Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection

Demirci, Müşerref Duygu Saçar; Adan, Aysun

doi:10.1101/2020.03.15.992438

Cited by 55 publications

(109 citation statements)

References 47 publications

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“…The authors claim that their scheme can achieve high levels of classification accuracy and discovers the most relevant relationships among over 5,000 viral genomes within a few minutes. Additionally, the research in [93] suggests an ML-based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpin which can impact the COVID-19 virus. Learning can help to realize potential miRNA based interactions between the viral miRNAs and human genes as well as human miRNAs and viral genes, which are important to identify the mechanisms behind the SARS-CoV-2 infections.…”

Section: Coronavirus Diagnosis and Treatmentmentioning

confidence: 99%

Blockchain and AI-based Solutions to Combat Coronavirus (COVID-19)-like Epidemics: A Survey

Nguyen¹,

Ding²,

Pathirana³

et al. 2020

Preprint

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The beginning of 2020 has seen the emergence of coronavirus outbreak caused by a novel virus called SARS-CoV-2. The sudden explosion and uncontrolled worldwide spread of COVID-19 show the limitations of existing healthcare systems to timely handle public health emergencies. In such contexts, innovative technologies such as blockchain and Artificial Intelligence (AI) have emerged as promising solutions for fighting coronavirus epidemic. On the one hand, blockchain can combat pandemics by enabling early detection of outbreaks, protecting user privacy, and ensuring reliable medical supply chain during the outbreak tracking. On the other hand, AI provides intelligent solutions for identifying symptoms caused by coronavirus for treatments and supporting drug manufacturing. Motivated by these, in this paper we present an extensive survey on the use of blockchain and AI for combating coronavirus (COVID-19) epidemics based on the rapidly emerging literature. First, we introduce a new conceptual architecture which integrates blockchain and AI specific for COVID-19 fighting. Particularly, we highlight the key solutions that blockchain and AI can provide to combat the COVID-19 outbreak. Then, we survey the latest research efforts on the use of blockchain and AI for COVID-19 fighting in a wide range of applications. The newly emerging projects and use cases enabled by these technologies to deal with coronavirus pandemic are also presented. Finally, we point out challenges and future directions that motivate more research efforts to deal with future coronavirus-like epidemics.

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Section: Coronavirus Diagnosis and Treatmentmentioning

confidence: 99%

Blockchain and AI-based Solutions to Combat Coronavirus (COVID-19)-like Epidemics: A Survey

Nguyen¹,

Ding²,

Pathirana³

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Human miRs have been associated with a variety of pathophysiological pathways and demonstrate differential expression during viral infections [93,94]. Recently, a few computational studies have shed light on the interplay between human miRs and SARS-CoV-2 target genes indicating a crucial role in regulating the viral load in host cells [95,96]. However, a comprehensive understanding of the functional role of host miRs during SARS-CoV-2 infection has remained elusive until now.…”

Section: Sars-cov-2 Genome Titrates the Abundance Of Functionally Impmentioning

confidence: 99%

“…However, a comprehensive understanding of the functional role of host miRs during SARS-CoV-2 infection has remained elusive until now. Recently, a machine learning based study predicted that miRs could impact SARS-CoV-2 infection through several mechanisms such as interfering with replication, translation and by modulation of the host gene expression [95]. In this study, we used computational approach to investigate the potential binding sites of human miRs in SARS-CoV-2 genome using FIMO [82].…”

Section: Sars-cov-2 Genome Titrates the Abundance Of Functionally Impmentioning

confidence: 99%

“…5A, Table S5). Among the human miRs likely to be sequestered on SARS-CoV-2 genome, miR-374a-3p has recently been predicted to target SARS-CoV-2 gene, in particular it has been shown to target gene encoding the spike protein which is essential for virus entry into the host cell [95,97]. In addition to targeting the spike protein encoding genes, miR-374a-3p is also predicted to target the ORF1ab in the SARS-CoV-2 genome that encodes for 5'viral replicase, based on the function similarity of SARS-CoV-2 coding genes with SARS-CoV [98].…”

Section: Sars-cov-2 Genome Titrates the Abundance Of Functionally Impmentioning

confidence: 99%

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Role of SARS-CoV-2 in altering the RNA binding protein and miRNA directed post-transcriptional regulatory networks in humans

Srivastava

Daulatabad

Srivastava

et al. 2020

Preprint

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AbstractThe outbreak of a novel coronavirus SARS-CoV2 responsible for COVID-19 pandemic has caused worldwide public health emergency. Due to the constantly evolving nature of the coronaviruses, SARS-CoV-2 mediated alteration on post-transcriptional gene regulation across human tissues remains elusive. In this study, we systematically dissected the crosstalk and dysregulation of human post-transcriptional regulatory networks governed by RNA binding proteins (RBPs) and micro-RNAs (miRs), due to SARS-CoV-2 infection. We uncovered that 13 out of 29 SARS-CoV-2 encoded proteins directly interact with 51 human RBPs of which majority of them were abundantly expressed in gonadal tissues and immune cells. We further performed functional analysis of differentially expressed genes in mock treated versus SARS-CoV-2 infected lung cells that revealed an enrichment for immune response, cytokine mediated signaling, and metabolism associated genes. This study also characterized the alternative splicing events in SARS-CoV-2 infected cells compared to control demonstrating that skipped exons and mutually exclusive exons were the most abundant events that potentially contributed to differential outcomes in response to viral infection. Motif enrichment analysis on the RNA genomic sequence of SARS-CoV-2 clearly revealed an enrichment for RBPs such as SRSFs, PCBPs, ELAVs and HNRNPs illustrating the sponging of RBPs by SARS-CoV-2 genome. Similar analysis to study the interactions of miRs with SARS-CoV-2 revealed the potential for several miRs to be sponged, suggesting that these interactions may contribute to altered pos-transcriptional regulation across human tissues. Given the need to understand the interactions of SARS-CoV-2 with key pos-transcriptional regulators in the human genome, this study provides a systematic analysis to dissect the role of dysregulated post-transcriptional regulatory networks controlled by RBPs and miRs, across tissues types during SARS-CoV2 infection.

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“…Additionally, SARS-CoV and SARS-CoV-2 express short RNAs that resemble miRNAs and could impact upon host house-keeping or immune defence processes [19][20][21]. More recently, several studies have proposed that host miRNAs bind SARS-CoV-2 transcripts [19,21,22]. However, host miRNAs inhibition of viral replication is relevant only if the identified miRNAs are expressed in target host cells.…”

Section: Introductionmentioning

confidence: 99%

Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting

Rad

McLellan

2020

Preprint

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The SARS-CoV-2 virus is a recently-emerged zoonotic pathogen already well adapted to transmission and replication in humans. Although the mutation rate is limited, recently introduced mutations in SARS-CoV-2 have the potential to alter viral fitness. In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral life cycle, or interfere with sequences targeted by host miRNAs. We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary structure. Filtering to targets matching miRNAs expressed in SARS-CoV-2 permissive host cells, we identified twelve separate target sequences in the SARS-CoV-2 genome; eight of these targets have been lost through conserved mutations. A genomic site targeted by the highly abundant miR-197-5p, overexpressed in patients with cardiovascular disease, is lost by a conserved mutation. Our results are compatible with a model that SARS-CoV-2 replication within the human host could be constrained by host miRNA defence. The impact of these and further mutations on secondary structures, miRNA targets or potential splice sites offers a new context in which to view future SARS-CoV-2 evolution, and a potential platform for engineered viral attenuation and antigen presentation.

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Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection

Cited by 55 publications

References 47 publications

Blockchain and AI-based Solutions to Combat Coronavirus (COVID-19)-like Epidemics: A Survey

Blockchain and AI-based Solutions to Combat Coronavirus (COVID-19)-like Epidemics: A Survey

Role of SARS-CoV-2 in altering the RNA binding protein and miRNA directed post-transcriptional regulatory networks in humans

Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting

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