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Kirk NM, Liang Y, Ly H. Pathogenesis and virulence of coronavirus disease: Comparative pathology of animal models for COVID-19. Virulence 2024; 15:2316438. [PMID: 38362881 PMCID: PMC10878030 DOI: 10.1080/21505594.2024.2316438] [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: 10/20/2023] [Accepted: 02/04/2024] [Indexed: 02/17/2024] Open
Abstract
Animal models that can replicate clinical and pathologic features of severe human coronavirus infections have been instrumental in the development of novel vaccines and therapeutics. The goal of this review is to summarize our current understanding of the pathogenesis of coronavirus disease 2019 (COVID-19) and the pathologic features that can be observed in several currently available animal models. Knowledge gained from studying these animal models of SARS-CoV-2 infection can help inform appropriate model selection for disease modelling as well as for vaccine and therapeutic developments.
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Affiliation(s)
- Natalie M. Kirk
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
| | - Yuying Liang
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
| | - Hinh Ly
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
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2
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Cai C, Huang Y, Li L, Miu KK, Wang Z, Deng Y, Cai Y, Li J, Wu L, Zhu H, Gao Y, Chen J, Xiao W, Lu L. Angiogenesis-related immune response may be the prelude to the syndesmophyte formation in Ankylosing spondylitis. Int Immunopharmacol 2024; 133:112040. [PMID: 38631220 DOI: 10.1016/j.intimp.2024.112040] [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] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Ankylosing spondylitis (AS) is a chronic autoimmune arthritis that mainly affects spine joints. To date, the pathogenesis of AS remains unclear, although immune cells and innate immune response cytokines have been suggested to be crucial players. METHODS By adopting a single-cell RNA sequencing approach in the AS cynomolgus model, we profiled and characterized PBMC proportions along disease progression. RESULTS Here, our primary focus was on the activation of an immune cascade-initiating lymphocyte subtype known as CD4+CXCR5+ T follicular helper (Tfh) cells. These Tfhs demonstrated a localized residence in AS bone lesion as an ectopic lymphoid structure. Moreover, Tfhs would serve as an upstream initiator for a pro-angiogenic cascade. Then, an expansion in CD14+ monocytes and DC cells subsets resulted in enhanced expression of angiogenesis genes in these AS cynomolgus monkeys. With a confirmed higher abundance of TNF-α accompanying H-type vascular invasion in the osteophytic region, pronounced expansion of Tfhs at such lesion site signaling for monocytes and DCs intrusion is considered as the prelude to the characteristic angiogenic bony outgrowth in AS known as syndesmophytes. CONCLUSIONS We explored the intimate relationship between local inflammation and bone formation in AS from the perspective of nascent vascularisation. Hence, our study lays the foundation for elucidating a unified AS pathogenesis through the immune-angiogenesis-osteogenesis axis.
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Affiliation(s)
- Chunmei Cai
- School of Life Science and Biopharmacy, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yuye Huang
- School of Life Science and Biopharmacy, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Liyan Li
- School of Life Science and Biopharmacy, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Kai Kei Miu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong SAR, China
| | - Zhangting Wang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong SAR, China
| | - Yujie Deng
- Guangzhou National Laboratory, Guangzhou, China
| | - Yanzhen Cai
- School of Life Science and Biopharmacy, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jinxiu Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Liang Wu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Hepeng Zhu
- School of Life Science and Biopharmacy, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yang Gao
- Department of Pharmacy & State Key Laboratory of Ophthalmology, Zhongshan Ophthalmological Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jun Chen
- School of Life Science and Biopharmacy, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wende Xiao
- Guangzhou First People's Hospital, Spine Surgery, Guangzhou 510180, China.
| | - Li Lu
- School of Life Science and Biopharmacy, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, China.
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3
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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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4
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Sun Y, Chen F, Ma H, Wang D, Wang D, Zhang J, Jiang Z, Xia R, Tian T, Zhang W. Exploring the immune characteristions of CRKP pneumonia at single-cell level. Comput Biol Med 2024; 177:108574. [PMID: 38772102 DOI: 10.1016/j.compbiomed.2024.108574] [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: 12/14/2023] [Revised: 04/08/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024]
Abstract
The immune dysregulation associated with carbapenem-resistant Klebsiella pneumoniae (CRKP) severity was investigated through single-cell RNA sequencing (scRNA-seq) of 5 peripheral blood samples from 3 patients with moderate and severe CRKP pneumonia. Additionally, scRNA-seq datasets from two individuals with COVID-19 were included for comparative analysis. The dynamic characterization and functional properties of each immune cell type were examined by delineating the transcriptional profiles of immune cells throughout the transition from moderate to severe conditions. Overall, most immune cells in CRKP patients exhibited a robust interferon-α response and inflammatory reaction compared to healthy controls, mirroring observations in COVID-19 patients. Furthermore, cell signatures associated with NK cells, macrophages, and monocytes were identified in CRKP progression including PTPRCAP for NK cells, C1QB for macrophages, and S100A12 for both macrophages and monocytes. In summary, this study offers a comprehensive scRNA-seq resource for illustrating the dynamic immune response patterns during CRKP progression, thereby shedding light on the associations between CRKP and COVID-19.
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Affiliation(s)
- Yajiao Sun
- Department of Respiratory Medicine, First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China; Department of Respiratory Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Fuhui Chen
- Department of Respiratory Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Hui Ma
- Department of Respiratory Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, 315500, China
| | - Dongjie Wang
- Department of Respiratory Medicine, First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Dong Wang
- Department of Respiratory Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Jingwen Zhang
- Department of Respiratory Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Zhe Jiang
- Department of Respiratory Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Rongyao Xia
- Department of Respiratory Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Tian Tian
- Department of Respiratory Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Wei Zhang
- Department of Respiratory Medicine, First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
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5
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O'Leary K, Zheng D. Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs. NPJ Syst Biol Appl 2024; 10:36. [PMID: 38580667 PMCID: PMC10997786 DOI: 10.1038/s41540-024-00364-2] [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] [Received: 12/07/2023] [Accepted: 03/27/2024] [Indexed: 04/07/2024] Open
Abstract
By profiling gene expression in individual cells, single-cell RNA-sequencing (scRNA-seq) can resolve cellular heterogeneity and cell-type gene expression dynamics. Its application to time-series samples can identify temporal gene programs active in different cell types, for example, immune cells' responses to viral infection. However, current scRNA-seq analysis has limitations. One is the low number of genes detected per cell. The second is insufficient replicates (often 1-2) due to high experimental cost. The third lies in the data analysis-treating individual cells as independent measurements leads to inflated statistics. To address these, we explore a new computational framework, specifically whether "metacells" constructed to maintain cellular heterogeneity within individual cell types (or clusters) can be used as "replicates" for increasing statistical rigor. Toward this, we applied SEACells to a time-series scRNA-seq dataset from peripheral blood mononuclear cells (PBMCs) after SARS-CoV-2 infection to construct metacells, and used them in maSigPro for quadratic regression to find significantly differentially expressed genes (DEGs) over time, followed by clustering expression velocity trends. We showed that such metacells retained greater expression variances and produced more biologically meaningful DEGs compared to either metacells generated randomly or from simple pseudobulk methods. More specifically, this approach correctly identified the known ISG15 interferon response program in almost all PBMC cell types and many DEGs enriched in the previously defined SARS-CoV-2 infection response pathway. It also uncovered additional and more cell type-specific temporal gene expression programs. Overall, our results demonstrate that the metacell-pseudoreplicate strategy could potentially overcome the limitation of 1-2 replicates.
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Affiliation(s)
- Kevin O'Leary
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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6
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Zou Y, Sun X, Wang Y, Wang Y, Ye X, Tu J, Yu R, Huang P. Integrating single-cell RNA sequencing data to genome-wide association analysis data identifies significant cell types in influenza A virus infection and COVID-19. Brief Funct Genomics 2024; 23:110-117. [PMID: 37340787 DOI: 10.1093/bfgp/elad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 02/23/2023] [Accepted: 06/01/2023] [Indexed: 06/22/2023] Open
Abstract
With the global pandemic of COVID-19, the research on influenza virus has entered a new stage, but it is difficult to elucidate the pathogenesis of influenza disease. Genome-wide association studies (GWASs) have greatly shed light on the role of host genetic background in influenza pathogenesis and prognosis, whereas single-cell RNA sequencing (scRNA-seq) has enabled unprecedented resolution of cellular diversity and in vivo following influenza disease. Here, we performed a comprehensive analysis of influenza GWAS and scRNA-seq data to reveal cell types associated with influenza disease and provide clues to understanding pathogenesis. We downloaded two GWAS summary data, two scRNA-seq data on influenza disease. After defining cell types for each scRNA-seq data, we used RolyPoly and LDSC-cts to integrate GWAS and scRNA-seq. Furthermore, we analyzed scRNA-seq data from the peripheral blood mononuclear cells (PBMCs) of a healthy population to validate and compare our results. After processing the scRNA-seq data, we obtained approximately 70 000 cells and identified up to 13 cell types. For the European population analysis, we determined an association between neutrophils and influenza disease. For the East Asian population analysis, we identified an association between monocytes and influenza disease. In addition, we also identified monocytes as a significantly related cell type in a dataset of healthy human PBMCs. In this comprehensive analysis, we identified neutrophils and monocytes as influenza disease-associated cell types. More attention and validation should be given in future studies.
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Affiliation(s)
- Yixin Zou
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xifang Sun
- Department of Mathematics, School of Science, Xi'an Shiyou University, Xi'an, China
| | - Yifan Wang
- Department of Infectious Disease, Jurong Hospital Affiliated to Jiangsu University, Jurong, China
| | - Yidi Wang
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiangyu Ye
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Junlan Tu
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Rongbin Yu
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Peng Huang
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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Su R, Li X, Xiao J, Xu J, Tian J, Liu T, Hu Y. UiO-66 nanoparticles combat influenza A virus in mice by activating the RIG-I-like receptor signaling pathway. J Nanobiotechnology 2024; 22:99. [PMID: 38461229 PMCID: PMC10925002 DOI: 10.1186/s12951-024-02358-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: 12/30/2023] [Accepted: 02/20/2024] [Indexed: 03/11/2024] Open
Abstract
The Influenza A virus (IAV) is a zoonotic pathogen that infects humans and various animal species. Infection with IAV can cause fever, anorexia, and dyspnea and is often accompanied by pneumonia characterized by an excessive release of cytokines (i.e., cytokine storm). Nanodrug delivery systems and nanoparticles are a novel approach to address IAV infections. Herein, UiO-66 nanoparticles (NPs) are synthesized using a high-temperature melting reaction. The in vitro and in vivo optimal concentrations of UiO-66 NPs for antiviral activity are 200 μg mL-1 and 60 mg kg-1, respectively. Transcriptome analysis revealed that UiO-66 NPs can activate the RIG-I-like receptor signaling pathway, thereby enhancing the downstream type I interferon antiviral effect. These NPs suppress inflammation-related pathways, including the FOXO, HIF, and AMPK signaling pathways. The inhibitory effect of UiO-66 NPs on the adsorption and entry of IAV into A549 cells is significant. This study presents novel findings that demonstrate the effective inhibition of IAV adsorption and entry into cells via UiO-66 NPs and highlights their ability to activate the cellular RIG-I-like receptor signaling pathway, thereby exerting an anti-IAV effect in vitro or in mice. These results provide valuable insights into the mechanism of action of UiO-66 NPs against IAV and substantial data for advancing innovative antiviral nanomedicine.
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Affiliation(s)
- Ruijing Su
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Xinsen Li
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Jin Xiao
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Zhongmu Institutes of China Animal Husbandry Industry Co., Ltd, Beijing, People's Republic of China
| | - Jiawei Xu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Jijing Tian
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Tianlong Liu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Yanxin Hu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
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8
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Wu Q, Leng X, Zhang Q, Zhu YZ, Zhou R, Liu Y, Mei C, Zhang D, Liu S, Chen S, Wang X, Lin A, Lin X, Liang T, Shen L, Feng XH, Xia B, Xu P. IRF3 activates RB to authorize cGAS-STING-induced senescence and mitigate liver fibrosis. SCIENCE ADVANCES 2024; 10:eadj2102. [PMID: 38416816 PMCID: PMC10901380 DOI: 10.1126/sciadv.adj2102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/23/2024] [Indexed: 03/01/2024]
Abstract
Cytosolic double-stranded DNA surveillance by cyclic GMP-AMP synthase (cGAS)-Stimulator of Interferon Genes (STING) signaling triggers cellular senescence, autophagy, biased mRNA translation, and interferon-mediated immune responses. However, detailed mechanisms and physiological relevance of STING-induced senescence are not fully understood. Here, we unexpectedly found that interferon regulatory factor 3 (IRF3), activated during innate DNA sensing, forms substantial endogenous complexes in the nucleus with retinoblastoma (RB), a key cell cycle regulator. The IRF3-RB interaction attenuates cyclin-dependent kinase 4/6 (CDK4/6)-mediated RB hyperphosphorylation that mobilizes RB to deactivate E2 family (E2F) transcription factors, thereby driving cells into senescence. STING-IRF3-RB signaling plays a notable role in hepatic stellate cells (HSCs) within various murine models, pushing activated HSCs toward senescence. Accordingly, IRF3 global knockout or conditional deletion in HSCs aggravated liver fibrosis, a process mitigated by the CDK4/6 inhibitor. These findings underscore a straightforward yet vital mechanism of cGAS-STING signaling in inducing cellular senescence and unveil its unexpected biology in limiting liver fibrosis.
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Affiliation(s)
- Qirou Wu
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiaohong Leng
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Qian Zhang
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Ye-Zhang Zhu
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ruyuan Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yutong Liu
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Chen Mei
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Dan Zhang
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shengduo Liu
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, University School of Medicine, Zhejiang University, Hangzhou 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 310058, China
| | - Shasha Chen
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiaojian Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Aifu Lin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xia Lin
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Li Shen
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xin-Hua Feng
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Department of Thoracic Cancer, Affiliated Hangzhou Cancer Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Bing Xia
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Pinglong Xu
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, University School of Medicine, Zhejiang University, Hangzhou 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 310058, China
- Department of Thoracic Cancer, Affiliated Hangzhou Cancer Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
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Chattopadhyay P, Mehta P, Soni J, Tardalkar K, Joshi M, Pandey R. Cell-specific housekeeping role of lncRNAs in COVID-19-infected and recovered patients. NAR Genom Bioinform 2024; 6:lqae023. [PMID: 38426128 PMCID: PMC10903533 DOI: 10.1093/nargab/lqae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
A plethora of studies have demonstrated the roles of lncRNAs in modulating disease severity and outcomes during infection. However, the spatio-temporal expression of these lncRNAs is poorly understood. In this study, we used single-cell RNA-seq to understand the spatio-temporal expression dynamics of lncRNAs across healthy, SARS-CoV-2-infected, and recovered individuals and their functional role in modulating the disease and recovery. We identified 203 differentially expressed lncRNAs, including cell type-specific ones like MALAT1, NEAT1, ZFAS1, SNHG7, SNHG8, and SNHG25 modulating immune function in classical monocyte, NK T, proliferating NK, plasmablast, naive, and activated B/T cells. Interestingly, we found invariant lncRNAs (no significant change in expression across conditions) regulating essential housekeeping functions (for example, HOTAIR, NRAV, SNHG27, SNHG28, and UCA1) in infected and recovered individuals. Despite similar repeat element abundance, variant lncRNAs displayed higher Alu content, suggesting increased interactions with proximal and distal genes, crucial for immune response modulation. The comparable repeat abundance but distinct expression levels of variant and invariant lncRNAs highlight the significance of investigating the regulatory mechanisms of invariant lncRNAs. Overall, this study offers new insights into the spatio-temporal expression patterns and functional roles of lncRNAs in SARS-CoV-2-infected and recovered individuals while highlighting the importance of invariant lncRNAs in the disease context.
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Affiliation(s)
- Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Jyoti Soni
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Kishore Tardalkar
- Department of Stem Cells & Regenerative Medicine, D.Y. Patil Education Society, Kadamwadi, Kolhapur-416003,Maharashtra, India
| | - Meghnad Joshi
- Department of Stem Cells & Regenerative Medicine, D.Y. Patil Education Society, Kadamwadi, Kolhapur-416003,Maharashtra, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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10
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Li J, Xu Y, Zhang J, Zhang Z, Guo H, Wei D, Wu C, Hai T, Sun HX, Zhao Y. Single-cell transcriptomic analysis reveals transcriptional and cell subpopulation differences between human and pig immune cells. Genes Genomics 2024; 46:303-322. [PMID: 37979077 DOI: 10.1007/s13258-023-01456-9] [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: 08/16/2023] [Accepted: 09/26/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND The pig is a promising donor candidate for xenotransplantation. Understanding the differences between human and swine immune systems is critical for addressing xenotransplant rejection and hematopoietic reconstitution. The gene transcriptional profile differences between human and pig immune cell subpopulations have not been studied. To assess the similarities and differences between pigs and humans at the levels of gene transcriptional profiles or cell subpopulations are important for better understanding the cross-species similarity of humans and pigs, and it would help establish the fundamental principles necessary to genetically engineer donor pigs and improve xenotransplantation. OBJECTIVE To assess the gene transcriptional similarities and differences between pigs and humans. METHODS Two pigs and two healthy humans' PBMCs were sorted for 10 × genomics single-cell sequence. We generated integrated human-pig scRNA-seq data from human and pig PBMCs and defined the overall gene expression landscape of pig peripheral blood immune cell subpopulations by updating the set of human-porcine homologous genes. The subsets of immune cells were detected by flow cytometry. RESULTS There were significantly less T cells, NK cells and monocytes but more B cells in pig peripheral blood than those in human peripheral blood. High oxidative phosphorylation, HIF-1, glycolysis, and lysosome-related gene expressions in pig CD14+ monocytes were observed, whereas pig CD14+ monocytes exhibited lower levels of cytokine receptors and JAK-STAT-related genes. Pig activated CD4+T cells decreased cell adhesion and inflammation, while enriched for migration and activation processes. Porcine GNLY+CD8+T cells reduced cytotoxicity and increased proliferation compared with human GNLY+CD8+T cells. Pig CD2+CD8+γδT cells were functionally homologous to human CD2+CD4+ γδT cells. Pig CD2-CD8-γδT cells expressed genes with quiescent and precursor characteristics, while CD2-CD8+γδT cells expressed migration and memory-related molecules. Pig CD24+ and CD5+B cells are associated with inflammatory responses. CONCLUSION Our research with integrated scRNA-seq assays identified the different distribution of pig immune cell subpopulations and the different transcriptional profiles of human and pig immune cells. This study enables a deeper understanding of the development and function of porcine immune cells.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
- BGI-Beijing, Beijing, 102601, China
| | - Yanan Xu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Jiayu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Immunology, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Zhaoqi Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Han Guo
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong Wei
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changhong Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Tang Hai
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- Beijing Farm Animal Research Center, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hai-Xi Sun
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- BGI-Beijing, Beijing, 102601, China.
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
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11
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Xu J, Hu Y, Zhao J, Kong X, Xia S, Dai S, Ding L, Bu T, Cao Y, Liu M, Yan L, Xiao Q, Guo H, Yuan Y, Xu D, Ding K. Single-cell sequencing reveals alterations in the peripheral blood mononuclear cell landscape and monocyte status during colorectal adenocarcinoma formation. Clin Transl Med 2024; 14:e1609. [PMID: 38488463 PMCID: PMC10941536 DOI: 10.1002/ctm2.1609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/11/2024] [Accepted: 02/17/2024] [Indexed: 03/18/2024] Open
Affiliation(s)
- Jiasheng Xu
- Department of Colorectal SurgeryThe Second Hospital of Zhejiang University School of Medicine (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, and Key Laboratory of Medical Molecular Biology)Zhejiang UniversityHangzhouChina
- Zhejiang University Cancer InstituteHangzhouChina
| | - Yeting Hu
- Department of Colorectal SurgeryThe Second Hospital of Zhejiang University School of Medicine (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, and Key Laboratory of Medical Molecular Biology)Zhejiang UniversityHangzhouChina
- Zhejiang University Cancer InstituteHangzhouChina
| | - Jie Zhao
- The State Key Laboratory of Neurology and Oncology Drug DevelopmentJiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd.NanjingChina
| | - Xiangxing Kong
- Department of Colorectal SurgeryThe Second Hospital of Zhejiang University School of Medicine (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, and Key Laboratory of Medical Molecular Biology)Zhejiang UniversityHangzhouChina
- Zhejiang University Cancer InstituteHangzhouChina
| | - Sijian Xia
- The State Key Laboratory of Neurology and Oncology Drug DevelopmentJiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd.NanjingChina
| | - Siqi Dai
- Department of Colorectal SurgeryThe Second Hospital of Zhejiang University School of Medicine (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, and Key Laboratory of Medical Molecular Biology)Zhejiang UniversityHangzhouChina
- Zhejiang University Cancer InstituteHangzhouChina
| | - Lei Ding
- Department of Colorectal SurgeryThe Second Hospital of Zhejiang University School of Medicine (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, and Key Laboratory of Medical Molecular Biology)Zhejiang UniversityHangzhouChina
- Zhejiang University Cancer InstituteHangzhouChina
| | - Tongtong Bu
- Department of Colorectal SurgeryThe Second Hospital of Zhejiang University School of Medicine (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, and Key Laboratory of Medical Molecular Biology)Zhejiang UniversityHangzhouChina
- Zhejiang University Cancer InstituteHangzhouChina
| | - Yue Cao
- Department of Colorectal SurgeryThe Second Hospital of Zhejiang University School of Medicine (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, and Key Laboratory of Medical Molecular Biology)Zhejiang UniversityHangzhouChina
- Zhejiang University Cancer InstituteHangzhouChina
| | - Manjiao Liu
- The State Key Laboratory of Neurology and Oncology Drug DevelopmentJiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd.NanjingChina
| | - Linlin Yan
- The State Key Laboratory of Neurology and Oncology Drug DevelopmentJiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd.NanjingChina
| | - Qian Xiao
- Department of Colorectal SurgeryThe Second Hospital of Zhejiang University School of Medicine (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, and Key Laboratory of Medical Molecular Biology)Zhejiang UniversityHangzhouChina
- Zhejiang University Cancer InstituteHangzhouChina
| | - Hao Guo
- The State Key Laboratory of Neurology and Oncology Drug DevelopmentJiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd.NanjingChina
| | - Ying Yuan
- The Department of Medical Oncologythe Second Affiliated Hospital of Zhejiang UniversityHangzhouChina
| | - Dong Xu
- Department of Colorectal SurgeryThe Second Hospital of Zhejiang University School of Medicine (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, and Key Laboratory of Medical Molecular Biology)Zhejiang UniversityHangzhouChina
- Zhejiang University Cancer InstituteHangzhouChina
| | - Kefeng Ding
- Department of Colorectal SurgeryThe Second Hospital of Zhejiang University School of Medicine (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, and Key Laboratory of Medical Molecular Biology)Zhejiang UniversityHangzhouChina
- Zhejiang University Cancer InstituteHangzhouChina
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12
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Song M, Liu X, Shen W, Wang Z, Wu J, Jiang J, Liu Y, Xu T, Bian T, Zhang M, Sun W, Huang M, Ji N. IFN-γ decreases PD-1 in T lymphocytes from convalescent COVID-19 patients via the AKT/GSK3β signaling pathway. Sci Rep 2024; 14:5038. [PMID: 38424104 PMCID: PMC10904811 DOI: 10.1038/s41598-024-55191-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024] Open
Abstract
Post-COVID-19 syndrome may be associated with the abnormal immune status. Compared with the unexposed age-matched elder group, PD-1 in the CD8+ T cells from recovered COVID-19 patients was significantly lower. IFN-γ in the plasma of COVID-19 convalescent patients was increased, which inhibited PD-1 expression in CD8+ T cells from COVID-19 convalescent patients. scRNA-seq bioinformatics analysis revealed that AKT/GSK3β may regulate the INF-γ/PD-1 axis in CD8+ T cells from COVID-19 convalescent patients. In parallel, an IFN-γ neutralizing antibody reduced AKT and increased GSK3β in PBMCs. An AKT agonist (SC79) significantly decreased p-GSK3β. Moreover, AKT decreased PD-1 on CD8+ T cells, and GSK3β increased PD-1 on CD8+ T cells according to flow cytometry analysis. Collectively, we demonstrated that recovered COVID-19 patients may develop long COVID. Increased IFN-γ in the plasma of recovered Wuhan COVID-19 patients contributed to PD-1 downregulation on CD8+ T cells by regulating the AKT/GSK3β signaling pathway.
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Affiliation(s)
- Meijuan Song
- Department of Respiratory and Critical Care Medicine, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, China
| | - Xiangqun Liu
- Department of Respiratory and Critical Care Medicine, The Xuzhou Municipal Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Weiyu Shen
- Department of Respiratory and Critical Care Medicine, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Zhengxia Wang
- Department of Respiratory and Critical Care Medicine, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, China
| | - Jingjing Wu
- Department of Respiratory and Critical Care Medicine, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, China
| | - Jingxian Jiang
- Department of Respiratory and Critical Care Medicine, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, China
| | - Yanan Liu
- Department of Respiratory and Critical Care Medicine, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, China
| | - Tingting Xu
- Department of Respiratory and Critical Care Medicine, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, China
| | - Tao Bian
- Department of Respiratory and Critical Care Medicine, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Mingshun Zhang
- Jiangsu Province Engineering Research Center of Antibody Drug, NHC Key Laboratory of Antibody Technique, Department of Immunology, Nanjing Medical University, Nanjing, China.
| | - Wei Sun
- Department of Respiratory and Critical Care Medicine, Xishan People's Hospital of Wuxi City, Wuxi, China.
| | - Mao Huang
- Department of Respiratory and Critical Care Medicine, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, China.
| | - Ningfei Ji
- Department of Respiratory and Critical Care Medicine, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, China.
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13
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Li W, Bazaz SR, Mayoh C, Salomon R. Analytical Workflows for Single-Cell Multiomic Data Using the BD Rhapsody Platform. Curr Protoc 2024; 4:e963. [PMID: 38353375 DOI: 10.1002/cpz1.963] [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: 02/16/2024]
Abstract
The conversion of raw sequencing reads to biologically relevant data in high-throughput single-cell RNA sequencing experiments is a complex and involved process. Drawing meaning from thousands of individual cells to provide biological insight requires ensuring not only that the data are of the highest quality but also that the signal can be separated from noise. In this article, we describe a detailed analytical workflow, including six pipelines, that allows high-quality data analysis in single-cell multiomics. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Image analysis Basic Protocol 2: Sequencing quality control and generation of a gene expression matrix Basic Protocol 3: Gene expression matrix data pre-processing and analysis Basic Protocol 4: Advanced analysis Basic Protocol 5: Conversion to flow cytometry standard (FCS) format Basic Protocol 6: Visualization using graphical interfaces.
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Affiliation(s)
- Wenyan Li
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Sajad Razavi Bazaz
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Robert Salomon
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
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14
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Hao Y, Stuart T, Kowalski MH, Choudhary S, Hoffman P, Hartman A, Srivastava A, Molla G, Madad S, Fernandez-Granda C, Satija R. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat Biotechnol 2024; 42:293-304. [PMID: 37231261 PMCID: PMC10928517 DOI: 10.1038/s41587-023-01767-y] [Citation(s) in RCA: 124] [Impact Index Per Article: 124.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/28/2023] [Indexed: 05/27/2023]
Abstract
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. However, most reference datasets are constructed from single-cell RNA-sequencing data and cannot be used to annotate datasets that do not measure gene expression. Here we introduce 'bridge integration', a method to integrate single-cell datasets across modalities using a multiomic dataset as a molecular bridge. Each cell in the multiomic dataset constitutes an element in a 'dictionary', which is used to reconstruct unimodal datasets and transform them into a shared space. Our procedure accurately integrates transcriptomic data with independent single-cell measurements of chromatin accessibility, histone modifications, DNA methylation and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to improve computational scalability and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach, implemented in version 5 of our Seurat toolkit ( http://www.satijalab.org/seurat ), broadens the utility of single-cell reference datasets and facilitates comparisons across diverse molecular modalities.
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Affiliation(s)
- Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Tim Stuart
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Madeline H Kowalski
- New York Genome Center, New York, NY, USA
- Institute for System Genetics, NYU Langone Medical Center, New York, NY, USA
| | - Saket Choudhary
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Paul Hoffman
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Austin Hartman
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Avi Srivastava
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | | | - Shaista Madad
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Carlos Fernandez-Granda
- Center for Data Science, New York University, New York, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Rahul Satija
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
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15
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Soni J, Chattopadhyay P, Mehta P, Mohite R, Tardalkar K, Joshi M, Pandey R. Dynamics of Whole Transcriptome Analysis (WTA) and Surface markers expression (AbSeq) in Immune Cells of COVID-19 Patients and Recovered captured through Single Cell Genomics. Front Med (Lausanne) 2024; 11:1297001. [PMID: 38357647 PMCID: PMC10864604 DOI: 10.3389/fmed.2024.1297001] [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: 09/19/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Single-cell multi-omics studies, such as multidimensional transcriptomics (whole transcriptomic analysis, WTA), and surface marker analysis (antibody sequencing, AbSeq), have turned out to be valuable techniques that offer inaccessible possibilities for single-cell profiling of mRNA, lncRNA, and proteins. Methods We used this technique to understand the dynamics of mRNA and protein-level differences in healthy, COVID-19-infected and recovered individuals using peripheral blood mononuclear cells (PBMCs). Our results demonstrate that compared to mRNA expression, protein abundance is a better indicator of the disease state. Results We demonstrate that compared to mRNA expression, protein abundance is a better indicator of the disease state. We observed high levels of cell identity and regulatory markers, CD3E, CD4, CD8A, CD5, CD7, GITR, and KLRB1 in healthy individuals, whereas markers related to cell activation, CD38, CD28, CD69, CD62L, CD14, and CD16 elevated in the SARS-CoV-2 infected patients at both WTA and AbSeq levels. Curiously, in recovered individuals, there was a high expression of cytokine and chemokine receptors (CCR5, CCR7, CCR4, CXCR3, and PTGRD2). We also observed variations in the expression of markers within cell populations under different states. Discussion Furthermore, our study emphasizes the significance of employing an oligo-based method (AbSeq) that can help in diagnosis, prognosis, and protection from disease/s by identifying cell surface markers that are unique to different cell types or states. It also allows simultaneous study of a vast array of markers, surpassing the constraints of techniques like FACS to query the vast repertoire of proteins.
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Affiliation(s)
- Jyoti Soni
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ramakant Mohite
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Kishore Tardalkar
- Department of Stem Cells & Regenerative Medicine, D. Y. Patil Education Society, Kolhapur, India
| | - Meghnad Joshi
- Department of Stem Cells & Regenerative Medicine, D. Y. Patil Education Society, Kolhapur, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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16
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Lin QXX, Rajagopalan D, Gamage AM, Tan LM, Venkatesh PN, Chan WOY, Kumar D, Agrawal R, Chen Y, Fong SW, Singh A, Sun LJ, Tan SY, Chai LYA, Somani J, Lee B, Renia L, Ng LFP, Ramanathan K, Wang LF, Young B, Lye D, Singhal A, Prabhakar S. Longitudinal single cell atlas identifies complex temporal relationship between type I interferon response and COVID-19 severity. Nat Commun 2024; 15:567. [PMID: 38238298 PMCID: PMC10796319 DOI: 10.1038/s41467-023-44524-0] [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: 08/05/2022] [Accepted: 12/18/2023] [Indexed: 01/22/2024] Open
Abstract
Due to the paucity of longitudinal molecular studies of COVID-19, particularly those covering the early stages of infection (Days 1-8 symptom onset), our understanding of host response over the disease course is limited. We perform longitudinal single cell RNA-seq on 286 blood samples from 108 age- and sex-matched COVID-19 patients, including 73 with early samples. We examine discrete cell subtypes and continuous cell states longitudinally, and we identify upregulation of type I IFN-stimulated genes (ISGs) as the predominant early signature of subsequent worsening of symptoms, which we validate in an independent cohort and corroborate by plasma markers. However, ISG expression is dynamic in progressors, spiking early and then rapidly receding to the level of severity-matched non-progressors. In contrast, cross-sectional analysis shows that ISG expression is deficient and IFN suppressors such as SOCS3 are upregulated in severe and critical COVID-19. We validate the latter in four independent cohorts, and SOCS3 inhibition reduces SARS-CoV-2 replication in vitro. In summary, we identify complexity in type I IFN response to COVID-19, as well as a potential avenue for host-directed therapy.
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Affiliation(s)
- Quy Xiao Xuan Lin
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Deepa Rajagopalan
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Akshamal M Gamage
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Le Min Tan
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Prasanna Nori Venkatesh
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Wharton O Y Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Dilip Kumar
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
| | - Ragini Agrawal
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Yao Chen
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Louisa J Sun
- Alexandra Hospital, Singapore, 159964, Singapore
| | - Seow-Yen Tan
- Changi General Hospital, Singapore, 529889, Singapore
| | - Louis Yi Ann Chai
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore, 119228, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Jyoti Somani
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore, 119228, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Bernett Lee
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Kollengode Ramanathan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- National University Hospital, Singapore, 119074, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore, 168753, Singapore
| | - Barnaby Young
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- National Centre for Infectious diseases, Singapore, 308442, Singapore
- Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - David Lye
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- National Centre for Infectious diseases, Singapore, 308442, Singapore
- Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - Amit Singhal
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore.
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore.
| | - Shyam Prabhakar
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore.
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17
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Vaivode K, Saksis R, Litvina HD, Niedra H, Spriņģe ML, Krūmiņa U, Kloviņš J, Rovite V. Single-Cell RNA Sequencing Reveals Alterations in Patient Immune Cells with Pulmonary Long COVID-19 Complications. Curr Issues Mol Biol 2024; 46:461-468. [PMID: 38248331 PMCID: PMC10814809 DOI: 10.3390/cimb46010029] [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: 11/16/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024] Open
Abstract
Since the emergence of the COVID-19 pandemic, the effects of SARS-CoV-2 have been extensively researched. While much is already known about the acute phase of the infection, increasing attention has turned to the prolonged symptoms experienced by a subset of individuals, commonly referred to as long COVID-19 patients. This study aims to delve deeper into the immune landscape of patients with prolonged symptoms by implementing single-cell mRNA analysis. A 71-year-old COVID-19 patient presenting with persistent viral pneumonia was recruited, and peripheral blood samples were taken at 3 and 2 years post-acute infection onset. Patients and control peripheral blood mononuclear cells (PBMCs) were isolated and single-cell sequenced. Immune cell population identification was carried out using the ScType script. Three months post-COVID-19 patients' PBMCs contained a significantly larger immature neutrophil population compared to 2-year and control samples. However, the neutrophil balance shifted towards a more mature profile after 18 months. In addition, a notable increase in the CD8+ NKT-like cells could be observed in the 3-month patient sample as compared to the later one and control. The subsequent change in these cell populations over time may be an indicator of an ongoing failure to clear the SARS-CoV-2 infection and, thus, lead to chronic COVID-19 complications.
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Affiliation(s)
| | | | | | | | | | | | - Jānis Kloviņš
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia (M.L.S.)
| | - Vita Rovite
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia (M.L.S.)
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18
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Bragazzi Cunha J, Leix K, Sherman EJ, Mirabelli C, Frum T, Zhang CJ, Kennedy AA, Lauring AS, Tai AW, Sexton JZ, Spence JR, Wobus CE, Emmer BT. Type I interferon signaling induces a delayed antiproliferative response in respiratory epithelial cells during SARS-CoV-2 infection. J Virol 2023; 97:e0127623. [PMID: 37975674 PMCID: PMC10734423 DOI: 10.1128/jvi.01276-23] [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: 08/29/2023] [Accepted: 10/22/2023] [Indexed: 11/19/2023] Open
Abstract
ABSTRACT Disease progression during SARS-CoV-2 infection is tightly linked to the fate of lung epithelial cells, with severe cases of COVID-19 characterized by direct injury of the alveolar epithelium and an impairment in its regeneration from progenitor cells. The molecular pathways that govern respiratory epithelial cell death and proliferation during SARS-CoV-2 infection, however, remain unclear. We now report a high-throughput CRISPR screen for host genetic modifiers of the survival and proliferation of SARS-CoV-2-infected Calu-3 respiratory epithelial cells. The top four genes identified in our screen encode components of the same type I interferon (IFN-I) signaling complex—IFNAR1, IFNAR2, JAK1, and TYK2. The fifth gene, ACE2, was an expected control encoding the SARS-CoV-2 viral receptor. Surprisingly, despite the antiviral properties of IFN-I signaling, its disruption in our screen was associated with an increase in Calu-3 cell fitness. We validated this effect and found that IFN-I signaling did not sensitize SARS-CoV-2-infected cultures to cell death but rather inhibited the proliferation of surviving cells after the early peak of viral replication and cytopathic effect. We also found that IFN-I signaling alone, in the absence of viral infection, was sufficient to induce this delayed antiproliferative response in both Calu-3 cells and iPSC-derived type 2 alveolar epithelial cells. Together, these findings highlight a cell autonomous antiproliferative response by respiratory epithelial cells to persistent IFN-I signaling during SARS-CoV-2 infection. This response may contribute to the deficient alveolar regeneration that has been associated with COVID-19 lung injury and represents a promising area for host-targeted therapeutic development.
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Affiliation(s)
- Juliana Bragazzi Cunha
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Kyle Leix
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Emily J. Sherman
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Tristan Frum
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Charles J. Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew A. Kennedy
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Adam S. Lauring
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Andrew W. Tai
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- VA Ann Arbor Healthcare System, Ann Arbor, Michigan, USA
| | - Jonathan Z. Sexton
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R. Spence
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Brian T. Emmer
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
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19
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Guo J, Zhang Y, Gao Y, Li S, Xu G, Tian Z, Xu Q, Li X, Li Y, Zhang Y. Systematical analyses of large-scale transcriptome reveal viral infection-related genes and disease comorbidities. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2023; 51:453-465. [PMID: 37651591 DOI: 10.1080/21691401.2023.2252477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/02/2023]
Abstract
Perturbation of transcriptome in viral infection patients is a recurrent theme impacting symptoms and mortality, yet a detailed understanding of pertinent transcriptome and identification of robust biomarkers is not complete. In this study, we manually collected 23 datasets related to 6,197 blood transcriptomes across 16 types of respiratory virus infections. We applied a comprehensive systems biology approach starting with whole-blood transcriptomes combined with multilevel bioinformatics analyses to characterize the expression, functional pathways, and protein-protein interaction (PPI) networks to identify robust biomarkers and disease comorbidities. Robust gene markers of infection with different viruses were identified, which can accurately classify the normal and infected patients in train and validation cohorts. The biological processes (BP) of different viruses showed great similarity and enriched in infection and immune response pathways. Network-based analyses revealed that a variety of viral infections were associated with nervous system diseases, neoplasms and metabolic diseases, and significantly correlated with brain tissues. In summary, our manually collected transcriptomes and comprehensive analyses reveal key molecular markers and disease comorbidities in the process of viral infection, which could provide a valuable theoretical basis for the prevention of subsequent public health events for respiratory virus infections.
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Affiliation(s)
- Jing Guo
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, Hainan, China
| | - Ya Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, Hainan, China
| | - Yueying Gao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, Hainan, China
| | - Si Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, Hainan, China
| | - Gang Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, Hainan, China
| | - Zhanyu Tian
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, Hainan, China
| | - Qi Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, Hainan, China
| | - Xia Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, Hainan, China
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongsheng Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, Hainan, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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20
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Chen C, Guo Q, Liu Y, Hou Q, Liao M, Guo Y, Zang Y, Wang F, Liu H, Luan X, Liang Y, Guan Z, Li Y, Liu H, Dong X, Zhang X, Liu J, Xu Q. Single-cell and spatial transcriptomics reveal POSTN + cancer-associated fibroblasts correlated with immune suppression and tumour progression in non-small cell lung cancer. Clin Transl Med 2023; 13:e1515. [PMID: 38115703 PMCID: PMC10731139 DOI: 10.1002/ctm2.1515] [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: 06/01/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Cancer-associated fibroblasts (CAFs) are potential targets for cancer therapy. Due to the heterogeneity of CAFs, the influence of CAF subpopulations on the progression of lung cancer is still unclear, which impedes the translational advances in targeting CAFs. METHODS We performed single-cell RNA sequencing (scRNA-seq) on tumour, paired tumour-adjacent, and normal samples from 16 non-small cell lung cancer (NSCLC) patients. CAF subpopulations were analyzed after integration with published NSCLC scRNA-seq data. SpaTial enhanced resolution omics-sequencing (Stereo-seq) was applied in tumour and tumour-adjacent samples from seven NSCLC patients to map the architecture of major cell populations in tumour microenvironment (TME). Immunohistochemistry (IHC) and multiplexed IHC (mIHC) were used to validate marker gene expression and the association of CAFs with immune infiltration in TME. RESULTS A subcluster of myofibroblastic CAFs, POSTN+ CAFs, were significantly enriched in advanced tumours and presented gene expression signatures related to extracellular matrix remodeling, tumour invasion pathways and immune suppression. Stereo-seq and mIHC demonstrated that POSTN+ CAFs were in close localization with SPP1+ macrophages and were associated with the exhausted phenotype and lower infiltration of T cells. POSTN expression or the abundance of POSTN+ CAFs were associated with poor prognosis of NSCLC. CONCLUSIONS Our study identified a myofibroblastic CAF subpopulation, POSTN+ CAFs, which might associate with SPP1+ macrophages to promote the formation of desmoplastic architecture and participate in immune suppression. Furthermore, we showed that POSTN+ CAFs associated with cancer progression and poor clinical outcomes and may provide new insights on the treatment of NSCLC.
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Affiliation(s)
- Chao Chen
- Department of Thoracic SurgeryPeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhenChina
| | - Qiang Guo
- BGI ResearchHangzhouChina
- BGI ResearchShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yang Liu
- BGI ResearchHangzhouChina
- BGI ResearchShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Qinghua Hou
- Department of Thoracic SurgeryPeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhenChina
| | - Mengying Liao
- Department of PathologyPeking University Shenzhen HospitalShenzhenChina
| | - Yanying Guo
- BGI ResearchHangzhouChina
- BGI ResearchShenzhenChina
| | - Yupeng Zang
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | | | - Huanyu Liu
- Department of PathologyPeking University Shenzhen HospitalShenzhenChina
| | - Xinyu Luan
- Department of Thoracic SurgeryPeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhenChina
| | - Yanling Liang
- BGI ResearchShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Zhuojue Guan
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yanling Li
- Central Laboratory of Peking University Shenzhen HospitalShenzhenChina
| | - Haozhen Liu
- Department of Thoracic SurgeryPeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhenChina
| | - Xuan Dong
- BGI ResearchHangzhouChina
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of GenomicsBGI ResearchShenzhenChina
| | - Xiuqing Zhang
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of GenomicsBGI ResearchShenzhenChina
| | - Jixian Liu
- Department of Thoracic SurgeryPeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhenChina
| | - Qumiao Xu
- BGI ResearchHangzhouChina
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of GenomicsBGI ResearchShenzhenChina
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21
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Yang Y, Du T, Yu W, Zhou Y, Yang C, Kuang D, Wang J, Tang C, Wang H, Zhao Y, Yang H, Huang Q, Wu D, Li B, Sun Q, Liu H, Lu S, Peng X. Single-cell transcriptomic atlas of distinct early immune responses induced by SARS-CoV-2 Proto or its variants in rhesus monkey. MedComm (Beijing) 2023; 4:e432. [PMID: 38020713 PMCID: PMC10661830 DOI: 10.1002/mco2.432] [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: 07/25/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
Immune responses induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection play a critical role in the pathogenesis and outcome of coronavirus disease 2019 (COVID-19). However, the dynamic profile of immune responses postinfection by SARS-CoV-2 variants of concern (VOC) is not fully understood. In this study, peripheral blood mononuclear cells single-cell sequencing was performed to determine dynamic profiles of immune response to Prototype, Alpha, Beta, and Delta in a rhesus monkey model. Overall, all strains induced dramatic changes in both cellular subpopulations and gene expression levels at 1 day postinfection (dpi), which associated function including adaptive immune response, innate immunity, and IFN response. COVID-19-related genes revealed different gene profiles at 1 dpi among the four SARS-CoV-2 strains, including genes reported in COVID-19 patients with increased risk of autoimmune disease and rheumatic diseases. Delta-infected animal showed inhibition of translation pathway. B cells, T cells, and monocytes showed much commonality rather than specificity among the four strains. Monocytes were the major responders to SARS-CoV-2 infection, and the response lasted longer in Alpha than the other strains. Thus, this study reveals the early immune responses induced by SARS-CoV-2 Proto or its variants in nonhuman primates, which is important information for controlling rapidly evolving viruses.
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Affiliation(s)
- Yun Yang
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
| | - Tingfu Du
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
| | - Wenhai Yu
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
| | - Yanan Zhou
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
| | - Chengyun Yang
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
| | - Dexuan Kuang
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
| | - Junbin Wang
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
| | - Cong Tang
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
| | - Haixuan Wang
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
| | - Yuan Zhao
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
| | - Hao Yang
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
| | - Qing Huang
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
| | - Daoju Wu
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
| | - Bai Li
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
| | - Qiangming Sun
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College)Ministry of EducationBeijingChina
| | - Hongqi Liu
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College)Ministry of EducationBeijingChina
| | - Shuaiyao Lu
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College)Ministry of EducationBeijingChina
| | - Xiaozhong Peng
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical SchoolKunmingChina
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College)Ministry of EducationBeijingChina
- State Key Laboratory of Medical Molecular BiologyDepartment of Molecular Biology and BiochemistryInstitute of Basic Medical SciencesMedical Primate Research CenterNeuroscience CenterChinese Academy of Medical SciencesSchool of Basic MedicinePeking Union Medical CollegeBeijingChina
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22
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Angioni R, Bonfanti M, Caporale N, Sánchez-Rodríguez R, Munari F, Savino A, Pasqualato S, Buratto D, Pagani I, Bertoldi N, Zanon C, Ferrari P, Ricciardelli E, Putaggio C, Ghezzi S, Elli F, Rotta L, Scardua A, Weber J, Cecatiello V, Iorio F, Zonta F, Cattelan AM, Vicenzi E, Vannini A, Molon B, Villa CE, Viola A, Testa G. RAGE engagement by SARS-CoV-2 enables monocyte infection and underlies COVID-19 severity. Cell Rep Med 2023; 4:101266. [PMID: 37944530 PMCID: PMC10694673 DOI: 10.1016/j.xcrm.2023.101266] [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: 07/08/2022] [Revised: 03/16/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023]
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has fueled the COVID-19 pandemic with its enduring medical and socioeconomic challenges because of subsequent waves and long-term consequences of great concern. Here, we chart the molecular basis of COVID-19 pathogenesis by analyzing patients' immune responses at single-cell resolution across disease course and severity. This approach confirms cell subpopulation-specific dysregulation in COVID-19 across disease course and severity and identifies a severity-associated activation of the receptor for advanced glycation endproducts (RAGE) pathway in monocytes. In vitro THP1-based experiments indicate that monocytes bind the SARS-CoV-2 S1-receptor binding domain (RBD) via RAGE, pointing to RAGE-Spike interaction enabling monocyte infection. Thus, our results demonstrate that RAGE is a functional receptor of SARS-CoV-2 contributing to COVID-19 severity.
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Affiliation(s)
- Roberta Angioni
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; Fondazione Istituto di Ricerca Pediatrica - Città Della Speranza, 35127 Padova, Italy
| | - Matteo Bonfanti
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Nicolò Caporale
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy; Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Ricardo Sánchez-Rodríguez
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; Fondazione Istituto di Ricerca Pediatrica - Città Della Speranza, 35127 Padova, Italy
| | - Fabio Munari
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; Fondazione Istituto di Ricerca Pediatrica - Città Della Speranza, 35127 Padova, Italy
| | - Aurora Savino
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | | | - Damiano Buratto
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Isabel Pagani
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Nicole Bertoldi
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; Fondazione Istituto di Ricerca Pediatrica - Città Della Speranza, 35127 Padova, Italy
| | - Carlo Zanon
- Fondazione Istituto di Ricerca Pediatrica - Città Della Speranza, 35127 Padova, Italy
| | - Paolo Ferrari
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | | | - Cristina Putaggio
- Infectious Disease Unit, Padova University Hospital, 35128 Padova, Italy
| | - Silvia Ghezzi
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Francesco Elli
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy
| | - Luca Rotta
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | | | - Janine Weber
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | | | - Francesco Iorio
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China; Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | | | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | | | - Barbara Molon
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; Fondazione Istituto di Ricerca Pediatrica - Città Della Speranza, 35127 Padova, Italy
| | - Carlo Emanuele Villa
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy; Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Antonella Viola
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; Fondazione Istituto di Ricerca Pediatrica - Città Della Speranza, 35127 Padova, Italy.
| | - Giuseppe Testa
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy; Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy.
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23
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Wang DX, Dong ZJ, Deng SX, Tian YM, Xiao YJ, Li X, Ma XR, Li L, Li P, Chang HZ, Liu L, Wang F, Wu Y, Gao X, Zheng SS, Gu HM, Zhang YN, Wu JB, Wu F, Peng Y, Zhang XW, Zhan RY, Gao LX, Sun Q, Guo X, Zhao XD, Luo JH, Zhou R, Han L, Shu Y, Zhao JW. GDF11 slows excitatory neuronal senescence and brain ageing by repressing p21. Nat Commun 2023; 14:7476. [PMID: 37978295 PMCID: PMC10656444 DOI: 10.1038/s41467-023-43292-1] [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: 02/17/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
As a major neuron type in the brain, the excitatory neuron (EN) regulates the lifespan in C. elegans. How the EN acquires senescence, however, is unknown. Here, we show that growth differentiation factor 11 (GDF11) is predominantly expressed in the EN in the adult mouse, marmoset and human brain. In mice, selective knock-out of GDF11 in the post-mitotic EN shapes the brain ageing-related transcriptional profile, induces EN senescence and hyperexcitability, prunes their dendrites, impedes their synaptic input, impairs object recognition memory and shortens the lifespan, establishing a functional link between GDF11, brain ageing and cognition. In vitro GDF11 deletion causes cellular senescence in Neuro-2a cells. Mechanistically, GDF11 deletion induces neuronal senescence via Smad2-induced transcription of the pro-senescence factor p21. This work indicates that endogenous GDF11 acts as a brake on EN senescence and brain ageing.
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Affiliation(s)
- Di-Xian Wang
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China
- Center of Cryo-Electron Microscopy, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Zhao-Jun Dong
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China
- Center of Cryo-Electron Microscopy, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Sui-Xin Deng
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, 201508, Shanghai, China
| | | | - Yu-Jie Xiao
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, 201508, Shanghai, China
| | - Xinran Li
- The Global Scientific and Technological Innovation Center and the MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Xiao-Ru Ma
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China
- Center of Cryo-Electron Microscopy, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Liang Li
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, 201508, Shanghai, China
| | - Pengxiao Li
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai; Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | | | | | - Fan Wang
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China
- Center of Cryo-Electron Microscopy, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Yang Wu
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China
- Center of Cryo-Electron Microscopy, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Xiang Gao
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China
- Center of Cryo-Electron Microscopy, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Shuang-Shuang Zheng
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China
- Center of Cryo-Electron Microscopy, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Hui-Min Gu
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China
- Center of Cryo-Electron Microscopy, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Ya-Nan Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jian-Bin Wu
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China
- Center of Cryo-Electron Microscopy, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Fan Wu
- Department of Neurosurgery, the First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, 310003, Hangzhou, China
| | - Yonglin Peng
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai; Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Xiao-Wen Zhang
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China
- Center of Cryo-Electron Microscopy, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Ren-Ya Zhan
- Department of Neurosurgery, the First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, 310003, Hangzhou, China
| | - Li-Xia Gao
- Department of Neurology of the Second Affiliated Hospital, Interdisciplinary Institute of Neuroscience and Technology, Zhejiang University School of Medicine, 310020, Hangzhou, China
| | - Qiming Sun
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xing Guo
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xiao-Dong Zhao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai; Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Jian-Hong Luo
- Department of Neurobiology and Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Zhejiang, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lei Han
- BGI Research, 310030, Hangzhou, China.
| | - Yousheng Shu
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, 201508, Shanghai, China.
| | - Jing-Wei Zhao
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China.
- Center of Cryo-Electron Microscopy, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
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24
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Huang Z, Brodeur KE, Chen L, Du, Wobma H, Hsu EE, Liu M, Chang JC, Chang MH, Chou J, Day-Lewis M, Dedeoglu F, Halyabar O, Lederer JA, Li T, Lo MS, Lu M, Meidan E, Newburger JW, Randolph AG, Son MB, Sundel RP, Taylor ML, Wu H, Zhou Q, Canna SW, Wei K, Henderson LA, Nigrovic PA, Lee PY. Type I interferon signature and cycling lymphocytes in macrophage activation syndrome. J Clin Invest 2023; 133:e165616. [PMID: 37751296 PMCID: PMC10645381 DOI: 10.1172/jci165616] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 09/19/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUNDMacrophage activation syndrome (MAS) is a life-threatening complication of Still's disease (SD) characterized by overt immune cell activation and cytokine storm. We aimed to further understand the immunologic landscape of SD and MAS.METHODWe profiled PBMCs from people in a healthy control group and patients with SD with or without MAS using bulk RNA-Seq and single-cell RNA-Seq (scRNA-Seq). We validated and expanded the findings by mass cytometry, flow cytometry, and in vitro studies.RESULTSBulk RNA-Seq of PBMCs from patients with SD-associated MAS revealed strong expression of genes associated with type I interferon (IFN-I) signaling and cell proliferation, in addition to the expected IFN-γ signal, compared with people in the healthy control group and patients with SD without MAS. scRNA-Seq analysis of more than 65,000 total PBMCs confirmed IFN-I and IFN-γ signatures and localized the cell proliferation signature to cycling CD38+HLA-DR+ cells within CD4+ T cell, CD8+ T cell, and NK cell populations. CD38+HLA-DR+ lymphocytes exhibited prominent IFN-γ production, glycolysis, and mTOR signaling. Cell-cell interaction modeling suggested a network linking CD38+HLA-DR+ lymphocytes with monocytes through IFN-γ signaling. Notably, the expansion of CD38+HLA-DR+ lymphocytes in MAS was greater than in other systemic inflammatory conditions in children. In vitro stimulation of PBMCs demonstrated that IFN-I and IL-15 - both elevated in MAS patients - synergistically augmented the generation of CD38+HLA-DR+ lymphocytes, while Janus kinase inhibition mitigated this response.CONCLUSIONMAS associated with SD is characterized by overproduction of IFN-I, which may act in synergy with IL-15 to generate CD38+HLA-DR+ cycling lymphocytes that produce IFN-γ.
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Affiliation(s)
- Zhengping Huang
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Rheumatology and Immunology, Guangdong Second Provincial General Hospital, Southern Medical University, Guangzhou, China
| | - Kailey E. Brodeur
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Liang Chen
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Du
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Rheumatology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Holly Wobma
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Evan E. Hsu
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Meng Liu
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Rheumatology and Immunology, Guangdong Second Provincial General Hospital, Southern Medical University, Guangzhou, China
| | - Joyce C. Chang
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Margaret H. Chang
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Janet Chou
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Megan Day-Lewis
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Fatma Dedeoglu
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Olha Halyabar
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - James A. Lederer
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Tianwang Li
- Department of Rheumatology and Immunology, Guangdong Second Provincial General Hospital, Southern Medical University, Guangzhou, China
| | - Mindy S. Lo
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Meiping Lu
- Department of Rheumatology, Immunology and Allergy, Zhejiang University School of Medicine, Hangzhou, China
| | - Esra Meidan
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Adrienne G. Randolph
- Department of Anesthesiology, Critical Care, and Pain Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mary Beth Son
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Robert P. Sundel
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Maria L. Taylor
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Huaxiang Wu
- Department of Rheumatology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Qing Zhou
- The MOE Key Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Scott W. Canna
- Division of Rheumatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lauren A. Henderson
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Peter A. Nigrovic
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Pui Y. Lee
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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25
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Dooley NL, Chabikwa TG, Pava Z, Loughland JR, Hamelink J, Berry K, Andrew D, Soon MSF, SheelaNair A, Piera KA, William T, Barber BE, Grigg MJ, Engwerda CR, Lopez JA, Anstey NM, Boyle MJ. Single cell transcriptomics shows that malaria promotes unique regulatory responses across multiple immune cell subsets. Nat Commun 2023; 14:7387. [PMID: 37968278 PMCID: PMC10651914 DOI: 10.1038/s41467-023-43181-7] [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: 11/23/2022] [Accepted: 11/02/2023] [Indexed: 11/17/2023] Open
Abstract
Plasmodium falciparum malaria drives immunoregulatory responses across multiple cell subsets, which protects from immunopathogenesis, but also hampers the development of effective anti-parasitic immunity. Understanding malaria induced tolerogenic responses in specific cell subsets may inform development of strategies to boost protective immunity during drug treatment and vaccination. Here, we analyse the immune landscape with single cell RNA sequencing during P. falciparum malaria. We identify cell type specific responses in sub-clustered major immune cell types. Malaria is associated with an increase in immunosuppressive monocytes, alongside NK and γδ T cells which up-regulate tolerogenic markers. IL-10-producing Tr1 CD4 T cells and IL-10-producing regulatory B cells are also induced. Type I interferon responses are identified across all cell types, suggesting Type I interferon signalling may be linked to induction of immunoregulatory networks during malaria. These findings provide insights into cell-specific and shared immunoregulatory changes during malaria and provide a data resource for further analysis.
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Affiliation(s)
- Nicholas L Dooley
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Environment and Sciences, Griffith University, Brisbane, QLD, Australia
| | | | - Zuleima Pava
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Julianne Hamelink
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- University of Queensland, Brisbane, QLD, Australia
| | - Kiana Berry
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Queensland University of Technology, Brisbane, QLD, Australia
| | - Dean Andrew
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Megan S F Soon
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Arya SheelaNair
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Kim A Piera
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Timothy William
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
- Subang Jaya Medical Centre, Selangor, Malaysia
| | - Bridget E Barber
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
| | - Matthew J Grigg
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
| | | | - J Alejandro Lopez
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Environment and Sciences, Griffith University, Brisbane, QLD, Australia
| | - Nicholas M Anstey
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
| | - Michelle J Boyle
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
- School of Environment and Sciences, Griffith University, Brisbane, QLD, Australia.
- University of Queensland, Brisbane, QLD, Australia.
- Queensland University of Technology, Brisbane, QLD, Australia.
- Burnet Institute, Melbourne, VIC, Australia.
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26
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Kushwaha ND, Mohan J, Kushwaha B, Ghazi T, Nwabuife JC, Koorbanally N, Chuturgoon AA. A comprehensive review on the global efforts on vaccines and repurposed drugs for combating COVID-19. Eur J Med Chem 2023; 260:115719. [PMID: 37597435 DOI: 10.1016/j.ejmech.2023.115719] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/31/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023]
Abstract
The recently discovered coronavirus, known as SARS-CoV-2, is a highly contagious and potentially lethal viral infection that was declared a pandemic by the World Health Organization on March 11, 2020. Since the beginning of the pandemic, an unprecedented number of COVID-19 vaccine candidates have been investigated for their potential to manage the pandemic. Herein, we reviewed vaccine development and the associated research effort, both traditional and forward-looking, to demonstrate the advantages and disadvantages of their technology, in addition to their efficacy limitations against mutant SARS-CoV-2. Moreover, we report repurposed drug discovery, which mainly focuses on virus-based and host-based targets, as well as their inhibitors. SARS-CoV-2 targets include the main protease (Mpro), and RNA-dependent RNA-polymerase (RdRp), which are the most well-studied and conserved across coronaviruses, enabling the development of broad-spectrum inhibitors of these enzymes.
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Affiliation(s)
- Narva Deshwar Kushwaha
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA.
| | - Jivanka Mohan
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Babita Kushwaha
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Terisha Ghazi
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Joshua C Nwabuife
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Neil Koorbanally
- School of Chemistry, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Anil A Chuturgoon
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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27
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Jeong K, Kim Y, Jeon J, Kim K. Subtyping of COVID-19 samples based on cell-cell interaction in single cell transcriptomes. Sci Rep 2023; 13:19629. [PMID: 37949890 PMCID: PMC10638268 DOI: 10.1038/s41598-023-46350-2] [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: 08/11/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
In single-cell transcriptome analysis, numerous biomarkers related to COVID-19 severity, including cell subtypes, genes, and pathways, have been identified. Nevertheless, most studies have focused on severity groups based on clinical features, neglecting immunological heterogeneity within the same severity level. In this study, we employed sample-level clustering using cell-cell interaction scores to investigate patient heterogeneity and uncover novel subtypes. The clustering results were validated using external datasets, demonstrating superior reproducibility and purity compared to gene expression- or gene set enrichment-based clustering. Furthermore, the cell-cell interaction score-based clusters exhibited a strong correlation with the WHO ordinal severity score based on clinical characteristics. By characterizing the identified subtypes through known COVID-19 severity-associated biomarkers, we discovered a "Severe-like moderate" subtype. This subtype displayed clinical features akin to moderate cases; however, molecular features, such as gene expression and cell-cell interactions, resembled those of severe cases. Notably, all patients who progressed from moderate to severe belonged to this subtype, underscoring the significance of cell-cell interactions in COVID-19 patient heterogeneity and severity.
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Affiliation(s)
- Kyeonghun Jeong
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yooeun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jaemin Jeon
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kwangsoo Kim
- Department of Transdisciplinary Medicine, Institute of Convergence Medicine with Innovative Technology, Seoul National University Hospital, Seoul, 03080, Republic of Korea.
- Department of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.
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28
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Hou W, Ji Z, Chen Z, Wherry EJ, Hicks SC, Ji H. A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples. Nat Commun 2023; 14:7286. [PMID: 37949861 PMCID: PMC10638410 DOI: 10.1038/s41467-023-42841-y] [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] [Received: 07/11/2021] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Pseudotime analysis with single-cell RNA-sequencing (scRNA-seq) data has been widely used to study dynamic gene regulatory programs along continuous biological processes. While many methods have been developed to infer the pseudotemporal trajectories of cells within a biological sample, it remains a challenge to compare pseudotemporal patterns with multiple samples (or replicates) across different experimental conditions. Here, we introduce Lamian, a comprehensive and statistically-rigorous computational framework for differential multi-sample pseudotime analysis. Lamian can be used to identify changes in a biological process associated with sample covariates, such as different biological conditions while adjusting for batch effects, and to detect changes in gene expression, cell density, and topology of a pseudotemporal trajectory. Unlike existing methods that ignore sample variability, Lamian draws statistical inference after accounting for cross-sample variability and hence substantially reduces sample-specific false discoveries that are not generalizable to new samples. Using both real scRNA-seq and simulation data, including an analysis of differential immune response programs between COVID-19 patients with different disease severity levels, we demonstrate the advantages of Lamian in decoding cellular gene expression programs in continuous biological processes.
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Affiliation(s)
- Wenpin Hou
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Zhicheng Ji
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Zeyu Chen
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephanie C Hicks
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
| | - Hongkai Ji
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
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29
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Ge Y, Zhang C, Qu Y, Ding L, Zhang X, Zhang Z, Jin C, Wang XN, Wang Z. Synthesis and pharmacodynamic evaluation of naphthalene derivatives against influenza A virus in vitro and in vivo. Eur J Med Chem 2023; 259:115660. [PMID: 37517205 DOI: 10.1016/j.ejmech.2023.115660] [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: 04/19/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 08/01/2023]
Abstract
Influenza A virus is a highly mutable pathogenic pathogen that could cause a global pandemic. It is necessary to find new anti-influenza drugs to resist influenza epidemics due to the seasonal popularity of a certain area every year. Naphthalene derivatives had potential antiviral activity. A series of naphthalene derivatives were synthesized via the metal-free intramolecular hydroarylation reactions of alkynes. Evaluation of their biological efficacy showed that compound 2-aminonaphthalene 4d had better antiviral activity in vitro than ribavirin. By studying the mechanism of action of 2-aminonaphthalene 4din vivo and in vitro, we found that 4d had antiviral activity to three different subtype influenza viruses of A/Weiss/43 (H1N1), A/Virginia/ATCC2/2009 (H1N1) and A/California/2/2014 (H3N2). Compound 4d had the best effect after viral adsorption, and mainly played in the early stage of virus replication. 2-Aminonaphthalene 4d could reduce the replication of virus by inhibiting the NP and M proteins of virus. Compound 4d cut down ROS accumulation, autophagy and apoptosis induced by influenza virus. Inflammatory response mediated by RIG-1 pathway were suppressed in the cell and mice. In addition, the pathological changes of lung tissue and virus titer in mice were reduced by the administration of 4d. Therefore, naphthalene derivative 4d is a potential drug for the treatment of influenza A virus infection.
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Affiliation(s)
- Yongzhuang Ge
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Key Laboratory of "Runliang" Antiviral Medicines Research and Development, Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Chaofeng Zhang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Key Laboratory of "Runliang" Antiviral Medicines Research and Development, Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ying Qu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Key Laboratory of "Runliang" Antiviral Medicines Research and Development, Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lixia Ding
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Key Laboratory of "Runliang" Antiviral Medicines Research and Development, Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xinbo Zhang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Key Laboratory of "Runliang" Antiviral Medicines Research and Development, Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhongmou Zhang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Key Laboratory of "Runliang" Antiviral Medicines Research and Development, Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Chengyun Jin
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Key Laboratory of "Runliang" Antiviral Medicines Research and Development, Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiao-Na Wang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Key Laboratory of "Runliang" Antiviral Medicines Research and Development, Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Zhenya Wang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Key Laboratory of "Runliang" Antiviral Medicines Research and Development, Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
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Bosquillon de Jarcy L, Akbil B, Mhlekude B, Leyens J, Postmus D, Harnisch G, Jansen J, Schmidt ML, Aigner A, Pott F, Chua RL, Krist L, Gentile R, Mühlemann B, Jones TC, Niemeyer D, Fricke J, Keil T, Pischon T, Janke J, Conrad C, Iacobelli S, Drosten C, Corman VM, Ralser M, Eils R, Kurth F, Sander L, Goffinet C. 90K/LGALS3BP expression is upregulated in COVID-19 but may not restrict SARS-CoV-2 infection. Clin Exp Med 2023; 23:3689-3700. [PMID: 37162650 PMCID: PMC10170455 DOI: 10.1007/s10238-023-01077-2] [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: 01/08/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Glycoprotein 90K, encoded by the interferon-stimulated gene LGALS3BP, displays broad antiviral activity. It reduces HIV-1 infectivity by interfering with Env maturation and virion incorporation, and increases survival of Influenza A virus-infected mice via antiviral innate immune signaling. Its antiviral potential in SARS-CoV-2 infection remains largely unknown. Here, we analyzed the expression of 90K/LGALS3BP in 44 hospitalized COVID-19 patients at multiple levels. We quantified 90K protein concentrations in serum and PBMCs as well as LGALS3BP mRNA levels. Complementary, we analyzed two single cell RNA-sequencing datasets for expression of LGALS3BP in respiratory specimens and PBMCs from COVID-19 patients. Finally, we analyzed the potential of 90K to interfere with SARS-CoV-2 infection of HEK293T/ACE2, Calu-3 and Caco-2 cells using authentic virus. 90K protein serum concentrations were significantly elevated in COVID-19 patients compared to uninfected sex- and age-matched controls. Furthermore, PBMC-associated concentrations of 90K protein were overall reduced by SARS-CoV-2 infection in vivo, suggesting enhanced secretion into the extracellular space. Mining of published PBMC scRNA-seq datasets uncovered monocyte-specific induction of LGALS3BP mRNA expression in COVID-19 patients. In functional assays, neither 90K overexpression in susceptible cell lines nor exogenous addition of purified 90K consistently inhibited SARS-CoV-2 infection. Our data suggests that 90K/LGALS3BP contributes to the global type I IFN response during SARS-CoV-2 infection in vivo without displaying detectable antiviral properties in vitro.
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Affiliation(s)
- Laure Bosquillon de Jarcy
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 , Berlin, Germany
- Speciality Network: Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Bengisu Akbil
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 , Berlin, Germany
| | - Baxolele Mhlekude
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 , Berlin, Germany
| | - Johanna Leyens
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Dylan Postmus
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 , Berlin, Germany
| | - Greta Harnisch
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Jenny Jansen
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Marie L Schmidt
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Annette Aigner
- Institute of Biometry and Clinical Epidemiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Fabian Pott
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 , Berlin, Germany
| | - Robert Lorenz Chua
- Center for Digital Health, Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany, Charitéplatz 1, 10117, Berlin, Germany
| | - Lilian Krist
- Institute of Social Medicine, Epidemiology and Health Economics, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | | | - Barbara Mühlemann
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Terence C Jones
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Department of Zoology, Centre for Pathogen Evolution, University of Cambridge, Downing St., Cambridge, CB2 3EJ, UK
| | - Daniela Niemeyer
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- German Center for Infection Research, Associated Partner Charité, Berlin, Germany
| | - Julia Fricke
- Institute of Social Medicine, Epidemiology and Health Economics, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Thomas Keil
- Institute of Social Medicine, Epidemiology and Health Economics, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Josef-Schneiderstr. 2, 97080, Würzburg, Germany
- State Institute of Health, Bavarian Health and Food Safety Authority, Eggenreuther Weg 43, 91058, Erlangen, Germany
| | - Tobias Pischon
- Molecular Epidemiology Research Group, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Biobank Technology Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Core Facility Biobank, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10178, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, 10117, Berlin, Germany
| | - Jürgen Janke
- Biobank Technology Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Christian Conrad
- Center for Digital Health, Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany, Charitéplatz 1, 10117, Berlin, Germany
| | | | - Christian Drosten
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- German Center for Infection Research, Associated Partner Charité, Berlin, Germany
| | - Victor M Corman
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- German Center for Infection Research, Associated Partner Charité, Berlin, Germany
| | - Markus Ralser
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, NW11AT, UK
| | - Roland Eils
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 , Berlin, Germany
- Center for Digital Health, Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany, Charitéplatz 1, 10117, Berlin, Germany
- German Center for Lung Research (DZL), 35392, Gießen, Germany
- Health Data Science Unit, Heidelberg University Hospital and BioQuant, 69120, Heidelberg, Germany
| | - Florian Kurth
- Speciality Network: Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany
- Department of Medicine, University Medical Center, Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Leif Sander
- Speciality Network: Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- German Center for Lung Research (DZL), 35392, Gießen, Germany
| | - Christine Goffinet
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 , Berlin, Germany.
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Han X, Wang B, Situ C, Qi Y, Zhu H, Li Y, Guo X. scapGNN: A graph neural network-based framework for active pathway and gene module inference from single-cell multi-omics data. PLoS Biol 2023; 21:e3002369. [PMID: 37956172 PMCID: PMC10681325 DOI: 10.1371/journal.pbio.3002369] [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: 02/14/2023] [Revised: 11/27/2023] [Accepted: 10/07/2023] [Indexed: 11/15/2023] Open
Abstract
Although advances in single-cell technologies have enabled the characterization of multiple omics profiles in individual cells, extracting functional and mechanistic insights from such information remains a major challenge. Here, we present scapGNN, a graph neural network (GNN)-based framework that creatively transforms sparse single-cell profile data into the stable gene-cell association network for inferring single-cell pathway activity scores and identifying cell phenotype-associated gene modules from single-cell multi-omics data. Systematic benchmarking demonstrated that scapGNN was more accurate, robust, and scalable than state-of-the-art methods in various downstream single-cell analyses such as cell denoising, batch effect removal, cell clustering, cell trajectory inference, and pathway or gene module identification. scapGNN was developed as a systematic R package that can be flexibly extended and enhanced for existing analysis processes. It provides a new analytical platform for studying single cells at the pathway and network levels.
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Affiliation(s)
- Xudong Han
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Medicine, Southeast University, Nanjing, China
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Bing Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Medicine, Southeast University, Nanjing, China
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Chenghao Situ
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Yaling Qi
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Hui Zhu
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Yan Li
- Department of Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Medicine, Southeast University, Nanjing, China
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
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Barilli A, Recchia Luciani G, Visigalli R, Sala R, Soli M, Dall’Asta V, Rotoli BM. Cytokine-Induced iNOS in A549 Alveolar Epithelial Cells: A Potential Role in COVID-19 Lung Pathology. Biomedicines 2023; 11:2699. [PMID: 37893073 PMCID: PMC10603955 DOI: 10.3390/biomedicines11102699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND In COVID-19, an uncontrolled inflammatory response might worsen lung damage, leading to acute respiratory distress syndrome (ARDS). Recent evidence points to the induction of inducible nitric oxide synthase (NOS2/iNOS) as a component of inflammatory response since NOS2 is upregulated in critical COVID-19 patients. Here, we explore the mechanisms underlying the modulation of iNOS expression in human alveolar cells. METHODS A549 WT and IRF1 KO cells were exposed to a conditioned medium of macrophages treated with SARS-CoV-2 spike S1. Additionally, the effect of IFNγ, IL-1β, IL-6, and TNFα, either alone or combined, was addressed. iNOS expression was assessed with RT-qPCR and Western blot. The effect of baricitinib and CAPE, inhibitors of JAK/STAT and NF-kB, respectively, was also investigated. RESULTS Treatment with a conditioned medium caused a marked induction of iNOS in A549 WT and a weak stimulation in IRF1 KO. IFNγ induced NOS2 and synergistically cooperated with IL-1β and TNFα. The inhibitory pattern of baricitinb and CAPE indicates that cytokines activate both IRF1 and NF-κB through the JAK/STAT1 pathway. CONCLUSIONS Cytokines secreted by S1-activated macrophages markedly induce iNOS, whose expression is suppressed by baricitinib. Our findings sustain the therapeutic efficacy of this drug in COVID-19 since, besides limiting the cytokine storm, it also prevents NOS2 induction.
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Affiliation(s)
- Amelia Barilli
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (A.B.)
| | - Giulia Recchia Luciani
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (A.B.)
| | - Rossana Visigalli
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (A.B.)
| | - Roberto Sala
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (A.B.)
| | - Maurizio Soli
- Immunohematology and Transfusion Medicine, University Hospital of Parma, 43125 Parma, Italy
| | - Valeria Dall’Asta
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (A.B.)
| | - Bianca Maria Rotoli
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (A.B.)
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Carlini F, Lusi V, Rizzi C, Assogna F, Laroni A. Cladribine Tablets Mode of Action, Learning from the Pandemic: A Narrative Review. Neurol Ther 2023; 12:1477-1490. [PMID: 37421556 PMCID: PMC10444742 DOI: 10.1007/s40120-023-00520-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 06/16/2023] [Indexed: 07/10/2023] Open
Abstract
Multiple sclerosis (MS) is an immune-mediated disease of the central nervous system, characterized by chronic, inflammatory, demyelinating, and neurodegenerative processes. MS management relies on disease-modifying drugs that suppress/modulate the immune system. Cladribine tablets (CladT) have been approved by different health authorities for patients with various forms of relapsing MS. The drug has been demonstrated to deplete CD4+ and CD8+ T-cells, with a higher effect described in the former, and to decrease total CD19+, CD20+, and naive B-cell counts. COVID-19 is expected to become endemic, suggesting its potential infection risk for immuno-compromised patients, including MS patients treated with disease-modifying drugs. We report here the available data on disease-modifying drug-treated-MS patients and COVID-19 infection and vaccination, with a focus on CladT. MS patients treated with CladT are not at higher risk of developing severe COVID-19. While anti-SARS-CoV-2 vaccination is recommended in all MS patients with guidelines addressing vaccination timing according to the different disease-modifying drugs, no vaccination timing restrictions seem to be necessary for cladribine, based on its mechanism of action and available evidence. Published data suggest that CladT treatment does not impact the production of anti-SARS-CoV-2 antibodies after COVID-19 vaccination, possibly due to its relative sparing effect on naïve B-cells and the rapid B-cell reconstitution following treatment. Slightly lower specific T-cell responses are likely not impacting the risk of breakthrough COVID-19. It could be stated that cladribine's transient effect on innate immune cells likely contributes to maintaining an adequate first line of defense against the SARS-CoV-2 virus.
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Affiliation(s)
- Federico Carlini
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, Genoa, Italy
| | - Valeria Lusi
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, Genoa, Italy
| | - Caterina Rizzi
- Merck Serono S.P.A., Italy an Affiliate of Merck KGaA, Piazza del Pigneto 9, Rome, Italy
| | - Francesco Assogna
- Merck Serono S.P.A., Italy an Affiliate of Merck KGaA, Piazza del Pigneto 9, Rome, Italy
| | - Alice Laroni
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, Genoa, Italy.
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, Largo Daneo 3, Genoa, Italy.
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Tian L, Xie Y, Xie Z, Tian J, Tian W. AtacAnnoR: a reference-based annotation tool for single cell ATAC-seq data. Brief Bioinform 2023; 24:bbad268. [PMID: 37497729 DOI: 10.1093/bib/bbad268] [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: 03/14/2023] [Revised: 06/14/2023] [Accepted: 07/04/2023] [Indexed: 07/28/2023] Open
Abstract
Here, we present AtacAnnoR, a two-round annotation method for scATAC-seq data using well-annotated scRNA-seq data as reference. We evaluate AtacAnnoR's performance against six competing methods on 11 benchmark datasets. Our results show that AtacAnnoR achieves the highest mean accuracy and the highest mean balanced accuracy and performs particularly well when unpaired scRNA-seq data are used as the reference. Furthermore, AtacAnnoR implements a 'Combine and Discard' strategy to further improve annotation accuracy when annotations of multiple references are available. AtacAnnoR has been implemented in an R package and can be directly integrated into currently popular scATAC-seq analysis pipelines.
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Affiliation(s)
- Lejin Tian
- State Key Laboratory of Genetic Engineering, Department of Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yunxiao Xie
- State Key Laboratory of Genetic Engineering, Department of Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhaobin Xie
- State Key Laboratory of Genetic Engineering, Department of Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | | | - Weidong Tian
- State Key Laboratory of Genetic Engineering, Department of Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
- Children's Hospital of Fudan University, Shanghai, China
- Children's Hospital of Shandong University, Jinan, China
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Zhang Y, Shen J, Cheng W, Roy B, Zhao R, Chai T, Sheng Y, Zhang Z, Chen X, Liang W, Hu W, Liao Q, Pan S, Zhuang W, Zhang Y, Chen R, Mei J, Wei H, Fang X. Microbiota-mediated shaping of mouse spleen structure and immune function characterized by scRNA-seq and Stereo-seq. J Genet Genomics 2023; 50:688-701. [PMID: 37156441 DOI: 10.1016/j.jgg.2023.04.012] [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: 01/12/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
Gut microbes exhibit complex interactions with their hosts and shape an organism's immune system throughout its lifespan. As the largest secondary lymphoid organ, the spleen has a wide range of immunological functions. To explore the role of microbiota in regulating and shaping the spleen, we employ scRNA-seq and Stereo-seq technologies based on germ-free (GF) mice to detect differences in tissue size, anatomical structure, cell types, functions, and spatial molecular characteristics. We identify 18 cell types, 9 subtypes of T cells, and 7 subtypes of B cells. Gene differential expression analysis reveals that the absence of microorganisms results in alterations in erythropoiesis within the red pulp region and congenital immune deficiency in the white pulp region. Stereo-seq results demonstrate a clear hierarchy of immune cells in the spleen, including marginal zone (MZ) macrophages, MZ B cells, follicular B cells and T cells, distributed in a well-defined pattern from outside to inside. However, this hierarchical structure is disturbed in GF mice. Ccr7 and Cxcl13 chemokines are specifically expressed in the spatial locations of T cells and B cells, respectively. We speculate that the microbiota may mediate the structural composition or partitioning of spleen immune cells by modulating the expression levels of chemokines.
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Affiliation(s)
- Yin Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Juan Shen
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Wei Cheng
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Bhaskar Roy
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Ruizhen Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Tailiang Chai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yifei Sheng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Zhao Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Xueting Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | | | - Weining Hu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Qijun Liao
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Shanshan Pan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Wen Zhuang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Yangrui Zhang
- BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Rouxi Chen
- BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Junpu Mei
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Hong Wei
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
| | - Xiaodong Fang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China.
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Bader SM, Cooney JP, Sheerin D, Taiaroa G, Harty L, Davidson KC, Mackiewicz L, Dayton M, Wilcox S, Whitehead L, Rogers KL, Georgy SR, Coussens AK, Grimley SL, Corbin V, Pitt M, Coin L, Pickering R, Thomas M, Allison CC, McAuley J, Purcell DFJ, Doerflinger M, Pellegrini M. SARS-CoV-2 mouse adaptation selects virulence mutations that cause TNF-driven age-dependent severe disease with human correlates. Proc Natl Acad Sci U S A 2023; 120:e2301689120. [PMID: 37523564 PMCID: PMC10410703 DOI: 10.1073/pnas.2301689120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/13/2023] [Indexed: 08/02/2023] Open
Abstract
The diversity of COVID-19 disease in otherwise healthy people, from seemingly asymptomatic infection to severe life-threatening disease, is not clearly understood. We passaged a naturally occurring near-ancestral SARS-CoV-2 variant, capable of infecting wild-type mice, and identified viral genomic mutations coinciding with the acquisition of severe disease in young adult mice and lethality in aged animals. Transcriptomic analysis of lung tissues from mice with severe disease elucidated a host antiviral response dominated mainly by interferon and IL-6 pathway activation in young mice, while in aged animals, a fatal outcome was dominated by TNF and TGF-β signaling. Congruent with our pathway analysis, we showed that young TNF-deficient mice had mild disease compared to controls and aged TNF-deficient animals were more likely to survive infection. Emerging clinical correlates of disease are consistent with our preclinical studies, and our model may provide value in defining aberrant host responses that are causative of severe COVID-19.
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Affiliation(s)
- Stefanie M. Bader
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - James P. Cooney
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - Dylan Sheerin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - George Taiaroa
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Leigh Harty
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Kathryn C. Davidson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - Liana Mackiewicz
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
| | - Merle Dayton
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
| | - Stephen Wilcox
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - Lachlan Whitehead
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - Kelly L. Rogers
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - Smitha Rose Georgy
- Anatomic Pathology, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Melbourne, VIC3030, Australia
| | - Anna K. Coussens
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - Samantha L. Grimley
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Vincent Corbin
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Miranda Pitt
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Lachlan Coin
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Raelene Pickering
- Department of Diabetes, Monash University, Central Clinical School, Level 5, Alfred Centre, Melbourne, VIC3004, Australia
| | - Merlin Thomas
- Department of Diabetes, Monash University, Central Clinical School, Level 5, Alfred Centre, Melbourne, VIC3004, Australia
| | - Cody C. Allison
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
| | - Julie McAuley
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Damian F. J. Purcell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Marcel Doerflinger
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - Marc Pellegrini
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
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Qin D, Yu F, Wu D, Han C, Yao X, Yang L, Yang X, Wang Q, He D, Zhao B. The underlying molecular mechanisms and biomarkers between periodontitis and COVID-19. BMC Oral Health 2023; 23:524. [PMID: 37495990 PMCID: PMC10369766 DOI: 10.1186/s12903-023-03150-4] [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: 02/20/2023] [Accepted: 06/20/2023] [Indexed: 07/28/2023] Open
Abstract
OBJECTIVE Emerging evidence shows the clinical consequences of patient with COVID-19 and periodontitis are not promising, and periodontitis is a risk factor. Periodontitis and COVID-19 probably have a relationship. Hence, this study aimed to identify the common molecular mechanism that may help to devise potential therapeutic strategies in the future. MATERIAL AND METHODS We analyzed two RNA-seq datasets for differential expressed genes, enrichment of biological processes, transcription factors (TFs) and deconvolution-based immune cell types in periodontitis, COVID-19 and healthy controls. Relationships between TFs and mRNA were established by Pearson correlation analysis, and the common TFs-mRNA regulatory network and nine co-upregulated TFs of the two diseases was obtained. The RT-PCR detected the TFs. RESULTS A total of 1616 and 10201 differentially expressed gene (DEGs) from periodontitis and COVID-19 are found. Moreover, nine shared TFs and common biological processes associated with lymphocyte activation involved in immune response were identified across periodontitis and COVID-19. The cell type enrichment revealed elevated plasma cells among two diseases. The RT-PCR further confirmed the nine TFs up-regulation in periodontitis. CONCLUSION The pathogenesis of periodontitis and COVID-19 is closely related to the expression of TFs and lymphocyte activation, which can provide potential targets for treatment.
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Affiliation(s)
- Danlei Qin
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
- Department of Medical Imaging, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Feiyan Yu
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
| | - Dongchao Wu
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
| | - Chong Han
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
| | - Xuemin Yao
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
| | - Lulu Yang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
| | - Xi Yang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
| | - Qianqian Wang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China
| | - Dongning He
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China.
| | - Bin Zhao
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No 63, New South Road, Yingze District, Taiyuan, 030001, Shanxi, China.
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Luo H, Yan J, Zhang D, Zhou X. Identification of cuproptosis-related molecular subtypes and a novel predictive model of COVID-19 based on machine learning. Front Immunol 2023; 14:1152223. [PMID: 37533853 PMCID: PMC10393044 DOI: 10.3389/fimmu.2023.1152223] [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: 01/27/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023] Open
Abstract
Background To explicate the pathogenic mechanisms of cuproptosis, a newly observed copper induced cell death pattern, in Coronavirus disease 2019 (COVID-19). Methods Cuproptosis-related subtypes were distinguished in COVID-19 patients and associations between subtypes and immune microenvironment were probed. Three machine algorithms, including LASSO, random forest, and support vector machine, were employed to identify differentially expressed genes between subtypes, which were subsequently used for constructing cuproptosis-related risk score model in the GSE157103 cohort to predict the occurrence of COVID-19. The predictive values of the cuproptosis-related risk score were verified in the GSE163151 cohort, GSE152418 cohort and GSE171110 cohort. A nomogram was created to facilitate the clinical use of this risk score, and its validity was validated through a calibration plot. Finally, the model genes were validated using lung proteomics data from COVID-19 cases and single-cell data. Results Patients with COVID-19 had higher significantly cuproptosis level in blood leukocytes compared to patients without COVID-19. Two cuproptosis clusters were identified by unsupervised clustering approach and cuproptosis cluster A characterized by T cell receptor signaling pathway had a better prognosis than cuproptosis cluster B. We constructed a cuproptosis-related risk score, based on PDHA1, PDHB, MTF1 and CDKN2A, and a nomogram was created, which both showed excellent predictive values for COVID-19. And the results of proteomics showed that the expression levels of PDHA1 and PDHB were significantly increased in COVID-19 patient samples. Conclusion Our study constructed and validated an cuproptosis-associated risk model and the risk score can be used as a powerful biomarker for predicting the existence of SARS-CoV-2 infection.
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Affiliation(s)
- Hong Luo
- Department of Tuberculosis and Respiratory, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology; Hubei Clinical Research Center for Infectious Diseases; Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences; Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, China
| | - Jisong Yan
- Department of Tuberculosis and Respiratory, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology; Hubei Clinical Research Center for Infectious Diseases; Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences; Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, China
| | - Dingyu Zhang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, China
- Center for Translational Medicine, Wuhan Jinyintan Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
| | - Xia Zhou
- Department of Tuberculosis and Respiratory, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology; Hubei Clinical Research Center for Infectious Diseases; Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences; Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, China
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Xie J, Gu A, He H, Zhao Q, Yu Y, Chen J, Cheng Z, Zhou P, Zhou Q, Jin M. Autoimmune thyroid disease disrupts immune homeostasis in the endometrium of unexplained infertility women-a single-cell RNA transcriptome study during the implantation window. Front Endocrinol (Lausanne) 2023; 14:1185147. [PMID: 37501789 PMCID: PMC10368980 DOI: 10.3389/fendo.2023.1185147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/23/2023] [Indexed: 07/29/2023] Open
Abstract
Objective Autoimmune thyroid disease (AITD) is known to be associated with unexplained infertility in women. Although the presence of antithyroid antibodies have been speculated to be a marker of an immune imbalance that might lead to implantation failure, its underlying mechanism influencing the endometrial receptivity remains to be elucidated. In this study, we used single-cell RNA sequencing (scRNA-seq) to dissect immune microenvironment in endometrium of AITD patients during window of implantation (WOI). Methods We collected CD45+ immune cell populations of endometrium samples of unexplained infertile women with AITD (n=3), as well as samples of AITD- controls (n=3). The cells were then processed with 10X Genomics Chromium for further analysis. Results We characterized 28 distinct immune cell subtypes totally, and uncovered differences in the composition and gene expression patterns between AITD patients and controls. The proportions of T CD4+, cNK, ILC3, T CD8+ GZMK+, T CD8+ Cytotoxic and ILC3 CD3E - cells were increased, and CD366+ uNK1 was decreased in AITD+ patients. And the abnormal expression of GNLY and chemokines was observed in AITD patients. In addition, uNK and T CD8+ Cytotoxic cells showed lower cytotoxicity but activation of immune response. Genes enriched in cell adhesion of ILC3 and Tregs were downregulated, while the number of ILC3 and Tregs were increased. Conclusion Immune imbalance exists in endometrium during WOI, which may impact embryo implantation.
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Affiliation(s)
- Jilai Xie
- Second Affiliated Hospital, School of Medicine, Zhejiang University, Department of Reproductive Medicine, Hangzhou, China
| | - Aiyuan Gu
- Ministry of Education (MOE) Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Huangyi He
- Ministry of Education (MOE) Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Qiaohang Zhao
- Second Affiliated Hospital, School of Medicine, Zhejiang University, Department of Reproductive Medicine, Hangzhou, China
| | - Ya Yu
- Second Affiliated Hospital, School of Medicine, Zhejiang University, Department of Reproductive Medicine, Hangzhou, China
| | - Jian Chen
- Second Affiliated Hospital, School of Medicine, Zhejiang University, Department of Reproductive Medicine, Hangzhou, China
| | - Zhangliang Cheng
- Ministry of Education (MOE) Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Ping Zhou
- Second Affiliated Hospital, School of Medicine, Zhejiang University, Department of Reproductive Medicine, Hangzhou, China
| | - Qi Zhou
- Second Affiliated Hospital, School of Medicine, Zhejiang University, Department of Reproductive Medicine, Hangzhou, China
- Ministry of Education (MOE) Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Min Jin
- Second Affiliated Hospital, School of Medicine, Zhejiang University, Department of Reproductive Medicine, Hangzhou, China
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Carroll TM, Chadwick JA, Owen RP, White MJ, Kaplinsky J, Peneva I, Frangou A, Xie PF, Chang J, Roth A, Amess B, James SA, Rei M, Fuchs HS, McCann KJ, Omiyale AO, Jacobs BA, Lord SR, Norris-Bulpitt S, Dobbie ST, Griffiths L, Ramirez KA, Ricciardi T, Macri MJ, Ryan A, Venhaus RR, Van den Eynde BJ, Karydis I, Schuster-Böckler B, Middleton MR, Lu X. Tumor monocyte content predicts immunochemotherapy outcomes in esophageal adenocarcinoma. Cancer Cell 2023; 41:1222-1241.e7. [PMID: 37433281 DOI: 10.1016/j.ccell.2023.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 04/07/2023] [Accepted: 06/14/2023] [Indexed: 07/13/2023]
Abstract
For inoperable esophageal adenocarcinoma (EAC), identifying patients likely to benefit from recently approved immunochemotherapy (ICI+CTX) treatments remains a key challenge. We address this using a uniquely designed window-of-opportunity trial (LUD2015-005), in which 35 inoperable EAC patients received first-line immune checkpoint inhibitors for four weeks (ICI-4W), followed by ICI+CTX. Comprehensive biomarker profiling, including generation of a 65,000-cell single-cell RNA-sequencing atlas of esophageal cancer, as well as multi-timepoint transcriptomic profiling of EAC during ICI-4W, reveals a novel T cell inflammation signature (INCITE) whose upregulation correlates with ICI-induced tumor shrinkage. Deconvolution of pre-treatment gastro-esophageal cancer transcriptomes using our single-cell atlas identifies high tumor monocyte content (TMC) as an unexpected ICI+CTX-specific predictor of greater overall survival (OS) in LUD2015-005 patients and of ICI response in prevalent gastric cancer subtypes from independent cohorts. Tumor mutational burden is an additional independent and additive predictor of LUD2015-005 OS. TMC can improve patient selection for emerging ICI+CTX therapies in gastro-esophageal cancer.
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Affiliation(s)
- Thomas M Carroll
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Joseph A Chadwick
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Richard P Owen
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Michael J White
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Joseph Kaplinsky
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Iliana Peneva
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Anna Frangou
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, University of Oxford, Oxford, UK
| | - Phil F Xie
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Jaeho Chang
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Andrew Roth
- Department of Pathology and Molecular Medicine, University of British Columbia, Vancouver, Canada; Department of Computer Science, University of British Columbia, Vancouver, Canada; Department of Molecular Oncology, BC Cancer, Vancouver, Canada
| | - Bob Amess
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Sabrina A James
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Margarida Rei
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Hannah S Fuchs
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Katy J McCann
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Ayo O Omiyale
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | | | - Simon R Lord
- Department of Oncology, University of Oxford, Oxford, UK
| | - Stewart Norris-Bulpitt
- Early Phase Clinical Trials Unit, Cancer & Haematology Centre, Churchill Hospital, Oxford, UK
| | - Sam T Dobbie
- Oncology Clinical Trials Office (OCTO), Department of Oncology, University of Oxford, Oxford, UK
| | - Lucinda Griffiths
- Oncology Clinical Trials Office (OCTO), Department of Oncology, University of Oxford, Oxford, UK
| | | | | | | | | | | | - Benoit J Van den Eynde
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK; Ludwig Institute for Cancer Research, Brussels, Belgium; de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Ioannis Karydis
- Cancer Sciences Unit, University of Southampton and Cancer Care Group, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | - Mark R Middleton
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK; Department of Oncology, University of Oxford, Oxford, UK; Early Phase Clinical Trials Unit, Cancer & Haematology Centre, Churchill Hospital, Oxford, UK.
| | - Xin Lu
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.
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Gordon-Lipkin EM, Banerjee P, Franco JLM, Tarasenko T, Kruk S, Thompson E, Gildea DE, Zhang S, Wolfsberg TG, Flegel WA, McGuire PJ. Primary oxidative phosphorylation defects lead to perturbations in the human B cell repertoire. Front Immunol 2023; 14:1142634. [PMID: 37483601 PMCID: PMC10361569 DOI: 10.3389/fimmu.2023.1142634] [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: 01/11/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction The majority of studies on oxidative phosphorylation in immune cells have been performed in mouse models, necessitating human translation. To understand the impact of oxidative phosphorylation (OXPHOS) deficiency on human immunity, we studied children with primary mitochondrial disease (MtD). Methods scRNAseq analysis of peripheral blood mononuclear cells was performed on matched children with MtD (N = 4) and controls (N = 4). To define B cell function we performed phage display immunoprecipitation sequencing on a cohort of children with MtD (N = 19) and controls (N = 16). Results Via scRNAseq, we found marked reductions in select populations involved in the humoral immune response, especially antigen presenting cells, B cell and plasma populations, with sparing of T cell populations. MTRNR2L8, a marker of bioenergetic stress, was significantly elevated in populations that were most depleted. mir4485, a miRNA contained in the intron of MTRNR2L8, was co-expressed. Knockdown studies of mir4485 demonstrated its role in promoting survival by modulating apoptosis. To determine the functional consequences of our findings on humoral immunity, we studied the antiviral antibody repertoire in children with MtD and controls using phage display and immunoprecipitation sequencing. Despite similar viral exposomes, MtD displayed antiviral antibodies with less robust fold changes and limited polyclonality. Discussion Overall, we show that children with MtD display perturbations in the B cell repertoire which may impact humoral immunity and the ability to clear viral infections.
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Affiliation(s)
- Eliza M. Gordon-Lipkin
- Metabolism, Infection and Immunity Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Payal Banerjee
- Metabolism, Infection and Immunity Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jose Luis Marin Franco
- Metabolism, Infection and Immunity Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Tatiana Tarasenko
- Metabolism, Infection and Immunity Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Shannon Kruk
- Metabolism, Infection and Immunity Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Elizabeth Thompson
- Metabolism, Infection and Immunity Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Derek E. Gildea
- Bioinformatics and Scientific Programming Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Suiyuan Zhang
- Bioinformatics and Scientific Programming Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Tyra G. Wolfsberg
- Bioinformatics and Scientific Programming Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | | | - Willy A. Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Peter J. McGuire
- Metabolism, Infection and Immunity Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
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Derbois C, Palomares MA, Deleuze JF, Cabannes E, Bonnet E. Single cell transcriptome sequencing of stimulated and frozen human peripheral blood mononuclear cells. Sci Data 2023; 10:433. [PMID: 37414801 PMCID: PMC10326076 DOI: 10.1038/s41597-023-02348-z] [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: 03/27/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023] Open
Abstract
Peripheral blood mononuclear cells (PBMCs) are blood cells that are a critical part of the immune system used to fight off infection, defending our bodies from harmful pathogens. In biomedical research, PBMCs are commonly used to study global immune response to disease outbreak and progression, pathogen infections, for vaccine development and a multitude of other clinical applications. Over the past few years, the revolution in single-cell RNA sequencing (scRNA-seq) has enabled an unbiased quantification of gene expression in thousands of individual cells, which provides a more efficient tool to decipher the immune system in human diseases. In this work, we generate scRNA-seq data from human PBMCs at high sequencing depth (>100,000 reads/cell) for more than 30,000 cells, in resting, stimulated, fresh and frozen conditions. The data generated can be used for benchmarking batch correction and data integration methods, and to study the effect of freezing-thawing cycles on the quality of immune cell populations and their transcriptomic profiles.
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Affiliation(s)
- Céline Derbois
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Marie-Ange Palomares
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Eric Cabannes
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Eric Bonnet
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France.
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Zhang J, Shu X, Deng R, Yang Z, Shu M, Ou X, Zhang X, Wu Z, Zeng H, Shao L. Transcriptome Changes of Hematopoietic Stem and Progenitor Cells in the Peripheral Blood of COVID-19 Patients by scRNA-seq. Int J Mol Sci 2023; 24:10878. [PMID: 37446049 DOI: 10.3390/ijms241310878] [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: 05/18/2023] [Revised: 06/19/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) threatens public health all over the world. It is well-accepted that the immune cells in peripheral blood are widely involved in the pathological process of COVID-19. However, hematopoietic stem and progenitor cells (HSPCs), as the main source of peripheral immune cells, have not been well studied during COVID-19 infection. We comprehensively revealed the transcriptome changes of peripheral blood HSPCs after COVID-19 infection and vaccination by single-cell RNA-seq. Compared with healthy individuals, the proportion of HSPCs in COVID-19 patients significantly increased. The increase in the proportion of HSPCs might be partly attributed to the enhancement of the HSPCs proliferation upon COVID-19 infection. However, the stemness damage of HSPCs is reflected by the decrease of differentiation signal, which can be used as a potential specific indicator of the severity and duration of COVID-19 infection. Type I interferon (IFN-I) and translation signals in HSPCs were mostly activated and inhibited after COVID-19 infection, respectively. In addition, the response of COVID-19 vaccination to the body is mild, while the secondary vaccination strengthens the immune response of primary vaccination. In conclusion, our study provides new insights into understanding the immune mechanism of COVID-19 infection.
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Affiliation(s)
- Jinfu Zhang
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Xin Shu
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Rong Deng
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Zihao Yang
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Manling Shu
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Xiangying Ou
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Xuan Zhang
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Zhenyu Wu
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Huihong Zeng
- Department of Histology and Embryology, School of Basic Medicine, Nanchang University, Nanchang 330006, China
| | - Lijian Shao
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
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Loy CJ, Sotomayor-Gonzalez A, Servellita V, Nguyen J, Lenz J, Bhattacharya S, Williams ME, Cheng AP, Bliss A, Saldhi P, Brazer N, Streithorst J, Suslovic W, Hsieh CJ, Bahar B, Wood N, Foresythe A, Gliwa A, Bhakta K, Perez MA, Hussaini L, Anderson EJ, Chahroudi A, Delaney M, Butte AJ, DeBiasi RL, Rostad CA, De Vlaminck I, Chiu CY. Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C. Cell Rep Med 2023; 4:101034. [PMID: 37279751 PMCID: PMC10121104 DOI: 10.1016/j.xcrm.2023.101034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/28/2022] [Accepted: 04/11/2023] [Indexed: 06/08/2023]
Abstract
Differential host responses in coronavirus disease 2019 (COVID-19) and multisystem inflammatory syndrome in children (MIS-C) remain poorly characterized. Here, we use next-generation sequencing to longitudinally analyze blood samples from pediatric patients with COVID-19 or MIS-C across three hospitals. Profiling of plasma cell-free nucleic acids uncovers distinct signatures of cell injury and death between COVID-19 and MIS-C, with increased multiorgan involvement in MIS-C encompassing diverse cell types, including endothelial and neuronal cells, and an enrichment of pyroptosis-related genes. Whole-blood RNA profiling reveals upregulation of similar pro-inflammatory pathways in COVID-19 and MIS-C but also MIS-C-specific downregulation of T cell-associated pathways. Profiling of plasma cell-free RNA and whole-blood RNA in paired samples yields different but complementary signatures for each disease state. Our work provides a systems-level view of immune responses and tissue damage in COVID-19 and MIS-C and informs future development of new disease biomarkers.
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Affiliation(s)
- Conor J Loy
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joan Lenz
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Sanchita Bhattacharya
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Alexandre P Cheng
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Andrew Bliss
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Prachi Saldhi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Noah Brazer
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jessica Streithorst
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Charlotte J Hsieh
- Division of Pediatric Infectious Diseases and Global Health, Department of Pediatrics, University of California San Francisco, Oakland, CA 94609
| | - Burak Bahar
- Children's National Hospital, Washington, DC 20010, USA
| | - Nathan Wood
- UCSF Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Abiodun Foresythe
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amelia Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kushmita Bhakta
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Maria A Perez
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Laila Hussaini
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Evan J Anderson
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA; Department of Medicine, Emory University School of Medicine, Atlanta, GA 30307, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Meghan Delaney
- Children's National Hospital, Washington, DC 20010, USA; The George Washington University School of Medicine, Washington, DC 20052, USA
| | - Atul J Butte
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Roberta L DeBiasi
- Children's National Hospital, Washington, DC 20010, USA; The George Washington University School of Medicine, Washington, DC 20052, USA
| | - Christina A Rostad
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA.
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA.
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Vengalil A, Nizamutdinov D, Su M, Huang JH. Mechanisms of SARS-CoV-2-induced Encephalopathy and Encephalitis in COVID-19 Cases. Neurosci Insights 2023; 18:26331055231172522. [PMID: 37255742 PMCID: PMC10225804 DOI: 10.1177/26331055231172522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/12/2023] [Indexed: 06/01/2023] Open
Abstract
The SARS-CoV-2 virus caused an unprecedented pandemic around the globe, infecting 36.5 million people and causing the death of over 1 million in the United States of America alone. COVID-19 patients demonstrated respiratory symptoms, cardiovascular complications, and neurologic symptoms, which in most severe cases included encephalopathy and encephalitis. Hypoxia and the uncontrolled proliferation of cytokines are commonly recognized to cause encephalopathy, while the retrograde trans-synaptic spread of the virus is thought to cause encephalitis in SARS-CoV-2-induced pathogenesis. Although recent research revealed some mechanisms explaining the development of neurologic symptoms, it still remains unclear whether interactions between these mechanisms exist. This review focuses on the discussion and analysis of previously reported hypotheses of SARS-CoV-2-induced encephalopathy and encephalitis and looks into possible overlaps between the pathogenesis of both neurological outcomes of the disease. Promising therapeutic approaches to prevent and treat SARS-CoV-2-induced neurological complications are also covered. More studies are needed to further investigate the dominant mechanism of pathogenesis for developing more effective preventative measures in COVID-19 cases with the neurologic presentation.
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Affiliation(s)
- Aaron Vengalil
- Neurosurgery, Texas A&M University,
College of Medicine, Temple, TX, USA
| | - Damir Nizamutdinov
- Neurosurgery, Texas A&M University,
College of Medicine, Temple, TX, USA
- Neurosurgery, Baylor Scott and White
Health, Neuroscience Institute, Temple, TX, USA
| | - Matthew Su
- Department of BioSciences, Rice
University, Houston, TX, USA
| | - Jason H Huang
- Neurosurgery, Texas A&M University,
College of Medicine, Temple, TX, USA
- Neurosurgery, Baylor Scott and White
Health, Neuroscience Institute, Temple, TX, USA
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García-García A, Pérez de Diego R, Flores C, Rinchai D, Solé-Violán J, Deyà-Martínez À, García-Solis B, Lorenzo-Salazar JM, Hernández-Brito E, Lanz AL, Moens L, Bucciol G, Almuqamam M, Domachowske JB, Colino E, Santos-Perez JL, Marco FM, Pignata C, Bousfiha A, Turvey SE, Bauer S, Haerynck F, Ocejo-Vinyals JG, Lendinez F, Prader S, Naumann-Bartsch N, Pachlopnik Schmid J, Biggs CM, Hildebrand K, Dreesman A, Cárdenes MÁ, Ailal F, Benhsaien I, Giardino G, Molina-Fuentes A, Fortuny C, Madhavarapu S, Conway DH, Prando C, Schidlowski L, Martínez de Saavedra Álvarez MT, Alfaro R, Rodríguez de Castro F, Meyts I, Hauck F, Puel A, Bastard P, Boisson B, Jouanguy E, Abel L, Cobat A, Zhang Q, Casanova JL, Alsina L, Rodríguez-Gallego C. Humans with inherited MyD88 and IRAK-4 deficiencies are predisposed to hypoxemic COVID-19 pneumonia. J Exp Med 2023; 220:e20220170. [PMID: 36880831 PMCID: PMC9998661 DOI: 10.1084/jem.20220170] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 11/11/2022] [Accepted: 01/30/2023] [Indexed: 03/08/2023] Open
Abstract
X-linked recessive deficiency of TLR7, a MyD88- and IRAK-4-dependent endosomal ssRNA sensor, impairs SARS-CoV-2 recognition and type I IFN production in plasmacytoid dendritic cells (pDCs), thereby underlying hypoxemic COVID-19 pneumonia with high penetrance. We report 22 unvaccinated patients with autosomal recessive MyD88 or IRAK-4 deficiency infected with SARS-CoV-2 (mean age: 10.9 yr; 2 mo to 24 yr), originating from 17 kindreds from eight countries on three continents. 16 patients were hospitalized: six with moderate, four with severe, and six with critical pneumonia, one of whom died. The risk of hypoxemic pneumonia increased with age. The risk of invasive mechanical ventilation was also much greater than in age-matched controls from the general population (OR: 74.7, 95% CI: 26.8-207.8, P < 0.001). The patients' susceptibility to SARS-CoV-2 can be attributed to impaired TLR7-dependent type I IFN production by pDCs, which do not sense SARS-CoV-2 correctly. Patients with inherited MyD88 or IRAK-4 deficiency were long thought to be selectively vulnerable to pyogenic bacteria, but also have a high risk of hypoxemic COVID-19 pneumonia.
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Affiliation(s)
- Ana García-García
- Pediatric Allergy and Clinical Immunology Dept., Clinical Immunology and Primary Immunodeficiencies Unit, Hospital Sant Joan de Déu, Barcelona, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children, Institut de Recerca Sant Joan de Déu, Barcelona, Barcelona, Spain
- Clinical Immunology Unit, Hospital Sant Joan de Déu-Hospital Clínic Barcelona, Barcelona, Spain
| | - Rebeca Pérez de Diego
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, La Paz Hospital, Madrid, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Dept. of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Jordi Solé-Violán
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Dept. of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Dept. of Intensive Care Medicine, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Àngela Deyà-Martínez
- Pediatric Allergy and Clinical Immunology Dept., Clinical Immunology and Primary Immunodeficiencies Unit, Hospital Sant Joan de Déu, Barcelona, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children, Institut de Recerca Sant Joan de Déu, Barcelona, Barcelona, Spain
- Clinical Immunology Unit, Hospital Sant Joan de Déu-Hospital Clínic Barcelona, Barcelona, Spain
| | - Blanca García-Solis
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, La Paz Hospital, Madrid, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Elisa Hernández-Brito
- Dept. of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Anna-Lisa Lanz
- Dept. of Pediatrics, Division of Pediatric Immunology and Rheumatology, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Leen Moens
- Laboratory for Inborn Errors of Immunity, Dept. of Microbiology, Immunology and Transplantation KU Leuven, Leuven, Belgium
| | - Giorgia Bucciol
- Laboratory for Inborn Errors of Immunity, Dept. of Microbiology, Immunology and Transplantation KU Leuven, Leuven, Belgium
- Dept. of Pediatrics, Childhood Immunology, UZ Leuven, Leuven, Belgium
| | - Mohamed Almuqamam
- Dept. of Pediatrics, Drexel University College of Medicine, St Christopher’s Hospital for Children, Philadelphia, PA, USA
| | | | - Elena Colino
- Unidad de Enfermedades Infecciosas, Complejo Hospitalario Universitario Insular-Materno Infantil, Las Palmas de Gran Canaria, Spain
| | - Juan Luis Santos-Perez
- Unidad de Gestión Clínica de Pediatría y Cirugía Pediátrica, Hospital Virgen de las Nieves-IBS, Granada, Spain
| | - Francisco M. Marco
- Dept. of Immunology, Alicante University General Hospital Doctor Balmis, Alicante, Spain
- Alicante Institute for Health and Biomedical Research, Alicante, Spain
| | - Claudio Pignata
- Dept. of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | - Aziz Bousfiha
- Dept. of Pediatric Infectious Diseases and Clinical Immunology, Ibn Rushd University Hospital, Casablanca, Morocco
- Clinical Immunology, Autoimmunity and Inflammation Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Stuart E. Turvey
- Dept. of Paediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Stefanie Bauer
- Clinic for Children and Adolescents. Dept. of Hematology and Oncology. University Clinic Erlangen, Erlangen, Germany
| | - Filomeen Haerynck
- Dept. of Pediatric Immunology and Pulmonology, Centre for Primary Immune Deficiency Ghent, Ghent University Hospital, Ghent, Belgium
- Dept. of Internal Medicine and Pediatrics, PID Research Laboratory, Ghent University, Ghent, Belgium
| | | | - Francisco Lendinez
- Dept. of Pediatric Oncohematology, Hospital Materno Infantil Torrecárdenas, Almería, Spain
| | - Seraina Prader
- Division of Immunology and Children’s Research Center, University Children’s Hospital Zurich, Zurich, Switzerland; University of Zurich, Zurich, Switzerland
| | - Nora Naumann-Bartsch
- Clinic for Children and Adolescents. Dept. of Hematology and Oncology. University Clinic Erlangen, Erlangen, Germany
| | - Jana Pachlopnik Schmid
- Division of Immunology and Children’s Research Center, University Children’s Hospital Zurich, Zurich, Switzerland; University of Zurich, Zurich, Switzerland
| | - Catherine M. Biggs
- Dept. of Paediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Kyla Hildebrand
- Dept. of Paediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | | | - Miguel Ángel Cárdenes
- Dept. of Internal Medicine, Unit of Infectious Diseases, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Fatima Ailal
- Dept. of Pediatric Infectious Diseases and Clinical Immunology, Ibn Rushd University Hospital, Casablanca, Morocco
- Clinical Immunology, Autoimmunity and Inflammation Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Ibtihal Benhsaien
- Dept. of Pediatric Infectious Diseases and Clinical Immunology, Ibn Rushd University Hospital, Casablanca, Morocco
- Clinical Immunology, Autoimmunity and Inflammation Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Giuliana Giardino
- Dept. of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | | | - Claudia Fortuny
- Study Group for Immune Dysfunction Diseases in Children, Institut de Recerca Sant Joan de Déu, Barcelona, Barcelona, Spain
- Pediatric Infectious Diseases Unit, Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER of Epidemiology and Public Health, Madrid, Spain; Translational Research Network in Pediatric Infectious Diseases, Madrid, Spain
- Dept. of Surgery and Surgical Specializations, Facultat de Medicina i Ciències de la Salut, University of Barcelona, Barcelona, Spain
| | - Swetha Madhavarapu
- Dept. of Pediatrics, Drexel University College of Medicine, St Christopher’s Hospital for Children, Philadelphia, PA, USA
| | - Daniel H. Conway
- Dept. of Pediatrics, Drexel University College of Medicine, St Christopher’s Hospital for Children, Philadelphia, PA, USA
| | - Carolina Prando
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Hospital Pequeno Príncipe, Curitiba, Brazil
| | - Laire Schidlowski
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Hospital Pequeno Príncipe, Curitiba, Brazil
| | | | - Rafael Alfaro
- Dept. of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Felipe Rodríguez de Castro
- Dept. of Medical and Surgical Sciences, School of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
- Dept. of Respiratory Diseases, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Isabelle Meyts
- Laboratory for Inborn Errors of Immunity, Dept. of Microbiology, Immunology and Transplantation KU Leuven, Leuven, Belgium
- Dept. of Pediatrics, Childhood Immunology, UZ Leuven, Leuven, Belgium
| | - Fabian Hauck
- Dept. of Pediatrics, Division of Pediatric Immunology and Rheumatology, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Paul Bastard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- Pediatric Hematology and Immunology Unit, Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Laia Alsina
- Pediatric Allergy and Clinical Immunology Dept., Clinical Immunology and Primary Immunodeficiencies Unit, Hospital Sant Joan de Déu, Barcelona, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children, Institut de Recerca Sant Joan de Déu, Barcelona, Barcelona, Spain
- Clinical Immunology Unit, Hospital Sant Joan de Déu-Hospital Clínic Barcelona, Barcelona, Spain
- Dept. of Surgery and Surgical Specializations, Facultat de Medicina i Ciències de la Salut, University of Barcelona, Barcelona, Spain
| | - Carlos Rodríguez-Gallego
- Dept. of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Dept. of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Dept. of Medical and Surgical Sciences, School of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
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Pechous RD, Malaviarachchi PA, Banerjee SK, Byrum SD, Alkam DH, Ghaffarieh A, Kurten RC, Kennedy JL, Zhang X. An ex vivo human precision-cut lung slice platform provides insight into SARS-CoV-2 pathogenesis and antiviral drug efficacy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537373. [PMID: 37131640 PMCID: PMC10153187 DOI: 10.1101/2023.04.18.537373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
COVID-19 has claimed millions of lives since the emergence of SARS-CoV-2, and lung disease appears the primary cause of the death in COVID-19 patients. However, the underlying mechanisms of COVID-19 pathogenesis remain elusive, and there is no existing model where the human disease can be faithfully recapitulated and conditions for the infection process can be experimentally controlled. Herein we report the establishment of an ex vivo human precision-cut lung slice (hPCLS) platform for studying SARS-CoV-2 pathogenicity and innate immune responses, and for evaluating the efficacy of antiviral drugs against SARS-CoV-2. We show that while SARS-CoV-2 continued to replicate during the course of infection of hPCLS, infectious virus production peaked within 2 days, and rapidly declined thereafter. Although most proinflammatory cytokines examined were induced by SARS-CoV-2 infection, the degree of induction and types of cytokines varied significantly among hPCLS from individual donors, reflecting the heterogeneity of human populations. In particular, two cytokines (IP-10 and IL-8) were highly and consistently induced, suggesting a role in the pathogenesis of COVID-19. Histopathological examination revealed focal cytopathic effects late in the infection. Transcriptomic and proteomic analyses identified molecular signatures and cellular pathways that are largely consistent with the progression of COVID-19 in patients. Furthermore, we show that homoharringtonine, a natural plant alkaloid derived from Cephalotoxus fortunei , not only inhibited virus replication but also production of pro-inflammatory cytokines, and ameliorated the histopathological changes of the lungs caused by SARS-CoV-2 infection, demonstrating the usefulness of the hPCLS platform for evaluating antiviral drugs. SIGNIFICANCE Here we established an ex vivo human precision-cut lung slice platform for assessing SARS-CoV-2 infection, viral replication kinetics, innate immune response, disease progression, and antiviral drugs. Using this platform, we identified early induction of specific cytokines, especially IP-10 and IL-8, as potential predictors for severe COVID-19, and uncovered a hitherto unrecognized phenomenon that while infectious virus disappears at late times of infection, viral RNA persists and lung histopathology commences. This finding may have important clinical implications for both acute and post-acute sequelae of COVID-19. This platform recapitulates some of the characteristics of lung disease observed in severe COVID-19 patients and is therefore a useful platform for understanding mechanisms of SARS-CoV-2 pathogenesis and for evaluating the efficacy of antiviral drugs.
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48
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Sun Q, Li X, Kuang E. Subversion of autophagy machinery and organelle-specific autophagy by SARS-CoV-2 and coronaviruses. Autophagy 2023; 19:1055-1069. [PMID: 36005882 PMCID: PMC10012907 DOI: 10.1080/15548627.2022.2116677] [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: 03/14/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 12/09/2022] Open
Abstract
As a new emerging severe coronavirus, the knowledge on the SARS-CoV-2 and COVID-19 remains very limited, whereas many concepts can be learned from the homologous coronaviruses. Macroautophagy/autophagy is finely regulated by SARS-CoV-2 infection and plays important roles in SARS-CoV-2 infection and pathogenesis. This review will explore the subversion and mechanism of the autophagy-related machinery, vacuoles and organelle-specific autophagy during infection of SARS-CoV-2 and coronaviruses to provide meaningful insights into the autophagy-related therapeutic strategies for infectious diseases of SARS-CoV-2 and coronaviruses.
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Affiliation(s)
- Qinqin Sun
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xiaojuan Li
- College of Clinic Medicine, Hubei University of Chinese Medicine, Wuhan, Hubei, China
| | - Ersheng Kuang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Ministry of Education, Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Guangzhou, Guangdong, China
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49
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Vasaikar SV, Savage AK, Gong Q, Swanson E, Talla A, Lord C, Heubeck AT, Reading J, Graybuck LT, Meijer P, Torgerson TR, Skene PJ, Bumol TF, Li XJ. A comprehensive platform for analyzing longitudinal multi-omics data. Nat Commun 2023; 14:1684. [PMID: 36973282 PMCID: PMC10041512 DOI: 10.1038/s41467-023-37432-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
Longitudinal bulk and single-cell omics data is increasingly generated for biological and clinical research but is challenging to analyze due to its many intrinsic types of variations. We present PALMO ( https://github.com/aifimmunology/PALMO ), a platform that contains five analytical modules to examine longitudinal bulk and single-cell multi-omics data from multiple perspectives, including decomposition of sources of variations within the data, collection of stable or variable features across timepoints and participants, identification of up- or down-regulated markers across timepoints of individual participants, and investigation on samples of same participants for possible outlier events. We have tested PALMO performance on a complex longitudinal multi-omics dataset of five data modalities on the same samples and six external datasets of diverse background. Both PALMO and our longitudinal multi-omics dataset can be valuable resources to the scientific community.
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Affiliation(s)
| | - Adam K Savage
- Allen Institute for Immunology, Seattle, WA, 98109, USA
| | - Qiuyu Gong
- Allen Institute for Immunology, Seattle, WA, 98109, USA
| | - Elliott Swanson
- Allen Institute for Immunology, Seattle, WA, 98109, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Aarthi Talla
- Allen Institute for Immunology, Seattle, WA, 98109, USA
| | - Cara Lord
- Allen Institute for Immunology, Seattle, WA, 98109, USA
- GlaxoSmithKline, Collegeville, PA, 19426, USA
| | | | | | | | - Paul Meijer
- Allen Institute for Immunology, Seattle, WA, 98109, USA
| | | | - Peter J Skene
- Allen Institute for Immunology, Seattle, WA, 98109, USA
| | | | - Xiao-Jun Li
- Allen Institute for Immunology, Seattle, WA, 98109, USA.
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50
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Pan T, Cao G, Tang E, Zhao Y, Penaloza-MacMaster P, Fang Y, Huang J. A single-cell atlas reveals shared and distinct immune responses and metabolic profiles in SARS-CoV-2 and HIV-1 infections. Front Genet 2023; 14:1105673. [PMID: 36992700 PMCID: PMC10040851 DOI: 10.3389/fgene.2023.1105673] [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: 11/22/2022] [Accepted: 03/01/2023] [Indexed: 03/16/2023] Open
Abstract
Introduction: Within the inflammatory immune response to viral infection, the distribution and cell type-specific profiles of immune cell populations and the immune-mediated viral clearance pathways vary according to the specific virus. Uncovering the immunological similarities and differences between viral infections is critical to understanding disease progression and developing effective vaccines and therapies. Insight into COVID-19 disease progression has been bolstered by the integration of single-cell (sc)RNA-seq data from COVID-19 patients with data from related viruses to compare immune responses. Expanding this concept, we propose that a high-resolution, systematic comparison between immune cells from SARS-CoV-2 infection and an inflammatory infectious disease with a different pathophysiology will provide a more comprehensive picture of the viral clearance pathways that underscore immunological and clinical differences between infections. Methods: Using a novel consensus single-cell annotation method, we integrate previously published scRNA-seq data from 111,566 single PBMCs from 7 COVID-19, 10 HIV-1+, and 3 healthy patients into a unified cellular atlas. We compare in detail the phenotypic features and regulatory pathways in the major immune cell clusters. Results: While immune cells in both COVID-19 and HIV-1+ cohorts show shared inflammation and disrupted mitochondrial function, COVID-19 patients exhibit stronger humoral immunity, broader IFN-I signaling, elevated Rho GTPase and mTOR pathway activity, and downregulated mitophagy. Discussion: Our results indicate that differential IFN-I signaling regulates the distinct immune responses in the two diseases, revealing insight into fundamental disease biology and potential therapeutic candidates.
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Affiliation(s)
- Tony Pan
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
| | - Guoshuai Cao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
| | - Erting Tang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
| | - Yu Zhao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
| | | | - Yun Fang
- Biological Sciences Division, University of Chicago, Chicago, IL, United States
| | - Jun Huang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
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