key: cord-0814576-fmp02jwy authors: Wu, Yen-Hung; Yeh, I-Jeng; Phan, Nam Nhut; Yen, Meng-Chi; Hung, Jui-Hsiang; Chiao, Chung-Chieh; Chen, Chien-Fu; Sun, Zhengda; Hsu, Hui-Ping; Wang, Chih-Yang; Lai, Ming-Derg title: Gene signatures and potential therapeutic targets of Middle East respiratory syndrome coronavirus (MERS-CoV)-infected human lung adenocarcinoma epithelial cells date: 2021-03-26 journal: J Microbiol Immunol Infect DOI: 10.1016/j.jmii.2021.03.007 sha: dc2b87ceb5dbb3db1e68e96be4f920c8eba89e17 doc_id: 814576 cord_uid: fmp02jwy Background Pathogenic coronaviruses include Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), and SARS-CoV-2. These viruses have induced outbreaks worldwide, and there are currently no effective medications against them. Therefore, there is an urgent need to develop potential drugs against coronaviruses. Methods High-throughput technology is widely used to explore differences in messenger (m)RNA and micro (mi)RNA expression profiles, especially to investigate protein-protein interactions and search for new therapeutic compounds. We integrated miRNA and mRNA expression profiles in MERS-CoV-infected cells and compared them to mock-infected controls from public databases. Results Through the bioinformatics analysis, there were 251 upregulated genes and eight highly differentiated miRNAs that overlapped in the two datasets. External validation verified that these genes had high expression in MERS-CoV-infected cells, including RC3H1, NF-κB, CD69, TNFAIP3, LEAP-2, DUSP10, CREB5, CXCL2, etc. We revealed that immune, olfactory or sensory system-related, and signal-transduction networks were discovered from upregulated mRNAs in MERS-CoV-infected cells. In total, 115 genes were predicted to be related to miRNAs, with the intersection of upregulated mRNAs and miRNA-targeting prediction genes such as TCF4, NR3C1, and POU2F2. Through the Connectivity Map (CMap) platform, we suggested potential compounds to use against MERS-CoV infection, including diethylcarbamazine, harpagoside, bumetanide, enalapril, and valproic acid. Conclusions The present study illustrates the crucial roles of miRNA-mRNA interacting networks in MERS-CoV-infected cells. The genes we identified are potential targets for treating MERS-CoV infection; however, these could possibly be extended to other coronavirus infections. and mRNA expression were integrated to explore the miRNA-mRNA interactive network. Bioinfor matics and high-thr oughput database analysis 96 We searched GEO databases for available datasets comparing MERS-CoV-infected and 97 mock-infected epithelial cells of human lung adenocarcinomas. Two high-throughput 98 datasets (GSE65574 and GSE139516) with differential expression data for mRNAs and 99 miRNAs were acquired from National Center for Biotechnology Information (NCBI) GEO 100 databases, 7,13 and the GSE56677 dataset was used for external validation. 8 The raw data 101 were downloaded, and we used CLC Genomics Workbench v10.1 for analysis. 14, 15 The 102 Database for Annotation, Visualization and Integrated Discovery (DAVID, vers. 6.8) 103 includes gene functional classifications, various processes and pathways in gene ontology 104 (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG). We used an 105 agglomeration algorithm in DAVID to cluster genes into different groups according to their 106 biological functions, signaling pathways, as well as the associated diseases. The top 5% of 107 highly expressed mRNAs in MERS-CoV-infected cells were compared to mock-infected 108 controls, and the p value was set at 0.05 according to previous methods. 16-21 Significantly 109 differentially expressed genes were input to the GO database and gene set enrichment 110 analysis (GSEA) software to construct biological networks or regulatory pathways, and the 111 cutoff point of significant enrichment was set to p < 0.05. 112 J o u r n a l P r e -p r o o f Analyses using miRNA-tar geting pr ediction databases 113 We used miRWalk 2.0 to predict potential miRNA-targeted genes; this program contains 114 eight different software packages: mirWalk, MicroT4, miRanda, miRDB, miRmap, 115 RNA22, RNAhybrid, and TargetScan. 22 The miRmap score is the repression strength of 116 miRNA binding to its target mRNA. We set the cutoff of the miRmap score to > 99, and the 117 top 5% of significantly highly expressed miRNAs from MERS-CoV-infected cells 118 compared to mock-infected controls were analyzed. The results were imported into miRtest, 119 which evaluates both individual miRNAs and their target mRNAs in the same analysis for 120 consistency. 121 122 Investigation of pr otein-pr otein inter actions (PPIs) 123 The Search Tool for the Retrieval of Interacting Genes (STRING) software contains 124 protein-protein interaction (PPI) networks from 5090 organisms, 24.6 million proteins, and 125 more than 2000 million interactions. 23 We used STRING (vers. 11.0) to analyze PPIs based 126 on the top 5% of genes with highly differential expression. The k-means clustering 127 algorithm was selected to classify the proteins into different groups. The top 5% of highly expressed mRNAs in MERS-CoV-infected cells were compared to 147 the mock-infected controls. There were 1636 mRNAs selected from the GSE65574 dataset 148 and 2831 mRNAs from the GSE139516 dataset ( Figure 2A ). We compared these data in a 149 Venn diagram and found that there were 251 upregulated genes in MERS-CoV-infected 150 cells that overlapped in these two datasets. These genes were uploaded into KEGG; the 151 associated pathways are shown in Figure 2B . We also used GO software to analyze 152 pathways to connected biological processes ( Figure Journal of M icrobiology, Immunology and Infection (2020). 5 2 4 Gene signatures and 4 8 3 potential therapeutic targets of am ino acid m etabolism in estrogen receptor-positive breast cancer PSM B5 plays a dual role in 4 8 6 cancer developm ent and im munosuppression Overexpressed gene signature EPH receptor A/B fam ily in cancer patients-com prehensive analyses from the public high Novel signaling pathways regulate SARS-CoV and SARS-CoV-2 infectious disease. M edicine (Baltimore) SARS-CoV)-2 infection induces dysregulation of im m unity: in silico gene 4 9 7 expression analysis SARS-CoV-2 infection in children: Transmission 525 dynamics and clinical characteristics The emerging novel Middle East respiratory syndrome 527 coronavirus: the "knowns" and "unknowns" Comparative therapeutic 530 efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against MERS-CoV COVID-19: 533 consider cytokine storm syndromes and immunosuppression Antiviral potential 535 of ERK/MAPK and PI3K/AKT/mTOR signaling modulation for Middle East respiratory syndrome 536 coronavirus infection as identified by temporal kinome analysis Targeting Coronaviral 539 Replication and Cellular JAK2 Mediated Dominant NF-kappaB Activation for Comprehensive and 540 Ultimate Inhibition of Olfactory disorder in 542 patients infected with SARS-CoV-2 Utility of Olfactory 544 test as screening tool for COVID-19: A pilot study Extra-respiratory manifestations of COVID-546 19 Human cytomegalovirus induces and 548 exploits Roquin to counteract the IRF1-mediated antiviral state Severe acute respiratory syndrome 551 coronavirus papain-like protease ubiquitin-like domain and catalytic domain regulate antagonism of 552 IRF3 and NF-κB signaling Phenotypical and 554 functional alteration of unconventional T cells in severe COVID-19 patients Transcriptome analysis of duck 557 embryo fibroblasts for the dynamic response to duck tembusu virus infection and dual regulation of 558 apoptosis genes Immune activation in HIV/HCV-560 infected patients is associated with low-level expression of liver expressed antimicrobial peptide-2 561 (LEAP-2) DUSP10 negatively regulates the 563 inflammatory response to rhinovirus through interleukin-1β signaling Epigenetically regulated miR-449a 565 enhances hepatitis B virus replication by targeting cAMP-responsive element binding protein 5 and 566 modulating hepatocytes phenotype LOCATION: Location of neuroinflammation is important in 568 pathogenesis of schizophrenia Host transcriptome-guided drug 570 repurposing for COVID-19 treatment: a meta-analysis based approach Detection and 572 characterization of microRNA expression profiling and its target genes in response to canine 573 parvovirus in Crandell Reese Feline Kidney cells Screening for differentially expressed miRNAs 575 in Aedes albopictus (Diptera: Culicidae) exposed to DENV-2 and their effect on replication of DENV-576 2 in C6/36 cells Circulating microRNAs as potential biomarkers of 578 HBV infection persistence Mediated Proliferation of Human Chondrocytes Through PI3K/Akt Pathway Human MiR-4660 regulates the expression of 583 alanine-glyoxylate aminotransferase and may be a biomarker for idiopathic oxalosis KSHV vPK inhibits Wnt signaling via preventing interactions between 586 beta-catenin and TCF4 Growth retardation induced by avian 588 leukosis virus subgroup J associated with down-regulated Wnt/beta-catenin pathway Catenin/TCF-4 signaling 591 regulates susceptibility of macrophages and resistance of monocytes to HIV-1 productive infection Role of β-catenin/TCF-4 signaling in HIV replication and 594 pathogenesis: insights to informing novel anti-HIV molecular therapeutics HIV and symptoms of 597 depression are independently associated with impaired glucocorticoid signaling Host genes associated 600 with HIV-1 replication in lymphatic tissue Expression of transcription factor 602 genes after influenza A virus infection Epstein-Barr virus nuclear 604 antigen 3C binds to BATF/IRF4 or SPI1/IRF4 composite sites and recruits Sin3A to repress CDKN2A Effect of 607 diethylcarbamazine on HIV load, CD4%, and CD4/CD8 ratio in HIV-infected adult Tanzanians with 608 or without lymphatic filariasis: randomized double-blind and placebo-controlled cross-over trial 611 Border and imported bancroftian filariases: baseline seroprevalence in sentinel populations exposed 612 to infections with Wuchereria bancrofti and concomitant HIV at the start of diethylcarbamazine mass 613 treatment in Thailand Is the anti-filarial drug diethylcarbamazine useful to treat 615 COVID-19? Medical Hypotheses Antiviral activity of 617 seven iridoids, three saikosaponins and one phenylpropanoid glycoside extracted from Bupleurum 618 rigidum and Scrophularia scorodonia Ambroxol inhibits 620 rhinovirus infection in primary cultures of human tracheal epithelial cells. Archives of pharmacal 621 research Antioxidant therapy as a potential approach to severe influenza-associated 623 complications Identification of old drugs as potential 625 inhibitors of HIV-1 integrase -human LEDGF/p75 interaction via molecular docking Diseases Treated with Combined Antiretroviral Therapy (cART) 631 Inhibition of herpes virus infection in oligodendrocyte cultured cells by valproic acid Interferon-Induced Transmembrane Protein (IFITM3) Is Upregulated Explicitly in SARS-CoV-2 635 Infected Lung Epithelial Cells A new advanced in silico drug discovery method for novel coronavirus 637 (SARS-CoV-2) with tensor decomposition-based unsupervised feature extraction Identification of amitriptyline HCl, 640 flavin adenine dinucleotide, azacitidine and calcitriol as repurposing drugs for influenza A H5N1 641 virus-induced lung injury Repurposing Drugs for COVID-19: An Approach for Treatment in the Pandemic. Alternative therapies 644 in health and medicine Related enteric viruses have different 646 requirements for host microbiota in mice Inhibition of HIV-1 Protease by Evidence-Based Complementary and Alternative M edicine The gendered im pact of coronavirus disease The European Journal of Contraception & Reproductive Health Care International Consensus Guidelines for Advanced Breast Cancer (ABC 4)dagger The role of the glycosyl m oiety of m yricetin derivatives in anti-HIV-1 activity in vitro Developm ent of chem ical inhibitors of the SARS coronavirus: viral helicase 6 5 7 as a potential target im m u n e, o lfa cto ry , a n d sen so ry sy stem s a n d cellu la r resp o n se-rela ted p a th w a y s.