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Serum miR-181b-5p predicts ascites onset in patients with compensated cirrhosis. JHEP Rep 2021; 3:100368. [PMID: 34712934 PMCID: PMC8531668 DOI: 10.1016/j.jhepr.2021.100368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/19/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022] Open
Abstract
Background & Aims Treatment with non-selective beta-blockers (NSBBs) reduces the risk of ascites, which is the most common decompensating event in cirrhosis. This study aimed to assess the ability of a serum microRNA (miRNA) signature to predict ascites formation and the hemodynamic response to NSBBs in compensated cirrhosis. Methods Serum levels of miR-452-5p, miR-429, miR-885-5p, miR-181b-5p, and miR-122-5p were analyzed in patients with compensated cirrhosis (N = 105). Hepatic venous pressure gradient (HVPG) was measured at baseline, after intravenous propranolol, and 1 year after randomization to NSBBs (n = 52) or placebo (n = 53) (PREDESCI trial). miRNAs were analyzed at baseline and at 1 year. Results Nineteen patients (18%) developed ascites, of whom 17 developed ascites after 1 year. miR-181b-5p levels at 1 year, but not at baseline, were higher in patients that developed ascites. The AUC of miR-181b-5p at 1 year to predict ascites was 0.7 (95% CI 0.59–0.78). miR-429 levels were lower at baseline in acute HVPG responders to NSBBs (AUC 0.65; 95% CI, 0.53–0.76), but levels at baseline and at 1 year were not associated with the HVPG response to NSBBs at 1 year. Conclusions Serum miR-181b-5p is a promising non-invasive biomarker to identify patients with compensated cirrhosis at risk of ascites development. Lay summary Ascites marks the transition from the compensated to decompensated stage in cirrhosis and indicates a worsening in prognosis. There are currently no easily accessible tools to identify patients with compensated cirrhosis at risk of developing ascites. We evaluated the levels of novel molecules termed microRNAs in the blood of patients with compensated cirrhosis and observed that miR-181b-5p can predict which patients are going to develop ascites. miR-181b-5p appears to be a useful serum biomarker to anticipate ascites onset. Low serum miR-181b-5p indicates low risk of ascites in compensated cirrhosis. Low serum miR-429 reflects acute hemodynamic response to non-selective beta-blockers.
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MicroRNA-regulated transcriptome analysis identifies four major subtypes with prognostic and therapeutic implications in prostate cancer. Comput Struct Biotechnol J 2021; 19:4941-4953. [PMID: 34527198 PMCID: PMC8433071 DOI: 10.1016/j.csbj.2021.08.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
MicroRNA (miRNA) deregulation plays a critical role in the heterogeneous development of prostate cancer (PCa) by tuning mRNA levels. Herein, we aimed to characterize the molecular features of PCa by clustering the miRNA-regulated transcriptome with non-negative matrix factorization. Using 478 PCa samples from The Cancer Genome Atlas, four molecular subtypes (S-I, S-II, S-III, and S-IV) were identified and validated in two merged microarray and RNAseq datasets with 656 and 252 samples, respectively. Interestingly, the four subtypes showed distinct clinical and biological features after comprehensive analyses of clinical features, multiomic profiles, immune infiltration, and drug sensitivity. S-I is basal/stem/mesenchymal-like and immune-excluded with marked transforming growth factor β, epithelial-mesenchymal transition and hypoxia signals, increased sensitivity to olaparib, and intermediate prognosis. S-II is luminal/metabolism-active and responsive to androgen deprivation therapy with frequent TMPRSS2-ERG fusion and a good prognosis. S-III is characterized by moderate proliferative and metabolic activity, sensitivity to taxane-based chemotherapy, and intermediate prognosis. S-IV is highly proliferative with moderate EMT and stemness, frequent deletions of TP53, PTEN and RB, and the poorest prognosis; it is also immune-inflamed and sensitive to anti-PD-L1 therapy. Overall, based on miRNA-regulated gene profiles, this study identified four distinct PCa subtypes that could improve risk stratification at diagnosis and provide therapeutic guidance.
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Key Words
- ADT, androgen deprivation therapy
- AR, androgen receptor
- AUC, Area under the dose-response curve
- BCR, biochemical recurrence
- CAFs, cancer-associated fibroblasts
- CCLs, cancer cell lines
- CTLA-4, cytotoxic T-lymphocyte associated protein-4
- DEmiRs, differentially expressed miRNAs
- DFS, disease-free survival
- EMT, epithelial-mesenchymal transition
- FDR, false discovery rate
- GEO, Gene Expression Omnibus
- GEP, gene expression profile
- GO, Gene Ontology
- GSEA, Gene Set Enrichment Analysis
- Heterogeneity
- ICB, immune checkpoint blockade
- IFN, interferon
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MDSCs, myeloid-derived suppressor cells
- MIRcor, miRNA-correlated
- Molecular subtypes
- NEPC, neuroendocrine prostate cancer
- NMF, non-negative matrix factorization
- NTP, Nearest template prediction
- OS, overall survival
- PCa, prostate cancer
- PD-1, programmed cell death protein-1
- PD-L1, programmed death-ligand 1
- Prostate cancer
- SCNAs, somatic copy number alterations
- SubMap, Subclass mapping
- TCGA, The Cancer Genome Atlas
- TGFβ, transforming growth factor β
- TMB, tumor mutation burden
- TNAs, tumor neoantigens
- Tregs, regulatory T cells
- k-NN, K-nearest neighbor
- mCRPC, metastatic castration-resistant prostate cancer
- miRNAs
- miRNAs, microRNAs
- ssGSEA, single-sample gene set enrichment analysis
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Novel vectors and approaches for gene therapy in liver diseases. JHEP Rep 2021; 3:100300. [PMID: 34159305 PMCID: PMC8203845 DOI: 10.1016/j.jhepr.2021.100300] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/23/2021] [Accepted: 04/18/2021] [Indexed: 12/13/2022] Open
Abstract
Gene therapy is becoming an increasingly valuable tool to treat many genetic diseases with no or limited treatment options. This is the case for hundreds of monogenic metabolic disorders of hepatic origin, for which liver transplantation remains the only cure. Furthermore, the liver contains 10-15% of the body's total blood volume, making it ideal for use as a factory to secrete proteins into the circulation. In recent decades, an expanding toolbox has become available for liver-directed gene delivery. Although viral vectors have long been the preferred approach to target hepatocytes, an increasing number of non-viral vectors are emerging as highly efficient vehicles for the delivery of genetic material. Herein, we review advances in gene delivery vectors targeting the liver and more specifically hepatocytes, covering strategies based on gene addition and gene editing, as well as the exciting results obtained with the use of RNA as a therapeutic molecule. Moreover, we will briefly summarise some of the limitations of current liver-directed gene therapy approaches and potential ways of overcoming them.
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Key Words
- AAT, α1-antitrypsin
- AAV, adeno-associated virus
- AHP, acute hepatic porphyrias
- AIP, acute intermittent porphyria
- ALAS1, aminolevulic synthase 1
- APCs, antigen-presenting cells
- ASGCT, American Society of Gene and Cell Therapy
- ASGPR, asialoglycoprotein receptor
- ASOs, antisense oligonucleotides
- Ad, adenovirus
- CBS, cystathionine β-synthase
- CN, Crigel-Najjar
- CRISPR, clustered regularly interspaced short palindromic repeats
- CRISPR/Cas9, CRISPR associated protein 9
- DSBs, double-strand breaks
- ERT, enzyme replacement therapy
- FH, familial hypercholesterolemia
- FSP27, fat-specific protein 27
- GO, glycolate oxidase
- GSD1a, glycogen storage disorder 1a
- GT, gene therapy
- GUSB, β-glucuronidase
- GalNAc, N-acetyl-D-galactosamine
- HDAd, helper-dependent adenovirus
- HDR, homology-directed repair
- HT, hereditary tyrosinemia
- HemA/B, haemophilia A/B
- IDS, iduronate 2-sulfatase
- IDUA, α-L-iduronidase
- IMLD, inherited metabolic liver diseases
- ITR, inverted terminal repetition
- LDH, lactate dehydrogenase
- LDLR, low-density lipoprotein receptor
- LNP, Lipid nanoparticles
- LTR, long terminal repeat
- LV, lentivirus
- MMA, methylmalonic acidemia
- MPR, metabolic pathway reprograming
- MPS type I, MPSI
- MPS type VII, MPSVII
- MPS, mucopolysaccharidosis
- NASH, non-alcoholic steatohepatitis
- NHEJ, non-homologous end joining
- NHPs, non-human primates
- Non-viral vectors
- OLT, orthotopic liver transplantation
- OTC, ornithine transcarbamylase
- PA, propionic acidemia
- PB, piggyBac
- PCSK9, proprotein convertase subtilisin/kexin type 9
- PEG, polyethylene glycol
- PEI, polyethyleneimine
- PFIC3, progressive familial cholestasis type 3
- PH1, Primary hyperoxaluria type 1
- PKU, phenylketonuria
- RV, retrovirus
- S/MAR, scaffold matrix attachment regions
- SB, Sleeping Beauty
- SRT, substrate reduction therapy
- STK25, serine/threonine protein kinase 25
- TALEN, transcription activator-like effector nucleases
- TTR, transthyretin
- UCD, urea cycle disorders
- VLDLR, very-low-density lipoprotein receptor
- WD, Wilson’s disease
- ZFN, zinc finger nucleases
- apoB/E, apolipoprotein B/E
- dCas9, dead Cas9
- efficacy
- gene addition
- gene editing
- gene silencing
- hepatocytes
- immune response
- lncRNA, long non-coding RNA
- miRNAs, microRNAs
- siRNA, small-interfering RNA
- toxicity
- viral vectors
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Recent advances in nanomedicines for the treatment of ischemic stroke. Acta Pharm Sin B 2021; 11:1767-1788. [PMID: 34386320 PMCID: PMC8343119 DOI: 10.1016/j.apsb.2020.11.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/27/2020] [Accepted: 09/13/2020] [Indexed: 12/20/2022] Open
Abstract
Ischemic stroke is a cerebrovascular disease normally caused by interrupted blood supply to the brain. Ischemia would initiate the cascade reaction consisted of multiple biochemical events in the damaged areas of the brain, where the ischemic cascade eventually leads to cell death and brain infarction. Extensive researches focusing on different stages of the cascade reaction have been conducted with the aim of curing ischemic stroke. However, traditional treatment methods based on antithrombotic therapy and neuroprotective therapy are greatly limited for their poor safety and treatment efficacy. Nanomedicine provides new possibilities for treating stroke as they could improve the pharmacokinetic behavior of drugs in vivo, achieve effective drug accumulation at the target site, enhance the therapeutic effect and meanwhile reduce the side effect. In this review, we comprehensively describe the pathophysiology of stroke, traditional treatment strategies and emerging nanomedicines, summarize the barriers and methods for transporting nanomedicine to the lesions, and illustrate the latest progress of nanomedicine in treating ischemic stroke, with a view to providing a new feasible path for the treatment of cerebral ischemia.
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Key Words
- AEPO, asialo-erythropoietin
- APOE, apolipoprotein E
- BBB, blood‒brain barrier
- BCECs, brain capillary endothelial cells
- Blood‒brain barrier
- CAT, catalase
- COX-1, cyclooxygenase-1
- CXCR-4, C-X-C chemokine receptor type 4
- Ce-NPs, ceria nanoparticles
- CsA, cyclosporine A
- DAMPs, damage-associated molecular patterns
- GFs, growth factors
- GPIIb/IIIa, glycoprotein IIb/IIIa
- HMGB1, high mobility group protein B1
- Hb, hemoglobin
- ICAM-1, intercellular adhesion molecule-1
- IL-1β, interleukin-1β
- IL-6, interleukin-6
- Ischemic cascade
- LFA-1, lymphocyte function-associated antigen-1
- LHb, liposomal Hb
- MCAO, middle cerebral artery occlusion
- MMPs, matrix metalloproteinases
- MSC, mesenchymal stem cell
- NF-κB, nuclear factor-κB
- NGF, nerve growth factor
- NMDAR, N-methyl-d-aspartate receptor
- NOS, nitric oxide synthase
- NPs, nanoparticles
- NSCs, neural stem cells
- Nanomedicine
- Neuroprotectant
- PBCA, poly-butylcyanoacrylate
- PCMS, poly (chloromethylstyrene)
- PEG, poly-ethylene-glycol
- PEG-PLA, poly (ethylene-glycol)-b-poly (lactide)
- PLGA NPs, poly (l-lactide-co-glycolide) nanoparticles
- PSD-95, postsynaptic density protein-95
- PSGL-1, P-selectin glycoprotein ligand-1
- RBCs, red blood cells
- RES, reticuloendothelial system
- RGD, Arg-Gly-Asp
- ROS, reactive oxygen species
- Reperfusion
- SDF-1, stromal cell-derived factor-1
- SHp, stroke homing peptide
- SOD, superoxide dismutase
- SUR1-TRPM4, sulfonylurea receptor 1-transient receptor potential melastatin-4
- Stroke
- TEMPO, 2,2,6,6-tetramethylpiperidine-1-oxyl
- TIA, transient ischemic attack
- TNF-α, tumor necrosis factor-α
- Thrombolytics
- cRGD, cyclic Arg-Gly-Asp
- e-PAM-R, arginine-poly-amidoamine ester
- iNOS, inducible nitric oxide synthase
- miRNAs, microRNAs
- nNOS, neuron nitric oxide synthase
- siRNA, small interfering RNA
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Review on circular RNAs and new insights into their roles in cancer. Comput Struct Biotechnol J 2021; 19:910-928. [PMID: 33598105 PMCID: PMC7851342 DOI: 10.1016/j.csbj.2021.01.018] [Citation(s) in RCA: 164] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) are a very interesting class of conserved single-stranded RNA molecules derived from exonic or intronic sequences by precursor mRNA back-splicing. Unlike canonical linear RNAs, circRNAs form covalently closed, continuous stable loops without a 5'end cap and 3'end poly(A) tail, and therefore are resistant to exonuclease digestion. The majority of circRNAs are highly abundant, and conserved across different species with a tissue or developmental-stage-specific expression. circRNAs have been shown to play important roles as microRNA sponges, regulators of gene splicing and transcription, RNA-binding protein sponges and protein/peptide translators. Emerging evidence reveals that circRNAs function in various human diseases, particularly cancers, and may function as better predictive biomarkers and therapeutic targets for cancer treatment. In consideration of their potential clinical relevance, circRNAs have become a new research hotspot in the field of tumor pathology. In the present study, the current understanding of the biogenesis, characteristics, databases, research methods, biological functions subcellular distribution, epigenetic regulation, extracellular transport and degradation of circRNAs was discussed. In particular, the multiple databases and methods involved in circRNA research were first summarized, and the recent advances in determining the potential roles of circRNAs in tumor growth, migration and invasion, which render circRNAs better predictive biomarkers, were described. Furthermore, future perspectives for the clinical application of circRNAs in the management of patients with cancer were proposed, which could provide new insights into circRNAs in the future.
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Key Words
- AML, acute myloid leukemia
- BSJ, back-splice junction
- Biomarker
- CLL, chronic lymphocytic leukemia
- CML, chronic myeloid leukemia
- CRC, colorectal cancer
- Cancer
- Circular RNAs
- EIciRNAs, exon–intron RNAs
- EMT, epithelial-mesenchymal transition
- Functions
- GC, gastric cancer
- HCC, hepatocellular carcinoma
- ISH, in situ hybridization
- LUAD, lung adenocarcinoma
- MER, miRNA response elements
- MM, multiple myeloma
- NSCLC, non-small cell lung cancer
- PCR, polymerase chain reaction
- PDAC, pancreatic ductal adenocarcinoma
- RBP, RNA-binding protein
- RNA, ribonucleic acid
- RNase, ribonuclease
- RT-PCR, reverse transcription-PCR
- TNM, tumor node metastases
- UTR, untranslated regions
- ccRCC, clear cell renal cell carcinoma
- ceRNAs, endogenous RNAs
- ciRNAs, circular intronic RNAs
- ciRS-7, circular RNA sponge for miR-7
- circRNAs, circular RNAs
- ecircRNAs, exonic circular RNAs
- lncRNAs, long ncRNA
- miRNAs, microRNAs
- ncRNAs, noncoding RNAs
- qPCR, quantitative PCR
- rRNA, ribosomal RNA
- siRNAs, small interfering RNAs
- snRNA, small nuclear RNA
- tricRNAs, tRNA intronic circRNAs
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Application of "omics" sciences to the prediction of bone metastases from breast cancer: State of the art. J Bone Oncol 2020; 26:100337. [PMID: 33240786 PMCID: PMC7672315 DOI: 10.1016/j.jbo.2020.100337] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/23/2020] [Accepted: 10/29/2020] [Indexed: 11/28/2022] Open
Abstract
Breast cancer (BC) is the first cause of cancer-related death in women. Most patients with advanced BC develop bone metastases (BM). Omics technologies have been applied to identify putative BM “predicting” biomarkers. Prospective studies are needed before any clinical application of such biomarkers.
Breast cancer (BC) is the most frequent malignancy and the first cause of cancer-related death in women. The majority of patients with advanced BC develop skeletal metastases which may ultimately lead to serious complications, termed skeletal-related events, that often dramatically impact on quality of life and survival. Therefore, the identification of biomarkers able to stratify BC patient risk to develop bone metastases (BM) is fundamental to define personalized diagnostic and therapeutic strategies, possibly at the earliest stages of the disease. In this regard, the advent of “omics” sciences boosted the investigation of several putative biomarkers of BC osteotropism, including deregulated genes, proteins and microRNAs. The present review revisits the current knowledge on BM development in BC and the most recent studies exploring potential BM-predicting biomarkers, based on the application of omics sciences to the study of primary breast malignancies.
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Key Words
- ADAMTS1, a disintegrin-like and metalloproteinase with thrombospondin type 1
- ALP, alkaline phosphatase
- BALP (BSAP), bone-specific alkaline phosphatase
- BC, breast cancer
- BM, bone metastases
- BOLCs, breast osteoblast-like cells
- BTM, bone turnover markers
- Biomarkers
- Bone metastases
- Breast cancer
- CAPG, capping-protein
- CCN3, cellular communication network factor 3
- CDH11, cadherin-11
- CNV, copy number variation
- CTGF, connective tissue-derived growth factor
- CTSK, cathepsin K
- CTX, C-telopeptide
- CXCL, C-X-C-ligand
- CXCR, C–X–C motif chemokine receptor
- DEGs, differentially expressed genes
- DOCK4, dedicator of cytokinesis protein 4
- DPD, deoxypyridoline
- DTC, disseminated tumour cells
- EMT, epithelial-to-mesenchymal transition
- ER, estrogen receptor
- ERRα, estrogen-related receptor alpha
- FAK, focal adhesion kinase
- FGF, fibroblast growth factor
- FST, follistatin
- GIPC1, PDZ domain-containing protein member 1
- HR, hazard ratio
- Her, human epidermal growth factor
- ICAM-1, intercellular adhesion molecule 1
- IGF, insulin-like growth factor
- IHC, immunohistochemistry
- IL, interleukin
- LC/MS/MS, liquid chromatography/mass spectrometry/mass spectrometry
- MAF, v-maf avian muscolo aponeurotic fibro-sarcoma oncogene homolog
- MDA-MB, MD Anderson metastatic BC
- MMP1, matrix metalloproteinase-1
- NTX, N-telopeptide
- OPG, osteoprotegerin
- Omics sciences
- Osteotropism
- P1CP, pro-collagen type I C-terminal
- P1NP, pro-collagen type I N-terminal
- PDGF, platelet-derived growth factor
- PRG1, proteoglycan-1
- PTH-rP, parathyroid hormone-related protein
- PYD, pyridoline
- PgR, progesterone receptor
- PlGF, placental growth factor
- RANK, receptor activator of nuclear factor к-B
- RT-PCR, real time-PCR
- SILAC-MS, stable isotope labelling by amino acids in cell culture-mass spectrometry
- SNPs, single nucleotide polymorphisms
- SPP1, osteopontin
- SREs, skeletal-related events
- TCGA, the cancer genome atlas
- TGF-β, transforming growth factor beta
- TNF-α, tumor necrosis factor-α
- TRACP-5b, tartrate resistant acid phosphatase-5b
- VEGF, vascular endothelial growth factor
- ZNF217, zinc-finger protein 217
- miRNAs, microRNAs
- ncRNAs, noncoding RNA
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Long non-coding RNA BLACAT1 expedites osteosarcoma cell proliferation, migration and invasion via up-regulating SOX12 through miR-608. J Bone Oncol 2020; 25:100314. [PMID: 33005563 PMCID: PMC7519359 DOI: 10.1016/j.jbo.2020.100314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 12/26/2022] Open
Abstract
BLACAT1 promotes cell proliferation, migration and invasion, and dampens cell apoptosis in OS. BLACAT1 sponges miR-608 in OS. SOX12 is the target of miR-608. BLACA1 promotes OS cell growth and migration via targeting miR-608/SOX12 axis.
Background Osteosarcoma is the most common type of bone malignancy. Increasing evidence indicated that long non-coding RNAs (lncRNAs) possess multiple functions in the development of cancer and can be used as indicators of prognosis and diagnosis. LncRNA BLACAT1 has been found to promote the proliferation of breast cancer cells. However, the role of BLACAT1 in osteosarcoma remains largely unknown. Methods QRT-PCR analysis was employed to evaluate mRNA expressions. Western blot was performed to measure relevant protein level. Colony formation and EdU assays were conducted to certify proliferative ability. TUNEL assay was finalized to assess apoptotic cells. Wound-healing and transwell assays were utilized for the exploration of migrating and invasive abilities. The subcellular distribution of BLACAT1 was studied by nucleus-cytoplasm separation assay. Relevant mechanical experiments were combined to elucidate molecular relationship between molecules. Results BLACAT1 was highly expressed in osteosarcoma. BLACAT1 promoted the proliferation and migration of osteosarcoma cells. BLACAT1 acted as a sponge for miR-608 to augment the expression of Sex determining region Y-box protein 12 (SOX12), the direct target of miR-608. Further, inhibiting miR-608 recovered the repressive effect of silenced BLACAT1 on the malignant behaviors of osteosarcoma cells. Conclusion This study highlighted the contribution of BLACAT1/miR-608/SOX12 axis to the progression of osteosarcoma, suggesting novel targets for osteosarcoma therapy.
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Key Words
- ANOVA, analysis of variance
- ATCC, American type culture collection
- BLACAT1
- DMEM, Dulbecco’s modified Eagle’s medium
- FBS, fetal bovine serum
- FISH, Fluorescence in situ hybridization
- HRP, horseradish peroxidase
- Mut, mutant
- OS, osteosarcoma
- Osteosarcoma
- PVDF, polyvinylidene fluoride
- RIPA, radioimmunoprecipitation assay
- RT-qPCR, RNA extraction and quantitative real-time polymerase chain reaction
- SD, standard deviation
- SDS-PAGE, sulphate-polyacrylamide gel electrophoresis
- SOX, sex-determining region Y (SRY)-box
- SOX12
- SOX12, sex determining region Y-box protein 12
- WT, wild-type
- ceRNAs, competing endogenous RNAs
- lncRNAs, long non-coding RNAs
- mRNA, messenger RNA
- miR-608
- miRNAs, microRNAs
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Early microRNA indicators of PPARα pathway activation in the liver. Toxicol Rep 2020; 7:805-815. [PMID: 32642447 PMCID: PMC7334544 DOI: 10.1016/j.toxrep.2020.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/01/2020] [Accepted: 06/19/2020] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNA species that play key roles in post-transcriptional regulation of gene expression. MiRNAs also serve as a promising source of early biomarkers for different environmental exposures and health effects, although there is limited information linking miRNA changes to specific target pathways. In this study, we measured liver miRNAs in male B6C3F1 mice exposed to a known chemical activator of the peroxisome proliferator-activated receptor alpha (PPARα) pathway, di(2-ethylhexyl) phthalate (DEHP), for 7 and 28 days at concentrations of 0, 750, 1500, 3000, or 6000 ppm in feed. At the highest dose tested, DEHP altered 61 miRNAs after 7 days and 171 miRNAs after 28 days of exposure, with 48 overlapping miRNAs between timepoints. Analysis of these 48 common miRNAs indicated enrichment in PPARα–related targets and other pathways related to liver injury and cancer. Four of the 10 miRNAs exhibiting a clear dose trend were linked to the PPARα pathway: mmu-miRs-125a-5p, -182−5p, -20a−5p, and -378a−3p. mmu-miRs-182−5p and -378a−3p were subsequently measured using digital drop PCR across a dose range for DEHP and two related phthalates with weaker PPARα activity, di-n-octyl phthalate and n-butyl benzyl phthalate, following 7-day exposures. Analysis of mmu-miRs-182−5p and -378a−3p by transcriptional benchmark dose analysis correctly identified DEHP as having the greatest potency. However, benchmark dose estimates for DEHP based on these miRNAs (average 163; range 126−202 mg/kg-day) were higher on average than values for PPARα target genes (average 74; range 29−183 mg/kg-day). These findings identify putative miRNA biomarkers of PPARα pathway activity and suggest that early miRNA changes may be used to stratify chemical potency.
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Key Words
- AIC, Akaike Information Criterion
- ALT, alanine aminotransferase
- AOP, adverse outcome pathway
- AST, aspartate aminotransferase
- Acox1, acyl-Coenzyme A oxidase 1
- Adverse outcome pathway (AOP)
- AhR, aryl hydrocarbon receptor
- BBP, n-butyl benzyl phthalate
- BMD, benchmark dose
- BMDA, apical-based benchmark dose
- BMDL, BMD lower confidence interval
- BMDT, transcriptional-based benchmark dose
- BMR, benchmark response
- BROD, benzyloxyresorufin O-debenzylation
- Benchmark dose (BMD)
- Biomarkers
- CAR, constitutive androstane receptor
- DEGs, differentially expressed genes
- DEHP, di (2-thylhexyl) phthalate
- DEmiRs, differentially expressed miRNAs
- DNOP, di-n-octyl phthalate
- EPA, U.S. Environmental Protection Agency
- EROD, ethoxyresorufin O-dealkylation
- GEO, Gene Expression Omnibus
- HCA, hepatocellular adenoma
- HCC, hepatocellular carcinoma
- Hepatocellular carcinoma
- IPA, Ingenuity Pathway Analysis
- Liver toxicity
- MOA, mode of action
- MicroRNAs
- Mode of action (MOA)
- Nrf2, nuclear receptor erythroid 2-like 2
- POD, point-of-departure
- PPARα, peroxisome proliferator-activated receptor alpha
- PROD, pentoxyresorufin O-depentylation
- PXR, pregnane X receptor
- Peroxisome proliferator-activated receptor alpha (PPARα)
- Phthalate
- SDH, sorbitol dehydrogenase
- TMM, trimmed mean of M-values
- ddPCR, droplet digital polymerase chain reaction
- mRNA, messenger RNA
- miRNAs, microRNAs
- mtDNA, mitochondrial
- rRNA, ribosomal RNA
- smallRNA-seq, small RNA sequencing
- tRNA, transfer RNA
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Long filopodia and tunneling nanotubes define new phenotypes of breast cancer cells in 3D cultures. Matrix Biol Plus 2020; 6-7:100026. [PMID: 33543024 PMCID: PMC7852320 DOI: 10.1016/j.mbplus.2020.100026] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer cell invasion into the surrounding extracellular matrix (ECM) takes place when cell-cell junctions are disrupted upon epithelial-to-mesenchymal transition (EMT). Both cancer cell-stroma and cell-cell crosstalk are essential to support the continuous tumor invasion. Cancer cells release microvesicles and exosomes containing bioactive molecules and signal peptides, which are recruited by neighboring cells or carried to distant sites, thus supporting intercellular communication and cargo transfer. Besides this indirect communication mode, cancer cells can develop cytoplasmic intercellular protrusions or tunneling nanotubes (TNTs), which allow the direct communication and molecular exchange between connected distinct cells. Using scanning electron microscopy (SEM) we show for the first time that MDA-MB-231 (high metastatic potential) and shERβ MDA-MB-231 (low metastatic potential) breast cancer cells cultured on fibronectin and collagen type I or 17β-estradiol (E2) develop TNTs and very long flexible filopodia. Interestingly, the less aggressive shERβ MDA-MB-231 cells treated with E2 in 3D collagen matrix showed the highest development of TNTs and filopodia. TNTs were often associated to adhering exosomes and microvesicles surfing from one cell to another, but no filopodia exhibited vesicle-like cytoplasmic structures on their surface. Moreover, E2 affected the expression of matrix macromolecules and cell effectors mostly in the presence of ERβ. Our novel data highlights the significance of matrix substrates and the presence of E2 and ERβ in the formation of cellular protrusion and the production of surface structures, defining novel phenotypes that unravel nodal reports for breast cancer progression.
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Key Words
- 3D, three dimensional
- Breast cancer
- CAFs, cancer-associated fibroblasts
- E2, 17β-estradiol
- ECM, extracellular matrix
- EMT, epithelial-to-mesenchymal transition
- ER, estrogen receptor
- Estrogen receptor beta
- FGF, fibroblast growth factor
- FIB-SEM, focused-ion beam scanning electron microscopy
- Filopodia
- HGF, hepatocyte growth factor
- Intercellular communication
- MMPs, matrix metalloproteinases
- SEM, scanning electron microscope
- Scanning electron microscopy
- TGFβ, transforming growth factor beta
- TNTs, tunneling nanotubes
- Tunneling nanotubes
- miRNAs, microRNAs
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10
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Comprehensive biological function analysis of lncRNAs in hepatocellular carcinoma. Genes Dis 2020; 8:157-167. [PMID: 33997162 PMCID: PMC8099694 DOI: 10.1016/j.gendis.2019.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/16/2019] [Accepted: 12/31/2019] [Indexed: 12/19/2022] Open
Abstract
Thousands of long non-coding RNAs (lncRNAs) have been discovered in human genomes by gene chip, next-generation sequencing, and/or other methods in recent years, which represent a significant subset of the universal genes involved in a wide range of biological functions. An abnormal expression of lncRNAs is associated with the growth, invasion, and metastasis of various types of human cancers, including hepatocellular carcinoma (HCC), which is an aggressive, highly malignant, and invasive tumor, and a poor prognosis in China. With a more in-depth understanding of lncRNA research for HCC and the emergence of new molecular-targeted therapies, the diagnosis, treatment, and prognosis of HCC will be considerably improved. Therefore, this review is expected to provide recommendations and directions for future lncRNA research for HCC.
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11
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Hydrophobic sand is a viable method of urine collection from the rat for extracellular vesicle biomarker analysis. Mol Genet Metab Rep 2019; 21:100505. [PMID: 31467851 PMCID: PMC6710715 DOI: 10.1016/j.ymgmr.2019.100505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Previously we have shown in rats a new method of urine collection, hydrophobic sand, to be an acceptable alternate in place of the traditional method using metabolic cages. Hydrophobic sand is non-toxic, induces similar or lower levels of stress in the rat, and does not contaminate clinical urine markers nor metal concentrations in collected samples (Hoffman et al., 2017 and 2018). Urine is often used in humans and many animal models as a readily-attainable biosample which contains proteins and microRNAs (miRNAs) within extracellular vesicles (EVs) that can be isolated to indicate changes in health. In order to ensure hydrophobic sand did not in any way contaminate or disrupt the extraction and analysis of these EVs and miRNAs, we used urine samples from the same 8 rats in the within-subjects crossover experiment comparing hydrophobic sand and metabolic cage collection methods. We isolated EVs and miRNAs from the urine set and examined their quantity and quality between the urine collection methods. We found no significant differences in particle size, particle concentration, total RNA, or the type and abundance of miRNAs contained within the urine EVs due to urine collection method, suggesting hydrophobic sand represents an easy-to-use, non-invasive method to collect rodent urine for EVs and biomarker studies.
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12
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Circular RNAs in the cardiovascular system. Noncoding RNA Res 2018; 3:1-11. [PMID: 30159434 PMCID: PMC6084836 DOI: 10.1016/j.ncrna.2018.02.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/16/2018] [Accepted: 02/22/2018] [Indexed: 02/06/2023] Open
Abstract
Until recently considered as rare, circular RNAs (circRNAs) are emerging as important regulators of gene expression. They are ubiquitously expressed and represent a novel branch of the family of non-coding RNAs. Recent investigations showed that circRNAs are regulated in the cardiovascular system and participate in its physiological and pathological development. In this review article, we will provide an overview of the role of circRNAs in cardiovascular health and disease. After a description of the biogenesis of circRNAs, we will summarize what is known of the expression, regulation and function of circRNAs in the cardiovascular system. We will then address some technical aspects of circRNAs research, discussing how artificial intelligence may aid in circRNAs research. Finally, the potential of circRNAs as biomarkers of cardiovascular disease will be addressed and directions for future research will be proposed.
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Key Words
- Artificial intelligence
- Biomarker
- CRISPR, clustered regularly interspaced short palindromic repeats
- CV, cardiovascular
- Cardiovascular disease
- Cardiovascular system
- Circular RNAs
- DCM, dilated cardiomyopathy
- EMT, epithelial-mesenchymal transition
- Non-coding RNAs
- RNA-seq, RNA sequencing
- RPAD, RNase R treatment followed by polyadenylation and poly(A)+ RNA depletion
- RT-qPCR, reverse transcription quantitative polymerase chain reaction
- circRNAs, circular RNAs
- lncRNAs, long non-coding RNAs
- miRNAs, microRNAs
- ncRNAs, non-coding RNAs
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13
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Non-coding RNAs are promising targets for stem cell-based cancer therapy. Noncoding RNA Res 2017; 2:83-87. [PMID: 30159424 PMCID: PMC6096406 DOI: 10.1016/j.ncrna.2017.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/19/2017] [Accepted: 05/19/2017] [Indexed: 12/19/2022] Open
Abstract
The term “non-coding RNA” (ncRNA) is generally used to indicate RNA that does not encode a protein and includes several classes of RNAs, such as microRNA and long non-coding RNA. Several lines of evidence suggest that ncRNAs appear to be involved in a hidden layer of biological procedures that control various levels of gene expression in physiology and development including stem cell biology. Stem cells have recently constituted a revolution in regenerative medicine by providing the possibility of generating suitable cell types for therapeutic use. Here, we review the recent progress that has been made in elaborating the interaction between ncRNAs and tissue/cancer stem cells, discuss related technical and biological challenges, and highlight plausible solutions to surmount these difficulties. This review particularly emphasises the involvement of ncRNAs in stem cell biology and in vivo modulation to treat and cure specific pathological disorders especially in cancer. We believe that a better understanding of the molecular machinery of ncRNAs as related to pluripotency, cellular reprogramming, and lineage-specific differentiation is essential for progress of cancer therapy.
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Key Words
- CD, cytosine deaminase
- CSC, cancer stem cell
- EMT, epithelial to mesenchymal transition
- ESCs, embryonic stem cells
- MET, mesenchymal to epithelial transition
- MSCs, mesenchymal stem cells
- Non-coding RNA
- Stem cell-based therapy
- T-UCR, transcribed ultraconserved region
- Transcribed ultraconserved region
- iPSCs, induced pluripotent stem cells
- lincRNA, long inverting non-coding RNA
- lncRNA, long ncRNA
- miRNAs, microRNAs
- ncRNAs, non-coding RNAs
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14
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Transcriptional regulation of microRNA-100, -146a, and -150 genes by p53 and NFκB p65/RelA in mouse striatal STHdh(Q7)/ Hdh(Q7) cells and human cervical carcinoma HeLa cells. RNA Biol 2016; 12:457-77. [PMID: 25757558 DOI: 10.1080/15476286.2015.1014288] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
MicroRNA (miRNA) genes generally share many features common to those of protein coding genes. Various transcription factors (TFs) and co-regulators are also known to regulate miRNA genes. Here we identify novel p53 and NFκB p65/RelA responsive miRNAs and demonstrate that these 2 TFs bind to the regulatory sequences of miR-100, -146a and -150 in both mouse striatal and human cervical carcinoma cells and regulate their expression. p53 represses the miRNAs while NFκB p65/RelA induces them. Further, we provide evidence that exogenous p53 inhibits NFκB p65/RelA activity by reducing its nuclear content and competing with it for CBP binding. This suggests for the existence of a functional cross-talk between the 2 TFs in regulating miRNA expression. Moreover, promoter occupancy assay reveals that exogenous p53 excludes NFκB p65/RelA from its binding site in the upstream sequence of miR-100 gene thereby causing its repression. Thus, our work identifies novel p53 and NFκB p65/RelA responsive miRNAs in human and mouse and uncovers possible mechanisms of co-regulation of miR-100. It is to be mentioned here that cross-talks between p53 and NFκB p65/RelA have been observed to define the outcome of several biological processes and that the pro-apoptotic effect of p53 and the pro-survival functions of NFκB can be largely mediated via the biological roles of the miRNAs these TFs regulate. Our observation with cell lines thus provides an important platform upon which further work is to be done to establish the biological significance of such co-regulation of miRNAs by p53 and NFκB p65/RelA.
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Key Words
- ChIP, Chromatin immunoprecipitation
- Co-IP, Co-immunoprecipitation
- NFκB p65/RelA
- NFκB, nuclear factor kappa-light-chain-enhancer of activated B cells
- RLU, Relative light unit
- RNA POL II, RNA Polymerase II
- RNA POL III, RNA Polymerase III
- RT-PCR, Reverse transcription polymerase chain reaction
- TF, Transcriptional factor
- TFBS
- Transcription factor binding site
- WB, Western blot
- miR-100
- miR-146a
- miR-150
- miRNA gene regulation
- miRNAs, microRNAs
- microRNA
- p53
- p53, tumor protein 53
- p65, RELA, RELA
- transcription factor
- v-rel avian reticuloendotheliosis viral oncogene homolog A
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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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16
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miR-214-mediated downregulation of RNF8 induces chromosomal instability in ovarian cancer cells. Cell Cycle 2015; 13:3519-28. [PMID: 25483088 DOI: 10.4161/15384101.2014.958413] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Defective DNA damage response (DDR) is frequently associated with carcinogenesis. Abrogation of DDR leads to chromosomal instability, a most common characteristic of tumors. However, the molecular mechanisms underlying regulation of DDR are still elusive. The ubiquitin ligase RNF8 mediates the ubiquitination of γH2AX and recruits 53BP1 and BRCA1 to DNA damage sites which promotes DDR and inhibits chromosomal instability. Though RNF8 is a key player involved in DDR, regulation of its expression is still poorly understood. Here, we show that miR-214 could abrogate DDR by repressing RNF8 expression through direct binding to 3'-untranslated region (3' UTR) of RNF8 mRNA in human ovarian cancer cells. Antagonizing miR-214 by expressing its inhibitors in A2780 cells significantly increased RNF8 expression and thus promoted DNA damage repair. Consistent with the role of miR-214 in regulating RNF8 expression, the impaired DNA repair induced by miR-214 overexpression can be rescued by overexpressing RNF8 mRNA lacking the 3' UTR. Together, our results indicate that down-regulation of RNF8 mediated by miR-214 impedes DNA damage response to induce chromosomal instability in ovarian cancers, which may facilitate the understanding of mechanisms underlying chromosomal instability.
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17
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Computational analysis of miRNA-target community network reveals cross talk among different metabolisms. GENOMICS DATA 2015; 5:292-6. [PMID: 26484271 PMCID: PMC4584007 DOI: 10.1016/j.gdata.2015.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/26/2015] [Indexed: 02/03/2023]
Abstract
To date, only a few conserved miRNAs have been predicted in hexaploid (AABBDD) bread wheat and till now community behavior among miRNA is still in dark. Analysis of publically available 1287279 ESTs from NCBI resulted 262 putative pre-miRNAs and 39 novel mature miRNAs. A total 22,468 targets were identified on 21 chromosomes. MiRNA target community was identified for genomes with different levels of cross talks. Gene ontology of these community targets suggests their differential involvement in different metabolisms along with common and stringent involvement in nitrogen metabolism.
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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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Epigenetic analysis of sporadic and Lynch-associated ovarian cancers reveals histology-specific patterns of DNA methylation. Epigenetics 2015; 9:1577-87. [PMID: 25625843 PMCID: PMC4622692 DOI: 10.4161/15592294.2014.983374] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Diagnosis and treatment of epithelial ovarian cancer is challenging due to the poor understanding of the pathogenesis of the disease. Our aim was to investigate epigenetic mechanisms in ovarian tumorigenesis and, especially, whether tumors with different histological subtypes or hereditary background (Lynch syndrome) exhibit differential susceptibility to epigenetic inactivation of growth regulatory genes. Gene candidates for epigenetic regulation were identified from the literature and by expression profiling of ovarian and endometrial cancer cell lines treated with demethylating agents. Thirteen genes were chosen for methylation-specific multiplex ligation-dependent probe amplification assays on 104 (85 sporadic and 19 Lynch syndrome-associated) ovarian carcinomas. Increased methylation (i.e., hypermethylation) of variable degree was characteristic of ovarian carcinomas relative to the corresponding normal tissues, and hypermethylation was consistently more prominent in non-serous than serous tumors for individual genes and gene sets investigated. Lynch syndrome-associated clear cell carcinomas showed the highest frequencies of hypermethylation. Among endometrioid ovarian carcinomas, lower levels of promoter methylation of RSK4, SPARC, and HOXA9 were significantly associated with higher tumor grade; thus, the methylation patterns showed a shift to the direction of high-grade serous tumors. In conclusion, we provide evidence of a frequent epigenetic inactivation of RSK4, SPARC, PROM1, HOXA10, HOXA9, WT1-AS, SFRP2, SFRP5, OPCML, and MIR34B in the development of non-serous ovarian carcinomas of Lynch and sporadic origin, as compared to serous tumors. Our findings shed light on the role of epigenetic mechanisms in ovarian tumorigenesis and identify potential targets for translational applications.
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20
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Epigenetic regulation of drug metabolism and transport. Acta Pharm Sin B 2015; 5:106-12. [PMID: 26579435 PMCID: PMC4629221 DOI: 10.1016/j.apsb.2015.01.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/04/2015] [Accepted: 01/06/2015] [Indexed: 12/18/2022] Open
Abstract
The drug metabolism is a biochemical process on modification of pharmaceutical substances through specialized enzymatic systems. Changes in the expression of drug-metabolizing enzyme genes can affect drug metabolism. Recently, epigenetic regulation of drug-metabolizing enzyme genes has emerged as an important mechanism. Epigenetic regulation refers to heritable factors of genomic modifications that do not involve changes in DNA sequence. Examples of such modifications include DNA methylation, histone modifications, and non-coding RNAs. This review examines the widespread effect of epigenetic regulations on genes involved in drug metabolism, and also suggests a network perspective of epigenetic regulation. The epigenetic mechanisms have important clinical implications and may provide insights into effective drug development and improve safety of drug therapy.
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Key Words
- CAR, constitutive androstane receptor
- DNA methylation
- DNMTs, DNA methyltransferases
- Drug metabolism
- Epigenetics
- H3K27me3, histone 3 lysine 27 trimethylation
- H3K36me3, histone 3 lysine 36 trimethylation
- H3K4me1, histone 3 lysine 4 monomethylation
- H3K4me2, histone 3 lysine 4 dimethylation
- H3K4me3, histone 3 lysine 4 trimethylation
- H3K9me2, histone 3 lysine 9 dimethylation
- H3K9me3, histone 3 lysine 9 trimethylation
- HATs, histone acetyltransferases
- HDAC, histone deacetylases
- Histone modification
- Non-coding RNA
- P450s, cytochrome P450s
- SULTs, sulfotransferases
- TSS, transcription start sites
- Transporter
- UGTs, UDP-glucuronosyltransferases
- UTR, untranslated region
- lncRNAs, long non-coding RNAs
- miRNAs, microRNAs
- ncRNAs, non-coding RNAs
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21
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Identification of post-transcriptional regulatory networks during myeloblast-to-monocyte differentiation transition. RNA Biol 2015; 12:690-700. [PMID: 25970317 PMCID: PMC4615388 DOI: 10.1080/15476286.2015.1044194] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/17/2015] [Accepted: 04/20/2015] [Indexed: 01/24/2023] Open
Abstract
Treatment of leukemia cells with 1,25-dihydroxyvitamin D3 may overcome their differentiation block and lead to the transition from myeloblasts to monocytes. To identify microRNA-mRNA networks relevant for myeloid differentiation, we profiled the expression of mRNAs and microRNAs associated to the low- and high-density ribosomal fractions in leukemic cells and in their differentiated monocytic counterpart. Intersection between mRNAs shifted across the fractions after treatment with putative target genes of modulated microRNAs showed a series of molecular networks relevant for the monocyte cell fate determination, as for example the post-transcriptional regulation of the Polo-like kinase 1 (PLK1) by miR-22-3p and let-7e-5p.
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Key Words
- AGO2, argonaute 2
- AML
- AML, acute myeloid leukemia
- ECL methods, enhanced chemiluminescence methods
- GAPDH, glyceraldehyde 3-phosphate dehydrogenase
- GFP, green fluorescent protein
- HPCs, haematopoietic progenitor cells
- KPNA2, karyopherin α, 2
- NBT assay, nitroblue tetrazolium assay
- PLK1
- PLK1, polo-like kinase 1
- PMSF, phenylmethylsulfonyl fluoride
- RAB10, member RAS oncogene family 10
- RAB5C, member RAS oncogene family 5C
- RT-qPCR, quantitative reverse transcription polymerase chain reaction
- SF2A1, splicing factor 2A1
- TFs, transcription factors
- VitD3, 1,25-dihydroxyvitamin D3
- miRNAs, microRNAs
- microRNAs
- myeloid differentiation
- ribosomal/polysomal fractions
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