LitCovid-sentences  

PMC:7321036 / 5738-13874 JSONTXT 12 Projects

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Id Subject Object Predicate Lexical cue
T36 0-84 Sentence denotes Phosphorylation Signaling Represents a Primary Host Response to SARS-CoV-2 Infection
T37 85-331 Sentence denotes To determine how SARS-CoV-2 hijacks host-protein signaling, a global phosphoproteomics experiment was performed in Vero E6 cells, a cell line originating from the kidney of a female African green monkey (Chlorocebus sabaeus) (Osada et al., 2014).
T38 332-443 Sentence denotes This cell line was selected because of its high susceptibility to SARS-CoV-2 infection (Harcourt et al., 2020).
T39 444-610 Sentence denotes Cells were harvested in biological triplicate at 6 time points after SARS-CoV-2 infection (0, 2, 4, 8, 12, or 24 h) or after mock infection at 0 or 24 h (Figure 1 A).
T40 611-809 Sentence denotes Using a data-independent acquisition (DIA) proteomics approach, each sample was then partitioned and analyzed for changes in global protein abundance or phosphorylation (data available in Table S1).
T41 810-978 Sentence denotes Chlorocebus sabaeus and human protein sequences were aligned, and phosphorylation sites and protein identifiers were mapped to their respective human protein orthologs.
T42 979-1184 Sentence denotes Phosphorylation fold changes calculated using the 0- or 24-h mock control were highly comparable (correlation coefficient r = 0.77); therefore, the 0-h mock control was used for all subsequent comparisons.
T43 1185-1278 Sentence denotes Figure 1 Global Proteomics of Phosphorylation and Abundance Changes upon SARS-CoV-2 Infection
T44 1279-1337 Sentence denotes (A) Vero E6 cells were infected with SARS-CoV-2 (MOI 1.0).
T45 1338-1437 Sentence denotes After 1 h of viral uptake, cells were harvested (0 h) or, subsequently, after 2, 4, 8, 12, or 24 h.
T46 1438-1573 Sentence denotes As a control, Vero E6 cells were also mock infected for 1 h and harvested immediately thereafter (0 h) or after 24 h of mock infection.
T47 1574-1629 Sentence denotes All conditions were performed in biological triplicate.
T48 1630-1713 Sentence denotes Following cell harvest, cells were lysed, and proteins were digested into peptides.
T49 1714-1978 Sentence denotes Aliquots of all samples were analyzed by mass spectrometry (MS) to measure changes in protein abundance upon infection, whereas the remaining sample was enriched for phosphorylated peptides and subsequently analyzed to measure changes in phosphorylation signaling.
T50 1979-2027 Sentence denotes A DIA approach was used for all MS acquisitions.
T51 2028-2140 Sentence denotes Last, all phosphorylation sites and protein identifiers were mapped to their respective human protein orthologs.
T52 2141-2234 Sentence denotes (B) Principal-component analysis (PCA) of phosphorylation replicates after removing outliers.
T53 2235-2254 Sentence denotes See also Figure S1.
T54 2255-2425 Sentence denotes (C) Correlation of protein abundance (AB) and phosphorylation sites (PHs) between replicates within a biological condition (red) and across biological conditions (black).
T55 2426-2571 Sentence denotes Boxplots depict median (horizonal lines), interquartile range (boxes), maximum and minimum values (vertical lines), and outliers (solid circles).
T56 2572-2647 Sentence denotes (D) Median AB of individual SARS-CoV-2 proteins in the protein AB analysis.
T57 2648-2733 Sentence denotes (E) The number of significantly regulated PH groups across the infection time course.
T58 2734-2799 Sentence denotes (F) Volcano plot of PH group quantification 24 h after infection.
T59 2800-2884 Sentence denotes (G) The number of significantly regulated proteins across the infection time course.
T60 2885-2952 Sentence denotes (H) Volcano plot of protein AB quantification 24 h after infection.
T61 2953-3111 Sentence denotes (I) Gene Ontology enrichment analysis of all significantly changing proteins in terms of AB divided into two sets: downregulated (blue) and upregulated (red).
T62 3112-3330 Sentence denotes (J) Proportion of significantly regulated PH groups with a correlated (i.e., same direction, AB match) or anticorrelated (i.e., opposite direction, AB mismatch) significant or insignificant (gray) change in protein AB.
T63 3331-3630 Sentence denotes In (E)–(H), all infection time points are compared with the mock infection at 0 h, and significantly regulated proteins are defined as (absolute value of log2(infection/mock) > 1 and adjusted p < 0.05 or when only detected in infected or mock based on replicate and MS feature counts; STAR Methods).
T64 3631-3650 Sentence denotes See also Figure S1.
T65 3651-3881 Sentence denotes Quality control filtering of the data was performed, and two samples from each of the phosphorylation and protein abundance datasets were removed because of poor correlation with their respective replicates (Figures S1 A and S1B).
T66 3882-4097 Sentence denotes Principal component analysis (PCA) of the remaining samples revealed good separation of mock and infected samples as well as high quantitative reproducibility between biological replicates (Figures 1B, 1C, and S1C).
T67 4098-4248 Sentence denotes In total, high-quality quantification of 4,624 human-orthologous phosphorylation sites and 3,036 human-orthologous proteins was obtained (Figure S1D).
T68 4249-4417 Sentence denotes Successful infection was confirmed by the observation of a dramatic increase in viral protein abundance over the course of a 24-h infection period (Figures 1D and S1E).
T69 4418-4439 Sentence denotes Figure S1 Proteomics:
T70 4440-4525 Sentence denotes Quality Control (QC), Orthology, Enrichments, and Viral Proteins, Related to Figure 1
T71 4526-4751 Sentence denotes (A) Principal component analysis computed on intensities summarized by MSstats at the level of phosphorylation site groups within (from left to right) all runs, with one outlier run removed, and with two outlier runs removed.
T72 4752-4990 Sentence denotes Outlier runs are labeled 00Hr.2 and 02.Hr.2. (B) Principal components analysis computed on protein intensities as summarized by MSstats (from left to right) within all runs, with one outlier run removed, and with two outlier runs removed.
T73 4991-5123 Sentence denotes Outlier runs are both labeled 00Hr.2; one is mock and the other is infected. (C) Coefficient of variance boxplot for each condition.
T74 5124-5355 Sentence denotes Black lines depict the median and their values are indicated above each boxplot. (D) Mapping detected and quantifiable proteins and phosphorylation sites from the green monkey (Chlorocebus sabaeus) protein sequences to human genes.
T75 5356-5672 Sentence denotes Proteins and sites were considered quantifiable if MSstats computed a non-infinite fold change for any time point or if an infinite log2 fold change passes criteria for inclusion in any time point. (E) Intensities of viral proteins as summarized over all peptide ion fragments by MSstats, averaged across replicates.
T76 5673-5972 Sentence denotes The MSstats summarization is based on the median intensity of all fragments after data pre-processing (STAR Methods). (F) Gene Ontology enrichment analysis for proteins significantly regulated in terms of abundance upon infection, separated by time point and direction of phosphorylation regulation.
T77 5973-6133 Sentence denotes All terms with significant over-representation (adjusted p value < 0.01) in the regulated gene set are kept, and redundant terms are removed (see STAR Methods).
T78 6134-6394 Sentence denotes Numbers in cells indicate the number of genes that match the term for a given time point and direction. (G) Gene Ontology enrichment analysis for significantly phosphorylated proteins upon infection, separated by time point and direction of protein regulation.
T79 6395-6419 Sentence denotes Details same as for (F).
T80 6420-6712 Sentence denotes As expected, an increase was observed in the number of significantly regulated phosphorylation sites and proteins over the infection time course, with the majority of regulation occurring at the level of phosphorylation (Figures 1E and 1F) as opposed to protein abundance (Figures 1G and 1H).
T81 6713-6852 Sentence denotes Of the few proteins that significantly increased in abundance upon infection, the vast majority were SARS-CoV-2 viral proteins (Figure 1H).
T82 6853-6919 Sentence denotes In contrast, the majority of host proteins decreased in abundance.
T83 6920-7110 Sentence denotes This finding is consistent with mechanisms of host mRNA nuclear export and/or host mRNA translation inhibition, which are common in viral infections (Kuss et al., 2013; Walsh and Mohr 2011).
T84 7111-7260 Sentence denotes Gene Ontology enrichment analysis of significantly downregulated proteins revealed several terms related to platelet regulation (Figures 1I and S1F).
T85 7261-7514 Sentence denotes Several downregulated host proteins are known to be involved in platelet regulation, thrombosis, and prevention of blood coagulation, including APOH, CD9, TSPAN14, AHSG, SERPINA1, and A2M (Mather et al., 2016; Mangin et al., 2009; Taggart et al., 2000).
T86 7515-7686 Sentence denotes The downregulation of these proteins suggests that they may mechanistically contribute to symptoms of blood coagulation and stroke in COVID-19 patients (Han et al., 2020).
T87 7687-7780 Sentence denotes Lastly, the contribution of protein abundance to phosphorylation level changes was evaluated.
T88 7781-8136 Sentence denotes For nearly all cases of a significantly changed phosphorylation site, no corresponding significant change in protein abundance was observed (Figure 1J), further suggesting that phosphorylation signaling represents a primary host response over this time course of infection as opposed to transcriptional regulation, which would influence protein abundance.