Upregulation of Long Non-Coding RNA DRAIC Correlates with Adverse Features of Breast Cancer

Multifaced roles of the long non-coding RNA DRAIC in cancer progression

Long non-coding RNAs (lncRNA) are functional RNAs, with over 200 nucleotides in length and lacking protein-coding potential. Studies have indicated that lncRNAs are important gene regulators under physiological conditions. Aberrant lncRNA expression is associated with the initiation and progression of various diseases, including cancers. High-throughput transcriptome analyses have revealed thousands of lncRNAs as putative tumor suppressors or promoters in various cancers, but the detailed molecular mechanisms of each lncRNA remain unclear. Downregulated RNA In Cancer, inhibitor of cell invasion and migration (DRAIC) (also known as LOC145837 and RP11-279F6.1) is a lncRNA that inhibits or promotes cancer progression with several modes of action. DRAIC was originally identified as a tumor-suppressive lncRNA in prostate adenocarcinoma. Subsequent studies also revealed that it has an anti-tumor role in glioblastoma, triple-negative breast cancer, and stomach adenocarcinoma. However, DRAIC exhibits oncogenic functions in other malignancies, such as lung adenocarcinoma and esophageal carcinoma, indicating its highly context-dependent effects on cancer progression and clinical outcomes. DRAIC and its associated pathways regulate various biological processes, including proliferation, invasion, metastasis, autophagy, and neuroendocrine function. This review introduces the multifaceted roles of DRAIC, particularly in cancer progression, and discusses its biological significance and clinical implications.

A contrast set mining based approach for cancer subtype analysis

The task of detecting common and unique characteristics among different cancer subtypes is an important focus of research that aims to improve personalized therapies. Unlike current approaches mainly based on predictive techniques, our study aims to improve the knowledge about the molecular mechanisms that descriptively led to cancer, thus not requiring previous knowledge to be validated. Here, we propose an approach based on contrast set mining to capture high-order relationships in cancer transcriptomic data. In this way, we were able to extract valuable insights from several cancer subtypes in the form of highly specific genetic relationships related to functional pathways affected by the disease. To this end, we have divided several cancer gene expression databases by the subtype associated with each sample to detect which gene groups are related to each cancer subtype. To demonstrate the potential and usefulness of the proposed approach we have extensively analysed RNA-Seq gene expression data from breast, kidney, and colon cancer subtypes. The possible role of the obtained genetic relationships was further evaluated through extensive literature research, while its prognosis was assessed via survival analysis, finding gene expression patterns related to survival in various cancer subtypes. Some gene associations were described in the literature as potential cancer biomarkers while other results have been not described yet and could be a starting point for future research.

The current advances of lncRNAs in breast cancer immunobiology research

Breast cancer is the most frequently diagnosed malignancy and the leading cause of cancer-related death in women worldwide. Breast cancer development and progression are mainly associated with tumor-intrinsic alterations in diverse genes and signaling pathways and with tumor-extrinsic dysregulations linked to the tumor immune microenvironment. Significantly, abnormal expression of lncRNAs affects the tumor immune microenvironment characteristics and modulates the behavior of different cancer types, including breast cancer. In this review, we provide the current advances about the role of lncRNAs as tumor-intrinsic and tumor-extrinsic modulators of the antitumoral immune response and the immune microenvironment in breast cancer, as well as lncRNAs which are potential biomarkers of tumor immune microenvironment and clinicopathological characteristics in patients, suggesting that lncRNAs are potential targets for immunotherapy in breast cancer.

The emerging potentials of lncRNA DRAIC in human cancers

Long non-coding RNA (lncRNA) is a subtype of noncoding RNA that has more than 200 nucleotides. Numerous studies have confirmed that lncRNA is relevant during multiple biological processes through the regulation of various genes, thus affecting disease progression. The lncRNA DRAIC, a newly discovered lncRNA, has been found to be abnormally expressed in a variety of diseases, particularly cancer. Indeed, the dysregulation of DRAIC expression is closely related to clinicopathological features. It was also reported that DRAIC is key to biological functions such as cell proliferation, autophagy, migration, and invasion. Furthermore, DRAIC is of great clinical significance in human disease. In this review, we discuss the expression signature, clinical characteristics, biological functions, relevant mechanisms, and potential clinical applications of DRAIC in several human diseases.

DRAIC promotes growth of breast cancer by sponging miR-432-5p to upregulate SLBP

Mounting evidence suggests that lncRNAs can exert functions in cancer progression in multiple manners. In recent years, competing endogenous RNA (ceRNA) has been widely reported in human cancers as a lncRNA-dominant molecular pathway. The current study aimed at proving the role of lncRNA downregulated RNA in cancer (DRAIC) in breast cancer (BRCA) progression. To be specific, qRT-PCR assay was conducted to measure the expression of DRAIC and other downstream target genes. It was uncovered that DRAIC was expressed at a high level in BRCA cells. Functional analyses, including CCK-8, colony formation, and EdU assays demonstrated that DRAIC depletion suppressed BRCA cell proliferation. In addition, cell apoptosis was promoted due to DRAIC knockdown. The inhibitory effect of DRAIC reduction on BRCA cell migration and invasion was proven by transwell assays. Mechanistically, DRAIC was confirmed to predominantly distribute in the cytoplasm and could interact with miR-432-5p. In addition, stem-loop binding protein (SLBP) was verified to be a downstream target of miR-432-5p and was positively regulated by DRAIC. Taken together, DRAIC sponged miR-432-5p to enhance SLBP expression, by which malignant behaviors of BRCA cells were promoted. Our findings may help to provide a promising therapeutic target for BRCA patients.

A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response

Cancer cells within a tumour have heterogeneous phenotypes and exhibit dynamic plasticity. How to evaluate such heterogeneity and its impact on outcome and drug response is still unclear. Here, we transcriptionally profile 35,276 individual cells from 32 breast cancer cell lines to yield a single cell atlas. We find high degree of heterogeneity in the expression of biomarkers. We then train a deconvolution algorithm on the atlas to determine cell line composition from bulk gene expression profiles of tumour biopsies, thus enabling cell line-based patient stratification. Finally, we link results from large-scale in vitro drug screening in cell lines to the single cell data to computationally predict drug responses starting from single-cell profiles. We find that transcriptional heterogeneity enables cells with differential drug sensitivity to co-exist in the same population. Our work provides a framework to determine tumour heterogeneity in terms of cell line composition and drug response.

The tumor-suppressive long noncoding RNA DRAIC inhibits protein translation and induces autophagy by activating AMPK

Long noncoding RNAs (lncRNAs) are long RNA transcripts that do not code for proteins and have been shown to play a major role in cellular processes through diverse mechanisms. DRAIC, a lncRNA that is downregulated in castration-resistant advanced prostate cancer, inhibits the NF-κB pathway by inhibiting the IκBα kinase. Decreased DRAIC expression predicted poor patient outcome in gliomas and seven other cancers. We now report that DRAIC suppresses invasion, migration, colony formation and xenograft growth of glioblastoma-derived cell lines. DRAIC activates AMP-activated protein kinase (AMPK) by downregulating the NF-κB target gene GLUT1, and thus represses mTOR, leading to downstream effects, such as a decrease in protein translation and increase in autophagy. DRAIC, therefore, has an effect on multiple signal transduction pathways that are important for oncogenesis, namely, the NF-κB pathway and AMPK-mTOR-S6K/ULK1 pathway. The regulation of NF-κB, protein translation and autophagy by the same lncRNA explains the tumor-suppressive role of DRAIC in different cancers and reinforces the importance of lncRNAs as emerging regulators of signal transduction pathways. This article has an associated First Person interview with the first author of the paper.

An updated review on the therapeutic, diagnostic, and prognostic value of long non-coding RNAs in gastric cancer

As a novel group of non-coding RNAs, long non-coding RNA (lncRNAs) can substantially regulate various biological processes. Downregulated tumor-suppressive lncRNAs and upregulated oncogenic lncRNAs (onco-lncRNAs) have been implicated in gastric cancer (GC) development. These dysregulations have been associated with decreased chemosensitivity, inhibited apoptosis, and increased tumor migration in GC. Besides, growing evidence indicates that lncRNAs can be a valuable diagnostic and prognostic biomarker, and their expression levels are substantially associated with the clinicopathological features of affected patients. The current study aims to review the recent findings of the tumor-suppressive lncRNAs and onco-lncRNAs in GC development and highlight their therapeutic, diagnostic, and prognostic values in treating GC cells. Besides, it intends to highlight the future direction of lncRNAs in treating GC.

Prognostic Value of lncRNA DRAIC and miR-3940-3p in Lung Adenocarcinoma and Their Effect on Lung Adenocarcinoma Cell Progression

Purpose

Lung adenocarcinoma (LUAD) is a most common malignant tumor, even worse for diseases with relatively poor prognosis. Non-coding RNAs have the potential to be biomarkers for the prognosis of various cancers. LncRNA DRAIC and miR-3940-3p have been screened as dysregulated RNAs in LUAD. The clinical significance and biological function of lncRNA DRAIC and miR-3940-3p in LUAD were assessed in this study.

Patients and Methods

A total of 122 cases of LUAD patients with complete clinical information were enrolled. The expression levels of lncRNA DRAIC and miR-3940-3p were determined via RT-qPCR in LUAD tissues and cells. The relationship between lncRNA DRAIC or miR-3940-3p expression and the clinicopathological features of patients was analyzed based on the Pearson Chi-square test. For the prognostic value, the Kaplan–Meier plot and multi-variate Cox proportional regression analysis were introduced. Finally, the effect of lnc DRAIC and miR-3940-3p on the LUAD cellular function was investigated by CCK-8 and Transwell assay.

Results

lnc DRAIC was upregulated in LUAD tissues and cells, but miR-3940-3p was downregulated. Both of them showed significant associations with and TNM stage, lymph node metastasis, and a poor prognosis. Lnc-DRAIC and miR-3940-3p have the potential as independent prognostic factors for LUAD. Furthermore, the inhibition of lnc DRAIC can inhibit cell proliferation, migration, and invasion of LUAD partly as a ceRNA of miR-3940-3p.

Conclusion

lncRNA DRAIC/miR-3940-3p axis may be involved in the progression of LUAD and can be developed to promising prognostic factors, which may provide new insights into the treatment of LUAD.

Identification and Roles of miR-29b-1-3p and miR29a-3p-Regulated and Non-Regulated lncRNAs in Endocrine-Sensitive and Resistant Breast Cancer Cells

Despite improvements in the treatment of endocrine-resistant metastatic disease using combination therapies in patients with estrogen receptor α (ERα) primary tumors, the mechanisms underlying endocrine resistance remain to be elucidated. Non-coding RNAs (ncRNAs), including microRNAs (miRNA) and long non-coding RNAs (lncRNA), are targets and regulators of cell signaling pathways and their exosomal transport may contribute to metastasis. Previous studies have shown that a low expression of miR-29a-3p and miR-29b-3p is associated with lower overall breast cancer survival before 150 mos. Transient, modest overexpression of miR-29b1-3p or miR-29a-3p inhibited MCF-7 tamoxifen-sensitive and LCC9 tamoxifen-resistant cell proliferation. Here, we identify miR-29b-1/a-regulated and non-regulated differentially expressed lncRNAs in MCF-7 and LCC9 cells using next-generation RNA seq. More lncRNAs were miR-29b-1/a-regulated in LCC9 cells than in MCF-7 cells, including DANCR, GAS5, DSCAM-AS1, SNHG5, and CRND. We examined the roles of miR-29-regulated and differentially expressed lncRNAs in endocrine-resistant breast cancer, including putative and proven targets and expression patterns in survival analysis using the KM Plotter and TCGA databases. This study provides new insights into lncRNAs in endocrine-resistant breast cancer.

Long non-coding RNA regulating androgen receptor signaling in breast and prostate cancer

The human genome transcribe an array of RNAs that do not encode proteins and may act as mediators in the regulation of gene expression. Long non-coding RNAs (lncRNAs) are a group of non-coding RNAs consisting of more than 200 nucleotides of RNA transcripts that play important role in tumor development. Numerous lncRNAs have been characterized as functional transcripts associated with several biological processes and pathologic stages. Although the biological function and molecular mechanisms of lncRNAs remains to be explored, recent studies demonstrate aberrant expression of several lncRNAs linked with various human cancers. The present review summarizes the current knowledge of lncRNA expression patterns and mechanisms that contribute to carcinogenesis. In particular, we focus on lncRNAs regulating androgen receptor signaling pathways in prostate and breast cancer subtype having prognostic and therapeutic implications.

Thyroid Hormone Receptor Beta Induces a Tumor-Suppressive Program in Anaplastic Thyroid Cancer

The thyroid hormone receptor beta (TRβ), a key regulator of cellular growth and differentiation, is frequently dysregulated in cancers. Diminished expression of TRβ is noted in thyroid, breast, and other solid tumors and is correlated with more aggressive disease. Restoration of TRβ levels decreased tumor growth supporting the concept that TRβ could function as a tumor suppressor. Yet, the TRβ tumor suppression transcriptome is not well delineated and the impact of TRβ is unknown in aggressive anaplastic thyroid cancer (ATC). Here, we establish that restoration of TRβ expression in the human ATC cell line SW1736 (SW-TRβ) reduces the aggressive phenotype, decreases cancer stem cell populations and induces cell death in a T3-dependent manner. Transcriptomic analysis of SW-TRβ cells via RNA sequencing revealed distinctive expression patterns induced by ligand-bound TRβ and revealed novel molecular signaling pathways. Of note, liganded TRβ repressed multiple nodes in the PI3K/AKT pathway, induced expression of thyroid differentiation markers, and promoted proapoptotic pathways. Our results further revealed the JAK1-STAT1 pathway as a novel, T3-mediated, antitumorigenic pathway that can be activated in additional ATC lines. These findings elucidate a TRβ-driven tumor suppression transcriptomic signature, highlight unexplored therapeutic options for ATC, and support TRβ activation as a promising therapeutic option in cancers. IMPLICATIONS: TRβ-T3 induced a less aggressive phenotype and tumor suppression program in anaplastic thyroid cancer cells revealing new potential therapeutic targets.

Regulatory effect of LncRNA DRAIC/miR-149-5p/NFIB molecular network on autophagy of esophageal cancer cells and its biological behavior

OBJECTIVE

This experiment will explore the effect of LncRNA DRAIC/miR-149-5p/NFIB molecular network on esophageal cancer (EC) cells' biological behavior and autophagy.

METHODS

We bought human EC cells and normal esophageal epithelial cells HEEC. DRAIC, miR-149-5p and NFIB protein expression were tested. The low expression plasmid of DRAIC and empty vector of DRAIC, miR-149-5p miR-mimics, miR-149-5p inhibitors and negative control groups, NFIB high expression plasmid, NFIB low expression plasmid and empty vector were transfected into EC cells (Eca-109 and EC9706) to detect changes in cell biological behavior and autophagy protein expression. The targeted relationship between DRAIC/miR-149-5p/NFIB was verified through dual-luciferase report and pull-down experiment.

RESULTS

DRAIC and NFIB showed high expression in EC cells, while miR-149-5p showed low expression. Down-regulating DRAIC, NFIB and over-expressing miR-149-5p can inhibit EC cells' proliferation and invasion, and improve apoptosis and autophagy. Dual-luciferase report and pull-down experiment confirmed that DRAIC targeted miR-149-5p regulation, and down-regulating DRAIC could reverse miR-149-5p inhibitor's effect on the biological behavior of EC cells. However, dual-luciferase report revealed that miR-149-5p directly targeted NFIB, and miR-149-5p inhibitor could weaken the effect of down-regulating NFIB on apoptosis and autophagy of EC cells. Moreover, DRAIC has an effect on the autophagy of EC cells through miR-149-5p/NFIB.

CONCLUSION

LncRNA DRAIC is relevant to cell biology and autophagy of EC. In the future, DRAIC may be developed as a key gene for EC diagnosis and treatment.

Long noncoding RNAs and their link to cancer

The central dogma of molecular biology, developed from the study of simple organisms such as Escherichia coli, has up until recently been that RNA functions mainly as an information intermediate between a DNA sequence (gene), localized in the cell nucleus, serving as a template for the transcription of messenger RNAs, which in turn translocate into the cytoplasm and act as blueprints for the translation of their encoded proteins. There are a number of classes of non-protein coding RNAs (ncRNAs) which are essential for gene expression to function. The specific number of ncRNAs within the human genome is unknown. ncRNAs are classified on the basis of their size. Transcripts shorter than 200 nucleotides, referred to as ncRNAs, which group includes miRNAs, siRNAs, piRNAs, etc, have been extensively studied. Whilst transcripts with a length ranging between 200 nt up to 100 kilobases, referred to as lncRNAs, make up the second group, and are recently receiving growing concerns. LncRNAs play important roles in a variety of biological processes, regulating physiological functions of organisms, including epigenetic control of gene regulation, transcription and post-transcription, affecting various aspects of cellular homeostasis, including proliferation, survival, migration and genomic stability. LncRNAs are also capable of tuning gene expression and impact cellular signalling cascades, play crucial roles in promoter-specific gene regulation, and X-chromosome inactivation. Furthermore, it has been reported that lncRNAs interact with DNA, RNA, and/or protein molecules, and regulate chromatin organisation, transcriptional and post-transcriptional regulation. Consequently, they are differentially expressed in tumours, and they are directly linked to the transformation of healthy cells into tumour cells. As a result of their key functions in a wide range of biological processes, lncRNAs are becoming rising stars in biology and medicine, possessing potential active roles in various oncologic diseases, representing a gold mine of potential new biomarkers and drug targets.

LncRNA DRAIC inhibits proliferation and metastasis of gastric cancer cells through interfering with NFRKB deubiquitination mediated by UCHL5

Background

Long non-coding RNA (lncRNA) as a widespread and pivotal epigenetic molecule participates in the occurrence and progression of malignant tumors. DRAIC, a kind of lncRNA whose coding gene location is on 15q23 chromatin, has been found to be weakly expressed in a variety of malignant tumors and acts as a suppressor, but its characteristics and role in gastric cancer (GC) remain to be elucidated.

Methods

Sixty-seven primary GC tissues and paired paracancerous normal tissues were collected. Bioinformatics is used to predict the interaction molecules of DRAIC. DRAIC and NFRKB were overexpressed or interfered exogenously in GC cells by lentivirus or transient transfection. Quantitative real-time PCR (qPCR) and western blotting were used to evaluate the expression of DRAIC, UCHL5 and NFRKB. The combinations of DRAIC and NFRKB or UCHL5 and NFRKB were verified by RNA-IP and Co-IP assays. Ubiquitination-IP and the treatment of MG132 and CHX were used to detect the ubiquitylation level of NFRKB. The CCK-8 and transwell invasion and migration assays measured the proliferation, migration and invasion of GC cells.

Results

DRAIC is down-regulated in GC tissues and cell lines while its potential interacting molecules UCHL5 and NFRKB are up-regulated, and DRAIC is positively correlated with NFRKB protein instead of mRNA. Lower DRAIC and higher UCHL5 and NFRKB indicated advanced progression of GC patients. DRAIC could increase NFRKB protein significantly instead of NFRKB mRNA and UCHL5, and bind to UCHL5. DRAIC combined with UCHL5 and attenuated binding of UCHL5 and NFRKB, meanwhile promoting the degradation of NFRKB via ubiquitination, and then inhibited the proliferation and metastasis of GC cells, which can be rescued by oeNFRKB.

Conclusion

DRAIC suppresses GC proliferation and metastasis via interfering with the combination of UCHL5 and NFRKB and mediating ubiquitination degradation.

Long noncoding RNA DRAIC acts as a microRNA-122 sponge to facilitate nasopharyngeal carcinoma cell proliferation, migration and invasion via regulating SATB1

Increasing evidences have revealed that long noncoding RNAs (lncRNAs) are frequently involved in various cancers. However, the expression and function of lncRNA DRAIC in nasopharyngeal carcinoma (NPC) remain unknown. In this study, we found that DRAIC was significantly increased in NPC tissues. Increased expression of DRAIC was positively correlated with advanced clinical stages of NPC patients. Functional assays revealed that ectopic expression of DRAIC enhances NPC cell growth, migration and invasion. DRAIC knockdown represses NPC cell growth, migration and invasion. Mechanistically, we identified two miR-122 binding sites on DRAIC. RNA pull-down, RNA immunoprecipitation, and dual-luciferase reporter assays confirmed the binding of DRAIC to miR-122. Via binding of miR-122, DRAIC upregulated the expression of miR-122 target SATB1, which was abolished by the mutation of miR-122 binding sites on SATB1. Moreover, the oncogenic roles of DRAIC on NPC were reversed by the mutation of miR-122 binding sites on SATB1, simultaneous overexpression of miR-122, or depletion of SATB1. In addition, the expression of SATB1 was also increased and positively associated with that of DRAIC in NPC tissues. In conclusion, these findings revealed the important roles of DRAIC-miR-122-SATB1 axis in NPC and suggested that DRAIC may be a potential therapeutic target for NPC.

Long Noncoding RNA DRAIC Inhibits Prostate Cancer Progression by Interacting with IKK to Inhibit NF-κB Activation

DRAIC is a 1.7 kb spliced long noncoding RNA downregulated in castration-resistant advanced prostate cancer. Decreased DRAIC expression predicts poor patient outcome in prostate and seven other cancers, while increased DRAIC represses growth of xenografted tumors. Here, we show that cancers with decreased DRAIC expression have increased NF-κB target gene expression. DRAIC downregulation increased cell invasion and soft agar colony formation; this was dependent on NF-κB activation. DRAIC interacted with subunits of the IκB kinase (IKK) complex to inhibit their interaction with each other, the phosphorylation of IκBα, and the activation of NF-κB. These functions of DRAIC mapped to the same fragment containing bases 701-905. Thus, DRAIC lncRNA inhibits prostate cancer progression through suppression of NF-κB activation by interfering with IKK activity. SIGNIFICANCE: A cytoplasmic tumor-suppressive lncRNA interacts with and inhibits a major kinase that activates an oncogenic transcription factor in prostate cancer. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/5/950/F1.large.jpg.

Weighted Gene Coexpression Network Analysis Reveals the Critical lncRNAs and mRNAs in Development of Hirschsprung's Disease

Hirschsprung's disease (HSCR) is a common newborn defect. This study aimed to identify critical genes involved in the development of HSCR. Differently expressed genes (DEGs) of public data set GSE98502 were analyzed using paired t-test. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using Database for Annotation, Visualization and Integrated Discovery (DAVID) 6.8. Besides, Coexpression network of long noncoding RNAs (lncRNAs)-mRNAs (message RNA) were constructed using weighted gene coexpression network analysis. The key modules were filtered out by calculating the module-trait correlations. Then, hub genes were screened and the expression of these genes was further validated in an independent data set GSE96854. We identified 864 DEGs enriched in 19 GO biological functions such as negative regulation of growth and regulation of heart contraction; 11 KEGG pathways such as mineral absorption and protein digestion and absorption. lncRNAs-mRNAs coexpressed network was constructed, including 8 modules and 177 genes. Hub lncRNAs, including LINC00619, LINC00924, LINC00261, and DRAIC, were identified. Hub mRNAs, including CYCS, CCND1, BDKRB, ITGA6, and TNNC1, were mainly enriched in cancer pathways, p53 signaling pathway, and calcium signaling pathway. The expressions of the hub mRNAs were successfully validated by another independent GSE96854 data set. Our findings indicated the hub lncRNAs, including LINC00619, LINC00924, LINC00261, and DRAIC, as well as hub mRNAs, including CYCS, CCND1, BDKRB, ITGA6, and TNNC1, might involve in the progression of HSCR, and these genes might provide new clinical biomarkers for risk evaluation of HSCR.