immunity and shares numerous interactions with components of the haemostatic pathway, helping to maintain physiological equilibrium. The term 'immunothrombosis' was introduced in 2013 to embrace this process, and has become an area of much recent interest. What is less apparent in the literature however is an appreciation of the clinical manifestations of the coagulation-complement interaction and the consequences of dysregulation of either system, as seen in many inflammatory and thrombotic disease states, such as sepsis, trauma, atherosclerosis, antiphospholipid syndrome (APS), paroxysmal nocturnal haemoglobinuria (PNH) and some thrombotic microangiopathies to name a few. The growing appreciation of this immunothrombotic phenomenon will foster the drive for novel therapies in these disease states, including anticoagulants as immunomodulators and targeted molecular therapies.
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Affiliation(s)
- Charithani B Keragala
- Molecular Neurotrauma and Haemostasis, Australian Centre for Blood Diseases, Monash University, Melbourne, Vic., Australia
| | - Dominik F Draxler
- Molecular Neurotrauma and Haemostasis, Australian Centre for Blood Diseases, Monash University, Melbourne, Vic., Australia
| | - Zoe K McQuilten
- Transfusion Research Unit and Australian and New Zealand Intensive Care Research Centre, Department of Epidemiology and Preventative Medicine, Monash University, Melbourne, Vic., Australia
| | - Robert L Medcalf
- Molecular Neurotrauma and Haemostasis, Australian Centre for Blood Diseases, Monash University, Melbourne, Vic., Australia
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Rother N, Pieterse E, Lubbers J, Hilbrands L, van der Vlag J. Acetylated Histones in Apoptotic Microparticles Drive the Formation of Neutrophil Extracellular Traps in Active Lupus Nephritis. Front Immunol 2017; 8:1136. [PMID: 28959262 PMCID: PMC5604071 DOI: 10.3389/fimmu.2017.01136] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/29/2017] [Indexed: 12/03/2022] Open
Abstract
Objective Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by the presence of autoantibodies against nuclear components. Lupus nephritis (LN) is the major cause of morbidity and mortality in patients with SLE. Central to the pathogenesis of SLE is the accumulation of cellular waste, especially apoptotic microparticles (MPs), which stimulates diverse immune reactions including the formation of neutrophil extracellular traps (NETs). In this study, we investigated the content of MPs from SLE patients with and without (active) LN, their capacity to stimulate NET release, and assessed the molecular mechanisms underlying MP-induced NETosis. Methods MPs from SLE patients with biopsy-proven active LN, remissive LN, without LN, and healthy controls were characterized by flow cytometry. Isolated neutrophils were exposed to MPs derived from either patient plasma or apoptotic human umbilical vein endothelial cells, and NET release was quantified by immunofluorescence imaging, spectrofluorometry or an in-house developed NET ELISA. Results MPs from SLE patients with active LN contain higher levels of acetylated chromatin compared to MPs from those with remissive LN, without LN, or healthy controls. MPs enriched in hyperacetylated chromatin are more potent in inducing NETosis when compared to MPs containing moderate acetylated chromatin. The release of NETs in response to MPs occurs rapidly in a concentration-dependent manner and proceeds independent from the formation of reactive oxygen species (ROS). Conclusion Our data suggest that MPs containing acetylated chromatin drive ROS-independent NET release in SLE patients with active LN, which may lead to the glomerular deposition of NETs and subsequent NET-driven LN.
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Affiliation(s)
- Nils Rother
- Department of Nephrology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Elmar Pieterse
- Department of Nephrology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jelle Lubbers
- Department of Nephrology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Luuk Hilbrands
- Department of Nephrology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Johan van der Vlag
- Department of Nephrology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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Cornett EM, Dickson BM, Rothbart SB. Analysis of Histone Antibody Specificity with Peptide Microarrays. J Vis Exp 2017. [PMID: 28809825 DOI: 10.3791/55912] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Post-translational modifications (PTMs) on histone proteins are widely studied for their roles in regulating chromatin structure and gene expression. The mass production and distribution of antibodies specific to histone PTMs has greatly facilitated research on these marks. As histone PTM antibodies are key reagents for many chromatin biochemistry applications, rigorous analysis of antibody specificity is necessary for accurate data interpretation and continued progress in the field. This protocol describes an integrated pipeline for the design, fabrication and use of peptide microarrays for profiling the specificity of histone antibodies. The design and analysis aspects of this procedure are facilitated by ArrayNinja, an open-source and interactive software package we recently developed to streamline the customization of microarray print formats. This pipeline has been used to screen a large number of commercially available and widely used histone PTM antibodies, and data generated from these experiments are freely available through an online and expanding Histone Antibody Specificity Database. Beyond histones, the general methodology described herein can be applied broadly to the analysis of PTM-specific antibodies.
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39
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Identification of autoreactive B cells with labeled nucleosomes. Sci Rep 2017; 7:602. [PMID: 28377609 PMCID: PMC5428865 DOI: 10.1038/s41598-017-00664-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/28/2017] [Indexed: 12/15/2022] Open
Abstract
The pathogenesis of autoimmune diseases has not been completely elucidated yet, and only a few specific treatments have been developed so far. In autoimmune diseases mediated by pathogenic autoantibodies, such as systemic lupus erythematosus, the specific detection and analysis of autoreactive B cells is crucial for a better understanding of the physiopathology. Biological characterization of these cells may help to define new therapeutic targets. Very few techniques allowing the precise detection of autoreactive B cells have been described so far. Herein we propose a new flow cytometry technique for specific detection of anti-nucleosome B cells, which secrete autoantibodies in systemic lupus erythematosus, using labeled nucleosomes. We produced different fluorochrome-labeled nucleosomes, characterized them, and finally tested them in flow cytometry. Nucleosomes labeled via the cysteines present in H3 histone specifically bind to autoreactive B cells in the anti-DNA transgenic B6.56R mice model. The present work validates the use of fluorochrome-labeled nucleosomes via cysteines to identify anti-nucleosome B cells and offers new opportunities for the description of autoreactive B cell phenotype.
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