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1.
Proc Natl Acad Sci U S A ; 119(33): e2208144119, 2022 Aug 16.
Article in English | MEDLINE | ID: covidwho-1984601

ABSTRACT

Pattern recognition molecules (PRMs) form an important part of innate immunity, where they facilitate the response to infections and damage by triggering processes such as inflammation. The pentraxin family of soluble PRMs comprises long and short pentraxins, with the former containing unique N-terminal regions unrelated to other proteins or each other. No complete high-resolution structural information exists about long pentraxins, unlike the short pentraxins, where there is an abundance of both X-ray and cryoelectron microscopy (cryo-EM)-derived structures. This study presents a high-resolution structure of the prototypical long pentraxin, PTX3. Cryo-EM yielded a 2.5-Å map of the C-terminal pentraxin domains that revealed a radically different quaternary structure compared to other pentraxins, comprising a glycosylated D4 symmetrical octameric complex stabilized by an extensive disulfide network. The cryo-EM map indicated α-helices that extended N terminal of the pentraxin domains that were not fully resolved. AlphaFold was used to predict the remaining N-terminal structure of the octameric PTX3 complex, revealing two long tetrameric coiled coils with two hinge regions, which was validated using classification of cryo-EM two-dimensional averages. The resulting hybrid cryo-EM/AlphaFold structure allowed mapping of ligand binding sites, such as C1q and fibroblast growth factor-2, as well as rationalization of previous biochemical data. Given the relevance of PTX3 in conditions ranging from COVID-19 prognosis, cancer progression, and female infertility, this structure could be used to inform the understanding and rational design of therapies for these disorders and processes.


Subject(s)
COVID-19 , Serum Amyloid P-Component , C-Reactive Protein/metabolism , Complement Activation , Cryoelectron Microscopy , Female , Humans , Immunity, Innate , Ligands , Serum Amyloid P-Component/chemistry , Serum Amyloid P-Component/metabolism
2.
Nat Immunol ; 23(2): 275-286, 2022 02.
Article in English | MEDLINE | ID: covidwho-1661973

ABSTRACT

The humoral arm of innate immunity includes diverse molecules with antibody-like functions, some of which serve as disease severity biomarkers in coronavirus disease 2019 (COVID-19). The present study was designed to conduct a systematic investigation of the interaction of human humoral fluid-phase pattern recognition molecules (PRMs) with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Of 12 PRMs tested, the long pentraxin 3 (PTX3) and mannose-binding lectin (MBL) bound the viral nucleocapsid and spike proteins, respectively. MBL bound trimeric spike protein, including that of variants of concern (VoC), in a glycan-dependent manner and inhibited SARS-CoV-2 in three in vitro models. Moreover, after binding to spike protein, MBL activated the lectin pathway of complement activation. Based on retention of glycosylation sites and modeling, MBL was predicted to recognize the Omicron VoC. Genetic polymorphisms at the MBL2 locus were associated with disease severity. These results suggest that selected humoral fluid-phase PRMs can play an important role in resistance to, and pathogenesis of, COVID-19, a finding with translational implications.


Subject(s)
COVID-19/immunology , Immunity, Humoral , Receptors, Pattern Recognition/immunology , SARS-CoV-2/immunology , Animals , C-Reactive Protein/immunology , C-Reactive Protein/metabolism , COVID-19/metabolism , COVID-19/virology , Case-Control Studies , Chlorocebus aethiops , Complement Activation , Coronavirus Nucleocapsid Proteins/genetics , Coronavirus Nucleocapsid Proteins/immunology , Coronavirus Nucleocapsid Proteins/metabolism , Female , Glycosylation , HEK293 Cells , Host-Pathogen Interactions , Humans , Male , Mannose-Binding Lectin/genetics , Mannose-Binding Lectin/immunology , Mannose-Binding Lectin/metabolism , Phosphoproteins/genetics , Phosphoproteins/immunology , Phosphoproteins/metabolism , Polymorphism, Genetic , Protein Binding , Receptors, Pattern Recognition/genetics , Receptors, Pattern Recognition/metabolism , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , SARS-CoV-2/pathogenicity , Serum Amyloid P-Component/immunology , Serum Amyloid P-Component/metabolism , Signal Transduction , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/metabolism , Vero Cells
3.
Nat Commun ; 12(1): 3406, 2021 06 07.
Article in English | MEDLINE | ID: covidwho-1260941

ABSTRACT

Prognostic characteristics inform risk stratification in intensive care unit (ICU) patients with coronavirus disease 2019 (COVID-19). We obtained blood samples (n = 474) from hospitalized COVID-19 patients (n = 123), non-COVID-19 ICU sepsis patients (n = 25) and healthy controls (n = 30). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA was detected in plasma or serum (RNAemia) of COVID-19 ICU patients when neutralizing antibody response was low. RNAemia is associated with higher 28-day ICU mortality (hazard ratio [HR], 1.84 [95% CI, 1.22-2.77] adjusted for age and sex). RNAemia is comparable in performance to the best protein predictors. Mannose binding lectin 2 and pentraxin-3 (PTX3), two activators of the complement pathway of the innate immune system, are positively associated with mortality. Machine learning identified 'Age, RNAemia' and 'Age, PTX3' as the best binary signatures associated with 28-day ICU mortality. In longitudinal comparisons, COVID-19 ICU patients have a distinct proteomic trajectory associated with mortality, with recovery of many liver-derived proteins indicating survival. Finally, proteins of the complement system and galectin-3-binding protein (LGALS3BP) are identified as interaction partners of SARS-CoV-2 spike glycoprotein. LGALS3BP overexpression inhibits spike-pseudoparticle uptake and spike-induced cell-cell fusion in vitro.


Subject(s)
COVID-19/prevention & control , Critical Care/statistics & numerical data , Proteomics/methods , RNA, Viral/genetics , SARS-CoV-2/genetics , Adult , Animals , Antibodies, Neutralizing/immunology , Antigens, Neoplasm/metabolism , Biomarkers, Tumor/metabolism , C-Reactive Protein/metabolism , COVID-19/metabolism , COVID-19/virology , Female , HEK293 Cells , Humans , Kaplan-Meier Estimate , Male , Middle Aged , RNA, Viral/blood , SARS-CoV-2/metabolism , SARS-CoV-2/physiology , Serum Amyloid P-Component/metabolism , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/metabolism , Viral Load/immunology
5.
Cells ; 10(5)2021 05 12.
Article in English | MEDLINE | ID: covidwho-1234671

ABSTRACT

Macrophages play a key role in induction of inflammatory responses. These inflammatory responses are mostly considered to be instigated by activation of pattern recognition receptors (PRRs) or cytokine receptors. However, recently it has become clear that also antibodies and pentraxins, which can both activate Fc receptors (FcRs), induce very powerful inflammatory responses by macrophages that can even be an order of magnitude greater than PRRs. While the physiological function of this antibody-dependent inflammation (ADI) is to counteract infections, undesired activation or over-activation of this mechanism will lead to pathology, as observed in a variety of disorders, including viral infections such as COVID-19, chronic inflammatory disorders such as Crohn's disease, and autoimmune diseases such as rheumatoid arthritis. In this review we discuss how physiological ADI provides host defense by inducing pathogen-specific immunity, and how erroneous activation of this mechanism leads to pathology. Moreover, we will provide an overview of the currently known signaling and metabolic pathways that underlie ADI, and how these can be targeted to counteract pathological inflammation.


Subject(s)
Antibodies/metabolism , C-Reactive Protein/metabolism , Inflammation/immunology , Serum Amyloid P-Component/metabolism , Antibodies/immunology , C-Reactive Protein/immunology , Host-Pathogen Interactions/immunology , Humans , Immunity, Innate , Inflammation/metabolism , Inflammation/microbiology , Macrophages/immunology , Macrophages/metabolism , Metabolic Networks and Pathways/immunology , Receptors, Fc/metabolism , Serum Amyloid P-Component/immunology , Signal Transduction/immunology
7.
Nat Immunol ; 22(1): 19-24, 2021 01.
Article in English | MEDLINE | ID: covidwho-1065905

ABSTRACT

Long pentraxin 3 (PTX3) is an essential component of humoral innate immunity, involved in resistance to selected pathogens and in the regulation of inflammation1-3. The present study was designed to assess the presence and significance of PTX3 in Coronavirus Disease 2019 (COVID-19)4-7. RNA-sequencing analysis of peripheral blood mononuclear cells, single-cell bioinformatics analysis and immunohistochemistry of lung autopsy samples revealed that myelomonocytic cells and endothelial cells express high levels of PTX3 in patients with COVID-19. Increased plasma concentrations of PTX3 were detected in 96 patients with COVID-19. PTX3 emerged as a strong independent predictor of 28-d mortality in multivariable analysis, better than conventional markers of inflammation, in hospitalized patients with COVID-19. The prognostic significance of PTX3 abundance for mortality was confirmed in a second independent cohort (54 patients). Thus, circulating and lung myelomonocytic cells and endothelial cells are a major source of PTX3, and PTX3 plasma concentration can serve as an independent strong prognostic indicator of short-term mortality in COVID-19.


Subject(s)
C-Reactive Protein/genetics , COVID-19/genetics , Gene Expression Profiling/methods , Macrophages/metabolism , SARS-CoV-2/isolation & purification , Serum Amyloid P-Component/genetics , A549 Cells , Adult , C-Reactive Protein/metabolism , COVID-19/epidemiology , COVID-19/virology , Cell Line, Tumor , Cells, Cultured , Cohort Studies , Endothelial Cells/metabolism , Epidemics , Female , Humans , Male , Middle Aged , Monocytes/metabolism , Neutrophils/metabolism , Prognosis , SARS-CoV-2/physiology , Serum Amyloid P-Component/metabolism
8.
Turk J Med Sci ; 51(2): 448-453, 2021 04 30.
Article in English | MEDLINE | ID: covidwho-976380

ABSTRACT

Background/aim: The purpose of this study is to evaluate serum pentraxin-3 (PTX-3) levels in Sars-CoV-2 virus infection (COVID-19) patients and to investigate whether PTX-3 predicts the disease prognosis. Materials and methods: This study was conducted on 88 confirmed COVID-19 patients who were hospitalized due to symptomatic pneumonia between April 15 and August 15, 2020. The patients were divided into two groups as survived patients and non-survived patients. Both groups were compared according to demographic features, comorbid conditions and measurement of the PTX-3 and other laboratory parameters of the patients. Results: Of 88 patients with COVID-19, 59 (67%) were discharged with complete cure and 29 (33%) resulted in death. 46 (52.3%) of the patients were men. PTX-3 median value (IQR) was 3.66 ng/mL (0.9­27.9) in all patients, 3.3 ng/mL (0.9­27.9) in survivors and 3.91 ng/mL (1.9­23.2) in nonsurvivors which was significantly higher (P = 0.045). As a receiver operating characteristic curve analysis the cut-off value of PTX-3 for predicting mortality in patients was 3.73 with 65% sensitivity and 65% specificity (AUC: 0.646, 95% CI: 0.525­ 0.767, P = 0.045). Also, we found significant cut-off values with respect to D-dimer, D-dimer/PTX-3, high-sensitivity troponin, high- sensitivity troponin/PTX-3, lymphocyte, PTX-3/lymphocyte, procalcitonin, procalcitonin/PTX-3, CRP, and CRP/PTX-3 (P < 0.05). Conclusion: In this study, as far as we know, for the first time, we have shown PTX-3 as the new mortality biomarker for COVID-19 disease.


Subject(s)
C-Reactive Protein/metabolism , COVID-19/metabolism , Serum Amyloid P-Component/metabolism , Adult , Aged , Aged, 80 and over , Area Under Curve , Biomarkers/metabolism , COVID-19/mortality , Female , Fibrin Fibrinogen Degradation Products/metabolism , Humans , Lymphocyte Count , Male , Middle Aged , Mortality , Procalcitonin/metabolism , Prognosis , ROC Curve , SARS-CoV-2 , Troponin/metabolism , Young Adult
9.
Nat Immunol ; 22(1): 19-24, 2021 01.
Article in English | MEDLINE | ID: covidwho-933698

ABSTRACT

Long pentraxin 3 (PTX3) is an essential component of humoral innate immunity, involved in resistance to selected pathogens and in the regulation of inflammation1-3. The present study was designed to assess the presence and significance of PTX3 in Coronavirus Disease 2019 (COVID-19)4-7. RNA-sequencing analysis of peripheral blood mononuclear cells, single-cell bioinformatics analysis and immunohistochemistry of lung autopsy samples revealed that myelomonocytic cells and endothelial cells express high levels of PTX3 in patients with COVID-19. Increased plasma concentrations of PTX3 were detected in 96 patients with COVID-19. PTX3 emerged as a strong independent predictor of 28-d mortality in multivariable analysis, better than conventional markers of inflammation, in hospitalized patients with COVID-19. The prognostic significance of PTX3 abundance for mortality was confirmed in a second independent cohort (54 patients). Thus, circulating and lung myelomonocytic cells and endothelial cells are a major source of PTX3, and PTX3 plasma concentration can serve as an independent strong prognostic indicator of short-term mortality in COVID-19.


Subject(s)
C-Reactive Protein/genetics , COVID-19/genetics , Gene Expression Profiling/methods , Macrophages/metabolism , SARS-CoV-2/isolation & purification , Serum Amyloid P-Component/genetics , A549 Cells , Adult , C-Reactive Protein/metabolism , COVID-19/epidemiology , COVID-19/virology , Cell Line, Tumor , Cells, Cultured , Cohort Studies , Endothelial Cells/metabolism , Epidemics , Female , Humans , Male , Middle Aged , Monocytes/metabolism , Neutrophils/metabolism , Prognosis , SARS-CoV-2/physiology , Serum Amyloid P-Component/metabolism
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