key: cord-0942915-k4vcqw77
authors: Guterres, Alexandro; de Azeredo Lima, Carlos Henrique; Miranda, Renan Lyra; Gadelha, Mônica Roberto
title: What is the potential function of microRNAs as biomarkers and therapeutic targets in COVID-19?
date: 2020-06-08
journal: Infect Genet Evol
DOI: 10.1016/j.meegid.2020.104417
sha: 57b8934877509e6c5a1bb5394be7cd183cb14914
doc_id: 942915
cord_uid: k4vcqw77

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19, a pandemic associated with substantial morbidity and mortality. Despite of this, no vaccine or approved drug is available to eradicate the virus. In this manuscript, we present an alternative study area that may contribute to development of diagnostic biomarkers and therapeutic targets for COVID-19. We analyzed sixty SARS-CoV-2 genomes to identify regions that could work as virus-encoded miRNA seed sponges and potentially bind to human miRNA seed sites and prevent interaction with their native targets thereby relieving native miRNA suppression. MicroRNAs (miRNAs) are evolutionally conserved single-stranded RNAs that regulate gene expression at the posttranscriptional level by disrupting translation. MiRNAs are key players in variety of biological processes that regulate differentiation, development and activation of immune cells in both innate and adaptive immunity. We find 34 miRNAs for positive-sense viral RNA and 45 miRNAs for negative-sense that can strongly bind to certain key SARS-CoV-2 genes. The disruption and dysfunction of miRNAs may perturb the immune response and stimulate the release of inflammatory cytokines altering the cellular response to viral infection. Previous studies demonstrate that miRNAs have the potential to be used as diagnostic and therapeutic biomarkers. Therefore, its discovery and validation are essential for improving the diagnosis of infection and clinical monitoring in COVID-19.

The SARS-CoV-2 outbreak started on December 2019 in China and rapidly spread worldwide. This novel coronavirus can cause severe acute respiratory syndrome and became an international health emergency. Initial outbreaks in China involved 13.8% cases with severe, and 6.1% with critical courses (WHO, 2020) . The immune response is vital for the control and resolution of SARS-CoV-02 infections, while it can also lead to cellular damage, associated with an exacerbated immune response. There is a complex network of interaction between the virus and infected host cells, in which microRNAs (miRNAs) have been revealed to play a pivotal role (Girardi et al., 2018; Rupaimoole and Slack, 2017) .

MicroRNAs, the smallest endogenous regulatory non-coding RNAs, play a central role in cell differentiation, proliferation and survival by binding to complementary target mRNAs leading to translational inhibition or degradation. miRNAs are the crucial factor in a diverse biological processes such as antiviral defense, oncogenesis and cell development (Bartel, 2004) . The miRNA-binding sites within viral genomes are mostly located in the 5'and 3'non-translated regions (NTRs) but have recently been found in the coding regions of viral proteins (Girardi et al., 2018; Trobaugh et al., 2014; Zheng et al., 2013) . Various RNA viruses mimic or block the binding between a host miRNA and its target transcript, a phenomenon mediated by the miRNA seed site at the 5′ end of miRNA. We analyzed sixty SARS-CoV-2 genomes to identify regions that could work as virus-encoded miRNA seed sponges and potentially bind to human miRNA seed sites and prevent interaction with their native targets thereby relieving native miRNA suppression.

We searched for miRNAs that shared 100% identity of the 8mer seed region (Ellwanger et al., 2011) with SARS-CoV-02 genome regions, both positive and negative-sense. Currently, the human genome contains 2.654 mature sequences of miRNAs in miRBase database and > 1000 showed 100% of similarity between their seed sequences, important specific gene silencing motifs, and regions from the viral RNA. We refined the search for miRNAs that interact with the SARS-CoV-2 genome with a perfect alignment of 11 nucleotides encompassing the seed region. Thus, we find 34 miRNAs for positive-sense viral RNA and 45 miRNAs for negative-sense that can strongly bind to certain key SARS-CoV-2 genes. Once a candidate miRNA has been found, it becomes essential to identify its targets to understand the molecular mechanisms underlying the effect on the infection. We therefore conducted a literature review in this study to reveal the potential of these miRNAs in the immunopathogenesis and potential treatment possibilities of SARS-CoV-2 disease. Notably, these miRNAs play an important role in studies with pulmonary and cardiac disorders, including lung cancer, asthma, pneumonia, cardiac fibrosis, among others (Table 1) . For example, Bertrams and collaborators analyzed transcriptional networks of peripheral blood mononuclear cells to identify central regulators and potential biomarkers in community-acquired pneumonia (CAP), and acute exacerbations (AE) that are episodes of aggravated chronic obstructive pulmonary disease (COPD) symptoms and often co-occur with respiratory infection. They identified several microRNAs, e.g. miR-545-3p and miR-519c-3p, which separated AECOPD and CAP (Bertrams et al., 2020) . Already, Huang and collaborators show that a host miRNA, miR-1290, is induced through the extracellular signal-regulated kinase pathway upon Influenza A (IAV) virus infection and is associated with increased viral titers in human cells and ferret animal models. These findings point to a host species-specific mechanism by which IAV Table 1 MicroRNAs that plays a significant role in different mechanisms with based on the scientific literature. In silico analyzes were not considered. Many of the microRNAs that exhibited a perfect alignment of 11 nucleotides encompassing the seed region have not yet been found with their expression changed. Therefore, there were no scientific data about them. 

upregulates miR-1290 to disrupt vimentin expression and retain virus ribonucleoprotein in the nucleus, thereby enhancing viral polymerase activity and viral replication (Huang et al., 2019) .

The differentially expressed (DE) miRNAs exhibit promising potential for COVID-19 screening. MiRNAs levels can be monitored at different stages during the progression of the infection on severely ill patients. DE miRNA between early stages of infection and late stages could potentially be used to aid anticipate prognosis. Thus, these small RNA molecules may function as favorable clinical biomarkers for distinguishing the different clinical progressions of COVID-19, treatment strategy selection, and outcomes. For example, SARS-CoV-2 infection leads to fast activation of innate immune cells and change in the levels of many pro-inflammatory effector cytokines, such as TNF, IL-1β, IL-6, IL-8, G-CSF and GM-CSF, as well as chemokines, such as MCP1, IP10 and MIP1α, that are elevated in patients with COVID-19 (Huang et al., 2020) . The deregulated expression of some miRNAs can modulate translation of transcripts occasioning in a decrease in the levels of immunomodulating factors that can inhibit or originate the inflammatory response, thus acting as molecular brake to regulate inflammation (Boldin et al., 2011) . The expression levels of these miRNAs may offer promising diagnostic value and severity prediction of inflammatory response for COVID-19.

The role of cellular miRNAs is crucial when they are proviral, or when a longer, persistent infection is established. A fantastic example of use microRNAs is a significant reduction in virus titres (> 300-fold) without no sign of a rebound in viral titres, even after discontinuation of treatments in the Hepatitis C virus infection (Rupaimoole and Slack, 2017) . The miRNA-based therapeutics for Hepatitis C virus infection is performed using a antimiR (AntimiR-122), which had designed to bind directly to the mature strand of the targeted miRNA-122 and thus to induce a functional blockade. The miR-122 upregulates the replication of the Hepatitis C virus RNA genome, having a key role in promoting viral RNA stability (Jopling, 2005) . miRNAs can be used as an entry gate into regulatory networks that could be explored to find new unconventional therapeutic targets. Moreover, the use of antisense oligonucleotides to block viral genome, can be the most straightforward and easy to implement way toward new drugs therapy. For example, in one study researchers developed four artificial microRNAs (amiRNAs) that were designed to target different regions of Chikungunya virus (CHIKV) genome. These amiRNAs significantly inhibited CHIKV replication significantly (up to 99.8%) (Saha et al., 2016) . In medicine, miRNAs have been revealed as novel, highly promising biomarkers and as attractive tools and targets for novel therapeutic approaches. As candidate miRNAs begin to proceed toward clinical trials in virology field, the landscape of both diagnostic and interventional medicine will arguably continue to evolve.

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior -Brasil (CAPES) -Finance Code 001. National Council for Scientific and Technological Development -CNPq.