Characterization of a carcinogenesis-associated long non-coding RNA

Genome-Wide Association Study Identifying a Novel Gene Related to a History of Febrile Convulsions in Patients With Focal Epilepsy

BACKGROUND AND PURPOSE

The risk factors for developing epilepsy following febrile convulsion (FC) have been studied extensively, but the underlying genetic components remain largely unexplored. Our objective here was to identify the risk loci related to FC through a genome-wide association study of Korean epilepsy patients.

METHODS

We examined associations between a history of FC and single-nucleotide polymorphisms (SNPs) in data obtained from 125 patients with focal epilepsy: 28 with an FC history and 97 without an FC history.

RESULTS

Among 288,394 SNPs, 5 candidate SNPs showed p<1×10⁻⁴. Regional association plots of these SNPs identified a novel locus adjacent to PROX1 that is implicated in hippocampal neurogenesis and epileptogenesis. The allele frequencies of the SNPs upstream of PROX1 including two candidate SNPs (rs1159179 and rs7554295 on chromosome 1) differed significantly between the groups with and without an FC history. In contrast, the allele frequencies of the SNPs inside PROX1 showed no differences, indicating dysregulated expression of PROX1 rather than a functional alteration in the PROX1 protein.

CONCLUSIONS

This novel discovery of SNPs upstream of PROX1 suggests that the dysregulated expression of PROX1 contributes to the development of focal epilepsy following FC. We propose that these SNPs are potential genetic markers for focal epilepsy following FC, and that PROX1 represents a potential therapeutic target of antiseizure medications.

In silico identification and functional study of long non-coding RNA involved in acute hepatopancreatic necrosis disease caused by Vibrio parahaemolyticus infection in white shrimp, Litopenaeus vannamei

Acute hepatopancreatic necrosis disease (AHPND) caused by toxin-producing Vibrio parahaemolyticus (VpAHPND) has severely affected shrimp production. Long non-coding RNA (lncRNA), a regulatory non-coding RNA, which can play important function in shrimp disease responses. This study aimed to identify and investigate the role of lncRNA involved in VpAHPND infection in Pacific white shrimp, Litopenaeus vannamei. From a total of 368,736 de novo assembled transcripts, 67,559 were identified as putative lncRNAs, and only 72 putative lncRNAs showed differential expression between VpAHPND-infected and normal shrimp. The six candidate lncRNAs were validated for their expression profiles during VpAHPND infection and tissue distribution using RT-qPCR. The role of lnc2088 in response to VpAHPND infection was investigated through RNA interference. The result indicated that the suppression of lnc2088 expression led to an increase in shrimp mortality after VpAHPND infection. To explore the set of genes involved in lnc2088 knockdown, RNA sequencing was performed. A total of 275 differentially expressed transcripts were identified in the hepatopancreas of lnc2088 knockdown shrimp. The expression profiles of five candidate metabolic and immune-related genes were validated in lnc2088 knockdown and VpAHPND-infected shrimp. The result showed that the expression of ChiNAG was significantly increased, while that of NCBP1, WIPF2, and NFKB1 was significantly downregulated in ds2088-injected shrimp. Additionally, the expression of NFKB1, NCBP1 and WIPF2 was significantly increased, whereas that of ChiNAG and CUL5 were significantly decreased after infection with VpAHPND. Our work identified putative lncRNA profiles in L. vannamei in response to VpAHPND infection and investigated the role of lncRNA in shrimp immunity.

Expression characteristics and potential function of non-coding RNA in mouse cortical cells

Non-coding RNAs (ncRNAs) play essential regulatory functions in various physiological and pathological processes in the brain. To systematically characterize the ncRNA profile in cortical cells, we downloaded single-cell SMART-Seq v4 data of mouse cerebral cortex. Our results revealed that the ncRNAs alone are sufficient to define the identity of most cortical cell types. We identified 1,600 ncRNAs that exhibited cell type specificity, even yielding to distinguish microglia from perivascular macrophages with ncRNA. Moreover, we characterized cortical layer and region specific ncRNAs, in line with the results by spatial transcriptome (ST) data. By constructing a co-expression network of ncRNAs and protein-coding genes, we predicted the function of ncRNAs. By integrating with genome-wide association studies data, we established associations between cell type-specific ncRNAs and traits related to neurological disorders. Collectively, our study identified differentially expressed ncRNAs at multiple levels and provided the valuable resource to explore the functions and dysfunctions of ncRNAs in cortical cells.

Long non-coding RNAs affecting cell metabolism in cancer

Metabolic reprogramming is commonly recognized as one important hallmark of cancers. Cancer cells present significant alteration of glucose metabolism, oxidative phosphorylation, and lipid metabolism. Recent findings demonstrated that long non-coding RNAs control cancer development and progression by modulating cell metabolism. Here, we give an overview of breast cancer metabolic reprogramming and the role of long non-coding RNAs in driving cancer-specific metabolic alteration.

c-Myc-Regulated lncRNA-IGFBP4 Suppresses Autophagy in Cervical Cancer-Originated HeLa Cells

LncRNAs are known to regulate a plethora of key events of cellular processes; however, little is known about the function of lncRNAs in autophagy. Here in the current study, we report lncRNA-IGFBP4 which has previously been known to regulate the proliferation and reprogramming of cancer cells, but its role in autophagy is not yet known. We found that serum starvation provokes autophagy-induced downregulation of lncRNA-IGFBP4 levels. Next, we determined that c-Myc can negatively regulate lncRNA-IGFBP4 in HeLa cells. Phenotypically, we found that upon depletion of lncRNA-IGFBP4, the HeLa cells undergo autophagy through ULK1/Beclin1 signaling. Furthermore, through TCGA data analysis, we found lncRNA-IGFB4 overexpressed in most cancers including cervical cancer. Based on these findings, we conclude that c-Myc maintains cellular homeostasis through negatively regulating lncRNA-IGFBP4 in cervical cancer cells.

LINC01857 promotes the proliferation, migration, and invasion of gastric cancer cells via regulating miR-4731-5p/HOXC6

The great importance of long non-coding RNAs (lncRNAs) in tumorigenesis has been acknowledged gradually. LINC01857 is previously reported to be highly expressed in gastric cancer (GC), while the regulatory mechanism of LINC01857 in gastric cancer is largely unknown. In this study, we detected high expression of LINC01857 from the gastric cancer microarray GSE109476. Additionally, LINC01857 expression is remarkably up-regulated in gastric cancer cell lines (AGS, MKN-45, HGC-27 and SGC-7901) compared to the normal gastric mucosal cell line GES-1. Functionally, LINC01857 knockdown suppressed the proliferation, migration, invasion, and epithelial-mesenchymal transformation (EMT) of GC cells, while LINC01857 overexpression promoted the proliferation, migration, invasion and EMT of GC cells. Furthermore, our data demonstrate that LINC01857 targeted miR-4731-5p and subsequently increased the expression of HOXC6 in GC. Rescue experiments showed that miR-4731-5p inhibition and HOXC6 overexpression could reverse the biological behavior of GC cells induced by LINC01857 knockdown. In conclusion, we demonstrated that LINC01857 sponged miR-4731-5p to promote the expression of HOXC6 and eventually acts as an oncogene in GC.

The molecular mechanism of METTL3 promoting the malignant progression of lung cancer

Lung cancer remains one of the major causes of cancer-related death globally. Recent studies have shown that aberrant m6A levels caused by METTL3 are involved in the malignant progression of various tumors, including lung cancer. The m6A modification, the most abundant RNA chemical modification, regulates RNA stabilization, splicing, translation, decay, and nuclear export. The methyltransferase complex plays a key role in the occurrence and development of many tumors by installing m6A modification. In this complex, METTL3 is the first identified methyltransferase, which is also the major catalytic enzyme. Recent findings have revealed that METTL3 is remarkably associated with different aspects of lung cancer progression, influencing the prognosis of patients. In this review, we will focus on the underlying mechanism of METT3 in lung cancer and predict the future work and potential clinical application of targeting METTL3 for lung cancer therapy.

Long noncoding RNASEH1-AS1 exacerbates the progression of non-small cell lung cancer by acting as a ceRNA to regulate microRNA-516a-5p/FOXK1 and thereby activating the Wnt/β-catenin signaling pathway

BACKGROUND

Till now, no study has focused on the functions of RNASEH1 antisense RNA 1 (RNASEH1-AS1) in non-small cell lung cancer (NSCLC). Accordingly, we measured the expression of RNASEH1-AS1 in NSCLC and characterized its functions in detail. Finally, our research elucidated the mechanisms that occurred downstream of RNASEH1-AS1.

METHODS

RNASEH1-AS1 expression was examined utilizing TCGA database and qRT-PCR. Functional experiments were conducted to study the tumor-associated functions of RNASEH1-AS1. The targeting relationship among RNASEH1-AS1, microRNA-516a-5p (miR-516a-5p), and forkhead box K1 (FOXK1) was revealed utilizing RNA immunoprecipitation and luciferase reporter assays.

RESULTS

Utilizing TCGA database and our own cohort, we found a significantly increased level of RNASEH1-AS1 in NSCLC. The high level of RNASEH1-AS1 was markedly related with poor clinical outcomes. Knockdown of RNASEH1-AS1 expression inhibited NSCLC cell growth, metastatic capacities, and epithelial-mesenchymal transition and promoted the apoptosis in vitro, whereas RNASEH1-AS1 overexpression exerted the opposite effects. Additionally, knocking down RNASEH1-AS1 expression suppressed tumor growth in vivo. RNASEH1-AS1 was confirmed to act as a miR-516a-5p sponge, consequently upregulating FOXK1 expression in NSCLC cells. As revealed by the subsequent rescue experiments, the miR-516a-5p/FOXK1 axis served as a downstream effector of RNASEH1-AS1. In addition, by controlling the miR-516a-5p/FOXK1 axis, RNASEH1-AS1 was capable of activating the Wnt/β-catenin pathway.

CONCLUSION

RNASEH1-AS1 exacerbated the oncogenicity of NSCLC by affecting the miR-516a-5p/FOXK1 axis and consequently promoting the activation of Wnt/β-catenin pathway. Our newly identified RNASEH1-AS1/miR-516a-5p/FOXK1/Wnt/β-catenin network may offer an interesting foundation for NSCLC treatment in the clinic.

Long Non-Coding RNA Small Nucleolar RNA Host Gene 14 Enhances Pancreatic-β-Cell Function by Sponging MicroRNA-206 and Thereby Upregulating Insulin-Like Growth Factor-1

Diabetes mellitus (DM) characterised by pancreatic β-cell dysfunction and insulin resistance is already prevalent worldwide, and the complications of DM increased the mortality of diabetic patients. More and more reports showed that long non-coding RNA (lncRNA) plays key roles in DM, and in this study we explored the effect of long non-coding RNA SNHG14 (SNHG14) in DM. Quantitative reverse transcription PCR (qRT-PCR) was used to analyze the expression of SNHG14 and microRNA (miR)-206 in peripheral blood from 60 pairs of healthy and DM samples. Then the effect of SNHG14 on the insulin secretion of pancreatic β-cells was investigated. Moreover, the effects of SNHG14 on the viability and apoptosis of pancreatic β-cells were determined by 3-(4, 5)-dimethylthiahiazo (-z-y1)-3, 5-di- phenytetrazoliumromide (MTT) assay and flow cytometry (FCM) respectively using INS-1 cells transfected with SNHG14-plasmid and/or miR-206 mimic. Bioinformatics and Daul luciferase reporter assay were used to confirm the direct target of miR-206. Our data showed that SNHG14 level was decreased but miR-206 was increased significantly in the peripheral blood of DM patients. Furthermore, over-expression of SNHG14 enhanced insulin secretion and cell viability but inhibited apoptosis of pancreatic β-cells, whereas, miR-206 over-expression reversed these effects. In addition, insulin-like growth factor-1 (IGF1) was proved to be regulated by miR-206 negatively and over-expression of SNHG14 increased the expression of IGF1 and IGF1R in pancreatic β-cells. In conclusion, we found that SNHG14 was significantly down-regulated in DM patients, and SNHG14/miR-206/IGF1 may serve as a potential candidate for the clinical target of DM.

Long non-coding RNA SNHG17 promotes lung adenocarcinoma progression by targeting the microRNA-193a-5p/NETO2 axis

Long non-coding RNAs (lncRNAs) play vital roles in human cancers. It has been reported that lncRNA SNHG17 expression is dysregulated in different types of cancer and involved in cancer progression. However, the role of SNHG17 in lung adenocarcinoma (LUAD) remains unclear. The present study aimed to investigate the role of SNHG17 in LUAD. Reverse transcription-quantitative (RT-q) PCR analysis was performed to detect SNHG17 expression in LUAD tissues and cells. The effects of SNHG17 on cancer cell migration, invasion, proliferation and epithelial-to-mesenchymal transition (EMT) were assessed via Transwell, MTT and western blot assays, respectively. The interactions between SNHG17 and microRNA (miRNA/miR)-193a-5p, miR-193a-5p and neuropilin and tolloid-like 2 (NETO2) were assessed via the dual-luciferase reporter assay. NETO2 expression and its potential role in LUAD were analyzed via RT-qPCR analysis and the UALCAN database. The results demonstrated that SNHG17 expression was significantly upregulated in LUAD tissues and cells, and high SNHG17 expression was associated with tumor-node-metastasis stage and poor prognosis of patients with LUAD. SNHG17 knockdown inhibited cell migration, invasion, proliferation and the EMT process. In addition, the results revealed that SNHG17 functions as a competing endogenous RNA of miR-193a-5p. The results of the dual-luciferase reporter assay confirmed that miR-193a-5p can directly target SNHG17. NETO2 was also predicted as a target protein of miR-193a-5p, which was confirmed via the dual-luciferase reporter assay. The roles of NETO2 knockdown in cancer cells were rescued following transfection with miR-193a-5p inhibitor or overexpression of SNHG17. Notably, high NETO2 expression was associated with poor prognosis of patients with LUAD. Bioinformatics analysis demonstrated that the promoter methylation level of NETO2 decreased in LUAD. Taken together, the results of the present study suggest that SNHG17 expression is upregulated in LUAD tissues and cells, and SNHG17 exerts tumor promoting effect by targeting the miR-193a-5p/NETO2 axis.

Functions of noncoding RNAs in glial development

Glia are widely distributed in the central nervous system and are closely related to cell metabolism, signal transduction, support, cell migration, and other nervous system development processes and functions. Glial development is complex and essential, including the processes of proliferation, differentiation, and migration, and requires precise regulatory networks. Noncoding RNAs (ncRNAs) can be deeply involved in glial development through gene regulation. Here, we review the regulatory roles of ncRNAs in glial development. We briefly describe the classification and functions of noncoding RNAs and focus on microRNAs (miRNAs) and long ncRNAs (lncRNAs), which have been reported to participate extensively during glial formation. The highlight of this summary is that miRNAs and lncRNAs can participate in and regulate the signaling pathways of glial development. The review not only describes how noncoding RNAs participate in nervous system development but also explains the processes of glial development, providing a foundation for subsequent studies on glial development and new insights into the pathogeneses of related neurological diseases.

Long non-coding RNA profile in banana shrimp, Fenneropenaeus merguiensis and the potential role of lncPV13 in vitellogenesis

The long non-coding RNAs (lncRNAs) have been known to play important roles in several biological processes as well as in reproduction. This study aimed to identify lncRNA in ovary female banana shrimp, Fenneropenaeus merguiensis, and investigate the potential role of lncPV13 in the vitellogenesis. After the in silico identification of the ovarian transcriptome, a total of 24,733 putative lncRNAs were obtained, and only 147 putative lncRNAs were significantly differentially expressed among the ovarian development stages. To validate the in silico identification of lncRNAs, the 16 lncRNAs with the highest differential expression in the transcriptome analysis were evaluated by RT-qPCR. The 6 lncRNAs showed higher expression levels in the mature stage than in the previtellogenic stage and were found in several tissues such as in eyestalks, brains, thoracic ganglia, gills, and muscle. Furthermore, most candidate lncRNAs were amplifiable in Litopenaeus vannamei's and Penaeus monodon's DNA but not in Macrobrachium rosenbergii's DNA, suggesting some lncRNAs are expressed in a species-specific manner among penaeid shrimp. In this study, the lncPV13 was investigated for its vitellogenin regulating function by RNA interference. The result indicates that the lncPV13 expression was suppressed in the ovary on day 7 after the injection of double-stranded RNA specific to lncPV13 (dslncPV13), while vitellogenin (Vg) expression was significantly decreased. In contrast, the gonad inhibiting hormone (GIH) expression was significantly increased in the lncPV13 knockdown shrimp. However, the oocyte proliferation was not significantly different between control and lncPV13 knockdown shrimp. This suggests that lncPV13 regulate Vg synthesis through GIH inhibition. Finally, our findings provide lncRNA information and potential lncRNAs involved in the vitellogenesis of female banana shrimp.

IGFBP-4: A promising biomarker for lung cancer

Background: Insulin-like growth factor binding protein-4 (IGFBP-4), a member of the insulin-like growth factor (IGF) family, transports, and regulates the activity of IGFs. The pregnancy-associated plasma protein-A (PAPP-A) has proteolytic activity towards IGFBP-4, and both proteins have been associated with a variety of cancers, including lung cancer. Thus, we aimed to evaluate the use of IGFBP-4 and PAPP-A as potential biomarkers for lung cancer. Methods: Eighty-three volunteers, including 60 patients with lung cancer and 23 healthy individuals, were included in this study. The patients with lung cancer were selected based on their treatment status, histological subgroup, and stage of the disease. Enzyme-linked immunosorbent assays were used to assess the serum levels of IGFBP-4 and PAPPA, whereas the IGF-1 levels were measured using a chemiluminescent immunometric assay. Results: The serum IGFBP-4 levels in all patient groups, regardless of the treatment status and histological differences, were significantly higher than those in the control group (p<0.005). However, the serum PAPP-A levels in the untreated patient group were found to be higher than those in the control group, but this difference was not statistically significant (p=0.086). Conclusions: The serum PAPP-A and IGFBP-4 levels are elevated in lung cancer. However, IGFBP-4 may have better potential than PAPP-A as a lung cancer biomarker.

Doxorubicin hydrochloride enhanced antitumour effect of CEA-regulated oncolytic virotherapy in live cancer cells and a mouse model

Oncolytic adenovirus (OA) has attracted increasing attention due to their specific proliferation in tumour cells and resulting in lysis of tumour cells. To further improve the antitumour effect of OA, in this study, we combined CD55-TRAIL-IETD-MnSOD (CD55-TMn), a CEA-controlled OA constructed previously, and chemotherapy to investigate their synergistic effect and possible mechanisms. MTT assay was performed to detect antitumour effects. Hoechst 33 342 and flow cytometric analysis were used to examine cell apoptosis. Western blotting was performed to examine cell pyroptosis and apoptosis mechanism. Animal experiment was used to detect antitumour effect of doxorubicin hydrochloride (Dox) combined with CD55-TMn in vivo. We firstly found that Dox promotes gene expression mediated by CEA-regulated OA and virus progeny replication by activating phosphorylation of Smad3, and Dox can enhance antitumour effect of CEA-regulated CD55-TMn by promoting cell apotopsis and cell pyroptosis. Thus, our results provide an experimental and theoretical basis on tumour therapy by combination treatment of the oncolytic virotherapy and chemotherapy and it is expected to become a novel strategy for liver cancer therapy.

Regulation of Glycolysis by Non-coding RNAs in Cancer: Switching on the Warburg Effect

The “Warburg effect” describes the reprogramming of glucose metabolism away from oxidative phosphorylation toward aerobic glycolysis, and it is one of the hallmarks of cancer cells. Several factors can be involved in this process, but in this review, the roles of non-coding RNAs (ncRNAs) are highlighted in several types of human cancer. ncRNAs, including microRNAs, long non-coding RNAs, and circular RNAs, can all affect metabolic enzymes and transcription factors to promote glycolysis and modulate glucose metabolism to enhance the progression of tumors. In particular, the 5′-AMP-activated protein kinase (AMPK) and the phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathways are associated with alterations in ncRNAs. A better understanding of the roles of ncRNAs in the Warburg effect could ultimately lead to new therapeutic approaches for suppressing cancer.

LINC00857 knockdown inhibits cell proliferation and induces apoptosis via involving STAT3 and MET oncogenic proteins in esophageal adenocarcinoma

Esophageal adenocarcinoma (EAC) is one of the leading causes of cancer-related death worldwide, and the molecular biology of this cancer remains poorly understood. Recent evidence indicates that long non-coding RNAs are dysregulated in a variety of cancers including EAC. In this study, siRNA mediated gene knockdown, Western blot, RT-PCR, as well as oncogenic function assay were performed. We found that the cell proliferation, colony formation, invasion and migration were decreased after LINC00857 knockdown in EAC cell lines. We also found that knockdown LINC00857 could induce apoptosis. Mechanistically, we found that the MET, STAT3, c-Myc and p-CREB proteins were decreased after LINC00857 knockdown. Our study suggests that LINC00857 may play an important oncogenic role in EAC via STAT3 and MET signaling.

Expression of Long Noncoding RNA YIYA Promotes Glycolysis in Breast Cancer

Long noncoding RNA (lncRNA) is yet to be linked to cancer metabolism. Here, we report that upregulation of the lncRNA LINC00538 (YIYA) promotes glycolysis, cell proliferation, and tumor growth in breast cancer. YIYA is associated with the cytosolic cyclin-dependent kinase CDK6 and regulated CDK6-dependent phosphorylation of the fructose bisphosphatase PFK2 (PFKFB3) in a cell-cycle-independent manner. In breast cancer cells, these events promoted catalysis of glucose 6-phosphate to fructose-2,6-bisphosphate/fructose-1,6-bisphosphate. CRISPR/Cas9-mediated deletion of YIYA or CDK6 silencing impaired glycolysis and tumor growth in vivo In clinical specimens of breast cancer, YIYA was expressed in approximately 40% of cases where it correlated with CDK6 expression and unfavorable survival outcomes. Our results define a functional role for lncRNA in metabolic reprogramming in cancer, with potential clinical implications for its therapeutic targeting.Significance: These findings offer a first glimpse into how a long-coding RNA influences cancer metabolism to drive tumor growth. Cancer Res; 78(16); 4524-32. ©2018 AACR.

Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS

Causal genes and variants within genome-wide association study (GWAS) loci can be identified by integrating GWAS statistics with expression quantitative trait loci (eQTL) and determining which variants underlie both GWAS and eQTL signals. Most analyses, however, consider only the marginal eQTL signal, rather than dissect this signal into multiple conditionally independent signals for each gene. Here we show that analyzing conditional eQTL signatures, which could be important under specific cellular or temporal contexts, leads to improved fine mapping of GWAS associations. Using genotypes and gene expression levels from post-mortem human brain samples (n = 467) reported by the CommonMind Consortium (CMC), we find that conditional eQTL are widespread; 63% of genes with primary eQTL also have conditional eQTL. In addition, genomic features associated with conditional eQTL are consistent with context-specific (e.g., tissue-, cell type-, or developmental time point-specific) regulation of gene expression. Integrating the 2014 Psychiatric Genomics Consortium schizophrenia (SCZ) GWAS and CMC primary and conditional eQTL data reveals 40 loci with strong evidence for co-localization (posterior probability > 0.8), including six loci with co-localization of conditional eQTL. Our co-localization analyses support previously reported genes, identify novel genes associated with schizophrenia risk, and provide specific hypotheses for their functional follow-up.

lncRNA CCAT1 promotes cell proliferation, migration, and invasion by down-regulation of miR-143 in FTC-133 thyroid carcinoma cell line

Thyroid cancer is a common malignant tumor. Long non-coding RNA colon cancer-associated transcript 1 (lncRNA CCAT1) is highly expressed in many cancers; however, the molecular mechanism of CCAT1 in thyroid cancer remains unclear. Hence, this study aimed to investigate the effect of CCAT1 on human thyroid cancer cell line FTC-133. FTC-133 cells were transfected with CCAT1 expressing vector, CCAT1 shRNA, miR-143 mimic, and miR-143 inhibitor, respectively. After different treatments, cell viability, proliferation, migration, invasion, and apoptosis were measured. Moreover, the regulatory relationship of CCAT1 and miR-143, as well as miR-143 and VEGF were tested using dual-luciferase reporter assay. The relative expressions of CCAT1, miR-143, and VEGF were tested by qRT-PCR. The expressions of apoptosis-related factors and corresponding proteins in PI3K/AKT and MAPK pathways were analyzed using western blot analysis. The results suggested that CCAT1 was up-regulated in the FTC-133 cells. CCAT1 suppression decreased FTC-133 cell viability, proliferation, migration, invasion, and miR-143 expression, while it increased apoptosis and VEGF expression. CCAT1 might act as a competing endogenous RNA (ceRNA) for miR-143. Moreover, CCAT1 activated PI3K/AKT and MAPK signaling pathways through inhibition of miR-143. This study demonstrated that CCAT1 exhibited pro-proliferative and pro-metastasis functions on FTC-133 cells and activated PI3K/AKT and MAPK signaling pathways via down-regulation of miR-143. These findings will provide a possible target for clinical treatment of thyroid cancer.

Long non-coding RNAs: novel prognostic biomarkers for liver metastases in patients with early stage colorectal cancer

Liver metastasis is the primary cause of death for colorectal cancer (CRC) patients. To investigate the prognostic value of long non-coding RNAs (lncRNAs) on colorectal liver metastases, quantitative reverse-transcriptase PCR (quantitative RT-PCR) was performed on 15 lncRNAs in 51 stage IV CRC with liver metastases and 57 stage I/II CRC specimens. The expression levels of four lncRNAs (GAS5, H19, MEG3 and Yiya) were significantly different between liver metastases and primary tumors of stage IV CRC patients. Furthermore, the high expression levels of GAS5 and Yiya were significantly associated with future occurrence of liver metastases in early stage CRC patients. Kaplan-Meier analysis showed that the high expression levels of GAS5 or Yiya were correlated with poor prognosis of early stage CRC patients (p = 0.0206 and 0.0005 for GAS5 and Yiya, respectively). Yiya expression was proved to be an independent prognostic indicator of colorectal liver metastases in a multivariate analysis (relative risk = 10.7; p < 0.0001). Our study revealed that GAS5 and Yiya were promising prognostic biomarkers of liver metastases for early stage CRC patients.

Overexpression of lncRNA IGFBP4-1 reprograms energy metabolism to promote lung cancer progression

BACKGROUND

Reprogrammed energy metabolism as an emerging hallmark of cancer has recently drawn special attention since it facilitate cell growth and proliferation. Recently, long noncoding RNAs (lncRNAs) have been served as key regulators implicated in tumor development and progression by promoting proliferation, invasion and metastasis. However, the associations of lncRNAs with cellular energy metabolism in lung cancer (LC) need to be clarified.

METHODS

Here, we conducted bioinformatics analysis and found insulin-like growth factor binding protein 4-1 (IGFBP4-1) as a new candidate lncRNA located in the upstream region of IGFBP4 gene. The expression levels of lnc-IGFBP4-1, mRNA levels of IGFBP4 in 159 paired lung cancer samples and adjacent, histological normal tissues by qRT-PCR. Over-expression and RNA interference (RNAi) approaches were adopted to investigate the biological functions of lnc-IGFBP4-1. The intracellular ATP level was measured using the Cell Titer-Glo Luminescent Cell Viability Assay kit, and changes in metabolic enzymes were examined in cancer cells and normal pulmonary epithelial cells with qRT-PCR.

RESULTS

Our results showed that lnc-IGFBP4-1 was significantly up-regulated in LC tissues compared with corresponding non-tumor tissues (P < 0.01), and its expression level was significantly correlated with TNM stage (P < 0.01) and lymph node metastasis (P < 0.05). Further investigation showed that overexpression of lnc-IGFBP4-1 significantly promoted LC cell proliferation in vitro and in vivo, while downregulation of endogenous lnc-IGFBP4-1 could inhibited cell proliferation and induce apoptosis. Moreover, we found lnc-IGFBP4-1 could influences ATP production levels and expression of enzymes including HK2, PDK1 and LDHA, in addition, decline in both ATP production and these enzymes in response to 2-DG and 2-DG-combined Rho123, respectively, was observed in lnc-IGFBP4-1-overespressing LC cells, indicative of an enhanced aerobic glycolysis rate. Finally, lnc-IGFBP4-1 was observed to negatively correlate with gene IGFBP4, and lower expression level of IGFPB4 was found after lnc-IGFBP4-1-overexpression was transfected into PC9 cells, higher expression level of IGFPB4 was also found after lnc-IGFBP4-1-downregulation was transfected into GLC-82 cells, which indicates that IGFBP4 may exert its targeting function regulated by lnc-IGFBP4-1.

CONCLUSIONS

Taken together, these findings provide the first evidence that lnc-IGFBP4-1 is significantly up-regulated in LC tissues and plays a positive role in cell proliferation and metastasis through possible mechanism of reprogramming tumor cell energy metabolism, which suggests that lnc-IGFBP4-1 may be a promising biomarker in LC development and progression and as a potential therapeutic target for LC intervention.

Non‑coding RNAs and ovarian diseases (Review)

Non-coding RNAs (ncRNAs) are a diverse family of untranslated transcripts, which serve important roles in numerous biological processes. ncRNAs are emerging as major mediators of gene expression with crucial regulatory functions. Ovarian diseases have a wide variety of clinical pathological types, which have serious impacts on women's health. In this review, current studies on ncRNAs are summarized with respect to ovarian diseases. Understanding of the role of ncRNAs in ovarian diseases is currently limited; further studies on the molecular mechanisms by which abnormal expression of ncRNAs contributes to ovarian diseases will aid in the identification of ncRNAs as novel diagnostic markers and therapeutic targets for ovarian diseases.

LncRNApred: Classification of Long Non-Coding RNAs and Protein-Coding Transcripts by the Ensemble Algorithm with a New Hybrid Feature

As a novel class of noncoding RNAs, long noncoding RNAs (lncRNAs) have been verified to be associated with various diseases. As large scale transcripts are generated every year, it is significant to accurately and quickly identify lncRNAs from thousands of assembled transcripts. To accurately discover new lncRNAs, we develop a classification tool of random forest (RF) named LncRNApred based on a new hybrid feature. This hybrid feature set includes three new proposed features, which are MaxORF, RMaxORF and SNR. LncRNApred is effective for classifying lncRNAs and protein coding transcripts accurately and quickly. Moreover,our RF model only requests the training using data on human coding and non-coding transcripts. Other species can also be predicted by using LncRNApred. The result shows that our method is more effective compared with the Coding Potential Calculate (CPC). The web server of LncRNApred is available for free at http://mm20132014.wicp.net:57203/LncRNApred/home.jsp.

High expression of long non-coding RNA SBF2-AS1 promotes proliferation in non-small cell lung cancer

Background

Recent evidence has proven that long noncoding RNAs (lncRNAs) play important roles in cancer biology, while few lncRNAs have been characterized in NSCLC. Here, we characterized a novel lncRNA, SBF2 antisense RNA 1 (SBF2-AS1), in non-small cell lung cancer (NSCLC).

Methods

Quantitative real-time PCR was used to quantify SBF2-AS1 expression in NSCLC tissues and cell lines. The correlation of SBF2-AS1 expression with clinicopathologic features was analyzed in a cohort NSCLC patient. Loss of function and gain of function studies were performed to determine the effects of SBF2-AS1 on proliferation and metastasis of NSCLC cells. RNA immunoprecipitation and chromosome immunoprecipitation assay was performed to confirm the interaction between SBF2-AS1 with protein and chromosome.

Results

We confirmed that SBF2-AS1 was significantly upregulated in NSCLC compared with corresponding non-tumor tissues, and a high expression level of SBF2-AS1 was correlated with lymph node metastasis and advanced TNM stage. Using siRNAs specifically targeting SBF2-AS1 and plasmid vector, we successfully silenced and overexpressed SBF2-AS1 in NSCCLC cell lines and investigated its biological function both in vitro and in vivo. After the silencing of SBF2-AS1, the metastasis of NSCLC cells was significantly inhibited, the silencing of SBF2-AS1 decreased the proliferation of NSCLC cells, and the cell cycle was arrested at the G1 phase; while overexpression promoted proliferation ability. Xenograft tumor models revealed that the silencing of SBF2-AS1 inhibited tumor growth in vivo. We speculated that SBF2-AS1 might negatively regulate P21. RNA immunoprecipitation discovered that SBF2-AS2 could bind with a core component of polycomb repressive complex2, SUZ12. Additionally chromatin immunoprecipitation assay demonstrated that, after silencing SBF2-AS1, the enrichment of SUZ12 and trimethylation of histone 3 lysine 27 decreased at the promoter region of P21.

Conclusions

We demonstrated that SBF2-AS1 is upregulated in NSCLC and promotes proliferation of NSCLC tumor cells. SBF2-AS1 may serve as a novel biomarker and potential therapeutic target for NSCLC patients.

Long noncoding RNAs and tumorigenesis: genetic associations, molecular mechanisms, and therapeutic strategies

The human genome contains a large number of nonprotein-coding sequences. Recently, new discoveries in the functions of nonprotein-coding sequences have demonstrated that the "Dark Genome" significantly contributes to human diseases, especially with regard to cancer. Of particular interest in this review are long noncoding RNAs (lncRNAs), which comprise a class of nonprotein-coding transcripts that are longer than 200 nucleotides. Accumulating evidence indicates that a large number of lncRNAs exhibit genetic associations with tumorigenesis, tumor progression, and metastasis. Our current understanding of the molecular bases of these lncRNAs that are associated with cancer indicate that they play critical roles in gene transcription, translation, and chromatin modification. Therapeutic strategies based on the targeting of lncRNAs to disrupt their expression or their functions are being developed. In this review, we briefly summarize and discuss the genetic associations and the aberrant expression of lncRNAs in cancer, with a particular focus on studies that have revealed the molecular mechanisms of lncRNAs in tumorigenesis. In addition, we also discuss different therapeutic strategies that involve the targeting of lncRNAs.

Natural antisense RNAs are involved in the regulation of CD45 expression in autoimmune diseases

CD45 is a transmembrane protein tyrosine phosphatase that is specifically expressed in hematopoietic cells and can initiate signal transduction via the dephosphorylation of tyrosine. Alternatively spliced transcript variants of this gene encode distinct isoforms, which indicate different functional states of CD45. Among these variants, CD45RO, which contains neither exon 4, 5, or 6, is over-expressed in lymphocytes in autoimmune diseases, including systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, and type I diabetes. The CD45 RO serves as a marker of the immune response activity and lymphocyte development. Previous studies have indicated that exon splicing is generally correlated with local hypermethylated DNA and acetylated histone modification, while autoimmune diseases are commonly associated with global hypomethylation and histone deacetylation in lymphocytes. Thus, the question arises of how exons 4, 5, and 6 of CD45RO are excluded under the status of global DNA hypomethylation and histone deacetylation in these autoimmune diseases. On the basis of the analyses of the context sequence of CD45 and its natural antisense RNA in GenBank, we proposed that the long noncoding RNA encoded by the natural antisense gene of CD45 contributes to the expressional regulation of the CD45RO splicing variant via recruitment of DNA methyltransferase and histone modification modulators specific to the sense gene CD45; thus, it is associated with the over-expression of CD45RO and the functional regulation of lymphocytes in the pathogenic development of autoimmune diseases.

Osteopontin enhances the expression of HOTAIR in cancer cells via IRF1

Osteopontin (OPN), a secreted phosphoglycoprotein, plays important roles in tumor growth, invasion, and metastasis for many types of cancers. The long, noncoding RNA HOTAIR has been strongly associated with the invasion and metastasis of cancer cells. In this study, we found that recombinant human OPN could induce HOTAIR expression in a time- and dose-dependent manner, and our data also showed that OPN transcriptionally activated the expression of HOTAIR in cancer cells. Furthermore, through chromatin immunoprecipitation and luciferase activity assays, we found that IRF1 could bind to the HOTAIR promoter region and decrease its transcriptional activity, and cellular overexpression of IRF1 downregulated the level of HOTAIR. The receptor CD44 has also been verified as a regulator of OPN-induced HOTAIR expression. Interestingly, our data demonstrated that OPN could regulate PI3K/AKT and IRF1 expression and signaling, thereby influencing the expression of HOTAIR. In hepatocellular carcinoma samples, levels of HOTAIR correlated with the expression of OPN and IRF1. We therefore conclude that OPN, as an extracellular matrix protein, can stimulate the expression of HOTAIR by attenuating the inhibitory effect of IRF1, and this results in promotion of the invasion and metastasis of cancer cells.

Non-coding RNAs in hepatitis C-induced hepatocellular carcinoma: Dysregulation and implications for early detection, diagnosis and therapy

Hepatitis C virus (HCV) infection is one of main causes of hepatocellular carcinoma (HCC) and the prevalence of HCV-associated HCC is on the rise worldwide. It is particularly important and helpful to identify potential markers for screening and early diagnosis of HCC among high-risk individuals with chronic hepatitis C, and to identify target molecules for the prevention and treatment of HCV-associated-HCC. Small non-coding RNAs, mainly microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) with size greater than 200 nucleotides, are likely to play important roles in a variety of biological processes, including development and progression of HCC. For the most part their underlying mechanisms of action remain largely unknown. In recent years, with the advance of high-resolution of microarray and application of next generation sequencing techniques, a significant number of non-coding RNAs (ncRNAs) associated with HCC, particularly caused by HCV infection, have been found to be differentially expressed and to be involved in pathogenesis of HCV-associated HCC. In this review, we focus on recent studies of ncRNAs, especially miRNAs and lncRNAs related to HCV-induced HCC. We summarize those ncRNAs aberrantly expressed in HCV-associated HCC and highlight the potential uses of ncRNAs in early detection, diagnosis and therapy of HCV-associated HCC. We also discuss the limitations of recent studies, and suggest future directions for research in the field. miRNAs, lncRNAs and their target genes may represent new candidate molecules for the prevention, diagnosis and treatment of HCC in patients with HCV infection. Studies of the potential uses of miRNAs and lncRNAs as diagnostic tools or therapies are still in their infancy.

MALAT-1 interacts with hnRNP C in cell cycle regulation

As a conserved non-coding RNA gene, transcripts of MALAT-1 localize predominately in the nucleus. However in G2/M cell cycle phase, MALAT-1 transcripts were surprisingly found to translocate from the nucleus into the cytoplasm. Investigation also found that in this process MALAT-1 interacts with an abundant nuclear factor, hnRNP C protein. Using a loss-of-function assay, we found that down-regulation of MALAT-1 expression compromised the cytoplasmic translocation of hnRNP C in the G2/M phase and resulted in G2/M arrest. In addition to characterize the physiological interaction between MALAT-1 and hnRNP C, our study also highlights the role of MALAT-1 in cell cycle regulation.

Long noncoding RNAs-related diseases, cancers, and drugs

Long noncoding RNA (lncRNA) function is described in terms of related gene expressions, diseases, and cancers as well as their polymorphisms. Potential modulators of lncRNA function, including clinical drugs, natural products, and derivatives, are discussed, and bioinformatic resources are summarized. The improving knowledge of the lncRNA regulatory network has implications not only in gene expression, diseases, and cancers, but also in the development of lncRNA-based pharmacology.

Long non-coding RNA: a new player in cancer

Emerging evidence showed that long non-coding RNAs (lncRNAs) play important roles in a wide range of biological processes and dysregulated lncRNAs are involved in many complex human diseases, including cancer. Although a few lncRNAs’ functions in cancer have been characterized, the detailed regulatory mechanisms of majority of lncRNAs in cancer initiation and progression remain largely unknown. In this review, we summarized recent progress on the mechanisms and functions of lncRNAs in cancer, especially focusing on the oncogenic and tumor suppressive roles of the newly identified lncRNAs, and the pathways these novel molecules might be involved in. Their potentials as biomarkers for diagnosis and prognosis in cancer are also discussed in this paper.

RNA-seq identified a super-long intergenic transcript functioning in adipogenesis

RNA transcripts are generally classified into polyA-plus and polyA-minus subgroups due to the presence or absence of a polyA tail at the 3′ end. Even though a number of physiologically and pathologically important polyA-minus RNAs have been recently identified, a systematic analysis of the expression and function of these transcripts in adipogenesis is still elusive. To study the potential function of the polyA-minus RNAs in adipogenesis, a dynamic expressional profiling was performed in the induced differentiation of 3T3-L1 cells. In addition to identifying thousands of novel intergenic transcripts, differentiation-synchronized expression was characterized for many of them. Among these, several large intergenic transcripts were found to be upregulated by more than 19-fold during differentiation. Further study demonstrated a fat tissue-specific expression pattern for these regions and identified an adipogenesis-associated long non-coding RNA. Collectively, these lines of evidence contribute to the characterization of a super-long intergenic transcript functioning in adipogenesis.

Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges

The numerous genome sequencing projects produced unprecedented amount of data providing significant information to the discovery of novel non-coding RNA (ncRNA). Several ncRNAs have been described to control gene expression and display important role during cell differentiation and homeostasis. In the last decade, high throughput methods in conjunction with approaches in bioinformatics have been used to identify, classify, and evaluate the expression of hundreds of ncRNA in normal and pathological states, such as cancer. Patient outcomes have been already associated with differential expression of ncRNAs in normal and tumoral tissues, providing new insights in the development of innovative therapeutic strategies in oncology. In this review, we present and discuss bioinformatics advances in the development of computational approaches to analyze and discover ncRNA data in oncology using high throughput sequencing technologies.