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Diz-de Almeida S, Cruz R, Luchessi AD, Lorenzo-Salazar JM, de Heredia ML, Quintela I, González-Montelongo R, Nogueira Silbiger V, Porras MS, Tenorio Castaño JA, Nevado J, Aguado JM, Aguilar C, Aguilera-Albesa S, Almadana V, Almoguera B, Alvarez N, Andreu-Bernabeu Á, Arana-Arri E, Arango C, Arranz MJ, Artiga MJ, Baptista-Rosas RC, Barreda-Sánchez M, Belhassen-Garcia M, Bezerra JF, Bezerra MAC, Boix-Palop L, Brion M, Brugada R, Bustos M, Calderón EJ, Carbonell C, Castano L, Castelao JE, Conde-Vicente R, Cordero-Lorenzana ML, Cortes-Sanchez JL, Corton M, Darnaude MT, De Martino-Rodríguez A, Del Campo-Pérez V, de Bustamante AD, Domínguez-Garrido E, Eirós R, Fariñas MC, Fernandez-Nestosa MJ, Fernández-Robelo U, Fernández-Rodríguez A, Fernández-Villa T, Gago-Dominguez M, Gil-Fournier B, Gómez-Arrue J, Álvarez BG, Bernaldo de Quirós FG, González-Neira A, González-Peñas J, Gutiérrez-Bautista JF, Herrero MJ, Herrero-Gonzalez A, Jimenez-Sousa MA, Lattig MC, Borja AL, Lopez-Rodriguez R, Mancebo E, Martín-López C, Martín V, Martinez-Nieto O, Martinez-Lopez I, Martinez-Resendez MF, Martinez-Perez A, Mazzeu JF, Macías EM, Minguez P, Cuerda VM, Oliveira SF, Ortega-Paino E, Parellada M, Paz-Artal E, Santos NPC, Pérez-Matute P, Perez P, Pérez-Tomás ME, Perucho T, Pinsach-Abuin M, Pita G, Pompa-Mera EN, Porras-Hurtado GL, Pujol A, León SR, Resino S, Fernandes MR, Rodríguez-Ruiz E, Rodriguez-Artalejo F, Rodriguez-Garcia JA, Ruiz-Cabello F, Ruiz-Hornillos J, Ryan P, Soria JM, Souto JC, Tamayo E, Tamayo-Velasco A, Taracido-Fernandez JC, Teper A, Torres-Tobar L, Urioste M, Valencia-Ramos J, Yáñez Z, Zarate R, de Rojas I, Ruiz A, Sánchez P, Real LM, Guillen-Navarro E, Ayuso C, Parra E, Riancho JA, Rojas-Martinez A, Flores C, Lapunzina P, Carracedo Á. Novel risk loci for COVID-19 hospitalization among admixed American populations. eLife 2024; 13:RP93666. [PMID: 39361370 PMCID: PMC11449485 DOI: 10.7554/elife.93666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024] Open
Abstract
The genetic basis of severe COVID-19 has been thoroughly studied, and many genetic risk factors shared between populations have been identified. However, reduced sample sizes from non-European groups have limited the discovery of population-specific common risk loci. In this second study nested in the SCOURGE consortium, we conducted a genome-wide association study (GWAS) for COVID-19 hospitalization in admixed Americans, comprising a total of 4702 hospitalized cases recruited by SCOURGE and seven other participating studies in the COVID-19 Host Genetic Initiative. We identified four genome-wide significant associations, two of which constitute novel loci and were first discovered in Latin American populations (BAZ2B and DDIAS). A trans-ethnic meta-analysis revealed another novel cross-population risk locus in CREBBP. Finally, we assessed the performance of a cross-ancestry polygenic risk score in the SCOURGE admixed American cohort. This study constitutes the largest GWAS for COVID-19 hospitalization in admixed Latin Americans conducted to date. This allowed to reveal novel risk loci and emphasize the need of considering the diversity of populations in genomic research.
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Affiliation(s)
- Silvia Diz-de Almeida
- ERN-ITHACA-European Reference Network, Soria, Spain
- Pediatric Neurology Unit, Department of Pediatrics, Navarra Health Service Hospital, Pamplona, Spain
- CIBERER, ISCIII, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Raquel Cruz
- ERN-ITHACA-European Reference Network, Soria, Spain
- Pediatric Neurology Unit, Department of Pediatrics, Navarra Health Service Hospital, Pamplona, Spain
- CIBERER, ISCIII, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Andre D Luchessi
- Universidade Federal do Rio Grande do Norte, Departamento de Analises Clinicas e Toxicologicas, Natal, Brazil
| | - José M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | | | - Inés Quintela
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | | | - Vivian Nogueira Silbiger
- Universidade Federal do Rio Grande do Norte, Departamento de Analises Clinicas e Toxicologicas, Natal, Brazil
| | - Marta Sevilla Porras
- CIBERER, ISCIII, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz IDIPAZ, Madrid, Spain
| | - Jair Antonio Tenorio Castaño
- ERN-ITHACA-European Reference Network, Soria, Spain
- CIBERER, ISCIII, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz IDIPAZ, Madrid, Spain
| | - Julian Nevado
- ERN-ITHACA-European Reference Network, Soria, Spain
- CIBERER, ISCIII, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz IDIPAZ, Madrid, Spain
| | - Jose María Aguado
- Unit of Infectious Diseases, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Spanish Network for Research in Infectious Diseases (REIPI RD16/0016/0002), Instituto de Salud Carlos III, Madrid, Spain
- CIBERINFEC, ISCIII, Madrid, Spain
| | | | - Sergio Aguilera-Albesa
- Pediatric Neurology Unit, Department of Pediatrics, Navarra Health Service Hospital, Pamplona, Spain
- Navarra Health Service, NavarraBioMed Research Group, Pamplona, Spain
| | | | - Berta Almoguera
- CIBERER, ISCIII, Madrid, Spain
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Nuria Alvarez
- Spanish National Cancer Research Centre, Human Genotyping-CEGEN Unit, Madrid, Spain
| | - Álvaro Andreu-Bernabeu
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón (IiSGM), Madrid, Spain
- School of Medicine, Universidad Complutense, Madrid, Spain
| | - Eunate Arana-Arri
- Biocruces Bizkai HRI, Bizkaia, Spain
- Cruces University Hospital, Osakidetza, Bizkaia, Spain
| | - Celso Arango
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón (IiSGM), Madrid, Spain
- School of Medicine, Universidad Complutense, Madrid, Spain
- Centre for Biomedical Network Research on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - María J Arranz
- Fundació Docència I Recerca Mutua Terrassa, Barcelona, Spain
| | | | - Raúl C Baptista-Rosas
- Hospital General de Occidente, Zapopan Jalisco, Mexico
- Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá Jalisco, Mexico
- Centro de Investigación Multidisciplinario en Salud, Universidad de Guadalajara, Tonalá Jalisco, Mexico
| | - María Barreda-Sánchez
- Universidad Católica San Antonio de Murcia (UCAM), Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain
| | - Moncef Belhassen-Garcia
- Hospital Universitario de Salamanca-IBSAL, Servicio de Medicina Interna-Unidad de Enfermedades Infecciosas, Salamanca, Spain
| | - Joao F Bezerra
- Escola Tecnica de Saúde, Laboratorio de Vigilancia Molecular Aplicada, Brasilia, Brazil
| | - Marcos A C Bezerra
- Federal University of Pernambuco, Genetics Postgraduate Program, Recife, Brazil
| | | | - María Brion
- Instituto de Investigación Sanitaria de Santiago (IDIS), Xenética Cardiovascular, Santiago de Compostela, Spain
- CIBERCV, ISCIII, Madrid, Spain
| | - Ramón Brugada
- CIBERCV, ISCIII, Madrid, Spain
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), Girona, Spain
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain
- Hospital Josep Trueta, Cardiology Service, Girona, Spain
| | - Matilde Bustos
- Institute of Biomedicine of Seville (IBiS), Consejo Superior de Investigaciones Científicas (CSIC)- University of Seville- Virgen del Rocio University Hospital, Seville, Spain
| | - Enrique J Calderón
- Institute of Biomedicine of Seville (IBiS), Consejo Superior de Investigaciones Científicas (CSIC)- University of Seville- Virgen del Rocio University Hospital, Seville, Spain
- Departamento de Medicina, Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Seville, Spain
- CIBERESP, ISCIII, Madrid, Spain
| | - Cristina Carbonell
- Hospital Universitario de Salamanca-IBSAL, Servicio de Medicina Interna, Salamanca, Spain
- Universidad de Salamanca, Salamanca, Spain
| | - Luis Castano
- CIBERER, ISCIII, Madrid, Spain
- Biocruces Bizkai HRI, Bizkaia, Spain
- Osakidetza, Cruces University Hospital, Bizkaia, Spain
- Centre for Biomedical Network Research on Diabetes and Metabolic Associated Diseases (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
- University of Pais Vasco, UPV/EHU, Bizkaia, Spain
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigacion Sanitaria Galicia Sur, Xerencia de Xestion Integrada de Vigo-Servizo Galego de Saúde, Vigo, Spain
| | | | - M Lourdes Cordero-Lorenzana
- Servicio de Medicina intensiva, Complejo Hospitalario Universitario de A Coruña (CHUAC), Sistema Galego de Saúde (SERGAS), A Coruña, Spain
| | - Jose L Cortes-Sanchez
- Tecnológico de Monterrey, Monterrey, Mexico
- Department of Microgravity and Translational Regenerative Medicine, Otto von Guericke University, Magdeburg, Germany
| | - Marta Corton
- CIBERER, ISCIII, Madrid, Spain
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | | | - Alba De Martino-Rodríguez
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
- Instituto Investigación Sanitaria Aragón (IIS-Aragon), Zaragoza, Spain
| | - Victor Del Campo-Pérez
- Preventive Medicine Department, Instituto de Investigacion Sanitaria Galicia Sur, Xerencia de Xestion Integrada de Vigo-Servizo Galego de Saúde, Vigo, Spain
| | | | | | - Rocío Eirós
- Hospital Universitario de Salamanca-IBSAL, Servicio de Cardiología, Salamanca, Spain
| | - María Carmen Fariñas
- IDIVAL, Cantabria, Spain
- Hospital U M Valdecilla, Cantabria, Spain
- Universidad de Cantabria, Cantabria, Spain
| | | | - Uxía Fernández-Robelo
- Urgencias Hospitalarias, Complejo Hospitalario Universitario de A Coruña (CHUAC), Sistema Galego de Saúde (SERGAS), A Coruña, Spain
| | - Amanda Fernández-Rodríguez
- CIBERINFEC, ISCIII, Madrid, Spain
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Tania Fernández-Villa
- CIBERESP, ISCIII, Madrid, Spain
- Grupo de Investigación en Interacciones Gen-Ambiente y Salud (GIIGAS) - Instituto de Biomedicina (IBIOMED), Universidad de León, León, Spain
| | - Manuela Gago-Dominguez
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS), Santiago de Compostela, Spain
- IDIS, Seongnam, Republic of Korea
| | | | - Javier Gómez-Arrue
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
- Instituto Investigación Sanitaria Aragón (IIS-Aragon), Zaragoza, Spain
| | - Beatriz González Álvarez
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
- Instituto Investigación Sanitaria Aragón (IIS-Aragon), Zaragoza, Spain
| | | | - Anna González-Neira
- Spanish National Cancer Research Centre, Human Genotyping-CEGEN Unit, Madrid, Spain
| | - Javier González-Peñas
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón (IiSGM), Madrid, Spain
- School of Medicine, Universidad Complutense, Madrid, Spain
- Centre for Biomedical Network Research on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan F Gutiérrez-Bautista
- Hospital Universitario Virgen de las Nieves, Servicio de Análisis Clínicos e Inmunología, Granada, Spain
| | - María José Herrero
- IIS La Fe, Plataforma de Farmacogenética, Valencia, Spain
- Universidad de Valencia, Departamento de Farmacología, Valencia, Spain
| | - Antonio Herrero-Gonzalez
- Data Analysis Department, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - María A Jimenez-Sousa
- CIBERINFEC, ISCIII, Madrid, Spain
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María Claudia Lattig
- Universidad de los Andes, Facultad de Ciencias, Bogotá, Colombia
- SIGEN Alianza Universidad de los Andes - Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | | | - Rosario Lopez-Rodriguez
- CIBERER, ISCIII, Madrid, Spain
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Esther Mancebo
- Hospital Universitario 12 de Octubre, Department of Immunology, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Transplant Immunology and Immunodeficiencies Group, Madrid, Spain
| | | | - Vicente Martín
- CIBERESP, ISCIII, Madrid, Spain
- Grupo de Investigación en Interacciones Gen-Ambiente y Salud (GIIGAS) - Instituto de Biomedicina (IBIOMED), Universidad de León, León, Spain
| | - Oscar Martinez-Nieto
- SIGEN Alianza Universidad de los Andes - Fundación Santa Fe de Bogotá, Bogotá, Colombia
- Fundación Santa Fe de Bogota, Departamento Patologia y Laboratorios, Bogotá, Colombia
| | - Iciar Martinez-Lopez
- Unidad de Genética y Genómica Islas Baleares, Islas Baleares, Spain
- Hospital Universitario Son Espases, Unidad de Diagnóstico Molecular y Genética Clínica, Islas Baleares, Spain
| | | | - Angel Martinez-Perez
- Genomics of Complex Diseases Unit, Research Institute of Hospital de la Santa Creu i Sant Pau, IIB Sant Pau, Barcelona, Spain
| | - Juliana F Mazzeu
- Universidade de Brasília, Faculdade de Medicina, Brasília, Brazil
- Programa de Pós-Graduação em Ciências Médicas (UnB), Brasília, Brazil
- Programa de Pós-Graduação em Ciencias da Saude (UnB), Brazila, Brazil
| | | | - Pablo Minguez
- CIBERER, ISCIII, Madrid, Spain
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Victor Moreno Cuerda
- Hospital Universitario Mostoles, Medicina Interna, Madrid, Spai, Spain
- Universidad Francisco de Vitoria, Madrid, Spain
| | - Silviene F Oliveira
- Programa de Pós-Graduação em Ciencias da Saude (UnB), Brazila, Brazil
- Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
- Programa de Pós-Graduação em Biologia Animal (UnB), Brasília, Brazil
- Programa de Pós-Graduação Profissional em Ensino de Biologia (UnB), Brasília, Brazil
| | - Eva Ortega-Paino
- Spanish National Cancer Research Centre, CNIO Biobank, Madrid, Spain
| | - Mara Parellada
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón (IiSGM), Madrid, Spain
- School of Medicine, Universidad Complutense, Madrid, Spain
- Centre for Biomedical Network Research on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - Estela Paz-Artal
- Hospital Universitario 12 de Octubre, Department of Immunology, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Transplant Immunology and Immunodeficiencies Group, Madrid, Spain
- Universidad Complutense de Madrid, Department of Immunology, Ophthalmology and ENT, Madrid, Spain
| | - Ney P C Santos
- Universidade Federal do Pará, Núcleo de Pesquisas em Oncologia, Belém, Brazil
| | - Patricia Pérez-Matute
- Infectious Diseases, Microbiota and Metabolism Unit, CSIC Associated Unit, Center for Biomedical Research of La Rioja (CIBIR), Logroño, Spain
| | | | - M Elena Pérez-Tomás
- Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain
| | | | - Mellina Pinsach-Abuin
- CIBERCV, ISCIII, Madrid, Spain
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), Girona, Spain
| | - Guillermo Pita
- Spanish National Cancer Research Centre, Human Genotyping-CEGEN Unit, Madrid, Spain
| | - Ericka N Pompa-Mera
- Instituto Mexicano del Seguro Social (IMSS), Centro Médico Nacional Siglo XXI, Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Mexico City, Mexico
- Instituto Mexicano del Seguro Social (IMSS), Centro Médico Nacional La Raza, Hospital de Infectología, Mexico City, Mexico
| | | | - Aurora Pujol
- CIBERER, ISCIII, Madrid, Spain
- Bellvitge Biomedical Research Institute (IDIBELL), Neurometabolic Diseases Laboratory, L'Hospitalet de Llobregat, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | | | - Salvador Resino
- CIBERINFEC, ISCIII, Madrid, Spain
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Marianne R Fernandes
- Universidade Federal do Pará, Núcleo de Pesquisas em Oncologia, Belém, Brazil
- Hospital Ophir Loyola, Departamento de Ensino e Pesquisa, Belém, Brazil
| | - Emilio Rodríguez-Ruiz
- IDIS, Seongnam, Republic of Korea
- Unidad de Cuidados Intensivos, Hospital Clínico Universitario de Santiago (CHUS), Sistema Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Fernando Rodriguez-Artalejo
- CIBERESP, ISCIII, Madrid, Spain
- Department of Preventive Medicine and Public Health, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
- IdiPaz (Instituto de Investigación Sanitaria Hospital Universitario La Paz), Madrid, Spain
- IMDEA-Food Institute, CEI UAM+CSIC, Madrid, Spain
| | | | - Francisco Ruiz-Cabello
- IDIS, Seongnam, Republic of Korea
- Instituto de Investigación Biosanitaria de Granada (ibs GRANADA), Granada, Spain
- Universidad de Granada, Departamento Bioquímica, Biología Molecular e Inmunología III, Granada, Spain
| | - Javier Ruiz-Hornillos
- Hospital Infanta Elena, Allergy Unit, Valdemoro, Madrid, Spain
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Faculty of Medicine, Universidad Francisco de Vitoria, Madrid, Spain
| | - Pablo Ryan
- CIBERINFEC, ISCIII, Madrid, Spain
- Hospital Universitario Infanta Leonor, Madrid, Spain
- Complutense University of Madrid, Madrid, Spain
- Gregorio Marañón Health Research Institute (IiSGM), Madrid, Spain
| | - José Manuel Soria
- Genomics of Complex Diseases Unit, Research Institute of Hospital de la Santa Creu i Sant Pau, IIB Sant Pau, Barcelona, Spain
| | - Juan Carlos Souto
- Haemostasis and Thrombosis Unit, Hospital de la Santa Creu i Sant Pau, IIB Sant Pau, Barcelona, Spain
| | - Eduardo Tamayo
- Hospital Clinico Universitario de Valladolid, Servicio de Anestesiologia y Reanimación, Valladolid, Spain
- Universidad de Valladolid, Departamento de Cirugía, Valladolid, Spain
| | - Alvaro Tamayo-Velasco
- Hospital Clinico Universitario de Valladolid, Servicio de Hematologia y Hemoterapia, Valladolid, Spain
| | - Juan Carlos Taracido-Fernandez
- Data Analysis Department, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Alejandro Teper
- Hospital de Niños Ricardo Gutierrez, Buenos Aires, Argentina
| | | | - Miguel Urioste
- Spanish National Cancer Research Centre, Familial Cancer Clinical Unit, Madrid, Spain
| | | | - Zuleima Yáñez
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla, Colombia
| | - Ruth Zarate
- Centro para el Desarrollo de la Investigación Científica, Asunción, Paraguay
| | - Itziar de Rojas
- Centre for Biomedical Network Research on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Research Center and Memory clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Agustín Ruiz
- Centre for Biomedical Network Research on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Research Center and Memory clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Pascual Sánchez
- CIEN Foundation/Queen Sofia Foundation Alzheimer Center, Madrid, Spain
| | - Luis Miguel Real
- Hospital Universitario de Valme, Unidad Clínica de Enfermedades Infecciosas y Microbiología, Sevilla, Spain
| | - Encarna Guillen-Navarro
- Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain
- Sección Genética Médica - Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Servicio Murciano de Salud, Murcia, Spain
- Departamento Cirugía, Pediatría, Obstetricia y Ginecología, Facultad de Medicina, Universidad de Murcia (UMU), Murcia, Spain
- Grupo Clínico Vinculado, Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ayuso
- CIBERER, ISCIII, Madrid, Spain
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Esteban Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Canada
| | - José A Riancho
- CIBERER, ISCIII, Madrid, Spain
- IDIVAL, Cantabria, Spain
- Hospital U M Valdecilla, Cantabria, Spain
- Universidad de Cantabria, Cantabria, Spain
| | | | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Instituto de Investigación Sanitaria de Canarias, Santa Cruz de Tenerife, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Centre for Biomedical Network Research on Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Pablo Lapunzina
- ERN-ITHACA-European Reference Network, Soria, Spain
- CIBERER, ISCIII, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz IDIPAZ, Madrid, Spain
| | - Ángel Carracedo
- CIBERER, ISCIII, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS), Santiago de Compostela, Spain
- IDIS, Seongnam, Republic of Korea
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Kawamoto H, Saito-Sasaki N, Sawada Y. Recurrent Merkel Cell Carcinoma Following COVID-19 Treatment. Cureus 2024; 16:e64863. [PMID: 39156288 PMCID: PMC11330325 DOI: 10.7759/cureus.64863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2024] [Indexed: 08/20/2024] Open
Abstract
Merkel cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer influenced by the immune system. Recent studies suggest that viral infections, notably COVID-19, may exacerbate such malignancies. This case report explores potential mechanisms by which SARS-CoV-2, the virus responsible for COVID-19, could influence the behavior and proliferation of malignant tumor cells. Emerging evidence indicates that COVID-19 may disrupt immune surveillance and modulation, which are critical in controlling the spread and severity of cancers, including MCC. Additionally, the cytokine storm induced by COVID-19 is proposed to facilitate tumorigenic activity, potentially enhancing MCC aggressiveness. By integrating clinical findings with contemporary immunological and virological theories, this report aims to contribute to the understanding of COVID-19's impact on cancer progression, specifically MCC, emphasizing the need for comprehensive management strategies in cancer patients during the pandemic.
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Affiliation(s)
- Hirofumi Kawamoto
- Dermatology, University of Occupational and Environmental Health, Kitakyushu, JPN
| | - Natsuko Saito-Sasaki
- Dermatology, University of Occupational and Environmental Health, Kitakyushu, JPN
| | - Yu Sawada
- Dermatology, University of Occupational and Environmental Health, Kitakyushu, JPN
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Israelow B, Iwasaki A. First encounter with SARS-CoV-2: immune portraits of COVID susceptibility. Nature 2024; 631:33-35. [PMID: 38898251 DOI: 10.1038/d41586-024-01644-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
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Lindeboom RGH, Worlock KB, Dratva LM, Yoshida M, Scobie D, Wagstaffe HR, Richardson L, Wilbrey-Clark A, Barnes JL, Kretschmer L, Polanski K, Allen-Hyttinen J, Mehta P, Sumanaweera D, Boccacino JM, Sungnak W, Elmentaite R, Huang N, Mamanova L, Kapuge R, Bolt L, Prigmore E, Killingley B, Kalinova M, Mayer M, Boyers A, Mann A, Swadling L, Woodall MNJ, Ellis S, Smith CM, Teixeira VH, Janes SM, Chambers RC, Haniffa M, Catchpole A, Heyderman R, Noursadeghi M, Chain B, Mayer A, Meyer KB, Chiu C, Nikolić MZ, Teichmann SA. Human SARS-CoV-2 challenge uncovers local and systemic response dynamics. Nature 2024; 631:189-198. [PMID: 38898278 PMCID: PMC11222146 DOI: 10.1038/s41586-024-07575-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
The COVID-19 pandemic is an ongoing global health threat, yet our understanding of the dynamics of early cellular responses to this disease remains limited1. Here in our SARS-CoV-2 human challenge study, we used single-cell multi-omics profiling of nasopharyngeal swabs and blood to temporally resolve abortive, transient and sustained infections in seronegative individuals challenged with pre-Alpha SARS-CoV-2. Our analyses revealed rapid changes in cell-type proportions and dozens of highly dynamic cellular response states in epithelial and immune cells associated with specific time points and infection status. We observed that the interferon response in blood preceded the nasopharyngeal response. Moreover, nasopharyngeal immune infiltration occurred early in samples from individuals with only transient infection and later in samples from individuals with sustained infection. High expression of HLA-DQA2 before inoculation was associated with preventing sustained infection. Ciliated cells showed multiple immune responses and were most permissive for viral replication, whereas nasopharyngeal T cells and macrophages were infected non-productively. We resolved 54 T cell states, including acutely activated T cells that clonally expanded while carrying convergent SARS-CoV-2 motifs. Our new computational pipeline Cell2TCR identifies activated antigen-responding T cells based on a gene expression signature and clusters these into clonotype groups and motifs. Overall, our detailed time series data can serve as a Rosetta stone for epithelial and immune cell responses and reveals early dynamic responses associated with protection against infection.
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Affiliation(s)
- Rik G H Lindeboom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Lisa M Dratva
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - David Scobie
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Helen R Wagstaffe
- Department of Infectious Disease, Imperial College London, London, UK
| | - Laura Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Josephine L Barnes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | | | | | - Puja Mehta
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | | | - Waradon Sungnak
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Microbiology, Faculty of Science, and Integrative Computational BioScience Center, Mahidol University, Bangkok, Thailand
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Ensocell Therapeutics, BioData Innovation Centre, Wellcome Genome Campus, Hinxton, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Rakesh Kapuge
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ben Killingley
- Department of Infectious Diseases, University College London Hospital, London, UK
| | | | | | | | | | - Leo Swadling
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
| | | | - Samuel Ellis
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Claire M Smith
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Vitor H Teixeira
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Sam M Janes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Rachel C Chambers
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Robert Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Mahdad Noursadeghi
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Benny Chain
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Andreas Mayer
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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5
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Shahbaz MA, Kuivanen S, Lampinen R, Mussalo L, Hron T, Závodná T, Ojha R, Krejčík Z, Saveleva L, Tahir NA, Kalapudas J, Koivisto AM, Penttilä E, Löppönen H, Singh P, Topinka J, Vapalahti O, Chew S, Balistreri G, Kanninen KM. Human-derived air-liquid interface cultures decipher Alzheimer's disease-SARS-CoV-2 crosstalk in the olfactory mucosa. J Neuroinflammation 2023; 20:299. [PMID: 38098019 PMCID: PMC10722731 DOI: 10.1186/s12974-023-02979-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND The neurological effects of the coronavirus disease of 2019 (COVID-19) raise concerns about potential long-term consequences, such as an increased risk of Alzheimer's disease (AD). Neuroinflammation and other AD-associated pathologies are also suggested to increase the risk of serious SARS-CoV-2 infection. Anosmia is a common neurological symptom reported in COVID-19 and in early AD. The olfactory mucosa (OM) is important for the perception of smell and a proposed site of viral entry to the brain. However, little is known about SARS-CoV-2 infection at the OM of individuals with AD. METHODS To address this gap, we established a 3D in vitro model of the OM from primary cells derived from cognitively healthy and AD individuals. We cultured the cells at the air-liquid interface (ALI) to study SARS-CoV-2 infection under controlled experimental conditions. Primary OM cells in ALI expressed angiotensin-converting enzyme 2 (ACE-2), neuropilin-1 (NRP-1), and several other known SARS-CoV-2 receptor and were highly vulnerable to infection. Infection was determined by secreted viral RNA content and confirmed with SARS-CoV-2 nucleocapsid protein (NP) in the infected cells by immunocytochemistry. Differential responses of healthy and AD individuals-derived OM cells to SARS-CoV-2 were determined by RNA sequencing. RESULTS Results indicate that cells derived from cognitively healthy donors and individuals with AD do not differ in susceptibility to infection with the wild-type SARS-CoV-2 virus. However, transcriptomic signatures in cells from individuals with AD are highly distinct. Specifically, the cells from AD patients that were infected with the virus showed increased levels of oxidative stress, desensitized inflammation and immune responses, and alterations to genes associated with olfaction. These results imply that individuals with AD may be at a greater risk of experiencing severe outcomes from the infection, potentially driven by pre-existing neuroinflammation. CONCLUSIONS The study sheds light on the interplay between AD pathology and SARS-CoV-2 infection. Altered transcriptomic signatures in AD cells may contribute to unique symptoms and a more severe disease course, with a notable involvement of neuroinflammation. Furthermore, the research emphasizes the need for targeted interventions to enhance outcomes for AD patients with viral infection. The study is crucial to better comprehend the relationship between AD, COVID-19, and anosmia. It highlights the importance of ongoing research to develop more effective treatments for those at high risk of severe SARS-CoV-2 infection.
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Affiliation(s)
- Muhammad Ali Shahbaz
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Suvi Kuivanen
- Department of Virology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Institute of Virology, 10117, Berlin, Germany
| | - Riikka Lampinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Laura Mussalo
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Tomáš Hron
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20, Prague, Czech Republic
| | - Táňa Závodná
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine, Czech Academy of Sciences, 142 20, Prague, Czech Republic
| | - Ravi Ojha
- Department of Virology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Zdeněk Krejčík
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine, Czech Academy of Sciences, 142 20, Prague, Czech Republic
| | - Liudmila Saveleva
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Numan Ahmad Tahir
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Juho Kalapudas
- Department of Neurology, Neuro Centre, Kuopio University Hospital, 70210, Kuopio, Finland
| | - Anne M Koivisto
- Department of Neurology, Neuro Centre, Kuopio University Hospital, 70210, Kuopio, Finland
- Brain Research Unit, Department of Neurology, School of Medicine, University of Eastern Finland, 70210, Kuopio, Finland
- Department of Neurology and Geriatrics, Helsinki University Hospital and Neurosciences, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Elina Penttilä
- Department of Otorhinolaryngology, University of Eastern Finland and Kuopio University Hospital, 70210, Kuopio, Finland
| | - Heikki Löppönen
- Department of Otorhinolaryngology, University of Eastern Finland and Kuopio University Hospital, 70210, Kuopio, Finland
| | | | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine, Czech Academy of Sciences, 142 20, Prague, Czech Republic
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Sweelin Chew
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Giuseppe Balistreri
- Department of Virology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- The Queensland Brain Institute, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Katja M Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210, Kuopio, Finland.
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6
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Premraj A, Aleyas AG, Nautiyal B, Rasool TJ. Viperin from the dromedary camel: First report of an antiviral interferon-responsive gene from camelids. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104754. [PMID: 37295628 DOI: 10.1016/j.dci.2023.104754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023]
Abstract
Viral infections activate pattern recognition receptors in the host, triggering an innate immune response that involves the production of interferons, which, in turn, stimulates the expression of antiviral effector genes. Viperin is one of the most highly induced interferon-stimulated genes and displays broad antiviral activity, especially against tick-borne viruses. Of late, camelid-borne zoonotic viruses have been on the rise in the Arabian Peninsula, but research into camelid antiviral effector genes has been limited. This is the first report of an interferon-responsive gene from the mammalian suborder Tylopoda to which modern camels belong. From camel kidney cells treated with dsRNA mimetic, we cloned viperin cDNA encoding 361 amino acid protein. Sequence analysis of camel viperin reveals high levels of amino acid conservation, particularly within the RSAD domain. Compared to kidney, the relative mRNA expression of viperin was higher in blood, lung, spleen, lymph nodes, and intestines. The in-vitro expression of viperin was induced by poly(I:C) and interferon treatment in camel kidney cell lines. Viperin expression was subdued in camel kidney cells infected with the camelpox virus during the early stages of infection, suggesting possible suppression by the virus. Overexpression of camel viperin through transient transfection significantly enhanced the resistance of cultured camel kidney cell lines to infection with camelpox virus. Research into the role of viperin in host immunity against emerging viral pathogens of camels will provide insight into novel mechanisms of antiviral activity of the protein, viral immune evasion strategies, and enable the development of better antivirals.
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Affiliation(s)
- Avinash Premraj
- Camel Biotechnology Center, Presidential Camels & Camel Racing Affairs Centre, Department of the President's Affairs, PO Box 17292, Al Ain, United Arab Emirates
| | - Abi George Aleyas
- Camel Biotechnology Center, Presidential Camels & Camel Racing Affairs Centre, Department of the President's Affairs, PO Box 17292, Al Ain, United Arab Emirates
| | - Binita Nautiyal
- Camel Biotechnology Center, Presidential Camels & Camel Racing Affairs Centre, Department of the President's Affairs, PO Box 17292, Al Ain, United Arab Emirates
| | - Thaha Jamal Rasool
- Camel Biotechnology Center, Presidential Camels & Camel Racing Affairs Centre, Department of the President's Affairs, PO Box 17292, Al Ain, United Arab Emirates.
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7
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Ogarek N, Oboza P, Olszanecka-Glinianowicz M, Kocelak P. SARS-CoV-2 infection as a potential risk factor for the development of cancer. Front Mol Biosci 2023; 10:1260776. [PMID: 37753372 PMCID: PMC10518417 DOI: 10.3389/fmolb.2023.1260776] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/31/2023] [Indexed: 09/28/2023] Open
Abstract
The COVID-19 pandemic has a significant impact on public health and the estimated number of excess deaths may be more than three times higher than documented in official statistics. Numerous studies have shown an increased risk of severe COVID-19 and death in patients with cancer. In addition, the role of SARS-CoV-2 as a potential risk factor for the development of cancer has been considered. Therefore, in this review, we summarise the available data on the potential effects of SARS-CoV-2 infection on oncogenesis, including but not limited to effects on host signal transduction pathways, immune surveillance, chronic inflammation, oxidative stress, cell cycle dysregulation, potential viral genome integration, epigenetic alterations and genetic mutations, oncolytic effects and reactivation of dormant cancer cells. We also investigated the potential long-term effects and impact of the antiviral therapy used in COVID-19 on cancer development and its progression.
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Affiliation(s)
- Natalia Ogarek
- Pathophysiology Unit, Department of Pathophysiology, Faculty of Medical Sciences in Katowice, The Medical University of Silesia, Katowice, Poland
| | - Paulina Oboza
- Students’ Scientific Society at the Pathophysiology Unit, Department of Pathophysiology, Faculty of Medical Sciences in Katowice, The Medical University of Silesia, Katowice, Poland
| | - Magdalena Olszanecka-Glinianowicz
- Health Promotion and Obesity Management Unit, Department of Pathophysiology, Faculty of Medical Sciences in Katowice, The Medical University of Silesia, Katowice, Poland
| | - Piotr Kocelak
- Pathophysiology Unit, Department of Pathophysiology, Faculty of Medical Sciences in Katowice, The Medical University of Silesia, Katowice, Poland
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8
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Gao S, Zhang L, Wang H. Characterizing the key genes of COVID-19 that regulate tumor immune microenvironment and prognosis in hepatocellular carcinoma. Funct Integr Genomics 2023; 23:262. [PMID: 37540264 DOI: 10.1007/s10142-023-01184-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/05/2023]
Abstract
Hepatocellular carcinoma (HCC), a highly heterogeneous malignant tumor associated with a poor prognosis, is a common cause of cancer-related deaths worldwide, with a limited survival benefit for patients despite ongoing therapeutic breakthroughs. Coronavirus disease 2019 (COVID-19), a severe infectious disease caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), is a global pandemic and a serious threat to human health. The increased susceptibility to SARS-CoV-2 infection and a poor prognosis in patients with cancer necessitate the exploration of the potential link between the two. No studies have investigated the relationship of COVID-19 genes with the prognosis and tumor development in patients with HCC. We screened prognosis-related COVID-19 genes in HCC, performed molecular typing, developed a stable and reliable COVID-19 genes signature for predicting survival, characterized the immune microenvironment in HCC patients, and explored new molecular therapeutic targets. Datasets of HCC patients, including RNA sequencing data and clinical information, were obtained from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and Gene Expression Omnibus (GEO) databases. Prognosis-related COVID-19 genes were identified by univariate Cox analysis. Molecular typing of HCC was performed using the consensus non-negative matrix factorization method (cNMF), followed by the analysis of survival, tumor microenvironment, and pathway enrichment for each subtype. Prognostic signatures were constructed using LASSO-Cox regression models, and receiver operating characteristic (ROC) curves were used to validate the predictive performance of the signature. The same approach was used for the test and external validation sets. Seven software packages were applied to determine the abundance of immune infiltration in HCC patients and investigate its relationship with the risk scores. Gene set enrichment analysis (GSEA) was used to explore the potential mechanisms by which the COVID-19 genes affect hepatocarcinogenesis and prognosis. Three types of machine learning methods were combined to identify the most critical genes in the signature and localize their expression at the single cell level. We identified 53 prognosis-related COVID-19 genes and classified HCC into two molecular subtypes (C1, C2) by using the NMF method. The prognosis of C2 was significantly better than that of C1, and the two subtypes differed remarkably in terms of the tumor immune microenvironment and biological functions. The 17 COVID-19 genes were screened using the LASSO regression method to develop a 17 COVID-19 genes signature, which demonstrated a good predictive performance for 1-, 2- and 3-year OS of patients with HCC. The risk score as an independent prognostic factor for HCC has better predictive accuracy than traditional clinical variables. Patients in the TCGA cohort were categorized by risk score into the high- and low-risk groups, with the high-risk group mainly enriched in the immune modulation-related pathways and the low-risk group mainly enriched in the metabolism-related pathways, suggesting that the COVID-19 genes may affect disease progression and prognosis by regulating the tumor immune microenvironment and metabolism in HCC. NOL10 was identified as the most critical gene in the signature and hypothesized to be a potential therapeutic target for HCC. Objectively, the COVID-19 genes signature developed in this study, as an independent prognostic factor in HCC patients, is closely associated with the prognosis and tumor immune microenvironment of HCC patients and indicates that they may regulate the development of HCC in multiple ways, providing us with new perspectives for understanding the molecular mechanisms of HCC and finding effective therapeutic targets.
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Affiliation(s)
- Shuang Gao
- Division of Life Sciences and Medicine, Ward 4 of the Department of Oncology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Lei Zhang
- Department of Oncology Surgery, The Second Affiliated Hospital of Bengbu Medical University, Bengbu, 233080, Anhui, China
| | - Huiyan Wang
- Division of Life Sciences and Medicine, Department of Laboratory Diagnostics, the First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China.
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Costanzo M, De Giglio MAR, Roviello GN. Deciphering the Relationship between SARS-CoV-2 and Cancer. Int J Mol Sci 2023; 24:ijms24097803. [PMID: 37175509 PMCID: PMC10178366 DOI: 10.3390/ijms24097803] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Some viruses are known to be associated with the onset of specific cancers. These microorganisms, oncogenic viruses or oncoviruses, can convert normal cells into cancer cells by modulating the central metabolic pathways or hampering genomic integrity mechanisms, consequently inhibiting the apoptotic machinery and/or enhancing cell proliferation. Seven oncogenic viruses are known to promote tumorigenesis in humans: human papillomavirus (HPV), hepatitis B and C viruses (HBV, HCV), Epstein-Barr virus (EBV), human T-cell leukemia virus 1 (HTLV-1), Kaposi sarcoma-associated herpesvirus (KSHV), and Merkel cell polyomavirus (MCPyV). Recent research indicates that SARS-CoV-2 infection and COVID-19 progression may predispose recovered patients to cancer onset and accelerate cancer development. This hypothesis is based on the growing evidence regarding the ability of SARS-CoV-2 to modulate oncogenic pathways, promoting chronic low-grade inflammation and causing tissue damage. Herein, we summarize the main relationships known to date between virus infection and cancer, providing a summary of the proposed biochemical mechanisms behind the cellular transformation. Mechanistically, DNA viruses (such as HPV, HBV, EBV, and MCPyV) encode their virus oncogenes. In contrast, RNA viruses (like HCV, HTLV-1) may encode oncogenes or trigger host oncogenes through cis-/-trans activation leading to different types of cancer. As for SARS-CoV-2, its role as an oncogenic virus seems to occur through the inhibition of oncosuppressors or controlling the metabolic and autophagy pathways in the infected cells. However, these effects could be significant in particular scenarios like those linked to severe COVID-19 or long COVID. On the other hand, looking at the SARS-CoV-2─cancer relationship from an opposite perspective, oncolytic effects and anti-tumor immune response were triggered by SARS-CoV-2 infection in some cases. In summary, our work aims to recall comprehensive attention from the scientific community to elucidate the effects of SARS-CoV-2 and, more in general, β-coronavirus infection on cancer susceptibility for cancer prevention or supporting therapeutic approaches.
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Affiliation(s)
- Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore s.c.ar.l., Via G. Salvatore 486, 80145 Naples, Italy
| | | | - Giovanni Nicola Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Via P. Castellino 111, 80131 Naples, Italy
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10
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Li J, Huang F, Ma Q, Guo W, Feng K, Huang T, Cai YD. Identification of genes related to immune enhancement caused by heterologous ChAdOx1-BNT162b2 vaccines in lymphocytes at single-cell resolution with machine learning methods. Front Immunol 2023; 14:1131051. [PMID: 36936955 PMCID: PMC10017451 DOI: 10.3389/fimmu.2023.1131051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
The widely used ChAdOx1 nCoV-19 (ChAd) vector and BNT162b2 (BNT) mRNA vaccines have been shown to induce robust immune responses. Recent studies demonstrated that the immune responses of people who received one dose of ChAdOx1 and one dose of BNT were better than those of people who received vaccines with two homologous ChAdOx1 or two BNT doses. However, how heterologous vaccines function has not been extensively investigated. In this study, single-cell RNA sequencing data from three classes of samples: volunteers vaccinated with heterologous ChAdOx1-BNT and volunteers vaccinated with homologous ChAd-ChAd and BNT-BNT vaccinations after 7 days were divided into three types of immune cells (3654 B, 8212 CD4+ T, and 5608 CD8+ T cells). To identify differences in gene expression in various cell types induced by vaccines administered through different vaccination strategies, multiple advanced feature selection methods (max-relevance and min-redundancy, Monte Carlo feature selection, least absolute shrinkage and selection operator, light gradient boosting machine, and permutation feature importance) and classification algorithms (decision tree and random forest) were integrated into a computational framework. Feature selection methods were in charge of analyzing the importance of gene features, yielding multiple gene lists. These lists were fed into incremental feature selection, incorporating decision tree and random forest, to extract essential genes, classification rules and build efficient classifiers. Highly ranked genes include PLCG2, whose differential expression is important to the B cell immune pathway and is positively correlated with immune cells, such as CD8+ T cells, and B2M, which is associated with thymic T cell differentiation. This study gave an important contribution to the mechanistic explanation of results showing the stronger immune response of a heterologous ChAdOx1-BNT vaccination schedule than two doses of either BNT or ChAdOx1, offering a theoretical foundation for vaccine modification.
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Affiliation(s)
- Jing Li
- School of Computer Science, Baicheng Normal University, Baicheng, Jilin, China
| | - FeiMing Huang
- School of Life Sciences, Shanghai University, Shanghai, China
| | - QingLan Ma
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Tao Huang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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11
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Prognostic Value of Catestatin in Severe COVID-19: An ICU-Based Study. J Clin Med 2022; 11:jcm11154496. [PMID: 35956112 PMCID: PMC9369405 DOI: 10.3390/jcm11154496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 02/04/2023] Open
Abstract
Catestatin is a pleiotropic peptide with a wide range of immunomodulatory effects. Considering that patients with a severe COVID-19 infection have a major immunological dysregulation, the aim of this study was to evaluate catestatin levels in patients with COVID-19 treated in the intensive care unit (ICU) and to compare them between the fatal and non-fatal outcomes. The study included 152 patients with severe COVID-19, out of which 105 had a non-fatal outcome and 47 had a fatal outcome. Serum catestatin levels were estimated by an enzyme-linked immunosorbent assay in a commercially available diagnostic kit. The results show that catestatin levels were significantly lower in the fatal group compared to the non-fatal group (16.6 ± 7.8 vs. 23.2 ± 9.2 ng/mL; p < 0.001). Furthermore, there was a significant positive correlation between serum catestatin levels and vitamin D levels (r = 0.338; p < 0.001) while there was also a significant positive correlation between serum catestatin levels and growth differentiation factor-15 (GDF-15) levels (r = −0.345; p < 0.001). Furthermore, multivariate logistic regression showed that catestatin, GDF-15 and leukocyte count were significant predictors for COVID-19 survival. These findings imply that catestatin could be playing a major immunomodulatory role in the complex pathophysiology of the COVID-19 infection and that serum catestatin could also be a predictor of a poor COVID-19 outcome.
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Goubran H, Stakiw J, Seghatchian J, Ragab G, Burnouf T. SARS-CoV-2 and cancer: the intriguing and informative cross-talk. Transfus Apher Sci 2022; 61:103488. [PMID: 35753906 PMCID: PMC9192107 DOI: 10.1016/j.transci.2022.103488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 virus has significantly disrupted and burdened the diagnostic workup and delivery of care, including transfusion, to cancer patients across the globe. Furthermore, cancer patients suffering from solid tumors or hematologic malignancies were more prone to the infection and had higher morbidity and mortality than the rest of the population. Major signaling pathways have been identified at the intersection of SARS-CoV-2 and cancer cells, often leading to tumor progression or alteration of the tumor response to therapy. The reactivation of oncogenic viruses has also been alluded to in the context and following COVID-19. Paradoxically, certain tumors responded better following the profound infection-induced immune modulation. Unveiling the mechanisms of the virus-tumor cell interactions will lead to a better understanding of the pathophysiology of both cancer progression and virus propagation. It would be challenging to monitor, through the different cancer registries, retrospectively, the response of patients who have been previously exposed to the virus in contrast to those who have not contracted the infection.
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Affiliation(s)
- Hadi Goubran
- Saskatoon Cancer Centre and College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Julie Stakiw
- Saskatoon Cancer Centre and College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Jerard Seghatchian
- International Consultancy in Blood Components Quality/Safety, Audit/Inspection and DDR Strategy, London, UK
| | - Gaafar Ragab
- Internal Medicine Department, Rheumatology, and Clinical Immunology Unit, Faculty of Medicine, Cairo University, Cairo, Egypt; School of Medicine, Newgiza University (NGU), Giza, Egypt
| | - Thierry Burnouf
- Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan; International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan.
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Kountouras J, Gialamprinou D, Kotronis G, Papaefthymiou A, Economidou E, Soteriades ES, Vardaka E, Chatzopoulos D, Tzitiridou-Chatzopoulou M, Papazoglou DD, Doulberis M. Ofeleein i mi Vlaptin-Volume II: Immunity Following Infection or mRNA Vaccination, Drug Therapies and Non-Pharmacological Management at Post-Two Years SARS-CoV-2 Pandemic. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:309. [PMID: 35208631 PMCID: PMC8874934 DOI: 10.3390/medicina58020309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/06/2022] [Accepted: 02/14/2022] [Indexed: 12/15/2022]
Abstract
The persistence of the coronavirus disease 2019 (COVID-19) pandemic has triggered research into limiting transmission, morbidity and mortality, thus warranting a comprehensive approach to guide balanced healthcare policies with respect to people's physical and mental health. The mainstay priority during COVID-19 is to achieve widespread immunity, which could be established through natural contact or vaccination. Deep knowledge of the immune response combined with recent specific data indicates the potential inferiority of induced immunity against infection. Moreover, the prevention of transmission has been founded on general non-pharmacological measures of protection, albeit debate exists considering their efficacy and, among other issues, their socio-psychological burden. The second line of defense is engaged after infection and is supported by a plethora of studied agents, such as antibiotics, steroids and non-steroid anti-inflammatory drugs, antiviral medications and other biological agents that have been proposed, though variability in terms of benefits and adverse events has not allowed distinct solutions, albeit certain treatments might have a role in prevention and/or treatment of the disease. This narrative review summarizes the existing literature on the advantages and weaknesses of current COVID-19 management measures, thus underlining the necessity of acting based on the classical principle of "ofeleein i mi vlaptin", that is, to help or not to harm.
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Affiliation(s)
- Jannis Kountouras
- Second Medical Clinic, School of Medicine, Ippokration Hospital, Aristotle University of Thessaloniki, 54652 Thessaloniki, Central Macedonia, Greece; (A.P.); (E.V.); (D.C.); (M.T.-C.); (M.D.)
| | - Dimitra Gialamprinou
- Second Neonatal Department and NICU, Papageorgiou General Hospital, Aristotle University of Thessaloniki, 56403 Thessaloniki, Central Macedonia, Greece;
| | - Georgios Kotronis
- Department of Internal Medicine, General Hospital Aghios Pavlos of Thessaloniki, 55134 Thessaloniki, Central Macedonia, Greece;
| | - Apostolis Papaefthymiou
- Second Medical Clinic, School of Medicine, Ippokration Hospital, Aristotle University of Thessaloniki, 54652 Thessaloniki, Central Macedonia, Greece; (A.P.); (E.V.); (D.C.); (M.T.-C.); (M.D.)
- Department of Gastroenterology, University Hospital of Larisa, Mezourlo, 41110 Larisa, Thessaly, Greece
| | - Eleftheria Economidou
- School of Economics and Management, Healthcare Management Program, Open University of Cyprus, Nicosia 12794, Cyprus; (E.E.); (E.S.S.)
| | - Elpidoforos S. Soteriades
- School of Economics and Management, Healthcare Management Program, Open University of Cyprus, Nicosia 12794, Cyprus; (E.E.); (E.S.S.)
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Environmental and Occupational Medicine and Epidemiology (EOME), Boston, MA 02115, USA
| | - Elisabeth Vardaka
- Second Medical Clinic, School of Medicine, Ippokration Hospital, Aristotle University of Thessaloniki, 54652 Thessaloniki, Central Macedonia, Greece; (A.P.); (E.V.); (D.C.); (M.T.-C.); (M.D.)
- Department of Nutritional Sciences and Dietetics, School of Health Sciences, International Hellenic University, 57400 Thessaloniki, Central Macedonia, Greece
| | - Dimitrios Chatzopoulos
- Second Medical Clinic, School of Medicine, Ippokration Hospital, Aristotle University of Thessaloniki, 54652 Thessaloniki, Central Macedonia, Greece; (A.P.); (E.V.); (D.C.); (M.T.-C.); (M.D.)
| | - Maria Tzitiridou-Chatzopoulou
- Second Medical Clinic, School of Medicine, Ippokration Hospital, Aristotle University of Thessaloniki, 54652 Thessaloniki, Central Macedonia, Greece; (A.P.); (E.V.); (D.C.); (M.T.-C.); (M.D.)
- Midwifery Department, School of Healthcare Sciences, University of West Macedonia, Koila, 50100 Kozani, Central Macedonia, Greece
| | - Dimitrios David Papazoglou
- Department of Cardiovascular Surgery, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland;
| | - Michael Doulberis
- Second Medical Clinic, School of Medicine, Ippokration Hospital, Aristotle University of Thessaloniki, 54652 Thessaloniki, Central Macedonia, Greece; (A.P.); (E.V.); (D.C.); (M.T.-C.); (M.D.)
- Division of Gastroenterology and Hepatology, Medical University Department, Kantonsspital Aarau, 5001 Aarau, Switzerland
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Vyavahare S, Kumar S, Cantu N, Kolhe R, Bollag WB, McGee-Lawrence ME, Hill WD, Hamrick MW, Isales CM, Fulzele S. Tryptophan-Kynurenine Pathway in COVID-19-Dependent Musculoskeletal Pathology: A Minireview. Mediators Inflamm 2021; 2021:2911578. [PMID: 34621138 PMCID: PMC8492288 DOI: 10.1155/2021/2911578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/09/2021] [Accepted: 09/21/2021] [Indexed: 12/28/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), affecting multiple organ systems, including the respiratory tract and lungs. Several studies have reported that the tryptophan-kynurenine pathway is altered in COVID-19 patients. The tryptophan-kynurenine pathway plays a vital role in regulating inflammation, metabolism, immune responses, and musculoskeletal system biology. In this minireview, we surmise the effects of the kynurenine pathway in COVID-19 patients and how this pathway might impact muscle and bone biology.
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Affiliation(s)
- Sagar Vyavahare
- Department of Cell Biology and Anatomy, Augusta University, Augusta, GA, USA
| | - Sandeep Kumar
- Department of Cell Biology and Anatomy, Augusta University, Augusta, GA, USA
| | - Nicholas Cantu
- Department of Medicine, Augusta University, Augusta, GA, USA
| | - Ravindra Kolhe
- Department of Pathology, Augusta University, Augusta, GA, USA
| | - Wendy B. Bollag
- Department of Physiology, Augusta University, Augusta, GA, USA
- Center for Healthy Aging, Augusta University, Augusta, GA, USA
| | - Meghan E. McGee-Lawrence
- Department of Cell Biology and Anatomy, Augusta University, Augusta, GA, USA
- Center for Healthy Aging, Augusta University, Augusta, GA, USA
| | - William D. Hill
- Department of Pathology, Medical University of South Carolina, Charleston, SC, USA
| | - Mark W. Hamrick
- Department of Cell Biology and Anatomy, Augusta University, Augusta, GA, USA
- Center for Healthy Aging, Augusta University, Augusta, GA, USA
| | - Carlos M. Isales
- Department of Medicine, Augusta University, Augusta, GA, USA
- Center for Healthy Aging, Augusta University, Augusta, GA, USA
| | - Sadanand Fulzele
- Department of Cell Biology and Anatomy, Augusta University, Augusta, GA, USA
- Department of Medicine, Augusta University, Augusta, GA, USA
- Center for Healthy Aging, Augusta University, Augusta, GA, USA
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