Long non-coding RNA UCA1 promotes breast tumor growth by suppression of p27 (Kip1)

Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines

The CRISPR/Cas has been recently shown to be a powerful genome-editing tool in a variety of organisms. However, these studies are mainly focused on protein-coding genes. The present study aims to determine whether this technology can be applied to non-coding genes. One of the challenges for knockout of non-coding genes is that a small deletion or insertion generated by the standard CRISPR/Cas system may not necessarily lead to functional loss of a given non-coding gene because of lacking an open reading frame, especially in polyploidy human cell lines. To overcome this challenge, we adopt a selection system that allows for marker genes to integrate into the genome through homologous recombination (HR). Moreover, we construct a dual guide RNA vector that can make two cuts simultaneously at designated sites such that a large fragment can be deleted. With these approaches, we are able to successfully generate knockouts for miR-21, miR-29a, lncRNA-21A, UCA1 and AK023948 in various human cell lines. Finally, we show that the HR-mediated targeting efficiency can be further improved by suppression of the non-homologous end joining pathway. Together, these results demonstrate the feasibility of knockout for non-coding genes by the CRISPR/Cas system in human cell lines.

Keeping abreast with long non-coding RNAs in mammary gland development and breast cancer

The majority of the human genome is transcribed, even though only 2% of transcripts encode proteins. Non-coding transcripts were originally dismissed as evolutionary junk or transcriptional noise, but with the development of whole genome technologies, these non-coding RNAs (ncRNAs) are emerging as molecules with vital roles in regulating gene expression. While shorter ncRNAs have been extensively studied, the functional roles of long ncRNAs (lncRNAs) are still being elucidated. Studies over the last decade show that lncRNAs are emerging as new players in a number of diseases including cancer. Potential roles in both oncogenic and tumor suppressive pathways in cancer have been elucidated, but the biological functions of the majority of lncRNAs remain to be identified. Accumulated data are identifying the molecular mechanisms by which lncRNA mediates both structural and functional roles. LncRNA can regulate gene expression at both transcriptional and post-transcriptional levels, including splicing and regulating mRNA processing, transport, and translation. Much current research is aimed at elucidating the function of lncRNAs in breast cancer and mammary gland development, and at identifying the cellular processes influenced by lncRNAs. In this paper we review current knowledge of lncRNAs contributing to these processes and present lncRNA as a new paradigm in breast cancer development.

Overexpression of long non-coding RNA UCA1 predicts a poor prognosis in patients with esophageal squamous cell carcinoma

INTRODUCTION

Long non-coding RNAs (lncRNAs) have been shown to have important regulatory roles in cancer biology, and the lncRNA UCA1 is upregulated in several cancers such as bladder cancer, breast cancer and colorectal cancer, however, the contributions of UCA1 to esophageal cancer remain largely unknown.

METHODS

Expression levels of lncRNA UCA1 in esophageal squamous cell carcinoma (ESCC) patients and esophageal cancer cell lines were evaluated by quantitative real-time PCR (qRT-PCR), and its association with overall survival of patients was analyzed by statistical analysis. Small interfering RNA was used to suppress UCA1 expression in esophageal cancer cell line. In vitro assays were conducted to further explore its underlying roles in tumor progression.

RESULTS

The relative level of UCA1 was significantly higher in ESCC tissues compared to the adjacent non-tumor tissues, and remarkably higher expression of UCA1 was found in esophageal cancer cell lines compared with the immortalized esophageal epithelial cell line NE1. The ESCC patients with higher UCA1 expression had an advanced clinical stage and a poorer prognosis than those with lower expression. In vitro assays, our data indicated that downregulation of UCA1 decrease cell proliferation, migration, and invasion ability.

CONCLUSIONS

lncRNA UCA1 might be considered as a novel molecule involved in ESCC progression, which provides a potential prognostic biomarker and therapeutic target.

Regulation of lncRNA expression

Long non-coding RNAs (lncRNAs) are series of transcripts with important biological functions. Various diseases have been associated with aberrant expression of lncRNAs and the related dysregulation of mRNAs. In this review, we highlight the mechanisms of dynamic lncRNA expression. The chromatin state contributes to the low and specific expression of lncRNAs. The transcription of non-coding RNA genes is regulated by many core transcription factors applied to protein-coding genes. However, specific DNA sequences may allow their unsynchronized transcription with their location-associated mRNAs. Additionally, there are multiple mechanisms involved in the post-transcriptional regulation of lncRNAs. Among these, microRNAs might have indispensible regulatory effects on lncRNAs, based on recent discoveries.

Molecular function and regulation of long non-coding RNAs: paradigms with potential roles in cancer

Different long non-coding RNAs (lncRNAs) are transcribed within the genome. Although initially argued to be spurious transcriptional noise, these RNAs play important roles in biological pathways, as shown by different studies. Also, there are some reports about the role of lncRNAs in different cancers. They can contribute to the development and progression of cancer by the functioning as oncogene or/and tumor suppressor molecules. In this review, we point to some important lncRNAs as examples which seem to be involved in cancer initiation/progression.

Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer

BACKGROUND

Long intergenic non-coding RNAs (lncRNAs) represent an emerging and under-studied class of transcripts that play a significant role in human cancers. Due to the tissue- and cancer-specific expression patterns observed for many lncRNAs it is believed that they could serve as ideal diagnostic biomarkers. However, until each tumor type is examined more closely, many of these lncRNAs will remain elusive.

RESULTS

Here we characterize the lncRNA landscape in lung cancer using publicly available transcriptome sequencing data from a cohort of 567 adenocarcinoma and squamous cell carcinoma tumors. Through this compendium we identify over 3,000 unannotated intergenic transcripts representing novel lncRNAs. Through comparison of both adenocarcinoma and squamous cell carcinomas with matched controls we discover 111 differentially expressed lncRNAs, which we term lung cancer-associated lncRNAs (LCALs). A pan-cancer analysis of 324 additional tumor and adjacent normal pairs enable us to identify a subset of lncRNAs that display enriched expression specific to lung cancer as well as a subset that appear to be broadly deregulated across human cancers. Integration of exome sequencing data reveals that expression levels of many LCALs have significant associations with the mutational status of key oncogenes in lung cancer. Functional validation, using both knockdown and overexpression, shows that the most differentially expressed lncRNA, LCAL1, plays a role in cellular proliferation.

CONCLUSIONS

Our systematic characterization of publicly available transcriptome data provides the foundation for future efforts to understand the role of LCALs, develop novel biomarkers, and improve knowledge of lung tumor biology.

Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer

Background

Long intergenic non-coding RNAs (lncRNAs) represent an emerging and under-studied class of transcripts that play a significant role in human cancers. Due to the tissue- and cancer-specific expression patterns observed for many lncRNAs it is believed that they could serve as ideal diagnostic biomarkers. However, until each tumor type is examined more closely, many of these lncRNAs will remain elusive.

Results

Here we characterize the lncRNA landscape in lung cancer using publicly available transcriptome sequencing data from a cohort of 567 adenocarcinoma and squamous cell carcinoma tumors. Through this compendium we identify over 3,000 unannotated intergenic transcripts representing novel lncRNAs. Through comparison of both adenocarcinoma and squamous cell carcinomas with matched controls we discover 111 differentially expressed lncRNAs, which we term lung cancer-associated lncRNAs (LCALs). A pan-cancer analysis of 324 additional tumor and adjacent normal pairs enable us to identify a subset of lncRNAs that display enriched expression specific to lung cancer as well as a subset that appear to be broadly deregulated across human cancers. Integration of exome sequencing data reveals that expression levels of many LCALs have significant associations with the mutational status of key oncogenes in lung cancer. Functional validation, using both knockdown and overexpression, shows that the most differentially expressed lncRNA, LCAL1, plays a role in cellular proliferation.

Conclusions

Our systematic characterization of publicly available transcriptome data provides the foundation for future efforts to understand the role of LCALs, develop novel biomarkers, and improve knowledge of lung tumor biology.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0429-8) contains supplementary material, which is available to authorized users.

Functional significance of long non-coding RNAs in breast cancer

Most of the genome is transcribed to transcripts of no protein-coding potential. However, these transcripts do not represent transcriptional 'noise', rather they play an important role in cellular metabolism and development. Non-coding transcripts of 200 bases to 100 kb length are termed as long non-coding RNAs, majority of which are yet to be characterised thoroughly. Long non-coding RNAs (lncRNAs) play a significant role in cellular process ranging from transcriptional to post-transcriptional regulation. In this review, we highlight the recent efforts to characterise the major functions of lncRNAs in breast cancer. lncRNA expression is altered in several cancer types. Further, the aberrant regulation of lncRNAs promotes tumour development as they are involved in several cancer-associated pathways.

Coordinated control of senescence by lncRNA and a novel T-box3 co-repressor complex

Cellular senescence is a crucial tumor suppressor mechanism. We discovered a CAPERα/TBX3 repressor complex required to prevent senescence in primary cells and mouse embryos. Critical, previously unknown roles for CAPERα in controlling cell proliferation are manifest in an obligatory interaction with TBX3 to regulate chromatin structure and repress transcription of CDKN2A-p16^INK and the RB pathway. The IncRNA UCA1 is a direct target of CAPERα/TBX3 repression whose overexpression is sufficient to induce senescence. In proliferating cells, we found that hnRNPA1 binds and destabilizes CDKN2A-p16^INK mRNA whereas during senescence, UCA1 sequesters hnRNPA1 and thus stabilizes CDKN2A-p16^INK. Thus CAPERα/TBX3 and UCA1 constitute a coordinated, reinforcing mechanism to regulate both CDKN2A-p16^INK transcription and mRNA stability. Dissociation of the CAPERα/TBX3 co-repressor during oncogenic stress activates UCA1, revealing a novel mechanism for oncogene-induced senescence. Our elucidation of CAPERα and UCA1 functions in vivo provides new insights into senescence induction, and the oncogenic and developmental properties of TBX3.

DOI:http://dx.doi.org/10.7554/eLife.02805.001

Cell division and growth are essential for survival. But it is equally important that cells can stop dividing, because failing to do so can lead to the uncontrolled tumor growth seen in cancer. One such quality control mechanism is called senescence, which stops the growth and multiplication of cells that are old, damaged or behaving in ways that may harm the organism. All cells eventually stop dividing and undergo senescence, but a number of factors may trigger the process early, such as DNA damage, stress or the appearance of cancer-causing proteins.

Senescence can be harmful if it occurs too early in life and interferes with normal growth. Severe birth defects—including fatal heart problems and limb malformations—occur if senescence is inappropriately triggered early in development. Mutations in a gene encoding a protein called TBX3 have been linked to these severe birth defects.

Normally, TBX3 stops the production of other proteins that trigger senescence in early development, and helps to maintain stable conditions in adult cells. Understanding how it does so could help scientists understand normal cell function and aging, and also help to find ways to trigger senescence in cancerous cells.

Kumar et al. found that a protein called CAPERα—for short Coactivator of AP1 and Estrogen Receptor—forms a complex with TBX3 that stops cells dividing in living organisms in at least two different ways. One way is by altering how DNA is folded. The other way involves a non-coding strand of RNA from a gene called UCA1: this RNA prevents the degradation of proteins that stop cell division.

In normal proliferating cells, the CAPERα/TBX3 protein complex prevents the production of UCA1 RNA. In contrast, in cells that received a cancer causing stimulus, TBX3 and CAPERα physically separate: this activates production of UCA1 RNA and causes senescence. Further studies will be required to establish exactly how the CAPERα/TBX3 protein complex interacts with DNA and RNA to control senescence and prevent cancer.

DOI:http://dx.doi.org/10.7554/eLife.02805.002

Natural antisense transcripts

Recent years have seen the increasing understanding of the crucial role of RNA in the functioning of the eukaryotic genome. These discoveries, fueled by the achievements of the FANTOM, and later GENCODE and ENCODE consortia, led to the recognition of the important regulatory roles of natural antisense transcripts (NATs) arising from what was previously thought to be 'junk DNA'. Roughly defined as non-coding regulatory RNA transcribed from the opposite strand of a coding gene locus, NATs are proving to be a heterogeneous group with high potential for therapeutic application. Here, we attempt to summarize the rapidly growing knowledge about this important non-coding RNA subclass.

Regulation of mammary epithelial cell homeostasis by lncRNAs

The epithelial cells of the mammary gland develop primarily after birth and undergo surges of hormonally regulated proliferation, differentiation, and apoptosis during both puberty and pregnancy. Thus, the mammary gland is a useful model to study fundamental processes of development and adult tissue homeostasis, such as stem and progenitor cell regulation, cell fate commitment, and differentiation. Long noncoding RNAs (lncRNAs) are emerging as prominent regulators of these essential processes, as their extraordinary versatility allows them to modulate gene expression via diverse mechanisms at both transcriptional and post-transcriptional levels. Not surprisingly, lncRNAs are also aberrantly expressed in cancer and promote tumorigenesis by disrupting vital cellular functions, such as cell cycle, survival, and migration. In this review, we first broadly summarize the functions of lncRNAs in mammalian development and cancer. Then we focus on what is currently known about the role of lncRNAs in mammary gland development and breast cancer. This article is part of a Directed Issue entitled: The Non-coding RNA Revolution.