Noncoding RNAs in the development, diagnosis, and prognosis of colorectal cancer

Long non-coding RNA SNHG15 interacts with and stabilizes transcription factor Slug and promotes colon cancer progression

Slug is a fast-turnover transcription factor critical for controlling cell fate and cancer cell invasion and metastasis. The stability of Slug is important and maintained by diverse mechanisms. In this study, we presented a paradigm of this activity by identifying long noncoding RNA (lncRNA) small nucleolar RNA host gene 15 (SNHG15) that binds to and stabilizes Slug in colon cancer cells. LncRNA SNHG15 transcription is upregulated in a variety of human cancers according to The Cancer Genome Atlas. Here, ectopic expression of SNHG15 promoted colon cancer cell migration in vitro, accelerated xenografted tumor growth in vivo, and elevated levels of SNHG15 were associated with poor prognosis for colon cancer patients. Mechanistically, SNHG15 maintains Slug stability in living cells by impeding its ubiquitination and degradation through interaction with the zinc finger domain of Slug. These findings revealed a novel mechanism underlying the control of Slug stability by demonstrating that oncogenic lncRNA SNHG15 interacts with and blocks Slug degradation via the ubiquitin-proteasome system.

MicroRNA-6869-5p acts as a tumor suppressor via targeting TLR4/NF-κB signaling pathway in colorectal cancer

Many studies have implicated that microRNAs (miRNAs), as non-coding RNAs, play important roles in the development and progression of colorectal cancer (CRC). However, little is known about the role of a newly identified miRNA, miR-6869-5p, in CRC. We aim to investigate the modifying effects and underlying mechanisms of miR-6869-5 in colorectal carcinogenesis and progression. Significantly reduced levels of miR-6869-5p were observed in both serum exosomes tumor tissue samples from patients with CRC. The prediction of targets of miR-6869-5p in databases of targetscan, microRNA. ORG and miRDBA revealed that toll-like receptor 4 (TLR4) is a potential target for this miRNA. MiR-6869-5p could inhibit cell proliferation and the production of inflammatory cytokines (TNF-α and IL-6) in CRC cells via directly targeting TLR4. The protective effect of miR-6869-5p from colorectal carcinogenesis was dependent on TLR4/NF-κB signaling pathway. In addition, the 3-year survival was poor among CRC patients with decreased levels of miR-6869-5p in serum exosomes. Thus, miR-6869-5p may serve as a tumor suppressor in CRC, and serum exosomal miR-6869-5p is a promising circulating biomarker for the prediction of CRC prognosis.

Drosophila as a Model to Gain Insight into the Role of lncRNAs in Neurological Disorders

It is now clear that the majority of transcription in humans results in the production of long non-protein-coding RNAs (lncRNAs) with a variable length spanning from 200 bp up to several kilobases. To date, we have a limited understanding of the lncRNA function, but a huge number of evidences have suggested that lncRNAs represent an outstanding asset for cells. In particular, temporal and spatial expression of lncRNAs appears to be important for proper neurological functioning. Stunningly, abnormal lncRNA function has been found as being critical for the onset of neurological disorders. This chapter focus on the lncRNAs with a role in diseases affecting the central nervous system with particular regard for the lncRNAs causing those neurodegenerative diseases that exhibit dementia and/or motor dysfunctions. A specific section will be dedicated to the human neuronal lncRNAs that have been modelled in Drosophila. Finally, even if only few examples have been reported so far, an overview of the Drosophila lncRNAs with neurological functions will be also included in this chapter.

Hepatitis B virus x protein induces epithelial-mesenchymal transition of hepatocellular carcinoma cells by regulating long non-coding RNA

BACKGROUND

It has been widely accepted that hepatitis B virus X protein (HBx) plays an important role in hepatocellular carcinoma (HCC). This study aimed to explore the function of long non-coding RNAs (lncRNAs) in the epithelial-mesenchymal transition (EMT) induced by HBx.

METHODS

The association between HBx and EMT markers was detected using immunohistochemistry in HCC tissues. The effect of HBx on HCC EMT was assessed through morphological analysis, transwell assay, metastatic in vivo study and detection of EMT markers. LncRNA microarray was used to screen the differently expressed lncRNAs. Small interfering RNA and Western blot were used to analyse the function and mechanism of the locked lncRNA.

RESULTS

HBx was negatively correlated with the epithelial marker E-cadherin but positively correlated with the mesenchymal marker vimentin in HCC tissues. HBx induced the mesenchymal phenotype and improved the metastatic ability of HCC cells. Meanwhile, HBx down-regulated E-cadherin, whereas it up-regulated vimentin. In HCC cells, HBx altered the expression of 2002 lncRNAs by more than 2-fold. One of them was ZEB2-AS1. Inhibition of ZEB2-AS1 can compensate for the EMT phenotype and reverse the expression of EMT markers regulated by HBx. Additionally, HBx affected the Wnt signalling pathway.

CONCLUSIONS

HBx promotes HCC cell metastasis by inducing EMT, which is at least partly mediated by lncRNAs.

Knockdown of lncRNA-XIST enhances the chemosensitivity of NSCLC cells via suppression of autophagy

Drug resistance is the major factor contributing to the failure of chemotherapy in non-small cell lung cancer (NSCLC) patients. Emerging evidence suggests that autophagy plays a vital role in the chemoresistance of many types of tumors. However, the exact mechanism underlying the chemoresistance of NSCLC is still elusive, and it is unclear whether lncRNA-XIST is involved in autophagy and chemoresistance of NSCLC. In the present study, we demonstrated that lncRNA-XIST was overexpressed in NSCLC tumor samples, and knockdown of lncRNA-XIST significantly decreased autophagy by regulation of ATG7 as determined by qPCR and by western blotting. Furthermore, we found that miR-17 was upregulated following knockdown of lncRNA-XIST, and miR-17 mimics decreased the protein levels of ATG7 by directly targeting the 3'-untranslated region of ATG7 mRNA as determined by RT-qPCR and by western blotting. Furthermore, we found that the expression level of lncRNA-XIST was markedly increased in cisplatin-resistant A549 cells as determined by q-PCR. Knockdown of lncRNA-XIST restored the chemosensitivity of cisplatin-resistant A549 cells to cisplatin, which was reversed by miR-17 inhibitor and overexpression of ATG7 as determined by CCK8 assays. This study provides evidence that lncRNA-XIST may be a potential marker of poor response to cisplatin chemotherapy in NSCLC patients and the pathway 'lncRNA-XIST/miR-17/autophagy' may be a promising target for patients with chemoresistant NSCLC.

Differential Expression of Long Noncoding RNAs in Normal and Inflamed Human Dental Pulp

INTRODUCTION

Dental pulp inflammation is an excellent model for the interaction between tissue inflammation and regenerative processes. It is worthwhile to better understand molecular signaling of repair and regeneration in inflammatory processes. Emerging evidence suggests that long noncoding RNA (lncRNA) participates in immune system inflammatory processes. Here we investigate the expression of lncRNAs in pulpitis, the inflammation of dental pulp tissue, and identify lncRNAs that possibly participate in inflammation responses and odontogenesis.

METHODS

Integrated comparative lncRNA microarray was used to examine lncRNA and mRNA expression between inflamed and normal human pulp tissue. The differential expression of lncRNAs and mRNAs was then validated by quantitative real-time polymerase chain reaction. A bioinformatics analysis was performed to predict the function of differentially expressed lncRNAs and mRNAs.

RESULTS

Our data indicated 752 lncRNAs were significantly differentially expressed (fold change > 2.0; P < .05) in inflamed pulp tissues compared with normal pulp tissues, including 338 upregulated and 414 downregulated lncRNAs. Among the 646 differentially expressed mRNAs (fold change > 2.0; P < .05), 460 were upregulated, and 186 were downregulated. The differentially downregulated genes are enriched for gene ontology terms related to odontogenesis and cell development in biological processes, whereas the differentially upregulated genes are related to immune and inflammation processes.

CONCLUSIONS

LncRNAs are differentially expressed in inflamed human pulp tissue compared with normal pulp tissue, indicating that lncRNAs may play key roles in pulpitis pathogenesis and development.

Diagnosis, prognosis and bioinformatics analysis of lncRNAs in hepatocellular carcinoma

This study aims to comprehensively analyze the diagnosis and prognosis of lncRNAs in hepatocellular carcinoma (HCC). From the Gene Expression Omnibus database, we screened out and analyzed the differently expressed lncRNAs and related mRNAs using bioinformatics methods. The expressions of lncRNAs were validated in tumor tissues, cell lines and the Cancer Genome Atlas database. At the same time, we also conducted an exploratory analysis on the diagnostic and prognostic ability of lncRNAs in HCC. In this study, we found that most of the targeted mRNAs promote the biological process of cell division, cellular component of nucleoplasm, molecular function of protein binding, which were significantly associated with 12 KEGG pathways. LncRNA CRNDE and LINC01419 also had significant diagnostic value in HCC. In particular, the sensitivity, specificity and area under the curve of CRNDE were 71.0%, 87.1% and 0.701 (95% CI: 0.543-0.860), respectively. In addition, the high expression of CRNDE and GBAP1 predicated poor prognosis, while the high expression of LINC01093 suggested the opposite outcome. Through the comprehensive analysis of lncRNAs, it provided an important reference for the early diagnosis, prognosis evaluation, pathogenesis and targeted therapy of HCC.

Prognostic value of long noncoding RNA ZFAS1 in various carcinomas: a meta-analysis

A number of studies have revealed that zinc finger antisense 1 (ZFAS1), a long noncoding RNA (lncRNA), is aberrantly regulated in various cancers, and high ZFAS1 expression is associated with poor prognosis and increased risk of lymph node metastasis (LNM). This meta-analysis was conducted to identify the potential value of ZFAS1 as a biomarker for cancer prognosis. We searched electronic database PubMed, Web of Science, and China Wanfang Data (up to June 1, 2017) to collect all relevant studies and explore the association of ZFAS1 expression with overall survival (OS) and LNM. The results showed that cancer patients with high ZFAS1 expression had a worse OS than those with low ZFAS1 expression (HR: 1.94, 95% confidence interval [CI]: 1.41–2.47, P < 0.001), and high ZFAS1 expression was significantly associated with LNM (OR: 2.60, 95% CI: 1.54–4.42, P < 0.001). Subgroup analysis revealed that high ZFAS1 expression was significantly related to high incidence of LNM in subgroups of sample size more than 88 (OR: 3.16, 95% CI: 2.06–4.86, P < 0.001), non-digestive system malignancies (OR: 4.05, 95% CI: 2.49–6.60, P < 0.001), and studies reported in 2017 (OR: 4.86, 95% CI: 2.67–8.84, P < 0.001) without significant heterogeneity. Further meta-regression by the covariates showed that tumor type, sample size, quality score, cut off value and publication year did not result in the inter-study heterogeneity. In conclusion, the present meta-analysis demonstrates that high ZFAS1 expression may potentially serve as a reliable biomarker for poor clinical outcome in various cancers.

Innate immunity in Sjögren's syndrome

Sjögren's syndrome (SS) is an autoimmune disease of exocrine tissue that primarily affects women. Although patients typically experience xerostomia and xerophthalmia, numerous systemic disease manifestations are seen. Innate immune hyperactivity is integral to many autoimmune diseases, including SS. Results from SS mouse models suggest that innate immune dysregulation drives disease and this is a seminal event in SS pathogenesis. Findings in SS patients corroborate those in mouse models, as innate immune cells and pathways are dysregulated both in exocrine tissue and in peripheral blood. We will review the role of the innate immune system in SS pathogenesis. We will discuss the etiology of SS with an emphasis on innate immune dysfunction. Moreover, we will review the innate cells that mediate inflammation in SS, the pathways implicated in disease, and the potential mechanisms governing their dysregulation. Finally, we will discuss emerging therapeutic approaches to target dysregulated innate immune signaling in SS.

Energy sensing pathways: Bridging type 2 diabetes and colorectal cancer?

The recently rapid increase of obesity and type 2 diabetes mellitus has caused great burden to our society. A positive association between type 2 diabetes and risk of colorectal cancer has been reported by increasing epidemiological studies. The molecular mechanism of this connection remains elusive. However, type 2 diabetes may result in abnormal carbohydrate and lipid metabolism, high levels of circulating insulin, insulin growth factor-1, and adipocytokines, as well as chronic inflammation. All these factors could lead to the alteration of energy sensing pathways such as the AMP activated kinase (PRKA), mechanistic (mammalian) target of rapamycin (mTOR), SIRT1, and autophagy signaling pathways. The resulted impaired SIRT1 and autophagy signaling pathway could increase the risk of gene mutation and cancer genesis by decreasing genetic stability and DNA mismatch repair. The dysregulated mTOR and PRKA pathway could remodel cell metabolism during the growth and metastasis of cancer in order for the cancer cell to survive the unfavorable microenvironment such as hypoxia and low blood supply. Moreover, these pathways may be coupling metabolic and epigenetic alterations that are central to oncogenic transformation. Further researches including molecular pathologic epidemiologic studies are warranted to better address the precise links between these two important diseases.

Cancer-type OATP1B3 mRNA has the potential to become a detection and prognostic biomarker for human colorectal cancer

AIM

We aimed to clarify diagnostic and prognostic biomarker potentials of cancer-type organic anion transporting polypeptide 1B3 (Ct-OATP1B3) mRNA in colorectal cancer (CRC) patients.

PATIENTS & METHODS

Ct-OATP1B3 mRNA levels in 97 CRC and adjacent normal colon tissues were measured by real-time PCR. The receiver operating characteristic curve analysis and the Kaplan-Meier curve analysis were performed to characterize its biomarker potentials.

RESULTS

Ct-OATP1B3 mRNA showed noticeable diagnostic power (the area under the receiver operating characteristic = 0.91) in the CRC patients. Additionally, the higher/lower mRNA expression was clearly associated with better/poorer overall survival in the CRC patients (p < 0.05).

CONCLUSION

Ct-OATP1B3 mRNA has the potential to be a tissue-based biomarker for definitive diagnosis and prognostic stratification in CRC.

MiR-218 suppresses the metastasis and EMT of HCC cells via targeting SERBP1

Hepatocellular carcinoma (HCC) is the leading cause of cancer-related deaths worldwide. Although many efforts for treating HCC have been made, the survival rate remains unsatisfied. Accumulating evidence indicates that microRNA-218 (miR-218) functions as a tumor suppressor and involves in many biological processes such as tumor initiation, development, and metastasis in certain types of human cancers. However, the potential function and underlying molecular mechanism of miR-218 in HCC still remains to be elucidated. Since HCC is a genetic disease, exploring the mechanisms of the pathogeny and integration are essential for the discovery of novel treatment targets for HCC. Therefore, the aim of the present study was to investigate the abnormal expression level of miR-218 in clinical HCC tissues and HCC cells, and to evaluate its function and underlying mechanisms in HCC. Our results revealed that miR-218 expression was significantly downregulated in HCC tissues and cell lines. Gain-of-function and loss-of-function assays indicated that forced expression of miR-218 in HCC cells inhibited cell migration/invasion and reversed epithelial-mesenchymal transition (EMT) to mesenchymal-epithelial transition (MET), while deletion of miR-218 promoted cell migration/invasion and contributed to the EMT phenotype formation. Bioinformatics analysis and luciferase reporter assay confirmed that serpine mRNA binding protein 1 (SERBP1) was a target gene of miR-218 and rescue assay further confirmed that SERBP1 involved in the function of miR-218 in HCC. All these results suggested that miR-218/SERBP1 signal pathway could inhibit the malignant phenotype formation and that targeting this pathway may be a potential novel way for HCC therapeutics.

Specific microRNA-mRNA Regulatory Network of Colon Cancer Invasion Mediated by Tissue Kallikrein-Related Peptidase 6

Metastatic colon cancer is a major cause of deaths among colorectal cancer (CRC) patients. Elevated expression of kallikrein 6 (KLK6), a member of a kallikrein subfamily of peptidase S1 family serine proteases, has been reported in CRC and is associated with low patient survival rates and poor disease prognosis. We knocked down KLK6 expression in HCT116 colon cancer cells to determine the significance of KLK6 expression for metastatic dissemination and to identify the KLK6-associated microRNAs (miRNAs) signaling networks in metastatic colon cancer. KLK6 suppression resulted in decreased cells invasion in vitro with a minimal effect on the cell growth and viability. In vivo, animals with orthotopic colon tumors deficient in KLK6 expression had the statistically significant increase in survival rates (P = .005) and decrease in incidence of distant metastases. We further performed the integrated miRNA and messenger RNA (mRNA) expression profiling to identify functional miRNA-mRNA interactions associated with KLK6-mediated invasiveness of colon cancer.

Through bioinformatics analysis we identified and functionally validated the top two up-regulated miRNAs, miR-182 and miR-203, and one down-regulated miRNA, miRNA-181d, and their seven mRNA effectors. The established miRNA-mRNA interactions modulate cellular proliferation, differentiation and epithelial–mesenchymal transition (EMT) in KLK6-expressing colon cancer cells via the TGF-β signaling pathway and RAS-related GTP-binding proteins. We confirmed the potential tumor suppressive properties of miR-181d and miR-203 in KLK6-expressing HCT116 cells using Matrigel invasion assay. Our data provide experimental evidence that KLK6 controls metastasis formation in colon cancer via specific downstream network of miRNA-mRNA effectors.

Meta-signature LncRNAs serve as novel biomarkers for colorectal cancer: integrated bioinformatics analysis, experimental validation and diagnostic evaluation

The aim of this study is to explore the differentially expressed lncRNAs, which may have potential biological function and diagnostic value in colorectal cancer (CRC). Through integrated data mining, we finally identified nine differentially expressed lncRNAs and their potential mRNA targets. After a series of bioinformatics analyses, we screened significant pathways and GO terms that are related to the up-regulated and down-regulated transcripts respectively. Meanwhile, the nine lncRNAs were validated in 30 paired tissues and cell lines by qRT-PCR and the results were basically consistent with the microarray data. We also tested the nine lncRNAs in the serum of 30 CRC patients matched with the CRC tissue, 30 non-cancer patients and 30 health controls. Finally, we found that BLACAT1 was significant for the diagnosis of CRC. The area under the curve (AUC), sensitivity and specificity were 0.858 (95% CI: 0.765-0.951), 83.3% and 76.7% respectively between CRC patients and health controls. Moreover, BLACAT1 also had distinct value to discriminate CRC from other non-cancer diseases. The results indicated that the differentially expressed lncRNAs and their potential target transcripts could be considered as potential therapeutic targets for CRC patients. Meanwhile, lncRNA BLACAT1 might represent a new supplementary biomarker for the diagnosis of CRC.

Potentials of Long Noncoding RNAs (LncRNAs) in Sarcoma: From Biomarkers to Therapeutic Targets

Sarcoma includes some of the most heterogeneous tumors, which make the diagnosis, prognosis and treatment of these rare yet diverse neoplasms especially challenging. Long noncoding RNAs (lncRNAs) are important regulators of cancer initiation and progression, which implies their potential as neoteric prognostic and diagnostic markers in cancer, including sarcoma. A relationship between lncRNAs and sarcoma pathogenesis and progression is emerging. Recent studies demonstrate that lncRNAs influence sarcoma cell proliferation, metastasis, and drug resistance. Additionally, lncRNA expression profiles are predictive of sarcoma prognosis. In this review, we summarize contemporary advances in the research of lncRNA biogenesis and functions in sarcoma. We also highlight the potential for lncRNAs to become innovative diagnostic and prognostic biomarkers as well as therapeutic targets in sarcoma.

Seven LncRNA-mRNA based risk score predicts the survival of head and neck squamous cell carcinoma

Dysregulation of mRNAs and long non-coding RNAs (lncRNAs) is one of the most important features of carcinogenesis and cancer development. However, studies integrating the expression of mRNAs and lncRNAs to predict the survival of head and neck squamous cell carcinoma (HNSC) are still limited, hitherto. In current work, we identified survival related mRNAs and lncRNAs in three datasets (TCGA dataset, E-TABM-302, GSE41613). By random forest, seven gene signatures (six mRNAs and lncRNA) were further selected to develop the risk score model. The risk score was significantly associated with survival in both training and testing datasets (E-TABM-302, GSE41613, and E-MTAB-1324). Furthermore, correlation analyses showed that the risk score is independent from clinicopathological features. According to Cox multivariable hazard model and nomogram, the risk score contributes the most to survival than the other clinical information, including gender, age, histologic grade, and alcohol taking. The Gene Set Enrichment Analysis (GSEA) indicates that the risk score is associated with cancer related pathways. In summary, the lncRNA-mRNA based risk score model we developed successfully predicts the survival of 755 HNSC samples in five datasets and two platforms. It is independent from clinical information and performs better than clinical information for prognosis.

Comprehensive investigation of a novel differentially expressed lncRNA expression profile signature to assess the survival of patients with colorectal adenocarcinoma

Growing evidence has shown that long non-coding RNAs (lncRNAs) can serve as prospective markers for survival in patients with colorectal adenocarcinoma. However, most studies have explored a limited number of lncRNAs in a small number of cases. The objective of this study is to identify a panel of lncRNA signature that could evaluate the prognosis in colorectal adenocarcinoma based on the data from The Cancer Genome Atlas (TCGA). Altogether, 371 colon adenocarcinoma (COAD) patients with complete clinical data were included in our study as the test cohort. A total of 578 differentially expressed lncRNAs (DELs) were observed, among which 20 lncRNAs closely related to overall survival (OS) in COAD patients were identified using a Cox proportional regression model. A risk score formula was developed to assess the prognostic value of the lncRNA signature in COAD with four lncRNAs (LINC01555, RP11-610P16.1, RP11-108K3.1 and LINC01207), which were identified to possess the most remarkable correlation with OS in COAD patients. COAD patients with a high-risk score had poorer OS than those with a low-risk score. The multivariate Cox regression analyses confirmed that the four-lncRNA signature could function as an independent prognostic indicator for COAD patients, which was largely mirrored in the validating cohort with rectal adenocarcinoma (READ) containing 158 cases. In addition, the correlative genes of LINC01555 and LINC01207 were enriched in the cAMP signaling and mucin type O-Glycan biosynthesis pathways. With further validation in the future, our study indicates that the four-lncRNA signature could serve as an independent biomarker for survival of colorectal adenocarcinoma.