1
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Dong H, Hao Y, Gao P. Vitamin D level in COVID-19 patients has positive correlations with autophagy and negative correlations with disease severity. Front Pharmacol 2024; 15:1388348. [PMID: 38783947 PMCID: PMC11112027 DOI: 10.3389/fphar.2024.1388348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Background and Objectives There is still incomplete understanding of the pathogenesis of COVID-19. Calcitriol, the main form of vitamin D in serum, regulates immune responses and increases resistance to pathogens, but the mechanism by which it protects against COVID-19 is uncertain. Autophagy has antiviral effects and helps to maintain homeostasis, but its specific role in COVID-19 is also uncertain. Both vitamin D and autophagy have important functions in the lung microenvironment. This study examined the relationship of serum vitamin D and autophagy-related proteins in patients with COVID-19 and evaluated their potential use as biomarkers. Methods Blood samples from COVID-19 patients at the Second Hospital of Jilin University were collected. The levels of vitamin D, autophagy-related proteins (Becline 1 [BECN1] and autophagy-related 7 [ATG7]), and inflammatory markers (TNF-α and IL-1β) were measured using enzyme-linked immunosorbent assays. Results We examined 25 patients with mild/moderate COVID-19 and 27 patients with severe/critical COVID-19. The group with severe/critical COVID-19 had more abnormalities in many laboratory indicators, including lower levels of autophagy markers (BECN1 and ATG7) and vitamin D, and higher levels of inflammatory markers (TNF-α and IL-1β). Partial correlation analysis showed that vitamin D had strong positive correlations with ATG7 (r = 0.819, p < 0.001) and BECN1 (r = 0.900, p < 0.001). Conclusion Our results demonstrated that the vitamin D level had significant negative correlations with COVID-19 severity and strong positive correlations with autophagy. These findings enhance our understanding of the pathogenesis of COVID-19, and provide a theoretical basis for clinical interventions that target autophagy and vitamin D.
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Affiliation(s)
| | | | - Peng Gao
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, Jilin, China
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2
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Stylianou N, Sebina I, Matigian N, Monkman J, Doehler H, Röhl J, Allenby M, Nam A, Pan L, Rockstroh A, Sadeghirad H, Chung K, Sobanski T, O'Byrne K, Almeida ACSF, Rebutini PZ, Machado‐Souza C, Stonoga ETS, Warkiani ME, Salomon C, Short K, McClements L, de Noronha L, Huang R, Belz GT, Souza‐Fonseca‐Guimaraes F, Clifton V, Kulasinghe A. Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies placental dysfunction signatures. Clin Transl Immunology 2024; 13:e1488. [PMID: 38322491 PMCID: PMC10846628 DOI: 10.1002/cti2.1488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 02/08/2024] Open
Abstract
Objectives Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus infection in pregnancy is associated with higher incidence of placental dysfunction, referred to by a few studies as a 'preeclampsia-like syndrome'. However, the mechanisms underpinning SARS-CoV-2-induced placental malfunction are still unclear. Here, we investigated whether the transcriptional architecture of the placenta is altered in response to SARS-CoV-2 infection. Methods We utilised whole-transcriptome, digital spatial profiling, to examine gene expression patterns in placental tissues from participants who contracted SARS-CoV-2 in the third trimester of their pregnancy (n = 7) and those collected prior to the start of the coronavirus disease 2019 (COVID-19) pandemic (n = 9). Results Through comprehensive spatial transcriptomic analyses of the trophoblast and villous core stromal cell subpopulations in the placenta, we identified SARS-CoV-2 to promote signatures associated with hypoxia and placental dysfunction. Notably, genes associated with vasodilation (NOS3), oxidative stress (GDF15, CRH) and preeclampsia (FLT1, EGFR, KISS1, PAPPA2) were enriched with SARS-CoV-2. Pathways related to increased nutrient uptake, vascular tension, hypertension and inflammation were also enriched in SARS-CoV-2 samples compared to uninfected controls. Conclusions Our findings demonstrate the utility of spatially resolved transcriptomic analysis in defining the underlying pathogenic mechanisms of SARS-CoV-2 in pregnancy, particularly its role in placental dysfunction. Furthermore, this study highlights the significance of digital spatial profiling in mapping the intricate crosstalk between trophoblasts and villous core stromal cells, thus shedding light on pathways associated with placental dysfunction in pregnancies with SARS-CoV-2 infection.
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Affiliation(s)
- Nataly Stylianou
- Australian Prostate Cancer Research Centre – Queensland, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of HealthQueensland University of TechnologyBrisbaneQLDAustralia
| | - Ismail Sebina
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | | | - James Monkman
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Hadeel Doehler
- Australian Prostate Cancer Research Centre – Queensland, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of HealthQueensland University of TechnologyBrisbaneQLDAustralia
| | - Joan Röhl
- Faculty of Health Sciences and MedicineBond UniversityRobinaQLDAustralia
| | - Mark Allenby
- BioMimetic Systems Engineering Lab, School of Chemical EngineeringUniversity of Queensland (UQ)St LuciaQLDAustralia
| | - Andy Nam
- Nanostring Technologies, Inc.SeattleWAUSA
| | - Liuliu Pan
- Nanostring Technologies, Inc.SeattleWAUSA
| | - Anja Rockstroh
- Australian Prostate Cancer Research Centre – Queensland, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of HealthQueensland University of TechnologyBrisbaneQLDAustralia
| | - Habib Sadeghirad
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Kimberly Chung
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Thais Sobanski
- Australian Prostate Cancer Research Centre – Queensland, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of HealthQueensland University of TechnologyBrisbaneQLDAustralia
| | - Ken O'Byrne
- Princess Alexandra HospitalWoolloongabbaQLDAustralia
| | | | - Patricia Zadorosnei Rebutini
- Postgraduate Program of Health Sciences, School of MedicinePontifícia Universidade Católica do Paraná ´ –PUCPRCuritibaBrazil
| | - Cleber Machado‐Souza
- Postgraduate Program in Biotechnology Applied in Health of Children and AdolescentInstituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno PríncipeCuritibaBrazil
| | | | - Majid E Warkiani
- School of Life Sciences & Institute for Biomedical Materials and Devices, Faculty of ScienceUniversity of Technology SydneySydneyNSWAustralia
| | - Carlos Salomon
- Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Kirsty Short
- School of Chemistry and Molecular Biosciences, Faculty of ScienceThe University of QueenslandSt LuciaQLDAustralia
| | - Lana McClements
- School of Life Sciences & Institute for Biomedical Materials and Devices, Faculty of ScienceUniversity of Technology SydneySydneyNSWAustralia
| | - Lucia de Noronha
- Postgraduate Program of Health Sciences, School of MedicinePontifícia Universidade Católica do Paraná ´ –PUCPRCuritibaBrazil
| | - Ruby Huang
- School of Medicine, College of MedicineNational Taiwan UniversityTaipeiTaiwan
| | - Gabrielle T Belz
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | | | - Vicki Clifton
- Mater Medical Research InstituteUniversity of QueenslandBrisbaneQLDAustralia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
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3
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Trapé J, Fernández-Galán E, Auge JM, Carbonell-Prat M, Filella X, Miró-Cañís S, González-Fernández C. Factors influencing blood tumor marker concentrations in the absence of neoplasia. Tumour Biol 2024; 46:S35-S63. [PMID: 38517826 DOI: 10.3233/tub-220023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024] Open
Abstract
BACKGROUND Tumor markers (TMs) are a heterogeneous group of molecules used in the diagnosis, prognosis and follow-up of cancer patients. During neoplastic differentiation, cells can either directly synthesize or induce the synthesis of TMs, and the release of these molecules into the bloodstream allows their quantification in biological fluids. Although very small concentrations of TMs are usually present in the serum or plasma of healthy subjects, increased concentrations may also be found in the presence of benign diseases or due to technical interference, producing false positive results. MATERIAL AND METHODS AND RESULTS Our review analyses the causes of false positives described between January 1970 to February 2023 for the TMs most frequently used in clinical practice: α-fetoprotein (AFP), β2-microglobulin (β2-M), cancer antigen 15-3 (CA 15-3), cancer antigen CA 19-9 (CA 19-9), cancer antigen CA 72-4 (CA 72-4), cancer antigen 125 (CA 125), carcinoembryonic antigen (CEA), chromogranin A (CgA), choriogonadotropin (hCG), cytokeratin 19 fragment (CYFRA 21-1), neuron-specific enolase (NSE), human epididymis protein 4 (HE4), serum HER2 (sHER2), squamous cell carcinoma antigen (SCCA), protein induced by vitamin K absence-II (PIVKA-II), Pro-gastrin-releasing peptide (Pro-GRP), prostate-specific antigen (PSA), Protein S-100 (S-100) and thyroglobulin (Tg). A total of 247 references were included. CONCLUSIONS A better understanding of pathophysiological processes and other conditions that affect the concentration of TMs might improve the interpretation of results and their clinical application.
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Affiliation(s)
- Jaume Trapé
- Department of Laboratory Medicine, Althaia Xarxa Assistencial Universitària de Manresa, Manresa, Catalonia, Spain
- Tissue Repair and Regeneration Laboratory, Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central, Barcelona, Spain
- Faculty of Medicine, University of Vic - Central University of Catalonia, Vic, Spain
| | - Esther Fernández-Galán
- Department of Biochemistry and Molecular Genetics - Hospital Clinic de Barcelona, Barcelona, Spain
| | - Josep Maria Auge
- Department of Biochemistry and Molecular Genetics - Hospital Clinic de Barcelona, Barcelona, Spain
| | | | - Xavier Filella
- Department of Biochemistry and Molecular Genetics - Hospital Clinic de Barcelona, Barcelona, Spain
| | - Sílvia Miró-Cañís
- Laboratori d'Anàlisis Clíniques, CLILAB Diagnòstics, Vilafranca del Penedès, Spain
| | - Carolina González-Fernández
- Department of Laboratory Medicine, Althaia Xarxa Assistencial Universitària de Manresa, Manresa, Catalonia, Spain
- Gastrointestinal Oncology, Endoscopy and Surgery Research Group, Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central, Barcelona, Spain
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4
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Gong S, Ma R, Zhu T, Ge X, Xie R, Tao Q, Shi C. Elevated serum beta-2 microglobulin level predicts short-term poor prognosis of patients with de novo acute omicron variant COVID-19 infection. Front Cell Infect Microbiol 2023; 13:1204326. [PMID: 37520437 PMCID: PMC10373586 DOI: 10.3389/fcimb.2023.1204326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Background The devastating coronavirus disease of 2019 (COVID-2019) epidemic has been declared a public health emergency, resulting in a worldwide pandemic. The omicron variety is the most common epidemic mutant strain in the globe. Serum beta-2 microglobulin (β2-MG) is associated with endothelial cell injury and has value in monitoring the progression of inflammation in infected individuals. Nonetheless, the potential functions of β2-MG in omicron remain elusive. Methods To investigate the prognostic value of serum β2-MG levels at diagnosis, we retrospectively analyzed a cohort of 240 people with omicron. Over the course of 65 days, all patients were monitored, and death was the primary outcome. Patients were allocated to two groups: those with high and low β2-MG levels. The Kaplan-Meier method was used to examine OS, and the log-rank test was used to compare them. Univariate and multivariate Cox hazard models were used to determine the prognostic significance. Results Our results revealed that β2-MG was significantly elevated in omicron. β2-MG levels in severe patients were higher than in mild-to-moderate patients, and the difference was statistically significant. Timely, interleukin-6 (IL-6) and interleukin-10 (IL-10) were observed to be significantly increased in individuals exhibiting elevated levels of β2-MG. In addition, patients exhibiting elevated levels of β2-MG demonstrated a statistically significant decrease in overall survival (OS, P < 0.0001). An elevated β2-MG level (≥4.72 mg/l) was found to be an independent, adverse prognostic factor for OS in omicron patients, according to multivariate Cox proportional hazards regression analysis (P = 0.001). Conclusion Serum β2-MG level at initial diagnosis was significantly correlated with omicron severity and prognosis. Thus, we propose that β2-MG may be an independent poor additional prognostic factor in patients with omicron.
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Affiliation(s)
- Shengping Gong
- Cancer Radiotherapy and Chemotherapy Center, the First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Ruishuang Ma
- Cancer Radiotherapy and Chemotherapy Center, the First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Ting Zhu
- Cancer Radiotherapy and Chemotherapy Center, the First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Xiaoqin Ge
- Cancer Radiotherapy and Chemotherapy Center, the First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Rongrong Xie
- Cancer Radiotherapy and Chemotherapy Center, the First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Qingsong Tao
- Cancer Radiotherapy and Chemotherapy Center, the First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Cong Shi
- Laboratory of Stem Cell Transplantation, the First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, the First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
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5
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Qin R, He L, Yang Z, Jia N, Chen R, Xie J, Fu W, Chen H, Lin X, Huang R, Luo T, Liu Y, Yao S, Jiang M, Li J. Identification of Parameters Representative of Immune Dysfunction in Patients with Severe and Fatal COVID-19 Infection: a Systematic Review and Meta-analysis. Clin Rev Allergy Immunol 2023; 64:33-65. [PMID: 35040086 PMCID: PMC8763427 DOI: 10.1007/s12016-021-08908-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2021] [Indexed: 01/26/2023]
Abstract
Abnormal immunological indicators associated with disease severity and mortality in patients with COVID-19 have been reported in several observational studies. However, there are marked heterogeneities in patient characteristics and research methodologies in these studies. We aimed to provide an updated synthesis of the association between immune-related indicators and COVID-19 prognosis. We conducted an electronic search of PubMed, Scopus, Ovid, Willey, Web of Science, Cochrane library, and CNKI for studies reporting immunological and/or immune-related parameters, including hematological, inflammatory, coagulation, and biochemical variables, tested on hospital admission of COVID-19 patients with different severities and outcomes. A total of 145 studies were included in the current meta-analysis, with 26 immunological, 11 hematological, 5 inflammatory, 4 coagulation, and 10 biochemical variables reported. Of them, levels of cytokines, including IL-1β, IL-1Ra, IL-2R, IL-4, IL-6, IL-8, IL-10, IL-18, TNF-α, IFN-γ, IgA, IgG, and CD4+ T/CD8+ T cell ratio, WBC, neutrophil, platelet, ESR, CRP, ferritin, SAA, D-dimer, FIB, and LDH were significantly increased in severely ill patients or non-survivors. Moreover, non-severely ill patients or survivors presented significantly higher counts of lymphocytes, monocytes, lymphocyte/monocyte ratio, eosinophils, CD3+ T,CD4+T and CD8+T cells, B cells, and NK cells. The currently updated meta-analysis primarily identified a hypercytokinemia profile with the severity and mortality of COVID-19 containing IL-1β, IL-1Ra, IL-2R, IL-4, IL-6, IL-8, IL-10, IL-18, TNF-α, and IFN-γ. Impaired innate and adaptive immune responses, reflected by decreased eosinophils, lymphocytes, monocytes, B cells, NK cells, T cells, and their subtype CD4+ and CD8+ T cells, and augmented inflammation, coagulation dysfunction, and nonpulmonary organ injury, were marked features of patients with poor prognosis. Therefore, parameters of immune response dysfunction combined with inflammatory, coagulated, or nonpulmonary organ injury indicators may be more sensitive to predict severe patients and those non-survivors.
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Affiliation(s)
- Rundong Qin
- grid.470124.4Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Li He
- grid.470124.4Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Zhaowei Yang
- grid.470124.4Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Nan Jia
- grid.470124.4Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Ruchong Chen
- grid.470124.4Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Jiaxing Xie
- grid.470124.4Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Wanyi Fu
- grid.470124.4Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Hao Chen
- grid.470124.4Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Xinliu Lin
- grid.470124.4Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Renbin Huang
- grid.470124.4Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Tian Luo
- grid.470124.4Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Yukai Liu
- grid.470124.4Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Siyang Yao
- grid.470124.4Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Mei Jiang
- grid.470124.4National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Jing Li
- grid.470124.4Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
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6
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COVID-19 Salivary Protein Profile: Unravelling Molecular Aspects of SARS-CoV-2 Infection. J Clin Med 2022; 11:jcm11195571. [PMID: 36233441 PMCID: PMC9570692 DOI: 10.3390/jcm11195571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/18/2022] Open
Abstract
COVID-19 is the most impacting global pandemic of all time, with over 600 million infected and 6.5 million deaths worldwide, in addition to an unprecedented economic impact. Despite the many advances in scientific knowledge about the disease, much remains to be clarified about the molecular alterations induced by SARS-CoV-2 infection. In this work, we present a hybrid proteomics and in silico interactomics strategy to establish a COVID-19 salivary protein profile. Data are available via ProteomeXchange with identifier PXD036571. The differential proteome was narrowed down by the Partial Least-Squares Discriminant Analysis and enrichment analysis was performed with FunRich. In parallel, OralInt was used to determine interspecies Protein-Protein Interactions between humans and SARS-CoV-2. Five dysregulated biological processes were identified in the COVID-19 proteome profile: Apoptosis, Energy Pathways, Immune Response, Protein Metabolism and Transport. We identified 10 proteins (KLK 11, IMPA2, ANXA7, PLP2, IGLV2-11, IGHV3-43D, IGKV2-24, TMEM165, VSIG10 and PHB2) that had never been associated with SARS-CoV-2 infection, representing new evidence of the impact of COVID-19. Interactomics analysis showed viral influence on the host immune response, mainly through interaction with the degranulation of neutrophils. The virus alters the host’s energy metabolism and interferes with apoptosis mechanisms.
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7
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Lv Y, Zhang T, Cai J, Huang C, Zhan S, Liu J. Bioinformatics and systems biology approach to identify the pathogenetic link of Long COVID and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Front Immunol 2022; 13:952987. [PMID: 36189286 PMCID: PMC9524193 DOI: 10.3389/fimmu.2022.952987] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global crisis. Although many people recover from COVID-19 infection, they are likely to develop persistent symptoms similar to those of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) after discharge. Those constellations of symptoms persist for months after infection, called Long COVID, which may lead to considerable financial burden and healthcare challenges. However, the mechanisms underlying Long COVID and ME/CFS remain unclear. Methods We collected the genes associated with Long COVID and ME/CFS in databases by restricted screening conditions and clinical sample datasets with limited filters. The common genes for Long COVID and ME/CFS were finally obtained by taking the intersection. We performed several advanced bioinformatics analyses based on common genes, including gene ontology and pathway enrichment analyses, protein–protein interaction (PPI) analysis, transcription factor (TF)–gene interaction network analysis, transcription factor–miRNA co-regulatory network analysis, and candidate drug analysis prediction. Results We found nine common genes between Long COVID and ME/CFS and gained a piece of detailed information on their biological functions and signaling pathways through enrichment analysis. Five hub proteins (IL-6, IL-1B, CD8A, TP53, and CXCL8) were collected by the PPI network. The TF–gene and TF–miRNA coregulatory networks were demonstrated by NetworkAnalyst. In the end, 10 potential chemical compounds were predicted. Conclusion This study revealed common gene interaction networks of Long COVID and ME/CFS and predicted potential therapeutic drugs for clinical practice. Our findings help to identify the potential biological mechanism between Long COVID and ME/CFS. However, more laboratory and multicenter evidence is required to explore greater mechanistic insight before clinical application in the future.
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Affiliation(s)
- Yongbiao Lv
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Tian Zhang
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Junxiang Cai
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Chushuan Huang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shaofeng Zhan
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianbo Liu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Jianbo Liu,
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8
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Bruiners N, Guerrini V, Ukey R, Dikdan RJ, Yang JH, Mishra PK, Onyuka A, Handler D, Vieth J, Carayannopoulos M, Guo S, Pollen M, Pinter A, Tyagi S, Feingold D, Philipp C, Libutti SK, Gennaro ML. Longitudinal Analysis of Biologic Correlates of COVID-19 Resolution: Case Report. Front Med (Lausanne) 2022; 9:915367. [PMID: 35783607 PMCID: PMC9240225 DOI: 10.3389/fmed.2022.915367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
While the biomarkers of COVID-19 severity have been thoroughly investigated, the key biological dynamics associated with COVID-19 resolution are still insufficiently understood. We report a case of full resolution of severe COVID-19 due to convalescent plasma transfusion. Following transfusion, the patient showed fever remission, improved respiratory status, and rapidly decreased viral burden in respiratory fluids and SARS-CoV-2 RNAemia. Longitudinal unbiased proteomic analysis of plasma and single-cell transcriptomics of peripheral blood cells conducted prior to and at multiple times after convalescent plasma transfusion identified the key biological processes associated with the transition from severe disease to disease-free state. These included (i) temporally ordered upward and downward changes in plasma proteins reestablishing homeostasis and (ii) post-transfusion disappearance of a subset of monocytes characterized by hyperactivated Interferon responses and decreased TNF-α signaling. Monitoring specific dysfunctional myeloid cell subsets in peripheral blood may provide prognostic keys in COVID-19.
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Affiliation(s)
- Natalie Bruiners
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Valentina Guerrini
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Rahul Ukey
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
| | - Ryan J. Dikdan
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
| | - Jason H. Yang
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, United States
- Center for Emerging and Re-emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Pankaj Kumar Mishra
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
| | - Alberta Onyuka
- Global Tuberculosis Institute, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Deborah Handler
- Global Tuberculosis Institute, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Joshua Vieth
- Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, United States
| | - Mary Carayannopoulos
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Shuang Guo
- Division of Hematology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Maressa Pollen
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Abraham Pinter
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Sanjay Tyagi
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Daniel Feingold
- Department of Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Claire Philipp
- Division of Hematology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Steven K. Libutti
- Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, United States
- *Correspondence: Steven K. Libutti
| | - Maria Laura Gennaro
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, United States
- Maria Laura Gennaro
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Bruiners N, Guerrini V, Ukey R, Dikdan R, Yang J, Mishra PK, Onyuka A, Handler D, Vieth J, Carayannopulos M, Guo S, Pollen M, Pinter A, Tyagi S, Feingold D, Philipp C, Libutti S, Gennaro ML. Biologic correlates of beneficial convalescent plasma therapy in a COVID-19 patient reveal disease resolution mechanisms. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.02.03.22269612. [PMID: 35132422 PMCID: PMC8820674 DOI: 10.1101/2022.02.03.22269612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND While the biomarkers of COVID-19 severity have been thoroughly investigated, the key biological dynamics associated with COVID-19 resolution are still insufficiently understood. MAIN BODY We report a case of full resolution of severe COVID-19 due to convalescent plasma transfusion in a patient with underlying multiple autoimmune syndrome. Following transfusion, the patient showed fever remission, improved respiratory status, and rapidly decreased viral burden in respiratory fluids and SARS-CoV-2 RNAemia. Longitudinal unbiased proteomic analysis of plasma and single-cell transcriptomics of peripheral blood cells conducted prior to and at multiple times after convalescent plasma transfusion identified the key biological processes associated with the transition from severe disease to disease-free state. These included (i) temporally ordered upward and downward changes in plasma proteins reestablishing homeostasis and (ii) post-transfusion disappearance of a particular subset of dysfunctional monocytes characterized by hyperactivated Interferon responses and decreased TNF-α signaling. CONCLUSIONS Monitoring specific subsets of innate immune cells in peripheral blood may provide prognostic keys in severe COVID-19. Moreover, understanding disease resolution at the molecular and cellular level should contribute to identify targets of therapeutic interventions against severe COVID-19.
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Affiliation(s)
- Natalie Bruiners
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Valentina Guerrini
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Rahul Ukey
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Ryan Dikdan
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Jason Yang
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103
- Center for Emerging and Re-emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Pankaj Kumar Mishra
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Alberta Onyuka
- Global Tuberculosis Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Deborah Handler
- Global Tuberculosis Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Joshua Vieth
- Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08903
| | - Mary Carayannopulos
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901
| | - Shuang Guo
- Division of Hematology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901
| | - Maressa Pollen
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901
| | - Abraham Pinter
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Sanjay Tyagi
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Daniel Feingold
- Department of Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901
| | - Claire Philipp
- Division of Hematology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901
| | - Steven Libutti
- Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08903
| | - Maria Laura Gennaro
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103
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Single-Cell and Bulk RNASeq Profiling of COVID-19 Patients Reveal Immune and Inflammatory Mechanisms of Infection-Induced Organ Damage. Viruses 2021; 13:v13122418. [PMID: 34960687 PMCID: PMC8706409 DOI: 10.3390/v13122418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 02/07/2023] Open
Abstract
The SARS-CoV-2 virus’s ability to induce hypercytokinemia and cause multiple organ failure makes it imperative to find effective treatments. To understand the mechanism of viral infection and its effects on organ tissues, we analyzed multiple single-cell and bulk RNAseq data from COVID-19 patients’ organ samples. Various levels of severity of infection were accounted for, with comparative analyses between mild, moderate, and severely infected patients. Our analysis uncovered an upregulation of the innate immune response via several inflammatory genes, IL-2, IL-6, IL-8, IL-17A, and NF-κB. Consequently, we found that the upregulation of these downstream effects can lead to organ injury. The downregulated pathways such as eukaryotic initiation factor 2 (eIF2) and eIF4-mediated host translation, were found to lead to an increased viral translation. We also found that the loss of inhibitory peptides can suppress an overactive innate immune response via NF-κB and interleukin-mediated pathways. Investigation of viral-host protein mapping showed that the interaction of viral proteins with host proteins correlated with the down- and upregulation of host pathways such as decreased eIF2-mediated host translation and increased hypertrophy and fibrosis. Inflammation was increased via the stimulation of pro-inflammatory cytokines and suppression of host translation pathways that led to reduced inflammatory inhibitors. Cardiac hypertrophy and organ fibrosis were the results of increased inflammation in organs of severe and critical patients. Finally, we identified potential therapeutic targets for the treatment of COVID-19 and its deleterious effects on organs. Further experimental investigation would conclusively determine the effects of COVID-19 infection on organs other than the lungs and the effectiveness of the proposed therapeutic targets.
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Alveolar-like Macrophages Attenuate Respiratory Syncytial Virus Infection. Viruses 2021; 13:v13101960. [PMID: 34696391 PMCID: PMC8540499 DOI: 10.3390/v13101960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 01/26/2023] Open
Abstract
Respiratory Syncytial Virus (RSV) is the leading cause of acute lower respiratory infections in young children and infection has been linked to the development of persistent lung disease in the form of wheezing and asthma. Despite substantial research efforts, there are no RSV vaccines currently available and an effective monoclonal antibody targeting the RSV fusion protein (palivizumab) is of limited general use given the associated expense. Therefore, the development of novel approaches to prevent RSV infection is highly desirable to improve pediatric health globally. We have developed a method to generate alveolar-like macrophages (ALMs) from pluripotent stem cells. These ALMs have shown potential to promote airway innate immunity and tissue repair and so we hypothesized that ALMs could be used as a strategy to prevent RSV infection. Here, we demonstrate that ALMs are not productively infected by RSV and prevent the infection of epithelial cells. Prevention of epithelial infection was mediated by two different mechanisms: phagocytosis of RSV particles and release of an antiviral soluble factor different from type I interferon. Furthermore, intratracheal administration of ALMs protected mice from subsequent virus-induced weight loss and decreased lung viral titres and inflammation, indicating that ALMs can impair the pathogenesis of RSV infection. Our results support a prophylactic role for ALMs in the setting of RSV infection and warrant further studies on stem cell-derived ALMs as a novel cell-based therapy for pulmonary viral infections.
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Risk Factors for SARS-CoV-2 Infection Severity in Abu Dhabi. J Epidemiol Glob Health 2021; 11:344-353. [PMID: 34734381 PMCID: PMC8381146 DOI: 10.1007/s44197-021-00006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 08/06/2021] [Indexed: 11/24/2022] Open
Abstract
Background Prediction models are essential for informing screening, assessing prognosis, and examining options for treatment. This study aimed to assess the risk of SARS-CoV-2 infection severity in the Abu Dhabi population. Methods This is a mixed retrospective cohort study and case–control study to explore the associated factors of receiving treatment in the community, being hospitalized, or requiring complex hospital care among patients with a diagnosis of SARS-CoV-2. Of 641 patients included, 266 were hospitalized; 135 were hospitalized and either died or required complex care, i.e., required ICU admission, intubation, or oxygen and 131 did not develop severe disease requiring complex care. The third group (“controls”) were 375 patients who were not hospitalized. Logistic regression analyses were used to study predictors of disease severity. Results Among hospitalized patients older age and low oxygen saturation at admission were the consistent and strongest predictors of an adverse outcome. Risk factors for the death in addition to age and low oxygen saturation were elevated white blood count and low reported physical activity. Chronic kidney disease and diabetes were also associated with more severe disease in logistic regression. The mortality rate among those with less than 30 min per week of physical activity was 4.9%, while the mortality rate was 0.35% for those with physical activity > 30 min at least once a week. The interval from the onset of symptoms to admission and mortality was found to have a significant inverse relationship, with worse survival for shorter intervals. Conclusion Oxygen saturation is an important measure that should be introduced at screening sites and used in the risk assessment of patients with SARS-CoV-2. In addition, an older age was a consistent factor in all adverse outcomes, and other factors, such as low physical activity, elevated WBC, CKD, and DM, were also identified as risk factors.
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