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Capendale PE, García-Rodríguez I, Ambikan AT, Mulder LA, Depla JA, Freeze E, Koen G, Calitz C, Sood V, Vieira de Sá R, Neogi U, Pajkrt D, Sridhar A, Wolthers KC. Parechovirus infection in human brain organoids: host innate inflammatory response and not neuro-infectivity correlates to neurologic disease. Nat Commun 2024; 15:2532. [PMID: 38514653 PMCID: PMC10958052 DOI: 10.1038/s41467-024-46634-9] [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: 11/16/2023] [Accepted: 02/29/2024] [Indexed: 03/23/2024] Open
Abstract
Picornaviruses are a leading cause of central nervous system (CNS) infections. While genotypes such as parechovirus A3 (PeV-A3) and echovirus 11 (E11) can elicit severe neurological disease, the highly prevalent PeV-A1 is not associated with CNS disease. Here, we expand our current understanding of these differences in PeV-A CNS disease using human brain organoids and clinical isolates of the two PeV-A genotypes. Our data indicate that PeV-A1 and A3 specific differences in neurological disease are not due to infectivity of CNS cells as both viruses productively infect brain organoids with a similar cell tropism. Proteomic analysis shows that PeV-A infection significantly alters the host cell metabolism. The inflammatory response following PeV-A3 (and E11 infection) is significantly more potent than that upon PeV-A1 infection. Collectively, our findings align with clinical observations and suggest a role for neuroinflammation, rather than viral replication, in PeV-A3 (and E11) infection.
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Affiliation(s)
- Pamela E Capendale
- OrganoVIR Labs, Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Reproduction and Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Inés García-Rodríguez
- OrganoVIR Labs, Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Reproduction and Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Anoop T Ambikan
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Lance A Mulder
- OrganoVIR Labs, Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Reproduction and Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Josse A Depla
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- UniQure Biopharma B.V., Department of Research & Development, Paasheuvelweg 25A, Amsterdam, The Netherlands
| | - Eline Freeze
- OrganoVIR Labs, Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Reproduction and Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Gerrit Koen
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Carlemi Calitz
- OrganoVIR Labs, Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Reproduction and Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Vikas Sood
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Renata Vieira de Sá
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Ujjwal Neogi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Dasja Pajkrt
- OrganoVIR Labs, Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Reproduction and Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Adithya Sridhar
- OrganoVIR Labs, Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Reproduction and Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands
| | - Katja C Wolthers
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
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Ramachandran PS, Okaty BW, Riehs M, Wapniarski A, Hershey D, Harb H, Zia M, Haas EA, Alexandrescu S, Sleeper LA, Vargas SO, Gorman MP, Campman S, Mena OJ, Levert K, Hyland K, Goldstein RD, Wilson MR, Haynes RL. Multiomic Analysis of Neuroinflammation and Occult Infection in Sudden Infant Death Syndrome. JAMA Neurol 2024; 81:240-247. [PMID: 38285456 PMCID: PMC10825787 DOI: 10.1001/jamaneurol.2023.5387] [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: 08/14/2023] [Accepted: 11/10/2023] [Indexed: 01/30/2024]
Abstract
Importance Antemortem infection is a risk factor for sudden infant death syndrome (SIDS)-the leading postneonatal cause of infant mortality in the developed world. Manifestations of infection and inflammation are not always apparent in clinical settings or by standard autopsy; thus, enhanced resolution approaches are needed. Objective To ascertain whether a subset of SIDS cases is associated with neuroinflammation and occult infection. Design, Setting, and Participants In this case-control study, postmortem fluids from SIDS cases and controls collected between July 2011 and November 2018 were screened for elevated inflammatory markers, specifically cerebrospinal fluid (CSF) neopterin and CSF and serum cytokines. CSF, liver, and brain tissue from SIDS cases with elevated CSF neopterin were subjected to metagenomic next-generation sequencing (mNGS) to probe for infectious pathogens. Brainstem tissue from a subset of these cases was analyzed by single-nucleus RNA sequencing (snRNAseq) to measure cell type-specific gene expression associated with neuroinflammation and infection. All tissue and fluid analyses were performed from April 2019 to January 2023 in a pathology research laboratory. Included was autopsy material from infants dying of SIDS and age-matched controls dying of known causes. Exposures There were no interventions or exposures. Main Outcomes and Measures CSF neopterin levels were measured by high-performance liquid chromatography. Cytokines were measured by multiplex fluorometric assay. mNGS was performed on liver, CSF, brain, and brainstem tissue. snRNAseq was performed on brainstem tissue. Results A cohort of 71 SIDS cases (mean [SD] age, 55.2 [11.4] postconceptional weeks; 42 male [59.2%]) and 20 controls (mean [SD] age, 63.2 [16.9] postconceptional weeks; 11 male [55.0%]) had CSF and/or serum available. CSF neopterin was screened in 64 SIDS cases and 15 controls, with no exclusions. Tissues from 6 SIDS cases were further analyzed. For CSF neopterin measures, SIDS samples were from infants with mean (SD) age of 54.5 (11.3) postconceptional weeks (38 male [59.4%]) and control samples were from infants with mean (SD) age of 61.5 (17.4) postconceptional weeks (7 male [46.7%]). A total of 6 SIDS cases (9.3%) with high CSF neopterin were identified, suggestive of neuroinflammation. mNGS detected human parechovirus 3 (HPeV3) in tissue and CSF from 1 of these 6 cases. snRNAseq of HPeV3-positive brainstem tissue (medulla) revealed dramatic enrichment of transcripts for genes with predominately inflammatory functions compared with 3 age-matched SIDS cases with normal CSF neopterin levels. Conclusions and Relevance Next-generation molecular tools in autopsy tissue provide novel insight into pathogens that go unrecognized by normal autopsy methodology, including in infants dying suddenly and unexpectedly.
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Affiliation(s)
- Prashanth S. Ramachandran
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco
- The Peter Doherty Institute for Immunity and Infection, University of Melbourne, Melbourne, Victoria, Australia
- The Royal Melbourne Hospital, University of Melbourne, Melbourne, Victoria, Australia
- Now with St Vincent’s Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin W. Okaty
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Molly Riehs
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts
| | - Anne Wapniarski
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco
| | - Daniel Hershey
- Department of Pediatrics, Division of Pediatric Hospital Medicine, University of California San Diego, Rady Childrens Hospital, San Diego
| | - Hani Harb
- Department of Immunology, Boston Children’s Hospital, Boston, Massachusetts
- Now with Institute for Medical Microbiology and Virology, Technical University Dresden, Germany
| | - Maham Zia
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco
| | - Elisabeth A. Haas
- Department of Research, Rady Children’s Hospital, San Diego, California
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts
| | - Lynn A. Sleeper
- Department of Cardiology, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Sara O. Vargas
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts
| | - Mark P. Gorman
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Steven Campman
- San Diego County Medical Examiner Office, San Diego, California
| | - Othon J. Mena
- San Diego County Medical Examiner Office, San Diego, California
- Now with Ventura County Medical Examiner Office, Ventura, California
| | - Keith Levert
- Medical Neurogenetics Laboratories, a Labcorp company, Atlanta, Georgia
| | - Keith Hyland
- Medical Neurogenetics Laboratories, a Labcorp company, Atlanta, Georgia
| | - Richard D. Goldstein
- Robert’s Program on Sudden Unexpected Death in Pediatrics, Division of General Pediatrics, Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco
| | - Robin L. Haynes
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts
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