Colon cancer associated transcripts in human cancers. Biomed Pharmacother. 2017;94:531-540. [PMID: 28779711 DOI: 10.1016/j.biopha.2017.07.073]

LncRNA MYLK antisense RNA 1 activates cell division cycle 42/Neutal Wiskott-Aldrich syndrome protein pathway via microRNA-101-5p to accelerate epithelial-to-mesenchymal transition of colon cancer cells

Long noncoding RNA MYLK antisense RNA 1 (MYLK-AS1) is the crux in multiple diseases. Therefore, the purpose of this study was to investigate the possible mechanism of MYLK-AS1. A total of 62 colon cancer (CC) specimens and paired adjacent normal tissues were collected, and the expression of MYLK-AS1, microRNA (miR)-101-5p/cell division cycle 42 (CDC42) was detected. CC cell lines were transfected with MYLK-AS1, miR-101-5p, CDC42-related plasmids, and the biological functions and markers of epithelial-mesenchymal transition (EMT) were analyzed. The binding relationship between MYLK-AS1, miR-101-5p, and CDC42 was evaluated. In CC tissues and cell lines, MYLK-AS1 and CDC42 were highly expressed, and miR-101-5p was lowly expressed. Inhibition of MYLK-AS1 or upregulation of miR-101-5p can inhibit CC cell growth and EMT. miR-101-5p inhibited CDC42/N-wasp axis activation in CC cells by targeting CDC42. Knockdown of CDC42 or upregulation of miR-101-5p partially reversed the effects caused by upregulation of MYLK-AS1. MYLK-AS1, which is significantly upregulated in CC, may be a molecular sponge for miR-101-5p, and MYLK-AS1 promotes the activation of the CDC42/N-wasp axis in CC cells by targeting CDC42 through miR-101-5p, which in turn promotes tumor development. MYLK-AS1 may be a potential biomarker and target for CC therapy.

Emerging roles of miR-145 in gastrointestinal cancers: A new paradigm

Gastrointestinal (GI) carcinomas are a group of cancers affecting the GI tract and digestive organs, such as the gastric, liver, bile ducts, pancreas, small intestine, esophagus, colon, and rectum. MicroRNAs (miRNAs) are small functional non-coding RNAs (ncRNAs) which are involved in regulating the expression of multiple target genes; mainly at the post-transcriptional level, via complementary binding to their 3'-untranslated region (3'-UTR). Increasing evidence has shown that miRNAs have critical roles in modulating of various physiological and pathological cellular processes and regulating the occurrence and development of human malignancies. Among them, miR-145 is recognized for its anti-oncogenic properties in various cancers, including GI cancers. MiR-145 has been implicated in diverse biological processes of cancers through the regulation of target genes or signaling, including, proliferation, differentiation, tumorigenesis, angiogenesis, apoptosis, metastasis, and therapy resistance. In this review, we have summarized the role of miR-145 in selected GI cancers and also its downstream molecules and cellular processes targets, which could lead to a better understanding of the miR-145 in these cancers. In conclusion, we reveal the potential diagnostic, prognostic, and therapeutic value of miR-145 in GI cancer, and hope to provide new ideas for its application as a biomarker as well as a therapeutic target for the treatment of these cancer.

Pertinence of glioma and single nucleotide polymorphism of TERT, CCDC26, CDKN2A/B and RTEL1 genes in glioma: a meta-analysis

Background

Previous genetic-epidemiological studies considered TERT (rs2736100), CCDC26 (rs4295627), CDKN2A/B (rs4977756) and RTEL1 (rs6010620) gene polymorphisms as the risk factors specific to glioma. However, the data samples of previous genetic-epidemiological studies are modest to determine whether they have definite association with glioma.

Method

The study paid attention to systematically searching databases of PubMed, Embase, Web of Science (WoS), Scopus, Cochrane Library and Google Scholars. Meta-analysis under 5 genetic models, namely recessive model (RM), over-dominant model (O-DM), allele model (AM), co-dominant model (C-DM) and dominant model (DM) was conducted for generating odds ratios (ORs) and 95% confidence intervals (CIs). That was accompanied by subgroup analyses according to various racial groups. The software STATA 17.0 MP was implemented in the study.

Result

21 articles were collected. According to data analysis results, in four genetic models (AM, RM, DM and C-DM) TERT gene rs2736100 polymorphism, CCDC26 gene rs4295627 polymorphism, CDKN2A/B gene rs4977756 polymorphism and RTEL1 gene rs6010620 polymorphisms increased the risk of glioma in Caucasians to different degrees. In Asian populations, the CCDC26 gene rs4295627 polymorphism and CDKN2A/B gene rs4977756 polymorphism did not exhibit a relevance to the risk of glioma. It is suggested to cautiously explain these results as the sample size is small.

Conclusion

The current meta-analysis suggested that the SNP of TERT (rs2736100), CCDC26 (rs4295627), CDKN2A/B (rs4977756) and RTEL1 (rs6010620) genes in glioma might increase risk of glioma, but there are ethnic differences. Further studies evaluating these polymorphisms and glioma risk are warranted.

CCAT 1- A Pivotal Oncogenic Long Non-Coding RNA in Colorectal Cancer

Colorectal cancer (CRC) is ranked as the third most common cancer and second deadliest cancer in both men and women in the world. Currently, the cure rate and 5-year survival rate of CRC patients remain relatively low. Therefore, discovering a novel molecular biomarker that can be used to improve CRC screening, diagnosis, prognosis, and treatment would be beneficial. Long non-coding RNA colon cancer-associated transcript 1 (CCAT 1) has been found overexpressed in CRC and is associated with CRC tumorigenesis and treatment outcome. CCAT 1 has a high degree of specificity and sensitivity, it is readily detected in CRC tissues and is significantly overexpressed in both premalignant and malignant CRC tissues. Besides, CCAT 1 is associated with clinical manifestation and advanced features of CRC, such as lymph node metastasis, high tumor node metastasis stage, differentiation, invasion, and distant metastasis. In addition, they can upregulate oncogenic c-MYC and negatively modulate microRNAs via different mechanisms of action. Furthermore, dysregulated CCAT 1 also enhances the chemoresistance in CRC cells while downregulation of them reverses the malignant phenotypes of cancer cells. In brief, CCAT 1 serves as a potential screening, diagnostic and prognostic biomarker in CRC, it also serves as a potential therapeutic marker to treat CRC patients.

Therapeutic impact of thymoquninone to alleviate ischemic brain injury via Nrf2/HO-1 pathway

Introduction: Reactive oxygen species (ROS)-mediated inflammation plays a crucial role in ischemic brain injury. Therefore, the activation of the nuclear erythroid 2 related protein and heme-oxygenase-1 (Nrf2/HO-1) pathway by thymoquinone (TQ) could ameliorate ischemic brain damage.Areas covered: The photo-thrombotic method was employed to assess the impact of TQ in attenuating ischemic brain damage in C57BL/6 J mice and thy1-YFP-16 transgenic mice. In vitro study of TQ efficiency to attenuate the oxygen-glucose deprivation/reoxygenation (OGD/R) induced cell death by fluorescence-activated cell sorting (FACs) analysis was also analyzed. The protein expression levels of Nrf2/HO-1, inflammatory, and apoptotic were evaluated by immunofluorescence and western blot techniques. Besides, mRNA expression level of inducible nitric oxide synthase (iNOS), proto-oncogene (c-MYC), proto-oncogene (c-FOS), 5-hydroxytryptamine receptors (5-HT), and autophagy-related 5 (Atg5) were evaluated by RT-qPCR. The dendritic spine density of YFP slices was determined by confocal microscope.Results: Our in vivo and in vitro results indicated that TQ significantly mitigates brain damage and motor dysfunction after ischemic stroke. These observations coincided with curtailed cell death, inflammation, oxidative stress, apoptosis, and autophagy. Most importantly, Nrf2/HO-1 signaling pathway activation by TQ was vital in the modulation of the above processes. Lastly, we found TQ to have minimal toxicity in liver tissue.Conclusion: Our study gives credence to TQ as a promising intervention therapy for cerebral ischemia that decreases inflammation, oxidative stress, and neuronal cell death via the Nrf2/HO-1 pathway, along with modulation of apoptotic and autophagic processes.

N6-Methylandenosine-Related lncRNAs in Tumor Microenvironment Are Potential Prognostic Biomarkers in Colon Cancer

Background

LncRNA dysregulation and the tumor microenvironment (TME) have been shown to play a vital role in the progression and prognosis of colon cancer (CC). We aim to reveal the potential molecular mechanism from the perspective of lncRNA in the TME and provide the candidate biomarkers for CC prognosis.

Methods

ESTIMATE analysis was used to divide the CC patients into high and low immune or stromal score groups. The expression array of lncRNA was re-annotated by Seqmap. Microenvironment-associated lncRNAs were filtered through differential analysis. The m6A-associated lncRNAs were screened by Pearson correlation analysis. Lasso Cox regression analyses were performed to construct the m6A- and tumor microenvironment-related lncRNA prognostic model (m6A-TME-LM). Survival analysis was used to assess the prognostic efficacy of candidate lncRNAs. Enrichment analyses annotated the candidate genes’ functions.

Results

We obtained 25 common differentially expressed lncRNAs (DELs) associated with immune microenvironment and m6A-related genes for subsequent lasso analysis. Four out of these DELs were selected for the m6A-TME-LM. All the four lncRNAs were related to overall survival, and a test set testified the result. Further stratification analysis of the m6A-TME-LM retained its ability to predict OS for male and chemotherapy adjuvant patients and performed an excellent prognostic efficacy in the TNM stage III and IV subgroups. Network analysis also found the four lncRNAs mediated co-expression network was associated with tumor development.

Conclusion

We constructed the m6A-TME-LM, which could provide a better prognostic prediction of CC.

Enhancer-derived long non-coding RNAs CCAT1 and CCAT2 at rs6983267 has limited predictability for early stage colorectal carcinoma metastasis

Up-regulation of long non-coding RNAs (lncRNAs), colon-cancer associated transcript (CCAT) 1 and 2, was associated with worse prognosis in colorectal cancer (CRC). Nevertheless, their role in predicting metastasis in early-stage CRC is unclear. We measured the expression of CCAT1, CCAT2 and their oncotarget, c-Myc, in 150 matched mucosa-tumour samples of early-stage microsatellite-stable Chinese CRC patients with definitive metastasis status by multiplex real-time RT-PCR assay. Expression of CCAT1, CCAT2 and c-Myc were significantly up-regulated in the tumours compared to matched mucosa (p < 0.0001). The expression of c-Myc in the tumours was significantly correlated to time to metastasis [hazard ratio = 1.47 (1.10–1.97)] and the risk genotype (GG) of rs6983267, located within CCAT2. Expression of c-Myc and CCAT2 in the tumour were also significantly up-regulated in metastasis-positive compared to metastasis-negative patients (p = 0.009 and p = 0.04 respectively). Nevertheless, integrating the expression of CCAT1 and CCAT2 by the Random Forest classifier did not improve the predictive values of ColoMet19, the mRNA-based predictor for metastasis previously developed on the same series of tumours. The role of these two lncRNAs is probably mitigated via their oncotarget, c-Myc, which was not ranked high enough previously to be included in ColoMet19.

Long Non-Coding RNA LINC00239 Functions as a Competitive Endogenous RNA by Sponging microRNA-484 and Enhancing KLF12 Expression to Promote the Oncogenicity of Colorectal Cancer

Background

Long intergenic non-protein coding RNA 239 (LINC00239) is an oncogenic long non-coding RNA in acute myeloid leukemia. We aimed to determine LINC00239 expression in colorectal cancer (CRC) and examine the influences of LINC00239 on tumor behaviors of CRC cells. Furthermore, the mechanism underlying the actions of LINC00239 in CRC was unveiled in detail.

Materials and Methods

Quantitative real-time polymerase chain reaction was used to detect LINC00239 expression in CRC tissues and cell lines. CRC cell proliferation, apoptosis, migration, and invasion were investigated by cell counting kit-8 assays, flow cytometry, and cell migration and invasion assays, respectively. Tumor xenograft experiments were performed to evaluate the tumor growth of CRC cells in vivo. The interactions among LINC00239, microRNA-484 (miR-484), and kruppel-like factor 12 (KLF12) were analyzed by bioinformatics prediction, RNA immunoprecipitation and luciferase reporter assay.

Results

LINC00239 was upregulated in CRC tissues and cell lines. LINC00239 knockdown impaired CRC cell proliferation, migration, and invasion and promoted apoptosis in vitro. Additionally, LINC00239 deficiency inhibited CRC growth in vivo. Mechanistically, LINC00239 functioned as a competing endogenous RNA by directly sponging miR-484, thereby enhancing KLF12 expression. Rescue experiments further corroborated that miR-484 inhibition or KLF12 overexpression reversed the inhibitory actions of LINC00239 knockdown in CRC cells.

Conclusion

The LINC00239/miR-484/KLF12 pathway executed critical roles in CRC oncogenicity and may provide potential targets for CRC treatments.

LncRNA SLC7A11-AS1 Contributes to Lung Cancer Progression Through Facilitating TRAIP Expression by Inhibiting miR-4775

Purpose

Long non-coding RNAs (lncRNAs) are important regulators of lung cancer. This article introduced a novel lncRNA, SLC7A11-AS1, whose effects on lung cancer development have been explored.

Methods

Lung cancer tissues and normal tissues of 47 patients were collected. Bronchial epithelial cell line (BEAS-2B) and lung cancer cell lines (H520, H596, A549 and H1299) were cultured. H1299 and A549 cells were transfected with siSLC7A11-AS1 or siNC. The proliferation, migration and invasion of H1299 and A549 cells were detected by CCK-8 assay and Transwell experiment. Caspase-3 activity in H1299 and A549 cells was researched using caspase-3 activity detection kit. Dual-luciferase reporter gene assay and RNA pull-down assay were performed to explore the relationship between SLC7A11-AS1 and miR-4775. SLC7A11-AS1, miR-4775 and TRAIP mRNA expressions in tissues/cells were detected by qRT-PCR.

Results

The up-regulated SLC7A11-AS1 in lung cancer patients was associated with metastasis and advanced tumor stage (P < 0.05). SLC7A11-AS1 was significantly up-regulated in lung cancer cells (P < 0.05). Silencing of SLC7A11-AS1 prominently inhibited H1299 and A549 cells proliferation, migration and invasion in vitro (P < 0.05). SLC7A11-AS1 acted as a sponge to inhibit miR-4775 expression in H1299 and A549 cells. Meanwhile, TRAIP expression in H1299 and A549 cells was directly and negatively regulated by miR-4775. Inhibition of miR-4775 or overexpression of TRAIP in H1299 and A549 cells remarkably reversed the reduced proliferation, migration and invasion induced by SLC7A11-AS1 silencing (P < 0.05).

Conclusion

SLC7A11-AS1 promoted lung cancer development by enhancing TRAIP expression via suppressing miR-4775.

Long noncoding RNA EPB41L4A-AS1 functions as an oncogene by regulating the Rho/ROCK pathway in colorectal cancer

Colorectal cancer (CRC) is one of the most common malignant tumors worldwide. In terms of cancer-related death, colon cancer ranks second and third among men and women, respectively, and the incidence is increasing annually. Accumulating evidence have indicated that long noncoding RNA (lncRNA) plays an important role in tumorigenesis. In this study, we found that lncRNA EPB41L4A-AS1 was highly expressed in CRC tissues and was associated with poor prognosis and tumor metastasis in patients with CRC. In vitro studies showed that the knockdown of EPB41L4A-AS1 inhibited the proliferation, migration, invasion, and epithelial-mesenchymal transition of CRC cells. Mechanically, we found that EPB41L4A-AS1 may participate in the development of CRC by activating the Rho/Rho-associated protein kinase signaling pathway. Collectively, these results demonstrated that EPB41L4A-AS1 can promote the proliferation, invasion, and migration of CRC, and it may be a novel biomarker for the diagnosis and targeted treatment of CRC.

A Comprehensive Exploration of the lncRNA CCAT2: A Pan-Cancer Analysis Based on 33 Cancer Types and 13285 Cases

Whether the lncRNA CCAT2 expression level affects the clinical progression and outcome of cancer patients has not yet been fully elucidated. There is still an inconsistent view regarding the correlation between CCAT2 expression and clinicopathological factors, including survival data. Besides, the regulation mechanism of CCAT2 in human cancer is still unclear. Our study analyzed a large number of publication data and TCGA databases to identify the association of CCAT2 expression with clinicopathological factors and to explore the regulatory mechanisms in human cancers. We designed a comprehensive study to determine the expression of CCAT2 in human cancer by designing a meta-analysis of 20 selected studies and the TCGA database, using StataSE 12.0 to explore the relationship between CCAT2 expression and both the prognosis and clinicopathological features of 33 cancer types and 13285 tumor patients. Moreover, we performed GO and KEGG pathway enrichment analyses on potential target genes of CCAT2 collected from GEPIA and LncRNA2Target V2.0. The level of CCAT2 expression in tumor tissues is higher than that in paired normal tissues and is significantly associated with a poor prognosis in cancer patients. Besides, overexpression of CCAT2 was significantly associated with tumor size, clinical stage, and TNM classification. Meanwhile, CCAT2 expression is the highest in stage II of human cancer, followed by stage III. Finally, 111 validated target gene symbols were identified, and GO and KEGG demonstrated that the CCAT2 validation target was significantly enriched in several pathways, including microRNAs in the cancer pathway. In summary, CCAT2 can be a potential biomarker associated with the progression and prognosis of human cancer.

CARLo-5 as an oncogenic gene in endometrial carcinoma

The long noncoding RNA CARLo-5 is dysregulated in multiple types of human cancers. High CARLo-5 is a promising predictive factor for various cancers, including endometrial carcinoma (EC). Our previous study showed that the expression level of CARLo-5 was associated with advanced FIGO stage (The International Federation of Gynecology and Obstetrics), lymph node metastasis, and the poor survival of patients with EC. In the present study, we demonstrated that the downregulation of CARLo-5 could affect the proliferation, cell cycle, migration, and invasion of EC cell lines HEC-1B and KLE cells. The oncogenic activity of CARLo-5 was also confirmed with in vivo data. Mechanistically, CARLo-5 could affect the expression of CDK/CDKN1A and MMP2/9, which have been reported to be regulated by CARLo-5 and associated with cell cycle and motility. In conclusion, this study is the first to discover the biological function and mechanism of CARLo-5 in regulating the biological characteristics of EC cells. Targeting CARLo-5 and its pathway might provide new biomarkers or potential therapies target for patients with EC. Environ. Mol. Mutagen. 61:256-265, 2020. © 2019 Wiley Periodicals, Inc.

LncARSR sponges miR-129-5p to promote proliferation and metastasis of bladder cancer cells through increasing SOX4 expression

Emerging evidences have indicated that long non-coding RNAs (lncRNAs) are potential biomarkers, playing important roles in the development of cancer. LncRNA Activated in RCC with Sunitinib Resistance (lncARSR) is a novel lncRNA that functions as a potential biomarker and is involved in the progression of cancers. However, the clinical significance and molecular mechanism of lncARSR in bladder cancer (Bca) remains unknow. In this study, we discovered that lncARSR was significantly up-regulated in bladder cancer. In addition, increased expression of lncARSR was positively correlated with higher histological grade and larger tumor size. Further experiments demonstrated that suppression of lncARSR attenuated the proliferation, migration, invasion and epithelial-mesenchymal transition (EMT) process of Bca cells. Mechanistically, lncARSR was mainly located in the cytoplasm and acted as a miRNA sponge to positively modulate the expression of Sex-determining region Y-related high-mobility-group box transcription factor 4 (SOX4) via sponging miR-129-5p and subsequently promoted the proliferation and metastasis of Bca cells, thus playing an oncogenic role in Bca pathogenesis. In conclusion, our study indicated that lncARSR plays a critical regulatory role in Bca cells and lncARSR may serve as a potential diagnostic biomarker and therapeutic target for bladder cancer.

lncRNA CCAT2 promotes radiotherapy resistance for human esophageal carcinoma cells via the miR‑145/p70S6K1 and p53 pathway

The long non‑coding RNA colon cancer‑associated transcript 2 (CCAT2) is abnormally expressed in various types of malignant tumor tissues and considered to be an oncogene, including for esophageal cancer (EC). Radiotherapy is an important and widely used cancer treatment. However, some patients with EC do not respond to radiotherapy. This study was designed to investigate effects of CCAT2 expression on radiotherapy dynamics for EC cells and to explore underlying molecular mechanisms. Reverse transcription‑quantitative PCR was used to measure CCAT2 expression in EC tissues, normal esophageal mucosa, EC cells and normal human esophageal epithelial cells. TUNEL assays were used to assess the effect of CCAT2 on X‑ray‑induced apoptosis of EC cells. Protein expression was detected by western blot. CCAT2 was highly expressed in EC tissues and EC cells, and was negatively associated with radiotherapy efficacy in patients with EC. In vitro, knockdown of CCAT2 enhanced radiosensitivity of EC cells and promoted apoptosis by increasing Bax/Bcl2 and active‑caspase 3/caspase 3 following X‑ray treatment. In addition, CCAT2 negatively regulated miR‑145 and P70 ribosomal protein S6 kinase 1 (p70S6K1) expression, and inhibited phosphorylation of Akt, ERK and p70S6K1 in EC cells. After X‑ray treatment, CCAT2 negatively regulated protein levels of p53, P21 and c‑Myc. These results showed that CCAT2 promoted the radiotherapy resistance of EC cells via negative regulation of the miR‑145/p70S6K1 and the p53 signaling pathways and associated elements may be potential targets for improving the sensitivity of EC radiotherapy.

Genomic alterations in high-risk chronic lymphocytic leukemia frequently affect cell cycle key regulators and NOTCH1-regulated transcription

To identify genomic alterations contributing to the pathogenesis of high-risk chronic lymphocytic leukemia (CLL) beyond the well-established role of TP53 aberrations, we comprehensively analyzed 75 relapsed/refractory and 71 treatment-naïve high-risk cases from prospective clinical trials by single nucleotide polymorphism arrays and targeted next-generation sequencing. Increased genomic complexity was a hallmark of relapsed/refractory and treatment-naïve high-risk CLL. In relapsed/refractory cases previously exposed to the selective pressure of chemo(immuno)therapy, gain(8)(q24.21) and del(9)(p21.3) were particularly enriched. Both alterations affect key regulators of cell-cycle progression, namely MYC and CDKN2A/B. While homozygous CDKN2A/B loss has been directly associated with Richter transformation, we did not find this association for heterozygous loss of CDKN2A/B. Gains in 8q24.21 were either focal gains in a MYC enhancer region or large gains affecting the MYC locus, but only the latter type was highly enriched in relapsed/refractory CLL (17%). In addition to a high frequency of NOTCH1 mutations (23%), we found recurrent genetic alterations in SPEN (4% mutated), RBPJ (8% deleted) and SNW1 (8% deleted), all affecting a protein complex that represses transcription of NOTCH1 target genes. We investigated the functional impact of these alterations on HES1, DTX1 and MYC gene transcription and found derepression of these NOTCH1 target genes particularly with SPEN mutations. In summary, we provide new insights into the genomic architecture of high-risk CLL, define novel recurrent DNA copy number alterations and refine knowledge on del(9p), gain(8q) and alterations affecting NOTCH1 signaling. This study was registered at ClinicalTrials.gov with number NCT01392079.

Identification of differentially expressed genes regulated by methylation in colon cancer based on bioinformatics analysis

BACKGROUND

DNA methylation, acknowledged as a key modification in the field of epigenetics, regulates gene expression at the transcriptional level. Aberrant methylation in DNA regulatory regions could upregulate oncogenes and downregulate tumor suppressor genes without changing the sequences. However, studies of methylation in the control of gene expression are still inadequate. In the present research, we performed bioinformatics analysis to clarify the function of methylation and supply candidate methylation-related biomarkers and drivers for colon cancer.

AIM

To identify and analyze methylation-regulated differentially expressed genes (MeDEGs) in colon cancer by bioinformatics analysis.

METHODS

We downloaded RNA expression profiles, Illumina Human Methylation 450K BeadChip data, and clinical data of colon cancer from The Cancer Genome Atlas project. MeDEGs were identified by analyzing the gene expression and methylation levels using the edgeR and limma package in R software. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed in the DAVID database and KEGG Orthology-Based Annotation System 3.0, respectively. We then conducted Kaplan–Meier survival analysis to explore the relationship between methylation and expression and prognosis. Gene set enrichment analysis (GSEA) and investigation of protein-protein interactions (PPI) were performed to clarify the function of prognosis-related genes.

RESULTS

A total of 5 up-regulated and 81 down-regulated genes were identified as MeDEGs. GO and KEGG pathway analyses indicated that MeDEGs were enriched in multiple cancer-related terms. Furthermore, Kaplan–Meier survival analysis showed that the prognosis was negatively associated with the methylation status of glial cell-derived neurotrophic factor (GDNF) and reelin (RELN). In PPI networks, GDNF and RELN interact with neural cell adhesion molecule 1. Besides, GDNF can interact with GDNF family receptor alpha (GFRA1), GFRA2, GFRA3, and RET. RELN can interact with RAFAH1B1, disabled homolog 1, very low-density lipoprotein receptor, lipoprotein receptor-related protein 8, and NMDA 2B. Based on GSEA, hypermethylation of GDNF and RELN were both significantly associated with pathways including “RNA degradation,” “ribosome,” “mismatch repair,” “cell cycle” and “base excision repair.”

CONCLUSION

Aberrant DNA methylation plays an important role in colon cancer progression. MeDEGs that are associated with the overall survival of patients may be potential targets in tumor diagnosis and treatment.

Effect of lncRNA THOR on proliferation and migration of colon cancer cells

The effect of long non-coding RNA (lncRNA) THOR on proliferation and migration of colon cancer cells was investigated. Lentiviral vector expressing lncRNA THOR shRNA was used to establish colon cancer SW620 lncRNA THOR knockdown cell line (experimental group), and at the same time, a control vector cell line (control group) was established by empty vector virus. Proliferation ability of the two groups was analyzed by CCK8 and EdU methods. Migration ability of the cells was analyzed by Transwell method. Xenograft tumor method was used to analyze the in vivo proliferation ability of the two groups of cells. mRNA levels of lncRNA THOR target genes were analyzed by reverse transcription-quantitative PCR (RT-qPCR). Compared with control cells, the cell proliferation ability of the experimental group was significantly decreased (P<0.05). Compared with the control group, the cell migration ability of the experimental group was significantly decreased (P<0.05). The tumor growth rate of the experimental group in the mice was significantly lower than that of the control group (P<0.05). Compared with the control group, mRNA levels of lncRNA THOR target genes IGF2BP1, SOX9 and c-myc in the experimental group were significantly downregulated (P<0.05). The results indicated that lncRNA THOR knockdown can significantly downregulate the expression of genes involved in tumor proliferation and migration, promote tumor cell proliferation and migration, indicating that lncRNA THOR plays an important role in colon cancer.

NEAT1 promotes colon cancer progression through sponging miR-495-3p and activating CDK6 in vitro and in vivo

Recently, increasing evidence has indicated lncRNAs are powerful regulators in the progression of multiple tumors. Dysregulation of lncRNA NEAT1 has been recognized in many cancer types. Meanwhile, the studies on NEAT1 function have suggested that NEAT1 can serve as a crucial oncogene. Nevertheless, the investigation of NEAT1 in colon cancer is still few. In our study, the function of NEAT1 was studied in colon cancer. As we observed, NEAT1 level was obviously elevated in colon cancer cells. Then, HCT-116 and SW620 cells were stably infected with shRNA-NEAT1 for 48 hr. As exhibited, silence of NEAT1 could greatly repress colon cancer cell progression. Apoptosis of colon cancer cells was triggered and the cell cycle progression was remarkably inhibited by downregulation of NEAT1. Interestingly, as exhibited, miR-495-3p was obviously decreased in colon cancer cells and it significantly suppressed colon cancer progression. Subsequently, miR-495-3p was predicted as a target of NEAT1. CDK6 was speculated as the target of miR-495-3p and miR-495-3p modulated its expression negatively. Finally, it was indicated that NEAT1 promoted colon cancer development through modulating miR-495-3p and CDK6 in vivo. Taken these together, we reported that NEAT1 could sponge miR-495-3p to contribute to colon cancer progression through activating CDK6.

Correlation of ERK/MAPK signaling pathway with proliferation and apoptosis of colon cancer cells

The role of extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) signaling pathway in the proliferation and apoptosis of human colon cancer cells was studied. The transduction process of ERK/MAPK signaling pathway was inhibited using methyl ethyl ketone (MEK) inhibitor U0126. Promoting effect of hepatocyte growth factor (HGF) on proliferation of human colon cancer cells was detected via Cell Counting Kit 8 (CCK8), the cycle and apoptosis of human colon cancer cells were detected via flow cytometry, and the migration of human colon cancer cells was detected via wound healing assay. The results revealed that after drug treatment for 48 h, there were statistically significant differences in 4 and 8 µmol/l U0126 experimental group compared with control group (P<0.05). Compared with those in control group, G1 phase, S phase, G2 phase and proliferation index (PI) in 2, 4 and 8 µmol/l U0126 group had statistically significant differences (P<0.05). There were statistically significant differences in comparison of G1 phase, S phase, G2 phase and PI between control and 8 µmol/l U0126 group (P<0.05). Compared with that in control group, the cell migration distance in 8 µmol/l U0126 group had a statistically significant difference after drug treatment for 24 h (P<0.05). After drug treatment for 48 and 72 h, the cell migration distance in 4 and 8 µmol/l U0126 group was significantly reduced, and the differences were statistically significant compared with that in control group (P<0.05). In conclusion, ERK/MAPK signaling pathway is involved in the effects of HGF of promoting proliferation and regulating cell cycle and apoptosis of human colon cancer cells, providing a new approach for the treatment of colon cancer.

The emerging roles of long non-coding RNA in gallbladder cancer tumorigenesis

Accumulating evidence suggests that long non-coding RNAs (lncRNAs) have important regulatory functions in gallbladder cancer (GBC) tumorigenesis and can serve as potential novel markers and/or targets for GBC. In this review, we critically discuss the emerging alteration of lncRNAs in GBC, the lncRNAs induced epigenetic regulation, the interaction of lncRNAs with microRNAs and lncRNAs effects on tumor-related signaling pathways. Additionally, contributions of lncRNAs in epithelial-mesenchymal transition process and energy metabolism reprogramming in GBC are also addressed. This may pave new ways towards the determination of GBC pathogenesis and lead to the development of new preventive and therapeutic strategies for GBC.

GAPLINC is a predictor of poor prognosis and regulates cell migration and invasion in osteosarcoma

Gastric adenocarcinoma predictive long intergenic non-coding (GAPLINC) is a novel long non-coding RNA (lncRNA) and has been found to function as an oncogenic lncRNA in gastric cancer, colorectal cancer, and bladder cancer. The expression status and biological function of GAPLINC in osteosarcoma are still unknown. Thus, we analyzed the association between GAPLINC expression and clinicopathological characteristics in osteosarcoma clinical samples, and conducted loss-of-function study in osteosarcoma cell lines. In our results, GAPLINC expression is elevated in osteosarcoma tissues and cell lines, and correlated with advanced Enneking stage, present distant metastasis, and poor histological grade. Survival analyses indicated that GAPLINC expression was negatively associated with overall survival, and GAPLINC high-expression was an independent risk factor in osteosarcoma patients. The in vitro studies showed knockdown of GAPLINC depressed osteosarcoma cell migration and invasion via inhibiting CD44 expression, but no effect on cell proliferation. In conclusion, GAPLINC may serve as a potential biomarker for predicting prognosis and developing therapy for osteosarcoma.

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.

Microarray‑based bioinformatics analysis of the prospective target gene network of key miRNAs influenced by long non‑coding RNA PVT1 in HCC

The long non-coding RNA (lncRNA) PVT1 plays vital roles in the tumorigenesis and development of various types of cancer. However, the potential expression profiling, functions and pathways of PVT1 in HCC remain unknown. PVT1 was knocked down in SMMC-7721 cells, and a miRNA microarray analysis was performed to detect the differentially expressed miRNAs. Twelve target prediction algorithms were used to predict the underlying targets of these differentially expressed miRNAs. Bioinformatics analysis was performed to explore the underlying functions, pathways and networks of the targeted genes. Furthermore, the relationship between PVT1 and the clinical parameters in HCC was confirmed based on the original data in the TCGA database. Among the differentially expressed miRNAs, the top two upregulated and downregulated miRNAs were selected for further analysis based on the false discovery rate (FDR), fold-change (FC) and P-values. Based on the TCGA database, PVT1 was obviously highly expressed in HCC, and a statistically higher PVT1 expression was found for sex (male), ethnicity (Asian) and pathological grade (G3+G4) compared to the control groups (P<0.05). Furthermore, Gene Ontology (GO) analysis revealed that the target genes were involved in complex cellular pathways, such as the macromolecule biosynthetic process, compound metabolic process, and transcription. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the MAPK and Wnt signaling pathways may be correlated with the regulation of the four candidate miRNAs. The results therefore provide significant information on the differentially expressed miRNAs associated with PVT1 in HCC, and we hypothesized that PVT1 may play vital roles in HCC by regulating different miRNAs or target gene expression (particularly MAPK8) via the MAPK or Wnt signaling pathways. Thus, further investigation of the molecular mechanism of PVT1 in HCC is needed.

Overexpression of CRNDE promotes the progression of bladder cancer

Accumulating evidences indicate that long non-coding RNAs (lncRNAs) are indispensable in cancer initiation and progression. Dysregulation of functional lncRNAs can promote the development of cancers. Previous research have revealed that augmented expression of CRNDE caused poor prognosis of cancer patients and facilitate the tumor progress in various cancers. Nevertheless, the underlying roles of CRNDE in bladder cancer progression are not entirely clear. To further identify the effects CRNDE in bladder cancer progression, we performed the gain and loss of function assay. In this work, we have presented evidence that CRNDE was significantly increased in bladder cancer, and overexpressed expression of CRNDE was positively related with advanced TNM stage of bladder cancer patients. In addition, in vitro experiments showed that CRNDE strengthened cell migration/proliferation and inhibited cell apoptosis in bladder cancer. To sum up, our results exhibited new understand into the role of lncRNA CRNDE in the development of bladder cancer.

Long non-coding RNA DLX6-AS1 aggravates hepatocellular carcinoma carcinogenesis by modulating miR-203a/MMP-2 pathway

Long non-coding RNAs (lncRNAs) have been wildly verified to modulate multiple tumorigenesis, especially hepatocellular carcinoma (HCC). In present study, our team aims to investigate the role of lncRNA DLX6-AS1 in the HCC carcinogenesis. Results of early-stage experiments found that DLX6-AS1 expression level was up-regulated in 60 cases of HCC tissue samples compared with adjacent normal tissue. Moreover, the aberrant overexpression of DLX6-AS1 indicated the poor prognosis of HCC patients. Loss-of-function experiments revealed that DLX6-AS1 knockdown inhibited the proliferation, migration and invasion of HCC cells in vitro, and decreased the tumor growth in vivo. Bioinformatics analysis predicted that miR-203a potentially targeted DLX6-AS1 3'-UTR, suggesting the interaction between miR-203a and DLX6-AS1. Furthermore, miR-203a also targeted MMP-2 mRNA 3'-UTR, which was validated by luciferase reporter assay. Taken together, our study discovered the oncogenic role of DLX6-AS1 in clinical specimens and cellular experiments, showing the potential DLX6-AS1/miR-203a/MMP-2 pathway. This results and findings provide a novel insight for HCC tumorigenesis.