A new avenue for obtaining insight into the functional characteristics of long noncoding RNAs associated with estrogen receptor signaling

Estrogen Receptor and Vascular Aging

Cardiovascular diseases remain an age-related pathology in both men and women. These pathologies are 3-fold more frequent in men than in women before menopause, although this difference progressively decreases after menopause. The vasculoprotective role of estrogens are well established before menopause, but the consequences of their abrupt decline on the cardiovascular risk at menopause remain debated. In this review, we will attempt to summarize the main clinical and experimental studies reporting the protective effects of estrogens against cardiovascular diseases, with a particular focus on atherosclerosis, and the impact of aging and estrogen deprivation on their endothelial actions. The arterial actions of estrogens, but also part of that of androgens through their aromatization into estrogens, are mediated by the estrogen receptor (ER)α and ERβ. ERs belong to the nuclear receptor family and act by transcriptional regulation in the nucleus, but also exert non-genomic/extranuclear actions. Beside the decline of estrogens at menopause, abnormalities in the expression and/or function of ERs in the tissues, and particularly in arteries, could contribute to the failure of classic estrogens to protect arteries during aging. Finally, we will discuss how recent insights in the mechanisms of action of ERα could contribute to optimize the hormonal treatment of the menopause.

Identification and characterization of functional long noncoding RNAs in cancer

Long noncoding RNAs (lncRNAs) have emerged as key regulators in a variety of cellular processes that influence disease states. In particular, many lncRNAs are genetically or epigenetically deregulated in cancer. However, whether lncRNA alterations are passengers acquired during cancer progression or can act as tumorigenic drivers is a topic of ongoing investigation. In this review, we examine the current methodologies underlying the identification of cancer-associated lncRNAs and highlight important considerations for evaluating their biological significance as cancer drivers.

GPER-regulated lncRNA-Glu promotes glutamate secretion to enhance cellular invasion and metastasis in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is a group of breast cancer with heterogeneity and poor prognosis and effective therapeutic targets are not available currently. TNBC has been recognized as estrogen-independent breast cancer, while the novel estrogen receptor, namely G protein-coupled estrogen receptor (GPER), was claimed to mediate estrogenic actions in TNBC tissues and cell lines. Through mRNA microarrays, lncRNA microarrays, and bioinformatics analysis, we found that GPER is activated by 17β-estradiol (E2) and GPER-specific agonist G1, which downregulates a novel lncRNA (termed as lncRNA-Glu). LncRNA-Glu can inhibit glutamate transport activity and transcriptional activity of its target gene VGLUT2 via specific binding. GPER-mediated reduction of lncRNA-Glu promotes glutamate transport activity and transcriptional activity of VGLUT2. Furthermore, GPER-mediated activation of cAMP-PKA signaling contributes to glutamate secretion. LncRNA-Glu-VGLUT2 signaling synergizes with cAMP-PKA signaling to increase autologous glutamate secretion in TNBC cells, which activates glutamate N-methyl-D-aspartate receptor (NMDAR) and its downstream CaMK and MEK-MAPK pathways, thus enhancing cellular invasion and metastasis in vitro and in vivo. Our data provide new insights into GPER-mediated glutamate secretion and its downstream signaling NMDAR-CaMK/MEK-MAPK during TNBC invasion. The mechanisms we discovered may provide new targets for clinical therapy of TNBC.

Microenvironment-regulated lncRNA-HAL is able to promote stemness in breast cancer cells

Multicellular Tumor Spheroids culture (MCTS) is an in vitro model mimicking the characteristics of the tumor microenvironment, such as hypoxia and acidosis, resulting in the presence of both proliferating and quiescent cell populations. lncRNA's is a novel group of regulatory molecules that participates in the acquisition of tumorigenic phenotypes. In the present work we evaluated the oncogenic association of an uncharacterized lncRNA (lncRNA-HAL) in the tumorigenic phenotype induced by the MCTS microenvironment. We measured lncRNA-HAL expression level in MCF-7-MCTS populations and under different hypoxic conditions by RT-qPCR. Afterwards, we silenced lncRNA-HAL expression by shRNAs and evaluated its effect in MCF-7 transcriptome (by RNAseq) and validated the modified cellular processes by proliferation, migration, and stem cells assays. Finally, we analyzed which proteins interacts with lncRNA-HAL by ChIRP assay, to propose a possible molecular mechanism for this lncRNA. We found that lncRNA-HAL is overexpressed in the internal quiescent populations (p27 positive populations) of MCF-7-MCTS, mainly in the quiescent stem cell population, being hypoxia one of the microenvironmental cues responsible of its overexpression. Transcriptome analysis of lncRNA-HAL knockdown MCF7 cells revealed that lncRNA-HAL effect is associated with proliferation, migration and cell survival mechanisms; moreover, lncRNA-HAL silencing increased cell proliferation and impaired cancer stem cell proportion and function, resulting in decreased tumor grafting in vivo. In addition, we found that this lncRNA was overexpressed in triple-negative breast cancer patients. Analysis by ChIRP assay showed that this nuclear lncRNA binds to histones and hnRNPs suggesting a participation at the chromatin level and transcriptional regulation. The results obtained in the present work suggest that the function of lncRNA-HAL is associated with quiescent stem cell populations, which in turn is relevant due to its implications in cancer cell survival and resistance against treatment in vivo. Altogether, our data highlights a new lncRNA whose expression is regulated by the tumor microenvironment and associated to stemness in breast cancer.

lnCAR: A Comprehensive Resource for lncRNAs from Cancer Arrays

Long noncoding RNAs (lncRNA) have emerged as promising biomarkers in cancer diagnosis, treatment, and prognosis. Recent studies suggest that a large number of coding gene expression microarray probes could be reannotated as lncRNAs. Microarray, once the most cutting-edge high-throughput gene expression technology, has been used for thousands of cancer studies and has brought invaluable resources for studying the functions of lncRNA in cancer development. However, a comprehensive lncRNA resource based on microarray data is still lacking. Here, we present lnCAR (lncRNAs from cancer arrays), a comprehensive open resource for providing expression profiles and prognostic landscape of lncRNAs derived from reannotation of public microarray data. Currently, lnCAR contains 52,300 samples for differential expression analysis and 12,883 samples for survival analysis from 10 cancer types. lnCAR allows users to interactively explore any annotated or novel lncRNAs. We believe lnCAR will serve as a valuable resource for the community focused on lncRNA research in cancer. SIGNIFICANCE: lnCAR, a new interactive tool of reannotated public cancer-related microarray data, provides expression profiles and prognostic landscapes of lncRNAs across thousands of samples and multiple cancer types.

Diosgenin protects against alveolar bone loss in ovariectomized rats via regulating long non-coding RNAs

The present study assessed the changes in long non-coding (lnc)RNA and mRNA expression profiles when diosgenin (DIO) exerted a potential osteoprotective effect on the alveolar bone of ovariectomized (OVX) rats. Female Wistar rats underwent a sham operation (SHAM group) or ovariectomy. OVX rats were treated using vehicle (OVX group), DIO (DIO group) or estradiol valerate (EV group) for 12 weeks. After treatment, the biomarkers of bone turnover in plasma and the microstructure of alveolar bone were assessed. lncRNA microarrays were applied to assess lncRNA and mRNA expression profiles in alveolar bone in the OVX and DIO group rats. Subsequently, the differentially expressed mRNAs associated with the comprehensive bone metabolism pathway in Ingenuity Pathway Analysis (IPA) were identified and regarded as key mRNAs. Based on some of the key mRNAs and all the differentially expressed lncRNAs, a coexpression network was established and this network was further analyzed to identify the top 6 lncRNAs with the highest closeness scores (pivotal lncRNAs). Finally, 6 modules showing interactions between pivotal lncRNAs and key mRNAs were constructed. All of the pivotal lncRNAs and key mRNAs were validated with reverse transcription-quantitative polymerase chain reaction. The present findings demonstrated that DIO suppressed the loss of alveolar bone in OVX rats, and the changes to the expression of some lncRNAs or mRNAs occurred in the alveolar bone of the rats in the DIO group. Twenty-four key mRNAs were identified during pathway analysis. Furthermore, 8/24 key mRNAs (Ctnnb1, Smad4, Tcf2, Sp7, Il1b, Il1r1, Tnf and Tnfrsf1a) were used to establish a coexpression network, which included 1,656 nodes and 5,341 edges. During network analysis, 6 pivotal lncRNAs (XR_008346, MRuc007iji, MRAK157089, MRAK076413, MRAK143591 and AB036696) were obtained, and 6 modules illustrating pivotal lncRNA-key mRNA interactions were identified. These results revealed that the anti-osteoporotic effect of DIO on alveolar bone may be associated with the promotion of a bone formation process through increasing the signaling of the Wnt and BMPs pathways and the inhibition of the bone resorption process through decreasing stimulators of osteoclastogenesis. To conclude, several pivotal lncRNAs may serve important roles in these processes via regulating some key mRNAs in the bone metabolism pathway.

The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases

Well characterized the connections among diseases, long non-coding RNAs (lncRNAs) and drugs are important for elucidating the key roles of lncRNAs in biological mechanisms in various biological states. In this study, we constructed a database called LNCmap (LncRNA Connectivity Map), available at http://www.bio-bigdata.com/LNCmap/, to establish the correlations among diseases, physiological processes, and the action of small molecule therapeutics by attempting to describe all biological states in terms of lncRNA signatures. By reannotating the microarray data from the Connectivity Map database, the LNCmap obtained 237 lncRNA signatures of 5916 instances corresponding to 1262 small molecular drugs. We provided a user-friendly interface for the convenient browsing, retrieval and download of the database, including detailed information and the associations of drugs and corresponding affected lncRNAs. Additionally, we developed two enrichment analysis methods for users to identify candidate drugs for a particular disease by inputting the corresponding lncRNA expression profiles or an associated lncRNA list and then comparing them to the lncRNA signatures in our database. Overall, LNCmap could significantly improve our understanding of the biological roles of lncRNAs and provide a unique resource to reveal the connections among drugs, lncRNAs and diseases.