key: cord-0899419-ii8rchl4
authors: Tiwari, Ritudhwaj; Mishra, Anurag R.; Mikaeloff, Flora; Gupta, Soham; Mirazimi, Ali; Byrareddy, Siddappa N.; Neogi, Ujjwal; Nayak, Debasis
title: In silico and In vitro Studies Reveal Complement System Drives Coagulation Cascade in SARS-CoV-2 Pathogenesis
date: 2020-11-11
journal: Comput Struct Biotechnol J
DOI: 10.1016/j.csbj.2020.11.005
sha: 9486c9a344edca218658ce3d5c590de0569116e2
doc_id: 899419
cord_uid: ii8rchl4

The emergence and continued spread of SARS-CoV-2 have resulted in a public health emergency across the globe. The lack of knowledge on the precise mechanism of viral pathogenesis is impeding medical intervention. In this study, we have taken both in silico and in vitro experimental approaches to unravel the mechanism of viral pathogenesis associated with complement and coagulation pathways. Based on the structural similarities of viral and host proteins, we initially generated a protein-protein interactome profile. Further computational analysis combined with Gene Ontology (GO) analysis and KEGG pathway analysis predicted key annotated pathways associated with viral pathogenesis. These include MAPK signaling, complement, and coagulation cascades, endocytosis, PD-L1 expression, PD-1 checkpoint pathway in cancer and C-type lectin receptor signaling pathways. Degree centrality analysis pinned down to MAPK1, MAPK3, AKT1, and SRC are crucial drivers of signaling pathways and often overlap with the associated pathways. Most strikingly, the complement and coagulation cascade and platelet activation pathways are interconnected, presumably directing thrombotic activity observed in severe or critical cases of COVID-19. This is complemented by in vitro studies of Huh7 cell infection and analysis of the transcriptome and proteomic profile of gene candidates during viral infection. The most known candidates associated with complement and coagulation cascade signaling by KEGG pathway analysis showed significant up-regulated fold change during viral infection. Collectively both in silico and in vitro studies suggest complement and coagulation cascade signaling are a mechanism for intravascular coagulation, thrombotic changes, and associated complications in severe COVID-19 patients.

Coronavirus disease 2019 (COVID-19) is a respiratory disease that primarily manifests with pneumonia-like symptoms, gastrointestinal symptoms and is occasionally associated with multiorgan failure. [1, 2] The causative agent SARS-CoV-2 is an enveloped positive-sense, single-stranded RNA betacoronavirus, which belongs to the Coronaviridae family. Six human coronaviruses (HCoVs) were previously identified. However, over the past two decades, highly pathogenic HCoVs have emerged. These include SARS-CoV in 2002 with a mortality rate of 10% and MERS-CoV emerged in 2012 with a case fatality rate of 36%. [3, 4] Although the overall mortality rate due to the current SARS-CoV-2 is relatively lower, the virus seemingly spreads more efficiently, thus making it far more challenging to contain and increasing its pandemic potential. Despite continuous research activities, efficacious vaccines or antivirals may be months or even years away. To understand the pathophysiology of the virus and develop new therapeutics, it is necessary to develop a broad understanding of hostpathogen interactions; like how SARS-CoV-2 uses the host machinery during infection, and apply this information towards developing both new drugs and repurposing existing drugs.

In this study, we utilized in silico methods for predicting the interactions between SARS-CoV-2 and the host proteins followed by transcriptomics and proteomics analysis of the SARS-CoV-2 infected Huh7 cell-line. The approach is based on protein structural similarity.

We predicted an interaction map for SARS-CoV-2 cellular co-localization information by mining previously published data sets of coronaviruses and other respiratory disease-causing RNA viruses. [5] [6] [7] Collectively, with the knowledge of protein-protein interactions of SARS-CoV-2, these predictions provide an additional platform for a better understanding of viral pathogenesis and identification of potential clinical targets. Gene enrichment analysis of these interacting host proteins advocates that cytokine storm and neutrophil degranulation drive acute respiratory disease syndrome (ARDS) in SARS CoV-2 patients. Most strikingly, the complement and coagulation cascade are interconnected and potentially crucial drivers of the innate immune response against SARS-CoV-2. This prediction was further validated by the KEGG pathway in gene set enrichment analysis of combined transcriptomics and proteomics data sets from in vitro SARS-CoV-2 infections in cell lines as reported earlier. [8] Thus the current study helps us to understand the molecular mechanism of the SARS-CoV-2 infection and its role in pathogenesis through the combined activation of cytokine storm, neutrophil degranulation, and the complement system.

The ORF7a, ORF8, N, ORF10) were curated from Zhang Lab, which modeled these structures by using I-TASSER. [9] Each of the structures for SARS-CoV-2 proteins were compared with proteins of known structure for structural similarities using the DaliLite v.5 webservers. [10] The PDB codes obtained from Dali were mapped to their corresponding Uniprot ID and gene Name by DAVID Gene ID Conversion or Uniprot ID mapping. [11, 12] Gene Ontology (GO) analysis of these proteins was performed using the g: Profiler tool and Reactome database.

Their interaction networks and degree centrality calculations were annotated using the STRING and CytoNCA tool in Cytoscape. [13] [14] [15] [16] 

We determined the structural similarities among SARS-CoV-2 and human proteins from

DaliLite v. 5 webservers. [10] The Dali server compares 3D structural coordinates of two PDB entries by an alignment of alpha carbon distance matrices, allowing for differences in domain order, and finally produces a structural similarity score. In the current study, we submitted each SARS-CoV-2 protein (PDB and Zhang Lab) into the Dali web server that searched against the entire PDB dataset for structurally-similar proteins with a z-score above 2.0. As a result, we retrieved all the proteins having structures similar to SARS-CoV-2 proteins available in the PDB database. From these results, we then filtered to only include those structures pertaining to human host. These human SARS-CoV-2-similar proteins are hence referred to as "hSARS-CoV-2 similar" proteins.

To predict the human endogenous proteins interacting with the SARS-CoV-2 proteins, we investigated the target proteins interacting with the hSARS-CoV-2 similar proteins during various cellular processes. We found known interactions between hSARS-CoV-2 similar proteins and target human endogenous proteins using data from the BIOGRID, HPRD, and MINT database. [17] [18] [19] These datasets are sourced from literature-curated interactions among human proteins. It is presumed that these cellular proteins, which are known to interact with human protein (similar to SARS-CoV-2 structures), might also interact with SARS-CoV-2 proteins due to their structural similarity.

The assumed host protein interactors of the SARS-CoV-2 proteome were shortlisted based on their functionality and cellular localization. The interactor host proteins were primarily annotated on the basis of protein localization, since theoretically, the two proteins must share at least one cellular compartment for direct communication among them. In our study, cellular compartments were chosen based on published literature and availability in the UniProt database, suggesting the localization of viral proteins in the host cell. Classified proteins from CC study were then submitted to the g:Profiler and Reactome database to retrieve the list of terms enriched with these proteins and the biological pathways, including them. [13, 15] 

As Dali might contain multiple PDB structures of the same protein, repetition in the interaction predictions could surface. Some SARS-CoV-2 proteins have multiple PDB structures resulting in similar repetitive interaction predictions. Hence, prediction count based on a pair of human Uniprot accessions and SARS-CoV-2 protein name was set as "single" score. The predicted interactions supported by the data obtained from experimental studies carried out for SARS-CoV-2 and datasets from related RNA viruses obtained from our VHFIDB database (www.vhfidb.com) create a very comprehensive and manually curated database, containing 9921 host factors information for 72 viral species.

We re-analyzed the proteo-transcriptomics data of SARS-CoV-2 infected (1 MOI) Huh7 cells to identify the temporal changes resulted from infection over time. [8] Briefly, Huh7 cells infected with SARS-CoV-2 were collected at 24, 48, and 72 h in triplicates. Transcripts and protein abundance were quantified using RNA-seq and LC-MS/MS methods. To identify the relative genes changes, temporal differential abundance analysis was performed using a univariate time series model from the R package LIMMA. In the LIMMA design matrix, separated coefficients were associated with time and replicates to extract the difference as a contrast. Moderated paired t-test using LIMMA with adjustment for replicates was used.

Benjamini-Hochberg (BH) adjustment was applied, and only proteins and transcripts with adjusted p values <0.05 were selected. Eighty-five genes associated with KEGG pathway "Complement and coagulation cascades -Homo sapiens" were retrieved from the KEGG database (https://www.genome.jp/kegg-bin). The proteins and transcripts associated with complement and coagulation networks were created separately with Cytoscape ver 3.6.1. For each node, fold change and q-value from LIMMA were added to the network template file.

Edges between nodes were taken from the string database (https://string-db.org/) with high evidence (interaction score > 700), and interactions retrieved from experiments and databases only. Nodes refer to connected objects in the network and edges to the connections between nodes. Heatmap was created using R package heatmap 2.

To identify the list of human host proteins having structural similarity to SARS-CoV-2 proteins, we employed a previously established protocol [20] by collecting the available PDB structures of viral proteins and predicted structures from the Zhang lab. [9] The viral protein structure was then submitted to DaliLite v.5 web servers for predicting structure similarity to human proteins. We refer to these identified human proteins bearing a domain of high structural similarity to the SARS-CoV-2 protein as "SARS-CoV-2 -similar". Next, we determined the known interactions for these SARS-CoV-2 -similar human (hSARS-CoV-2) proteins. The structural similarity analysis identified 3,735 human proteins (hSARS-CoV-2) similar to the 16 SARS-CoV-2 proteins. Next, we identified all possible interaction partners for these proteins and identified the interacting partners of the 16 proteins of SARS-CoV-2 from all interacting partners of the hSARS-CoV-2 similar proteins downloaded from three different databases (HPRD, BIOGRID, and MINT). A total of 57,359 unique interaction partners were identified for these 16 SARS-CoV-2 proteins, involving 12,872 unique human interacting proteins (Supplementary Table 1 ). To further enrich the protein pool, we used two different kinds of filters (cellular compartment analysis (CC), and literature analysis). First, we used GO cellular compartment (CC) annotation to refine and filter the candidates using the cellular localization pattern. This exercise reduced the number of unique interaction partners to 19,047, with 6,876 unique proteins (Supplementary Table 2 ). Later we curated the data by analyzing the RNA virus dataset, filtered, and obtained 5,903 unique interaction partners with 2,647 unique proteins. This information was subsequently used for the functional pathway analysis and for determining the role played by genes in associated pathways.

We compared our predictions with a previously published study by Gordon et al.. Experimental data sets published in this study showed SARS-CoV-2 and human proteins resulted in 332 unique interactions. When we aligned our interacting protein list with that from Gordon et al., we noticed around 91% overlap with our primary interacting list and about 54% genes with our CC and literature filtered list. ( Figure S1) 

Next, we performed gene enrichment analysis by using the g: GOSt tool of g: Profiler. g:

GOSt is the core tool for performing functional enrichment analysis on the input gene list. [15] It mapped a handler-provided list of genes to find relevant information sources and detect statistically significant enriched biological processes and pathways. At first, we uploaded the SARS CoV-2 interactors protein lists in. g: GOSt tools and manually selected GO: biological process (GO: BP), KEGG pathways, and Reactome database in data source option and set threshold value at .05. Finally, we got g: GOSt multi-query Manhattan plot, which shows significantly enriched GO: BP, KEGG terms and Reactome enhanced data 

Coronavirus can evade the host innate immune response by interacting with key components of signaling pathways. The GO enrichment analysis of predicted candidates showed 369 host genes associated with the innate immune system to interact with SARS-CoV-2 proteins (Supplementary Table 3 ). In silico analysis revealed that viral proteins like S, NSP13, NSP15, NSP7, NSP8, NSP 5, and NSP4 interact with mitochondrial antiviral-signaling protein (MAVS), an important intermediate of RIG-I signaling-mediated IFN-I production.

This interaction of the viral proteins with MAVS can inhibit IFN-I production. For example, blocking CARD-CARD domain interaction between RIG-I and MAVS, thereby promotes proteasomal degradation of MAVS or interferes with the recruitment of tumor necrosis factor receptor-associated factor (TRAF) family proteins. [21] Notably, the same viral proteins can also interact with TRIM-25 E3 ligase, which is essential for the ubiquitination of RIG-I and activation of the signaling cascade (Table S1 ). The SARS-CoV-2 proteins can also interact with effector targets of the RIG-I signaling like IRF3 and IRF7 and inhibit its translocation to the nucleus and downregulate IFN-I production. [22] We also observed that viral protein might interact with components of TLR-mediated IFN response like TRAF6 and IRAK1. [23] The IFN-I signaling can also activate mitogen-activated protein kinase (MAPK) signaling regulating several cellular processes ranging from inflammation, cell differentiation, stress to apoptosis, and metabolism. On the other hand, the MAPK signaling pathway is activated by several viruses. Interestingly, MAPK is essential for coronavirus replication and associated with the production of the inflammatory cytokines ( Figure 2 ). [24, 25] In this context, the degree centrality analysis of the predicted 369 host genes revealed that the MAPK signaling Table 3 ). The degree centrality analysis of these genes suggests that cellular tumor antigen p53 (TP53), followed by tumor necrosis factor (TNF), mitogen-activated protein kinase 3 (MAPK3), and mitogen-activated protein kinase 1 (MAPK1) have crucial and central roles in cytokine signaling ( Figure 3A ) ( Table 1) . TNFα is a potent pro-inflammatory factor and a key regulator of immune cell functions. In viral infections, TNFα can induce pro-inflammatory cytokine production and activate TNFdependent pathways. This primarily directs NF-κB-mediated cytokine production, ie; IL6, IL4. [28] Also, SARS-CoV-2 viral proteins can stimulate the MAPK and NF-κB pathways ( Figure 3A) , leading to the induction of IL6 production. Neutrophils are present during many lung diseases associated with acute respiratory distress syndrome (ARDS) and may be involved in severe lung injury [29] in COVID-19 patients. Table 2) .

VAMP8 is a member of the soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor (SNARE) family of fusion proteins. It confines to secretory granules, and degranulation is inhibited in VAMP8-deficient macrophages and mast cells. [31] VAMP8 is also expressed in human neutrophils and may follow a similar mechanism of degranulation. [32] The complement system also activates neutrophils degranulation. The

C5a triggers the phagocytic NADPH-oxidative burst and enhances phagocytosis and the release of granule molecules from neutrophils and macrophages. [33, 34] 

Extra-pulmonary microvascular injury associated with blood thickening and clotting is being dimer level, a fibrinolysis-specific degradation product. [36] , [37] The thrombocytopenia and elevated D-dimer can be described by the extreme activation of the coagulation cascade and platelets. [38] In our KEGG pathway and gene enrichment analysis, we discovered two highly enriched, prothrombotic, i.e., Complement and coagulation cascade, and platelet activation pathways, presumably directing thrombotic activities in severe COVID-19 patients. Our analysis shows that 52 proteins related to Complement and coagulation cascades interact with SARS-CoV-2 proteins (Supplementary Table 3 ). Degree centrality analysis of these genes suggests that

Kininogen-1 (KNG1), followed by C3, and Fibrinogen gamma chain (FGG), play a crucial role in activating Complement and coagulation cascades (Figure 4) (Table 3 ). Our study suggests that among all SARS-CoV-2 proteins, the spike protein showed high weighted interaction with proteins associated with complement and coagulation cascade and could activate proteolytic processing of C3. The C3 hydrolysis leads to C3a and C3b, and subsequently further cleavage of C5 into C5a and C5b. Activation and generation of C3a and C5a are well-known inducers for the production of inflammatory cytokines that leads to tissue damage in the lungs. The alteration of cellular membranes is essential in platelet activation, which is required for the primary clot formation. Association of the complement C5b-9 complex into the cell membrane activates platelets and results in the appearance of procoagulant lipids. [39] Modification of the phospholipid is also required for the tissue factor (TF)-based coagulation pathway. TF starts the extrinsic pathway of coagulation and is highly expressed in various tissues, including the brain, lung, kidney, and placenta. [40] . Our analysis showed that the activated complement substrate, specifically C5, can cause an increase in the expression of functionally active TF in leukocytes and endothelial cells ( Figure 5 ). [41] Although neutrophils carry TF on their membranes, it is unclear whether they can produce TF alone. It is tempting to speculate that the enhanced coagulation process observed in SARS-CoV-2 infection is due to higher neutrophils degranulation. and C3b, and further C3b cleaves C5 into C5a and C5b. C3a and C5a induce inflammatory cytokine production.

Further, C3a, C5a, and C5b9 activate the coagulation pathway. C5a also activates IL6 and TNF alpha production, which magnifies the coagulation pathway.

Our The network was annotated with transcriptomics ( Figure 6C ) and proteomics data ( Figure   6D ). Among 85 genes associated with complement and coagulation, 59 transcripts were detected, of which 44 showed significant changes in the transcriptomics data set. While in the proteomics data set, 36 proteins were detected, and 28 showed significant changes (Supplementary Table 5 ). There was a considerable overlap of 24 genes/proteins as shown in 

In the study, we established a network of protein-protein interactions between the host and SARS-CoV-2 proteins by using a protein structure-based computational approach. The GO analysis of these proteins identified their involvement primarily in the innate immune system, cytokine signaling, MAPK signaling pathway, neutrophils degranulation, complement, and coagulation cascades. On further analysis, we discovered that all these pathways overlap considerably with a key set of highly connected genes. The degree centrality analysis revealed that MAPK1, MAPK3, AKT1, and SRC genes are crucial for these pathways and overlapped maximally. This information suggests the existence of a nexus of robust inflammatory events upon SARS-CoV-2 infection. As MAPKs are heterogeneous kinases capable of phosphorylation of serine and threonine residues present in many proteins, the emergence of MAPK-associated pathways are seen as the likely reason for a profound proinflammatory cytokines production: stimulation and induction of strong innate response in the host. We also discovered that to counter IFN-I, a few SARS-CoV-2 proteins may interact with IFN-I signaling pathway associated proteins like MAVS, IRF3, TRIM21, TRAF6, and IRK1 and could inhibit their functions. [23, 42] By combining these observations, we suggest that the MAPK signaling pathway is central to the innate immune response to SARS-CoV-2 infection and associated pathophysiology. We have also found some other enriched pathways, which may be crucial for SARS-CoV-2 mediated pathogenesis, such as PD-L1 expression and PD-1 checkpoint pathway in cancer and C-type lectin receptor signaling pathways. A recent clinical study shows that PD-L1 expression is associated with COVID-19 patient severity. It is highly activated in COVID-19 severe patients. [43] and it was reported earlier that PD-1 and PD-L1 are vital mediators in T cell depletion in sepsis and cancer patients. [44, 45] Our observations are in line with clinically approved drug Camrelizumab (human anti-programmed cell death 1 (PD-1) monoclonal antibody) with thymosin which is already in use against SARS-Cov-2. [46] Similarly, C-type lectin receptor signaling pathways are also enriched in our study and might be associated with the induction of the proinflammatory response after virus infection. [47] Clinical studies and case reports suggest the COVID-19 disease severity is associated with the degree of ARDS, lung injury, hypoxia, thrombosis, ischemia, and reperfusion injury.

These pathological manifestations are also observed along with the increased cytokine storm, neutrophils degranulation, and activation of components of the complement and coagulation pathway. [48, 49] We show highly enriched pathways supporting these clinical observations and further unravel the plausible mechanism behind these phenomena. The degree centrality analysis shows cytokine-associated pathways are regulated by key players such as TP53, are strongly associated with the coagulation process. TNF is a potent enhancer of TF expression on monocytes, and IL-6 enhances the production and thrombogenicity of platelets [53] . Therefore, they can also decrease the anticoagulant factors like thrombomodulin, the endothelial cell protein C receptor, and PS. [53] Activation of the complement system, Among the viral proteins, spike protein interacts with complement components such as with C3, C4A, C5, and ORF 3a product interacts with mannose-binding lectin2 (MBL2). This observation is in line with earlier studies conducted on SARS-CoV-1, which revealed a direct interaction with MBL2 and activation of the complement system. [55, 56] The C3 is a key regulatory protein of the complement system. This notion is supported by a recent study on SARS-CoV-2, which revealed that activation of complement component C3 exacerbates disease pathology in SARS-CoV associated ARDS. Mice deficient with C3 (C3 -/-) exhibited significantly lower respiratory dysfunction despite having equivalent viral loads in the lungs.

This was associated with significantly fewer neutrophils and inflammatory monocytes present in the lungs of C3 -/compared to the control mice. Subsequent investigations exhibited reduced lung pathology and lower cytokine and chemokine levels in the tissue and the sera of C3 -/mice. [57] Thus, the Complement system chemoattractant property may cause neutrophilia in damaged tissue. Based on previous studies and our experimental results, we propose the complement system, along with neutrophils, significantly modulate the thrombogenesis pathway during SARS-CoV-2 infection.

Complement system plays a crucial role during the entire course of pathological events during COVID-19 disease progression. A recent study shows that anti-C3 inhibitor AMY-101 successfully treats COVID-19 patients. [58] This supports our findings that the complement system is a key pathway of the innate immune system associated with SARS-CoV-2 mediated pathogenesis. [59] We propose active research on antiviral drug discovery front targeting the key molecules on the complement and coagulation cascade pathway. Our study is limited to in silico and in vitro experiments and warrants further detailed clinical studies including samples obtained from critically ill COVID-19 patients. Further, future studies with animal models with genetically modified hosts could also be helpful in unraveling the exact mechanism of this phenomenon. 

Supplementary 

A novel coronavirus outbreak of global health concern

A Novel Coronavirus from Patients with Pneumonia in China

A novel coronavirus associated with severe acute respiratory syndrome

A decade after SARS: strategies for controlling emerging coronaviruses

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

The SARS-coronavirus-host interactome: identification of cyclophilins as target for pan-coronavirus inhibitors

Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients

Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells

Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1

Benchmarking fold detection by DaliLite v.5

UniProt: a worldwide hub of protein knowledge

Database for Annotation, Visualization, and Integrated Discovery

Reactome pathway analysis: a highperformance in-memory approach

Cytoscape Automation: empowering workflow-based network analysis

Profiler-a web server for functional interpretation of gene lists (2016 update)

The STRING database in 2017: qualitycontrolled protein-protein association networks, made broadly accessible

The BioGRID interaction database: 2019 update

Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis

MINT: the Molecular INTeraction database

Mapping protein interactions between Dengue virus and its human and insect hosts

Regulation of MAVS Expression and Signaling Function in the Antiviral Innate Immune Response

The SARS coronavirus papain like protease can inhibit IRF3 at a post activation step that requires deubiquitination activity

SARS-coronavirus open reading frame-9b suppresses innate immunity by targeting mitochondria and the MAVS/TRAF3/TRAF6 signalosome

Role of MAPK/MNK1 signaling in virus replication

Mitogen-activated protein kinases in innate immunity

The Global Phosphorylation Landscape of SARS-CoV-2 Infection

Cucurbitacin E inhibits TNF-α-induced inflammatory cytokine production in human synoviocyte MH7A cells via suppression of PI3K/Akt/NF-κB pathways

A Role for Neutrophils in Viral Respiratory Disease

Targeting potential drivers of COVID-19: Neutrophil extracellular traps

VAMP-8 segregates mast cell-preformed mediator exocytosis from cytokine trafficking pathways

Combinatorial SNARE complexes modulate the secretion of cytoplasmic granules in human neutrophils

Antisense Knockdown of Sphingosine Kinase 1 in Human Macrophages Inhibits C5a Receptor-Dependent Signal Transduction, Ca<sup>2+</sup> Signals, Enzyme Release, Cytokine Production, and Chemotaxis

Anaphylatoxin signaling in human neutrophils. A key role for sphingosine kinase

Complement associated microvascular injury and thrombosis in the pathogenesis of severe COVID-19 infection: a report of five cases

Clinical Characteristics of Coronavirus Disease 2019 in China

Incidence of asymptomatic deep vein thrombosis in patients with COVID-19 pneumonia and elevated D-dimer levels

Procoagulant activity during viral infections

The Human Platelet as an Innate Immune Cell: Interactions Between Activated Platelets and the Complement System

Functional tissue factor is entirely cell surface expressed on lipopolysaccharide-stimulated human blood monocytes and a constitutively tissue factor-producing neoplastic cell line

C5 chemotactic fragment induces leukocyte production of tissue factor activity: a link between complement and coagulation

Interplay between SARS-CoV-2 and the type I interferon response

Proteomic blood profiling in mild, severe and critical COVID-19 patients

PD-L1/PD-1 Co-Stimulation, a Brake for T cell Activation and a T cell Differentiation Signal

PD-L1 engagement on T cells promotes selftolerance and suppression of neighboring macrophages and effector T cells in cancer

Ongoing Clinical Trials for the Management of the COVID-19 Pandemic

Activation of C-Type Lectin Receptor and (RIG)-I-Like Receptors Contributes to Proinflammatory Response in Middle East Respiratory Syndrome Coronavirus-Infected Macrophages

COVID-19 cytokine storm: the interplay between inflammation and coagulation

Complement as a target in COVID-19?

COVID-19 and its implications for thrombosis and anticoagulation

Coagulation, inflammation, and apoptosis: different roles for protein S and the protein S-C4b binding protein complex

Liver inflammation and regeneration: two distinct biological phenomena or parallel pathophysiologic processes?

Role of inflammation in atrial fibrillation pathophysiology and management

IFN-I Independent Antiviral Immune Response to Vesicular Stomatitis Virus Challenge in Mouse Brain

A Single Asparagine-Linked Glycosylation Site of the Severe Acute Respiratory Syndrome Coronavirus Spike Glycoprotein Facilitates Inhibition by Mannose-Binding Lectin through Multiple Mechanisms

The case of Complement activation in COVID-19 multiorgan impact

Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis

The first case of COVID-19 treated with the complement C3 inhibitor AMY-101

Complement associated microvascular injury and thrombosis in the pathogenesis of severe COVID-19 infection: a report of five cases

We would like to acknowledge the contribution of all the authors of the Appelberg et al. 

The authors have declared no competing interests.Author's statment RT 

The authors whose names are listed above certify that they have NO affiliations with or involvement in any organization or entity with any financial interest (such as honoraria; educational grants; participation in speakers' bureaus; membership, employment, consultancies, stock ownership, or other equity interest; and expert testimony or patentlicensing arrangements), or non-financial interest (such as personal or professional relationships, affiliations, knowledge or beliefs) in the subject matter or materials discussed in this manuscript.Highlights  The structural similarity analysis identified 3,735 human proteins (hSARS-CoV-2) similar to the 16 SARS-CoV-2 proteins.  MAPK1, MAPK3, AKT1, and SRC proteins are the critical drivers of signaling pathways and often overlap with the associated pathways during SARS-CoV-2 infection.  Several viral proteins interact with MAVS, TRAF6, IRAK1, IRF3, and IRF7 and inhibit IFN-I and ISGs production.  TP53, TNF, MAPK3 proteins in Cytokines storm and VAMP8, ITGAM, and STOM in Neutrophils degranulation are regulatory proteins associated with the ARDS.  Proteomics data showed 28 candidates associated with complement and coagulation cascade during SARS-CoV-2 infection.  Our study suggests that therapeutic targeting of the downstream proteins of the complement system can mitigate SARS-CoV-2 pathogenesis.