key: cord-304792-8sdxqmkb authors: Khan, Md. Abdullah-Al-Kamran; Islam, Abul Bashar Mir Md. Khademul title: SARS-CoV-2 proteins exploit host’s genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology date: 2020-05-08 journal: bioRxiv DOI: 10.1101/2020.05.06.050260 sha: doc_id: 304792 cord_uid: 8sdxqmkb The constant rise of the death toll and cases of COVID-19 has made this pandemic a serious threat to human civilization. Understanding of host-SARS-CoV-2 interaction in viral pathogenesis is still in its infancy. In this study we aimed to correlate how SARS-CoV-2 utilizes its proteins for tackling the host immune response; parallelly, how host epigenetic factors might play a role in this pathogenesis was also investigated. We have utilized a blend of computational and knowledgebase approach to elucidate the interplay between host and SARS-CoV-2. Integrating the experimentally validated host interactome proteins and differentially expressed host genes due to SARS-CoV-2 infection, we have taken a blend of computational and knowledgebase approach to delineate the interplay between host and SARS-CoV-2 in various signaling pathways. Also, we have shown how host epigenetic factors are involved in the deregulation of gene expression. Strikingly, we have found that several transcription factors and other epigenetic factors can modulate some immune signaling pathways, helping both host and virus. We have identified miRNA hsa-miR-429 whose transcription factor was also upregulated and targets were downregulated and this miRNA can have pivotal role in suppression of host immune responses. While searching for the pathways in which viral proteins interact with host proteins, we have found pathways like-HIF-1 signaling, autophagy, RIG-I signaling, Toll-like receptor signaling, Fatty acid oxidation/degradation, Il-17 signaling etc significantly associated. We observed that these pathways can be either hijacked or suppressed by the viral proteins, leading to the improved viral survival and life-cycle. Moreover, pathways like-Relaxin signaling in lungs suggests aberration by the viral proteins might lead to the lung pathophysiology found in COVID-19. Also, enrichment analyses suggest that deregulated genes in SARS-CoV-2 infection are involved in heart development, kidney development, AGE-RAGE signaling pathway in diabetic complications etc. might suggest why patients with comorbidities are becoming more prone to SARS-CoV-2 infection. Our results suggest that SARS-CoV-2 integrates its proteins in different immune signaling pathway and other cellular signaling pathways for developing efficient immune evasion mechanisms, while leading the host to more complicated disease condition. Our findings would help in designing more targeted therapeutic interventions against SARS-CoV-2. Though several human coronaviruses outbreaks caused severe public health crisis over the 79 past few decades, the recent coronavirus disease (COVID-19) outbreak caused by the Severe 80 Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has beaten the records of the 81 previous and still the case counts are still on the upswing. About 210 countries and territories 82 around the globe has been affected by this outbreak and around a total of 2 millions of people 83 are already infected with SARS-CoV-2 and the number is steadily rising till the date of 84 writing this article (Worldometer, 2020) . Out of the closed cases, almost 20% of the patients 85 have suffered death and about 5% of the active cases are in critical conditions (Worldometer, 86 2020) . Though the death rates from COVID-19 was estimated to be as small as 3.4% (WHO, 87 2020), at present the global fatality rate is changing very rapidly; therefore, more 88 comprehensive studies needto be done for the efficient controlling to overturn this pandemic. 89 Coronaviruses are single stranded positive sense, enveloped RNA virus having ~30Kb 90 genome (Lu et al., 2020) . Amongst the four genera, SARS-CoV-2 (Accession no. 91 NC_045512.2) belong to the betacoronavirus genus and it has ~29.9Kb genome encoding 11 92 genes (NCBI-Gene, 2020 between SARS-CoV and SARS-CoV-2; as in SARS-CoV-2, there have been 380 amino acids 98 substitution, deletion of ORF8a, elongation of ORF8b, and truncation of ORF3b observed 99 (Lu et al., 2020) . 100 Though the overall mortality rate from SARS-CoV is higher than that of SARS-CoV-2, 101 several unique features of SARS-CoV-2 like-increased incubation period and dormancy 102 inside the host, thus spreading more efficiently (Lauer et al., 2020) . This suggests that SARS-103 CoV-2 might be using some immune evasion strategies to maintain its survival and essential 104 functions within its host. 105 Upon viral infection, host innate immune system detects the virion particles and elicits the 106 first sets of antiviral responses (Katze et al., 2008) to eliminate the viral threats. However, 107 viruses itself have generated various modes of actions to evade those immune response by 108 modulating the host's intracellular signaling pathways (Kikkert, 2020) . This arm-wrestling 109 between the host and the infecting virus results in the immunopathogenesis. Different human 110 coronaviruses also show similar features of host-pathogen interactions, which ranges from the 111 viral entry, replication, transcription, translation, assembly to the evasion from host innate 112 immune response (Fung and Liu, 2019) . Not only this but also different antiviral cellular 113 responses like-autophagy (Ahmad et al., 2018) , apoptosis (Barber, 2001) etc. can also be 114 moderated by the virus to ensure its survival inside the host cells. Apart from these, several 115 other host-virus interactions are also observed like-modulation of the activity of host 116 transcription factors (Lyles, 2000) , host epigenetic factors (e.g. histone modifications, host 117 miRNAs etc.) (Adhya and Basu, 2010) . All of these multifaceted interactions can lead to the 118 ultimate pathogenesis and progression of the disease. 119 The interplay between different human coronaviruses and host was previously reported (Fung 120 and Liu, 2019), however, SARS-CoV-2 interactions with the host immune response and its 121 outcome in the pathogenesis are still to be elucidated. Gordon We have obtained the transcription factors (TFs) which bind to the given promoters from 181 Cistrome data browser (Zheng et al., 2018 ) that provides TFs from experimental ChIP-seq 182 data. We utilized "Toolkit for CistromeDB", uploaded the 5Kb upstream promoter with 1Kb 183 downstream from transcription start site (TSS) BED file of the deregulated genes and fixed 184 the peak number parameter to "All peaks in each sample". 185 We extracted the experimentally validated target genes of human miRNAs from miRTarBase 187 database (Huang et al., 2019a) . 188 We have downloaded the experimentally validated TFs which bind to miRNA promoters and 190 module it. We have considered those TFs that are expressed itself and that can 'activate' or 191 'regulated' miRNAs. 192 We used EpiFactors database (Medvedeva et al., 2015) to find human genes related to 194 epigenetic activity. 195 We have utilized KEGG mapper tool (Kanehisa and Sato, 2020) for the mapping of 197 deregulated genes SARS-CoV-2 interacting host proteins in different cellular pathways. We 198 then searched and targeted the pathways which are found to be enriched for SARS-CoV-2 199 deregulated genes. From these pathway information, we have manually sketched the 200 pathways to provide a brief overview of the interplay between SARS-CoV-2 and host 201 immune response, their outcomes in the viral pathogenesis. 202 differentially expressed genes showed that deregulated genes of SARS-CoV-2 infection can 214 exert biological functions like-regulation of inflammatory response, negative regulation of 215 type-I interferon, response to interferon-gamma, interferon-gamma mediated signaling, 216 NIK/NF-kappaB signaling, regulation of apoptotic process, cellular response to hypoxia, 217 angiogenesis, negative regulation of inflammatory response, zinc ion binding, calcium ion 218 binding etc. which were not enriched for SARS-CoV infection ( Figure 1A , 1B). Also, 219 different organ specific functions like-heart development, kidney development etc. were only 220 enriched for differentially expressed genes in SARS-CoV-2 infection ( Figure 1A ). 221 Deregulated genes of SARS-CoV-2 infection were found to be related to pathways like-NF-222 kappaB signaling, Jak-STAT signaling, RIG-I-like receptor signaling, Natural killer cell 223 mediated cytotoxicity, Phagosome, HIF-1 signaling, Calcium signaling, GnRH signaling, 224 Arachidonic acid metabolism, Insulin signaling, Adrenergic signaling in cardiomyocytes, 225 PPAR signaling etc. ( Figure 1C , Supplementary figure 1, 2) which were found to be absent 226 for SARS-CoV infection. 227 CoV 3p, hsa-miR-146a-5p, hsa-miR-155-5p, hsa-miR-146b-5p, hsa-miR-27a-3p, hsa-miR-146b-260 3p, hsa-miR-141-5p) were found to be targeting in both infections. 261 Although there are some similarities between SARS-CoV and SARS-CoV-2 genetic 286 architecture, it is yet to know if they modulate common host pathways. Also, it is largely 287 unknown how SARS-CoV-2 uniquely exhibit some unique clinical features even having 288 much similarities of the viral genes. 289 As now the probable genetic and epigenetic regulators behind the differential gene expression 290 have been identified, we aimed to explore how these deregulated genes are playing a role in 291 the battle between virus and host. To obtain a detailed idea of the outcomes resulting from 292 viral-host interactions and how SARS-CoV-2 uses its proteins to evade host innate immune 293 response, we have mapped the significantly deregulated genes and host interacting protein in 294 different overrepresented functional pathways using KEGG mapper ( Phagosome ( Figure 13A ), Arachidonic acid metabolism ( Figure 13B ), PVR signaling ( Figure 302 14) etc., aberration of these pathways might provide SARS-CoV-2 an edge over the host 303 immune response. Also, SARS-CoV-2 can prevent the Relaxin downstream signaling ( Figure 304 15) which plays a crucial role in lung's overall functionality and its abnormal regulation 305 might results in the respiratory complications found in COVID-19. 306 From previous studies we have compiled information on deregulated genes (Blanco -Melo et 307 al., 2020) and virus-host interactome (Gordon et al., 2020) in SARS-CoV-2 infection, 308 however, to get detailed pictures of the affected pathways, which is still remained obscure, 309 we have investigated how our identified host genetic and epigenetic factors are playing a role 310 and how viruses are utilizing those. Giving a closer look we have found some pathways 311 which SARS-CoV-2 might be using but not SARS-CoV. Figure 13A) . 357 Apoptosis is one important intracellular host immune response to reduce further spread of 360 viruses from the infected cells (Barber, 2001) . Several signaling pathways are involved to 361 elicit this apoptotic response inside the infected cells which can be suppressed by the viral 362 proteins, for example-NSP12 is found to target RIP1, thus it might fail to relay signaling to 363 CASP8/FADD mediated apoptosis, and necrosis by RIP1/RIP3 complex ( Figure 8) ; NSP5 364 might block glutathione peroxidase which is involved in 15(S)-HETE production and 365 ultimately 15-oxoETE production, thus apoptotic induction by these metabolites through 366 PPARγ signaling axis will not take place ( which in turn results in vascular remodeling and leakage of inflammatory cytokines (Powell 400 and Rokach, 2015). 5-oxoETE another arachidonic acid metabolism product that can also 401 induce inflammation (Powell and Rokach, 2015) , production of both compounds might be 402 hindered by SARS-CoV-2 NSP5 as it interacts with an upstream metabolic enzyme 403 glutathione peroxidase ( Figure 13B ). 404 Previously it was reported that IL-17 signaling enhances antiviral immune responses (Ma et 405 al., 2019). SARS-CoV-2 NSP13 can bind IL-17 receptor and inhibit the downstream 406 signaling from IL-17 receptor to TRAF6 for activating NFκB/MAPKs/CEBPB signaling axis, 407 thus decreasing the antiviral inflammatory responses (Figure 11 ). 408 During acute viral infections Toll-like receptor 4 (TLR4) signaling plays important roles in 409 eliciting inflammatory responses (Olejnik et al., 2018) . SARS-CoV-2 protein NSP13 interacts 410 with TBK1 which might reduce the signaling from IRF7, resulting in less IFN-I productions; 411 while NSP12 interacts with RIP1; as a result, the activation of downstream NFκB and 412 MAPKs (p38 and JNK) pathways and induction of inflammatory responses from these 413 pathways will be stalled ( Figure 12) . 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