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Alcalde-Herraiz M, Català M, Prats-Uribe A, Paredes R, Xie J, Prieto-Alhambra D. Genome-wide association studies of COVID-19 vaccine seroconversion and breakthrough outcomes in UK Biobank. Nat Commun 2024; 15:8739. [PMID: 39384777 PMCID: PMC11464770 DOI: 10.1038/s41467-024-52890-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 09/23/2024] [Indexed: 10/11/2024] Open
Abstract
Understanding the genetic basis of COVID-19 vaccine seroconversion is crucial to study the role of genetics on vaccine effectiveness. In our study, we used UK Biobank data to find the genetic determinants of COVID-19 vaccine-induced seropositivity and breakthrough infections. We conducted four genome-wide association studies among vaccinated participants for COVID-19 vaccine seroconversion and breakthrough susceptibility and severity. Our findings confirmed a link between the HLA region and seroconversion after the first and second doses. Additionally, we identified 10 genomic regions associated with breakthrough infection (SLC6A20, ST6GAL1, MUC16, FUT6, MXI1, MUC4, HMGN2P18-KRTCAP2, NFKBIZ and APOC1), and one with breakthrough severity (APOE). No significant evidence of genetic colocalisation was found between those traits. Our study highlights the roles of individual genetic make-up in the varied antibody responses to COVID-19 vaccines and provides insights into the potential mechanisms behind breakthrough infections occurred even after the vaccination.
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Affiliation(s)
- Marta Alcalde-Herraiz
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK
| | - Martí Català
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK
| | - Albert Prats-Uribe
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK
| | - Roger Paredes
- Department of Infectious Diseases and Institut de Recerca de la Sida IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
- Centre for Global Health and Diseases, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - JunQing Xie
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK
| | - Daniel Prieto-Alhambra
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK.
- Department of Medical Informatics, Erasmus University Medical Centre, Rotterdam, The Netherlands.
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Le Pen J, Paniccia G, Kinast V, Moncada-Velez M, Ashbrook AW, Bauer M, Hoffmann HH, Pinharanda A, Ricardo-Lax I, Stenzel AF, Rosado-Olivieri EA, Dinnon KH, Doyle WC, Freije CA, Hong SH, Lee D, Lewy T, Luna JM, Peace A, Schmidt C, Schneider WM, Winkler R, Yip EZ, Larson C, McGinn T, Menezes MR, Ramos-Espiritu L, Banerjee P, Poirier JT, Sànchez-Rivera FJ, Cobat A, Zhang Q, Casanova JL, Carroll TS, Glickman JF, Michailidis E, Razooky B, MacDonald MR, Rice CM. A genome-wide arrayed CRISPR screen identifies PLSCR1 as an intrinsic barrier to SARS-CoV-2 entry that recent virus variants have evolved to resist. PLoS Biol 2024; 22:e3002767. [PMID: 39316623 DOI: 10.1371/journal.pbio.3002767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 07/25/2024] [Indexed: 09/26/2024] Open
Abstract
Interferons (IFNs) play a crucial role in the regulation and evolution of host-virus interactions. Here, we conducted a genome-wide arrayed CRISPR knockout screen in the presence and absence of IFN to identify human genes that influence Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. We then performed an integrated analysis of genes interacting with SARS-CoV-2, drawing from a selection of 67 large-scale studies, including our own. We identified 28 genes of high relevance in both human genetic studies of Coronavirus Disease 2019 (COVID-19) patients and functional genetic screens in cell culture, with many related to the IFN pathway. Among these was the IFN-stimulated gene PLSCR1. PLSCR1 did not require IFN induction to restrict SARS-CoV-2 and did not contribute to IFN signaling. Instead, PLSCR1 specifically restricted spike-mediated SARS-CoV-2 entry. The PLSCR1-mediated restriction was alleviated by TMPRSS2 overexpression, suggesting that PLSCR1 primarily restricts the endocytic entry route. In addition, recent SARS-CoV-2 variants have adapted to circumvent the PLSCR1 barrier via currently undetermined mechanisms. Finally, we investigate the functional effects of PLSCR1 variants present in humans and discuss an association between PLSCR1 and severe COVID-19 reported recently.
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Affiliation(s)
- Jérémie Le Pen
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Gabrielle Paniccia
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Volker Kinast
- Department of Medical Microbiology and Virology, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
- Department for Molecular and Medical Virology, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Marcela Moncada-Velez
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
| | - Alison W Ashbrook
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Michael Bauer
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - H-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Ana Pinharanda
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Inna Ricardo-Lax
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Ansgar F Stenzel
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Edwin A Rosado-Olivieri
- Laboratory of Synthetic Embryology, The Rockefeller University, New York, New York, United States of America
| | - Kenneth H Dinnon
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - William C Doyle
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Catherine A Freije
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Seon-Hui Hong
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Danyel Lee
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Tyler Lewy
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Joseph M Luna
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Avery Peace
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Carltin Schmidt
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
| | - William M Schneider
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Roni Winkler
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Elaine Z Yip
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Chloe Larson
- Fisher Drug Discovery Resource Center, The Rockefeller University, New York, New York, United States of America
| | - Timothy McGinn
- Fisher Drug Discovery Resource Center, The Rockefeller University, New York, New York, United States of America
| | - Miriam-Rose Menezes
- Fisher Drug Discovery Resource Center, The Rockefeller University, New York, New York, United States of America
| | - Lavoisier Ramos-Espiritu
- Fisher Drug Discovery Resource Center, The Rockefeller University, New York, New York, United States of America
| | - Priyam Banerjee
- Bio-Imaging Resource Center, The Rockefeller University, New York, New York, United States of America
| | - John T Poirier
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York, United States of America
| | - Francisco J Sànchez-Rivera
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Aurélie Cobat
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Qian Zhang
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, New York, United States of America
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, New York, United States of America
| | - J Fraser Glickman
- Fisher Drug Discovery Resource Center, The Rockefeller University, New York, New York, United States of America
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Brandon Razooky
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Margaret R MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
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Akbari A, Barton AR, Gazal S, Li Z, Kariminejad M, Perry A, Zeng Y, Mittnik A, Patterson N, Mah M, Zhou X, Price AL, Lander ES, Pinhasi R, Rohland N, Mallick S, Reich D. Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.14.613021. [PMID: 39314480 PMCID: PMC11419161 DOI: 10.1101/2024.09.14.613021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
We present a method for detecting evidence of natural selection in ancient DNA time-series data that leverages an opportunity not utilized in previous scans: testing for a consistent trend in allele frequency change over time. By applying this to 8433 West Eurasians who lived over the past 14000 years and 6510 contemporary people, we find an order of magnitude more genome-wide significant signals than previous studies: 347 independent loci with >99% probability of selection. Previous work showed that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution, but in the last ten millennia, many hundreds of alleles have been affected by strong directional selection. Discoveries include an increase from ~0% to ~20% in 4000 years for the major risk factor for celiac disease at HLA-DQB1; a rise from ~0% to ~8% in 6000 years of blood type B; and fluctuating selection at the TYK2 tuberculosis risk allele rising from ~2% to ~9% from ~5500 to ~3000 years ago before dropping to ~3%. We identify instances of coordinated selection on alleles affecting the same trait, with the polygenic score today predictive of body fat percentage decreasing by around a standard deviation over ten millennia, consistent with the "Thrifty Gene" hypothesis that a genetic predisposition to store energy during food scarcity became disadvantageous after farming. We also identify selection for combinations of alleles that are today associated with lighter skin color, lower risk for schizophrenia and bipolar disease, slower health decline, and increased measures related to cognitive performance (scores on intelligence tests, household income, and years of schooling). These traits are measured in modern industrialized societies, so what phenotypes were adaptive in the past is unclear. We estimate selection coefficients at 9.9 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.
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Affiliation(s)
- Ali Akbari
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alison R Barton
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven Gazal
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Zheng Li
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - Annabel Perry
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yating Zeng
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Alissa Mittnik
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Alkes L Price
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ron Pinhasi
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
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Moreno-Grau S, Vernekar M, Lopez-Pineda A, Mas-Montserrat D, Barrabés M, Quinto-Cortés CD, Moatamed B, Lee MTM, Yu Z, Numakura K, Matsuda Y, Wall JD, Ioannidis AG, Katsanis N, Takano T, Bustamante CD. Polygenic risk score portability for common diseases across genetically diverse populations. Hum Genomics 2024; 18:93. [PMID: 39218908 PMCID: PMC11367857 DOI: 10.1186/s40246-024-00664-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Polygenic risk scores (PRS) derived from European individuals have reduced portability across global populations, limiting their clinical implementation at worldwide scale. Here, we investigate the performance of a wide range of PRS models across four ancestry groups (Africans, Europeans, East Asians, and South Asians) for 14 conditions of high-medical interest. METHODS To select the best-performing model per trait, we first compared PRS performances for publicly available scores, and constructed new models using different methods (LDpred2, PRS-CSx and SNPnet). We used 285 K European individuals from the UK Biobank (UKBB) for training and 18 K, including diverse ancestries, for testing. We then evaluated PRS portability for the best models in Europeans and compared their accuracies with respect to the best PRS per ancestry. Finally, we validated the selected PRS models using an independent set of 8,417 individuals from Biobank of the Americas-Genomelink (BbofA-GL); and performed a PRS-Phewas. RESULTS We confirmed a decay in PRS performances relative to Europeans when the evaluation was conducted using the best-PRS model for Europeans (51.3% for South Asians, 46.6% for East Asians and 39.4% for Africans). We observed an improvement in the PRS performances when specifically selecting ancestry specific PRS models (phenotype variance increase: 1.62 for Africans, 1.40 for South Asians and 0.96 for East Asians). Additionally, when we selected the optimal model conditional on ancestry for CAD, HDL-C and LDL-C, hypertension, hypothyroidism and T2D, PRS performance for studied populations was more comparable to what was observed in Europeans. Finally, we were able to independently validate tested models for Europeans, and conducted a PRS-Phewas, identifying cross-trait interplay between cardiometabolic conditions, and between immune-mediated components. CONCLUSION Our work comprehensively evaluated PRS accuracy across a wide range of phenotypes, reducing the uncertainty with respect to which PRS model to choose and in which ancestry group. This evaluation has let us identify specific conditions where implementing risk-prioritization strategies could have practical utility across diverse ancestral groups, contributing to democratizing the implementation of PRS.
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Affiliation(s)
- Sonia Moreno-Grau
- Galatea Bio, Inc, 14350 Commerce Way, Miami Lakes, FL, 33146, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, 1265 Welch Road, Stanford, CA, 94305, USA
| | - Manvi Vernekar
- Genomelink, Inc, 2150 Shattuck Avenue, Berkeley, CA, 94704, USA
| | - Arturo Lopez-Pineda
- Galatea Bio, Inc, 14350 Commerce Way, Miami Lakes, FL, 33146, USA
- , Amphora Health. Batallon Independencia 80, Morelia, Michoacan, 58260, Mexico
- Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autonoma de México, Antigua Carretera a Pátzcuaro No. 8701, Col. Ex Hacienda de San José de la Huerta, Morelia, Michoacán, C.P. 58190, Mexico
| | | | - Míriam Barrabés
- Galatea Bio, Inc, 14350 Commerce Way, Miami Lakes, FL, 33146, USA
| | | | - Babak Moatamed
- Galatea Bio, Inc, 14350 Commerce Way, Miami Lakes, FL, 33146, USA
| | | | - Zhenning Yu
- Genomelink, Inc, 2150 Shattuck Avenue, Berkeley, CA, 94704, USA
| | | | - Yuta Matsuda
- Genomelink, Inc, 2150 Shattuck Avenue, Berkeley, CA, 94704, USA
| | - Jeffrey D Wall
- Galatea Bio, Inc, 14350 Commerce Way, Miami Lakes, FL, 33146, USA
| | - Alexander G Ioannidis
- Galatea Bio, Inc, 14350 Commerce Way, Miami Lakes, FL, 33146, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, 1265 Welch Road, Stanford, CA, 94305, USA
- University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | | | - Tomohiro Takano
- Genomelink, Inc, 2150 Shattuck Avenue, Berkeley, CA, 94704, USA.
- Japan: Awakens Japan K.K. (Japanese subsidiary of Genomelink, Inc.), 2-11-3, Meguro, Meguro-ku, 1530063, Tokyo, Japan.
| | - Carlos D Bustamante
- Galatea Bio, Inc, 14350 Commerce Way, Miami Lakes, FL, 33146, USA.
- Department of Biomedical Data Science, Stanford University School of Medicine, 1265 Welch Road, Stanford, CA, 94305, USA.
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Zheng K, Chong AY, Mentzer AJ. How could our genetics impact COVID-19 vaccine response? Expert Rev Clin Immunol 2024; 20:1027-1039. [PMID: 38676712 DOI: 10.1080/1744666x.2024.2346584] [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: 12/22/2023] [Accepted: 04/19/2024] [Indexed: 04/29/2024]
Abstract
INTRODUCTION The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has posed unprecedented global health challenges since its emergence in December 2019. The rapid availability of vaccines has been estimated to save millions of lives, but there is variation in how individuals respond to vaccines, influencing their effectiveness at an individual, and population level. AREAS COVERED This review focuses on human genetic factors influencing the immune response and effectiveness of vaccines, highlighting the importance of associations across the HLA locus. Genome-Wide Association Studies (GWAS) and other genetic association analyses have identified statistically significant associations between specific HLA alleles including HLA-DRB1*13, DBQ1*06, and A*03 impacting antibody responses and the risk of breakthrough infections post-vaccination. Relationships between these associations and potential mechanisms and links with risks of natural infection or disease are explored, and this review concludes by emphasizing how understanding the mechanisms of these genetic determinants may inform the development of tailored vaccination strategies. EXPERT OPINION Although complex, we believe these findings from the SARS-CoV2 pandemic offer a unique opportunity to understand the relationships between HLA and infection and vaccine response, with a goal of optimizing individual protection against COVID-19 in the ongoing pandemic, and possibly influencing wider vaccine development in the future.
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Affiliation(s)
- Keyi Zheng
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Amanda Y Chong
- Centre for Human Genetics, University of Oxford, Oxford, UK
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Bröer A, Hu Z, Kukułowicz J, Yadav A, Zhang T, Dai L, Bajda M, Yan R, Bröer S. Cryo-EM structure of ACE2-SIT1 in complex with tiagabine. J Biol Chem 2024; 300:107687. [PMID: 39159813 PMCID: PMC11414674 DOI: 10.1016/j.jbc.2024.107687] [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: 02/01/2024] [Revised: 08/03/2024] [Accepted: 08/07/2024] [Indexed: 08/21/2024] Open
Abstract
The pharmacology of amino acid transporters in the SLC6 family is poorly developed compared to that of the neurotransmitter transporters. To identify new inhibitors of the proline transporter SIT1 (SLC6A20), its expression in Xenopus laevis oocytes was optimized. Trafficking of SIT1 was augmented by co-expression of angiotensin-converting enzyme 2 (ACE2) in oocytes but there was no strict requirement for co-expression of ACE2. A pharmacophore-guided screen identified tiagabine as a potent non-competitive inhibitor of SIT1. To understand its binding mode, we determined the cryo-electron microscopy (cryo-EM) structure of ACE2-SIT1 bound with tiagabine. The inhibitor binds close to the orthosteric proline binding site, but due to its size extends into the cytosolic vestibule. This causes the transporter to adopt an inward-open conformation, in which the intracellular gate is blocked. This study provides the first structural insight into inhibition of SIT1 and generates tools for a better understanding of the ACE2-SIT1 complex. These findings may have significance for SARS-CoV-2 binding to its receptor ACE2 in human lung alveolar cells where SIT1 and ACE2 are functionally expressed.
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Affiliation(s)
- Angelika Bröer
- Research School of Biology, Australian National University, Canberra, Australia
| | - Ziwei Hu
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jędrzej Kukułowicz
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Cracow, Poland
| | - Aditya Yadav
- Research School of Biology, Australian National University, Canberra, Australia
| | - Ting Zhang
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lu Dai
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Marek Bajda
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Cracow, Poland
| | - Renhong Yan
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China.
| | - Stefan Bröer
- Research School of Biology, Australian National University, Canberra, Australia.
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7
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Leist SR, Schäfer A, Risemberg EL, Bell TA, Hock P, Zweigart MR, Linnertz CL, Miller DR, Shaw GD, de Villena FPM, Ferris MT, Valdar W, Baric RS. Sarbecovirus disease susceptibility is conserved across viral and host models. Virus Res 2024; 346:199399. [PMID: 38823688 PMCID: PMC11225686 DOI: 10.1016/j.virusres.2024.199399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 04/15/2024] [Accepted: 05/15/2024] [Indexed: 06/03/2024]
Abstract
Coronaviruses have caused three severe epidemics since the start of the 21st century: SARS, MERS and COVID-19. The severity of the ongoing COVID-19 pandemic and increasing likelihood of future coronavirus outbreaks motivates greater understanding of factors leading to severe coronavirus disease. We screened ten strains from the Collaborative Cross mouse genetic reference panel and identified strains CC006/TauUnc (CC006) and CC044/Unc (CC044) as coronavirus-susceptible and resistant, respectively, as indicated by variable weight loss and lung congestion scores four days post-infection. We generated a genetic mapping population of 755 CC006xCC044 F2 mice and exposed the mice to one of three genetically distinct mouse-adapted coronaviruses: clade 1a SARS-CoV MA15 (n=391), clade 1b SARS-CoV-2 MA10 (n=274), and clade 2 HKU3-CoV MA (n=90). Quantitative trait loci (QTL) mapping in SARS-CoV MA15- and SARS-CoV-2 MA10-infected F2 mice identified genetic loci associated with disease severity. Specifically, we identified seven loci associated with variation in outcome following infection with either virus, including one, HrS43, that is present in both groups. Three of these QTL, including HrS43, were also associated with HKU3-CoV MA outcome. HrS43 overlaps with a QTL previously reported by our lab that is associated with SARS-CoV MA15 outcome in CC011xCC074 F2 mice and is also syntenic with a human chromosomal region associated with severe COVID-19 outcomes in humans GWAS. The results reported here provide: (a) additional support for the involvement of this locus in SARS-CoV MA15 infection, (b) the first conclusive evidence that this locus is associated with susceptibility across the Sarbecovirus subgenus, and (c) demonstration of the relevance of mouse models in the study of coronavirus disease susceptibility in humans.
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Affiliation(s)
- Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, United States
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, United States
| | - Ellen L Risemberg
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, United States; Department of Genetics, University of North Carolina at Chapel Hill, United States
| | - Timothy A Bell
- Department of Genetics, University of North Carolina at Chapel Hill, United States
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, United States
| | - Mark R Zweigart
- Department of Epidemiology, University of North Carolina at Chapel Hill, United States
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, United States
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, United States
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, United States
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, United States
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, United States.
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, United States.
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, United States; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, United States.
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8
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Kosmicki JA, Marcketta A, Sharma D, Di Gioia SA, Batista S, Yang XM, Tzoneva G, Martinez H, Sidore C, Kessler MD, Horowitz JE, Roberts GHL, Justice AE, Banerjee N, Coignet MV, Leader JB, Park DS, Lanche R, Maxwell E, Knight SC, Bai X, Guturu H, Baltzell A, Girshick AR, McCurdy SR, Partha R, Mansfield AJ, Turissini DA, Zhang M, Mbatchou J, Watanabe K, Verma A, Sirugo G, Ritchie MD, Salerno WJ, Shuldiner AR, Rader DJ, Mirshahi T, Marchini J, Overton JD, Carey DJ, Habegger L, Reid JG, Economides A, Kyratsous C, Karalis K, Baum A, Cantor MN, Rand KA, Hong EL, Ball CA, Siminovitch K, Baras A, Abecasis GR, Ferreira MAR. Genetic risk factors for COVID-19 and influenza are largely distinct. Nat Genet 2024; 56:1592-1596. [PMID: 39103650 PMCID: PMC11319199 DOI: 10.1038/s41588-024-01844-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 06/24/2024] [Indexed: 08/07/2024]
Abstract
Coronavirus disease 2019 (COVID-19) and influenza are respiratory illnesses caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses, respectively. Both diseases share symptoms and clinical risk factors1, but the extent to which these conditions have a common genetic etiology is unknown. This is partly because host genetic risk factors are well characterized for COVID-19 but not for influenza, with the largest published genome-wide association studies for these conditions including >2 million individuals2 and about 1,000 individuals3-6, respectively. Shared genetic risk factors could point to targets to prevent or treat both infections. Through a genetic study of 18,334 cases with a positive test for influenza and 276,295 controls, we show that published COVID-19 risk variants are not associated with influenza. Furthermore, we discovered and replicated an association between influenza infection and noncoding variants in B3GALT5 and ST6GAL1, neither of which was associated with COVID-19. In vitro small interfering RNA knockdown of ST6GAL1-an enzyme that adds sialic acid to the cell surface, which is used for viral entry-reduced influenza infectivity by 57%. These results mirror the observation that variants that downregulate ACE2, the SARS-CoV-2 receptor, protect against COVID-19 (ref. 7). Collectively, these findings highlight downregulation of key cell surface receptors used for viral entry as treatment opportunities to prevent COVID-19 and influenza.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Giorgio Sirugo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | | | | | - Alina Baum
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
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9
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Kovanda A, Lukežič T, Maver A, Vokač Križaj H, Čižek Sajko M, Šelb J, Rijavec M, Bidovec-Stojković U, Bitežnik B, Rituper B, Korošec P, Peterlin B. Genomic Landscape of Susceptibility to Severe COVID-19 in the Slovenian Population. Int J Mol Sci 2024; 25:7674. [PMID: 39062917 PMCID: PMC11277002 DOI: 10.3390/ijms25147674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Determining the genetic contribution of susceptibility to severe SARS-CoV-2 infection outcomes is important for public health measures and individualized treatment. Through intense research on this topic, several hundred genes have been implicated as possibly contributing to the severe infection phenotype(s); however, the findings are complex and appear to be population-dependent. We aimed to determine the contribution of human rare genetic variants associated with a severe outcome of SARS-CoV-2 infections and their burden in the Slovenian population. A panel of 517 genes associated with severe SARS-CoV-2 infection were obtained by combining an extensive review of the literature, target genes identified by the COVID-19 Host Genetic Initiative, and the curated Research COVID-19 associated genes from PanelApp, England Genomics. Whole genome sequencing was performed using PCR-free WGS on DNA from 60 patients hospitalized due to severe COVID-19 disease, and the identified rare genomic variants were analyzed and classified according to the ACMG criteria. Background prevalence in the general Slovenian population was determined by comparison with sequencing data from 8025 individuals included in the Slovenian genomic database (SGDB). Results show that several rare pathogenic/likely pathogenic genomic variants in genes CFTR, MASP2, MEFV, TNFRSF13B, and RNASEL likely contribute to the severe infection outcomes in our patient cohort. These results represent an insight into the Slovenian genomic diversity associated with a severe COVID-19 outcome.
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Affiliation(s)
- Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tadeja Lukežič
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Hana Vokač Križaj
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Mojca Čižek Sajko
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Julij Šelb
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
| | - Matija Rijavec
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
| | | | - Barbara Bitežnik
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
| | - Boštjan Rituper
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
| | - Peter Korošec
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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10
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Farag N, Noë A, Patrinos D, Zawati MH. Mapping the Apps: Ethical and Legal Issues with Crowdsourced Smartphone Data using mHealth Applications. Asian Bioeth Rev 2024; 16:437-470. [PMID: 39022376 PMCID: PMC11250705 DOI: 10.1007/s41649-024-00296-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/03/2024] [Accepted: 04/14/2024] [Indexed: 07/20/2024] Open
Abstract
More than 5 billion people in the world own a smartphone. More than half of these have been used to collect and process health-related data. As such, the existing volume of potentially exploitable health data is unprecedentedly large and growing rapidly. Mobile health applications (apps) on smartphones are some of the worst offenders and are increasingly being used for gathering and exchanging significant amounts of personal health data from the public. This data is often utilized for health research purposes and for algorithm training. While there are advantages to utilizing this data for expanding health knowledge, there are associated risks for the users of these apps, such as privacy concerns and the protection of their data. Consequently, gaining a deeper comprehension of how apps collect and crowdsource data is crucial. To explore how apps are crowdsourcing data and to identify potential ethical, legal, and social issues (ELSI), we conducted an examination of the Apple App Store and the Google Play Store in North America and Europe to identify apps that could potentially gather health data through crowdsourcing. Subsequently, we analyzed their privacy policies, terms of use, and other related documentation to gain insights into the utilization of users' data and the possibility of repurposing it for research or algorithm training purposes. More specifically, we reviewed privacy policies to identify clauses pertaining to the following key categories: research, data sharing, privacy/confidentiality, commercialization, and return of findings. Based on the results of these app search, we developed an App Atlas that presents apps which crowdsource data for research or algorithm training. We identified 46 apps available in the European and Canadian markets that either openly crowdsource health data for research or algorithm training or retain the legal or technical capability to do so. This app search showed an overall lack of consistency and transparency in privacy policies that poses challenges to user comprehensibility, trust, and informed consent. A significant proportion of applications presented contradictions or exhibited considerable ambiguity. For instance, the vast majority of privacy policies in the App Atlas contain ambiguous or contradictory language regarding the sharing of users' data with third parties. This raises a number of ethico-legal concerns which will require further academic and policy attention to ensure a balance between protecting individual interests and maximizing the scientific utility of crowdsourced data. This article represents a key first step in better understanding these concerns and bringing attention to this important issue. Supplementary Information The online version contains supplementary material available at 10.1007/s41649-024-00296-3.
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Affiliation(s)
- Nada Farag
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Alycia Noë
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Dimitri Patrinos
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Ma’n H. Zawati
- Centre of Genomics and Policy, McGill University, Montreal, Canada
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11
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Johnston KJ, Signer R, Huckins LM. Chronic Overlapping Pain Conditions and Nociplastic Pain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.06.27.23291959. [PMID: 38766033 PMCID: PMC11100847 DOI: 10.1101/2023.06.27.23291959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Chronic Overlapping Pain Conditions (COPCs) are a subset of chronic pain conditions commonly comorbid with one another and more prevalent in women and assigned female at birth (AFAB) individuals. Pain experience in these conditions may better fit with a new mechanistic pain descriptor, nociplastic pain, and nociplastic type pain may represent a shared underlying factor among COPCs. We applied GenomicSEM common-factor genome wide association study (GWAS) and multivariate transcriptome-wide association (TWAS) analyses to existing GWAS output for six COPCs in order to find genetic variation associated with nociplastic type pain, followed by genetic correlation (linkage-disequilibrium score regression), gene-set and tissue enrichment analyses. We found 24 independent single nucleotide polymorphisms (SNPs), and 127 unique genes significantly associated with nociplastic type pain, and showed nociplastic type pain to be a polygenic trait with significant SNP-heritability. We found significant genetic overlap between multisite chronic pain and nociplastic type pain, and to a smaller extent with rheumatoid arthritis and a neuropathic pain phenotype. Tissue enrichment analyses highlighted cardiac and thyroid tissue, and gene set enrichment analyses emphasized potential shared mechanisms in cognitive, personality, and metabolic traits and nociplastic type pain along with distinct pathology in migraine and headache. We use a well-powered network approach to investigate nociplastic type pain using existing COPC GWAS output, and show nociplastic type pain to be a complex, heritable trait, in addition to contributing to understanding of potential mechanisms in development of nociplastic pain.
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Affiliation(s)
- Keira J.A. Johnston
- Department of Psychiatry, Yale School of Medicine, Yale University, New Haven, CT 06511, USA
| | - Rebecca Signer
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Laura M. Huckins
- Department of Psychiatry, Yale School of Medicine, Yale University, New Haven, CT 06511, USA
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12
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López-Bielma MF, Falfán-Valencia R, Fierro-Piña A, Abarca-Rojano E, Córdoba-Lanus E, Fricke-Galindo I, Romero-Villaseñor P, Buendía-Roldán I, Chávez-Galán L, Jaime-Capetillo ME, Pérez-Rubio G. Genetic variants in ATP2B2 as risk factors for mortality in patients unrelated but not associated with families with severe COVID-19. Heliyon 2024; 10:e29493. [PMID: 38628728 PMCID: PMC11019202 DOI: 10.1016/j.heliyon.2024.e29493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Introduction The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus Disease 2019 (COVID-19). The disease has a wide range of clinical manifestations, from asymptomatic to severe. Ancestral contribution, sex, immune response, and genetic factors influence the presentation of the disease. The objective of the present study was to validate these genetic variants in patients with severe COVID-19 who died and in survivor patients. Methods: Single nucleotide variants (SNVs) in six genes: ATPase plasma membrane Ca2+ transporting 2 (ATP2B2), transmembrane serine protease 2 (TMPRSS2), dedicator of cytokinesis 2 (DOCK2), (interferon alpha and beta receptor subunit 2) IFNAR2, tumor necrosis factor receptor superfamily, member 1A (TNFRSF1A), and tumor necrosis factor receptor superfamily, member 1B (TNFRSF1B), were explored in two groups: the first consisted of severe COVID-19-related patients (familial cases from 58 families, n = 130), and the second group of unrelated severe COVID-19 patients (n = 1045). In each study group, death was evaluated as the outcome. Results In non-related patients with severe COVID-19, carriers of GG genotype (rs2289274) in the ATP2B2 gene showed a high-risk probability of non-surviving (OR = 1.43). Survival analysis to 75 days indicates that carriers of GG have a higher risk than GA or AA genotypes (p = 0.0059). The haplotype GG (rs2289273-rs2289274) in ATP2B2 was found to be associated with a high risk of death in severe non-related COVID-19 patients. No significant associations were found between severe COVID-19-related patients and SNVs in ATP2B2, TMPRSS2, DOCK2, IFNAR2, TNFRSF1A, or TNFRSF1B. Conclusions Unrelated patients with severe COVID-19 that carry the GG genotype (rs2289274) in ATP2B2 showed a high death risk. Survival analysis to 75 days indicates that carriers of GG have a higher risk of non-survival compared to GA or AA genotypes.
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Affiliation(s)
- María Fernanda López-Bielma
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Aurelio Fierro-Piña
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Edgar Abarca-Rojano
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico
| | - Elizabeth Córdoba-Lanus
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, 38296, San Cristóbal de La Laguna, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Ingrid Fricke-Galindo
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Priscila Romero-Villaseñor
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Ivette Buendía-Roldán
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Leslie Chávez-Galán
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - María Esther Jaime-Capetillo
- Clinical Laboratory Service, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, 14080, Mexico
| | - Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
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13
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Chan MMY, Gale DP. Using genomics to understand severe COVID-19. Nephrol Dial Transplant 2024; 39:731-734. [PMID: 38081206 DOI: 10.1093/ndt/gfad262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Indexed: 09/18/2024] Open
Affiliation(s)
- Melanie M Y Chan
- UCL Department of Renal Medicine, University College London, London, UK
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK
| | - Daniel P Gale
- UCL Department of Renal Medicine, University College London, London, UK
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14
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Chávez-Vélez E, Álvarez-Nava F, Torres-Vinueza A, Balarezo-Díaz T, Pilataxi K, Acosta-López C, Peña IZ, Narváez K. Single nucleotide variants in the CCL2, OAS1 and DPP9 genes and their association with the severity of COVID-19 in an Ecuadorian population. Front Cell Infect Microbiol 2024; 14:1322882. [PMID: 38694517 PMCID: PMC11061356 DOI: 10.3389/fcimb.2024.1322882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/15/2024] [Indexed: 05/04/2024] Open
Abstract
COVID-19 has a broad clinical spectrum, ranging from asymptomatic-mild form to severe phenotype. The severity of COVID-19 is a complex trait influenced by various genetic and environmental factors. Ethnic differences have been observed in relation to COVID-19 severity during the pandemic. It is currently unknown whether genetic variations may contribute to the increased risk of severity observed in Latin-American individuals The aim of this study is to investigate the potential correlation between gene variants at CCL2, OAS1, and DPP9 genes and the severity of COVID-19 in a population from Quito, Ecuador. This observational case-control study was conducted at the Carrera de Biologia from the Universidad Central del Ecuador and the Hospital Quito Sur of the Instituto Ecuatoriano de Seguridad Social (Quito-SUR-IESS), Quito, Ecuador. Genotyping for gene variants at rs1024611 (A>G), rs10774671 (A>G), and rs10406145 (G>C) of CCL2, OAS1, and DPP9 genes was performed on 100 COVID-19 patients (43 with severe form and 57 asymptomatic-mild) using RFLP-PCR. The genotype distribution of all SNVs throughout the entire sample of 100 individuals showed Hardy Weinberg equilibrium (P=0.53, 0.35, and 0.4 for CCL2, OAS1, and DPP9, respectively). The HWE test did not find any statistically significant difference in genotype distribution between the study and control groups for any of the three SNVs. The multivariable logistic regression analysis showed that individuals with the GG of the CCL2 rs1024611 gene variant had an increased association with the severe COVID-19 phenotype in a recessive model (P = 0.0003, OR = 6.43, 95% CI 2.19-18.89) and for the OAS1 rs10774671 gene variant, the log-additive model showed a significant association with the severe phenotype of COVID-19 (P=0.0084, OR=3.85, 95% CI 1.33-11.12). Analysis of haplotype frequencies revealed that the coexistence of GAG at CCL2, OAS1, and DPP9 variants, respectively, in the same individual increased the presence of the severe COVID-19 phenotype (OR=2.273, 95% CI: 1.271-4.068, P=0.005305). The findings of the current study suggests that the ethnic background affects the allele and genotype frequencies of genes associated with the severity of COVID-19. The experience with COVID-19 has provided an opportunity to identify an ethnicity-based approach to recognize genetically high-risk individuals in different populations for emerging diseases.
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Affiliation(s)
- Erik Chávez-Vélez
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Francisco Álvarez-Nava
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Alisson Torres-Vinueza
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Thalía Balarezo-Díaz
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Kathya Pilataxi
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Camila Acosta-López
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Ivonne Z. Peña
- Unidad de Cuidados Críticos de Adultos, Hospital Quito Sur del Instituto Ecuatoriano de Securidad Social, Quito, Ecuador
| | - Katherin Narváez
- Unidad de Cuidados Críticos de Adultos, Hospital Quito Sur del Instituto Ecuatoriano de Securidad Social, Quito, Ecuador
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15
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Yin Y, Zhang Y, Sun L, Wang S, Zeng Y, Gong B, Huang L, He Y, Yang Z. Association analysis of genetic variants in critical patients with COVID-19 and validation in a Chinese population. Virol Sin 2024; 39:347-350. [PMID: 38403118 DOI: 10.1016/j.virs.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Affiliation(s)
- Yi Yin
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610213, China; Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Zhang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Lelin Sun
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Shuqiang Wang
- Infectious Disease Department, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Yong Zeng
- Department of Ophthalmology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Bo Gong
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Lulin Huang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
| | - Yongquan He
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
| | - Zhenglin Yang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610213, China; Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Skerenova M, Cibulka M, Dankova Z, Holubekova V, Kolkova Z, Lucansky V, Dvorska D, Kapinova A, Krivosova M, Petras M, Baranovicova E, Baranova I, Novakova E, Liptak P, Banovcin P, Bobcakova A, Rosolanka R, Janickova M, Stanclova A, Gaspar L, Caprnda M, Prosecky R, Labudova M, Gabbasov Z, Rodrigo L, Kruzliak P, Lasabova Z, Matakova T, Halasova E. Host genetic variants associated with COVID-19 reconsidered in a Slovak cohort. Adv Med Sci 2024; 69:198-207. [PMID: 38555007 DOI: 10.1016/j.advms.2024.03.007] [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: 06/28/2023] [Revised: 11/15/2023] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
We present the results of an association study involving hospitalized coronavirus disease 2019 (COVID-19) patients with a clinical background during the 3rd pandemic wave of COVID-19 in Slovakia. Seventeen single nucleotide variants (SNVs) in the eleven most relevant genes, according to the COVID-19 Host Genetics Initiative, were investigated. Our study confirms the validity of the influence of LZTFL1 and 2'-5'-oligoadenylate synthetase (OAS)1/OAS3 genetic variants on the severity of COVID-19. For two LZTFL1 SNVs in complete linkage disequilibrium, rs17713054 and rs73064425, the odds ratios of baseline allelic associations and logistic regressions (LR) adjusted for age and sex ranged in the four tested designs from 2.04 to 2.41 and from 2.05 to 3.98, respectively. The OAS1/OAS3 haplotype 'gttg' carrying a functional allele G of splice-acceptor variant rs10774671 manifested its protective function in the Delta pandemic wave. Significant baseline allelic associations of two DPP9 variants in all tested designs and two IFNAR2 variants in the Omicron pandemic wave were not confirmed by adjusted LR. Nevertheless, adjusted LR showed significant associations of NOTCH4 rs3131294 and TYK2 rs2304256 variants with severity of COVID-19. Hospitalized patients' reported comorbidities were not correlated with genetic variants, except for obesity, smoking (IFNAR2), and hypertension (NOTCH4). The results of our study suggest that host genetic variations have an impact on the severity and duration of acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Considering the differences in allelic associations between pandemic waves, they support the hypothesis that every new SARS-CoV-2 variant may modify the host immune response by reconfiguring involved pathways.
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Affiliation(s)
- Maria Skerenova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Michal Cibulka
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Zuzana Dankova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Veronika Holubekova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Zuzana Kolkova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Vincent Lucansky
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Dana Dvorska
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Kapinova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Michaela Krivosova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Martin Petras
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Eva Baranovicova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Ivana Baranova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Elena Novakova
- Department of Microbiology and Immunology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Peter Liptak
- Clinic of Internal Medicine- Gastroenterology, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Peter Banovcin
- Clinic of Internal Medicine- Gastroenterology, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Anna Bobcakova
- Clinic of Pneumology and Phthisiology, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Robert Rosolanka
- Clinic of Infectology and Travel Medicine, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Maria Janickova
- Clinic of Stomatology and Maxillofacial Surgery, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Stanclova
- Department of Pathological Anatomy, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Ludovit Gaspar
- Faculty of Health Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Martin Caprnda
- 1st Department of Internal Medicine, Faculty of Medicine, Comenius University and University Hospital, Bratislava, Slovakia
| | - Robert Prosecky
- 2nd Department of Internal Medicine, Faculty of Medicine, Masaryk University and St. Anne'S University Hospital, Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital and Masaryk University, Brno, Czech Republic
| | - Monika Labudova
- Faculty of Health Care and Social Work, University of Trnava in Trnava, Slovakia
| | - Zufar Gabbasov
- National Medical Research Centre for Cardiology, Moscow, Russia
| | - Luis Rodrigo
- Faculty of Medicine, University of Oviedo and Central University Hospital of Asturias (HUCA), Oviedo, Spain
| | - Peter Kruzliak
- Faculty of Medicine, University of Oviedo and Central University Hospital of Asturias (HUCA), Oviedo, Spain; Research and Development Services, Olomouc, Czech Republic.
| | - Zora Lasabova
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Tatiana Matakova
- Department of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Erika Halasova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia.
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Park JK, Brake MA, Schulman S. Human Genetic Variation in F3 and Its Impact on Tissue Factor-Dependent Disease. Semin Thromb Hemost 2024; 50:188-199. [PMID: 37201535 DOI: 10.1055/s-0043-1769079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Tissue factor (TF) is the primary initiator of blood coagulation in humans. As improper intravascular TF expression and procoagulant activity underlie numerous thrombotic disorders, there has been longstanding interest in the contribution of heritable genetic variation in F3, the gene encoding TF, to human disease. This review seeks to comprehensively and critically synthesize small case-control studies focused on candidate single nucleotide polymorphisms (SNPs), as well as modern genome-wide association studies (GWAS) seeking to discover novel associations between variants and clinical phenotypes. Where possible, correlative laboratory studies, expression quantitative trait loci, and protein quantitative trait loci are evaluated to glean potential mechanistic insights. Most disease associations implicated in historical case-control studies have proven difficult to replicate in large GWAS. Nevertheless, SNPs linked to F3, such as rs2022030, are associated with increased F3 mRNA expression, monocyte TF expression after endotoxin exposure, and circulating levels of the prothrombotic biomarker D-dimer, consistent with the central role of TF in the initiation of blood coagulation.
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Affiliation(s)
- Jin K Park
- Division of Health, Sciences, and Technology, Massachusetts Institute of Technology and Harvard Medical School, Boston, Massachusetts
| | - Marisa A Brake
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Sol Schulman
- Division of Health, Sciences, and Technology, Massachusetts Institute of Technology and Harvard Medical School, Boston, Massachusetts
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
- Division of Hematology and Hematologic Malignancies, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
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Coelho RDCC, Martins CLELP, Pastana LF, Rodrigues JCG, Aguiar KEC, Cohen-Paes ADN, Gellen LPA, de Moraes FCA, Calderaro MCL, de Assunção LA, Monte N, Pereira EEB, Ribeiro-dos-Santos AM, Ribeiro-do-Santos Â, Rodriguez Burbano RM, de Souza SJ, Guerreiro JF, de Assumpção PP, dos Santos SEB, Fernandes MR, dos Santos NPC. Molecular Profile of Variants Potentially Associated with Severe Forms of COVID-19 in Amazonian Indigenous Populations. Viruses 2024; 16:359. [PMID: 38543725 PMCID: PMC10974871 DOI: 10.3390/v16030359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 05/23/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an infection caused by SARS-CoV-2. Genome-wide association studies (GWASs) have suggested a strong association of genetic factors with the severity of the disease. However, many of these studies have been completed in European populations, and little is known about the genetic variability of indigenous peoples' underlying infection by SARS-CoV-2. The objective of the study is to investigate genetic variants present in the genes AQP3, ARHGAP27, ELF5L, IFNAR2, LIMD1, OAS1 and UPK1A, selected due to their association with the severity of COVID-19, in a sample of indigenous people from the Brazilian Amazon in order to describe potential new and already studied variants. We performed the complete sequencing of the exome of 64 healthy indigenous people from the Brazilian Amazon. The allele frequency data of the population were compared with data from other continental populations. A total of 66 variants present in the seven genes studied were identified, including a variant with a high impact on the ARHGAP27 gene (rs201721078) and three new variants located in the Amazon Indigenous populations (INDG) present in the AQP3, IFNAR2 and LIMD1 genes, with low, moderate and modifier impact, respectively.
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Affiliation(s)
- Rita de Cássia Calderaro Coelho
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
| | - Carlliane Lima e Lins Pinto Martins
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
| | - Lucas Favacho Pastana
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
| | - Juliana Carla Gomes Rodrigues
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
| | - Kaio Evandro Cardoso Aguiar
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
| | - Amanda de Nazaré Cohen-Paes
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
| | - Laura Patrícia Albarello Gellen
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
| | - Francisco Cezar Aquino de Moraes
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
| | - Maria Clara Leite Calderaro
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
| | - Letícia Almeida de Assunção
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
| | - Natasha Monte
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
| | - Esdras Edgar Batista Pereira
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
| | - André Maurício Ribeiro-dos-Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belém 66077-830, PA, Brazil; (A.M.R.-d.-S.); (Â.R.-d.-S.); (J.F.G.)
| | - Ândrea Ribeiro-do-Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belém 66077-830, PA, Brazil; (A.M.R.-d.-S.); (Â.R.-d.-S.); (J.F.G.)
| | - Rommel Mario Rodriguez Burbano
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
- Ophir Loyola Hospital, Pará State Department of Health, Belém 66063-240, PA, Brazil
| | - Sandro José de Souza
- Brain Institute, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil;
| | - João Farias Guerreiro
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belém 66077-830, PA, Brazil; (A.M.R.-d.-S.); (Â.R.-d.-S.); (J.F.G.)
| | - Paulo Pimentel de Assumpção
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
| | - Sidney Emanuel Batista dos Santos
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belém 66077-830, PA, Brazil; (A.M.R.-d.-S.); (Â.R.-d.-S.); (J.F.G.)
| | - Marianne Rodrigues Fernandes
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
- Ophir Loyola Hospital, Pará State Department of Health, Belém 66063-240, PA, Brazil
| | - Ney Pereira Carneiro dos Santos
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (R.d.C.C.C.); (C.L.e.L.P.M.); (L.F.P.); (J.C.G.R.); (K.E.C.A.); (A.d.N.C.-P.); (L.P.A.G.); (F.C.A.d.M.); (M.C.L.C.); (L.A.d.A.); (N.M.); (E.E.B.P.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.); (M.R.F.)
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belém 66077-830, PA, Brazil; (A.M.R.-d.-S.); (Â.R.-d.-S.); (J.F.G.)
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Zhang Z, Wang S, Jiang L, Wei J, Lu C, Li S, Diao Y, Fang Z, He S, Tan T, Yang Y, Zou K, Shi J, Lin J, Chen L, Bao C, Fei J, Fang H. Priority index for critical Covid-19 identifies clinically actionable targets and drugs. Commun Biol 2024; 7:189. [PMID: 38366110 PMCID: PMC10873402 DOI: 10.1038/s42003-024-05897-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 02/07/2024] [Indexed: 02/18/2024] Open
Abstract
While genome-wide studies have identified genomic loci in hosts associated with life-threatening Covid-19 (critical Covid-19), the challenge of resolving these loci hinders further identification of clinically actionable targets and drugs. Building upon our previous success, we here present a priority index solution designed to address this challenge, generating the target and drug resource that consists of two indexes: the target index and the drug index. The primary purpose of the target index is to identify clinically actionable targets by prioritising genes associated with Covid-19. We illustrate the validity of the target index by demonstrating its ability to identify pre-existing Covid-19 phase-III drug targets, with the majority of these targets being found at the leading prioritisation (leading targets). These leading targets have their evolutionary origins in Amniota ('four-leg vertebrates') and are predominantly involved in cytokine-cytokine receptor interactions and JAK-STAT signaling. The drug index highlights opportunities for repurposing clinically approved JAK-STAT inhibitors, either individually or in combination. This proposed strategic focus on the JAK-STAT pathway is supported by the active pursuit of therapeutic agents targeting this pathway in ongoing phase-II/III clinical trials for Covid-19.
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Affiliation(s)
- Zhiqiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lulu Jiang
- Translational Health Sciences, University of Bristol, Bristol, BS1 3NY, UK
| | - Jianwen Wei
- Network and Information Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chang Lu
- MRC London Institute of Medical Sciences, Imperial College London, London, W12 0HS, UK
| | - Shengli Li
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201620, China
| | - Yizhu Diao
- College of Finance and Statistics, Hunan University, Changsha, 410079, Hunan, China
| | - Zhongcheng Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuo He
- College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Tingting Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yisheng Yang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Kexin Zou
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiantao Shi
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - James Lin
- Network and Information Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liye Chen
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK.
| | - Chaohui Bao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Department of General Surgery, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, 200020, China.
| | - Jian Fei
- Department of General Surgery, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, 200020, China.
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Sandi JD, Levy JI, Tapela K, Zeller M, Yeboah JA, Saka DF, Grant DS, Awandare GA, Quashie PK, Andersen KG, Paemka L. Upper Airway Epithelial Tissue Transcriptome Analysis Reveals Immune Signatures Associated with COVID-19 Severity in Ghanaians. J Immunol Res 2024; 2024:6668017. [PMID: 38375062 PMCID: PMC10876312 DOI: 10.1155/2024/6668017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/04/2023] [Accepted: 01/03/2024] [Indexed: 02/21/2024] Open
Abstract
The immunological signatures driving the severity of coronavirus disease 19 (COVID-19) in Ghanaians remain poorly understood. We performed bulk transcriptome sequencing of nasopharyngeal samples from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-infected Ghanaians with mild and severe COVID-19, as well as healthy controls to characterize immune signatures at the primary SARS-CoV-2 infection site and identify drivers of disease severity. Generally, a heightened antiviral response was observed in SARS-CoV-2-infected Ghanaians compared with uninfected controls. COVID-19 severity was associated with immune suppression, overexpression of proinflammatory cytokines, including CRNN, IL1A, S100A7, and IL23A, and activation of pathways involved in keratinocyte proliferation. SAMD9L was among the differentially regulated interferon-stimulated genes in our mild and severe disease cohorts, suggesting that it may play a critical role in SARS-CoV-2 pathogenesis. By comparing our data with a publicly available dataset from a non-African (Indians) (GSE166530), an elevated expression of antiviral response-related genes was noted in COVID-19-infected Ghanaians. Overall, the study describes immune signatures driving COVID-19 severity in Ghanaians and identifies immune drivers that could serve as potential prognostic markers for future outbreaks or pandemics. It further provides important preliminary evidence suggesting differences in antiviral response at the upper respiratory interface in sub-Saharan Africans (Ghanaians) and non-Africans, which could be contributing to the differences in disease outcomes. Further studies using larger datasets from different populations will expand on these findings.
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Affiliation(s)
- John Demby Sandi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology (BCMB), School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Faculty of Laboratory Medicine, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Kenema Government Hospital, Kenema, Sierra Leone
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, San Diego, California 92037, USA
| | - Kesego Tapela
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology (BCMB), School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, San Diego, California 92037, USA
| | - Joshua Afari Yeboah
- Department of Biochemistry, Cell and Molecular Biology (BCMB), School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Daniel Frimpong Saka
- Department of Biochemistry, Cell and Molecular Biology (BCMB), School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Donald S. Grant
- Faculty of Laboratory Medicine, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Kenema Government Hospital, Kenema, Sierra Leone
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology (BCMB), School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Peter K. Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology (BCMB), School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, San Diego, California 92037, USA
| | - Lily Paemka
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology (BCMB), School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
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21
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Asteris PG, Gandomi AH, Armaghani DJ, Tsoukalas MZ, Gavriilaki E, Gerber G, Konstantakatos G, Skentou AD, Triantafyllidis L, Kotsiou N, Braunstein E, Chen H, Brodsky R, Touloumenidou T, Sakellari I, Alkayem NF, Bardhan A, Cao M, Cavaleri L, Formisano A, Guney D, Hasanipanah M, Khandelwal M, Mohammed AS, Samui P, Zhou J, Terpos E, Dimopoulos MA. Genetic justification of COVID-19 patient outcomes using DERGA, a novel data ensemble refinement greedy algorithm. J Cell Mol Med 2024; 28:e18105. [PMID: 38339761 PMCID: PMC10863978 DOI: 10.1111/jcmm.18105] [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: 06/12/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 02/12/2024] Open
Abstract
Complement inhibition has shown promise in various disorders, including COVID-19. A prediction tool including complement genetic variants is vital. This study aims to identify crucial complement-related variants and determine an optimal pattern for accurate disease outcome prediction. Genetic data from 204 COVID-19 patients hospitalized between April 2020 and April 2021 at three referral centres were analysed using an artificial intelligence-based algorithm to predict disease outcome (ICU vs. non-ICU admission). A recently introduced alpha-index identified the 30 most predictive genetic variants. DERGA algorithm, which employs multiple classification algorithms, determined the optimal pattern of these key variants, resulting in 97% accuracy for predicting disease outcome. Individual variations ranged from 40 to 161 variants per patient, with 977 total variants detected. This study demonstrates the utility of alpha-index in ranking a substantial number of genetic variants. This approach enables the implementation of well-established classification algorithms that effectively determine the relevance of genetic variants in predicting outcomes with high accuracy.
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Affiliation(s)
- Panagiotis G. Asteris
- Computational Mechanics Laboratory, School of Pedagogical and Technological EducationAthensGreece
| | - Amir H. Gandomi
- Faculty of Engineering & ITUniversity of Technology SydneySydneyNew South WalesAustralia
- University Research and Innovation Center (EKIK), Óbuda UniversityBudapestHungary
| | - Danial J. Armaghani
- School of Civil and Environmental EngineeringUniversity of Technology SydneySydneyNew South WalesAustralia
| | - Markos Z. Tsoukalas
- Computational Mechanics Laboratory, School of Pedagogical and Technological EducationAthensGreece
| | - Eleni Gavriilaki
- 2nd Propedeutic Department of Internal MedicineAristotle University of ThessalonikiThessalonikiGreece
| | - Gloria Gerber
- Hematology DivisionJohns Hopkins UniversityBaltimoreUSA
| | - Gerasimos Konstantakatos
- Computational Mechanics Laboratory, School of Pedagogical and Technological EducationAthensGreece
| | - Athanasia D. Skentou
- Computational Mechanics Laboratory, School of Pedagogical and Technological EducationAthensGreece
| | - Leonidas Triantafyllidis
- Computational Mechanics Laboratory, School of Pedagogical and Technological EducationAthensGreece
| | - Nikolaos Kotsiou
- 2nd Propedeutic Department of Internal MedicineAristotle University of ThessalonikiThessalonikiGreece
| | | | - Hang Chen
- Hematology DivisionJohns Hopkins UniversityBaltimoreUSA
| | | | | | - Ioanna Sakellari
- Hematology Department – BMT UnitG Papanicolaou HospitalThessalonikiGreece
| | | | - Abidhan Bardhan
- Civil Engineering DepartmentNational Institute of Technology PatnaPatnaIndia
| | - Maosen Cao
- Department of Engineering MechanicsHohai UniversityNanjingChina
| | - Liborio Cavaleri
- Department of Civil, Environmental, Aerospace and Materials EngineeringUniversity of PalermoPalermoItaly
| | - Antonio Formisano
- Department of Structures for Engineering and ArchitectureUniversity of Naples “Federico II”NaplesItaly
| | - Deniz Guney
- Engineering FacultySan Diego State UniversitySan DiegoCaliforniaUSA
| | - Mahdi Hasanipanah
- Department of Geotechnics and Transportation, Faculty of Civil EngineeringUniversiti Teknologi MalaysiaJohor BahruMalaysia
| | - Manoj Khandelwal
- Institute of Innovation, Science and SustainabilityFederation University AustraliaBallaratVictoriaAustralia
| | | | - Pijush Samui
- Civil Engineering DepartmentNational Institute of Technology PatnaPatnaIndia
| | - Jian Zhou
- School of Resources and Safety EngineeringCentral South UniversityChangshaChina
| | - Evangelos Terpos
- Department of Clinical Therapeutics, Medical School, Faculty of MedicineNational Kapodistrian University of AthensAthensGreece
| | - Meletios A. Dimopoulos
- Department of Clinical Therapeutics, Medical School, Faculty of MedicineNational Kapodistrian University of AthensAthensGreece
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22
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Cruz Cisneros MC, Anderson EJ, Hampton BK, Parotti B, Sarkar S, Taft-Benz S, Bell TA, Blanchard M, Dillard JA, Dinnon KH, Hock P, Leist SR, Madden EA, Shaw GD, West A, Baric RS, Baxter VK, Pardo-Manuel de Villena F, Heise MT, Ferris MT. Host Genetic Variation Impacts SARS-CoV-2 Vaccination Response in the Diversity Outbred Mouse Population. Vaccines (Basel) 2024; 12:103. [PMID: 38276675 PMCID: PMC10821422 DOI: 10.3390/vaccines12010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
The COVID-19 pandemic led to the rapid and worldwide development of highly effective vaccines against SARS-CoV-2. However, there is significant individual-to-individual variation in vaccine efficacy due to factors including viral variants, host age, immune status, environmental and host genetic factors. Understanding those determinants driving this variation may inform the development of more broadly protective vaccine strategies. While host genetic factors are known to impact vaccine efficacy for respiratory pathogens such as influenza and tuberculosis, the impact of host genetic variation on vaccine efficacy against COVID-19 is not well understood. To model the impact of host genetic variation on SARS-CoV-2 vaccine efficacy, while controlling for the impact of non-genetic factors, we used the Diversity Outbred (DO) mouse model. We found that DO mice immunized against SARS-CoV-2 exhibited high levels of variation in vaccine-induced neutralizing antibody responses. While the majority of the vaccinated mice were protected from virus-induced disease, similar to human populations, we observed vaccine breakthrough in a subset of mice. Importantly, we found that this variation in neutralizing antibody, virus-induced disease, and viral titer is heritable, indicating that the DO serves as a useful model system for studying the contribution of genetic variation of both vaccines and disease outcomes.
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Affiliation(s)
- Marta C. Cruz Cisneros
- Genetics and Molecular Biology Curriculum, University of North Carolina, Chapel Hill, NC 27599, USA; (M.C.C.C.); (B.K.H.)
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Elizabeth J. Anderson
- Division of Comparative Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (E.J.A.); (V.K.B.)
| | - Brea K. Hampton
- Genetics and Molecular Biology Curriculum, University of North Carolina, Chapel Hill, NC 27599, USA; (M.C.C.C.); (B.K.H.)
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Breantié Parotti
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Sanjay Sarkar
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Sharon Taft-Benz
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Timothy A. Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Matthew Blanchard
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Jacob A. Dillard
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
| | - Kenneth H. Dinnon
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Sarah R. Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.)
| | - Emily A. Madden
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
| | - Ginger D. Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.)
| | - Ralph S. Baric
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.)
| | - Victoria K. Baxter
- Division of Comparative Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (E.J.A.); (V.K.B.)
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mark T. Heise
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
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23
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Fam BSDO, Feira MF, Cadore NA, Sbruzzi R, Hünemeier T, Abel L, Zhang Q, Casanova JL, Vianna FSL. Human genetic determinants of COVID-19 in Brazil: challenges and future plans. Genet Mol Biol 2024; 46:e20230128. [PMID: 38226654 DOI: 10.1590/1678-4685-gmb-2023-0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 11/14/2023] [Indexed: 01/17/2024] Open
Abstract
COVID-19 pandemic represented a worldwide major challenge in different areas, and efforts undertaken by the scientific community led to the understanding of some of the genetic determinants that influence the different COVID-19 outcomes. In this paper, we review the studies about the role of human genetics in COVID-19 severity and how Brazilian studies also contributed to those findings. Rare variants in genes related to Inborn Errors of Immunity (IEI) in the type I interferons pathway, and its phenocopies, have been described as being causative of severe outcomes. IEI and its phenocopies are present in Brazil, not only in COVID-19 patients, but also in autoimmune conditions and severe reactions to yellow fever vaccine. In addition, studies focusing on common variants and GWAS studies encompassing worldwide patients have found several loci associated with COVID-19 severity. A GWAS study including only Brazilian COVID-19 patients identified a new locus 1q32.1 associated with COVID-19 severity. Thus, more comprehensive studies considering the Brazilian genomic diversity should be performed, since they can help to reveal not only what are the genetic determinants that contribute to the different outcomes for COVID-19 in the Brazilian population, but in the understanding of human genetics in different health conditions.
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Affiliation(s)
- Bibiana S de Oliveira Fam
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Marilea Furtado Feira
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Nathan Araujo Cadore
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Renan Sbruzzi
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Tábita Hünemeier
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas/Universitat Pompeu Fabra), Barcelona, Spain
| | - Laurent Abel
- The Rockefeller University, Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Qian Zhang
- The Rockefeller University, Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Jean-Laurent Casanova
- The Rockefeller University, Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- Necker Hospital for Sick Children, Department of Pediatrics, Paris, France
| | - Fernanda Sales Luiz Vianna
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
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24
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Hoseinnezhad T, Soltani N, Ziarati S, Behboudi E, Mousavi MJ. The role of HLA genetic variants in COVID-19 susceptibility, severity, and mortality: A global review. J Clin Lab Anal 2024; 38:e25005. [PMID: 38251811 PMCID: PMC10829690 DOI: 10.1002/jcla.25005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic has had a profound global impact, with variations in susceptibility, severity, and mortality rates across different regions. While many factors can contribute to the spread and impact of the disease, specifically human leukocyte antigen (HLA) genetic variants have emerged as potential contributors to COVID-19 outcomes. METHODS In this comprehensive narrative review, we conducted a thorough literature search to identify relevant studies investigating the association between HLA genetic variants and COVID-19 outcomes. Additionally, we analyzed allelic frequency data from diverse populations to assess differences in COVID-19 incidence and severity. RESULTS Our review provides insights into the immunological mechanisms involving HLA-mediated responses to COVID-19 and highlights potential research directions and therapeutic interventions. We found evidence suggesting that certain HLA alleles, such as HLA-A02, may confer a lower risk of COVID-19, while others, like HLA-C04, may increase the risk of severe symptoms and mortality. Furthermore, our analysis of allele frequency distributions revealed significant variations among different populations. CONCLUSION Considering host genetic variations, particularly HLA genetic variants, is crucial for understanding COVID-19 susceptibility and severity. These findings have implications for personalized treatment and interventions based on an individual's genetic profile. However, further research is needed to unravel the precise mechanisms underlying the observed associations and explore the potential for targeted therapies or preventive measures based on HLA genetic variants.
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Affiliation(s)
- Taraneh Hoseinnezhad
- Student Research CommitteeBushehr University of Medical SciencesBushehrIran
- Department of Hematology, School of Para‐MedicineBushehr University of Medical SciencesBushehrIran
| | - Nasrin Soltani
- Student Research CommitteeBushehr University of Medical SciencesBushehrIran
- Department of Hematology, School of Para‐MedicineBushehr University of Medical SciencesBushehrIran
| | - Sarina Ziarati
- Student Research CommitteeBushehr University of Medical SciencesBushehrIran
| | - Emad Behboudi
- Department of Basic Medical SciencesKhoy University of Medical SciencesKhoyIran
| | - Mohammad Javad Mousavi
- Department of Hematology, School of Para‐MedicineBushehr University of Medical SciencesBushehrIran
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25
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Holdenrieder S, Dos Santos Ferreira CE, Izopet J, Theel ES, Wieser A. Clinical and laboratory considerations: determining an antibody-based composite correlate of risk for reinfection with SARS-CoV-2 or severe COVID-19. Front Public Health 2023; 11:1290402. [PMID: 38222091 PMCID: PMC10788057 DOI: 10.3389/fpubh.2023.1290402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/30/2023] [Indexed: 01/16/2024] Open
Abstract
Much of the global population now has some level of adaptive immunity to SARS-CoV-2 induced by exposure to the virus (natural infection), vaccination, or a combination of both (hybrid immunity). Key questions that subsequently arise relate to the duration and the level of protection an individual might expect based on their infection and vaccination history. A multi-component composite correlate of risk (CoR) could inform individuals and stakeholders about protection and aid decision making. This perspective evaluates the various elements that need to be accommodated in the development of an antibody-based composite CoR for reinfection with SARS-CoV-2 or development of severe COVID-19, including variation in exposure dose, transmission route, viral genetic variation, patient factors, and vaccination status. We provide an overview of antibody dynamics to aid exploration of the specifics of SARS-CoV-2 antibody testing. We further discuss anti-SARS-CoV-2 immunoassays, sample matrices, testing formats, frequency of sampling and the optimal time point for such sampling. While the development of a composite CoR is challenging, we provide our recommendations for each of these key areas and highlight areas that require further work to be undertaken.
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Affiliation(s)
- Stefan Holdenrieder
- Institute of Laboratory Medicine, German Heart Centre Munich, Technical University Munich, Munich, Germany
| | | | - Jacques Izopet
- Laboratory of Virology, Toulouse University Hospital and INFINITY Toulouse Institute for Infections and Inflammatory Diseases, INSERM UMR 1291 CNRS UMR 5051, University Toulouse III, Toulouse, France
| | - Elitza S. Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Munich, Germany
- Faculty of Medicine, Max Von Pettenkofer Institute, LMU Munich, Munich, Germany
- Immunology, Infection and Pandemic Research, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Munich, Germany
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26
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Carriazo S, Abasheva D, Duarte D, Ortiz A, Sanchez-Niño MD. SCARF Genes in COVID-19 and Kidney Disease: A Path to Comorbidity-Specific Therapies. Int J Mol Sci 2023; 24:16078. [PMID: 38003268 PMCID: PMC10671056 DOI: 10.3390/ijms242216078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/29/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), which has killed ~7 million persons worldwide. Chronic kidney disease (CKD) is the most common risk factor for severe COVID-19 and one that most increases the risk of COVID-19-related death. Moreover, CKD increases the risk of acute kidney injury (AKI), and COVID-19 patients with AKI are at an increased risk of death. However, the molecular basis underlying this risk has not been well characterized. CKD patients are at increased risk of death from multiple infections, to which immune deficiency in non-specific host defenses may contribute. However, COVID-19-associated AKI has specific molecular features and CKD modulates the local (kidney) and systemic (lung, aorta) expression of host genes encoding coronavirus-associated receptors and factors (SCARFs), which SARS-CoV-2 hijacks to enter cells and replicate. We review the interaction between kidney disease and COVID-19, including the over 200 host genes that may influence the severity of COVID-19, and provide evidence suggesting that kidney disease may modulate the expression of SCARF genes and other key host genes involved in an effective adaptive defense against coronaviruses. Given the poor response of certain CKD populations (e.g., kidney transplant recipients) to SARS-CoV-2 vaccines and their suboptimal outcomes when infected, we propose a research agenda focusing on CKD to develop the concept of comorbidity-specific targeted therapeutic approaches to SARS-CoV-2 infection or to future coronavirus infections.
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Affiliation(s)
- Sol Carriazo
- Division of Nephrology, Department of Medicine, University Health Network, University of Toronto, Toronto, ON M5G 2C4, Canada;
- RICORS2040, 28049 Madrid, Spain;
| | - Daria Abasheva
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, 28049 Madrid, Spain; (D.A.); (D.D.)
| | - Deborah Duarte
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, 28049 Madrid, Spain; (D.A.); (D.D.)
| | - Alberto Ortiz
- RICORS2040, 28049 Madrid, Spain;
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, 28049 Madrid, Spain; (D.A.); (D.D.)
- Departamento de Medicina, Facultad de Medicina, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Maria Dolores Sanchez-Niño
- RICORS2040, 28049 Madrid, Spain;
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, 28049 Madrid, Spain; (D.A.); (D.D.)
- Departamento de Farmacología, Facultad de Medicina, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Bi X, Liang W, Zhao Q, Wang J. SSLpheno: a self-supervised learning approach for gene-phenotype association prediction using protein-protein interactions and gene ontology data. Bioinformatics 2023; 39:btad662. [PMID: 37941450 PMCID: PMC10666204 DOI: 10.1093/bioinformatics/btad662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/17/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023] Open
Abstract
MOTIVATION Medical genomics faces significant challenges in interpreting disease phenotype and genetic heterogeneity. Despite the establishment of standardized disease phenotype databases, computational methods for predicting gene-phenotype associations still suffer from imbalanced category distribution and a lack of labeled data in small categories. RESULTS To address the problem of labeled-data scarcity, we propose a self-supervised learning strategy for gene-phenotype association prediction, called SSLpheno. Our approach utilizes an attributed network that integrates protein-protein interactions and gene ontology data. We apply a Laplacian-based filter to ensure feature smoothness and use self-supervised training to optimize node feature representation. Specifically, we calculate the cosine similarity of feature vectors and select positive and negative sample nodes for reconstruction training labels. We employ a deep neural network for multi-label classification of phenotypes in the downstream task. Our experimental results demonstrate that SSLpheno outperforms state-of-the-art methods, especially in categories with fewer annotations. Moreover, our case studies illustrate the potential of SSLpheno as an effective prescreening tool for gene-phenotype association identification. AVAILABILITY AND IMPLEMENTATION https://github.com/bixuehua/SSLpheno.
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Affiliation(s)
- Xuehua Bi
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China
- Medical Engineering and Technology College, Xinjiang Medical University, Urumqi 830017, China
| | - Weiyang Liang
- College of Information Science and Engineering, Xinjiang University, Urumqi 830046, China
| | - Qichang Zhao
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China
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28
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Azarfar F, Abbasi B, Jalali A, Abbasian MH. Investigation of the relationship between monocyte chemoattractant protein 1 rs1024611 variant and severity of COVID-19. Cytokine 2023; 171:156367. [PMID: 37713941 DOI: 10.1016/j.cyto.2023.156367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/17/2023]
Abstract
BACKGROUND Higher expression of Monocyte Chemoattractant Protein 1 (MCP-1) was reported in several studies. The clinical severity of Coronavirus disease 2019 (COVID-19) could be affected by genetic polymorphisms in MCP-1. This study aimed to examine the impact of MCP-1 2518A/G polymorphism and clinical parameters with COVID-19 severity. METHODS The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used for MCP-1 rs1024611 (A/G) genotyping in 116 outpatients, hospitalized, and ICU patients. The biochemical and hematological profiles were collected from the patient's medical records. RESULTS Based on the statistical analysis, there was no significant relationship between the -2518A/G (rs1024611) genetic polymorphism in the regulatory region of the MCP-1 gene and the severity of the COVID-19. Multivariate logistic regression analysis has shown that the severity of COVID-19 infection was associated with decreased levels of eosinophils, neutrophils, lymphocytes, and, monocyte and higher levels of SGPT, SGOT, NLR, CRP, ferritin, urea, and D-Dimer (P < 0.05). CONCLUSION The MCP-1 gene polymorphism had no impact on COVID-19 severity. However, to confirm these results, a large-scale study needs to be conducted.
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Affiliation(s)
- Fatemeh Azarfar
- Department of Biology, Faculty of Sciences, Arak University, Arak, Iran
| | - Bahareh Abbasi
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Amir Jalali
- Department of Biology, Faculty of Sciences, Arak University, Arak, Iran.
| | - Mohammad Hadi Abbasian
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
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Breno M, Noris M, Rubis N, Parvanova AI, Martinetti D, Gamba S, Liguori L, Mele C, Piras R, Orisio S, Valoti E, Alberti M, Diadei O, Bresin E, Rigoldi M, Prandini S, Gamba T, Stucchi N, Carrara F, Daina E, Benigni A, Remuzzi G. A GWAS in the pandemic epicenter highlights the severe COVID-19 risk locus introgressed by Neanderthals. iScience 2023; 26:107629. [PMID: 37731612 PMCID: PMC10507134 DOI: 10.1016/j.isci.2023.107629] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/29/2023] [Accepted: 08/11/2023] [Indexed: 09/22/2023] Open
Abstract
Large GWAS indicated that genetic factors influence the response to SARS-CoV-2. However, sex, age, concomitant diseases, differences in ancestry, and uneven exposure to the virus impacted the interpretation of data. We aimed to perform a GWAS of COVID-19 outcome in a homogeneous population who experienced a high exposure to the virus and with a known infection status. We recruited inhabitants of Bergamo province-that in spring 2020 was the epicenter of the SARS-Cov-2 pandemic in Europe-via an online questionnaire followed by personal interviews. Cases and controls were matched by age, sex and risk factors. We genotyped 1195 individuals and replicated the association at the 3p21.31 locus with severity, but with a stronger effect size that further increased in gravely ill patients. Transcriptome-wide association study highlighted eQTLs for LZTFL1 and CCR9. We also identified 17 loci not previously reported, suggestive for an association with either COVID-19 severity or susceptibility.
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Affiliation(s)
- Matteo Breno
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Marina Noris
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Nadia Rubis
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Aneliya Ilieva Parvanova
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Davide Martinetti
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Sara Gamba
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Lucia Liguori
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Caterina Mele
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Rossella Piras
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Silvia Orisio
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Elisabetta Valoti
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Marta Alberti
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Olimpia Diadei
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Elena Bresin
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Miriam Rigoldi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Silvia Prandini
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Tiziano Gamba
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Nadia Stucchi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Fabiola Carrara
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Erica Daina
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Ariela Benigni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Giuseppe Remuzzi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
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Lim JK, Njei B. Clinical and Histopathological Discoveries in Patients with Hepatic Injury and Cholangiopathy Who Have Died of COVID-19: Insights and Opportunities for Intervention. Hepat Med 2023; 15:151-164. [PMID: 37814605 PMCID: PMC10560482 DOI: 10.2147/hmer.s385133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/28/2023] [Indexed: 10/11/2023] Open
Abstract
The COVID-19 pandemic has had a profound impact on global health, necessitating a comprehensive understanding of its diverse manifestations. Cholangiopathy, a condition characterized by biliary dysfunction, has emerged as a significant complication in COVID-19 patients. In this review, we report the epidemiology of COVID-19, describe the hepatotropism of SARS-CoV-2, and present the histopathology of acute liver injury (ALI) in COVID-19. Additionally, we explore the relationship between pre-existing chronic liver disease and COVID-19, shedding light on the increased susceptibility of these individuals to develop cholangiopathy. Through an in-depth analysis of cholangiopathy in COVID-19 patients, we elucidate its clinical manifestations, diagnostic criteria, and underlying pathogenesis involving inflammation, immune dysregulation, and vascular changes. Furthermore, we provide a summary of studies investigating post-COVID-19 cholangiopathy, highlighting the long-term effects and potential management strategies for this condition, and discussing opportunities for intervention, including therapeutic targets, diagnostic advancements, supportive care, and future research needs.
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Affiliation(s)
- Joseph K Lim
- Yale Liver Center and Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Basile Njei
- Yale Liver Center and Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT, USA
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31
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Khoramipour M, Jalali A, Abbasi B, Hadi Abbasian M. Evaluation of the association between clinical parameters and ADAM33 and ORMDL3 asthma gene single-nucleotide polymorphisms with the severity of COVID-19. Int Immunopharmacol 2023; 123:110707. [PMID: 37499392 DOI: 10.1016/j.intimp.2023.110707] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/13/2023] [Accepted: 07/23/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND Coronavirus Disease of 2019 (COVID-19) is a contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Patients had varying clinical symptoms and disease severity (mild, moderate, severe, and critical). Several risk factors, including genetic polymorphisms, have been reported to be associated with disease risk and severity. This study aimed to investigate the association of two polymorphisms in the orosomucoid1-like 3 (ORMDL3) and a disintegrin and metalloprotease 33 (ADAM33) asthma-related genes with the severity of COVID-19. MATERIAL AND METHODS The study included 116 COVID-19 patients with a positive polymerase chain reaction (PCR) test for the SARS-CoV-2 Delta variant. 58 patients with moderate symptoms, 28 patients with severe symptoms, and 30 outpatients with mild symptoms. Genotyping of rs7216389 in the ORMDL3 and rs2280091 in ADAM33 genes was performed by polymerase chain reaction-restriction fragment length polymorphism. Furthermore, records of patients were studied for hematological profiles and biochemical markers. RESULTS No significant association was found between rs7216389 and rs2280091 and the severity of COVID-19 between different groups of COVID-19 patients. The serum levels of RBC and neutrophil-to-lymphocyte ratio were significantly increased; the erythrocyte sedimentation rate (ESR), and Aspartate transaminase (SGOT) were significantly decreased during treatment in intensive care unit (ICU) patients. The serum levels of red blood cells, Platelets, Urea, Alkaline phosphatase, ESR, Alanine transaminase (SGPT), and SGOT were significantly increased during treatment in hospitalized patients. The serum levels of inflammatory factors, including C-reactive protein (CRP), D-dimer, and Ferritin at the time of admission, were significantly higher in patients admitted to the ICU patients compared to the other group of patients. CONCLUSION The two polymorphisms studied in this research are not suitable markers for predicting the severity of COVID-19. However, there are significant differences in the amounts of some blood factors in different groups of COVID-19 patients (P < 0.05) and these factors can be used as a marker for the disease severity prediction.
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Affiliation(s)
- Mahsa Khoramipour
- Department of Biology, Faculty of Sciences, Arak University, Arak, Iran
| | - Amir Jalali
- Department of Biology, Faculty of Sciences, Arak University, Arak, Iran.
| | - Bahareh Abbasi
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohammad Hadi Abbasian
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
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32
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Uvarova AN, Stasevich EM, Ustiugova AS, Mitkin NA, Zheremyan EA, Sheetikov SA, Zornikova KV, Bogolyubova AV, Rubtsov MA, Kulakovskiy IV, Kuprash DV, Korneev KV, Schwartz AM. rs71327024 Associated with COVID-19 Hospitalization Reduces CXCR6 Promoter Activity in Human CD4 + T Cells via Disruption of c-Myb Binding. Int J Mol Sci 2023; 24:13790. [PMID: 37762093 PMCID: PMC10530726 DOI: 10.3390/ijms241813790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/11/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Single-nucleotide polymorphism rs71327024 located in the human 3p21.31 locus has been associated with an elevated risk of hospitalization upon SARS-CoV-2 infection. The 3p21.31 locus contains several genes encoding chemokine receptors potentially relevant to severe COVID-19. In particular, CXCR6, which is prominently expressed in T lymphocytes, NK, and NKT cells, has been shown to be involved in the recruitment of immune cells to non-lymphoid organs in chronic inflammatory and respiratory diseases. In COVID-19, CXCR6 expression is reduced in lung resident memory T cells from patients with severe disease as compared to the control cohort with moderate symptoms. We demonstrate here that rs71327024 is located within an active enhancer that augments the activity of the CXCR6 promoter in human CD4+ T lymphocytes. The common rs71327024(G) variant makes a functional binding site for the c-Myb transcription factor, while the risk rs71327024(T) variant disrupts c-Myb binding and reduces the enhancer activity. Concordantly, c-Myb knockdown in PMA-treated Jurkat cells negates rs71327024's allele-specific effect on CXCR6 promoter activity. We conclude that a disrupted c-Myb binding site may decrease CXCR6 expression in T helper cells of individuals carrying the minor rs71327024(T) allele and thus may promote the progression of severe COVID-19 and other inflammatory pathologies.
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Affiliation(s)
- Aksinya N. Uvarova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.M.S.); (A.S.U.); (N.A.M.); (E.A.Z.); (D.V.K.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (S.A.S.); (K.V.Z.); (M.A.R.)
| | - Ekaterina M. Stasevich
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.M.S.); (A.S.U.); (N.A.M.); (E.A.Z.); (D.V.K.)
| | - Alina S. Ustiugova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.M.S.); (A.S.U.); (N.A.M.); (E.A.Z.); (D.V.K.)
| | - Nikita A. Mitkin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.M.S.); (A.S.U.); (N.A.M.); (E.A.Z.); (D.V.K.)
| | - Elina A. Zheremyan
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.M.S.); (A.S.U.); (N.A.M.); (E.A.Z.); (D.V.K.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (S.A.S.); (K.V.Z.); (M.A.R.)
| | - Savely A. Sheetikov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (S.A.S.); (K.V.Z.); (M.A.R.)
- National Research Center for Hematology, 125167 Moscow, Russia;
| | - Ksenia V. Zornikova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (S.A.S.); (K.V.Z.); (M.A.R.)
- National Research Center for Hematology, 125167 Moscow, Russia;
| | | | - Mikhail A. Rubtsov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (S.A.S.); (K.V.Z.); (M.A.R.)
| | | | - Dmitry V. Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.M.S.); (A.S.U.); (N.A.M.); (E.A.Z.); (D.V.K.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (S.A.S.); (K.V.Z.); (M.A.R.)
| | - Kirill V. Korneev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.M.S.); (A.S.U.); (N.A.M.); (E.A.Z.); (D.V.K.)
- National Research Center for Hematology, 125167 Moscow, Russia;
| | - Anton M. Schwartz
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, 199 Abba Khoushy Avenue, Mount Carmel, Haifa 3498838, Israel;
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33
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Aquino Y, Bisiaux A, Li Z, O'Neill M, Mendoza-Revilla J, Merkling SH, Kerner G, Hasan M, Libri V, Bondet V, Smith N, de Cevins C, Ménager M, Luca F, Pique-Regi R, Barba-Spaeth G, Pietropaoli S, Schwartz O, Leroux-Roels G, Lee CK, Leung K, Wu JT, Peiris M, Bruzzone R, Abel L, Casanova JL, Valkenburg SA, Duffy D, Patin E, Rotival M, Quintana-Murci L. Dissecting human population variation in single-cell responses to SARS-CoV-2. Nature 2023; 621:120-128. [PMID: 37558883 PMCID: PMC10482701 DOI: 10.1038/s41586-023-06422-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Humans display substantial interindividual clinical variability after SARS-CoV-2 infection1-3, the genetic and immunological basis of which has begun to be deciphered4. However, the extent and drivers of population differences in immune responses to SARS-CoV-2 remain unclear. Here we report single-cell RNA-sequencing data for peripheral blood mononuclear cells-from 222 healthy donors of diverse ancestries-that were stimulated with SARS-CoV-2 or influenza A virus. We show that SARS-CoV-2 induces weaker, but more heterogeneous, interferon-stimulated gene activity compared with influenza A virus, and a unique pro-inflammatory signature in myeloid cells. Transcriptional responses to viruses display marked population differences, primarily driven by changes in cell abundance including increased lymphoid differentiation associated with latent cytomegalovirus infection. Expression quantitative trait loci and mediation analyses reveal a broad effect of cell composition on population disparities in immune responses, with genetic variants exerting a strong effect on specific loci. Furthermore, we show that natural selection has increased population differences in immune responses, particularly for variants associated with SARS-CoV-2 response in East Asians, and document the cellular and molecular mechanisms by which Neanderthal introgression has altered immune functions, such as the response of myeloid cells to viruses. Finally, colocalization and transcriptome-wide association analyses reveal an overlap between the genetic basis of immune responses to SARS-CoV-2 and COVID-19 severity, providing insights into the factors contributing to current disparities in COVID-19 risk.
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Affiliation(s)
- Yann Aquino
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Aurélie Bisiaux
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Zhi Li
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Mary O'Neill
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Javier Mendoza-Revilla
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Sarah Hélène Merkling
- Insect-Virus Interactions Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Gaspard Kerner
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Milena Hasan
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
| | - Valentina Libri
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
| | - Vincent Bondet
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Nikaïa Smith
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Camille de Cevins
- Université Paris Cité, Imagine Institute, Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Atip-Avenir Team, INSERM UMR1163, Paris, France
| | - Mickaël Ménager
- Université Paris Cité, Imagine Institute, Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Atip-Avenir Team, INSERM UMR1163, Paris, France
- Labtech Single-Cell@Imagine, Imagine Institute, INSERM UMR1163, Paris, France
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Giovanna Barba-Spaeth
- Structural Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Stefano Pietropaoli
- Structural Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | | | - Cheuk-Kwong Lee
- Hong Kong Red Cross Blood Transfusion Service, Hospital Authority, Hong Kong SAR, China
| | - Kathy Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Malik Peiris
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Roberto Bruzzone
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Université Paris Cité, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Université Paris Cité, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Maxime Rotival
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France.
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France.
- Chair Human Genomics and Evolution, Collège de France, Paris, France.
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de Araújo JLF, Bonifácio VF, Batista LM, de Ávila RE, Aguiar RS, Bastos-Rodrigues L, de Souza RP. Association of 3p21.31 Locus (CXCR6 and LZTFL1) with COVID-19 Outcomes in Brazilian Hospitalyzed Subjects. Curr Microbiol 2023; 80:319. [PMID: 37578643 DOI: 10.1007/s00284-023-03437-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
The 3p21.31 locus has been associated with severe COVID-19 prognosis in GWAS studies. Here, we evaluated whether three polymorphisms (LZTFL1 rs10490770, CXCR6 rs2234355 and rs2234358) in the reported locus were associated with the need for mechanical ventilation, hospitalization length and death in 102 COVID-19 hospitalized Brazilian subjects. No genetic association was found with the need for mechanical ventilation and hospitalization length. CXCR6 rs2234355 was associated with mortality under the codominance model, with carriers of the A/A genotype having a greater chance of death than A/G (OR: 10.5; 95% CI: 1.55-70.76). Our results further suggest that the CXCR6 genetic variant contributes to COVID-19 outcomes.
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Affiliation(s)
- João Locke Ferreira de Araújo
- Grupo de Pesquisa em Bioestatística e Epidemiologia Molecular, Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Victória Frigério Bonifácio
- Departamento de Nutrição, Escola de Enfermagem, Universidade Federal de Minas Gerais, Minas Gerais - Brazil, Belo Horizonte, MG, Brazil
| | - Lorena Medeiros Batista
- Departamento de Nutrição, Escola de Enfermagem, Universidade Federal de Minas Gerais, Minas Gerais - Brazil, Belo Horizonte, MG, Brazil
| | | | - Renato Santana Aguiar
- Grupo de Pesquisa em Bioestatística e Epidemiologia Molecular, Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
- Instituto D'OR de Pesquisa e Ensino, Rio de Janeiro, RJ, Brazil
| | - Luciana Bastos-Rodrigues
- Departamento de Nutrição, Escola de Enfermagem, Universidade Federal de Minas Gerais, Minas Gerais - Brazil, Belo Horizonte, MG, Brazil.
| | - Renan Pedra de Souza
- Grupo de Pesquisa em Bioestatística e Epidemiologia Molecular, Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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Cobat A, Zhang Q, Abel L, Casanova JL, Fellay J. Human Genomics of COVID-19 Pneumonia: Contributions of Rare and Common Variants. Annu Rev Biomed Data Sci 2023; 6:465-486. [PMID: 37196358 PMCID: PMC10879986 DOI: 10.1146/annurev-biodatasci-020222-021705] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection is silent or benign in most infected individuals, but causes hypoxemic COVID-19 pneumonia in about 10% of cases. We review studies of the human genetics of life-threatening COVID-19 pneumonia, focusing on both rare and common variants. Large-scale genome-wide association studies have identified more than 20 common loci robustly associated with COVID-19 pneumonia with modest effect sizes, some implicating genes expressed in the lungs or leukocytes. The most robust association, on chromosome 3, concerns a haplotype inherited from Neanderthals. Sequencing studies focusing on rare variants with a strong effect have been particularly successful, identifying inborn errors of type I interferon (IFN) immunity in 1-5% of unvaccinated patients with critical pneumonia, and their autoimmune phenocopy, autoantibodies against type I IFN, in another 15-20% of cases. Our growing understanding of the impact of human genetic variation on immunity to SARS-CoV-2 is enabling health systems to improve protection for individuals and populations.
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Affiliation(s)
- Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
- Howard Hughes Medical Institute, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland;
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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Farooqi R, Kooner JS, Zhang W. Associations between polygenic risk score and covid-19 susceptibility and severity across ethnic groups: UK Biobank analysis. BMC Med Genomics 2023; 16:150. [PMID: 37386504 PMCID: PMC10311902 DOI: 10.1186/s12920-023-01584-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND COVID-19 manifests with huge heterogeneity in susceptibility and severity outcomes. UK Black Asian and Minority Ethnic (BAME) groups have demonstrated disproportionate burdens. Some variability remains unexplained, suggesting potential genetic contribution. Polygenic Risk Scores (PRS) can determine genetic predisposition to disease based on Single Nucleotide Polymorphisms (SNPs) within the genome. COVID-19 PRS analyses within non-European samples are extremely limited. We applied a multi-ethnic PRS to a UK-based cohort to understand genetic contribution to COVID-19 variability. METHODS We constructed two PRS for susceptibility and severity outcomes based on leading risk-variants from the COVID-19 Host Genetics Initiative. Scores were applied to 447,382 participants from the UK-Biobank. Associations with COVID-19 outcomes were assessed using binary logistic regression and discriminative power was validated using incremental area under receiver operating curve (ΔAUC). Variance explained was compared between ethnic groups via incremental pseudo-R2 (ΔR2). RESULTS Compared to those at low genetic risk, those at high risk had a significantly greater risk of severe COVID-19 for White (odds ratio [OR] 1.57, 95% confidence interval [CI] 1.42-1.74), Asian (OR 2.88, 95% CI 1.63-5.09) and Black (OR 1.98, 95% CI 1.11-3.53) ethnic groups. Severity PRS performed best within Asian (ΔAUC 0.9%, ΔR2 0.98%) and Black (ΔAUC 0.6%, ΔR2 0.61%) cohorts. For susceptibility, higher genetic risk was significantly associated with COVID-19 infection risk for the White cohort (OR 1.31, 95% CI 1.26-1.36), but not for Black or Asian groups. CONCLUSIONS Significant associations between PRS and COVID-19 outcomes were elicited, establishing a genetic basis for variability in COVID-19. PRS showed utility in identifying high-risk individuals. The multi-ethnic approach allowed applicability of PRS to diverse populations, with the severity model performing well within Black and Asian cohorts. Further studies with larger sample sizes of non-White samples are required to increase statistical power and better assess impacts within BAME populations.
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Affiliation(s)
- Raabia Farooqi
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK.
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, W2 1PG, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
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Liang S, Gao H, He T, Li L, Zhang X, Zhao L, Chen J, Xie Y, Bao J, Gao Y, Dai E, Wang Y. Association between SUMF1 polymorphisms and COVID-19 severity. BMC Genom Data 2023; 24:34. [PMID: 37344788 DOI: 10.1186/s12863-023-01133-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND Evidence shows that genetic factors play important roles in the severity of coronavirus disease 2019 (COVID-19). Sulfatase modifying factor 1 (SUMF1) gene is involved in alveolar damage and systemic inflammatory response. Therefore, we speculate that it may play a key role in COVID-19. RESULTS We found that rs794185 was significantly associated with COVID-19 severity in Chinese population, under the additive model after adjusting for gender and age (for C allele = 0.62, 95% CI = 0.44-0.88, P = 0.0073, logistic regression). And this association was consistent with this in European population Genetics Of Mortality In Critical Care (GenOMICC: OR for C allele = 0.94, 95% CI = 0.90-0.98, P = 0.0037). Additionally, we also revealed a remarkable association between rs794185 and the prothrombin activity (PTA) in subjects (P = 0.015, Generalized Linear Model). CONCLUSIONS In conclusion, our study for the first time identified that rs794185 in SUMF1 gene was associated with the severity of COVID-19.
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Affiliation(s)
- Shaohui Liang
- Department of Respiratory, Hebei Chest Hospital, Shijiazhuang, 050000, Hebei, China
| | - Huixia Gao
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, 050021, Hebei, China
| | - Tongxin He
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Li Li
- Intensive Care Unit, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, 050021, Hebei, China
| | - Xin Zhang
- Department of Tuberculosis, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, 050021, Hebei, China
| | - Lei Zhao
- The Second Internal Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, 050021, Hebei, China
| | - Jie Chen
- Graduate School of Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Yanyan Xie
- Graduate School of Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Jie Bao
- Department of Respiratory, Hebei Chest Hospital, Shijiazhuang, 050000, Hebei, China
| | - Yong Gao
- Department of Respiratory, Hebei Chest Hospital, Shijiazhuang, 050000, Hebei, China
| | - Erhei Dai
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, 050021, Hebei, China.
| | - Yuling Wang
- Department of Tuberculosis, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, 050021, Hebei, China.
- Graduate School of Hebei Medical University, Shijiazhuang, 050017, Hebei, China.
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Huang YX, Tian T, Huang JX, Wang J, Sui C, Ni J. A shared genetic contribution to osteoarthritis and COVID-19 outcomes: a large-scale genome-wide cross-trait analysis. Front Immunol 2023; 14:1184958. [PMID: 37398645 PMCID: PMC10311546 DOI: 10.3389/fimmu.2023.1184958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023] Open
Abstract
Background Patients with osteoarthritis (OA) are exposed to an increased risk of adverse outcomes of COVID-19, and they tend to experience disruption in access to healthcare services and exercise facilities. However, a deep understanding of this comorbidity phenomenon and the underlying genetic architecture of the two diseases is still unclear. In this study, we aimed to untangle the relationship between OA and COVID-19 outcomes by conducting a large-scale genome-wide cross-trait analysis. Methods Genetic correlation and causal relationships between OA and COVID-19 outcomes (critical COVID-19, COVID-19 hospitalization, and COVID-19 infection) were estimated by linkage disequilibrium score regression and Mendelian Randomization approaches. We further applied Multi-Trait Analysis of GWAS and colocalization analysis to identify putative functional genes associated with both OA and COVID-19 outcomes. Results Significant positive genetic correlations between OA susceptibility and both critical COVID-19 (rg=0.266, P=0.0097) and COVID-19 hospitalization (rg=0.361, P=0.0006) were detected. However, there was no evidence to support causal genetic relationships between OA and critical COVID-19 (OR=1.17[1.00-1.36], P=0.049) or OA and COVID-19 hospitalization OR=1.08[0.97-1.20], P=0.143). These results were robustly consistent after the removal of obesity-related single nucleotide polymorphisms (SNPs). Moreover, we identified a strong association signal located near the FYCO1 gene (lead SNPs: rs71325101 for critical COVID-19, Pmeta=1.02×10-34; rs13079478 for COVID-19 hospitalization, Pmeta=1.09×10-25). Conclusion Our findings further confirmed the comorbidity of OA and COVID-19 severity, but indicate a non-causal impact of OA on COVID-19 outcomes. The study offers an instructive perspective that OA patients did not generate negative COVID-19 outcomes during the pandemic in a causal way. Further clinical guidance can be formulated to enhance the quality of self-management in vulnerable OA patients.
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Affiliation(s)
- Yi-Xuan Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Tian Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Ji-Xiang Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Jing Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Cong Sui
- Department of Orthopedics Trauma, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jing Ni
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
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Resztak JA, Wei J, Zilioli S, Sendler E, Alazizi A, Mair-Meijers HE, Wu P, Wen X, Slatcher RB, Zhou X, Luca F, Pique-Regi R. Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution. Genome Res 2023; 33:839-856. [PMID: 37442575 PMCID: PMC10519413 DOI: 10.1101/gr.276765.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/08/2023] [Indexed: 07/15/2023]
Abstract
Synthetic glucocorticoids, such as dexamethasone, have been used as a treatment for many immune conditions, such as asthma and, more recently, severe COVID-19. Single-cell data can capture more fine-grained details on transcriptional variability and dynamics to gain a better understanding of the molecular underpinnings of inter-individual variation in drug response. Here, we used single-cell RNA-seq to study the dynamics of the transcriptional response to glucocorticoids in activated peripheral blood mononuclear cells from 96 African American children. We used novel statistical approaches to calculate a mean-independent measure of gene expression variability and a measure of transcriptional response pseudotime. Using these approaches, we showed that glucocorticoids reverse the effects of immune stimulation on both gene expression mean and variability. Our novel measure of gene expression response dynamics, based on the diagonal linear discriminant analysis, separated individual cells by response status on the basis of their transcriptional profiles and allowed us to identify different dynamic patterns of gene expression along the response pseudotime. We identified genetic variants regulating gene expression mean and variability, including treatment-specific effects, and showed widespread genetic regulation of the transcriptional dynamics of the gene expression response.
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Affiliation(s)
- Justyna A Resztak
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Samuele Zilioli
- Department of Psychology, Wayne State University, Detroit, Michigan 48201, USA
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, Michigan 48201, USA
| | - Edward Sendler
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Henriette E Mair-Meijers
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Peijun Wu
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Richard B Slatcher
- Department of Psychology, University of Georgia, Athens, Georgia 30602, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA;
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
- Department of Biology, University of Rome "Tor Vergata," 00133 Rome, Italy
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA;
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
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40
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Córdova-Palomera A, Siffel C, DeBoever C, Wong E, Diogo D, Szalma S. Assessing the potential of polygenic scores to strengthen medical risk prediction models of COVID-19. PLoS One 2023; 18:e0285991. [PMID: 37235597 DOI: 10.1371/journal.pone.0285991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
As findings on the epidemiological and genetic risk factors for coronavirus disease-19 (COVID-19) continue to accrue, their joint power and significance for prospective clinical applications remains virtually unexplored. Severity of symptoms in individuals affected by COVID-19 spans a broad spectrum, reflective of heterogeneous host susceptibilities across the population. Here, we assessed the utility of epidemiological risk factors to predict disease severity prospectively, and interrogated genetic information (polygenic scores) to evaluate whether they can provide further insights into symptom heterogeneity. A standard model was trained to predict severe COVID-19 based on principal component analysis and logistic regression based on information from eight known medical risk factors for COVID-19 measured before 2018. In UK Biobank participants of European ancestry, the model achieved a relatively high performance (area under the receiver operating characteristic curve ~90%). Polygenic scores for COVID-19 computed from summary statistics of the Covid19 Host Genetics Initiative displayed significant associations with COVID-19 in the UK Biobank (p-values as low as 3.96e-9, all with R2 under 1%), but were unable to robustly improve predictive performance of the non-genetic factors. However, error analysis of the non-genetic models suggested that affected individuals misclassified by the medical risk factors (predicted low risk but actual high risk) display a small but consistent increase in polygenic scores. Overall, the results indicate that simple models based on health-related epidemiological factors measured years before COVID-19 onset can achieve high predictive power. Associations between COVID-19 and genetic factors were statistically robust, but currently they have limited predictive power for translational settings. Despite that, the outcomes also suggest that severely affected cases with a medical history profile of low risk might be partly explained by polygenic factors, prompting development of boosted COVID-19 polygenic models based on new data and tools to aid risk-prediction.
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Affiliation(s)
- Aldo Córdova-Palomera
- Takeda Development Center Americas, Inc., San Diego, California, United States of America
| | - Csaba Siffel
- Takeda Development Center Americas, Inc., San Diego, California, United States of America
| | - Chris DeBoever
- Takeda Development Center Americas, Inc., San Diego, California, United States of America
| | - Emily Wong
- Takeda Development Center Americas, Inc., San Diego, California, United States of America
| | - Dorothée Diogo
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts, United States of America
| | - Sandor Szalma
- Takeda Development Center Americas, Inc., San Diego, California, United States of America
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Sugiyama M. Tools and factors predictive of the severity of COVID-19. Glob Health Med 2023; 5:78-84. [PMID: 37128224 PMCID: PMC10130545 DOI: 10.35772/ghm.2022.01046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 02/10/2023] [Accepted: 02/28/2023] [Indexed: 05/03/2023]
Abstract
The outbreak of the novel coronavirus infection caused worldwide confusion. The problem with this infection is that it causes severe illness in some patients, resulting in a high rate of death if appropriate treatment is not given. If patients with severe illness that requires treatment are appropriately identified, treatment can be focused on these patients. However, in the early days of the COVID-19 outbreak, the inability to predict and diagnose the disease led to hospitals being overwhelmed. Therefore, various methods for the diagnosis of severe disease were developed early on, and various methods are still being investigated to predict high-risk patients. The currently available prediction methods are divided into those that predict the onset of severe disease and those used to determine the severity of the disease. Specifically, the main methods include genetic factors, serum humoral factors, laboratory tests, and diagnostic imaging. Since each of these factors has different features, using them in combination is likely to be advantageous.
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Affiliation(s)
- Masaya Sugiyama
- Address correspondence to:Masaya Sugiyama, Department of Viral Pathogenesis and Controls, National Center for Global Health and Medicine, 1-7- 1 Kohnodai, Ichikawa 272-0817, Japan. E-mail:
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Liatsos GD. SARS-CoV-2 induced liver injury: Incidence, risk factors, impact on COVID-19 severity and prognosis in different population groups. World J Gastroenterol 2023; 29:2397-2432. [PMID: 37179584 PMCID: PMC10167898 DOI: 10.3748/wjg.v29.i16.2397] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/17/2023] [Accepted: 04/07/2023] [Indexed: 04/24/2023] Open
Abstract
Liver is unlikely the key organ driving mortality in coronavirus disease 2019 (COVID-19) however, liver function tests (LFTs) abnormalities are widely observed mostly in moderate and severe cases. According to this review, the overall prevalence of abnormal LFTs in COVID-19 patients ranges from 2.5% to 96.8% worldwide. The geographical variability in the prevalence of underlying diseases is the determinant for the observed discrepancies between East and West. Multifactorial mechanisms are implicated in COVID-19-induced liver injury. Among them, hypercytokinemia with "bystander hepatitis", cytokine storm syndrome with subsequent oxidative stress and endotheliopathy, hypercoagulable state and immuno-thromboinflammation are the most determinant mechanisms leading to tissue injury. Liver hypoxia may also contribute under specific conditions, while direct hepatocyte injury is an emerging mechanism. Except for initially observed severe acute respiratory distress syndrome corona virus-2 (SARS-CoV-2) tropism for cholangiocytes, more recent cumulative data show SARS-CoV-2 virions within hepatocytes and sinusoidal endothelial cells using electron microscopy (EM). The best evidence for hepatocellular invasion by the virus is the identification of replicating SARS-CoV-2 RNA, S protein RNA and viral nucleocapsid protein within hepatocytes using in-situ hybridization and immunostaining with observed intrahepatic presence of SARS-CoV-2 by EM and by in-situ hybridization. New data mostly derived from imaging findings indicate possible long-term sequelae for the liver months after recovery, suggesting a post-COVID-19 persistent live injury.
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Affiliation(s)
- George D Liatsos
- Department of Internal Medicine, Hippokration General Hospital, Athens 11527, Attiki, Greece
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Huang X, Yao M, Tian P, Wong JYY, Li Z, Liu Z, Zhao JV. Genome-wide cross-trait analysis and Mendelian randomization reveal a shared genetic etiology and causality between COVID-19 and venous thromboembolism. Commun Biol 2023; 6:441. [PMID: 37085521 PMCID: PMC10120502 DOI: 10.1038/s42003-023-04805-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 04/04/2023] [Indexed: 04/23/2023] Open
Abstract
Venous thromboembolism occurs in up to one-third of patients with COVID-19. Venous thromboembolism and COVID-19 may share a common genetic architecture, which has not been clarified. To fill this gap, we leverage summary-level genetic data from the latest COVID-19 host genetics consortium and UK Biobank and examine the shared genetic etiology and causal relationship between COVID-19 and venous thromboembolism. The cross-trait and co-localization analyses identify 2, 3, and 4 shared loci between venous thromboembolism and severe COVID-19, COVID-19 hospitalization, SARS-CoV-2 infection respectively, which are mapped to ABO, ADAMTS13, FUT2 genes involved in coagulation functions. Enrichment analysis supports shared biological processes between COVID-19 and venous thromboembolism related to coagulation and immunity. Bi-directional Mendelian randomization suggests that venous thromboembolism was associated with higher risk of three COVID-19 traits, and SARS-CoV-2 infection was associated with a higher risk of venous thromboembolism. Our study provides timely evidence for the genetic etiology between COVID-19 and venous thromboembolism (VTE). Our findings contribute to the understanding of COVID-19 and VTE etiology and provide insights into the prevention and comorbidity management of COVID-19.
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Affiliation(s)
- Xin Huang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Minhao Yao
- Department of Statistics and Actuarial Science, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Peixin Tian
- Department of Statistics and Actuarial Science, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jason Y Y Wong
- Epidemiology and Community Health Branch, National Heart Lung and Blood Institute, Bethesda, MD, USA
| | - Zilin Li
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Zhonghua Liu
- Department of Biostatistics, Columbia University, New York, NY, USA.
| | - Jie V Zhao
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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Bucciol G, Meyts I. Inherited and acquired errors of type I interferon immunity govern susceptibility to COVID-19 and multisystem inflammatory syndrome in children. J Allergy Clin Immunol 2023; 151:832-840. [PMID: 36841740 PMCID: PMC9951110 DOI: 10.1016/j.jaci.2023.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/02/2023] [Accepted: 02/01/2023] [Indexed: 02/27/2023]
Abstract
Since the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)/coronavirus disease 2019 (COVID-19) pandemic, global sequencing efforts have led in the field of inborn errors of immunity, and inspired particularly by previous research on life-threatening influenza, they have revealed that known and novel inborn errors affecting type I interferon immunity underlie critical COVID-19 in up to 5% of cases. In addition, neutralizing autoantibodies against type I interferons have been identified in up to 20% of patients with critical COVID-19 who are older than 80 years and 20% of fatal cases, with a higher prevalence in men and individuals older than 70 years. Also, inborn errors impairing regulation of type I interferon responses and RNA degradation have been found as causes of multisystem inflammatory syndrome in children, a life-threatening hyperinflammatory condition complicating otherwise mild initial SARS-CoV-2 infection in children and young adults. Better understanding of these immunologic mechanisms can aid in designing treatments for severe COVID-19, multisystem inflammatory syndrome in children, long COVID, and neuro-COVID.
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Affiliation(s)
- Giorgia Bucciol
- Laboratory of Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, Leuven, Belgium; Childhood Immunology, Department of Pediatrics, Leuven University Hospitals, Leuven, Belgium
| | - Isabelle Meyts
- Laboratory of Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, Leuven, Belgium; Childhood Immunology, Department of Pediatrics, Leuven University Hospitals, Leuven, Belgium.
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Liu Z, Dai W, Wang S, Yao Y, Zhang H. Deep learning identified genetic variants for COVID-19-related mortality among 28,097 affected cases in UK Biobank. Genet Epidemiol 2023; 47:215-230. [PMID: 36691909 PMCID: PMC10006374 DOI: 10.1002/gepi.22515] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/19/2022] [Accepted: 01/11/2023] [Indexed: 01/25/2023]
Abstract
Analysis of host genetic components provides insights into the susceptibility and response to viral infection such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19). To reveal genetic determinants of susceptibility to COVID-19 related mortality, we train a deep learning model to identify groups of genetic variants and their interactions that contribute to the COVID-19 related mortality risk using the UK Biobank data (28,097 affected cases and 1656 deaths). We refer to such groups of variants as super variants. We identify 15 super variants with various levels of significance as susceptibility loci for COVID-19 mortality. Specifically, we identify a super variant (odds ratio [OR] = 1.594, p = 5.47 × 10-9 ) on Chromosome 7 that consists of the minor allele of rs76398985, rs6943608, rs2052130, 7:150989011_CT_C, rs118033050, and rs12540488. We also discover a super variant (OR = 1.353, p = 2.87 × 10-8 ) on Chromosome 5 that contains rs12517344, rs72733036, rs190052994, rs34723029, rs72734818, 5:9305797_GTA_G, and rs180899355.
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Affiliation(s)
- Zihuan Liu
- Department of Biostatistics, Yale University, 300 George Street, Ste 523, New Haven, CT, 06511
| | - Wei Dai
- Department of Biostatistics, Yale University, 300 George Street, Ste 523, New Haven, CT, 06511
| | - Shiying Wang
- Department of Biostatistics, Yale University, 300 George Street, Ste 523, New Haven, CT, 06511
| | - Yisha Yao
- Department of Biostatistics, Yale University, 300 George Street, Ste 523, New Haven, CT, 06511
| | - Heping Zhang
- Department of Biostatistics, Yale University, 300 George Street, Ste 523, New Haven, CT, 06511
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Cappadona C, Rimoldi V, Paraboschi EM, Asselta R. Genetic susceptibility to severe COVID-19. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 110:105426. [PMID: 36934789 PMCID: PMC10022467 DOI: 10.1016/j.meegid.2023.105426] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the coronavirus disease 2019 (COVID-19) pandemic. Clinical manifestations of the disease range from an asymptomatic condition to life-threatening events and death, with more severe courses being associated with age, male sex, and comorbidities. Besides these risk factors, intrinsic characteristics of the virus as well as genetic factors of the host are expected to account for COVID-19 clinical heterogeneity. Genetic studies have long been recognized as fundamental to identify biological mechanisms underlying congenital diseases, to pinpoint genes/proteins responsible for the susceptibility to different inherited conditions, to highlight targets of therapeutic relevance, to suggest drug repurposing, and even to clarify causal relationships that make modifiable some environmental risk factors. Though these studies usually take long time to be concluded and, above all, to translate their discoveries to patients' bedside, the scientific community moved really fast to deliver genetic signals underlying different COVID-19 phenotypes. In this Review, besides a concise description of COVID-19 symptomatology and of SARS-CoV-2 mechanism of infection, we aimed to recapitulate the current literature in terms of host genetic factors that specifically associate with an increased severity of the disease.
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Affiliation(s)
- Claudio Cappadona
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele - Milan 20090, Italy
| | - Valeria Rimoldi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele - Milan 20090, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan 20089, Italy
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele - Milan 20090, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan 20089, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele - Milan 20090, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan 20089, Italy.
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Jankovic M, Nikolic D, Novakovic I, Petrovic B, Lackovic M, Santric-Milicevic M. miRNAs as a Potential Biomarker in the COVID-19 Infection and Complications Course, Severity, and Outcome. Diagnostics (Basel) 2023; 13:1091. [PMID: 36980399 PMCID: PMC10047241 DOI: 10.3390/diagnostics13061091] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/08/2023] [Accepted: 03/12/2023] [Indexed: 03/15/2023] Open
Abstract
During the last three years, since the emergence of the COVID-19 pandemic, a significant number of scientific publications have focused on resolving susceptibility to the infection, as well as the course of the disease and potential long-term complications. COVID-19 is widely considered as a multisystem disease and a variety of socioeconomic, medical, and genetic/epigenetic factors may contribute to the disease severity and outcome. Furthermore, the SARS-COV-2 infection may trigger pathological processes and accelerate underlying conditions to clinical entities. The development of specific and sensitive biomarkers that are easy to obtain will allow for patient stratification, prevention, prognosis, and more individualized treatments for COVID-19. miRNAs are proposed as promising biomarkers for different aspects of COVID-19 disease (susceptibility, severity, complication course, outcome, and therapeutic possibilities). This review summarizes the most relevant findings concerning miRNA involvement in COVID-19 pathology. Additionally, the role of miRNAs in wide range of complications due to accompanied and/or underlying health conditions is discussed. The importance of understanding the functional relationships between different conditions, such as pregnancy, obesity, or neurological diseases, with COVID-19 is also highlighted.
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Affiliation(s)
- Milena Jankovic
- Neurology Clinic, University Clinical Center of Serbia, 11000 Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Dejan Nikolic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Department of Physical Medicine and Rehabilitation, University Children's Hospital, 11000 Belgrade, Serbia
| | - Ivana Novakovic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Bojana Petrovic
- Clinic of Gynecology and Obstetrics, University Clinical Center of Serbia, 11000 Belgrade, Serbia
| | - Milan Lackovic
- Department of Obstetrics and Gynecology, University Hospital "Dragisa Misovic", 11000 Belgrade, Serbia
| | - Milena Santric-Milicevic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Institute of Social Medicine, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Faculty of Medicine, School of Public Health and Health Management, University of Belgrade, 11000 Belgrade, Serbia
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Mattiola I, Diefenbach A. Regulation of innate immune system function by the microbiome: Consequences for tumor immunity and cancer immunotherapy. Semin Immunol 2023; 66:101724. [PMID: 36758379 DOI: 10.1016/j.smim.2023.101724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/03/2023] [Accepted: 01/17/2023] [Indexed: 02/10/2023]
Abstract
Innate effector cells are immune cells endowed with host protective features and cytotoxic functions. By sensing the tissue environment, innate cells have an important role in regulating the transition from homeostasis to inflammation and the establishment of pathological states, including the onset and development of cancer. The tumor microenvironment induces molecular and functional modifications in innate cells, dampening their capability to initiate and sustain anti-tumor immune responses. Emerging studies clearly showed a contribution of the microbiota in modulating the functions of innate cells in cancer. Commensal microorganisms can not only directly interact with innate cells in the tumor microenvironment but can also exert immunomodulatory features from non-tumor sites through the release of microbial products. The microbiota can mediate the priming of innate cells at mucosal tissues and determine the strength of immune responses mediated by such cells when they migrate to non-mucosal tissues, having an impact on cancer. Finally, several evidences reported a strong contribution of the microbiota in promoting innate immune responses during anti-cancer therapies leading to enhanced therapeutic efficacy. In this review, we considered the current knowledge on the role of the microbiota in shaping host innate immune responses in cancer.
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Affiliation(s)
- Irene Mattiola
- Laboratory of Innate Immunity, Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Germany; Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany.
| | - Andreas Diefenbach
- Laboratory of Innate Immunity, Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Germany; Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany; Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
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Gazeau S, Deng X, Ooi HK, Mostefai F, Hussin J, Heffernan J, Jenner AL, Craig M. The race to understand immunopathology in COVID-19: Perspectives on the impact of quantitative approaches to understand within-host interactions. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2023; 9:100021. [PMID: 36643886 PMCID: PMC9826539 DOI: 10.1016/j.immuno.2023.100021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/16/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
The COVID-19 pandemic has revealed the need for the increased integration of modelling and data analysis to public health, experimental, and clinical studies. Throughout the first two years of the pandemic, there has been a concerted effort to improve our understanding of the within-host immune response to the SARS-CoV-2 virus to provide better predictions of COVID-19 severity, treatment and vaccine development questions, and insights into viral evolution and the impacts of variants on immunopathology. Here we provide perspectives on what has been accomplished using quantitative methods, including predictive modelling, population genetics, machine learning, and dimensionality reduction techniques, in the first 26 months of the COVID-19 pandemic approaches, and where we go from here to improve our responses to this and future pandemics.
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Affiliation(s)
- Sonia Gazeau
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
| | - Xiaoyan Deng
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
| | - Hsu Kiang Ooi
- Digital Technologies Research Centre, National Research Council Canada, Toronto, Canada
| | - Fatima Mostefai
- Montréal Heart Institute Research Centre, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Julie Hussin
- Montréal Heart Institute Research Centre, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Jane Heffernan
- Modelling Infection and Immunity Lab, Mathematics Statistics, York University, Toronto, Canada
- Centre for Disease Modelling (CDM), Mathematics Statistics, York University, Toronto, Canada
| | - Adrianne L Jenner
- School of Mathematical Sciences, Queensland University of Technology, Brisbane Australia
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
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50
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Murali R, Wanjari UR, Mukherjee AG, Gopalakrishnan AV, Kannampuzha S, Namachivayam A, Madhyastha H, Renu K, Ganesan R. Crosstalk between COVID-19 Infection and Kidney Diseases: A Review on the Metabolomic Approaches. Vaccines (Basel) 2023; 11:vaccines11020489. [PMID: 36851366 PMCID: PMC9959335 DOI: 10.3390/vaccines11020489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, a respiratory disorder. Various organ injuries have been reported in response to this virus, including kidney injury and, in particular, kidney tubular injury. It has been discovered that infection with the virus does not only cause new kidney disease but also increases treatment difficulty and mortality rates in people with kidney diseases. In individuals hospitalized with COVID-19, urinary metabolites from several metabolic pathways are used to distinguish between patients with acute kidney injury (AKI) and those without. This review summarizes the pathogenesis, pathophysiology, treatment strategies, and role of metabolomics in relation to AKI in COVID-19 patients. Metabolomics is likely to play a greater role in predicting outcomes for patients with kidney disease and COVID-19 with varying levels of severity in the near future as data on metabolic profiles expand rapidly. Here, we also discuss the correlation between COVID-19 and kidney diseases and the available metabolomics approaches.
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Affiliation(s)
- Reshma Murali
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Uddesh Ramesh Wanjari
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Anirban Goutam Mukherjee
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- Correspondence: (A.V.G.); (R.G.)
| | - Sandra Kannampuzha
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Arunraj Namachivayam
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Harishkumar Madhyastha
- Department of Cardiovascular Physiology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Kaviyarasi Renu
- Center of Molecular Medicine and Diagnostics (COMMAND), Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Raja Ganesan
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
- Correspondence: (A.V.G.); (R.G.)
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