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Abstract
Hepatocellular carcinoma and cholangiocarcinoma are the most common primary liver tumours, whose incidence and associated mortality have increased over recent decades. Liver cancer is often diagnosed late when curative treatments are no longer an option. Characterising new molecular determinants of liver carcinogenesis is crucial for the development of innovative treatments and clinically relevant biomarkers. Recently, circular RNAs (circRNAs) emerged as promising regulatory molecules involved in cancer onset and progression. Mechanistically, circRNAs are mainly known for their ability to sponge and regulate the activity of microRNAs and RNA-binding proteins, although other functions are emerging (e.g. transcriptional and post-transcriptional regulation, protein scaffolding). In liver cancer, circRNAs have been shown to regulate tumour cell proliferation, migration, invasion and cell death resistance. Their roles in regulating angiogenesis, genome instability, immune surveillance and metabolic switching are emerging. Importantly, circRNAs are detected in body fluids. Due to their circular structure, circRNAs are often more stable than mRNAs or miRNAs and could therefore serve as promising biomarkers - quantifiable with high specificity and sensitivity through minimally invasive methods. This review focuses on the role and the clinical relevance of circRNAs in liver cancer, including the development of innovative biomarkers and therapeutic strategies.
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Key Words
- ASO, antisense oligonucleotide
- CCA, cholangiocarcinoma
- CLIP, cross-linking immunoprecipitation
- EMT, epithelial-to-mesenchymal transition
- EVs, extracellular vesicles
- HCC, hepatocellular carcinoma
- HN1, haematopoietic- and neurologic-expressed sequence 1
- IRES, internal ribosome entry sites
- NGS, next-generation sequencing
- QKI, Quaking
- RBP, RNA-binding protein
- RISC, RNA-induced silencing complex
- TAM, tumour-associated macrophage
- TSB, target site blockers
- biomarker
- cancer hallmarks
- cholangiocarcinoma
- circRNA
- circRNA, circular RNA
- hepatocellular carcinoma
- miRNA, microRNA
- shRNA, small-hairpin RNA
- snRNP, small nuclear ribonuclear proteins
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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: 93] [Impact Index Per Article: 46.5] [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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Long non-coding RNAs: From disease code to drug role. Acta Pharm Sin B 2021; 11:340-354. [PMID: 33643816 PMCID: PMC7893121 DOI: 10.1016/j.apsb.2020.10.001] [Citation(s) in RCA: 238] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 08/06/2020] [Accepted: 08/21/2020] [Indexed: 12/30/2022] Open
Abstract
Enormous studies have corroborated that long non-coding RNAs (lncRNAs) extensively participate in crucial physiological processes such as metabolism and immunity, and are closely related to the occurrence and development of tumors, cardiovascular diseases, nervous system disorders, nephropathy, and other diseases. The application of lncRNAs as biomarkers or intervention targets can provide new insights into the diagnosis and treatment of diseases. This paper has focused on the emerging research into lncRNAs as pharmacological targets and has reviewed the transition of lncRNAs from the role of disease coding to acting as drug candidates, including the current status and progress in preclinical research. Cutting-edge strategies for lncRNA modulation have been summarized, including the sources of lncRNA-related drugs, such as genetic technology and small-molecule compounds, and related delivery methods. The current progress of clinical trials of lncRNA-targeting drugs is also discussed. This information will form a latest updated reference for research and development of lncRNA-based drugs.
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Key Words
- AD, Alzheimer's disease
- ANRIL, antisense noncoding RNA gene at the INK4 locus
- ASO, antisense oligonucleotide
- ASncmtRNA
- ASncmtRNA, antisense noncoding mitochondrial RNA
- BCAR4, breast cancer anti-estrogen resistance 4
- BDNF-AS, brain-derived neurotrophic factor antisense
- CASC9, cancer susceptibility candidate 9
- CDK, cyclin dependent kinase 1
- CHRF, cardiac hypertrophy related factor
- CRISPR, clustered regularly interspaced short palindromic repeats
- Clinical trials
- DACH1, dachshund homolog 1
- DANCR, differentiation antagonizing non-protein coding RNA
- DKD, diabetic kidney disease
- DPF, diphenyl furan
- Delivery
- EBF3-AS, early B cell factor 3-antisense
- ENE, element for nuclear expression
- Erbb4-IR, Erb-B2 receptor tyrosine kinase 4-immunoreactivity
- FDA, U.S. Food and Drug Administration
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- GAS5, growth arrest specific 5
- Gene therapy
- HISLA, HIF-1α-stabilizing long noncoding RNA
- HOTAIR, HOX transcript antisense intergenic RNA
- HULC, highly upregulated in liver cancer
- LIPCAR, long intergenic noncoding RNA predicting cardiac remodeling
- LNAs, locked nucleic acids
- LncRNAs
- MALAT1, metastasis associated lung adenocarcinoma transcript 1
- MEG3, maternally expressed gene 3
- MHRT, myosin heavy chain associated RNA transcripts
- MM, multiple myeloma
- NEAT1, nuclear enriched abundant transcript 1
- NKILA, NF-kappaB interacting lncRNA
- NPs, nanoparticles
- Norad, non-coding RNA activated by DNA damage
- OIP5-AS1, opa-interacting protein 5 antisense transcript 1
- PD, Parkinson's disease
- PEG, polyethylene glycol
- PNAs, peptide nucleic acids
- PTO, phosphorothioate
- PVT1, plasmacytoma variant translocation 1
- RGD, arginine-glycine-aspartic acid peptide
- RISC, RNA-induced silencing complex
- SALRNA1, senescence associated long non-coding RNA 1
- SNHG1, small nucleolar RNA host gene 1
- Small molecules
- SncmtRNA, sense noncoding mitochondrial RNA
- THRIL, TNF and HNRNPL related immunoregulatory
- TTTY15, testis-specific transcript, Y-linked 15
- TUG1, taurine-upregulated gene 1
- TWIST1, twist family BHLH transcription factor 1
- Targeted drug
- TncRNA, trophoblast-derived noncoding RNA
- Translational medicine
- UCA1, urothelial carcinoma-associated 1
- UTF1, undifferentiated transcription factor 1
- XIST, X-inactive specific transcript
- lincRNA-p21, long intergenic noncoding RNA p21
- lncRNAs, long non-coding RNAs
- mtlncRNA, mitochondrial long noncoding RNA
- pHLIP, pH-low insertion peptide
- sgRNA, single guide RNA
- siRNAs, small interfering RNAs
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Small interfering RNA for cancer treatment: overcoming hurdles in delivery. Acta Pharm Sin B 2020; 10:2075-2109. [PMID: 33304780 PMCID: PMC7714980 DOI: 10.1016/j.apsb.2020.10.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/24/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
In many ways, cancer cells are different from healthy cells. A lot of tactical nano-based drug delivery systems are based on the difference between cancer and healthy cells. Currently, nanotechnology-based delivery systems are the most promising tool to deliver DNA-based products to cancer cells. This review aims to highlight the latest development in the lipids and polymeric nanocarrier for siRNA delivery to the cancer cells. It also provides the necessary information about siRNA development and its mechanism of action. Overall, this review gives us a clear picture of lipid and polymer-based drug delivery systems, which in the future could form the base to translate the basic siRNA biology into siRNA-based cancer therapies.
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Key Words
- 1,3-propanediol, PEG-b-PDMAEMA-b-Ppy
- 2-propylacrylicacid, PAH-b-PDMAPMA-b-PAH
- APOB, apolipoprotein B
- AQP-5, aquaporin-5
- AZEMA, azidoethyl methacrylate
- Atufect01, β-l-arginyl-2,3-l-diaminopropionicacid-N-palmityl-N-oleyl-amide trihydrochloride
- AuNPs, gold nanoparticles
- B-PEI, branched polyethlenimine
- BMA, butyl methacrylate
- CFTR, cystic fibrosis transmembrane conductance regulator gene
- CHEMS, cholesteryl hemisuccinate
- CHOL, cholesterol
- CMC, critical micelles concentration
- Cancer
- DC-Chol, 3β-[N-(N′,N′-dimethylaminoethane)carbamoyl]cholesterol
- DMAEMA, 2-dimethylaminoethyl methacrylate
- DNA, deoxyribonucleic acid
- DOPC, dioleylphosphatidyl choline
- DOPE, dioleylphosphatidyl ethanolamine
- DOTAP, N-[1-(2,3-dioleoyloxy)propyl]-N,N,N-trimethylammonium methyl-sulfate
- DOTMA, N-[1-(2,3-dioleyloxy)propy]-N,N,N-trimethylammoniumchloride
- DOX, doxorubicin
- DSGLA, N,N-dis-tearyl-N-methyl-N-2[N′-(N2-guanidino-l-lysinyl)] aminoethylammonium chloride
- DSPC, 1,2-distearoyl-sn-glycero-3-phosphocholine
- DSPE, 1,2-distearoyl-sn-glycero-3-phosphorylethanolamine
- DSPE-MPEG, 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] (ammonium salt)
- DSPE-PEG-Mal: 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[maleimide(polyethylene glycol)-2000] (mmmonium salt), EPR
- Liposomes
- Micelles
- N-acetylgalactosamine, HIF-1α
- Nanomedicine
- PE-PCL-b-PNVCL, pentaerythritol polycaprolactone-block-poly(N-vinylcaprolactam)
- PLA, poly-l-arginine
- PLGA, poly lactic-co-glycolic acid
- PLK-1, polo-like kinase 1
- PLL, poly-l-lysine
- PPES-b-PEO-b-PPES, poly(4-(phenylethynyl)styrene)-block-PEO-block-poly(4-(phenylethynyl)styrene)
- PTX, paclitaxel
- PiRNA, piwi-interacting RNA
- Polymer
- RES, reticuloendothelial system
- RGD, Arg-Gly-Asp peptide
- RISC, RNA-induced silencing complex
- RNA, ribonucleic acid
- RNAi, RNA interference
- RNAse III, ribonuclease III enzyme
- SEM, scanning electron microscope
- SNALP, stable nucleic acid-lipid particles
- SiRNA, short interfering rNA
- Small interfering RNA (siRNA)
- S–Au, thio‒gold
- TCC, transitional cell carcinoma
- TEM, transmission electron microscopy
- Tf, transferrin
- Trka, tropomyosin receptor kinase A
- USPIO, ultra-small superparamagnetic iron oxide nanoparticles
- UV, ultraviolet
- VEGF, vascular endothelial growth factor
- ZEBOV, Zaire ebola virus
- enhanced permeability and retention, Galnac
- hypoxia-inducible factor-1α, KSP
- kinesin spindle protein, LDI
- lipid-protamine-DNA/hyaluronic acid, MDR
- lysine ethyl ester diisocyanate, LPD/LPH
- messenger RNA, MTX
- methotrexate, NIR
- methoxy polyethylene glycol-polycaprolactone, mRNA
- methoxypoly(ethylene glycol), MPEG-PCL
- micro RNA, MPEG
- multiple drug resistance, MiRNA
- nanoparticle, NRP-1
- near-infrared, NP
- neuropilin-1, PAA
- poly(N,N-dimethylacrylamide), PDO
- poly(N-isopropyl acrylamide), pentaerythritol polycaprolactone-block-poly(N-isopropylacrylamide)
- poly(acrylhydrazine)-block-poly(3-dimethylaminopropyl methacrylamide)-block-poly(acrylhydrazine), PCL
- poly(ethylene glycol)-block-poly(2-dimethylaminoethyl methacrylate)-block poly(pyrenylmethyl methacrylate), PEG-b-PLL
- poly(ethylene glycol)-block-poly(l-lysine), PEI
- poly(ethylene oxide)-block-poly(2-(diethylamino)ethyl methacrylate)-stat-poly(methoxyethyl methacrylate), PEO-b-PCL
- poly(ethylene oxide)-block-poly(Ε-caprolactone), PE-PCL-b-PNIPAM
- poly(Ε-caprolactone), PCL-PEG
- poly(Ε-caprolactone)-polyethyleneglycol-poly(l-histidine), PCL-PEI
- polycaprolactone-polyethyleneglycol, PCL-PEG-PHIS
- polycaprolactone-polyethylenimine, PDMA
- polyethylenimine, PEO-b-P(DEA-Stat-MEMA
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Good or not good: Role of miR-18a in cancer biology. Rep Pract Oncol Radiother 2020; 25:808-819. [PMID: 32884453 DOI: 10.1016/j.rpor.2020.07.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/24/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023] Open
Abstract
miR-18a is a member of primary transcript called miR-17-92a (C13orf25 or MIR17HG) which also contains five other miRNAs: miR-17, miR-19a, miR-20a, miR-19b and miR-92a. This cluster as a whole shows specific characteristics, where miR-18a seems to be unique. In contrast to the other members, the expression of miR-18a is additionally controlled and probably functions as its own internal controller of the cluster. miR-18a regulates many genes involved in proliferation, cell cycle, apoptosis, response to different kinds of stress, autophagy and differentiation. The disturbances of miR-18a expression are observed in cancer as well as in different diseases or pathological states. The miR-17-92a cluster is commonly described as oncogenic and it is known as 'oncomiR-1', but this statement is a simplification because miR-18a can act both as an oncogene and a suppressor. In this review we summarize the current knowledge about miR-18a focusing on its regulation, role in cancer biology and utility as a potential biomarker.
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Key Words
- 5-FU, 5-fluorouracyl
- ACVR2A, activin A receptor type 2A
- AKT, AKT serine/threonine kinase
- AR, androgen receptor
- ATG7, autophagy related 7
- ATM, ATM serine/threonine kinase
- BAX, BCL2 associated Xapoptosis regulator
- BCL2, BCL2 apoptosis regulator
- BCL2L10, BCL2 like 10
- BDNF, brain derived neurotrophic factor
- BLCA, bladder urothelial carcinoma
- BRCA, breast cancer
- Biomarker
- Bp, base pair
- C-myc (MYCBP), MYC binding protein
- CASC2, cancer susceptibility 2
- CD133 (PROM1), prominin 1
- CDC42, cell division cycle 42
- CDKN1, Bcyclin dependent kinase inhibitor 1B
- COAD, colon adenocarcinoma
- Cancer
- Circulating miRNA
- DDR, DNA damage repair
- E2F family (E2F1, E2F2, E2F3), E2F transcription factors
- EBV, Epstein-Barr virus
- EMT, epithelial-to-mesenchymal transition
- ER, estrogen receptor
- ERBB (EGFR), epidermal growth factor receptor
- ESCA, esophageal carcinoma
- FENDRR, FOXF1 adjacent non-coding developmental regulatory RNA
- FER1L4, fer-1 like family member 4 (pseudogene)
- GAS5, growth arrest–specific 5
- HIF-1α (HIF1A), hypoxia inducible factor 1 subunit alpha
- HNRNPA1, heterogeneous nuclear ribonucleoprotein A1
- HNSC, head and neck squamous cell carcinoma
- HRR, homologous recombination-based DNA repair
- IFN-γ (IFNG), interferon gamma
- IGF1, insulin like growth factor 1
- IL6, interleukin 6
- IPMK, inositol phosphate multikinase
- KIRC, clear cell kidney carcinoma
- KIRP, kidney renal papillary cell carcinoma
- KRAS, KRAS proto-oncogene, GTPase
- LIHC, liver hepatocellular carcinoma
- LMP1, latent membrane protein 1
- LUAD, lung adenocarcinoma
- LUSC, lung squamous cell carcinoma
- Liquid biopsy
- MAPK, mitogen-activated protein kinase
- MCM7, minichromosome maintenance complex component 7
- MET, mesenchymal-to-epithelial transition
- MTOR, mechanistic target of rapamycin kinase
- N-myc (MYCN), MYCN proto-oncogene, bHLH transcription factor
- NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NOTCH2, notch receptor 2
- Oncogene
- PAAD, pancreatic adenocarcinoma
- PERK (EIF2AK3), eukaryotic translation initiation factor 2 alpha kinase 3
- PI3K (PIK3CA), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha
- PIAS3, protein inhibitor of activated STAT 3
- PRAD, prostate adenocarcinoma
- RISC, RNA-induced silencing complex
- SMAD2, SMAD family member 2
- SMG1, SMG1 nonsense mediated mRNA decay associated PI3K related kinase
- SNHG1, small nucleolar RNA host gene 1
- SOCS5, suppressor of cytokine signaling 5
- STAD, stomach adenocarcinoma
- STAT3, signal transducer and activator of transcription 3
- STK4, serine/threonine kinase 4
- Suppressor
- TCGA
- TCGA, The Cancer Genome Atlas
- TGF-β (TGFB1), transforming growth factor beta 1
- TGFBR2, transforming growth factor beta receptor 2
- THCA, papillary thyroid carcinoma
- TNM, Classification of Malignant Tumors: T - tumor / N - lymph nodes / M – metastasis
- TP53, tumor protein p53
- TP53TG1, TP53 target 1
- TRIAP1, p53-regulating inhibitor of apoptosis gene
- TSC1, TSC complex subunit 1
- UCA1, urothelial cancer associated 1
- UCEC, uterine corpus endometrial carcinoma
- UTR, untranslated region
- WDFY3-AS2, WDFY3 antisense RNA 2
- WEE1, WEE1 G2 checkpoint kinase
- WNT family, Wingless-type MMTV integration site family/Wnt family ligands
- ZEB1/ZEB2, zinc finger E-box binding homeobox 1 and 2
- ceRNA, competitive endogenous RNA
- cncRNA, protein coding and non-coding RNA
- lncRNA, long-non coding RNA
- miR-17-92a
- miR-18a
- miRNA
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MicroRNAs and Xenobiotic Toxicity: An Overview. Toxicol Rep 2020; 7:583-595. [PMID: 32426239 PMCID: PMC7225592 DOI: 10.1016/j.toxrep.2020.04.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/13/2020] [Accepted: 04/19/2020] [Indexed: 12/27/2022] Open
Abstract
miRNAs are key regulators of gene expression at both transcription and translation. The role of miRNAs in xenobiotic toxicity and its potential as biomarkers are being explored. In spite of numerous studies, the complex mechanism of miRNA biogenesis and its regulation remains unclear.
The advent of new technologies has paved the rise of various chemicals that are being employed in industrial as well as consumer products. This leads to the accumulation of these xenobiotic compounds in the environment where they pose a serious threat to both target and non-target species. miRNAs are one of the key epigenetic mechanisms that have been associated with toxicity by modulating the gene expression post-transcriptionally. Here, we provide a comprehensive view on miRNA biogenesis, their mechanism of action and, their possible role in xenobiotic toxicity. Further, we review the recent in vitro and in vivo studies involved in xenobiotic exposure induced miRNA alterations and the mRNA-miRNA interactions. Finally, we address the challenges associated with the miRNAs in toxicological studies.
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Key Words
- ADAMTS9, A disintegrin and metalloproteinase with thrombospondin motifs 9
- AHR, Aryl Hydrocarbon Receptor
- AMPK, Adenosine Monophosphate-activated protein kinase
- ARRB1, Arrestin beta 1
- Ag, Silver
- Al2O3, Aluminium oxide
- Au, Gold
- Aβ, Amyloid Beta
- BCB, Blood-cerebrospinal fluid barrier
- BNIP3−3, BCL2/adenovirus E1B 19 kDa protein-interacting protein 3
- BaP, Benzo[a]pyrene
- Biomarkers
- CCNB1, Cyclin B1
- CDC25A, M-phase inducer phosphatase 1
- CDC25C, M-phase inducer phosphatase 3
- CDK, Cyclin-dependent Kinase
- CDK1, Cyclin-dependent kinase 1
- CDK6, Cyclin-dependent kinase 6
- CDKN1b, Cyclin-dependent kinase Inhibitor 1B
- CEC, Contaminants of Emerging Concern
- COPD, Chronic obstructive pulmonary disease
- COX2, Cyclooxygenase-2
- CTGF, Connective Tissue Growth Factor
- DGCR8, DiGeorge syndrome chromosomal [or critical] region 8
- DNA, Deoxy ribonucleic acid
- DON, Deoxynivalenol
- ER, Endoplasmic Reticulum
- Environment
- Epigenetics
- Fadd, Fas-associated protein with death domain
- GTP, Guanosine triphosphate
- Gene regulation
- Grp78/BIP, Binding immunoglobulin protein
- HSPA1A, Heat shock 70 kDa protein 1
- Hpf, Hours post fertilization
- IL-6, Interleukin 6
- IL1R1, Interleukin 1 receptor, type 1
- LIN28B, Lin-28 homolog B
- LRP-1-, Low density lipoprotein receptor-related protein 1
- MAPK, Mitogen Activated Protein Kinase
- MC-LR, Microcystin-Leucine Arginine
- MC-RR, Microcystin-Arginine Arginine
- MRE, MicroRNA Response Elements
- Mn, Manganese
- NASH, Non-alcoholic steatohepatitis
- NET1, Neuroepithelial Cell Transforming 1
- NF- ҡB, Nuclear Factor kappa-light-chain-enhancer of activated B cells
- NFKBAP, NFKB Activating protein-1
- NMDAR, N-methyl-d-aspartate receptor
- NPs, Nanoparticles
- Non-coding RNAs
- Nrf2, Nuclear factor erythroid 2-related factor 2
- PDCD4, Programmed cell death protein 4
- PFAS, Poly-fluoroalkyl substances
- PM2.5, Particulate Matter2.5
- RISC, RNA-induced silencing complex
- RNA, Ribonucleic acid
- RNAi, RNA interference
- RNase III, Ribonuclease III
- SEMA6D, Semaphorin-6D
- SOLiD, Sequencing by Oligonucleotide Ligation and Detection
- SPIONs, Superparamagnetic Iron Oxide Nanoparticles
- SiO2, Silicon dioxide
- TCDD, 2,3,7,8-Tetrachlorodibenzodioxin
- TNF-α, Tumor necrosis factor – alpha
- TP53, Tumor protein 53
- TRBP, Transactivation Response RNA Binding Protein
- Toxicity
- UTR, Untranslated region
- WHO, World Health Organization
- Wnt, Wingless-related integration site
- ZEA, Zearalanone
- Zn, Zinc
- bcl2l11, B-cell lymphoma-2-like protein 11
- ceRNA, Competing endogenous RNA
- lncRNAs, Long non-coding RNA
- mRNA, Messenger RNA
- miRNA, MicroRNA
- qRT-PCR, quantitative Real Time-Polymerase Chain Reaction
- ripk 1, Receptor-interacting serine/threonine-protein kinase 1
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miR-200b restrains EMT and aggressiveness and regulates matrix composition depending on ER status and signaling in mammary cancer. Matrix Biol Plus 2020; 6-7:100024. [PMID: 33543022 PMCID: PMC7852204 DOI: 10.1016/j.mbplus.2020.100024] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/14/2020] [Accepted: 01/14/2020] [Indexed: 02/06/2023] Open
Abstract
Secreted microRNAs (miRNAs) reside in a complex regulatory network with extracellular matrix (ECM) macromolecules, which affect cell-cell communication, therefore miRNA expression highlights its significance in several aspects of human diseases, including cancer. miRNA-mediated regulation of breast cancer has received considerable attention due to evidence that shows miRNAs to mediate estrogen receptor (ER) status, metastasis, chemoresistance and epithelial-to-mesenchymal transition (EMT). miR-200b is a pluripotent miRNA, which is inversely regulated by ERα and ERβ in mammary cancer. It has been identified as tumor suppressor and EMT inhibitor serving as a critical biomarker, as its expression in breast tumor determines the disease-free survival, thus highlighting its roles in breast cancer invasion and metastasis. The main goal of this study was to investigate the role of miR-200b in modulating the behavior of breast cancer cells with different ER status. We demonstrate that estrogen signaling through ERs reduces miR-200b expression levels in ERα-positive breast cancer cells. Moreover, miR-200b upregulation reduces the aggressive phenotype of ERβ-positive breast cancer cells by inhibiting cell invasiveness and motility, followed by ECM reorganization as well as cytoskeletal and morphological changes concluded from deep inspection of cell topography. Future investigation towards the mechanistic perspective of miR-200b effects in the behavior of aggressive mammary cancer cells appears rewarding in order to expand our understanding of miR-200b as a novel mediator beyond breast cancer diagnosis and pharmaceutical targeting.
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Key Words
- Breast cancer
- ECM, extracellular matrix
- EGFR, epidermal growth factor receptor
- EMT, epithelial-to-mesenchymal-transition
- ER, estrogen receptor
- Erk, extracellular signal-regulated kinase
- Estrogen receptors
- Extracellular matrix
- GAG, glycosaminoglycan
- GF, growth factor
- HER2, human epidermal growth factor receptor 2
- IGF-IR, insulin-like growth factor receptor type I
- IL, interleukin
- MMP, matrix metalloproteinase
- PG, proteoglycan
- PR, progesterone receptor
- RISC, RNA-induced silencing complex
- SERM, selective estrogen receptor modulator
- TGFβ, transforming growth factor beta
- miR-200b
- miRNA, microRNA
- miRNAs
- pre-miRNA, precursor miRNA
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Biomaterial-based delivery systems of nucleic acid for regenerative research and regenerative therapy. Regen Ther 2019; 11:123-130. [PMID: 31338391 PMCID: PMC6626072 DOI: 10.1016/j.reth.2019.06.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/10/2019] [Accepted: 06/25/2019] [Indexed: 12/22/2022] Open
Abstract
Regenerative medicine is a new and promising medical method aiming at treating patients with defective or dysfunctional tissues by maintaining or enhancing the biological activity of cells. The development of biomaterial-based technologies, such as cell scaffolds and carriers for drug delivery system, are highly required to promote the regenerative research and regenerative therapy. Nucleic acids are one of the most feasible factors to efficiently modify the biological activity of cells. The effective and stable delivery of nucleic acids into cells is highly required to succeed in the modification. Biomaterials-based non-viral carriers or biological carriers, like exosomes, play an important role in the efficient delivery of nucleic acids. This review introduces the examples of regenerative research and regenerative therapy based on the delivery of nucleic acids with biomaterials technologies and emphasizes their importance to accomplish regenerative medicine. Modifying the activity of cells is important for regenerative medicine. Various nucleic acids regulate gene expression to modify the activity of cells. Intracellular delivery system is vital to the nucleic acids-based modification. Biomaterials are useful for the intracellular delivery of nucleic acids.
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Key Words
- Biomaterials
- CRISPR, clustered regularly interspaced short palindromic repeats
- Cas, CRISPR-associated systems
- Cell scaffold
- DDS, drug delivery system
- Drug delivery system
- ECM, extracellular matrix
- MSC, mesenchymal stem cells
- Nucleic acids
- PEG, polyethylene glycol
- PLGA, poly(d,l-lactic acid-co-glycolic acid)
- RISC, RNA-induced silencing complex
- RNAi, RNA interferince
- Regenerative research
- Regenerative therapy
- TALEN, transcription activator-like effector nuclease
- ZFN, zinc finger nucleases
- lncRNA, long non-coding RNA
- mRNA, messenger RNA
- miRNA, microRNA
- siRNA, small interfering RNA
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Development of precision medicine approaches based on inter-individual variability of BCRP/ ABCG2. Acta Pharm Sin B 2019; 9:659-674. [PMID: 31384528 PMCID: PMC6664102 DOI: 10.1016/j.apsb.2019.01.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 12/15/2022] Open
Abstract
Precision medicine is a rapidly-developing modality of medicine in human healthcare. Based on each patient׳s unique characteristics, more accurate dosages and drug selection can be made to achieve better therapeutic efficacy and less adverse reactions in precision medicine. A patient׳s individual parameters that affect drug transporter action can be used to develop a precision medicine guidance, due to the fact that therapeutic efficacy and adverse reactions of drugs can both be affected by expression and function of drug transporters on the cell membrane surface. The purpose of this review is to summarize unique characteristics of human breast cancer resistant protein (BCRP) and the genetic variability in the BCRP encoded gene ABCG2 in the development of precision medicine. Inter-individual variability of BCRP/ABCG2 can impact choices and outcomes of drug treatment for several diseases, including cancer chemotherapy. Several factors have been implicated in expression and function of BCRP, including genetic, epigenetic, physiologic, pathologic, and environmental factors. Understanding the roles of these factors in controlling expression and function of BCRP is critical for the development of precision medicine based on BCRP-mediated drug transport.
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Key Words
- 3′-UTR, 3′-untranslated region
- 5-aza-C, 5-aza-2′-deoxycytidine
- ABCG2, ATP-binding cassette subfamily G member 2
- ALL, acute lymphocytic leukemia
- AML, acute myeloid leukemia
- AUC, area under curve
- BCRP
- BCRP, breast cancer resistant protein
- Epigenetics
- FTC, fumitremorgin C
- Gene polymorphisms
- H3K4me3, histone H3 lysine 4 trimethylation
- H3K9me3, histone H3 lysine 9 trimethylation
- H3S10P, histone H3 serine 10 phosphorylation
- HDAC, histone deacetylase
- HIF-1α, hypoxia inducible factor 1 subunit alpha
- HIV-1, human immunodeficiency virus type-1
- HMG-CoA, β-hydroxy-β-methyl-glutaryl-coenzyme A
- MDR, multidrug resistance
- MDR1, multidrug resistance 1
- NBD, nucleotide binding domain
- P-gp, P-glycoprotein
- Physiologic factors
- Precision medicine
- RISC, RNA-induced silencing complex
- SNP, Single nucleotide polymorphism
- TKI, tyrosine kinase inhibitor
- Tat, transactivator protein
- miRNA, microRNA
- siRNA, small RNA interference
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Abstract
MicroRNAs (miRNAs) are important regulators of gene function and manipulation of miRNAs is a central component of basic research. Modulation of gene expression by miRNA gain-of-function can be based on different approaches including transfection with miRNA mimics; artificial, chemically modified miRNA-like small RNAs. These molecules are intended to mimic the function of a miRNA guide strand while bypassing the maturation steps of endogenous miRNAs. Due to easy accessibility through commercial providers this approach has gained popularity, and accuracy is often assumed without prior independent testing. Our in silico analysis of over-represented sequence motifs in microarray expression data and sequencing of AGO-associated small RNAs indicate, however, that miRNA mimics may be associated with considerable side-effects due to the unwanted activity of the miRNA mimic complementary strand.
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Key Words
- AGO, Argonaute
- Argonaute protein
- GEO, Gene Expression Omnibus
- HITS-CLIP, high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation
- OAS, oligoadenylate synthetase
- PKR, protein kinase R
- RISC, RNA-induced silencing complex
- RNA interference
- TLR3, Toll-like receptor 3
- mRNA, mRNA
- miRNA, microRNA
- microRNA
- mimic
- nt, nucleotide
- off-target effect
- passenger strand
- siRNA
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Abstract
Oncogene MYC is deregulated in many human cancers, especially in lymphoma. Previously, we showed that inauhzin (INZ) activates p53 and inhibits tumor growth. However, whether INZ could suppress cancer cell growth independently of p53 activity is still elusive. Here, we report that INZ(c), a second generation of INZ, suppresses c-Myc activity and thus inhibits growth of human lymphoma cells in a p53-independent manner. INZ(c) treatment decreased c-Myc expression at both mRNA and protein level, and suppressed c-Myc transcriptional activity in human Burkitt's lymphoma Raji cells with mutant p53. Also, we showed that overexpressing ectopic c-Myc rescues the inhibition of cell proliferation by INZ(c) in Raji cells, implicating c-Myc activity is targeted by INZ(c). Interestingly, the effect of INZ(c) on c-Myc expression was impaired by disrupting the targeting of c-Myc mRNA by miRNAs via knockdown of ribosomal protein (RP) L5, RPL11, or Ago2, a subunit of RISC complex, indicating that INZ(c) targets c-Myc via miRNA pathways. These results reveal a new mechanism that INZ
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Key Words
- Dox, doxorubicin
- FACS, Fluorescence-activated cell sorting
- GTP, guanosine triphosphate
- INZ, inauhzin
- Inauhzin
- MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
- PBS, Phosphate Buffered Saline
- PI, propidium iodide
- RISC, RNA-induced silencing complex
- RP, ribosomal protein
- RPL11
- RPL5
- UTR, untranslated region
- c-Myc
- lymphoma
- microRNA
- q-RT-PCR, Real-time reverse transcription polymerase chain reaction
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Prediction of microRNA target genes using an efficient genetic algorithm-based decision tree. FEBS Open Bio 2015; 5:877-84. [PMID: 26649272 PMCID: PMC4643183 DOI: 10.1016/j.fob.2015.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 09/29/2015] [Accepted: 10/05/2015] [Indexed: 11/27/2022] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression in almost all plants and animals. They play an important role in key processes, such as proliferation, apoptosis, and pathogen-host interactions. Nevertheless, the mechanisms by which miRNAs act are not fully understood. The first step toward unraveling the function of a particular miRNA is the identification of its direct targets. This step has shown to be quite challenging in animals primarily because of incomplete complementarities between miRNA and target mRNAs. In recent years, the use of machine-learning techniques has greatly increased the prediction of miRNA targets, avoiding the need for costly and time-consuming experiments to achieve miRNA targets experimentally. Among the most important machine-learning algorithms are decision trees, which classify data based on extracted rules. In the present work, we used a genetic algorithm in combination with C4.5 decision tree for prediction of miRNA targets. We applied our proposed method to a validated human datasets. We nearly achieved 93.9% accuracy of classification, which could be related to the selection of best rules.
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Abstract
MicroRNA (miRNA) comprise a large family of non-protein coding transcripts which regulate gene expression in diverse biological pathways of both plants and animals. We recently used a systematic proteomic approach to generate a protein interactome map of the human miRNA pathway involved in miRNA biogenesis and processing. The interactome expands the number of candidate proteins in the miRNA pathway and connects the network to other cellular processes. Functional analyses identified TRIM65 and at least 3 other proteins as novel regulators of the miRNA pathway. Biochemical studies established that TRIM65 forms stable complexes with TNRC6 proteins and these molecules co-localize in P-body-like structures. Gain of function and RNAi analyses reveal that TRIM65 negatively regulates miRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. The potential molecular mechanisms which regulate TRIM65 catalytic activity are discussed.
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Key Words
- AGO, Argonaute
- AP-MS, Affinity purification coupled with mass spectrometry
- DGCR8, DiGeorge syndrome critical region gene 8
- HCIP, High confidence interacting protein
- IMP-1, IGF2 mRNA-binding protein 1
- MOV10, Moloney leukemia virus 10
- MiRNA, microRNA
- PDCD4, Programmed cell death 4
- PTEN, Phosphatase and tensin homolog
- RISC, RNA-induced silencing complex
- RNA-induced silencing complex
- TARBP2, TAR (HIV-1) RNA binding protein 2
- TNRC6
- TNRC6, Trinucleotide repeat containing 6
- TRIM65, Tripartite Motif-Containing 65
- interactome
- proteomics
- tripartite motif proteins
- ubiquitin E3 ligase
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Abstract
microRNAs (miRNAs) are non coding RNAs with different biological functions and pathological implications. Given their role as post-transcriptional gene expression regulators, they are involved in several important physiological processes like development, cell differentiation and cell signaling. miRNAs act as modulators of gene expression programs in different diseases, particularly in cancer, where they act through the repression of genes which are critical for carcinogenesis. The expression level of mature miRNAs is the result of a fine mechanism of biogenesis, carried out by different enzymatic complexes that exert their function at transcriptional and post-transcriptional levels. In this review, we will focus our discussion on the alterations in the miRNA biogenesis machinery, and its impact on the establishment and development of cancer programs.
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Key Words
- Ago2, Argonaute 2 protein
- Ars2, Arsenic Resistance protein 2
- DGCR8, DiGeorge syndrome Critical Region 8 protein
- EMT, epithelial–mesenchymal transition
- KSRP, KH-type splicing regulatory protein
- MK2, MAPK-activated protein kinase 2
- PABP, poly(A)-binding protein
- PACT, kinase R–activating protein
- PRC2, Polycomb repressor complex
- RISC, RNA-induced silencing complex
- TRBP, TAR RNA binding protein
- TUT4, terminal uridine transferase-4
- XPO5, exportin 5
- cancer
- cellular signaling
- circRNA, circular RNA
- hnRNPs, heterogeneous nuclear ribonucleoproteins
- miRNA biogenesis
- miRNAs, microRNAs
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Staphylococcal nuclease domain containing-1 (SND1) promotes migration and invasion via angiotensin II type 1 receptor (AT1R) and TGFβ signaling. FEBS Open Bio 2014; 4:353-61. [PMID: 24918049 PMCID: PMC4050181 DOI: 10.1016/j.fob.2014.03.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/13/2014] [Accepted: 03/27/2014] [Indexed: 12/29/2022] Open
Abstract
Staphylococcal nuclease domain containing-1 (SND1) is overexpressed in human hepatocellular carcinoma (HCC) patients and promotes tumorigenesis by human HCC cells. We now document that SND1 increases angiotensin II type 1 receptor (AT1R) levels by increasing AT1R mRNA stability. This results in activation of ERK, Smad2 and subsequently the TGFβ signaling pathway, promoting epithelial-mesenchymal transition (EMT) and migration and invasion by human HCC cells. A positive correlation was observed between SND1 and AT1R expression levels in human HCC patients. Small molecule inhibitors of SND1, alone or in combination with AT1R blockers, might be an effective therapeutic strategy for late-stage aggressive HCC.
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Key Words
- ACE, angiotensin-I converting enzyme
- ACE-I, ACE inhibitors
- AT1R
- AT1R, angiotensin II type 1 receptor
- EMT, epithelial–mesenchymal transition
- FDR, false discovery rate
- HCC, human hepatocellular carcinoma
- Invasion
- LP, losartan potassium
- MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
- NASH, non-alcoholic steatohepatitis
- PAI-1
- PAI-1, plasminogen activator inhibitor-1
- RISC, RNA-induced silencing complex
- SND1
- SND1, Staphylococcal nuclease domain containing-1
- TGFβ
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Olfactory discrimination training up-regulates and reorganizes expression of microRNAs in adult mouse hippocampus. ASN Neuro 2010; 2:e00028. [PMID: 20309390 PMCID: PMC2832745 DOI: 10.1042/an20090055] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2009] [Revised: 01/14/2010] [Accepted: 01/18/2010] [Indexed: 12/01/2022] Open
Abstract
Adult male mice (strain C57Bl/6J) were trained to execute nose-poke responses for water reinforcement; then they were randomly assigned to either of two groups: olfactory discrimination training (exposed to two odours with reward contingent upon correctly responding to one odour) or pseudo-training (exposed to two odours with reward not contingent upon response). These were run in yoked fashion and killed when the discrimination-trained mouse reached a learning criterion of 70% correct responses in 20 trials, occurring after three sessions (a total of ∼40 min of training). The hippocampus was dissected bilaterally from each mouse (N = 7 in each group) and profiling of 585 miRNAs (microRNAs) was carried out using multiplex RT–PCR (reverse transcription–PCR) plates. A significant global up-regulation of miRNA expression was observed in the discrimination training versus pseudo-training comparison; when tested individually, 29 miRNAs achieved significance at P = 0.05. miR-10a showed a 2.7-fold increase with training, and is predicted to target several learning-related mRNAs including BDNF (brain-derived neurotrophic factor), CAMK2b (calcium/calmodulin-dependent protein kinase IIβ), CREB1 (cAMP-response-element-binding protein 1) and ELAVL2 [ELAV (embryonic lethal, abnormal vision, Drosophila)-like; Hu B]. Analysis of miRNA pairwise correlations revealed the existence of several miRNA co-expression modules that were specific to the training group. These in vivo results indicate that significant, dynamic and co-ordinated changes in miRNA expression accompany early stages of learning.
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Key Words
- BDNF, brain-derived neurotrophic factor
- Ct, threshold cycle value
- DHPG, (S)-3,5-dihydroxyphenylglycine
- LTP, long-term potentiation
- MEF2, myocyte enhancer factor-2
- NMDA, N-methyl-d-aspartate
- RISC, RNA-induced silencing complex
- RT-PCR, reverse transcription-PCR
- TLDA, TaqMan® Low Density Arrays
- TOP, terminal oligopyrimidine
- dicer
- learning
- miRNA, microRNA
- microRNA
- olfactory discrimination
- pre-miR, miRNA small hairpin precursor
- pri-miR, primary miRNA gene transcript
- snoRNA, small nucleolar RNA
- synaptic plasticity
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