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Castelli EC, de Castro MV, Naslavsky MS, Scliar MO, Silva NSB, Pereira RN, Ciriaco VAO, Castro CFB, Mendes-Junior CT, Silveira EDS, de Oliveira IM, Antonio EC, Vieira GF, Meyer D, Nunes K, Matos LRB, Silva MVR, Wang JYT, Esposito J, Cória VR, Magawa JY, Santos KS, Cunha-Neto E, Kalil J, Bortolin RH, Hirata MH, Dell’Aquila LP, Razuk-Filho A, Batista-Júnior PB, Duarte-Neto AN, Dolhnikoff M, Saldiva PHN, Passos-Bueno MR, Zatz M. MUC22, HLA-A, and HLA-DOB variants and COVID-19 in resilient super-agers from Brazil. Front Immunol 2022; 13:975918. [PMID: 36389712 PMCID: PMC9641602 DOI: 10.3389/fimmu.2022.975918] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/15/2022] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Although aging correlates with a worse prognosis for Covid-19, super elderly still unvaccinated individuals presenting mild or no symptoms have been reported worldwide. Most of the reported genetic variants responsible for increased disease susceptibility are associated with immune response, involving type I IFN immunity and modulation; HLA cluster genes; inflammasome activation; genes of interleukins; and chemokines receptors. On the other hand, little is known about the resistance mechanisms against SARS-CoV-2 infection. Here, we addressed polymorphisms in the MHC region associated with Covid-19 outcome in super elderly resilient patients as compared to younger patients with a severe outcome. METHODS SARS-CoV-2 infection was confirmed by RT-PCR test. Aiming to identify candidate genes associated with host resistance, we investigated 87 individuals older than 90 years who recovered from Covid-19 with mild symptoms or who remained asymptomatic following positive test for SARS-CoV-2 as compared to 55 individuals younger than 60 years who had a severe disease or died due to Covid-19, as well as to the general elderly population from the same city. Whole-exome sequencing and an in-depth analysis of the MHC region was performed. All samples were collected in early 2020 and before the local vaccination programs started. RESULTS We found that the resilient super elderly group displayed a higher frequency of some missense variants in the MUC22 gene (a member of the mucins' family) as one of the strongest signals in the MHC region as compared to the severe Covid-19 group and the general elderly control population. For example, the missense variant rs62399430 at MUC22 is two times more frequent among the resilient super elderly (p = 0.00002, OR = 2.24). CONCLUSION Since the pro-inflammatory basal state in the elderly may enhance the susceptibility to severe Covid-19, we hypothesized that MUC22 might play an important protective role against severe Covid-19, by reducing overactive immune responses in the senior population.
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Affiliation(s)
- Erick C. Castelli
- Department of Pathology, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Mateus V. de Castro
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Michel S. Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Marilia O. Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Nayane S. B. Silva
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Raphaela N. Pereira
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Viviane A. O. Ciriaco
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Camila F. B. Castro
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
- Centro Universitário Sudoeste Paulista, Avaré, Brazil
| | - Celso T. Mendes-Junior
- Departamento de Química, Faculdade de Filosofa, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Etiele de S. Silveira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Iuri M. de Oliveira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Eduardo C. Antonio
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gustavo F. Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratório de Saúde Humana In Silico, Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Canoas, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Larissa R. B. Matos
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Monize V. R. Silva
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Jaqueline Y. T. Wang
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Joyce Esposito
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Vivian R. Cória
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Jhosiene Y. Magawa
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Keity S. Santos
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Edecio Cunha-Neto
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Jorge Kalil
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Raul H. Bortolin
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Mário Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | | | | | - Amaro N. Duarte-Neto
- Department of Pathology, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Marisa Dolhnikoff
- Department of Pathology, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Paulo H. N. Saldiva
- Department of Pathology, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
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2
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Fu JM, Satterstrom FK, Peng M, Brand H, Collins RL, Dong S, Wamsley B, Klei L, Wang L, Hao SP, Stevens CR, Cusick C, Babadi M, Banks E, Collins B, Dodge S, Gabriel SB, Gauthier L, Lee SK, Liang L, Ljungdahl A, Mahjani B, Sloofman L, Smirnov AN, Barbosa M, Betancur C, Brusco A, Chung BHY, Cook EH, Cuccaro ML, Domenici E, Ferrero GB, Gargus JJ, Herman GE, Hertz-Picciotto I, Maciel P, Manoach DS, Passos-Bueno MR, Persico AM, Renieri A, Sutcliffe JS, Tassone F, Trabetti E, Campos G, Cardaropoli S, Carli D, Chan MCY, Fallerini C, Giorgio E, Girardi AC, Hansen-Kiss E, Lee SL, Lintas C, Ludena Y, Nguyen R, Pavinato L, Pericak-Vance M, Pessah IN, Schmidt RJ, Smith M, Costa CIS, Trajkova S, Wang JYT, Yu MHC, Cutler DJ, De Rubeis S, Buxbaum JD, Daly MJ, Devlin B, Roeder K, Sanders SJ, Talkowski ME. Rare coding variation provides insight into the genetic architecture and phenotypic context of autism. Nat Genet 2022; 54:1320-1331. [PMID: 35982160 PMCID: PMC9653013 DOI: 10.1038/s41588-022-01104-0] [Citation(s) in RCA: 137] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/24/2022] [Indexed: 01/11/2023]
Abstract
Some individuals with autism spectrum disorder (ASD) carry functional mutations rarely observed in the general population. We explored the genes disrupted by these variants from joint analysis of protein-truncating variants (PTVs), missense variants and copy number variants (CNVs) in a cohort of 63,237 individuals. We discovered 72 genes associated with ASD at false discovery rate (FDR) ≤ 0.001 (185 at FDR ≤ 0.05). De novo PTVs, damaging missense variants and CNVs represented 57.5%, 21.1% and 8.44% of association evidence, while CNVs conferred greatest relative risk. Meta-analysis with cohorts ascertained for developmental delay (DD) (n = 91,605) yielded 373 genes associated with ASD/DD at FDR ≤ 0.001 (664 at FDR ≤ 0.05), some of which differed in relative frequency of mutation between ASD and DD cohorts. The DD-associated genes were enriched in transcriptomes of progenitor and immature neuronal cells, whereas genes showing stronger evidence in ASD were more enriched in maturing neurons and overlapped with schizophrenia-associated genes, emphasizing that these neuropsychiatric disorders may share common pathways to risk.
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Affiliation(s)
- Jack M Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - F Kyle Satterstrom
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Minshi Peng
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lily Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Stephanie P Hao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Christine R Stevens
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Caroline Cusick
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mehrtash Babadi
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric Banks
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brett Collins
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sheila Dodge
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stacey B Gabriel
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Laura Gauthier
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuel K Lee
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lindsay Liang
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Alicia Ljungdahl
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Behrang Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Laura Sloofman
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrey N Smirnov
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mafalda Barbosa
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Catalina Betancur
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
- Medical Genetics Unit, 'Città della Salute e della Scienza' University Hospital, Turin, Italy
| | - Brian H Y Chung
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
| | - Michael L Cuccaro
- The John P Hussman Institute for Human Genomics, The University of Miami Miller School of Medicine, Miami, FL, USA
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology, , University of Trento, Trento, Italy
| | | | - J Jay Gargus
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Gail E Herman
- The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Irva Hertz-Picciotto
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Patricia Maciel
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal
| | - Dara S Manoach
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Maria Rita Passos-Bueno
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Antonio M Persico
- Interdepartmental Program 'Autism 0-90', 'Gaetano Martino' University Hospital, University of Messina, Messina, Italy
| | - Alessandra Renieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, , University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - James S Sutcliffe
- Department of Molecular Physiology & Biophysics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Flora Tassone
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA, USA
| | - Elisabetta Trabetti
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Verona, Italy
| | - Gabriele Campos
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Simona Cardaropoli
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Diana Carli
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Marcus C Y Chan
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Chiara Fallerini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, , University of Siena, Siena, Italy
| | - Elisa Giorgio
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Ana Cristina Girardi
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Emily Hansen-Kiss
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX, USA
| | - So Lun Lee
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Carla Lintas
- Service for Neurodevelopmental Disorders, University Campus Bio-medico of Rome, Rome, Italy
| | - Yunin Ludena
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Rachel Nguyen
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Margaret Pericak-Vance
- The John P Hussman Institute for Human Genomics, The University of Miami Miller School of Medicine, Miami, FL, USA
| | - Isaac N Pessah
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
- Department of Molecular Biosciences, University of California Davis, School of Veterinary Medicine, Davis, CA, USA
| | - Rebecca J Schmidt
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Moyra Smith
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Claudia I S Costa
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Jaqueline Y T Wang
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Mullin H C Yu
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Mark J Daly
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Kathryn Roeder
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA.
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA.
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3
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de Castro MV, Santos KS, Apostolico JS, Fernandes ER, Almeida RR, Levin G, Magawa JY, Nunes JPS, Bruni M, Yamamoto MM, Lima AC, Silva MVR, Matos LRB, Coria VR, Castelli EC, Scliar MO, Kuramoto A, Bruno FR, Jacintho LC, Nunes K, Wang JYT, Coelho VP, Neto MM, Maciel RMB, Naslavsky MS, Passos-Bueno MR, Boscardin SB, Rosa DS, Kalil J, Zatz M, Cunha-Neto E. Recurrence of COVID-19 associated with reduced T-cell responses in a monozygotic twin pair. Open Biol 2022; 12:210240. [PMID: 35104433 PMCID: PMC8807054 DOI: 10.1098/rsob.210240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Recurrence of COVID-19 in recovered patients has been increasingly reported. However, the immune mechanisms behind the recurrence have not been thoroughly investigated. The presence of neutralizing antibodies (nAbs) in recurrence/reinfection cases suggests that other types of immune response are involved in protection against recurrence. Here, we investigated the innate type I/III interferon (IFN) response, binding and nAb assays and T-cell responses to severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2) with IFN gamma (IFNγ) enzyme-linked spot assay (ELISPOT) in three pairs of young adult monozygotic (MZ) twins with previous confirmed COVID-19, one of them presenting a severe recurrence four months after the initial infection. Twin studies have been of paramount importance to comprehend the immunogenetics of infectious diseases. Each MZ twin pair was previously exposed to SARS-CoV-2, as seen by clinical reports. The six individuals presented similar overall recovered immune responses except for the recurrence case, who presented a drastically reduced number of recognized SARS-CoV-2 T-cell epitopes on ELISPOT as compared to her twin sister and the other twin pairs. Our results suggest that the lack of a broad T-cell response to initial infection may have led to recurrence, emphasizing that an effective SARS-CoV-2-specific T-cell immune response is key for complete viral control and avoidance of clinical recurrence of COVID-19.
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Affiliation(s)
- Mateus V. de Castro
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Keity S. Santos
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | - Juliana S. Apostolico
- Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Department of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Edgar R. Fernandes
- Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Department of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Rafael R. Almeida
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil
| | - Gabriel Levin
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil
| | - Jhosiene Y. Magawa
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | - João Paulo S. Nunes
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | - Mirian Bruni
- Department of Parasitology, Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Marcio M. Yamamoto
- Department of Parasitology, Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ariane C. Lima
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | - Monize V. R. Silva
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Larissa R. B. Matos
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Vivian R. Coria
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Erick C. Castelli
- School of Medicine, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Marilia O. Scliar
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Andreia Kuramoto
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | - Fernanda R. Bruno
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | - Lucas C. Jacintho
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | - Kelly Nunes
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jaqueline Y. T. Wang
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Veronica P. Coelho
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | | | | | - Michel S. Naslavsky
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Silvia B. Boscardin
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil,Department of Parasitology, Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Daniela S. Rosa
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Department of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Jorge Kalil
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil,Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Edecio Cunha-Neto
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil
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4
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Castelli EC, de Castro MV, Naslavsky MS, Scliar MO, Silva NSB, Andrade HS, Souza AS, Pereira RN, Castro CFB, Mendes-Junior CT, Meyer D, Nunes K, Matos LRB, Silva MVR, Wang JYT, Esposito J, Coria VR, Bortolin RH, Hirata MH, Magawa JY, Cunha-Neto E, Coelho V, Santos KS, Marin MLC, Kalil J, Mitne-Neto M, Maciel RMB, Passos-Bueno MR, Zatz M. MHC Variants Associated With Symptomatic Versus Asymptomatic SARS-CoV-2 Infection in Highly Exposed Individuals. Front Immunol 2021; 12:742881. [PMID: 34650566 PMCID: PMC8506217 DOI: 10.3389/fimmu.2021.742881] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/06/2021] [Indexed: 12/11/2022] Open
Abstract
Despite the high number of individuals infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) who develop coronavirus disease 2019 (COVID-19) symptoms worldwide, many exposed individuals remain asymptomatic and/or uninfected and seronegative. This could be explained by a combination of environmental (exposure), immunological (previous infection), epigenetic, and genetic factors. Aiming to identify genetic factors involved in immune response in symptomatic COVID-19 as compared to asymptomatic exposed individuals, we analyzed 83 Brazilian couples where one individual was infected and symptomatic while the partner remained asymptomatic and serum-negative for at least 6 months despite sharing the same bedroom during the infection. We refer to these as "discordant couples". We performed whole-exome sequencing followed by a state-of-the-art method to call genotypes and haplotypes across the highly polymorphic major histocompatibility complex (MHC) region. The discordant partners had comparable ages and genetic ancestry, but women were overrepresented (65%) in the asymptomatic group. In the antigen-presentation pathway, we observed an association between HLA-DRB1 alleles encoding Lys at residue 71 (mostly DRB1*03:01 and DRB1*04:01) and DOB*01:02 with symptomatic infections and HLA-A alleles encoding 144Q/151R with asymptomatic seronegative women. Among the genes related to immune modulation, we detected variants in MICA and MICB associated with symptomatic infections. These variants are related to higher expression of soluble MICA and low expression of MICB. Thus, quantitative differences in these molecules that modulate natural killer (NK) activity could contribute to susceptibility to COVID-19 by downregulating NK cell cytotoxic activity in infected individuals but not in the asymptomatic partners.
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Affiliation(s)
- Erick C. Castelli
- Department of Pathology, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
- Molecular Genetics and Bioinformatics Laboratory–Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Mateus V. de Castro
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Michel S. Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Marilia O. Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Nayane S. B. Silva
- Molecular Genetics and Bioinformatics Laboratory–Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Heloisa S. Andrade
- Molecular Genetics and Bioinformatics Laboratory–Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Andreia S. Souza
- Molecular Genetics and Bioinformatics Laboratory–Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Raphaela N. Pereira
- Molecular Genetics and Bioinformatics Laboratory–Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Camila F. B. Castro
- Molecular Genetics and Bioinformatics Laboratory–Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
- Centro Universitário Sudoeste Paulista, Avaré, Brazil
| | - Celso T. Mendes-Junior
- Departamento de Química, Faculdade de Filosofa, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Larissa R. B. Matos
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Monize V. R. Silva
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Jaqueline Y. T. Wang
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Joyce Esposito
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Vivian R. Coria
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Raul H. Bortolin
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Mario H. Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jhosiene Y. Magawa
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Edecio Cunha-Neto
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia - Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
| | - Verônica Coelho
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia - Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
| | - Keity S. Santos
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia - Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
| | - Maria Lucia C. Marin
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia - Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
| | - Jorge Kalil
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia - Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
| | | | | | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
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5
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Naslavsky MS, Scliar MO, Nunes K, Wang JYT, Yamamoto GL, Guio H, Tarazona-Santos E, Duarte YAO, Passos-Bueno MR, Meyer D, Zatz M. Biased pathogenic assertions of loss of function variants challenge molecular diagnosis of admixed individuals. Am J Med Genet C Semin Med Genet 2021; 187:357-363. [PMID: 34189818 DOI: 10.1002/ajmg.c.31931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/21/2021] [Accepted: 05/20/2021] [Indexed: 11/06/2022]
Abstract
Diagnosis of individuals affected by monogenic disorders was significantly improved by next-generation sequencing targeting clinically relevant genes. Whole exomes yield a large number of variants that require several filtering steps, prioritization, and pathogenicity classification. Among the criteria recommended by ACMG, those that rely on population databases critically affect analyses of individuals with underrepresented ancestries. Population-specific allelic frequencies need consideration when characterizing potential deleteriousness of variants. An orthogonal input for classification is annotation of variants previously classified as pathogenic as a criterion that provide supporting evidence widely sourced at ClinVar. We used a whole-genome dataset from a census-based cohort of 1,171 elderly individuals from São Paulo, Brazil, highly admixed, and unaffected by severe monogenic disorders, to investigate if pathogenic assertions in ClinVar are enriched with higher proportions of European ancestry, indicating bias. Potential loss of function (pLOF) variants were filtered from 4,250 genes associated with Mendelian disorders and annotated with ClinVar assertions. Over 1,800 single nucleotide pLOF variants were included, 381 had non-benign assertions. Among carriers (N = 463), average European ancestry was significantly higher than noncarriers (N = 708; p = .011). pLOFs in genomic contexts of non-European local ancestries were nearly three times less likely to have any ClinVar entry (OR = 0.353; p <.0001). Independent pathogenicity assertions are useful for variant classification in molecular diagnosis. However, European overrepresentation of assertions can promote distortions when classifying variants in non-European individuals, even in admixed samples with a relatively high proportion of European ancestry. The investigation and deposit of clinically relevant findings of diverse populations is fundamental improve this scenario.
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Affiliation(s)
- Michel S Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil.,Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
| | - Marília O Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Jaqueline Y T Wang
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Guilherme L Yamamoto
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil.,Instituto da Criança, Faculdade de Medicina da Universidade de São Paulo, São Paulo, São Paulo, Brazil.,Orthopedic Research Labs, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Laboratório DASA, São Paulo, São Paulo, Brazil
| | - Heinner Guio
- Instituto Nacional de Salud, Lima, Peru.,Universidad de Huánuco, Huánuco, Peru
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Mosaico Translational Genomics Initiative, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru.,Instituto de Estudos Avançados Transdisciplinares, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Yeda A O Duarte
- Medical-Surgical Nursing Department, School of Nursing, University of São Paulo, São Paulo, São Paulo, Brazil.,Epidemiology Department, Public Health School, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil.,Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil.,Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
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