Regulation of the apolipoprotein gene cluster by a long noncoding RNA

Long Non-Coding RNAs in Brown Adipose Tissue

Obesity has become a widespread disease that is harmful to human health. Fat homeostasis is essentially maintained by fat accumulation and energy expenditure. Studies on brown adipose tissue (BAT) represent a promising opportunity to identify a pharmaceutical intervention against obesity through increased energy expenditure. Long non-coding RNAs (lncRNAs) were thought to be critical regulators in a variety of biological processes. Recent studies have revealed that lncRNAs, including ones that are BAT-specific, conserved, and located at key protein-coding genes, function in brown adipogenesis, white adipose browning (ie, beige adipogenesis), and brown thermogenesis. In this review, we describe lncRNA properties and highlight functional lncRNAs in these biological processes, with the goal of establishing links between lncRNAs and BAT. Based on the advances of lncRNAs in the regulation of BAT, we discussed the advantages of potential lncRNA-based obesity drugs. Further BAT lncRNA-based drug development may provide new exciting approaches to defend obesity by regulation of fat homeostasis.

lncRNA FEZF1‑AS1 promotes migration, invasion and epithelial‑mesenchymal transition of retinoblastoma cells by targeting miR‑1236‑3p

Long non-coding RNAs (lncRNAs) and microRNAs (miRs) have been reported to regulate disease progression in numerous types of disease, including retinoblastoma (Rb). Therefore, the present study aimed to investigate the effects of the lncRNA FEZ family zinc finger 1 antisense RNA 1 (FEZF1-AS1) on Rb and to determine its possible mechanism of action. Reverse transcription-quantitative PCR and western blot analysis were conducted to detect the gene or protein expression. Cell Counting Kit-8, wound healing and transwell invasion assays were performed to estimate the capabilities of cell viability, invasion and migration. The potential association between FEZF1-AS1 and miR-1236-3p in Y79 cells was measured via dual-luciferase reporter assay. The results of the present study revealed that the levels of FEZF1-AS1 were significantly upregulated in different Rb cell lines, with the most prominent upregulation observed in Y79 cells. In addition, the cell viability, invasive and migratory abilities, and the ability to undergo epithelial-mesenchymal transition (EMT), were significantly inhibited following the transfection of short hairpin RNA (shRNA)-FEZF1-AS1 into Y79 cells. Further experimental validation confirmed that miR-1236-3p may be a direct target of FEZF1-AS1. Notably, the miR-1236-3p inhibitor was discovered to reverse the inhibitory effects of shRNA-FEZF1-AS1 on cell viability, invasion, migration and EMT. In conclusion, the findings of the present study suggested that lncRNA-FEZF1-AS1 may promote the viability, migration, invasion and EMT of Rb cells by modulating miR-1236-3p.

Our emerging understanding of the roles of long non-coding RNAs in normal liver function, disease, and malignancy

Long non-coding RNAs (lncRNAs) are important biological mediators that regulate numerous cellular processes. New experimental evidence suggests that lncRNAs play essential roles in liver development, normal liver physiology, fibrosis, and malignancy, including hepatocellular carcinoma and cholangiocarcinoma. In this review, we summarise our current understanding of the function of lncRNAs in the liver in both health and disease, as well as discuss approaches that could be used to target these non-coding transcripts for therapeutic purposes.

Noncoding RNAs in Cardiovascular Disease: Current Knowledge, Tools and Technologies for Investigation, and Future Directions: A Scientific Statement From the American Heart Association

BACKGROUND

The discovery that much of the non-protein-coding genome is transcribed and plays a diverse functional role in fundamental cellular processes has led to an explosion in the development of tools and technologies to investigate the role of these noncoding RNAs in cardiovascular health. Furthermore, identifying noncoding RNAs for targeted therapeutics to treat cardiovascular disease is an emerging area of research. The purpose of this statement is to review existing literature, offer guidance on tools and technologies currently available to study noncoding RNAs, and identify areas of unmet need.

METHODS

The writing group used systematic literature reviews (including MEDLINE, Web of Science through 2018), expert opinion/statements, analyses of databases and computational tools/algorithms, and review of current clinical trials to provide a broad consensus on the current state of the art in noncoding RNA in cardiovascular disease.

RESULTS

Significant progress has been made since the initial studies focusing on the role of miRNAs (microRNAs) in cardiovascular development and disease. Notably, recent progress on understanding the role of novel types of noncoding small RNAs such as snoRNAs (small nucleolar RNAs), tRNA (transfer RNA) fragments, and Y-RNAs in cellular processes has revealed a noncanonical function for many of these molecules. Similarly, the identification of long noncoding RNAs that appear to play an important role in cardiovascular disease processes, coupled with the development of tools to characterize their interacting partners, has led to significant mechanistic insight. Finally, recent work has characterized the unique role of extracellular RNAs in mediating intercellular communication and their potential role as biomarkers.

CONCLUSIONS

The rapid expansion of tools and pipelines for isolating, measuring, and annotating these entities suggests that caution in interpreting results is warranted until these methodologies are rigorously validated. Most investigators have focused on investigating the functional role of single RNA entities, but studies suggest complex interaction between different RNA molecules. The use of network approaches and advanced computational tools to understand the interaction of different noncoding RNA species to mediate a particular phenotype may be required to fully comprehend the function of noncoding RNAs in mediating disease phenotypes.

Microarray analysis of long non-coding RNA expression profiles in low high-density lipoprotein cholesterol disease

Background

Low high-density lipoprotein cholesterol (HDL-C) disease with unknown etiology has a high prevalence in the Xinjiang Kazak population. In this study, long noncoding RNAs (lncRNAs) that might play a role in low HDL-C disease were identified.

Methods

Plasma samples from 10 eligible individuals with low HDL disease and 10 individuals with normal HDL-C levels were collected. The lncRNA profiles for 20 Xinjiang Kazak individuals were measured using microarray analysis.

Results

Differentially expressed lncRNAs and mRNAs with fold-change values not less than 1.5 and FDR-adjusted P-values less than 0.05 were screened. Bioinformatic analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and network analyses, were used to determine relevant signaling pathways and predict potential target genes. In total, 381 lncRNAs and 370 mRNAs were differentially expressed based on microarray analysis. Compared with those in healthy individuals, several lncRNAs were upregulated or downregulated in patients with low HDL-C disease, among which TCONS_00006679 was most significantly upregulated and TCONS_00011823 was most significantly downregulated. GO and KEGG pathway analyses as well as co-expression networks of lncRNAs and mRNAs revealed that the platelet activation pathway and cardiovascular disease were associated with low HDL-C disease.

Conclusions

Potential target genes integrin beta-3 (ITGB3) and thromboxane A2 receptor (TBXA2R) were regulated by the lncRNAs AP001033.3–201 and AC068234.2–202, respectively. Both genes were associated with cardiovascular disease and were involved in the platelet activation pathway. AP001033.3–201 and AC068234.2–202 were associated with low HDL-C disease and could play a role in platelet activation in cardiovascular disease. These results reveal the potential etiology of dyslipidemia in the Xinjiang Kazakh population and lay the foundation for further validation using large sample sizes.

Non-coding RNAs, metabolic stress and adaptive mechanisms in cancer

Metabolic reprogramming in cancer describes the multifaceted alterations in metabolism that contribute to tumorigenesis. Major determinants of metabolic phenotypes are the changes in signalling pathways associated with oncogenic activation together with cues from the tumor microenvironment. Therein, depleted oxygen and nutrient levels elicit metabolic stress, requiring cancer cells to engage adaptive mechanisms. Non-coding RNAs (ncRNAs) act as regulatory elements within metabolic pathways and their widespread dysregulation in cancer contributes to altered metabolic phenotypes. Indeed, ncRNAs are the regulatory accomplices of many prominent effectors of metabolic reprogramming including c-MYC and HIFs that are activated by metabolic stress. By example, this review illustrates the range of ncRNAs mechanisms impacting these effectors throughout their DNA-RNA-protein lifecycle along with presenting the mechanistic roles of ncRNAs in adaptive responses to glucose, glutamine and lipid deprivation. We also discuss the facultative activation of metabolic enzymes by ncRNAs, a phenomenon which may reflect a broad but currently invisible level of metabolic regulation. Finally, the translational challenges associated with ncRNA discoveries are discussed, emphasizing the gaps in knowledge together with importance of understanding the molecular basis of ncRNA regulatory mechanisms.

Alzheimer's disease in the gut-Major changes in the gut of 5xFAD model mice with ApoA1 as potential key player

Alzheimer's disease (AD) affects around 33 million people worldwide, which makes it the most prominent form of dementia. The main focus of AD research has been on the central nervous system (CNS) for long, but in recent years, the gut gained more attention. The intestinal tract is innervated by the enteric nervous system (ENS), built of numerous different types of neurons showing great similarity to neurons of the CNS. It already has been demonstrated that the amyloid precursor protein, which plays a major role in AD pathology, is also expressed in these cells. We analyzed gut tissue of AD model mice (5xFAD) and the respective wild-type littermates at different pathological stages: pre-pathological, early pathological and late pathological. Our results show significant difference in function of the intestine of 5xFAD mice as compared to wild-type mice. Using a pathway array detecting 84 AD-related gene products, we found ApoA1 expression significantly altered in colon tissue of 5xFAD mice. Furthermore, we unveil ApoA1's beneficial impact on cell viability and calcium homeostasis of cultured enteric neurons of 5xFAD animals. With this study, we demonstrate that the intestine is altered in AD-like pathology and that ApoA1 might be one key player within the gut.

Direct Administration and Gene Modulation Using Antisense Oligonucleotides Within the CNS

Besides his vast contribution to the opioid receptor studies, Dr. G. W. Pasternak was among the early pioneers in the antisense oligonucleotide (ASO) field at the time when the crucial in vivo studies using ASO-mediated gene knockdown in the CNS were still impeded by the ASO's inability to cross the blood-brain barrier. This changed at the start of 1990s, when administration of oligonucleotides through intracerebroventricular or, later, intrathecal injection was undertaken at Cornell University Medical College and further developed in close collaboration with Pasternak lab. These early studies eventually led to the practical realization of the significant therapeutic potential of ASO-based drugs we see today.

LncRNA SNHG3 promotes bladder cancer proliferation and metastasis through miR-515-5p/GINS2 axis

Growing evidence suggests that long non‐coding RNAs (lncRNAs) are associated with carcinogenesis. LncRNA small nucleolar RNA host gene 3 (SNHG3) is up‐regulated in various cancers and positively associated with poor prognosis of these cancers. However, the precise role of lncRNA SNHG3 in bladder cancer (Bca) remains unclear. In our research, we first reported that lncRNA SNHG3 was up‐regulated in bladder cancer tissues and positively related to poor clinical prognosis. Moreover, knockdown of lncRNA SNHG3 significantly suppressed the proliferation, migration, invasion and EMT process of Bca cells in vitro and vivo. Mechanistically, we revealed that suppression of SNHG3 evidently enhanced miR‐515‐5p expression and decreased GINS2 expression at posttranscriptional levels. Moreover, SNHG3 positively regulated GINS2 expression by sponging miR‐515‐5p under a competing endogenous RNA (ceRNA) mechanism. To sum up, our study suggested lncRNA SNHG3 acted as a microRNA sponge and an oncogenic role in the progression of bladder cancer.

The Roles of Long Noncoding RNAs HNF1α-AS1 and HNF4α-AS1 in Drug Metabolism and Human Diseases

Long noncoding RNAs (lncRNAs) are RNAs with a length of over 200 nucleotides that do not have protein-coding abilities. Recent studies suggest that lncRNAs are highly involved in physiological functions and diseases. lncRNAs HNF1α-AS1 and HNF4α-AS1 are transcripts of lncRNA genes HNF1α-AS1 and HNF4α-AS1, which are antisense lncRNA genes located in the neighborhood regions of the transcription factor (TF) genes HNF1α and HNF4α, respectively. HNF1α-AS1 and HNF4α-AS1 have been reported to be involved in several important functions in human physiological activities and diseases. In the liver, HNF1α-AS1 and HNF4α-AS1 regulate the expression and function of several drug-metabolizing cytochrome P450 (P450) enzymes, which also further impact P450-mediated drug metabolism and drug toxicity. In addition, HNF1α-AS1 and HNF4α-AS1 also play important roles in the tumorigenesis, progression, invasion, and treatment outcome of several cancers. Through interacting with different molecules, including miRNAs and proteins, HNF1α-AS1 and HNF4α-AS1 can regulate their target genes in several different mechanisms including miRNA sponge, decoy, or scaffold. The purpose of the current review is to summarize the identified functions and mechanisms of HNF1α-AS1 and HNF4α-AS1 and to discuss the future directions of research of these two lncRNAs.

Machine Learning Supports Long Noncoding RNAs as Expression Markers for Endometrial Carcinoma

Uterine corpus endometrial carcinoma (UCEC) is the second most common type of gynecological tumor. Several research studies have recently shown the potential of different ncRNAs as biomarkers for prognostics and diagnosis in different types of cancers, including UCEC. Thus, we hypothesized that long noncoding RNAs (lncRNAs) could serve as efficient factors to discriminate solid primary (TP) and normal adjacent (NT) tissues in UCEC with high accuracy. We performed an in silico differential expression analysis comparing TP and NT from a set of samples downloaded from the Cancer Genome Atlas (TCGA) database, targeting highly differentially expressed lncRNAs that could potentially serve as gene expression markers. All analyses were performed in R software. The receiver operator characteristics (ROC) analyses and both supervised and unsupervised machine learning indicated a set of 14 lncRNAs that may serve as biomarkers for UCEC. Functions and putative pathways were assessed through a coexpression network and target enrichment analysis.

Identifying functional non-coding variants in APOA5/A4/C3/A1 gene cluster associated with coronary heart disease

Recent genome-wide association studies identified several polymorphisms in the APOA5/A4/C3/A1 gene cluster influencing lipids level and risk of coronary heart disease (CHD). However, few studies explored the molecular mechanism. The purposes of this study were to fine-map noncoding region between APOA1 and APOC3 and then explore the clinical relevance in CHD and potential underlying mechanisms. In this study, a 2.7-kb length of the non-coding region between APOA1 and APOC3 was screened and five polymorphisms were investigated in the case-control study. The molecular mechanism was explored. Our data confirmed the association between rs7123454, rs12721030, rs10750098, and rs12721028 with CHD in 828 patients and 828 controls and replicated it in an independent population of 405 patients and 405 controls. In addition, the rs10750098 and rs12721030 are significantly associated with decreased serum APOA1 levels (P = 4.2 × 10^-4 and P = 3.2 × 10^-5, combined analysis), while a significant association was observed between serum APOA1 level and CHD (OR: 0.43, 95% CI: 0.28-0.64, P < .01) with adjustment for clinical covariates and different population sets. In vitro evaluation of potential function of non-coding variants between APOA1 and APOC3 demonstrated that rs10750098 as being the most sufficient to confer the haplotype-specific effect on the regulation of APOs gene transcription. Our results strongly implicate the involvement of common noncoding DNA variants in APOA5/A4/C3/A1 gene cluster in the pathogenesis of dyslipidemia and the risk of CHD.

The novel long noncoding RNA Lnc19959.2 modulates triglyceride metabolism-associated genes through the interaction with Purb and hnRNPA2B1

Objective

Long noncoding RNAs (lncRNAs) are currently considered to have a vital and wide range of biological functions, but the molecular mechanism underlying triglycerides metabolism remains poorly understood. This study aims to identify novel lncRNAs differentially expressed in rat livers with hypertriglyceridemia and elucidated the function role in TG metabolism.

Methods

Differentially expressions of lncRNAs in rat livers with hypertriglyceridemia were identified by transcriptome sequencing and validated by real-time PCR. The role of lnc19959.2 in triglyceride metabolism was assessed both in vitro and in vivo. RNA pulldown and RIP assays were conducted to evaluate the interactions between lnc19959.2 and its target proteins. ChIP and Dual report assays were performed to detect the interactions between transcription factors and promoters of its target genes.

Results

We identified a novel lncRNA, and lnc19959.2 was upregulated in rat livers with hypertriglyceridemia. The knockdown of lnc19959.2 has profound TG lowering effects in vitro and in vivo. Subsequently, the genome-wide analysis identified that the knockdown of lnc19959.2 caused the deregulation of many genes during TG homeostasis. Further mechanism studies revealed that lnc19959.2 upregulated ApoA4 expression via ubiquitinated transcription inhibitor factor Purb, while it specifically interacted with hnRNPA2B1 to downregulate the expression of Cpt1a, Tm7sf2, and Gpam, respectively. In the upstream pathway, palmitate acid upregulated CCAAT/Enhancer-Binding Protein Beta (Cebpb) and facilitated its binding to the promoter of lnc19959.2, which resulted in significant promotion of lnc19959.2 transcriptional activity.

Conclusions

Our findings provide novel insights into a new layer regulatory complexity of an lncRNA modulating triglyceride homeostasis by a novel lncRNA lnc19959.2.

•

lnc19959.2 was identified as a novel LncRNA in hypertriglyceridemic rat liver.

•

lnc19959.2 was involved in triglyceride metabolism in vivo and in vitro.

•

lnc19959.2 upregulated ApoA4 expression via ubiquitinated transcription inhibitor factor Purb.

•

lnc19959.2 interacted with hnRNPA2B1 and cooperated with RNP II that controls expression of Cpt1a, Tm7sf2 and Gpam.

mTORC1-dependent protein synthesis and autophagy uncouple in the regulation of Apolipoprotein A-I expression

BACKGROUND

Apolipoprotein A-I (ApoA-I) is involved in reverse cholesterol transport as a major component of HDL, but also conveys anti-thrombotic, anti-oxidative, anti-inflammatory and immune-regulatory properties that are pertinent to its protective roles in cardiovascular, inflammatory and malignant pathologies. Despite the pleiotropy in ApoA-I functions, the regulation of intracellular ApoA-I levels remains poorly explored.

METHODS

HepG2 hepatoma cells and primary mouse hepatocytes were used as in vitro models to study the impact of genetic and chemical inhibitors of autophagy and the proteasome on ApoA-I by immunoblot, immunofluorescence and electron microscopy. Different growth conditions were implemented in conjunction with mTORC inhibitors to model the influence of nutrient scarcity versus sufficiency on ApoA-I regulation. Hepatic ApoA-I expression was also evaluated in high fat diet-fed mice displaying blockade in autophagy.

RESULTS

Under nutrient-rich conditions, basal ApoA-I levels in liver cells are sustained by the balancing act of autophagy and of mTORC1-dependent de novo protein synthesis. ApoA-I proteolysis occurs through a canonical autophagic pathway involving Beclin1 and ULK1 and the receptor protein p62/SQSTM1 that targets ApoA-I to autophagosomes. However, upon aminoacid insufficiency, suppression of ApoA-I synthesis prevails, rendering mTORC1 inactivation dispensable for autophagy-mediated ApoA-I proteolysis.

CONCLUSION

These data underscore the major contribution of post-transcriptional mechanisms to ApoA-I levels which differentially involve mTORC1-dependent signaling to protein synthesis and autophagy, depending on nutrient availability. Given the established role of ApoA-I in HDL-mediated reverse cholesterol transport, this mode of ApoA-I regulation may reflect a hepatocellular response to the organismal requirement for maintenance of cholesterol and lipid reserves under conditions of nutrient scarcity.

Understanding the mechanistic insight of arsenic exposure and decoding the histone cipher

BACKGROUND

The study of heritable epigenetic changes in arsenic exposure has intensified over the last decade. Groundwater arsenic contamination causes a great threat to humans and, to date, no accurate measure has been formulated for remediation. The fascinating possibilities of epi-therapeutics identify the need for an in-depth mechanistic understanding of the epigenetic landscape.

OBJECTIVE

In this comprehensive review, we have set to analyze major studies pertaining to histone post-translational modifications in arsenic-mediated disease development and carcinogenesis during last ten years (2008-2018).

RESULTS

The role of the specific histone marks in arsenic toxicity has been detailed. A comprehensive list that includes major arsenic-induced histone modifications identified for the last 10 years has been documented and details of different states of arsenic, organisms, exposure type, study platform, and findings were provided. An arsenic signature panel was suggested to help in early prognosis. An attempt has been made to identify the grey areas of research.

PROSPECTS

Future prospective multi-target analyses of the inter-molecular crosstalk among different histone marks are needed to be explored further in order to understand the mechanism of arsenic toxicity and carcinogenicity and to confirm the suitability of these epi-marks as prognostic markers.

Long noncoding RNAs APOA1-AS, IFNG-AS1, RMRP and their related biomolecules in Egyptian patients with relapsing-remitting multiple sclerosis: Relation to disease activity and patient disability

Lately, long noncoding (lnc) RNAs are increasingly appreciated for their involvement in multiple sclerosis (MS). In inflammation and autoimmunity, a role of apoprotein A1 (ApoA1), mediated by sphingosine 1-phosphate receptors (S1PRs), was reported. However, the epigenetic mechanisms regulating these biomolecules and their role in MS remains elusive. This case control study investigated the role of ApoA1, sphingosine kinase 1 and 2 (SPHK1 & 2), S1PR1 & 5, interferon-γ (IFN-γ) and interleukin 17 (IL17) in MS, beside three lncRNA: APOA1-AS, IFNG-AS1, and RMRP. Expression of SPHKs, S1PRs, and lncRNAs were measured in 72 relapsing-remitting MS patients (37 during relapse and 35 in remission) and 28 controls. Plasma levels of ApoA1, IFN-γ and IL17 were determined. The impact of these parameters on MS activity, relapse rate and patient disability was assessed. APOA1-AS, IFNG-AS1, SPHK1 & 2, and S1PR5 were upregulated in RRMS patients. Differences in ApoA1, SPHK2, and IL17 were observed between relapse and remission. Importantly, ApoA1, SPHK2, and IL17 were related to activity, while S1PR1 and IFN-γ were linked to disability, though, only IFN-γ was associated with relapse rate. Finally, an excellent diagnostic power of IFN-γ, IL17, SPHK1 and APOA1-AS was demonstrated, whereas SPHK2 showed promising prognostic power in predicting relapses.

Regulation of Glucose and Lipid Metabolism by Long Non-coding RNAs: Facts and Research Progress

Long non-coding RNAs (lncRNAs) are a type of non-coding RNA with a length that exceeds 200 nucleotides. Previous studies have shown that lncRNAs play an important role in the pathogenesis of various diseases. Research in both animal models and humans has begun to unravel the profound complexity of lncRNAs and demonstrated that lncRNAs exert direct effects on glucose and lipid metabolism both in vivo and in vitro. Such research has elucidated the regulatory role of lncRNAs in glucose and lipid metabolism in human disease. lncRNAs mediate glucose and lipid metabolism under physiological and pathological conditions and contribute to various metabolism disorders. This review provides an update on our understanding of the regulatory role of lncRNAs in glucose and lipid metabolism in various diseases. As our understanding of the function of lncRNAs improves, the future is promising for the development of new diagnostic biomarkers that utilize lncRNAs and treatments that target lncRNAs to improve clinical outcomes.

Long noncoding RNAs in lipid metabolism: literature review and conservation analysis across species

BACKGROUND

Lipids are important for the cell and organism life since they are major components of membranes, energy reserves and are also signal molecules. The main organs for the energy synthesis and storage are the liver and adipose tissue, both in humans and in more distant species such as chicken. Long noncoding RNAs (lncRNAs) are known to be involved in many biological processes including lipid metabolism.

RESULTS

In this context, this paper provides the most exhaustive list of lncRNAs involved in lipid metabolism with 60 genes identified after an in-depth analysis of the bibliography, while all "review" type articles list a total of 27 genes. These 60 lncRNAs are mainly described in human or mice and only a few of them have a precise described mode-of-action. Because these genes are still named in a non-standard way making such a study tedious, we propose a standard name for this list according to the rules dictated by the HUGO consortium. Moreover, we identified about 10% of lncRNAs which are conserved between mammals and chicken and 2% between mammals and fishes. Finally, we demonstrated that two lncRNA were wrongly considered as lncRNAs in the literature since they are 3' extensions of the closest coding gene.

CONCLUSIONS

Such a lncRNAs catalogue can participate to the understanding of the lipid metabolism regulators; it can be useful to better understand the genetic regulation of some human diseases (obesity, hepatic steatosis) or traits of economic interest in livestock species (meat quality, carcass composition). We have no doubt that this first set will be rapidly enriched in coming years.

LncRNA PU.1 AS regulates arsenic-induced lipid metabolism through EZH2/Sirt6/SREBP-1c pathway

Arsenic (As) is an omnipresent metalloid toxicant, which has elicited serious environmental pollution and health risky problems. Previous studies have uncovered that the As exposure could also cause markedly reduction of serum triglycerides in mice. However, the regulation mechanisms are still largely unknown. The present study is aimed to elucidate the molecular mechanisms of lncRNAs in As-induced lipid metabolic disequilibrium. We demonstrated that lncRNA PU.1 AS was significantly induced in the liver of As-feed mice companied with lower serum triglycerides contents; further in vitro experiment confirmed that PU.1 AS regulated liver cells lipid accumulation by nile red fluorescence staining. Intensive mechanistic investigations illustrated that PU.1 AS could interact with EZH2 protein to regulate its downstream target gene expression, and As-induced PU.1 AS attenuated EZH2-supppressed Sirt6 expression, thereafter leading to a decreased SREBP-1c protein expression, as well as the diminished synthesis of triglycerides in hepatocytes. In conclusion, this study provided a new lncRNA-related regulatory signaling pathway participating in As-induced abnormal lipid metabolism.

LncRNA MVIH knockdown inhibits the malignancy progression through downregulating miR-505 mediated HMGB1 and CCNE2 in acute myeloid leukemia

Background

This study aimed to investigate the regulatory role of long non-coding RNA associated with microvascular invasion in hepatocellular carcinoma (lnc-MVIH) in the progression of acute myeloid leukemia (AML) and the underlying mechanism.

Methods

Lnc-MVIH expression was detected in AML cell lines AML-193, KG-1, HL-60, OCI-AML2 and primary normal bone marrow mononuclear cells (BMMC). The effect of lnc-MVIH knockdown on cell proliferation, apoptosis and miR-505 expression were detected by transfection of lnc-MVIH shRNA and control shRNA into KG-1 cells. And the effect of miR-505 knockdown on lnc-MVIH, cell proliferation, cell apoptosis as well as potential miR-505 target genes [high mobility group box 1 (HMGB1) and cyclin E2 (CCNE2)] in lnc-MVIH knockdown treated KG-1 cells was assessed by transfection of lnc-MVIH shRNA and lnc-MVIH shRNA & miR-505 shRNA into KG-1 cells.

Results

Lnc-MVIH expression was elevated in AML-193, KG-1, OCI-AML2 cell lines, but similar in HL-60 cell line compared with primary normal BMMC. Lnc-MVIH knockdown inhibited cell proliferation but promoted cell apoptosis in KG-1 cells, meanwhile miR-505 expression was increased by lnc-MVIH knockdown in KG-1 cells. And in rescue experiments, miR-505 knockdown had no effect on expression of lnc-MVIH, while it increased the expressions of HMGB1 and CCNE2, promoted cell proliferation, inhibited cell apoptosis in lnc-MVIH knockdown treated KG-1 cells.

Conclusions

Lnc-MVIH knockdown inhibits cell proliferation but promotes cell apoptosis via regulating miR-505 mediated HMGB1 and CCNE2 in AML.

Long Non-Coding RNA MEG3 Promotes Apoptosis of Vascular Cells and is Associated with Poor Prognosis in Ischemic Stroke

Aim: This study focused on the expression pattern of long non-coding RNA maternally expressed gene 3 (MEG3) and its value in ischemic stroke (IS).

Methods: The expression pattern and the roles of MEG3 in the development of IS were explored in mice IS model and human brain microvascular endothelial cells (hBMECs). A case-control study, including 215 IS patients and 153 controls, was also conducted to investigate its prognostic value.

Results:In vivo study showed that MEG3 increased significantly in the IS group (P = 0.004), and its level remained stable within 3 to 48h after the onset of IS. Besides, the survival time of the mouse in the high MEG3 group was significantly lower than that in the low MEG3 group (P = 0.042). In vitro study showed that oxygen–glucose deprivation (OGD) treatment significantly up-regulated expressions of MEG3, Bax, and cleaved caspase-3, and further promoted apoptosis of hBMECs, while si-MEG3 blocked these effects. A human study showed that MEG3 increased markedly within 48h of IS onset and was positively associated with the National Institutes of Health Stroke Scale (r = 0.347, P < 0.001), modified Rankin Scale (r = 0.385, P < 0.001), high-sensitivity C-reactive protein (r = 0.221, P = 0.002) level, and infarct volume (r = 0.201, P = 0.006). Overall survival analysis showed that patients with higher MEG3 expression within 48h had a relatively poor prognosis (P < 0.001). Meanwhile, multivariate analysis revealed that MEG3 was an independent prognostic marker for unfavorable functional outcome and death in IS patients.

Conclusions: This study suggested that MEG3 might be considered as an intervention point and potential prognostic indicator for IS.

Invited Review: Long non-coding RNAs: important regulators in the development, function and disorders of the central nervous system

Genome-wide transcriptional studies have demonstrated that tens of thousands of long non-coding RNAs (lncRNA) genes are expressed in the central nervous system (CNS) and that they exhibit tissue- and cell-type specificity. Their regulated and dynamic expression and their co-expression with protein-coding gene neighbours have led to the study of the functions of lncRNAs in CNS development and disorders. In this review, we describe the general characteristics, localization and classification of lncRNAs. We also elucidate the examples of the molecular mechanisms of nuclear and cytoplasmic lncRNA actions in the CNS and discuss common experimental approaches used to identify and unveil the functions of lncRNAs. Additionally, we provide examples of lncRNA studies of cell differentiation and CNS disorders including CNS injuries and neurodegenerative diseases. Finally, we review novel lncRNA-based therapies. Overall, this review highlights the important biological roles of lncRNAs in CNS functions and disorders.

Long Noncoding RNAs in Atherosclerosis: JACC Review Topic of the Week

Atherosclerosis is a complex and chronic disease characterized by lipid deposition in the vessel wall that leads to an inflammatory and proliferative cascade involving smooth muscle, endothelial, and immune cells. Despite substantial improvements in our understanding of mechanisms contributing to atherosclerosis and overall reduction in cardiovascular mortality, the absolute disease burden remains substantially high. The recent discovery of a new group of mediators known as long noncoding ribonucleic acids (lncRNAs) offers a unique opportunity for the development of novel diagnostic and therapeutic tools in atherothrombotic disease. A number of studies suggest that lncRNAs are important mediators in health and disease, and rapidly accumulating evidence implicates lncRNAs in regulatory circuits controlling atherosclerosis. In this review, the authors outline important contributions of lncRNAs to atherosclerosis and its associated risk factors, including hypercholesterolemia, diabetes, hypertension, and obesity.

A DHX9-lncRNA-MDM2 interaction regulates cell invasion and angiogenesis of cervical cancer

Cervical cancer (CC) is the third most common carcinoma and the fourth leading cause of cancer-associated mortality in women. Here, we report that MDM2-DHX9 interaction mediates CC motility and angiogenesis in a long noncoding RNA-dependent fashion. A long noncoding RNA, named lnc-CCDST, is significantly downregulated in CC tissues, and binds to pro-oncogenic DHX9. DHX9 is upregulated in CC tissue, and promotes CC cell motility and angiogenesis. The lnc-CCDST and DHX9 interaction promotes DHX9 degradation through the ubiquitin proteasome pathway. Furthermore, DHX9 bound to E3 ubiquitin ligase MDM2, and this interaction is enhanced by lnc-CCDST. Thus, lnc-CCDST promotes DHX9 degradation by serving as a scaffold to facilitate the formation of MDM2 and DHX9 complexes. Moreover, HPV oncogenes E6 and E7 abolish the expression of lnc-CCDST resulting in the increase of DHX9. Our results have revealed a novel mechanism by which high-risk HPVs promote motility and angiogenesis of CC by inhibiting expression of lnc-CCDST to disrupt MDM2 and DHX9 interaction, and DHX9 degradation, and identified a potential therapeutic target for CC.

Apolipoprotein A-I (ApoA-I), Immunity, Inflammation and Cancer

Apolipoprotein A-I (ApoA-I), the major protein component of high-density lipoproteins (HDL) is a multifunctional protein, involved in cholesterol traffic and inflammatory and immune response regulation. Many studies revealing alterations of ApoA-I during the development and progression of various types of cancer suggest that serum ApoA-I levels may represent a useful biomarker contributing to better estimation of cancer risk, early cancer diagnosis, follow up, and prognosis stratification of cancer patients. In addition, recent in vitro and animal studies disclose a more direct, tumor suppressive role of ApoA-I in cancer pathogenesis, which involves anti-inflammatory and immune-modulatory mechanisms. Herein, we review recent epidemiologic, clinicopathologic, and mechanistic studies investigating the role of ApoA-I in cancer biology, which suggest that enhancing the tumor suppressive activity of ApoA-I may contribute to better cancer prevention and treatment.

Non-Coding RNAs and their Integrated Networks

Eukaryotic genomes are pervasively transcribed. Besides protein-coding RNAs, there are different types of non-coding RNAs that modulate complex molecular and cellular processes. RNA sequencing technologies and bioinformatics methods greatly promoted the study of ncRNAs, which revealed ncRNAs' essential roles in diverse aspects of biological functions. As important key players in gene regulatory networks, ncRNAs work with other biomolecules, including coding and non-coding RNAs, DNAs and proteins. In this review, we discuss the distinct types of ncRNAs, including housekeeping ncRNAs and regulatory ncRNAs, their versatile functions and interactions, transcription, translation, and modification. Moreover, we summarize the integrated networks of ncRNA interactions, providing a comprehensive landscape of ncRNAs regulatory roles.

Identification and characterization of a novel group of natural anti-sense transcripts from RNA1.2 gene locus of human cytomegalovirus

Background:

Natural anti-sense transcripts (NATs), which are transcribed from the complementary DNA strand of annotated genes, exert regulatory function of gene expression. Increasing studies recognized anti-sense transcription widespread throughout human cytomegalovirus (HCMV) genome, whereas the anti-sense transcription of RNA1.2 gene locus has never been investigated. In this study, the transcription of the RNA1.2 anti-sense strand was investigated in clinically isolated HCMV strain.

Methods:

Strand-specific high-through RNA-sequencing (RNA-seq) was performed to find possible anti-sense transcripts (ASTs). For analyzing and visualization of RNA-seq data sets, Integrative Genomics Viewer software was applied. To confirm these possibilities, Northern blotting and rapid amplification of cDNA ends (RACE) were used.

Results:

Transcription of the opposite strand of RNA1.2 gene locus was detected by RNA-sequencing using RNAs extracted from human embryonic lung fibroblasts infected with HCMV clinical isolate HAN. At least three HCMV NATs, named RNA1.2 AST 1, RNA1.2 AST2, and RNA1.2 AST3, were characterized by Northern blotting and RACE analyses. These RNA1.2 ASTs orientated from the complementary strand of RNA1.2 locus during the late phase of HCMV infection. The 5′- and 3′-termini of these transcripts were located within the opposite sequence of the predicted RNA1.2 gene.

Conclusion:

A cluster of novel NATs was transcribed from the opposite sequence of the HCMV RNA1.2 gene region.

The Dark That Matters: Long Non-coding RNAs as Master Regulators of Cellular Metabolism in Non-communicable Diseases

Non-coding RNAs are pivotal for many cellular functions, such as splicing, gene regulation, chromosome structure, and hormone-like activity. Here, we will report about the biology and the general molecular mechanisms associated with long non-coding RNAs (lncRNAs), a class of >200 nucleotides-long ribonucleic acid sequences, and their role in chronic non-transmissible diseases. In particular, we will summarize knowledge about some of the best-characterized lncRNAs, such as H19 and MALAT1, and how they regulate carbohydrate and lipid metabolism as well as protein synthesis and degradation. Evidence is discussed about how lncRNAs expression might affect cellular and organismal metabolism and whether their modulation could provide ground for the development of innovative treatments.

Regulation of Cholesterol Homeostasis by a Novel Long Non-coding RNA LASER

Genome-wide association studies (GWAS) have identified many genetic variants in genes related to lipid metabolism. However, how these variations affect lipid levels remains elusive. Long non-coding RNAs (lncRNAs) have been implicated in a variety of biological processes. We hypothesize lncRNAs are likely to be located within disease or trait-associated DNA regions to regulate lipid metabolism. The aim of this study was to investigate whether and how lncRNAs in lipid- associated DNA regions regulate cholesterol homeostasis in hepatocytes. In this study, we identified a novel long non-coding RNA in Lipid Associated Single nucleotide polymorphism gEne Region (LASER) by bioinformatic analysis. We report that LASER is highly expressed in both hepatocytes and peripheral mononuclear cells (PBMCs). Clinical studies showed that LASER expression is positively related with that of cholesterol containing apolipoprotein levels. In particular, we found that LASER is positively correlated with plasma PCSK9 levels in statin free patients. siRNAs mediated knock down of LASER dramatically reduces intracellular cholesterol levels and affects the expression of genes involved in cholesterol metabolism. Transcriptome analyses show that knockdown of LASER affects the expression of genes involved in metabolism pathways. We found that HNF-1α and PCSK9 were reduced after LASER knock-down. Interestingly, the reduction of PCSK9 can be blocked by the treatment of berberine, a natural cholesterol-lowering compound which functions as a HNF-1α antagonist. Mechanistically, we found that LASER binds to LSD1 (lysine-specific demethylase 1), a member of CoREST/REST complex, in nucleus. LASER knock-down enhance LSD1 targeting to genomic loci, resulting in decreased histone H3 lysine 4 mono-methylation at the promoter regions of HNF-1α gene. Conversely, LSD1 knock-down abolished the effect of LASER on HNF-1α and PCSK9 expressions. Finally, we found that statin treatment increased LASER expression, accompanied with increased PCSK9 expression, suggesting a feedback regulation of cholesterol on LASER expression. This observation may partly explain the statin escape during anti-cholesterol treatment. These findings identified a novel lncRNA in cholesterol homeostasis. Therapeutic targeting LASER might be an effective approach to augment the effect of statins on cholesterol levels in clinics.

Sex-Biased lncRNAs Inversely Correlate With Sex-Opposite Gene Coexpression Networks in Diversity Outbred Mouse Liver

Sex differences in liver gene expression are determined by pituitary growth hormone secretion patterns, which regulate sex-dependent liver transcription factors and establish sex-specific chromatin states. Hypophysectomy (hypox) identifies two major classes of liver sex-biased genes, defined by their sex-dependent positive or negative responses to pituitary hormone ablation. However, the mechanisms that underlie each hypox-response class are unknown. We sought to discover candidate, regulatory, long noncoding RNAs (lncRNAs) controlling responsiveness to hypox. We characterized gene structures and expression patterns for 15,558 mouse liver-expressed lncRNAs, including many sex-specific lncRNAs regulated during postnatal development or subject to circadian regulation. Using the high natural allelic variance of Diversity Outbred (DO) mice, we discovered tightly coexpressed clusters of sex-specific protein-coding genes (gene modules) in male and female DO liver. Remarkably, many gene modules were strongly enriched for sex-specific genes within a single hypox-response class, indicating that the genetic heterogeneity of DO mice encompasses responsiveness to hypox. Moreover, several distant gene modules were enriched for gene subsets of the same hypox-response class, highlighting the complex regulation of hypox-responsiveness. Finally, we identified eight sex-specific lncRNAs with strong negative regulatory potential, as indicated by their strong negative correlation of expression across DO mouse livers with that of protein-coding gene modules enriched for genes of the opposite sex bias and inverse hypox-response class. These findings reveal an important role for genetic factors in regulating responsiveness to hypox, and present testable hypotheses for the roles of sex-biased liver lncRNAs in controlling the sex-bias of liver gene expression.

KCNQ1OT1, HIF1A-AS2 and APOA1-AS are promising novel biomarkers for diagnosis of coronary artery disease

This study aimed to evaluate the potential of long noncoding RNAs (lncRNAs) as biomarkers for coronary artery disease (CAD). We measured the levels of three atherosclerosis- or cardiac-related lncRNAs in peripheral blood monocyte cells (PBMCs) from 20 CAD patients and 20 non-CAD control participants using real-time reverse transcription-polymerase chain reaction (real-time RT-PCR) methods. We found that the levels of lncRNA KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1), hypoxia-inducible factor 1 alpha-antisense RNA 2 (HIF1A-AS2) and apolipoprotein A-1 antisense RNA (APOA1-AS) were significantly increased in CAD patients (KCNQ1OT1 increased by 2.38-fold, P = 0.00042; HIF1A-AS2 increased by 2.00-fold, P = 0.0001; APOA1-AS increased by 4.52-fold, P = 0.000048). The area under the ROC curve was 0.865 for KCNQ1OT1, 0.852 for HIF1A-AS2, and 0.967 for APOA1-AS. Furthermore, the combination of lncRNAs resulted in a much higher AUC value of 0.990 for the prediction of CAD. Spearman's correlation analysis showed that APOA1-AS was positively correlated with NT-proBNP, CKMB, MYO and HsTnT, whereas HIF1A-AS2 was correlated with NT-proBNP and HsTnT. Hence, the elevation of KCNQ1OT1, HIF1A-AS2 and APOA1-AS predicts CAD and these molecules may be considered as novel biomarkers of CAD.

Knockdown of slincRAD leads to defective adipose development in vivo

The development of adipose tissue is a precisely coordinated cellular process, in which both protein-coding and non-coding genes are involved. To characterize the in vivo function of a novel long non-coding RNA (lncRNAs), loss-of-function assays were performed with slincRAD knockdown mice. Down-regulation of slincRAD expression was found to impair the development of adipose tissue, leading to a slim phenotype for both of the male and female mice. Compared to normal adipocytes, slincRAD knockdown cells had defective differentiation features, such as smaller sizes and decreased lipid production. For elder mice, slincRAD knockdown led to abnormal glucose and lipid metabolism. Therefore, a physiologically important lncRNA was characterized in the development of adipose tissue.

Circular RNAs: Diversity of Functions and a Regulatory Nova in Oral Medicine: A Pilot Review

Oral diseases, such as cancers, inflammation, loss of bone/tooth/soft tissues, are serious threats to human health since some can cause systemic disease and effective treatments are limited. Thus, discovering promising biomarkers for physiological and pathological processes in oral medicine, and identifying novel targets for therapy have become a most critical issue. Recently, circular RNAs (circRNAs), which were once thought to be a class of non-coding RNAs (ncRNAs), are found to be of coding potential. CircRNAs are highly present in the cytoplasm of eukaryotic cells and are key elements in the physiological and biological processes of various pathological conditions, and are also reflected in oral development and progress. Previous studies have indicated that circRNAs are involved in the initiation and development of different types of diseases and tissues (e.g., cancers, cardiovascular diseases, neural development, growth and development, wood healing, liver regeneration). Moreover, growing evidence demonstrates that circRNAs play vital roles in oral cancers and osteogenic differentiation of periodontal ligament stem cells (PDLSCs). Here, we focus on the biological characteristics of circRNAs, beginning with an overview of previous studies on the functional roles of circRNAs as diagnostic biomarkers and therapeutic targets in oral medicine. We hope this will give us a promising new comprehension of the underlying mechanisms occurring during related biological and pathological progress, and contribute to the development of effective diagnostic biomarkers and therapeutic targets for oral diseases.

Transcriptomic Analysis of Potential "lncRNA-mRNA" Interactions in Liver of the Marine Teleost Cynoglossus semilaevis Fed Diets With Different DHA/EPA Ratios

Long non-coding RNAs (lncRNA) have emerged as important regulators of lipid metabolism and have been shown to play multifaceted roles in controlling transcriptional gene regulation, but very little relevant information has been available in fish, especially in non-model fish species. With a feeding trial on a typical marine teleost tongue sole C. semilaevis followed by transcriptomic analysis, the present study investigated the possible involvement of lncRNA in hepatic mRNA expression in response to different levels of dietary DHA and EPA, which are two most important fatty acids for marine fish. An 80-day feeding trial was conducted in a flow-through seawater system, and in this trial three experimental diets differing basically in DHA/EPA ratio, i.e., 0.61 (D/E-0.61), 1.46 (D/E-1.46), and 2.75 (D/E-2.75), were randomly assigned to 9 tanks of experimental fish. A total of 124.04 G high quality genome-wide clean data about coding and non-coding transcripts was obtained in the analysis of hepatic transcriptome. Compared to diet D/E-0.61, D/E-1.46 up-regulated expression of 178 lncRNAs and 2629 mRNAs, and down-regulated that of 47 lncRNAs and 3059 mRNAs, while D/E-2.75 resulted in much less change in gene expression. The co-expression and co-localization analysis of differentially expressed (DE) lncRNA and mRNA among dietary groups were then conducted. The co-expressed DE lncRNA and mRNA were primarily enriched in GO terms such as Metabolic process, Intracellular organelle, Catalytic activity, and Oxidoreductase activity, as well as in KEGG pathways such as Ribosome and Oxidative phosphorylation. Overlap of co-expression and co-localization analysis, i.e., lncRNA–mRNA matches “XR_523541.1–solute carrier family 16, member 5 (slc16a5)” and “LNC_000285–bromodomain adjacent to zinc finger domain 2A (baz2a),” were observed in all inter-group comparisons, indicating that they might crucially mediate the effects of dietary DHA and EPA on hepatic gene expression in tongue sole. In conclusion, this was the first time in marine teleost to investigate the possible lncRNA–mRNA interactions in response to dietary fatty acids. The results provided novel knowledge of lncRNAs in non-model marine teleost, and will serve as important resources for future studies that further investigate the roles of lncRNAs in lipid metabolism of marine teleost.

MicroRNAs or Long Noncoding RNAs in Diagnosis and Prognosis of Coronary Artery Disease

Coronary artery disease (CAD) is the result of atherosclerotic plaque development in the wall of the coronary arteries. The underlying mechanism involves atherosclerosis of the arteries of the heart which is a relatively complex process comprising several steps. In CAD, atherosclerosis induces functional and structural changes. The pathogenesis of CAD results from various changes in and interactions between multiple cell types in the artery walls; these changes mainly include endothelial cell (EC) dysfunction, vascular smooth muscle cell (SMC) alteration, lipid deposition and macrophage activation. Various blood markers associated with an increased risk for cardiovascular endpoints have been identified; however, few have yet been shown to have a diagnostic impact or important clinical implications that would affect patient management. Noncoding RNAs, especially microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), can be stable in plasma and other body fluids and could therefore serve as biomarkers for some diseases. Many studies have shown that some miRNAs and lncRNAs play key roles in heart and vascular development and in cardiac pathophysiology. Thus, we summarize here the latest research progress, focusing on the molecular mechanism of miRNAs and lncRNAs in CAD, with the intent of seeking new targets for the treatment of heart disease.

Multi-Omics Approaches to Study Long Non-coding RNA Function in Atherosclerosis

Atherosclerosis is a complex inflammatory disease of the vessel wall involving the interplay of multiple cell types including vascular smooth muscle cells, endothelial cells, and macrophages. Large-scale genome-wide association studies (GWAS) and the advancement of next generation sequencing technologies have rapidly expanded the number of long non-coding RNA (lncRNA) transcripts predicted to play critical roles in the pathogenesis of the disease. In this review, we highlight several lncRNAs whose functional role in atherosclerosis is well-documented through traditional biochemical approaches as well as those identified through RNA-sequencing and other high-throughput assays. We describe novel genomics approaches to study both evolutionarily conserved and divergent lncRNA functions and interactions with DNA, RNA, and proteins. We also highlight assays to resolve the complex spatial and temporal regulation of lncRNAs. Finally, we summarize the latest suite of computational tools designed to improve genomic and functional annotation of these transcripts in the human genome. Deep characterization of lncRNAs is fundamental to unravel coronary atherosclerosis and other cardiovascular diseases, as these regulatory molecules represent a new class of potential therapeutic targets and/or diagnostic markers to mitigate both genetic and environmental risk factors.

Identification of a novel antisense RNA that regulates growth hormone receptor expression in chickens

Natural antisense transcripts (NATs) are widely present in mammalian genomes and act as pivotal regulator molecules of gene expression. However, studies on NATs in the chicken are relatively rare. We identified a novel antisense transcript in the chicken, designated GHR-AS-EST, transcribed from the growth hormone receptor (GHR) locus, which encodes a well-known regulatory molecule of muscle development and fat deposition. GHR-AS-EST is predominantly expressed in the chicken liver and muscle tissues. GHR-AS-EST sequence conservation among vertebrates is weak. GHR-AS-EST forms an RNA-RNA duplex with GHBP to increase its stability, and regulates the expression of GHR sense transcripts at both the mRNA and protein levels. Further, GHR-AS-EST promotes cell proliferation by stimulating the expression of signaling factors in the JAK2/STAT pathway, and contributes to fat deposition via downregulating the expression of signaling factors in the JAK2/SOCS pathway in LMH hepatocellular carcinoma cells. We expect that the discovery of a NAT for a regulatory gene associated with cell proliferation and lipolysis will further our understanding of the molecular regulation of both muscle development and fat deposition.

Role of long non-coding RNAs in metabolic control

Long non-coding RNAs (lncRNAs) have emerged as pivotal regulators of gene expression by influencing various biological processes including proliferation, apoptosis, differentiation, and senescence. Accumulating evidence implicates lncRNAs in the maintenance of metabolic homeostasis; dysregulation of certain lncRNAs promotes the progression of metabolic disorders such as diabetes, obesity, and cardiovascular diseases. In this review, we discuss our understanding of lncRNAs implicated in metabolic control, focusing on in particular diseases arising from chronic inflammation, insulin resistance, and lipid homeostasis. We have analyzed lncRNAs and their molecular targets involved in the pathogenesis of chronic liver disease, diabetes, and obesity, and have discussed the rising interest in lncRNAs as diagnostic and therapeutic targets improving metabolic homeostasis. This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen.

Long Noncoding RNA FEZF1-AS1 Promotes Proliferation and Inhibits Apoptosis in Ovarian Cancer by Activation of JAK-STAT3 Pathway

BACKGROUND Long noncoding RNAs (lncRNAs) have been acknowledged as important regulators in human cancers, including ovarian cancer. Several reports identified lncRNA FEZF1-AS1 as an oncogene in gastric cancer, colorectal carcinoma, and non-small cell lung cancer (NSCLC). However, the function of FEZF1-AS1 in ovarian cancer remains largely unknown. This study was aimed to investigate the role of FEZF1-AS1 in ovarian cancer. MATERIAL AND METHODS FEZF1-AS1 expression levels in pairs of ovarian cancer tissues and adjacent normal tissues were measured by quantitative real-time polymerase chain reaction (qRT-PCR). Kaplan-Meier curve analysis was used to determine the correlation between FEZF1-AS1 expression and prognosis in ovarian cancer patients. The effects of FEZF1-AS1 knockdown on ovarian cancer cell proliferation, cell-cycle, and apoptosis were analyzed by Cell Counting Kit-8 (CCK8) and Fluorescence activated Cell Sorting (FACS) assays. Western blot was utilized to assess the effect of FEZF1-AS1 on the activation of JAK-STAT3 pathway. RESULTS FEZF1-AS1 was overexpressed in ovarian cancer tissues compared to adjacent normal tissues. Consistently, FEZF1-AS1 expression was also upregulated in ovarian cancer cell lines compared with normal cell line. Furthermore, higher expression of FEZF1-AS1 in ovarian cancer patients contributed to poorer prognosis. FEZF1-AS1 knockdown significantly suppressed the proliferation and promoted apoptosis in ovarian cancer cells. In mechanism, FEZF1-AS1 regulated activation of JAK-STAT3 signaling pathway by modulating STAT3 phosphorylation. Knockdown of FEZF1-AS1 significantly impaired the phosphorylation of STAT3. CONCLUSIONS Our study demonstrated that FEZF1-AS1 exerted an oncogenic role in ovarian cancer via modulating JAK-STAT3 pathway.

Overexpression of lncRNA PANDAR predicts adverse prognosis in acute myeloid leukemia

Background and purpose

Abundant studies have shown that lncRNA PANDAR plays an oncogenic role in human solid tumors. Although abnormal expression of PANDAR has been well investigated in solid tumors, it was rarely studied in hematologic diseases. Hence, the aim of this study was to determine the PANDAR expression level and its clinical significance in patients with acute myeloid leukemia (AML).

Materials and methods

For detecting the expression level of PANDAR in 119 AML patients and 26 controls, real-time quantitative PCR was used in this study. The prognostic values were evaluated by using Kaplan-Meier analysis, Cox regression analyses, and logistic regression analysis.

Results

PANDAR was significantly overexpressed in AML and might be a promising biomarker which could distinguish AML from normal samples (P<0.001). Patients with high expression of PANDAR (PANDAR ^high) were older and showed higher bone marrow blasts than patients in PANDAR ^low group (P=0.029 and 0.032, respectively). Significant differences between these groups were also detected regarding risk group and karyotype finding (P=0.009 and 0.041, respectively). Importantly, PANDAR ^high patients presented a significant lower complete remission rate compared to PANDAR ^low patients (P<0.001). Furthermore, Kaplan-Meier analysis showed that PANDAR ^high patients had shorter overall survival compared to PANDAR ^low patients observing the whole AML cohort, and also in the non-M3 group of patients (P<0.001 and P=0.005, respectively). Multivariate analysis of Cox and logistic regression analysis confirmed that high PANDAR expression was an independent unfavorable risk factor for overall survival and complete remission in both observed patient groups.

Conclusion

These results revealed that PANDAR was overexpressed in AML, and that higher PANDAR expression was associated with poor clinical outcome. Our study therefore suggests that PANDAR expression is a promising biomarker for prognostic prediction for AML.

Long non-coding RNAs in coronary atherosclerosis

Coronary atherosclerosis (CAS), a leading cause of cardiovascular disease, is a major cause of death worldwide. CAS is a chronic disease in the aorta that can be caused by dyslipidemia, abnormal glucose metabolism, endothelial cell dysfunction, vascular smooth muscle cell (VSMC) or fibrous connective tissue hyperplasia, immune inflammatory reactions, and many other factors. The pathogenesis of CAS is not fully understood, as it is a complex lesion complicated by multiple factors. Damage-response theories have put forward endothelial cell (EC) injury as the initiating factor for CAS; the addition of lipid metabolism disorders may enhance monocyte adhesion, increase the proliferation and migration of fibroblasts and VSMCs, and accelerate the development of CAS. Furthermore, inflammatory and immune responses can create a vicious cycle of endothelial injury, which also plays key roles in the formation of CAS. Therefore, in order to elucidate the mechanisms controlling CAS, it is important to study the etiology of vascular cell dysfunction, abnormal energy and metabolism disorders, and immune and inflammatory reactions. Non-coding RNAs play regulatory roles in the pathogenesis of CAS, especially long non-coding RNAs (lncRNAs); lncRNAs have recently become a major focus for cardiovascular disease mechanisms, as they play numerous roles in the progression of CAS. Therefore, in this review, we discuss the role of lncRNAs in the pathogenesis of coronary CAS, and their role in the prevention and treatment of coronary CAS.

Long Noncoding RNAs: Advances in Lipid Metabolism

Long noncoding RNAs (lncRNAs) are an important group of pervasive noncoding RNAs (>200nt) proposed to be crucial regulators of numerous physiological and pathological processes. Through interactions with RNA, chromatin, and protein, lncRNAs modulate mRNA stability, chromatin structure, and the function of proteins (including transcription factors). In addition, to their well-known roles in the modulation of cell growth, apoptosis, neurological disease progression and cancer metastasis, these large molecules have also been identified as likely mediators of lipid metabolism. In particular, lncRNAs orchestrate adipogenesis; fatty acid, cholesterol, and phospholipid metabolism and transport; and the formation of high-density and low-density lipoproteins (HDLs and LDLs). LncRNAs also appear to target several transcription factors that play essential roles in the regulation of lipid metabolism, such as liver X receptors (LXRs), sterol regulatory element binding proteins (SREBPs), and peroxisome proliferator-activated receptor γ (PPARγ). Better understanding the regulatory roles of lncRNAs in dyslipidemia, atherosclerosis, and adipogenesis will reveal appropriate strategies to treat these diseases. In this review, we review recent progress in lncRNA-mediated regulation of lipid metabolism, as well as its role in the regulation of adipogenesis.

Epigenetics: An emerging field in the pathogenesis of nonalcoholic fatty liver disease

Nonalcoholic fatty liver disease (NAFLD) is a major health concern associated with increased mortality due to cardiovascular disease, type II diabetes, insulin resistance, liver disease, and malignancy. The molecular mechanism underlying these processes is not fully understood but involves hepatic fat accumulation and alteration of energy metabolism and inflammatory signals derived from various cell types including immune cells. During the last two decades, epigenetic mechanisms have emerged as important regulators of chromatin alteration and the reprogramming of gene expression. Recently, epigenetic mechanisms have been implicated in the pathogenesis of NAFLD and nonalcoholic steatohepatitis (NASH) genesis. Epigenetic mechanisms could be used as potential therapeutic targets and as noninvasive diagnostic biomarkers for NAFLD. These mechanisms can determine disease progression and prognosis in NAFLD. In this review, we discuss the role of epigenetic mechanisms in the progression of NAFLD and potential therapeutic targets for the treatment of NAFLD.

Long noncoding RNAs: regulation, function and cancer

Long noncoding RNAs (lncRNAs) are non-protein-coding RNA transcripts that exert a key role in many cellular processes and have potential toward addressing disease etiology. Here, we review existing noncoding RNA classes and then describe a variety of mechanisms and functions by which lncRNAs regulate gene expression such as chromatin remodeling, genomic imprinting, gene transcription and post-transcriptional processing. We also examine several lncRNAs that contribute significantly to pathogenesis, oncogenesis, tumor suppression and cell cycle arrest of diverse cancer types and also give a summary of the pathways that lncRNAs might be involved in.

Long non-coding RNAs regulation in adipogenesis and lipid metabolism: Emerging insights in obesity

Obesity is a widespread health problem that brings about various adipose tissue dysfunctions. The balance of energy storage and energy expenditure is critical for normal fat accumulation and lipid metabolism. Therefore, understanding the molecular basis of adipogenesis and thermogenesis is essential to maintain adipose development and lipid homeostasis. Increasing evidence demonstrated that lncRNAs (long non-coding RNAs), a class of non-protein coding RNAs of >200 nucleotides in length, are identified as key regulators in obesity-related biological processes through diverse regulatory mechanisms. In this review, we concentrate on recent and relevant studies on the roles of lncRNAs in regulation of white adipogenesis, brown adipocyte differentiation and lipid metabolism. In addition, the diagnostic and therapeutic potential of lncRNAs is highlighted, and that will make recommendations for the future application of lncRNAs in the treatment of obesity.

Non-coding RNAs in lipid metabolism

Cardiovascular disease (CVD), the leading cause of death and morbidity in the Western world, begins with lipid accumulation in the arterial wall, which is the initial step in atherogenesis. Alterations in lipid metabolism result in increased risk of cardiometabolic disorders, and treatment of lipid disorders remains the most common strategy aimed at reducing the incidence of CVD. Work done over the past decade has identified numerous classes of non-coding RNA molecules including microRNAs (miRNAs) and long-non-coding RNAs (lncRNAs) as critical regulators of gene expression involved in lipid metabolism and CVD, mostly acting at post-transcriptional level. A number of miRNAs, including miR-33, miR-122 and miR-148a, have been demonstrated to play important role in controlling the risk of CVD through regulation of cholesterol homeostasis and lipoprotein metabolism. lncRNAs are recently emerging as important regulators of lipid and lipoprotein metabolism. However, much additional work will be required to fully understand the impact of lncRNAs on CVD and lipid metabolism, due to the high abundance of lncRNAs and the poor-genetic conservation between species. This article reviews the role of miRNAs and lncRNAs in lipid and lipoprotein metabolism and their potential implications for the treatment of CVD.

Long noncoding RNAs in lipid metabolism

PURPOSE OF REVIEW

Noncoding RNAs have emerged as important regulators of cellular and systemic lipid metabolism. In particular, the enigmatic class of long noncoding RNAs have been shown to play multifaceted roles in controlling transcriptional and posttranscriptional gene regulation. In this review, we discuss recent advances, current challenges and future opportunities in understanding the roles of lncRNAs in the regulation of lipid metabolism during health and disease.

RECENT FINDINGS

Despite comprising the majority of the transcriptionally active regions of the human genome, lncRNA functions remain poorly understood, with fewer than 1% of human lncRNAs functionally characterized. Broadly defined as nonprotein coding transcripts greater than 200 nucleotides in length, lncRNAs execute their functions by forming RNA-DNA, RNA-protein, and RNA-RNA interactions that regulate gene expression through diverse mechanisms, including epigenetic remodeling of chromatin, transcriptional activation or repression, posttranscriptional regulation of mRNA, and modulation of protein activity. It is now recognized that in lipid metabolism, just as in other areas of biology, lncRNAs operate to regulate the expression of individual genes and gene networks at multiple different levels.

SUMMARY

The complexity revealed by recent studies showing how lncRNAs can alter systemic and cell-type-specific cholesterol and triglyceride metabolism make it clear that we have entered a new frontier for discovery that is both daunting and exciting.