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pmid:34531741
Identification of Novel Gene Signatures using Next-Generation Sequencing Data from COVID-19 Infection Models: Focus on Neuro-COVID and Potential Therapeutics.
Peter Natesan Pushparaj · Angham Abdulrahman Abdulkareem · Muhammad Imran Naseer
Frontiers in pharmacology · 2021 doi:10.3389/fphar.2021.688227
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Complete file
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The gene expression profiles of COVID-19 infection models can be used to decipher potential therapeutics for COVID-19 and related pathologies, such as Neuro-COVID. Here, we used the raw RNA-seq reads (Single-End) in quadruplicates derived using Illumina Next Seq 500 from SARS-CoV-infected primary human bronchial epithelium (NHBE) and mock-treated NHBE cells obtained from the Gene Expression Omnibus (GEO) (GSE147507), and the quality control (QC) was evaluated using the CLC Genomics Workbench 20.0 (Qiagen, United States) before the RNA-seq analysis using BioJupies web tool and iPathwayGuide for gene ontologies (GO), pathways, upstream regulator genes, small molecules, and natural products. Additionally, single-cell transcriptomics data (GSE163005) of meta clusters of immune cells from the cerebrospinal fluid (CSF), such as T-cells/natural killer cells (NK) (TcMeta), dendritic cells (DCMeta), and monocytes/granulocyte (monoMeta) cell types for comparison, namely, Neuro-COVID versus idiopathic intracranial hypertension (IIH), were analyzed using iPathwayGuide. L1000 fireworks display (L1000FWD) and L1000 characteristic direction signature search engine (L1000 CDS2) web tools were used to uncover the small molecules that could potentially reverse the COVID-19 and Neuro-COVID-associated gene signatures. We uncovered small molecules such as camptothecin, importazole, and withaferin A, which can potentially reverse COVID-19 associated gene signatures. In addition, withaferin A, trichostatin A, narciclasine, camptothecin, and JQ1 have the potential to reverse Neuro-COVID gene signatures. Furthermore, the gene set enrichment analysis (GSEA) preranked method and Metascape web tool were used to decipher and annotate the gene signatures that were potentially reversed by these small molecules. 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"access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[4]#T4", "version": null, "note": "Top identified molecular functions for each pruning type.", "structure": {"pmcid": "PMC8438179", "section_index": 12, "section_title": "iPathwayGuide Analysis of DEGs From COVID-19 and Neuro-COVID Infection Models", "row_count": 7, "column_count": 8}, "table": {"label": "TABLE 4", "caption": "Top identified molecular functions for each pruning type.", "rows": [["Pruning type: none", "Pruning type: high specificity", "Pruning type: smallest common denominator"], ["Go term", "p-value", "p-value (FDR)", "p-value (Bonferroni)", "Go term", "p-value", "Go term", "p-value"], ["Cytokine activity", "1.200e−7", "1.691e−4", "1.691e−4", "Cytokine activity", "0.061", "Cytokine activity", "1.691e−4"], ["Receptor regulator activity", "6.500e−7", "4.579e−4", "9.158e−4", "Chemokine activity", "0.061", "Serine hydrolase activity", "0.341"], ["Signaling receptor activator activity", "4.500e−6", "0.002", "0.006", "DNA replication origin binding", "0.341", "DNA replication origin binding", "0.341"], ["Receptor-ligand activity", "7.900e−6", "0.003", "0.011", "2’-5’-Oligodenylate synthetase activity", "0.341", "2’-5’-Oligodenylate synthetase activity", "0.341"], ["Chemokine activity", "6.000e−5", "0.017", "0.085", "Structural constituent of skin epidermis", "0.341", "Structural constituent of skin epidermis", "0.341"]], "row_count": 7, "column_count": 8, "numeric_cells": 27, "header_rows": 2, "locator": "section[12]/table-wrap[4]#T4"}}, {"id": "asset:table:pmid:34531741:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1070fad613596f673b427e54e108f9ab34c2f32aae68043728474ad3f424135c", "bytes": 959, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[5]#T5", "version": null, "note": "Top identified cellular components for each pruning type.", "structure": {"pmcid": "PMC8438179", "section_index": 12, "section_title": "iPathwayGuide Analysis of DEGs From COVID-19 and Neuro-COVID Infection Models", "row_count": 7, "column_count": 8}, "table": {"label": "TABLE 5", "caption": "Top identified cellular components for each pruning type.", "rows": [["Pruning type: none", "Pruning type: high specificity", "Pruning type: smallest common denominator"], ["Go term", "p-value", "p-value (FDR)", "p-value (Bonferroni)", "Go term", "p-value", "Go term", "p-value"], ["Cornified envelope", "3.600e−5", "0.024", "0.033", "Cornified envelope", "0.033", "Cornified envelope", "0.024"], ["Intermediate filament", "5.200e−5", "0.024", "0.048", "Intermediate filament", "0.279", "Intermediate filament", "0.024"], ["DNA packaging complex", "2.700e−4", "0.082", "0.247", "Blood microparticle", "0.485", "DNA packaging complex", "0.082"], ["Intermediate filament cytoskeleton", "0.001", "0.209", "0.924", "MCM complex", "0.492", "Blood microparticle", "0.364"], ["Extracellular matrix", "0.001", "0.209", "1.000", "Nucleosome", "0.492", "MCM complex", "0.470"]], "row_count": 7, "column_count": 8, "numeric_cells": 25, "header_rows": 2, "locator": "section[12]/table-wrap[5]#T5"}}, {"id": "asset:table:pmid:34531741:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f134bfa032bf8c8429f0938911d466c29cd4d2a7ea2f81d506825d1d52644295", "bytes": 1709, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[6]#T6", "version": null, "note": "Natural products and drugs with opposite molecular signatures based on L1000FWD web-based tool for querying gene expression signatures (SARS-CoV-2-NHBE vs. Mock-NHBE) against signatures created from human cell lines treated with over 20,000 small molecules and drugs for the LINCS project.", "structure": {"pmcid": "PMC8438179", "section_index": 12, "section_title": "iPathwayGuide Analysis of DEGs From COVID-19 and Neuro-COVID Infection Models", "row_count": 11, "column_count": 7}, "table": {"label": "TABLE 6", "caption": "Natural products and drugs with opposite molecular signatures based on L1000FWD web-based tool for querying gene expression signatures (SARS-CoV-2-NHBE vs. Mock-NHBE) against signatures created from human cell lines treated with over 20,000 small molecules and drugs for the LINCS project.", "rows": [["Signature ID", "Drug or natural product", "Similarity SCORE", "p-value", "q-value", "Z-score", "Combined score"], ["CPC006_PC3_6H:BRD-A36630025-001-02-6:0.35", "SN-38", "−0.0598", "1.04e−11", "2.02e−08", "1.79", "−19.61"], ["CPC011_A549_24H:BRD-K97514127-045-02-0:10", "Vinorelbine", "−0.0598", "2.32e−11", "3.82e−08", "1.72", "−18.26"], ["CPC015_MCF7_24H:BRD-K52075715-001-03-4:10", "Oxibendazole", "−0.0573", "2.91e−10", "3.37e−07", "1.67", "−15.88"], ["CPC019_HT29_6H:BRD-K67870070-001-01-4:10", "SA-247615", "−0.0560", "7.96e−11", "1.22e−07", "1.69", "−17.05"], ["ERG005_VCAP_6H:BRD-K88378636-001-02-8:20", "Withaferin A", "−0.0547", "1.28e−09", "1.19e−06", "1.65", "−14.71"], ["CPC012_MCF7_24H:BRD-K69496360-001-01-5:10", "BRD-K69496360", "−0.0522", "1.03e−08", "5.72e−06", "1.73", "−13.81"], ["CPC015_MCF7_24H:BRD-K47869605-001-18-9:10", "Podophyllotoxin", "−0.0509", "1.78e−08", "8.35e−06", "1.67", "−12.97"], ["CPC001_HCC515_24H:BRD-K82823804-001-01-7:10", "SA-792987", "−0.0509", "3.61e−08", "1.44e−05", "1.81", "−13.45"], ["MUC.CP003_MCF7_24H:BRD-K02407574-001-04-8:3.3333", "Parbendazole", "−0.0496", "8.46e−08", "2.85e−05", "1.62", "−11.45"], ["CPC002_PC3_6H:BRD-K06926592-001-01-7:10", "Tretinoin", "−0.0496", "7.24e−08", "2.54e−05", "1.79", "−12.80"]], "row_count": 11, "column_count": 7, "numeric_cells": 64, "header_rows": 1, "locator": "section[12]/table-wrap[6]#T6"}}, {"id": "asset:table:pmid:34531741:7", "role": "table", "format": 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from human cell lines treated with over 20,000 small molecules and drugs for the LINCS project.", "rows": [["Signature ID", "Drug or natural product", "Similarity score", "p-value", "q-value", "Z-score", "Combined score"], ["ERG005_VCAP_6H:BRD-K88378636-001-02-8:20", "Withaferin A", "−0.0492", "3.55e−16", "1.52e−11", "1.65", "−25.55"], ["CPC012_VCAP_24H:BRD-A59985574-003-01-9:10", "Topotecan", "−0.0303", "6.34e−05", "4.35e−01", "1.75", "−7.36"], ["CPC012_VCAP_24H:BRD-K62459624-001-08-7:10", "BRD-K62459624", "−0.0293", "1.66e−04", "8.86e−01", "1.77", "−6.69"], ["CPC006_HCC515_6H:BRD-K16406336-311-01-2:10", "Methylene-blue", "−0.0303", "8.54e−04", "1.00e+00", "1.77", "−5.43"], ["CPC011_PC3_6H:BRD-K04548931-003-11-6:10", "Pidorubicine", "−0.0278", "1.04e−03", "1.00e+00", "1.77", "−5.27"], ["NMH002_NPC_24H:BRD-K32610195-001-14-9:10", "Androstenedione", "−0.0269", "1.58e−03", "1.00e+00", "1.63", "−4.57"], ["CPC012_VCAP_24H:BRD-K56196992-001-01-2:10", "BRD-K56196992", "−0.0269", "9.60e−03", 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"−6.19"], ["CPC006_HCC515_6H:BRD-K16406336-311-01-2:10", "Methylene-blue", "−0.0330", "3.94e−04", "8.88e−01", "1.77", "−6.02"], ["CPC012_HCC515_6H:BRD-K56653679-001-01-2:10", "MD-041", "−0.0317", "4.22e−04", "9.03e−01", "1.72", "−5.81"], ["CVD001_HUH7_6H:BRD-K81142122-001-14-1:10", "STK-249718", "−0.0323", "3.91e−04", "8.88e-01", "1.62", "−5.52"], ["CPC004_HT29_6H:BRD-K77830450-001-02-4:10", "Forskolin", "−0.0264", "1.31e−03", "1.00e+00", "1.90", "−5.47"], ["CPC013_SKB_24H:BRD-K16798053-001-01-0:10", "ST-4029573", "−0.0277", "9.86e−04", "1.00e+00", "1.76", "−5.29"], ["CPC014_HA1E_6H:BRD-U66370498-000-01-0:10", "Androstanol", "−0.0264", "1.43e−03", "1.00e+00", "1.77", "−5.03"], ["CPC005_A375_24H:BRD-A78360835-001-01-1:10", "Cercosporin", "−0.0290", "2.06e−03", "1.00e+00", "1.82", "−4.90"], ["CPC014_HCC515_6H:BRD-A80960055-001-01-7:10", "Celastrol", "−0.0290", "2.78e−03", "1.00e+00", "1.72", "−4.40"]], "row_count": 11, "column_count": 7, "numeric_cells": 63, "header_rows": 1, "locator": 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