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Devadoss D, Acharya A, Manevski M, Houserova D, Cioffi MD, Pandey K, Nair M, Chapagain P, Mirsaeidi M, Borchert GM, Byrareddy SN, Chand HS. Immunomodulatory LncRNA on antisense strand of ICAM-1 augments SARS-CoV-2 infection-associated airway mucoinflammatory phenotype. iScience 2022; 25:104685. [PMID: 35789750 PMCID: PMC9242679 DOI: 10.1016/j.isci.2022.104685] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/25/2022] [Accepted: 06/23/2022] [Indexed: 01/20/2023] Open
Abstract
Noncoding RNAs are important regulators of mucoinflammatory response, but little is known about the contribution of airway long noncoding RNAs (lncRNAs) in COVID-19. RNA-seq analysis showed a more than 4-fold increased expression of IL-6, ICAM-1, CXCL-8, and SCGB1A1 inflammatory factors; MUC5AC and MUC5B mucins; and SPDEF, FOXA3, and FOXJ1 transcription factors in COVID-19 patient nasal samples compared with uninfected controls. A lncRNA on antisense strand to ICAM-1 or LASI was induced 2-fold in COVID-19 patients, and its expression was directly correlated with viral loads. A SARS-CoV-2-infected 3D-airway model largely recapitulated these clinical findings. RNA microscopy and molecular modeling indicated a possible interaction between viral RNA and LASI lncRNA. Notably, blocking LASI lncRNA reduced the SARS-CoV-2 replication and suppressed MUC5AC mucin levels and associated inflammation, and select LASI-dependent miRNAs (e.g., let-7b-5p and miR-200a-5p) were implicated. Thus, LASI lncRNA represents an essential facilitator of SARS-CoV-2 infection and associated airway mucoinflammatory response.
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Affiliation(s)
- Dinesh Devadoss
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Marko Manevski
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Dominika Houserova
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Michael D. Cioffi
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Madhavan Nair
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Mehdi Mirsaeidi
- Miller School of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of Miami, Miami, FL 33136, USA
| | - Glen M. Borchert
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Hitendra S. Chand
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
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Zoulikha M, Xiao Q, Boafo GF, Sallam MA, Chen Z, He W. Pulmonary delivery of siRNA against acute lung injury/acute respiratory distress syndrome. Acta Pharm Sin B 2022; 12:600-620. [PMID: 34401226 PMCID: PMC8359643 DOI: 10.1016/j.apsb.2021.08.009] [Citation(s) in RCA: 114] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/14/2021] [Accepted: 07/02/2021] [Indexed: 02/08/2023] Open
Abstract
The use of small interfering RNAs (siRNAs) has been under investigation for the treatment of several unmet medical needs, including acute lung injury/acute respiratory distress syndrome (ALI/ARDS) wherein siRNA may be implemented to modify the expression of pro-inflammatory cytokines and chemokines at the mRNA level. The properties such as clear anatomy, accessibility, and relatively low enzyme activity make the lung a good target for local siRNA therapy. However, the translation of siRNA is restricted by the inefficient delivery of siRNA therapeutics to the target cells due to the properties of naked siRNA. Thus, this review will focus on the various delivery systems that can be used and the different barriers that need to be surmounted for the development of stable inhalable siRNA formulations for human use before siRNA therapeutics for ALI/ARDS become available in the clinic.
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Key Words
- AAV, adeno-associated virus
- ALI/ARDS
- ALI/ARDS, acute lung injury/acute respiratory distress syndrome
- AM, alveolar macrophage
- ATI, alveolar cell type I
- ATII, alveolar cell type II
- AV, adenovirus
- Ago-2, argonaute 2
- CFDA, China Food and Drug Administration
- COPD, chronic obstructive pulmonary disease
- CPP, cell-penetrating peptide
- CS, cigarette smoke
- CXCR4, C–X–C motif chemokine receptor type 4
- Cellular uptake
- DAMPs, danger-associated molecular patterns
- DC-Chol, 3β-(N-(N′,N′-dimethylethylenediamine)-carbamoyl) cholesterol
- DDAB, dimethyldioctadecylammonium bromide
- DODAP, 1,2-dioleyl-3-dimethylammonium-propane
- DODMA, 1,2-dioleyloxy-N,N-dimethyl-3-aminopropane
- DOGS, dioctadecyl amido glycin spermine
- DOPC, 1,2-dioleoyl-sn-glycero-3-phosphocholine
- DOPE, 1,2-dioleoyl-l-α-glycero-3-phosphatidylethanolamine
- DOSPA, 2,3-dioleyloxy-N-[2-(sperminecarboxamido)ethyl]-N,N-dimethyl-1-propanaminium
- DOTAP, 1,2-dioleoyl-3-trimethylammonium-propane
- DOTMA, N-[1-(2,3-dioleoyloxy)propyl]-N,N,N-trimethylammonium
- DPI, dry powder inhaler
- DPPC, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine
- Drug delivery
- EC, endothelial cell
- EPC, egg phosphatidylcholine
- EXOs, exosomes
- Endosomal escape
- EpiC, epithelial cell
- FDA, US Food and Drug Administration
- HALI, hyperoxic acute lung injury
- HMGB1, high-mobility group box 1
- HMVEC, human primary microvascular endothelial cell
- HNPs, hybrid nanoparticles
- Hem-CLP, hemorrhagic shock followed by cecal ligation and puncture septic challenge
- ICAM-1, intercellular adhesion molecule-1
- IFN, interferons
- Inflammatory diseases
- LPS, lipopolysaccharides
- MEND, multifunctional envelope-type nano device
- MIF, macrophage migration inhibitory factor
- Myd88, myeloid differentiation primary response 88
- N/P ratio, nitrogen /phosphate ratio
- NETs, neutrophil extracellular traps
- NF-κB, nuclear factor kappa B
- NPs, nanoparticles
- Nanoparticles
- PAI-1, plasminogen activator inhibitor-1
- PAMAM, polyamidoamine
- PAMPs, pathogen-associated molecular patterns
- PD-L1, programmed death ligand-1
- PDGFRα, platelet-derived growth factor receptor-α
- PEEP, positive end-expiratory pressure
- PEG, polyethylene glycol
- PEI, polyethyleneimine
- PF, pulmonary fibrosis
- PFC, perfluorocarbon
- PLGA, poly(d,l-lactic-co-glycolic acid)
- PMs, polymeric micelles
- PRR, pattern recognition receptor
- PS, pulmonary surfactant
- Pulmonary administration
- RIP2, receptor-interacting protein 2
- RISC, RNA-induced silencing complex
- RNAi, RNA interference
- ROS, reactive oxygen species
- SLN, solid lipid nanoparticle
- SNALP, stable nucleic acid lipid particle
- TGF-β, transforming growth factor-β
- TLR, Toll-like receptor
- TNF-α, tumor necrosis factor-α
- VALI, ventilator-associated lung injury
- VILI, ventilator-induced lung injury
- dsDNA, double-stranded DNA
- dsRNA, double-stranded RNA
- eggPG, l-α-phosphatidylglycerol
- mRNA, messenger RNA
- miRNA, microRNA
- pDNA, plasmid DNA
- shRNA, short RNA
- siRNA
- siRNA, small interfering RNA
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Affiliation(s)
- Makhloufi Zoulikha
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Qingqing Xiao
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - George Frimpong Boafo
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Marwa A. Sallam
- Department of Industrial Pharmacy, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Zhongjian Chen
- Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, China
| | - Wei He
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, China
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Khan P, Siddiqui JA, Lakshmanan I, Ganti AK, Salgia R, Jain M, Batra SK, Nasser MW. RNA-based therapies: A cog in the wheel of lung cancer defense. Mol Cancer 2021; 20:54. [PMID: 33740988 PMCID: PMC7977189 DOI: 10.1186/s12943-021-01338-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
Lung cancer (LC) is a heterogeneous disease consisting mainly of two subtypes, non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC), and remains the leading cause of death worldwide. Despite recent advances in therapies, the overall 5-year survival rate of LC remains less than 20%. The efficacy of current therapeutic approaches is compromised by inherent or acquired drug-resistance and severe off-target effects. Therefore, the identification and development of innovative and effective therapeutic approaches are critically desired for LC. The development of RNA-mediated gene inhibition technologies was a turning point in the field of RNA biology. The critical regulatory role of different RNAs in multiple cancer pathways makes them a rich source of targets and innovative tools for developing anticancer therapies. The identification of antisense sequences, short interfering RNAs (siRNAs), microRNAs (miRNAs or miRs), anti-miRs, and mRNA-based platforms holds great promise in preclinical and early clinical evaluation against LC. In the last decade, RNA-based therapies have substantially expanded and tested in clinical trials for multiple malignancies, including LC. This article describes the current understanding of various aspects of RNA-based therapeutics, including modern platforms, modifications, and combinations with chemo-/immunotherapies that have translational potential for LC therapies.
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Affiliation(s)
- Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Apar Kishor Ganti
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE-68198, USA
- Division of Oncology-Hematology, Department of Internal Medicine, VA-Nebraska Western Iowa Health Care System, Omaha, NE, 68105, USA
- Division of Oncology-Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA, 91010, USA
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Surinder Kumar Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE-68198, USA
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA.
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE-68198, USA.
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Natarelli L, Parca L, Mazza T, Weber C, Virgili F, Fratantonio D. MicroRNAs and Long Non-Coding RNAs as Potential Candidates to Target Specific Motifs of SARS-CoV-2. Noncoding RNA 2021; 7:14. [PMID: 33670580 PMCID: PMC7931055 DOI: 10.3390/ncrna7010014] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
The respiratory system is one of the most affected targets of SARS-CoV-2. Various therapies have been utilized to counter viral-induced inflammatory complications, with diverse success rates. Pending the distribution of an effective vaccine to the whole population and the achievement of "herd immunity", the discovery of novel specific therapies is to be considered a very important objective. Here, we report a computational study demonstrating the existence of target motifs in the SARS-CoV-2 genome suitable for specific binding with endogenous human micro and long non-coding RNAs (miRNAs and lncRNAs, respectively), which can, therefore, be considered a conceptual background for the development of miRNA-based drugs against COVID-19. The SARS-CoV-2 genome contains three motifs in the 5'UTR leader sequence recognized by selective nucleotides within the seed sequence of specific human miRNAs. The seed of 57 microRNAs contained a "GGG" motif that promoted leader sequence-recognition, primarily through offset-6mer sites able to promote microRNAs noncanonical binding to viral RNA. Similarly, lncRNA H19 binds to the 5'UTR of the viral genome and, more specifically, to the transcript of the viral gene Spike, which has a pivotal role in viral infection. Notably, some of the non-coding RNAs identified in our study as candidates for inhibiting SARS-CoV-2 gene expression have already been proposed against diverse viral infections, pulmonary arterial hypertension, and related diseases.
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Affiliation(s)
- Lucia Natarelli
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU), 800336 Munich, Germany
| | - Luca Parca
- IRCCS Casa sollievo della Sofferenza, Laboratory of Bioinformatics, 71013 San Giovanni Rotondo (FG), Italy; (L.P.); (T.M.)
| | - Tommaso Mazza
- IRCCS Casa sollievo della Sofferenza, Laboratory of Bioinformatics, 71013 San Giovanni Rotondo (FG), Italy; (L.P.); (T.M.)
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU), 800336 Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 80336 Munich, Germany
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD Maastricht, The Netherlands
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | - Fabio Virgili
- Council for Agricultural Research and Economics, Research Center for Food and Nutrition, 00178 Rome, Italy;
| | - Deborah Fratantonio
- Biotechnology and Biopharmaceutics, Department of Biosciences, University of Bari Aldo Moro, 70125 Bari, Italy;
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Emerging Contribution of PancRNAs in Cancer. Cancers (Basel) 2020; 12:cancers12082035. [PMID: 32722129 PMCID: PMC7464463 DOI: 10.3390/cancers12082035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 02/06/2023] Open
Abstract
“Cancer” includes a heterogeneous group of diseases characterized by abnormal growth beyond natural boundaries. Neoplastic transformation of cells is orchestrated by multiple molecular players, including oncogenic transcription factors, epigenetic modifiers, RNA binding proteins, and coding and noncoding transcripts. The use of computational methods for global and quantitative analysis of RNA processing regulation provides new insights into the genomic and epigenomic features of the cancer transcriptome. In particular, noncoding RNAs are emerging as key molecular players in oncogenesis. Among them, the promoter-associated noncoding RNAs (pancRNAs) are noncoding transcripts acting in cis to regulate their host genes, including tumor suppressors and oncogenes. In this review, we will illustrate the role played by pancRNAs in cancer biology and will discuss the latest findings that connect pancRNAs with cancer risk and progression. The molecular mechanisms involved in the function of pancRNAs may open the path to novel therapeutic opportunities, thus expanding the repertoire of targets to be tested as anticancer agents in the near future.
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