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Loktionov AV, Kobzeva KA, Karpenko AR, Sergeeva VA, Orlov YL, Bushueva OY. GWAS-significant loci and severe COVID-19: analysis of associations, link with thromboinflammation syndrome, gene-gene, and gene-environmental interactions. Front Genet 2024; 15:1434681. [PMID: 39175753 PMCID: PMC11338913 DOI: 10.3389/fgene.2024.1434681] [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: 05/18/2024] [Accepted: 07/29/2024] [Indexed: 08/24/2024] Open
Abstract
Objective The aim of this study was to replicate associations of GWAS-significant loci with severe COVID-19 in the population of Central Russia, to investigate associations of the SNPs with thromboinflammation parameters, to analyze gene-gene and gene-environmental interactions. Materials and Methods DNA samples from 798 unrelated Caucasian subjects from Central Russia (199 hospitalized COVID-19 patients and 599 controls with a mild or asymptomatic course of COVID-19) were genotyped using probe-based polymerase chain reaction for 10 GWAS-significant SNPs: rs143334143 CCHCR1, rs111837807 CCHCR1, rs17078346 SLC6A20-LLZTFL1, rs17713054 SLC6A20-LLZTFL1, rs7949972 ELF5, rs61882275 ELF5, rs12585036 ATP11A, rs67579710 THBS3, THBS3-AS1, rs12610495 DPP9, rs9636867 IFNAR2. Results SNP rs17713054 SLC6A20-LZTFL1 was associated with increased risk of severe COVID-19 in the entire group (risk allele A, OR = 1.78, 95% CI = 1.22-2.6, p = 0.003), obese individuals (OR = 2.31, 95% CI = 1.52-3.5, p = 0.0002, (p bonf = 0.0004)), patients with low fruit and vegetable intake (OR = 1.72, 95% CI = 1.15-2.58, p = 0.01, (p bonf = 0.02)), low physical activity (OR = 1.93, 95% CI = 1.26-2.94, p = 0.0035, (p bonf = 0.007)), and nonsmokers (OR = 1.65, 95% CI = 1.11-2.46, p = 0.02). This SNP correlated with increased BMI (p = 0.006) and worsened thrombodynamic parameters (maximum optical density of the formed clot, D (p = 0.02), delayed appearance of spontaneous clots, Tsp (p = 0.02), clot size 30 min after coagulation activation, CS (p = 0.036)). SNP rs17078346 SLC6A20-LZTFL1 was linked with increased BMI (p = 0.01) and severe COVID-19 in obese individuals (risk allele C, OR = 1.72, 95% CI = 1.15-2.58, p = 0.01, (p bonf = 0.02)). SNP rs12610495 DPP9 was associated with increased BMI (p = 0.01), severe COVID-19 in obese patients (risk allele G, OR = 1.48, 95% CI = 1.09-2.01, p = 0.01, (p bonf = 0.02)), and worsened thrombodynamic parameters (time to the start of clot growth, Tlag (p = 0.01)). For rs7949972 ELF5, a protective effect against severe COVID-19 was observed in non-obese patients (effect allele T, OR = 0.67, 95% CI = 0.47-0.95, p = 0.02, (p bonf = 0.04)), improving thrombodynamic parameters (CS (p = 0.02), stationary spatial clot growth rates, Vst (p = 0.02)). Finally, rs12585036 ATP11A exhibited a protective effect against severe COVID-19 in males (protective allele A, OR = 0.51, 95% CI = 0.32-0.83, p = 0.004). SNPs rs67579710 THBS3, THBS3-AS1, rs17713054 SLC6A20-LZTFL1, rs7949972 ELF5, rs9636867 IFNAR2-were involved in two or more of the most significant G×G interactions (p perm ≤ 0.01). The pairwise combination rs67579710 THBS3, THBS3-AS1 × rs17713054 SLC6A20-LZTFL1 was a priority in determining susceptibility to severe COVID-19 (it was included in four of the top five most significant SNP-SNP interaction models). Conclusion Overall, this study represents a comprehensive molecular-genetic and bioinformatics analysis of the involvement of GWAS-significant loci in the molecular mechanisms of severe COVID-19, gene-gene and gene-environmental interactions, and provides evidence of their relationship with thromboinflammation parameters in patients hospitalized in intensive care units.
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Affiliation(s)
- Alexey Valerevich Loktionov
- Department of Anesthesia and Critical Care, Institute of Continuing Education, Kursk State Medical University, Kursk, Russia
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russia
| | - Ksenia Andreevna Kobzeva
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russia
| | - Andrey Romanovich Karpenko
- Department of Anesthesia and Critical Care, Institute of Continuing Education, Kursk State Medical University, Kursk, Russia
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russia
| | - Vera Alexeevna Sergeeva
- Department of Anesthesia and Critical Care, Institute of Continuing Education, Kursk State Medical University, Kursk, Russia
| | - Yuriy Lvovich Orlov
- Institute of Biodesign and Complex Systems Modeling, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Olga Yurievna Bushueva
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russia
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, Kursk, Russia
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Biddie SC, Weykopf G, Hird EF, Friman ET, Bickmore WA. DNA-binding factor footprints and enhancer RNAs identify functional non-coding genetic variants. Genome Biol 2024; 25:208. [PMID: 39107801 PMCID: PMC11304670 DOI: 10.1186/s13059-024-03352-1] [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: 03/06/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have revealed a multitude of candidate genetic variants affecting the risk of developing complex traits and diseases. However, the highlighted regions are typically in the non-coding genome, and uncovering the functional causative single nucleotide variants (SNVs) is challenging. Prioritization of variants is commonly based on genomic annotation with markers of active regulatory elements, but current approaches still poorly predict functional variants. To address this, we systematically analyze six markers of active regulatory elements for their ability to identify functional variants. RESULTS We benchmark against molecular quantitative trait loci (molQTL) from assays of regulatory element activity that identify allelic effects on DNA-binding factor occupancy, reporter assay expression, and chromatin accessibility. We identify the combination of DNase footprints and divergent enhancer RNA (eRNA) as markers for functional variants. This signature provides high precision, but with a trade-off of low recall, thus substantially reducing candidate variant sets to prioritize variants for functional validation. We present this as a framework called FINDER-Functional SNV IdeNtification using DNase footprints and eRNA. CONCLUSIONS We demonstrate the utility to prioritize variants using leukocyte count trait and analyze variants in linkage disequilibrium with a lead variant to predict a functional variant in asthma. Our findings have implications for prioritizing variants from GWAS, in development of predictive scoring algorithms, and for functionally informed fine mapping approaches.
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Affiliation(s)
- Simon C Biddie
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- NHS Lothian, Edinburgh, UK.
| | - Giovanna Weykopf
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Elias T Friman
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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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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Yaghmouri M, Safdari Lord J, Amini M, Yekaninejad MS, Izadi P. The association of rs17713054 with Neanderthal origin at 3p21.31 locus with the severity of COVID-19 in Iranian patients. Sci Rep 2024; 14:15058. [PMID: 38956433 PMCID: PMC11219939 DOI: 10.1038/s41598-024-65732-8] [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: 06/24/2023] [Accepted: 06/24/2024] [Indexed: 07/04/2024] Open
Abstract
Since the COVID-19 pandemic, the diversity of clinical manifestations in patients has been a tremendous challenge. It seems that genetic variations, as one of the players, contribute to the variety of symptoms. Genome-wide association studies have demonstrated the influence of certain genomic regions on the disease prognosis. Particularly, a haplotype at 3p21.31 locus, inherited from Neanderthals, showed an association with COVID-19 severity. Despite several studies regarding this haplotype, some key variants are not sufficiently addressed. In the present study, we investigated the association of rs17713054 at 3p21.31 with COVID-19 severity. We analyzed the genotype of 251 Iranian COVID-19 patients (151 patients with asymptomatic to mild form as control and 100 patients with severe to critical symptoms without any comorbidities as case group) using the ARMS-PCR method. Results demonstrated that the A allele confers an almost twofold increased risk for COVID-19 severity (P value = 0.008). The AA genotype also raises the risk by more than 11 times following the recessive model (P value = 0.013). In conclusion, the A allele in rs17713054 was a risk allele in Iranian patients and was independently associated with COVID-19 severity. More studies are beneficial to confirm these findings in other populations and to develop strategies for risk assessment, prevention, and personalized medicine.
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Affiliation(s)
- Mohammad Yaghmouri
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Safdari Lord
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Amini
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mir Saeed Yekaninejad
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Pantea Izadi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Strober BJ, Zhang MJ, Amariuta T, Rossen J, Price AL. Fine-mapping causal tissues and genes at disease-associated loci. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.01.23297909. [PMID: 37961337 PMCID: PMC10635248 DOI: 10.1101/2023.11.01.23297909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Heritable diseases often manifest in a highly tissue-specific manner, with different disease loci mediated by genes in distinct tissues or cell types. We propose Tissue-Gene Fine-Mapping (TGFM), a fine-mapping method that infers the posterior probability (PIP) for each gene-tissue pair to mediate a disease locus by analyzing GWAS summary statistics (and in-sample LD) and leveraging eQTL data from diverse tissues to build cis-predicted expression models; TGFM also assigns PIPs to causal variants that are not mediated by gene expression in assayed genes and tissues. TGFM accounts for both co-regulation across genes and tissues and LD between SNPs (generalizing existing fine-mapping methods), and incorporates genome-wide estimates of each tissue's contribution to disease as tissue-level priors. TGFM was well-calibrated and moderately well-powered in simulations; unlike previous methods, TGFM was able to attain correct calibration by modeling uncertainty in cis-predicted expression models. We applied TGFM to 45 UK Biobank diseases/traits (average N = 316K) using eQTL data from 38 GTEx tissues. TGFM identified an average of 147 PIP > 0.5 causal genetic elements per disease/trait, of which 11% were gene-tissue pairs. Implicated gene-tissue pairs were concentrated in known disease-critical tissues, and causal genes were strongly enriched in disease-relevant gene sets. Causal gene-tissue pairs identified by TGFM recapitulated known biology (e.g., TPO-thyroid for Hypothyroidism), but also included biologically plausible novel findings (e.g., SLC20A2-artery aorta for Diastolic blood pressure). Further application of TGFM to single-cell eQTL data from 9 cell types in peripheral blood mononuclear cells (PBMC), analyzed jointly with GTEx tissues, identified 30 additional causal gene-PBMC cell type pairs at PIP > 0.5-primarily for autoimmune disease and blood cell traits, including the biologically plausible example of CD52 in classical monocyte cells for Monocyte count. In conclusion, TGFM is a robust and powerful method for fine-mapping causal tissues and genes at disease-associated loci.
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Affiliation(s)
- Benjamin J. Strober
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martin Jinye Zhang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tiffany Amariuta
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jordan Rossen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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6
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Milne TA. Chromatin and aberrant enhancer activity in KMT2A rearranged acute lymphoblastic leukemia. Curr Opin Genet Dev 2024; 86:102191. [PMID: 38579381 DOI: 10.1016/j.gde.2024.102191] [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: 12/18/2023] [Revised: 03/11/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024]
Abstract
To make a multicellular organism, genes need to be transcribed at the right developmental stages and in the right tissues. DNA sequences termed 'enhancers' are crucial to achieve this. Despite concerted efforts, the exact mechanisms of enhancer activity remain elusive. Mixed lineage leukemia (MLL or KMT2A) rearrangements (MLLr), commonly observed in cases of acute lymphoblastic leukemia (ALL) and acute myeloid leukemia, produce novel in-frame fusion proteins. Recent work has shown that the MLL-AF4 fusion protein drives aberrant enhancer activity at key oncogenes in ALL, dependent on the continued presence of MLL-AF4 complex components. As well as providing some general insights into enhancer function, these observations may also provide an explanation for transcriptional heterogeneity observed in MLLr patients.
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Affiliation(s)
- Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
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Tang Y, Xu M, Luo B, Wang Y, Chen Y, Yu G, Yang G, Gao S, Wang P. Highly sensitive detection of a long-COVID-related SNP in LZTFL1 allele with Pyrococcus furiosus Argonaute in point-of-care settings. Acta Biochim Biophys Sin (Shanghai) 2024; 56:1089-1092. [PMID: 38804045 PMCID: PMC11322863 DOI: 10.3724/abbs.2024071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 04/22/2024] [Indexed: 05/29/2024] Open
Affiliation(s)
- Yixin Tang
- Jiangsu Key Laboratory of Marine Biological Resources and EnvironmentCo-Innovation Center of Jiangsu Marine Bio-industry TechnologyJiangsu Ocean UniversityLianyungang222005China
| | - Miao Xu
- Jiangsu Key Laboratory of Marine Biological Resources and EnvironmentCo-Innovation Center of Jiangsu Marine Bio-industry TechnologyJiangsu Ocean UniversityLianyungang222005China
| | - Bo Luo
- Jiangsu Key Laboratory of Marine Biological Resources and EnvironmentCo-Innovation Center of Jiangsu Marine Bio-industry TechnologyJiangsu Ocean UniversityLianyungang222005China
| | - Yue Wang
- Jiangsu Key Laboratory of Marine Biological Resources and EnvironmentCo-Innovation Center of Jiangsu Marine Bio-industry TechnologyJiangsu Ocean UniversityLianyungang222005China
| | - Yukang Chen
- Jiangsu Key Laboratory of Marine Biological Resources and EnvironmentCo-Innovation Center of Jiangsu Marine Bio-industry TechnologyJiangsu Ocean UniversityLianyungang222005China
| | - Guangxi Yu
- Jiangsu Key Laboratory of Marine Biological Resources and EnvironmentCo-Innovation Center of Jiangsu Marine Bio-industry TechnologyJiangsu Ocean UniversityLianyungang222005China
| | - Guang Yang
- Jiangsu Key Laboratory of Marine Biological Resources and EnvironmentCo-Innovation Center of Jiangsu Marine Bio-industry TechnologyJiangsu Ocean UniversityLianyungang222005China
| | - Song Gao
- Jiangsu Key Laboratory of Marine Biological Resources and EnvironmentCo-Innovation Center of Jiangsu Marine Bio-industry TechnologyJiangsu Ocean UniversityLianyungang222005China
| | - Pei Wang
- School of Marine and Biological EngineeringYancheng Teachers UniversityYancheng224007China
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8
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Cao J, Li C, Cui Z, Deng S, Lei T, Liu W, Yang H, Chen P. Spatial Transcriptomics: A Powerful Tool in Disease Understanding and Drug Discovery. Theranostics 2024; 14:2946-2968. [PMID: 38773973 PMCID: PMC11103497 DOI: 10.7150/thno.95908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/25/2024] [Indexed: 05/24/2024] Open
Abstract
Recent advancements in modern science have provided robust tools for drug discovery. The rapid development of transcriptome sequencing technologies has given rise to single-cell transcriptomics and single-nucleus transcriptomics, increasing the accuracy of sequencing and accelerating the drug discovery process. With the evolution of single-cell transcriptomics, spatial transcriptomics (ST) technology has emerged as a derivative approach. Spatial transcriptomics has emerged as a hot topic in the field of omics research in recent years; it not only provides information on gene expression levels but also offers spatial information on gene expression. This technology has shown tremendous potential in research on disease understanding and drug discovery. In this article, we introduce the analytical strategies of spatial transcriptomics and review its applications in novel target discovery and drug mechanism unravelling. Moreover, we discuss the current challenges and issues in this research field that need to be addressed. In conclusion, spatial transcriptomics offers a new perspective for drug discovery.
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Affiliation(s)
- Junxian Cao
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
| | - Caifeng Li
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zhao Cui
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shiwen Deng
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
| | - Tong Lei
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wei Liu
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Hongjun Yang
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
| | - Peng Chen
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
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9
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Woodall MNJ, Cujba AM, Worlock KB, Case KM, Masonou T, Yoshida M, Polanski K, Huang N, Lindeboom RGH, Mamanova L, Bolt L, Richardson L, Cakir B, Ellis S, Palor M, Burgoyne T, Pinto A, Moulding D, McHugh TD, Saleh A, Kilich E, Mehta P, O'Callaghan C, Zhou J, Barclay W, De Coppi P, Butler CR, Cortina-Borja M, Vinette H, Roy S, Breuer J, Chambers RC, Heywood WE, Mills K, Hynds RE, Teichmann SA, Meyer KB, Nikolić MZ, Smith CM. Age-specific nasal epithelial responses to SARS-CoV-2 infection. Nat Microbiol 2024; 9:1293-1311. [PMID: 38622380 PMCID: PMC11087271 DOI: 10.1038/s41564-024-01658-1] [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: 03/24/2023] [Accepted: 03/04/2024] [Indexed: 04/17/2024]
Abstract
Children infected with SARS-CoV-2 rarely progress to respiratory failure. However, the risk of mortality in infected people over 85 years of age remains high. Here we investigate differences in the cellular landscape and function of paediatric (<12 years), adult (30-50 years) and older adult (>70 years) ex vivo cultured nasal epithelial cells in response to infection with SARS-CoV-2. We show that cell tropism of SARS-CoV-2, and expression of ACE2 and TMPRSS2 in nasal epithelial cell subtypes, differ between age groups. While ciliated cells are viral replication centres across all age groups, a distinct goblet inflammatory subtype emerges in infected paediatric cultures and shows high expression of interferon-stimulated genes and incomplete viral replication. In contrast, older adult cultures infected with SARS-CoV-2 show a proportional increase in basaloid-like cells, which facilitate viral spread and are associated with altered epithelial repair pathways. We confirm age-specific induction of these cell types by integrating data from in vivo COVID-19 studies and validate that our in vitro model recapitulates early epithelial responses to SARS-CoV-2 infection.
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Affiliation(s)
| | | | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Tereza Masonou
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Ni Huang
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Liam Bolt
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Samuel Ellis
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Machaela Palor
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Thomas Burgoyne
- UCL Institute of Ophthalmology, University College London, London, UK
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Andreia Pinto
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Dale Moulding
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Timothy D McHugh
- UCL Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, UK
| | - Aarash Saleh
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Eliz Kilich
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Puja Mehta
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Jie Zhou
- Department of Infectious Disease, Imperial College London, London, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Paolo De Coppi
- Great Ormond Street UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Colin R Butler
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
| | | | - Heloise Vinette
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Sunando Roy
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Judith Breuer
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Rachel C Chambers
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Wendy E Heywood
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Kevin Mills
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Robert E Hynds
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory/Dept Physics, University of Cambridge, Cambridge, UK.
| | | | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK.
- University College London Hospitals NHS Foundation Trust, London, UK.
| | - Claire M Smith
- Great Ormond Street UCL Institute of Child Health, London, UK.
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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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11
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Angulo-Aguado M, Carrillo-Martinez JC, Contreras-Bravo NC, Morel A, Parra-Abaunza K, Usaquén W, Fonseca-Mendoza DJ, Ortega-Recalde O. Next-generation sequencing of host genetics risk factors associated with COVID-19 severity and long-COVID in Colombian population. Sci Rep 2024; 14:8497. [PMID: 38605121 PMCID: PMC11009356 DOI: 10.1038/s41598-024-57982-3] [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: 10/29/2023] [Accepted: 03/24/2024] [Indexed: 04/13/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) was considered a major public health burden worldwide. Multiple studies have shown that susceptibility to severe infections and the development of long-term symptoms is significantly influenced by viral and host factors. These findings have highlighted the potential of host genetic markers to identify high-risk individuals and develop target interventions to reduce morbimortality. Despite its importance, genetic host factors remain largely understudied in Latin-American populations. Using a case-control design and a custom next-generation sequencing (NGS) panel encompassing 81 genetic variants and 74 genes previously associated with COVID-19 severity and long-COVID, we analyzed 56 individuals with asymptomatic or mild COVID-19 and 56 severe and critical cases. In agreement with previous studies, our results support the association between several clinical variables, including male sex, obesity and common symptoms like cough and dyspnea, and severe COVID-19. Remarkably, thirteen genetic variants showed an association with COVID-19 severity. Among these variants, rs11385942 (p < 0.01; OR = 10.88; 95% CI = 1.36-86.51) located in the LZTFL1 gene, and rs35775079 (p = 0.02; OR = 8.53; 95% CI = 1.05-69.45) located in CCR3 showed the strongest associations. Various respiratory and systemic symptoms, along with the rs8178521 variant (p < 0.01; OR = 2.51; 95% CI = 1.27-4.94) in the IL10RB gene, were significantly associated with the presence of long-COVID. The results of the predictive model comparison showed that the mixed model, which incorporates genetic and non-genetic variables, outperforms clinical and genetic models. To our knowledge, this is the first study in Colombia and Latin-America proposing a predictive model for COVID-19 severity and long-COVID based on genomic analysis. Our study highlights the usefulness of genomic approaches to studying host genetic risk factors in specific populations. The methodology used allowed us to validate several genetic variants previously associated with COVID-19 severity and long-COVID. Finally, the integrated model illustrates the importance of considering genetic factors in precision medicine of infectious diseases.
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Affiliation(s)
- Mariana Angulo-Aguado
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Juan Camilo Carrillo-Martinez
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Nora Constanza Contreras-Bravo
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Adrien Morel
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | | | - William Usaquén
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, D.C, Colombia
| | - Dora Janeth Fonseca-Mendoza
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Oscar Ortega-Recalde
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia.
- Departamento de Morfología, Facultad de Medicina e Instituto de Genética, Universidad Nacional de Colombia, Bogotá, D.C, Colombia.
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12
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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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13
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Ma Y, Zhou Y, Jiang D, Dai W, Li J, Deng C, Chen C, Zheng G, Zhang Y, Qiu F, Sun H, Xing S, Han H, Qu J, Wu N, Yao Y, Su J. Integration of human organoids single-cell transcriptomic profiles and human genetics repurposes critical cell type-specific drug targets for severe COVID-19. Cell Prolif 2024; 57:e13558. [PMID: 37807299 PMCID: PMC10905359 DOI: 10.1111/cpr.13558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023] Open
Abstract
Human organoids recapitulate the cell type diversity and function of their primary organs holding tremendous potentials for basic and translational research. Advances in single-cell RNA sequencing (scRNA-seq) technology and genome-wide association study (GWAS) have accelerated the biological and therapeutic interpretation of trait-relevant cell types or states. Here, we constructed a computational framework to integrate atlas-level organoid scRNA-seq data, GWAS summary statistics, expression quantitative trait loci, and gene-drug interaction data for distinguishing critical cell populations and drug targets relevant to coronavirus disease 2019 (COVID-19) severity. We found that 39 cell types across eight kinds of organoids were significantly associated with COVID-19 outcomes. Notably, subset of lung mesenchymal stem cells increased proximity with fibroblasts predisposed to repair COVID-19-damaged lung tissue. Brain endothelial cell subset exhibited significant associations with severe COVID-19, and this cell subset showed a notable increase in cell-to-cell interactions with other brain cell types, including microglia. We repurposed 33 druggable genes, including IFNAR2, TYK2, and VIPR2, and their interacting drugs for COVID-19 in a cell-type-specific manner. Overall, our results showcase that host genetic determinants have cellular-specific contribution to COVID-19 severity, and identification of cell type-specific drug targets may facilitate to develop effective therapeutics for treating severe COVID-19 and its complications.
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Affiliation(s)
- Yunlong Ma
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Yijun Zhou
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Dingping Jiang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Wei Dai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Jingjing Li
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Chunyu Deng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Cheng Chen
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Gongwei Zheng
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Yaru Zhang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Fei Qiu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Haojun Sun
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Shilai Xing
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Haijun Han
- School of Medicine, Hangzhou City University, Hangzhou, China
| | - Jia Qu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Nan Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yinghao Yao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Jianzhong Su
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
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14
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Zeberg H, Jakobsson M, Pääbo S. The genetic changes that shaped Neandertals, Denisovans, and modern humans. Cell 2024; 187:1047-1058. [PMID: 38367615 DOI: 10.1016/j.cell.2023.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/20/2023] [Accepted: 12/20/2023] [Indexed: 02/19/2024]
Abstract
Modern human ancestors diverged from the ancestors of Neandertals and Denisovans about 600,000 years ago. Until about 40,000 years ago, these three groups existed in parallel, occasionally met, and exchanged genes. A critical question is why modern humans, and not the other two groups, survived, became numerous, and developed complex cultures. Here, we discuss genetic differences among the groups and some of their functional consequences. As more present-day genome sequences become available from diverse groups, we predict that very few, if any, differences will distinguish all modern humans from all Neandertals and Denisovans. We propose that the genetic basis of what constitutes a modern human is best thought of as a combination of genetic features, where perhaps none of them is present in each and every present-day individual.
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Affiliation(s)
- Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Physiology and Pharmacology, Karolinska Institutet, 17165 Stockholm, Sweden.
| | - Mattias Jakobsson
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Okinawa Institute of Science and Technology, Onnason 904-0495, Okinawa, Japan.
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15
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Wang S, Zhao N, Luo T, Kou S, Sun M, Chen K. Causality between COVID-19 and multiple myeloma: a two-sample Mendelian randomization study and Bayesian co-localization. Clin Exp Med 2024; 24:42. [PMID: 38400850 PMCID: PMC10894079 DOI: 10.1007/s10238-024-01299-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/18/2024] [Indexed: 02/26/2024]
Abstract
Infection is the leading cause of morbidity and mortality in patients with multiple myeloma (MM). Studying the relationship between different traits of Coronavirus 2019 (COVID-19) and MM is critical for the management and treatment of MM patients with COVID-19. But all the studies on the relationship so far were observational and the results were also contradictory. Using the latest publicly available COVID-19 genome-wide association studies (GWAS) data, we performed a bidirectional Mendelian randomization (MR) analysis of the causality between MM and different traits of COVID-19 (SARS-CoV-2 infection, COVID-19 hospitalization, and severe COVID-19) and use multi-trait analysis of GWAS(MTAG) to identify new associated SNPs in MM. We performed co-localization analysis to reveal potential causal pathways between diseases and over-representation enrichment analysis to find involved biological pathways. IVW results showed SARS-CoV-2 infection and COVID-19 hospitalization increased risk of MM. In the reverse analysis, the causal relationship was not found between MM for each of the different symptoms of COVID-19. Co-localization analysis identified LZTFL1, MUC4, OAS1, HLA-C, SLC22A31, FDX2, and MAPT as genes involved in COVID-19-mediated causation of MM. These genes were mainly related to immune function, glycosylation modifications and virus defense. Three novel MM-related SNPs were found through MTAG, which may regulate the expression of B3GNT6. This is the first study to use MR to explore the causality between different traits of COVID-19 and MM. The results of our two-way MR analysis found that SARS-CoV-2 infection and COVID-19 hospitalization increased the susceptibility of MM.
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Affiliation(s)
- Shuaiyuan Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory of Tumor Pathology, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Na Zhao
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Ting Luo
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Songzi Kou
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Miaomiao Sun
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Kuisheng Chen
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Henan Key Laboratory of Tumor Pathology, Zhengzhou University, Zhengzhou, 450052, Henan, China.
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16
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Hubáček JA, Šedová L, Hellerová V, Adámková V, Tóthová V. Increased prevalence of the COVID-19 associated Neanderthal mutations in the Central European Roma population. Ann Hum Biol 2024; 51:2341727. [PMID: 38771659 DOI: 10.1080/03014460.2024.2341727] [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: 12/18/2023] [Accepted: 03/26/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and subsequent COVID-19 has spread world-wide and become pandemic with about 7 million deaths reported so far. Interethnic variability of the disease has been described, but a significant part of the differences remain unexplained and may be attributable to genetic factors. AIM To analyse genetic factors potentially influencing COVID-19 susceptibility and severity in European Roma minority. SUBJECTS AND METHODS Two genetic determinants, within OAS-1 (2-prime,5-prime-oligoadenylate synthetase 1, a key protein in the defence against viral infection; it activates RNases that degrade viral RNAs; rs4767027 has been analysed) and LZTFL1 (leucine zipper transcription factor-like 1, expressed in the lung respiratory epithelium; rs35044562 has been analysed) genes were screened in a population-sample of Czech Roma (N = 302) and majority population (N = 2,559). RESULTS For both polymorphisms, Roma subjects were more likely carriers of at least one risky allele for both rs4767027-C (p < 0.001) and rs35044562-G (p < 0.00001) polymorphism. There were only 5.3% Roma subjects without at least one risky allele in comparison with 10.1% in the majority population (p < 0.01). CONCLUSIONS It is possible that different genetic background plays an important role in increased prevalence of COVID-19 in the Roma minority.
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Affiliation(s)
- Jaroslav A Hubáček
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
- 3rd Department of Internal Medicine, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lenka Šedová
- Faculty of Health and Social Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | - Věra Hellerová
- Faculty of Health and Social Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | - Věra Adámková
- Department of Preventive Cardiology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Valérie Tóthová
- Faculty of Health and Social Sciences, University of South Bohemia, České Budějovice, Czech Republic
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17
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Camps-Vilaró A, Pinsach-Abuin ML, Degano IR, Ramos R, Martí-Lluch R, Elosua R, Subirana I, Solà-Richarte C, Puigmulé M, Pérez A, Vilaró I, Cruz R, Diz-de Almeida S, Nogues X, Masclans JR, Güerri-Fernández R, Marin J, Tizon-Marcos H, Vaquerizo B, Brugada R, Marrugat J. Genetic characteristics involved in COVID-19 severity. The CARGENCORS case-control study and meta-analysis. J Med Virol 2024; 96:e29404. [PMID: 38293834 DOI: 10.1002/jmv.29404] [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: 09/13/2023] [Revised: 11/30/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
Pre-existing coronary artery disease (CAD), and thrombotic, inflammatory, or virus infectivity response phenomena have been associated with COVID-19 disease severity. However, the association of candidate single nucleotide variants (SNVs) related to mechanisms of COVID-19 complications has been seldom analysed. Our aim was to test and validate the effect of candidate SNVs on COVID-19 severity. CARGENCORS (CARdiovascular GENetic risk score for Risk Stratification of patients positive for SARS-CoV-2 [COVID-19] virus) is an age- and sex-matched case-control study with 818 COVID-19 cases hospitalized with hypoxemia, and 1636 controls with COVID-19 treated at home. The association between severity and SNVs related to CAD (n = 32), inflammation (n = 19), thrombosis (n = 14), virus infectivity (n = 11), and two published to be related to COVID-19 severity was tested with adjusted logistic regression models. Two external independent cohorts were used for meta-analysis (SCOURGE and UK Biobank). After adjustment for potential confounders, 14 new SNVs were associated with COVID-19 severity in the CARGENCORS Study. These SNVs were related to CAD (n = 10), thrombosis (n = 2), and inflammation (n = 2). We also confirmed eight SNVs previously related to severe COVID-19 and virus infectivity. The meta-analysis showed five SNVs associated with severe COVID-19 in adjusted analyses (rs11385942, rs1561198, rs6632704, rs6629110, and rs12329760). We identified 14 novel SNVs and confirmed eight previously related to COVID-19 severity in the CARGENCORS data. In the meta-analysis, five SNVs were significantly associated to COVID-19 severity, one of them previously related to CAD.
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Affiliation(s)
- Anna Camps-Vilaró
- Registre Gironí del Cor (REGICOR) Study Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Doctoral College, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Mel Lina Pinsach-Abuin
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IdIBGi), Salt, Spain
| | - Irene R Degano
- Registre Gironí del Cor (REGICOR) Study Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Institute for Research and Innovation in Life Sciences and Health in Central Catalonia (IRIS-CC), Vic, Spain
| | - Rafel Ramos
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain
- Vascular Health Research Group, Institut Universitari per a la Recerca en Atenció Primària Jordi Gol i Gurina, Girona, Spain
- Girona Biomedical Research Institute, Girona, Spain
- Primary Care Services, Catalan Institute of Health, Girona, Spain
| | - Ruth Martí-Lluch
- Vascular Health Research Group, Institut Universitari per a la Recerca en Atenció Primària Jordi Gol i Gurina, Girona, Spain
- Girona Biomedical Research Institute, Girona, Spain
| | - Roberto Elosua
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Cardiovascular Epidemiology and Genetics Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Isaac Subirana
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Cardiovascular Epidemiology and Genetics Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Clàudia Solà-Richarte
- Registre Gironí del Cor (REGICOR) Study Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Marta Puigmulé
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
| | - Alexandra Pérez
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IdIBGi), Salt, Spain
| | | | - Raquel Cruz
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia Diz-de Almeida
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Xavier Nogues
- Musculoskeletal Research Unit, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Internal Medicine, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable, Instituto de Salud Carlos III, Madrid, Spain
- Department of Medicine, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Joan R Masclans
- Critical Illness Research Group (GREPAC), Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Critical Care, Hospital del Mar, Barcelona, Spain
- Medicine and Life Sciences department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roberto Güerri-Fernández
- Department of Medicine, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Department of Infectious Diseases, Hospital del Mar Research Institute, Barcelona, Spain
| | - Judith Marin
- Critical Illness Research Group (GREPAC), Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Critical Care, Hospital del Mar, Barcelona, Spain
| | - Helena Tizon-Marcos
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Biomedical Research in Heart Diseases Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Cardiology, Hospital del Mar, Barcelona, Spain
| | - Beatriz Vaquerizo
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Department of Medicine, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Biomedical Research in Heart Diseases Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Cardiology, Hospital del Mar, Barcelona, Spain
| | - Ramon Brugada
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IdIBGi), Salt, Spain
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain
- Department of Cardiology, Hospital Josep Trueta & University of Girona, Girona, Spain
| | - Jaume Marrugat
- Registre Gironí del Cor (REGICOR) Study Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
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18
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Covill LE, Sendel A, Campbell TM, Piiroinen I, Enoksson SL, Borgström EW, Hansen S, Ma K, Marits P, Norlin AC, Smith CIE, Kåhlin J, Eriksson LI, Bergman P, Bryceson YT. Evaluation of Genetic or Cellular Impairments in Type I IFN Immunity in a Cohort of Young Adults with Critical COVID-19. J Clin Immunol 2024; 44:50. [PMID: 38231281 PMCID: PMC10794435 DOI: 10.1007/s10875-023-01641-1] [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: 11/23/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024]
Abstract
Several genetic and immunological risk factors for severe COVID-19 have been identified, with monogenic conditions relating to 13 genes of type I interferon (IFN) immunity proposed to explain 4.8% of critical cases. However, previous cohorts have been clinically heterogeneous and were not subjected to thorough genetic and immunological analyses. We therefore aimed to systematically investigate the prevalence of rare genetic variants causing inborn errors of immunity (IEI) and functionally interrogate the type I IFN pathway in young adults that suffered from critical COVID-19 yet lacked comorbidities. We selected and clinically characterized a cohort of 38 previously healthy individuals under 50 years of age who were treated in intensive care units due to critical COVID-19. Blood samples were collected after convalescence. Two patients had IFN-α autoantibodies. Genome sequencing revealed very rare variants in the type I IFN pathway in 31.6% of the patients, which was similar to controls. Analyses of cryopreserved leukocytes did not indicate any defect in plasmacytoid dendritic cell sensing of TLR7 and TLR9 agonists in patients carrying variants in these pathways. However, lymphocyte STAT phosphorylation and protein upregulation upon IFN-α stimulation revealed three possible cases of impaired type I IFN signaling in carriers of rare variants. Together, our results suggest a strategy of functional screening followed by genome analyses and biochemical validation to uncover undiagnosed causes of critical COVID-19.
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Affiliation(s)
- L E Covill
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - A Sendel
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - T M Campbell
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - I Piiroinen
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - S Lind Enoksson
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - E Wahren Borgström
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - S Hansen
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - K Ma
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - P Marits
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - A C Norlin
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - C I E Smith
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - J Kåhlin
- Division of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - L I Eriksson
- Division of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - P Bergman
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Y T Bryceson
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden.
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden.
- Broegelmann Laboratory, Department of Clinical Sciences, University of Bergen, Bergen, Norway.
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19
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Laplana M, Royo JL, Real LM. Genetic Association Studies in Host-Pathogen Interaction Analysis. Methods Mol Biol 2024; 2751:19-30. [PMID: 38265707 DOI: 10.1007/978-1-0716-3617-6_2] [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] [Indexed: 01/25/2024]
Abstract
Studying host-pathogen interactions at a molecular level has always been technically challenging. Identifying the different biochemical and genetic pathways involved in the different stages of infection traditionally require complex molecular biology tools and often the use of costly animal models. In this chapter, we illustrate a complementary approach to address host-pathogen interactions, taking advantage of the natural interindividual genetic diversity. The application of genetic association studies allows us to identify alleles involved in infection progression or resistance. Thus, this strategy may be useful to unravel new molecular pathways underlying host-pathogen interactions. Here we present the general steps that might be followed to plan, execute, and analyze a population-based study in order to identify genetic variants affecting human exposition to pathogens.
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Affiliation(s)
- Marina Laplana
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - José Luis Royo
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología. Facultad de Medicina, Universidad de Málaga, Málaga, Spain.
| | - Luis Miguel Real
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología. Facultad de Medicina, Universidad de Málaga, Málaga, Spain
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario de Valme, Sevilla, Spain
- Centro de Investigación en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Instituto de Biomedicina de Sevilla, Sevilla, Spain
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20
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Constantinescu-Bercu A, Lobiuc A, Căliman-Sturdza OA, Oiţă RC, Iavorschi M, Pavăl NE, Șoldănescu I, Dimian M, Covasa M. Long COVID: Molecular Mechanisms and Detection Techniques. Int J Mol Sci 2023; 25:408. [PMID: 38203577 PMCID: PMC10778767 DOI: 10.3390/ijms25010408] [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: 11/28/2023] [Revised: 12/25/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Long COVID, also known as post-acute sequelae of SARS-CoV-2 infection (PASC), has emerged as a significant health concern following the COVID-19 pandemic. Molecular mechanisms underlying the occurrence and progression of long COVID include viral persistence, immune dysregulation, endothelial dysfunction, and neurological involvement, and highlight the need for further research to develop targeted therapies for this condition. While a clearer picture of the clinical symptomatology is shaping, many molecular mechanisms are yet to be unraveled, given their complexity and high level of interaction with other metabolic pathways. This review summarizes some of the most important symptoms and associated molecular mechanisms that occur in long COVID, as well as the most relevant molecular techniques that can be used in understanding the viral pathogen, its affinity towards the host, and the possible outcomes of host-pathogen interaction.
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Affiliation(s)
- Adela Constantinescu-Bercu
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
| | - Andrei Lobiuc
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
| | - Olga Adriana Căliman-Sturdza
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
- Suceava Emergency Clinical County Hospital, 720224 Suceava, Romania
| | - Radu Cristian Oiţă
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Ştefan cel Mare University of Suceava, 720229 Suceava, Romania; (R.C.O.); (I.Ș.); (M.D.)
| | - Monica Iavorschi
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
| | - Naomi-Eunicia Pavăl
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
| | - Iuliana Șoldănescu
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Ştefan cel Mare University of Suceava, 720229 Suceava, Romania; (R.C.O.); (I.Ș.); (M.D.)
| | - Mihai Dimian
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Ştefan cel Mare University of Suceava, 720229 Suceava, Romania; (R.C.O.); (I.Ș.); (M.D.)
- Department of Computers, Electronics and Automation, Ştefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mihai Covasa
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
- Department of Basic Medical Sciences, College of Osteopathic Medicine, Western University of Health Sciences, Pomona, CA 91711, USA
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21
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Zhang L, Zhang X, Deng X, Wang P, Mo Y, Zhang Y, Tong X. Cytokines as drivers: Unraveling the mechanisms of epithelial-mesenchymal transition in COVID-19 lung fibrosis. Biochem Biophys Res Commun 2023; 686:149118. [PMID: 37931361 DOI: 10.1016/j.bbrc.2023.10.050] [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: 07/11/2023] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), like other viruses, can induce proliferation of myofibroblasts and even lead to fibrosis in the lung. Epithelial-mesenchymal transition (EMT) is thought to play an essential role in the pathogenesis of Coronavirus disease 19 (COVID-19). EMT is originally a critical process that regulates the development of different tissues in the embryo, but in inflammatory situations, EMT tries to be activated again to control inflammation or even heal inflammatory damage. However, in pathological situations, such as chronic viral infections (e.g., COVID-19) or pulmonary fibrosis initiation, this benign healing transforms into sinister nature, pushing the lung into the fibrotic process. Notably, the cytokines released by inflammatory cells and the chronic inflammatory microenvironment shared by fibrotic cells promote each other as critical factors in the induction of pathological EMT. In the induction of SARS-CoV-2 virus, cytokines are an essential mediator of EMT transformation, and a summary of whether COVID-19 patients, during the infection phase, have many persistent inflammatory mediators (cytokines) that are a causative factor of EMT has not yet appeared. The following common signaling drivers, including Transforming growth factor beta (TGF-β), cytokines, Notch signaling pathway, Wnt and hypoxia signaling pathways, drive the regulation of EMT. In this review, we will focus on 3 key EMT signaling pathways: TGF-β, Leucine zipper transcription factor like 1 (LZTFL1) and the common interleukin family expressed in the lung. TGF-β-induced SNAIL and LZTFL1 were identified as regulatory EMT in COVID-19. For cytokines, the interleukin family is a common inducer of EMT and plays an essential role in the formation of the microenvironment of fibrosis. We sought to demonstrate that cytokines act as "communicators" and build the "microenvironment" of fibrosis together with EMT as a "bridge" to induce EMT in fibrosis. The mechanisms utilized by these two pathways could serve as templates for other mesenchymal transformations and provide new potential therapeutic targets.
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Affiliation(s)
- Lanlan Zhang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China; State Key Laboratory of Respiratory Health and Multimorbidity, Chengdu, China.
| | - Xin Zhang
- Department of Gastroenterology, West China (Airport) Hospital of Sichuan University, Chengdu, China; Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China.
| | - Xiaoqian Deng
- Department of Anesthesiology, West China Hospital, Sichuan university, Chengdu, China
| | - Pengbo Wang
- School of Professional Studies, Columbia University, USA
| | - Yan Mo
- Department of Neurology Medicine, The Aviation Industry Corporation of China (AVIC) 363 Hospital, Chengdu, China
| | - Yuansheng Zhang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Xia Tong
- Department of Gastroenterology, West China (Airport) Hospital of Sichuan University, Chengdu, China; Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
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22
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Wang S, Peng H, Chen F, Liu C, Zheng Q, Wang M, Wang J, Yu H, Xue E, Chen X, Wang X, Fan M, Qin X, Wu Y, Li J, Ye Y, Chen D, Hu Y, Wu T. Identification of genetic loci jointly influencing COVID-19 and coronary heart diseases. Hum Genomics 2023; 17:101. [PMID: 37964352 PMCID: PMC10647050 DOI: 10.1186/s40246-023-00547-8] [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: 06/28/2023] [Accepted: 10/29/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND Comorbidities of coronavirus disease 2019 (COVID-19)/coronary heart disease (CHD) pose great threats to disease outcomes, yet little is known about their shared pathology. The study aimed to examine whether comorbidities of COVID-19/CHD involved shared genetic pathology, as well as to clarify the shared genetic variants predisposing risks common to COVID-19 severity and CHD risks. METHODS By leveraging publicly available summary statistics, we assessed the genetically determined causality between COVID-19 and CHD with bidirectional Mendelian randomization. To further quantify the causality contributed by shared genetic variants, we interrogated their genetic correlation with the linkage disequilibrium score regression method. Bayesian colocalization analysis coupled with conditional/conjunctional false discovery rate analysis was applied to decipher the shared causal single nucleotide polymorphisms (SNPs). FINDINGS Briefly, we observed that the incident CHD risks post COVID-19 infection were partially determined by shared genetic variants. The shared genetic variants contributed to the causality at a proportion of 0.18 (95% CI 0.18-0.19) to 0.23 (95% CI 0.23-0.24). The SNP (rs10490770) located near LZTFL1 suggested direct causality (SNPs → COVID-19 → CHD), and SNPs in ABO (rs579459, rs495828), ILRUN(rs2744961), and CACFD1(rs4962153, rs3094379) may simultaneously influence COVID-19 severity and CHD risks. INTERPRETATION Five SNPs located near LZTFL1 (rs10490770), ABO (rs579459, rs495828), ILRUN (rs2744961), and CACFD1 (rs4962153, rs3094379) may simultaneously influence their risks. The current study suggested that there may be shared mechanisms predisposing to both COVID-19 severity and CHD risks. Genetic predisposition to COVID-19 is a causal risk factor for CHD, supporting that reducing the COVID-19 infection risk or alleviating COVID-19 severity among those with specific genotypes might reduce their subsequent CHD adverse outcomes. Meanwhile, the shared genetic variants identified may be of clinical implications for identifying the target population who are more vulnerable to adverse CHD outcomes post COVID-19 and may also advance treatments of 'Long COVID-19.'
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Affiliation(s)
- Siyue Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Hexiang Peng
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Feng Chen
- Department of Intensive Care Unit, PLA Rocket Force Characteristic Medical Center, Beijing, 100088, China
| | - Chunfang Liu
- School of Public Health, Baotou Medical College, Baotou, 014040, China
| | - Qiwen Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Mengying Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Jiating Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Huan Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Enci Xue
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Xi Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Xueheng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Meng Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Xueying Qin
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Yiqun Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Jin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Ying Ye
- Department of Local Diseases Control and Prevention, Fujian Provincial Center for Disease Control and Prevention, Fuzhou, 350001, China
| | - Dafang Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Yonghua Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China.
| | - Tao Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China.
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23
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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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Jones RP, Ponomarenko A. COVID-19-Related Age Profiles for SARS-CoV-2 Variants in England and Wales and States of the USA (2020 to 2022): Impact on All-Cause Mortality. Infect Dis Rep 2023; 15:600-634. [PMID: 37888139 PMCID: PMC10606787 DOI: 10.3390/idr15050058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 10/28/2023] Open
Abstract
Since 2020, COVID-19 has caused serious mortality around the world. Given the ambiguity in establishing COVID-19 as the direct cause of death, we first investigate the effects of age and sex on all-cause mortality during 2020 and 2021 in England and Wales. Since infectious agents have their own unique age profile for death, we use a 9-year time series and several different methods to adjust single-year-of-age deaths in England and Wales during 2019 (the pre-COVID-19 base year) to a pathogen-neutral single-year-of-age baseline. This adjusted base year is then used to confirm the widely reported higher deaths in males for most ages above 43 in both 2020 and 2021. During 2020 (+COVID-19 but no vaccination), both male and female population-adjusted deaths significantly increased above age 35. A significant reduction in all-cause mortality among both males and females aged 75+ could be demonstrated in 2021 during the widespread COVID-19 vaccination period; however, deaths below age 75 progressively increased. This finding arises from a mix of vaccination coverage and year-of-age profiles of deaths for the different SARS-CoV-2 variants. In addition, specific effects of age around puberty were demonstrated, where females had higher deaths than males. There is evidence that year-of-birth cohorts may also be involved, indicating that immune priming to specific pathogen outbreaks in the past may have led to lower deaths for some birth cohorts. To specifically identify the age profile for the COVID-19 variants from 2020 to 2023, we employ the proportion of total deaths at each age that are potentially due to or 'with' COVID-19. The original Wuhan strain and the Alpha variant show somewhat limited divergence in the age profile, with the Alpha variant shifting to a moderately higher proportion of deaths below age 84. The Delta variant specifically targeted individuals below age 65. The Omicron variants showed a significantly lower proportion of overall mortality, with a markedly higher relative proportion of deaths above age 65, steeply increasing with age to a maximum around 100 years of age. A similar age profile for the variants can be seen in the age-banded deaths in US states, although they are slightly obscured by using age bands rather than single years of age. However, the US data shows that higher male deaths are greatly dependent on age and the COVID variant. Deaths assessed to be 'due to' COVID-19 (as opposed to 'involving' COVID-19) in England and Wales were especially overestimated in 2021 relative to the change in all-cause mortality. This arose as a by-product of an increase in COVID-19 testing capacity in late 2020. Potential structure-function mechanisms for the age-specificity of SARS-CoV-2 variants are discussed, along with potential roles for small noncoding RNAs (miRNAs). Using data from England, it is possible to show that the unvaccinated do indeed have a unique age profile for death from each variant and that vaccination alters the shape of the age profile in a manner dependent on age, sex, and the variant. The question is posed as to whether vaccines based on different variants carry a specific age profile.
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Affiliation(s)
| | - Andrey Ponomarenko
- Department of Biophysics, Informatics and Medical Instrumentation, Odessa National Medical University, Valikhovsky Lane 2, 65082 Odessa, Ukraine
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25
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Wang Y, Liu B, Zhao G, Lee Y, Buzdin A, Mu X, Zhao J, Chen H, Li X. Spatial transcriptomics: Technologies, applications and experimental considerations. Genomics 2023; 115:110671. [PMID: 37353093 PMCID: PMC10571167 DOI: 10.1016/j.ygeno.2023.110671] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/10/2023] [Accepted: 06/15/2023] [Indexed: 06/25/2023]
Abstract
The diverse cell types of an organ have a highly structured organization to enable their efficient and correct function. To fully appreciate gene functions in a given cell type, one needs to understand how much, when and where the gene is expressed. Classic bulk RNA sequencing and popular single cell sequencing destroy cell structural organization and fail to provide spatial information. However, the spatial location of gene expression or of the cell in a complex tissue provides key clues to comprehend how the neighboring genes or cells cross talk, transduce signals and work together as a team to complete the job. The functional requirement for the spatial content has been a driving force for rapid development of the spatial transcriptomics technologies in the past few years. Here, we present an overview of current spatial technologies with a special focus on the commercially available or currently being commercialized technologies, highlight their applications by category and discuss experimental considerations for a first spatial experiment.
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Affiliation(s)
- Ye Wang
- Clinical Laboratory, The Affiliated Qingdao Central Hospital of Medical College of Qingdao University, Qingdao 266042, China.
| | - Bin Liu
- Departments of Medical Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang 110042, China
| | - Gexin Zhao
- UCLA Technology Center for Genomics & Bioinformatics, Department of Pathology & Laboratory Medicine, 650 Charles E Young Dr., Los Angeles, CA 90095, USA
| | - YooJin Lee
- UCLA Technology Center for Genomics & Bioinformatics, Department of Pathology & Laboratory Medicine, 650 Charles E Young Dr., Los Angeles, CA 90095, USA
| | - Anton Buzdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; Moscow Institute of Physics and Technology, Moscow Region, 141701, Russia; World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Xiaofeng Mu
- Clinical Laboratory, The Affiliated Qingdao Central Hospital of Medical College of Qingdao University, Qingdao 266042, China
| | - Joseph Zhao
- UCLA Technology Center for Genomics & Bioinformatics, Department of Pathology & Laboratory Medicine, 650 Charles E Young Dr., Los Angeles, CA 90095, USA
| | - Hong Chen
- Heilongjiang Academy of Traditional Chinese Medicine, No. 142, Sanfu Street, Xiangfang District, Harbin City, Heilongjiang Province 150036, China
| | - Xinmin Li
- UCLA Technology Center for Genomics & Bioinformatics, Department of Pathology & Laboratory Medicine, 650 Charles E Young Dr., Los Angeles, CA 90095, USA.
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26
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Wang WJ, Chu LX, He LY, Zhang MJ, Dang KT, Gao C, Ge QY, Wang ZG, Zhao XW. Spatial transcriptomics: recent developments and insights in respiratory research. Mil Med Res 2023; 10:38. [PMID: 37592342 PMCID: PMC10433685 DOI: 10.1186/s40779-023-00471-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
The respiratory system's complex cellular heterogeneity presents unique challenges to researchers in this field. Although bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) have provided insights into cell types and heterogeneity in the respiratory system, the relevant specific spatial localization and cellular interactions have not been clearly elucidated. Spatial transcriptomics (ST) has filled this gap and has been widely used in respiratory studies. This review focuses on the latest iterative technology of ST in recent years, summarizing how ST can be applied to the physiological and pathological processes of the respiratory system, with emphasis on the lungs. Finally, the current challenges and potential development directions are proposed, including high-throughput full-length transcriptome, integration of multi-omics, temporal and spatial omics, bioinformatics analysis, etc. These viewpoints are expected to advance the study of systematic mechanisms, including respiratory studies.
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Affiliation(s)
- Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Liu-Xi Chu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Yong He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ming-Jing Zhang
- Orthopaedic Bioengineering Research Group, Division of Surgery and Interventional Science, University College London, London, HA7 4LP, UK
| | - Kai-Tong Dang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qin-Yu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Zhou-Guang Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Xiang-Wei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
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27
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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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28
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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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29
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Pi P, Zeng Z, Zeng L, Han B, Bai X, Xu S. Molecular mechanisms of COVID-19-induced pulmonary fibrosis and epithelial-mesenchymal transition. Front Pharmacol 2023; 14:1218059. [PMID: 37601070 PMCID: PMC10436482 DOI: 10.3389/fphar.2023.1218059] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/25/2023] [Indexed: 08/22/2023] Open
Abstract
As the outbreak of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first broke out in Hubei Province, China, at the end of 2019. It has brought great challenges and harms to global public health. SARS-CoV-2 mainly affects the lungs and is mainly manifested as pulmonary disease. However, one of the biggest crises arises from the emergence of COVID-19-induced fibrosis. At present, there are still many questions about how COVID-19 induced pulmonary fibrosis (PF) occurs and how to treat and regulate its long-term effects. In addition, as an important process of fibrosis, the effect of COVID-19 on epithelial-mesenchymal transition (EMT) may be an important factor driving PF. This review summarizes the main pathogenesis and treatment mechanisms of COVID-19 related to PF. Starting with the basic mechanisms of PF, such as EMT, transforming growth factor-β (TGF-β), fibroblasts and myofibroblasts, inflammation, macrophages, innate lymphoid cells, matrix metalloproteinases and tissue inhibitors of metalloproteinases, hedgehog pathway as well as Notch signaling. Further, we highlight the importance of COVID-19-induced EMT in the process of PF and provide an overview of the related molecular mechanisms, which will facilitate future research to propose new clinical therapeutic solutions for the treatment of COVID-19-induced PF.
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Affiliation(s)
- Peng Pi
- School of Sports Medicine and Rehabilitation, Beijing Sport University, Beijing, China
| | - Zhipeng Zeng
- School of Sports Medicine and Rehabilitation, Beijing Sport University, Beijing, China
| | - Liqing Zeng
- School of Sports Medicine and Rehabilitation, Beijing Sport University, Beijing, China
| | - Bing Han
- School of Sports Medicine and Rehabilitation, Beijing Sport University, Beijing, China
| | - Xizhe Bai
- College of Physical Education and Health, East China Normal University, Shanghai, China
| | - Shousheng Xu
- School of Sports Engineering, Beijing Sport University, Beijing, China
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30
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Udomsinprasert W, Nontawong N, Saengsiwaritt W, Panthan B, Jiaranai P, Thongchompoo N, Santon S, Runcharoen C, Sensorn I, Jittikoon J, Chaikledkaew U, Chantratita W. Host genetic polymorphisms involved in long-term symptoms of COVID-19. Emerg Microbes Infect 2023:2239952. [PMID: 37497655 PMCID: PMC10392286 DOI: 10.1080/22221751.2023.2239952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Host genetic polymorphisms are recognized as a critical determinant of diversity in clinical symptoms of Coronavirus disease 2019 (COVID-19). Accordingly, this study aimed to determine possible associations between single nucleotide polymorphisms (SNPs) in 37 candidate genes and clinical consequences of COVID-19 - especially long-term symptoms, Long COVID. A total of 260 COVID-19 patients, divided into mild (n=239) and severe (n=21) and further categorized based on the presence of Long COVID (no, n=211; yes, n=49), were recruited. Genotyping of selected polymorphisms in 37 genes responsible for viral entry, immune response, and inflammation was performed using MassARRAY system. Out of 37 SNPs, 9 including leucine zipper transcription factor like-1 (LZTFL1) rs10490770 C allele, LZTFL1 rs11385942 dupA allele, nicotinamide adenine dinucleotide synthetase-1 (NADSYN1) rs12785878 TT genotype, plexin A-4 (PLXNA4) rs1424597 AA genotype, LZTFL1 rs17713054 A allele, interleukin-10 (IL10) rs1800896 TC genotype and C allele, angiotensin converting enzyme-2 (ACE2) rs2285666 T allele, and plasmanylethanolamine desaturase-1 (PEDS1) rs6020298 GG genotype and G allele were significantly associated with an increased risk of developing Long COVID, whereas interleukin-10 receptor subunit beta (IL10RB) rs8178562 GG genotype was significantly associated with a reduced risk of Long COVID. Kaplan-Meier curve displayed that polymorphisms in the above genes were significantly associated with cumulative rate of Long COVID occurrence. Polymorphisms in LZTFL1 rs10490770, LZTFL1 rs11385942, LZTFL1 rs17713054, NADSYN1 rs12785878, PLXNA4 rs1424597, IL10 rs1800896, ACE2 rs2285666, PEDS1 rs6020298, and IL10RB rs8178562 appear to be genetic factors involved in development of Long COVID.
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Affiliation(s)
- Wanvisa Udomsinprasert
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | | | | | - Bhakbhoom Panthan
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Poramate Jiaranai
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Nartthawee Thongchompoo
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Siwalee Santon
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Chakkaphan Runcharoen
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Insee Sensorn
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Jiraphun Jittikoon
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Usa Chaikledkaew
- Social and Administrative Pharmacy Division, Department of Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Mahidol University Health Technology Assessment (MUHTA) Graduate Program, Mahidol University, Bangkok 10400, Thailand
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
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31
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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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Affiliation(s)
- Bruna Gomes
- From the Departments of Medicine, Genetics, and Biomedical Data Science, Stanford University, Stanford, CA (B.G., E.A.A.); and the Department of Cardiology, Pneumology, and Angiology, Heidelberg University Hospital, Heidelberg, Germany (B.G.)
| | - Euan A Ashley
- From the Departments of Medicine, Genetics, and Biomedical Data Science, Stanford University, Stanford, CA (B.G., E.A.A.); and the Department of Cardiology, Pneumology, and Angiology, Heidelberg University Hospital, Heidelberg, Germany (B.G.)
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Gu H, Liu Y, Zhao Y, Qu H, Li Y, Ahmed AA, Liu HY, Hu P, Cai D. Hepatic Anti-Oxidative Genes CAT and GPX4 Are Epigenetically Modulated by RORγ/NRF2 in Alphacoronavirus-Exposed Piglets. Antioxidants (Basel) 2023; 12:1305. [PMID: 37372035 DOI: 10.3390/antiox12061305] [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: 05/02/2023] [Revised: 06/12/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
As a member of alpha-coronaviruses, PEDV could lead to severe diarrhea and dehydration in newborn piglets. Given that lipid peroxides in the liver are key mediators of cell proliferation and death, the role and regulation of endogenous lipid peroxide metabolism in response to coronavirus infection need to be illuminated. The enzymatic activities of SOD, CAT, mitochondrial complex-I, complex-III, and complex-V, along with the glutathione and ATP contents, were significantly decreased in the liver of PEDV piglets. In contrast, the lipid peroxidation biomarkers, malondialdehyde, and ROS were markedly elevated. Moreover, we found that the peroxisome metabolism was inhibited by the PEDV infection using transcriptome analysis. These down-regulated anti-oxidative genes, including GPX4, CAT, SOD1, SOD2, GCLC, and SLC7A11, were further validated by qRT-PCR and immunoblotting. Because the nuclear receptor RORγ-driven MVA pathway is critical for LPO, we provided new evidence that RORγ also controlled the genes CAT and GPX4 involved in peroxisome metabolism in the PEDV piglets. We found that RORγ directly binds to these two genes using ChIP-seq and ChIP-qPCR analysis, where PEDV strongly repressed the binding enrichments. The occupancies of histone active marks such as H3K9/27ac and H3K4me1/2, together with active co-factor p300 and polymerase II at the locus of CAT and GPX4, were significantly decreased. Importantly, PEDV infection disrupted the physical association between RORγ and NRF2, facilitating the down-regulation of the CAT and GPX4 genes at the transcriptional levels. RORγ is a potential factor in modulating the CAT and GPX4 gene expressions in the liver of PEDV piglets by interacting with NRF2 and histone modifications.
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Affiliation(s)
- Haotian Gu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yaya Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yahui Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Huan Qu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yanhua Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Abdelkareem A Ahmed
- Biomedical Research Institute, Darfur University College, Nyala 56022, Sudan
| | - Hao-Yu Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
| | - Ping Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
| | - Demin Cai
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
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Mocci S, Littera R, Chessa L, Campagna M, Melis M, Ottelio CM, Piras IS, Lai S, Firinu D, Tranquilli S, Mascia A, Vacca M, Schirru D, Lecca LI, Rassu S, Cannas F, Sanna C, Carta MG, Sedda F, Giuressi E, Cipri S, Miglianti M, Perra A, Giglio S. A review of the main genetic factors influencing the course of COVID-19 in Sardinia: the role of human leukocyte antigen-G. Front Immunol 2023; 14:1138559. [PMID: 37342325 PMCID: PMC10277491 DOI: 10.3389/fimmu.2023.1138559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Introduction A large number of risk and protective factors have been identified during the SARS-CoV-2 pandemic which may influence the outcome of COVID-19. Among these, recent studies have explored the role of HLA-G molecules and their immunomodulatory effects in COVID-19, but there are very few reports exploring the genetic basis of these manifestations. The present study aims to investigate how host genetic factors, including HLA-G gene polymorphisms and sHLA-G, can affect SARS-CoV-2 infection. Materials and Methods We compared the immune-genetic and phenotypic characteristics between COVID-19 patients (n = 381) with varying degrees of severity of the disease and 420 healthy controls from Sardinia (Italy). Results HLA-G locus analysis showed that the extended haplotype HLA-G*01:01:01:01/UTR-1 was more prevalent in both COVID-19 patients and controls. In particular, this extended haplotype was more common among patients with mild symptoms than those with severe symptoms [22.7% vs 15.7%, OR = 0.634 (95% CI 0.440 - 0.913); P = 0.016]. Furthermore, the most significant HLA-G 3'UTR polymorphism (rs371194629) shows that the HLA-G 3'UTR Del/Del genotype frequency decreases gradually from 27.6% in paucisymptomatic patients to 15.9% in patients with severe symptoms (X2 = 7.095, P = 0.029), reaching the lowest frequency (7.0%) in ICU patients (X2 = 11.257, P = 0.004). However, no significant differences were observed for the soluble HLA-G levels in patients and controls. Finally, we showed that SARS-CoV-2 infection in the Sardinian population is also influenced by other genetic factors such as β-thalassemia trait (rs11549407C>T in the HBB gene), KIR2DS2/HLA-C C1+ group combination and the HLA-B*58:01, C*07:01, DRB1*03:01 haplotype which exert a protective effect [P = 0.005, P = 0.001 and P = 0.026 respectively]. Conversely, the Neanderthal LZTFL1 gene variant (rs35044562A>G) shows a detrimental consequence on the disease course [P = 0.001]. However, by using a logistic regression model, HLA-G 3'UTR Del/Del genotype was independent from the other significant variables [ORM = 0.4 (95% CI 0.2 - 0.7), PM = 6.5 x 10-4]. Conclusion Our results reveal novel genetic variants which could potentially serve as biomarkers for disease prognosis and treatment, highlighting the importance of considering genetic factors in the management of COVID-19 patients.
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Affiliation(s)
- Stefano Mocci
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
| | - Roberto Littera
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Luchino Chessa
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- Liver Unit, University Hospital, Cagliari, Italy
| | - Marcello Campagna
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Maurizio Melis
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
| | - Carla Maria Ottelio
- Anesthesia and Intensive Care Unit, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Ignazio S. Piras
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Sara Lai
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Davide Firinu
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Stefania Tranquilli
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Alessia Mascia
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Monica Vacca
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Daniele Schirru
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Luigi Isaia Lecca
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Stefania Rassu
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Federica Cannas
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Celeste Sanna
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Mauro Giovanni Carta
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Francesca Sedda
- Section of Pathology, Oncology and Molecular Pathology Unit, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Erika Giuressi
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Selene Cipri
- GeneMos-APS (Association for Social Advancement), Reggio Calabria, Italy
| | - Michela Miglianti
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Andrea Perra
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
- Section of Pathology, Oncology and Molecular Pathology Unit, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Sabrina Giglio
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
- Centre for Research University Services (CeSAR, Centro Servizi di Ateneo per la Ricerca), University of Cagliari, Monserrato, Italy
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Zhu D, Zhao R, Yuan H, Xie Y, Jiang Y, Xu K, Zhang T, Chen X, Suo C. Host Genetic Factors, Comorbidities and the Risk of Severe COVID-19. J Epidemiol Glob Health 2023; 13:279-291. [PMID: 37160831 PMCID: PMC10169198 DOI: 10.1007/s44197-023-00106-3] [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: 11/28/2022] [Accepted: 04/17/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was varied in disease symptoms. We aim to explore the effect of host genetic factors and comorbidities on severe COVID-19 risk. METHODS A total of 20,320 COVID-19 patients in the UK Biobank cohort were included. Genome-wide association analysis (GWAS) was used to identify host genetic factors in the progression of COVID-19 and a polygenic risk score (PRS) consisted of 86 SNPs was constructed to summarize genetic susceptibility. Colocalization analysis and Logistic regression model were used to assess the association of host genetic factors and comorbidities with COVID-19 severity. All cases were randomly split into training and validation set (1:1). Four algorithms were used to develop predictive models and predict COVID-19 severity. Demographic characteristics, comorbidities and PRS were included in the model to predict the risk of severe COVID-19. The area under the receiver operating characteristic curve (AUROC) was applied to assess the models' performance. RESULTS We detected an association with rs73064425 at locus 3p21.31 reached the genome-wide level in GWAS (odds ratio: 1.55, 95% confidence interval: 1.36-1.78). Colocalization analysis found that two genes (SLC6A20 and LZTFL1) may affect the progression of COVID-19. In the predictive model, logistic regression models were selected due to simplicity and high performance. Predictive model consisting of demographic characteristics, comorbidities and genetic factors could precisely predict the patient's progression (AUROC = 82.1%, 95% CI 80.6-83.7%). Nearly 20% of severe COVID-19 events could be attributed to genetic risk. CONCLUSION In this study, we identified two 3p21.31 genes as genetic susceptibility loci in patients with severe COVID-19. The predictive model includes demographic characteristics, comorbidities and genetic factors is useful to identify individuals who are predisposed to develop subsequent critical conditions among COVID-19 patients.
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Affiliation(s)
- Dongliang Zhu
- Department of Epidemiology & Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Renjia Zhao
- State Key Laboratory of Genetic Engineering, Zhangjiang Fudan International Innovation Center, Human Phenome Institute, Fudan University, Shanghai, China
| | - Huangbo Yuan
- State Key Laboratory of Genetic Engineering, Zhangjiang Fudan International Innovation Center, Human Phenome Institute, Fudan University, Shanghai, China
| | - Yijing Xie
- Department of Epidemiology & Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Yanfeng Jiang
- State Key Laboratory of Genetic Engineering, Zhangjiang Fudan International Innovation Center, Human Phenome Institute, Fudan University, Shanghai, China
- Fudan University Taizhou Institute of Health Sciences, Yaocheng Road 799, Taizhou, Jiangsu, China
| | - Kelin Xu
- Fudan University Taizhou Institute of Health Sciences, Yaocheng Road 799, Taizhou, Jiangsu, China
- Department of Biostatistics, School of Public Health, Fudan University, Shanghai, China
| | - Tiejun Zhang
- Department of Epidemiology & Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai, China
- Fudan University Taizhou Institute of Health Sciences, Yaocheng Road 799, Taizhou, Jiangsu, China
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering, Zhangjiang Fudan International Innovation Center, Human Phenome Institute, Fudan University, Shanghai, China
- Fudan University Taizhou Institute of Health Sciences, Yaocheng Road 799, Taizhou, Jiangsu, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
- Yiwu Research Institute of Fudan University, Yiwu, Zhejiang, China
| | - Chen Suo
- Department of Epidemiology & Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China.
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai, China.
- Fudan University Taizhou Institute of Health Sciences, Yaocheng Road 799, Taizhou, Jiangsu, China.
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Hamley JC, Li H, Denny N, Downes D, Davies JOJ. Determining chromatin architecture with Micro Capture-C. Nat Protoc 2023; 18:1687-1711. [PMID: 36991220 DOI: 10.1038/s41596-023-00817-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 01/11/2023] [Indexed: 03/30/2023]
Abstract
Micro Capture-C (MCC) is a chromatin conformation capture (3C) method for visualizing reproducible three-dimensional contacts of specified regions of the genome at base pair resolution. These methods are an established family of techniques that use proximity ligation to assay the topology of chromatin. MCC can generate data at substantially higher resolution than previous techniques through multiple refinements of the 3C method. Using a sequence agnostic nuclease, the maintenance of cellular integrity and full sequencing of the ligation junctions, MCC achieves subnucleosomal levels of resolution, which can be used to reveal transcription factor binding sites analogous to DNAse I footprinting. Gene dense regions, close-range enhancer-promoter contacts, individual enhancers within super-enhancers and multiple other types of loci or regulatory regions that were previously challenging to assay with conventional 3C techniques, are readily observed using MCC. MCC requires training in common molecular biology techniques and bioinformatics to perform the experiment and analyze the data. The protocol can be expected to be completed in a 3 week timeframe for experienced molecular biologists.
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Affiliation(s)
- Joseph C Hamley
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Hangpeng Li
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nicholas Denny
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Damien Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Oxford Biomedical Research Centre, Genomic Medicine and Cell and Gene Therapy Themes, Oxford, UK.
- National Institute of Health Research Blood and Transplant Research Unit, Oxford, UK.
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Edahiro R, Shirai Y, Takeshima Y, Sakakibara S, Yamaguchi Y, Murakami T, Morita T, Kato Y, Liu YC, Motooka D, Naito Y, Takuwa A, Sugihara F, Tanaka K, Wing JB, Sonehara K, Tomofuji Y, Namkoong H, Tanaka H, Lee H, Fukunaga K, Hirata H, Takeda Y, Okuzaki D, Kumanogoh A, Okada Y. Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity. Nat Genet 2023; 55:753-767. [PMID: 37095364 PMCID: PMC10181941 DOI: 10.1038/s41588-023-01375-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/15/2023] [Indexed: 04/26/2023]
Abstract
Mechanisms underpinning the dysfunctional immune response in severe acute respiratory syndrome coronavirus 2 infection are elusive. We analyzed single-cell transcriptomes and T and B cell receptors (BCR) of >895,000 peripheral blood mononuclear cells from 73 coronavirus disease 2019 (COVID-19) patients and 75 healthy controls of Japanese ancestry with host genetic data. COVID-19 patients showed a low fraction of nonclassical monocytes (ncMono). We report downregulated cell transitions from classical monocytes to ncMono in COVID-19 with reduced CXCL10 expression in ncMono in severe disease. Cell-cell communication analysis inferred decreased cellular interactions involving ncMono in severe COVID-19. Clonal expansions of BCR were evident in the plasmablasts of patients. Putative disease genes identified by COVID-19 genome-wide association study showed cell type-specific expressions in monocytes and dendritic cells. A COVID-19-associated risk variant at the IFNAR2 locus (rs13050728) had context-specific and monocyte-specific expression quantitative trait loci effects. Our study highlights biological and host genetic involvement of innate immune cells in COVID-19 severity.
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Affiliation(s)
- Ryuya Edahiro
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yuya Shirai
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Yusuke Takeshima
- Laboratory of Experimental Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Shuhei Sakakibara
- Laboratory of Immune Regulation, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Yuta Yamaguchi
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Teruaki Murakami
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Takayoshi Morita
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Yasuhiro Kato
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Yu-Chen Liu
- Laboratory of Human Immunology (Single Cell Genomics), WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Daisuke Motooka
- Laboratory of Human Immunology (Single Cell Genomics), WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Yoko Naito
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Ayako Takuwa
- Laboratory of Human Immunology (Single Cell Genomics), WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center and Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Kentaro Tanaka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - James B Wing
- Laboratory of Human Immunology (Single Cell Immunology), Immunology Frontier Research Center, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshihiko Tomofuji
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ho Namkoong
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Hiromu Tanaka
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Ho Lee
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Haruhiko Hirata
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Daisuke Okuzaki
- Laboratory of Human Immunology (Single Cell Genomics), WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
- Japan Agency for Medical Research and Development - Core Research for Evolutional Science and Technology (AMED-CREST), Osaka University, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan.
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan.
- Japan Agency for Medical Research and Development - Core Research for Evolutional Science and Technology (AMED-CREST), Osaka University, Osaka, Japan.
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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Badat M, Ejaz A, Hua P, Rice S, Zhang W, Hentges LD, Fisher CA, Denny N, Schwessinger R, Yasara N, Roy NBA, Issa F, Roy A, Telfer P, Hughes J, Mettananda S, Higgs DR, Davies JOJ. Direct correction of haemoglobin E β-thalassaemia using base editors. Nat Commun 2023; 14:2238. [PMID: 37076455 PMCID: PMC10115876 DOI: 10.1038/s41467-023-37604-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 03/23/2023] [Indexed: 04/21/2023] Open
Abstract
Haemoglobin E (HbE) β-thalassaemia causes approximately 50% of all severe thalassaemia worldwide; equating to around 30,000 births per year. HbE β-thalassaemia is due to a point mutation in codon 26 of the human HBB gene on one allele (GAG; glutamatic acid → AAG; lysine, E26K), and any mutation causing severe β-thalassaemia on the other. When inherited together in compound heterozygosity these mutations can cause a severe thalassaemic phenotype. However, if only one allele is mutated individuals are carriers for the respective mutation and have an asymptomatic phenotype (β-thalassaemia trait). Here we describe a base editing strategy which corrects the HbE mutation either to wildtype (WT) or a normal variant haemoglobin (E26G) known as Hb Aubenas and thereby recreates the asymptomatic trait phenotype. We have achieved editing efficiencies in excess of 90% in primary human CD34 + cells. We demonstrate editing of long-term repopulating haematopoietic stem cells (LT-HSCs) using serial xenotransplantation in NSG mice. We have profiled the off-target effects using a combination of circularization for in vitro reporting of cleavage effects by sequencing (CIRCLE-seq) and deep targeted capture and have developed machine-learning based methods to predict functional effects of candidate off-target mutations.
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Affiliation(s)
- Mohsin Badat
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Department of Clinical Haematology, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Ayesha Ejaz
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Peng Hua
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Siobhan Rice
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Weijiao Zhang
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lance D Hentges
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Oxford National Institute of Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Christopher A Fisher
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas Denny
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nirmani Yasara
- Department of Paediatrics, University of Kelaniya, Kelaniya, Sri Lanka
| | - Noemi B A Roy
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Fadi Issa
- Transplantation Research and Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Andi Roy
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Paul Telfer
- Department of Clinical Haematology, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Jim Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Douglas R Higgs
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- Department of Clinical Haematology, Royal London Hospital, Barts Health NHS Trust, London, UK.
- National Institute of Health Research Blood and Transplant Research Unit in Precision Cellular Therapeutics, Oxford, UK.
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Urbiola-Salvador V, Lima de Souza S, Grešner P, Qureshi T, Chen Z. Plasma Proteomics Unveil Novel Immune Signatures and Biomarkers upon SARS-CoV-2 Infection. Int J Mol Sci 2023; 24:ijms24076276. [PMID: 37047248 PMCID: PMC10093853 DOI: 10.3390/ijms24076276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/07/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Several elements have an impact on COVID-19, including comorbidities, age and sex. To determine the protein profile changes in peripheral blood caused by a SARS-CoV-2 infection, a proximity extension assay was used to quantify 1387 proteins in plasma samples among 28 Finnish patients with COVID-19 with and without comorbidities and their controls. Key immune signatures, including CD4 and CD28, were changed in patients with comorbidities. Importantly, several unreported elevated proteins in patients with COVID-19, such as RBP2 and BST2, which show anti-microbial activity, along with proteins involved in extracellular matrix remodeling, including MATN2 and COL6A3, were identified. RNF41 was downregulated in patients compared to healthy controls. Our study demonstrates that SARS-CoV-2 infection causes distinct plasma protein changes in the presence of comorbidities despite the interpatient heterogeneity, and several novel potential biomarkers associated with a SARS-CoV-2 infection alone and in the presence of comorbidities were identified. Protein changes linked to the generation of SARS-CoV-2-specific antibodies, long-term effects and potential association with post-COVID-19 condition were revealed. Further study to characterize the identified plasma protein changes from larger cohorts with more diverse ethnicities of patients with COVID-19 combined with functional studies will facilitate the identification of novel diagnostic, prognostic biomarkers and potential therapeutic targets for patients with COVID-19.
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Affiliation(s)
- Víctor Urbiola-Salvador
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, 80-307 Gdańsk, Pomerania, Poland
| | - Suiane Lima de Souza
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220 Oulu, North Ostrobothnia, Finland
| | - Peter Grešner
- Department of Translational Oncology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Medical University of Gdańsk, 80-211 Gdańsk, Pomerania, Poland
| | - Talha Qureshi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220 Oulu, North Ostrobothnia, Finland
| | - Zhi Chen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220 Oulu, North Ostrobothnia, Finland
- Correspondence:
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40
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Lu J, Fu LM, Cao Y, Fang Y, Cao JZ, Pan YH, Cen JJ, Liang YP, Chen ZH, Wei JH, Huang Y, Mumin MA, Xu QH, Wang YH, Zhu JQ, Liang H, Wang Z, Deng Q, Chen W, Jin XH, Liu ZP, Luo JH. LZTFL1 inhibits kidney tumor cell growth by destabilizing AKT through ZNRF1-mediated ubiquitin proteosome pathway. Oncogene 2023; 42:1543-1557. [PMID: 36966254 PMCID: PMC10039360 DOI: 10.1038/s41388-023-02666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/27/2023]
Abstract
LZTFL1 is a tumor suppressor located in chromosomal region 3p21.3 that is deleted frequently and early in various cancer types including the kidney cancer. However, its role in kidney tumorigenesis remains unknown. Here we hypothesized a tumor suppressive function of LZTFL1 in clear cell renal cell carcinoma (ccRCC) and its mechanism of action based on extensive bioinformatics analysis of patients' tumor data and validated it using both gain- and loss-functional studies in kidney tumor cell lines and patient-derive xenograft (PDX) model systems. Our studies indicated that LZTFL1 inhibits kidney tumor cell proliferation by destabilizing AKT through ZNRF1-mediated ubiquitin proteosome pathway and inducing cell cycle arrest at G1. Clinically, we found that LZTFL1 is frequently deleted in ccRCC. Downregulation of LZTFL1 is associated with a poor ccRCC outcome and may be used as prognostic maker. Furthermore, we show that overexpression of LZTFL1 in PDX via lentiviral delivery suppressed PDX growth, suggesting that re-expression of LZTFL1 may be a therapeutic strategy against ccRCC.
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Affiliation(s)
- Jun Lu
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Liang-Min Fu
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yun Cao
- Department of Pathology, Sun Yat-sen University Cancer Center of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yong Fang
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jia-Zheng Cao
- Department of Urology, Jiangmen Central Hospital, Jiangmen, Guangdong Province, People's Republic of China
| | - Yi-Hui Pan
- Department of Urology, The First People's Hospital of Changzhou, Changzhou, Jiangsu, People's Republic of China
| | - Jun-Jie Cen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yan-Ping Liang
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Zhen-Hua Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jin-Huan Wei
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yong Huang
- Department of Emergency, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Mukhtar Adan Mumin
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Quan-Hui Xu
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ying-Han Wang
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jiang-Quan Zhu
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Hui Liang
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, Guangdong Province, People's Republic of China
| | - Zhu Wang
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, Guangdong Province, People's Republic of China
| | - Qiong Deng
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, Guangdong Province, People's Republic of China
| | - Wei Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiao-Han Jin
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China.
| | - Zhi-Ping Liu
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Jun-Hang Luo
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China.
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41
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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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42
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A systematic review of artificial intelligence-based COVID-19 modeling on multimodal genetic information. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 179:1-9. [PMID: 36809830 PMCID: PMC9938959 DOI: 10.1016/j.pbiomolbio.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/21/2023]
Abstract
This study systematically reviews the Artificial Intelligence (AI) methods developed to resolve the critical process of COVID-19 gene data analysis, including diagnosis, prognosis, biomarker discovery, drug responsiveness, and vaccine efficacy. This systematic review follows the guidelines of Preferred Reporting for Systematic Reviews and Meta-Analyses (PRISMA). We searched PubMed, Embase, Web of Science, and Scopus databases to identify the relevant articles from January 2020 to June 2022. It includes the published studies of AI-based COVID-19 gene modeling extracted through relevant keyword searches in academic databases. This study included 48 articles discussing AI-based genetic studies for several objectives. Ten articles confer about the COVID-19 gene modeling with computational tools, and five articles evaluated ML-based diagnosis with observed accuracy of 97% on SARS-CoV-2 classification. Gene-based prognosis study reviewed three articles and found host biomarkers detecting COVID-19 progression with 90% accuracy. Twelve manuscripts reviewed the prediction models with various genome analysis studies, nine articles examined the gene-based in silico drug discovery, and another nine investigated the AI-based vaccine development models. This study compiled the novel coronavirus gene biomarkers and targeted drugs identified through ML approaches from published clinical studies. This review provided sufficient evidence to delineate the potential of AI in analyzing complex gene information for COVID-19 modeling on multiple aspects like diagnosis, drug discovery, and disease dynamics. AI models entrenched a substantial positive impact by enhancing the efficiency of the healthcare system during the COVID-19 pandemic.
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43
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Towards precision medicine: Omics approach for COVID-19. BIOSAFETY AND HEALTH 2023; 5:78-88. [PMID: 36687209 PMCID: PMC9846903 DOI: 10.1016/j.bsheal.2023.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic had a devastating impact on human society. Beginning with genome surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the development of omics technologies brought a clearer understanding of the complex SARS-CoV-2 and COVID-19. Here, we reviewed how omics, including genomics, proteomics, single-cell multi-omics, and clinical phenomics, play roles in answering biological and clinical questions about COVID-19. Large-scale sequencing and advanced analysis methods facilitate COVID-19 discovery from virus evolution and severity risk prediction to potential treatment identification. Omics would indicate precise and globalized prevention and medicine for the COVID-19 pandemic under the utilization of big data capability and phenotypes refinement. Furthermore, decoding the evolution rule of SARS-CoV-2 by deep learning models is promising to forecast new variants and achieve more precise data to predict future pandemics and prevent them on time.
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44
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Zsichla L, Müller V. Risk Factors of Severe COVID-19: A Review of Host, Viral and Environmental Factors. Viruses 2023; 15:175. [PMID: 36680215 PMCID: PMC9863423 DOI: 10.3390/v15010175] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The clinical course and outcome of COVID-19 are highly variable, ranging from asymptomatic infections to severe disease and death. Understanding the risk factors of severe COVID-19 is relevant both in the clinical setting and at the epidemiological level. Here, we provide an overview of host, viral and environmental factors that have been shown or (in some cases) hypothesized to be associated with severe clinical outcomes. The factors considered in detail include the age and frailty, genetic polymorphisms, biological sex (and pregnancy), co- and superinfections, non-communicable comorbidities, immunological history, microbiota, and lifestyle of the patient; viral genetic variation and infecting dose; socioeconomic factors; and air pollution. For each category, we compile (sometimes conflicting) evidence for the association of the factor with COVID-19 outcomes (including the strength of the effect) and outline possible action mechanisms. We also discuss the complex interactions between the various risk factors.
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Affiliation(s)
- Levente Zsichla
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
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45
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Papageorgiou L, Papakonstantinou E, Diakou I, Pierouli K, Dragoumani K, Bacopoulou F, Chrousos GP, Eliopoulos E, Vlachakis D. Semantic and Population Analysis of the Genetic Targets Related to COVID-19 and Its Association with Genes and Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1423:59-78. [PMID: 37525033 DOI: 10.1007/978-3-031-31978-5_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
SARS-CoV-2 is a coronavirus responsible for one of the most serious, modern worldwide pandemics, with lasting and multifaceted effects. By late 2021, SARS-CoV-2 has infected more than 180 million people and has killed more than 3 million. The virus gains entrance to human cells through binding to ACE2 via its surface spike protein and causes a complex disease of the respiratory system, termed COVID-19. Vaccination efforts are being made to hinder the viral spread, and therapeutics are currently under development. Toward this goal, scientific attention is shifting toward variants and SNPs that affect factors of the disease such as susceptibility and severity. This genomic grammar, tightly related to the dark part of our genome, can be explored through the use of modern methods such as natural language processing. We present a semantic analysis of SARS-CoV-2-related publications, which yielded a repertoire of SNPs, genes, and disease ontologies. Population data from the 1000 Genomes Project were subsequently integrated into the pipeline. Data mining approaches of this scale have the potential to elucidate the complex interaction between COVID-19 pathogenesis and host genetic variation; the resulting knowledge can facilitate the management of high-risk groups and aid the efforts toward precision medicine.
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Affiliation(s)
- Louis Papageorgiou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Flora Bacopoulou
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - George P Chrousos
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece.
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece.
- Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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46
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Barmania F, Mellet J, Holborn MA, Pepper MS. Genetic Associations with Coronavirus Susceptibility and Disease Severity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:119-140. [PMID: 37378764 DOI: 10.1007/978-3-031-28012-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19) global public health emergency, and the disease it causes is highly variable in its clinical presentation. Host genetic factors are increasingly recognised as a determinant of infection susceptibility and disease severity. Several initiatives and groups have been established to analyse and review host genetic epidemiology associated with COVID-19 outcomes. Here, we review the genetic loci associated with COVID-19 susceptibility and severity focusing on the common variants identified in genome-wide association studies.
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Affiliation(s)
- Fatima Barmania
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juanita Mellet
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Megan A Holborn
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Michael S Pepper
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
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47
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Srivastava A, Hollenbach JA. The immunogenetics of COVID-19. Immunogenetics 2022; 75:309-320. [PMID: 36534127 PMCID: PMC9762652 DOI: 10.1007/s00251-022-01284-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/19/2022] [Indexed: 12/23/2022]
Abstract
The worldwide coronavirus disease 2019 pandemic was sparked by the severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2) that first surfaced in December 2019 (COVID-19). The effects of COVID-19 differ substantially not just between patients individually but also between populations with different ancestries. In humans, the human leukocyte antigen (HLA) system coordinates immune regulation. Since HLA molecules are a major component of antigen-presenting pathway, they play an important role in determining susceptibility to infectious disease. It is likely that differential susceptibility to SARS-CoV-2 infection and/or disease course in COVID-19 in different individuals could be influenced by the variations in the HLA genes which are associated with various immune responses to SARS-CoV-2. A growing number of studies have identified a connection between HLA variation and diverse COVID-19 outcomes. Here, we review research investigating the impact of HLA on individual responses to SARS-CoV-2 infection and/or progression, also discussing the significance of MHC-related immunological patterns and its use in vaccine design.
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Affiliation(s)
- Anshika Srivastava
- grid.266102.10000 0001 2297 6811University of California San Francisco, San Francisco, CA USA
| | - Jill A. Hollenbach
- grid.266102.10000 0001 2297 6811University of California San Francisco, San Francisco, CA USA
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48
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Ferreira LC, Gomes CE, Rodrigues-Neto JF, Jeronimo SM. Genome-wide association studies of COVID-19: Connecting the dots. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 106:105379. [PMID: 36280088 PMCID: PMC9584840 DOI: 10.1016/j.meegid.2022.105379] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/01/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022]
Abstract
Genome-wide association studies (GWASs) are a research approach used to identify genetic variants associated with common diseases, like COVID-19. The lead genetic variants (n = 41) reported by the eleven largest COVID-19 GWASs are mapped to 22 different chromosomal regions. The loci 3q21.31 (LZTFL1 and chemokine receptor genes) and 9q34.2 (ABO), associated with disease severity and susceptibility to infection, respectively, were the most replicated findings across studies. Genes involved with mucociliary clearance (CEP97, FOXP4), viral-entry (ACE2, SLC6A20) and mucosal immunity (MIR6891) are associated with the risk of SARS-CoV-2 infection while genes of antiviral immune response (IFNAR2, OAS1), leukocyte trafficking (CCR9, CXCR6) and lung injury (DPP9, NOTCH4) are associated with severe disease. The biological processes underlying the risk of infection occur prominently, but not exclusively, in the upper airways whereas the severe COVID-19-associated processes in alveolar-capillary interface. The COVID-19 GWASs has unraveled key genetic mechanisms of SARS-CoV-2 pathogenesis, although the genetic basis of other COVID-19 related phenotypes (long COVID and neurological impairment) remains to be elucidated.
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Affiliation(s)
- Leonardo C. Ferreira
- Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN 59078-900, Brazil,Institute of Tropical Medicine, Federal University of Rio Grande do Norte, Natal, RN 59078-900, Brazil,Corresponding author at: Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN 59078-900, Brazil
| | - Carlos E.M. Gomes
- Department of Biophysics and Pharmacology, Federal University of Rio Grande do Norte, Natal, RN 59078-900, Brazil
| | - João F. Rodrigues-Neto
- Institute of Tropical Medicine, Federal University of Rio Grande do Norte, Natal, RN 59078-900, Brazil,Multicampi School of Medical Sciences, Federal University of Rio Grande do Norte, Caicó, RN 59078-900, Brazil
| | - Selma M.B. Jeronimo
- Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN 59078-900, Brazil,Institute of Tropical Medicine, Federal University of Rio Grande do Norte, Natal, RN 59078-900, Brazil,Institute of Science and Technology of Tropical Diseases, Natal, RN, Brazil
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Traspov AA, Minashkin MM, Poyarkov SV, Komarov AG, Shtinova IA, Speshilov GI, Karbyshev IA, Pozdniakova NV, Godkov MA. The rs17713054 and rs1800629 polymorphisms of genes LZTFL1 and TNF are associated with COVID-19 severity. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2022. [DOI: 10.24075/brsmu.2022.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Both genetic and non-genetic factors are responsible for high interindividual variability in response to SARS-CoV-2. Despite the fact that multiple genetic polymorphisms have been identified as risk factors of severe COVID-19, such polymorphisms are still insufficiently studied in the Russian population. The study was aimed to identify genetic determinants associated with severe COVID-19 in the sample of patients from the Russian Federation. The correlation of the rs17713054 polymorphism in gene LZTFL1 and rs1800629 polymorphism in gene TNF (tumor necrosis factor) with the COVID-19 severity was assessed. DNA samples obtained from 713 patients (324 males and 389 females) aged 18‒95 with COVID-19 of varying severity were analyzed. The rs1800629 polymorphism of gene TNF (OR = 1.5; p = 0.02) and rs17713054 polymorphism of gene LZTFL1 (OR = 1.60; p = 0.0043) were identified as risk factors of severe disease. The TNF polymorphism rs1800629 and LZTFL1 polymorphism rs17713054 could be considered as potential predictive biomarkers. The rs17713054 G > A polymorphism was strongly associated with severe disease. In the future the findings may provide the basis for the development of test-systems for prediction of the risk of severe viral respiratory diseases.
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Affiliation(s)
| | | | | | - AG Komarov
- State Budget Institution Of Health Of The City Of Moscow "Diagnostic Center (Center For Laboratory Research) Of The Department Of Health Of The City Of Moscow" Russian Federation, , Moscow
| | - IA Shtinova
- State Budget Institution Of Health Of The City Of Moscow "Diagnostic Center (Center For Laboratory Research) Of The Department Of Health Of The City Of Moscow" Russian Federation, , Moscow
| | - GI Speshilov
- State Budget Institution Of Health Of The City Of Moscow "Diagnostic Center (Center For Laboratory Research) Of The Department Of Health Of The City Of Moscow" Russian Federation, , Moscow
| | - IA Karbyshev
- State Budget Institution Of Health Of The City Of Moscow "Diagnostic Center (Center For Laboratory Research) Of The Department Of Health Of The City Of Moscow" Russian Federation, , Moscow
| | | | - MA Godkov
- Sklifosovsky Research Institute for Emergency Medicine, Moscow, Russia
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50
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Li P, Ke Y, Shen W, Shi S, Wang Y, Lin K, Guo X, Wang C, Zhang Y, Zhao Z. Targeted screening of genetic associations with COVID-19 susceptibility and severity. Front Genet 2022; 13:1073880. [PMID: 36531218 PMCID: PMC9747945 DOI: 10.3389/fgene.2022.1073880] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/18/2022] [Indexed: 07/26/2023] Open
Abstract
The COVID-19 pandemic has resulted in great morbidity and mortality worldwide and human genetic factors have been implicated in the susceptibility and severity of COVID-19. However, few replicate researches have been performed, and studies on associated genes mainly focused on genic regions while regulatory regions were a lack of in-depth dissection. Here, based on previously reported associated variants and genes, we designed a capture panel covering 1,238 candidate variants and 25 regulatory regions of 19 candidate genes and targeted-sequenced 96 mild and 145 severe COVID-19 patients. Genetic association analysis was conducted between mild and severe COVID-19 patients, between all COVID-19 patients and general population, or between severe COVID-19 patients and general population. A total of 49 variants were confirmed to be associated with susceptibility or severity of COVID-19 (p < 0.05), corresponding to 18 independent loci. Specifically, rs1799964 in the promoter of inflammation-related gene TNF, rs9975538 in the intron of interferon receptor gene IFNAR2, rs429358 in the exon of APOE, rs1886814 in the intron of FOXP4-AS1 and a list of variants in the widely reported 3p21.31 and ABO gene were confirmed. It is worth noting that, for the confirmed variants, the phenotypes of the cases and controls were highly consistent between our study and previous reports, and the confirmed variants identified between mild and severe patients were quite different from those identified between patients and general population, suggesting the genetic basis of susceptibility and severity of SARS-CoV-2 infection might be quite different. Moreover, we newly identified 67 significant associated variants in the 12 regulatory regions of 11 candidate genes (p < 0.05). Further annotation by RegulomeDB database and GTEx eQTL data filtered out two variants (rs11246060 and rs28655829) in the enhancer of broad-spectrum antiviral gene IFITM3 that might affect disease severity by regulating the gene expression. Collectively, we confirmed a list of previously reported variants and identified novel regulatory variants associated with susceptibility and severity of COVID-19, which might provide biological and clinical insights into COVID-19 pathogenesis and treatment.
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Affiliation(s)
- Ping Li
- Beijing Institute of Biotechnology, Beijing, China
| | - Yuehua Ke
- Center for Disease Control and Prevention of PLA, Beijing, China
| | - Wenlong Shen
- Beijing Institute of Biotechnology, Beijing, China
| | - Shu Shi
- Beijing Institute of Biotechnology, Beijing, China
| | - Yahao Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Kailin Lin
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Xinjie Guo
- Beijing Institute of Biotechnology, Beijing, China
| | - Changjun Wang
- Center for Disease Control and Prevention of PLA, Beijing, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, Beijing, China
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