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@#Introduction: Prediction and identification of miRNAs target genes are crucial for understanding the biology of miRNAs. Amidst reported long-coding RNA (lncRNA), the microRNA 195-497 cluster host gene (MIR497HG) regulation is mediated by multiple non-coding RNAs (ncRNAs) such as microRNAs (miRNAs). MIR497HG has been implicated as a tumour suppressor in various cancers. However, the impact of MIR497HG and its derived miRNAs is largely unknown and still needs to be further explored. Employing an experimental approach is often challenging since some lncRNAs are difficult to identify and isolate by the current isolation technique. Thus, bioinformatic tools are introduced to aid these problems. This study sought to search and identify the miRNAs targeting the 3’untranslated region (3’UTR) of MIR497HG. Methods: Here, bioinformatic tools were adopted to identify a unique list of miRNAs that potentially target the 3’UTR of MIR497HG. Results: A total of 57 candidate miRNAs that target the 3’UTR of MIR497HG were extracted using the miRDB. Meanwhile, STarMir predicted 291 miRNAs that potentially target the 3’UTR of MIR497HG. A common list of 36 miRNAs was obtained using the Venny 2.1.0 and further narrowed down using the LogitProb score of StarMir. Finally, a total 4 miRNAs (hsa-miR-3182, hsa-miR-7156-5p, hsa-miR-452-3p and hsa-miR-2117) were identified. The mRNA target of identified miRNAs was identified by TargetScan. Finally, Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of mRNA target was done using Enrichr. Conclusion: This finding could be useful in understanding the complex interaction between MIR497HG and its regulatory miRNA. In addition, a comparative analysis of computational miRNA-target predictions is provided in this study would potentially lay the foundations for miRNAs to be used for biomarkers in cancer research.
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Liver fibrosis is a key step in the progression of chronic liver diseases to liver cirrhosis and even liver cancer. In recent years， a large number of studies have shown the necessity of intervening in the process of liver fibrosis， and various anti-liver fibrosis drugs and active ingredients have been discovered. Non-coding RNAs also play an important role in the process of liver fibrosis， and searching for upstream non-coding RNAs that can regulate signaling pathways can provide new insights for anti-liver fibrosis treatment. This article introduces the process of liver fibrosis mediated by the TGF-β， Wnt/β-catenin， PI3K/Akt/mTOR， NF-κβ， Hippo， and MAPK signaling pathways， lists the latest anti-liver fibrosis drugs or active components in each signaling pathway， and summarizes the research advances in anti-liver fibrosis targets and drugs mediated by related non-coding RNAs， so as to provide new research ideas and treatment methods for anti-liver fibrosis treatment.
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Objective:To investigate the relationship between long non-coding RNA (lncRNA) DHRS4-AS1 and disease-free survival in osteosarcoma patients and the mechanisms of its effect on proliferation and migration of osteosarcoma cells in vitro.Methods:The data of DHRS4-AS1 transcriptome levels and survival status of osteosarcoma patients in GEPIA database were collected since the database was established, and the patients were divided into high DHRS4-AS1 expression group and low DHRS4-AS1 expression group based on the median DHRS4-AS1 transcriptome level, with 59 cases in each group, and the Kaplan-Meier method was used to analyze the disease-free survival of the two groups. Real-time fluorescence quantitative polymerase chain reaction (qRT-PCR) was used to detect the expression of DHRS4-AS1 in osteosarcoma cell lines MG-63, HOS, 143B, U-2OS, Saos2 and normal osteoblast cell line hFOB1.19, and the osteosarcoma cell line with the lowest DHRS4-AS1 expression level was selected for subsequent experiments. The plasmid carrying DHRS4-AS1 sequence and the plasmid carrying negative control sequence were transfected into the selected osteosarcoma cells as DHRS4-AS1 group and control group. CCK-8 method was used to detect the proliferation of each group of cells, and the absorbance value was used as the cell proliferation ability; cell scratch assay was used to detect the migration of each group of cells. The bioinformatics website starBase V2.0 was used to predict the target genes of DHRS4-AS1, and the dual luciferase reporter gene assay was used to verify the targeting relationship between DHRS4-AS1 and the target genes. The expression levels of target genes and downstream genes of osteosarcoma cells in control group and DHRS4-AS1 group were detected by qRT-PCR and Western blotting.Results:Survival analysis showed that the disease-free survival of osteosarcoma patients in the high DHRS4-AS1 expression group in GEPIA database was superior to that of the low DHRS4-AS1 expression group ( P < 0.001). Compared with normal osteoblastic hFOB1.19 cells, the expression level of DHRS4-AS1 was low in all osteosarcoma cells (all P < 0.01), with the lowest expression level of DHRS4-AS1 in U-2OS cells ( P < 0.001). Cell proliferation ability was reduced in U-2OS cells of the DHRS4-AS1 group after 1, 2, 3 and 4 d of culture compared with the control group (all P < 0.05). The migration rate of U-2OS cells in the DHRS4-AS1 group was lower than that in the control group [(31±6)% vs. (63±4)%, t = 4.38, P = 0.005]. starBase V2.0 website predicted that DHRS4-AS1 complementarily bound to miRNA-411-3p (miR-411-3p); dual luciferase reporter gene assay showed that miR-411-3p overexpression reduced the luciferase activity of the wild-type DHRS4-AS1 reporter gene ( P < 0.001), but had no effect on the luciferase activity of the mutant DHRS4-AS1 reporter gene ( P > 0.05). qRT-PCR showed that the relative expression of miR-411-3p in U-2OS cells of the DHRS4-AS1 group was low (0.22±0.06 vs. 1.06±0.23, t = 3.55, P = 0.012) and the relative expression of metastasis suppressor MTSS1 mRNA was high (5.58±1.03 vs. 1.06±0.22, t = 4.28, P = 0.005) compared with the control group; Western blotting showed that MTSS1 expression was elevated, and the expression levels of cell proliferation phenotype proteins CDK3 and cyclin C and cell migration phenotype proteins ZEB2 and KLF8 were low. Conclusions:Osteosarcoma patients with high expression of lncRNA DHRS4-AS1 have better disease-free survival, and its expression is low in osteosarcoma cell lines. DHRS4-AS1 may promote MTSS1 gene expression and inhibit cell proliferation and migration by targeting and down-regulating miR-411-3p expression in osteosarcoma cells.
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Objective:To investigate the correlation between Piwi-interacting RNA (piRNA) and diabetic nephropathy (DN).Methods:The differential expression profiles of piRNAs in renal tissues of patients with DN (experimental group) and renal tissues adjacent to tumors of patients with renal tumors (control group) were detected by high-throughput sequencing. The biological function of differentially expressed piRNAs was described by gene ontology and Kyoto encyclopedia of genes and genomes enrichment analysis. Real-time fluorescence quantitative PCR was used to detect the serum expression level of target piRNAs in patients with DN. Spearman correlation analysis was used to analyze the correlation between serum target piRNAs and clinical indexes of patients with DN.Results:The results of high throughput sequencing showed that there were 127 differentially expressed piRNAs between DN group and control group, with screening condition of |log 2(fold changes)|≥2 and P<0.05. Among them, there were 99 up-regulated piRNAs and 28 down-regulated piRNAs. The top 5 up-regulated piRNAs were piRNA-hsa-161686, piRNA-hsa-349255, piRNA-hsa-355720, piRNA-hsa-151229 and piRNA-hsa-154959, respectively. The top 5 down-regulated piRNAs were piRNA-hsa-1929960, piRNA-hsa-174194, piRNA-hsa- 148658, piRNA-hsa-172594 and piRNA-hsa-172421, respectively. The PCR verification results of 3 up-regulated genes and 3 down-regulated genes with low P values and high expression levels showed that serum expression level of piRNA-hsa-77976 was significantly down-regulated in patients with DN ( P=0.028), which was consistent with that of sequencing, while the expression levels of other genes were inconsistent with the sequencing results or had no statistical significance. Bioinformatics analysis results predicted that significantly differentially expressed piRNAs might participate in the regulation of DN through Rap1, Ras, PI3K-Akt and axon guiding pathways. The results of correlation analysis showed that the expression level of piRNA-hsa-77976 was negatively correlated with blood urea nitrogen ( r=-0.584, P=0.028), serum creatinine ( r=-0.637, P=0.014), cystatin C ( r=-0.738, P=0.003) and β2 microglobulin ( r=-0.822, P<0.001), and positively correlated with estimated glomerular filtration rate ( r=0.661, P=0.010). Conclusion:The differential expression of piRNA is closely related to DN, and may be used as a new biomarker for the diagnosis and prognosis of DN.
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Preeclampsia is a unique complication in the second and third trimesters of pregnancy, but its pathogenesis remains unclear and the early diagnosis and treatment methods are yet to be perfect. Termination of pregnancy at the right time is the only way to prevent its deterioration and avoid adverse pregnancy outcomes. In recent years, with the in-depth research, non-coding RNAs has been found to be involved in many important physiological and pathological processes such as proliferation and apoptosis of trophoblast cells and these non-coding RNAs can regulate each other to form an intricate and competitive endogenous RNA regulatory network. This article will introduce the biological roles of non-coding RNAs in regulating the invasion and proliferation of trophoblast cells in patients with preeclampsia and possible regulatory relationship between non-coding RNAs. Furthermore, the potential clinical value of non-coding RNAs as diagnostic biomarkers for preeclampsia and therapeutic targets are also elaborated.
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Pathological cardiac hypertrophy serves as a significant foundation for cardiac dysfunction and heart failure. Recently, growing evidence has revealed that microRNAs (miRNAs) play multiple roles in biological processes and participate in cardiovascular diseases. In the present research, we investigate the impact of miRNA-34c-5p on cardiac hypertrophy and the mechanism involved. The expression of miR-34c-5p was proved to be elevated in heart tissues from isoprenaline (ISO)-infused mice. ISO also promoted miR-34c-5p level in primary cultures of neonatal rat cardiomyocytes (NRCMs). Transfection with miR-34c-5p mimic enhanced cell surface area and expression levels of foetal-type genes atrial natriuretic factor (Anf) and β-myosin heavy chain (β-Mhc) in NRCMs. In contrast, treatment with miR-34c-5p inhibitor attenuated ISO-induced hypertrophic responses. Enforced expression of miR-34c-5p by tail intravenous injection of its agomir led to cardiac dysfunction and hypertrophy in mice, whereas inhibiting miR-34c-5p by specific antagomir could protect the animals against ISO-triggered hypertrophic abnormalities. Mechanistically, miR-34c-5p suppressed autophagic flux in cardiomyocytes, which contributed to the development of hypertrophy. Furthermore, the autophagy-related gene 4B (ATG4B) was identified as a direct target of miR-34c-5p, and miR-34c-5p was certified to interact with 3' untranslated region of Atg4b mRNA by dual-luciferase reporter assay. miR-34c-5p reduced the expression of ATG4B, thereby resulting in decreased autophagy activity and induction of hypertrophy. Inhibition of miR-34c-5p abolished the detrimental effects of ISO by restoring ATG4B and increasing autophagy. In conclusion, our findings illuminate that miR-34c-5p participates in ISO-induced cardiac hypertrophy, at least partly through suppressing ATG4B and autophagy. It suggests that regulation of miR-34c-5p may offer a new way for handling hypertrophy-related cardiac dysfunction.
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The immune checkpoint blockade (ICB) targeting on PD-1/PD-L1 has shown remarkable promise in treating cancers. However, the low response rate and frequently observed severe side effects limit its broad benefits. It is partially due to less understanding of the biological regulation of PD-L1. Here, we systematically and comprehensively summarized the regulation of PD-L1 from nuclear chromatin reorganization to extracellular presentation. In PD-L1 and PD-L2 highly expressed cancer cells, a new TAD (topologically associating domain) (chr9: 5,400,000-5,600,000) around CD274 and CD273 was discovered, which includes a reported super-enhancer to drive synchronous transcription of PD-L1 and PD-L2. The re-shaped TAD allows transcription factors such as STAT3 and IRF1 recruit to PD-L1 locus in order to guide the expression of PD-L1. After transcription, the PD-L1 is tightly regulated by miRNAs and RNA-binding proteins via the long 3'UTR. At translational level, PD-L1 protein and its membrane presentation are tightly regulated by post-translational modification such as glycosylation and ubiquitination. In addition, PD-L1 can be secreted via exosome to systematically inhibit immune response. Therefore, fully dissecting the regulation of PD-L1/PD-L2 and thoroughly detecting PD-L1/PD-L2 as well as their regulatory networks will bring more insights in ICB and ICB-based combinational therapy.
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Sorafenib, as the first-line treatment drug for advanced hepatocellular carcinoma (HCC), can effectively improve the prognosis of patients with HCC, but sorafenib resistance has become a major obstacle to the therapeutic outcome of HCC. Recent studies have shown that non-coding RNA plays a key role in sorafenib resistance in HCC. This article summarizes that non-coding RNA regulates the sensitivity of HCC to sorafenib by inducing the autophagy of hepatoma cells, promoting the proliferation of liver cancer stem cells, promoting the EMT process of hepatoma cells, inhibiting the apoptosis of hepatoma cells, and regulating the microenvironment of liver cancer tissue. It is pointed out that the molecular mechanism of non-coding RNA in regulating sorafenib resistance in HCC has potential clinical significance in overcoming sorafenib resistance in HCC.
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Liver fibrosis is the initial stage of the development of various chronic liver diseases into liver cirrhosis and is a reversible process. As a subset of extracellular vesicles that can carry active substances such as proteins, lipids, and RNA, exosomes are involved in intercellular signal communication and have attracted more and more attention in recent years. Studies have shown that non-coding RNAs in exosomes play an important role in the development and progression of liver fibrosis. This article discusses the mechanism of action of exosome long non- coding RNAs (including MALAT1, H19, GAS5, MEG3, PVT1, and P21), exosome short non-coding RNAs (including micro-RNA, small nucleolus RNA, PIWI-interacting RNA, and small interference RNA), and exosome circular RNA in the development and progression of liver fibrosis, and it is concluded that exosomes from different sources (such as hepatocytes and cholangiocytes) carrying non-coding RNAs mainly affect the activation, proliferation, migration, and transformation of hepatic stellate cells. In-depth studies of exosome non-coding RNAs in the future are expected to find potential new targets for the treatment of liver fibrosis.
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Liver fibrosis is the initial stage of the development of various chronic liver diseases into liver cirrhosis and is a reversible process. As a subset of extracellular vesicles that can carry active substances such as proteins, lipids, and RNA, exosomes are involved in intercellular signal communication and have attracted more and more attention in recent years. Studies have shown that non-coding RNAs in exosomes play an important role in the development and progression of liver fibrosis. This article discusses the mechanism of action of exosome long non- coding RNAs (including MALAT1, H19, GAS5, MEG3, PVT1, and P21), exosome short non-coding RNAs (including micro-RNA, small nucleolus RNA, PIWI-interacting RNA, and small interference RNA), and exosome circular RNA in the development and progression of liver fibrosis, and it is concluded that exosomes from different sources (such as hepatocytes and cholangiocytes) carrying non-coding RNAs mainly affect the activation, proliferation, migration, and transformation of hepatic stellate cells. In-depth studies of exosome non-coding RNAs in the future are expected to find potential new targets for the treatment of liver fibrosis.
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Bronchopulmonary dysplasia (BPD) is a common chronic respiratory complication in preterm infants without fully understand the mechanism or effective treatment,which could significantly affect the survival rate and prognosis of these infants.Studies have confirmed that epigenetic mechanisms,including histone modification,non-coding RNA and DNA methylation may play an essential role in the onset and development of BPD.And most related epigenetic changes are reversible,which might serve as a potential target for BPD treatment.Therefore,further studies on epigenetics will shed light on a better understanding of the pathogenesis,prevention,and treatment of BPD.
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A large number of studies in recent years have shown that long non-coding RNAs (lncRNAs) play an important regulatory role in the progression of liver fibrosis. This article briefly describes the definition, classification, and biological functions of lncRNAs and summarizes recent reports on the regulatory role of lncRNAs in liver fibrosis by acting as competitive endogenous RNA, including downregulated maternally expressed gene 3, growth arrest-specific transcript 5, and long intergenic non-coding RNA-p21 and upregulated lung adenocarcinoma-associated transcript 1, lncRNA-activated by transforming growth factor beta, plasmacytoma variant translocation 1, homeobox transcript antisense RNA, lncRNA-H19, and small nuclear RNA host gene 7, so as to provide insights into the diagnosis of liver fibrosis, the screening of therapeutic targets, and the development of clinical treatment regimens for the reversal of liver fibrosis.
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Bronchopulmonary dysplasia (BPD) is a common chronic respiratory complication in preterm infants without fully understand the mechanism or effective treatment, which could significantly affect the survival rate and prognosis of these infants. Studies have confirmed that epigenetic mechanisms, including histone modification, non-coding RNA and DNA methylation may play an essential role in the onset and development of BPD. And most related epigenetic changes are reversible, which might serve as a potential target for BPD treatment. Therefore, further studies on epigenetics will shed light on a better understanding of the pathogenesis, prevention, and treatment of BPD.
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ObjectiveTo screen out the key intergenic long non-coding RNAs (lncRNAs) in cholangiocarcinoma (CCA) and their association with patient prognosis. MethodsCCA expression and clinical data were obtained from The Cancer Genome Atlas (TCGA). High-throughput gene expression data in GSE107943 dataset were obtained from the Gene Expression Omnibus (GEO). R software was used to analyze differentially expressed genes and determine significantly differentially expressed lncRNAs between tumor and normal samples, and the key lncRNAs were screened out. The receiver operating characteristic (ROC) curve was used to analyze the value of gene expression in the diagnosis of CCA; the Kaplan-Meier survival curves were used to analyze prognosis; Gene Set Enrichment Analysis (GSEA) was used to investigate significantly enriched pathways; quantitative real-time PCR was used to verify gene expression in clinical samples. ResultsA total of 451 upregulated lncRNAs and 154 downregulated lncRNAs in both TCGA and GSE107943 dataset were screened out. The lncRNA RP11-488L18.10 in TCGA and GSE107943 dataset was highly abundant in tumor tissue. Based on TCGA and GSE107943 dataset, the ROC curve analysis of the association between lncRNA RP11-488L18.10 expression and CCA showed that the expression of lncRNA RP11-488L18.10 had an area under the ROC curve of 1 in TCGA (P＜0.000 1) and 0.9469 in GSE107943 (P＜0.000 1). In TCGA, the high expression of lncRNA RP11-488L18.10 significantly predicted overall survival rate (P=0.016) and recurrence-free survival rate (P=0.017) in patients with CCA; in GSE107943, the high expression of lncRNA RP11-488L18.10 significantly predicted overall survival rate (P=0.023) and recurrence-free survival rate (P=0.005) in patients with CCA. LncRNA RP11-488L18.10 was significantly positively correlated with MCM2. Compared with the adjacent tissue, CCA tissue had high expression of lncRNA RP11-488L18.10 (P=0.010) and MCM2 (P=0.023). ConclusionLncRNA RP11-488L18.10 is closely associated with the development and prognosis of CCA and thus may become a target for the diagnosis and treatment of CCA.
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Pregnane X receptor (PXR) is the major regulator of xenobiotic metabolism. PXR itself is controlled by various signaling molecules including glucocorticoids. Moreover, negative feed-back regulation has been proposed at the transcriptional level. We examined the involvement of the 3'-untranslated region (3'-UTR) of mRNA and microRNAs in PXR- and glucocorticoid receptor (GR)-mediated regulation of gene expression. PXR ligands were found to significantly downregulate mRNA expression in a set of 14 human hepatocyte cultures. Similarly, PXR was downregulated by PCN in the C57/BL6 mice liver. In mechanistic studies with the full-length 3'-UTR cloned into luciferase reporter or expression vectors, we showed that the 3'-UTR reduces PXR expression. From the miRNAs tested, miR-18a-5p inhibited both expression and gene induction. Importantly, we observed significant upregulation of miR-18a-5p expression 6 h after treatment with the PXR ligand rifampicin, which indicates a putative mechanism underlying negative feed-back regulation in hepatic cells. Additionally, glucocorticoids upregulated expression not only through the promoter region but also 3'-UTR regulation, which likely involves downregulation of miR-18a-5p. We conclude that miR-18a-5p is involved in the down-regulation of expression by its ligands and in the upregulation of mRNA expression by glucocorticoids in hepatic cells.
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Stanniocalcin-1 (STC1) is secreted by the variety of tissues having a major role in the regulation of calcium ions in the involuting mammary gland. The present work aims to sequence and structural characterization as well as expression profiling of STC1 gene in buffalo. Polymorphism identified in the 3-untranslated region (UTR) was analysed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) genotyping in riverine and swamp buffaloes. Expression profiling of STC1 was performed in different lactation stages of mammary gland and peripheral blood mononuclear cells to study the impact of 3'-UTR polymorphism on its expression. Different polymorphic sites were detected in the entire coding and noncoding regions of riverine and swamp buffaloes, including two INDELs. An identified polymorphic nucleotide locus A324G, having target sites for two miRNAs, namely bta-miR-2382 and bta-miR-1343, reported in cattle, was genotyped by PCR-RFLP to reveal variable allelic distribution among swamp and riverine buffaloes. Gene expression profiling across buffalo mammary tissues representing different lactation stages showed maximum expression of the STC1 gene in the involuting mammary gland. Ruminants’ specific genetic variation has been observed in STC1 and its implication in buffalo mammary gland involution as well as coregulation of gene expression throughmiRNA binding in the 3'-UTR is suggested.
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A large amount of non-coding RNA are found existing in eukaryotic transcriptome, which play an important role in regulating the expression of genes as well as participating in physiological and pathological process of various cells.In recent years,the research of ncRNA in diagnosis of breast cancer is extremely hot. In this review, the research of three types of peripheral blood ncRNAs as breast cancer diagnostic biomarkers were reviewed, including microRNA(miRNA), long non-coding RNA(lncRNA), and circular RNA(circRNA).Also,the prospect of ncRNA in clinical research and translational medicine of breast cancer was mentioned, in order to provide a new idea for breast cancer with the discovery of diagnostic markers in early detection and the monitoring of diagnosis and treatment process.
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Objective@#To sequence the 3′UTR of enterovirus 71 strains, investigate its foundation and impact in virulence by constructing a 3′UTR-replaced recombinant cDNA infectious clone.@*Methods@#Viral RNA of EV-A71 isolated viruses were extracted, and the nucleotide analysis was performed after sequencing. The 3′UTR of a full-length infectious clone of SDLY107 strain was replaced by its corresponding part of SDLY1 strain, and then the recombinant virus was constructed and identified.@*Results@#The nine isolated strains were classified into sub-genotype C4a of enterovirus (EV)-A71 by analysis, and nucleotide sequence homology for 3′UTR were 94%-100%. 3′UTR of EV-A71 strains may be associated with its pathogenicity. Identification of the rescued virus by sequencing and indirect immunofluorescence confirmed the successful construction of infectious recombinant virus.@*Conclusions@#Sequence analysis indicated that the 3′UTR may be involved in the pathogenicity of EV-A71. The recombinant virus SDLY107(1-3′UTR) was rescued successfully. Our study may provide evidence for further research on the influence of 3′UTR on the virulence of enterovirus 71.
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A large amount of non-coding RNA are found existing in eukaryotic transcriptome, which play an important role in regulating the expression of genes as well as participating in physiological and pathological process of various cells.In recent years,the research of ncRNA in diagnosis of breast cancer is extremely hot. In this review, the research of three types of peripheral blood ncRNAs as breast cancer diagnostic biomarkers were reviewed, including microRNA(miRNA), long non-coding RNA(lncRNA), and circular RNA(circRNA).Also,the prospect of ncRNA in clinical research and translational medicine of breast cancer was mentioned, in order to provide a new idea for breast cancer with the discovery of diagnostic markers in early detection and the monitoring of diagnosis and treatment process.
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Heart failure (HF) is a severe or advanced stage of heart disease with high mortality and readmission rates. The detection of biomarkers plays an important role in the diagnosis, treatment and clinical management of HF. In addition to the traditional biomarkers, the non-coding RNA markers such as miRNA, circRNA, and lncRNA have also shown better future applications in the diagnosis and differential diagnosis of HF, the severity and prognosis assessment, the risk assessment of cardiovascular events after discharge in patients with HF. These biomarkers will also contribute to personalized clinical management of HF.