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Article
Biochemistry & Molecular Biology
Chuanmiao Liu et al.
Summary: This study investigated whether individual variations in human leukocyte antigen (HLA) could alter the course of COVID-19 and be associated with its severity. Through HLA gene sequencing of 16 COVID-19 patients, it was found that HLA-DRB3*01:01, HLA-K*01:01, and HLA-K*01:02 variations were associated with the severity of COVID-19.
Review
Virology
Xiaoxiao Jin et al.
Summary: This review provides a comprehensive map of T-cell epitopes from SARS-CoV-2 antigens, the HLA supertypes that present these epitopes, and the strategies to screen and identify T-cell epitopes. A total of 1349 CD8+ T-cell epitopes and 790 CD4+ T-cell epitopes have been defined, mostly presented by common HLA supertypes. However, the currently defined T-cell epitope repertoire does not cover the HLA polymorphism of major populations in specific geographic regions.
Article
Biochemical Research Methods
Ayse Tugce Sahin et al.
Summary: This study identified potential early severity predictors of COVID-19 and established a protein network connecting viral and human proteins. The findings provide insights into the molecular details of viral perturbation and how the infection affects human physiology.
PROTEOMICS CLINICAL APPLICATIONS
(2023)
Article
Virology
Candace R. Fox et al.
Summary: This study reveals the role of complement (C') in human coronavirus OC43 infection. OC43 infection can activate C', but the lytic effect is relatively delayed. The presence of inhibitors on OC43-infected cells may contribute to this delayed lysis. Furthermore, the study also found that human antibodies play a crucial role in recruiting inhibitors to OC43-infected cells.
Review
Biochemistry & Molecular Biology
Michele Costanzo et al.
Summary: This review summarizes the diverse knowledge acquired through the application of COVIDomics techniques, focusing on proteomics and metabolomics studies, to identify common dysregulation in proteins, metabolites, and pathways in COVID-19 disease. Exploring the multiomics perspective and data integration may lead to new therapeutic solutions against the COVID-19 pandemic.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Gengyu Cen et al.
Summary: The purpose of this research was to explore the biological processes causing COVID-19-related stroke. By analyzing gene expression data, key genes associated with COVID-19-related stroke were identified and their importance in platelet activation, signaling pathways, and cell lineage was determined.
OXIDATIVE MEDICINE AND CELLULAR LONGEVITY
(2022)
Article
Immunology
Iker Valle Aramburu et al.
Summary: This study found that splenocyte death interferes with chromatin clearance in severe infection by releasing the DNase I inhibitor actin. Low NET clearance is associated with increased COVID-19 pathology and mortality. Defective chromatin clearance is implicated in the development of cardiovascular disease and COVID-19 susceptibility.
Article
Multidisciplinary Sciences
Zhichao Ai
Summary: This study re-analyzed scRNA-seq datasets of mouse and human neutrophils and identified distinct transcriptional regulatory networks underlying neutrophil differentiation and inflammatory responses. Neutrophil activation in COVID19 patients was associated with the activation of inflammation-specific TF modules, particularly IRF7. Neutrophil-mediated inflammatory responses positively correlated with the expression level of IRF7.
Article
Multidisciplinary Sciences
Jack S. Gisby et al.
Summary: This study collected blood samples from COVID-19 patients with end-stage kidney disease and performed proteomic and transcriptomic analysis to identify features associated with COVID-19 severity. The results suggest that the plasma proteome is a superior indicator of clinical severity compared to the PBMC transcriptome, and the decreasing trajectory of plasma LRRC15 may be associated with a more severe clinical course. Dysregulated gene expression related to vascular, platelet, and coagulation pathways was still observed in patients two months after the acute infection.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Fabiola Ciccosanti et al.
Summary: Proteomic analysis of plasma from COVID-19 patients reveals molecular changes associated with disease severity, including dysregulation of inflammatory response and selective induction of complement cascade factors. Higher levels of neutrophil granule proteins DEFA3 and LCN2 are confirmed in severe COVID-19 patients.
CLINICAL PROTEOMICS
(2022)
Article
Anesthesiology
Masahiko Oiwa et al.
Summary: The levels of HRG can serve as a biomarker for predicting postoperative complications. Therefore, HRG may be a useful tool for predicting postoperative complications.
BMC ANESTHESIOLOGY
(2022)
Article
Genetics & Heredity
Tommi Valikangas et al.
Summary: This study reanalyzed transcriptome data from multiple independent cohort studies and identified a COVID-19-specific signature consisting of 149 genes. The signature includes signals previously associated with the disease, such as immune response and cell cycle dysregulation, as well as potential new gene candidates related to COVID-19.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Ewa Pius-Sadowska et al.
Summary: The aim of this study was to examine the CMV status, select chemokines, and complement components in COVID-19 patients and analyze their changes over time. The results showed significant differences in chemokines and complement profiles between ICU and non-ICU patients, indicating their contribution to the development of severe COVID-19. Higher concentrations of CXCL8 and CCL2 in the plasma, along with CMV seropositivity, correlated with more severe courses of the disease. Therefore, CXCL8, CCL2, and CMV seropositivity should be considered as new prognostic factors for severe COVID-19.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Pharmacology & Pharmacy
M. Nishibori
Summary: This article summarizes recent advances in the understanding of the complex pathophysiology of sepsis, with a focus on neutrophil extracellular traps, their significant role in thrombosis/embolism, and the functional roles of plasma proteins.
JOURNAL OF PHARMACOLOGICAL SCIENCES
(2022)
Article
Immunology
Meshach Asare-Werehene et al.
Summary: This study demonstrates the utility of plasma gelsolin (pGSN) as a prognostic marker for COVID-19 disease outcome. Combining pGSN with cytokines and antibodies significantly improves test performance compared to conventional markers like CRP and ferritin. These findings have important implications for clinical management and health system interventions in response to COVID-19.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Medicine, General & Internal
Gabriella Captur et al.
Summary: This study reveals that SARS-CoV-2 infection affects the plasma proteome for at least 6 weeks, and the proteomic signature at the time of seroconversion can predict the likelihood of persistent symptoms related to the infection.
Article
Respiratory System
Julia Beimdiek et al.
Summary: The changes in specific plasma protein levels and N-glycosylation in COVID-19 patients highlight the complexity of the inflammatory process and warrant further investigation.
RESPIRATORY RESEARCH
(2022)
Article
Biology
Franziska Vollmy et al.
Summary: The study recorded serum proteome profiles of 33 severe COVID-19 patients and identified a panel of about a dozen proteins that showed significantly different abundance between survivors and non-survivors. Nine proteins were defined for mortality risk assessment, and the predictive power of this panel was found to perform well in predicting mortality in independent cohorts measured in other countries. Some proteins in the panel have been previously annotated as mortality markers in aging and other diseases caused by different pathogens.
LIFE SCIENCE ALLIANCE
(2021)
Article
Biochemistry & Molecular Biology
Katherine A. Overmyer et al.
Summary: The study conducted RNA-seq and high-resolution mass spectrometry on blood samples from COVID-19-positive and COVID-19-negative patients, identifying molecular features associated with disease severity and outcomes, offering pathophysiological insights and therapeutic suggestions. The observed dysregulation of platelet function, blood coagulation, acute phase response, and endotheliopathy further illuminated the unique COVID-19 phenotype. The findings are presented through a web-based tool enabling interactive exploration and machine learning prediction of COVID-19 severity.
Article
Multidisciplinary Sciences
Micah T. McClain et al.
Summary: In this study, McClain et al. used RNA sequencing to compare the peripheral blood transcriptome of subjects with SARS-CoV-2 and other respiratory infections. They found dysregulated immune responses in COVID-19 with both heterogeneous and conserved components.
NATURE COMMUNICATIONS
(2021)
Article
Immunology
Gautier Breville et al.
Summary: This study describes the potential pathogenic role of Ig4 autoantibodies in complement-mediated thrombotic microangiopathy in a patient with IgG4-related disease. The patient was successfully treated with plasmapheresis, corticosteroids, and cyclophosphamide, achieving remission. The results suggest a link between genetic predispositions such as CFHR1 and CFHR4 gene deletions and the formation of inhibitory anti-Factor H IgG4 antibodies.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Kavitha Mukund et al.
Summary: The study found that in COVID-19 patients, there is expansion and mobilization of the innate immune response while lymphoid cell types are reduced, especially in severe cases. Additionally, plasmablasts expand significantly in severe COVID-19 patients. The research also reveals the different subsets' responses to IFN-I and the increased aggregation potential of myeloid subsets.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Michal Kukla et al.
Summary: Analysis of liver biopsy specimens suggests that SARS-CoV-2 could cause liver damage, and changes in certain hepatokines and myokines may be associated with the development and severity of COVID-19.
Article
Biochemical Research Methods
Jee-Soo Lee et al.
Summary: This study identified potential early prognostic protein markers and 40 potential biomarkers that reflect the clinical progression of COVID-19. These findings provide insights into host response to SARS-CoV-2 infection and may support better prediction and monitoring of progression to severe COVID-19.
Review
Cardiac & Cardiovascular Systems
Saeed Samadizadeh et al.
Summary: The severity of COVID-19 varies significantly among individuals and populations, with differences in reported disease burdens and case fatality rates between countries. The influence of host, virus, and environment on the clinical outcome of the disease is complex and still not fully understood.
RESPIRATORY MEDICINE
(2021)
Article
Microbiology
Opeyemi S. Adeniji et al.
Summary: The study suggests that qualitative differences in SARS-CoV-2-specific antibody-mediated innate immune functions may contribute to COVID-19 severity, with higher ADCD associated with higher inflammation and higher ADCP associated with lower inflammation. Understanding these qualitative features of antibodies could be crucial for developing effective and safe COVID-19 therapeutics and vaccines.
Article
Multidisciplinary Sciences
Hamel Patel et al.
Summary: This study analyzed blood protein profiles of COVID-19 patients and identified six proteins associated with disease severity, offering potential early biomarkers and therapeutic targets for monitoring and treating the disease.
SCIENTIFIC REPORTS
(2021)
Review
Microbiology
Magdalena Ulanowska et al.
Summary: COVID-19, caused by SARS-CoV-2 virus, affects respiratory function and disrupts the coagulation system, leading to clotting and thrombotic events. Inflammation and cytokine storms are major causes of hemostasis disorders, with the use of anticoagulants such as heparin recommended to prevent and treat thrombosis. The relationship between blood platelets and COVID-19, as well as the potential use of antiplatelet drugs in COVID-19 cases, are also areas of focus in research.
Review
Genetics & Heredity
Maria Monticelli et al.
Summary: This study identified genetic variants related to COVID-19 risk factors through text mining and population distribution analysis, revealing associations between five polymorphisms and the number of COVID-19 cases and/or deaths in different countries. The findings suggest a potential role of these genetic variants, particularly in genes related to innate immunity, in individual responses to SARS-CoV-2 infection and the outcome of COVID-19. The results provide a basis for the design of a cost-effective assay for population screening of genetic risk factors during the COVID-19 pandemic.
EUROPEAN JOURNAL OF MEDICAL GENETICS
(2021)
Article
Gastroenterology & Hepatology
Jordi Merino et al.
Summary: The study found that a diet characterized by healthy plant-based foods was associated with a lower risk and severity of COVID-19. This association was particularly evident in areas with higher socioeconomic deprivation.
Article
Multidisciplinary Sciences
Peng Wu et al.
Summary: The authors conducted blood sampling and multi-omics analysis on COVID-19 patients of various disease severities, reporting a trans-omics landscape of COVID-19. The study found differences in characteristics between patients with different disease severities, suggesting potential clues for pathophysiology and therapeutic strategies of COVID-19.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Yukai Jing et al.
Summary: SARS-CoV-2 infection causes changes in the immune phenotype of B cells in recovered COVID-19 patients, with reduced CD19 expression and disrupted immune regulation, providing a new target for treating COVID-19.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2021)
Letter
Biochemistry & Molecular Biology
Ling Leng et al.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2021)
Article
Immunology
Thiago Carvalho et al.
Summary: The timeline of major scientific discoveries during the first year of the COVID-19 pandemic highlights the collaborative efforts that led to rapid progress in understanding the immune response to SARS-CoV-2. It showcases the unprecedented convergence of research efforts on COVID-19 and identifies gaps in knowledge for future investigations.
NATURE REVIEWS IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Daniel Blanco-Melo et al.
Article
Biochemistry & Molecular Biology
Bo Shen et al.
Article
Virology
Xiuqi Wei et al.
JOURNAL OF MEDICAL VIROLOGY
(2020)
Review
Medicine, General & Internal
Laure Wynants et al.
BMJ-BRITISH MEDICAL JOURNAL
(2020)
Article
Biochemistry & Molecular Biology
Christoph B. Messner et al.
Article
Immunology
Jeong Seok Lee et al.
SCIENCE IMMUNOLOGY
(2020)
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Multidisciplinary Sciences
Joonho Park et al.
SCIENTIFIC REPORTS
(2020)
Article
Biochemistry & Molecular Biology
Fan Zhang et al.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2020)
Article
Biochemistry & Molecular Biology
Uku Raudvere et al.
NUCLEIC ACIDS RESEARCH
(2019)
Article
Immunology
Zhiping Yang et al.
JOURNAL OF INFECTIOUS DISEASES
(2019)
Article
Biochemistry & Molecular Biology
Damian Szklarczyk et al.
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemical Research Methods
Eva Csosz et al.
JOURNAL OF PROTEOMICS
(2017)
Article
Respiratory System
Markos Minas et al.
COPD-JOURNAL OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE
(2013)
Article
Medicine, General & Internal
Hiroe Sato et al.
