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Cleaver J, Jeffery K, Klenerman P, Lim M, Handunnetthi L, Irani SR, Handel A. The immunobiology of herpes simplex virus encephalitis and post-viral autoimmunity. Brain 2024; 147:1130-1148. [PMID: 38092513 PMCID: PMC10994539 DOI: 10.1093/brain/awad419] [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: 07/20/2023] [Revised: 10/25/2023] [Accepted: 11/27/2023] [Indexed: 04/06/2024] Open
Abstract
Herpes simplex virus encephalitis (HSE) is the leading cause of non-epidemic encephalitis in the developed world and, despite antiviral therapy, mortality and morbidity is high. The emergence of post-HSE autoimmune encephalitis reveals a new immunological paradigm in autoantibody-mediated disease. A reductionist evaluation of the immunobiological mechanisms in HSE is crucial to dissect the origins of post-viral autoimmunity and supply rational approaches to the selection of immunotherapeutics. Herein, we review the latest evidence behind the phenotypic progression and underlying immunobiology of HSE including the cytokine/chemokine environment, the role of pathogen-recognition receptors, T- and B-cell immunity and relevant inborn errors of immunity. Second, we provide a contemporary review of published patients with post-HSE autoimmune encephalitis from a combined cohort of 110 patients. Third, we integrate novel mechanisms of autoimmunization in deep cervical lymph nodes to explore hypotheses around post-HSE autoimmune encephalitis and challenge these against mechanisms of molecular mimicry and others. Finally, we explore translational concepts where neuroglial surface autoantibodies have been observed with other neuroinfectious diseases and those that generate brain damage including traumatic brain injury, ischaemic stroke and neurodegenerative disease. Overall, the clinical and immunological landscape of HSE is an important and evolving field, from which precision immunotherapeutics could soon emerge.
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Affiliation(s)
- Jonathan Cleaver
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals, Oxford, OX3 9DU, UK
| | - Katie Jeffery
- Department of Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | - Ming Lim
- Children’s Neurosciences, Evelina London Children’s Hospital at Guy’s and St Thomas’ NHS Foundation Trust, London, SE1 7EH, UK
- Department Women and Children’s Health, School of Life Course Sciences, King’s College London, London, WC2R 2LS, UK
| | - Lahiru Handunnetthi
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Sarosh R Irani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals, Oxford, OX3 9DU, UK
| | - Adam Handel
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals, Oxford, OX3 9DU, UK
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Peter E, Honnorat J, Desestret V. Paraneoplastic neurologic syndrome associated with gynecologic and breast malignancies. HANDBOOK OF CLINICAL NEUROLOGY 2024; 200:409-417. [PMID: 38494293 DOI: 10.1016/b978-0-12-823912-4.00014-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Gynecologic and breast malignancies are the cancers most commonly associated with paraneoplastic neurologic syndromes, of which the foremost is Yo [Purkinje cell antibody, type 1 (PCA-1)] paraneoplastic cerebellar degeneration. Yo syndrome affects women in the sixth decade and manifests as a subacute severe cerebellar ataxia. The association of the typical clinical picture with the detection of Yo antibodies in a patient's serum or CSF defines the diagnosis. Yo syndrome is always associated with a cancer, and the search for the underlying tumor should focus on ovarian and breast cancers and be repeated overtime if negative. The Yo autoantibodies are directed against the Yo antigens, aberrantly overexpressed by tumor cells with frequent somatic mutations and gene amplifications. The massive infiltration of these tumors by immune cells suggests that they are the site of the immune tolerance breakdown, leading to the destruction of Purkinje cells harboring the Yo antigens. Despite a growing understanding of the immunologic mechanisms, efficient therapeutic options are still lacking. Anti-Ri and antiamphiphysin syndromes are rarer and associated with breast cancers; a wide variety of other rare paraneoplastic neurologic syndromes have been described in association with gynecologic and breast malignancies that, though sharing some similarities, may have specific immune and genetics features leading to the immune tolerance breakdown.
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Affiliation(s)
- Elise Peter
- French Reference Center for Paraneoplastic Neurological Syndromes, Hospices Civils de Lyon, Lyon, France; Synaptopathies and Autoantibodies (SynatAc) Team, Institut MeLis, Inserm U1314, UMR CNRS 5284, University Claude Bernard Lyon 1, Lyon, France
| | - Jérôme Honnorat
- French Reference Center for Paraneoplastic Neurological Syndromes, Hospices Civils de Lyon, Lyon, France; Synaptopathies and Autoantibodies (SynatAc) Team, Institut MeLis, Inserm U1314, UMR CNRS 5284, University Claude Bernard Lyon 1, Lyon, France.
| | - Virginie Desestret
- French Reference Center for Paraneoplastic Neurological Syndromes, Hospices Civils de Lyon, Lyon, France; Synaptopathies and Autoantibodies (SynatAc) Team, Institut MeLis, Inserm U1314, UMR CNRS 5284, University Claude Bernard Lyon 1, Lyon, France
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3
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Waters P, Mills JR, Fox H. Evolution of methods to detect paraneoplastic antibodies. HANDBOOK OF CLINICAL NEUROLOGY 2024; 200:113-130. [PMID: 38494273 DOI: 10.1016/b978-0-12-823912-4.00010-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
An adaptive immune response in less than 1% of people who develop cancer produces antibodies against neuronal proteins. These antibodies can be associated with paraneoplastic syndromes, and their accurate detection should instigate a search for a specific cancer. Over the years, multiple systems, from indirect immunofluorescence to live cell-based assays, have been developed to identify these antibodies. As the specific antigens were identified, high throughput, multi-antigen substrates such as line blots and ELISAs were developed for clinical laboratories. However, the evolution of assays required to identify antibodies to membrane targets has shone a light on the importance of antigen conformation for antibody detection. This chapter discusses the early antibody assays used to detect antibodies to nuclear and cytosolic targets and how new approaches are required to detect antibodies to membrane targets. The chapter presents recent data that support international recommendations against the sole use of line blots for antibody detection and highlights a new antigen-specific approach that appears promising for the detection of submembrane targets.
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Affiliation(s)
- Patrick Waters
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.
| | - John R Mills
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Hannah Fox
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
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4
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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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5
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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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6
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Bartley CM, Ngo TT, Duy Do L, Zekeridou A, Dandekar R, Muñiz-Castrillo S, Alvarenga BD, Zorn KC, Tubati A, Pinto AL, Browne WD, Hullett PW, Terrelonge M, Schubert RD, Piquet AL, Yang B, Montalvo Perero MJ, Kung AF, Mann SA, Shah MP, Geschwind MD, Gelfand JM, DeRisi JL, Pittock SJ, Honnorat J, Pleasure SJ, Wilson MR. Detection of High-Risk Paraneoplastic Antibodies against TRIM9 and TRIM67 Proteins. Ann Neurol 2023; 94:1086-1101. [PMID: 37632288 PMCID: PMC10842626 DOI: 10.1002/ana.26776] [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: 03/28/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
OBJECTIVE Co-occurring anti-tripartite motif-containing protein 9 and 67 autoantibodies (TRIM9/67-IgG) have been reported in only a very few cases of paraneoplastic cerebellar syndrome. The value of these biomarkers and the most sensitive methods of TRIM9/67-IgG detection are not known. METHODS We performed a retrospective, multicenter study to evaluate the cerebrospinal fluid and serum of candidate TRIM9/67-IgG cases by tissue-based immunofluorescence, peptide phage display immunoprecipitation sequencing, overexpression cell-based assay (CBA), and immunoblot. Cases in which TRIM9/67-IgG was detected by at least 2 assays were considered TRIM9/67-IgG positive. RESULTS Among these cases (n = 13), CBA was the most sensitive (100%) and revealed that all cases had TRIM9 and TRIM67 autoantibodies. Of TRIM9/67-IgG cases with available clinical history, a subacute cerebellar syndrome was the most common presentation (n = 7/10), followed by encephalitis (n = 3/10). Of these 10 patients, 70% had comorbid cancer (7/10), 85% of whom (n = 6/7) had confirmed metastatic disease. All evaluable cancer biopsies expressed TRIM9 protein (n = 5/5), whose expression was elevated in the cancerous regions of the tissue in 4 of 5 cases. INTERPRETATION TRIM9/67-IgG is a rare but likely high-risk paraneoplastic biomarker for which CBA appears to be the most sensitive diagnostic assay. ANN NEUROL 2023;94:1086-1101.
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Affiliation(s)
- Christopher M. Bartley
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, California
| | - Thomas T. Ngo
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Le Duy Do
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon and SynatAc Team, Institut MELiS, INSERM U1314/CNRS UMR 5284, Universités de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Anastasia Zekeridou
- Department of Neurology, Center MS and Autoimmune Neurology, Mayo Clinic
- Department of Laboratory Medicine and Pathology, Mayo Clinic
| | - Ravi Dandekar
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Sergio Muñiz-Castrillo
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon and SynatAc Team, Institut MELiS, INSERM U1314/CNRS UMR 5284, Universités de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Bonny D. Alvarenga
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Kelsey C. Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, California
| | - Asritha Tubati
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Anne-Laurie Pinto
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon and SynatAc Team, Institut MELiS, INSERM U1314/CNRS UMR 5284, Universités de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Weston D. Browne
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Patrick W. Hullett
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Mark Terrelonge
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Ryan D. Schubert
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Amanda L. Piquet
- Department of Neurology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, Colorado
| | - Binxia Yang
- Department of Laboratory Medicine and Pathology, Mayo Clinic
| | | | - Andrew F. Kung
- University of California San Francisco, School of Medicine, San Francisco, California
| | - Sabrina A. Mann
- Chan Zuckerberg Biohub, San Francisco, California
- Department of Biochemistry and Biophysics, University of California, San Francisco, California
| | - Maulik P. Shah
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Michael D. Geschwind
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Jeffrey M. Gelfand
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, California
- Department of Biochemistry and Biophysics, University of California, San Francisco, California
| | - Sean J. Pittock
- Department of Neurology, Center MS and Autoimmune Neurology, Mayo Clinic
- Department of Laboratory Medicine and Pathology, Mayo Clinic
| | - Jérôme Honnorat
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon and SynatAc Team, Institut MELiS, INSERM U1314/CNRS UMR 5284, Universités de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Samuel J. Pleasure
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Michael R. Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
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7
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Vogrig A, Pegat A, Villagrán-García M, Wucher V, Attignon V, Sohier E, Brevet M, Rogemond V, Pinto AL, Muñiz-Castrillo S, Peter E, Robert M, Picard G, Hopes L, Psimaras D, Terra A, Perrin C, Cogne D, Tabone-Eglinger S, Martinez S, Jury D, Valantin J, Gadot N, Auclair-Perrossier J, Viari A, Dubois B, Desestret V, Honnorat J. Different Genetic Signatures of Small-Cell Lung Cancer Characterize Anti-GABA B R and Anti-Hu Paraneoplastic Neurological Syndromes. Ann Neurol 2023; 94:1102-1115. [PMID: 37638563 DOI: 10.1002/ana.26784] [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: 04/24/2023] [Revised: 07/27/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]
Abstract
OBJECTIVE Small-cell lung cancer (SCLC) is the malignancy most frequently associated with paraneoplastic neurological syndromes (PNS) and can trigger different antibody responses against intracellular (Hu) or neuronal surface (GABAB R) antigens. Our aim was to clarify whether the genomic and transcriptomic features of SCLC are different in patients with anti-GABAB R or anti-Hu PNS compared with SCLC without PNS. METHODS A total of 76 SCLC tumor samples were collected: 34 anti-Hu, 14 anti-GABAB R, and 28 SCLC without PNS. The study consisted of 4 steps: (1) pathological confirmation; (2) next generation sequencing using a panel of 98 genes, including those encoding the autoantibodies targets ELAVL1-4, GABBR1-2, and KCTD16; (3) genome-wide copy number variation (CNV); and (4) whole-transcriptome RNA sequencing. RESULTS CNV analysis revealed that patients with anti-GABAB R PNS commonly have a gain in chromosome 5q, which contains KCTD16, whereas anti-Hu and control patients often harbor a loss. No significantly different number of mutations regarding any onconeural genes was observed. Conversely, the transcriptomic profile of SCLC was different, and the differentially expressed genes allowed effective clustering of the samples into 3 groups, reflecting the antibody-based classification, with an overexpression of KCTD16 specific to anti-GABAB R PNS. Pathway analysis revealed that tumors of patients with anti-GABAB R encephalitis were enriched in B-cell signatures, as opposed to those of patients with anti-Hu, in which T-cell- and interferon-γ-related signatures were overexpressed. INTERPRETATION SCLC genetic and transcriptomic features differentiate anti-GABAB R, anti-Hu, and non-PNS tumors. The role of KCTD16 appears to be pivotal in the tumor immune tolerance breakdown of anti-GABAB R PNS. ANN NEUROL 2023;94:1102-1115.
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Affiliation(s)
- Alberto Vogrig
- French Reference Center of Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Hôpital Neurologique, Bron, France
- Mechanisms in integrated life sciences Institute, (MeLiS), INSERM U1314, CNRS UMR 5284, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Clinical Neurology, Santa Maria della Misericordia University Hospital, Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Antoine Pegat
- Service ENMG et Pathologies Neuromusculaires, Hôpital Neurologique P. Wertheimer, Hospices Civils de Lyon, Bron, France
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, INMG, Université Claude Bernard Lyon 1, Faculté de Médecine Lyon Est, Lyon, France
| | - Macarena Villagrán-García
- French Reference Center of Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Hôpital Neurologique, Bron, France
- Mechanisms in integrated life sciences Institute, (MeLiS), INSERM U1314, CNRS UMR 5284, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Valentin Wucher
- French Reference Center of Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Hôpital Neurologique, Bron, France
- Mechanisms in integrated life sciences Institute, (MeLiS), INSERM U1314, CNRS UMR 5284, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Valéry Attignon
- Cancer Genomic Platform, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS, Centre Léon Bérard, Lyon, France
| | - Emilie Sohier
- Gilles Thomas Bioinformatics Platform, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS, Centre Léon Bérard, Lyon, France
- Fondation Synergie Lyon Cancer, Centre Léon Bérard, Lyon, France
| | - Marie Brevet
- Department of Pathology, Lyon Est Hospital, Hospices Civils de Lyon, Bron, France
| | - Veronique Rogemond
- French Reference Center of Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Hôpital Neurologique, Bron, France
- Mechanisms in integrated life sciences Institute, (MeLiS), INSERM U1314, CNRS UMR 5284, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Anne-Laurie Pinto
- French Reference Center of Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Hôpital Neurologique, Bron, France
- Mechanisms in integrated life sciences Institute, (MeLiS), INSERM U1314, CNRS UMR 5284, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Sergio Muñiz-Castrillo
- French Reference Center of Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Hôpital Neurologique, Bron, France
- Mechanisms in integrated life sciences Institute, (MeLiS), INSERM U1314, CNRS UMR 5284, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Stanford Center for Sleep Sciences and Medicine, Stanford University, Palo Alto, CA, USA
| | - Elise Peter
- French Reference Center of Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Hôpital Neurologique, Bron, France
- Mechanisms in integrated life sciences Institute, (MeLiS), INSERM U1314, CNRS UMR 5284, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Melisse Robert
- French Reference Center of Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Hôpital Neurologique, Bron, France
- Mechanisms in integrated life sciences Institute, (MeLiS), INSERM U1314, CNRS UMR 5284, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Géraldine Picard
- French Reference Center of Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Hôpital Neurologique, Bron, France
- Mechanisms in integrated life sciences Institute, (MeLiS), INSERM U1314, CNRS UMR 5284, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Lucie Hopes
- Department of Neurology, CHRU Nancy, Nancy, France
| | - Dimitri Psimaras
- Neurology 2 Department Mazarin, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Sorbonne Université, INSERM, CNRS, Paris Brain Institute, Institut du Cerveau et de la Moelle Épinière, ICM, Paris, France
| | - Anthony Terra
- Centre de Ressources Biologiques Hospices Civils de Lyon, Hôpital Neurologique, Bron, France
| | - Corinne Perrin
- Centre de Ressources Biologiques Hospices Civils de Lyon, Hôpital Neurologique, Bron, France
| | - Dominique Cogne
- Plateforme de Gestion des Echantillons Biologique, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS, Centre Léon Bérard, Lyon, France
| | - Severine Tabone-Eglinger
- Plateforme de Gestion des Echantillons Biologique, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS, Centre Léon Bérard, Lyon, France
| | - Séverine Martinez
- Plateforme de Gestion des Echantillons Biologique, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS, Centre Léon Bérard, Lyon, France
| | - Delphine Jury
- Plateforme de Gestion des Echantillons Biologique, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS, Centre Léon Bérard, Lyon, France
| | - Julie Valantin
- Plateforme Anatomopathologie Recherche, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS Centre Léon Bérard, Lyon, France
| | - Nicolas Gadot
- Plateforme Anatomopathologie Recherche, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS Centre Léon Bérard, Lyon, France
| | - Jessie Auclair-Perrossier
- Cancer Genomic Platform, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS, Centre Léon Bérard, Lyon, France
| | - Alain Viari
- Gilles Thomas Bioinformatics Platform, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS, Centre Léon Bérard, Lyon, France
| | - Bertrand Dubois
- Cancer Immune Surveillance and Therapeutic Targeting Team, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS, Centre Léon Bérard, Lyon, France
- Lyon Immunotherapy for Cancer Laboratory, Cancer Research Center of Lyon, Lyon, France
| | - Virginie Desestret
- French Reference Center of Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Hôpital Neurologique, Bron, France
- Mechanisms in integrated life sciences Institute, (MeLiS), INSERM U1314, CNRS UMR 5284, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Jérôme Honnorat
- French Reference Center of Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Hôpital Neurologique, Bron, France
- Mechanisms in integrated life sciences Institute, (MeLiS), INSERM U1314, CNRS UMR 5284, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
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Vorasoot N, Scharf M, Miske R, Thakolwiboon S, Dubey D, Mills JR, Pittock SJ, Zekeridou A, Ott A, McKeon A. CDR2 and CDR2L line blot performance in PCA-1/anti-Yo paraneoplastic autoimmunity. Front Immunol 2023; 14:1265797. [PMID: 37841252 PMCID: PMC10570841 DOI: 10.3389/fimmu.2023.1265797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Background Purkinje cytoplasmic autoantibody type 1 (PCA-1)/anti-Yo autoimmunity is a common high-risk paraneoplastic neurological disorder, traditionally attributed antigenically to cerebellar degeneration-related protein 2 (CDR2), predominantly affecting women with gynecologic or breast adenocarcinoma. Single-modality CDR2 testing may produce false-positive results. We assessed the performance characteristics of the more recently purported major PCA-1/Yo antigen, CDR2-like (CDR2L), side by side with CDR2, in a line blot format. Methods CDR2 and CDR2L were tested in six specimen groups (serum and cerebrospinal fluid (CSF)). Group 1, PCA-1/Yo mouse brain indirect immunofluorescence assay (IFA) positives; Group 2, PCA-1/Yo IFA mimics; Group 3, suspected CDR2 line blot false positives; Group 4, consecutive patient samples tested for neural antibodies over 1 year; Group 5, healthy subject serums; and Group 6, polyclonal (non-specific) immunoglobulin G (IgG)-positive serums. Results Group 1: Of 64 samples tested, all but two were CDR2 positive (both CSF samples) and all were CDR2L positive. In individual patients, CDR2L values were always higher than CDR2. The two "CDR2L-only" positives were CSF samples with low titer PCA-1/Yo by IFA with serum negativity but with typical clinical phenotype. Group 2: All 51 PCA-1/Yo mimics were CDR2/CDR2L negative. Group 3: Nine samples [six of 1289 (0.47%) serums and three of 700 CSF samples (0.43%) were PCA-1/Yo IFA negative/CDR2 positive; two of the six available (serums from the same patient) were also CDR2L positive; the other four CDR2L negative had low CDR2 values (17-22). Group 4: Twenty-two patients had unexpected CDR2 or CDR2L positivity; none had tissue IFA positivity. Eleven of the 2,132 serum (0.5%) and three of the 677 CSF (0.4%) samples were CDR2 positive; median value was 19 (range, 11-48). Seven of the 2,132 serum (0.3%) and three of the 677 CSF (0.4%) samples were CDR2L positive; median value was 18 (range, 11-96). Group 5: All 151 healthy serum samples were negative. Group 6: One of the 46 polyclonal serum samples was CDR2L positive. Optimum overall performance was accomplished by requiring both CDR2 and CDR2L positivity in serum (sensitivity, 100%; and specificity, 99.9%) and positivity for CDR2L in CSF (sensitivity, 100%; and specificity, 99.6%). Conclusion CDR2L provides additional PCA-1/anti-Yo sensitivity in CSF, and dual positivity with CDR2 provides additional specificity assurance in serum. Combining antigen-specific and tissue-based assays optimizes PCA-1/anti-Yo testing.
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Affiliation(s)
- Nisa Vorasoot
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Division of Neurology, Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Madeleine Scharf
- The Institute for Experimental Immunology, Affiliated to Euroimmun AG, Lubeck, Germany
| | - Ramona Miske
- The Institute for Experimental Immunology, Affiliated to Euroimmun AG, Lubeck, Germany
| | | | - Divyanshu Dubey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Department of Neurology, Mayo Clinic, Rochester, MN, United States
| | - John R. Mills
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Sean J. Pittock
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Department of Neurology, Mayo Clinic, Rochester, MN, United States
| | - Anastasia Zekeridou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Department of Neurology, Mayo Clinic, Rochester, MN, United States
| | - Anthonina Ott
- The Institute for Experimental Immunology, Affiliated to Euroimmun AG, Lubeck, Germany
| | - Andrew McKeon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Department of Neurology, Mayo Clinic, Rochester, MN, United States
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9
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McKeon A, Lesnick C, Vorasoot N, Buckley MW, Dasari S, Flanagan EP, Gilligan M, Lafrance-Corey R, Miske R, Pittock SJ, Scharf M, Yang B, Zekeridou A, Dubey D, Mills J. Utility of Protein Microarrays for Detection of Classified and Novel Antibodies in Autoimmune Neurologic Disease. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2023; 10:e200145. [PMID: 37550073 PMCID: PMC10406426 DOI: 10.1212/nxi.0000000000200145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/01/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND AND OBJECTIVES Neural antibodies are detected by tissue-based indirect immunofluorescence assay (IFA) in Mayo Clinic's Neuroimmunology Laboratory practice, but the process of characterizing and validating novel antibodies is lengthy. We report our assessment of human protein arrays. METHODS Assessment of arrays (81% human proteome coverage) was undertaken using diverse known positive samples (17 serum and 14 CSF). Samples from patients with novel neural antibodies were reflexed from IFA to arrays. Confirmatory assays were cell-based (CBA) or line blot. Epitope mapping was undertaken using phage display immunoprecipitation sequencing (PhiPSeq). RESULTS Control positive samples known to be reactive with linear epitopes of intracellular antigens (e.g., ANNA-1 [anti-Hu]) were readily identified by arrays in 20 of 21 samples. By contrast, 10 positive controls known to be enriched with antibodies against cell surface protein conformational epitopes (e.g., GluN1 subunit of NMDA-R) were indistinguishable from background signal. Three antibodies, previously characterized by other investigators (but unclassified in our laboratory), were unmasked in 4 patients using arrays (July-December 2022): Neurexin-3α, 1 patient; regulator of gene protein signaling (RGS)8, 1 patient; and seizure-related homolog like 2 (SEZ6L2), 2 patients. All were accompanied by previously reported phenotypes (encephalitis, 1; cerebellar ataxia, 3). Patient 1 had subacute onset of seizures and encephalopathy. Neurexin-3α ranked high in CSF (second ranked neural protein) but low in serum (660th overall). Neurexin-3α CBA was positive in both samples. Patient 2 presented with rapidly progressive cerebellar ataxia. RGS8 ranked the highest neural protein in available CSF sample by array (third overall). RGS8-specific line blot was positive. Patients 3 and 4 had rapidly progressive cerebellar ataxia. SEZ6L2 was the highest ranked neural antigen by arrays in all samples (CSF, 1, serum, 2; Patient 3, ranked 9th overall in CSF, 11th in serum; Patient 4, 6th overall in serum]). By PhIPSeq, diverse neurexin-3α epitopes (including cell surface) were detected in CSF from patient 1, but no SEZ6L2 peptides were detected for serum or CSF samples from Patient 3. DISCUSSION Individualized autoimmune neurologic diagnoses may be accelerated using protein arrays. They are optimal for detection of intracellular antigen-reactive antibodies, though certain cell surface-directed antibodies (neurexin-3α and SEZ6L2) may also be detected.
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Affiliation(s)
- Andrew McKeon
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany.
| | - Connie Lesnick
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Nisa Vorasoot
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Monica W Buckley
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Surendra Dasari
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Eoin P Flanagan
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Michael Gilligan
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Reghann Lafrance-Corey
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Ramona Miske
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Sean J Pittock
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Madeleine Scharf
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Binxia Yang
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Anastasia Zekeridou
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Divyanshu Dubey
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - John Mills
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
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10
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Hawes IA, Alvarenga BD, Browne W, Wapniarski A, Dandekar R, Bartley CM, Sowa GM, DeRisi JL, Cinque P, Dravid AN, Pleasure SJ, Gisslen M, Price RW, Wilson MR. Viral co-infection, autoimmunity, and CSF HIV antibody profiles in HIV central nervous system escape. J Neuroimmunol 2023; 381:578141. [PMID: 37418948 DOI: 10.1016/j.jneuroim.2023.578141] [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: 02/14/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 07/09/2023]
Abstract
Antiretroviral therapy (ART) suppresses plasma and cerebrospinal fluid (CSF) HIV replication. Neurosymptomatic (NS) CSF escape is a rare exception in which CNS HIV replication occurs in the setting of neurologic impairment. The origins of NS escape are not fully understood. We performed a case-control study of asymptomatic (AS) escape and NS escape subjects with HIV-negative subjects as controls in which we investigated differential immunoreactivity to self-antigens in the CSF of NS escape by employing neuroanatomic CSF immunostaining and massively multiplexed self-antigen serology (PhIP-Seq). Additionally, we utilized pan-viral serology (VirScan) to deeply profile the CSF anti-viral antibody response and metagenomic next-generation sequencing (mNGS) for pathogen detection. We detected Epstein-Barr virus (EBV) DNA more frequently in the CSF of NS escape subjects than in AS escape subjects. Based on immunostaining and PhIP-Seq, there was evidence for increased immunoreactivity against self-antigens in NS escape CSF. Finally, VirScan revealed several immunodominant epitopes that map to the HIV envelope and gag proteins in the CSF of AS and NS escape subjects. Whether these additional inflammatory markers are byproducts of an HIV-driven process or whether they independently contribute to the neuropathogenesis of NS escape will require further study.
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Affiliation(s)
- I A Hawes
- Weill Institute for Neurosciences, University of California San Francisco, CA, USA; Department of Neurology, University of California San Francisco, CA, USA; University of California San Francisco, Biomedical Sciences Graduate Program, CA, USA; University of California San Francisco, School of Medicine, CA, USA
| | - B D Alvarenga
- Weill Institute for Neurosciences, University of California San Francisco, CA, USA; Department of Neurology, University of California San Francisco, CA, USA
| | - W Browne
- Weill Institute for Neurosciences, University of California San Francisco, CA, USA; Department of Neurology, University of California San Francisco, CA, USA
| | - A Wapniarski
- Weill Institute for Neurosciences, University of California San Francisco, CA, USA; Department of Neurology, University of California San Francisco, CA, USA
| | - R Dandekar
- Weill Institute for Neurosciences, University of California San Francisco, CA, USA; Department of Neurology, University of California San Francisco, CA, USA
| | - C M Bartley
- Weill Institute for Neurosciences, University of California San Francisco, CA, USA; Department of Psychiatry and Behavioral Sciences, University of California San Francisco, CA, USA
| | - G M Sowa
- University of California San Francisco, School of Medicine, CA, USA; Department of Medicine, Northwestern University, Chicago, IL, United States of America
| | - J L DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California San Francisco, CA, USA
| | - P Cinque
- Infectious Diseases, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - A N Dravid
- Poona Hospital and Research Centre and Noble Hospital, Pune, India
| | - S J Pleasure
- Weill Institute for Neurosciences, University of California San Francisco, CA, USA; Department of Neurology, University of California San Francisco, CA, USA
| | - M Gisslen
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden; Department of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - R W Price
- Weill Institute for Neurosciences, University of California San Francisco, CA, USA; Department of Neurology, University of California San Francisco, CA, USA
| | - M R Wilson
- Weill Institute for Neurosciences, University of California San Francisco, CA, USA; Department of Neurology, University of California San Francisco, CA, USA.
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11
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Carlton LH, McGregor R, Moreland NJ. Human antibody profiling technologies for autoimmune disease. Immunol Res 2023; 71:516-527. [PMID: 36690876 PMCID: PMC9870766 DOI: 10.1007/s12026-023-09362-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023]
Abstract
Autoimmune diseases are caused by the break-down in self-tolerance mechanisms and can result in the generation of autoantibodies specific to human antigens. Human autoantigen profiling technologies such as solid surface arrays and display technologies are powerful high-throughput technologies utilised to discover and map novel autoantigens associated with disease. This review compares human autoantigen profiling technologies including the application of these approaches in chronic and post-infectious autoimmune disease. Each technology has advantages and limitations that should be considered when designing new projects to profile autoantibodies. Recent studies that have utilised these technologies across a range of diseases have highlighted marked heterogeneity in autoantibody specificity between individuals as a frequent feature. This individual heterogeneity suggests that epitope spreading maybe an important mechanism in the pathogenesis of autoimmune disease in general and likely contributes to inflammatory tissue damage and symptoms. Studies focused on identifying autoantibody biomarkers for diagnosis should use targeted data analysis to identify the rarer public epitopes and antigens, common between individuals. Thus, utilisation of human autoantigen profiling technology, combined with different analysis approaches, can illuminate both pathogenesis and biomarker discovery.
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Affiliation(s)
- Lauren H Carlton
- School of Medical Sciences, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
| | - Reuben McGregor
- School of Medical Sciences, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Nicole J Moreland
- School of Medical Sciences, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
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12
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Klepper A, Kung A, Vazquez SE, Mitchell A, Mann S, 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 J, 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 2023:2023.06.12.23291297. [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
Autoimmune hepatitis (AIH) is a severe autoimmune disease, characterized by the presence of autoantibodies. However, the role of autoantibodies in the pathophysiology of AIH remains uncertain. Here, we employed Phage Immunoprecipitation-Sequencing (PhIP-Seq) to identify novel autoantibodies in AIH. Using these results, a logistic regression classifier was able to predict which patients had AIH, indicating the presence of a distinct humoral immune signature. To further investigate the autoantibodies most specific to AIH, significant peptides were identified relative to a broad array of controls (298 patients with non-alcoholic fatty liver disease (NAFLD), primary biliary cholangitis (PBC), or healthy controls). Top ranked autoreactive targets included SLA, the target of a well-recognized autoantibody in AIH, and disco interacting protein 2 homolog A (DIP2A). The autoreactive fragment of DIP2A shares a 9-amino acid stretch nearly identical to the U27 protein of HHV-6B, a virus found in the liver. In addition, antibodies against peptides derived from the leucine rich repeat N-terminal (LRRNT) domain of the relaxin family peptide receptor 1 (RXFP1) were highly enriched and specific to AIH. The enriched peptides map to a motif adjacent to the receptor binding domain, which is required for RXFP1 signaling. RXFP1 is a G protein-coupled receptor that binds relaxin-2, an anti-fibrogenic molecule shown to reduce the myofibroblastic phenotype of hepatic stellate cells. Eight of nine patients with antibodies to RXFP1 had evidence of advanced fibrosis (F3 or greater). Furthermore, serum from AIH patients positive for anti-RFXP1 antibody was able to significantly inhibit relaxin-2 signaling in the human monocytic cell line, THP1. Depletion of IgG from anti-RXFP1 positive serum abrogated this effect. These data provide supporting evidence that HHV6 plays a role in the development of AIH and point to a potential pathogenic role for anti-RXFP1 IgG in some patients. Identification of anti-RXFP1 in patient serum may enable risk stratification of AIH patients for fibrosis progression and lead to the development of novel strategies for disease intervention.
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Affiliation(s)
| | - Andrew Kung
- University of California, San Francisco, USA
- Chan Zuckerberg Biohub; San Francisco, CA, USA
| | - Sara E Vazquez
- University of California, San Francisco, USA
- Chan Zuckerberg Biohub; San Francisco, CA, USA
| | - Anthea Mitchell
- University of California, San Francisco, USA
- Chan Zuckerberg Biohub; San Francisco, CA, USA
| | - Sabrina Mann
- University of California, San Francisco, USA
- Chan Zuckerberg Biohub; San Francisco, CA, USA
| | - Kelsey Zorn
- University of California, San Francisco, USA
| | | | - Swathi Kari
- University of California, San Francisco, USA
| | | | | | - Briton Lee
- University of California, San Francisco, USA
| | | | - Mandana Khalili
- University of California, San Francisco, USA
- UCSF Liver Center
| | - Monica Yang
- University of California, San Francisco, USA
| | | | - Jennifer Price
- University of California, San Francisco, USA
- UCSF Liver Center
| | - Emily Perito
- University of California, San Francisco, USA
- UCSF Liver Center
| | - Sandy Feng
- University of California, San Francisco, USA
- UCSF Liver Center
| | | | - Jennifer Lai
- University of California, San Francisco, USA
- UCSF Liver Center
| | | | - Ansgar W Lohse
- Medical Department, University Medical Center Hamburg-Eppendorf, Hamburg, DE
| | - Joseph DeRisi
- University of California, San Francisco, USA
- Chan Zuckerberg Biohub; San Francisco, CA, USA
| | - Michele Tana
- University of California, San Francisco, USA
- UCSF Liver Center
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13
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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: 6] [Impact Index Per Article: 6.0] [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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14
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Yoon YM, Velez TE, Upadhyay V, Vazquez SE, Lee CT, Selvan KC, Law CS, Blaine KM, Hollinger MK, Decker DC, Clark MR, Strek ME, Guzy RD, Adegunsoye A, Noth I, Wolters PJ, Anderson M, DeRisi JL, Shum AK, Sperling AI. Antigenic responses are hallmarks of fibrotic interstitial lung diseases independent of underlying etiologies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.08.23289640. [PMID: 37214861 PMCID: PMC10197719 DOI: 10.1101/2023.05.08.23289640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Interstitial lung diseases (ILD) are heterogeneous conditions that may lead to progressive fibrosis and death of affected individuals. Despite diversity in clinical manifestations, enlargement of lung-associated lymph nodes (LLN) in fibrotic ILD patients predicts worse survival. Herein, we revealed a common adaptive immune landscape in LLNs of all ILD patients, characterized by highly activated germinal centers and antigen-activated T cells including regulatory T cells (Tregs). In support of these findings, we identified serum reactivity to 17 candidate auto-antigens in ILD patients through a proteome-wide screening using phage immunoprecipitation sequencing. Autoantibody responses to actin binding LIM protein 1 (ABLIM1), a protein highly expressed in aberrant basaloid cells of fibrotic lungs, were correlated with LLN frequencies of T follicular helper cells and Tregs in ILD patients. Together, we demonstrate that end-stage ILD patients have converging immune mechanisms, in part driven by antigen-specific immune responses, which may contribute to disease progression.
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Affiliation(s)
- Young me Yoon
- University of Chicago, Department of Medicine, Chicago, IL 60637
| | - Tania E. Velez
- University of Virginia, Department of Medicine, Charlottesville, VA 22908
| | - Vaibhav Upadhyay
- University of California San Francisco, Department of Medicine, San Francisco, CA 94143
| | - Sara E. Vazquez
- University of California San Francisco and Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Cathryn T. Lee
- University of Chicago, Department of Medicine, Chicago, IL 60637
| | | | - Christopher S. Law
- University of California San Francisco, Department of Medicine, San Francisco, CA 94143
| | - Kelly M. Blaine
- University of Chicago, Department of Medicine, Chicago, IL 60637
| | - Maile K. Hollinger
- University of Chicago, Department of Medicine, Chicago, IL 60637
- University of Virginia, Department of Medicine, Charlottesville, VA 22908
| | - Donna C. Decker
- University of Chicago, Department of Medicine, Chicago, IL 60637
| | - Marcus R. Clark
- University of Chicago, Department of Medicine, Chicago, IL 60637
| | - Mary E. Strek
- University of Chicago, Department of Medicine, Chicago, IL 60637
| | - Robert D. Guzy
- University of Wisconsin at Madison, Department of Medicine, Madison, WI 53792
| | | | - Imre Noth
- University of Virginia, Department of Medicine, Charlottesville, VA 22908
| | - Paul J. Wolters
- University of California San Francisco, Department of Medicine, San Francisco, CA 94143
| | - Mark Anderson
- University of California San Francisco, Department of Medicine, San Francisco, CA 94143
| | - Joseph L. DeRisi
- University of California San Francisco and Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Anthony K. Shum
- University of California San Francisco, Department of Medicine, San Francisco, CA 94143
| | - Anne I. Sperling
- University of Chicago, Department of Medicine, Chicago, IL 60637
- University of Virginia, Department of Medicine, Charlottesville, VA 22908
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15
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McAlpine LS, Lifland B, Check JR, Angarita GA, Ngo TT, Chen P, Dandekar R, Alvarenga BD, Browne WD, Pleasure SJ, Wilson MR, Spudich SS, Farhadian SF, Bartley CM. Anti-SARS-CoV-2 and Autoantibody Profiling of a COVID-19 Patient With Subacute Psychosis Who Remitted After Treatment With Intravenous Immunoglobulin. Biol Psychiatry 2023; 93:e25-e29. [PMID: 36481066 PMCID: PMC9722219 DOI: 10.1016/j.biopsych.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Lindsay S McAlpine
- Department of Neurology, Yale University School of Medicine, New Haven, Connecticut
| | - Brooke Lifland
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Joseph R Check
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Gustavo A Angarita
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Thomas T Ngo
- Weill Institute for Neurosciences, University of California, San Francisco, California; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, California
| | - Peixi Chen
- Weill Institute for Neurosciences, University of California, San Francisco, California; Department of Neurology, University of California, San Francisco, California
| | - Ravi Dandekar
- Weill Institute for Neurosciences, University of California, San Francisco, California; Department of Neurology, University of California, San Francisco, California
| | - Bonny D Alvarenga
- Weill Institute for Neurosciences, University of California, San Francisco, California; Department of Neurology, University of California, San Francisco, California
| | - Weston D Browne
- Weill Institute for Neurosciences, University of California, San Francisco, California; Department of Neurology, University of California, San Francisco, California
| | - Samuel J Pleasure
- Weill Institute for Neurosciences, University of California, San Francisco, California; Department of Neurology, University of California, San Francisco, California
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, California; Department of Neurology, University of California, San Francisco, California
| | - Serena S Spudich
- Department of Neurology, Yale University School of Medicine, New Haven, Connecticut
| | - Shelli F Farhadian
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut
| | - Christopher M Bartley
- Weill Institute for Neurosciences, University of California, San Francisco, California; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, California.
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16
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Zhao J, Wu Y, Xiao T, Cheng C, Zhang T, Gao Z, Hu S, Ren Z, Yu X, Yang F, Li G. A specific anti-cyclin D1 intrabody represses breast cancer cell proliferation by interrupting the cyclin D1-CDK4 interaction. Breast Cancer Res Treat 2023; 198:555-568. [PMID: 36808524 DOI: 10.1007/s10549-023-06866-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/18/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND Cyclin D1 overexpression may contribute to development of various cancers, including breast cancer, and thus may serve as a key cancer diagnostic marker and therapeutic target. In our previous study, we generated a cyclin D1-specific single-chain variable fragment antibody (ADκ) from a human semi-synthetic single-chain variable fragment library. ADκ specifically interacted with recombinant and endogenous cyclin D1 proteins through an unknown molecular basis to inhibit HepG2 cell growth and proliferation. RESULTS Here, using phage display and in silico protein structure modeling methods combined with cyclin D1 mutational analysis, key residues that bind to ADκ were identified. Notably, residue K112 within the cyclin box was required for cyclin D1-ADκ binding. In order to elucidate the molecular mechanism underlying ADκ anti-tumor effects, a cyclin D1-specific nuclear localization signal-containing intrabody (NLS-ADκ) was constructed. When expressed within cells, NLS-ADκ interacted specifically with cyclin D1 to significantly inhibit cell proliferation, induce G1-phase arrest, and trigger apoptosis of MCF-7 and MDA-MB-231 breast cancer cells. Moreover, the NLS-ADκ-cyclin D1 interaction blocked binding of cyclin D1 to CDK4 and inhibited RB protein phosphorylation, resulting in altered expression of downstream cell proliferation-related target genes. CONCLUSION We identified amino acid residues in cyclin D1 that may play key roles in the ADκ-cyclin D1 interaction. A nuclear localization antibody against cyclin D1 (NLS-ADκ) was constructed and successfully expressed in breast cancer cells. NLS-ADκ exerted tumor suppressor effects via blocking the binding of CDK4 to cyclin D1 and inhibiting phosphorylation of RB. The results presented here demonstrate anti-tumor potential of intrabody-based cyclin D1-targeted breast cancer therapy.
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Affiliation(s)
- Jialiang Zhao
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Yan Wu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
- Medical Research Center, Binzhou Medical University Hospital, Binzhou, 256600, China
| | - Tong Xiao
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Cheng Cheng
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Tong Zhang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Ziyang Gao
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Siyuan Hu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Ze Ren
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Xinze Yu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Fang Yang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China.
| | - Guiying Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China.
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17
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Raghavan M, Kalantar KL, Duarte E, Teyssier N, Takahashi S, Kung AF, Rajan JV, Rek J, Tetteh KKA, Drakeley C, Ssewanyana I, Rodriguez-Barraquer I, Greenhouse B, DeRisi JL. Antibodies to repeat-containing antigens in Plasmodium falciparum are exposure-dependent and short-lived in children in natural malaria infections. eLife 2023; 12:e81401. [PMID: 36790168 PMCID: PMC10005774 DOI: 10.7554/elife.81401] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 02/14/2023] [Indexed: 02/16/2023] Open
Abstract
Protection against Plasmodium falciparum, which is primarily antibody-mediated, requires recurrent exposure to develop. The study of both naturally acquired limited immunity and vaccine induced protection against malaria remains critical for ongoing eradication efforts. Towards this goal, we deployed a customized P. falciparum PhIP-seq T7 phage display library containing 238,068 tiled 62-amino acid peptides, covering all known coding regions, including antigenic variants, to systematically profile antibody targets in 198 Ugandan children and adults from high and moderate transmission settings. Repeat elements - short amino acid sequences repeated within a protein - were significantly enriched in antibody targets. While breadth of responses to repeat-containing peptides was twofold higher in children living in the high versus moderate exposure setting, no such differences were observed for peptides without repeats, suggesting that antibody responses to repeat-containing regions may be more exposure dependent and/or less durable in children than responses to regions without repeats. Additionally, short motifs associated with seroreactivity were extensively shared among hundreds of antigens, potentially representing cross-reactive epitopes. PfEMP1 shared motifs with the greatest number of other antigens, partly driven by the diversity of PfEMP1 sequences. These data suggest that the large number of repeat elements and potential cross-reactive epitopes found within antigenic regions of P. falciparum could contribute to the inefficient nature of malaria immunity.
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Affiliation(s)
- Madhura Raghavan
- University of California, San FranciscoSan FranciscoUnited States
| | | | - Elias Duarte
- University of California, BerkeleyBerkeleyUnited States
| | - Noam Teyssier
- University of California, San FranciscoSan FranciscoUnited States
| | - Saki Takahashi
- University of California, San FranciscoSan FranciscoUnited States
| | - Andrew F Kung
- University of California, San FranciscoSan FranciscoUnited States
| | - Jayant V Rajan
- University of California, San FranciscoSan FranciscoUnited States
| | - John Rek
- Infectious Diseases Research CollaborationKampalaUganda
| | - Kevin KA Tetteh
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Chris Drakeley
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Isaac Ssewanyana
- Infectious Diseases Research CollaborationKampalaUganda
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Isabel Rodriguez-Barraquer
- University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Bryan Greenhouse
- University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Joseph L DeRisi
- University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
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18
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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: 1.0] [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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19
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Bartley CM, Ngo TT, Cadwell CR, Harroud A, Schubert RD, Alvarenga BD, Hawes IA, Zorn KC, Hunyh T, Teliska LH, Kung AF, Shah S, Gelfand JM, Chow FC, Rasband MN, Dubey D, Pittock SJ, DeRisi JL, Wilson MR, Pleasure SJ. Dual ankyrinG and subpial autoantibodies in a man with well-controlled HIV infection with steroid-responsive meningoencephalitis: A case report. Front Neurol 2023; 13:1102484. [PMID: 36756346 PMCID: PMC9900111 DOI: 10.3389/fneur.2022.1102484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/16/2022] [Indexed: 01/24/2023] Open
Abstract
Neuroinvasive infection is the most common cause of meningoencephalitis in people living with human immunodeficiency virus (HIV), but autoimmune etiologies have been reported. We present the case of a 51-year-old man living with HIV infection with steroid-responsive meningoencephalitis whose comprehensive pathogen testing was non-diagnostic. Subsequent tissue-based immunofluorescence with acute-phase cerebrospinal fluid revealed anti-neural antibodies localizing to the axon initial segment (AIS), the node of Ranvier (NoR), and the subpial space. Phage display immunoprecipitation sequencing identified ankyrinG (AnkG) as the leading candidate autoantigen. A synthetic blocking peptide encoding the PhIP-Seq-identified AnkG epitope neutralized CSF IgG binding to the AIS and NoR, thereby confirming a monoepitopic AnkG antibody response. However, subpial immunostaining persisted, indicating the presence of additional autoantibodies. Review of archival tissue-based staining identified candidate AnkG autoantibodies in a 60-year-old woman with metastatic ovarian cancer and seizures that were subsequently validated by cell-based assay. AnkG antibodies were not detected by tissue-based assay and/or PhIP-Seq in control CSF (N = 39), HIV CSF (N = 79), or other suspected and confirmed neuroinflammatory CSF cases (N = 1,236). Therefore, AnkG autoantibodies in CSF are rare but extend the catalog of AIS and NoR autoantibodies associated with neurological autoimmunity.
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Affiliation(s)
- Christopher M. Bartley
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Thomas T. Ngo
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Cathryn R. Cadwell
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Adil Harroud
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Ryan D. Schubert
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Bonny D. Alvarenga
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Isobel A. Hawes
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, United States
| | - Kelsey C. Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Trung Hunyh
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Lindsay H. Teliska
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Andrew F. Kung
- School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Shailee Shah
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, United States
- Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, United States
| | - Jeffrey M. Gelfand
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Felicia C. Chow
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Matthew N. Rasband
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Divyanshu Dubey
- Department of Neurology, Mayo Clinic Foundation, Rochester, MN, United States
- Department of Laboratory Medicine and Pathology, Mayo Clinic Foundation, Rochester, MN, United States
| | - Sean J. Pittock
- Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, United States
- Department of Neurology, Mayo Clinic Foundation, Rochester, MN, United States
- Department of Laboratory Medicine and Pathology, Mayo Clinic Foundation, Rochester, MN, United States
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Michael R. Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Samuel J. Pleasure
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
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20
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Chen J, Li H, Zhao T, Chen K, Chen MH, Sun Z, Xu W, Maas K, Lester B, Cong X. The impact of early life experiences and gut microbiota on neurobehavioral development among preterm infants: A longitudinal cohort study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.04.23284200. [PMID: 36711616 PMCID: PMC9882379 DOI: 10.1101/2023.01.04.23284200] [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] [Indexed: 01/09/2023]
Abstract
Objectives To investigate the impact of early life experiences and gut microbiota on neurobehavioral development among preterm infants during neonatal intensive care unit (NICU) hospitalization. Methods Preterm infants were followed from the NICU admission until their 28 th postnatal day or until discharge. Daily stool samples, painful/stressful experiences, feeding patterns, and other clinical and demographic data were collected. Gut microbiota was profiled using 16S rRNA sequencing, and operational taxonomic units (OTUs) were selected to predict the neurobehaviors. The neurobehavioral development was assessed by the Neonatal Neurobehavioral Scale (NNNS) at 36 to 38 weeks of post-menstrual age (PMA). Fifty-five infants who had NNNS measurements were included in the sparse log-contrast regression analysis. Results Preterm infants who experienced high level of pain/stress during the NICU hospitalization that were associated with higher NNNS stress/abstinence scores. Eight operational taxonomic units (OTUs) were identified to be associated with of NNNS subscales after controlling demographic and clinical features, feeding patterns, and painful/stressful experiences. These OTUs, taxa belong to seven genera including Enterobacteriaceae_unclassified, Escherichia-Shigella, Incertae_Sedis, Veillonella, Enterococcus, Clostridium_sensu_stricto_1 , and Streptococcus with five belonging to Firmicutes and two belonging to Proteobacteria phylum. The enriched abundance of Enterobacteriaceae_unclassified (OTU17) and Streptococcus (OTU28) were consistently associated with less optimal neurobehavioral outcomes. The other six OTUs were also associated with infant neurobehavioral responses depending on days at NICU stay. Conclusions This study explored the dynamic impact of specific OTUs on neurobehavioral development among preterm infants after controlling for early life experiences, i.e., acute and chronic pain/stress, and feeding in the NICU.
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Affiliation(s)
- Jie Chen
- Florida State University College of Nursing, Tallahassee, FL., United States
- School of Nursing, University of Connecticut, Storrs, CT., United States
| | - Hongfei Li
- Department of Statistics, University of Connecticut, Storrs, CT., United States
| | - Tingting Zhao
- School of Nursing, University of Connecticut, Storrs, CT., United States
| | - Kun Chen
- Department of Statistics, University of Connecticut, Storrs, CT., United States
| | - Ming-Hui Chen
- Department of Statistics, University of Connecticut, Storrs, CT., United States
| | - Zhe Sun
- Department of Statistics, University of Connecticut, Storrs, CT., United States
- Department of Biostatistics, Yale School of Public Health, New Haven, CT., United States
| | - Wanli Xu
- School of Nursing, University of Connecticut, Storrs, CT., United States
| | - Kendra Maas
- University of Connecticut, Microbial Analysis, Resources, and Services (MARS), Storrs, CT., United States
| | - Barry Lester
- Brown Center for the Study of Children at Risk, Departments of Psychiatry and Pediatrics, Warren Alpert Medical School of Brown University, Providence, RI., United States
| | - Xiaomei Cong
- School of Nursing, University of Connecticut, Storrs, CT., United States
- Yale University School of Nursing, Orange, CT., United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT., United States
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21
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Mandel-Brehm C, Vazquez SE, Liverman C, Cheng M, Quandt Z, Kung AF, Parent A, Miao B, Disse E, Cugnet-Anceau C, Dalle S, Orlova E, Frolova E, Alba D, Michels A, Oftedal BE, Lionakis MS, Husebye ES, Agarwal AK, Li X, Zhu C, Li Q, Oral E, Brown R, Anderson MS, Garg A, DeRisi JL. Autoantibodies to Perilipin-1 Define a Subset of Acquired Generalized Lipodystrophy. Diabetes 2023; 72:59-70. [PMID: 35709010 PMCID: PMC9797316 DOI: 10.2337/db21-1172] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023]
Abstract
Acquired lipodystrophy is often characterized as an idiopathic subtype of lipodystrophy. Despite suspicion of an immune-mediated pathology, biomarkers such as autoantibodies are generally lacking. Here, we used an unbiased proteome-wide screening approach to identify autoantibodies to the adipocyte-specific lipid droplet protein perilipin 1 (PLIN1) in a murine model of autoimmune polyendocrine syndrome type 1 (APS1). We then tested for PLIN1 autoantibodies in human subjects with acquired lipodystrophy with two independent severe breaks in immune tolerance (including APS1) along with control subjects using a specific radioligand binding assay and indirect immunofluorescence on fat tissue. We identified autoantibodies to PLIN1 in these two cases, including the first reported case of APS1 with acquired lipodystrophy and a second patient who acquired lipodystrophy as an immune-related adverse event following cancer immunotherapy. Lastly, we also found PLIN1 autoantibodies to be specifically enriched in a subset of patients with acquired generalized lipodystrophy (17 of 46 [37%]), particularly those with panniculitis and other features of autoimmunity. These data lend additional support to new literature that suggests that PLIN1 autoantibodies represent a marker of acquired autoimmune lipodystrophies and further link them to a break in immune tolerance.
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Affiliation(s)
- Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | - Sara E. Vazquez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Christopher Liverman
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Mickie Cheng
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Zoe Quandt
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Andrew F. Kung
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | - Audrey Parent
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Brenda Miao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Emmanuel Disse
- Endocrinology Diabetology and Nutrition Department, Lyon Sud Hospital, Hospices Civils de Lyon, Pierre-Bénite, France
- ImmuCare, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Lyon, France
| | - Christine Cugnet-Anceau
- Endocrinology Diabetology and Nutrition Department, Lyon Sud Hospital, Hospices Civils de Lyon, Pierre-Bénite, France
- ImmuCare, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Lyon, France
| | - Stéphane Dalle
- ImmuCare, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Lyon, France
- Dermatology Department, Lyon Sud Hospital, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Elizaveta Orlova
- Endocrinology Research Centre, Institute of Paediatric Endocrinology, Moscow, Russia
| | - Elena Frolova
- National Medical Research Center of Children’s Health, Moscow, Russia
| | - Diana Alba
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Aaron Michels
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO
| | - Bergithe E. Oftedal
- University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Michail S. Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Eystein S. Husebye
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science and K.G. Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway
| | - Anil K. Agarwal
- Division of Nutrition and Metabolic Diseases, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX
| | - Xilong Li
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX
| | - Chengsong Zhu
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX
| | - Quan Li
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX
| | - Elif Oral
- Division of Metabolism, Endocrinology & Diabetes and Caswell Diabetes Institute, University of Michigan, Ann Arbor, MI
| | - Rebecca Brown
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Mark S. Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Abhimanyu Garg
- Division of Nutrition and Metabolic Diseases, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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22
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Ramasubramanian B, Reddy VS, Chellappan V, Ramakrishna S. Emerging Materials, Wearables, and Diagnostic Advancements in Therapeutic Treatment of Brain Diseases. BIOSENSORS 2022; 12:1176. [PMID: 36551143 PMCID: PMC9775999 DOI: 10.3390/bios12121176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Among the most critical health issues, brain illnesses, such as neurodegenerative conditions and tumors, lower quality of life and have a significant economic impact. Implantable technology and nano-drug carriers have enormous promise for cerebral brain activity sensing and regulated therapeutic application in the treatment and detection of brain illnesses. Flexible materials are chosen for implantable devices because they help reduce biomechanical mismatch between the implanted device and brain tissue. Additionally, implanted biodegradable devices might lessen any autoimmune negative effects. The onerous subsequent operation for removing the implanted device is further lessened with biodegradability. This review expands on current developments in diagnostic technologies such as magnetic resonance imaging, computed tomography, mass spectroscopy, infrared spectroscopy, angiography, and electroencephalogram while providing an overview of prevalent brain diseases. As far as we are aware, there hasn't been a single review article that addresses all the prevalent brain illnesses. The reviewer also looks into the prospects for the future and offers suggestions for the direction of future developments in the treatment of brain diseases.
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Affiliation(s)
- Brindha Ramasubramanian
- Department of Mechanical Engineering, Center for Nanofibers & Nanotechnology, National University of Singapore, Singapore 117574, Singapore
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), #08-03, 2 Fusionopolis Way, Innovis, Singapore 138634, Singapore
| | - Vundrala Sumedha Reddy
- Department of Mechanical Engineering, Center for Nanofibers & Nanotechnology, National University of Singapore, Singapore 117574, Singapore
| | - Vijila Chellappan
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), #08-03, 2 Fusionopolis Way, Innovis, Singapore 138634, Singapore
| | - Seeram Ramakrishna
- Department of Mechanical Engineering, Center for Nanofibers & Nanotechnology, National University of Singapore, Singapore 117574, Singapore
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23
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Qi H, Xue JB, Lai DY, Li A, Tao SC. Current advances in antibody-based serum biomarker studies: From protein microarray to phage display. Proteomics Clin Appl 2022; 16:e2100098. [PMID: 36071670 DOI: 10.1002/prca.202100098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 08/16/2022] [Accepted: 09/05/2022] [Indexed: 12/30/2022]
Abstract
PURPOSE This review aims to summarize the technological advances in the field of antibody-based biomarker studies by proteome microarray and phage display. In addition, the possible development directions of this field are also discussed. EXPERIMENTAL DESIGN We have focused on the antibody profiling by proteome microarray and phage display, including the technological advances, the tools/resources constructed, and the characteristics of both platforms. RESULTS With the help of tools/resources and technological advances in proteome microarray and phage display, the efficiency of profiling antibody-based biomarkers in serum samples has been greatly improved. CONCLUSIONS In the past few years, proteome microarray and phage display, especially the latter one, have already demonstrated their capacity and efficiency for biomarker identification. In the near future, we believe that more antibody-based biomarkers could be identified, and some of them could eventually be developed into real clinical applications.
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Affiliation(s)
- Huan Qi
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Jun-Biao Xue
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Dan-Yun Lai
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Ang Li
- College of Life Sciences, Shanghai Normal 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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24
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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: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [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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25
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Moritz CP, Do LD, Tholance Y, Vallayer PB, Rogemond V, Joubert B, Ferraud K, La Marca C, Camdessanché JP, Honnorat J, Antoine JC. Conformation-stabilizing ELISA and cell-based assays reveal patient subgroups targeting three different epitopes of AGO1 antibodies. Front Immunol 2022; 13:972161. [DOI: 10.3389/fimmu.2022.972161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
Autoantibodies (Abs) are biomarkers for many disease conditions and are increasingly used to facilitate diagnosis and treatment decisions. To guarantee high sensitivity and specificity, the choice of their detection method is crucial. Via cell-based assays, we recently found 21 patients with neurological diseases positive for antibodies against argonaute (AGO), 10 of which having a neuropathy (NP). Here, we established a simple and conformation-sensitive ELISA with the aim to distinguish between AGO1 Abs against conformational epitopes and non-conformational epitopes and to reveal further characteristics of AGO1 antibodies in NP and autoimmune disease (AID). In a retrospective multicenter case/control and observational study, we tested 434 patients with NP, 274 disease controls with AID, and 116 healthy controls (HC) for AGO1 Abs via conformation-stabilizing ELISA. Seropositive patients were also tested for conformation-specificity via comparative denaturing/stabilizing ELISA (CODES-ELISA), CBA positivity, AGO1 titers and IgG subclasses, and AGO2 reactivity. These parameters were statistically compared among different epitope-specific patient groups. We found Abs in 44 patients, including 28/434 (6.5%) NP, 16/274 (5.8%) AID, and 0/116 (0%) HC. Serum reactivity was consistently higher for AGO1 than AGO2. Globally among the 44 AGO1 Abs-positive patients, 42 were also tested in CBA for AGO1 Abs positivity and 15 (35.7%) were positive. Furthermore, 43 were tested for conformation-specificity and 32 (74.4%) bound a conformational epitope. Among the subgroups of highly positive patients (ELISA z-score >14) with sera binding conformational epitopes (n=23), 14 patient sera were also CBA positive and 9 bound a second conformational but CBA-inaccessible epitope. A third, non-conformational epitope was bound by 11/43 (15.6%). Among the epitope-specific patient subgroups, we found significant differences regarding the Abs titers, IgG subclass, and AGO2 reactivity. When comparing AGO1 Abs-positive NP versus AID patients, we found the conformation-specific and CBA inaccessible epitope significantly more frequently in AID patients. We conclude that 1) conformational ELISA was more sensitive than CBA in detecting AGO1 Abs, 2) serum reactivity is higher for AGO1 than for AGO2 at least for NP patients, 3) AGO1 Abs might be a marker-of-interest in 6.5% of NP patients, 4) distinguishing epitopes might help finding different patient subgroups.
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26
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Mandel‐Brehm C, Benson LA, Tran B, Kung AF, Mann SA, Vazquez SE, Retallack H, Sample HA, Zorn KC, Khan LM, Kerr LM, McAlpine PL, Zhang L, McCarthy F, Elias JE, Katwa U, Astley CM, Tomko S, Dalmau J, Seeley WW, Pleasure SJ, Wilson MR, Gorman MP, DeRisi JL. ZSCAN1 Autoantibodies Are Associated with Pediatric Paraneoplastic ROHHAD. Ann Neurol 2022; 92:279-291. [PMID: 35466441 PMCID: PMC9329235 DOI: 10.1002/ana.26380] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Rapid-onset Obesity with Hypothalamic Dysfunction, Hypoventilation and Autonomic Dysregulation (ROHHAD), is a severe pediatric disorder of uncertain etiology resulting in hypothalamic dysfunction and frequent sudden death. Frequent co-occurrence of neuroblastic tumors have fueled suspicion of an autoimmune paraneoplastic neurological syndrome (PNS); however, specific anti-neural autoantibodies, a hallmark of PNS, have not been identified. Our objective is to determine if an autoimmune paraneoplastic etiology underlies ROHHAD. METHODS Immunoglobulin G (IgG) from pediatric ROHHAD patients (n = 9), non-inflammatory individuals (n = 100) and relevant pediatric controls (n = 25) was screened using a programmable phage display of the human peptidome (PhIP-Seq). Putative ROHHAD-specific autoantibodies were orthogonally validated using radioactive ligand binding and cell-based assays. Expression of autoantibody targets in ROHHAD tumor and healthy brain tissue was assessed with immunohistochemistry and mass spectrometry, respectively. RESULTS Autoantibodies to ZSCAN1 were detected in ROHHAD patients by PhIP-Seq and orthogonally validated in 7/9 ROHHAD patients and 0/125 controls using radioactive ligand binding and cell-based assays. Expression of ZSCAN1 in ROHHAD tumor and healthy human brain tissue was confirmed. INTERPRETATION Our results support the notion that tumor-associated ROHHAD syndrome is a pediatric PNS, potentially initiated by an immune response to peripheral neuroblastic tumor. ZSCAN1 autoantibodies may aid in earlier, accurate diagnosis of ROHHAD syndrome, thus providing a means toward early detection and treatment. This work warrants follow-up studies to test sensitivity and specificity of a novel diagnostic test. Last, given the absence of the ZSCAN1 gene in rodents, our study highlights the value of human-based approaches for detecting novel PNS subtypes. ANN NEUROL 2022;92:279-291.
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Affiliation(s)
- Caleigh Mandel‐Brehm
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | | | - Baouyen Tran
- Weill Institute for Neurosciences, Department of NeurologyUniversity of CaliforniaSan FranciscoCAUSA
| | - Andrew F. Kung
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | - Sabrina A. Mann
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | - Sara E. Vazquez
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | - Hanna Retallack
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | - Hannah A. Sample
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | - Kelsey C. Zorn
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | - Lillian M. Khan
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | - Lauren M. Kerr
- Department of NeurologyBoston Children's HospitalBostonMAUSA
| | - Patrick L. McAlpine
- Otolaryngology Head and Neck Surgery Research DivisionStanford UniversityStanfordCAUSA
| | | | | | | | - Umakanth Katwa
- Department of Pulmonary MedicineSleep Center, Boston Children's HospitalBostonMAUSA
| | - Christina M. Astley
- Division of Endocrinology & Computational EpidemiologyBoston Children's HospitalBostonMAUSA
| | - Stuart Tomko
- Department of NeurologyWashington UniversitySt. LouisMOUSA
| | - Josep Dalmau
- Catalan Institution for Research and Advanced Studies (ICREA), Hospital Clinic‐IdibapsUniversity of BarcelonaBarcelonaSpain
| | - William W. Seeley
- Memory and Aging Center, Department of NeurologyUniversity of CaliforniaSan FranciscoCAUSA
| | - Samuel J. Pleasure
- Weill Institute for Neurosciences, Department of NeurologyUniversity of CaliforniaSan FranciscoCAUSA
| | - Michael R. Wilson
- MAS, Weill Institute for Neurosciences, Department of NeurologyUniversity of CaliforniaSan FranciscoCAUSA
| | - Mark P. Gorman
- Department of NeurologyHarvard Medical SchoolBostonMAUSA
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
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Rasquinha MT, Lasrado N, Petro-Turnquist E, Weaver E, Venkataraman T, Anderson D, Laserson U, Larman HB, Reddy J. PhIP-Seq Reveals Autoantibodies for Ubiquitously Expressed Antigens in Viral Myocarditis. BIOLOGY 2022; 11:biology11071055. [PMID: 36101433 PMCID: PMC9312229 DOI: 10.3390/biology11071055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022]
Abstract
Simple Summary Myocarditis is the inflammation of the heart muscle, and viral infections are a common cause of this disease. Myocarditis in some patients can progress to dilated cardiomyopathy (DCM). The mouse model of coxsackievirus B3 (CVB3) is commonly used to understand this disease progression in DCM patients. In this paper, we have attempted to analyze antibodies for heart antigens that could be produced as a result of heart damage in animals infected with CVB3 using a technique called Phage ImmunoPrecipitation Sequencing (PhIP-Seq). The analyses led us to identify antibodies for several proteins that were not previously reported that may have relevance to human disease. Abstract Enteroviruses such as group B coxsackieviruses (CVB) are commonly suspected as causes of myocarditis that can lead to dilated cardiomyopathy (DCM), and the mouse model of CVB3 myocarditis is routinely used to understand DCM pathogenesis. Mechanistically, autoimmunity is suspected due to the presence of autoantibodies for select antigens. However, their role continues to be enigmatic, which also raises the question of whether the breadth of autoantibodies is sufficiently characterized. Here, we attempted to comprehensively analyze the autoantibody repertoire using Phage ImmunoPrecipitation Sequencing (PhIP-Seq), a versatile and high-throughput platform, in the mouse model of CVB3 myocarditis. First, PhIP-Seq analysis using the VirScan library revealed antibody reactivity only to CVB3 in the infected group but not in controls, thus validating the technique in this model. Second, using the mouse peptide library, we detected autoantibodies to 32 peptides from 25 proteins in infected animals that are ubiquitously expressed and have not been previously reported. Third, by using ELISA as a secondary assay, we confirmed antibody reactivity in sera from CVB3-infected animals to cytochrome c oxidase assembly factor 4 homolog (COA4) and phosphoinositide-3-kinase adaptor protein 1 (PIK3AP1), indicating the specificity of antibody detection by PhIP-Seq technology. Fourth, we noted similar antibody reactivity patterns in CVB3 and CVB4 infections, suggesting that the COA4- and PIK3AP1-reactive antibodies could be common to multiple CVB infections. The specificity of the autoantibodies was affirmed with influenza-infected animals that showed no reactivity to any of the antigens tested. Taken together, our data suggest that the autoantibodies identified by PhIP-Seq may have relevance to CVB pathogenesis, with a possibility that similar reactivity could be expected in human DCM patients.
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Affiliation(s)
- Mahima T. Rasquinha
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (M.T.R.); (N.L.)
| | - Ninaad Lasrado
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (M.T.R.); (N.L.)
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Erika Petro-Turnquist
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (E.P.-T.); (E.W.)
| | - Eric Weaver
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (E.P.-T.); (E.W.)
| | - Thiagarajan Venkataraman
- Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA;
| | - Daniel Anderson
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Uri Laserson
- Department of Genetics and Genomic Sciences and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - H. Benjamin Larman
- Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA;
- Correspondence: (H.B.L.); (J.R.); Tel.: +1-(410)-614-6525 (H.B.L); +1-(402)-472-8541 (J.R.)
| | - Jay Reddy
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (M.T.R.); (N.L.)
- Correspondence: (H.B.L.); (J.R.); Tel.: +1-(410)-614-6525 (H.B.L); +1-(402)-472-8541 (J.R.)
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28
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Vazquez SE, Mann SA, Bodansky A, Kung AF, Quandt Z, Ferré EMN, Landegren N, Eriksson D, Bastard P, Zhang S, Liu J, Mitchell A, Mandel-brehm C, Miao B, Sowa G, Zorn K, Chan AY, Shimizu C, Tremoulet A, Lynch K, Wilson MR, Kampe O, Dobbs K, Delmonte OM, Notarangelo LD, Burns JC, Casanova J, Lionakis MS, Torgerson TR, Anderson MS, Derisi JL. Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq.. [PMID: 35350199 PMCID: PMC8963698 DOI: 10.1101/2022.03.23.485509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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 COVID19. 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 PDYN in APS1 patients, and intestinally expressed proteins BEST4 and BTNL8 in IPEX patients. Remarkably, BEST4 antibodies were also found in 2 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 COVID19, 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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29
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Lanz TV, Brewer RC, Ho PP, Moon JS, Jude KM, Fernandez D, Fernandes RA, Gomez AM, Nadj GS, Bartley CM, Schubert RD, Hawes IA, Vazquez SE, Iyer M, Zuchero JB, Teegen B, Dunn JE, Lock CB, Kipp LB, Cotham VC, Ueberheide BM, Aftab BT, Anderson MS, DeRisi JL, Wilson MR, Bashford-Rogers RJ, Platten M, Garcia KC, Steinman L, Robinson WH. Clonally expanded B cells in multiple sclerosis bind EBV EBNA1 and GlialCAM. Nature 2022; 603:321-327. [PMID: 35073561 PMCID: PMC9382663 DOI: 10.1038/s41586-022-04432-7] [Citation(s) in RCA: 326] [Impact Index Per Article: 163.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/14/2022] [Indexed: 11/09/2022]
Abstract
Multiple sclerosis (MS) is a heterogenous autoimmune disease in which autoreactive lymphocytes attack the myelin sheath of the central nervous system. B lymphocytes in the cerebrospinal fluid (CSF) of patients with MS contribute to inflammation and secrete oligoclonal immunoglobulins1,2. Epstein-Barr virus (EBV) infection has been epidemiologically linked to MS, but its pathological role remains unclear3. Here we demonstrate high-affinity molecular mimicry between the EBV transcription factor EBV nuclear antigen 1 (EBNA1) and the central nervous system protein glial cell adhesion molecule (GlialCAM) and provide structural and in vivo functional evidence for its relevance. A cross-reactive CSF-derived antibody was initially identified by single-cell sequencing of the paired-chain B cell repertoire of MS blood and CSF, followed by protein microarray-based testing of recombinantly expressed CSF-derived antibodies against MS-associated viruses. Sequence analysis, affinity measurements and the crystal structure of the EBNA1-peptide epitope in complex with the autoreactive Fab fragment enabled tracking of the development of the naive EBNA1-restricted antibody to a mature EBNA1-GlialCAM cross-reactive antibody. Molecular mimicry is facilitated by a post-translational modification of GlialCAM. EBNA1 immunization exacerbates disease in a mouse model of MS, and anti-EBNA1 and anti-GlialCAM antibodies are prevalent in patients with MS. Our results provide a mechanistic link for the association between MS and EBV and could guide the development of new MS therapies.
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Affiliation(s)
- Tobias V. Lanz
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, United States, and the Geriatric Research, Education, and Clinical Centers (GRECC), VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, United States,Department of Neurology, Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany,Department of Neurology and National Center for Tumor Diseases, University Hospital Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - R. Camille Brewer
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, United States, and the Geriatric Research, Education, and Clinical Centers (GRECC), VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, United States
| | - Peggy P. Ho
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Beckman Center for Molecular Medicine, 279 Campus Drive, Stanford, CA 94305, United States
| | - Jae-Seung Moon
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, United States, and the Geriatric Research, Education, and Clinical Centers (GRECC), VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, United States
| | - Kevin M. Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Beckman Center for Molecular Medicine, 279 Campus Drive, Stanford, CA 94305, United States
| | - Daniel Fernandez
- Stanford ChEM-H Institute, Macromolecular Structure Knowledge Center, 290 Jane Stanford Way, Stanford, CA 94305, United States
| | - Ricardo A. Fernandes
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Beckman Center for Molecular Medicine, 279 Campus Drive, Stanford, CA 94305, United States
| | - Alejandro M. Gomez
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, United States, and the Geriatric Research, Education, and Clinical Centers (GRECC), VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, United States
| | - Gabriel-Stefan Nadj
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, United States, and the Geriatric Research, Education, and Clinical Centers (GRECC), VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, United States
| | - Christopher M. Bartley
- Hanna H. Gray Fellow, Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, United States,Weill Institute for Neurosciences, Department of Psychiatry and Behavioral Sciences, University of California San Francisco, 675 Nelson Rising Ln San Francisco, CA 94158, San Francisco, United States
| | - Ryan D. Schubert
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, 675 Nelson Rising Ln San Francisco, CA 94158, San Francisco, United States
| | - Isobel A. Hawes
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, 675 Nelson Rising Ln San Francisco, CA 94158, San Francisco, United States
| | - Sara E. Vazquez
- Department of Biochemistry and Biophysics, University of California San Francisco, 1700 4th Street, San Francisco, CA 94158, United States
| | - Manasi Iyer
- Department of Neurosurgery, Stanford University School of Medicine, 1201 Welsh Road, Stanford, CA, United States
| | - J. Bradley Zuchero
- Department of Neurosurgery, Stanford University School of Medicine, 1201 Welsh Road, Stanford, CA, United States
| | - Bianca Teegen
- Institute of Experimental Immunology, Euroimmun AG, Seekamp 31, 23560 Lübeck, Germany
| | - Jeffrey E. Dunn
- Division of Neuroimmunology, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, 213 Quarry Road, Stanford, CA, United States
| | - Christopher B. Lock
- Division of Neuroimmunology, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, 213 Quarry Road, Stanford, CA, United States
| | - Lucas B. Kipp
- Division of Neuroimmunology, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, 213 Quarry Road, Stanford, CA, United States
| | - Victoria C. Cotham
- Department of Biochemistry and Molecular Pharmacology, NYU Perlmutter Cancer Center, and NYU Langone Health Proteomics Laboratory, Division of Advanced Research Technologies, NYU School of Medicine, 430 East 29th St, New York, NY, 10016, United States
| | - Beatrix M. Ueberheide
- Department of Biochemistry and Molecular Pharmacology, NYU Perlmutter Cancer Center, and NYU Langone Health Proteomics Laboratory, Division of Advanced Research Technologies, NYU School of Medicine, 430 East 29th St, New York, NY, 10016, United States
| | - Blake T. Aftab
- Preclinical Science and Translational Medicine, Atara Biotherapeutics, 611 Gateway Blvd South San Francisco, CA 94080, United States
| | - Mark S. Anderson
- Department of Medicine, Diabetes Center, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143, United States
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, 1700 4th Street, San Francisco, CA 94158, United States,Chan Zuckerberg Biohub, University of California San Francisco, 499 Illinois Street, San Francisco, CA 94158, United States
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, 675 Nelson Rising Ln San Francisco, CA 94158, San Francisco, United States
| | - Rachael J.M. Bashford-Rogers
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Dr, Headington, Oxford OX3 7BN, United Kingdom
| | - Michael Platten
- Department of Neurology, Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany,Department of Neurology and National Center for Tumor Diseases, University Hospital Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany,DKTK Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - K. Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Beckman Center for Molecular Medicine, 279 Campus Drive, Stanford, CA 94305, United States
| | - Lawrence Steinman
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Beckman Center for Molecular Medicine, 279 Campus Drive, Stanford, CA 94305, United States
| | - William H. Robinson
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, United States, and the Geriatric Research, Education, and Clinical Centers (GRECC), VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, United States,Corresponding Author: William H. Robinson, Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, United States,
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30
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Abstract
Meningitis and encephalitis are inflammatory syndromes of the meninges and brain parenchyma, respectively, and may be identified either by finding definitive evidence of inflammation on tissue pathology or by cerebrocpinal fluid (CSF) analysis showing pleocytosis or intrathecal antibody synthesis. Clinicians evaluating undifferentiated meningitis or encephalitis should simultaneously consider autoimmune, infectious, and neoplastic causes, using patient risk factors, clinical syndrome, and diagnostic results including CSF and MRI findings to narrow the differential diagnosis. If an autoimmune cause is favored, an important early diagnostic question is whether a specific neural autoantibody is likely to be identified.
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Affiliation(s)
- Megan B Richie
- Department of Neurology, University of California San Francisco, 505 Parnassus Avenue, Box 0114, San Francisco, CA 94143, USA.
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31
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Bartley CM, Parikshak NN, Ngo TT, Alexander JA, Zorn KC, Alvarenga BA, Kang MK, Pedriali M, Pleasure SJ, Wilson MR. Case Report: A False Negative Case of Anti-Yo Paraneoplastic Myelopathy. Front Neurol 2021; 12:728700. [PMID: 34744969 PMCID: PMC8570369 DOI: 10.3389/fneur.2021.728700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/16/2021] [Indexed: 11/22/2022] Open
Abstract
The development of autoimmune antibody panels has improved the diagnosis of paraneoplastic neurological disorders (PNDs) of the brain and spinal cord. Here, we present a case of a woman with a history of breast cancer who presented with a subacute sensory ataxia that progressed over 18 months. Her examination and diagnostic studies were consistent with a myelopathy. Metabolic, infectious, and autoimmune testing were non-diagnostic. However, she responded to empirical immunosuppression, prompting further workup for an autoimmune etiology. An unbiased autoantibody screen utilizing phage display immunoprecipitation sequencing (PhIP-Seq) identified antibodies to the anti-Yo antigens cerebellar degeneration related protein 2 like (CDR2L) and CDR2, which were subsequently validated by immunoblot and cell-based overexpression assays. Furthermore, CDR2L protein expression was restricted to HER2 expressing tumor cells in the patient's breast tissue. Recent evidence suggests that CDR2L is likely the primary antigen in anti-Yo paraneoplastic cerebellar degeneration, but anti-Yo myelopathy is poorly characterized. By immunostaining, we detected neuronal CDR2L protein expression in the murine and human spinal cord. This case demonstrates the diagnostic utility of unbiased assays in patients with suspected PNDs, supports prior observations that anti-Yo PND can be associated with isolated myelopathy, and implicates CDR2L as a potential antigen in the spinal cord.
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Affiliation(s)
- Christopher M Bartley
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States.,Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Neelroop N Parikshak
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States.,Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Thomas T Ngo
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States.,Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Jessa A Alexander
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States.,Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Bonny A Alvarenga
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States.,Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Min K Kang
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States.,Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Massimo Pedriali
- Operative Unit of Surgical Pathology, Azienda Ospedaliera-Universitaria, Ferrara, Italy
| | - Samuel J Pleasure
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States.,Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States.,Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
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32
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Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Sunshine S, Liu J, Wu W, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CB, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander JR, Gallego JA, Lencz T, Walsh H, Wapniarski AE, Mohanty S, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, Pak J, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms. Cell Rep Med 2021; 2:100288. [PMID: 33969321 PMCID: PMC8091032 DOI: 10.1016/j.xcrm.2021.100288] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/03/2021] [Accepted: 04/22/2021] [Indexed: 12/17/2022]
Abstract
Individuals with coronavirus disease 2019 (COVID-19) frequently develop neurological symptoms, but the biological underpinnings of these phenomena are unknown. Through single-cell RNA sequencing (scRNA-seq) and cytokine analyses of cerebrospinal fluid (CSF) and blood from individuals with COVID-19 with neurological symptoms, we find compartmentalized, CNS-specific T cell activation and B cell responses. All affected individuals had CSF anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies whose target epitopes diverged from serum antibodies. In an animal model, we find that intrathecal SARS-CoV-2 antibodies are present only during brain infection and not elicited by pulmonary infection. We produced CSF-derived monoclonal antibodies from an individual with COVID-19 and found that these monoclonal antibodies (mAbs) target antiviral and antineural antigens, including one mAb that reacted to spike protein and neural tissue. CSF immunoglobulin G (IgG) from 5 of 7 patients showed antineural reactivity. This immune survey reveals evidence of a compartmentalized immune response in the CNS of individuals with COVID-19 and suggests a role of autoimmunity in neurologic sequelae of COVID-19.
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Affiliation(s)
- Eric Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Christopher M. Bartley
- Hanna H. Gray Fellow, Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - Ryan D. Chow
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Thomas T. Ngo
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - Ruoyi Jiang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 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
| | - Ravi Dandekar
- 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
| | - Rita P. Loudermilk
- 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
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- University of California, Berkeley—University of California, San Francisco Gradate Program in Bioengineering, Berkeley, CA, USA
| | - Wesley Wu
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Isobel A. Hawes
- 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
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Bonny D. Alvarenga
- 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
| | - Trung Huynh
- 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
| | - Lindsay McAlpine
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Nur-Taz Rahman
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Bertie Geng
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | | | - Benjamin Goldman-Israelow
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale University School of Medicine, New Haven, CT, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Brett S. Phinney
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Michelle Salemi
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Jessa R. Alexander
- 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
| | - Juan A. Gallego
- Institute for Behavioral Science, The Feinstein Institute for Medical Research, Manhasset, NY, USA
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, NY, USA
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Todd Lencz
- Institute for Behavioral Science, The Feinstein Institute for Medical Research, Manhasset, NY, USA
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, NY, USA
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Hannah Walsh
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Anne E. Wapniarski
- 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
| | - Subhasis Mohanty
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jon Klein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jieun Oh
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Aaron Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Serena Spudich
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Albert I. Ko
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Steven H. Kleinstein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - John Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Samuel J. Pleasure
- 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
| | - 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
| | - Shelli F. Farhadian
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
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Qi H, Ma M, Hu C, Xu ZW, Wu FL, Wang N, Lai DY, Li Y, Zhang H, Jiang HW, Meng QF, Guo S, Kang Y, Zhao X, Li H, Tao SC. Antibody Binding Epitope Mapping (AbMap) of Hundred Antibodies in a Single Run. Mol Cell Proteomics 2021; 20:100059. [PMID: 33109704 PMCID: PMC8027275 DOI: 10.1074/mcp.ra120.002314] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Antibodies play essential roles in both diagnostics and therapeutics. Epitope mapping is essential to understand how an antibody works and to protect intellectual property. Given the millions of antibodies for which epitope information is lacking, there is a need for high-throughput epitope mapping. To address this, we developed a strategy, Antibody binding epitope Mapping (AbMap), by combining a phage displayed peptide library with next-generation sequencing. Using AbMap, profiles of the peptides bound by 202 antibodies were determined in a single test, and linear epitopes were identified for >50% of the antibodies. Using spike protein (S1 and S2)-enriched antibodies from the convalescent serum of one COVID-19 patient as the input, both linear and potentially conformational epitopes of spike protein specific antibodies were identified. We defined peptide-binding profile of an antibody as the binding capacity (BiC). Conceptually, the BiC could serve as a systematic and functional descriptor of any antibody. Requiring at least one order of magnitude less time and money to map linear epitopes than traditional technologies, AbMap allows for high-throughput epitope mapping and creates many possibilities.
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Affiliation(s)
- Huan Qi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mingliang Ma
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China; School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chuansheng Hu
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhao-Wei Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fan-Lin Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China; School of Agriculture, Lu Dong University, Yantai, China
| | - Nan Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China; Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China
| | - Dan-Yun Lai
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Li
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hainan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - He-Wei Jiang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qing-Feng Meng
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shujuan Guo
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yani Kang
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaodong Zhao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Hua Li
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China; State Key Laboratory for Oncogenes, Shanghai Jiao Tong University, Shanghai, China.
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34
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Herdlevær I, Haugen M, Mazengia K, Totland C, Vedeler C. Paraneoplastic Cerebellar Degeneration: The Importance of Including CDR2L as a Diagnostic Marker. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2021; 8:8/2/e963. [PMID: 33531379 PMCID: PMC8057066 DOI: 10.1212/nxi.0000000000000963] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/09/2020] [Indexed: 12/20/2022]
Abstract
Objective Investigate the value of including cerebellar degeneration-related protein
2-like (CDR2L) as a marker in commercial diagnostic tests for
anti-Yo–associated paraneoplastic cerebellar degeneration (PCD). Methods We included sera and CSF samples from 24 patients with suspected PCD (6 of
whom had PCD with underlying gynecologic or breast cancer), who were
positive for Yo antibodies using the commercially available, paraneoplastic
neurologic syndromes (PNS) 14 Line Assay from Ravo Diagnostika. The samples
were further evaluated using the EUROLINE PNS 12 Ag Line Assay and a
cell-based assay (CBA) from Euroimmun. For confirmation of positive lineblot
results, we used indirect immunofluorescence of rat cerebellar sections. We
also tested all samples in 2 assays developed in-house: a CBA for CDR2L and
a Western blot analysis using recombinant cerebellar degeneration-related
protein 2 (CDR2) and CDR2L proteins. Results In PNS 14 and PNS 12 Ag Line Assays, anti-CDR2 reactivity was observed for 24
(100%) and 20 (83%) of the 24 samples, respectively. Thirteen of 24 subjects
(54%) were also positive using the Euroimmun CBA. Rat cerebellar
immunofluorescence was the best confirmatory test. In our in-house CBA for
CDR2L and Western blot for CDR2 and CDR2L, only the 6 patients with
confirmed PCD reacted with CDR2L. Conclusions Commercially available tests for Yo antibody detection have low specificity
for PCD because these assays use CDR2 as antigen. By adding a test for
CDR2L, which is the major Yo antigen, the accuracy of PCD diagnosis greatly
improved. Classification of Evidence This study provides Class III evidence that a CBA for CDR2L accurately
identifies patients with PCD.
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Affiliation(s)
- Ida Herdlevær
- From the Department of Neurology (I.H., M.H., C.T., C.V.), Haukeland University Hospital; Department of Clinical Medicine (I.H., K.M., C.V.), University of Bergen; and Departments of Neurology and Clinical Medicine (I.H., C.T., C.V.), Neuro-SysMed-Centre of Excellence for Experimental Therapy in Neurology, Bergen, Norway.
| | - Mette Haugen
- From the Department of Neurology (I.H., M.H., C.T., C.V.), Haukeland University Hospital; Department of Clinical Medicine (I.H., K.M., C.V.), University of Bergen; and Departments of Neurology and Clinical Medicine (I.H., C.T., C.V.), Neuro-SysMed-Centre of Excellence for Experimental Therapy in Neurology, Bergen, Norway
| | - Kibret Mazengia
- From the Department of Neurology (I.H., M.H., C.T., C.V.), Haukeland University Hospital; Department of Clinical Medicine (I.H., K.M., C.V.), University of Bergen; and Departments of Neurology and Clinical Medicine (I.H., C.T., C.V.), Neuro-SysMed-Centre of Excellence for Experimental Therapy in Neurology, Bergen, Norway
| | - Cecilie Totland
- From the Department of Neurology (I.H., M.H., C.T., C.V.), Haukeland University Hospital; Department of Clinical Medicine (I.H., K.M., C.V.), University of Bergen; and Departments of Neurology and Clinical Medicine (I.H., C.T., C.V.), Neuro-SysMed-Centre of Excellence for Experimental Therapy in Neurology, Bergen, Norway
| | - Christian Vedeler
- From the Department of Neurology (I.H., M.H., C.T., C.V.), Haukeland University Hospital; Department of Clinical Medicine (I.H., K.M., C.V.), University of Bergen; and Departments of Neurology and Clinical Medicine (I.H., C.T., C.V.), Neuro-SysMed-Centre of Excellence for Experimental Therapy in Neurology, Bergen, Norway
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35
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Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CB, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander J, Gallego JA, Lencz T, Walsh H, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.11.293464. [PMID: 32935102 PMCID: PMC7491516 DOI: 10.1101/2020.09.11.293464] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
One third of COVID-19 patients develop significant neurological symptoms, yet SARS-CoV-2 is rarely detected in central nervous system (CNS) tissue, suggesting a potential role for parainfectious processes, including neuroimmune responses. We therefore examined immune parameters in cerebrospinal fluid (CSF) and blood samples from a cohort of patients with COVID-19 and significant neurological complications. We found divergent immunological responses in the CNS compartment, including increased levels of IL-12 and IL-12-associated innate and adaptive immune cell activation. Moreover, we found increased proportions of B cells in the CSF relative to the periphery and evidence of clonal expansion of CSF B cells, suggesting a divergent intrathecal humoral response to SARS-CoV-2. Indeed, all COVID-19 cases examined had anti-SARS-CoV-2 IgG antibodies in the CSF whose target epitopes diverged from serum antibodies. We directly examined whether CSF resident antibodies target self-antigens and found a significant burden of CNS autoimmunity, with the CSF from most patients recognizing neural self-antigens. Finally, we produced a panel of monoclonal antibodies from patients' CSF and show that these target both anti-viral and anti-neural antigens-including one mAb specific for the spike protein that also recognizes neural tissue. This exploratory immune survey reveals evidence of a compartmentalized and self-reactive immune response in the CNS meriting a more systematic evaluation of neurologically impaired COVID-19 patients.
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Affiliation(s)
- Eric Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Christopher M. Bartley
- Hanna H. Gray Fellow, Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, CA, USA
| | - Ryan D. Chow
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Thomas T. Ngo
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, CA, USA
| | - Ruoyi Jiang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Colin R. Zamecnik
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Ravi Dandekar
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Rita P. Loudermilk
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Isobel A. Hawes
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Bonny D. Alvarenga
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Trung Huynh
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Lindsay McAlpine
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Nur-Taz Rahman
- Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Bertie Geng
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | | | - Benjamin Goldman-Israelow
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Brett S. Phinney
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, CA 95616, USA
| | - Michelle Salemi
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, CA 95616, USA
| | - Jessa Alexander
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Juan A. Gallego
- Institute for Behavioral Science, The Feinstein Institute for Medical Research, Manhasset, New York, USA
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, New York, USA
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York USA
| | - Todd Lencz
- Institute for Behavioral Science, The Feinstein Institute for Medical Research, Manhasset, New York, USA
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, New York, USA
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York USA
| | - Hannah Walsh
- Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jon Klein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jieun Oh
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Aaron Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Serena Spudich
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Albert I. Ko
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Steven H. Kleinstein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Samuel J. Pleasure
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Michael R. Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Shelli F. Farhadian
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
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36
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Herdlevær I, Kråkenes T, Schubert M, Vedeler CA. Localization of CDR2L and CDR2 in paraneoplastic cerebellar degeneration. Ann Clin Transl Neurol 2020; 7:2231-2242. [PMID: 33009713 PMCID: PMC7664253 DOI: 10.1002/acn3.51212] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/07/2020] [Accepted: 09/11/2020] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE Identify the subcellular location and potential binding partners of two cerebellar degeneration-related proteins, CDR2L and CDR2, associated with anti-Yo-mediated paraneoplastic cerebellar degeneration. METHODS Cancer cells, rat Purkinje neuron cultures, and human cerebellar sections were exposed to cerebrospinal fluid and serum from patients with paraneoplastic cerebellar degeneration with Yo antibodies and with several antibodies against CDR2L and CDR2. We used mass spectrometry-based proteomics, super-resolution microscopy, proximity ligation assay, and co-immunoprecipitation to verify the antibodies and to identify potential binding partners. RESULTS We confirmed the CDR2L specificity of Yo antibodies by mass spectrometry-based proteomics and found that CDR2L localized to the cytoplasm and CDR2 to the nucleus. CDR2L co-localized with the 40S ribosomal protein S6, while CDR2 co-localized with the nuclear speckle proteins SON, eukaryotic initiation factor 4A-III, and serine/arginine-rich splicing factor 2. INTERPRETATION We showed that Yo antibodies specifically bind to CDR2L in Purkinje neurons of PCD patients where they potentially interfere with the function of the ribosomal machinery resulting in disrupted mRNA translation and/or protein synthesis. Our findings demonstrating that CDR2L interacts with ribosomal proteins and CDR2 with nuclear speckle proteins is an important step toward understanding PCD pathogenesis.
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Affiliation(s)
- Ida Herdlevær
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of NeurologyHaukeland University HospitalBergenNorway
| | | | - Manja Schubert
- Department of NeurologyHaukeland University HospitalBergenNorway
| | - Christian A. Vedeler
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of NeurologyHaukeland University HospitalBergenNorway
- Departments of Neurology and Clinical MedicineNeuro‐SysMed ‐ Centre of Excellence for Experimental Therapy in NeurologyBergenNorway
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37
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Zamecnik CR, Rajan JV, Yamauchi KA, Mann SA, Loudermilk RP, Sowa GM, Zorn KC, Alvarenga BD, Gaebler C, Caskey M, Stone M, Norris PJ, Gu W, Chiu CY, Ng D, Byrnes JR, Zhou XX, Wells JA, Robbiani DF, Nussenzweig MC, DeRisi JL, Wilson MR. ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens. CELL REPORTS MEDICINE 2020; 1:100123. [PMID: 32995758 PMCID: PMC7513813 DOI: 10.1016/j.xcrm.2020.100123] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/17/2020] [Accepted: 09/21/2020] [Indexed: 12/25/2022]
Abstract
Comprehensive understanding of the serological response to SARS-CoV-2 infection is important for both pathophysiologic insight and diagnostic development. Here, we generate a pan-human coronavirus programmable phage display assay to perform proteome-wide profiling of coronavirus antigens enriched by 98 COVID-19 patient sera. Next, we use ReScan, a method to efficiently sequester phage expressing the most immunogenic peptides and print them onto paper-based microarrays using acoustic liquid handling, which isolates and identifies nine candidate antigens, eight of which are derived from the two proteins used for SARS-CoV-2 serologic assays: spike and nucleocapsid proteins. After deployment in a high-throughput assay amenable to clinical lab settings, these antigens show improved specificity over a whole protein panel. This proof-of-concept study demonstrates that ReScan will have broad applicability for other emerging infectious diseases or autoimmune diseases that lack a valid biomarker, enabling a seamless pipeline from antigen discovery to diagnostic using one recombinant protein source. ReScan is a whole proteome screen to isolate and identify serologic assay targets Antibodies to linear peptides in COVID-19 sera bind spike and nucleocapsid proteins Rapid workflow that seamlessly translates biomarkers into a functional diagnostic Multiplexing linear S and N SARS-CoV-2 peptides can increase diagnostic specificity
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Affiliation(s)
- Colin R Zamecnik
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Jayant V Rajan
- Division of Experimental Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, San Francisco, CA, USA
| | | | - Sabrina A Mann
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Rita P Loudermilk
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Gavin M Sowa
- University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Bonny D Alvarenga
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Philip J Norris
- Vitalant Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, San Francisco, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, San Francisco, USA
| | - Dianna Ng
- Department of Medicine, University of California, San Francisco, San Francisco, USA
| | - James R Byrnes
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, USA
| | - Xin X Zhou
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Michael R Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
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