ZFAS1: a long noncoding RNA associated with ribosomes in breast cancer cells

An update on the molecular mechanisms of ZFAS1 as a prognostic, diagnostic, or therapeutic biomarker in cancers

Zinc finger antisense 1 (ZFAS1), a newly discovered long noncoding RNA, is expressed in various tissues and organs and has been introduced an oncogenic gene in human malignancies. In various cancers, ZFAS1 regulates apoptosis, cell proliferation, the cell cycle, migration, translation, rRNA processing, and spliceosomal snRNP assembly; targets signaling cascades; and interacts with transcription factors via binding to key proteins and miRNAs, with conflicting findings on its effect on these processes. ZFAS1 is elevated in different types of cancer, like colorectal, colon, osteosarcoma, and gastric cancer. Considering the ZFAS1 expression pattern, it also has the potential to be a diagnostic or prognostic marker in various cancers. The current review discusses the mode of action of ZFAS1 in various human cancers and its regulation function related to chemoresistance comprehensively, as well as the potential role of ZFAS1 as an effective and noninvasive cancer-specific biomarker in tumor diagnosis, prognosis, and treatment. We expected that the current review could fill the current scientific gaps in the ZFAS1-related cancer causative mechanisms and improve available biomarkers.

Unveiling Polysomal Long Non-Coding RNA Expression on the First Day of Adipogenesis and Osteogenesis in Human Adipose-Derived Stem Cells

Understanding the intricate molecular mechanisms governing the fate of human adipose-derived stem cells (hASCs) is essential for elucidating the delicate balance between adipogenic and osteogenic differentiation in both healthy and pathological conditions. Long non-coding RNAs (lncRNAs) have emerged as key regulators involved in lineage commitment and differentiation of stem cells, operating at various levels of gene regulation, including transcriptional, post-transcriptional, and post-translational processes. To gain deeper insights into the role of lncRNAs' in hASCs' differentiation, we conducted a comprehensive analysis of the lncRNA transcriptome (RNA-seq) and translatome (polysomal-RNA-seq) during a 24 h period of adipogenesis and osteogenesis. Our findings revealed distinct expression patterns between the transcriptome and translatome during both differentiation processes, highlighting 90 lncRNAs that are exclusively regulated in the polysomal fraction. These findings underscore the significance of investigating lncRNAs associated with ribosomes, considering their unique expression patterns and potential mechanisms of action, such as translational regulation and potential coding capacity for microproteins. Additionally, we identified specific lncRNA gene expression programs associated with adipogenesis and osteogenesis during the early stages of cell differentiation. By shedding light on the expression and potential functions of these polysome-associated lncRNAs, we aim to deepen our understanding of their involvement in the regulation of adipogenic and osteogenic differentiation, ultimately paving the way for novel therapeutic strategies and insights into regenerative medicine.

Translational control by long non-coding RNAs

Long non-coding (lnc) RNAs, once considered as junk and useless, are now broadly recognized to have major functions in the cell. LncRNAs are defined as non-coding RNAs of more than 200 nucleotides, regulate all steps of gene expression. Their origin is diverse, they can arise from intronic, intergenic or overlapping region, in sense or antisense direction. LncRNAs are mainly described for their action on transcription, while their action at the translational level is more rarely cited. However, the bibliography in the field is more and more abundant. The present synopsis of lncRNAs involved in the control of translation reveals a wide field of regulation of gene expression, with at least nine distinct molecular mechanisms. Furthermore, it appears that all these lncRNAs are involved in various pathologies including cancer, cardiovascular and neurodegenerative diseases.

Role of long non-coding RNAs in cancer: From subcellular localization to nanoparticle-mediated targeted regulation

Long non-coding RNAs (lncRNAs) are a class of RNA transcripts more than 200 nucleotides in length that play crucial roles in cancer development and progression. With the rapid development of high-throughput sequencing technology, a considerable number of lncRNAs have been identified as novel biomarkers for predicting the prognosis of cancer patients and/or therapeutic targets for cancer therapy. In recent years, increasing evidence has shown that the biological functions and regulatory mechanisms of lncRNAs are closely associated with their subcellular localization. More importantly, based on the important roles of lncRNAs in regulating cancer progression (e.g., growth, therapeutic resistance, and metastasis) and the specific ability of nucleic acids (e.g., siRNA, mRNA, and DNA) to regulate the expression of any target genes, much effort has been exerted recently to develop nanoparticle (NP)-based nucleic acid delivery systems for in vivo regulation of lncRNA expression and cancer therapy. In this review, we introduce the subcellular localization and regulatory mechanisms of various functional lncRNAs in cancer and systemically summarize the recent development of NP-mediated nucleic acid delivery for targeted regulation of lncRNA expression and effective cancer therapy.

Translational landscape in human early neural fate determination

Gene expression regulation in eukaryotes is a multi-level process, including transcription, mRNA translation and protein turnover. Many studies have reported sophisticated transcriptional regulation during neural development, but the global translational dynamics are still ambiguous. Here, we differentiate human embryonic stem cells (ESCs) into neural progenitor cells (NPCs) with high efficiency and perform ribosome sequencing and RNA sequencing on both ESCs and NPCs. Data analysis reveals that translational controls engage in many crucial pathways and contribute significantly to regulation of neural fate determination. Furthermore, we show that the sequence characteristics of the untranslated region (UTR) might regulate translation efficiency. Specifically, genes with short 5'UTR and intense Kozak sequence are associated with high translation efficiency in human ESCs, whereas genes with long 3'UTR are related to high translation efficiency in NPCs. In addition, we have identified four biasedly used codons (GAC, GAT, AGA and AGG) and dozens of short open reading frames during neural progenitor differentiation. Thus, our study reveals the translational landscape during early human neural differentiation and provides insights into the regulation of cell fate determination at the translational level.

Inferring miRNA sponge modules across major neuropsychiatric disorders

The role of non-coding RNAs in neuropsychiatric disorders (NPDs) is an emerging field of study. The long non-coding RNAs (lncRNAs) are shown to sponge the microRNAs (miRNAs) from interacting with their target mRNAs. Investigating the sponge activity of lncRNAs in NPDs will provide further insights into biological mechanisms and help identify disease biomarkers. In this study, a large-scale inference of the lncRNA-related miRNA sponge network of pan-neuropsychiatric disorders, including autism spectrum disorder (ASD), schizophrenia (SCZ), and bipolar disorder (BD), was carried out using brain transcriptomic (RNA-Seq) data. The candidate miRNA sponge modules were identified based on the co-expression pattern of non-coding RNAs, sharing of miRNA binding sites, and sensitivity canonical correlation. miRNA sponge modules are associated with chemical synaptic transmission, nervous system development, metabolism, immune system response, ribosomes, and pathways in cancer. The identified modules showed similar and distinct gene expression patterns depending on the neuropsychiatric condition. The preservation of miRNA sponge modules was shown in the independent brain and blood-transcriptomic datasets of NPDs. We also identified miRNA sponging lncRNAs that may be potential diagnostic biomarkers for NPDs. Our study provides a comprehensive resource on miRNA sponging in NPDs.

A systematic review of the research progress of non-coding RNA in neuroinflammation and immune regulation in cerebral infarction/ischemia-reperfusion injury

Cerebral infarction/ischemia-reperfusion injury is currently the disease with the highest mortality and disability rate of cardiovascular disease. Current studies have shown that nerve cells die of ischemia several hours after ischemic stroke, which activates the innate immune response in the brain, promotes the production of neurotoxic substances such as inflammatory cytokines, chemokines, reactive oxygen species and − nitrogen oxide, and mediates the destruction of blood-brain barrier and the occurrence of a series of inflammatory cascade reactions. Meanwhile, the expression of adhesion molecules in cerebral vascular endothelial cells increased, and immune inflammatory cells such as polymorphonuclear neutrophils, lymphocytes and mononuclear macrophages passed through vascular endothelial cells and entered the brain tissue. These cells recognize antigens exposed by the central nervous system in the brain, activate adaptive immune responses, and further mediate secondary neuronal damage, aggravating neurological deficits. In order to reduce the above-mentioned damage, the body induces peripheral immunosuppressive responses through negative feedback, which increases the incidence of post-stroke infection. This process is accompanied by changes in the immune status of the ischemic brain tissue in local and systemic systems. A growing number of studies implicate noncoding RNAs (ncRNAs) as novel epigenetic regulatory elements in the dysfunction of various cell subsets in the neurovascular unit after cerebral infarction/ischemia-reperfusion injury. In particular, recent studies have revealed advances in ncRNA biology that greatly expand the understanding of epigenetic regulation of immune responses and inflammation after cerebral infarction/ischemia-reperfusion injury. Identification of aberrant expression patterns and associated biological effects of ncRNAs in patients revealed their potential as novel biomarkers and therapeutic targets for cerebral infarction/ischemia-reperfusion injury. Therefore, this review systematically presents recent studies on the involvement of ncRNAs in cerebral infarction/ischemia-reperfusion injury and neuroimmune inflammatory cascades, and elucidates the functions and mechanisms of cerebral infarction/ischemia-reperfusion-related ncRNAs, providing new opportunities for the discovery of disease biomarkers and targeted therapy. Furthermore, this review introduces clustered regularly interspaced short palindromic repeats (CRISPR)-Display as a possible transformative tool for studying lncRNAs. In the future, ncRNA is expected to be used as a target for diagnosing cerebral infarction/ischemia-reperfusion injury, judging its prognosis and treatment, thereby significantly improving the prognosis of patients.

Prostate cancer resistance leads to a global deregulation of translation factors and unconventional translation

Emerging evidence associates translation factors and regulators to tumorigenesis. However, our understanding of translational changes in cancer resistance is still limited. Here, we generated an enzalutamide-resistant prostate cancer (PCa) model, which recapitulated key features of clinical enzalutamide-resistant PCa. Using this model and poly(ribo)some profiling, we investigated global translation changes that occur during acquisition of PCa resistance. We found that enzalutamide-resistant cells exhibit an overall decrease in mRNA translation with a specific deregulation in the abundance of proteins involved in mitochondrial processes and in translational regulation. However, several mRNAs escape this translational downregulation and are nonetheless bound to heavy polysomes in enzalutamide-resistant cells suggesting active translation. Moreover, expressing these corresponding genes in enzalutamide-sensitive cells promotes resistance to enzalutamide treatment. We also found increased association of long non-coding RNAs (lncRNAs) with heavy polysomes in enzalutamide-resistant cells, suggesting that some lncRNAs are actively translated during enzalutamide resistance. Consistent with these findings, expressing the predicted coding sequences of known lncRNAs JPX, CRNDE and LINC00467 in enzalutamide-sensitive cells drove resistance to enzalutamide. Taken together, this suggests that aberrant translation of specific mRNAs and lncRNAs is a strong indicator of PCa enzalutamide resistance, which points towards novel therapeutic avenues that may target enzalutamide-resistant PCa.

Long non-coding RNAs in the pathogenesis of heart failure: A literature review

Heart failure (HF) is a common cardiovascular disorder and a major cause of mortality and morbidity in older people. The mechanisms underlying HF are still not fully understood, restricting novel therapeutic target discovery and drug development. Besides, few drugs have been shown to improve the survival of HF patients. Increasing evidence suggests that long non-coding RNAs (lncRNAs) serve as a critical regulator of cardiac physiological and pathological processes, regarded as a new target of treatment for HF. lncRNAs are versatile players in the pathogenesis of HF. They can interact with chromatin, protein, RNA, or DNA, thereby modulating chromatin accessibility, gene expressions, and signaling transduction. In this review, we summarized the current knowledge on how lncRNAs involve in HF and categorized them into four aspects based on their biological functions, namely, cardiomyocyte contractility, cardiac hypertrophy, cardiac apoptosis, and myocardial fibrosis. Along with the extensive laboratory data, RNA-based therapeutics achieved great advances in recent years. These indicate that targeting lncRNAs in the treatment of HF may provide new strategies and address the unmet clinical needs.

lncRNA MEG3 restrained the M1 polarization of microglia in acute spinal cord injury through the HuR/A20/NF-κB axis

The M1 polarization of microglia and neuroinflammation restrict the treatment of acute spinal cord injury (ASCI), and long non‐coding ribonucleic acid (lncRNA) maternally expressed gene 3 (MEG3) expression is lessened in ASCI. However, the function and mechanism of lncRNA MEG3 in the M1 polarization of microglia and neuroinflammation in ASCI are unclear. The expressions of lncRNA MEG3 in ASCI mouse spinal cord tissues and lipopolysaccharide (LPS)‐treated primary microglia and BV2 cells were quantified through a quantitative real‐time polymerase chain reaction. In‐vitro assays were conducted to explore the function of lncRNA MEG3 in the M1 polarization of microglia and neuroinflammation in ASCI. RNA degradation, RNA immunoprecipitation, RNA pull‐down, cycloheximide‐chase, and ubiquitination analyses were carried out to probe into the mechanism of lncRNA MEG3 in the M1 polarization of microglia and neuroinflammation in ASCI. The lncRNA MEG3 expression was lessened in the ASCI mouse spinal cord tissues and LPS‐treated primary microglia and BV2 cells, and the overexpression of lncRNA MEG3 restrained the M1 polarization of microglia and the neuroinflammation by regulating the NF‐κB signaling pathway. For the investigation of the potential mechanism of such, the overexpression of lncRNA MEG3 restrained the M1 polarization of microglia through the HuR/A20/NF‐κB axis and boosted the motor function recovery and neuroinflammation relief in the mice with SCI. The overexpression of lncRNA MEG3 restrained the M1 polarization of microglia through the HuR/A20/NF‐κB axis.

Ribosome-Associated ncRNAs (rancRNAs) Adjust Translation and Shape Proteomes

The regulation of protein synthesis is of extreme importance for cell survival in challenging environmental conditions. Modulating gene expression at the level of translation allows a swift and low-energy-cost response to external stimuli. In the last decade, an emerging class of regulatory ncRNAs, namely ribosome-associated non-coding RNAs (rancRNAs), has been discovered. These rancRNAs have proven to be efficient players in the regulation of translation as a first wave of stress adaptation by directly targeting the ribosome, the central enzyme of protein production. This underlying principle appears to be highly conserved, since rancRNAs are present in all three domains of life. Here, we review the major findings and mechanistic peculiarities of rancRNAs, a class of transcripts that is providing new and broader perspectives on the complexity of the ribosome and translation regulation.

Microproteins in skeletal muscle: hidden keys in muscle physiology

Recent advances in the transcriptomics, translatomics, and proteomics have led us to the exciting new world of functional endogenous microproteins. These microproteins have a small size and are derived from small open reading frames (smORFs) of RNAs previously annotated as non-coding (e.g. lncRNAs and circRNAs) as well as from untranslated regions and canonical mRNAs. The presence of these microproteins reveals a much larger translatable portion of the genome, shifting previously defined dogmas and paradigms. These findings affect our view of organisms as a whole, including skeletal muscle tissue. Emerging evidence demonstrates that several smORF-derived microproteins play crucial roles during muscle development (myogenesis), maintenance, and regeneration, as well as lipid and glucose metabolism and skeletal muscle bioenergetics. These microproteins are also involved in processes including physical activity capacity, cellular stress, and muscular-related diseases (i.e. myopathy, cachexia, atrophy, and muscle wasting). Given the role of these small proteins as important key regulators of several skeletal muscle processes, there are rich prospects for the discovery of new microproteins and possible therapies using synthetic microproteins.

Genomic and functional conservation of lncRNAs: lessons from flies

Over the last decade, the increasing interest in long non-coding RNAs (lncRNAs) has led to the discovery of these transcripts in multiple organisms. LncRNAs tend to be specifically, and often lowly, expressed in certain tissues, cell types and biological contexts. Although lncRNAs participate in the regulation of a wide variety of biological processes, including development and disease, most of their functions and mechanisms of action remain unknown. Poor conservation of the DNA sequences encoding for these transcripts makes the identification of lncRNAs orthologues among different species very challenging, especially between evolutionarily distant species such as flies and humans or mice. However, the functions of lncRNAs are unexpectedly preserved among different species supporting the idea that conservation occurs beyond DNA sequences and reinforcing the potential of characterising lncRNAs in animal models. In this review, we describe the features and roles of lncRNAs in the fruit fly Drosophila melanogaster, focusing on genomic and functional comparisons with human and mouse lncRNAs. We also discuss the current state of advances and limitations in the study of lncRNA conservation and future perspectives.

Long noncoding RNA and protein abundance in lncRNPs

Although long noncoding RNAs (lncRNAs) are generally expressed at low levels, emerging evidence has revealed that many play important roles in gene regulation by a variety of mechanisms as they engage with proteins. Given that the abundance of proteins often greatly exceeds that of their interacting lncRNAs, quantification of the relative abundance, or even the exact stoichiometry in some cases, within lncRNA-protein complexes is helpful for understanding of the mechanism(s) of action of lncRNAs. We discuss methods used to examine lncRNA and protein expression at the single cell, subcellular, and suborganelle levels, the average and local lncRNA concentration in cells, as well as how lncRNAs can modulate the functions of their interacting proteins even at a low stoichiometric concentration.

Dissecting the Biological Relevance and Clinical Impact of lncRNA MIAT in Multiple Myeloma

Simple Summary

The interest in the biological role and clinical impact of long non-coding RNAs (lncRNAs) in multiple myeloma (MM) is continuously expanding. Many studies, mainly involving solid tumors, have strongly suggested the MIAT oncogenic role; more recently, it has been suggested that MIAT may have a role in inducing Bortezomib resistance in MM. However, data concerning MIAT deregulation in MM are virtually absent. In this context, we investigated the expression pattern and the clinical relevance of the lncRNA MIAT in MM, taking advantage of the publicly available CoMMpass database. Our findings prompt further studies to elucidate better the significance of MIAT in MM.

Abstract

The biological impact of long non-coding RNAs (lncRNAs) in multiple myeloma (MM) is becoming an essential aspect of the investigation, which may contribute to understanding the disease’s complex pathobiology, providing novel potential therapeutic targets. Herein, we investigated the expression pattern and the clinical relevance of the lncRNA MIAT in MM, taking advantage of the publicly available CoMMpass database. MIAT expression in MM is highly heterogeneous and significantly associated with specific molecular lesions frequently occurring in MM. Transcriptome analyses of MM PCs from patients included in the CoMMpass database indicated a potential involvement of MIAT in different signaling pathways and ribosome biogenesis and assembly. These findings suggest that MIAT deregulation may play a pathogenetic role in MM by affecting both proliferation pathways and, indirectly, the translational process. Although MIAT expression levels seem not to be significantly associated with clinical outcome in multivariate analyses, high MIAT expression levels are associated with bortezomib resistance, this suggesting that MIAT targeting could overcome drug resistance in MM. These findings strongly prompt for further studies investigating the significance of MIAT in MM.

DeepLncLoc: a deep learning framework for long non-coding RNA subcellular localization prediction based on subsequence embedding

Long non-coding RNAs (lncRNAs) are a class of RNA molecules with more than 200 nucleotides. A growing amount of evidence reveals that subcellular localization of lncRNAs can provide valuable insights into their biological functions. Existing computational methods for predicting lncRNA subcellular localization use k-mer features to encode lncRNA sequences. However, the sequence order information is lost by using only k-mer features. We proposed a deep learning framework, DeepLncLoc, to predict lncRNA subcellular localization. In DeepLncLoc, we introduced a new subsequence embedding method that keeps the order information of lncRNA sequences. The subsequence embedding method first divides a sequence into some consecutive subsequences and then extracts the patterns of each subsequence, last combines these patterns to obtain a complete representation of the lncRNA sequence. After that, a text convolutional neural network is employed to learn high-level features and perform the prediction task. Compared with traditional machine learning models, popular representation methods and existing predictors, DeepLncLoc achieved better performance, which shows that DeepLncLoc could effectively predict lncRNA subcellular localization. Our study not only presented a novel computational model for predicting lncRNA subcellular localization but also introduced a new subsequence embedding method which is expected to be applied in other sequence-based prediction tasks. The DeepLncLoc web server is freely accessible at http://bioinformatics.csu.edu.cn/DeepLncLoc/, and source code and datasets can be downloaded from https://github.com/CSUBioGroup/DeepLncLoc.

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 Noncoding RNA ZFAS1 Promotes Progression of NSCLC via Regulating of miR-590-3p

The incidence and mortality rate of nonsmall cell lung cancer (NSCLC) are continuously increasing. Recently, the important roles of long noncoding ribonucleic acid (lncRNA) zinc finger antisense1 (ZFAS1) in the development of many disease have been proved. However, the roles of ZFAS1 in NSCLC are still not completely understood. Thus, this study aimed to explore the potential roles and underlying mechanisms of lncRNA ZFAS1 in the progression of NSCLC. Our results demonstrated that lncRNA ZFAS1 expression was significantly upregulated in NSCLC tissues and cell lines. Loss-of-function experiments revealed that lncRNA ZFAS1 inhibition could remarkably suppress NSCLC cells proliferation in vitro. Bioinformatic analysis and luciferase reporter assay revealed that lncRNA ZFAS1 directly interacted with miR-590-3p. Rescue experiments showed that miR-590-3p inhibitor reversed the cell proliferation function of lncRNA ZFAS1 knockdown in vitro. Furthermore, we confirmed that lncRNA ZFAS1 inhibited cell division cycle 42 (Cdc42) expression by regulating of miR-590-3p in NSCLC cells. Therefore, our study indicates that lncRNA ZFAS1/miR-590-3p axis is involved in NSCLC cell proliferation. It also suggests that lncRNA ZFAS1 is a putative tumor oncogene in NSCLC.

Long Intergenic Non-Coding RNAs in the Mammary Parenchyma and Fat Pad of Pre-Weaning Heifer Calves: Identification and Functional Analysis

Enhanced plane of nutrition at pre-weaning stage can promote the development of mammary gland especially heifer calves. Although several genes are involved in this process, long intergenic non-coding RNAs (lincRNAs) are regarded as key regulators in the regulated network and are still largely unknown. We identified and characterized 534 putative lincRNAs based on the published RNA-seq data, including heifer calves in two groups: fed enhanced milk replacer (EH, 1.13 kg/day, including 28% crude protein, 25% fat) group and fed restricted milk replacer (R, 0.45 kg/day, including 20% crude protein, 20% fat) group. Sub-samples from the mammary parenchyma (PAR) and mammary fat pad (MFP) were harvested from heifer calves. According to the information of these lincRNAs' quantitative trait loci (QTLs), the neighboring and co-expression genes were used to predict their function. By comparing EH vs R, 79 lincRNAs (61 upregulated, 18 downregulated) and 86 lincRNAs (54 upregulated, 32 downregulated) were differentially expressed in MFP and PAR, respectively. In MFP, some differentially expressed lincRNAs (DELs) are involved in lipid metabolism pathways, while, in PAR, among of DELs are involved in cell proliferation pathways. Taken together, this study explored the potential regulatory mechanism of lincRNAs in the mammary gland development of calves under different planes of nutrition.

The Role of LncRNAs in Translation

Long non-coding RNAs (lncRNAs), a group of non-protein coding RNAs with lengths of more than 200 nucleotides, exert their effects by binding to DNA, mRNA, microRNA, and proteins and regulate gene expression at the transcriptional, post-transcriptional, translational, and post-translational levels. Depending on cellular location, lncRNAs are involved in a wide range of cellular functions, including chromatin modification, transcriptional activation, transcriptional interference, scaffolding and regulation of translational machinery. This review highlights recent studies on lncRNAs in the regulation of protein translation by modulating the translational factors (i.e, eIF4E, eIF4G, eIF4A, 4E-BP1, eEF5A) and signaling pathways involved in this process as wells as their potential roles as tumor suppressors or tumor promoters.

MicroRNAs and long non-coding RNAs as novel regulators of ribosome biogenesis

Ribosome biogenesis is the fine-tuned, essential process that generates mature ribosomal subunits and ultimately enables all protein synthesis within a cell. Novel regulators of ribosome biogenesis continue to be discovered in higher eukaryotes. While many known regulatory factors are proteins or small nucleolar ribonucleoproteins, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) are emerging as a novel modulatory layer controlling ribosome production. Here, we summarize work uncovering non-coding RNAs (ncRNAs) as novel regulators of ribosome biogenesis and highlight their links to diseases of defective ribosome biogenesis. It is still unclear how many miRNAs or lncRNAs are involved in phenotypic or pathological disease outcomes caused by impaired ribosome production, as in the ribosomopathies, or by increased ribosome production, as in cancer. In time, we hypothesize that many more ncRNA regulators of ribosome biogenesis will be discovered, which will be followed by an effort to establish connections between disease pathologies and the molecular mechanisms of this additional layer of ribosome biogenesis control.

A systematic review of long non-coding RNAs with a potential role in breast cancer

The human transcriptome contains many non-coding RNAs (ncRNAs), which play important roles in gene regulation. Long noncoding RNAs (lncRNAs) are an important class of ncRNAs with lengths between 200 and 200,000 bases. Unlike mRNA, lncRNA lacks protein-coding features, specifically, open-reading frames, and start and stop codons. LncRNAs have been reported to play a role in the pathogenesis and progression of many cancers, including breast cancer (BC), acting as tumor suppressors or oncogenes. In this review, we systematically mined the literature to identify 65 BC-related lncRNAs. We then perform an integrative bioinformatics analysis to identify 14 lncRNAs with a potential regulatory role in BC. The biological function of these 14 lncRNAs, their regulatory mechanisms, and roles in the initiation and progression of BC are discussed in this review. Additionally, we elaborate on the current and future applications of lncRNAs as diagnostic and/or therapeutic biomarkers in BC.

Towards establishing extracellular vesicle-associated RNAs as biomarkers for HER2+ breast cancer

Extracellular vesicles (EVs) are emerging as key players in breast cancer progression and hold immense promise as cancer biomarkers. However, difficulties in obtaining sufficient quantities of EVs for the identification of potential biomarkers hampers progress in this area. To circumvent this obstacle, we cultured BT-474 breast cancer cells in a two-chambered bioreactor with CDM-HD serum replacement to significantly improve the yield of cancer cell-associated EVs and eliminate bovine EV contamination. Cancer-relevant mRNAs BIRC5 (Survivin) and YBX1, as well as long-noncoding RNAs HOTAIR, ZFAS1, and AGAP2-AS1 were detected in BT-474 EVs by quantitative RT-PCR. Bioinformatics meta-analyses showed that BIRC5 and HOTAIR RNAs were substantially upregulated in breast tumours compared to non-tumour breast tissue, warranting further studies to explore their usefulness as biomarkers in patient EV samples. We envision this effective procedure for obtaining large amounts of cancer-specific EVs will accelerate discovery of EV-associated RNA biomarkers for cancers including HER2+ breast cancer.

Towards establishing extracellular vesicle-associated RNAs as biomarkers for HER2+ breast cancer

Extracellular vesicles (EVs) are emerging as key players in breast cancer progression and hold immense promise as cancer biomarkers. However, difficulties in obtaining sufficient quantities of EVs for the identification of potential biomarkers hampers progress in this area. To circumvent this obstacle, we cultured BT-474 breast cancer cells in a two-chambered bioreactor with CDM-HD serum replacement to significantly improve the yield of cancer cell-associated EVs and eliminate bovine EV contamination. Cancer-relevant mRNAs BIRC5 (Survivin) and YBX1, as well as long-noncoding RNAs HOTAIR, ZFAS1, and AGAP2-AS1 were detected in BT-474 EVs by quantitative RT-PCR. Bioinformatics meta-analyses showed that BIRC5 and HOTAIR RNAs were substantially upregulated in breast tumours compared to non-tumour breast tissue, warranting further studies to explore their usefulness as biomarkers in patient EV samples. We envision this effective procedure for obtaining large amounts of cancer-specific EVs will accelerate discovery of EV-associated RNA biomarkers for cancers including HER2+ breast cancer.

Long non-coding RNA ZFAS1 promotes colorectal cancer tumorigenesis and development through DDX21-POLR1B regulatory axis

Increasing evidence supports long non-coding RNA-ZFAS1 as master protein regulators involved in a variety of human cancers. However, the molecular mechanism is not fully understood in colorectal cancer (CRC) and remains to be elucidated. Here, we uncovered a previously unreported mechanism linking RNA helicase DDX21 regulated by lncRNA ZFAS1 in control of POLR1B expression in CRC initiation and progression. Specifically, ZFAS1 exerted its oncogenic functions and was significantly up-regulated accompanied by elevated DDX21, POLR1B expression in CRC cells and tissues, which further closely associated with poor clinical outcomes. Notably, ZFAS1 knockdown dramatically suppressed CRC cell proliferation, invasion, migration, and increased cell apoptosis, which were contrary to the effect caused by ZFAS1 up-regulation. We further revealed that the inhibitory effect caused by ZFAS1 knockdown could be reversed by DDX21 overexpression in vitro and in vivo. Mechanistically, our research found that ZFAS1 could directly recruit DDX21 protein by harboring the specific motif (AAGA or CAGA). Finally, POLR1B was identified as the downstream target of DDX21 regulated by ZFAS1, which was also up-regulated in CRC cells and tissues and closely related to poor prognosis. The unrecognized ZFAS1/DDX21/POLR1B signaling regulation axis may provide new biomarkers and targets for CRC treatment and prognostic evaluation.

Emerging Roles of Long Noncoding RNAs in the Cytoplasmic Milieu

While the important functions of long noncoding RNAs (lncRNAs) in nuclear organization are well documented, their orchestrating and architectural roles in the cytoplasmic environment have long been underestimated. However, recently developed fractionation and proximity labelling approaches have shown that a considerable proportion of cellular lncRNAs is exported into the cytoplasm and associates nonrandomly with proteins in the cytosol and organelles. The functions of these lncRNAs range from the control of translation and mitochondrial metabolism to the anchoring of cellular components on the cytoskeleton and regulation of protein degradation at the proteasome. In the present review, we provide an overview of the functions of lncRNAs in cytoplasmic structures and machineries und discuss their emerging roles in the coordination of the dense intracellular milieu. It is becoming apparent that further research into the functions of these lncRNAs will lead to an improved understanding of the spatiotemporal organization of cytoplasmic processes during homeostasis and disease.

LncRNAs in Cancer: From garbage to Junk

Sequencing-based transcriptomics has significantly redefined the concept of genome complexity, leading to the identification of thousands of lncRNA genes identification of thousands of lncRNA genes whose products possess transcriptional and/or post-transcriptional regulatory functions that help to shape cell functionality and fate. Indeed, it is well-established now that lncRNAs play a key role in the regulation of gene expression through epigenetic and posttranscriptional mechanims. The rapid increase of studies reporting lncRNAs alteration in cancers has also highlighted their relevance for tumorigenesis. Herein we describe the most prominent examples of well-established lncRNAs having oncogenic and/or tumor suppressive activity. We also discuss how technical advances have provided new therapeutic strategies based on their targeting, and also report the challenges towards their use in the clinical settings.

Identification and analysis of key lncRNAs in malignant-transformed BEAS-2B cells induced with coal tar pitch by microarray analysis

This study aims to explore the key and differentially expressed long non-coding RNAs (lncRNAs) and elucidates their possible mechanisms in malignant-transformed Human bronchial epithelial (BEAS-2B) cells induced by coal tar pitch extracts (CTPE). BEAS-2B cells were stimulated with 2.4 μg/ml CTPE, then passaged for three times which were named CTPE1 and then passaged until passage 30 (CTPE30). The results showed that cells of CTPE30 appeared abnormal morphology. Furthermore, migration, clonality and proliferation of cells in CTPE group were significantly increased compared with those in control groups. However, the apoptosis of cells in CTPE group was inhibited. A total of 569 differentially expressed mRNAs and 707 differentially expressed lncRNAs were screened out, among which four lncRNAs were validated and were consistent with the microarray results. 32 target genes were screened out by Co-expression network. The study suggests that differentially expressed lncRNAs may play a potential role in lung carcinogenesis.

Competing Endogenous RNA Networks in the Epithelial to Mesenchymal Transition in Diffuse-Type of Gastric Cancer

Simple Summary

The diffuse-type of gastric cancer is associated with epithelial to mesenchymal transition. Loss of E-cadherin expression is the hallmark of this process and is largely due to the upregulation of the transcription factors ZEB1/2, Snail, Slug, and Twist1/2. However, miRNA and lncRNAs can also participate through these transcription factors which directly target E-cadherin. The competing endogenous RNA (ceRNA) network hypothesis state that lncRNA can sponge the miRNA pool that targets these transcripts. Based on the lack of said networks in the epithelial to mesenchymal transition, we performed a prediction analysis that resulted in novel ceRNA networks which will expand our knowledge of the molecular basis of the diffuse-type of gastric cancer.

Abstract

The diffuse-type of gastric cancer (DGC), molecularly associated with epithelial to mesenchymal transition (EMT), is increasing in incidence. Loss of E-cadherin expression is the hallmark of the EMT process and is largely due to the upregulation of the EMT-inducing transcription factors ZEB1/2, Snail, Slug, and Twist1/2. However, ncRNA, such as miRNA and lncRNAs, can also participate in the EMT process through the direct targeting of E-cadherin and other EMT-inducing transcription factors. Additionally, lncRNA can sponge the miRNA pool that targets these transcripts through competing endogenous RNA (ceRNA) networks. In this review, we focus on the role of ncRNA in the direct deregulation of E-cadherin, as well as EMT-inducing transcription factors. Based on the relevance of the ceRNA network hypothesis, and the lack of said networks in EMT, we performed a prediction analysis for all miRNAs and lncRNAs that target E-cadherin, as well as EMT-inducing transcription factors. This analysis resulted in novel predicted ceRNA networks for E-cadherin and EMT-inducing transcription factors (EMT-TFs), as well as the expansion of the molecular basis of the DGC.

LncRNA EGOT decreases breast cancer cell viability and migration via inactivation of the Hedgehog pathway

The long noncoding RNA (lncRNA) Eosinophil Granule Ontogeny Transcript (EGOT) has been reported to inhibit the proliferation and migration of glioma cells, and promote the development and progression of gastric cancer through the Hedgehog (Hh) signaling pathway. This study was conducted to assess the role of EGOT in the progression of breast cancer. We observed that EGOT is significantly down-regulated in breast cancer tissues and cell lines, and EGOT expression is negatively correlated with the Ki67 expression. Overexpression of EGOT in BT549 cells decreased cell viability and migration. In addition, overexpression of EGOT resulted in decreases in expression of key genes in the Hh pathway, including Gli1, smoothened protein, protein patched homolog 1 and Hedgehog-interacting protein (HHIP). Breast cancer tissues exhibited an increase in Gli1 expressions. Altered expression of Gli1, smoothened protein, protein patched homolog 1 and HHIP caused by EGOT overexpression were fully restored in cells transfected with plasmid complementory DNA (pcDNA) EGOT and treated with purmorphamine, an agonist of the Hh pathway. Cell viability and migration were also restored by purmorphamine. We conclude that lncRNA EGOT may inhibit breast cancer cell viability and migration via inactivation of the Hh pathway.

Noncoding RNA MaIL1 is an integral component of the TLR4-TRIF pathway

RNA has been proposed as an important scaffolding factor in the nucleus, aiding protein complex assembly in the dense intracellular milieu. Architectural contributions of RNA to cytosolic signaling pathways, however, remain largely unknown. Here, we devised a multidimensional gradient approach, which systematically locates RNA components within cellular protein networks. Among a subset of noncoding RNAs (ncRNAs) cosedimenting with the ubiquitin-proteasome system, our approach unveiled ncRNA MaIL1 as a critical structural component of the Toll-like receptor 4 (TLR4) immune signal transduction pathway. RNA affinity antisense purification-mass spectrometry (RAP-MS) revealed MaIL1 binding to optineurin (OPTN), a ubiquitin-adapter platforming TBK1 kinase. MaIL1 binding stabilized OPTN, and consequently, loss of MaIL1 blunted OPTN aggregation, TBK1-dependent IRF3 phosphorylation, and type I interferon (IFN) gene transcription downstream of TLR4. MaIL1 expression was elevated in patients with active pulmonary infection and was highly correlated with IFN levels in bronchoalveolar lavage fluid. Our study uncovers MaIL1 as an integral RNA component of the TLR4-TRIF pathway and predicts further RNAs to be required for assembly and progression of cytosolic signaling networks in mammalian cells.

LncRNA-mediated regulation of SOX9 expression in basal subtype breast cancer cells

Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer (BC) subtypes with a poor prognosis and high recurrence rate. Recent studies have identified vital roles played by several lncRNAs (long noncoding RNAs) in BC pathobiology. Cell type-specific expression of lncRNAs and their potential role in regulating the expression of oncogenic and tumor suppressor genes have made them promising cancer drug targets. By performing a transcriptome screen in an isogenic TNBC/basal subtype BC progression cell line model, we recently reported ∼1800 lncRNAs that display aberrant expression during breast cancer progression. Mechanistic studies on one such nuclear-retained lncRNA, linc02095, reveal that it promotes breast cancer proliferation by facilitating the expression of oncogenic transcription factor, SOX9. Both linc02095 and SOX9 display coregulated expression in BC patients as well in basal subtype BC cell lines. Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase II occupancy at the SOX9 gene body as well as defective SOX9 mRNA export, implying that linc02095 positively regulates SOX9 transcription and mRNA export. Finally, we identify a positive feedback loop in BC cells that controls the expression of both linc02095 and SOX9 Thus, our results unearth tumor-promoting activities of a nuclear lncRNA linc02095 by facilitating the expression of key oncogenic transcription factor in BC.

Long Non-Coding RNA EGOT Promotes the Malignant Phenotypes of Hepatocellular Carcinoma Cells and Increases the Expression of HMGA2 via Down-Regulating miR-33a-5p

Background

Chronic hepatitis C virus (HCV) infection is an important risk factor for hepatocellular carcinoma (HCC). EGOT is a long non-coding RNA (lncRNA) induced after HCV infection that increases viral replication by antagonizing the antiviral response. Interestingly, EGOT also acts as a crucial regulator in multiple cancers. However, its role in HCC remains unclear.

Methods

Real-time PCR (RT-PCR) was used to detect the expression of EGOT in HCC samples and cell lines. CCK-8 assay and colony formation assay were performed to evaluate the effect of EGOT on proliferation. Scratch healing assay and transwell assay were used to detect the changes of migration and invasion. Flow cytometry was used to detect the effect of EGOT on apoptosis. Interaction between EGOT and miR-33a-5p was determined by bioinformatics analysis, RT-PCR, and dual-luciferase reporter assay. Western blot was used to confirm that high mobility group protein A2 (HMGA2) could be modulated by EGOT.

Results

Compared with normal liver tissues, the expression level of EGOT in HCC tissues was significantly up-regulated. EGOT markedly regulated viability, migration and invasion of HCC cells. The expression level of EGOT was negatively correlated the expression level of miR-33a-5p. It is also confirmed that EGOT could specifically bind to miR-33a-5p and could reduce its expression, in turn, up-regulate the expression of HMGA2.

Conclusion

Our data imply that EGOT may be a novel therapeutic target for HCC, and highlights the key role of EGOT/miR-33a-5p/HMGA2 in the progression of this deadly disease.

The Long Non-coding RNA ZFAS1 Sponges miR-193a-3p to Modulate Hepatoblastoma Growth by Targeting RALY via HGF/c-Met Pathway

Hepatoblastoma (HB) is the most common and aggressive malignant hepatic neoplasm in childhood and the therapeutic outcomes remain undesirable due to its recurrence and metastasis. Recently, long non-coding RNA (lncRNA) zinc finger antisense 1 (ZFAS1) has been reported to be an oncogenic gene in multiple cancers. However, the expression status and specific role of ZFAS1 involved in cancer progression of human HB remain unknown. This study aimed to identify the role of ZFAS1/miR-193a-3p/RALY axis in the development of HB. Here we showed that the expression of ZFAS1 was significantly upregulated in both HB tissues and cell lines. High ZFAS1 expression was significantly associated with aggressive tumor phenotypes and poorer overall survival in HB. In vitro and in vivo function assays indicated that silencing of ZFAS1 significantly suppressed HB cell proliferation and invasion. Furthermore, miR-193a-3p was identified to be the target of ZFAS1. Subsequently, RALY was confirmed to be regulated by miR-193a-3p/ZFAS1 axis. Mechanistically, our results indicated that the ZFAS1 participated to the progression of HB via regulating the HGF/c-Met signaling. Collectively, these data demonstrated that ZFAS1 acted as an oncogene to promote initiation and progression of HB by regulating miR-193a-3p/RALY (RALY Heterogeneous Nuclear Ribonucleoprotein) axis via HGF/c-Met Pathway, which provides an efficient marker and new therapeutic target for HB.

Long noncoding RNA ZFAS1 promotes progression of papillary thyroid carcinoma by sponging miR-590-3p and upregulating HMGA2 expression

Background

Thyroid cancer is the most common endocrine malignancy, papillary thyroid carcinoma (PTC) is the main form of thyroid cancer. The long non-coding RNA (lncRNA) zinc finger antisense 1 (ZFAS1) is highly expressed in various cancer tissues and it has been shown to function as a tumor promoter in various cellular processes. However, the role of ZFAS1 in PTC is not well understood currently. Thus, this study aimed to explore the potential roles of ZFAS1 in the development and progression of PTC.

Material and methods

PTC tissues (n=80) and noncancerous tissues were collected. Gain- and loss-of-function assays were performed to determine the effect of ZFAS1 on proliferation in K-1 and TPC-1 cells. The ZFAS1/mir-590-3P/HMGA2 aixs were analysed in PTC cell lines.

Results

We found that the expression of ZFAS1 was increased in PTC tissues and four PTC cell lines (B-CPAP, IHH-4, TPC-1, and K-1). The gain- and loss-of-function assays showed that overexpressing ZFAS1 promoted cell proliferation and inhibited cell apoptosis in PTC cells in vitro. We demonstrated that knockdown of ZFAS1 inhibits tumor growth and upregulation of ZFAS1 promotes tumor growth in vivo. Bioinformatics analysis revealed that miR-590-3p targeted the 3ʹ-UTR of ZFAS1. The double luciferase reporter and RNA-binding protein immunoprecipitation assay demonstrated that miR-590-3p is a target of ZFAS1. Rescue experiments confirmed that miR-590-3p could reverse the effect of ZFAS1 on PTC cells. Moreover, we identified high mobility group AT-hook 2 (HMGA2) to be a downstream target of miR-590-3p and ZFAS1 which activates HMGA2 expression by sponging to miR-590-3p.

Conclusion

High ZFAS1 expression level was associated with the progression of PTC, and ZFAS1 contributed to PTC progression via miR-590-3p/HMGA2 regulatory aixs. Therefore, ZFAS1 might be a potential therapeutic target for PTC intervention.

Noncoding RNAs in development and teratology, with focus on effects of cannabis, cocaine, nicotine, and ethanol

Completion of the Human Genome Project has led to the identification of a large number of transcription start sites that are not paired with protein-coding genes, supporting the growing recognition of the abundance of encoded nonprotein-coding RNAs (ncRNAs) and their importance for speciation and species-specific development. Present in both plants and animals, ncRNAs vary in size, function, primary sequence, and secondary structure. While microRNAs (miRNAs) are the best known, there are a number of other ncRNAs (long[er] nonprotein-coding RNA, pseudogenes, circular RNAs, and so on) that have been shown to play an important role in the development either directly or via networks of proteins and other ncRNAs, including modulating the impact of miRNAs. Furthermore, these ncRNAs and their developmental regulatory networks are sensitive to teratogens such as ethanol, cannabis, cocaine, and nicotine. A better understanding of the developmental role of ncRNAs and their capacity to mediate teratogenesis is a necessary step in efforts to minimize the long-term consequences of developmental exposures to drugs-of-abuse. Moreover, with increasing awareness of the prevalence of polydrug use, experimental models will need to incorporate more complex drug exposure paradigms into meaningful assessments of developmental ncRNA function.

Global Positioning System: Understanding Long Noncoding RNAs through Subcellular Localization

The localization of long noncoding RNAs (lncRNAs) within the cell is the primary determinant of their molecular functions. LncRNAs are often thought of as chromatin-restricted regulators of gene transcription and chromatin structure. However, a rich population of cytoplasmic lncRNAs has come to light, with diverse roles including translational regulation, signaling, and respiration. RNA maps of increasing resolution and scope are revealing a subcellular world of highly specific localization patterns and hint at sequence-based address codes specifying lncRNA fates. We propose a new framework for analyzing sequencing-based data, which suggests that numbers of cytoplasmic lncRNA molecules rival those in the nucleus. New techniques promise to create high-resolution, transcriptome-wide maps associated with all organelles of the mammalian cell. Given its intimate link to molecular roles, subcellular localization provides a means of unlocking the mystery of lncRNA functions.

Long non-coding RNAs are emerging targets of phytochemicals for cancer and other chronic diseases

The long non-coding RNAs (lncRNAs) are the crucial regulators of human chronic diseases. Therefore, approaches such as antisense oligonucleotides, RNAi technology, and small molecule inhibitors have been used for the therapeutic targeting of lncRNAs. During the last decade, phytochemicals and nutraceuticals have been explored for their potential against lncRNAs. The common lncRNAs known to be modulated by phytochemicals include ROR, PVT1, HOTAIR, MALAT1, H19, MEG3, PCAT29, PANDAR, NEAT1, and GAS5. The phytochemicals such as curcumin, resveratrol, sulforaphane, berberine, EGCG, and gambogic acid have been examined against lncRNAs. In some cases, formulation of phytochemicals has also been used. The disease models where phytochemicals have been demonstrated to modulate lncRNAs expression include cancer, rheumatoid arthritis, osteoarthritis, and nonalcoholic fatty liver disease. The regulation of lncRNAs by phytochemicals can affect multi-steps of tumor development. When administered in combination with the conventional drugs, phytochemicals can also produce synergistic effects on lncRNAs leading to the sensitization of cancer cells. Phytochemicals target lncRNAs either directly or indirectly by affecting a wide variety of upstream molecules. However, the potential of phytochemicals against lncRNAs has been demonstrated mostly by preclinical studies in cancer models. How the modulation of lncRNAs by phytochemicals produce therapeutic effects on cancer and other chronic diseases is discussed in this review.

Control of nucleolar stress and translational reprogramming by lncRNAs

Under adverse environmental conditions, cells activate stress re-sponses that favour adaptation or, in case of irreversible damage, induce cell death. Multiple stress response pathways converge to downregulate ribo-some biogenesis and translation since these are the most energy consuming processes in the cell. This adaptive response allows preserving genomic stabil-ity and saving energy for the recovery. It follows that the nucleolus is a major sensor and integrator of stress responses that are then transmitted to the translation machinery through an intricate series of conserved events. Long non-coding RNAs (lncRNAs) are emerging as important regulators of stress-induced cascades, for their ability to mediate post-transcriptional responses. Consistently, many of them are specifically expressed under stress conditions and a few have been already functionally linked to these processes, thus fur-ther supporting a role in stress management. In this review we survey differ-ent archetypes of lncRNAs specifically implicated in the regulation of nucleo-lar functions and translation reprogramming during stress responses.

Zinc finger antisense 1: A long noncoding RNA with complex roles in human cancers

Zinc finger antisense 1 (ZFAS1), a newly identified long non-coding RNA, is a transcript antisense to the 5' end of the protein-coding gene zinc finger NFX1-type containing 1 which hosts three C/D-box small nucleolar RNAs (SNORDs) within sequential introns: Snord12, Snord12b, and Snord12c. ZFAS1 is dysregulated and acts as either an oncogene or a tumor suppressor in different human malignancies. ZFAS1 has been implicated in many aspects of carcinogenesis, including proliferation, invasion, metastasis, apoptosis, cell cycle, and drug resistance. The mechanisms underlying the effects of ZFAS1 are complex and involve multiple signaling pathways. In this review, the multiple pathological functions of ZFAS1 in diverse malignancies are systematically reviewed to elucidate the molecular basis of its biological roles and to provide new directions for future research.

LINC01585 functions as a regulator of gene expression by the CAMP/CREB signaling pathway in breast cancer

OBJECTIVE

Breast cancer is the leading cause of cancer death among women. Nowadays, long non-coding RNAs (lncRNAs) have been identified and emerged as critical bio-markers in breast cancer tumorigenesis and progression. However, only a handful of lncRNAs which are implicated in BC have been characterized. The underlying molecular mechanisms are still largely unknown.

METHODS

In this study, we explored 12 nominated lncRNAs at breast cancer susceptibility loci identified by genome-wide association studies to contribute to the risk and effects of breast cancer. We then analyzed these lncRNAs in a total of 132 pairs of breast cancer tissues and surrounding non-tumor tissues from southern China population.

RESULTS

Here, we report a novel lncRNA, LINC01585, is aberrantly down regulated during breast cancer (BC). Next, to explore the molecular mechanisms underlying the biological activity of LINC01585, we identified LINC01585 binding protein by RNA pull-down experiments. Functionally, we found that LINC01585 overexpression inhibited breast cancer proliferation and growth by prototypical experiments. Mechanistically, LINC01585 was located in nuclear and binding with NONO protein. Interestingly, when LINC01585 was down-expressed, NONO separated from LINC01585 and then interacted with CRTC. The complex promotes CAMP/CREB target gene transcription and thus promotes the growth of breast cancer.

CONCLUSIONS

A series of discoveries suggest to us that LINC01585 has a potential value in anti-carcinoma therapy and deserves further investigation.

ZFAS1: A novel vital oncogenic lncRNA in multiple human cancers

Long noncoding RNAs (lncRNAs) are a class of noncoding, endogenous, single‐stranded RNAs longer than 200 nucleotides in length that are transcribed by RNA polymerase II. Mounting evidence has indicated that lncRNAs play key roles in several physiological and pathological processes by modifying gene expression at the transcriptional, posttranscriptional, epigenetic, and translation levels. Many reports have demonstrated that lncRNAs function as potential oncogene or tumour suppressors and thus play vital regulatory roles in tumourigenesis and tumour progression. ZNFX1 antisense RNA 1 (ZFAS1), a novel lncRNA transcribed in the antisense orientation of zinc finger NFX1‐type containing 1(ZNFX1), was found to be increased in multiple cancers, such as gastric cancer and hepatocellular carcinoma, contributing to cancer development and progression. In the present review, we summarized recent progression on study of the functions and underlying molecular mechanisms of ZFAS1 related to occurrence and development of multiple cancers.

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.

Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

Background

Although the number of discovered long non-coding RNAs (lncRNAs) has increased dramatically, their biological roles have not been established. Many recent studies have used ribosome profiling data to assess the protein-coding capacity of lncRNAs. However, very little work has been done to identify ribosome-associated lncRNAs, here defined as lncRNAs interacting with ribosomes related to protein synthesis as well as other unclear biological functions.

Results

On average, 39.17% of expressed lncRNAs were observed to interact with ribosomes in human and 48.16% in mouse. We developed the ribosomal association index (RAI), which quantifies the evidence for ribosomal associability of lncRNAs over various tissues and cell types, to catalog 691 and 409 lncRNAs that are robustly associated with ribosomes in human and mouse, respectively. Moreover, we identified 78 and 42 lncRNAs with a high probability of coding peptides in human and mouse, respectively. Compared with ribosome-free lncRNAs, ribosome-associated lncRNAs were observed to be more likely to be located in the cytoplasm and more sensitive to nonsense-mediated decay.

Conclusion

Our results suggest that RAI can be used as an integrative and evidence-based tool for distinguishing between ribosome-associated and free lncRNAs, providing a valuable resource for the study of lncRNA functions.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4765-z) contains supplementary material, which is available to authorized users.

Role of long noncoding RNA ZFAS1 in proliferation, apoptosis and migration of chondrocytes in osteoarthritis

OBJECTIVE

This study aimed to investigate the role of long noncoding RNA (lncRNA) ZFAS1 in the development of osteoarthritis (OA) as well as to explore the potential molecular mechanisms.

MATERIAL AND METHODS

The expression of lncRNA ZFAS1 in OA chondrocytes was determined. After cell transfection, the effects of ZFAS1 overexpression on the viability, proliferation, apoptosis and migration of OA chondrocytes were detected. Additionally, the expression levels of Bcl-2, Bax, Caspase-3, and matrix metalloproteinases (MMP1 and MMP13) were determined. The expressions of Wnt3a signaling proteins, and the relationship between ZFAS1 and Wnt3a were detected as well.

RESULTS

The expression of ZFAS1 was down-regulated in OA chondrocytes compared with normal chondrocytes. Overexpression of ZFAS1 promoted the viability, proliferation and migration, and inhibited apoptosis and matrix synthesis of OA chondrocytes. Additionally, overexpressed ZFAS1 significantly decreased Wnt3a factors. The effects of ZFAS1 on OA chondrocytes were achieved by regulating Wnt3a signaling.

CONCLUSIONS

Our study demonstrates that ZFAS1 may promote chondrocyte proliferation, and migration, and decrease apoptosis and matrix synthesis in OA possible via targeting Wnt3a signaling. ZFAS1 provides a potential therapeutic target for OA treatment.

A link between expression level of long-non-coding RNA ZFAS1 in breast tissue of healthy women and obesity

BACKGROUND

Epidemiological and experimental literature indicates that the risk of breast cancer incidence is strongly linked to hormone-dependent factors, including reproductive history and obesity. However, the molecular mechanisms underlying the association between these factors and breast cancer risk are poorly understood. The aim of this study, therefore, was to determine whether obesity and reproductive history are associated with expression levels of two breast cancer-related long non-coding RNAs (lncRNAs), namely ZFAS1 and SRA1 in cancer-free breast tissues of women.

METHODS

In the current research, 145 healthy women were recruited, and the quantitative expression levels of the two lncRNAs were determined through qPCR assay after gathering the mammoplasty breast tissue samples.

RESULTS

It was found that women with body mass index (BMI)≥30 kg/m² and BMI 25-29 kg/m² show a low expression of ZFAS1 compared to the BMI<25 kg/m² (P=0.031 and P=0.027, respectively). Then, the correlation analysis disclosed a negative correlation of ZFAS1 low expression with increasing BMI (r=-0.194, P=0.019). Interestingly, this analysis demonstrated a negative correlation between low expression of the ZFAS1 and high BMI in women with menarche age below 14 (r=-221; P=0.028). Lastly, it was also revealed that there was a negative association of the low expression level of ZFAS1 with increasing BMI in women through regression models (B=-0.048, P=0.019).

CONCLUSIONS

These findings suggest interesting clues about the links between high BMI and the expression levels of ZFAS1 in non-diseased breasts that may help us better understand the underlying mechanisms through which obesity contributes to breast carcinogenesis. However, such results need more validations in future research.

Deciphering the roles of lncRNAs in breast development and disease

Breast cancer is the second leading cause of cancer related deaths in women. It is therefore important to understand the mechanisms underlying breast cancer development as well as raises the need for enhanced, non-invasive strategies for novel prognostic and diagnostic methods. The emergence of long non-coding RNAs (lncRNAs) as potential key players in neoplastic disease has received considerable attention over the past few years. This relatively new class of molecular regulators has been shown from ongoing research to act as critical players for key biological processes. Deregulated expression levels of lncRNAs have been observed in a number of cancers including breast cancer. Furthermore, lncRNAs have been linked to breast cancer initiation, progression, metastases and to limit sensitivity to certain targeted therapeutics. In this review we provide an update on the lncRNAs associated with breast cancer and mammary gland development and illustrate the versatility of such lncRNAs in gene control, differentiation and development both in normal physiological conditions and in diseased states. We also highlight the therapeutic and diagnostic potential of lncRNAs in cancer.