LncRNA-uc.167 influences cell proliferation, apoptosis and differentiation of P19 cells by regulating Mef2c

The molecular mechanisms of cardiac development and related diseases

Cardiac development is a complex and intricate process involving numerous molecular signals and pathways. Researchers have explored cardiac development through a long journey, starting with early studies observing morphological changes and progressing to the exploration of molecular mechanisms using various molecular biology methods. Currently, advancements in stem cell technology and sequencing technology, such as the generation of human pluripotent stem cells and cardiac organoids, multi-omics sequencing, and artificial intelligence (AI) technology, have enabled researchers to understand the molecular mechanisms of cardiac development better. Many molecular signals regulate cardiac development, including various growth and transcription factors and signaling pathways, such as WNT signaling, retinoic acid signaling, and Notch signaling pathways. In addition, cilia, the extracellular matrix, epigenetic modifications, and hypoxia conditions also play important roles in cardiac development. These factors play crucial roles at one or even multiple stages of cardiac development. Recent studies have also identified roles for autophagy, metabolic transition, and macrophages in cardiac development. Deficiencies or abnormal expression of these factors can lead to various types of cardiac development abnormalities. Nowadays, congenital heart disease (CHD) management requires lifelong care, primarily involving surgical and pharmacological treatments. Advances in surgical techniques and the development of clinical genetic testing have enabled earlier diagnosis and treatment of CHD. However, these technologies still have significant limitations. The development of new technologies, such as sequencing and AI technologies, will help us better understand the molecular mechanisms of cardiac development and promote earlier prevention and treatment of CHD in the future.

Long-chain noncoding RNA sequencing analysis reveals the molecular profiles of chemically induced mammary epithelial cells

Long noncoding RNAs (lncRNAs) were important regulators affecting the cellular reprogramming process. Previous studies from our group have demonstrated that small molecule compounds can induce goat ear fibroblasts to reprogram into mammary epithelial cells with lactation function. In this study, we used lncRNA-Sequencing (lncRNA-seq) to analyze the lncRNA expression profile of cells before and after reprogramming (CK vs. 5i8 d). The results showed that a total of 3,970 candidate differential lncRNAs were detected, 1,170 annotated and 2,800 new lncRNAs. Compared to 0 d cells, 738 lncRNAs were significantly upregulated and 550 were significantly downregulated in 8 d cells. Heat maps of lncrnas and target genes with significant differences showed that the fate of cell lineages changed. Functional enrichment analysis revealed that these differently expressed (DE) lncRNAs target genes were mainly involved in signaling pathways related to reprogramming and mammary gland development, such as the Wnt signaling pathway, PI3K-Akt signaling pathway, arginine and proline metabolism, ECM-receptor interaction, and MAPK signaling pathway. The accuracy of sequencing was verified by real-time fluorescence quantification (RT-qPCR) of lncRNAs and key candidate genes, and it was also demonstrated that the phenotype and genes of the cells were changed. Therefore, this study offers a foundation for explaining the molecular mechanisms of lncRNAs in chemically induced mammary epithelial cells.

Molecular regulatory mechanism of key LncRNAs in subclinical mastitic cows with folic acid supplementation

BACKGROUND

Folic acid is a water-soluble B vitamin (B9), which is closely related to the body's immune and other metabolic pathways. The folic acid synthesized by rumen microbes has been unable to meet the needs of high-yielding dairy cows. The incidence rate of subclinical mastitis in dairy herds worldwide ranged between 25%~65% with no obvious symptoms, but it significantly causes a decrease in lactation and milk quality. Therefore, this study aims at exploring the effects of folic acid supplementation on the expression profile of lncRNAs, exploring the molecular mechanism by which lncRNAs regulate immunity in subclinical mastitic dairy cows.

RESULTS

The analysis identified a total of 4384 lncRNA transcripts. Subsequently, differentially expressed lncRNAs in the comparison of two groups (SF vs. SC, HF vs. HC) were identified to be 84 and 55 respectively. Furthermore, the weighted gene co-expression network analysis (WGCNA) and the KEGG enrichment analysis result showed that folic acid supplementation affects inflammation and immune response-related pathways. The two groups have few pathways in common. One important lncRNA MSTRG.11108.1 and its target genes (ICAM1, CCL3, CCL4, etc.) were involved in immune-related pathways. Finally, through integrated analysis of lncRNAs with GWAS data and animal QTL database, we found that differential lncRNA and its target genes could be significantly enriched in SNPs and QTLs related to somatic cell count (SCC) and mastitis, such as MSTRG.11108.1 and its target gene ICAM1, CXCL3, GRO1.

CONCLUSIONS

For subclinical mastitic cows, folic acid supplementation can significantly affect the expression of immune-related pathway genes such as ICAM1 by regulating lncRNAs MSTRG.11108.1, thereby affecting related immune phenotypes. Our findings laid a ground foundation for theoretical and practical application for feeding folic acid supplementation in subclinical mastitic cows.

Ultra-conserved RNA: a novel biological tool with diagnostic and therapeutic potential

Ultra-conserved RNA (ucRNA) is a subset of long non-coding RNA, that is highly conserved among mice, rats and humans. UcRNA has attracted extensive attention in recent years for its potential biological significance in normal physiological function and diseases. However, due to the instability of RNA and the technical limitation, the function and mechanism of ucRNAs are largely unknown. Over the last two decades, researchers have made a lot of efforts to try to lift the veil of ucRNA in nervous, cardiovascular system and other systems as well as cancers. Since the concept of the glymphatic system is relatively new, we summarized here recent findings on the functions, regulation and the underlying mechanisms of ucRNAs in physiology and pathology. Meanwhile, pathology in some diseases is likely to contribute to abnormal expression of ucRNA in turn. We also discuss the technical challenges and bright prospects for future applications of ucRNAs in the diagnosis and treatment of diseases.

Overexpressing lnc240 Rescues Learning and Memory Dysfunction in Hepatic Encephalopathy Through miR-1264-5p/MEF2C Axis

Hepatic encephalopathy (HE) is a nervous system disease caused by severe liver diseases and different degrees of learning and memory dysfunction. Long non-coding RNA (lncRNA) is highly expressed in the brain and plays important roles in central nervous system diseases like Alzheimer's disease. In the present work, we found that the expression of lnc240 in the hippocampus of HE mice was significantly downregulated, but its pathogenesis in HE has not been clarified. This study aimed to explore the effects of lnc240 on the cognitive function of HE. The expression of lnc240, miR-1264-5p, and MEF2C was analyzed with RNA-seq and further determined by qRT-PCR in HE mouse. Double luciferase reporter gene testing confirmed the relationship between lnc240, MEF2C, and miR-1264-5p. The functional role of lnc240 and MEF2C in vitro and in vivo was evaluated by qRT-PCR, western blot analysis, immunofluorescence staining, Golgi staining, electrophysiology, and Morris water maze. The expression of lnc240 was decreased in HE mice. The overexpression of lnc240 could significantly downregulate miR-1264-5p and upregulate MEF2C, also increasing the amplitude and frequency of mEPSC in primary cultured hippocampal neurons. The overexpression of miR-1264-5p reversed the effect of lnc240 on MEF2C. Moreover, in vivo experiments have shown that the overexpression of lnc240 could improve HE mice's spatial learning and memory functions. Golgi staining suggested that overexpression of lnc240 could increase the density and maturity of dendritic spines in hippocampal neurons of HE mice. Lnc240 can regulate the expression of MEF2C through miR-1264-5p and regulate the synaptic plasticity of hippocampal neurons, thereby saving the learning and memory dysfunction in HE mice, suggesting that lnc240 might be a potential therapeutic target for the treatment of HE.

High expression of RNF169 is associated with poor prognosis in pancreatic adenocarcinoma by regulating tumour immune infiltration

Background: Pancreatic adenocarcinoma (PAAD) is a highly deadly and aggressive tumour with a poor prognosis. However, the prognostic value of RNF169 and its related mechanisms in PAAD have not been elucidated. In this study, we aimed to explore prognosis-related genes, especially RNF169 in PAAD and to identify novel potential prognostic predictors of PAAD. Methods: The GEPIA and UALCAN databases were used to investigate the expression and prognostic value of RNF169 in PAAD. The correlation between RNF169 expression and immune infiltration was determined by using TIMER and TISIDB. Correlation analysis with starBase was performed to identify a potential regulatory axis of lncRNA-miRNA-RNF169. Results: The data showed that the level of RNF169 mRNA expression in PAAD tissues was higher than that in normal tissues. High RNF169 expression was correlated with poor prognosis in PAAD. In addition, analysis with the TISIDB and TIMER databases revealed that RNF169 expression was positively correlated with tumour immune infiltration in PAAD. Correlation analysis suggested that the long non-coding RNA (lncRNA) AL049555.1 and the microRNA (miRNA) hsa-miR-324-5p were involved in the expression of RNF169, composing a potential regulatory axis to control the progression of PAAD. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that RNF169 plays a role in PAAD through pathways such as TNF, Hippo, JAK-STAT and Toll-like receptor signaling. Conclusion: In summary, the upregulation of RNF169 expression mediated by ncRNAs might influence immune cell infiltration in the microenvironment; thus, it can be used as a prognostic biomarker and a potential therapeutic target in PAAD.

The Emerging Role of Non-Coding RNAs in Osteogenic Differentiation of Human Bone Marrow Mesenchymal Stem Cells

Autologous bone marrow-derived mesenchymal stem cells (BMSCs) are more easily available and frequently used for bone regeneration in clinics. Osteogenic differentiation of BMSCs involves complex regulatory networks affecting bone formation phenomena. Non-coding RNAs (ncRNAs) refer to RNAs that do not encode proteins, mainly including microRNAs, long non-coding RNAs, circular RNAs, piwi-interacting RNAs, transfer RNA-derived small RNAs, etc. Recent in vitro and in vivo studies had revealed the regulatory role of ncRNAs in osteogenic differentiation of BMSCs. NcRNAs had both stimulatory and inhibitory effects on osteogenic differentiation of BMSCs. During the physiological condition, osteo-stimulatory ncRNAs are upregulated and osteo-inhibitory ncRNAs are downregulated. The opposite effects might occur during bone degenerative disease conditions. Intracellular ncRNAs and ncRNAs from neighboring cells delivered via exosomes participate in the regulatory process of osteogenic differentiation of BMSCs. In this review, we summarize the recent advances in the regulatory role of ncRNAs on osteogenic differentiation of BMSCs during physiological and pathological conditions. We also discuss the prospects of the application of modulation of ncRNAs function in BMSCs to promote bone tissue regeneration in clinics.

Post-Transcriptional Regulation of Molecular Determinants during Cardiogenesis

Cardiovascular development is initiated soon after gastrulation as bilateral precardiac mesoderm is progressively symmetrically determined at both sides of the developing embryo. The precardiac mesoderm subsequently fused at the embryonic midline constituting an embryonic linear heart tube. As development progress, the embryonic heart displays the first sign of left-right asymmetric morphology by the invariably rightward looping of the initial heart tube and prospective embryonic ventricular and atrial chambers emerged. As cardiac development progresses, the atrial and ventricular chambers enlarged and distinct left and right compartments emerge as consequence of the formation of the interatrial and interventricular septa, respectively. The last steps of cardiac morphogenesis are represented by the completion of atrial and ventricular septation, resulting in the configuration of a double circuitry with distinct systemic and pulmonary chambers, each of them with distinct inlets and outlets connections. Over the last decade, our understanding of the contribution of multiple growth factor signaling cascades such as Tgf-beta, Bmp and Wnt signaling as well as of transcriptional regulators to cardiac morphogenesis have greatly enlarged. Recently, a novel layer of complexity has emerged with the discovery of non-coding RNAs, particularly microRNAs and lncRNAs. Herein, we provide a state-of-the-art review of the contribution of non-coding RNAs during cardiac development. microRNAs and lncRNAs have been reported to functional modulate all stages of cardiac morphogenesis, spanning from lateral plate mesoderm formation to outflow tract septation, by modulating major growth factor signaling pathways as well as those transcriptional regulators involved in cardiac development.

Sox9 Promotes Cardiomyocyte Apoptosis After Acute Myocardial Infarction by Promoting miR-223-3p and Inhibiting MEF2C

Acute myocardial infarction (AMI) is a severe and even fatal cardiovascular disease. The effect of transcription factors on AMI is intensively explored. Our experiment attempts to probe the role of Sox9 in cardiomyocyte apoptosis after AMI. AMI cell model was established in AC16 cells by hypoxia treatment. Cell viability and apoptosis were assessed. Then, the levels of BAX, Bcl-2, Sox9, miR-223-3p, and MEF2C were detected. The binding relation between Sox9 and miR-223-3p and between miR-223-3p and MEF2C was verified. The expression of miR-223-3p was upregulated using the miR-223-3p mimic, and collaborative experiments were conducted as si-Sox9 or si-MEF2C was transfected into cells to inhibit the expression of Sox9 or MEF2C. Sox9 was highly expressed in cardiomyocyte apoptosis after hypoxia, while Sox9 silencing protected hypoxia-treated cardiomyocytes from apoptosis by enhancing cell viability, quenching apoptosis, and reducing activity of caspase-3 and caspase-9. Essentially, Sox9 bound to the miR-223-3p promoter region to upregulate its expression. miR-223-3p targeted MEF2C transcription. miR-223-3p overexpression and MEF2C silencing could counteract the suppressive role of Sox9 silencing in hypoxia-treated cardiomyocyte apoptosis. Sox9 exacerbated hypoxia-induced cardiomyocyte apoptosis by promoting miR-223-3p expression and inhibiting MEF2C transcription.

Spatiotemporal expression of long noncoding RNA Moshe modulates heart cell lineage commitment

The roles of long non-coding RNA (LncRNA) have been highlighted in various development processes including congenital heart defects (CHD). Here, we characterized the molecular function of LncRNA, Moshe (1010001N08ik-203), one of the Gata6 antisense transcripts located upstream of Gata6, which is involved in both heart development and the most common type of congenital heart defect, atrial septal defect (ASD). During mouse embryonic development, Moshe was first detected during the cardiac mesoderm stage (E8.5 to E9.5) where Gata6 is expressed and continues to increase at the atrioventricular septum (E12.5), which is involved in ASD. Functionally, the knock-down of Moshe during cardiogenesis caused significant repression of Nkx2.5 in cardiac progenitor stages and resulted in the increase in major SHF lineage genes, such as cardiac transcriptional factors (Isl1, Hand2, Tbx2), endothelial-specific genes (Cd31, Flk1, Tie1, vWF), a smooth muscle actin (a-Sma) and sinoatrial node-specific genes (Shox2, Tbx18). Chromatin Isolation by RNA Purification showed Moshe activates Nkx2.5 gene expression via direct binding to its promoter region. Of note, Moshe was conserved across species, including human, pig and mouse. Altogether, this study suggests that Moshe is a heart-enriched lncRNA that controls a sophisticated network of cardiogenesis by repressing genes in SHF via Nkx2.5 during cardiac development and may play an important role in ASD.

Comprehensive Overview of Non-coding RNAs in Cardiac Development

Cardiac development in the human embryo is characterized by the interactions of several transcription and growth factors leading the heart from a primordial linear tube into a synchronous contractile four-chamber organ. Studies on cardiogenesis showed that cell proliferation, differentiation, fate specification and morphogenesis are spatiotemporally coordinated by cell-cell interactions and intracellular signalling cross-talks. In recent years, research has focused on a class of inter- and intra-cellular modulators called non-coding RNAs (ncRNAs), transcribed from the noncoding portion of the DNA and involved in the proper formation of the heart. In this chapter, we will summarize the current state of the art on the roles of three major forms of ncRNAs [microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs)] in orchestrating the four sequential phases of cardiac organogenesis.

Research into the intervention effect of folic acid on arsenic-induced heart abnormalities in fetal rats during the periconception period

BACKGROUND

The incidence of CHD is the highest among birth defects and is increasing year to year. CHD seriously harms the health of infants and young children and presents a large economic burden to families and society. The pathogenesis of CHD and preventive measures are the focus of current research. Our research aimed to explore the intervention effect of folic acid on heart abnormalities resulting from sodium arsenic (NaAsO2) exposure during the periconception period.

METHODS

Sixty 35-day-old female SD rats were randomly divided into 5 groups with 12 rats in each group. Group A was the control group. The rats were given distilled water and ordinary chow. The rats in group B were given distilled water containing 75 mg/L NaAsO2 and ordinary chow. The rats in groups C, D, and E were given distilled water containing 75 mg/L NaAsO2 and chow containing 0.53 mg/kg, 5.3 mg/kg, and 10.6 mg/kg folic acid, respectively. The general condition of the embryos and the histopathology of the embryonic hearts were examined. The acetylation levels of histone H3K9 in heart tissues and the expression levels of Mef2C (which is related to heart development) were observed.

RESULTS

The embryo weight and placental weight of groups B-E were significantly lower than those of group A (P < 0.05). The heart malformation rate of the fetal rats in groups B-E was significantly higher than that of the fetal rats in group A (P < 0.05). We found that the level of H3K9 acetylation in fetal rat cardiomyocytes in groups B-E was significantly higher than that in group A (P < 0.05) and that the level of H3K9 acetylation in groups C-E was lower than that in group B (P < 0.05). The mRNA level of Mef2C in fetal rat cardiomyocytes in group B-E was significantly higher than that in group A (P < 0.05), and the mRNA level of Mef2C in groups C-E was significantly lower than that in group B (P < 0.05).

CONCLUSION

Supplementation with folic acid during the periconception period can interfere with the toxic effects of arsenic on the heart. The mechanism may be that lowering the acetylation levels of histone H3K9 in heart tissues leads to decreased expression levels of Mef2C, which may play a protective role in heart development in fetal rats.

Non-coding RNAs as Epigenetic Gene Regulators in Cardiovascular Diseases

Epigenetic gene regulations can be considered as de-novo initiation of abnormal molecular signaling events whose regulation is otherwise required during normal or specific developmental stages of the organisms. Primarily, three different mechanisms have been identified to participate in epigenetic gene regulations which include, DNA methylation, non-coding RNA species (microRNAs [miRNA], and long non-coding RNAs [LNC-RNA]) and histone modifications. These de-novo epigenetic mechanisms have been associated with altered normal cellular functions which eventually facilitate normal cells to transition into an abnormal phenotype. Among the three modes of regulation, RNA species which are usually considered to be less stable, can be speculated to initiate instant alterations in gene expression compared to DNA methylation or histone modifications. However, LNC-RNAs appear to be more stable in the cells than the other RNA species. Moreover, there is increasing literature which clearly suggests that a single specific LNC-RNA can regulate multiple mechanisms and disease phenotypes. With specific focus on cardiovascular diseases, here we attempt to provide UpToDate information on the functional role of miRNAs and LNC-RNAs. Here we discuss the role of these epigenetic mediators in different components of cardiovascular disease which include physiopathological heart development, athersclerosis, retenosis, diabetic hearts, myocardial infarction, ischemia-reperfusion, heart valve disease, aortic aneurysm, osteogenesis, angiogenesis and hypoxia in the heart. While there is abundant literature support that shows the involvement of many LNC-RNAs and miRNAs in cardiovascular diseases, very few RNA species have been identified which regulate epigenetic mechanisms which is the current focus in this article. Understanding the role of these RNA species in regulating epigenetic mechanisms in different cell types causing cardiovascular disease, would advance the field and promote disease prevention approaches that are aimed to target epigenetic mechanisms.

Differential chamber-specific expression and regulation of long non-coding RNAs during cardiac development

Cardiovascular development is governed by a complex interplay between inducting signals such as Bmps and Fgfs leading to activation of cardiac specific transcription factors such as Nkx2.5, Mef2c and Srf that orchestrate the initial steps of cardiogenesis. Over the last decade we have witnessed the discovery of novel layers of gene regulation, i.e. post-transcriptional regulation exerted by non-coding RNAs. The function role of small non coding RNAs has been widely demonstrated, e.g. miR-1 knockout display several cardiovascular abnormalities during embryogenesis. More recently long non-coding RNAs have been also reported to modulate gene expression and function in the developing heart, as exemplified by the embryonic lethal phenotypes of Fendrr and Braveheart knock out mice, respectively. In this study, we investigated the differential expression profile during cardiogenesis of previously reported lncRNAs in heart development. Our data revealed that Braveheart, Fendrr, Carmen display a preferential adult expression while Miat, Alien, H19 preferentially display chamber-specific expression at embryonic stages. We also demonstrated that these lncRNAs are differentially regulated by Nkx2.5, Srf and Mef2c, Pitx2 > Wnt > miRNA signaling pathway and angiotensin II and thyroid hormone administration. Importantly isoform-specific expression and distinct nuclear vs cytoplasmic localization of Braveheart, Carmen and Fendrr during chamber morphogenesis is observed, suggesting distinct functional roles of these lncRNAs in atrial and ventricular chambers. Furthermore, we demonstrate by in situ hybridization a dynamic epicardial, myocardial and endocardial expression of H19 during cardiac development. Overall our data support novel roles of these lncRNAs in different temporal and tissue-restricted fashion during cardiogenesis.

Long noncoding RNA FAM3D-AS1 inhibits development of colorectal cancer through NF-κB signaling pathway

Although numerous differential long noncoding RNAs (IncRNAs) have been identified, the relationship between lncRNA and colorectal cancer (CRC) still remains largely unclear. In the present study, we investigated the function and provided a possible mechanism of lncRNA FAM3D-AS1 in CRC. CCK8, transwell, and trypan blue staining were used to evaluate the proliferation, invasion, and cell death rates. Real-time PCR was used to elucidate the expression level of FAM3D-AS1. We found that lncRNA FAM3D-AS1 located in cytoplasm. Overexpression of FAM3D-AS1 significantly inhibited the cell proliferation, cell survival rates, and invaded cells. We also provided evidence that FAM3D-AS1 reversed the EMT process. Moreover, we proved that FAM3D-AS1 inhibits CRC development through NF-κB signaling pathway. Taken together, we performed functional analysis of FAM3D-AS1 and provided a possible mechanism in the development of CRC. Our study provided new targets for clinical treatment.

Exploration of the Differentially Expressed Long Noncoding RNAs and Genes of Morphine Tolerance via Bioinformatic Analysis

Morphine tolerance is one of the most common complications in patients with chronic pain. Many patients with morphine tolerance have poor efficacy in the treatment of primary pain, and are accompanied by the side effects. Previous studies have found that many mechanisms are involved in morphine tolerance, but few researches could fully explain morphine tolerance, and no effective treatment for morphine tolerance has been found. One expression profiling data set was downloaded from the Gene Expression Omnibus (GEO) database. The probes would be transformed into the homologous gene symbol by means of the platform's annotation information. GEO2R was used to search for differentially expressed long noncoding RNAs (lncRNAs) and differentially expressed genes (DEGs) that were differentially expressed between spinal cord samples. Receiver operator characteristic curve analysis was performed to determine the ability of the hub lncRNAs to predict morphine tolerance. Through the principal component analysis, the intragroup data repeatability is fine in the GSE110115. A total of 10 genes were identified as hub genes from the protein-protein interaction network with degrees ≥10. Compared with the normal saline group, the expression levels of LncRNA XR_006440, XR_009493, AF196267, MRAK150340, and MRAK037188 were more downregulated, while the expression levels of MRAK046606, XR_005988, DQ266361, uc.167-, and uc.468+ were more upregulated in the morphine tolerance group. LncRNAs and DEGs were differentially expressed between the morphine tolerance group and nonmorphine tolerance group, which may be involved in the development of morphine tolerance, especially LncRNA DQ266361, uc.167-, and Mmp9, CCL7 genes.

Long noncoding RNA uc.4 inhibits cell differentiation in heart development by altering DNA methylation

In previous studies, we have demonstrated that long noncoding RNA uc.4 may influence the cell differentiation through the TGF-β signaling pathway, suppressed the heart development of zebrafish and resulting cardiac malformation. DNA methylation plays a significant role in the heart development and disordered of DNA methylation may cause disruption of control of gene promoter. In this study, methylated DNA immunoprecipitation was performed to identify the different expression levels of methylation regions. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were also performed to identify the possible biological process and pathway that uc.4 may join, associated with Rap1 signaling pathway, gonadotropin-releasing hormone signaling pathway, and Calcium signaling pathway. We found that the distribution of differentially methylated regions peaks was mainly located in intergenic and intron regions. Altogether, our result showed that differentially methylated genes are significantly expressed in uc.4-overexpression cells, providing valuable data for further exploration of the role of uc.4 in heart development.

Effects of long non-coding RNA uc.245 on cardiomyocyte-like differentiation in P19 cells via FOG2

Each year, cardiac diseases may cause a high morbidity and mortality worldwide. Long non-coding RNAs (lncRNAs) that contained ultra-conserved elements (UCEs) may play important roles on cardiomyocytes differentiation. Further investigations underlying mechanisms of lncRNA-UC regulating embryonic heart development are necessary. In this study, we investigated the effects of lnc-uc.245 on proliferation, migration, apoptosis, and cardiomyocyte-like differentiation in P19 cells with DMSO stimulation, and hypothesized that lnc-uc.245 would influence cardiomyocytes differentiation via FOG2. Lentiviral vectors of pGPU6/GFP/Neo-uc.245 and pGPU6/GFP/Neo-shRNA-uc.245 were respectively transfected into P19 cells to overexpress or silence uc.245. MTT assay, Annexin V-FITC/PI double-staining, scratch test and transwell assay were performed and the results showed that uc.245 overexpression could significantly suppress P19 cell proliferation, migration, cardiomyocyte-like differentiation but promote cell apoptosis. Contrarily, sh-uc.245 treatment caused the opposite changes. Uc.245 overexpression obviously downregulated the expression of cardiomyogenic-specific molecular markers (cTnI, ANP, α-MHC, Nkx2.5, GATA4, MEF2C) but remarkably upregulated the expression of FOG2. Subsequently, we transfected the recombinant vectors loaded FOG2 or shRRNA-FOG2 into P19 cells to further address the functional significance of FOG2 in uc.245-regulated cardiomyocyte-like differentiation. Interestingly, we found that overexpressing of FOG2 promoted cell proliferation, migration, and inhibited apoptosis both in uc.245 overexpressed and silenced P19 cells, especially in uc.245 silenced cell line. In addition, sh-FOG2 promoted cardiomyocyte-like differentiation and upregulated the expression of cardiomyogenic-specific markers at the gene and protein levels both in uc.245 overexpressed and silenced P19 cells. Similarly, this upregulation effect of sh-FOG2 was more obvious after uc.245 silencing. These findings suggest that FOG2 is a key mediator during uc.245-regulated differentiation of P19 cells into cardiomyocytes. It is expected that lnc-uc.245/FOG2 will become a promising therapeutic target for cardiac diseases.

Differential Analysis of lncRNA, miRNA and mRNA Expression Profiles and the Prognostic Value of lncRNA in Esophageal Cancer

Integrative central axis of lncRNA-miRNA-mRNA plays pivotal roles in tumor development and progression. However, the regulatory role of lncRNA-miRNA-mRNA in esophageal cancer remains elusive. TCGA database was utilized to investigate the differential expression of lncRNA, miRNA and mRNA in esophageal cancer (ESCA) and normal esophageal tissues, and GEO database was used to further validate the expression profile of key genes. Differential lncRNAs in TCGA database were submitted to Starbase, and lncRNAs related to overall survival were analyzed using Kaplan-Meier and log-rank test. We found 145 lncRNAs, 112 miRNAs and 2000 protein coding mRNAs were differentially expressed in ESCA samples, which were tightly involved in chromosome segregation, extracellular matrix assembly by GO assay, and KEGG assay revealed the correlation of differentially expressed genes with cell cycle, apoptosis and cGMP-PKG signaling pathway. Furthermore, there were 291 nodes in ceRNA network, which consisted of 40 lncRNAs, 28 miRNAs and 233 mRNAs, and formed 677 relations. Furthermore, 6 of 10 lncRNAs in TCGA database were consistent with GEO database, and expressions of 10 mRNAs in TCGA database all exhibited the same tendency with GEO database. Notably, we found 8 lncRNAs (WDFY3-AS2, CASC8, UGDH-AS1, RAP2C-AS1, AC007128.1, AC016205.1, AC092803.2 and AC079949.2) were correlated with overall survival of the patients with ESCA. The key differentially expressed genes participate in the development and progression of ESCA, and thus the elucidation of functions of lncRNA-miRNA-mRNA will provide new novel therapeutic target for the patients with ESCA.

Role of lncRNA uc.457 in the differentiation and maturation of cardiomyocytes

Congenital heart disease (CHD) is the most common type of birth defect, and the leading cause of fetal mortality. The long noncoding RNA (lncRNA) uc.457 is differentially expressed in cardiac tissue from patients with a ventricular septal defect; however, its role in cardiac development and CHD remains unknown. In the present study, the role of uc.457 in the differentiation and maturation of cardiomyocytes was investigated. Bioinformatics approaches were employed to analyze putative transcription factor (TF) regulation, histone modifications and the biological functions of uc.457. Subsequently, uc.457 overexpression and small interfering RNA‑mediated knockdown were performed to evaluate the functional role of the lncRNA in the dimethyl sulfoxide‑induced differentiation of P19 cells into cardiomyocytes. Bioinformatics analyses predicted that uc.457 binds to TFs associated with cardiomyocyte growth and cardiac development. Cell Counting Kit‑8 assays demonstrated that uc.457 overexpression inhibited cell proliferation, whereas knockdown of uc.457 enhanced the proliferation of differentiating cardiomyocytes. Additionally, reverse transcription‑quantitative polymerase chain reaction and western blot analyses revealed that overexpression of uc.457 suppressed the mRNA and protein expression of histone cell cycle regulation defective homolog A, natriuretic peptide A, cardiac muscle troponin T and myocyte‑specific enhancer factor 2C. Collectively, the results indicated that overexpression of uc.457 inhibited the differentiation and proliferation of cardiomyocytes, suggesting that dysregulated uc.457 expression may be associated with CHD.

The Role of Non-Coding RNA in Congenital Heart Diseases

Cardiovascular development is a complex developmental process starting with the formation of an early straight heart tube, followed by a rightward looping and the configuration of atrial and ventricular chambers. The subsequent step allows the separation of these cardiac chambers leading to the formation of a four-chambered organ. Impairment in any of these developmental processes invariably leads to cardiac defects. Importantly, our understanding of the developmental defects causing cardiac congenital heart diseases has largely increased over the last decades. The advent of the molecular era allowed to bridge morphogenetic with genetic defects and therefore our current understanding of the transcriptional regulation of cardiac morphogenesis has enormously increased. Moreover, the impact of environmental agents to genetic cascades has been demonstrated as well as of novel genomic mechanisms modulating gene regulation such as post-transcriptional regulatory mechanisms. Among post-transcriptional regulatory mechanisms, non-coding RNAs, including therein microRNAs and lncRNAs, are emerging to play pivotal roles. In this review, we summarize current knowledge on the functional role of non-coding RNAs in distinct congenital heart diseases, with particular emphasis on microRNAs and long non-coding RNAs.

Expression profiling of lncRNAs and mRNAs reveals regulation of muscle growth in the Pacific abalone, Haliotis discus hannai

Long non-coding RNAs (lncRNAs) are known to play a major role in the epigenetic regulation of muscle development. Unfortunately there is little understanding of the mechanisms with which they regulate muscle growth in abalone. Therefore, we used RNA-seq to study the muscle transcriptomes of six Haliotis discus hannai specimens: three large (L_HD group) and three small (S_HD group). We identified 2463 lncRNAs in abalone muscle belonging to two subtypes: 160 anti-sense lncRNAs and 2303 intergenic lncRNAs (lincRNAs). In the L_HD group, we identified 204 significantly differentially expressed lncRNAs (55 upregulated and 149 downregulated), and 2268 significantly differentially expressed mRNAs (994 upregulated and 1274 downregulated), as compared to the S_HD group. The bioinformatics analysis indicated that lncRNAs were relate to cell growth, regulation of growth, MAPK signaling pathway, TGF-β signaling pathway, PI3K-Akt and insulin signaling pathway, which involved in regulating muscle growth. These findings contribute to understanding the possible regulatory mechanisms of muscle growth in Pacific abalone.

Expression profile of long non‑coding RNAs in cardiomyocytes exposed to acute ischemic hypoxia

Acute myocardial infarction (AMI) is a life-threatening disease and seriously influences patient quality of life. Long non-coding RNAs (lncRNAs), an emerging class of non-coding genes, have attracted attention in research, however, whether lncRNAs serve a function in acute ischemic hypoxia remains to be elucidated. In the present study, an lncRNA microarray was used to analyze differential lncRNA expression in acute ischemic hypoxia. A total of 323 lncRNAs were identified, 168 of which were upregulated and 155 of which were downregulated. Gene Ontology and Pathway analyses were also used to identify the potential functions of dysregulated lncRNAs; it was predicted that these dysregulated lncRNAs may contribute to the initiation of AMI. It was demonstrated that an lncRNA termed sloyfley may influence acute ischemic hypoxia through its neighboring gene Peg3, which has been linked to brain ischemia hypoxia. In summary, the present study identified numerous lncRNAs, which may provide further opportunities for the development of novel therapeutic strategies.

Altered DNA Methylation of Long Noncoding RNA uc.167 Inhibits Cell Differentiation in Heart Development

In previous studies, we have demonstrated the function of uc.167 in the heart development. DNA methylation plays a crucial role in regulating the expression of developmental genes during embryonic development. In this study, the methylomic landscape was investigated in order to identify the DNA methylation alterations. Methylated DNA immunoprecipitation (MeDIP) was performed to examine the differences in methylation status of overexpressed uc.167 in P19 cells. GO and KEGG pathway analyses of differentially methylated genes were also conducted. We found that the distribution of differentially methylated regions (DMRs) peaks in different components of genome was mainly located in intergenic regions and intron. The biological process associated with uc.167 was focal adhesion and Rap1 signaling pathway. MEF2C was significantly decreased in uc.167 overexpressed group, suggesting that uc.167 may influence the P19 differentiation through MEF2C reduction. Taken together, our findings revealed that the effect of uc.167 on P19 differentiation may be attributed to the altered methylation of specific genes.

LncRNA uc.48+ is involved in the diabetic immune and inflammatory responses mediated by P2X7 receptor in RAW264.7 macrophages

High glucose combined with high FFAs can contribute to the unfavorable development of type 2 diabetes mellitus (T2DM) and monocytes/macrophages are important in the occurrence and development of T2DM, which is regarded as a type of low‑grade inflammation. Although our previous study demonstrated that increased expression of P2X7 receptor (P2X7R) in peripheral blood monocytes may alter the innate immune system and that long non‑coding (lnc)RNA uc.48+ was involved in diabetic neuropathic pain, the involvement of uc.48+ mediated by the P2X7R in monocyte/macrophages during T2DM has not been reported. In the present study, the effectsof uc.48+ small interference RNA (siRNA) on factors, including the mRNA and protein expression of P2X7R, apoptosis and proliferation, levels of reactive oxygen species (ROS), cytokine levels, and expression of phosphorylated (p‑) extracellular signal‑regulated kinase (ERK)1/2, were examined in RAW264.7 macrophages following exposure to high glucose and high plasma free fatty acids (FFAs). After RAW264.7 cells were transfected with uc.48+ siRNA under high glucose conditions and FFAs treatment, the mRNA expression levels of uc.48+ and P2X7 receptor were detected by reverse transcription‑polymerase chain reaction. The protein mass of P2X7 receptor and ERK signaling pathway were assessed by western blotting. ROS and calcium concentrations, and culture supernatant cytokine content [tumor necrosis factor‑α, interleukin (IL)‑10, IL‑1β] were detected by fluorescent probes and ELISA respectively. Cell viability and apoptosis were determined by MTS test and flow cytometry, respectively. It was found that treatment of RAW264.7 cells with high glucose and FFAs, which exhibited increased expression of uc.48+, evoked P2X7R‑mediated immune and inflammatory responses through several means, including cytokine secretion, ROS formation, and activation of the ERK signaling pathway. The uc.48+ siRNA regulated these factors and thus influenced the course and outcome of the immune and inflammatory responses mediated by P2X7R.

The role of long non-coding RNAs in cardiac development and disease

Cells display a set of RNA molecules at one time point, reflecting thus the cellular transcriptional steady state, configuring therefore its transcriptome. It is basically composed of two different classes of RNA molecules; protein-coding RNAs (cRNAs) and protein non-coding RNAs (ncRNAs). Sequencing of the human genome and subsequently the ENCODE project identified that more than 80% of the genome is transcribed in some type of RNA. Importantly, only 3% of these transcripts correspond to protein-coding RNAs, pointing that ncRNAs are as important or even more as cRNAs. ncRNAs have pivotal roles in development, differentiation and disease. Non-coding RNAs can be classified into two distinct classes according to their length; i.e., small (<200 nt) and long (>200 nt) noncoding RNAs. The structure, biogenesis and functional roles of small non-coding RNA have been widely studied, particularly for microRNAs (miRNAs). In contrast to microRNAs, our current understanding of long non-coding RNAs (lncRNAs) is limited. In this manuscript, we provide state-of-the art review of the functional roles of long non-coding RNAs during cardiac development as well as an overview of the emerging role of these ncRNAs in distinct cardiac diseases.

MEF2 signaling and human diseases

The members of myocyte Enhancer Factor 2 (MEF2) protein family was previously believed to function in the development of heart and muscle. Recent reports indicate that they are also closely associated with development and progression of many human diseases. Although their role in cancer biology is well established, the molecular mechanisms underlying their action is yet largely unknown. MEF2 family is closely associated with various signaling pathways, including Ca²⁺ signaling, MAP kinase signaling, Wnt signaling, PI3K/Akt signaling, etc. microRNAs also contribute to regulate the activities of MEF2. In this review, we summarize the known molecular mechanism by which MEF2 family contribute to human diseases.

LncRNA PlncRNA‑1 regulates proliferation and differentiation of hair follicle stem cells through TGF‑β1‑mediated Wnt/β‑catenin signal pathway

The present study demonstrated that hair follicle stem cells (HFSc) have multidirectional differentiation potential and participate in skin wound healing processes. Long non‑coding RNAs (lncRNAs) are defined as non‑protein coding transcripts longer than 200 nucleotides, which are important in the proliferation and differentiation of cells. The purpose of the present study was to investigate the role of PlncRNA‑1 in the proliferation and differentiation of HFSc. Results revealed that PlncRNA‑1, transforming growth factor (TGF)‑β1, Wnt and β‑catenin expression levels were significantly downregulated in HFSc. PlncRNA‑1 transfection promoted proliferation and differentiation of HFSc. TGF‑β1, Wnt and β‑catenin expression levels were upregulated in HFSc following transfection of PlncRNA‑1. Results demonstrated that TGF‑β1 inhibitor LY2109761 blocked proliferation and differentiation of HFSc promoted by PlncRNA‑1 transfection. In addition, TGF‑β1 inhibitor LY2109761 led to decreased Wnt and β‑catenin expression levels in HFSc. Furthermore, PlncRNA‑1 transfection stimulated the cell cycle of HFSc, whereas TGF‑β1 inhibitor LY2109761 inhibited the cell cycle of HFSc and decreased the acceleration of the cell cycle induced by PlncRNA‑1 transfection. In conclusion, these findings suggest that PlncRNA‑1 may promote proliferation and differentiation of HFSc through upregulation of TGF‑β1‑mediated Wnt/β‑catenin signaling pathway.

Impact of miR-26b on cardiomyocyte differentiation in P19 cells through regulating canonical/non-canonical Wnt signalling

BACKGROUND AND OBJECTIVES

The control of cardiomyocyte differentiation is tightly linked to microRNAs (miRNAs), which have been emerging as important players in heart development. However, the regulation mechanisms mediated by miRNAs in early heart development remains speculative. Here, we evaluated the impact of miR-26b during the progression of cardiomyocyte differentiation from the P19 cell line.

MATERIALS AND METHODS

The overexpression of miR-26b in P19 cells was performed by transduction with lentivirus vector. The levels of cardiac-related genes during P19 cell differentiation were detected using quantitative real-time PCR for mRNA abundance and Western blots for protein expression. ICG-001 was applied to elucidate the role of β-catenin on P19 cells differentiation. The Cell Counting kit-8 (CCK-8) was used to monitor the cell proliferation. The target genes of miR-26b were validated using the dual luciferase reporter system.

RESULTS

Overexpression of miR-26b upregulates the expression level of cardiomyocyte-related genes such as Gata4, cTNT, α-MHC and α-Actinin that comprehensively represent cardiomyocyte differentiation by effecting Wnt5a signalling and Gsk3β activity. However, ICG-001 blocks the differentiation along with inhibition of the cell proliferation. In addition, miR-26b also regulates CyclinD1 to promote P19 cell proliferation, thereby, demonstrating the rapid aggregation and differentiation programming of these cells into cardiomyocytic types.

CONCLUSIONS

Our results indicated that miR-26b exerts a role on promoting cardiomyocyte differentiation of P19 cells by controlling the canonical and non-canonical Wnt signalling.

A lncRNA Perspective into (Re)Building the Heart

Our conception of the human genome, long focused on the 2% that codes for proteins, has profoundly changed since its first draft assembly in 2001. Since then, an unanticipatedly expansive functionality and convolution has been attributed to the majority of the genome that is transcribed in a cell-type/context-specific manner into transcripts with no apparent protein coding ability. While the majority of these transcripts, currently annotated as long non-coding RNAs (lncRNAs), are functionally uncharacterized, their prominent role in embryonic development and tissue homeostasis, especially in the context of the heart, is emerging. In this review, we summarize and discuss the latest advances in understanding the relevance of lncRNAs in (re)building the heart.