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1.
Cells ; 10(12)2021 12 08.
Article in English | MEDLINE | ID: covidwho-1598446

ABSTRACT

Organ-specific proteins (OSPs) possess great medical potential both in clinics and in biomedical research. Applications of them-such as alanine transaminase, aspartate transaminase, and troponins-in clinics have raised certain concerns of their organ specificity. The dynamics and diversity of protein expression in heterogeneous human populations are well known, yet their effects on OSPs are less addressed. Here, we used mice as a model and implemented a breadth study to examine the panorgan proteome for potential variations in organ specificity in different genetic backgrounds. Using reasonable resources, we generated panorgan proteomes of four in-bred mouse strains. The results revealed a large diversity that was more profound among OSPs than among proteomes overall. We defined a robustness score to quantify such variation and derived three sets of OSPs with different stringencies. In the meantime, we found that the enriched biological functions of OSPs are also organ-specific and are sensitive and useful to assess the quality of OSPs. We hope our breadth study can open doors to explore the molecular diversity and dynamics of organ specificity at the protein level.


Subject(s)
Organ Specificity/genetics , Proteins/genetics , Proteome/genetics , Proteomics , Animals , Genetic Variation/genetics , Humans , Mice
2.
PLoS One ; 16(11): e0259165, 2021.
Article in English | MEDLINE | ID: covidwho-1581791

ABSTRACT

The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry (MS) based proteomics for the detection of SARS-CoV-2 proteins in both research samples and clinical specimens. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) MS in infected Vero E6 cells. For tryptic peptides of Nucleocapsid protein, the limit of detection was estimated to be in the mid-attomole range (9E-13 g). Next, this PRM methodology was applied to the detection of viral proteins in various COVID-19 patient clinical specimens, such as sputum and nasopharyngeal swabs. SARS-CoV-2 proteins were detected in these samples with high sensitivity in all specimens with PCR Ct values <24 and in several samples with higher CT values. A clear relationship was observed between summed MS peak intensities for SARS-CoV-2 proteins and Ct values reflecting the abundance of viral RNA. Taken together, these results suggest that targeted MS based proteomics may have the potential to be used as an additional tool in COVID-19 diagnostics.


Subject(s)
COVID-19/diagnosis , Proteomics , SARS-CoV-2/isolation & purification , Viral Proteins/isolation & purification , Animals , COVID-19/pathology , COVID-19/virology , Chlorocebus aethiops , Humans , Mass Spectrometry , Nucleocapsid/genetics , Nucleocapsid/isolation & purification , Phosphoproteins/genetics , Phosphoproteins/isolation & purification , Proteome/genetics , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , Sputum/virology , Vero Cells , Viral Proteins/genetics
3.
EBioMedicine ; 70: 103525, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1356203

ABSTRACT

BACKGROUND: While our battle with the COVID-19 pandemic continues, a multitude of Omics data have been generated from patient samples in various studies. Translation of these data into clinical interventions against COVID-19 remains to be accomplished. Exploring host response to COVID-19 in the upper respiratory tract can unveil prognostic markers and therapeutic targets. METHODS: We conducted a meta-analysis of published transcriptome and proteome profiles of respiratory samples of COVID-19 patients to shortlist high confidence upregulated host factors. Subsequently, mRNA overexpression of selected genes was validated in nasal swabs from a cohort of COVID-19 positive/negative, symptomatic/asymptomatic individuals. Guided by this analysis, we sought to check for potential drug targets. An FDA-approved drug, Auranofin, was tested against SARS-CoV-2 replication in cell culture and Syrian hamster challenge model. FINDINGS: The meta-analysis and validation in the COVID-19 cohort revealed S100 family genes (S100A6, S100A8, S100A9, and S100P) as prognostic markers of severe COVID-19. Furthermore, Thioredoxin (TXN) was found to be consistently upregulated. Auranofin, which targets Thioredoxin reductase, was found to mitigate SARS-CoV-2 replication in vitro. Furthermore, oral administration of Auranofin in Syrian hamsters in therapeutic as well as prophylactic regimen reduced viral replication, IL-6 production, and inflammation in the lungs. INTERPRETATION: Elevated mRNA level of S100s in the nasal swabs indicate severe COVID-19 disease, and FDA-approved drug Auranofin mitigated SARS-CoV-2 replication in preclinical hamster model. FUNDING: This study was supported by the DBT-IISc partnership program (DBT (IED/4/2020-MED/DBT)), the Infosys Young Investigator award (YI/2019/1106), DBT-BIRAC grant (BT/CS0007/CS/02/20) and the DBT-Wellcome Trust India Alliance Intermediate Fellowship (IA/I/18/1/503613) to ST lab.


Subject(s)
COVID-19/genetics , Nasopharynx/virology , Proteome/genetics , Transcriptome/genetics , Adult , Animals , Biomarkers/metabolism , COVID-19/pathology , COVID-19/virology , Cell Line , Chlorocebus aethiops , Cohort Studies , Female , HEK293 Cells , Humans , Inflammation/genetics , Inflammation/virology , Interleukin-6/genetics , Male , Mesocricetus , Middle Aged , Nasopharynx/pathology , Pandemics , Prognosis , RNA, Messenger/genetics , SARS-CoV-2/pathogenicity , Up-Regulation/genetics , Vero Cells , Virus Replication/genetics
4.
Genes (Basel) ; 11(6)2020 06 26.
Article in English | MEDLINE | ID: covidwho-1280752

ABSTRACT

Ivermectin (IVM), an antiparasitic drug, has a positive effect against Anisakis simplex s.s. infection and has been used for the treatment and prevention of anisakiasis in humans. However, the molecular mechanism of action of IVM on A. simplex s.s. remains unknown. Herein, tandem mass tag (TMT) labeling and extensive liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analysis were used to identify the effect of IVM on the proteome of A. simplex s.s. in vitro. During the study, 3433 proteins, of which 1247 had at least two protein unique peptides, were identified. Comparative proteomics analysis revealed that 59 proteins were differentially regulated (DRPs) in IVM-treated larvae, of which 14 proteins were upregulated and 38 were downregulated after 12 h of culture, but after 24 h, 12 proteins were upregulated and 22 were downregulated. The transcription level of five randomly selected DRPs was determined by real-time PCR as a supplement to the proteomic data. The functional enrichment analysis showed that most of the DRPs were involved in oxidoreductase activity, immunogenicity, protein degradation, and other biological processes. This study has, for the first time, provided comprehensive proteomics data on A. simplex s.s. response to IVM and might deliver new insight into the molecular mechanism by which IVM acts on invasive larvae of A. simplex s.s.


Subject(s)
Anisakiasis/genetics , Anisakis/drug effects , Ivermectin/pharmacology , Proteome/genetics , Animals , Anisakiasis/drug therapy , Anisakiasis/parasitology , Anisakis/pathogenicity , Chromatography, Liquid , Gene Expression Regulation/drug effects , Humans , Larva/drug effects , Larva/pathogenicity , Proteomics , Tandem Mass Spectrometry
5.
Infect Genet Evol ; 93: 104973, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1275585

ABSTRACT

SARS-CoV-2 is currently causing major havoc worldwide with its efficient transmission and propagation. To track the emergence as well as the persistence of mutations during the early stage of the pandemic, a comparative analysis of SARS-CoV-2 whole proteome sequences has been performed by considering manually curated 31,389 whole genome sequences from 84 countries. Among the 7 highly recurring (percentage frequency≥10%) mutations (Nsp2:T85I, Nsp6:L37F, Nsp12:P323L, Spike:D614G, ORF3a:Q57H, N protein:R203K and N protein:G204R), N protein:R203K and N protein: G204R are co-occurring (dependent) mutations. Nsp12:P323L and Spike:D614G often appear simultaneously. The highly recurring Spike:D614G, Nsp12:P323L and Nsp6:L37F as well as moderately recurring (percentage frequency between ≥1 and <10%) ORF3a:G251V and ORF8:L84S mutations have led to4 major clades in addition to a clade that lacks high recurring mutations. Further, the occurrence of ORF3a:Q57H&Nsp2:T85I, ORF3a:Q57H and N protein:R203K&G204R along with Nsp12:P323L&Spike:D614G has led to 3 additional sub-clades. Similarly, occurrence of Nsp6:L37F and ORF3a:G251V together has led to the emergence of a sub-clade. Nonetheless, ORF8:L84S does not occur along with ORF3a:G251V or Nsp6:L37F. Intriguingly, ORF3a:G251V and ORF8:L84S are found to occur independent of Nsp12:P323L and Spike:D614G mutations. These clades have evolved during the early stage of the pandemic and have disseminated across several countries. Further, Nsp10 is found to be highly resistant to mutations, thus, it can be exploited for drug/vaccine development and the corresponding gene sequence can be used for the diagnosis. Concisely, the study reports the SARS-CoV-2 antigens diversity across the globe during the early stage of the pandemic and facilitates the understanding of viral evolution.


Subject(s)
COVID-19/virology , Mutation , SARS-CoV-2/physiology , Viral Proteins/genetics , Viral Proteins/metabolism , Biological Evolution , COVID-19/epidemiology , Hospitalization , Humans , Proteome/genetics , Proteome/metabolism , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus/genetics , Virus Replication/genetics , Whole Genome Sequencing
6.
Mol Cell ; 81(13): 2851-2867.e7, 2021 07 01.
Article in English | MEDLINE | ID: covidwho-1240514

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control its life cycle remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively the cellular and viral RBPs that are involved in SARS-CoV-2 infection. We reveal that SARS-CoV-2 infection profoundly remodels the cellular RNA-bound proteome, which includes wide-ranging effects on RNA metabolic pathways, non-canonical RBPs, and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Among them are several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.


Subject(s)
COVID-19/metabolism , Proteome/metabolism , RNA, Viral/metabolism , RNA-Binding Proteins/metabolism , SARS-CoV-2/physiology , Viral Proteins/metabolism , Virus Replication/physiology , A549 Cells , COVID-19/genetics , Humans , Proteome/genetics , RNA, Viral/genetics , RNA-Binding Proteins/genetics , Viral Proteins/genetics
7.
Proteomics ; 21(11-12): e2000278, 2021 06.
Article in English | MEDLINE | ID: covidwho-1212777

ABSTRACT

In managing patients with coronavirus disease 2019 (COVID-19), early identification of those at high risk and real-time monitoring of disease progression to severe COVID-19 is a major challenge. We aimed to identify potential early prognostic protein markers and to expand understanding of proteome dynamics during clinical progression of the disease. We performed in-depth proteome profiling on 137 sera, longitudinally collected from 25 patients with COVID-19 (non-severe patients, n = 13; patients who progressed to severe COVID-19, n = 12). We identified 11 potential biomarkers, including the novel markers IGLV3-19 and BNC2, as early potential prognostic indicators of severe COVID-19. These potential biomarkers are mainly involved in biological processes associated with humoral immune response, interferon signalling, acute phase response, lipid metabolism, and platelet degranulation. We further revealed that the longitudinal changes of 40 proteins persistently increased or decreased as the disease progressed to severe COVID-19. These 40 potential biomarkers could effectively reflect the clinical progression of the disease. Our findings provide some new insights into host response to SARS-CoV-2 infection, which are valuable for understanding of COVID-19 disease progression. This study also identified potential biomarkers that could be further validated, which may support better predicting and monitoring progression to severe COVID-19.


Subject(s)
COVID-19 , Host-Pathogen Interactions/genetics , Proteome , Transcriptome/genetics , Aged , Biomarkers/blood , COVID-19/diagnosis , COVID-19/genetics , COVID-19/metabolism , Disease Progression , Female , Gene Expression Profiling , Humans , Longitudinal Studies , Male , Middle Aged , Prognosis , Proteome/analysis , Proteome/genetics , Proteome/metabolism , Proteomics
8.
J Proteome Res ; 20(5): 2224-2239, 2021 05 07.
Article in English | MEDLINE | ID: covidwho-1118785

ABSTRACT

The outbreak of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has posed a serious threat to global public health. The mechanism of pathogenesis and the host immune response to SARS-CoV-2 infection are largely unknown. In the present study, we applied a quantitative proteomic technology to identify and quantify the ubiquitination changes that occur in both the virus and the Vero E6 cells during SARS-CoV-2 infection. By applying label-free, quantitative liquid chromatography with tandem mass spectrometry proteomics, 8943 lysine ubiquitination sites on 3086 proteins were identified, of which 138 sites on 104 proteins were quantified as significantly upregulated, while 828 sites on 447 proteins were downregulated at 72 h post-infection. Bioinformatics analysis suggested that SARS-CoV-2 infection might modulate host immune responses through the ubiquitination of important proteins, including USP5, IQGAP1, TRIM28, and Hsp90. Ubiquitination modification was also observed on 11 SAR-CoV-2 proteins, including proteins involved in virus replication and inhibition of the host innate immune response. Our study provides new insights into the interaction between SARS-CoV-2 and the host as well as potential targets for the prevention and treatment of COVID-19.


Subject(s)
COVID-19 , Proteome , Humans , Proteome/genetics , Proteomics , SARS-CoV-2 , Ubiquitin
9.
J Proteome Res ; 19(12): 4735-4746, 2020 12 04.
Article in English | MEDLINE | ID: covidwho-1065786

ABSTRACT

According to the 2020 Metrics of the HUPO Human Proteome Project (HPP), expression has now been detected at the protein level for >90% of the 19 773 predicted proteins coded in the human genome. The HPP annually reports on progress made throughout the world toward credibly identifying and characterizing the complete human protein parts list and promoting proteomics as an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2020-01 classified 17 874 proteins as PE1, having strong protein-level evidence, up 180 from 17 694 one year earlier. These represent 90.4% of the 19 773 predicted coding genes (all PE1,2,3,4 proteins in neXtProt). Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), was reduced by 230 from 2129 to 1899 since the neXtProt 2019-01 release. PeptideAtlas is the primary source of uniform reanalysis of raw mass spectrometry data for neXtProt, supplemented this year with extensive data from MassIVE. PeptideAtlas 2020-01 added 362 canonical proteins between 2019 and 2020 and MassIVE contributed 84 more, many of which converted PE1 entries based on non-MS evidence to the MS-based subgroup. The 19 Biology and Disease-driven B/D-HPP teams continue to pursue the identification of driver proteins that underlie disease states, the characterization of regulatory mechanisms controlling the functions of these proteins, their proteoforms, and their interactions, and the progression of transitions from correlation to coexpression to causal networks after system perturbations. And the Human Protein Atlas published Blood, Brain, and Metabolic Atlases.


Subject(s)
Proteome , Proteomics , Databases, Protein , Genome, Human , Humans , Mass Spectrometry , Proteome/genetics
10.
Int J Biol Macromol ; 170: 820-826, 2021 Feb 15.
Article in English | MEDLINE | ID: covidwho-996949

ABSTRACT

In this study, analysis of changes of SARS-CoV-2 ORF3a protein during pandemic is reported. ORF3a, a conserved coronavirus protein, is involved in virus replication and release. A set of 70,752 high-quality SARS-CoV-2 genomes available in GISAID databank at the end of August 2020 have been scanned. All ORF3a mutations in the virus genomes were grouped according to the collection date interval and over the entire data set. The considered intervals were: start of collection-February, March, April, May, June, July and August 2020. The top five most frequent variants were examined within each collection interval. Overall, seventeen variants have been isolated. Ten of the seventeen mutant sites occur within the transmembrane (TM) domain of ORF3a and are in contact with the central pore or side tunnels. The other variant sites are in different places of the ORF3a structure. Within the entire sample, the five most frequent mutations are V13L, Q57H, Q57H + A99V, G196V and G252V. The same analysis identified 28 sites identically conserved in all the genome isolates. These sites are possibly involved in stabilization of monomer, dimer, tetramerization and interaction with other cellular components. The results here reported can be helpful to understand virus biology and to design new therapeutic strategies.


Subject(s)
COVID-19/virology , Mutation , SARS-CoV-2/genetics , Viroporin Proteins/genetics , Amino Acid Sequence , COVID-19/epidemiology , Conserved Sequence , Databases, Genetic , Evolution, Molecular , Genome, Viral , Humans , Models, Molecular , Pandemics , Protein Structure, Quaternary , Proteome/genetics , SARS-CoV-2/chemistry , SARS-CoV-2/physiology , Time Factors , Viroporin Proteins/chemistry , Viroporin Proteins/physiology
11.
J Proteome Res ; 19(11): 4275-4290, 2020 11 06.
Article in English | MEDLINE | ID: covidwho-974861

ABSTRACT

SARS-CoV-2 (COVID-19) has infected millions of people worldwide, with lethality in hundreds of thousands. The rapid publication of information, both regarding the clinical course and the viral biology, has yielded incredible knowledge of the virus. In this review, we address the insights gained for the SARS-CoV-2 proteome, which we have integrated into the Viral Integrated Structural Evolution Dynamic Database, a publicly available resource. Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. This inhibition has the potential to not only regulate about 10% of all biological transcripts through altered ribosomal biology but also associate with viral-induced genetics, where suppressed human variants are activated to drive dominant, negative outcomes within cells. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics.


Subject(s)
Betacoronavirus , Coronavirus Infections , Host-Pathogen Interactions , Pandemics , Pneumonia, Viral , Proteome , Ribosomes , COVID-19 , Coronavirus Infections/genetics , Coronavirus Infections/metabolism , Coronavirus Infections/virology , Databases, Genetic , Gene Expression Profiling , Humans , Pneumonia, Viral/genetics , Pneumonia, Viral/metabolism , Pneumonia, Viral/virology , Proteome/genetics , Proteome/metabolism , Ribosomes/genetics , Ribosomes/metabolism , Ribosomes/virology , SARS-CoV-2 , Transcriptome , Viral Proteins
12.
Comput Biol Med ; 128: 104158, 2021 01.
Article in English | MEDLINE | ID: covidwho-950964

ABSTRACT

The COVID-19 pandemic has affected 215 countries and territories around the world with 60,187,347 coronavirus cases and 17,125,719 currently infected patients confirmed as of the November 25, 2020. Currently, many countries are working on developing new vaccines and therapeutic drugs for this novel virus strain, and a few of them are in different phases of clinical trials. The advancement in high-throughput sequence technologies, along with the application of bioinformatics, offers invaluable knowledge on genomic characterization and molecular pathogenesis of coronaviruses. Recent multi-disciplinary studies using bioinformatics methods like sequence-similarity, phylogenomic, and computational structural biology have provided an in-depth understanding of the molecular and biochemical basis of infection, atomic-level recognition of the viral-host receptor interaction, functional annotation of important viral proteins, and evolutionary divergence across different strains. Additionally, various modern immunoinformatic approaches are also being used to target the most promiscuous antigenic epitopes from the SARS-CoV-2 proteome for accelerating the vaccine development process. In this review, we summarize various important computational tools and databases available for systematic sequence-structural study on coronaviruses. The features of these public resources have been comprehensively discussed, which may help experimental biologists with predictive insights useful for ongoing research efforts to find therapeutics against the infectious COVID-19 disease.


Subject(s)
COVID-19/epidemiology , COVID-19/genetics , Computational Biology , Pandemics , Proteome/genetics , SARS-CoV-2/genetics , Computer Simulation , Humans
13.
Nucleic Acids Res ; 49(D1): D480-D489, 2021 01 08.
Article in English | MEDLINE | ID: covidwho-944363

ABSTRACT

The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.


Subject(s)
Computational Biology/methods , Data Curation/methods , Databases, Protein , Knowledge Bases , Proteome/metabolism , Proteomics/methods , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/virology , Humans , Internet , Molecular Sequence Annotation/methods , Pandemics , Proteome/genetics , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , SARS-CoV-2/physiology , User-Computer Interface , Viral Proteins/genetics , Viral Proteins/metabolism
14.
Mol Cell ; 80(6): 1104-1122.e9, 2020 12 17.
Article in English | MEDLINE | ID: covidwho-933377

ABSTRACT

Human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative pathogen of the COVID-19 pandemic, exerts a massive health and socioeconomic crisis. The virus infects alveolar epithelial type 2 cells (AT2s), leading to lung injury and impaired gas exchange, but the mechanisms driving infection and pathology are unclear. We performed a quantitative phosphoproteomic survey of induced pluripotent stem cell-derived AT2s (iAT2s) infected with SARS-CoV-2 at air-liquid interface (ALI). Time course analysis revealed rapid remodeling of diverse host systems, including signaling, RNA processing, translation, metabolism, nuclear integrity, protein trafficking, and cytoskeletal-microtubule organization, leading to cell cycle arrest, genotoxic stress, and innate immunity. Comparison to analogous data from transformed cell lines revealed respiratory-specific processes hijacked by SARS-CoV-2, highlighting potential novel therapeutic avenues that were validated by a high hit rate in a targeted small molecule screen in our iAT2 ALI system.


Subject(s)
Alveolar Epithelial Cells/metabolism , COVID-19/metabolism , Phosphoproteins/metabolism , Proteome/metabolism , SARS-CoV-2/metabolism , Alveolar Epithelial Cells/pathology , Alveolar Epithelial Cells/virology , Animals , Antiviral Agents , COVID-19/drug therapy , COVID-19/genetics , COVID-19/pathology , Chlorocebus aethiops , Cytopathogenic Effect, Viral , Cytoskeleton , Drug Evaluation, Preclinical , Humans , Induced Pluripotent Stem Cells/metabolism , Induced Pluripotent Stem Cells/pathology , Induced Pluripotent Stem Cells/virology , Phosphoproteins/genetics , Protein Transport , Proteome/genetics , SARS-CoV-2/genetics , Signal Transduction , Vero Cells
15.
Proteomics ; 20(24): e2000229, 2020 12.
Article in English | MEDLINE | ID: covidwho-897888

ABSTRACT

Proteins and peptides serve as biomarkers in the context of multiple pathologies. The hypothesis that protein or peptide biomarkers may also be of value in the context of the Covid-19 pandemic appears self-evident. Proteome based biomarkers are not expected to display significant added value in the detection of viral infection but appear well suited to address a major unmet need: the prognosis of the course of disease, to guide appropriate, timely intervention. Based on similar approaches in the context of other diseases and using a CE-MS platform, urinary peptides are investigated for their value as biomarkers to assess disease progression after SARS-CoV-2 infection. The manuscript presented in this issue of Proteomics reports first results, indicating that urine peptides may be of substantial value in the assessment and prediction of severity of the Covid-19 disease course on an individual level. While the findings are not entirely surprising, the report does stand out from all others by a well-defined context-of-use, and, what is more, by presenting an already initiated validation study that may, if successful, result in immediate implementation of this proteomics-based diagnostic test. This approach should serve as positive example for the planning and execution of clinical proteomics studies.


Subject(s)
COVID-19/urine , Peptides/urine , Proteome/genetics , Proteomics , Biomarkers/urine , COVID-19/genetics , COVID-19/therapy , COVID-19/virology , Humans , Pandemics , Peptides/genetics , SARS-CoV-2 , Severity of Illness Index
16.
Nucleic Acids Res ; 49(D1): D412-D419, 2021 01 08.
Article in English | MEDLINE | ID: covidwho-894614

ABSTRACT

The Pfam database is a widely used resource for classifying protein sequences into families and domains. Since Pfam was last described in this journal, over 350 new families have been added in Pfam 33.1 and numerous improvements have been made to existing entries. To facilitate research on COVID-19, we have revised the Pfam entries that cover the SARS-CoV-2 proteome, and built new entries for regions that were not covered by Pfam. We have reintroduced Pfam-B which provides an automatically generated supplement to Pfam and contains 136 730 novel clusters of sequences that are not yet matched by a Pfam family. The new Pfam-B is based on a clustering by the MMseqs2 software. We have compared all of the regions in the RepeatsDB to those in Pfam and have started to use the results to build and refine Pfam repeat families. Pfam is freely available for browsing and download at http://pfam.xfam.org/.


Subject(s)
Computational Biology/statistics & numerical data , Databases, Protein , Proteins/metabolism , Proteome/metabolism , Animals , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/virology , Computational Biology/methods , Epidemics , Humans , Internet , Models, Molecular , Protein Structure, Tertiary , Proteins/chemistry , Proteins/genetics , Proteome/classification , Proteome/genetics , Repetitive Sequences, Amino Acid/genetics , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Sequence Analysis, Protein/methods
18.
FEBS J ; 288(17): 5190-5200, 2021 09.
Article in English | MEDLINE | ID: covidwho-887379

ABSTRACT

Up to 10-20% of patients with coronavirus disease 2019 (COVID-19) develop a severe pulmonary disease due to immune dysfunction and cytokine dysregulation. However, the extracellular proteomic characteristics in respiratory tract of these critical COVID-19 patients still remain to be investigated. In the present study, we performed a quantitative proteomic analysis of the bronchoalveolar lavage fluid (BALF) from patients with critical COVID-19 and from non-COVID-19 controls. Our study identified 358 differentially expressed BALF proteins (P < 0.05), among which 41 were significantly changed after using the Benjamini-Hochberg correction (q < 0.05). The up-regulated signaling was found to be mainly involved in inflammatory signaling and response to oxidative stress. A series of increased extracellular factors including Tenascin-C (TNC), Mucin-1 (KL-6 or MUC1), Lipocalin-2 (LCN2), periostin (POSTN), Chitinase 3-like 1 (CHI3L1 or YKL40), and S100A12, and the antigens including lymphocyte antigen 6D/E48 antigen (LY6D), CD9 antigen, CD177 antigen, and prostate stem cell antigen (PSCA) were identified, among which the proinflammatory factors TNC and KL-6 were further validated in serum of another thirty-nine COVID-19 patients and healthy controls, showing high potentials of being biomarkers or therapeutic candidates for COVID-19. This BALF proteome associated with COVID-19 would also be a valuable resource for researches on anti-inflammatory medication and understanding the molecular mechanisms of host response. DATABASE: Proteomic raw data are available in ProteomeXchange (http://proteomecentral.proteomexchange.org) under the accession number PXD022085, and in iProX (www.iprox.org) under the accession number IPX0002429000.


Subject(s)
Bronchoalveolar Lavage Fluid , COVID-19/genetics , Proteome/genetics , SARS-CoV-2/genetics , Adult , COVID-19/pathology , COVID-19/virology , Critical Illness , Female , Humans , Lung/metabolism , Lung/pathology , Male , Middle Aged , Proteomics , SARS-CoV-2/pathogenicity
19.
Proc Natl Acad Sci U S A ; 117(45): 28336-28343, 2020 11 10.
Article in English | MEDLINE | ID: covidwho-882991

ABSTRACT

Coronavirus disease 2019 (COVID-19), the global pandemic caused by SARS-CoV-2, has resulted thus far in greater than 933,000 deaths worldwide; yet disease pathogenesis remains unclear. Clinical and immunological features of patients with COVID-19 have highlighted a potential role for changes in immune activity in regulating disease severity. However, little is known about the responses in human lung tissue, the primary site of infection. Here we show that pathways related to neutrophil activation and pulmonary fibrosis are among the major up-regulated transcriptional signatures in lung tissue obtained from patients who died of COVID-19 in Wuhan, China. Strikingly, the viral burden was low in all samples, which suggests that the patient deaths may be related to the host response rather than an active fulminant infection. Examination of the colonic transcriptome of these patients suggested that SARS-CoV-2 impacted host responses even at a site with no obvious pathogenesis. Further proteomics analysis validated our transcriptome findings and identified several key proteins, such as the SARS-CoV-2 entry-associated protease cathepsins B and L and the inflammatory response modulator S100A8/A9, that are highly expressed in fatal cases, revealing potential drug targets for COVID-19.


Subject(s)
COVID-19/metabolism , Proteome/metabolism , Transcriptome , Aged , Aged, 80 and over , COVID-19/genetics , COVID-19/immunology , COVID-19/pathology , Colon/metabolism , Fatal Outcome , Female , Humans , Lung/metabolism , Lung/pathology , Lung/virology , Male , Middle Aged , Neutrophil Activation , Proteome/genetics , SARS-CoV-2/pathogenicity , Viral Load
20.
Arch Virol ; 166(1): 101-113, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-882387

ABSTRACT

Avian infectious bronchitis virus is one of the most important gammacoronaviruses, which causes a highly contagious disease. In this study, we investigated changes in the proteome of kidney tissue of specific-pathogen-free (SPF) chickens that were infected with an isolate of the nephrotropic variant 2 genotype (IS/1494/06) of avian coronavirus. Twenty 1-day-old SPF White Leghorn chickens were randomly divided into two groups, each comprising 10 chickens, which were kept in separate positive-pressure isolators. Chickens in group A served as a virus-free control group up to the end of the experiment, whereas chickens in group B were inoculated with 0.1 ml of 104.5 EID50 of the IBV/chicken/Iran/UTIVO-C/2014 isolate of IBV, and kidney tissue samples were collected at 2 and 7 days post-inoculation (dpi) from both groups. Sequencing of five protein spots at 2 dpi and 22 spots at 7 dpi that showed differential expression by two-dimensional electrophoresis (2DE) along with fold change greater than 2 was done by MS-MALDI/TOF/TOF. Furthermore, the corresponding protein-protein interaction (PPI) networks at 2 and 7 dpi were identified to develop a detailed understanding of the mechanism of molecular pathogenesis. Topological graph analysis of this undirected PPI network revealed the effect of 10 genes in the 2 dpi PPI network and nine genes in the 7 dpi PPI network during virus pathogenesis. Proteins that were found by 2DE analysis and MS/TOF-TOF mass spectrometry to be down- or upregulated were subjected to PPI network analysis to identify interactions with other cellular components. The results show that cellular metabolism was altered due to viral infection. Additionally, multifunctional heat shock proteins with a significant role in host cell survival may be employed circuitously by the virus to reach its target. The data from this study suggest that the process of pathogenesis that occurs during avian coronavirus infection involves the regulation of vital cellular processes and the gradual disruption of critical cellular functions.


Subject(s)
Coronavirus Infections/pathology , Coronavirus Infections/veterinary , Infectious bronchitis virus/genetics , Kidney/pathology , Proteome/genetics , Animals , Chickens , Coronavirus Infections/virology , Infectious bronchitis virus/classification , Infectious bronchitis virus/isolation & purification , Kidney/virology , Poultry Diseases/virology , Proteomics , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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