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Shi Q, Zhang P, Hu Q, Zhang T, Hou R, Yin S, Zou Y, Chen F, Jiao S, Si L, Zheng B, Chen Y, Zhan T, Liu Y, Zhu W, Qi N. Role of TOMM34 on NF-κB activation-related hyperinflammation in severely ill patients with COVID-19 and influenza. EBioMedicine 2024; 108:105343. [PMID: 39276680 DOI: 10.1016/j.ebiom.2024.105343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 08/21/2024] [Accepted: 09/02/2024] [Indexed: 09/17/2024] Open
Abstract
BACKGROUND Highly pathogenic respiratory RNA viruses such as SARS-CoV-2 and its associated syndrome COVID-19 pose a tremendous threat to the global public health. Innate immune responses to SARS-CoV-2 depend mainly upon the NF-κB-mediated inflammation. Identifying unknown host factors driving the NF-κB activation and inflammation is crucial for the development of immune intervention strategies. METHODS Published single-cell RNA sequencing (scRNA-seq) data was used to analyze the differential transcriptome profiles of bronchoalveolar lavage (BAL) cells between healthy individuals (n = 27) and patients with severe COVID-19 (n = 21), as well as the differential transcriptome profiles of peripheral blood mononuclear cells (PBMCs) between healthy individuals (n = 22) and severely ill patients with COVID-19 (n = 45) or influenza (n = 16). Loss-of-function and gain-of-function assays were performed in diverse viruses-infected cells and male mice models to identify the role of TOMM34 in antiviral innate immunity. FINDINGS TOMM34, together with a list of genes encoding pro-inflammatory cytokines and antiviral immune proteins, was transcriptionally upregulated in circulating monocytes, lung epithelium and innate immune cells from individuals with severe COVID-19 or influenza. Deficiency of TOMM34/Tomm34 significantly impaired the type I interferon responses and NF-κB-mediated inflammation in various human/murine cell lines, murine bone marrow-derived macrophages (BMDMs) and in vivo. Mechanistically, TOMM34 recruits TRAF6 to facilitate the K63-linked polyubiquitination of NEMO upon viral infection, thus promoting the downstream NF-κB activation. INTERPRETATION In this study, viral induction of TOMM34 is positively correlated with the hyperinflammation in severely ill patients with COVID-19 and influenza. Our findings also highlight the physiological role of TOMM34 in the innate antiviral signallings. FUNDING A full list of funding sources can be found in the acknowledgements section.
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Affiliation(s)
- Qiwen Shi
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Pengfei Zhang
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China
| | - Qingtao Hu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Tianxin Zhang
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China
| | - Ruixia Hou
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Shengxiang Yin
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China
| | - Yilin Zou
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China
| | - Fenghua Chen
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Shuang Jiao
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China
| | - Lanlan Si
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Bangjin Zheng
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China
| | - Yichao Chen
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China
| | - Tingzhu Zhan
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yongxiang Liu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China.
| | - Wenting Zhu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China.
| | - Nan Qi
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China; Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China.
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2
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Jia R, Li Z, Hu S, Chang H, Zeng M, Liu P, Lu L, Xu M, Zhai X, Qian M, Xu J. Immunological characterization and comparison of children with COVID-19 from their adult counterparts at single-cell resolution. Front Immunol 2024; 15:1358725. [PMID: 39148728 PMCID: PMC11325098 DOI: 10.3389/fimmu.2024.1358725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 07/17/2024] [Indexed: 08/17/2024] Open
Abstract
Introduction The immunological characteristics that could protect children with coronavirus disease 2019 (COVID-19) from severe or fatal illnesses have not been fully understood yet. Methods Here, we performed single-cell RNA sequencing (scRNA-seq) analysis on peripheral blood samples of 15 children (8 with COVID-19) and compared them to 18 adults (13 with COVID-19). Results The child-adult integrated single cell data indicated that children with the disease presented a restrained response to type I interferon in most of the major immune cell types, along with suppression of upstream interferon regulatory factor and toll-like receptor expression in monocytes, which was confirmed by in vitro interferon stimulation assays. Unlike adult patients, children with COVID-19 showed lower frequencies of activated proinflammatory CD14+ monocytes, possibly explaining the rareness of cytokine storm in them. Notably, natural killer (NK) cells in pediatric patients displayed potent cytotoxicity with a rich expression of cytotoxic molecules and upregulated cytotoxic pathways, whereas the cellular senescence, along with the Notch signaling pathway, was significantly downregulated in NK cells, all suggesting more robust cytotoxicity in NK cells of children than adult patients that was further confirmed by CD107a degranulation assays. Lastly, a modest adaptive immune response was evident with more naïve T cells but less activated and proliferated T cells while less naïve B cells but more activated B cells in children over adult patients. Conclusion Conclusively, this preliminary study revealed distinct cell frequency and activation status of major immune cell types, particularly more robust NK cell cytotoxicity in PBMC that might help protect children from severe COVID-19.
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Affiliation(s)
- Ran Jia
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Zifeng Li
- Department of Hematology and Oncology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Shiwen Hu
- Department of Hematology and Oncology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Hailing Chang
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Mei Zeng
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Pengcheng Liu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Lijuan Lu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Menghua Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xiaowen Zhai
- Department of Hematology and Oncology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Maoxiang Qian
- Institute of Pediatrics and Department of Hematology and Oncology, Children's Hospital of Fudan University, National Children's Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jin Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
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3
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Zhang Y, Xu F, Wang T, Han Z, Shang H, Han K, Zhu P, Gao S, Wang X, Xue Y, Huang C, Chen Y, Liu G. Shared genetics and causal association between plasma levels of SARS-CoV-2 entry receptor ACE2 and Alzheimer's disease. CNS Neurosci Ther 2024; 30:e14873. [PMID: 39056224 PMCID: PMC11273102 DOI: 10.1111/cns.14873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/26/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is the highest risk of COVID-19 infection, hospitalization, and mortality. However, it remains largely unclear about the link between AD and COVID-19 outcomes. ACE2 is an entry receptor for SARS-CoV-2. Circulating ACE2 is a novel biomarker of death and associated with COVID-19 outcomes. METHODS Here, we explored the shared genetics and causal association between AD and plasma ACE2 levels using large-scale genome-wide association study, gene expression, expression quantitative trait loci, and high-throughput plasma proteomic profiling datasets. RESULTS We found a significant causal effect of genetically increased circulating ACE2 on increased risk of AD. Cross-trait association analysis identified 19 shared genetic variants, and three variants rs3104412, rs2395166, and rs3135344 at chromosome 6p21.32 were associated with COVID-19 infection, hospitalization, and severity. We mapped 19 variants to 117 genes, which were significantly upregulated in lung, spleen, and small intestine, downregulated in brain tissues, and involved in immune system, immune disease, and infectious disease pathways. The plasma proteins corresponding to LST1, AGER, TNXB, and APOC1 were predominantly associated with COVID-19 infection, ventilation, and death. CONCLUSION Together, our findings suggest the shared genetics and causal association between AD and plasma ACE2 levels, which may partially explain the link between AD and COVID-19.
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Affiliation(s)
- Yan Zhang
- Department of PathologyThe Affiliated Hospital of Weifang Medical UniversityWeifangChina
| | - Fang Xu
- Department of Neurology, Xuanwu Hospital, National Center for Neurological DisordersCapital Medical UniversityBeijingChina
| | - Tao Wang
- Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina
- Chinese Institute for Brain ResearchBeijingChina
| | - Zhifa Han
- Center of Respiratory Medicine, China–Japan Friendship Hospital, National Center for Respiratory Medicine, Institute of Respiratory MedicineChinese Acadamy of Medical Sciences, National Clinical Research Center for Respiratory DiseasesBeijingChina
| | - Hong Shang
- Department of NeurologyThe Fourth Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Kevin Han
- Department of StatisticsStanford UniversityStanfordCaliforniaUSA
| | - Ping Zhu
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain DisordersCapital Medical UniversityBeijingChina
| | - Shan Gao
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain DisordersCapital Medical UniversityBeijingChina
| | - Xiaojie Wang
- Department of NeurologyShenzhen Qianhai Shekou Free Trade Zone HospitalShenzhenChina
| | - Yanli Xue
- School of Biomedical EngineeringCapital Medical UniversityBeijingChina
| | - Chen Huang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese MedicineMacau University of Science and TechnologyMacao SARChina
| | - Yan Chen
- Department of Epidemiology and Biostatistics, School of Public HealthWannan Medical CollegeWuhuChina
- Institute of Chronic Disease Prevention and ControlWannan Medical CollegeWuhuChina
| | - Guiyou Liu
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain DisordersCapital Medical UniversityBeijingChina
- Department of Epidemiology and Biostatistics, School of Public HealthWannan Medical CollegeWuhuChina
- Institute of Chronic Disease Prevention and ControlWannan Medical CollegeWuhuChina
- Beijing Key Laboratory of Hypoxia Translational Medicine, National Engineering Laboratory of Internet Medical Diagnosis and Treatment Technology, Xuanwu HospitalCapital Medical UniversityBeijingChina
- Taishan Vocational College of NursingTaianChina
- Brain HospitalShengli Oilfield Central HospitalDongyingChina
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4
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Gray-Gaillard SL, Solis SM, Chen HM, Monteiro C, Ciabattoni G, Samanovic MI, Cornelius AR, Williams T, Geesey E, Rodriguez M, Ortigoza MB, Ivanova EN, Koralov SB, Mulligan MJ, Herati RS. SARS-CoV-2 inflammation durably imprints memory CD4 T cells. Sci Immunol 2024; 9:eadj8526. [PMID: 38905326 DOI: 10.1126/sciimmunol.adj8526] [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: 07/25/2023] [Accepted: 05/30/2024] [Indexed: 06/23/2024]
Abstract
Memory CD4 T cells are critical to human immunity, yet it is unclear whether viral inflammation during memory formation has long-term consequences. Here, we compared transcriptional and epigenetic landscapes of Spike (S)-specific memory CD4 T cells in 24 individuals whose first exposure to S was via SARS-CoV-2 infection or mRNA vaccination. Nearly 2 years after memory formation, S-specific CD4 T cells established by infection remained enriched for transcripts related to cytotoxicity and for interferon-stimulated genes, likely because of a chromatin accessibility landscape altered by inflammation. Moreover, S-specific CD4 T cells primed by infection had reduced proliferative capacity in vitro relative to vaccine-primed cells. Furthermore, the transcriptional state of S-specific memory CD4 T cells was minimally altered by booster immunization and/or breakthrough infection. Thus, infection-associated inflammation durably imprints CD4 T cell memory, which affects the function of these cells and may have consequences for long-term immunity.
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Affiliation(s)
- Sophie L Gray-Gaillard
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Sabrina M Solis
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Han M Chen
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Clarice Monteiro
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Grace Ciabattoni
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Marie I Samanovic
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Amber R Cornelius
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Tijaana Williams
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Emilie Geesey
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Miguel Rodriguez
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Mila Brum Ortigoza
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Ellie N Ivanova
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Sergei B Koralov
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Mark J Mulligan
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Ramin Sedaghat Herati
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
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5
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Cooper L, Xu H, Polmear J, Kealy L, Szeto C, Pang ES, Gupta M, Kirn A, Taylor JJ, Jackson KJL, Broomfield BJ, Nguyen A, Gago da Graça C, La Gruta N, Utzschneider DT, Groom JR, Martelotto L, Parish IA, O'Keeffe M, Scharer CD, Gras S, Good-Jacobson KL. Type I interferons induce an epigenetically distinct memory B cell subset in chronic viral infection. Immunity 2024; 57:1037-1055.e6. [PMID: 38593796 PMCID: PMC11096045 DOI: 10.1016/j.immuni.2024.03.016] [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: 03/08/2023] [Revised: 11/02/2023] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
Memory B cells (MBCs) are key providers of long-lived immunity against infectious disease, yet in chronic viral infection, they do not produce effective protection. How chronic viral infection disrupts MBC development and whether such changes are reversible remain unknown. Through single-cell (sc)ATAC-seq and scRNA-seq during acute versus chronic lymphocytic choriomeningitis viral infection, we identified a memory subset enriched for interferon (IFN)-stimulated genes (ISGs) during chronic infection that was distinct from the T-bet+ subset normally associated with chronic infection. Blockade of IFNAR-1 early in infection transformed the chromatin landscape of chronic MBCs, decreasing accessibility at ISG-inducing transcription factor binding motifs and inducing phenotypic changes in the dominating MBC subset, with a decrease in the ISG subset and an increase in CD11c+CD80+ cells. However, timing was critical, with MBCs resistant to intervention at 4 weeks post-infection. Together, our research identifies a key mechanism to instruct MBC identity during viral infection.
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Affiliation(s)
- Lucy Cooper
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Hui Xu
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jack Polmear
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Liam Kealy
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Christopher Szeto
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Ee Shan Pang
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Mansi Gupta
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Alana Kirn
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Benjamin J Broomfield
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia; Division of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Angela Nguyen
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Catarina Gago da Graça
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Nicole La Gruta
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Daniel T Utzschneider
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Joanna R Groom
- Division of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Luciano Martelotto
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia; University of Melbourne Centre for Cancer Research, Victoria Comprehensive Cancer Centre, Melbourne, VIC, Australia
| | - Ian A Parish
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia; John Curtin School of Medical Research, ANU, Canberra, ACT, Australia
| | - Meredith O'Keeffe
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Christopher D Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Kim L Good-Jacobson
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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6
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Zheng C, Wang Y, Cheng Y, Wang X, Wei H, King I, Li Y. scNovel: a scalable deep learning-based network for novel rare cell discovery in single-cell transcriptomics. Brief Bioinform 2024; 25:bbae112. [PMID: 38555470 PMCID: PMC10981759 DOI: 10.1093/bib/bbae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/05/2024] [Accepted: 02/20/2024] [Indexed: 04/02/2024] Open
Abstract
Single-cell RNA sequencing has achieved massive success in biological research fields. Discovering novel cell types from single-cell transcriptomics has been demonstrated to be essential in the field of biomedicine, yet is time-consuming and needs prior knowledge. With the unprecedented boom in cell atlases, auto-annotation tools have become more prevalent due to their speed, accuracy and user-friendly features. However, existing tools have mostly focused on general cell-type annotation and have not adequately addressed the challenge of discovering novel rare cell types. In this work, we introduce scNovel, a powerful deep learning-based neural network that specifically focuses on novel rare cell discovery. By testing our model on diverse datasets with different scales, protocols and degrees of imbalance, we demonstrate that scNovel significantly outperforms previous state-of-the-art novel cell detection models, reaching the most AUROC performance(the only one method whose averaged AUROC results are above 94%, up to 16.26% more comparing to the second-best method). We validate scNovel's performance on a million-scale dataset to illustrate the scalability of scNovel further. Applying scNovel on a clinical COVID-19 dataset, three potential novel subtypes of Macrophages are identified, where the COVID-related differential genes are also detected to have consistent expression patterns through deeper analysis. We believe that our proposed pipeline will be an important tool for high-throughput clinical data in a wide range of applications.
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Affiliation(s)
- Chuanyang Zheng
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, China
| | - Yixuan Wang
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, China
| | - Yuqi Cheng
- College of Computing, Georgia Institute of Technology, Atlanta, GA, USA
| | - Xuesong Wang
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, China
| | - Hongxin Wei
- MLR Lab, Southern University of Science and Technology
| | - Irwin King
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, China
| | - Yu Li
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, China
- The CUHK Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China
- Institute for Medical Enginering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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7
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Kole A, Bag AK, Pal AJ, De D. Generic model to unravel the deeper insights of viral infections: an empirical application of evolutionary graph coloring in computational network biology. BMC Bioinformatics 2024; 25:74. [PMID: 38365632 PMCID: PMC10874019 DOI: 10.1186/s12859-024-05690-0] [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: 11/22/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
PURPOSE Graph coloring approach has emerged as a valuable problem-solving tool for both theoretical and practical aspects across various scientific disciplines, including biology. In this study, we demonstrate the graph coloring's effectiveness in computational network biology, more precisely in analyzing protein-protein interaction (PPI) networks to gain insights about the viral infections and its consequences on human health. Accordingly, we propose a generic model that can highlight important hub proteins of virus-associated disease manifestations, changes in disease-associated biological pathways, potential drug targets and respective drugs. We test our model on SARS-CoV-2 infection, a highly transmissible virus responsible for the COVID-19 pandemic. The pandemic took significant human lives, causing severe respiratory illnesses and exhibiting various symptoms ranging from fever and cough to gastrointestinal, cardiac, renal, neurological, and other manifestations. METHODS To investigate the underlying mechanisms of SARS-CoV-2 infection-induced dysregulation of human pathobiology, we construct a two-level PPI network and employed a differential evolution-based graph coloring (DEGCP) algorithm to identify critical hub proteins that might serve as potential targets for resolving the associated issues. Initially, we concentrate on the direct human interactors of SARS-CoV-2 proteins to construct the first-level PPI network and subsequently applied the DEGCP algorithm to identify essential hub proteins within this network. We then build a second-level PPI network by incorporating the next-level human interactors of the first-level hub proteins and use the DEGCP algorithm to predict the second level of hub proteins. RESULTS We first identify the potential crucial hub proteins associated with SARS-CoV-2 infection at different levels. Through comprehensive analysis, we then investigate the cellular localization, interactions with other viral families, involvement in biological pathways and processes, functional attributes, gene regulation capabilities as transcription factors, and their associations with disease-associated symptoms of these identified hub proteins. Our findings highlight the significance of these hub proteins and their intricate connections with disease pathophysiology. Furthermore, we predict potential drug targets among the hub proteins and identify specific drugs that hold promise in preventing or treating SARS-CoV-2 infection and its consequences. CONCLUSION Our generic model demonstrates the effectiveness of DEGCP algorithm in analyzing biological PPI networks, provides valuable insights into disease biology, and offers a basis for developing novel therapeutic strategies for other viral infections that may cause future pandemic.
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Affiliation(s)
- Arnab Kole
- Department of Computer Application, The Heritage Academy, Kolkata, W.B., 700107, India.
| | - Arup Kumar Bag
- Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | | | - Debashis De
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, Nadia, W.B., 741249, India
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8
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McClain MT, Zhbannikov I, Satterwhite LL, Henao R, Giroux NS, Ding S, Burke TW, Tsalik EL, Nix C, Balcazar JP, Petzold EA, Shen X, Woods CW. Epigenetic and transcriptional responses in circulating leukocytes are associated with future decompensation during SARS-CoV-2 infection. iScience 2024; 27:108288. [PMID: 38179063 PMCID: PMC10765013 DOI: 10.1016/j.isci.2023.108288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 08/03/2023] [Accepted: 10/18/2023] [Indexed: 01/06/2024] Open
Abstract
To elucidate host response elements that define impending decompensation during SARS-CoV-2 infection, we enrolled subjects hospitalized with COVID-19 who were matched for disease severity and comorbidities at the time of admission. We performed combined single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) on peripheral blood mononuclear cells (PBMCs) at admission and compared subjects who improved from their moderate disease with those who later clinically decompensated and required invasive mechanical ventilation or died. Chromatin accessibility and transcriptomic immune profiles were markedly altered between the two groups, with strong signals in CD4+ T cells, inflammatory T cells, dendritic cells, and NK cells. Multiomic signature scores at admission were tightly associated with future clinical deterioration (auROC 1.0). Epigenetic and transcriptional changes in PBMCs reveal early, broad immune dysregulation before typical clinical signs of decompensation are apparent and thus may act as biomarkers to predict future severity in COVID-19.
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Affiliation(s)
- Micah T. McClain
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710, USA
- Durham Veterans Affairs Medical Center, Durham, NC 27705, USA
| | - Ilya Zhbannikov
- Department of Medicine, Clinical Research Unit, Duke University Medical Center, Durham, NC 27710, USA
| | - Lisa L. Satterwhite
- Department of Civil and Environmental Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Ricardo Henao
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicholas S. Giroux
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Shengli Ding
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Thomas W. Burke
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Christina Nix
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710, USA
| | - Jorge Prado Balcazar
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Elizabeth A. Petzold
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiling Shen
- Terasaki Institute for Biological Innovation, Los Angeles, CA 90024, USA
| | - Christopher W. Woods
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710, USA
- Durham Veterans Affairs Medical Center, Durham, NC 27705, USA
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9
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Huang B, Huang J, Chiang NH, Chen Z, Lui G, Ling L, Kwan MYW, Wong JSC, Mak PQ, Ling JWH, Lam ICS, Ng RWY, Wang X, Gao R, Hui DSC, Ma SL, Chan PKS, Tang NLS. Interferon response and profiling of interferon response genes in peripheral blood of vaccine-naive COVID-19 patients. Front Immunol 2024; 14:1315602. [PMID: 38268924 PMCID: PMC10806211 DOI: 10.3389/fimmu.2023.1315602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/18/2023] [Indexed: 01/26/2024] Open
Abstract
Introduction There is insufficient understanding on systemic interferon (IFN) responses during COVID-19 infection. Early reports indicated that interferon responses were suppressed by the coronavirus (SARS-CoV-2) and clinical trials of administration of various kinds of interferons had been disappointing. Expression of interferon-stimulated genes (ISGs) in peripheral blood (better known as interferon score) has been a well-established bioassay marker of systemic IFN responses in autoimmune diseases. Therefore, with archival samples of a cohort of COVID-19 patients collected before the availability of vaccination, we aimed to better understand this innate immune response by studying the IFN score and related ISGs expression in bulk and single cell RNAs sequencing expression datasets. Methods In this study, we recruited 105 patients with COVID-19 and 30 healthy controls in Hong Kong. Clinical risk factors, disease course, and blood sampling times were recovered. Based on a set of five commonly used ISGs (IFIT1, IFIT2, IFI27, SIGLEC1, IFI44L), the IFN score was determined in blood leukocytes collected within 10 days after onset. The analysis was confined to those blood samples collected within 10 days after disease onset. Additional public datasets of bulk gene and single cell RNA sequencing of blood samples were used for the validation of IFN score results. Results Compared to the healthy controls, we showed that ISGs expression and IFN score were significantly increased during the first 10 days after COVID infection in majority of patients (71%). Among those low IFN responders, they were more commonly asymptomatic patients (71% vs 25%). 22 patients did not mount an overall significant IFN response and were classified as low IFN responders (IFN score < 1). However, early IFN score or ISGs level was not a prognostic biomarker and could not predict subsequent disease severity. Both IFI27 and SIGLEC1 were monocyte-predominant expressing ISGs and IFI27 were activated even among those low IFN responders as defined by IFN score. In conclusion, a substantial IFN response was documented in this cohort of COVID-19 patients who experience a natural infection before the vaccination era. Like innate immunity towards other virus, the ISGs activation was observed largely during the early course of infection (before day 10). Single-cell RNA sequencing data suggested monocytes were the cell-type that primarily accounted for the activation of two highly responsive ISGs (IFI44L and IFI27). Discussion As sampling time and age were two major confounders of ISG expression, they may account for contradicting observations among previous studies. On the other hand, the IFN score was not associated with the severity of the disease.
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Affiliation(s)
- Baozhen Huang
- Department of Chemical Pathology, and Li Ka Shing Institute of Health Science, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jinghan Huang
- Department of Chemical Pathology, and Li Ka Shing Institute of Health Science, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Nim Hang Chiang
- Department of Chemical Pathology, and Li Ka Shing Institute of Health Science, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Grace Lui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Mike Yat Wah Kwan
- Paediatric Infectious Disease Unit, Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, Hong Kong SAR, China
| | - Joshua Sung Chih Wong
- Paediatric Infectious Disease Unit, Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, Hong Kong SAR, China
| | - Phoebe Qiaozhen Mak
- Paediatric Infectious Disease Unit, Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, Hong Kong SAR, China
| | - Janet Wan Hei Ling
- Paediatric Infectious Disease Unit, Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, Hong Kong SAR, China
| | - Ivan Cheuk San Lam
- Paediatric Infectious Disease Unit, Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, Hong Kong SAR, China
| | - Rita Wai Yin Ng
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Xingyan Wang
- Department of Chemical Pathology, and Li Ka Shing Institute of Health Science, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Ruonan Gao
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - David Shu-Cheong Hui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Suk Ling Ma
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Paul K. S. Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Nelson Leung Sang Tang
- Department of Chemical Pathology, and Li Ka Shing Institute of Health Science, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Hong Kong, Hong Kong SAR, China
- Functional Genomics and Biostatistical Computing Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China
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10
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Liu H, Wang J, Li S, Sun Y, Zhang P, Ma J. The unfolded protein response pathway as a possible link in the pathogenesis of COVID-19 and sepsis. Arch Virol 2024; 169:20. [PMID: 38191819 DOI: 10.1007/s00705-023-05948-7] [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: 09/22/2023] [Accepted: 11/10/2023] [Indexed: 01/10/2024]
Abstract
The global impact of the COVID-19 pandemic has been substantial. Emerging evidence underscores a strong clinical connection between COVID-19 and sepsis. Numerous studies have identified the unfolded protein response (UPR) pathway as a crucial pathogenic pathway for both COVID-19 and sepsis, but it remains to be investigated whether this signaling pathway operates as a common pathogenic mechanism for both COVID-19 and sepsis. In this study, single-cell RNA-seq data and transcriptome data for COVID-19 and sepsis cases were downloaded from GEO (Gene Expression Omnibus). By analyzing the single-cell transcriptome data, we identified B cells as the critical cell subset and the UPR pathway as the critical signaling pathway. Based on the transcriptome data, a machine learning diagnostic model was then constructed using the interleaved genes of B-cell-related and UPR-pathway-related genes. We validated the diagnostic model using both internal and external datasets and found the accuracy and stability of this model to be extremely strong. Even after integrating our algorithmic model with the patient's clinical status, it continued to yield identical results, further emphasizing the reliability of this model. This study provides a novel molecular perspective on the pathogenesis of sepsis and COVID-19 at the single-cell level and suggests that these two diseases may share a common mechanism.
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Affiliation(s)
- Hong Liu
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Junyi Wang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong, China
| | - Shaofeng Li
- School of Pharmacy, Key Laboratory of Nano-carbon Modified Film Technology of Henan Province, Diagnostic Laboratory of Animal Diseases, Xinxiang University, Xinxiang, China
| | - Yanmei Sun
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Peng Zhang
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jiahao Ma
- School of Pharmacy, Key Laboratory of Nano-carbon Modified Film Technology of Henan Province, Diagnostic Laboratory of Animal Diseases, Xinxiang University, Xinxiang, China.
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11
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Lee Y, Song J, Jeong Y, Choi E, Ahn C, Jang W. Meta-analysis of single-cell RNA-sequencing data for depicting the transcriptomic landscape of chronic obstructive pulmonary disease. Comput Biol Med 2023; 167:107685. [PMID: 37976829 DOI: 10.1016/j.compbiomed.2023.107685] [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: 07/24/2023] [Revised: 10/17/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a respiratory disease characterized by airflow limitation and chronic inflammation of the lungs that is a leading cause of death worldwide. Since the complete pathological mechanisms at the single-cell level are not fully understood yet, an integrative approach to characterizing the single-cell-resolution landscape of COPD is required. To identify the cell types and mechanisms associated with the development of COPD, we conducted a meta-analysis using three single-cell RNA-sequencing datasets of COPD. Among the 154,011 cells from 16 COPD patients and 18 healthy subjects, 17 distinct cell types were observed. Of the 17 cell types, monocytes, mast cells, and alveolar type 2 cells (AT2 cells) were found to be etiologically implicated in COPD based on genetic and transcriptomic features. The most transcriptomically diversified states of the three etiological cell types showed significant enrichment in immune/inflammatory responses (monocytes and mast cells) and/or mitochondrial dysfunction (monocytes and AT2 cells). We then identified three chemical candidates that may potentially induce COPD by modulating gene expression patterns in the three etiological cell types. Overall, our study suggests the single-cell level mechanisms underlying the pathogenesis of COPD and may provide information on toxic compounds that could be potential risk factors for COPD.
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Affiliation(s)
- Yubin Lee
- Department of Life Sciences, Dongguk University, Seoul, 04620, Republic of Korea.
| | - Jaeseung Song
- Department of Life Sciences, Dongguk University, Seoul, 04620, Republic of Korea.
| | - Yeonbin Jeong
- Department of Life Sciences, Dongguk University, Seoul, 04620, Republic of Korea.
| | - Eunyoung Choi
- Department of Life Sciences, Dongguk University, Seoul, 04620, Republic of Korea.
| | - Chulwoo Ahn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| | - Wonhee Jang
- Department of Life Sciences, Dongguk University, Seoul, 04620, Republic of Korea.
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12
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Liu Y, Yang Y, Wang G, Wang D, Shao PL, Tang J, He T, Zheng J, Hu R, Liu Y, Xu Z, Niu D, Lv J, Yang J, Xiao H, Wu S, He S, Tang Z, Liu Y, Tang M, Jiang X, Yuan J, Dai H, Zhang B. Multiplexed discrimination of SARS-CoV-2 variants via plasmonic-enhanced fluorescence in a portable and automated device. Nat Biomed Eng 2023; 7:1636-1648. [PMID: 37735541 DOI: 10.1038/s41551-023-01092-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 08/17/2023] [Indexed: 09/23/2023]
Abstract
Portable assays for the rapid identification of lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to aid large-scale efforts in monitoring the evolution of the virus. Here we report a multiplexed assay in a microarray format for the detection, via isothermal amplification and plasmonic-gold-enhanced near-infrared fluorescence, of variants of SARS-CoV-2. The assay, which has single-nucleotide specificity for variant discrimination, single-RNA-copy sensitivity and does not require RNA extraction, discriminated 12 lineages of SARS-CoV-2 (in three mutational hotspots of the Spike protein) and detected the virus in nasopharyngeal swabs from 1,034 individuals at 98.8% sensitivity and 100% specificity, with 97.6% concordance with genome sequencing in variant discrimination. We also report a compact, portable and fully automated device integrating the entire swab-to-result workflow and amenable to the point-of-care detection of SARS-CoV-2 variants. Portable, rapid, accurate and multiplexed assays for the detection of SARS-CoV-2 variants and lineages may facilitate variant-surveillance efforts.
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Affiliation(s)
- Ying Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Guanghui Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dou Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Pan-Lin Shao
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target and Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiahu Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Tingzhen He
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jintao Zheng
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Ruibin Hu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yiyi Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Ziyi Xu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dan Niu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jiahui Lv
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jingkai Yang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Hongjun Xiao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Shuai Wu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Shuang He
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Zhongrong Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yan Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | | | - Xingyu Jiang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
| | - Jing Yuan
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China.
| | - Hongjie Dai
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Bo Zhang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
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13
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Yuan D, Mancuso N. SuSiE PCA: A scalable Bayesian variable selection technique for principal component analysis. iScience 2023; 26:108181. [PMID: 37953948 PMCID: PMC10638022 DOI: 10.1016/j.isci.2023.108181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/20/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
Latent factor models, like principal component analysis (PCA), provide a statistical framework to infer low-rank representation in various biological contexts. However, feature selection is challenging when this low-rank structure manifests from a sparse subspace. We introduce SuSiE PCA, a scalable sparse latent factor approach that evaluates uncertainty in contributing variables through posterior inclusion probabilities. We validate our model in extensive simulations and demonstrate that SuSiE PCA outperforms other approaches in signal detection and model robustness. We apply SuSiE PCA to multi-tissue expression quantitative trait loci (eQTLs) data from GTEx v8 and identify tissue-specific factors and their contributing eGenes. We further investigate its performance on the large-scale perturbation data and find that SuSiE PCA identifies modules with a higher enrichment of ribosome-related genes than sparse PCA (false discovery rate [FDR] = 9.2 × 10 - 82 vs. 1.4 × 10 - 33 ), while being ∼ 18x faster. Overall, SuSiE PCA provides an efficient tool to identify relevant features in high-dimensional biological data.
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Affiliation(s)
- Dong Yuan
- Biostatistics Division, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Nicholas Mancuso
- Biostatistics Division, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
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14
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Amrute JM, Lai L, Ma P, Koenig AL, Kamimoto K, Bredemeyer A, Shankar TS, Kuppe C, Kadyrov FF, Schulte LJ, Stoutenburg D, Kopecky BJ, Navankasattusas S, Visker J, Morris SA, Kramann R, Leuschner F, Mann DL, Drakos SG, Lavine KJ. Defining cardiac functional recovery in end-stage heart failure at single-cell resolution. NATURE CARDIOVASCULAR RESEARCH 2023; 2:399-416. [PMID: 37583573 PMCID: PMC10426763 DOI: 10.1038/s44161-023-00260-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/01/2023] [Indexed: 08/17/2023]
Abstract
Recovery of cardiac function is the holy grail of heart failure therapy yet is infrequently observed and remains poorly understood. In this study, we performed single-nucleus RNA sequencing from patients with heart failure who recovered left ventricular systolic function after left ventricular assist device implantation, patients who did not recover and non-diseased donors. We identified cell-specific transcriptional signatures of recovery, most prominently in macrophages and fibroblasts. Within these cell types, inflammatory signatures were negative predictors of recovery, and downregulation of RUNX1 was associated with recovery. In silico perturbation of RUNX1 in macrophages and fibroblasts recapitulated the transcriptional state of recovery. Cardiac recovery mediated by BET inhibition in mice led to decreased macrophage and fibroblast Runx1 expression and diminished chromatin accessibility within a Runx1 intronic peak and acquisition of human recovery signatures. These findings suggest that cardiac recovery is a unique biological state and identify RUNX1 as a possible therapeutic target to facilitate cardiac recovery.
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Affiliation(s)
- Junedh M. Amrute
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- These authors contributed equally: Junedh M. Amrute, Lulu Lai
| | - Lulu Lai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- These authors contributed equally: Junedh M. Amrute, Lulu Lai
| | - Pan Ma
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew L. Koenig
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrea Bredemeyer
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Thirupura S. Shankar
- Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT, USA
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology and Division of Nephrology, RWTH Aachen University, Aachen, Germany
| | - Farid F. Kadyrov
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Linda J. Schulte
- Division of Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Dylan Stoutenburg
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Benjamin J. Kopecky
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sutip Navankasattusas
- Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT, USA
| | - Joseph Visker
- Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT, USA
| | - Samantha A. Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology and Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Florian Leuschner
- Department of Cardiology, University Hospital Heidelberg, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg, Heidelberg, Germany
| | - Douglas L. Mann
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Stavros G. Drakos
- Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT, USA
| | - Kory J. Lavine
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
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15
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Girard TJ, Antunes L, Zhang N, Amrute JM, Subramanian R, Eldem I, Remy KE, Mazer M, Erlich EC, Cruchaga C, Steed AL, Randolph GJ, Di Paola J. Peripheral blood mononuclear cell tissue factor (F3 gene) transcript levels and circulating extracellular vesicles are elevated in severe coronavirus 2019 (COVID-19) disease. J Thromb Haemost 2023; 21:629-638. [PMID: 36696180 PMCID: PMC9773443 DOI: 10.1016/j.jtha.2022.11.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 10/20/2022] [Accepted: 11/01/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with excessive coagulation, thrombosis, and mortality. OBJECTIVE To provide insight into mechanisms that contribute to excessive coagulation in coronavirus 2019 (COVID-19) disease. PATIENTS/METHODS Blood from COVID-19 patients was investigated for coagulation-related gene expression and functional activities. RESULTS Single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells from severe COVID-19 patients revealed a 5.2-fold increase in tissue factor (TF [F3 gene]) transcript expression levels (P < .05), the trigger of extrinsic coagulation; a 7.7-fold increase in C1-inhibitor (SERPING1 gene; P < .01) transcript expression levels, an inhibitor of intrinsic coagulation; and a 4.4-fold increase in anticoagulant thrombomodulin (TM [THBD gene]) transcript expression levels (P < .001). Bulk RNA-seq analysis of sorted CD14+ monocytes on an independent cohort of COVID-19 patients confirmed these findings (P < .05). Indicative of excessive coagulation, 41% of COVID-19 patients' plasma samples contained high D-dimer levels (P < .0001); of these, 19% demonstrated extracellular vesicle TF activity (P = .109). COVID-19 patients' ex vivo plasma-based thrombin generation correlated positively with D-dimer levels (P < .01). Plasma procoagulant extracellular vesicles were elevated ∼9-fold in COVID-19 patients (P < .01). Public scRNA-seq data sets from bronchoalveolar lung fluid and our peripheral blood mononuclear cell scRNA-seq data show CD14+ monocytes/macrophages TF transcript expression levels are elevated in severe but not mild or moderate COVID-19 patients. CONCLUSIONS Beyond local lung injury, SARS-CoV-2 infection increases systemic TF (F3) transcript levels and elevates circulating extracellular vesicles that likely contribute to disease-associated coagulation, thrombosis, and related mortality.
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Affiliation(s)
- Thomas J Girard
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lilian Antunes
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nan Zhang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Junedh M Amrute
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Renumathi Subramanian
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Irem Eldem
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kenneth E Remy
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Monty Mazer
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Emma C Erlich
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ashley L Steed
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gwendalyn J Randolph
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jorge Di Paola
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.
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16
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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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Brown B, Ojha V, Fricke I, Al-Sheboul SA, Imarogbe C, Gravier T, Green M, Peterson L, Koutsaroff IP, Demir A, Andrieu J, Leow CY, Leow CH. Innate and Adaptive Immunity during SARS-CoV-2 Infection: Biomolecular Cellular Markers and Mechanisms. Vaccines (Basel) 2023; 11:408. [PMID: 36851285 PMCID: PMC9962967 DOI: 10.3390/vaccines11020408] [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: 12/18/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/16/2023] Open
Abstract
The coronavirus 2019 (COVID-19) pandemic was caused by a positive sense single-stranded RNA (ssRNA) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, other human coronaviruses (hCoVs) exist. Historical pandemics include smallpox and influenza, with efficacious therapeutics utilized to reduce overall disease burden through effectively targeting a competent host immune system response. The immune system is composed of primary/secondary lymphoid structures with initially eight types of immune cell types, and many other subtypes, traversing cell membranes utilizing cell signaling cascades that contribute towards clearance of pathogenic proteins. Other proteins discussed include cluster of differentiation (CD) markers, major histocompatibility complexes (MHC), pleiotropic interleukins (IL), and chemokines (CXC). The historical concepts of host immunity are the innate and adaptive immune systems. The adaptive immune system is represented by T cells, B cells, and antibodies. The innate immune system is represented by macrophages, neutrophils, dendritic cells, and the complement system. Other viruses can affect and regulate cell cycle progression for example, in cancers that include human papillomavirus (HPV: cervical carcinoma), Epstein-Barr virus (EBV: lymphoma), Hepatitis B and C (HB/HC: hepatocellular carcinoma) and human T cell Leukemia Virus-1 (T cell leukemia). Bacterial infections also increase the risk of developing cancer (e.g., Helicobacter pylori). Viral and bacterial factors can cause both morbidity and mortality alongside being transmitted within clinical and community settings through affecting a host immune response. Therefore, it is appropriate to contextualize advances in single cell sequencing in conjunction with other laboratory techniques allowing insights into immune cell characterization. These developments offer improved clarity and understanding that overlap with autoimmune conditions that could be affected by innate B cells (B1+ or marginal zone cells) or adaptive T cell responses to SARS-CoV-2 infection and other pathologies. Thus, this review starts with an introduction into host respiratory infection before examining invaluable cellular messenger proteins and then individual immune cell markers.
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Affiliation(s)
| | | | - Ingo Fricke
- Independent Immunologist and Researcher, 311995 Lamspringe, Germany
| | - Suhaila A Al-Sheboul
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
- Department of Medical Microbiology, International School of Medicine, Medipol University-Istanbul, Istanbul 34810, Turkey
| | | | - Tanya Gravier
- Independent Researcher, MPH, San Francisco, CA 94131, USA
| | | | | | | | - Ayça Demir
- Faculty of Medicine, Afyonkarahisar University, Istanbul 03030, Turkey
| | - Jonatane Andrieu
- Faculté de Médecine, Aix–Marseille University, 13005 Marseille, France
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, USM, Penang 11800, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine, (INFORMM), Universiti Sains Malaysia, USM, Penang 11800, Malaysia
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Avila-Ponce de León U, Vazquez-Jimenez A, Cervera A, Resendis-González G, Neri-Rosario D, Resendis-Antonio O. Machine Learning and COVID-19: Lessons from SARS-CoV-2. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:311-335. [PMID: 37378775 DOI: 10.1007/978-3-031-28012-2_17] [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
Currently, methods in machine learning have opened a significant number of applications to construct classifiers with capacities to recognize, identify, and interpret patterns hidden in massive amounts of data. This technology has been used to solve a variety of social and health issues against coronavirus disease 2019 (COVID-19). In this chapter, we present some supervised and unsupervised machine learning techniques that have contributed in three aspects to supplying information to health authorities and diminishing the deadly effects of the current worldwide outbreak on the population. First is the identification and construction of powerful classifiers capable of predicting severe, moderate, or asymptomatic responses in COVID-19 patients starting from clinical or high-throughput technologies. Second is the identification of groups of patients with similar physiological responses to improve the triage classification and inform treatments. The final aspect is the combination of machine learning methods and schemes from systems biology to link associative studies with mechanistic frameworks. This chapter aims to discuss some practical applications in the use of machine learning techniques to handle data coming from social behavior and high-throughput technologies, associated with COVID-19 evolution.
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Affiliation(s)
- Ugo Avila-Ponce de León
- Programa de Doctorado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, Mexico
| | - Aarón Vazquez-Jimenez
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, Mexico
| | - Alejandra Cervera
- Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, Mexico
| | - Galilea Resendis-González
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, Mexico
| | - Daniel Neri-Rosario
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, Mexico
| | - Osbaldo Resendis-Antonio
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, Mexico.
- Coordinación de la Investigación Científica - Red de Apoyo a la Investigación - Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico.
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Dang W, Tao Y, Xu X, Zhao H, Zou L, Li Y. The role of lung macrophages in acute respiratory distress syndrome. Inflamm Res 2022; 71:1417-1432. [PMID: 36264361 PMCID: PMC9582389 DOI: 10.1007/s00011-022-01645-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/22/2022] [Accepted: 09/14/2022] [Indexed: 11/25/2022] Open
Abstract
Acute respiratory distress syndrome (ARDS) is an acute and diffuse inflammatory lung injury in a short time, one of the common severe manifestations of the respiratory system that endangers human life and health. As an innate immune cell, macrophages play a key role in the inflammatory response. For a long time, the role of pulmonary macrophages in ARDS has tended to revolve around the polarization of M1/M2. However, with the development of single-cell RNA sequencing, fate mapping, metabolomics, and other new technologies, a deeper understanding of the development process, classification, and function of macrophages in the lung are acquired. Here, we discuss the function of pulmonary macrophages in ARDS from the two dimensions of anatomical location and cell origin and describe the effects of cell metabolism and intercellular interaction on the function of macrophages. Besides, we explore the treatments for targeting macrophages, such as enhancing macrophage phagocytosis, regulating macrophage recruitment, and macrophage death. Considering the differences in responsiveness of different research groups to these treatments and the tremendous dynamic changes in the gene expression of monocyte/macrophage, we discussed the possibility of characterizing the gene expression of monocyte/macrophage as the biomarkers. We hope that this review will provide new insight into pulmonary macrophage function and therapeutic targets of ARDS.
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Affiliation(s)
- Wenpei Dang
- Department of Intensive Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
- Department of Emergency, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Yiming Tao
- Department of Intensive Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
- Department of Emergency, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Xinxin Xu
- Department of Intensive Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
- Department of Emergency, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Hui Zhao
- Department of Intensive Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
- Department of Emergency, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Lijuan Zou
- Department of Intensive Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
- Department of Emergency, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Yongsheng Li
- Department of Intensive Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China.
- Department of Emergency, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China.
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Giannella A, Riccetti S, Sinigaglia A, Piubelli C, Razzaboni E, Di Battista P, Agostini M, Dal Molin E, Manganelli R, Gobbi F, Ceolotto G, Barzon L. Circulating microRNA signatures associated with disease severity and outcome in COVID-19 patients. Front Immunol 2022; 13:968991. [PMID: 36032130 PMCID: PMC9403711 DOI: 10.3389/fimmu.2022.968991] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/20/2022] [Indexed: 12/14/2022] Open
Abstract
Background SARS-CoV-2 induces a spectrum of clinical conditions ranging from asymptomatic infection to life threatening severe disease. Host microRNAs have been involved in the cytokine storm driven by SARS-CoV-2 infection and proposed as candidate biomarkers for COVID-19. Methods To discover signatures of circulating miRNAs associated with COVID-19, disease severity and mortality, small RNA-sequencing was performed on serum samples collected from 89 COVID-19 patients (34 severe, 29 moderate, 26 mild) at hospital admission and from 45 healthy controls (HC). To search for possible sources of miRNAs, investigation of differentially expressed (DE) miRNAs in relevant human cell types in vitro. Results COVID-19 patients showed upregulation of miRNAs associated with lung disease, vascular damage and inflammation and downregulation of miRNAs that inhibit pro-inflammatory cytokines and chemokines, angiogenesis, and stress response. Compared with mild/moderate disease, patients with severe COVID-19 had a miRNA signature indicating a profound impairment of innate and adaptive immune responses, inflammation, lung fibrosis and heart failure. A subset of the DE miRNAs predicted mortality. In particular, a combination of high serum miR-22-3p and miR-21-5p, which target antiviral response genes, and low miR-224-5p and miR-155-5p, targeting pro-inflammatory factors, discriminated severe from mild/moderate COVID-19 (AUROC 0.88, 95% CI 0.80-0.95, p<0.0001), while high leukocyte count and low levels of miR-1-3p, miR-23b-3p, miR-141-3p, miR-155-5p and miR-4433b-5p predicted mortality with high sensitivity and specificity (AUROC 0.95, 95% CI 0.89-1.00, p<0.0001). In vitro experiments showed that some of the DE miRNAs were modulated directly by SARS-CoV-2 infection in permissive lung epithelial cells. Conclusions We discovered circulating miRNAs associated with COVID-19 severity and mortality. The identified DE miRNAs provided clues on COVID-19 pathogenesis, highlighting signatures of impaired interferon and antiviral responses, inflammation, organ damage and cardiovascular failure as associated with severe disease and death.
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Affiliation(s)
| | - Silvia Riccetti
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Chiara Piubelli
- Department of Infectious-Tropical Diseases and Microbiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Elisa Razzaboni
- Department of Infectious-Tropical Diseases and Microbiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Piero Di Battista
- Maternal and Child Health Department, University of Padova, Padova, Italy
| | - Matteo Agostini
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Riccardo Manganelli
- Department of Molecular Medicine, University of Padova, Padova, Italy
- Microbiology and Virology Unit, Padova University Hospital, Padova, Italy
| | - Federico Gobbi
- Department of Infectious-Tropical Diseases and Microbiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Sacro Cuore Don Calabria Hospital, Verona, Italy
| | | | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padova, Italy
- Microbiology and Virology Unit, Padova University Hospital, Padova, Italy
- *Correspondence: Luisa Barzon,
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Severe COVID-19 is characterised by inflammation and immature myeloid cells early in disease progression. Heliyon 2022; 8:e09230. [PMID: 35386227 PMCID: PMC8973020 DOI: 10.1016/j.heliyon.2022.e09230] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/20/2021] [Accepted: 03/28/2022] [Indexed: 12/21/2022] Open
Abstract
SARS-CoV-2 infection causes a wide spectrum of disease severity. Identifying the immunological characteristics of severe disease and the risk factors for their development are important in the management of COVID-19. This study aimed to identify and rank clinical and immunological features associated with progression to severe COVID-19 in order to investigate an immunological signature of severe disease. One hundred and eight patients with positive SARS-CoV-2 PCR were recruited. Routine clinical and laboratory markers were measured, as well as myeloid and lymphoid whole-blood immunophenotyping and measurement of the pro-inflammatory cytokines IL-6 and soluble CD25. All analysis was carried out in a routine hospital diagnostic laboratory. Univariate analysis demonstrated that severe disease was most strongly associated with elevated CRP and IL-6, loss of DLA-DR expression on monocytes and CD10 expression on neutrophils. Unbiased machine learning demonstrated that these four features were strongly associated with severe disease, with an average prediction score for severe disease of 0.925. These results demonstrate that these four markers could be used to identify patients developing severe COVID-19 and allow timely delivery of therapeutics. Severe COVID-19 is characterised by a combination of emergency myelopoiesis and inflammation. These changes can be rapidly identified in a diagnostic laboratory, facilitating intervention. This disease signature was derived from a cohort of patients with a wide range of ages, frailty and COVID-19 severity.
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