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van Beek N, Holtsche MM, Atefi I, Olbrich H, Schmitz MJ, Pruessmann J, Vorobyev A, Schmidt E. State-of-the-art diagnosis of autoimmune blistering diseases. Front Immunol 2024; 15:1363032. [PMID: 38903493 PMCID: PMC11187241 DOI: 10.3389/fimmu.2024.1363032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/15/2024] [Indexed: 06/22/2024] Open
Abstract
Autoimmune blistering disorders (AIBDs) are a heterogeneous group of approximately a dozen entities comprising pemphigus and pemphigoid disorders and dermatitis herpetiformis. The exact diagnosis of AIBDs is critical for both prognosis and treatment and is based on the clinical appearance combined with the detection of tissue-bound and circulating autoantibodies. While blisters and erosions on the skin and/or inspectable mucosal surfaces are typical, lesions may be highly variable with erythematous, urticarial, prurigo-like, or eczematous manifestations. While direct immunofluorescence microscopy (IFM) of a perilesional biopsy is still the diagnostic gold standard, the molecular identification of the major target antigens opened novel therapeutic avenues. At present, most AIBDs can be diagnosed by the detection of autoantigen-specific serum antibodies by enzyme-linked immunosorbent assay (ELISA) or indirect IFM when the clinical picture is known. This is achieved by easily available and highly specific and sensitive assays employing recombinant immunodominant fragments of the major target antigens, i.e., desmoglein 1 (for pemphigus foliaceus), desmoglein 3 (for pemphigus vulgaris), envoplakin (for paraneoplastic pemphigus), BP180/type XVII collagen (for bullous pemphigoid, pemphigoid gestationis, and mucous membrane pemphigoid), laminin 332 (for mucous membrane pemphigoid), laminin β4 (for anti-p200 pemphigoid), type VII collagen (for epidermolysis bullosa acquisita and mucous membrane pemphigoid), and transglutaminase 3 (for dermatitis herpetiformis). Indirect IFM on tissue substrates and in-house ELISA and immunoblot tests are required to detect autoantibodies in some AIBD patients including those with linear IgA disease. Here, a straightforward modern approach to diagnosing AIBDs is presented including diagnostic criteria according to national and international guidelines supplemented by long-term in-house expertise.
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Affiliation(s)
- Nina van Beek
- Department of Dermatology, Allergology and Venerology, University of Lübeck, Lübeck, Germany
| | - Maike M. Holtsche
- Department of Dermatology, Allergology and Venerology, University of Lübeck, Lübeck, Germany
| | - Ingeborg Atefi
- Department of Dermatology, Allergology and Venerology, University of Lübeck, Lübeck, Germany
| | - Henning Olbrich
- Department of Dermatology, Allergology and Venerology, University of Lübeck, Lübeck, Germany
| | - Marie J. Schmitz
- Department of Dermatology, Allergology and Venerology, University of Lübeck, Lübeck, Germany
| | - Jasper Pruessmann
- Department of Dermatology, Allergology and Venerology, University of Lübeck, Lübeck, Germany
| | - Artem Vorobyev
- Department of Dermatology, Allergology and Venerology, University of Lübeck, Lübeck, Germany
| | - Enno Schmidt
- Department of Dermatology, Allergology and Venerology, University of Lübeck, Lübeck, Germany
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
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2
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Liblau RS, Latorre D, Kornum BR, Dauvilliers Y, Mignot EJ. The immunopathogenesis of narcolepsy type 1. Nat Rev Immunol 2024; 24:33-48. [PMID: 37400646 DOI: 10.1038/s41577-023-00902-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2023] [Indexed: 07/05/2023]
Abstract
Narcolepsy type 1 (NT1) is a chronic sleep disorder resulting from the loss of a small population of hypothalamic neurons that produce wake-promoting hypocretin (HCRT; also known as orexin) peptides. An immune-mediated pathology for NT1 has long been suspected given its exceptionally tight association with the MHC class II allele HLA-DQB1*06:02, as well as recent genetic evidence showing associations with polymorphisms of T cell receptor genes and other immune-relevant loci and the increased incidence of NT1 that has been observed after vaccination with the influenza vaccine Pandemrix. The search for both self-antigens and foreign antigens recognized by the pathogenic T cell response in NT1 is ongoing. Increased T cell reactivity against HCRT has been consistently reported in patients with NT1, but data demonstrating a primary role for T cells in neuronal destruction are currently lacking. Animal models are providing clues regarding the roles of autoreactive CD4+ and CD8+ T cells in the disease. Elucidation of the pathogenesis of NT1 will allow for the development of targeted immunotherapies at disease onset and could serve as a model for other immune-mediated neurological diseases.
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Affiliation(s)
- Roland S Liblau
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, Toulouse, France.
- Department of Immunology, Toulouse University Hospitals, Toulouse, France.
| | | | - Birgitte R Kornum
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yves Dauvilliers
- National Reference Center for Orphan Diseases, Narcolepsy, Idiopathic Hypersomnia and Kleine-Levin Syndrome, Department of Neurology, Gui-de-Chauliac Hospital, CHU de Montpellier, Montpellier, France
- INSERM Institute for Neurosciences of Montpellier, Montpellier, France
| | - Emmanuel J Mignot
- Stanford University, Center for Narcolepsy, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, USA.
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3
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Seitz V, Gennermann K, Elezkurtaj S, Groth D, Schaper S, Dröge A, Lachmann N, Berg E, Lenze D, Kühl AA, Husemann C, Kleo K, Horst D, Lennerz V, Hennig S, Hummel M, Schumann M. Specific T-cell receptor beta-rearrangements of gluten-triggered CD8 + T-cells are enriched in celiac disease patients' duodenal mucosa. Clin Immunol 2023; 256:109795. [PMID: 37769786 DOI: 10.1016/j.clim.2023.109795] [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: 07/13/2023] [Revised: 09/12/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Celiac disease (CeD) is an autoimmune disorder affecting the small intestine with gluten as disease trigger. Infections including Influenza A, increase the CeD risk. While gluten-specific CD4+ T-cells, recognizing HLA-DQ2/DQ8 presented gluten-peptides, initiate and sustain the celiac immune response, CD8+ α/β intraepithelial T-cells elicit mucosal damage. Here, we subjected TCRs from a cohort of 56 CeD patients and 22 controls to an analysis employing 749 published CeD-related TCRβ-rearrangements derived from gluten-specific CD4+ T-cells and gluten-triggered peripheral blood CD8+ T-cells. We show, that in addition to TCRs from gluten-specific CD4+ T-cells, TCRs of gluten-triggered CD8+ T-cells are significantly enriched in CeD duodenal tissue samples. TCRβ-rearrangements of gluten-triggered CD8+ T-cells were even more expanded in patients than TCRs from gluten-specific CD4+ T-cells (p < 0.0002) and highest in refractory CeD. Sequence alignments with TCR-antigen databases suggest that a subgroup of these most likely indirectly gluten-triggered TCRs recognize microbial, viral, and autoantigens.
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Affiliation(s)
- V Seitz
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; HS Diagnomics GmbH, Berlin, Germany
| | | | - S Elezkurtaj
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - D Groth
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - A Dröge
- HS Diagnomics GmbH, Berlin, Germany
| | - N Lachmann
- Centre for Tumor Medicine, Histocompatibility & Immunogenetics Laboratory, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - E Berg
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - D Lenze
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - A A Kühl
- iPATH.Berlin - Core Unit of the Charité Universitätsmedizin Berlin, corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - C Husemann
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - K Kleo
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - D Horst
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - S Hennig
- HS Diagnomics GmbH, Berlin, Germany
| | - M Hummel
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Schumann
- Medizinische Klinik m. S. Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
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4
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Peric S, Zlatar J, Nikolic L, Ivanovic V, Pesovic J, Petrovic Djordjevic I, Sreckovic S, Savic-Pavicevic D, Meola G, Rakocevic-Stojanovic V. Autoimmune Diseases in Patients With Myotonic Dystrophy Type 2. Front Neurol 2022; 13:932883. [PMID: 35923829 PMCID: PMC9341519 DOI: 10.3389/fneur.2022.932883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/20/2022] [Indexed: 11/18/2022] Open
Abstract
Introduction Myotonic dystrophy type 2 (DM2) is a rare autosomal dominant multisystemic disease with highly variable clinical presentation. Several case reports and one cohort study suggested a significant association between DM2 and autoimmune diseases (AIDs). Aim The aim of this study is to analyze the frequency and type of AIDs in patients with DM2 from the Serbian DM registry. Patients and Methods A total of 131 patients with DM2 from 108 families were included, [62.6% women, mean age at DM2 onset 40.4 (with standard deviation 13) years, age at entering the registry 52 (12.8) years, and age at analysis 58.4 (12.8) years]. Data were obtained from Akhenaten, the Serbian registry for DM, and through the hospital electronic data system. Results Upon entering the registry, 35 (26.7%) of the 131 patients with DM2 had AIDs including Hashimoto thyroiditis (18.1%), rheumatoid arthritis, diabetes mellitus type 1, systemic lupus, Sjogren's disease, localized scleroderma, psoriasis, celiac disease, Graves's disease, neuromyelitis optica, myasthenia gravis, and Guillain-Barre syndrome. At the time of data analysis, one additional patient developed new AIDs, so eventually, 36 (28.8%) of 125 DM2 survivors had AIDs. Antinuclear antibodies (ANAs) were found in 14 (10.7%) of 63 tested patients, including 12 without defined corresponding AID (all in low titers, 1:40 to 1:160). Antineutrophil cytoplasmic antibodies (ANCAs) were negative in all 50 tested cases. The percentage of women was significantly higher among patients with AIDs (82.9% vs. 55.2%, p <0.01). Conclusion AIDs were present in as high as 30% of the patients with DM2. Thus, screening for AIDs in DM2 seems reasonable. Presence of AIDs and/or ANAs may lead to under-diagnosis of DM2.
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Affiliation(s)
- Stojan Peric
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- *Correspondence: Stojan Peric ; orcid.org/0000-0002-2979-556X
| | - Jelena Zlatar
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Luka Nikolic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Vukan Ivanovic
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Jovan Pesovic
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Ivana Petrovic Djordjevic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- Cardiology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Svetlana Sreckovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- Anaesthesiology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Dusanka Savic-Pavicevic
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Giovanni Meola
- Department of Neurorehabilitation Sciences, Casa Di Cura del Policlinico, Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Vidosava Rakocevic-Stojanovic
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
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5
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Song Y, Lee S, Bell D, Goudey B, Zhou R. Binding Affinity Calculations of Gluten Peptides to HLA Risk Modifiers: DQ2.5 versus DQ7.5. J Phys Chem B 2022; 126:5151-5160. [PMID: 35796490 DOI: 10.1021/acs.jpcb.2c00962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Free energy perturbation (FEP) calculations can predict relative binding affinities of an antigen and its point mutants to the same human leukocyte antigen (HLA) with high accuracy (e.g., within 1.0 kcal/mol to experiment); however, a more challenging task is to compare binding affinities of wholly different antigens binding to completely different HLAs using FEP. Researchers have used a variety of different FEP schemes to compute and compare absolute binding affinities, with varied success. Here, we propose and assess a unifying scheme to compute the relative binding affinities of different antigens binding to completely different HLAs using absolute binding affinity FEP calculations. We apply our affinity calculation technique to HLA-antigen-T-cell receptor (TCR) systems relevant to celiac disease (CeD) by investigating binding affinity differences between HLA-DQ2.5 (enhanced CeD risk) and HLA-DQ7.5 (CeD protective) in the binary (HLA-gliadin) and ternary (HLA-gliadin-TCR) binding complexes for three gliadin derived epitopes: glia-α1, glia-α2, and glia-ω1. Based on FEP calculations with our carefully designed thermodynamic cycles, we demonstrate that HLA-DQ2.5 has higher binding affinity than HLA-DQ7.5 for gliadin and enhanced binding affinity with a common TCR, agreeing with known results that the HLA-DQ2.5 serotype exhibits increased risk for CeD. Our findings reveal that our proposed absolute binding affinity FEP method is appropriate for predicting HLA binding for disparate antigens with different genotypes. We also discuss atomic-level details of HLA genotypes interacting with gluten peptides and TCRs in regard to the pathogenesis of CeD.
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Affiliation(s)
- Yi Song
- College of Life Sciences, Department of Physics, and Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China
| | - Sangyun Lee
- Computational Biology Center, IBM Thomas J Watson Research Center, Yorktown Heights, New York 10598, United States
| | - David Bell
- Computational Biology Center, IBM Thomas J Watson Research Center, Yorktown Heights, New York 10598, United States.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Benjamin Goudey
- School of Computing and Information Systems, The University of Melbourne, Melbourne 3010, Australia
| | - Ruhong Zhou
- College of Life Sciences, Department of Physics, and Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China.,Computational Biology Center, IBM Thomas J Watson Research Center, Yorktown Heights, New York 10598, United States.,Department of Chemistry, Columbia University, New York, New York 10027, United States
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6
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Chang D, O’Shea D, Therrien A, Silvester JA. Review article: Becoming and being coeliac-special considerations for childhood, adolescence and beyond. Aliment Pharmacol Ther 2022; 56 Suppl 1:S73-S85. [PMID: 35815825 PMCID: PMC9441244 DOI: 10.1111/apt.16851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/10/2022] [Accepted: 02/13/2022] [Indexed: 12/09/2022]
Abstract
Classically considered a disease of early childhood characterised by malabsorption and failure to thrive, coeliac disease is now recognised to arise in genetically susceptible individuals at any age. Although permissive HLA genotypes are the strongest predictor of coeliac disease, they are not sufficient. Several prospective cohort studies enrolling genetically at-risk infants have investigated the role of potential triggers of coeliac disease autoimmunity, such as timing of gluten introduction, viral infections and dietary patterns. Much less is known about triggers of coeliac disease in adulthood. Better understanding of factors leading to coeliac disease may be helpful in the management of those with potential coeliac disease (elevated serum celiac antibodies without villous atrophy in the small intestine), many of whom initiate a gluten-free diet without demonstration of villous atrophy. There are a range of clinical presentations of celiac disease in childhood and patterns of coeliac serology, including fluctuation and spontaneous reversion on a gluten-containing diet, vary. There is a current debate over best strategies to manage adults and children with potential coeliac disease to avoid over-treatment and under-treatment. Childhood and adolescence carry unique issues pertaining to the diagnosis and management of coeliac disease, and include nutrition and growth, rescreening, repeat biopsy, dietary adherence concerns and transition to adult care. In conclusion, while coeliac disease has similar pathogenesis and general clinical manifestations in paediatric and adult populations, diagnostic and management approaches need to adapt to the developmental stages.
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Affiliation(s)
- Denis Chang
- 1. Boston Children’s Hospital, Boston, MA,2. Harvard Celiac Research Program, Harvard Medical School, Boston, MA
| | - Delia O’Shea
- 1. Boston Children’s Hospital, Boston, MA,2. Harvard Celiac Research Program, Harvard Medical School, Boston, MA
| | - Amelie Therrien
- 2. Harvard Celiac Research Program, Harvard Medical School, Boston, MA,3. Beth Israel Deaconess Medical Center, Boston, MA
| | - Jocelyn A Silvester
- 1. Boston Children’s Hospital, Boston, MA,2. Harvard Celiac Research Program, Harvard Medical School, Boston, MA,3. Beth Israel Deaconess Medical Center, Boston, MA
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7
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Paavola S, Lindfors K, Kivelä L, Cerqueira J, Huhtala H, Saavalainen P, Tauschi R, Kaukinen K, Kurppa K. Presence of high-risk HLA genotype is the most important individual risk factor for coeliac disease among at-risk relatives. Aliment Pharmacol Ther 2021; 54:805-813. [PMID: 34278595 DOI: 10.1111/apt.16534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/07/2021] [Accepted: 07/02/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Family screening has been advocated as a means to reduce the major underdiagnosis of coeliac disease. However, the precise risk of the disease in relatives and the impact of patient- and relative-related individual factors remain obscure. AIMS To investigate the individual risk of coeliac disease among patients' relatives. METHODS Altogether 2943 relatives of 624 index patients were assessed for the presence of previous coeliac disease diagnosis, or were screened for the disease. Coeliac disease-associated human leucocyte antigen (HLA) genotype was determined from all participants. The association between individual factors and new screening positivity was assessed by logistic regression. RESULTS There were 229 previously diagnosed non-index relatives with coeliac disease and 2714 non-affected (2067 first-degree, 647 more distant) relatives. Of these 2714 relatives, 129 (4.8%) were screening-positive (first-degree 5.1%, second-degree 3.6%, more distant 3.5%). The combined prevalence of the previously diagnosed and now detected cases in relatives was 12.2% (6.3% clinically detected, 5.9% screen-detected). In univariate analysis, age <18 years at diagnosis (odds ratio 1.60, 95% CI 1.04-2.45) in index, and age 41-60 years (1.73, 1.10-2.73), being a sibling (1.65, 1.06-2.59) and having the high-risk genotype (3.22, 2.01-5.15 DQ2.5/2.5 or DQ2.5/2.2 vs other risk alleles) in relatives were associated with screening positivity. Only high-risk HLA remained significant (2.94, 1.80-4.78) in multivariable analysis. CONCLUSIONS Unrecognised coeliac disease was common among at-risk relatives even in a country with an active case-finding policy, and also in relatives more distant than first-degree. The presence of a high-risk genotype was the most important predictor for screening positivity. ClinicalTrials.gov identifier NCT03136731.
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Affiliation(s)
- Saana Paavola
- Faculty of Medicine and Health Technology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Katri Lindfors
- Faculty of Medicine and Health Technology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Laura Kivelä
- Faculty of Medicine and Health Technology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Juliana Cerqueira
- Faculty of Medicine and Health Technology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Heini Huhtala
- Faculty of Social Sciences, University of Tampere, Tampere, Finland
| | - Päivi Saavalainen
- Translational Immunology Research Program, and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Riku Tauschi
- Faculty of Medicine and Health Technology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Katri Kaukinen
- Faculty of Medicine and Health Technology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Kalle Kurppa
- Faculty of Medicine and Health Technology, University of Tampere and Tampere University Hospital, Tampere, Finland.,The University Consortium of Seinäjoki, Seinäjoki, Finland
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8
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Bell DR, Chen SH. Toward Guided Mutagenesis: Gaussian Process Regression Predicts MHC Class II Antigen Mutant Binding. J Chem Inf Model 2021; 61:4857-4867. [PMID: 34375111 DOI: 10.1021/acs.jcim.1c00458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antigen-specific immunotherapies (ASI) require successful loading and presentation of antigen peptides into the major histocompatibility complex (MHC) binding cleft. One route of ASI design is to mutate native antigens for either stronger or weaker binding interaction to MHC. Exploring all possible mutations is costly both experimentally and computationally. To reduce experimental and computational expense, here we investigate the minimal amount of prior data required to accurately predict the relative binding affinity of point mutations for peptide-MHC class II (pMHCII) binding. Using data from different residue subsets, we interpolate pMHCII mutant binding affinities by Gaussian process (GP) regression of residue volume and hydrophobicity. We apply GP regression to an experimental data set from the Immune Epitope Database, and theoretical data sets from NetMHCIIpan and Free Energy Perturbation calculations. We find that GP regression can predict binding affinities of nine neutral residues from a six-residue subset with an average R2 coefficient of determination value of 0.62 ± 0.04 (±95% CI), average error of 0.09 ± 0.01 kcal/mol (±95% CI), and with an receiver operating characteristic (ROC) AUC value of 0.92 for binary classification of enhanced or diminished binding affinity. Similarly, metrics increase to an R2 value of 0.69 ± 0.04, average error of 0.07 ± 0.01 kcal/mol, and an ROC AUC value of 0.94 for predicting seven neutral residues from an eight-residue subset. Our work finds that prediction is most accurate for neutral residues at anchor residue sites without register shift. This work holds relevance to predicting pMHCII binding and accelerating ASI design.
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Affiliation(s)
- David R Bell
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Serena H Chen
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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