Role of long non-coding RNAs in metabolic control

Bioactive alkaloidal and phenolic phytochemicals as promising epidrugs for diabetes mellitus 2: A review of recent development

Type 2 diabetes (T2D) remains a major chronic metabolic disorder affecting hundreds of millions of the global population, mostly among adults, engendering high rates of morbidity and mortality. It is characterized by complex aetiologies including insulin deficiency and resistance, and hyperglycemia, and these significantly constitute therapeutic challenges. Several pathways have been implicated in its pathophysiology and treatment including the epigenetic regulatory mechanism, notably, deoxyribonucleic acid (DNA) methylation/demethylation, histone modification, non-coding ribonucleic acid (ncRNA) modulation and other relevant pathways. Many studies have recently documented the implications of phytochemicals on the aforementioned biomarkers in the pathogenesis and treatment of T2D. In this review, the cellular and molecular mechanisms of the epigenetic effects of some bioactive alkaloidal and phenolic phytochemicals as potential therapeutic alternatives for T2D have been overviewed from the recent literature (2019-2024). From the survey, the natural product-based compounds, C1-C32 were curated as potent epigenetic modulators for T2D. Their cellular and molecular mechanisms of anti-T2D activities with relevant epigenetic biomarkers were revealed. Although, more comprehensive experimental analyses are observably required for validating their activity and toxicological indices. Thus, perspectives and challenges were enumerated for such demanding future translational studies. The review reveals advances in scientific efforts towards reversing the global trend of T2D through epigenetic phytotherapeutics.

Long non-coding RNA TINCR suppresses growth and epithelial-mesenchymal transition by inhibiting Wnt/β-catenin signaling pathway in human pancreatic cancer PANC-1 cells: Insights from in vitro and in vivo studies

There is increasing evidence that long non-coding RNAs (lncRNAs) play a crucial role in the development and progression of malignant tumors, particularly pancreatic cancer. In this study, the influence of the lncRNA TINCR on the behavior of human pancreatic cancer cells was investigated with the aim of deciphering its role in growth, migration, and invasion. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to investigate TINCR expression in pancreatic cancer cells. Ectopic expression of TINCR in PANC-1 cells was induced to evaluate the effects on cell viability and apoptosis, examining the apoptotic genes Bax and Bcl-2. Migration and invasion assays were used to measure the impact of TINCR on these cellular processes. In vivo studies using a xenograft mouse model examined the effects of TINCR on tumor growth, epithelial-to-mesenchymal transition (EMT) markers, and the Wnt/β-catenin signaling pathway. PANC-1 cells showed strikingly low TINCR expression compared to other pancreatic cancer cell lines. Ectopic TINCR expression reduced the viability of PANC-1 cells primarily by inducing apoptosis, as evidenced by increased Bax and decreased Bcl-2 expression. Overexpression of TINCR significantly increased the percentage of apoptotic cells. It also decreased the migration and invasion ability of PANC-1 cells, as demonstrated in wound healing and transwell assays. In addition, overexpression of TINCR-suppressed proteins is associated with the Wnt/β-catenin signaling pathway in PANC-1 cells. In the xenograft mouse model, overexpression of TINCR inhibited tumor growth, EMT markers, and proteins associated with the Wnt/β-catenin pathway. This study sheds light on the tumour-suppressive role of TINCR in PANC-1 cells and suggests its potential as a therapeutic target. These results shed light on the molecular mechanisms underlying the impact of TINCR on pancreatic cancer and offer promising opportunities for innovative therapeutic strategies to improve outcomes in this serious malignancy.

The interaction between MALAT1 and TUG1 with dietary fatty acid quality indices on visceral adiposity index and body adiposity index

We aimed to investigate the interaction between the transcript levels of taurine-upregulated gene 1 (TUG1) and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and the Cholesterol-Saturated Fat Index (CSI) in relation to the visceral adiposity index (VAI) and body adiposity index (BAI). This cross-sectional study involved 346 women classified as obese and overweight, aged between 18 and 48 years. Dietary intake and the quality of dietary fat were assessed using a validated and reliable 147-item semi-quantitative food frequency questionnaire, with the Cholesterol-Saturated Fat Index (CSI) used as an indicator. Transcription levels of MALAT1 and TUG1 were evaluated through real-time polymerase chain reaction following the criteria outlined in the Minimum Information for Publication of Quantitative standards. Serum profiles were measured using standard protocols. We observed a positive association between transcription level of MALAT1 and VAI in both crude (β = 3.646, 95% CI 1.950-5.341, p < 0.001) and adjusted (β = 8.338, 95% CI 6.110-10.566, p < 0.001) models. Furthermore, after adjusting for confounders, a significant positive interaction was noted between MALAT1 expression and CSI on BAI (β: 0.130, 95% CI 0.019, 0.240, p = 0.022), with a marginal positive interaction observed on VAI (β: 0.718, 95% CI - 0.028, 1.463, p = 0.059). It seems that there may be a positive interaction between MALAT1 transcription level and CSI on VAI and BAI among overweight and obese women. However, no associations were seen between TUG1 mRNA level and the above-mentioned outcomes. Further functional studies are still required to elucidate this concept.

The Role of Genetic Variants in the Long Non-Coding RNA Genes MALAT1 and H19 in the Pathogenesis of Childhood Obesity

Long non-coding RNAs (lncRNAs) play important roles in the maintenance of metabolic homeostasis. Recently, many studies have suggested that lncRNAs, such as Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) and Imprinted Maternally Expressed Transcript (H19), might participate in the pathogenesis of metabolic disorders such as obesity. We conducted a case-control study with 150 Russian children and adolescents aged between 5 and 17 years old in order to assess the statistical association between the single nucleotide polymorphisms (SNPs) rs3200401 in MALAT1 and rs217727 in H19, and the risk of developing obesity in this population. We further explored the possible association of rs3200401 and rs217727 with BMI Z-score and insulin resistance. The MALAT1 rs3200401 and H19 rs217727 SNPs were genotyped using Taqman SNP genotyping assay. The MALAT1 rs3200401 SNP was identified as a risk factor for childhood obesity (p < 0.05) under the dominant and allelic models, and the CT heterozygous genotype was associated with the risk of increased BMI and with insulin resistance. The H19 rs217727 SNP had no significant association with obesity risk (all p > 0.05). Our findings thus suggest that MALAT1 SNP rs3200401 is a potential indicator of obesity susceptibility and pathogenesis in children and adolescents.

The function of long non-coding RNA in non-alcoholic fatty liver disease

Non-alcoholic fatty liver disease is a disease that is currently prevalent in the world, increasingly becoming the mainstay of liver diseases. And its prevalence is rapidly increasing, but its pathogenesis is not entirely understood. Long non-coding RNAs have increasingly gained attention as science has progressed in recent years. Studies have shown that long non-coding RNAs are involved in a variety of biological processes in vivo, such as proliferation, differentiation, and apoptosis, and can affect disease by regulating gene expression. This review explores the biological processes involving long non-coding RNAs, including lipid metabolism, glucose metabolism, liver fibrosis, and apoptosis. In addition, we summarize how the different long non-coding RNAs involved in each process function. Finally, the shortcomings of long non-coding RNAs as potential therapeutic targets are briefly described. In conclusion, this article provides a clear visualization of the link that exists between long non-coding RNAs and non-alcoholic fatty liver disease.

Circular RNAs-New Kids on the Block in Cancer Pathophysiology and Management

The ever-increasing number of cancer cases and persistently high mortality underlines the urgent need to acquire new perspectives for developing innovative therapeutic approaches. As the research on protein-coding genes brought significant yet only incremental progress in the development of anticancer therapy, much attention is now devoted to understanding the role of non-coding RNAs (ncRNAs) in various types of cancer. Recent years have brought about the awareness that ncRNAs recognized previously as "dark matter" are, in fact, key players in shaping cancer development. Moreover, breakthrough discoveries concerning the role of a new group of ncRNAs, circular RNAs, have evidenced their high importance in many diseases, including malignancies. Therefore, in the following review, we focus on the role of circular RNAs in cancer, particularly in cancer stem-like cells, summarize their mechanisms of action, and provide an overview of the state-of-the-art toolkits to study them.

Identify Functional lncRNAs in Nonalcoholic Fatty Liver Disease by Constructing a ceRNA Network

Aim: To identify functional long noncoding RNAs (lncRNAs) by constructing a NAFLD-related lncRNA-miRNA-mRNA network (NLMMN) based on the hypothesis that lncRNAs, as competitive endogenous RNAs (ceRNAs), are able to regulate mRNA functions by competitive binding to shared miRNAs. Methods: The "Limma R package" was used to identify differentially expressed lncRNAs and mRNAs (DElncRNAs and DEmRNAs). The "miRcode online tool" was used to predict the potential interactions between DElncRNAs or DEmRNAs using Perl, and "multiMiR R package" was used to predict the potential interactions between DElncRNAs and miRNAs. The NLMMN was viewed by Cytoscape. The DEmRNAs were further analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to identify functional lncRNAs in human liver tissue and FFAs-induced fat-overloading HepG2 cells. The role of functional lncRNA was explored in the HepG2 cell line. Results: A total of 336 DElncRNAs (154 upregulated and 182 downregulated, |log 2 (fold change) |>0.655 and P < 0.05) and 399 DEmRNAs (152 upregulated and 247 downregulated, |log 2 (fold change) |>0.608 and P < 0.05) were identified. A total of 142 DElncRNA-miRNA interaction pairs and 643 miRNA-DEmRNA interaction pairs were retained to construct the NLMMN, which contained 19 lncRNAs, 47 miRNAs, and 228 mRNAs. The results of GO and KEGG enrichment analyses were related to an extracellular matrix (ECM). Two upregulated lncRNAs (LINC00240 and RBMS3-AS3) and one downregulated lncRNA (ALG9-IT1) were identified by qRT-PCR in liver tissues. But only LINC00240 was significantly upregulated in fat-overloading HepG2 cells. Overexpression of LINC00240 did not affect lipid accumulation but increased the reactive oxygen species (ROS) content in HepG2 cells. Conclusion: LINC00240, RBMS3-AS3, and ALG9-IT1 might be novel functional lncRNAs that attenuate liver fibrosis in NAFLD by influencing the ECM through the ceRNA network. Among them, LINC00240 might have a key role.

An Unanticipated Modulation of Cyclin-Dependent Kinase Inhibitors: The Role of Long Non-Coding RNAs

It is now definitively established that a large part of the human genome is transcribed. However, only a scarce percentage of the transcriptome (about 1.2%) consists of RNAs that are translated into proteins, while the large majority of transcripts include a variety of RNA families with different dimensions and functions. Within this heterogeneous RNA world, a significant fraction consists of sequences with a length of more than 200 bases that form the so-called long non-coding RNA family. The functions of long non-coding RNAs range from the regulation of gene transcription to the changes in DNA topology and nucleosome modification and structural organization, to paraspeckle formation and cellular organelles maturation. This review is focused on the role of long non-coding RNAs as regulators of cyclin-dependent kinase inhibitors’ (CDKIs) levels and activities. Cyclin-dependent kinases are enzymes necessary for the tuned progression of the cell division cycle. The control of their activity takes place at various levels. Among these, interaction with CDKIs is a vital mechanism. Through CDKI modulation, long non-coding RNAs implement control over cellular physiology and are associated with numerous pathologies. However, although there are robust data in the literature, the role of long non-coding RNAs in the modulation of CDKIs appears to still be underestimated, as well as their importance in cell proliferation control.

Long non-coding RNAs in metabolic disorders: pathogenetic relevance and potential biomarkers and therapeutic targets

BACKGROUND

It has been suggested that dysregulation of long non-coding RNAs (lncRNAs) could be associated with the incidence and development of metabolic disorders.

AIM

Accordingly, this narrative review described the molecular mechanisms of lncRNAs in the development of metabolic diseases including insulin resistance, diabetes, obesity, non-alcoholic fatty liver disease (NAFLD), cirrhosis, and coronary artery diseases (CAD). Furthermore, we investigated the up-to-date findings on the association of deregulated lncRNAs in the metabolic disorders, and potential use of lncRNAs as biomarkers and therapeutic targets.

CONCLUSION

LncRNAs/miRNA/regulatory proteins axis plays a crucial role in progression of metabolic disorders and may be used in development of therapeutic and diagnostic approaches.

Transcriptional characterization of subcutaneous adipose tissue in obesity affected women highlights metabolic dysfunction and implications for lncRNAs

Obesity is a complex disease with multifactorial causes, and its prevalence is becoming a serious health crisis. For this reason, there is a crucial need to identify novel targets and players. With this aim in mind, we analyzed via RNA-sequencing the subcutaneous adipose tissue of normal weight and obesity-affected women, highlighting the differential expression in the two tissues. We specifically focused on long non-coding RNAs, as 6 of these emerged as dysregulated in the diseased-tissue (COL4A2-AS2, RPS21-AS, PELATON, ITGB2-AS1, ACER2-AS and CTEPHA1). For each of them, we performed both a thorough in silico dissection and in vitro validation, to predict their function during adipogenesis. We report the lncRNAs expression during adipose derived stem cells differentiation to adipocytes as model of adipogenesis and their potential modulation by adipogenesis-related transcription factors (C/EBPs and PPARγ). Moreover, inhibiting CTEPHA1 expression we investigated its impact on adipogenesis-related transcription factors, showing its significative dysregulation of C/EBPα expression. Lastly, we dissected the subcellular localization, pathway involvement and disease-correlation for coding differentially expressed genes. Together, these findings highlight a transcriptional deregulation at the basis of obesity, impacted by both coding and long non-coding RNAs.

Non-Coding RNAs: Novel Players in Insulin Resistance and Related Diseases

The rising prevalence of metabolic diseases related to insulin resistance (IR) have stressed the urgent need of accurate and applicable tools for early diagnosis and treatment. In the last decade, non-coding RNAs (ncRNAs) have gained growing interest because of their potential role in IR modulation. NcRNAs are variable-length transcripts which are not translated into proteins but are involved in gene expression regulation. Thanks to their stability and easy detection in biological fluids, ncRNAs have been investigated as promising diagnostic and therapeutic markers in metabolic diseases, such as type 2 diabetes mellitus (T2D), obesity and non-alcoholic fatty liver disease (NAFLD). Here we review the emerging role of ncRNAs in the development of IR and related diseases such as obesity, T2D and NAFLD, and summarize current evidence concerning their potential clinical application.

Role of long non-coding RNAs in adipogenesis: State of the art and implications in obesity and obesity-associated diseases

Obesity is an evolutionary, chronic, and relapsing disease that consists of a pathological accumulation of adipose tissue able to increase morbidity for high blood pressure, type 2 diabetes, metabolic syndrome, and obstructive sleep apnea in adults, children, and adolescents. Despite intense research over the last 20 years, obesity remains today a disease with a complex and multifactorial etiology. Recently, long non-coding RNAs (lncRNAs) are emerging as interesting new regulators as different lncRNAs have been found to play a role in early and late phases of adipogenesis and to be implicated in obesity-associated complications onset. In this review, we discuss the most recent advances on the role of lncRNAs in adipocyte biology and in obesity-associated complications. Indeed, more and more researchers are focusing on investigating the underlying roles that these molecular modulators could play. Even if a significant number of evidence is correlation-based, with lncRNAs being differentially expressed in a specific disease, recent works are now focused on deeply analyzing how lncRNAs can effectively modulate the disease pathogenesis onset and progression. LncRNAs possibly represent new molecular markers useful in the future for both the early diagnosis and a prompt clinical management of patients with obesity.

LncRNA CASC2 Alleviates Sepsis-induced Acute Lung Injury by Regulating the miR-152-3p/PDK4 Axis

Background: Acute lung injury (ALI) is an early complication of sepsis and it is also considered as an important cause of high mortality in sepsis patients. This research aimed to explore the potential role and mechanism of long non-coding RNA (lncRNA) cancer susceptibility candidate 2 (CASC2) in sepsis-induced ALI. Methods: The levels of CASC2, microRNA-152-3p (miR-152-3p) and pyruvate dehydrogenase kinase 4 (PDK4) in sepsis patients and LPS-treated HPAEpiC were detected by quantitative real-time PCR and western blot. Cell viability and apoptosis were assessed by Counting Kit-8 (CCK-8) assay and flow cytometry. The concentrations of inflammatory factors were tested by Enzyme-linked immunosorbent assay. Oxidative stress was evaluated by the levels of reactive oxygen species and superoxide dismutase using corresponding commercial kits. The targeting relationship between miR-152-3p and CASC2 or PDK4 was verified by dual-luciferase reporter, RNA immunoprecipitation (RIP) and RNA pull-down assays.Results: CASC2 and PDK4 were down-regulated, while miR-152-3p was up-regulated in sepsis patients and LPS-stimulated HPAEpiC. Overexpression of CASC2 relieved the LPS-resulted cell viability inhibition, apoptosis promotion, inflammatory and oxidative damages in HPAEpiC. In addition, miR-152-3p was a miRNA target of CASC2 and CASC2 alleviated cell injury in LPS-disposed HPAEpiC by sponging miR-152-3p. Moreover, miR-152-3p directly targeted PDK4 and CASC2 increased the PDK4 expression by depending on the sponge effect on miR-152-3p. Meanwhile, inhibition of miR-152-3p attenuated LPS-triggered HPAEpiC injury by upregulating the level of PDK4.Conclusion: These results suggested that CASC2 ameliorated the LPS-induced injury in HPAEpiC via regulating miR-152-3p/PDK4 pathway.

LINC00511/miRNA-143-3p Modulates Apoptosis and Malignant Phenotype of Bladder Carcinoma Cells via PCMT1

Bladder cancer has easy recurrence characteristics, but its occurrence and development mechanism are still unclear. Non-coding RNA is a kind of RNA that exists widely and cannot be translated into proteins, which has played a key role in the regulation of biological functions of tumor cells. However, the regulation mechanism of non-coding RNA on bladder tumors is not fully understood. By microarray analysis and database analysis, we found that LINC00511 was significantly highly expressed in bladder cancer. The expressions of LINC00511, miR-143-3p, and PCMT in bladder cancer tissues and cells were detected by quantitative reverse transcription–polymerase chain reaction. The relationship between the expressions of miR-143-3p and PCMT1 and the clinicopathological parameters of the tumor was analyzed. The proliferation and invasion of bladder cancer cells were detected by MTT assay and Transwell assay. The expression levels of E-cadherin and vimentin in bladder cancer cells were detected by Western blot. Cell apoptosis was detected by flow cytometry. In vivo, TCCSUP or SW780 cells were inoculated into BALB/c nude mice to detect tumor volume and weight. Bioinformatics and dual luciferase reporter gene were used to analyze the relationship between LINC00511 and miR-143-3p and its downstream target gene PCMT1. The results showed that LINC00511 could target miR-143-3p/PCMT1 to regulate the proliferation, migration, and apoptosis of bladder cancer TCCSUP or SW780 cells and promote the occurrence and development of bladder cancer.

Long noncoding RNAs-a new dimension in the molecular architecture of the bile acid/FXR pathway

Bile acids, regarded as the body's detergent for digesting lipids, also function as critical signaling molecules that regulate cholesterol and triglyceride levels in the body. Bile acids are the natural ligands of the nuclear receptor, FXR, which controls an intricate network of cellular pathways to maintain metabolic homeostasis. In recent years, growing evidence supports that many cellular actions of the bile acid/FXR pathway are mediated by long non-coding RNAs (lncRNAs), and lncRNAs are in turn powerful regulators of bile acid levels and FXR activities. In this review, we highlight the substantial progress made in the understanding of the functional and mechanistic role of lncRNAs in bile acid metabolism and how lncRNAs connect bile acid activity to additional metabolic processes. We also discuss the potential of lncRNA studies in elucidating novel molecular mechanisms of the bile acid/FXR pathway and the promise of lncRNAs as potential diagnostic markers and therapeutic targets for diseases associated with altered bile acid metabolism.

The role of miRNA, lncRNA and circRNA in the development of intervertebral disk degeneration (Review)

Intervertebral disc degeneration (IVDD) is a degenerative musculoskeletal disorder with multiple causative factors, such as age, genetics, mechanics and life style. IVDD contributes to non-specific lower back pain (NLBP), which is a globally prevalent and debilitating musculoskeletal disorder. NLBP has a substantial impact on medical resources and creates an economic burden for the public. Dysregulated phenotypes of nucleus pulposus (NP) cells and endplate chondrocytes, such as proliferation, senescence and apoptosis, along with aberrant expression of extracellular matrix components, including type II collagen and aggrecan, are involved in the pathological process of IVDD. Evidence indicates that non-coding RNAs, mainly microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), play a vital role in the development of IVDD. In the present review, the potential molecular mechanisms of miRNAs, lncRNAs and circRNAs in the initiation and progression of IVDD were described based on the latest literature. Furthermore, ways to influence the functions of NP cells and endplate chondrocytes in IVDD were also summarized. The presented insights suggested that non-coding RNAs may function as potential targets for the treatment of IVDD.

Upregulated lncRNA HCG18 in Patients with Non-Alcoholic Fatty Liver Disease and Its Regulatory Effect on Insulin Resistance

PURPOSE

Non-alcoholic fatty liver disease (NAFLD) is a disease associated with genetic-environmental-metabolic stress, which severely damages the liver function of patients. This study aimed to explore the significance and probable functions of HCG18 in NAFLD.

PATIENTS AND METHODS

The expression of HCG18 and miR-197-3p was tested by qRT-PCR. The clinical signification of HCG18 was provided by the ROC curve and Pearson correlation. The corresponding mechanism was punctuated by the luciferase reporter assay and HFD-managed mice.

RESULTS

HCG18 expression was higher in the patients with NAFLD than in controls and in individuals with HOMA-IR score ≥2.5 than those with HOMA-IR score <2.5. HCG18 expression in NAFLD patients was related to BMI, HOMA-IR, ALT, FBG, TC, and TG. HCG18 showed satisfactory predictive accuracy in differentiating NAFLD patients and patients with HOMA-IR ≥2.5. Besides, HCG18 had protective impacts on blood glucose and fat deposition but not on body weight. MiR-197-3p is a direct gene of HCG18, and a reverse correlation was found between miR-197-3p and HCG18. Furthermore, miR-197-3p regulated the influence of HCG18 on insulin resistance and lipid accumulation.

CONCLUSION

Increased levels of HCG18 might be an alternate indicator for NAFLD patients. The HCG18-miR-197-3p axis exerted effects on the progression of fat sedimentation and glucose disorder in NAFLD.

Genome-wide identification and characterization of novel long non-coding RNA in Ruminal tissue affected with sub-acute Ruminal acidosis from Holstein cattle

Sub-acute ruminal acidosis is a type of metabolic disorder in which affected cattle show a considerable depression of rumen pH. This leads to a dramatic decline in productivity and consequent loss of income for many dairy farms. The objective of the present study is to identify and characterize novel long non-coding RNAs (lncRNAs) in Holstein cattle affected by sub-acute ruminal acidosis. Two replicates from six animals were sequenced that bioinformatically analyzed. Results showed 6679 novel lncRNAs among which 12 intergenic lncRNAs showed differential expression (p value ≤0.05). GO and KEGG analysis revealed that calcium signaling and G protein couple-receptor pathways may be involved in regulating metabolic processes during sub-acute ruminal acidosis. Furthermore, other biological processes including transmembrane transport, adult behavior, neuroactive ligand-receptor interaction, GABAergic synapse, cholinergic synapse were significantly enriched. The present data suggest that these differentially expressed lncRNAs may play regulatory roles in modulating biological processes associated with sub-acute ruminal acidosis in cattle rumen.

Long Non-coding RNA Maternally Expressed 3 Increases the Expression of Neuron-Specific Genes by Targeting miR-128-3p in All-Trans Retinoic Acid-Induced Neurogenic Differentiation From Amniotic Epithelial Cells

MicroRNA (miR)-128-3p is a brain-enriched miRNA that participates in the regulation of neural cell differentiation and the protection of neurons, but the mechanisms by which miR-128-3p regulates its target and downstream genes to influence cell fate from adult stem cells are poorly understood. In this study, we show down-regulation of miR-128-3p during all-trans retinoic acid (ATRA)-induced neurogenic differentiation from amniotic epithelial cells (AECs). We investigated miR-128-3p in both the Notch pathway and in the expression of neuron-specific genes predicted to be involved in miR-128-3p signaling to elucidate its role in the genetic regulation of downstream neurogenic differentiation. Our results demonstrate that miR-128-3p is a negative regulator for the transcription of the neuron-specific genes β III-tubulin, neuron-specific enolase (NSE), and polysialic acid-neural cell adhesion molecule (PSA-NCAM) via targeting Jagged 1 to inhibit activation of the Notch signaling pathway. We also used bioinformatics algorithms to screen for miR-128-3p interactions with long non-coding (lnc) RNA and circular RNA as competing endogenous RNAs to further elucidate underlying down-regulated molecular mechanisms. The lncRNA maternally expressed 3 is up-regulated by the ATRA/cAMP/CREB pathway, and it, in turn, is directly down-regulated by miR-128-3p to increase the amount of neuron differentiation. Endogenous miRNAs are, therefore, involved in neurogenic differentiation from AECs and should be considered during the development of effective cell transplant therapies for the treatment of neurodegenerative disease.

Prognostic significance of long non-coding RNAs in clear cell renal cell carcinoma: A meta-analysis

BACKGROUND

Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer in adults, and patients with advanced ccRCC have a 5-year survival rate of <30%. The poor prognosis of ccRCC is closely related to its lacking of potential therapeutic and prognostic biomarkers. This meta-analysis aimed to elucidate the precise prognostic value of long non-coding RNAs (lncRNAs) in patients with ccRCC.

METHODS

A literature search was performed in related databases up to January 31, 2019. Hazard ratios (HRs) and corresponding 95% confidence intervals (CIs) were calculated to explore the relationship between special lncRNAs expression and survival in patients with ccRCC.

RESULTS

After literature researching, a total of 16 studies, including 13 lncRNAs were identified. The data from studies that investigated the association between lncRNA expression and survival outcomes in patients with ccRCC were extracted. Results revealed that lncRNAs expression was significantly associated with poor overall survival (OS) outcome in patients with ccRCC (HR = 1.71, 95%CI = 1.40-2.01 in up-regulated subgroup; HR = 0.53, 95% CI = 0.25-0.80 in down-regulated subgroup). The overexpression of PVT1 was significantly associated with poor OS in ccRCC (HR = 1.51, 95% CI = 1.02-2.00). Meanwhile, up-regulation of LUCAT1 was significantly related to worse OS in ccRCC patients (HR = 1.51, 95% CI = 1.01-2.00).

CONCLUSIONS

These results suggest that lncRNAs could be used to predict unfavorable prognosis and function as potential prognostic biomarkers in ccRCC.

Crosstalk between microRNAs, the putative target genes and the lncRNA network in metabolic diseases

MicroRNAs (miRNAs/miRs) are small non-coding RNAs (ncRNAs) that regulate gene expression. Emerging knowledge has suggested that miRNAs have a role in the pathogenesis of metabolic disorders, supporting the hypothesis that miRNAs may represent potential biomarkers or targets for this set of diseases. However, the current evidence is often controversial. Therefore, the aim of the present study was to determine the associations between miRNAs-target genes, miRNA-long ncRNAs (lncRNAs), and miRNAs-small molecules in human metabolic diseases, including obesity, type 2 diabetes and non-alcoholic fatty liver disease. The metabolic disease-related miRNAs were obtained from the Human MicroRNA Disease Database (HMDD) and miR2Disease database. A search on the databases Matrix Decomposition and Heterogeneous Graph Inference (MDHGI) and DisGeNET were also performed. miRNAs target genes were obtained from three independent sources: Microcosm, TargetScan and miRTarBase. The interactions between miRNAs-lncRNA and miRNA-small molecules were performed using the miRNet web tool. The network analyses were performed using Cytoscape software. As a result, a total of 20 miRNAs were revealed to be associated with metabolic disorders in the present study. Notably, 6 miRNAs (miR-17-5p, miR-29c-3p, miR-34a-5p, miR-103a-3p, miR-107 and miR-132-3p) were found in the four resources (HMDD, miR2Disease, MDHGI, and DisGeNET) used for these analyses, presenting a stronger association with the diseases. Furthermore, the target genes of these miRNAs participate in several pathways previously associated with metabolic diseases. In addition, interactions between miRNA-lncRNA and miRNA-small molecules were also found, suggesting that some molecules can modulate gene expression via such an indirect way. Thus, the results of this data mining and integration analysis provide further information on the possible molecular basis of the metabolic disease pathogenesis as well as provide a path to search for potential biomarkers and therapeutic targets concerning metabolic diseases.