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Krainer J, Hendling M, Siebenhandl S, Fuehner S, Kessel C, Verweyen E, Vierlinger K, Foell D, Schönthaler S, Weinhäusel A. Patients with Systemic Juvenile Idiopathic Arthritis (SJIA) Show Differences in Autoantibody Signatures Based on Disease Activity. Biomolecules 2023; 13:1392. [PMID: 37759792 PMCID: PMC10527260 DOI: 10.3390/biom13091392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Systemic juvenile idiopathic arthritis (SJIA) is a severe rheumatic disease in children. It is a subgroup of juvenile idiopathic arthritis (JIA; MIM #604302), which is the most common rheumatic disease in children. The diagnosis of SJIA often comes with a significant delay, and the classification between autoinflammatory and autoimmune disease is still discussed. In this study, we analyzed the immunological responses of patients with SJIA, using human proteome arrays presenting immobilized recombinantly expressed human proteins, to analyze the involvement of autoantibodies in SJIA. Results from group comparisons show several differentially reactive antigens involved in inflammatory processes. Intriguingly, many of the identified antigens had a high reactivity against proteins involved in the NF-κB pathway, and it is also notable that many of the detected DIRAGs are described as dysregulated in rheumatoid arthritis. Our data highlight novel proteins and pathways potentially dysregulated in SJIA and offer a unique approach to unraveling the underlying disease pathogenesis in this chronic arthropathy.
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Affiliation(s)
- Julie Krainer
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Michaela Hendling
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Sandra Siebenhandl
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Sabrina Fuehner
- Pediatric Rheumatology & Immunology, University Children’s Hospital, 48149 Münster, Germany; (S.F.); (C.K.); (E.V.); (D.F.)
| | - Christoph Kessel
- Pediatric Rheumatology & Immunology, University Children’s Hospital, 48149 Münster, Germany; (S.F.); (C.K.); (E.V.); (D.F.)
| | - Emely Verweyen
- Pediatric Rheumatology & Immunology, University Children’s Hospital, 48149 Münster, Germany; (S.F.); (C.K.); (E.V.); (D.F.)
| | - Klemens Vierlinger
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Dirk Foell
- Pediatric Rheumatology & Immunology, University Children’s Hospital, 48149 Münster, Germany; (S.F.); (C.K.); (E.V.); (D.F.)
| | - Silvia Schönthaler
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Andreas Weinhäusel
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
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Kuehn J, Schleifenbaum S, Hendling M, Siebenhandl S, Krainer J, Fuehner S, Hellige A, Park C, Hinze C, Wittkowski H, Holzinger D, Thurner L, Weinhäusel A, Foell D, Kessel C. Aberrant Naive CD4-Positive T Cell Differentiation in Systemic Juvenile Idiopathic Arthritis Committed to B Cell Help. Arthritis Rheumatol 2022; 75:826-841. [PMID: 36409585 DOI: 10.1002/art.42409] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 11/03/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022]
Abstract
OBJECTIVE Systemic juvenile idiopathic arthritis (JIA) features characteristics of autoinflammation and autoimmunity, culminating in chronic arthritis. In this study, we hypothesized that aberrant or incomplete polarization of T helper cells contributes to disease pathology. METHODS Cells or serum samples were obtained from healthy controls (n = 72) and systemic JIA patients (n = 171). Isolated naive T helper cells were cultured under Th1, Th17, and T follicular helper (Tfh) or T peripheral helper (Tph)-polarizing conditions and were partly cocultured with allogenic memory B cells. Cell samples were then analyzed for surface marker, transcription factor, and cytokine expression, as well as plasmablast generation. Serum samples were subjected to multiplexed bead and self-antigen arrays and enzyme-linked immunosorbent assays, and all data were compared to retrospective RNA profiling analyses. RESULTS Differentiation of systemic JIA-naive T helper cells toward Th1 cells resulted in low expression levels of interferon-γ (IFNγ) and eomesodermin, which was associated in part with disease duration. In contrast developing Th1 cells in patients with systemic JIA were found to produce elevated levels of interleukin-21 (IL-21), which negatively correlated with cellular expression of IFNγ and eomesodermin. In both in vitro and ex vivo analyses, IL-21 together with programmed cell death 1 (PD-1), inducible T cell costimulator (ICOS), and CXCR5 expression induced naive T helper cells from systemic JIA patients to polarize toward a Tfh/Tph cell phenotype. Retrospective analysis of whole-blood RNA-sequencing data demonstrated that Bcl-6, a master transcription factor in Tfh/Tph cell differentiation, was overexpressed specifically in patients with systemic JIA. Naive T helper cells from systemic JIA patients which were stimulated in vitro promoted B cellular plasmablast generation, and self-antigen array data indicated that IgG reactivity profiles of patients with systemic JIA differed from those of healthy controls. CONCLUSION In the pathogenesis of systemic JIA, skewing of naive T helper cell differentiation toward a Tfh/Tph cell phenotype may represent an echo of autoimmunity, which may indicate the mechanisms driving progression toward chronic destructive arthritis.
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Affiliation(s)
- Julia Kuehn
- Pediatric Rheumatology and Immunology, University Children's Hospital, Muenster, Germany
| | - Susanne Schleifenbaum
- Pediatric Rheumatology and Immunology, University Children's Hospital, Muenster, Germany
| | - Michaela Hendling
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, Austrian Institute of Technology, Vienna, Austria
| | - Sandra Siebenhandl
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, Austrian Institute of Technology, Vienna, Austria
| | - Julie Krainer
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, Austrian Institute of Technology, Vienna, Austria
| | - Sabrina Fuehner
- Pediatric Rheumatology and Immunology, University Children's Hospital, Muenster, Germany
| | - Antje Hellige
- Pediatric Rheumatology and Immunology, University Children's Hospital, Muenster, Germany
| | - Carolin Park
- Pediatric Rheumatology and Immunology, University Children's Hospital, Muenster, Germany
| | - Claas Hinze
- Pediatric Rheumatology and Immunology, University Children's Hospital, Muenster, Germany
| | - Helmut Wittkowski
- Pediatric Rheumatology and Immunology, University Children's Hospital, Muenster, Germany
| | - Dirk Holzinger
- Department of Pediatric Hematology-Oncology, University of Duisburg-Essen, Essen, Germany, and Department of Applied Health Sciences, University of Applied Sciences Bochum, Bochum, Germany
| | - Lorenz Thurner
- José Carreras Center for Immunology and Gene Therapy and Internal Medicine I, Saarland University Medical School, Homburg, Germany
| | - Andreas Weinhäusel
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, Austrian Institute of Technology, Vienna, Austria
| | - Dirk Foell
- Pediatric Rheumatology and Immunology, University Children's Hospital, Muenster, Germany
| | - Christoph Kessel
- Pediatric Rheumatology and Immunology, University Children's Hospital, Muenster, Germany
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Hendling M, Barišić I. Computational Design of Multiplex Oligonucleotide-Based Assays. Methods Mol Biol 2021; 2189:19-30. [PMID: 33180290 DOI: 10.1007/978-1-0716-0822-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The success of any oligonucleotide-based experiment strongly depends on the accurate design of the components. Oli2go is a user-friendly web tool that provides efficient multiplex oligonucleotide design including specificity and primer dimer checks. Its fully automated workflow involves important design steps that use specific parameters to produce high-quality oligonucleotides. This chapter describes how these steps are computationally implemented by oli2go.
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Affiliation(s)
- Michaela Hendling
- Center for Health & Bioresources, Molecular Diagnostics, Austrian Institute of Technology GmbH, Vienna, Austria.
| | - Ivan Barišić
- Center for Health & Bioresources, Molecular Diagnostics, Austrian Institute of Technology GmbH, Vienna, Austria
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Hendling M, Barišić I. In-silico Design of DNA Oligonucleotides: Challenges and Approaches. Comput Struct Biotechnol J 2019; 17:1056-1065. [PMID: 31452858 PMCID: PMC6700205 DOI: 10.1016/j.csbj.2019.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 11/13/2022] Open
Abstract
DNA oligonucleotides are essential components of a high number of technologies in molecular biology. The key event of each oligonucleotide-based assay is the specific binding between oligonucleotides and their target DNA. However, single-stranded DNA molecules also tend to bind to unintended targets or themselves. The probability of such unspecific binding increases with the complexity of an assay. Therefore, accurate data management and design workflows are necessary to optimize the in-silico design of primers and probes. Important considerations concerning computational infrastructure and run time need to be made for both data management and the design process. Data retrieval, data updates, storage, filtering and analysis are the main parts of a sequence data management system. Each part needs to be well-implemented as the resulting sequences form the basis for the oligonucleotide design. Important key features, such as the oligonucleotide length, melting temperature, secondary structures and primer dimer formation, as well as the specificity, should be considered for the in-silico selection of oligonucleotides. The development of an efficient oligonucleotide design workflow demands the right balance between the precision of the applied computer models, the general expenditure of time, and computational workload. This paper gives an overview of important parameters during the design process, starting from the data retrieval, up to the design parameters for optimized oligonucleotide design.
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Affiliation(s)
- Michaela Hendling
- Austrian Institute of Technology GmbH, Center for Health & Bioresources, Molecular Diagnostics, Giefinggasse 4, 1210 Vienna, Austria
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Hendling M, Pabinger S, Peters K, Wolff N, Conzemius R, Barišić I. Oli2go: an automated multiplex oligonucleotide design tool. Nucleic Acids Res 2018; 46:W252-W256. [PMID: 29718464 PMCID: PMC6030895 DOI: 10.1093/nar/gky319] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/04/2018] [Accepted: 04/17/2018] [Indexed: 01/11/2023] Open
Abstract
The success of widely used oligonucleotide-based experiments, ranging from PCR to microarray, strongly depends on an accurate design. The design process involves a number of steps, which use specific parameters to produce high quality oligonucleotides. Oli2go is an efficient, user friendly, fully automated multiplex oligonucleotide design tool, which performs primer and different hybridization probe designs as well as specificity and cross dimer checks in a single run. The main improvement to existing oligonucleotide design web-tools is that oli2go combines multiple steps in an all-in-one solution, where other web applications only accomplish parts of the whole design workflow. Especially, the oli2go specificity check is not only performed against a single species (e.g. mouse), but against bacteria, viruses, fungi, invertebrates, plants, protozoa, archaea and sequences from whole genome shotgun sequence projects and environmental samples, at once. This allows the design of highly specific oligonucleotides in multiplex applications, which is further assured by performing dimer checks not only on the primers themselves, but in an all-against-all fashion. The software is freely accessible to all users at http://oli2go.ait.ac.at/.
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Affiliation(s)
- Michaela Hendling
- AIT Austrian Institute of Technology, Center for Health, and Bioresources, Molecular Diagnostics, Muthgasse 11, 1190 Vienna, Austria
| | - Stephan Pabinger
- AIT Austrian Institute of Technology, Center for Health, and Bioresources, Molecular Diagnostics, Muthgasse 11, 1190 Vienna, Austria
| | - Konrad Peters
- University of Vienna, Faculty of Informatics, Währinger Straße 29, 1090 Vienna, Austria
| | - Noa Wolff
- AIT Austrian Institute of Technology, Center for Health, and Bioresources, Molecular Diagnostics, Muthgasse 11, 1190 Vienna, Austria
| | - Rick Conzemius
- AIT Austrian Institute of Technology, Center for Health, and Bioresources, Molecular Diagnostics, Muthgasse 11, 1190 Vienna, Austria
| | - Ivan Barišić
- AIT Austrian Institute of Technology, Center for Health, and Bioresources, Molecular Diagnostics, Muthgasse 11, 1190 Vienna, Austria
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Hendling M, Krenn M, Haller MA, Loefler S, Kern H, Mayr W. Compliance monitoring of home based electrical stimulation training of elderly subjects. ACTA ACUST UNITED AC 2013; 58 Suppl 1:/j/bmte.2013.58.issue-s1-A/bmt-2013-4006/bmt-2013-4006.xml. [PMID: 24042616 DOI: 10.1515/bmt-2013-4006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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