key: cord-0782464-o84vpqzr
authors: Farshbaf, Alieh; Mohtasham, Nooshin; Zare, Reza; Mohajertehran, Farnaz; Rezaee, Seyed Abdolrahim
title: Potential therapeutic approaches of microRNAs for COVID-19: Challenges and opportunities
date: 2020-12-30
journal: J Oral Biol Craniofac Res
DOI: 10.1016/j.jobcr.2020.12.006
sha: 8c194879def36131dd29669ffcb866620accc916
doc_id: 782464
cord_uid: o84vpqzr

The coronavirus disease 2019 (COVID-19) emerges as current outbreak cause by Novel Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2). This infection affects respiratory system and provides uncontrolled systemic inflammatory response as cytokine storm. The main concern about SARS-CoV-2 pandemic is high viral pathogenicity with no specific drugs. MicroRNAs (miRs) as small non-coding RNAs (21–25 nt) regulate gene expression. The SARS-CoV-2 encoded-miRs affect human genes that involved in transcription, translation, apoptosis, immune response and inflammation. Also, they alter self-gene regulation and hijacked host miRs that provide protective environment to maintain its latency. On the other hand, Host miRs play critical role in viral gene expression to restrict infection. Over expression/inhibition of miRs might result in cell cycle irregularity, impaired immune response or cancer. In this manner, exact role of each miR should be specified. Mimic encoded-miRs like antagomirs showed successful result in phases of clinical trial prevent from negative effects of viral encoded-miRs. Products of mimic miRs are inexpensive corresponds to synthesis of primer; they are short and nanoscale in size. Although SARS-CoV-2 genome is undergoing evaluation, detection of exact molecular pathogenesis open up opportunities to for vaccine development. Salivaomics can evaluate SARS-CoV-2 genome, transcriptome, proteome and biomarkers like miRs in oral related and cancer disease. In this review, we studied the challenge and opportunities of miRs in therapeutic approach for SARS-CoV-2 infection, then overviewed the role of miRs in saliva droplet during SARS-CoV-2 infection and related cancer.

Novel Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) that emerges as current viral outbreak is caused by beta coronavirus, a member of Coronaviridae family. For this reason, symptoms of upper respiratory tract reveals. 2 Clinical symptoms are various following SARS-CoV-2 infection, most of the patient present fever, dry cough and tiredness. In addition, dyspnea, lung invasive lesions in chest radiographs, loss of smell or taste senses, ache and pains and diarrhea are observed. 3 Based on the first genome sequencing information, SARS-CoV-2 is a positive single strand RNA (+ssRNA) with 29891 nt length genome and low GC content that encoding 9860 amino acid. 4 The genome of SARS-CoV-2 be made up 11 open reading frames (ORFs) encode 16 nonstructural proteins and structural protein including spike glycoprotein (S), membrane (M), small envelope (E), nucleocapsid (N) and six accessory proteins (3a, 6, 7a, 7b, 8, and 10). 5 The spike protein play crucial role in viral infection because its receptor binding domains (RBDs) connected to the ACE2 receptor in mucosa cell and entry into the host cell and result in pneumonia. 6 Release a large number of systemic pro-inflammatory cytokine and chemokine by immune host cell following stimulated secretion of viral invasion provide deadly uncontrolled systemic inflammatory response. This cytokine storm including IL-6, TNFα, IL-1β, IL-8 and IL2R result in Acute Respiratory Distress Syndrome (ARDS) that is the main cause of death in COVID-19 patients. 7 Current evidence approved SARS-CoV-2 genome got mutations that almost are point mutation.

Position of mutation affect RNA secondary structure and cryptic splice site that help to virus avoided to target by host microRNAs and provide viral fitness. 8 J o u r n a l P r e -p r o o f MicroRNAs (miRs) are non-coding RNAs, small endogenous molecules (21-25 nt length), that regulate gene expression by inhibition of translation process or mRNA degradation depending upon their complementarity. They play a key role post-transcriptionally by binding to 3ʹ UTR of specific target mRNAs. 9 It is demonstrated that more than half human mRNA transcripts are regulated by miRs and a single mRNA can target by multiple miRs and controversy one miR can bind to several target mRNAs. 10 More than 2500 miRs are involved in human gene regulation that involve in various biological pathway like proliferation, differentiation, cancer, development, cell death and metabolism. In addition, previous studies declared host miRs play critical role in viral infection by modulate virus pathogenesis. To induce this antiviral effects, miRs can bind to both 3ʹ UTR and protein coding region of virus transcripts and alter viral tissue tropism or replication, transcription and translation. 11 On the other hand, viral-encoded miRs modulate self-gene regulation and also affect host gene expression. This can provide protective environment for life cycle of virus and maintain its latency. In this manner, some viruses able to escape from host immune response and can survive. Viral and host miRs interaction provide a cross talk between two regulatory systems result in infection. So, understand of this novel miR regulatory system can evident therapeutic approach.

The main concern about SARS-CoV-2 pandemic is high viral pathogenicity with no specific drugs that increased mortality rate and threat human health. Moreover, none of previous infection exhibited pandemic health crisis like SARS-CoV-2. 12 Although there is a complicated interaction between host cell and viral infection but detection of molecular SARS-CoV-2 pathogenesis help us to find out more new ways of therapeutic approaches. In this review, we investigate the molecular pathogenesis of SARS-CoV-2 that provide by miRs regulatory system as small non-coding RNAs that produce in virus and host cells and then overview the role of miRs in saliva droplet during SARS-CoV-2 infection and related cancers.

So far, more than 300 viral miRs are detected which affect host and self-gene expression. The first viral encoded-miRs identified in Epstein -Barr virus (EBV) infected cells that regulate gene expression involved in immune response. 13 Previous studies demonstrated some viruses encoded miRs that downregulate crucial genes involve in cell process and induce lung infection. 14 It was forecasted among 90 mature SARS-CoV-2 encoded miRs that bind to 3' UTR region of human genes, 40 miRs banded to 73 human J o u r n a l P r e -p r o o f genes. Result of gene ontology (GO) analysis showed these genes play role in Notch signaling, DNA endodeoxyribonuclease and deoxyribonuclease activities, cellular response to peptide hormone stimulus and modulation of fatty acid metabolism. 15 The mentioned pathways participate in apoptosis process that helps to development of viral infection. The virus applies some strategy to defeat apoptotic defense. For example, cation transport regulator-like protein 1 (CHAC1) gene as proapoptotic enzyme that involve in Notch signaling is target by SARS-CoV-2 encoded miR named as MD2-5p. Another gene, RAD9A -as a checkpoint in cell arrest during DNA damage and repair requirement-interact with BAX and Bcl-2 and targeted by MR147-3p. 16 It was demonstrated SARS-CoV-2 miRs silence P53, as an apoptosis inducer, and BMPR2 genes that involve in pathogenesis of respiratory infection. 17 Other study predicted 26 mature SARS-CoV-2 miRs affect human genes in apoptosis and also EGF, FGF receptor signaling, angiogenesis and VEGF pathway. 18 Likewise, it was shown 30 viral miRs can target 1367 human genes in transcription, metabolism, immune system and some pathway like Wnt and EGFR. 19 Some SARS-CoV-2 encoded-miRs affect human genes are listed in table 1.

It was reported SARS-CoV-2 encoded miRs can target 5ʹ UTR of human genes like promoter and enhancer regions and activated gene expression. More upregulation of gene expression is observed in immune response specially chemokine signaling and cytoskeleton related protein.

Also, among various tissues that infected by SARS-CoV-2 lung is more gene targeted by viral miRs and spleen and gut go after lung 15 . In addition, alignment of SARS-CoV-2 encoded-miRs and human miRs with high similarity showed they are involved in same pathway that affects pathophysiology, inflammation and clinical features. 14 Overall, the host gene expression can alter in SARS-CoV-2-infected cells in compare to normal. One of the challenges is viral escape from host inhibition following several ways: 1) block host miRs function, 2) avoidance to be target by host miRs following own 3' UTR sequence modification with mutation or length shortness that cannot bind complementary, 3) provide secondary structure with too long 3' UTR sequence. Another challenge is hijacked host miRs that help virus to modulate cell biological process, also function of target genes affect by hijacked miRs can alter similarly. It was assumed 28 human miRs hijacked by SARS-CoV-2 and affects more than 800 genes. Most of this hijacked human miRs predicted significantly interfering with immune response in COVID-19 patients. 15 CDC reported 80% of COVID-19 related death is observed among adult individuals ≥ 65 years with severe outcome in United States. 22 It was predicted one of the probable reason that aged adult present sever COVID-19 or more mortality is miR expression levels go down. It was assumed SARS-CoV-2 can replicate and produce essential particles parallels low overall miR expression in aged individuals similar to previous reports. 23 It should be consider some illness like cardiovascular and lung related disease can alter expression of human miR repertoires significantly, so affect SARS-CoV-2 and host cell interaction. 24 This is one of the reasons that some people are classified as high risk groups that should be more careful about their self. Some problems with COVID-19 patients like oxygen dependent, ventilation needs and Shortness of breath increase pulmonary hypertension and chronic lung diseases that linked to miR-1307-3p involved in TGF-β signaling. It has been proposed miR-1307 as a therapeutic target in SARS-CoV-2 infection because TGF-β play crucial role in lung development and mentioned diseases. 25 It was suggested 3 critical human miRs can apply for COVID-19 therapeutic strategies because they bind complete complementary to SARS-CoV-2 gRNA without any side effect on host genes, they are miRs 5197-3p, 4778-3p and 6864-5p. The miRs 5197-5p was identified especially as more effective on viral infection such as SARS-CoV, MERS-CoV and COVID-19 and also propose for hepatitis B and herpes simplex virus (HSV-1) infections. 24 In table 2 we listed some altered human encoded-miRs expression and related genes affected in SARS-CoV-2 infection in lung. 24, 25 The role of miRs as saliva biomarker in pathogenesis of viral infection and cancer J o u r n a l P r e -p r o o f Microdroplets are tiny particles (10 µm) carrying the SARS-CoV-2 and can transmit to others via exhale, loud conversation and sneezing. 26 As mention above, expression of miRs can alter in different condition like viral infection or cancer. Moreover, miRs are present in liquid body such as saliva, tear, urine and plasma. One of the reasons that is used the plasma from recovered COVID-19 patients is presence of antiviral miRs in addition to antibodies following previous SARS-CoV-2 infection. 27 In viral infection, like SARS-CoV-2, profile of miR expression change and investigation of this alternation can obtain by liquid body such as saliva. Saliva collection provides advantage including rapid, non-invasive, stable diagnosis with reliable indication and early diagnosis before signs appear. In addition, an advanced technique named "salivaomics" can evaluate genome, transcriptome, proteome and biomarkers such as miRs in oral related and cancer disease. 28 The human miRs can use as biomarkers for viral infection and cancer diagnosis, because they are regulator and impact gene related expression. In table 3 we mentioned some human miRs target SARS-CoV-2 genome and involve in cancer. In this manner, they can be utilized for prognostic approach. Up to date, some studies approved implement of miRs as biomarkers in head and neck squamous cell carcinomas (HNSCCs) including Oral, hypopharyngeal, esophageal and tongue squamous cell carcinomas. 29 We previous reported the validity of saliva biomarkers presence in HNSCC in compare to blood and other tissues. [30] [31] [32] The salivary miRs are extricated from normal or tumor cells and also during apoptosis or emitted of exosome or microvesicles. 33 They demonstrated high potential utility in disease monitoring. For example, profile of salivary miR expression identified significant decreasing of miR-139 in tongue SCC in compare to control group. Furthermore, the levels of miR-139 expression return to normal after surgery and indicated miR-139 play tumor suppressor role with biomarker potential. 34 Interestingly, outcome of a diagnostic validity study demonstrated 93% overall agreement in saliva specimen in compare to nasopharyngeal aspirate in detection of viral respiratory infection like SARS-CoV-2. 35

Current evidence approved microRNAs affect regulation of viral gene expression to restrict infection. In this review, we studied the challenge and opportunities of miRs as smallest noncoding RNAs in SARS-CoV-2 infection. The dual role of host miRs cannot be declined, they can play role as antiviral regulatory factors and also interact with viral miRs that benefice for virus replication and propagation. Based on insilico analysis seems first function is more possible, but J o u r n a l P r e -p r o o f in vitro and in vivo studies are needed to validate obtained data. 23 It was detected difference of gene expression between healthy and SARS-CoV-2 infected lung cells associated with regulatory role of miRs in some crucial pathways, like as TGF-β. Alternation in TGF-β pathway stimulates host response as cytokine storm and affect immune defense, and also cause clinical features. 36 Increasing of host miRs to target SARS-CoV-2 genes like S, M, N, E and ORF1ab will be obstruct viral entry and replication. In figure 1 we mentioned some human miRs target SARS-CoV-2 genome that product structural protein. As well, reduction of host miRs provides environment for more viral replication and accessibility for the host immune system. So, modification of host-miR levels alters specific cellular processes that are crucial for control of infection. 19 Therapeutic approach based on replacement of mimic miRs can apply to increase low host miR levels to suppress viral infection or take modified miRs products that cannot be degraded and uptake from the cells effectively. 37 Previous studies indicated intranasal inhalation of mimic miRs protect animal from viral respiratory infection. 38, 39 Target delivery with least toxicity is crucial in miR-based therapeutic strategies. It should be considered over expression/inhibition of miRs might result in cell cycle irregularity, impaired immune response or cancer. In this manner, exact role of each miR should be specified. 40 Although result of genome analysis estimated ~78.7% sequence homology between SARS-CoV and COVID-19, 41 but target of host miRs for both viral genomes can significantly be difference.

Recent study demonstrated 848 and 873 human miRs target SARS and COVID-19 genomes respectively that only 588 common human miRs target both viral sequences. Also, they estimated only 315 miRs were unique for isolated COVID-19 that obtained from different geographical region. 23 Recent studies evaluated SARS-CoV-2 strain mutations in different geographical region and find out viral genome get more mutated. Mutations mediate host immune response and affect virus survival with more pathogenicity. 24 Furthermore, evolution of SARS-CoV-2 genome helps virus to overcome host antiviral response special miRs as essential regulatory molecular pathway. On the other hand, virus can get advantage of host miRs to suppress own replication to escape from immune response but promote its transmission stronger.

After successful transmission, the virus can rapidly mutate own strains to elevate host specificity to avoid host miRs interaction following RNA polymerase activity without proofreading. 21 Altogether 810 mutations are discovered in SARS-CoV-2 genome consists of 646 SNPs, 19 indels, 145 deletions and also 33 sequence of pre-miRs overlapped with these mutations. And J o u r n a l P r e -p r o o f also, more than half mutation was predicated synonym and most of them were substitution of C/G to U. Outcome of these variations might attenuate phenotype of SARS-CoV-2 with reducing viral miRs repertories and affect miR-binding site and their regulatory role in defense mechanism. 15 Detection of new SARS-CoV-2 mutations should be considered because genetic variation in SARS-CoV-2 genome prevent from vaccine development. 42 Similarly, this virus is undergoing evolution, natural selection effect and purifying selection, 43 so detection and evaluation of exact molecular pathogenesis open up opportunities to apply best therapeutic approaches. There are challenges in modification of host miR levels or replacement of mimic miRs that should be considered their side effects. Selected miRs should be effective, safe and well tolerated by patients. Moreover, design and products of mimic miRs are inexpensive corresponds to synthesis of primer sequence, they are short and nanoscale in size that can deliver by exosomes. 44 The protein-protein interaction network between human and SARS-CoV-2 was identified by affinity-purification mass spectrometry, the outcome of this study can help us to focus on miRs that target translation inhibitors and sigma 1, 2 receptors. 45

The effects of miR based therapeutic approaches approved in viral infection. Alternation in human miRs expression including overexpression or mimic replacement, inhibition or suppression helps to block viral entry or replication in host cells. Target SARS-CoV-2 genes such as S, M, N, E and ORF1ab by increasing host miRs attenuate viral latency. In contrast, decreasing in human miRs against SARS-CoV-2 infection provide more viral replication and accessibility for immune system. The crucial challenge for selection of candidate human miRs against SARS-CoV-2 infection is the side effects following alternation of gene. More investigation assists to least the side effects. On the other hand, the impact of SARS-CoV-2 encoded-miRs on host genes should not be ignored. As a solution, potential therapeutic of antagomirs as the small molecular inhibitors can be evaluated for SARS-CoV-2 infection. The stability, effective delivery, higher binding affinity and uptake with less degradation by nuclease are the common problem in target miRs therapy process. The SARS-CoV-2 genome sequence discovery and its alignment with the other correlated Coronaviridae family help us to help from previous therapeutic approaches. Salivaomics present high potential utility in detection of biomarker such as miRs; it can help in vaccine development for SARS-CoV-2.

J o u r n a l P r e -p r o o f This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

The authors declare that there are no conflicts of interest 15 J o u r n a l P r e -p r o o f 

Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense

A Novel Coronavirus from Patients with Pneumonia in China

Coronavirus disease 2019 (COVID-19): a clinical update

A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses

The architecture of SARS-CoV-2 transcriptome

Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

Translationassociated mutational U-pressure in the first ORF of SARS-CoV-2 and other coronaviruses

MicroRNAs: small RNAs with a big role in gene regulation

The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): The Perspectives of clinical immunologists from China

On the Importance of Host MicroRNAs During Viral Infection

Novel SARS-CoV-2 outbreak and COVID19 disease; a systemic review on the global pandemic

Epstein-Barr virus-encoded microRNAs as regulators in host immune responses

MicroRNAs as mediators of viral evasion of the immune system

Implications of the virus-encoded miRNA and host miRNA in the pathogenicity of SARS

Human cytomegalovirus miR-UL36-5p inhibits apoptosis via downregulation of adenine nucleotide translocator 3 in cultured cells

Genome-wide computational prediction of miRNAs in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) revealed target genes involved in pulmonary vasculature and antiviral innate immunity

Consequences of BMPR2 Deficiency in the Pulmonary Vasculature and Beyond: Contributions to Pulmonary Arterial Hypertension

Safety, tolerability, and antiviral effect of RG-101 in patients with chronic hepatitis C: a phase 1B, double-blind, randomised controlled trial

Team CC-R. Severe Outcomes Among Patients with Coronavirus Disease 2019 (COVID-19) -United States

COVID-19 Virulence in Aged Patients Might Be Impacted by the Host Cellular MicroRNAs Abundance/Profile

The Prediction of miRNAs in SARS-CoV-2 Genomes: hsa-miR Databases Identify 7 Key miRs Linked to Host Responses and Virus Pathogenicity-Related KEGG Pathways Significant for Comorbidities

Exosome-Derived MiRNAs as Biomarkers of the Development and Progression of Intracranial Aneurysms

COVID 19 can spread through breathing, talking, study estimates

Plasma MicroRNA as a novel diagnostic

A Review of Salivary Diagnostics and Its Potential Implication in Detection of Covid-19

The microRNA signatures: aberrantly expressed microRNAs in head and neck squamous cell carcinoma

Overexpression of High-Mobility Motor Box 1 in the Blood and Tissues of Patients with Head and Neck Squamous Cell Carcinoma

Overexpression of Lactate Dehydrogenase in the Saliva and Tissues of Patients with Head and Neck Squamous Cell Carcinoma

The promise of stem cell markers in the diagnosis and therapy of epithelial dysplasia and oral squamous cell carcinoma

Human salivary microRNAs in

Tumor-suppressive function of miR-139-5p in esophageal squamous cell carcinoma

Saliva as a diagnostic specimen for testing respiratory virus by a point-of-care molecular assay: a diagnostic validity study

Severe acute respiratory syndrome-associated coronavirus nucleocapsid protein interacts with Smad3 and modulates transforming growth factor-beta signaling

Evaluation and Treatment Coronavirus (COVID-19). StatPearls. Treasure Island FL: © 2020

Endogenous Cellular MicroRNAs Mediate Antiviral Defense against Influenza A Virus

Cellular miR-130b inhibits replication of porcine reproductive and respiratory syndrome virus in vitro and in vivo

The role of microRNAs in respiratory viral infection: friend or foe

The establishment of reference sequence for SARS-CoV-2 and variation analysis

Don't rush to deploy COVID-19 vaccines and drugs without sufficient safety guarantees

Emergence of SARS-CoV-2 through recombination and strong purifying selection

Engineering of Exosomes to Target Cancer Metastasis

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

Signal Strength Alters T-DC Activation and Interaction Times and Directs the Outcome of Differentiation

Implications of SARS-CoV-2 Mutations for Genomic RNA Structure and Host microRNA Targeting

The effect of miR-338-3p on HBx deletion-mutant (HBx-d382) mediated liver-cell proliferation through CyclinD1 regulation

The EGFR/miR-338-3p/EYA2 axis controls breast tumor growth and lung metastasis

Epigenetic silencing of miR-338-3p contributes to tumorigenicity in gastric cancer by targeting SSX2IP

How miRNAs can protect humans from coronaviruses COVID-19

Role and mechanism of miR-4778-3p and its targets NR2C2 and Med19 in cervical cancer radioresistance

A panel of MicroRNA signature as a tool for predicting survival of patients with urothelial carcinoma of the bladder

Microarray expression profiling and bioinformatics analysis of circular RNA expression in lung squamous cell carcinoma

MiR-15b-5p Regulates Collateral Artery Formation by Targeting AKT3 (Protein Kinase B-3)

miR-15a-5p suppresses inflammation and fibrosis of peritoneal mesothelial cells induced by peritoneal dialysis via targeting VEGFA

Downregulation of exosome-encapsulated miR-548c-5p is associated with poor prognosis in colorectal cancer

miR-548d-3p inhibits osteosarcoma by downregulating KRAS

MiR-409-3p Inhibits Cell Proliferation and Invasion of Osteosarcoma by Targeting Zinc-Finger E-Box-Binding Homeobox-1

miR-30b-5p acts as a tumor suppressor microRNA in esophageal squamous cell carcinoma

Functional analysis of miR-21-3p, miR-30b-5p and miR-150-5p shuttled by extracellular vesicles from diabetic subjects reveals their association with diabetic retinopathy

Downregulation of miR-505-3p predicts poor bone metastasis-free survival in prostate cancer

Targeting the circulating microRNA signature of obesity

Potential Involvement of MiR-30e-3p in Myocardial Injury Induced by Coronary Microembolization via Autophagy Activation

miR-23c suppresses tumor growth of human hepatocellular carcinoma by attenuating ERBB2IP

Expression Signature and Role of miR-30d-5p in Non-Small Cell Lung Cancer: a Comprehensive Study Based on in Silico Analysis of Public Databases and in Vitro Experiments

The potential value of miR-1 and miR-374b as biomarkers for colorectal cancer

PIK3C2A is a gene-specific target of microRNA-518a-5p in imatinib mesylate-resistant gastrointestinal stromal tumor

MicroRNA Regulatory Network as Biomarkers of Late Seizure in Patients with Spontaneous Intracerebral Hemorrhage

Post-transcriptional control of miRNA biogenesis

Role of O-glycosylation and expression of CD43 and CD45 on the surfaces of effector T cells in human T cell leukemia virus type 1 cell-to-cell infection

Site-specific glycosylation of Ebola virus glycoprotein by human polypeptide GalNAc-transferase 1 induces cell adhesion defects

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Identifying the miRNA signature associated with survival time in patients with lung adenocarcinoma using miRNA expression profiles

Incomplete cellular reprogramming of colorectal cancer cells elicits an epithelial/mesenchymal hybrid phenotype

Differential expression of microRNA and arachidonic acid metabolism in aspirin-treated human cardiac and peri-cardiac fat-derived mesenchymal stem cells

Transforming growth factor-beta signaling across ages: from distorted lung development to chronic obstructive pulmonary disease

Profiling of circulating microRNAs in children with recent onset of type 1 diabetes

MicroRNA-1468-5p inhibits glioma cell proliferation and induces cell cycle arrest by targeting RRM1

MicroRNA-129-3p functions as a tumor suppressor in serous ovarian cancer by targeting BZW1

J o u r n a l P r e -p r o o f