Prognostic value of long non-coding RNA HOTAIR in various cancers

Non-coding RNAs in Cancer: Mechanistic insights and therapeutic implications

Non-coding RNAs have gathered significant attention for their unique roles in biological regulation. Across a broad spectrum of developmental processes and diseases, particularly in human malignancies, ncRNAs play pivotal roles in regulatory mechanisms. MicroRNAs, long noncoding RNAs, and small nucleolar RNAs stand out among the diverse forms of ncRNAs that have been implicated in cancer. MiRNAs, classified as short non-coding RNAs, modulate gene expression by binding to messenger RNA molecules, thereby inhibiting their translation. Altered miRNA expression has been associated with the onset and progression of various malignancies, including lung, breast, and prostate cancer. In contrast, lncRNAs, characterized as longer ncRNAs, exert control over gene expression through various mechanisms, such as chromatin remodelling and gene silencing. This review offers a comprehensive examination of the numerous ncRNAs that have emerged as crucial regulators of gene expression, playing implicated roles in the initiation and progression of diverse cancers.

miRNA-1246, HOTAIR, and IL-39 signature as potential diagnostic biomarkers in breast cancer

The molecular alterations in noncoding RNA can lead to a cellular storm that is correlated to higher mortality and morbidity rates and contributes to the progression and metastasis of cancer. Herein, we aim to evaluate the expression levels and correlations of microRNA-1246 (miR-1246), HOX transcript antisense RNA (HOTAIR), and interleukin-39 (IL-39) in patients with breast cancer (BC). In this study, 130 participants were recruited, including 90 breast cancer patients and 40 healthy control participants. Serum levels of miR-1246 and HOTAIR expression were assessed by quantitative real-time polymerase chain reaction (qRT-PCR). Also, the level of IL-39 expression was evaluated using a Western blot. All BC participants demonstrated a remarkable elevation in miR-1246 and HOTAIR expression levels. Moreover, IL-39 expression levels demonstrated a noticeable decline in BC patients. Furthermore, the differential expression fold of miR-1246 and HOTAIR revealed a strong positive correlation among breast cancer patients. In addition, a negative relationship between the IL-39 and the miR-1246 and HOTAIR differential expression was also noticed. This study revealed that HOTAIR/miR-1246 exerts an oncogenic impact in patients with breast cancer. The expression levels of circulation miR-1246, HOTAIR, and IL-39 could be considered early diagnostic biomarkers in BC patients.

Long Noncoding RNAs and Human Liver Disease

Long noncoding RNAs (lncRNAs) are pervasively transcribed in the genome, exhibit a diverse range of biological functions, and exert effects through a variety of mechanisms. The sheer number of lncRNAs in the human genome has raised important questions about their potential biological significance and roles in human health and disease. Technological and computational advances have enabled functional annotation of a large number of lncRNAs. Though the number of publications related to lncRNAs has escalated in recent years, relatively few have focused on those involved in hepatic physiology and pathology. We provide an overview of evolving lncRNA classification systems and characteristics and highlight important advances in our understanding of the contribution of lncRNAs to liver disease, with a focus on nonalcoholic steatohepatitis, hepatocellular carcinoma, and cholestatic liver disease. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

There and Back Again: Hox Clusters Use Both DNA Strands

Bilaterian animals operate the clusters of Hox genes through a rich repertoire of diverse mechanisms. In this review, we will summarize and analyze the accumulated data concerning long non-coding RNAs (lncRNAs) that are transcribed from sense (coding) DNA strands of Hox clusters. It was shown that antisense regulatory RNAs control the work of Hox genes in cis and trans, participate in the establishment and maintenance of the epigenetic code of Hox loci, and can even serve as a source of regulatory peptides that switch cellular energetic metabolism. Moreover, these molecules can be considered as a force that consolidates the cluster into a single whole. We will discuss the examples of antisense transcription of Hox genes in well-studied systems (cell cultures, morphogenesis of vertebrates) and bear upon some interesting examples of antisense Hox RNAs in non-model Protostomia.

Associations between HOTAIR polymorphisms rs4759314, rs920778, rs1899663, and rs7958904 and risk of primary ovarian insufficiency in Korean women

BACKGROUND

We investigated the association between the Hox transcript antisense RNA (HOTAIR) polymorphisms rs4759314, rs920778, rs1899663, and rs7958904 and primary ovarian insufficiency (POI) in Korean women.

METHODS

We conducted a case-control study of 134 Korean women with POI and 383 control individuals with at least one live birth and no history of pregnancy loss.

RESULTS

The GT genotype of rs1899663 was associated with a decreased risk of POI compared with other genotypes at that locus. In addition, compared with the wild-type homozygous genotypes, the combination of the AA genotype of rs4759314 and the GC genotype of rs7958904 was associated with a decreased risk of POI (P < 0.05), whereas the combination of the GG genotype of rs1899663 and the GC genotype of rs7958904 was associated with an increased risk of POI (P = 0.003). Haplotype analysis revealed that certain haplotypes involving some or all of the polymorphisms were associated with a decreased risk of POI, whereas other haplotypes were associated with an increased risk of POI. Serum levels of luteinizing hormone, follicle-stimulating hormone, and estradiol differed between patients with POI and control individuals (P < 0.05).

CONCLUSIONS

Our results suggest that the HOTAIR polymorphisms rs4759314, rs920778, rs1899663, and rs7958904 are involved in POI.

miR-200c overexpression inhibits the invasion and tumorigenicity of epithelial ovarian cancer cells by suppressing lncRNA HOTAIR in mice

Epithelial ovarian cancer (EOC) is a common ovarian cancer in gynecological cancers today. It has been found that microRNAs and long-chain noncoding RNA (lncRNA) regulate the gene transcriptional expression in cells. However, it is not well understood that the upstream and downstream regulatory molecules of lncRNA HOX antisense intergenic RNA (HOTAIR). The effects of miR-200c overexpression on the invasion and nude mouse tumorigenicity, as well as lncRNA HOTAIR and snail expression of EOC SKOV3 cells, should be further explored. The expression of miR-200c and lncRNA HOTAIR was detected by reverse transcription PCR (RT-PCR) in EOC SKOV3 cells. The whole miR-200c gene fragment was cloned into a lentiviral plasmid vector. The miR-200c expression in transducted SKOV3 cells with reconstructed miR-200c lentivirus was significantly higher than the negative control (P < .01). The lentivirus-miR-200c-SKOV3 cells show that the invasion ability was significantly decreased compared with the negative control (P < .01). The nude mouse tumorigenicity was significantly decreased compared with that of the control group (P < .01). The snail protein expression in lentivirus-miR-200c-SKOV3 xenograft tumor was significantly decreased compared with the negative control lentivirus-SKOV3 group (P < .05). The miR-200c overexpression significantly decreased the expressions of lncRNA HOTAIR and snail, but increased E-cadherin expression in the lentivirus-miR-200c transducted SKOV3 cells of xenograft tumor, compared with the negative control (P < .05). The miR-200c overexpression in SKOV3 cells with transducted lentivirus-miR-200c can inhibit lncRNA HOTAIR expression, decrease snail, increase E-cadherin and significantly reduce the invasion and tumorigenicity of EOC SKOV3 cells. These results suggest that the miR-200c and lncRNA HOTAIR could be effective therapeutic targets for human epithelial ovarian cancer treatment.

HOTAIR as a Prognostic Predictor for Diverse Human Cancers: A Meta- and Bioinformatics Analysis

Several studies suggest that upregulated expression of the long non-coding RNA HOX transcript antisense RNA (HOTAIR) is a negative predictive biomarker for numerous cancers. Herein, we performed a meta-analysis to further investigate the prognostic value of HOTAIR expression in diverse human cancers. To this end, a systematic literature review was conducted in order to select scientific studies relevant to the association between HOTAIR expression and clinical outcomes, including overall survival (OS), recurrence-free survival (RFS)/disease-free survival (DFS), and progression-free survival (PFS)/metastasis-free survival (MFS) of cancer patients. Collectively, 53 eligible studies including a total of 4873 patients were enrolled in the current meta-analysis. Pooled hazard ratios (HRs) with their corresponding 95% confidence intervals (CIs) were calculated to assess the relationship between HOTAIR and cancer patients’ survival. Elevated HOTAIR expression was found to be significantly associated with OS, RFS/DFS and PFS/MFS in diverse types of cancers. These findings were also corroborated by the results of bioinformatics analysis on overall survival. Therefore, based on our findings, HOTAIR could serve as a potential biomarker for the prediction of cancer patient survival in many different types of human cancers.

Diagnostic efficacy of long non-coding RNA in lung cancer: a systematic review and meta-analysis

The detection of long non-coding RNA (lncRNA) is a novel method for lung cancer diagnosis. However, the diagnostic efficacy of lncRNA in different studies is inconsistent. Therefore, we conducted this meta-analysis to elucidate the diagnostic efficacy of lncRNA in identification of lung cancer including small cell lung cancer. The online PubMed, Medline, EMBASE, CNKI and Wanfang literature databases were searched to identify all related articles about the diagnostic efficacy of lncRNA for lung cancer. 28 articles including 3044 patients with lung cancer and 2598 controls were enrolled in our meta-analysis. lncRNA sustained a high diagnostic efficacy, pooled sensitivity of 0.82 (95% CI 0.79 to 0.84), specificity of 0.82 (95% CI 0.78 to 0.84) and area under the curve (AUC) of 0.88 (95% CI 0.85 to 0.91) in identification of patients with lung cancer from controls. Furthermore, the diagnostic efficacy of paralleled lncRNA was better than single lncRNA (sensitivity: 0.86 vs 0.80; specificity: 0.88 vs 0.78; AUC: 0.93 vs 0.86). MALAT1 had a better diagnostic efficacy than GAS5 (AUC: 0.90 vs 0.81; sensitivity: 0.83 vs 0.70; specificity: 0.83 vs 0.78). lncRNA in tissues was observed to achieve lower diagnostic efficacy than that in plasma or serum (AUC: 0.87 vs 0.90 vs 0.90) when stratified by sample types. In summary, our meta-analysis suggests that lncRNA might be a promising biomarker(s) for identifying lung cancer and the combination of lncRNA or with other biomarkers had a better diagnostic efficacy.

Prognostic role of lncRNA TUG1 for cancer outcome: Evidence from 840 cancer patients

LncRNA TUG1 has been demonstrated to be aberrantly expressed in several types of cancer and maybe serve as a prognostic marker for cancer patients. However, most individual studies have been limited by small sample sizes and controversial results. Therefore, this meta analysis was conducted to analyze available data to delineate the potential clinical application of lncRNA TUG1 on cancer prognosis, lymph node metastasis and tumor progression. Up to February 20, 2017, literature collections were conducted by comprehensive searching electronic databases, including Cochrane Library, PubMed, Embase, BioMed Central, Springer, ScienceDirect, ISI Web of Knowledge, together with three Chinese databases. The hazard ratios (HR) with 95% confidence interval (95% CI) were calculated to assess the strength of the association. Eight studies with a total of 840 cancer patients were included in the present meta analysis. The results indicated that elevated lncRNA TUG1 significantly predicted unfavorable overall survival (OS) (HR = 2.06, 95% CI: 1.23–3.45, P = 0.006), but failed to show incline to lymph node metastasis (HR: 1.16, 95% CI: 0.82–1.62, P = 0.40) and disease progression (III/IV vs. I/II: HR 1.16, 95% CI: 0.74–1.81, P = 0.52). In stratified analyses, a significantly unfavorable OS associated with elevated lncRNA TUG1 was observed in both bladder cancer (HR = 2.98, 95% CI: 1.84–4.83, P < 0.0001) and other system cancer (HR = 2.63, 95% CI: 1.42–4.87, P = 0.002), but not respiratory system cancer (HR = 0.93, 95% CI: 0.30–2.82, P = 0.895). The results indicated that increased lncRNA TUG1 was an independent prognostic biomarker for unfavorable OS but may not susceptible to lymph node metastasis and tumor progression in cancer patients.

Prognostic role of the long non-coding RNA, SPRY4 Intronic Transcript 1, in patients with cancer: a meta-analysis

Recent studies have emphasized the important role of long non-coding RNAs (lncRNAs) in cancer development. The present study performed a meta-analysis to investigate whether lncRNA, SPRY4 Intronic Transcript 1(SPRY4-IT1) can be served as a potential biomarker for prognosis in human cancers. The eligible studies were collected by searching multiple online databases (Pubmed, EMBASE, CNKI, Web of Science and Google Scholar) and meta-analysis was performed to explore the association between the expression levels of SPRY4-IT1 and overall survival (OS), disease-free survival (DFS) and clinicopathological parameters. A total of 1329 patients from 13 studies were included for meta-analysis. The meta-analysis results showed that high expression level of SPRY4-IT1 was significantly associated with shorter OS in cancer patients (HR = 3.20, 95% CI: 2.59-3.90, P<0.001) except in the patients with non-small cell lung cancer (NSCLC). Increased SPRY4-IT1 expression level was correlated with shorter DFS in patients with gastric cancer and ovarian cancer. SPRY4-IT1 expression level was not correlated with the clinicopathological parameters including age (P = 0.37), gender (P = 0.87), tumor size (P = 0.47) and invasion depth (P = 0.52), and increased SPRY4-IT1 expression level was significantly associated with distant metastasis (odds ratio (OR) = 1.96, 95% CI: 1.24-3.08, P = 0.004), lymph node metastasis (OR = 3.96, 95% CI: 1.48-5.54, P<0.001), advanced tumor/node/metastasis stage (OR = 3.72, 95% CI = 2.91-4.76, P<0.001) and poor tumor differentiation (OR = 1.86, 95% CI = 1.35-2.58, P<0.001) in cancer patients except in patients with NSCLC. In summary, the meta-analysis results suggested that increased expression level of SPRY4-IT1 was positively associated with unfavorable prognosis and advanced features of cancers in cancer patients but not in patients with NSCLC.

Natural Antisense Transcripts: Molecular Mechanisms and Implications in Breast Cancers

Natural antisense transcripts are RNA sequences that can be transcribed from both DNA strands at the same locus but in the opposite direction from the gene transcript. Because strand-specific high-throughput sequencing of the antisense transcriptome has only been available for less than a decade, many natural antisense transcripts were first described as long non-coding RNAs. Although the precise biological roles of natural antisense transcripts are not known yet, an increasing number of studies report their implication in gene expression regulation. Their expression levels are altered in many physiological and pathological conditions, including breast cancers. Among the potential clinical utilities of the natural antisense transcripts, the non-coding|coding transcript pairs are of high interest for treatment. Indeed, these pairs can be targeted by antisense oligonucleotides to specifically tune the expression of the coding-gene. Here, we describe the current knowledge about natural antisense transcripts, their varying molecular mechanisms as gene expression regulators, and their potential as prognostic or predictive biomarkers in breast cancers.

Prognostic Role of Long Noncoding RNA BANCR in Solid Tumors: A Meta-Analysis

Accumulating studies have reported that long noncoding RNA BRAF-activated nonprotein coding RNA plays vital role in various cancers. However, the prognostic values of BRAF-activated nonprotein coding RNA in solid tumors remain controversial. Thus, we assessed the prognostic values of BRAF-activated nonprotein coding RNA by this meta-analysis. We comprehensively searched PubMed, Web of Science, Medline, China National Knowledge Infrastructure (CNKI), and the Cochrane Library at November 2016. After carefully screening, we ultimately included 14 studies in this meta-analysis. This meta-analysis brought all relevant articles into determining the association of BRAF-activated nonprotein coding RNA expression with overall survival and clinicopathologic features. The results showed that high BRAF-activated nonprotein coding RNA expression significantly shorten the overall survival of solid tumors (pooled hazard ratios 1.66, 95% confidence interval: 1.19-2.32). Moreover, high BRAF-activated nonprotein coding RNA expression was also strongly associated with advanced tumor stage (odds ratios = 2.57, 95% confidence interval: 1.14-5.79), differentiation grade (odds ratio = 1.71, 95% confidence interval: 1.26-2.31), lymph node metastasis (odds ratio = 2.67, 95% confidence interval: 1.93-3.70, P < .001), and distant metastasis (odds ratio = 2.98, 95% confidence interval: 1.76-5.07, P = .02). In conclusion, this meta-analysis demonstrated that high BRAF-activated nonprotein coding RNA expression may be a potential novel biomarker for indicating a poor prognosis and progression in human solid tumors.

High expression of long non‑coding HOTAIR correlated with hepatocarcinogenesis and metastasis

HOX transcript antisense RNA (HOTAIR), a newly discovered long noncoding RNA (lncRNA), has been reported to be a poor prognostic marker in many types of cancers. The current study attempted to investigate the biological roles and clinicopathlogical implications of HOTAIR in hepatocellular carcinoma (HCC), as well as understand the molecular mechanisms of HOTAIR in HCC progression. HOTAIR expression in 95 HCC patients with paired HCC tissues and adjacent non‑cancer tissues were investigated using quantitative reverse transcription‑polymerase chain reaction. The association between HOTAIR expression and clinicopathological features was assessed. The effects of HOTAIR were examined in vitro assays by silencing the lncRNA. Pathway analyses were performed to illustrate the biological functions of the HOTAIR and coexpression genes. The expression level of HOTAIR was observed significantly higher in the HCC tissue than the adjacent non‑tumor tissue. HOTAIR expression levels were significantly higher in tumor samples from patients with distant metastasis, advanced stage, portal vein tumor embolus, vasoinvasion, tumor capsular infiltration or positive nm23 expression than those from patients without these conditions, correspondingly. The silencing of HOTAIR in liver cancer cells induced the inhibition of cell proliferation and promotion of apoptosis. Several pathways such as extracellular matrix‑receptor interaction, focal adhesion, pathways in cancer were annotated with the HOTAIR and coexpression genes. In summary, the present analysis indicates that HOTAIR might be an oncogene in HCC. It functions though promoting tumor cell growth and inhibiting apoptosis. HOTAIR may potentially be involved in HCC metastatic progression by several pathways correlated to cell adhesion, and may be a therapeutic target in future.

The Value of lncRNA NEAT1 as a Prognostic Factor for Survival of Cancer Outcome: A Meta-Analysis

The present meta-analysis aimed to analyze available data to identify the prognostic role of NEAT1 in multiple carcinomas. A systematic search was performed by using several computerized databases from inception to June 7, 2017. The quantity of the publications was assessed according to MOOSE checklist. Pooled HRs with 95% CI was calculated to summarize the effect. A total of 12 studies with 3,262 cancer patients were pooled in the analysis to evaluate the prognostic value of NEAT1 in multiple tumors. High expression levels of NEAT1 were demonstrated to be associated with poor OS (HR = 1.71, 95%CI: 1.37-2.14, P < 0.001) and tumor progression (III/IV vs. I/II: HR 1.76, 95%CI: 1.40-2.21, P < 0.00001). Subgroup analysis showed that NEAT1 detection method (qRT-PCR) and sample size (more or less than 100) did not alter the predictive value of NEAT1 on OS in various cancers. According to the meta-regression results, the large heterogeneity of meta-analysis may be attributed to the differences of NEAT1 detection method. Furthermore, elevated NEAT1 expression significantly predicted lymph node metastasis (HR: 2.10, 95%CI: 1.32-3.33, P = 0.002) and distant metastasis (HR: 2.80, 95%CI: 1.60-4.91, P = 0.0003) respectively. The results indicate that NEAT1 expression level is a prognostic biomarker for OS and metastasis in general tumors.

Clinicopathological and prognostic significance of homeobox transcript antisense RNA expression in various cancers: A meta-analysis

BACKGROUND

Increased expression of the homeobox (HOX) transcript antisense RNA (HOTAIR) has been reported in multiple types of malignancies and enhances the proliferation and migration of cancer cells. However, the association between HOTAIR expression and tumor progression and prognosis remains controversial. We performed a meta-analysis to clarify the association between the expression of HOTAIR and the clinicopathological features and prognosis in different cancers.

METHODS

A systematic search of the PubMed, Web of Science, EMBASE, and Ovid databases was conducted, up to September 2016, for eligible studies involving HOTAIR expression and malignancies. The odds ratios (ORs), hazard ratios (HRs), and corresponding 95% confidence intervals (CIs) were calculated using fixed- or random-effect models. Any publication bias was evaluated using Begg and Egger tests, and adjusted using the trim and fill method if a bias existed.

RESULTS

A total of 4116 patients from 44 studies were included in our meta-analysis. The results showed that high HOTAIR expression was associated with an advanced clinical tumor stage (OR = 3.90, 95% CI = 3.02-5.03, P < .001), lymph node metastasis (OR = 3.11, 95% CI = 2.15-4.49, P < .001), poor differentiation of the tumor (OR = 1.56, 95% CI = 1.01-2.41, P = .03), and worse prognosis (HR = 2.16, 95% CI = 1.73-2.69, P < .001) in different cancer types. HOTAIR expression was more predictive in monitoring the clinical tumor stage of patients and there was no significant heterogeneity or publication bias found in the analysis.

CONCLUSION

Our meta-analysis suggests that HOTAIR is positively correlated with tumor development and negatively correlated with clinical outcome. Thus, an increase in HOTAIR expression may be a potential biomarker for tumor progression and evaluation of prognosis.

Prioritization of non-coding disease-causing variants and long non-coding RNAs in liver cancer

There are multiple bioinformatics tools available for the detection of coding driver mutations in cancers. However, the prioritization of pathogenic non-coding variants remains a challenging and demanding task. The present study was performed to discriminate non-coding disease-causing mutations and prioritize potential cancer-implicated long non-coding RNAs (lncRNAs) in liver cancer using a logistic regression model. A logistic regression model was constructed by combining 19,153 disease-associated ClinVar and human gene mutation database pathogenic variants as the response variable and non-coding features as the predictor variable. Genome-wide association study (GWAS) disease or trait-associated variants and recurrent somatic mutations were used to validate the model. Non-coding gene features with the highest fractions of load were characterized and potential cancer-associated lncRNA candidates were prioritized by combining the fraction of high-scoring regions and average score predicted by the logistic regression model. H3K9me3 and conserved regions were the most negatively and positively informative for the model, respectively. The area under the receiver operating characteristic curve of the model was 0.92. The average score of GWAS disease-associated variants was significantly increased compared with neutral single nucleotide polymorphisms (5.8642 vs. 5.4707; P<0.001), the average score of recurrent somatic mutations of liver cancer was significantly increased compared with non-recurrent somatic mutations (5.4101 vs. 5.2768; P=0.0125). The present study found regions in lncRNAs and introns/untranslated regions of protein coding genes where mutations are most likely to be damaging. In total, 847 lncRNAs were filtered out from the background. Characterization of this subset of lncRNAs showed that these lncRNAs are more conservative, less mutated and more highly expressed compared with other control lncRNAs. In addition, 23 of these lncRNAs were differentially expressed between 12 pairs of liver cancer and adjacent normal specimens. The logistic regression model is a useful tool to prioritize non-coding pathogenic variants and lncRNAs, and paves the way for the detection of non-coding driver lncRNAs in liver cancer.

Long noncoding RNAs are novel potential prognostic biomarkers for esophageal squamous cell carcinoma: an overview

Esophageal squamous cell carcinoma (ESCC) still has a poor prognosis. The prognostic biomarkers of ESCC are not yet well established. Long noncoding RNAs (lncRNAs) have recently been intensively investigated in various cancers including ESCC, and are found to be closely correlated to ESCC. Dysregulated expression of lncRNAs was widely observed in ESCC tumor tissue and was closely related to the tumorigenesis and progression of ESCC. More and more studies have found that lncRNAs were significantly correlated with the prognosis and diagnosis of patients with ESCC. Therefore, all those accumulating evidence indicated that lncRNAs could serve as a prognostic biomarker of ESCC. In this, we summarized the relation between lncRNAs and ESCC as well as the potential biomarker role of lncRNAs in ESCC, especially the prognostic value of lncRNAs. Our current review highlighted the need of further studies to explore the biomarker functions as well as therapeutic values of lncRNAs in ESCC.

Long noncoding RNA SPRY4-IT1 promotes malignant development of colorectal cancer by targeting epithelial-mesenchymal transition

The clinical significance and biological functions of long noncoding RNA SPRY4 intronic transcript 1 (SPRY4-IT1) in colorectal cancer (CRC) remain largely unclear. Herein, we are the first to report that the SPRY4-IT1 was significantly upregulated in CRC tissues, serum, and cells. Higher SPRY4-IT1 expression was markedly associated with advanced Tumor Node Metastasis (TNM) stage in a cohort of 84 CRC patients. Multivariate analyses indicated that SPRY4-IT1 expression could be useful as an independent predictor for overall survival. Further in vitro experiments revealed that knockdown of SPRY4-IT1 inhibited the proliferation, migration, and invasion of CRC cells and induced cell cycle arrestment. Moreover, we confirmed that the expression of epithelial–mesenchymal transition-related genes was modulated through alteration of SPRY4-IT1 expression. These results suggest that SPRY4-IT1, as an oncogenic regulator, may serve as a candidate prognostic marker and potential target for CRC therapies.

Long Noncoding RNAs in Lung Cancer

Despite great progress in research and treatment options, lung cancer remains the leading cause of cancer-related deaths worldwide. Oncogenic driver mutations in protein-encoding genes were defined and allow for personalized therapies based on genetic diagnoses. Nonetheless, diagnosis of lung cancer mostly occurs at late stages, and chronic treatment is followed by a fast onset of chemoresistance. Hence, there is an urgent need for reliable biomarkers and alternative treatment options. With the era of whole genome and transcriptome sequencing technologies, long noncoding RNAs emerged as a novel class of versatile, functional RNA molecules. Although for most of them the mechanism of action remains to be defined, accumulating evidence confirms their involvement in various aspects of lung tumorigenesis. They are functional on the epigenetic, transcriptional, and posttranscriptional level and are regulators of pathophysiological key pathways including cell growth, apoptosis, and metastasis. Long noncoding RNAs are gaining increasing attention as potential biomarkers and a novel class of druggable molecules. It has become clear that we are only beginning to understand the complexity of tumorigenic processes. The clinical integration of long noncoding RNAs in terms of prognostic and predictive biomarker signatures and additional cancer targets could provide a chance to increase the therapeutic benefit. Here, we review the current knowledge about the expression, regulation, biological function, and clinical relevance of long noncoding RNAs in lung cancer.

Expression Specificity of Disease-Associated lncRNAs: Toward Personalized Medicine

Long noncoding RNAs (lncRNAs) perform diverse regulatory functions in transcription, translation' chromatin modification, and cellular organization. Misregulation of lncRNAs is found linked to various human diseases. Compared to protein-coding RNAs' lncRNAs are more specific to organs, tissues, cell types, developmental stages, and disease conditions' making them promising candidates as diagnostic and prognostic biomarkers and as gene therapy targets. The functional annotation of mammalian genome (FANTOM) consortium utilizes cap analysis of gene expression (CAGE) method to quantify genome-wide activities of promoters and enhancers of coding and noncoding RNAs across a large collection of human and mouse tissues' cell types' diseases, and time-courses. The project discovered widespread transcription of major lncRNA classes, including lncRNAs derived from enhancers' bidirectional promoters' antisense lncRNAs' and repetitive elements. Results from FANTOM project enable assessment of lncRNA expression specificity across tissue and disease conditions' based on differential promoter and enhancer usage. More than 85 % of disease-related SNPs are within noncoding regions and are strikingly overrepresented in enhancer and promoter regions, suggestive of the importance of lncRNA loci at these SNP harboring regions to human diseases. In this chapter' we discuss lncRNA expression specificity' review diverse functions of disease-associated lncRNAs' and present perspectives on their potential therapeutic applications for personalized medicine. The future development of lncRNA applications relies on technologies to identify and validate their functions' structures' and mechanisms. Comprehensive understanding of genome-wide interaction networks of lncRNAs with proteins, chromatins, and other RNAs in regulating cellular processes will allow personalized medicine to use lncRNAs as highly specific biomarkers in diagnosis' prognosis, and therapeutic targets.

Long noncoding RNAs as novel predictors of survival in human cancer: a systematic review and meta-analysis

Background

Expression of various long noncoding RNAs (lncRNAs) may affect cancer prognosis. Here, we aim to gather and examine all evidence on the potential role of lncRNAs as novel predictors of survival in human cancer.

Methods

We systematically searched through PubMed, to identify all published studies reporting on the association between any individual lncRNA or group of lncRNAs with prognosis in human cancer (death or other clinical outcomes). Where appropriate, we then performed quantitative synthesis of those results using meta-analytic methods to identify the true effect size of lncRNAs on cancer prognosis. The reliability of those results was then examined using measures of heterogeneity and testing for selective reporting biases.

Results

Three hundred ninety-two studies were screened to eventually identify 111 eligible studies on 127 datasets. In total, these represented 16,754 independent participants pertaining to 53 individual and 6 grouped lncRNAs within a total of 19 cancer sites. Overall, 83 % of the studies we identified addressed overall survival and 32 % of the studies addressed recurrence-free survival. For overall survival, 96 % (88/92) of studies identified a statistically significant association of lncRNA expression to prognosis. Meta-analysis of 6 out of 7 lncRNAs for which three or more studies were available, identified statistically significant associations with overall survival. The lncRNA HOTAIR was by far the most broadly studied lncRNA (n = 29; of 111 studies) and featured a summary hazard ratio (HR) of 2.22 (95 % confidence interval (CI), 1.86–2.65) with modest heterogeneity (I² = 49 %; 95 % CI, 14–79 %). Prominent excess significance was demonstrated across all meta-analyses (p-value = 0.0003), raising the possibility of substantial selective reporting biases.

Conclusions

Multiple lncRNAs have been shown to be strongly associated with prognosis in diverse cancers, but substantial bias cannot be excluded in this field and larger studies are needed to understand whether these prognostic information may eventually be useful.

Electronic supplementary material

The online version of this article (doi:10.1186/s12943-016-0535-1) contains supplementary material, which is available to authorized users.

TUG1: a pivotal oncogenic long non-coding RNA of human cancers

Long non-coding RNAs (lncRNAs) are a group greater than 200 nucleotides in length. An increasing number of studies has shown that lncRNAs play important roles in diverse cellular processes, including proliferation, differentiation, apoptosis, invasion and chromatin remodelling. In this regard, deregulation of lncRNAs has been documented in human cancers. TUG1 is a recently identified oncogenic lncRNA whose aberrant upregulation has been detected in different types of cancer, including B-cell malignancies, oesophageal squamous cell carcinoma, bladder cancer, hepatocellular carcinoma and osteosarcoma. In these malignancies, knock-down of TUG1 has been shown to suppress cell proliferation, invasion and/or colony formation. Interestingly, TUG1 has been found to be downregulated in non-small cell lung carcinoma, indicative of its tissue-specific function in tumourigenesis. Pertinent to clinical practice, TUG1 may act as a prognostic biomarker for tumours. In this review, we summarize current knowledge concerning the role of TUG1 in tumour progression and discuss mechanisms associated with it.

Current Insights into Long Non-Coding RNAs in Renal Cell Carcinoma

Renal cell carcinoma (RCC) represents a deadly disease with rising mortality despite intensive therapeutic efforts. It comprises several subtypes in terms of distinct histopathological features and different clinical presentations. Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts in the genome which vary in expression levels and length and perform diverse functions. They are involved in the inititation, evolution and progression of primary cancer, as well as in the development and spread of metastases. Recently, several lncRNAs were described in RCC. This review emphasises the rising importance of lncRNAs in RCC. Moreover, it provides an outlook on their therapeutic potential in the future.

Quantitative Assessment of the Polymorphisms in the HOTAIR lncRNA and Cancer Risk: A Meta-Analysis of 8 Case-Control Studies

HOX transcript antisense intergenic RNA (HOTAIR) is a long non-coding RNA (lncRNA) that functions as an oncogenic molecule in different cancer cells. Genetic variants of HOTAIR may affect the activity of certain regulatory factors and further regulate the aberrant expression of HOTAIR, which might be underlying mechanisms that affect tumour susceptibility and prognosis. Recently, several studies have been performed to examine the possible link between polymorphisms in HOTAIR and cancer risk; however, the results have been inconclusive. Therefore, we performed a meta-analysis to estimate the associations between HOTAIR polymorphisms (rs920778, rs4759314 and rs1899663) and cancer risk. Eight studies comprising 7,151 cases and 8,740 controls were included in our study. Overall, no significant associations between the HOTAIR polymorphisms (rs920778, rs4759314 and rs1899663) and cancer risk were observed. However, in further stratified analyses, the variant T allele of rs920778 exhibited a significant increased risk of developing digestive cancers (dominant model: OR = 1.44; 95% CI = 1.31–1.59). These findings provided evidence that HOTAIR rs920778 may modify the susceptibility to certain cancer types. Further studies incorporating subjects with different ethnic backgrounds combined with re-sequencing of the marked region and functional evaluations are warranted.

HOTAIR and its surrogate DNA methylation signature indicate carboplatin resistance in ovarian cancer

BACKGROUND

Understanding carboplatin resistance in ovarian cancer is critical for the improvement of patients' lives. Multipotent mesenchymal stem cells or an aggravated epithelial to mesenchymal transition phenotype of a cancer are integrally involved in pathways conferring chemo-resistance. Long non-coding RNA HOTAIR (HOX transcript antisense intergenic RNA) is involved in mesenchymal stem cell fate and cancer biology.

METHODS

We analyzed HOTAIR expression and associated surrogate DNA methylation (DNAme) in 134 primary ovarian cancer cases (63 received carboplatin, 55 received cisplatin and 16 no chemotherapy). We validated our findings by HOTAIR expression and DNAme analysis in a multicentre setting of five additional sets, encompassing 946 ovarian cancers. Chemo-sensitivity has been assessed in cell culture experiments.

RESULTS

HOTAIR expression was significantly associated with poor survival in carboplatin-treated patients with adjusted hazard ratios for death of 3.64 (95 % confidence interval [CI] 1.78-7.42; P < 0.001) in the discovery and 1.63 (95 % CI 1.04-2.56; P = 0.032) in the validation set. This effect was not seen in patients who did not receive carboplatin (0.97 [95 % CI 0.52-1.80; P = 0.932]). HOTAIR expression or its surrogate DNAme signature predicted poor outcome in all additional sets of carboplatin-treated ovarian cancer patients while HOTAIR expressors responded preferentially to cisplatin (multivariate interaction P = 0.008).

CONCLUSIONS

Non-coding RNA HOTAIR or its more stable DNAme surrogate may indicate the presence of a subset of cells which confer resistance to carboplatin and can serve as (1) a marker to personalise treatment and (2) a novel target to overcome carboplatin resistance.

Regulatory Roles of Non-Coding RNAs in Colorectal Cancer

Non-coding RNAs (ncRNAs) have recently gained attention because of their involvement in different biological processes. An increasing number of studies have demonstrated that mutations or abnormal expression of ncRNAs are closely associated with various diseases including cancer. The present review is a comprehensive examination of the aberrant regulation of ncRNAs in colorectal cancer (CRC) and a summary of the current findings on ncRNAs, including long ncRNAs, microRNAs, small interfering RNAs, small nucleolar RNAs, small nuclear RNAs, Piwi-interacting RNAs, and circular RNAs. These ncRNAs might become novel biomarkers and targets as well as potential therapeutic tools for the treatment of CRC in the near future and this review may provide important clues for further research on CRC and for the selection of effective therapeutic targets.

Prognostic role of HOTAIR in four estrogen-dependent malignant tumors: a meta-analysis

Background

HOX transcript antisense intergenic RNA (HOTAIR), a long non-coding RNA transcribed from the antisense strand of the HOXC gene locus, has been shown to be overexpressed in various carcinomas and is thought to be an indicator of poor prognosis. Recently, HOTAIR was found to be an estrogen-responsive gene. We therefore conducted a meta-analysis to systematically summarize and clarify the association between HOTAIR expression and prognosis in the four main estrogen-dependent tumors.

Methods

A systematic search of studies that examined the association and prognostic impact of HOTAIR in four of the main estrogen-dependent tumors was conducted in PubMed and Embase. Hazard ratios (HRs) and 95% confidence intervals (95% CIs) were calculated to pool the effect size.

Results

A total of 1,200 patients from eight eligible studies were included. The current study found an association between HOTAIR expression and overall survival (OS) in four estrogen-dependent tumor types (HR, 1.99; 95% CI: 1.02–3.90; P_{Heterogeneity}=0.001). Subgroup analyses indicated that high HOTAIR expression appeared to be a potential prognostic biomarker in non-breast cancer patients (HR, 2.72; 95% CI: 1.65–4.48). There was also an increased risk in Asian populations (HR, 2.55; 95% CI: 1.62–4.00) compared with Caucasian populations (HR, 1.19; 95% CI: 0.16–8.83) and in patients without preoperative treatment (HR, 2.55; 95% CI: 1.62–4.00) compared with patients with preoperative treatment (HR, 1.19; 95% CI: 0.16–8.83). In addition, the HRs of patients with high HOTAIR expression for metastasis-free survival (MFS), relapse-free survival (RFS), and disease-free survival (DFS) were 2.30 (P=0.120), 1.39 (P=0.000), and 2.53 (P=0.714), respectively, but there were insufficient data to fully confirm these associations.

Conclusion

HOTAIR may be a predictor of poor prognosis in four of the main estrogen-dependent tumors, especially in cervical, ovarian, and endometrial cancer patients without preoperative treatment in Asian populations. It is important to note that the prognostic value of HOTAIR in MFS, RFS, and DFS should be interpreted with caution due to the limited sample size and sample heterogeneity. Well-designed and larger-scale studies are needed to validate our findings.

LncRNA MALAT1 overexpression is an unfavorable prognostic factor in human cancer: evidence from a meta-analysis

Long non-coding RNAs (lncRNAs) have been suggested to serve as an important role in tumor development and progression. The aim of this study was to analyse the association between lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and cancer patients' overall survival. We systematically and carefully searched the studies from electronic databases and seriously identified according to eligibility criteria. The correlation between lncRNA MALAT1 expression and overall survival in human cancers was evaluated through Review Manager. A total of 8 studies which included 792 cancer patients were included in the final analysis. Meta-analysis showed that lncRNA MALAT1 overexpression was correlated with a poor overall survival and the pooled hazard ratio (HR) and corresponding 95% confidence interval (CI) was 1.94 (95% CI 1.59-2.38). From subgroup analyses, we present evidence that lncRNA MALAT1 overexpression was an unfavorable prognostic factor for patients' overall survival in non-small cell lung cancer and pancreatic cancer, the pooled HRs (95% CI) were 1.86 (95% CI 1.27-2.73) and 1.78 (95% CI 1.30-2.44), respectively. In conclusion, lncRNA MALAT1 is a potential prognostic factor in human cancers.