A novel lncRNA, GASL1, inhibits cell proliferation and restricts E2F1 activity

Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency

Although many long non-coding RNAs (lncRNAs) exhibit lineage-specific expression, the vast majority remain functionally uncharacterized in the context of development. Here, we report the first described human embryonic stem cell (hESC) lines to repress (CRISPRi) or activate (CRISPRa) transcription during differentiation into all three germ layers, facilitating the modulation of lncRNA expression during early development. We performed an unbiased, genome-wide CRISPRi screen targeting thousands of lncRNA loci expressed during endoderm differentiation. While dozens of lncRNA loci were required for proper differentiation, most differentially expressed lncRNAs were not, supporting the necessity for functional screening instead of relying solely on gene expression analyses. In parallel, we developed a clustering approach to infer mechanisms of action of lncRNA hits based on a variety of genomic features. We subsequently identified and validated FOXD3-AS1 as a functional lncRNA essential for pluripotency and differentiation. Taken together, the cell lines and methodology described herein can be adapted to discover and characterize novel regulators of differentiation into any lineage.

Role of Long Non-Coding RNAs in Pulmonary Arterial Hypertension

Pulmonary arterial hypertension (PAH) is a debilitating condition of the pulmonary circulatory system that occurs in patients of all ages and if untreated, eventually leads to right heart failure and death. Despite existing medical treatment options that improve survival and quality of life, the disease remains incurable. Thus, there is an urgent need to develop novel therapies to treat this disease. Emerging evidence suggests that long non-coding RNAs (lncRNAs) play critical roles in pulmonary vascular remodeling and PAH. LncRNAs are implicated in pulmonary arterial endothelial dysfunction by modulating endothelial cell proliferation, angiogenesis, endothelial mesenchymal transition, and metabolism. LncRNAs are also involved in inducing different pulmonary arterial vascular smooth muscle cell phenotypes, such as cell proliferation, apoptosis, migration, regulation of the phenotypic switching, and cell cycle. LncRNAs are essential regulators of gene expression that affect various diseases at the chromatin, transcriptional, post-translational, and even post-translational levels. Here, we focus on the role of LncRNAs and their molecular mechanisms in the pathogenesis of PAH. We also discuss the current research challenge and potential biomarker and therapeutic potentials of lncRNAs in PAH.

A novel E2F1-regulated lncRNA, LAPAS1, is required for S phase progression and cell proliferation

The transcription factor E2F1 induces both proliferation and apoptosis and is a critical downstream target of the tumor suppressor RB.

Long non-coding RNAs (lncRNAs) are major regulators of many cellular processes, including cell cycle progression and cell proliferation. However, the mode of action as well as the transcriptional regulation of most lncRNAs are only beginning to be understood.

Here, we report that a novel human lncRNA, LAPAS1, is an E2F1- regulated lncRNA that affects S phase progression. Inhibition of LAPAS1 expression increases percentage of S phase cells, and its silencing in synchronized cells delays their progression through S phase. In agreement with its suggested role in cell cycle progression, prolonged inhibition of LAPAS1 attenuates proliferation of human cancer cells.

Our data demonstrate that LAPAS1 predominantly functions in trans to repress expression of Sphingolipid Transporter 2 (SPNS2). Importantly, knockdown of SPNS2 rescues the effect of LAPAS1 silencing on cell cycle and cell proliferation.

Notably, low levels of LAPAS1 are associated with increased survival of kidney cancer patients.

Summarily, we identify LAPAS1 as a novel E2F-regulated lncRNA that has a potential role in human cancer and regulates cell-cycle progression and cell proliferation, at least in part, via regulation of SPNS2.

The novel target of esophageal squamous cell carcinoma: lncRNA GASL1 regulates cell migration, invasion and cell cycle stagnation by inactivating the Wnt3a/β-catenin signaling

Long non-coding RNA (lncRNA) Growth-Arrest Associated LncRNA 1 (GASL1) is a lncRNA with a suppressive role in glioma, prostate carcinoma and gastric carcinoma, whereas its involvement in esophageal cancer is unknown. In the present study, we used RT-qPCR to detect the expression of GASL1 in esophageal cancer cell carcinoma (ESCC) cell lines, and constructed the overexpression and interference plasmids of GASL1 and the interference plasmid of DKK1. CCK8 was used to detect the cell proliferation level, clone formation experiment was used to detect the cell clonal formation ability, flow cytometry was used to detect the cell cycle level, and wound healing and Transwell experiments were respectively used to detect the cell invasion and migration. The interference and overexpression plasmids of GASL1 were injected into mice subcutaneously for tumor-bearing experiment. The body weight, tumor growth curve, and tumor weight of mice were recorded, and western blot was used to detect the expression of proliferation-, invasion-, and migration-related proteins and the expression of Wnt3a/β-catenin signal-related proteins in tumor tissues. LncRNA GASL1 was down-regulated in ESCC cell lines, and GASL1 inhibited ESCC cell progression and regulated cell cycle arrest in ESCC cells. In vivo, GASL1 inhibited tumor growth. GASL1 decreased the protein levels of DDK1, Wnt3a, β-catenin, and c-MYC in ESCC cell lines. Interfering DKK1 activates Wnt3a/β--catenin signal to reverse the inhibitory effects of GASL1 on proliferation, cell cycle acceleration, invasion, and migration. In conclusion, lncRNA GASL1 regulates cell migration, invasion and cell cycle stagnation by inactivating the wnt/β-catenin signaling.

The effect of LncRNA SNHG16 on vascular smooth muscle cells in CHD by targeting miRNA-218-5p

PURPOSE

To explore the role of SNHG16 in coronary heart disease (CHD) and its effect on vascular smooth muscle cells via miR-218-5p.

METHODS

A quantitative real time polymerase chain reaction (qRT-PCR) assay was carried out to determine the expression of serum SNHG16 and miR-218-5p in the observation group before and after treatment and in the control group. Then, receiver operating characteristic (ROC) curves were drawn to analyze the value of SNHG16 and miR-218-5p in the diagnosis and prognosis prediction of CHD. Furthermore, purchased coronary artery smooth muscle cells (HCASMC) were transfected with SNHG16 mimics, SNHG16 inhibitor, miR-218-5p mimics, miR-218-5p inhibitor, or negative control, and then the cell proliferation, migration, apoptosis, and apoptosis-related proteins (Bax, Bcl-2, and Caspase-3) and Wnt/β-catenin signaling pathway-related proteins (c-myc and β-catenin) in the cells were detected.

RESULTS

Both SNHG16 and miR-218-5 had good predictive value for the development and recurrence of CHD (P < 0.001). In addition, cell experiments showed that inhibition of SNHG16 weakened the proliferation and migration of HCASMC cells and intensified their apoptosis, SNHG16 and miR-218-5p had the same binding sites, and the dual luciferase reporter assay revealed that the fluorescence activity of HG16-WT was inhibited by transfected miR-mimics, but enhanced by transfected miR-inhibitor (both P < 0.050). Furthermore, the rescue experiment revealed that the effect of inhibiting SNHG16 on HCASMC cells was completely reversed by miR-218-5p (P > 0.050).

CONCLUSIONS

Highly expressed SNHG16 targetedly regulates miR-218-5p and promotes the proliferation and migration of HCASMC via the Wnt/β-catenin signaling pathway, giving rise to CHD.

Long noncoding RNA Linc00337 functions as an E2F1 co-activator and promotes cell proliferation in pancreatic ductal adenocarcinoma

BACKGROUND

Long noncoding RNA (lncRNA) Linc00337 has been implicated in lung, gastric, colorectal and esophageal squamous cell carcinoma progression via various mechanisms; however, its clinicopathological significance and role in pancreatic ductal adenocarcinoma (PDAC) progression remains largely unknown.

METHODS

Multiple approaches such as bioinformatic analysis, Transfection, quantitative real-time-PCR, Western blotting, animal studies, RNA-immunoprecipitation (RIP), RNA-pulldown and RNA-Fluorescence in situ hybridization (RNA-FISH) and were utilized to explore the role of Linc00337 in PDAC.

RESULTS

Here we identified Linc00337 is an oncogenic lncRNA during PDAC progression. We found that the expression of Linc00337 is elevated in PDAC tissues and the higher Linc00337 predicts dismal prognosis. Functionally, Linc00337 promotes PDAC cell proliferation and cell cycle transition both in vitro and in vivo. Mechanistically, Linc00337 binds to E2F1 and functions as an E2F1 coactivator to trigger the targets expression during PDAC progression.

CONCLUSION

Our results demonstrate a reciprocal regulation mechanism between Linc00337 and E2F1 in PDAC progression and report the clinical value of Linc00337 for PDAC prognosis and treatment.

Long non-coding RNA GASL1 restrains gastric carcinoma cell proliferation and metastasis by sponging microRNA-106a

Background: Gastric carcinoma (GC) is a common malignant tumor. Recently, it has been found that long non-coding RNAs (lncRNAs) play important role in cancer. In this paper, we investigated the effects and mechanism of lncRNA GASL1 in GC cells. Methods: GASL1 level in GC cells was up-regulated via cell transfection. Cell proliferation, migration, invasion were detected by CCK-8, BrdU, Transwell assays and western blot. In addition, the regulation of GASL1 on microRNA (miR)-106a level was detected using RT-qPCR and the binding between GASL1 and miR-106a was confirmed by bioinformatic prediction and luciferase reporter assay. The effects of overexpressing miR-106a on GASL1-regulated GC cell behaviors were further explored. Moreover, western blot also was used to detect the pathway-related proteins. Results: Overexpression of GASL1 decreased the viability and BrdU levels. Meanwhile, CyclinD1 level was decreased while p53 and p21 levels were strengthened by overexpression of GASL1. On cell metastasis, up-regulation of GASL1 decreased cell migration, invasion and related proteins matrix metalloproteinase (MMP)-9 and Vimentin levels. Meanwhile, silencing GASL1 exerted opposite effects on GC cells. Moreover, GASL1 negatively regulated and targeted miR-106a. Up-regulation of miR-106a weakened the functions of GASL1 in cell proliferation and metastasis. Besides, GASL1 decreased the relate-protein levels of PI3K/AKT and ras/raf/MEK/ERK pathways while miR-106a weakened these changes. ConclusionGASL1 restrained GC cell proliferation and metastasis and blocked PI3K/AKT and ras/raf/MEK/ERK pathways by sponging miR-106a.

HOXB-AS1 accelerates the tumorigenesis of glioblastoma via modulation of HOBX2 and HOBX3 at transcriptional and posttranscriptional levels

Glioblastoma (GBM) is the most universal and invasive brain tumor among adults. Increasing studies have reported that long noncoding RNAs play vital roles in regulating downstream molecules at the transcriptional or posttranscriptional level in tumor progression. The purpose of the current research was to inquire the modulation mechanism by which homeobox B cluster antisense RNA 1 (HOXB-AS1) functioned in GBM. Our study first discovered the lifted expression of HOXB-AS1 and its nearby genes HOXB2 and HOXB3 in GBM and the positive relationship between HOXB-AS1 and HOXB2 or HOXB3. Loss-of-function assays and in vivo study detected that silencing of HOXB-AS1, HOXB2, or HOXB3 restrained the proliferation and induced the apoptosis in GBM. In addition, mechanism experiments demonstrated that HOXB-AS1 recruited interleukin enhancer-binding factor 3 (ILF3) to regulate HOXB2 and HOXB3 expression at the transcriptional level, and HOXB-AS1 sponged miR-186-5p to modulate HOXB2 and HOXB3 expression at posttranscriptional level. Finally, the regulatory mechanism of HOXB-AS1 in GBM was certified through rescue experiments. Our results indicated that HOXB-AS1 boost the HOXB2 or HOXB3 expression at the transcriptional and posttranscriptional levels. We detected the HOXB-AS1-ILF3-HOXB2/HOXB3 axis and HOXB-AS1-miR-186-5p-HOXB2/HOXB3 axis driving the GBM progression, which might generate more effective diagnostic biomarkers and therapeutic targets for patients with GBM.

LINC00667/miR-449b-5p/YY1 axis promotes cell proliferation and migration in colorectal cancer

Background

Long non-coding RNAs (lncRNAs) have been defined as vital regulators in the progression of human cancers, including colorectal cancer (CRC). Long intergenic non-protein coding RNA 667 (LINC00667) is a tumor promoter in several cancer types, while its role in CRC remains to be unmasked. This study focused on exploring the potential function and regulatory mechanism of LINC00667 in CRC.

Methods

qRT-PCR analysis was applied to detect the expression of LINC00667 in CRC cells. Loss-of function assays revealed the role of LINC00667 silencing in regulating CRC cell proliferation, apoptosis and migration. In vivo study demonstrated the effect of LINC00667 silencing on CRC cell growth. Mechanism experiments were conducted to determine the upstream or the downstream molecular mechanism of LINC00667 in CRC cells.

Results

LINC00667 was expressed at high level in CRC cells. LINC00667 knockdown significantly inhibited CRC cell growth and migration. YY1 transcription factor induced the upregulation of LINC00667 in CRC cells by transcriptionally activating LINC00667. In addition, miR-449b-5p could interact with LINC00667 in CRC cells. Intriguingly, miR-449b-5p directly targeted to YY1, thus inhibiting YY1 expression. YY1 recovered the CRC cell functions impaired by LINC00667 silencing.

Conclusions

LINC00667 is transcriptionally activated by YY1 and promotes cell proliferation and migration in CRC by sponging miR-449b-5p to upregulate YY1.

Identification of Key Players Involved in CoCl2 Hypoxia Induced Pulmonary Artery Hypertension in vitro

Background

The proliferation of human pulmonary artery smooth muscle cells (HPASMCs) induced by hypoxia was considered as the main cause of pulmonary arterial hypertension (PAH). This study aimed to explore potential genes and long non-coding RNAs (lncRNAs) involved in the mechanism of hypoxia-induced PAH.

Methods

CoCl₂ was utilized to induce hypoxia in HPASMCs, and then cell proliferation, apoptosis, and expression of hypoxia-inducible factors (HIF)-1α were determined. Meanwhile, the RNA isolated from CoCl₂-treated cells and control cells were sequenced and differentially expressed genes/lncRNA (DEGs/DELs) were screened, followed by protein-protein interaction (PPI) construction, functional enrichment analyses, and lncRNA-target prediction. Finally, the expression of key genes and lncRNAs were validated using quantitative real-time PCR and western blotting.

Results

CoCl₂ treatment could significantly increase the expression of HIF-1α and the proliferation of HPASMCs. A total of 360 DEGs and 57 DELs were identified between CoCl₂ treated and control cells. Functional enrichment analysis showed that up-regulated DEGs and DELs’ targets, including LDHA, PFKP, and VEGFA, were significantly enriched in biological processes related to hypoxia or oxygen levels, and the downregulated DEGs and DELs’ targets were significantly enriched in extracellular-matrix-related biological processes. In addition, LDHA, PFKP, and VEGFA exhibited a strong relationship with miR-100HG and TSPEAR-AS2 in lncRNA-target network. The protein level of LDHA, PFKP, and VEGFA were all increased.

Conclusion

LDHA, PFKP, VEGFA, and lncRNA miR-100HG and TSPEAR-AS2 probably played crucial roles in the pathogenesis of CoCl₂ hypoxia-induced-HAP, which might serve as promising therapeutic targets for PAH.

A classification model for lncRNA and mRNA based on k-mers and a convolutional neural network

Background

Long-chain non-coding RNA (lncRNA) is closely related to many biological activities. Since its sequence structure is similar to that of messenger RNA (mRNA), it is difficult to distinguish between the two based only on sequence biometrics. Therefore, it is particularly important to construct a model that can effectively identify lncRNA and mRNA.

Results

First, the difference in the k-mer frequency distribution between lncRNA and mRNA sequences is considered in this paper, and they are transformed into the k-mer frequency matrix. Moreover, k-mers with more species are screened by relative entropy. The classification model of the lncRNA and mRNA sequences is then proposed by inputting the k-mer frequency matrix and training the convolutional neural network. Finally, the optimal k-mer combination of the classification model is determined and compared with other machine learning methods in humans, mice and chickens. The results indicate that the proposed model has the highest classification accuracy. Furthermore, the recognition ability of this model is verified to a single sequence.

Conclusion

We established a classification model for lncRNA and mRNA based on k-mers and the convolutional neural network. The classification accuracy of the model with 1-mers, 2-mers and 3-mers was the highest, with an accuracy of 0.9872 in humans, 0.8797 in mice and 0.9963 in chickens, which is better than those of the random forest, logistic regression, decision tree and support vector machine.

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles in cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling their effects on the activity of transcription factors, RNA-binding proteins, and microRNAs in 5,185 TCGA tumors and 1,019 ENCODE assays. Our predictions included hundreds of candidate onco- and tumor-suppressor lncRNAs (cancer lncRNAs) whose somatic alterations account for the dysregulation of dozens of cancer genes and pathways in each of 14 tumor contexts. To demonstrate proof of concept, we showed that perturbations targeting OIP5-AS1 (an inferred tumor suppressor) and TUG1 and WT1-AS (inferred onco-lncRNAs) dysregulated cancer genes and altered proliferation of breast and gynecologic cancer cells. Our analysis indicates that, although most lncRNAs are dysregulated in a tumor-specific manner, some, including OIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergistically dysregulate cancer pathways in multiple tumor contexts.

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Hundreds of lncRNAs target cancer genes and pathways in each tumor context

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lncRNA copy numbers are predictive of target cancer gene dysregulation

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Most lncRNAs are predicted to be transcriptional or post-transcriptional specialists

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lncRNAs are predicted to synergistically regulate proliferation pathways in cancer

Involvement of GASL1 in postoperative distant recurrence of gastric adenocarcinoma after gastrectomy distal resection and the possible mechanism

As a cancer-related long noncoding RNA, functionality of GASL1 has only been characterized in liver cancer. Our study aimed to investigate the possible involvement of GASL1 in postoperative recurrence of gastric adenocarcinoma. A total of 112 gastric adenocarcinoma patients with a tumor located in the distal third who received gastrectomy distal resection in The Second Hospital of Dalian Medical University from January 2012 to January 2015 were included in this study. Patients were followed up for 3 years. Another 56 healthy people were also included to serve as a control group. Blood was extracted from each subject on the day of discharge, on the day of diagnosis of recurrence or at the end of follow-up. The GASL1 expression vector was transfected into gastric adenocarcinoma cell lines. It was observed that plasma levels of GASL1 were significantly lower, while plasma levels of transforming growth factor-β1 (TGF-β1) were significantly higher in patients than in healthy controls on the day of discharge. Patients with distant recurrence showed significantly lower plasma levels of GASL1 and significantly higher plasma levels of TGF-β1 compared with patients with local recurrence and patients without recurrence. During follow-up, plasma levels of GASL1 and TGF-β1 were negatively correlated in patients with distant recurrence but not in other groups of patients. GASL1 overexpression inhibited, while TGF-β1 treatment promoted cell migration and invasion. Overexpression of GASL1 led to downregulated and GASL1 knockdown led to upregulated TGF-β1. However, TGF-β1 showed no significant effects on GASL1 expression. We conclude that GASL1 may participate in the distant recurrence of gastric adenocarcinoma through the interactions with TGF-β1.

LncRNA MAFG-AS1 boosts the proliferation of lung adenocarcinoma cells via regulating miR-744-5p/MAFG axis

Lung adenocarcinoma (LUAD) is typically featured by a low 5-year survival rate, hence there is a necessary to investigate new biomarkers in LUAD progression. Competing endogenous RNA (ceRNA) network has been widely reported in the regulation of tumor processes, which is also the main direction of this paper. Based on the data of GEPIA database, lncRNA MAFG-AS1 was upregulated in LUAD tissues, which was associated with poor prognosis of patients. Proliferation or apoptosis of LUAD cells were measured by CCK-8, EdU and caspase-3 activity assays followed by Western blot. The results indicated that silencing of MAFG-AS1 suppressed cell proliferation but induced cell apoptosis. RNA FISH staining showing the cytoplasmic localization of MAFG-AS1 in LUAD cells. Mechanism detection revealed that MAFG-AS1 served as a molecular sponge of miR-744-5p to upregulate its nearby gene MAF bZIP transcription factor G (MAFG) in LUAD cells. Functionally, MAFG overexpression attenuated the cellular processes mediated by MAFG-AS1 knockdown. In summary, this study unveiled the MAFG-AS1/miR-744-5p/MAFG axis in LUAD, providing a potent and promising therapeutic target for LUAD patients.

LncRNA GASL1 is downregulated in chronic heart failure and regulates cardiomyocyte apoptosis

Background

TGF-β1 contributes to chronic heart failure. It is known that lncRNA GASL1 can inactivate TGF-β1 in cancer biology.

Methods

All the participants were enrolled in the First People’s Hospital of Zhaoqing during the period June 2012 to June 2013. ELISA, RT-qPCR, vectors, transient transfections and western blot were carried out during the research.

Results

We found that plasma levels of TGF-β1 were significantly higher, while levels of GASL1 in plasma were significantly lower in chronic heart failure (CHF) patients compared to the control group. TGF-β1 and GASL1 were inversely correlated in CHF patients. Low pretreatment plasma levels of GASL1 were closely associated with poor survival of CHF patients. GASL1 expression was not significantly affected by TGF-β1 overexpression in cardiomyocytes, while cardiomyocytes with GASL1 overexpression showed downregulated TGF-β1. Overexpression of GASL1 led to a decreased, while TGF-β1 overexpression led to an increased apoptotic rate of cardiomyocytes under H₂O₂ treatment. In addition, TGF-β1 overexpression attenuated the effect of GASL1 overexpression.

Conclusion

In conclusion, GASL1 was downregulated in CHF. GASL1 overexpression may improve CHF by inhibiting cardiomyocyte apoptosis through the inactivation of TGF-β1.

Long non-coding RNA GASL1 may inhibit the proliferation of glioma cells by inactivating the TGF-β signaling pathway

Growth-arrest-associated long non-coding RNA (lncRNA) 1 (GASL1) is an lncRNA with a tumor suppression role in osteosarcoma, whereas its involvement in other malignancies is unknown. In the present study, tumor tissues and adjacent healthy tissues were collected from patients with glioma, and blood samples were collected from patients and healthy controls to detect the expression of GASL1. All patients were followed up for 5 years, and the diagnostic and prognostic values for glioma were evaluated by receiver operating characteristic curve analysis and survival curve analysis, respectively. Potential associations between serum GASL1 and clinicopathological data of patients with glioma were investigated using χ² testing. A GASL1 expression vector and short hairpin RNA targeting GASL1 were transfected into glioma cells and the effects on TGF-β1 expression and cell proliferation were investigated by western blotting and Cell Counting Kit-8 assay. Glioma tumor tissue exhibited significantly lower GASL1 expression compared with in adjacent healthy tissue. Serum levels of GASL1 were lower in patients compared with in healthy controls. Serum GASL1 was identified to be a sensitive biomarker for glioma cancer, and a low expression level of GASL1 was associated with a decreased postoperative survival rate. In glioma cell lines with GASL1 overexpression, TGF-β1 expression was decreased and proliferation was inhibited. GASL1 knockdown in glioma cell lines led to increased TGF-β1 expression and proliferation. TGF-β1 treatment had no effect on GASL1 expression, but TGF-β1 treatment partially rescued the inhibition of proliferation in cells overexpressing GASL1. Therefore, GASL1 may inhibit tumor growth of glioma by inactivating the TGF-β signaling pathway.

Long Noncoding RNA SBF2-AS1 Is Critical for Tumorigenesis of Early-Stage Lung Adenocarcinoma

Emerging evidence demonstrates that long non-coding RNAs (lncRNAs) are deeply involved in the development of various cancers. This study identified that SBF2-AS1, an early-stage-specific lncRNA, is critical for the tumorigenesis of lung adenocarcinoma (LUAD). We first analyzed LUAD transcriptome data from The Cancer Genome Atlas and the GEO database by weighted gene co-expression network analysis (WGCNA). Five early LUAD-specific lncRNAs were filtered out, and only SBF2-AS1 was upregulated in LUAD. High expression of SBF2-AS1 indicates poor survival of LUAD, especially the early-stage LUAD, but not lung squamous cell carcinoma. SBF2-AS1 promotes LUAD cells proliferation in vitro, and RNA-sequencing data shows that many cell-cycle-related genes were downregulated after SBF2-AS1 knockdown. Mechanically, SBF2-AS1 could competitively bind with miR-338-3p and miR-362-3p to increase E2F1 expression. Finally, we show that the SBF2-AS1-miR-338-3p/362-3p-E2F1 axis could promote LUAD tumorigenesis in vitro and in vivo. Our study demonstrates that SBF2-AS1, an early-stage-specific lncRNA, promotes LUAD tumorigenesis by sponging miR-338-3p and miR-362-3p and increasing E2F1 expression. The SBF2-AS1-miR-338-3p/362-3p-E2F1 regulatory axis may serve as a prognostic marker and potential therapeutic target for LUAD.

LncRNA GASL1 inhibits growth and promotes expression of apoptosis-associated proteins in prostate carcinoma cells through GLUT-1

Growth-arrest-associated long non-coding (lnc)RNA 1 (GASL1) is as newly identified lncRNA that is associated with liver cancer. The present study aimed to investigate the role of GASL1 in prostate carcinoma (PC). Expression levels of GASL1 in prostate tissues and sera from patients with PC and from healthy subjects were detected by reverse transcription-quantitative polymerase chain reaction. Receiver operating characteristic and survival curve analyses were performed to evaluate the diagnostic and prognostic values of GASL1 for patients with PC. A GASL1 expression vector was transfected into PC cells prior to assessment of cell proliferation and expression of B cell lymphoma 2 (Bcl-2) and glucose transporter 1 (GLUT-1) by Cell Counting Kit-8 and western blotting, respectively. The results demonstrated that GASL1 was significantly downregulated in the tissue and serum of patients with PC compared to those of healthy subjects. In addition, GASL1 was used to distinguish patients with PC from healthy controls, and low expression levels of GASL1 were associated with short survival time. Expression levels of GASL1 were significantly associated with tumor size. GASL1 overexpression inhibited PC cell growth. Overexpression of GASL1 upregulated Bcl-2 expression and downregulated GLUT-1 expression. In conclusion, these data suggested that lncRNA GASL1 may inhibit PC cell proliferation by targeting GLUT-1.

LncRNA GASL1 inhibits tumor growth in gastric carcinoma by inactivating the Wnt/β-catenin signaling pathway

Growth arrest associated lncRNA 1 (GASL1) is a newly discovered tumor suppressor long non-coding RNA (lncRNA) in osteosarcoma; however its role in other malignancies remains unknown. The aim of the present study was to investigate the involvement of GASL1 in gastric cancer. In the current study, gastric cancer tissue and adjacent healthy tissue samples were collected from patients with gastric carcinoma, and blood samples were collected from patients with gastric carcinoma and healthy controls to detect the expression of serum GASL1. All patients were followed up for 5 years and the diagnostic and prognostic value of GASL1 for gastric carcinoma was evaluated by ROC and survival curve analyses, respectively. The chi-square test was used to analyze the correlation between serum levels of GASL1 and the clinicopathological features of patients with gastric carcinoma. A GASL1 expression vector and GASL1 small interfering RNA were transfected into gastric cancer cell lines and the effects on β-catenin expression and cell proliferation were examined by western blot and cell proliferation assays, respectively. The expression level of lncRNA GASL1 was significantly downregulated in gastric cancer tissues compared with adjacent normal tissues from patients with gastric carcinoma. In addition, serum levels of GASL1 were significantly decreased in patients with gastric carcinoma when compared with healthy controls. Serum GASL1 levels distinguished patients with gastric carcinoma from healthy controls, and low expression levels of GASL1 were associated with decreased postoperative survival time. GASL1 overexpression downregulated, while GASL1 knockdown upregulated β-catenin expression. GASL1 overexpression inhibited, and GASL1 knockdown promoted gastric cancer cell proliferation. In addition, treatment with a Wnt agonist demonstrated no significant effect on GASL1 expression, however the inhibitory effect of GASL1 overexpression on cell proliferation was reduced following treatment with the Wnt agonist. In conclusion, the GASL1 lncRNA may inhibit tumor growth in patients with gastric carcinoma by inactivating the Wnt/β-catenin signaling pathway.

LincK contributes to breast tumorigenesis by promoting proliferation and epithelial-to-mesenchymal transition

BACKGROUND

Increasing evidence has demonstrated that mesenchymal stem cells (MSCs) play a role in the construction of tumor microenvironments. Co-culture between tumor cells and MSCs provides an easy and useful platform for mimicking tumor microenvironments and identifying the important members involved in tumor progress. The long non-coding RNAs (lncRNAs) have been shown to regulate different tumorigenic processes. In this study, we aimed to examine functional lncRNA deregulations associated with breast cancer malignancy instigated by MSC-MCF-7 co-culture.

METHODS

The microarrays were used to profile the expression changes of lncRNAs in MCF-7 cells during epithelial-mesenchymal transition (EMT) induced by co-culture with MSCs. We found that an intergenic lncRNA KB-1732A1.1 (termed LincK, partly overlapped with GASL1) was significantly elevated. To investigate the biological function of LincK, the expression of EMT markers, cell migration, invasion, proliferation, and colony formation were evaluated in vitro and xenograft assay in nude mice were performed in vivo. Furthermore, we detected LincK expression in clinical samples using RNAscope® technology and verified aberrant expression of LincK in breast cancer data sets from The Cancer Genome Atlas (TCGA) by bioinformatic analysis. The underlying mechanisms of LincK were investigated using mRNA microarray analyses, Western blot, RNA pull down, and RNA immunoprecipitation.

RESULTS

LincK induced an EMT progress in breast cancer cells (BCC) MCF-7, MDA-MB-453, and MDA-MB-231. The depletion of LincK decreased the growth, migration, and invasion in BCC, whereas the overexpression of LincK exerted the opposite effects. Moreover, knockdown of LincK repressed tumorigenesis, and ectopic expression of LincK promoted tumor growth in MCF-7 xenograft model. LincK ablation in MDA-MB-231 cells dramatically impaired lung metastasis when incubated intravenously into nude mice. Further, LincK was frequently elevated in breast cancer compared with normal breast tissue in clinical samples. Mechanistically, LincK may share common miRNA response elements with PBK and ZEB1 and regulate the effects of miR-200 s.

CONCLUSION

LincK plays a significant role in regulating EMT and tumor growth and could be a potential therapeutic target in breast cancer.

Expression of a Novel Long Noncoding RNA (lncRNA), GASL1, is Downregulated in Patients with Intracranial Aneurysms and Regulates the Proliferation of Vascular Smooth Muscle Cells In Vitro

BACKGROUND Preliminary microarray data in our laboratory indicated that the novel long noncoding RNA (lncRNA), GASL1, was downregulated in patients with intracranial aneurysms. This study aimed to investigate the expression of lncRNA GASL1 in patients with intracranial aneurysms and its role in the regulation of vascular smooth muscle cell (VSMC) proliferation by transforming growth factor-β1 (TGF-β1). MATERIAL AND METHODS The study included 68 patients with unruptured intracranial aneurysms and 56 healthy volunteers. In both groups, serum levels of TGF-β1 were measured using an enzyme-linked immunoassay (ELISA) and Western blot. Human VSMCs in vitro underwent lncRNA GASL1 overexpression using the insertion of an EcoRI-EcoRI fragment into the pIRSE2 vector. Cell viability and proliferation were measured by a cell counting kit-8 (CCK-8) assay. RNA extraction and quantitative real-time polymerase chain reaction (qRT-PCR) determined GASL1 expression. RESULTS ROC curve analysis showed that downregulation of GASL1 effectively distinguished patients with intracranial aneurysm from healthy controls. Blood GASL1 and TGF-β1 were negatively correlated in patients with intracranial aneurysm but not in healthy people. GASL1 overexpression promoted proliferation of human vascular smooth muscle cells (VSMCs) and downregulated TGF-β1 expression, while exogenous TGF-β1 reduced VSMCs proliferation but showed no effects on GASL1 expression.  CONCLUSIONS Expression of the novel lncRNA, GASL1, was downregulated in patients with intracranial aneurysms and regulated the proliferation of VSMCs in vitro by targeting TGF-β1.

NR2C2-uORF targeting UCA1-miR-627-5p-NR2C2 feedback loop to regulate the malignant behaviors of glioma cells

Accumulating evidence has highlighted the potential role of non-coding RNAs (ncRNAs) and upstream open-reading frames (uORFs) in the biological behaviors of glioblastoma. Here, we elucidated the function and possible molecular mechanisms of the effect of some ncRNAs and NR2C2-uORF on the biological behaviors of gliomas. Quantitative real-time PCR was conducted to profile the cell expression of lnc-UCA1 and microRNA-627-5p (miR-627-5p) in glioma tissues and cells. Western blot assay was used to determine the expression levels of NR2C2, SPOCK1, and NR2C2-uORF in glioma tissues and cells. Stable knockdown of lnc-UCA1 or overexpression of miR-627-5p in glioma cell lines (U87 and U251) were established to explore the function of lnc-UCA1 and miR-627-5p in glioma cells. Further, Dual luciferase report assay was used to investigate the correlation between lnc-UCA1 and miR-627-5p. Cell Counting Kit-8, transwell assays, and flow cytometry were used to investigate lnc-UCA1 and miR-627-5p function including cell proliferation, migration and invasion, and apoptosis, respectively. ChIP assays were used to ascertain the correlations between NR2C2 and SPOCK1 as well as NR2C2 between lnc-UCA1. This study confirmed that lnc-UCA1 was up-regulated in glioma tissues and cells. UCA1 knockdown inhibited the malignancies of glioma cells by reducing proliferation, migration, and invasion, but inducing apoptosis. We found that lnc-UCA1 acted as miR-627-5p sponge in a sequence-specific manner. Meanwhile, upregulated lnc-UCA1 inhibited miR-627-5p expression. In addition, miR-627-5p targeted 3'UTR of NR2C2 and down-regulated its expression. Moreover, UCA1 knockdown impaired NR2C2 expression by upregulating miR-627-5p. An uORF was identified in mRNA 5'UTR of NR2C2 and overexpression of whom negatively regulated NR2C2 expression. Remarkably, lnc-UCA1 knockdown combined with uORF overepression and NR2C2 knockdown led to severe tumor suppression in vivo. This study demonstrated that the NR2C2-uORF impaired the pivotal roles that UCA1-miR-627-5p-NR2C2 feedback loop had in regulating the malignancies of glioma cells by targeting NR2C2 directly. And this may provide a potential therapeutic strategy for treating glioma.

LncRNA DLEU1 contributes to colorectal cancer progression via activation of KPNA3

Background

Accumulating evidences show that long noncoding RNAs (lncRNA) play essential roles in the development and progression of various malignancies. However, their functions remains poorly understood and many lncRNAs have not been defined in colorectal cancer (CRC). In this study, we investigated the role of DLEU1 in CRC.

Methods

Quantitative real-time PCR was used to detect the expression of DLEU1 and survival analysis was adopted to explore the association between DLEU1 expression and the prognosis of CRC patients. CRC cells were stably transfected with lentivirus approach and cell proliferation, migration, invasion and cell apoptosis, as well as tumorigenesis in nude mice were performed to assess the effects of DLEU1 in BCa. Biotin-coupled probe pull down assay, RNA immunoprecipitation and Fluorescence in situ hybridization assays were conducted to confirm the relationship between DLEU1 and SMARCA1.

Results

Here we revealed that DLEU1 was crucial for activation of KPNA3 by recruiting SMARCA1, an essential subunit of the NURF chromatin remodeling complex, in CRC. DLEU1 was indispensible for the deposition of SMARCA1 at the promoter of KPNA3 gene. Increased expression of DLEU1 and KPNA3 was observed in human CRC tissues. And higher expression of DLEU1 or KPNA3 in patients indicates lower survival rate and poorer prognosis. DLEU1 knockdown remarkably inhibited CRC cell proliferation, migration and invasion in vitro and in vivo while overexpressing KPNA3 in the meantime reversed it.

Conclusions

Our results identify DLEU1 as a key regulator by a novel DLEU1/SMARCA1/KPNA3 axis in CRC development and progression, which may provide a potential biomarker and therapeutic target for the management of CRC.

Electronic supplementary material

The online version of this article (10.1186/s12943-018-0873-2) contains supplementary material, which is available to authorized users.

RNA-Sequencing of Primary Retinoblastoma Tumors Provides New Insights and Challenges Into Tumor Development

Retinoblastoma is rare tumor of the retina caused by the homozygous loss of the Retinoblastoma 1 tumor suppressor gene (RB1). Loss of the RB1 protein, pRB, results in de-regulated activity of the E2F transcription factors, chromatin changes and developmental defects leading to tumor development. Extensive microarray profiles of these tumors have enabled the identification of genes sensitive to pRB disruption, however, this technology has a number of limitations in the RNA profiles that they generate. The advent of RNA-sequencing has enabled the global profiling of all of the RNA within the cell including both coding and non-coding features and the detection of aberrant RNA processing events. In this perspective, we focus on discussing how RNA-sequencing of rare Retinoblastoma tumors will build on existing data and open up new area's to improve our understanding of the biology of these tumors. In particular, we discuss how the RB-research field may be to use this data to determine how RB1 loss results in the expression of; non-coding RNAs, causes aberrant RNA processing events and how a deeper analysis of metabolic RNA changes can be utilized to model tumor specific shifts in metabolism. Each section discusses new opportunities and challenges associated with these types of analyses and aims to provide an honest assessment of how understanding these different processes may contribute to the treatment of Retinoblastoma.

LncRNA BCAR4 promotes colon cancer progression via activating Wnt/β-catenin signaling

BCAR4 (Breast Cancer Anti-Estrogen Resistance 4) is a long noncoding RNA that was identified as an oncogene in breast cancer. In our research, we found that the expression level of BCAR4 was upregulated in colon cancer tissues compared to paired normal tissues. What's more, higher BCAR4 expression was correlated with lower survival rate in patients with colon cancer. Mechanistically, we showed that BCAR4 activated Wnt/β-catenin signaling in colon cancer by protecting β-catenin from degradation. We also showed that BCAR4 overexpression promoted cell proliferation and migration in colon cancer. However, silencing BCAR4 inhibited cell growth and promoted apoptosis. Besides, BCAR4 knockdown decreased tumor growth in vivo. These findings indicate that BCAR4 facilitated colon cancer progression by enhancing cell proliferation and inhibiting apoptosis via BCAR4/β-catenin axis. BCAR4 may be a useful new target for treatment of patients with colon cancer.