Long noncoding RNA HOTAIR as an independent prognostic marker in cancer: a meta-analysis

Polycomb repressive complex 2 and its core component EZH2: potential targeted therapeutic strategies for head and neck squamous cell carcinoma

The polycomb group (PcG) comprises a set of proteins that exert epigenetic regulatory effects and play crucial roles in diverse biological processes, ranging from pluripotency and development to carcinogenesis. Among these proteins, enhancer of zeste homolog 2 (EZH2) stands out as a catalytic component of polycomb repressive complex 2 (PRC2), which plays a role in regulating the expression of homologous (Hox) genes and initial stages of x chromosome inactivation. In numerous human cancers, including head and neck squamous cell carcinoma (HNSCC), EZH2 is frequently overexpressed or activated and has been identified as a negative prognostic factor. Notably, EZH2 emerges as a significant gene involved in regulating the STAT3/HOTAIR axis, influencing HNSCC proliferation, differentiation, and promoting metastasis by modulating related oncogenes in oral cancer. Currently, various small molecule compounds have been developed as inhibitors specifically targeting EZH2 and have gained approval for treating refractory tumors. In this review, we delve into the epigenetic regulation mediated by EZH2/PRC2 in HNSCC, with a specific focus on exploring the potential roles and mechanisms of EZH2, its crucial contribution to targeted drug therapy, and its association with cancer markers and epithelial-mesenchymal transition. Furthermore, we aim to unravel its potential as a therapeutic strategy for oral squamous cell carcinoma.

HCC-Related lncRNAs: Roles and Mechanisms

Hepatocellular carcinoma (HCC) presents a significant global health threat, particularly in regions endemic to hepatitis B and C viruses, and because of the ongoing pandemic of obesity causing metabolic-dysfunction-related fatty liver disease (MAFLD), a precursor to HCC. The molecular intricacies of HCC, genetic and epigenetic alterations, and dysregulated signaling pathways facilitate personalized treatment strategies based on molecular profiling. Epigenetic regulation, encompassing DNA methyltion, histone modifications, and noncoding RNAs, functions as a critical layer influencing HCC development. Long noncoding RNAs (lncRNAs) are spotlighted for their diverse roles in gene regulation and their potential as diagnostic and therapeutic tools in cancer. In this review, we explore the pivotal role of lncRNAs in HCC, including MAFLD and viral hepatitis, the most prevalent risk factors for hepatocarcinogenesis. The dysregulation of lncRNAs is implicated in HCC progression by modulating chromatin regulation and transcription, sponging miRNAs, and influencing structural functions. The ongoing studies on lncRNAs contribute to a deeper comprehension of HCC pathogenesis and offer promising routes for precision medicine, highlighting the utility of lncRNAs as early biomarkers, prognostic indicators, and therapeutic targets.

Long noncoding RNA HOTAIR regulates the stemness of breast cancer cells via activation of the NF-κB signaling pathway

Breast cancer is the most prevalent cancer among women, and it is characterized by a high rate of tumor development and heterogeneity. Breast cancer stem cells (CSCs) may well contribute to these pathological properties, but the mechanisms underlying their self-renewal and maintenance are still elusive. Here, we found that the long noncoding RNA HOTAIR is highly expressed in breast CSCs. HOTAIR is required for breast CSC self-renewal and tumor propagation. Mechanistically, we demonstrate that HOTAIR recruits the PRC2 protein complex to the promoter of IκBα to inhibit its expression, leading to activation of the NF-κB signaling pathway. The activated NF-κB signaling promotes downstream c-Myc and Cyclin D1 expression. Furthermore, our analysis of clinical samples from the GEPIA database indicated that the IκBα level, as well as the survival rate of patients, with high HOTAIR expression was significantly lower than that of patients with relatively low HOTAIR expression. Our data suggest that HOTAIR-mediated NF-κB signaling primes breast CSC self-renewal and tumor propagation. In sum, we have identified HOTAIR-based NF-κB signaling regulatory circuit that promotes tumorigenic activity in breast CSCs, further indicating that HOTAIR could be a promising target for clinical treatment of breast cancers.

Long noncoding RNA HOTAIR polymorphisms and susceptibility to bipolar disorder: a preliminary case-control study

Recent studies have shown that long noncoding RNAs contribute to the pathogenesis of bipolar disorder (BD). In this study, we genotyped four HOX Transcript Antisense Intergenic RNA (HOTAIR) gene polymorphisms to investigate if these variations could affect the risk of BD and its clinical subtypes. A total of 357 subjects, comprised of 194 BD patients and 163 age-matched healthy controls, were enrolled. Genotyping was carried out using PCR-RFLP and ARMS-PCR methods. We detected significant associations between the HOTAIR gene rs1899663 G/T, rs12826786 C/T, rs4759314 A/G, and rs920778 C/T polymorphism and the risk of BD under allelic, recessive, dominant, and codominant contrasted genetic models. The CT genotype of rs920778 C/T, GT genotype of rs1899663 G/T, and CT genotype of rs12826786 C/T polymorphisms enhanced the risk of BD type II (BDII). In contrast, the GG genotype of rs4759314 A/G polymorphism significantly diminished BDII risk by 83%. A positive association was noticed between CTTA and CTCG haplotypes of rs920778/rs1899663/rs12826786/rs4759314 and BD risk. Our findings reveal an interactive effect of HOTAIR polymorphisms on the development of BD and its subtypes. Further functional studies are needed to elucidate the role of these variations on HOTAIR expression and epigenetic status.

Long noncoding RNAs (lncRNAs) in human lymphomas

Lymphomas are a diverse group of haematologic malignancies, which occur in infection-fighting cells of the lymphatic system. Long non-coding RNAs (lncRNAs) are non-coding RNAs, which have recently received significant attention as the main mediators of gene expression. In this review, we summarize the current knowledge on lncRNAs involved in lymphomas, their molecular functions, as well as their potential clinical value. Relevant literature was identified by a PubMed search of English language papers using the following terms: Lymphoma, LncRNA, leukemia, proliferation, apoptosis, and prognosis. LncRNAs are imperative for lymphoma carcinogenesis through affecting apoptosis, cell proliferation, invasion, and response to chemotherapy. The expression level of lncRNAs can affect chemotherapy-induced apoptosis. Taken together, lncRNA dysregulation in lymphoma cells is not only an epiphenomenon but also lncRNA transcription is critically related to the initiation and progression of lymphomas. Aberrant expression of lncRNAs can lead to the transformation of normal lymphocytes into lymphoma cells.

HOTAIR beyond repression: In protein degradation, inflammation, DNA damage response, and cell signaling

Long noncoding RNAs (lncRNAs) are pervasively transcribed from the mammalian genome as transcripts that are usually >200 nucleotides long. LncRNAs generally do not encode proteins but are involved in a variety of physiological processes, principally as epigenetic regulators. HOX transcript antisense intergenic RNA (HOTAIR) is a well-characterized lncRNA that has been implicated in several cancers and in various other diseases. HOTAIR is a repressor lncRNA and regulates various repressive chromatin modifications. However, recent studies have revealed additional functions of HOTAIR in regulation of protein degradation, microRNA (miRNA) sponging, NF-κB activation, inflammation, immune signaling, and DNA damage response. Herein, we have summarized the diverse functions and modes of action of HOTAIR in protein degradation, inflammation, DNA repair, and diseases, beyond its established functions in gene silencing.

Long noncoding RNA LINC00978 acts as a potential diagnostic biomarker in patients with colorectal cancer

Colorectal cancer (CRC) as a lethal malignancy has been associated with dysregulation of several genes and pathways. Long noncoding RNAs (lncRNAs) play an important role in gene expression regulation. In the current research, we aim to evaluate the expression of LINC00978 in CRC samples and adjacent tissues. Using Quantitative Real-Time PCR (qRT-PCR) method, we assessed the expression levels of LINC00978 and β-catenin in 70 pairs of CRC and adjacent tissues. Moreover, the association between clinicopathological features and the LINC00978 expression levels was investigated. To assess the diagnostic power of LINC00978 expression in CRC, receiver operating characteristic (ROC) curve was plotted. The relationship between LINC00978 and β-catenin expression levels was evaluated using correlation analysis. A markedly increased level of LINC00978 and β-catenin expression levels was observed in CRC samples compared with adjacent tissues (P < 0.0001). No significant association was detected between LINC00978 expression level and the patient's clinicopathological features. The results of Pearson's correlation coefficient highlighted a positive correlation between LINC00978 and β-catenin expression (r² = 0.4695, P < 0.0001). According to the area under curve (AUC) value, LINC00978 expression differentiates CRC samples from the adjacent tissues (AUC = 0.81, P < 0.0001). The present results suggest that LINC00978 may play a critical role in CRC progression via Wnt pathway. The potential role of LINC00978 as a diagnostic biomarker needs to be further investigated in future studies.

Hypoxia-Induced Non-Coding RNAs Controlling Cell Viability in Cancer

Hypoxia, a characteristic of the tumour microenvironment, plays a crucial role in cancer progression and therapeutic response. The hypoxia-inducible factors (HIF-1α, HIF-2α, and HIF-3α), are the master regulators in response to low oxygen partial pressure, modulating hypoxic gene expression and signalling transduction pathways. HIFs’ activation is sufficient to change the cell phenotype at multiple levels, by modulating several biological activities from metabolism to the cell cycle and providing the cell with new characteristics that make it more aggressive. In the past few decades, growing numbers of studies have revealed the importance of non-coding RNAs (ncRNAs) as molecular mediators in the establishment of hypoxic response, playing important roles in regulating hypoxic gene expression at the transcriptional, post-transcriptional, translational, and posttranslational levels. Here, we review recent findings on the different roles of hypoxia-induced ncRNAs in cancer focusing on the data that revealed their involvement in tumour growth.

Long non-coding RNA HOTAIR regulates myeloid differentiation through the upregulation of p21 via miR-17-5p in acute myeloid leukaemia

Long non-coding RNA HOTAIR has been reported to play a key role in regulating various biological processes in various cancers. However, the roles and mechanisms of HOTAIR in acute myeloid leukaemia (AML) are still unclear and need to be investigated. In this study, we induced differentiation of four AML cell lines by all-trans retinoic acid (ATRA) and found HOTAIR was significantly upregulated in the process. Chromatin immunoprecipitation (ChIP) assays indicated that C/EBPβ upregulated HOTAIR during ATRA induced differentiation in HL-60 cells. By gain- and loss-of-function analysis, we then observed that HOTAIR expression was positively correlated with ATRA-induced differentiation and negatively regulated G1 phase arrest in HL-60 cells. In addition, we found that HOTAIR promoted ATRA-induced differentiation via the regulation of the cell cycle regulator p21 via miR-17-5p. Moreover, we detected the expression of HOTAIR in 84 de novo AML patients, HOTAIR was found significantly downregulated in the AML patients compared to the iron deficiency anaemia (IDA) control group, negatively correlated with the platelet level in M2 patients. In all, our data suggest that HOTAIR may be subtype-specific in AML-M2 patients, also HOTAIR regulates AML differentiation by C/EBPBβ/HOTAIR/miR-17-5p/p21 pathway. The findings of the present study provide a novel insight into the mechanism of lncRNA-mediated differentiation and indicate that HOTAIR may be a promising therapeutic target for leukaemia, especially for AML with M2 type.Abbreviation: AML: acute myeloid leukaemia; APL: acute promyelocytic leukaemia; ATRA: all-trans retinoic acid; CCK8: cell Counting Kit-8; CDKs: cyclin-dependent kinases ; CeRNA: competing endogenous RNAs; ChIP: chromatin immunoprecipitation; CHX: cycloheximide; FAB: French-American-British; FCM: flow cytometry; HOTAIR: HOX transcript antisense RNA; IDA: iron-deficiency anemia; lncRNA: long non-coding RNA; 3'UTR: 3'untranslated region; MT: Mutation type; WT: Wild type; qRT-PCR: Quantitative real-time PCR.

Long non-coding RNA GAS5 in human cancer

Long non-coding RNAs (lncRNAs) constitute a group of >200-nucleotide ncRNA molecules. lncRNAs regulate several cell functions, such as proliferation, apoptosis, invasion and metastasis. Meanwhile, lncRNAs are abnormally expressed in human malignancies, where they suppress or promote tumor growth. The present study focused on growth arrest-specific transcript 5 (GAS5), a well-known lncRNA that acts as a tumor suppressor but is suppressed in multiple types of cancer, including mammary carcinoma, prostate cancer, colorectal cancer, gastric cancer, melanoma, esophageal squamous cell carcinoma, lung cancer, ovarian cancer, cervical cancer, gliomas, osteosarcoma, pancreatic cancer, bladder cancer, kidney cancer, papillary thyroid carcinoma, neuroblastoma, endometrial cancer and liver cancer. Notably, GAS5 is overexpressed in liver cancer, potentially functioning as an oncogene. In the present study, the diagnostic and therapeutic roles of GAS5 in different tumors were reviewed, with a summary of the potential clinical application of the lncRNA, which may help identify novel study directions for GAS5.

Long non-coding RNA TINCR as potential biomarker and therapeutic target for cancer

Despite the recent scientific advances made in cancer diagnostics and therapeutics, cancer still remains the second leading cause of death worldwide. Thus, there is a need to identify new potential biomarkers/molecular targets to improve the diagnosis and treatment of cancer patients. In this regard, long non-coding RNAs (lncRNAs), a type of non-coding RNA molecule, have been found to play important roles in diverse biological processes, including tumorigenesis, and may provide new biomarkers and/or molecular targets for the improved detection of treatment of cancer. For example, one lncRNA, tissue differentiation-inducing non-protein coding RNA (TINCR) has been found to be significantly dysregulated in many cancers, and has an impact on tumor development and progression through targeting pivotal molecules in cancer-associated signaling pathways. Hence, based on recent discoveries, herein, we discuss the regulatory functions and the underlying mechanisms of how TINCR regulates signaling pathways attributed to cancer hallmarks associated with the pathogenesis of various human cancers. We also highlight studies assessing its potential clinical utility as a biomarker/target for early detection, cancer risk stratification, and personalized cancer therapies.

Silencing of Long Non-Coding RNA-HCG18 Inhibits the Tumorigenesis of Gastric Cancer Through Blocking PI3K/Akt Pathway

PURPOSE

Long non-coding RNAs (lncRNAs) play critical regulatory roles in the tumorigenesis of GC. This study aimed to investigate the regulatory effect and mechanism of lncRNA-HCG18 on GC.

METHODS

The expression of lncRNA-HCG18 was detected in GC tissues and cell lines by qRT-PCR. LncRNA-HCG18 was silenced in AGS and MGC803 cells by the transfection of lncRNA-HCG18 siRNA (si-HCG18). MTT, transwell and Annexin V-PI double staining assay were performed to assess the proliferation, migration, invasion and apoptosis of GC cells. The expression of PI3K/Akt pathway-, apoptosis-, and migration-related proteins were detected by Western blot. An activator of PI3K/Akt pathway 740 Y-P was used to activate the PI3K/Akt pathway in AGS cells. A human tumor xenograft model was established in mice to evaluate the effects of si-HCG18 in vivo.

RESULTS

LncRNA-HCG18 was overexpressed in GC tissues and cells. Up-regulation of lncRNA-HCG18 was positively correlated with the stage of tumor node metastasis and invasion depth. Silencing of lncRNA-HCG18 suppressed the proliferation, migration and invasion, and induced the apoptosis of GC cells. Silencing of lncRNA-HCG18 blocked the PI3K/Akt pathway. The intervention of 740Y-P reversed the anti-tumor effect of lncRNA-HCG18 on GC cells. In addition, silencing of lncRNA-HCG18 suppressed the growth of GC xenografts in mice.

CONCLUSION

Silencing of lncRNA-HCG18 inhibited the tumorigenesis of GC through blocking the PI3K/Akt pathway, suggesting a novel therapeutic target for GC.

Prognostic and Clinicopathological Significance of Long Non-coding RNA PANDAR Expression in Cancer Patients: A Meta-Analysis

Background: Long non-coding RNA PANDAR is an emerging non-coding RNA mapping to 6p21.2. It underlies metastatic progression and chromosomal instability in a variety of cancers. Despite the fact that recent studies have revealed that lncRNA PANDAR may be a potential prognostic biomarker for patients with cancer, there has still been controversy on the prognostic value of PANDAR. Methods: Databases of PubMed, Embase, SinoMed, and Web of Science were carefully searched and the literature which investigated the prognostic value of PANDAR expression among human cancers was collected for further analysis. Odds ratios (ORs) or hazards ratios (HRs) with 95% confidence intervals (CIs) were pooled to estimate the relation between PANDAR expression and survival or clinicopathological characteristics of cancer patients. Results: There were 13 eligible studies in total, with 1,465 patients enlisted in this meta-analysis. All the eligible studies complied with the case-control study. The outcome showed that the elevated expression level of PANDAR was significantly related to poor overall survival (OS) (pooled HR 1.72, 95%CI 1.14-2.60). However, high or low expression of PANDAR did not differ in the prediction of event-free survival (EFS). Moreover, we discovered that high PANDAR expression was closely related to decreased OS in colorectal cancer (pooled HR 3.43, 95%CI 2.06-5.72) and reduced expression level of PANDAR was markedly related to poor OS (pooled HR 0.65, 95%CI 0.45-0.88) in non-small cell lung cancer. However, the expression level of PANDAR had no significant association with OS in renal cell carcinoma (pooled HR 1.19, 95%CI 0.56-2.50). Moreover, after analysis, we discovered that the high expression level of PANDAR was associated closely with the depth of invasion (pooled OR 3.95, 95%CI 2.36-6.63), lymph node metastasis (pooled OR 1.92, 95%CI 0.93-3.98), tumor stage (pooled OR 2.05, 95%CI 0.99-4.27), and distant metastasis (pooled OR 2.87, 95%CI 1.60-5.16). Conclusions: Our study revealed that increased PANDAR expression may serve as an adverse prognostic biomarker for cancer patients, thus helping the clinical decision-making process.

Long non-coding RNA XIST predicting advanced clinical parameters in cancer: A Meta-Analysis and case series study in a single institution

Dysregulated expression of long non-coding RNA X-inactive specific transcript (lncRNA-XIST) has been indicated in various cancer types. In the present study, a meta-analysis was conducted to evaluate the potential role of lncRNA-XIST in predicting the clinicopathological parameters of patients with cancer. Eligible studies were obtained through a systematic search of PubMed, Web of Science, Embase and the Cochrane Library, of articles published prior to January 2019. The combined odds ratio and 95% confidence interval were calculated to determine the association between lncRNA-XIST expression and patient outcome. In addition, 45 pairs of osteosarcoma (OS) tissues and adjacent healthy tissues from a single institution were analyzed for the expression of lncRNA-XIST, and its association with clinicopathological features; ultimately, a total of 1,869 cancer patients from 25 studies were assessed. The results demonstrated that high expression levels of lncRNA-XIST were significantly associated with lymphatic metastasis, larger tumor size, advanced cancer stage and distant metastasis. However, sex was not associated with lncRNA-XIST expression level. In the OS patient cohort, it was demonstrated that lncRNA-XIST was highly expressed in OS tissues, which negatively correlated with patient prognosis. The present study indicated that lncRNA-XIST may serve as a potential biomarker for advanced clinical parameters in human cancer.

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.

Four lncRNAs associated with breast cancer prognosis identified by coexpression network analysis

Previous studies on long noncoding RNA (lncRNA) have made breakthroughs in the treatment of several tumors, and these findings have brought attention to the lncRNA signature of breast cancer. Increased understanding of genomic architecture and achievement of innovative therapeutic strategies has prompted creation of a novel oncological model for the treatment of solid cancers. In this study, we systematically analyzed the transcriptome of breast cancer tissues to gain more in-depth knowledge of tumor biology. Gene coexpression relationships were studied in 206 samples from The Cancer Genome Atlas database, and nine coexpression modules were identified. After screening and analysis, we identified four important prognosis-related lncRNAs (HOTAIR, SNHG16, HCP5, and TINCR), and constructed a prognostic model, one (HCP5) of which has not previously been identified in the context of breast cancer. Importantly, an understanding of prognosis facilitates precise disease risk assessment and advances the selection of strategies for risk-adaptive management. These findings broaden the landscape of carcinogenic lncRNAs in breast cancer, providing insights into the biological significance and clinical application of lncRNAs in breast cancer.

ZFAS1: a novel tumor-related long non-coding RNA

Long non-coding RNAs (lncRNA) are classified as a kind of RNA, which are longer than 200 nucleotides in length and cannot be translated into proteins. Multiple studies have demonstrated that lncRNAs are involved in various cellular processes, including proliferation, differentiation, cell death, and metastasis. In addition, aberrant expression of lncRNAs has been discovered in human tumors, where they function as either oncogenes or tumor suppressor genes. Among numerous lncRNAs, we focus on ZNFX1 antisense RNA 1 (ZFAS1), a well-known lncRNA that is aberrant overexpression in various tumors, including melanoma, esophageal squamous cell carcinoma, non-small cell lung cancer, gastric cancer, colon cancer, and Hepatocellular carcinoma, in which it functions as oncogene. In contrast, ZFAS1 is downregulated in breast cancer, which may function as tumor suppressor gene. In this review, we provide an overview of current evidence concerning the role and potential clinical utilities of ZFAS1 in human cancers.

Expression profile analysis of antisense long non-coding RNA identifies WDFY3-AS2 as a prognostic biomarker in diffuse glioma

BACKGROUND

Increasing evidence has shown that long non-coding RNAs (lncRNAs) are important prognostic biomarkers and epigenetic regulators with critical roles in cancer initiation and progression. However, the expression and clinical prognostic value of antisense lncRNAs in diffuse glioma patients remain unknown.

METHODS

Here, we profiled differentially expressed antisense lncRNAs in glioma using RNA sequencing data from Chinese Glioma Genome Atlas database. Cox regression was performed to evaluate the prognostic value. Gene oncology (GO) and gene set enrichment analysis (GSEA) were used for functional analysis of antisense LncRNAs.

RESULTS

Expression profiling identified 169 aberrantly expressed antisense lncRNAs between lower grade glioma (LGG) (grade II and III) and glioblastoma multiforme (GBM), 113 antisense lncRNAs between LGG IDH-wt and IDH-mut samples, and 70 antisense lncRNAs between GBM IDH-wt and IDH-mut samples, respectively. Among them, three antisense lncRNAs (WDFY3-AS2, MCM3AP-AS1 and LBX2-AS1) were significantly associated with prognosis and malignant progression of patients. WDFY3-AS2, the top one of downregulated antisense lncRNAs in GBM with fold change of 0.441 (P < 0.001), showed specific decreased expression in classical, mesenchymal, LGG IDH-wt, GBM IDH-wt or MGMT promoter unmethylated stratified patients. Chi square test found that WDFY3-AS2 was significantly associated with the clinical and molecular features of glioma. Univariate and multivariate Cox regression analysis indicated that WDFY3-AS2 was independently correlated with overall survival (OS) of patients. Kaplan-Meier analysis found that patients with high WDFY3-AS2 expression had longer OS than the low expression ones in the stratified cohorts. Additionally, GO and GSEA showed that gene sets correlated with WDFY3-AS2 expression were involved in regulation of synaptic transmission, glutamate receptor and TNF signaling pathway.

CONCLUSION

Our findings provided convincing evidence that WDFY3-AS2 is a novel valuable prognostic biomarker for diffuse glioma.

Identification of aberrantly expressed long non-coding RNAs in stomach adenocarcinoma

Aim

Stomach adenocarcinoma (STAD) is a common malignancy worldwide. This study aimed to identify the aberrantly expressed long non-coding RNAs (lncRNAs) in STAD.

Results

Total of 74 DElncRNAs and 449 DEmRNAs were identified in STAD compared with paired non-tumor tissues. The DElncRNA/DEmRNA co-expression network was constructed, which covered 519 nodes and 2993 edges. The qRT-PCR validation results of DElncRNAs were consistent with our bioinformatics analysis based on RNA-sequencing. The DEmRNAs co-expressed with DElncRNAs were significantly enriched in gastric acid secretion, complement and coagulation cascades, pancreatic secretion, cytokine-cytokine receptor interaction and Jak-STAT signaling pathway. The expression levels of the nine candidate DElncRNAs in TCGA database were compatible with our RNA-sequencing. FEZF1-AS1, HOTAIR and LINC01234 had the potential diagnosis value for STAD.

Materials and Methods

The lncRNA and mRNA expression profile of 3 STAD tissues and 3 matched adjacent non-tumor tissues was obtained through high-throughput RNA-sequencing. Differentially expressed lncRNAs/mRNAs (DElncRNAs/DEmRNAs) were identified in STAD. DElncRNA/DEmRNA co-expression network construction, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to predict the biological functions of DElncRNAs. Quantitative real-time polymerase chain reaction (qRT-PCR) was subjected to validate the expression levels of DEmRNAs and DElncRNAs. Moreover, the expression of DElncRNAs was validated through The Cancer Genome Atlas (TCGA) database. The diagnosis value of candidate DElncRNAs was accessed by receiver operating characteristic (ROC) analysis.

Conclusions

Our work might provide useful information for exploring the tumorigenesis mechanism of STAD and pave the road for identification of diagnostic biomarkers in STAD.

STAT3/HOTAIR Signaling Axis Regulates HNSCC Growth in an EZH2-dependent Manner

Purpose: PI3K and STAT3 are frequently activated in cancer progression. However, little is known about the underlying mechanisms by which PI3K and STAT3 regulate head and neck squamous cell cancer (HNSCC) growth. The lncRNA HOX transcript antisense RNA (HOTAIR) was found to modulate the progression of HNSCC. In this study, we attempted to establish the correlation of PI3K/STAT3/HOTAIR signaling with the progression of HNSCC and its sensitivity toward platinum-based and targeted anti-EGFR combination therapy.Experimental Design: We first analyzed the STAT3/HOTAIR and PI3K/AKT level in human HNSCC samples. We then activated or suppressed STAT3/HOTAIR and determined the effects on HNSCC cell proliferation in vitro and the growth of UM1 xenograft tumor, an orthotopic model of HNSCC. The sensitivity of HNSCC cells toward cisplatin and cetuximab was determined by in vitro assays.Results: HNSCC samples showed significantly robust expression/activation of STAT3, HOTAIR, PI3K, and AKT, compared with normal squamous epithelium. STAT3 inhibition with WP1066 decreased HOTAIR level and sensitized HNSCC to cisplatin or cetuximab. STAT3 promoted HOTAIR transcription and its interaction with pEZH2-S21, resulting in enhanced growth of HNSCC cells. In addition, overexpression of HOTAIR promoted the growth of UM1 xenograft tumors in vivoConclusions: Our results suggest that STAT3 signaling promotes HNSCC progression via regulating HOTAIR and pEZH2-S21 in HNSCC with PI3K overexpression/activation. These findings provide a rationale to target the STAT3/HOTAIR/pEZH2-S21 regulatory axis for treating patients with HNSCC. Clin Cancer Res; 24(11); 2665-77. ©2018 AACR.

Altered long non-coding RNAs predict worse outcome in osteosarcoma patients: evidence from a meta-analysis

Long non-coding RNAs (lncRNAs) are emerging as promising prognostic biomarkers in an expanding list of malignant neoplasms. Here, we sought to investigate the strength of associations between lncRNA signatures and clinical outcomes in osteosarcoma. We conducted a systematic search of the online databases from inception to July 2016. Hazard ratios (HRs) with corresponding 95% confidence intervals (CIs) for the primary endpoints of overall survival (OS), progression-free survival (PFS) or event-free survival (EFS) were extracted and meta-analyzed. Our results manifested that altered lncRNAs expression was markedly associated with worse OS (univariate analysis: HR = 3.20, 95% CI: 2.42-4.24, P = 0.000; multivariate analysis: HR = 2.66, 95% CI: 1.92-3.69, P = 0.000), PFS (HR = 2.05, 95% CI: 1.32-3.18, P = 0.001) and EFS (HR = 4.37, 95% CI: 1.64-11.66, P = 0.003) times among osteosarcoma patients. In the pooled analyses stratified by clinicopathological features, levels of lncRNAs were closely correlated with tumor size (pooled P = 0.001), tumor stage (pooled P = 0.003), and distant metastasis (pooled P = 0.002) in osteosarcoma. The results obtained in our work suggest that altered lncRNA signatures predict unfavorable clinical outcomes and are acceptable to be potential prognostic biomarkers in forecasting prognosis of osteosarcoma.

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.

Association between the HOTAIR polymorphisms and cancer risk: an updated meta-analysis

Purpose

LncRNA HOTAIR plays an important role in many cancer. Several studies have shown that some HOTAIR SNPs might be associated with tumor risk in case-control studies, but the results are inconsistent and inconclusive. Therefore, it is necessary to better evaluate association between the HOTAIR SNPs and the risk of cancer.

Results

rs920778, rs7958904 and rs874945 but not rs4759314 and rs1899663 loci were significantly related to cancer risk, among of which rs920778 and rs874945 increased and rs7958904 decreased cancer risk, respectively. Moreover, rs920778 is significantly susceptible in both Asian population and digestive cancer risks.

Materials and Methods

Data were collected from PubMed, Embase and Web of Science. A total of 11 case-control studies were selected for the quantitative analysis. Software Stata (Version 12) was used to calculate Odds ratios (ORs) and 95% confidence intervals (CIs) to evaluate the strength of the associations. Subgroup analysis, sensitivity analysis, and publication bias were also performed. Five HOTAIR SNPs were finally enrolled in the study.

Conclusions

HOTAIR SNP rs920778, rs7958904 and rs874945 are susceptible to cancer risk. SNP rs920778 is also a useful risk factor in evaluation of Asian population and digestive cancer. In addition, the cancer risk SNP rs874945 is first reported in the meta-analysis.

Association of HOTAIR polymorphisms rs4759314 and rs920778 with cancer susceptibility on the basis of ethnicity and cancer type

Polymorphisms in the HOX transcript antisense intergenic RNA (HOTAIR) have been recently associated with susceptibility to different cancers. Here, a meta-analysis was performed to derive a more precise estimation of the involvement of HOTAIR polymorphisms in cancer development. Data from cases (n = 7,772) and controls (n = 9,075) were extracted from eligible studies (n = 10) identified in a comprehensive literature search conducted in PubMed, Embase, and the Web of Science databases through January 20, 2016. Overall, association between polymorphism rs920778 and increased cancer risk was significant in allele contrast (odds ratio (OR) = 1.239, 95% confidence interval (CI) = 1.032 - 1.487) and recessive models (OR = 1.614, 95% CI = 1.082 - 2.406). In subgroup analysis based on ethnicity, a significant association between polymorphism rs920778 and cancer susceptibility was observed in Asians under all models, but was most compelling under recessive (OR = 2.128, 95% CI = 1.417 - 3.197) and homozygous models (OR = 2.764, 95% CI = 2.221 - 3.440). Subgroup analysis by cancer type revealed a significant association between polymorphism rs4759314 and susceptibility to gastric cancer in allele contrast (OR = 1.262, 95% CI = 1.073 - 1.486), dominant (OR = 1.280, 95% CI = 1.060 - 1.547), and heterozygous models (OR = 1.288, 95% CI = 1.057 - 1.570). In conclusion, the results indicated that HOTAIR polymorphism rs920778 was more generally associated with cancer risk, particularly in Asians, while rs4759314 was a risk factor for gastric cancer.

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.

Targeting LncRNA HOTAIR suppresses cancer stemness and metastasis in oral carcinomas stem cells through modulation of EMT

Increasing evidence indicates that long non-coding RNAs (lncRNAs) regulate diverse cellular processes, such as cell growth, apoptosis and tumorigenesis. However, the functional roles of lncRNAs and mechanistic analysis of their interplays with oncogenic pathways in oral cancer remain largely unknown. In the current study, we examined the significance of lncRNA HOTAIR (HOX transcript antisense RNA) in tumor progression of oral squamous cell carcinomas (OSCC). We found the expression of HOTAIR was upregulated in tumor tissues, especially in the metastatic samples. And it was also observed in metastatic OSCC cell lines. Silence of HOTAIR in oral carcinomas stem cells (OCSC) significantly inhibited their cancer stemness, invasiveness and tumourigenicity in xenotransplantation models. By contrast, overexpression of HOTAIR in OSCC enhanced their metastatic potential and epithelial-mesenchymal transition (EMT) characteristics. And we showed that the expression of HOTAIR was positively related to mesenchymal markers and inversely correlated with epithelial marker in clinical samples. Moreover, Kaplan-Meier survival analysis suggested that high level of HOTAIR was a strong predictor of poor survival in OSCC patients. Collectively, our data demonstrated that HOTAIR-mediated cancer stemness and metastasis are associated with the regulation of EMT and HOTAIR may serve as a therapeutic target in OSCC.

Trends of long noncoding RNA research from 2007 to 2016: a bibliometric analysis

Purpose

This study aims to analyze the scientific output of long noncoding RNA (lncRNA) research and construct a model to evaluate publications from the past decade qualitatively and quantitatively.

Methods

Publications from 2007 to 2016 were retrieved from the Web of Science Core Collection database. Microsoft Excel 2016 and CiteSpace IV software were used to analyze publication outputs, journals, countries, institutions, authors, citation counts, ESI top papers, H-index, and research frontiers.

Results

A total of 3,008 papers on lncRNA research were identified published by June 17, 2017. The journal, Oncotarget (IF2016, 5.168) ranked first in the number of publications. China had the largest number of publications (1,843), but the United States showed its dominant position in both citation frequency (45,120) and H-index (97). Zhang Y (72 publications) published the most papers, and Guttman M (1,556 citations) had the greatest co-citation counts. The keyword “database” ranked first in research frontiers.

Conclusion

The annual number of publications rapidly increased in the past decade. China showed its significant progress in lncRNA research, but the United States was the actual leading country in this field. Many Chinese institutions engaged in lncRNA research but significant collaborations among them were not noted. Guttman M, Mercer TR, Rinn JL, and Gupta RA were identified as good candidates for research collaboration. “Database,” “Xist RNA,” and “Genome-wide association study” should be closely observed in this field.

Decreased expression of long non-coding RNA LOC728290 in human hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a leading cause of cancer-associated mortality worldwide. Despite progress in the diagnosis and treatment of HCC, prognosis remains unfavorable. Long non-coding RNAs (lncRNAs) are emerging as important factors in tumorigenesis and cancer progression; however, the underlying molecular mechanisms and clinical significance of lncRNAs in HCC remain largely unknown. The present study examined the expression pattern and clinical significance of a novel lncRNA, LOC728290, in HCC. Expression of LOC728290 was markedly decreased in HCC tissues compared with adjacent non-tumor liver tissues, as detected using the reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The area under the receiver operating characteristic curve for LOC728290 was 0.728. The expression of LOC728290 was associated with the level of α-fetoprotein and microvascular invasion. Furthermore, patients with low LOC728290 expression exhibited decreased recurrence-free survival times (P<0.05) compared with those with high LOC728290 expression. The results of the present study indicated that downregulation of LOC728290 in patients with HCC may be a powerful tumor biomarker, with potential clinical applications in prognosis as well as a therapeutic target.

Prognostic value of long non-coding RNA CCAT1 expression in patients with cancer: A meta-analysis

Background

LncRNA CCAT1 is significantly overexpressed in various types of cancers, suggesting that it might be associated with prognosis and clinicopathological features in patients with cancer.

Methods

A comprehensive search was performed in Pubmed, Web of Science, OVID and CNKI databases. We also retrieved articles from other sources, such as retrieving from the reference lists of relevant articles. Eligible studies were included based on defined exclusion and inclusion criteria to perform a meta-analysis. STATA 14.0 was used to estimate pooled hazard ratios (HRs) with 95% confidence interval (95% CI), the heterogeneity among studies and publication bias to judge the prognostic value.

Results

A total of 1587 patients from 11 eligible studies were included in the meta-analysis. The results showed that high expression level of CCAT1 was significantly associated with shorter overall survival in cancer patients (HR 2.335, 95% CI:1.551–3.517); in the subgroup analysis, region (China or UK), sample size (more or less than 100), type of cancer (digestive or non-digestive disease) and paper quality (score more or less than 7) did not alter the association between CCAT1 expression and cancer prognosis but preoperative treatment did. And CCAT1 expression was an independent prognostic marker for overall survival in patients with cancer (pooled HR 2.195, 95%CI:1.316–3.664) using Cox multivariate analyses. The clinicopathological parameters analysis further showed that increased expression level of CCAT1 was correlated with tumor size, lymph node metastasis, TNM stage, distant metastasis, microvascular invasion and capsular formation in relevant cancers.

Conclusions

The meta-analysis results from present study suggested that increased expression level of CCAT1 was associated with poor prognosis and can serve as an independent biomarker. And the expression level of CCAT1 was associated with clinicopathological features in relevant cancers.

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.

CCAT2: A novel oncogenic long non-coding RNA in human cancers

Colon cancer-associated transcript 2 (CCAT2) was originally identified as an oncogenic long non-coding RNA in colorectal cancer. Since its discovery, the oncogenic role of CCAT2 has been increasingly demonstrated in human cancers. In this connection, CCAT2 upregulation is frequently reported and very often associated with tumour progression and poor clinical outcomes. Functionally, knockdown of CCAT2 could induce cancer cell apoptosis and suppress cell proliferation and invasiveness, suggesting that CCAT2 might be a therapeutic target. The present review summarized current literature concerning the expression and functional role of CCAT2 in human malignancies.

Expression of long non-coding RNA-HOTAIR in oral squamous cell carcinoma Tca8113 cells and its associated biological behavior

As a long noncoding RNA, HOX transcript antisense intergenic RNA (HOTAIR) is highly expressed in many types of tumors. However, its expression and function in oral squamous cell carcinoma (OSCC) cells and tissues remains largely unknown. We herein studied the biological functions of HOTAIR in OSCC Tca8113 cells. Real-time quantitative PCR showed that HOTAIR, p21 and p53 mRNA expressions in doxorubicin (DOX)-treated or γ-ray-irradiated Tca8113 cells were up-regulated. Knockdown of p53 expression inhibited DOX-induced HOTAIR up-regulation, suggesting that DNA damage-induced HOTAIR expression may be associated with p53. Transfection and CCK-8 assays showed that compared with the control group, overexpression of HOTAIR promoted the proliferation of Tca8113 cells, while interfering with its expression played an opposite role. Flow cytometry exhibited that HOTAIR overexpression decreased the rate of DOX-induced apoptosis. When HOTAIR expression was inhibited by siRNA, the proportions of cells in G₂/M and S phases increased and decreased respectively. Meanwhile, the rate of DOX-induced apoptosis rose. DNA damage-induced HOTAIR expression facilitated the proliferation of Tca8113 cells and decreased their apoptosis. However, whether the up-regulation depends on p53 still needs in-depth studies.

Long noncoding RNA, tissue differentiation-inducing nonprotein coding RNA is upregulated and promotes development of esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is one of the major causes of cancer death worldwide, especially in Eastern Asia. Due to the poor prognosis, it is necessary to further dissect the underlying mechanisms and explore therapeutic targets of ESCC. Recently, studies show that long noncoding RNAs (lncRNAs) have critical roles in diverse biological processes, including tumorigenesis. Increasing evidence indicates that some lncRNAs are widely involved in the development and progression of ESCC, such as HOTAIR, SPRY4-IT1 and POU3F3. An emerging lncRNA, tissue differentiation-inducing nonprotein coding RNA (TINCR), has been studied in human cutaneous squamous cell carcinoma and has critical biological function, but its role in ESCC remains unknown. Here, we evaluated the expression profile of TINCR and its biological function in ESCC. In a cohort of 56 patients, TINCR was significantly overexpressed in ESCC tissues compared with paired adjacent normal tissues. Further, in vitro silencing TINCR via small interfering RNA (siRNA) inhibited the proliferation, migration and invasion of ESCC cells. Meantime, siRNA treatment induced apoptosis and blocked the progression of cell cycle. Taken together, our study suggests that TINCR promotes proliferation, migration and invasion of ESCC cells, acting as a potential oncogene of ESCC.

Long Non-coding RNA HOTAIR Expression in Diffuse Large B-Cell Lymphoma: In Relation to Polycomb Repressive Complex Pathway Proteins and H3K27 Trimethylation

BACKGROUND

A long non-coding RNA hox transcript antisense intergenic RNA (HOTAIR) is involved in epigenetic regulation through chromatin remodeling by recruiting polycomb repressive complex 2 (PRC2) proteins (EZH2, SUZ12, and EED) that induce histone H3 trimethylation at lysine 27 (H3K27me3). Deregulation of c-MYC and interaction between c-MYC and EZH2 are well known in lymphomagenesis; however, little is known about the expression status of HOTAIR in diffuse large B-cell lymphomas (DLBCLs).

METHODS

The expression status of PRC2 (EZH2, SUZ12, and EED), H3K27me3, c-MYC, and BCL2 was analyzed using immunohistochemistry (n = 231), and HOTAIR was investigated by a quantification real-time polymerase chain reaction method (n = 164) in DLBCLs.

RESULTS

The present study confirmed the positive correlation among PRC2 proteins, H3K27me3, and c-MYC in DLBCLs. Expression level of HOTAIR was also positively correlated to EZH2 (p < .05, respectively). Between c-MYC and HOTAIR, and between c- MYC/BCL2 co-expression and HOTAIR, however, negative correlation was observed in DLBCLs (p < .05, respectively). High level of H3K27me3 was determined as an independent prognostic marker in poor overall survival (hazard ratio, 2.0; p = .023) of DLBCL patients. High expression of HOTAIR, however, was associated with favorable overall survival (p = .004) in the univariate analysis, but the impact was not significant in the multivariate analysis. The favorable outcome of DLBCL with HOTAIR high expression levels may be related to the negative correlation with c- MYC expression or c-MYC/BCL2 co-expression.

CONCLUSIONS

HOTAIR expression could be one of possible mechanisms for inducing H3K27me3 via EZH2-related PRC2 activation, and induced H3K27me3 may be strongly related to aggressive DLBCLs which show poor patient outcome.

Meta-analysis of the prognostic value of abnormally expressed lncRNAs in hepatocellular carcinoma

Many long noncoding RNAs (lncRNAs) have been reported to be abnormally expressed in hepatocellular carcinoma (HCC), and may have the potential to serve as prognostic markers. In this study, a meta-analysis was conducted to systematically evaluate the prognostic value of various lncRNAs in HCC. Eligible literatures were systematically collected from PubMed, Embase, Web of Science, and Cochrane Library (up to December 30, 2015). The main outcomes including overall survival, relapse-free survival, and disease-free survival were analyzed. Pooled hazard ratios (HRs) and 95% confidence intervals (95% CIs) were calculated using random- or fixed-effects models. A total of 2,991 patients with HCC in People’s Republic of China from 27 studies were included in the analysis. The level of lncRNAs showed a significant association with clinical outcomes. Abnormally elevated lncRNA transcription level predicted poor overall survival (HR: 1.68, 95% CI: 1.20–2.34, P=0.002; I²=75.5%, P=0.000) and relapse-free survival (HR: 2.08, 95% CI: 1.65–2.61, P<0.001; I²=24.0%, P=0.215), while no association was observed with disease-free survival of HCC patients (HR: 1.39, 95% CI: 0.51–3.78, P=0.524; I²=81.3%, P=0.005). Subgroup analysis further showed that lncRNA transcription level was significantly associated with tumor size (relative risk [RR]: 1.19, 95% CI: 1.01–1.39, P=0.035), microvascular invasion (RR: 1.44, 95% CI: 1.10–1.89, P=0.009), and portal vein tumor thrombus (RR: 1.50, 95% CI: 1.03–2.20, P=0.036). Publication bias and sensitivity analysis further confirmed the stability of our results. Our present meta-analysis indicates that abnormal lncRNA transcription level may serve as a promising indicator for prognostic evaluation of patients with HCC in People’s Republic of China.

Meta-analysis of the prognostic value of abnormally expressed lncRNAs in hepatocellular carcinoma

Many long noncoding RNAs (lncRNAs) have been reported to be abnormally expressed in hepatocellular carcinoma (HCC), and may have the potential to serve as prognostic markers. In this study, a meta-analysis was conducted to systematically evaluate the prognostic value of various lncRNAs in HCC. Eligible literatures were systematically collected from PubMed, Embase, Web of Science, and Cochrane Library (up to December 30, 2015). The main outcomes including overall survival, relapse-free survival, and disease-free survival were analyzed. Pooled hazard ratios (HRs) and 95% confidence intervals (95% CIs) were calculated using random- or fixed-effects models. A total of 2,991 patients with HCC in People's Republic of China from 27 studies were included in the analysis. The level of lncRNAs showed a significant association with clinical outcomes. Abnormally elevated lncRNA transcription level predicted poor overall survival (HR: 1.68, 95% CI: 1.20-2.34, P=0.002; I (2)=75.5%, P=0.000) and relapse-free survival (HR: 2.08, 95% CI: 1.65-2.61, P<0.001; I (2)=24.0%, P=0.215), while no association was observed with disease-free survival of HCC patients (HR: 1.39, 95% CI: 0.51-3.78, P=0.524; I (2)=81.3%, P=0.005). Subgroup analysis further showed that lncRNA transcription level was significantly associated with tumor size (relative risk [RR]: 1.19, 95% CI: 1.01-1.39, P=0.035), microvascular invasion (RR: 1.44, 95% CI: 1.10-1.89, P=0.009), and portal vein tumor thrombus (RR: 1.50, 95% CI: 1.03-2.20, P=0.036). Publication bias and sensitivity analysis further confirmed the stability of our results. Our present meta-analysis indicates that abnormal lncRNA transcription level may serve as a promising indicator for prognostic evaluation of patients with HCC in People's Republic of China.

The bright side of dark matter: lncRNAs in cancer

The traditional view of genome organization has been upended in the last decade with the discovery of vast amounts of non-protein-coding transcription. After initial concerns that this "dark matter" of the genome was transcriptional noise, it is apparent that a subset of these noncoding RNAs are functional. Long noncoding RNA (lncRNA) genes resemble protein-coding genes in several key aspects, and they have myriad molecular functions across many cellular pathways and processes, including oncogenic signaling. The number of lncRNA genes has recently been greatly expanded by our group to triple the number of protein-coding genes; therefore, lncRNAs are likely to play a role in many biological processes. Based on their large number and expression specificity in a variety of cancers, lncRNAs are likely to serve as the basis for many clinical applications in oncology.

Clinical prognostic value of metastasis-associated lung adenocarcinoma transcript 1 in various human cancers: an updated meta-analysis

BACKGROUND

Many studies have investigated the prognostic value of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) in human cancers. However, these studies were often limited by small sample sizes. Therefore, we performed this updated meta-analysis to summarize the potential value of MALAT1 as a biomarker for early treatment and to predict survival in various human malignant neoplasms, through the inclusion of the latest literature and improved methodology.

METHODS

Twelve eligible articles were systematically obtained from PubMed, Medline, Embase, Web of Science, China National Knowledge Infrastructure and the Cochrane Library, from inception up to June 30, 2015. Survival was assessed using pooled hazard ratios (HRs) and 95% confidence intervals (95% CIs).

RESULTS

By combining the results of 12 studies, we found elevated MALAT1 expression was associated with poor survival in most cancers, with a pooled HR of 1.90 (95% CI, 1.56-2.30) for overall survival (OS) and 3.06 (95% CI, 2.06-4.56) for recurrence-free survival/disease-free survival. Subgroup analyses according to ethnicity, tumor type, assay method, sample size, HR-calculation method and analysis type did not affect the predictive role of MALAT1 for OS in various cancer types. Further, by combining results from studies that used multivariate analyses, we found elevated MALAT1 was an independent prognostic factor for OS (HR = 1.98; 95% CI, 1.58-2.48).

CONCLUSIONS

MALAT1 could serve as a potential prognostic biomarker in various cancers and may be a potential therapeutic target for the treatment and early detection of recurrence.

The Long Noncoding RNA MALAT-1 is A Novel Biomarker in Various Cancers: A Meta-analysis Based on the GEO Database and Literature

Background: MALAT-1 is significantly overexpressed in various cancers, suggesting that it might be a potential biomarker of cancer.

Methods: A meta-analysis was performed using microarray data obtained via the Affymetrix Human Genome U133 Plus 2.0 platform found in the Gene Expression Omnibus (GEO) database and data obtained through a systematic search of PubMed and Web of Science. The pooled odds ratio (OR) and hazard ratio (HR) with 95% CI (Confidence interval) were used to judge the value of biomarkers.

Results: A total of 28 studies were included in this meta-analysis, comprising a total of 3573 patients. MALAT-1 was significantly linked with over survival (OS) (HR=1.58, 95%CI: 1.12-2.23), recurrence-free survival (RFS) (HR=2.32, 95% CI: 1.68-3.19) and death-free survival (DFS) (HR=3.28, 95% CI: 1.52-7.09). We found that MALAT-1 was a risk factor in the prognoses of lung cancer (HR=1.54, 95%CI: 1.01-2.34), digestive system cancer (HR=2.16, 95% CI: 1.34-3.48) and ovarian cancer (HR=3.98, 95% CI: 1.54-10.25). In contrast, MALAT-1 was a safe factor in the prognosis of B cell lineage cancer (HR=0.45, 95% CI: 0.33-0.61). MALAT-1 was also a risk factor of RFS in breast cancer (HR=1.97, 95% CI: 1.25-3.09) and the TNM stage in pancreatic cancer (OR=3.65, 95% CI: 1.86-7.18) and glioma (OR=4.30, 95% CI: 1.90-9.73) and was a safe factor in colorectal cancer (OR=0.17, 95% CI: 0.08-0.35). MALAT-1 was significantly associated with lymph node metastasis in clear cell carcinoma (OR=5.04, 95% CI: 2.36-10.78) and distant metastasis in pancreatic cancer (OR=11.64, 95% CI: 2.13-63.78).

Conclusions: MALAT-1 can serve as a molecular marker in different types of cancers.

Long Non-Coding RNAs As Potential Novel Prognostic Biomarkers in Colorectal Cancer

Colorectal cancer (CRC) is the fourth most common cause of death worldwide. Surgery is usually the first line of treatment for patients with CRC but many tumors with similar histopathological features show significantly different clinical outcomes. The discovery of robust prognostic biomarkers in patients with CRC is imperative to achieve more effective treatment strategies and improve patient's care. Recent progress in next generation sequencing methods and transcriptome analysis has revealed that a much larger part of the genome is transcribed into RNA than previously assumed. Collectively referred to as non-coding RNAs (ncRNAs), some of these RNA molecules such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been shown to be altered and to play critical roles in tumor biology. This discovery leads to exciting possibilities for personalized cancer diagnosis, and therapy. Many lncRNAs are tissue and cancer-type specific and have already revealed to be useful as prognostic markers. In this review, we focus on recent findings concerning aberrant expression of lncRNAs in CRC tumors and emphasize their prognostic potential in CRC. Further studies focused on the mechanisms of action of lncRNAs will contribute to the development of novel biomarkers for diagnosis and disease progression.

The tumour hypoxia induced non-coding transcriptome

Recent investigations have highlighted the importance of the non-coding genome in regions of hypoxia in tumours. Such regions are frequently found in solid tumours, and are associated with worse patient survival and therapy resistance. Hypoxia stabilises the transcription factors, hypoxia inducible factors (HIF1α and HIF2α) which coordinate transcriptomic changes that occur in hypoxia. The changes in gene expression induced by HIF1α and HIF2α contribute to many of the hallmarks of cancer phenotypes and enable tumour growth, survival and invasion in the hypoxic tumour microenvironment. Non-coding RNAs, in particular microRNAs (miRNAs), which regulate mRNA stability and translation, and long-non-coding RNAs (lncRNAs), which have diverse functions including chromatin modification and transcriptional regulation, are also important in enabling the key hypoxia regulated processes. They have roles in the regulation of metabolism, angiogenesis, autophagy, invasion and metastasis in the hypoxic microenvironment. Furthermore, HIF1α and HIF2α expression and stabilisation are also regulated by both miRNAs and lncRNAs. Here we review the recent developments in the expression, regulation and functions of miRNAs, lncRNAs and other non-coding RNA classes in tumour hypoxia.

LncRNAs and Esophageal Squamous Cell Carcinoma - Implications for Pathogenesis and Drug Development

LncRNAs are a group of ncRNA species longer than 200 nt, which have fundamental regulatory roles in diverse cellular processes and diseases progression. Esophageal cancer is a serious malignancy with respect to prognosis and mortality rate. It is among the five leading cancer types for the cancer deaths in males of middle age in the United States. In China, esophageal cancer is the fourth most frequently diagnosed cancer and the fourth leading cause of cancer death. The molecular mechanisms of esophageal cancer development are not fully understood, but emerging studies point out that lncRNAs may actively associate with the pathogenesis. In this review, we first provided an introduction of lncRNAs classifications. Then we focused on the recent findings on lncRNA expression and function in esophageal cancer development. Implications for pathogenesis and potential drug developments will also be discussed.

Hypoxia/lncRNA-AK123072/EGFR pathway induced metastasis and invasion in gastric cancer

OBJECTIVE

To investigate the role of long noncoding RNAs (lncRNAs) in hypoxia-induced gastric cancer (GC) metastasis and invasion.

METHODS

We investigated the differentially expressed lncRNAs resulting from hypoxia-induced GC and normoxia conditions using microarrays and validated our results through real-time quantitative polymerase chain reaction. The role of the targeting lncRNA was further detected by in vivo and in vitro assays.

RESULTS

We found an lncRNA, AK123072, which was up-regulated by hypoxia. AK123072 was frequently up-regulated in GC samples and promoted GC migration and invasion in vivo and in vitro. Furthermore, AK123072 could mediate the metastasis of hypoxia-induced GC cells. Next, we identified EGFR, which was a metastasis-related gene regulated by AK123072. In addition, we found that the expression of EGFR was positively correlated with that of AK123072 in the clinical GC samples used in our study. Furthermore, we found that the EGFR gene CpG island methylation was significantly increased in GC cells depleted of AK123072. Intriguingly, EGFR expression was also increased by hypoxia, and EGFR up-regulation by AK123072 mediated hypoxia-induced GC cell metastasis.

CONCLUSION

Our results identified hypoxia/lncRNA-AK123072/EGFR pathway in gastric cancer pathogenesis and this might help in the development of new therapeutics in clinics.

A functional HOTAIR rs12826786 C>T polymorphism is associated with breast cancer susceptibility and poor clinicopathological characteristics in a Turkish population: a hospital-based case-control study

Hox transcript antisense intergenic RNA (HOTAIR), a long non-coding RNA (lncRNA), is pervasively overexpressed and correlated with tumor invasion, progression, metastasis, and poor prognosis in various human cancers including breast cancer (BC) that plays a role as an oncogenic molecule. A common functional single-nucleotide polymorphism (SNP) (rs12826786 C>T) at the HOTAIR promoter has been reported to influence HOTAIR expression and gastric adenocarcinoma susceptibility, but relation of HOTAIR rs12826786 C>T polymorphism with BC susceptibility and clinicopathological characteristics has yet to be reported. To explore the association of the HOTAIR rs12826786 C>T polymorphism with the risk of BC in a Turkish population, a hospital-based case-control study was carried out consisting of 123 BC patients and 122 age-matched healthy controls. HOTAIR rs12826786 C>T polymorphism was determined by real-time polymerase chain reaction (PCR) using TaqMan assay. We found that women carrying TT genotype of HOTAIR rs12826786 C>T polymorphism had an increased risk of developing BC in both codominant (odds ratio (OR) = 2.24, 95 % confidence interval (CI) 1.05-4.81, P = 0.02) and recessive (OR = 2.49, 95 % CI 1.25-4.97, P = 0.008) inheritance models. Moreover, TT genotype of HOTAIR rs12826786 C>T polymorphism was significantly related with multiple clinicopathological characteristics concerned with worse BC progression such as advanced TNM stage (III and IV), larger tumor size (T3 and T4), and distant metastasis (M1), as well as poor histological grade (III) (P < 0.05). Because of our results put forward for the first time that TT genotype of HOTAIR rs12826786 C>T polymorphism might play crucial roles in genetic susceptibility and poor prognosis for BC in Turkish population, further independent studies are needed to confirm our results in a larger series, as well as in patients of distinct populations.

Genome-wide differential expression of synaptic long noncoding RNAs in autism spectrum disorder

A genome-wide differential expression of long noncoding RNAs (lncRNAs) was identified in blood specimens of autism spectrum disorder (ASD). A total of 3929 lncRNAs were found to be differentially expressed in ASD peripheral leukocytes, including 2407 that were upregulated and 1522 that were downregulated. Simultaneously, 2591 messenger RNAs (mRNAs), including 1789 upregulated and 821 downregulated, were also identified in ASD leukocytes. Functional pathway analysis of these lncRNAs revealed neurological pathways of the synaptic vesicle cycling, long-term depression and long-term potentiation to be primarily involved. Thirteen synaptic lncRNAs, including nine upregulated and four downregulated, and 19 synaptic mRNAs, including 12 upregulated and seven downregulated, were identified as being differentially expressed in ASD. Our identification of differential expression of synaptic lncRNAs and mRNAs suggested that synaptic vesicle transportation and cycling are important for the delivery of synaptosomal protein(s) between presynaptic and postsynaptic membranes in ASD. Finding of 19 lncRNAs, which are the antisense, bi-directional and intergenic, of HOX genes may lead us to investigate the role of HOX genes involved in the development of ASD. Discovery of the lncRNAs of SHANK2-AS and BDNF-AS, the natural antisense of genes SHANK2 and BDNF, respectively, indicates that in addition to gene mutations, deregulation of lncRNAs on ASD-causing gene loci presents a new approach for exploring possible epigenetic mechanisms underlying ASD. Our study also opened a new avenue for exploring the use of lncRNA(s) as biomarker(s) for the early detection of ASD.

Noncoding Genomics in Gastric Cancer and the Gastric Precancerous Cascade: Pathogenesis and Biomarkers

Gastric cancer is the fifth most common cancer and the third leading cause of cancer-related death, whose patterns vary among geographical regions and ethnicities. It is a multifactorial disease, and its development depends on infection by Helicobacter pylori (H. pylori) and Epstein-Barr virus (EBV), host genetic factors, and environmental factors. The heterogeneity of the disease has begun to be unraveled by a comprehensive mutational evaluation of primary tumors. The low-abundance of mutations suggests that other mechanisms participate in the evolution of the disease, such as those found through analyses of noncoding genomics. Noncoding genomics includes single nucleotide polymorphisms (SNPs), regulation of gene expression through DNA methylation of promoter sites, miRNAs, other noncoding RNAs in regulatory regions, and other topics. These processes and molecules ultimately control gene expression. Potential biomarkers are appearing from analyses of noncoding genomics. This review focuses on noncoding genomics and potential biomarkers in the context of gastric cancer and the gastric precancerous cascade.

Prognostic value of long noncoding RNA HOTAIR in digestive system malignancies

BACKGROUND AND AIM

HOX transcript antisense intergenic RNA (HOTAIR), a well-known long noncoding RNA, has been found to play significant roles in several tumors. However, the clinical application value of HOTAIR in digestive system malignancies remains to be clarified. We aimed to explore comprehensively the potential role of HOTAIR as a prognostic indicator in digestive system malignancies.

METHODS

Systematic search was performed in Pubmed, Embase, Cochrane Library, and Web of Science until July 5, 2014. A quantitative meta-analysis was conducted with standard statistical methods for eligible papers on the prognostic value of HOTAIR in digestive system cancers.

RESULTS

A total of 1059 patients from 13 studies were included in the meta-analysis. A significant association was found between HOTAIR abundance and poor overall survival (OS) of patients with digestive system malignancies, with pooled hazard ratio (HR) of 2.587 (95% confidence interval [CI]: 2.054-3.259, P < 0.001). By combining HRs from Cox multivariate analyses, we found HOTAIR was an independent prognostic factor for OS without obvious heterogeneity (HR: 2.405, 95% CI: 1.883-3.0722, P < 0.001). Subgroup analysis showed that tumor type, histology type, region, publication year, sample size, and quality score did not alter the predictive value of HOTAIR as an independent factor for survival. Meta-regression and sensitivity analysis both suggested the reliability of our findings. A slight publication bias was observed. After adjustment by nonparametric "trim-and-fill" method, the corrected HRs had no significant change.

CONCLUSION

HOTAIR could be exploited as a novel prognostic biomarker for patients with digestive system malignancies.

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.