key: cord-0838890-az4pgi9k authors: Turjya, Rafeed Rahman; Khan, Md. Abdullah-Al-Kamran; Islam, Abul Bashar Mir Md. Khademul title: Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection date: 2020-06-29 journal: bioRxiv DOI: 10.1101/2020.06.29.177204 sha: 0e716c5eb2e5f666dc031813f26b657baa71eb7f doc_id: 838890 cord_uid: az4pgi9k Background Since December 2019, the world is experiencing an unprecedented crisis due to a novel coronavirus, SARS-CoV-2. Owing to poor understanding of pathogenicity, the virus is eluding treatment and complicating recovery. Regulatory roles of long non-coding RNAs (lncRNAs) during viral infection and associated antagonism of host antiviral immune responses has become more evident in last decade. To elucidate possible functions of lncRNAs in the COVID-19 pathobiology, we have utilized RNA-seq dataset of SARS-CoV-2 infected lung epithelial cells. Results Our analyses uncover 21 differentially expressed lncRNAs whose functions are broadly involved in cell survival and regulation of gene expression. By network enrichment analysis we find that these lncRNAs can directly interact with differentially expressed protein-coding genes ADAR, EDN1, KYNU, MALL, TLR2 and YWHAG; and also AKAP8L, EXOSC5, GDF15, HECTD1, LARP4B, LARP7, MIPOL1, UPF1, MOV10 and PRKAR2A, host genes that interact with SARS-CoV-2 proteins. These genes are involved in cellular signaling, metabolism, immune response and RNA homeostasis. Since lncRNAs have been known to sponge microRNAs and protect expression of upregulated genes, we also identified 9 microRNAs that are induced in viral infections; however, some lncRNAs are able to block their usual suppressive effect on overexpressed genes and consequently contribute to host defense and cell survival. Conclusions Our investigation determines that deregulated lncRNAs in SARS-CoV-2 infection are involved in viral proliferation, cellular survival, and immune response, ultimately determining disease outcome and this information could drive the search for novel RNA therapeutics as a treatment option. By mid-May 2020, the confirmed cases of COVID-19 have crossed 4 million (1), making it 58 one of the largest pandemics in modern times. Since the first reported case at Wuhan, China 59 in December 2019 (2), this viral disease has been responsible for more than 300,000 deaths 60 worldwide (1), and the number is steadily rising. The causative agent behind the disease is a 61 novel beta-coronavirus (3), which has been named SARS Coronavirus 2 i.e. SARS-CoV-2 62 due to its similarity to the earlier SARS-CoV first detected in 2002 (4). The rapid spread of 63 the virus, the ever-increasing death toll, and absence of a sufficient treatment strategy has 64 affected societies and economies all over the globe. 65 The molecular mechanism of SARS-CoV-2 is complex and interrelated with host 66 mechanisms, as is common with most pathogenic viruses (5). It is possible that infected lung performing RNA-seq analysis to identify differentially expressed (DE) genes. But no such 103 study yet concluded the possible outcomes of the deregulated lncRNAs in SARS-CoV-2. In 104 our present study we have identified lncRNAs that are differentially expressed in SARS-105 CoV-2 infected cell's transcriptome compared to uninfected cells, and then correlated the 106 putative effects of the deregulated lncRNAs in the tug-of-war between SARS-CoV-2 and the 107 host. We have also investigated the possible aftermaths of lncRNA deregulation in COVID-108 19 disease pathobiology. 109 To investigate the probable deregulation of lncRNAs in SARS-CoV-2 infection, firstly we 112 have analyzed the 24 hours post-infection transcriptome data of SARS-CoV-2 infected 113 NHBE cells. Analyzing the RNA-seq data led to identification of 687 DE genes and 114 intriguingly, amongst those DE genes, we discovered 21 lncRNA genes, 9 of them 115 upregulated while 12 were downregulated (Figure 1 ). We now sought to elucidate the putative effects of these deregulated lncRNAs in SARS-119 CoV-2 infection. In order to achieve that, we built a network of the deregulated lncRNAs 120 along with their interacting protein coding target genes. Among the differentially expressed 121 protein-coding genes, 6 were found to interact with the DE lncRNAs which (Table 1) . There 122 are direct RNA-RNA interactions for 4 genes, and RNA-protein interactions for the rest 123 ( Figure 2 ). These lncRNA interacting protein coding genes have potential roles during the 124 viral infections (Table 1) Innate immune response against the infection is inevitable, but the complex interactions 306 underlying its activation and effect may have been the target of lncRNAs.HECTD1 is an E3 307 ubiquitin-protein ligase that interacts with Nsp8. As it is involved in class I MHC mediated 308 antigen processing and presentation and innate immune system, the binding may lead to 309 modulation of that response. In case of HECTD1 mRNA, absence of RNA-RNA interaction 310 with downregulated KCNQ1OT1 lncRNA can facilitate the response. PTGES2 gene was 311 upregulated and also found to interact with SARS-CoV-2 Nsp7 protein. As it is involved in 312 innate immune system and signaling pathways, this binding may exert an indirect influence. were analyzed using NetworkAnalyst 3.0 (88) tools for functional overrepresentation and 386 network enrichment. miRNAs that mostly targeted upregulated genes were finally selected. 387 Not applicable. 395 Publicly available data were utilized. Analyses generated data are deposited as supplementary 397 files. 398 The authors declare that they have no competing interests. 400 Funding 401 This research did not receive any specific grant from funding agencies in the public, 402 commercial, or not-for-profit sectors. 403 EXOSC5 is a non-catalytic component of the RNA exosome complex which has 3' to 5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events (121). Protein-RNA GDF15is a member of the Glial cell-derived neurotropic factor (GDNF) family which binds to GDNF family receptor α -like (GFRAL) protein, a transmembrane receptor exclusively expressed in the hind brain (122). The protein is expressed in a broad range of cell types, acts as a pleiotropic cytokine and is involved in the stress response program of cells after cellular injury (123). Increased protein levels are associated with disease states such as tissue hypoxia, inflammation, acute injury and oxidative stress (124, 125). MEG3 RNA-RNA HECTD1 is an E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates and mediates 'Lys-63'-linked polyubiquitination of HSP90AA1 which leads to its intracellular localization and reduced secretion (126). The protein is involved in class I MHC mediated antigen processing and presentation and innate immune system. KCNQ1OT1 RNA-RNA LARP4Bencodes a La-module containing factor that can bind AU-rich RNA sequence directly and promotes mRNA accumulation and translation (127). It was deemed a candidate tumor suppressor gene in glioma, as it was consistently decreased in human glioma stem cells and cell lines compared with normal neural stem cells. LARP4B overexpression strongly inhibited cell proliferation by inducing mitotic arrest and apoptosis andCDKN1A and BAX were upregulated (128). Nsp12 Protein-RNA LARP7 works as a negative transcriptional regulator of polymerase II genes, acting by means of the 7SK RNP system (129). This snRNP complex inhibits a cyclin-dependent kinase, positive transcription elongation factor b, which is required for paused RNA polymerase II at a promoter to begin transcription elongation (130). Protein-RNA PRKAR2A is the cAMP-dependent protein kinase type II-alpha regulatory subunit, which works as the regulatory subunit of the cAMP-dependent protein kinases involved in cAMP signaling in cells (131). 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