1
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Dong MH, Mei ZC, Zhou LQ, Heming M, Xu LL, Liu YX, Pang XW, Chu YH, Cai SB, Ye H, Shang K, Xiao J, Meyer Zu Hörste G, Wang W, Qin C, Tian DS. Anti-BCMA CAR-T cell therapy in relapsed/refractory chronic inflammatory demyelinating polyneuropathy. MED 2025:100704. [PMID: 40425008 DOI: 10.1016/j.medj.2025.100704] [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: 02/26/2025] [Revised: 04/14/2025] [Accepted: 04/29/2025] [Indexed: 05/29/2025]
Abstract
BACKGROUND Chronic inflammatory demyelinating polyneuropathy (CIDP) presents a significant therapeutic challenge, with up to 15% of patients being refractory to first-line treatments. METHODS Anti-B cell maturation antigen chimeric antigen receptor T (CAR-T) cell therapy was applied to two patients with highly relapsed and refractory CIDP, followed by safety and efficacy evaluation. Multi-omics analyses were performed on samples of peripheral blood mononuclear cells (PBMCs) collected before and after infusion. FINDINGS Both patients had no severe adverse events and achieved drug-free remission within 6 months post-CAR-T therapy. Patient 1 experienced disease recurrence 12 months post infusion following a severe infection of COVID-19, while patient 2 maintained remission over 24 months. Relapse was accompanied by reactivation of pathogenic B cells and recurrence of autoantibodies/peptides targeting axons or myelin. Metabolic reprogramming of B cells characterized by overglycolysis was linked to disease relapse, which could be modulated by regulatory factor X5. CONCLUSION This study demonstrates the safety and potential of anti-BCMA CAR-T cell therapy in treating refractory CIDP and provides insights into the molecular mechanisms underlying patient responses (ClinicalTrials.gov: NCT04561557). FUNDING Ministry of Science and Technology China Brain Initiative grant STI2030-Major Projects 2022ZD0204700 (to W.W.), National Natural Science Foundation of China grants 82371404 and 82071380 (to D.-S.T.) and 82471353 and 82271341 (to C.Q.), Knowledge Innovation Program of Wuhan Shuguang Project 2022020801020454 (to C.Q.), and Key Research and Development Program of Hubei Provincial Department of Science and Technology 2023BCB148 (to D.-S.T.). The clinical trial was funded by Nanjing IASO Biotechnology Co., Ltd.
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Affiliation(s)
- Ming-Hao Dong
- Department of Neurology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhi-Cheng Mei
- Department of Neurology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Luo-Qi Zhou
- Department of Neurology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Michael Heming
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Lu-Lu Xu
- Department of Neurology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yu-Xin Liu
- Department of Neurology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiao-Wei Pang
- Department of Neurology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yun-Hui Chu
- Department of Neurology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Song-Bai Cai
- Nanjing IASO Biotherapeutics Ltd., Nanjing, China
| | - Huan Ye
- Nanjing IASO Biotherapeutics Ltd., Nanjing, China
| | - Ke Shang
- Department of Neurology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jun Xiao
- Department of Neurology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Gerd Meyer Zu Hörste
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
| | - Wei Wang
- Department of Neurology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Chuan Qin
- Department of Neurology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Dai-Shi Tian
- Department of Neurology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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2
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Hörstke NV, Vogl T. Deciphering the autoreactome: Massively parallelized methods for autoantibody detection in humans. J Immunol Methods 2025; 541:113876. [PMID: 40339788 DOI: 10.1016/j.jim.2025.113876] [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: 11/18/2024] [Revised: 05/05/2025] [Accepted: 05/05/2025] [Indexed: 05/10/2025]
Abstract
Autoantibodies have a substantial impact on human health ranging from autoimmune diseases to cancer diagnostics. Knowledge of the antigens recognized can allow for more accurate diagnostics, a better understanding of pathogeneses and thus improved prevention, as well as laying the foundation for the development of new therapies. A critical step to acquire this knowledge is to detect the exact self-antigens targeted by autoantibodies out of the pool of 20,000 human proteins against which reactivities could be observed. Here, we review established and emerging methods for highly parallelized autoantigen detection such as human proteome microarrays, serological identification of antigens by screening of cDNA expression libraries (SEREX), serological proteome analysis (SERPA), phage display immunoprecipitation sequencing (PhIP-Seq), parallel analysis of translated ORFs (PLATO), and rapid extracellular antigen profiling (REAP). We highlight advantages and limitations of these methods, aiming to give a guideline to choose the appropriate method for a certain application.
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Affiliation(s)
- Nicolai V Hörstke
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090 Vienna, Austria
| | - Thomas Vogl
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090 Vienna, Austria.
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3
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Pala F, Notarangelo LD, Lionakis MS. Thymic inborn errors of immunity. J Allergy Clin Immunol 2025; 155:368-376. [PMID: 39428079 PMCID: PMC11805638 DOI: 10.1016/j.jaci.2024.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 10/08/2024] [Accepted: 10/11/2024] [Indexed: 10/22/2024]
Abstract
The thymus is crucial for optimal T-cell development by facilitating the generation and selection of a diverse repertoire of T cells that can recognize foreign antigens while promoting tolerance to self-antigens. A number of inborn errors of immunity causing complete or partial defects in thymic development (athymia) and/or impaired thymic function have been increasingly recognized that manifest clinically with a combination of life-threatening infections, severe multiorgan autoimmunity, and/or cardiac, craniofacial, ectodermal, and endocrine abnormalities. The introduction of newborn screening programs and the advent of thymic transplantation show promise for early detection and improving the outcomes of patients with certain thymic inborn errors of immunity. We discuss our current understanding of the genetics, immunopathogenesis, diagnosis, and treatment of inborn errors of immunity that impair thymic development and/or function.
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Affiliation(s)
- Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
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4
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Bosticardo M, Dobbs K, Delmonte OM, Martins AJ, Pala F, Kawai T, Kenney H, Magro G, Rosen LB, Yamazaki Y, Yu HH, Calzoni E, Lee YN, Liu C, Stoddard J, Niemela J, Fink D, Castagnoli R, Ramba M, Cheng A, Riley D, Oikonomou V, Shaw E, Belaid B, Keles S, Al-Herz W, Cancrini C, Cifaldi C, Baris S, Sharapova S, Schuetz C, Gennery AR, Freeman AF, Somech R, Choo S, Giliani SC, Güngör T, Drozdov D, Meyts I, Moshous D, Neven B, Abraham RS, El-Marsafy A, Kanariou M, King A, Licciardi F, Cruz-Muñoz ME, Palma P, Poli C, Adeli M, Algeri M, Alroqi FJ, Bastard P, Bergerson JRE, Booth C, Brett A, Burns SO, Butte MJ, Padem N, de la Morena M, Dbaibo G, de Ravin SS, Dimitrova D, Djidjik R, Dorna MB, Dutmer CM, Elfeky R, Facchetti F, Fuleihan RL, Geha RS, Gonzalez-Granado LI, Haljasmägi L, Ale H, Hayward A, Hifanova AM, Ip W, Kaplan B, Kapoor N, Karakoc-Aydiner E, Kärner J, Keller MD, Dávila Saldaña BJ, Kiykim A, Kuijpers TW, Kuznetsova EE, Latysheva EA, Leiding JW, Locatelli F, Alva-Lozada G, McCusker C, Celmeli F, Morsheimer M, Ozen A, Parvaneh N, Pasic S, Plebani A, Preece K, Prockop S, Sakovich IS, Starkova EE, et alBosticardo M, Dobbs K, Delmonte OM, Martins AJ, Pala F, Kawai T, Kenney H, Magro G, Rosen LB, Yamazaki Y, Yu HH, Calzoni E, Lee YN, Liu C, Stoddard J, Niemela J, Fink D, Castagnoli R, Ramba M, Cheng A, Riley D, Oikonomou V, Shaw E, Belaid B, Keles S, Al-Herz W, Cancrini C, Cifaldi C, Baris S, Sharapova S, Schuetz C, Gennery AR, Freeman AF, Somech R, Choo S, Giliani SC, Güngör T, Drozdov D, Meyts I, Moshous D, Neven B, Abraham RS, El-Marsafy A, Kanariou M, King A, Licciardi F, Cruz-Muñoz ME, Palma P, Poli C, Adeli M, Algeri M, Alroqi FJ, Bastard P, Bergerson JRE, Booth C, Brett A, Burns SO, Butte MJ, Padem N, de la Morena M, Dbaibo G, de Ravin SS, Dimitrova D, Djidjik R, Dorna MB, Dutmer CM, Elfeky R, Facchetti F, Fuleihan RL, Geha RS, Gonzalez-Granado LI, Haljasmägi L, Ale H, Hayward A, Hifanova AM, Ip W, Kaplan B, Kapoor N, Karakoc-Aydiner E, Kärner J, Keller MD, Dávila Saldaña BJ, Kiykim A, Kuijpers TW, Kuznetsova EE, Latysheva EA, Leiding JW, Locatelli F, Alva-Lozada G, McCusker C, Celmeli F, Morsheimer M, Ozen A, Parvaneh N, Pasic S, Plebani A, Preece K, Prockop S, Sakovich IS, Starkova EE, Torgerson T, Verbsky J, Walter JE, Ward B, Wisner EL, Draper D, Myint-Hpu K, Truong PM, Lionakis MS, Similuk MB, Walkiewicz MA, Klion A, Holland SM, Oguz C, Bogunovic D, Kisand K, Su HC, Tsang JS, Kuhns D, Villa A, Rosenzweig SD, Pittaluga S, Notarangelo LD. Multiomics dissection of human RAG deficiency reveals distinctive patterns of immune dysregulation but a common inflammatory signature. Sci Immunol 2025; 10:eadq1697. [PMID: 39792639 DOI: 10.1126/sciimmunol.adq1697] [Show More Authors] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 12/12/2024] [Indexed: 01/30/2025]
Abstract
Human recombination-activating gene (RAG) deficiency can manifest with distinct clinical and immunological phenotypes. By applying a multiomics approach to a large group of RAG-mutated patients, we aimed at characterizing the immunopathology associated with each phenotype. Although defective T and B cell development is common to all phenotypes, patients with hypomorphic RAG variants can generate T and B cells with signatures of immune dysregulation and produce autoantibodies to a broad range of self-antigens, including type I interferons. T helper 2 (TH2) cell skewing and a prominent inflammatory signature characterize Omenn syndrome, whereas more hypomorphic forms of RAG deficiency are associated with a type 1 immune profile both in blood and tissues. We used cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) analysis to define the cell lineage-specific contribution to the immunopathology of the distinct RAG phenotypes. These insights may help improve the diagnosis and clinical management of the various forms of the disease.
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Affiliation(s)
- Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tomoki Kawai
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Heather Kenney
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Gloria Magro
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lindsey B Rosen
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yasuhiro Yamazaki
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hsin-Hui Yu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Enrica Calzoni
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yu Nee Lee
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, 52621 Tel HaShomer, Israel
| | - Can Liu
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jennifer Stoddard
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Julie Niemela
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Danielle Fink
- Neutrophil Monitoring Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Riccardo Castagnoli
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Meredith Ramba
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Aristine Cheng
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Deanna Riley
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vasileios Oikonomou
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elana Shaw
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brahim Belaid
- Department of Medical Immunology, Beni Messous University Hospital Center, Faculty of Pharmacy, University of Algiers, Algiers, Algeria
| | - Sevgi Keles
- Division of Pediatric Allergy and Immunology, Meram Faculty of Medicine, Necmettin Erbakan University, Konya, Turkey
| | - Waleed Al-Herz
- Department of Pediatrics, College of Medicine, Kuwait University, Safat, Kuwait City, Kuwait
- Allergy and Clinical Immunology Unit, Pediatric Department, Al-Sabah Hospital, Kuwait City, Kuwait
| | - Caterina Cancrini
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Research Unit of Primary Immunodeficiencies, Academic Department of Pediatrics, Bambino Gesu' Children's Hospital, Scientific Institute for Research and Heathcare (IRCCS), Rome, Italy
| | - Cristina Cifaldi
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Safa Baris
- Faculty of Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
- Isil Berat Barlan Center for Translational Medicine, Istanbul Jeffrey Modell Foundation Diagnostic Center for Primary Immune Deficiencies, Istanbul, Turkey
| | - Svetlana Sharapova
- Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Catharina Schuetz
- Department of Paediatrics, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Andrew R Gennery
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Raz Somech
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, 52621 Tel HaShomer, Israel
| | - Sharon Choo
- Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Silvia C Giliani
- Angelo Nocivelli Institute for Molecular Medicine, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Laboratory Department, Spedali Civili, Brescia, Italy
- National Center for Gene Therapy and Drugs based on RNA Technology, CN3, Brescia, Italy
| | - Tayfun Güngör
- Division of Hematology/Oncology/Immunology, Gene-Therapy, and Stem Cell Transplantation, University Children's Hospital Zürich, Zürich, Switzerland
- Eleonore Foundation & Children's Research Center (CRC), Zürich, Switzerland
| | - Daniel Drozdov
- Division of Hematology/Oncology/Immunology, Gene-Therapy, and Stem Cell Transplantation, University Children's Hospital Zürich, Zürich, Switzerland
- Eleonore Foundation & Children's Research Center (CRC), Zürich, Switzerland
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Kantonsspital Aarau, Aarau, Switzerland
| | - Isabelle Meyts
- Department of Immunology and Microbiology, Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
- University Hospitals Leuven and ERN-RITA Core Center, Leuven, Belgium
| | - Despina Moshous
- Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
- Institut Imagine, Université Paris Cité, Paris, France
| | - Benedicte Neven
- Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
- Institut Imagine, Université Paris Cité, Paris, France
| | - Roshini S Abraham
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Aisha El-Marsafy
- Department of Pediatrics, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Maria Kanariou
- Department of Immunology-Histocompatibility, Specialized & Referral Center for Primary Immunodeficiencies-Paediatric Immunology, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Alejandra King
- Departamento de Pediatría, Hospital Luis Calvo Mackenna, Santiago, Chile
| | - Francesco Licciardi
- Immuno-reumatologia, Pediatria Specialistica Universitaria, Ospedale Infantile Regina Margherita, Torino, Italy
| | - Mario E Cruz-Muñoz
- Facultad de Medicina, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Paolo Palma
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Clinical Immunology and Vaccinology Unit, Children's Hospital "Bambino Gesu," Rome, Italy
| | - Cecilia Poli
- Faculty of Medicine, Clínica Alemana Universidad del Desarrollo Roberto del Rio, Santiago, Chile
| | - Mehdi Adeli
- Department of Immunology, Sidra Medicine, Ar-Rayyan, Qatar
| | - Mattia Algeri
- Department of Hematology/Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
- Catholic University of the Sacred Heart, Rome, Italy
| | - Fayhan J Alroqi
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Paul Bastard
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Claire Booth
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Ana Brett
- Hospital Pediátrico, Unidade Local de Saúde de Coimbra, Coimbra, Portugal
- Clínica Universitária de Pediatria, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Siobhan O Burns
- Institute of Immunity and Transplantation, University College London, London, UK
- Department of Immunology, Royal Free London NHS Foundation Trust, London, UK
| | - Manish J Butte
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nurcicek Padem
- Division of Pediatric Pulmonology, Allergy-Immunology and Sleep Medicine, Riley Hospital for Children/Indiana University, Indianapolis, IN, USA
| | - M de la Morena
- Division of Immunology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - Ghassan Dbaibo
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon
| | - Suk See de Ravin
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dimana Dimitrova
- Experimental Transplantation and Immunotherapy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Reda Djidjik
- Department of Medical Immunology, Beni Messous University Hospital Center, Faculty of Pharmacy, University of Algiers, Algiers, Algeria
| | - Mayra B Dorna
- Division of Allergy and Immunology, Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Cullen M Dutmer
- Allergy and Immunology Section, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Reem Elfeky
- Department of Clinical Immunology, Royal Free Hospital, London, UK
| | - Fabio Facchetti
- Section of Pathology, Department of Molecular and Translational Medicine, University of Brescia, Spedali Civili di Brescia, Brescia, Italy
| | - Ramsay L Fuleihan
- Division of Allergy & Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Raif S Geha
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA
| | - Luis I Gonzalez-Granado
- Primary Immunodeficiency Unit, Pediatrics, Hospital 12 Octubre, Madrid, Spain
- Instituto de Investigation Hospital 12 Octubre (imas12), Madrid, Spain
- School of Medicine Complutense University, Madrid, Spain
| | - Liis Haljasmägi
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Hanadys Ale
- Division of Immunology, Allergy and Rheumatology, Joe DiMaggio Children's Hospital, Memorial Healthcare System, Hollywood, FL, USA
- Florida International University Herbert Wertheim College of Medicine, Miami, FL, USA
| | - Anthony Hayward
- Division of Infectious Diseases, Department of Pediatrics, Brown University and Rhode Island Hospital, Providence, RI, USA
| | - Anna M Hifanova
- Department of Pediatric Infectious Diseases and Pediatric Immunology, Shupyk National Healthcare University of Ukraine, Kiev, Ukraine
| | - Winnie Ip
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Blanka Kaplan
- Division of Allergy, Asthma and Immunology, Cohen Children's Medical Center, Northwell Health, New Hyde Park, NY, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Neena Kapoor
- Children's Hospital of Los Angeles, Los Angeles, CA, USA
| | - Elif Karakoc-Aydiner
- Faculty of Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
- Isil Berat Barlan Center for Translational Medicine, Istanbul Jeffrey Modell Foundation Diagnostic Center for Primary Immune Deficiencies, Istanbul, Turkey
| | - Jaanika Kärner
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Michael D Keller
- Division of Allergy and Immunology, Children's National Hospital, Washington, DC, USA
| | | | - Ayça Kiykim
- Division of Pediatric Allergy and Immunology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Taco W Kuijpers
- Department of Pediatric Immunology, Amsterdam UMC Locatie AMC, Amsterdam, Netherlands
| | | | - Elena A Latysheva
- Immunopathology Department, NRC Institute of Immunology FMBA, Pigorov Russian National Research Medical University, Moscow, Russia
| | - Jennifer W Leiding
- Division of Allergy and Immunology, Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA
- Institute for Clinical and Translational Research, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA
- Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA
| | - Franco Locatelli
- Department of Hematology/Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
- Catholic University of the Sacred Heart, Rome, Italy
| | - Guisela Alva-Lozada
- Allergy and Immunology Division Hospital Nacional Edgardo Rebagliati Martins, Lima, Peru
| | - Christine McCusker
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre, Montreal, QC, Canada
| | - Fatih Celmeli
- Immunology and Allergy Diseases, Saglık Bilimleri University, Antalya Training and Research Hospital Pediatric, Antalya, Turkey
| | - Megan Morsheimer
- Division of Allergy, Immunology and Transplantation, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ahmet Ozen
- Faculty of Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
- Isil Berat Barlan Center for Translational Medicine, Istanbul Jeffrey Modell Foundation Diagnostic Center for Primary Immune Deficiencies, Istanbul, Turkey
| | - Nima Parvaneh
- Infectious Disease Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Srdjan Pasic
- Department of Pediatric Immunology, Mother and Child Health Institute, Medical Faculty, University of Belgrade, Belgrade, Serbia
| | | | - Kahn Preece
- Department of Immunology, John Hunter Children's Hospital, Newcastle, NSW, Australia
| | - Susan Prockop
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Inga S Sakovich
- Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Elena E Starkova
- Clinical Department, Regional Clinical Hospital No. 2, Orenburg, Russia
| | | | - James Verbsky
- Division of Rheumatology, Department of Pediatrics, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, WI, USA
| | - Jolan E Walter
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA
| | - Brant Ward
- Division of Rheumatology, Allergy and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Elizabeth L Wisner
- Division of Allergy Immunology, Department of Pediatrics, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, USA
| | - Deborah Draper
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Katherine Myint-Hpu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Pooi M Truong
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Morgan B Similuk
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Magdalena A Walkiewicz
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy Klion
- Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cihan Oguz
- Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dusan Bogunovic
- Center for Genetic Errors of Immunity, Columbia University Medical Center, New York City, NY, USA
| | - Kai Kisand
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Douglas Kuhns
- Neutrophil Monitoring Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Anna Villa
- Milan Unit, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Milan, Italy
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Stefania Pittaluga
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Wolff ASB, Oftedal BE. Aire Mutations and Autoimmune Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2025; 1471:223-246. [PMID: 40067589 DOI: 10.1007/978-3-031-77921-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2025]
Abstract
Autoimmune diseases were first recognized by Mackay and Macfarlane Burnet in 1962 (Burnet and Mackay 1962). It is defined as the failure of an organism to tolerate its own cells and tissue, resulting in an aberrant immune response by lymphocytes (T-cell-driven disease) and/or antibodies (B-cell-driven disease). Autoimmune diseases can be divided into systemic autoimmune diseases and specific organ- or body-system diseases, including the endocrine, gastro-intestinal, and neurological systems, and it's not uncommon for individuals to experience multiple autoimmune conditions simultaneously. Autoimmune diseases affect ~10% of the population (Conrad et al. 2023), causing chronic suffering, vital organ failure, and premature death at the level of cancer and cardiovascular diseases. The rising incidence of these disorders poses a significant challenge to healthcare systems, underscoring the critical need to elucidate disease mechanisms and translate these into effective diagnostic tests and therapeutics. Current therapeutic strategies are predominantly confined to symptomatic relief through replacement therapy and broad-spectrum anti-inflammatory drugs, often resulting in increased disease burden, diminished life quality, and elevated mortality rates. Most autoimmune diseases are likely a result of a combination of different genetic and environmental factors. However, there are a few exemptions, like the autoimmune polyendocrine syndrome type 1 (APS-1) caused by mutations in the Autoimmune Regulator (AIRE) gene.
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Affiliation(s)
- Anette S B Wolff
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
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6
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Bellos E, Santillo D, Vantourout P, Jackson HR, Duret A, Hearn H, Seeleuthner Y, Talouarn E, Hodeib S, Patel H, Powell O, Yeoh S, Mustafa S, Habgood-Coote D, Nichols S, Estramiana Elorrieta L, D’Souza G, Wright VJ, Estrada-Rivadeneyra D, Tremoulet AH, Dummer KB, Netea SA, Condino-Neto A, Lau YL, Núñez Cuadros E, Toubiana J, Holanda Pena M, Rieux-Laucat F, Luyt CE, Haerynck F, Mège JL, Chakravorty S, Haddad E, Morin MP, Metin Akcan Ö, Keles S, Emiroglu M, Alkan G, Tüter Öz SK, Elmas Bozdemir S, Morelle G, Volokha A, Kendir-Demirkol Y, Sözeri B, Coskuner T, Yahsi A, Gulhan B, Kanik-Yuksek S, Bayhan GI, Ozkaya-Parlakay A, Yesilbas O, Hatipoglu N, Ozcelik T, Belot A, Chopin E, Barlogis V, Sevketoglu E, Menentoglu E, Gayretli Aydin ZG, Bloomfield M, AlKhater SA, Cyrus C, Stepanovskiy Y, Bondarenko A, Öz FN, Polat M, Fremuth J, Lebl J, Geraldo A, Jouanguy E, Carter MJ, Wellman P, Peters M, Pérez de Diego R, Edwards LA, Chiu C, Noursadeghi M, Bolze A, Shimizu C, Kaforou M, Hamilton MS, Herberg JA, Schmitt EG, Rodriguez-Palmero A, Pujol A, Kim J, Cobat A, Abel L, Zhang SY, Casanova JL, Kuijpers TW, Burns JC, Levin M, Hayday AC, Sancho-Shimizu V. Heterozygous BTNL8 variants in individuals with multisystem inflammatory syndrome in children (MIS-C). J Exp Med 2024; 221:e920240699. [PMID: 39576310 PMCID: PMC11586762 DOI: 10.1084/jem.20240699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 08/27/2024] [Accepted: 09/27/2024] [Indexed: 11/24/2024] Open
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a rare condition following SARS-CoV-2 infection associated with intestinal manifestations. Genetic predisposition, including inborn errors of the OAS-RNAseL pathway, has been reported. We sequenced 154 MIS-C patients and utilized a novel statistical framework of gene burden analysis, "burdenMC," which identified an enrichment for rare predicted-deleterious variants in BTNL8 (OR = 4.2, 95% CI: 3.5-5.3, P < 10-6). BTNL8 encodes an intestinal epithelial regulator of Vγ4+γδ T cells implicated in regulating gut homeostasis. Enrichment was exclusive to MIS-C, being absent in patients with COVID-19 or bacterial disease. Using an available functional test for BTNL8, rare variants from a larger cohort of MIS-C patients (n = 835) were tested which identified eight variants in 18 patients (2.2%) with impaired engagement of Vγ4+γδ T cells. Most of these variants were in the B30.2 domain of BTNL8 implicated in sensing epithelial cell status. These findings were associated with altered intestinal permeability, suggesting a possible link between disrupted gut homeostasis and MIS-C-associated enteropathy triggered by SARS-CoV-2.
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Affiliation(s)
- Evangelos Bellos
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Dilys Santillo
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
- Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Pierre Vantourout
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London, UK
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - Heather R. Jackson
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Amedine Duret
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Henry Hearn
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Université Paris Cité, Paris, France
| | - Estelle Talouarn
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Université Paris Cité, Paris, France
| | - Stephanie Hodeib
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
- Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Harsita Patel
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Oliver Powell
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Sophya Yeoh
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Sobia Mustafa
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Dominic Habgood-Coote
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Samuel Nichols
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Leire Estramiana Elorrieta
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Giselle D’Souza
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Victoria J. Wright
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Diego Estrada-Rivadeneyra
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Adriana H. Tremoulet
- Department of Pediatrics, Kawasaki Disease Research Center, University of California San Diego, La Jolla, CA, USA
- Rady Children’s Hospital-San Diego, San Diego, CA, USA
| | - Kirsten B. Dummer
- Department of Pediatrics, Kawasaki Disease Research Center, University of California San Diego, La Jolla, CA, USA
- Rady Children’s Hospital-San Diego, San Diego, CA, USA
| | - Stejara A. Netea
- Department of Pediatric Immunology, Rheumatology and Infectious Disease, Emma Children’s Hospital, Amsterdam University Medical Center (AmsterdamUMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Antonio Condino-Neto
- Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Esmeralda Núñez Cuadros
- Department of Pediatrics, Regional University Hospital of Málaga, IBIMA Research Institute, Málaga, Spain
| | - Julie Toubiana
- Department of General Pediatrics and Infectious Diseases, Necker-Enfants Malades University Hospital, AP-HP, Université Paris Cité, Paris, France
| | | | - Frédéric Rieux-Laucat
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163-Institut Imagine, Paris, France
- Imagine Institute, Paris Descartes-Sorbonne Université Paris Cité, Paris, France
| | - Charles-Edouard Luyt
- Intensive Care Unit, AP-HP Pitié-Salpêtrière Hospital, Paris University, Paris, France
| | | | | | - Samya Chakravorty
- Biocon Bristol Myers Squibb Research and Development Center, Syngene Intl. Ltd., Bengaluru, India
- Bristol Myers Squibb, Lawrenceville, NJ, USA
- Emory University Department of Pediatrics and Human Genetics, Atlanta GA, USA
| | - Elie Haddad
- CHU Sainte-Justine Azrieli Research Center, Montreal, Canada
- Department of Microbiology, Infectious Diseases and Immunology, University of Montreal, Montreal, Canada
- Department of Pediatrics, University of Montreal, Montreal, Canada
| | | | - Özge Metin Akcan
- Division of Pediatric Infectious Diseases, Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Sevgi Keles
- Division of Pediatric Allergy and Immunology, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Melike Emiroglu
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Selcuk University Faculty of Medicine, Konya, Turkey
| | - Gulsum Alkan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Selcuk University Faculty of Medicine, Konya, Turkey
| | - Sadiye Kübra Tüter Öz
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Selcuk University Faculty of Medicine, Konya, Turkey
| | - Sefika Elmas Bozdemir
- Division of Pediatric Allergy and Immunology, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Guillaume Morelle
- Department of General Paediatrics, Hôpital Bicêtre, AP-HP, University of Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Alla Volokha
- Pediatric Infectious Disease and Pediatric Immunology Department, Shupyk National Healthcare University, Kyiv, Ukraine
| | - Yasemin Kendir-Demirkol
- Department of Pediatric Genetics, Umraniye Education and Research Hospital, Health Sciences University, İstanbul, Turkey
| | - Betul Sözeri
- Division of Pediatric Rheumatology, Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Taner Coskuner
- Division of Pediatric Rheumatology, Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Aysun Yahsi
- Department of Pediatric Infectious Diseases, Ankara City Hospital, Ankara, Turkey
| | - Belgin Gulhan
- Department of Pediatric Infectious Diseases, Ankara City Hospital, Ankara, Turkey
| | - Saliha Kanik-Yuksek
- Department of Pediatric Infectious Diseases, Ankara City Hospital, Ankara, Turkey
| | | | | | - Osman Yesilbas
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Nevin Hatipoglu
- Pediatric Infectious Diseases Unit, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Alexandre Belot
- Service de Rhumatologie Pédiatrique, Hôpital Femme-Mère-Enfant, Groupement Hospitalier Est – Bâtiment “Pinel”, Bron, France
| | - Emilie Chopin
- CBC BIOTEC Biobank, GHE, Hospices Civils de Lyon, Lyon, France
| | - Vincent Barlogis
- La Timone Children Hospital, Aix-Marseille University, APHM, Marseille, France
| | - Esra Sevketoglu
- Univeristy of Health Sciences Turkiye Bakirkoy Dr. Sadi Konuk Research and Training Hospital Pediatirc Intensive Care Department, Istanbul, Türkiye
| | - Emin Menentoglu
- Univeristy of Health Sciences Turkiye Bakirkoy Dr. Sadi Konuk Research and Training Hospital Pediatirc Intensive Care Department, Istanbul, Türkiye
| | - Zeynep Gokce Gayretli Aydin
- Division of Pediatric Infectious Disease, Department of Pediatrics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Marketa Bloomfield
- Department of Immunology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
- Department of Paediatrics, 1st Faculty of Medicine, Charles University in Prague and Thomayer University Hospital, Prague, Czech Republic
| | - Suzan A. AlKhater
- College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- Department of Pediatrics, King Fahad Hospital of the University, Al-Khobar, Saudi Arabia
| | - Cyril Cyrus
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Yuriy Stepanovskiy
- Department of Pediatrics, Immunology, Infectious, and Rare Diseases at the International European University, Kyiv, Ukraine
| | - Anastasiia Bondarenko
- Department of Pediatrics, Immunology, Infectious, and Rare Diseases at the International European University, Kyiv, Ukraine
| | - Fatma Nur Öz
- Department of Pediatric Infectious Disease, SBU Ankara Dr. Sami Ulus Maternity Child Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Meltem Polat
- Department of Pediatric Infectious Diseases, Gazi University School of Medicine, Ankara, Turkey
| | - Jiří Fremuth
- Department of Pediatrics - PICU, Faculty of Medicine in Pilsen, Charles University in Prague, Prague, Czech Republic
| | - Jan Lebl
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Amyrath Geraldo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Université Paris Cité, Paris, France
- Department of Pediatircs, Germans Trias i Pujol Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Rockefeller University, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Université Paris Cité, Paris, France
- Department of Pediatircs, Germans Trias i Pujol Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Rockefeller University, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Michael J. Carter
- Paediatric Intensive Care, Evelina London Children’s Hospital, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
- Department of Women and Children’s Health, School of Life Course Sciences, King’s College London, St Thomas’ Hospital, London, UK
| | - Paul Wellman
- Paediatric Intensive Care, Evelina London Children’s Hospital, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
| | - Mark Peters
- Paediatric Intensive Care Unit, Great Ormond Street Hospital for Children NHS Foundation Trust and NIHR Biomedical Research Centre, London, UK
- University College London Great Ormond St Institute of Child Health, London, UK
| | - Rebeca Pérez de Diego
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, University Hospital “La Paz”, Madrid, Spain
| | - Lindsey Ann Edwards
- Centre Host Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, Guy’s Tower, Guy’s Hospital, London, UK
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | | | - Chisato Shimizu
- Department of Pediatrics, Kawasaki Disease Research Center, University of California San Diego, La Jolla, CA, USA
- Rady Children’s Hospital-San Diego, San Diego, CA, USA
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Melissa Shea Hamilton
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Jethro A. Herberg
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Erica G. Schmitt
- Division of Rheumatology and Immunology, Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA
| | - Agusti Rodriguez-Palmero
- Department of Pediatircs, Germans Trias i Pujol Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Centre for Biomedical Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Centre for Biomedical Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
- Catalan Institution of Research and Advanced Studies, Barcelona, Spain
| | - Jihoon Kim
- Department of Biomedical Informatics, University of California, San Diego, CA, USA
- Section of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Université Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Université Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Université Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163 Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Université Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Rockefeller University, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Taco W. Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Disease, Emma Children’s Hospital, Amsterdam University Medical Center (AmsterdamUMC), University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Hematology, Sanquin Research and Landsteiner Laboratory at the AmsterdamUMC, Amsterdam Institute for Infection and Immunity, AmsterdamUMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jane C. Burns
- Department of Pediatrics, Kawasaki Disease Research Center, University of California San Diego, La Jolla, CA, USA
- Rady Children’s Hospital-San Diego, San Diego, CA, USA
| | - Michael Levin
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Adrian C. Hayday
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London, UK
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - Vanessa Sancho-Shimizu
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
- Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
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Liu Y, Bao L, Sodha D, Li J, Mansini A, Djalilian AR, Li X, Qian H, Ishii N, Hashimoto T, Amber KT. Ocular Mucous Membrane Pemphigoid Demonstrates a Distinct Autoantibody Profile from Those of Other Autoimmune Blistering Diseases: A Preliminary Study. Antibodies (Basel) 2024; 13:91. [PMID: 39584991 PMCID: PMC11586953 DOI: 10.3390/antib13040091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 10/28/2024] [Accepted: 11/08/2024] [Indexed: 11/26/2024] Open
Abstract
Background: Ocular predominant mucous membrane pemphigoid (oMMP) is a severe subtype of autoimmune blistering disease (AIBD), which can result in scarring and vision loss. The diagnosis of oMMP is challenging as patients often have undetectable levels of circulating autoantibodies by conventional assays. Likewise, the principal autoantigen in oMMP has been an area of debate. Methods: In this preliminary experiment, we performed Phage Immunoprecipitation Sequencing (PhIP-seq) on sera from patients with oMMP, as well as non-ocular MMP, bullous pemphigoid, and mucocutaneous-type pemphigus vulgaris. Results: We identified several autoantigens unique to oMMP relative to other AIBDs. We then cross-referenced these antigens against previously published single-nuclei datasets, as well as the International Mouse Phenotyping Consortium Database. Several protein hits identified in our study demonstrated enriched expression on the anterior surface epithelia, including TNKS1BP1, SEC16B, FNBP4, CASZ1, GOLGB1, DOT1L, PRDM 15, LARP4B, and RPL6. Likewise, a previous study of mouse knockout models of murine analogs CASZ1, HIP1, and ELOA2 reported that these mice showed abnormalities in terms of the ocular surface and development in the eyes. Notably, PhIP-seq failed to identify the canonical markers of AIBDs such as BP180, BP230, desmogleins 1 and 3, or integrin β4, indicating that the patient autoantibodies react with conformational epitopes rather than linear epitopes. Conclusions: oMMP patients demonstrate a unique autoantibody repertoire relative to the other AIBDs. Further validation of the identified autoantibodies will shed light on their potentially pathogenic role.
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Affiliation(s)
- Yingzi Liu
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92617, USA
| | - Lei Bao
- Department of Dermatology, Rush University Medical Center, Chicago, IL 60612, USA
| | - Dharm Sodha
- Department of Dermatology, Rush University Medical Center, Chicago, IL 60612, USA
| | - Jing Li
- Department of Dermatology, Rush University Medical Center, Chicago, IL 60612, USA
| | - Adrian Mansini
- Department of Dermatology, Rush University Medical Center, Chicago, IL 60612, USA
| | - Ali R. Djalilian
- Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Xiaoguang Li
- Central Laboratory, Dermatology Hospital of Jiangxi Province, Dermatology Institute of Jiangxi Province, and the Affiliated Dermatology Hospital of Nanchang University, Nanchang 331332, China
| | - Hua Qian
- Central Laboratory, Dermatology Hospital of Jiangxi Province, Dermatology Institute of Jiangxi Province, and the Affiliated Dermatology Hospital of Nanchang University, Nanchang 331332, China
| | - Norito Ishii
- Department of Dermatology, Kurume University School of Medicine, Kurume University Institute of Cutaneous Cell Biology, Kurume 830-0011, Japan
| | - Takashi Hashimoto
- Department of Dermatology, Graduate School of Medicine, Osaka Metropolitan University, Osaka 545-8585, Japan
| | - Kyle T. Amber
- Department of Dermatology, Rush University Medical Center, Chicago, IL 60612, USA
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8
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Li LY, Keles A, Homeyer MA, Prüss H. Antibodies in neurological diseases: Established, emerging, explorative. Immunol Rev 2024; 328:283-299. [PMID: 39351782 PMCID: PMC11659937 DOI: 10.1111/imr.13405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2024]
Abstract
Within a few years, autoantibodies targeting the nervous system resulted in a novel disease classification. For several of them, which we termed 'established', direct pathogenicity has been proven and now guides diagnostic pathways and early immunotherapy. For a rapidly growing number of further anti-neuronal autoantibodies, the role in disease is less clear. Increasing evidence suggests that they could contribute to disease, by playing a modulating role on brain function. We therefore suggest a three-level classification of neurological autoantibodies according to the degree of experimentally proven pathogenicity and strength of clinical association: established, emerging, explorative. This may facilitate focusing on clinical constellations in which autoantibody-mediated mechanisms have not been assumed previously, including autoimmune psychosis and dementia, cognitive impairment in cancer, and neurodegenerative diseases. Based on recent data reviewed here, humoral autoimmunity may represent an additional "super-system" for brain health. The "brain antibody-ome", that is, the composition of thousands of anti-neuronal autoantibodies, may shape neuronal function not only in disease, but even in healthy aging. Towards this novel concept, extensive research will have to elucidate pathogenicity from the atomic to the clinical level, autoantibody by autoantibody. Such profiling can uncover novel biomarkers, enhance our understanding of underlying mechanisms, and identify selective therapies.
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Affiliation(s)
- Lucie Y. Li
- Department of Neurology and Experimental NeurologyCharité – Universitätsmedizin BerlinBerlinGermany
- German Center for Neurodegenerative Diseases (DZNE) BerlinBerlinGermany
| | - Amelya Keles
- Department of Neurology and Experimental NeurologyCharité – Universitätsmedizin BerlinBerlinGermany
- German Center for Neurodegenerative Diseases (DZNE) BerlinBerlinGermany
| | - Marie A. Homeyer
- Department of Neurology and Experimental NeurologyCharité – Universitätsmedizin BerlinBerlinGermany
- German Center for Neurodegenerative Diseases (DZNE) BerlinBerlinGermany
| | - Harald Prüss
- Department of Neurology and Experimental NeurologyCharité – Universitätsmedizin BerlinBerlinGermany
- German Center for Neurodegenerative Diseases (DZNE) BerlinBerlinGermany
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9
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Klepper A, Asaki J, Kung AF, Vazquez SE, Bodansky A, Mitchell A, Mann SA, Zorn K, Avila-Vargas I, Kari S, Tekeste M, Castro J, Lee B, Duarte M, Khalili M, Yang M, Wolters P, Price J, Perito E, Feng S, Maher JJ, Lai JC, Weiler-Normann C, Lohse AW, DeRisi J, Tana M. Novel autoantibody targets identified in patients with autoimmune hepatitis (AIH) by PhIP-Seq reveals pathogenic insights. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.06.12.23291297. [PMID: 37398174 PMCID: PMC10312872 DOI: 10.1101/2023.06.12.23291297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Background and Aims Autoimmune hepatitis (AIH) is a severe disease characterized by elevated immunoglobin levels. However, the role of autoantibodies in the pathophysiology of AIH remains uncertain. Methods Phage Immunoprecipitation-Sequencing (PhIP-seq) was employed to identify autoantibodies in the serum of patients with AIH (n = 115), compared to patients with other liver diseases (metabolic associated steatotic liver disease (MASH) n = 178, primary biliary cholangitis (PBC), n = 26, or healthy controls, n = 94). Results Logistic regression using PhIP-seq enriched peptides as inputs yielded a classification AUC of 0.81, indicating the presence of a predictive humoral immune signature for AIH. Embedded within this signature were disease relevant targets, including SLA/LP, the target of a well-recognized autoantibody in AIH, disco interacting protein 2 homolog A (DIP2A), and the relaxin family peptide receptor 1 (RXFP1). The autoreactive fragment of DIP2A was a 9-amino acid stretch nearly identical to the U27 protein of human herpes virus 6 (HHV-6). Fine mapping of this epitope suggests the HHV-6 U27 sequence is preferentially enriched relative to the corresponding DIP2A sequence. Antibodies against RXFP1, a receptor involved in anti-fibrotic signaling, were also highly specific to AIH. The enriched peptides are within a motif adjacent to the receptor binding domain, required for signaling and serum from AIH patients positive for anti-RFXP1 antibody was able to significantly inhibit relaxin-2 singling. Depletion of IgG from anti-RXFP1 positive serum abrogated this effect. Conclusions These data provide evidence for a novel serological profile in AIH, including a possible functional role for anti-RXFP1, and antibodies that cross react with HHV6 U27 protein.
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Affiliation(s)
- Arielle Klepper
- Department of Medicine, University of California, San Francisco, USA
- UCSF Liver Center
| | - James Asaki
- Department of Biochemistry, University of California, San Francisco, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, USA
| | - Andrew F Kung
- Department of Biochemistry, University of California, San Francisco, USA
| | - Sara E Vazquez
- Department of Dermatology, Mass General Hospital, Boston, MA
| | - Aaron Bodansky
- Department of Pediatrics, University of California, San Francisco, USA
| | | | - Sabrina A Mann
- Department of Biochemistry, University of California, San Francisco, USA
- Chan Zuckerberg Biohub; San Francisco, CA, USA
| | - Kelsey Zorn
- Department of Biochemistry, University of California, San Francisco, USA
| | | | - Swathi Kari
- Department of Medicine, University of California, San Francisco, USA
| | - Melawit Tekeste
- Department of Medicine, University of California, San Francisco, USA
| | - Javier Castro
- Department of Medicine, University of California, San Francisco, USA
| | - Briton Lee
- Department of Medicine, University of California, San Francisco, USA
| | - Maria Duarte
- Department of Medicine, University of California, San Francisco, USA
- UCSF Liver Center
| | - Mandana Khalili
- Department of Medicine, University of California, San Francisco, USA
- UCSF Liver Center
| | - Monica Yang
- Department of Medicine, University of California, San Francisco, USA
| | - Paul Wolters
- Department of Medicine, University of California, San Francisco, USA
| | - Jennifer Price
- Department of Medicine, University of California, San Francisco, USA
- UCSF Liver Center
| | - Emily Perito
- Department of Pediatrics, University of California, San Francisco, USA
- UCSF Liver Center
| | - Sandy Feng
- Department of Surgery, University of California, San Francisco, USA
- UCSF Liver Center
| | - Jacquelyn J Maher
- Department of Medicine, University of California, San Francisco, USA
- UCSF Liver Center
| | - Jennifer C Lai
- Department of Medicine, University of California, San Francisco, USA
- UCSF Liver Center
| | | | - Ansgar W Lohse
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joseph DeRisi
- Department of Biochemistry, University of California, San Francisco, USA
- Chan Zuckerberg Biohub; San Francisco, CA, USA
| | - Michele Tana
- Department of Medicine, University of California, San Francisco, USA
- UCSF Liver Center
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10
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Agarwal S, Bodansky A, Xing C, Anderson MS, Garg A. Partial Lipodystrophy Affecting the Extremities in a Young Woman With Autoimmune Polyglandular Syndrome 1. JCEM CASE REPORTS 2024; 2:luae166. [PMID: 39318439 PMCID: PMC11421462 DOI: 10.1210/jcemcr/luae166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Indexed: 09/26/2024]
Abstract
Autoimmune polyglandular syndrome 1 (APS1) is an autosomal recessive disorder due to biallelic pathogenic variants in the autoimmune regulator (AIRE) gene that manifests with chronic mucocutaneous candidiasis, primary hypoparathyroidism, and adrenal insufficiency. We report a 39-year-old woman with APS1 who developed partial lipodystrophy during adulthood. She presented with diaper rashes, oral thrush, and tetany during infancy due to candidiasis and hypoparathyroidism. During childhood, she developed hypothyroidism, primary adrenal insufficiency, and ovarian insufficiency. At age 14, she received a sibling-matched allogenic bone marrow transplant due to multiple antibiotic-refractory fungal infections. At age 35, her serum triglycerides were 914 mg/dL (10.32 mmol/L) and she had loss of subcutaneous fat from the upper and lower extremities and hips. A whole-body dual-energy x-ray absorptiometry revealed lower-extremity fat at less than the first percentile. Whole-exome sequencing on DNA extracted from saliva revealed pathogenic variants, p.Leu28Pro and p.Arg257* in AIRE but none in the known lipodystrophy genes. Phage-immunoprecipitation-sequencing revealed the presence of autoantibodies to MAGEB1, MAGEB4, and RFX6, which have been previously reported in APS1. Our case suggests that patients with APS1 may develop partial lipodystrophy due to autoantibodies against novel adipocyte-expressed proteins. A causal relationship of high levels of autoantibodies in our patient to adipose tissue-expressed ODC1, NUCKS1, or FNBP1L and lipodystrophy remains uncertain.
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Affiliation(s)
- Shubham Agarwal
- Division of Endocrinology, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390-8537, USA
| | - Aaron Bodansky
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Chao Xing
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Peter O’Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Abhimanyu Garg
- Division of Endocrinology, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390-8537, USA
- Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX 75390, USA
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11
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Mosavie M, Rynne J, Fish M, Smith P, Jennings A, Singh S, Millar J, Harvala H, Mora A, Kaloyirou F, Griffiths A, Hopkins V, Washington C, Estcourt LJ, Roberts D, Shankar-Hari M. Changes in Phenotypic and Molecular Features of Naïve and Central Memory T Helper Cell Subsets following SARS-CoV-2 Vaccination. Vaccines (Basel) 2024; 12:1040. [PMID: 39340069 PMCID: PMC11435719 DOI: 10.3390/vaccines12091040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 09/02/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024] Open
Abstract
Molecular changes in lymphocytes following SARS-CoV-2 vaccination are incompletely understood. We hypothesized that studying the molecular (transcriptomic, epigenetic, and T cell receptor (TCR) repertoire) changes in CD4+ T cells following SARS-CoV-2 vaccination could inform protective mechanisms and refinement of future vaccines. We tested this hypothesis by reporting alterations in CD4+ T cell subsets and molecular features of CD4+ naïve and CD4+ central memory (CM) subsets between the unvaccinated and vaccinated groups. Compared with the unvaccinated, the vaccinated had higher HLA-DR expression in CD4+ T subsets, a greater number of differentially expressed genes (DEGs) that overlapped with key differentially accessible regions (DARs) along the chromatin linked to inflammasome activation, translation, regulation (of apoptosis, inflammation), and significant changes in clonal architecture beyond SARS-CoV-2 specificity. Several of these differences were more pronounced in the CD4+CM subset. Taken together, our observations imply that the COVID-19 vaccine exerts its protective effects via modulation of acute inflammation to SARS-CoV-2 challenge.
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Affiliation(s)
- Mia Mosavie
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, 4-5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Jennifer Rynne
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, 4-5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Matthew Fish
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Peter Smith
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, 4-5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Aislinn Jennings
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, 4-5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Shivani Singh
- Department of Medicine, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London W6 8RF, UK
| | - Jonathan Millar
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, 4-5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Heli Harvala
- Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
- Microbiology Services, Colindale, NHS Blood and Transplant, Colindale NW9 5BG, UK
| | - Ana Mora
- Heart Lung Research Institute Clinical Research Facility, Cambridge CB2 0BB, UK
| | - Fotini Kaloyirou
- Statistics and Clinical Research, NHS Blood and Transplant, Cambridge CB2 0PT, UK
| | - Alexandra Griffiths
- Statistics and Clinical Research, NHS Blood and Transplant, Bristol BS34 7QH, UK
| | - Valerie Hopkins
- Statistics and Clinical Research, NHS Blood and Transplant, Cambridge CB2 0PT, UK
| | | | - Lise J Estcourt
- Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - David Roberts
- Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Manu Shankar-Hari
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, 4-5 Little France Drive, Edinburgh EH16 4UU, UK
- Department of Critical Care Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
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12
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Huang Z, Gunarathne SMS, Liu W, Zhou Y, Jiang Y, Li S, Huang J. PhIP-Seq: methods, applications and challenges. FRONTIERS IN BIOINFORMATICS 2024; 4:1424202. [PMID: 39295784 PMCID: PMC11408297 DOI: 10.3389/fbinf.2024.1424202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 08/22/2024] [Indexed: 09/21/2024] Open
Abstract
Phage-immunoprecipitation sequencing (PhIP-Seq) technology is an innovative, high-throughput antibody detection method. It enables comprehensive analysis of individual antibody profiles. This technology shows great potential, particularly in exploring disease mechanisms and immune responses. Currently, PhIP-Seq has been successfully applied in various fields, such as the exploration of biomarkers for autoimmune diseases, vaccine development, and allergen detection. A variety of bioinformatics tools have facilitated the development of this process. However, PhIP-Seq technology still faces many challenges and has room for improvement. Here, we review the methods, applications, and challenges of PhIP-Seq and discuss its future directions in immunological research and clinical applications. With continuous progress and optimization, PhIP-Seq is expected to play an even more important role in future biomedical research, providing new ideas and methods for disease prevention, diagnosis, and treatment.
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Affiliation(s)
- Ziru Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | | | - Wenwen Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuwei Zhou
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuqing Jiang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Shiqi Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
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13
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Deguine J, Xavier RJ. B cell tolerance and autoimmunity: Lessons from repertoires. J Exp Med 2024; 221:e20231314. [PMID: 39093312 PMCID: PMC11296956 DOI: 10.1084/jem.20231314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
Adaptive immune cell function is regulated by a highly diverse receptor recombined from variable germline-encoded segments that can recognize an almost unlimited array of epitopes. While this diversity enables the recognition of any pathogen, it also poses a risk of self-recognition, leading to autoimmunity. Many layers of regulation are present during both the generation and activation of B cells to prevent this phenomenon, although they are evidently imperfect. In recent years, our ability to analyze immune repertoires at scale has drastically increased, both through advances in sequencing and single-cell analyses. Here, we review the current knowledge on B cell repertoire analyses, focusing on their implication for autoimmunity. These studies demonstrate that a failure of tolerance occurs at multiple independent checkpoints in different autoimmune contexts, particularly during B cell maturation, plasmablast differentiation, and within germinal centers. These failures are marked by distinct repertoire features that may be used to identify disease- or patient-specific therapeutic approaches.
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Affiliation(s)
- Jacques Deguine
- Immunology Program, Broad Institute of Massachusetts Institute of Technology and Harvard , Cambridge, MA, USA
| | - Ramnik J Xavier
- Immunology Program, Broad Institute of Massachusetts Institute of Technology and Harvard , Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School , Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
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14
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Upadhyay V, Yoon YM, Vazquez SE, Velez TE, Jones KD, Lee CT, Law CS, Wolters PJ, Lee S, Yang MM, Farrand E, Noth I, Strek ME, Anderson MS, DeRisi JL, Sperling AI, Shum AK. Phage Immunoprecipitation-Sequencing Reveals CDHR5 Autoantibodies in Select Patients With Interstitial Lung Disease. ACR Open Rheumatol 2024; 6:568-580. [PMID: 38952015 PMCID: PMC11506559 DOI: 10.1002/acr2.11696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/10/2024] [Accepted: 04/26/2024] [Indexed: 07/03/2024] Open
Abstract
OBJECTIVE Interstitial lung diseases (ILDs) are a heterogeneous group of disorders that can develop in patients with connective tissue diseases. Establishing autoimmunity in ILD impacts prognosis and treatment. Patients with ILD are screened for autoimmunity by measuring antinuclear autoantibodies, rheumatoid factors, and other nonspecific tests. However, this approach may miss autoimmunity that manifests as autoantibodies to tissue antigens not previously defined in ILD. METHODS We use Phage Immunoprecipitation-Sequencing (PhIP-Seq) to conduct an autoantibody discovery screen of patients with ILD and controls. We screened for novel autoantigen candidates using PhIP-Seq. We next developed a radio-labeled binding assay and validated the leading candidate in 398 patients with ILD recruited from two academic medical centers and 138 blood bank individuals that formed our reference cohort. RESULTS PhIP-Seq identified 17 novel autoreactive targets, and machine learning classifiers derived from these targets discriminated ILD serum from controls. Among the 17 candidates, we validated CDHR5 and found CDHR5 autoantibodies in patients with rheumatologic disorders and importantly, patients not previously diagnosed with autoimmunity. Using survival and transplant free-survival data available from one of the two centers, patients with CDHR5 autoantibodies showed worse survival compared with other patients with connective tissue disease ILD. CONCLUSION We used PhIP-Seq to define a novel CDHR5 autoantibody in a subset of select patients with ILD. Our data complement a recent study showing polymorphisms in the CDHR5-IRF7 gene locus strongly associated with titer of anticentromere antibodies in systemic sclerosis, creating a growing body of evidence suggesting a link between CDHR5 and autoimmunity.
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Affiliation(s)
| | | | - Sara E. Vazquez
- University of California San Francisco and Chan Zuckerberg Biohub
| | - Tania E. Velez
- University of Chicago, Illinois, and University of VirginiaCharlottesville
| | | | | | | | | | | | | | | | - Imre Noth
- University of VirginiaCharlottesville
| | | | | | - Joseph L. DeRisi
- University of California San Francisco and Chan Zuckerberg Biohub
| | - Anne I. Sperling
- University of Chicago, Illinois, and University of VirginiaCharlottesville
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15
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Sundell GN, Tao SC. Phage Immunoprecipitation and Sequencing-a Versatile Technique for Mapping the Antibody Reactome. Mol Cell Proteomics 2024; 23:100831. [PMID: 39168282 PMCID: PMC11417174 DOI: 10.1016/j.mcpro.2024.100831] [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: 04/10/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024] Open
Abstract
Characterizing the antibody reactome for circulating antibodies provide insight into pathogen exposure, allergies, and autoimmune diseases. This is important for biomarker discovery, clinical diagnosis, and prognosis of disease progression, as well as population-level insights into the immune system. The emerging technology phage display immunoprecipitation and sequencing (PhIP-seq) is a high-throughput method for identifying antigens/epitopes of the antibody reactome. In PhIP-seq, libraries with sequences of defined lengths and overlapping segments are bioinformatically designed using naturally occurring proteins and cloned into phage genomes to be displayed on the surface. These libraries are used in immunoprecipitation experiments of circulating antibodies. This can be done with parallel samples from multiple sources, and the DNA inserts from the bound phages are barcoded and subjected to next-generation sequencing for hit determination. PhIP-seq is a powerful technique for characterizing the antibody reactome that has undergone rapid advances in recent years. In this review, we comprehensively describe the history of PhIP-seq and discuss recent advances in library design and applications.
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Affiliation(s)
- Gustav N Sundell
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.
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16
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Bodansky A, Mettelman RC, Sabatino JJ, Vazquez SE, Chou J, Novak T, Moffitt KL, Miller HS, Kung AF, Rackaityte E, Zamecnik CR, Rajan JV, Kortbawi H, Mandel-Brehm C, Mitchell A, Wang CY, Saxena A, Zorn K, Yu DJL, Pogorelyy MV, Awad W, Kirk AM, Asaki J, Pluvinage JV, Wilson MR, Zambrano LD, Campbell AP, Thomas PG, Randolph AG, Anderson MS, DeRisi JL. Molecular mimicry in multisystem inflammatory syndrome in children. Nature 2024; 632:622-629. [PMID: 39112696 PMCID: PMC11324515 DOI: 10.1038/s41586-024-07722-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/14/2024] [Indexed: 08/16/2024]
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a severe, post-infectious sequela of SARS-CoV-2 infection1,2, yet the pathophysiological mechanism connecting the infection to the broad inflammatory syndrome remains unknown. Here we leveraged a large set of samples from patients with MIS-C to identify a distinct set of host proteins targeted by patient autoantibodies including a particular autoreactive epitope within SNX8, a protein involved in regulating an antiviral pathway associated with MIS-C pathogenesis. In parallel, we also probed antibody responses from patients with MIS-C to the complete SARS-CoV-2 proteome and found enriched reactivity against a distinct domain of the SARS-CoV-2 nucleocapsid protein. The immunogenic regions of the viral nucleocapsid and host SNX8 proteins bear remarkable sequence similarity. Consequently, we found that many children with anti-SNX8 autoantibodies also have cross-reactive T cells engaging both the SNX8 and the SARS-CoV-2 nucleocapsid protein epitopes. Together, these findings suggest that patients with MIS-C develop a characteristic immune response to the SARS-CoV-2 nucleocapsid protein that is associated with cross-reactivity to the self-protein SNX8, demonstrating a mechanistic link between the infection and the inflammatory syndrome, with implications for better understanding a range of post-infectious autoinflammatory diseases.
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Affiliation(s)
- Aaron Bodansky
- Department of Pediatrics, Division of Critical Care, University of California San Francisco, San Francisco, CA, USA
| | - Robert C Mettelman
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Joseph J Sabatino
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Sara E Vazquez
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Janet Chou
- Division of Immunology, Department of Pediatrics, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Tanya Novak
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Anesthesia, Harvard Medical School, Boston, MA, USA
| | - Kristin L Moffitt
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatric, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Haleigh S Miller
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, CA, USA
| | - Andrew F Kung
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, CA, USA
| | - Elze Rackaityte
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Colin R Zamecnik
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Jayant V Rajan
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Hannah Kortbawi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Aditi Saxena
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - David J L Yu
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mikhail V Pogorelyy
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Walid Awad
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Allison M Kirk
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - James Asaki
- Biomedical Sciences Program, University of California San Francisco, San Francisco, CA, USA
| | - John V Pluvinage
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Laura D Zambrano
- COVID-19 Response Team and Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Angela P Campbell
- COVID-19 Response Team and Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Paul G Thomas
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adrienne G Randolph
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Anesthesia, Harvard Medical School, Boston, MA, USA
| | - Mark S Anderson
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Francisco, San Francisco, CA, USA.
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA.
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17
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Apoorva, Singh SK. A tale of endurance: bats, viruses and immune dynamics. Future Microbiol 2024; 19:841-856. [PMID: 38648093 PMCID: PMC11382704 DOI: 10.2217/fmb-2023-0233] [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: 10/21/2023] [Accepted: 02/09/2024] [Indexed: 04/25/2024] Open
Abstract
The emergence of highly zoonotic viral infections has propelled bat research forward. The viral outbreaks including Hendra virus, Nipah virus, Marburg virus, Ebola virus, Rabies virus, Middle East respiratory syndrome coronavirus, SARS-CoV and the latest SARS-CoV-2 have been epidemiologically linked to various bat species. Bats possess unique immunological characteristics that allow them to serve as a potential viral reservoir. Bats are also known to protect themselves against viruses and maintain their immunity. Therefore, there is a need for in-depth understanding into bat-virus biology to unravel the major factors contributing to the coexistence and spread of viruses.
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Affiliation(s)
- Apoorva
- Molecular Biology Unit, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Sunit Kumar Singh
- Molecular Biology Unit, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
- Dr. B R Ambedkar Center for Biomedical Research, University of Delhi (North Campus), New Delhi, 110007, India
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18
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Bodansky A, Yu DJ, Rallistan A, Kalaycioglu M, Boonyaratanakornkit J, Green DJ, Gauthier J, Turtle CJ, Zorn K, O’Donovan B, Mandel-Brehm C, Asaki J, Kortbawi H, Kung AF, Rackaityte E, Wang CY, Saxena A, de Dios K, Masi G, Nowak RJ, O’Connor KC, Li H, Diaz VE, Saloner R, Casaletto KB, Gontrum EQ, Chan B, Kramer JH, Wilson MR, Utz PJ, Hill JA, Jackson SW, Anderson MS, DeRisi JL. Unveiling the proteome-wide autoreactome enables enhanced evaluation of emerging CAR T cell therapies in autoimmunity. J Clin Invest 2024; 134:e180012. [PMID: 38753445 PMCID: PMC11213466 DOI: 10.1172/jci180012] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024] Open
Abstract
Given the global surge in autoimmune diseases, it is critical to evaluate emerging therapeutic interventions. Despite numerous new targeted immunomodulatory therapies, comprehensive approaches to apply and evaluate the effects of these treatments longitudinally are lacking. Here, we leveraged advances in programmable-phage immunoprecipitation methodology to explore the modulation, or lack thereof, of autoantibody profiles, proteome-wide, in both health and disease. Using a custom set of over 730,000 human-derived peptides, we demonstrated that each individual, regardless of disease state, possesses a distinct and complex constellation of autoreactive antibodies. For each individual, the set of resulting autoreactivites constituted a unique immunological fingerprint, or "autoreactome," that was remarkably stable over years. Using the autoreactome as a primary output, we evaluated the relative effectiveness of various immunomodulatory therapies in altering autoantibody repertoires. We found that therapies targeting B cell maturation antigen (BCMA) profoundly altered an individual's autoreactome, while anti-CD19 and anti-CD20 therapies had minimal effects. These data both confirm that the autoreactome comprises autoantibodies secreted by plasma cells and strongly suggest that BCMA or other plasma cell-targeting therapies may be highly effective in treating currently refractory autoantibody-mediated diseases.
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Affiliation(s)
- Aaron Bodansky
- Department of Pediatrics, Division of Critical Care, and
| | - David J.L. Yu
- Diabetes Center, School of Medicine, UCSF, San Francisco, California, USA
| | - Alysa Rallistan
- Department of Medicine, Division of Immunology and Rheumatology, and
| | - Muge Kalaycioglu
- Institute of Immunity, Transplantation, and Infection, Stanford University, Stanford, California, USA
| | - Jim Boonyaratanakornkit
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
- University of Washington School of Medicine, Seattle, Washington, USA
| | - Damian J. Green
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
- University of Washington School of Medicine, Seattle, Washington, USA
| | - Jordan Gauthier
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
- University of Washington School of Medicine, Seattle, Washington, USA
| | - Cameron J. Turtle
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
- University of Washington School of Medicine, Seattle, Washington, USA
| | | | | | | | | | - Hannah Kortbawi
- Department of Biochemistry and Biophysics
- Medical Scientist Training Program, and
| | - Andrew F. Kung
- Department of Biochemistry and Biophysics
- Biological and Medical Informatics Program, UCSF, San Francisco, California, USA
| | | | - Chung-Yu Wang
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, USA
| | - Aditi Saxena
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, USA
| | - Kimberly de Dios
- Diabetes Center, School of Medicine, UCSF, San Francisco, California, USA
| | - Gianvito Masi
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Richard J. Nowak
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Kevin C. O’Connor
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Hao Li
- Department of Biochemistry and Biophysics
| | - Valentina E. Diaz
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences
| | - Rowan Saloner
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences
| | - Kaitlin B. Casaletto
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences
| | - Eva Q. Gontrum
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences
| | - Brandon Chan
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences
| | - Joel H. Kramer
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences
| | - Michael R. Wilson
- Weill Institute for Neurosciences, and
- Department of Neurology, UCSF, San Francisco, California, USA
| | - Paul J. Utz
- Department of Medicine, Division of Immunology and Rheumatology, and
| | - Joshua A. Hill
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
- University of Washington School of Medicine, Seattle, Washington, USA
| | - Shaun W. Jackson
- Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
- Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Mark S. Anderson
- Diabetes Center, School of Medicine, UCSF, San Francisco, California, USA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, USA
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19
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Zamecnik CR, Sowa GM, Abdelhak A, Dandekar R, Bair RD, Wade KJ, Bartley CM, Kizer K, Augusto DG, Tubati A, Gomez R, Fouassier C, Gerungan C, Caspar CM, Alexander J, Wapniarski AE, Loudermilk RP, Eggers EL, Zorn KC, Ananth K, Jabassini N, Mann SA, Ragan NR, Santaniello A, Henry RG, Baranzini SE, Zamvil SS, Sabatino JJ, Bove RM, Guo CY, Gelfand JM, Cuneo R, von Büdingen HC, Oksenberg JR, Cree BAC, Hollenbach JA, Green AJ, Hauser SL, Wallin MT, DeRisi JL, Wilson MR. An autoantibody signature predictive for multiple sclerosis. Nat Med 2024; 30:1300-1308. [PMID: 38641750 PMCID: PMC11980355 DOI: 10.1038/s41591-024-02938-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Although B cells are implicated in multiple sclerosis (MS) pathophysiology, a predictive or diagnostic autoantibody remains elusive. In this study, the Department of Defense Serum Repository (DoDSR), a cohort of over 10 million individuals, was used to generate whole-proteome autoantibody profiles of hundreds of patients with MS (PwMS) years before and subsequently after MS onset. This analysis defines a unique cluster in approximately 10% of PwMS who share an autoantibody signature against a common motif that has similarity with many human pathogens. These patients exhibit antibody reactivity years before developing MS symptoms and have higher levels of serum neurofilament light (sNfL) compared to other PwMS. Furthermore, this profile is preserved over time, providing molecular evidence for an immunologically active preclinical period years before clinical onset. This autoantibody reactivity was validated in samples from a separate incident MS cohort in both cerebrospinal fluid and serum, where it is highly specific for patients eventually diagnosed with MS. This signature is a starting point for further immunological characterization of this MS patient subset and may be clinically useful as an antigen-specific biomarker for high-risk patients with clinically or radiologically isolated neuroinflammatory syndromes.
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Affiliation(s)
- Colin R Zamecnik
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Gavin M Sowa
- University of California, San Francisco School of Medicine, San Francisco, CA, USA
- Department of Medicine, McGaw Medical Center of Northwestern University, Chicago, IL, USA
| | - Ahmed Abdelhak
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Ravi Dandekar
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Rebecca D Bair
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kristen J Wade
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher M Bartley
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kerry Kizer
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Danillo G Augusto
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Asritha Tubati
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Refujia Gomez
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Camille Fouassier
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Chloe Gerungan
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Colette M Caspar
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jessica Alexander
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Anne E Wapniarski
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Rita P Loudermilk
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Erica L Eggers
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Kirtana Ananth
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Nora Jabassini
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Sabrina A Mann
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA
| | - Nicholas R Ragan
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Adam Santaniello
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Roland G Henry
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Sergio E Baranzini
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Scott S Zamvil
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph J Sabatino
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Riley M Bove
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Chu-Yueh Guo
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey M Gelfand
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Richard Cuneo
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - H-Christian von Büdingen
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jorge R Oksenberg
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Bruce A C Cree
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jill A Hollenbach
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Ari J Green
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen L Hauser
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mitchell T Wallin
- Department of Veterans Affairs, Multiple Sclerosis Center of Excellence, Washington, DC, USA
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA
| | - Michael R Wilson
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
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20
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Peel JN, Yang R, Le Voyer T, Gervais A, Rosain J, Bastard P, Behere A, Cederholm A, Bodansky A, Seeleuthner Y, Conil C, Ding JY, Lei WT, Bizien L, Soudee C, Migaud M, Ogishi M, Yatim A, Lee D, Bohlen J, Perpoint T, Perez L, Messina F, Genet R, Karkowski L, Blot M, Lafont E, Toullec L, Goulvestre C, Mehlal-Sedkaoui S, Sallette J, Martin F, Puel A, Jouanguy E, CONSTANCES cohort, 3C-Dijon Study, Etablissement du Sang study group, Anderson MS, Landegren N, Tiberghien P, Abel L, Boisson-Dupuis S, Bustamante J, Ku CL, Casanova JL. Neutralizing IFN-γ autoantibodies are rare and pathogenic in HLA-DRB1*15:02 or 16:02 individuals. J Clin Invest 2024; 134:e178263. [PMID: 38470480 PMCID: PMC11014650 DOI: 10.1172/jci178263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/01/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUNDWeakly virulent environmental mycobacteria (EM) can cause severe disease in HLA-DRB1*15:02 or 16:02 adults harboring neutralizing anti-IFN-γ autoantibodies (nAIGAs). The overall prevalence of nAIGAs in the general population is unknown, as are the penetrance of nAIGAs in HLA-DRB1*15:02 or 16:02 individuals and the proportion of patients with unexplained, adult-onset EM infections carrying nAIGAs.METHODSThis study analyzed the detection and neutralization of anti-IFN-γ autoantibodies (auto-Abs) from 8,430 healthy individuals of the general population, 257 HLA-DRB1*15:02 or 16:02 carriers, 1,063 patients with autoimmune disease, and 497 patients with unexplained severe disease due to EM.RESULTSWe found that anti-IFN-γ auto-Abs detected in 4,148 of 8,430 healthy individuals (49.2%) from the general population of an unknown HLA-DRB1 genotype were not neutralizing. Moreover, we did not find nAIGAs in 257 individuals carrying HLA-DRB1* 15:02 or 16:02. Additionally, nAIGAs were absent in 1,063 patients with an autoimmune disease. Finally, 7 of 497 patients (1.4%) with unexplained severe disease due to EM harbored nAIGAs.CONCLUSIONThese findings suggest that nAIGAs are isolated and that their penetrance in HLA-DRB1*15:02 or 16:02 individuals is low, implying that they may be triggered by rare germline or somatic variants. In contrast, the risk of mycobacterial disease in patients with nAIGAs is high, confirming that these nAIGAs are the cause of EM disease.FUNDINGThe Laboratory of Human Genetics of Infectious Diseases is supported by the Howard Hughes Medical Institute, the Rockefeller University, the St. Giles Foundation, the National Institutes of Health (NIH) (R01AI095983 and U19AIN1625568), the National Center for Advancing Translational Sciences (NCATS), the NIH Clinical and Translational Science Award (CTSA) program (UL1 TR001866), the French National Research Agency (ANR) under the "Investments for the Future" program (ANR-10-IAHU-01), the Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence (ANR-10-LABX-62-IBEID), ANR-GENMSMD (ANR-16-CE17-0005-01), ANR-MAFMACRO (ANR-22-CE92-0008), ANRSECTZ170784, the French Foundation for Medical Research (FRM) (EQU201903007798), the ANRS-COV05, ANR GENVIR (ANR-20-CE93-003), and ANR AI2D (ANR-22-CE15-0046) projects, the ANR-RHU program (ANR-21-RHUS-08-COVIFERON), the European Union's Horizon 2020 research and innovation program under grant agreement no. 824110 (EASI-genomics), the Square Foundation, Grandir - Fonds de solidarité pour l'enfance, the Fondation du Souffle, the SCOR Corporate Foundation for Science, the Battersea & Bowery Advisory Group, William E. Ford, General Atlantic's Chairman and Chief Executive Officer, Gabriel Caillaux, General Atlantic's Co-President, Managing Director, and Head of business in EMEA, and the General Atlantic Foundation, Institut National de la Santé et de la Recherche Médicale (INSERM) and of Paris Cité University. JR was supported by the INSERM PhD program for doctors of pharmacy (poste d'accueil INSERM). JR and TLV were supported by the Bettencourt-Schueller Foundation and the MD-PhD program of the Imagine Institute. MO was supported by the David Rockefeller Graduate Program, the Funai Foundation for Information Technology (FFIT), the Honjo International Scholarship Foundation (HISF), and the New York Hideyo Noguchi Memorial Society (HNMS).
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Affiliation(s)
- Jessica N. Peel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Rui Yang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Tom Le Voyer
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
- Clinical Immunology Department, Assistance Publique Hôpitaux de Paris (AP-HP), Saint-Louis Hospital, Paris, France
| | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
- Study Center for Primary Immunodeficiencies and
| | - Paul Bastard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistante Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Anish Behere
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Axel Cederholm
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Aaron Bodansky
- Department of Pediatric Critical Care Medicine and
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Clément Conil
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Jing-Ya Ding
- Laboratory of Human Immunology and Infectious Disease, Graduate Institute of Clinical Medical Sciences; Center for Molecular and Clinical Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Te Lei
- Laboratory of Human Immunology and Infectious Disease, Graduate Institute of Clinical Medical Sciences; Center for Molecular and Clinical Immunology, Chang Gung University, Taoyuan, Taiwan
- Department of Pediatrics, Hsinchu Municipal MacKay Children’s Hospital, Hsinchu, Taiwan
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Camille Soudee
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Ahmad Yatim
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Danyel Lee
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Jonathan Bohlen
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Thomas Perpoint
- Infectious and Tropical Diseases Service, Hospices Civils of Lyon, Lyon, France
| | - Laura Perez
- Immunology and Rheumatology Unit, Prof. Dr. Juan P. Garrahan National Hospital of Pediatrics, Buenos Aires, Argentina
| | - Fernando Messina
- Mycology Unit, Dr. Francisco J. Muñiz Hospital, Buenos Aires, Argentina
| | - Roxana Genet
- Infectious Diseases Service, Regional Hospital of Metz-Thionville, France
| | - Ludovic Karkowski
- Deparement of Internal Medicine, Sainte Anne Armed Forces Teaching Hospital, Toulon, France
| | - Mathieu Blot
- Department of Infectious Diseases, Dijon-Bourgogne University Hospital, Dijon, France
| | - Emmanuel Lafont
- Department of Infectious Diseases and Tropical Medicine, Paris Cité University, Necker Hospital for Sick Children and
| | - Laurie Toullec
- Laboratory of Immunology, Cochin hospital, AP-HP, Paris, France
| | | | | | | | | | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | | | - 3C-Dijon Study
- Details are available in the Supplemental Acknowledgments
| | | | - Mark S. Anderson
- Department of Pediatric Critical Care Medicine and
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Nils Landegren
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Centre for Molecular Medicine, Department of Medicine (Solna), Karolinska Institute, Stockholm, Sweden
| | - Pierre Tiberghien
- Etablissement Français Du Sang, La Plaine Saint-Denis, France
- 20UMR1098 RIGHT, INSERM, EFS, Université de Franche-Comté, Besançon, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
- Study Center for Primary Immunodeficiencies and
| | - Cheng-Lung Ku
- Laboratory of Human Immunology and Infectious Disease, Graduate Institute of Clinical Medical Sciences; Center for Molecular and Clinical Immunology, Chang Gung University, Taoyuan, Taiwan
- Department of Nephrology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistante Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Howard Hughes Medical Institute, New York, New York, USA
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21
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Bacchetta R, Roncarolo MG. IPEX syndrome from diagnosis to cure, learning along the way. J Allergy Clin Immunol 2024; 153:595-605. [PMID: 38040040 DOI: 10.1016/j.jaci.2023.11.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/17/2023] [Accepted: 11/24/2023] [Indexed: 12/03/2023]
Abstract
In the past 2 decades, a significant number of studies have been published describing the molecular and clinical aspects of immune dysregulation polyendocrinopathy enteropathy X-linked (IPEX) syndrome. These studies have refined our knowledge of this rare yet prototypic genetic autoimmune disease, advancing the diagnosis, broadening the clinical spectrum, and improving our understanding of the underlying immunologic mechanisms. Despite these advances, Forkhead box P3 mutations have devastating consequences, and treating patients with IPEX syndrome remains a challenge, even with safer strategies for hematopoietic stem cell transplantation and gene therapy becoming a promising reality. The aim of this review was to highlight novel features of the disease to further advance awareness and improve the diagnosis and treatment of patients with IPEX syndrome.
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Affiliation(s)
- Rosa Bacchetta
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, Calif; Center for Definitive and Curative Medicine (CDCM), Stanford University School of Medicine, Stanford, Calif.
| | - Maria Grazia Roncarolo
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, Calif; Center for Definitive and Curative Medicine (CDCM), Stanford University School of Medicine, Stanford, Calif; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, Calif
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22
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Borna S, Meffre E, Bacchetta R. FOXP3 deficiency, from the mechanisms of the disease to curative strategies. Immunol Rev 2024; 322:244-258. [PMID: 37994657 DOI: 10.1111/imr.13289] [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] [Indexed: 11/24/2023]
Abstract
FOXP3 gene is a key transcription factor driving immune tolerance and its deficiency causes immune dysregulation, polyendocrinopathy, enteropathy X-linked syndrome (IPEX), a prototypic primary immune regulatory disorder (PIRD) with defective regulatory T (Treg) cells. Although life-threatening, the increased awareness and early diagnosis have contributed to improved control of the disease. IPEX currently comprises a broad spectrum of clinical autoimmune manifestations from severe early onset organ involvement to moderate, recurrent manifestations. This review focuses on the mechanistic advancements that, since the IPEX discovery in early 2000, have informed the role of the human FOXP3+ Treg cells in controlling peripheral tolerance and shaping the overall immune landscape of IPEX patients and carrier mothers, contributing to defining new treatments.
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Affiliation(s)
- Simon Borna
- Department of Pediatrics, Division of Hematology, Oncology Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Eric Meffre
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California, USA
| | - Rosa Bacchetta
- Department of Pediatrics, Division of Hematology, Oncology Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Center for Definitive and Curative Medicine (CDCM), Stanford University School of Medicine, Stanford, California, USA
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23
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Filimonova I, Innocenti G, Vogl T. Phage Immunoprecipitation Sequencing (PhIP-Seq) for Analyzing Antibody Epitope Repertoires Against Food Antigens. Methods Mol Biol 2024; 2717:101-122. [PMID: 37737980 DOI: 10.1007/978-1-0716-3453-0_7] [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] [Indexed: 09/23/2023]
Abstract
While thousands of food and environmental allergens have been reported, conventional methods for allergy testing typically rely on measuring immunoglobulin E (IgE) binding against panels of dozens to hundreds of antigens. Beyond IgE, also the specificity of other Ig (sub-)classes such as IgG4, has gained interest because of a potential protective role toward allergy.Phage immunoprecipitation sequencing (PhIP-Seq) allows to study hundreds of thousands of rationally selected peptide antigens and to resolve binding specificities of different Ig classes. This technology combines synthetic DNA libraries encoding antigens, with the display on the surface of T7 bacteriophages and next-generation sequencing (NGS) for quantitative readouts. Thereby binding of entire Ig repertoires can be measured to detect the exact epitopes of food allergens and to study potential cross-reactivity.In this chapter, we provide a summary of both the key experimental steps and various strategies for analyzing PhIP-Seq datasets, as well as comparing the advantages and disadvantages of this methodology for measuring antibody responses against food antigens.
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Affiliation(s)
- Ioanna Filimonova
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria
| | - Gabriel Innocenti
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria
| | - Thomas Vogl
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria.
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24
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Bodansky A, Yu DJL, Rallistan A, Kalaycioglu M, Boonyaratanakornkit J, Green DJ, Gauthier J, Turtle CJ, Zorn K, O’Donovan B, Mandel-Brehm C, Asaki J, Kortbawi H, Kung AF, Rackaityte E, Wang CY, Saxena A, de Dios K, Masi G, Nowak RJ, O’Connor KC, Li H, Diaz VE, Casaletto KB, Gontrum EQ, Chan B, Kramer JH, Wilson MR, Utz PJ, Hill JA, Jackson SW, Anderson MS, DeRisi JL. Unveiling the autoreactome: Proteome-wide immunological fingerprints reveal the promise of plasma cell depleting therapy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.19.23300188. [PMID: 38196603 PMCID: PMC10775319 DOI: 10.1101/2023.12.19.23300188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
The prevalence and burden of autoimmune and autoantibody mediated disease is increasing worldwide, yet most disease etiologies remain unclear. Despite numerous new targeted immunomodulatory therapies, comprehensive approaches to apply and evaluate the effects of these treatments longitudinally are lacking. Here, we leverage advances in programmable-phage immunoprecipitation (PhIP-Seq) methodology to explore the modulation, or lack thereof, of proteome-wide autoantibody profiles in both health and disease. We demonstrate that each individual, regardless of disease state, possesses a distinct set of autoreactivities constituting a unique immunological fingerprint, or "autoreactome", that is remarkably stable over years. In addition to uncovering important new biology, the autoreactome can be used to better evaluate the relative effectiveness of various therapies in altering autoantibody repertoires. We find that therapies targeting B-Cell Maturation Antigen (BCMA) profoundly alter an individual's autoreactome, while anti-CD19 and CD-20 therapies have minimal effects, strongly suggesting a rationale for BCMA or other plasma cell targeted therapies in autoantibody mediated diseases.
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Affiliation(s)
- Aaron Bodansky
- Department of Pediatrics, Division of Critical Care, University of California San Francisco, San Francisco, CA
| | - David JL Yu
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA
| | - Alysa Rallistan
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305
| | - Muge Kalaycioglu
- Institute of Immunity, Transplantation, and Infection (ITI), Stanford University, Stanford, CA 94305
| | - Jim Boonyaratanakornkit
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- University of Washington School of Medicine, Seattle, WA, USA
| | - Damian J. Green
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- University of Washington School of Medicine, Seattle, WA, USA
| | - Jordan Gauthier
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- University of Washington School of Medicine, Seattle, WA, USA
| | - Cameron J. Turtle
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- University of Washington School of Medicine, Seattle, WA, USA
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
| | - Brian O’Donovan
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
| | - Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
| | - James Asaki
- Biomedical Sciences Program, University of California San Francisco, San Francisco, CA
| | - Hannah Kortbawi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA
| | - Andrew F. Kung
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, CA
| | - Elze Rackaityte
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
| | | | | | - Kimberly de Dios
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA
| | - Gianvito Masi
- Department of Neurology, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT
| | | | - Kevin C. O’Connor
- Department of Neurology, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
| | - Valentina E. Diaz
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Kaitlin B. Casaletto
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Eva Q. Gontrum
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Brandon Chan
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Joel H. Kramer
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Michael R. Wilson
- Weill Institute for Neurosciences, University of California San Francisco; San Francisco, CA
- Department of Neurology, University of California San Francisco; San Francisco, CA
| | - Paul J. Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305
| | - Joshua A. Hill
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- University of Washington School of Medicine, Seattle, WA, USA
| | - Shaun W. Jackson
- Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
- Seattle Children’s Research Institute, Seattle, WA
- Pediatrics, University of Washington School of Medicine, Seattle, WA
| | - Mark S. Anderson
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub SF, San Francisco, CA
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25
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Rackaityte E, Proekt I, Miller HS, Ramesh A, Brooks JF, Kung AF, Mandel-Brehm C, Yu D, Zamecnik CR, Bair R, Vazquez SE, Sunshine S, Abram CL, Lowell CA, Rizzuto G, Wilson MR, Zikherman J, Anderson MS, DeRisi JL. Validation of a murine proteome-wide phage display library for identification of autoantibody specificities. JCI Insight 2023; 8:e174976. [PMID: 37934865 PMCID: PMC10795829 DOI: 10.1172/jci.insight.174976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
Autoimmunity is characterized by loss of tolerance to tissue-specific as well as systemic antigens, resulting in complex autoantibody landscapes. Here, we introduce and extensively validate the performance characteristics of a murine proteome-wide library for phage display immunoprecipitation and sequencing (PhIP-seq) in profiling mouse autoantibodies. This library was validated using 7 genetically distinct mouse lines across a spectrum of autoreactivity. Mice deficient in antibody production (Rag2-/- and μMT) were used to model nonspecific peptide enrichments, while cross-reactivity was evaluated using anti-ovalbumin B cell receptor-restricted OB1 mice as a proof of principle. The PhIP-seq approach was then utilized to interrogate 3 distinct autoimmune disease models. First, serum from Lyn-/- IgD+/- mice with lupus-like disease was used to identify nuclear and apoptotic bleb reactivities. Second, serum from nonobese diabetic (NOD) mice, a polygenic model of pancreas-specific autoimmunity, was enriched in peptides derived from both insulin and predicted pancreatic proteins. Lastly, Aire-/- mouse sera were used to identify numerous autoantigens, many of which were also observed in previous studies of humans with autoimmune polyendocrinopathy syndrome type 1 carrying recessive mutations in AIRE. These experiments support the use of murine proteome-wide PhIP-seq for antigenic profiling and autoantibody discovery, which may be employed to study a range of immune perturbations in mouse models of autoimmunity profiling.
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Affiliation(s)
| | | | - Haleigh S. Miller
- Department of Biochemistry and Biophysics
- Biological and Medical Informatics Program
| | - Akshaya Ramesh
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Jeremy F. Brooks
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, and
| | - Andrew F. Kung
- Department of Biochemistry and Biophysics
- Biological and Medical Informatics Program
| | | | - David Yu
- Diabetes Center, School of Medicine
| | - Colin R. Zamecnik
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Rebecca Bair
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Sara E. Vazquez
- Department of Biochemistry and Biophysics
- Diabetes Center, School of Medicine
| | | | - Clare L. Abram
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
| | | | - Gabrielle Rizzuto
- Human Oncology & Pathogenesis Program and Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Julie Zikherman
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, and
| | | | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics
- Chan Zuckerberg Biohub, San Francisco, California, USA
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26
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Buck AM, Deitchman AN, Takahashi S, Lu S, Goldberg SA, Bodansky A, Kung A, Hoh R, Williams MC, Kerbleski M, Maison DP, Deveau TM, Munter SE, Lombardo J, Wrin T, Petropoulos CJ, Durstenfeld MS, Hsue PY, Daniel Kelly J, Greenhouse B, Martin JN, Deeks SG, Peluso MJ, Henrich TJ. The breadth of the neutralizing antibody response to original SARS-CoV-2 infection is linked to the presence of Long COVID symptoms. J Med Virol 2023; 95:e29216. [PMID: 37988251 PMCID: PMC10754238 DOI: 10.1002/jmv.29216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/23/2023]
Abstract
The associations between longitudinal dynamics and the breadth of SARS-CoV-2 neutralizing antibody (nAb) response with various Long COVID phenotypes before vaccination are not known. The capacity of antibodies to cross-neutralize a variety of viral variants may be associated with ongoing pathology and persistent symptoms. We measured longitudinal neutralizing and cross-neutralizing antibody responses to pre- and post-SARS-CoV-2 Omicron variants in participants infected early in the COVID-19 pandemic, before widespread rollout of SARS-CoV-2 vaccines. Cross-sectional regression models adjusted for clinical covariates and longitudinal mixed-effects models were used to determine the impact of the breadth and rate of decay of neutralizing responses on the development of Long COVID symptoms, as well as Long COVID phenotypes. We identified several novel relationships between SARS-CoV-2 antibody neutralization and the presence of Long COVID symptoms. Specifically, we show that, although nAb responses to the original, infecting strain of SARS-CoV-2 were not associated with Long COVID in cross-sectional analyses, cross-neutralization ID50 levels to the Omicron BA.5 variant approximately 4 months following acute infection was independently and significantly associated with greater odds of Long COVID and with persistent gastrointestinal and neurological symptoms. Longitudinal modeling demonstrated significant associations in the overall levels and rates of decay of neutralization capacity with Long COVID phenotypes. A higher proportion of participants had antibodies capable of neutralizing Omicron BA.5 compared with BA.1 or XBB.1.5 variants. Our findings suggest that relationships between various immune responses and Long COVID are likely complex but may involve the breadth of antibody neutralization responses.
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Affiliation(s)
- Amanda M. Buck
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Amelia N. Deitchman
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, CA, United States
| | - Saki Takahashi
- Division of HIV, ID and Global Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, United States
| | - Sarah A. Goldberg
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, United States
| | - Aaron Bodansky
- Division of Pediatric Critical Care Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Andrew Kung
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States
| | - Rebecca Hoh
- Division of HIV, ID and Global Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Meghann C. Williams
- Division of HIV, ID and Global Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Marian Kerbleski
- Division of HIV, ID and Global Medicine, University of California San Francisco, San Francisco, CA, United States
| | - David P. Maison
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Tyler-Marie Deveau
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Sadie E. Munter
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, United States
| | - James Lombardo
- Division of HIV, ID and Global Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Terri Wrin
- Monogram Biosciences, South San Francisco, CA, United States
| | | | - Matthew S. Durstenfeld
- Division of Cardiology, University of California San Francisco, San Francisco, CA, United States
| | - Priscilla Y. Hsue
- Division of Cardiology, University of California San Francisco, San Francisco, CA, United States
| | - J. Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, United States
| | - Bryan Greenhouse
- Division of HIV, ID and Global Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, United States
| | - Steven G. Deeks
- Division of HIV, ID and Global Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Michael J. Peluso
- Division of HIV, ID and Global Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Timothy J. Henrich
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, United States
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27
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Cusick JK, Alcaide J, Shi Y. The RELT Family of Proteins: An Increasing Awareness of Their Importance for Cancer, the Immune System, and Development. Biomedicines 2023; 11:2695. [PMID: 37893069 PMCID: PMC10603948 DOI: 10.3390/biomedicines11102695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
This review highlights Receptor Expressed in Lymphoid Tissues (RELT), a Tumor Necrosis Factor Superfamily member, and its two paralogs, RELL1 and RELL2. Collectively, these three proteins are referred to as RELTfms and have gained much interest in recent years due to their association with cancer and other human diseases. A thorough knowledge of their physiological functions, including the ligand for RELT, is lacking, yet emerging evidence implicates RELTfms in a variety of processes including cytokine signaling and pathways that either promote cell death or survival. T cells from mice lacking RELT exhibit increased responses against tumors and increased inflammatory cytokine production, and multiple lines of evidence indicate that RELT may promote an immunosuppressive environment for tumors. The relationship of individual RELTfms in different cancers is not universal however, as evidence indicates that individual RELTfms may be risk factors in certain cancers yet appear to be protective in other cancers. RELTfms are important for a variety of additional processes related to human health including microbial pathogenesis, inflammation, behavior, reproduction, and development. All three proteins have been strongly conserved in all vertebrates, and this review aims to provide a clearer understanding of the current knowledge regarding these interesting proteins.
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Affiliation(s)
- John K. Cusick
- College of Medicine, California Northstate University, Elk Grove, CA 95757, USA
| | - Jessa Alcaide
- College of Medicine, California Northstate University, Elk Grove, CA 95757, USA
| | - Yihui Shi
- College of Medicine, California Northstate University, Elk Grove, CA 95757, USA
- California Pacific Medical Center Research Institute, Sutter Bay Hospitals, San Francisco, CA 94107, USA
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28
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Vanker M, Särekannu K, Fekkar A, Jørgensen SE, Haljasmägi L, Kallaste A, Kisand K, Lember M, Peterson P, Menon M, Hussell T, Knight S, Moore-Stanley J, Bastard P, Zhang SY, Mogensen TH, Philippot Q, Zhang Q, Puel A, Casanova JL, Kisand K. Autoantibodies Neutralizing Type III Interferons Are Uncommon in Patients with Severe Coronavirus Disease 2019 Pneumonia. J Interferon Cytokine Res 2023; 43:379-393. [PMID: 37253131 PMCID: PMC10517334 DOI: 10.1089/jir.2023.0003] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/07/2023] [Indexed: 06/01/2023] Open
Abstract
Autoantibodies (AABs) neutralizing type I interferons (IFN) underlie about 15% of cases of critical coronavirus disease 2019 (COVID-19) pneumonia. The impact of autoimmunity toward type III IFNs remains unexplored. We included samples from 1,002 patients with COVID-19 (50% with severe disease) and 1,489 SARS-CoV-2-naive individuals. We studied the prevalence and neutralizing capacity of AABs toward IFNλ and IFNα. Luciferase-based immunoprecipitation method was applied using pooled IFNα (subtypes 1, 2, 8, and 21) or pooled IFNλ1-IFNλ3 as antigens, followed by reporter cell-based neutralization assay. In the SARS-CoV-2-naive cohort, IFNλ AABs were more common (8.5%) than those targeting IFNα2 (2.9%) and were related with older age. In the COVID-19 cohort the presence of autoreactivity to IFNλ did not associate with severe disease [odds ratio (OR) 0.84; 95% confidence interval (CI) 0.40-1.73], unlike to IFNα (OR 4.88; 95% CI 2.40-11.06; P < 0.001). Most IFNλ AAB-positive COVID-19 samples (67%) did not neutralize any of the 3 IFNλ subtypes. Pan-IFNλ neutralization occurred in 5 patients (0.50%), who all suffered from severe COVID-19 pneumonia, and 4 of them neutralized IFNα2 in addition to IFNλ. Overall, AABs to type III IFNs are rarely neutralizing, and do not seem to predispose to severe COVID-19 pneumonia on their own.
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Affiliation(s)
- Martti Vanker
- Institute of Biomedicine and Translational Medicine; Institute of Clinical Medicine; University of Tartu, Tartu, Estonia
| | - Karita Särekannu
- Institute of Biomedicine and Translational Medicine; Institute of Clinical Medicine; University of Tartu, Tartu, Estonia
| | - Arnaud Fekkar
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Service de Parasitologie-Mycologie, Groupe Hospitalier Pitié Salpêtrière, AP-HP, Paris, France
| | - Sofie Eg Jørgensen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus N, Denmark
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Liis Haljasmägi
- Institute of Biomedicine and Translational Medicine; Institute of Clinical Medicine; University of Tartu, Tartu, Estonia
| | - Anne Kallaste
- Department of Internal Medicine, Tartu University Hospital, Tartu, Estonia
| | - Kalle Kisand
- Department of Internal Medicine, Institute of Clinical Medicine; University of Tartu, Tartu, Estonia
| | - Margus Lember
- Department of Internal Medicine, Tartu University Hospital, Tartu, Estonia
- Department of Internal Medicine, Institute of Clinical Medicine; University of Tartu, Tartu, Estonia
| | - Pärt Peterson
- Institute of Biomedicine and Translational Medicine; Institute of Clinical Medicine; University of Tartu, Tartu, Estonia
| | - Madhvi Menon
- Lydia Becker Institute of Immunology and Inflammation, Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Tracy Hussell
- Lydia Becker Institute of Immunology and Inflammation, Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Sean Knight
- Lydia Becker Institute of Immunology and Inflammation, Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Respiratory Department, Salford Care Organisation, Northern Care Alliance Foundation Trust, Manchester, United Kingdom
| | - James Moore-Stanley
- Lydia Becker Institute of Immunology and Inflammation, Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Trine H. Mogensen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus N, Denmark
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France
- Howard Hughes Medical Institute, New York, New York, USA
| | - Kai Kisand
- Institute of Biomedicine and Translational Medicine; Institute of Clinical Medicine; University of Tartu, Tartu, Estonia
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29
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Bodansky A, Wang CY, Saxena A, Mitchell A, Kung AF, Takahashi S, Anglin K, Huang B, Hoh R, Lu S, Goldberg SA, Romero J, Tran B, Kirtikar R, Grebe H, So M, Greenhouse B, Durstenfeld MS, Hsue PY, Hellmuth J, Kelly JD, Martin JN, Anderson MS, Deeks SG, Henrich TJ, DeRisi JL, Peluso MJ. Autoantigen profiling reveals a shared post-COVID signature in fully recovered and long COVID patients. JCI Insight 2023; 8:e169515. [PMID: 37288661 PMCID: PMC10393220 DOI: 10.1172/jci.insight.169515] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/03/2023] [Indexed: 06/09/2023] Open
Abstract
Some individuals do not return to baseline health following SARS-CoV-2 infection, leading to a condition known as long COVID. The underlying pathophysiology of long COVID remains unknown. Given that autoantibodies have been found to play a role in severity of SARS-CoV-2 infection and certain other post-COVID sequelae, their potential role in long COVID is important to investigate. Here, we apply a well-established, unbiased, proteome-wide autoantibody detection technology (T7 phage-display assay with immunoprecipitation and next-generation sequencing, PhIP-Seq) to a robustly phenotyped cohort of 121 individuals with long COVID, 64 individuals with prior COVID-19 who reported full recovery, and 57 pre-COVID controls. While a distinct autoreactive signature was detected that separated individuals with prior SARS-CoV-2 infection from those never exposed to SARS-CoV-2, we did not detect patterns of autoreactivity that separated individuals with long COVID from individuals fully recovered from COVID-19. These data suggest that there are robust alterations in autoreactive antibody profiles due to infection; however, no association of autoreactive antibodies and long COVID was apparent by this assay.
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Affiliation(s)
- Aaron Bodansky
- Division of Pediatric Critical Care Medicine, UCSF, San Francisco, California, USA
| | - Chung-Yu Wang
- Chan Zuckerberg Biohub Network, San Francisco, California, USA
| | - Aditi Saxena
- Chan Zuckerberg Biohub Network, San Francisco, California, USA
| | - Anthea Mitchell
- Chan Zuckerberg Biohub Network, San Francisco, California, USA
| | | | - Saki Takahashi
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine
| | | | - Beatrice Huang
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine
| | - Scott Lu
- Department of Epidemiology and Biostatistics
| | | | - Justin Romero
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine
| | - Brandon Tran
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine
| | - Raushun Kirtikar
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine
| | - Halle Grebe
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine
| | - Matthew So
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine
| | - Bryan Greenhouse
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine
| | | | | | | | | | | | | | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine
| | - Timothy J. Henrich
- Division of Experimental Medicine, Department of Medicine, UCSF, San Francisco, California, USA
| | | | - Michael J. Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine
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30
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Upadhyay V, Yoon YM, Vazquez SE, Velez TE, Jones KD, Lee CT, Law CS, Wolters PJ, Lee S, Yang MM, Farrand E, Noth I, Strek ME, Anderson M, DeRisi J, Sperling AI, Shum AK. PhIP-Seq uncovers novel autoantibodies and unique endotypes in interstitial lung disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538091. [PMID: 37163026 PMCID: PMC10168232 DOI: 10.1101/2023.04.24.538091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Interstitial lung diseases (ILDs) are a heterogeneous group of disorders that can develop in patients with connective tissue diseases (CTD). Establishing autoimmunity in ILD impacts prognosis and treatment. ILD patients are screened for autoimmunity by assaying for anti-nuclear autoantibodies, rheumatoid factors and other non-specific tests. However, this approach has not been rigorously validated and may miss autoimmunity that manifests as autoantibodies to tissue antigens not previously defined in ILD. Here, we use Phage Immunoprecipitation-Sequencing (PhIP-Seq) to conduct a large, multi-center unbiased autoantibody discovery screen of ILD patients and controls. PhIP-Seq identified 17 novel autoreactive targets, and machine learning classifiers derived from these targets discriminated ILD serum from controls. Among these 17 candidates, we validated Cadherin Related Family Member 5 (CDHR5) as an autoantigen and found CDHR5 autoantibodies in patients with rheumatologic disorders and importantly, subjects not previously diagnosed with autoimmunity. Lung tissue of CDHR5 autoreactive patients showed transcriptional profiles consistent with activation of NFκB signaling and upregulation of chitotriosidase (CHIT1), a molecular pathway linked to fibrosis. Our study shows PhIP-Seq uncovers novel autoantibodies in ILD patients not revealed by standard clinical tests. Furthermore, CDHR5 autoantibodies may define a novel molecular endotype of ILD characterized by inflammation and fibrosis.
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31
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Bodansky A, Wang CY, Saxena A, Mitchell A, Takahashi S, Anglin K, Huang B, Hoh R, Lu S, Goldberg SA, Romero J, Tran B, Kirtikar R, Grebe H, So M, Greenhouse B, Durstenfeld MS, Hsue PY, Hellmuth J, Kelly JD, Martin JN, Anderson MS, Deeks SG, Henrich TJ, DeRisi JL, Peluso MJ. Autoantigen profiling reveals a shared post-COVID signature in fully recovered and Long COVID patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.06.23285532. [PMID: 36798288 PMCID: PMC9934805 DOI: 10.1101/2023.02.06.23285532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Some individuals do not return to baseline health following SARS-CoV-2 infection, leading to a condition known as Long COVID. The underlying pathophysiology of Long COVID remains unknown. Given that autoantibodies have been found to play a role in severity of COVID infection and certain other post-COVID sequelae, their potential role in Long COVID is important to investigate. Here we apply a well-established, unbiased, proteome-wide autoantibody detection technology (PhIP-Seq) to a robustly phenotyped cohort of 121 individuals with Long COVID, 64 individuals with prior COVID-19 who reported full recovery, and 57 pre-COVID controls. While a distinct autoreactive signature was detected which separates individuals with prior COVID infection from those never exposed to COVID, we did not detect patterns of autoreactivity that separate individuals with Long COVID relative to individuals fully recovered from SARS-CoV-2 infection. These data suggest that there are robust alterations in autoreactive antibody profiles due to infection; however, no association of autoreactive antibodies and Long COVID was apparent by this assay.
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Affiliation(s)
- Aaron Bodansky
- Division of Pediatric Critical Care Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | - Saki Takahashi
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Khamal Anglin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Beatrice Huang
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Justin Romero
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Brandon Tran
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Raushun Kirtikar
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Halle Grebe
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew So
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Bryan Greenhouse
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew S Durstenfeld
- Division of Cardiology, University of California, San Francisco, San Francisco, CA, USA
| | - Priscilla Y Hsue
- Division of Cardiology, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Hellmuth
- Department of Neurology University of California, San Francisco, San Francisco, CA, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
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32
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Vazquez SE, Mann SA, Bodansky A, Kung AF, Quandt Z, Ferré EMN, Landegren N, Eriksson D, Bastard P, Zhang SY, Liu J, Mitchell A, Proekt I, Yu D, Mandel-Brehm C, Wang CY, Miao B, Sowa G, Zorn K, Chan AY, Tagi VM, Shimizu C, Tremoulet A, Lynch K, Wilson MR, Kämpe O, Dobbs K, Delmonte OM, Bacchetta R, Notarangelo LD, Burns JC, Casanova JL, Lionakis MS, Torgerson TR, Anderson MS, DeRisi JL. Autoantibody discovery across monogenic, acquired, and COVID-19-associated autoimmunity with scalable PhIP-seq. eLife 2022; 11:e78550. [PMID: 36300623 PMCID: PMC9711525 DOI: 10.7554/elife.78550] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Phage immunoprecipitation sequencing (PhIP-seq) allows for unbiased, proteome-wide autoantibody discovery across a variety of disease settings, with identification of disease-specific autoantigens providing new insight into previously poorly understood forms of immune dysregulation. Despite several successful implementations of PhIP-seq for autoantigen discovery, including our previous work (Vazquez et al., 2020), current protocols are inherently difficult to scale to accommodate large cohorts of cases and importantly, healthy controls. Here, we develop and validate a high throughput extension of PhIP-seq in various etiologies of autoimmune and inflammatory diseases, including APS1, IPEX, RAG1/2 deficiency, Kawasaki disease (KD), multisystem inflammatory syndrome in children (MIS-C), and finally, mild and severe forms of COVID-19. We demonstrate that these scaled datasets enable machine-learning approaches that result in robust prediction of disease status, as well as the ability to detect both known and novel autoantigens, such as prodynorphin (PDYN) in APS1 patients, and intestinally expressed proteins BEST4 and BTNL8 in IPEX patients. Remarkably, BEST4 antibodies were also found in two patients with RAG1/2 deficiency, one of whom had very early onset IBD. Scaled PhIP-seq examination of both MIS-C and KD demonstrated rare, overlapping antigens, including CGNL1, as well as several strongly enriched putative pneumonia-associated antigens in severe COVID-19, including the endosomal protein EEA1. Together, scaled PhIP-seq provides a valuable tool for broadly assessing both rare and common autoantigen overlap between autoimmune diseases of varying origins and etiologies.
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Affiliation(s)
- Sara E Vazquez
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
- School of Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Sabrina A Mann
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Aaron Bodansky
- Department of Pediatric Critical Care Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Andrew F Kung
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Zoe Quandt
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
- Department of Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Elise MN Ferré
- Fungal Pathogenesis Unit, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Nils Landegren
- Department of Medicine, Karolinska University Hospital, Karolinska InstituteStockholmSweden
- Science for life Laboratory, Department of Medical Sciences, Uppsala UniversityUppsalaSweden
| | - Daniel Eriksson
- Department of Medical Biochemistry and Microbiology, Uppsala UniversityUppsalaSweden
- Centre for Molecular Medicine, Department of Medicine, Karolinska InstitutetStockholmSweden
| | - Paul Bastard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller UniversityNew YorkUnited States
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick ChildrenParisFrance
- Imagine Institute, University of ParisParisFrance
- Department of Pediatrics, Necker Hospital for Sick ChildrenParisFrance
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller UniversityNew YorkUnited States
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick ChildrenParisFrance
- Imagine Institute, University of ParisParisFrance
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, San FranciscoSan FranciscoUnited States
| | - Anthea Mitchell
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Irina Proekt
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - David Yu
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Chung-Yu Wang
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Brenda Miao
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Gavin Sowa
- School of Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Alice Y Chan
- Department of Pediatrics, Division of Pediatric Allergy, Immunology, Bone and Marrow Transplantation, Division of Pediatric Rheumatology, University of California, San FranciscoSan FranciscoUnited States
| | - Veronica M Tagi
- Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
| | - Chisato Shimizu
- Kawasaki Disease Research Center, Rady Children’s Hospital and Department of Pediatrics, University of California, San DiegoLa JollaUnited States
| | - Adriana Tremoulet
- Kawasaki Disease Research Center, Rady Children’s Hospital and Department of Pediatrics, University of California, San DiegoLa JollaUnited States
| | - Kara Lynch
- Department of Laboratory Medicine, University of California, San FranciscoSan FranciscoUnited States
- Zuckerberg San Francisco GeneralSan FranciscoUnited States
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
| | - Olle Kämpe
- Department of Medicine, Karolinska University Hospital, Karolinska InstituteStockholmSweden
- Department of Clinical Science and KG Jebsen Center for Autoimmune Disorders, University of BergenBergenNorway
- Center of Molecular Medicine, and Department of Endocrinology, Metabolism and Diabetes, Karolinska University HospitalStockholmSweden
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Rosa Bacchetta
- Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Jane C Burns
- Kawasaki Disease Research Center, Rady Children’s Hospital and Department of Pediatrics, University of California, San DiegoLa JollaUnited States
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller UniversityNew YorkUnited States
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick ChildrenParisFrance
- Imagine Institute, University of ParisParisFrance
- Department of Pediatrics, Necker Hospital for Sick ChildrenParisFrance
- Howard Hughes Medical InstituteNew YorkUnited States
| | - Michail S Lionakis
- Fungal Pathogenesis Unit, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Troy R Torgerson
- Seattle Children's Research InstituteSeattleUnited States
- Department of Pediatrics, University of WashingtonSeattleUnited States
| | - Mark S Anderson
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
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