NEAT1: A novel cancer‐related long non‐coding RNA

Abstract

Aberrant overexpression of the long non‐coding RNA NEAT1 (nuclear paraspeckle assembly transcript 1) has been documented in different types of solid tumours, such as lung cancer, oesophageal cancer, colorectal cancer and hepatocellular carcinoma, in which its high levels are associated with poor prognosis. In contrast, NEAT1 is downregulated in acute promyelocytic leukaemia where it promotes leucocyte differentiation. In this review, we provide an overview of current evidence concerning the oncogenic role and potential clinical utilities of NEAT1. Further investigations are warranted to elucidate the upstream and downstream mechanisms of NEAT1 overexpression.

1. Introduction

While recent genome‐wide studies indicated that about 70% of human genome is transcribed into RNA, and only less than 2% of the human genome codes for protein.1, 2, 3 With the completion of the Encyclopedia of DNA Elements (ENCODE) project, it is now known non‐coding RNAs (ncRNAs), including short and long non‐coding RNAs (lncRNAs), are key regulatory RNAs transcribed from non‐protein‐coding DNA sequences.4, 5, 6 LncRNAs are ncRNAs that are longer than 200 nucleotides in length.7, 8 Accumulating evidence has shown that lncRNAs are aberrantly expressed in cancer and play critical roles in tumourigenesis.9, 10 In this connection, lncRNAs have been shown to regulate cellular processes that are pertinent to cancer development, including cell cycle progression, apoptosis and metastasis.11, 12, 13 Importantly, many studies have shown that lncRNAs might serve as biomarkers for cancer diagnosis and prognostication.14, 15

Nuclear paraspeckle assembly transcript 1 (NEAT1) is a novel lncRNA localized specifically to nuclear paraspeckles,16 which are irregularly shaped compartments found in the nucleus’ interchromatin space.17 NEAT1 expression is upregulated in many human malignancies, including lung, oesophageal and gastric cancers but downregulated in acute promyelocytic leukaemia.18, 19, 20, 21, 22 The present review summarizes the deregulation of NEAT1 in human cancers in relation to its associated mechanisms and potential clinical utilities.

2. NEAT1: Structure and biological functions

NEAT1 is transcribed from the familial tumour syndrome multiple endocrine neoplasia type 1 locus, which is located on chromosome 11. The NEAT1 gene encodes two transcriptional variants, namely NEAT1‐1 (3.7 kb in length) and NEAT1‐2 (23 kb in length) (Figure  1). The two variants, both localized to nuclear paraspeckles, share the same promoter with different 3′‐end processing mechanisms.23 NEAT1 is an important nuclear component in which its knockdown results in the disintegration of paraspeckles. Although the exact function of nuclear paraspeckles remains unclear,24 they have been implicated in the development of corpus luteum and mammary gland as well as myeloid differentiation.25 At the cellular level, nuclear paraspeckles have been shown to migrate from the nucleus to the cytoplasm and participates in regulation of gene expression by keeping mRNAs in the nucleus for editing.26, 27 The subcellular localization of NEAT1 as detected by RNA fluorescence in situ hybridization is shown in this paper. 28

Figure 1.

Genomic structure of NEAT1‐1 and NEAT1‐2. A screenshot was captured from UCSC genome browser

2.1. Non‐small cell lung cancers

Lung cancer makes up 13% of all new cancer diagnosis and contributes to ~1.6 million deaths worldwide in 2012. Lung cancer will continue to be the top cancer killer over the next three decades. Twice as many people will be living with lung cancer in 2040 compared to 2010. About 80% of lung cancers are non‐small cell lung cancers (NSCLC). Current management of lung cancer depends on its histological (adenocarcinoma, large‐cell, squamous cell carcinoma) and molecular (EGFR activating mutation and ALK rearrangement) subtype.29 For NSCLC, surgery remains the standard treatment in stage I and II diseases. Concurrent chemoradiotherapy is the therapeutic standard in patients with locally advanced NSCLC. Platinum‐based chemotherapy also improves survival in patients with metastatic NSCLC. In addition, specific subsets of NSCLC patients will benefit from targeted agents, including bevacizumab (vascular endothelial growth factor antibody), erlotinib and gefitinib (tyrosine kinase inhibitors of epidermal growth factor receptor) and crizotinib (tyrosine kinase inhibitor of anaplastic lymphoma kinase). The efficacy of immunotherapy with pembrolizumab (a humanized monoclonal antibody against programmed death 1) has also been demonstrated in advanced, PD‐L1‐positive NSCLC.30

The expression and clinicopathological significance of NEAT1 have been profiled in NSCLCs. The relative levels of NEAT1 were significantly elevated in NSCLC tissues compared with the adjacent non‐cancer lung tissues. Moreover, higher NEAT1 expression was positively correlated with patient age, vascular invasion, lymphatic metastasis and tumour‐node‐metastasis (TNM) staging.31 Another study showed that circulating NEAT1 levels were significantly higher in NSCLC patients’ plasma.32 These results suggested that increased NEAT1 expression might be associated with progression of NSCLC where circulating NEAT1 could be used as a diagnostic marker. NEAT1 has also been shown to enhance the sensitivity of NSCLC cells to cisplatin by upregulating CTR1 (copper transporter 1). Mechanistically, NEAT1 function as a competing endogenous lncRNA by sponging hsa‐miR‐98‐5p to alleviate its repression on CTR1.33 In addition, NEAT1 could sponge hsa‐miR‐377‐3p to derepress E2F3, which is a key oncogene in promoting NSCLC.34

2.2. Oesophageal squamous cell carcinoma

Oesophageal cancer is the Eighth most common cancer worldwide, with more than 480 000 new cases and 400 000 deaths annually. Two major histological subtypes of oesophageal cancer, namely oesophageal squamous cell carcinoma (ESCC) and oesophageal adenocarcinoma, account for more than 95% of all cases. The former is the most dominant type of oesophageal cancer in most countries outside the US and is associated with cigarette smoking and alcohol consumption. Although multiple modalities, including chemotherapy (docetaxel, cisplatin plus 5‐fluorouracil), radiotherapy and surgery, have been proposed for the treatment of ESCC, prognostic outcomes of most cases remain unsatisfactory with the overall 3‐year survival rates less than 50% even with surgery.35

NEAT1 expression was higher in ESCC tissues and cell lines as compared with their normal counterparts. In addition, elevated NEAT1 levels were significantly correlated with tumour size, clinical stage and lymph node metastasis. High expression of NEAT1 was also significantly associated with poor overall survival in ESCC patients independent of other clinicopathological parameters. Functional characterization demonstrated that increased NEAT1 expression could promote ESCC cell proliferation, migration and invasion. These findings indicated that high NEAT1 expression is a predictive factor for unfavourable clinical outcomes in ESCC patients in which NEAT1 functions as an oncogene.19

2.3. Laryngeal squamous cell carcinoma

Laryngeal cancer is the Eleventh most common cancer worldwide, in which laryngeal squamous cell carcinoma (LSCC) accounts for approximately 85%–90% of all cases. Despite therapeutic advances in recent years, the clinical outcome for patients with advanced laryngeal cancer remains dismal and has not improved in the past two decades.36

NEAT1 expression was significantly upregulated in LSCC compared with the adjacent non‐neoplastic tissues. Moreover, higher NEAT1 expression was associated with advanced clinical stage and lymph nodemetastasis. NEAT1 knockdown significantly suppressed cell proliferation and increased apoptosis in LSCC cell lines. More importantly, the growth of LSCC xenografts was significantly retarded in mice injected with lentivirus expressing NEAT1 small‐interfering RNA. Mechanistically, NEAT1 knockdown upregulated miR‐107 to repress CDK6 (a cyclin‐dependent kinase) expression in LSCC cells. These data suggested that NEAT1 overexpression is oncogenic in the development of LSCC in which NEAT1 might serve as a potential therapeutic target.37

2.4. Colorectal cancer

Colorectal cancer (CRC) is the third most common cancer and the fourth leading cause of cancer‐related death worldwide. It has been estimated that about one‐fifth of patients present with metastases at diagnosis, and more than half of the remainder eventually developed disseminating disease. These subsets of patients usually survive less than 5 years due to metastasis.38 Early diagnosis of CRC with non‐invasive methods is therefore an area of active investigation.39

NEAT1 expression was elevated in 72% (172/239) of CRC tissues relative to corresponding normal counterparts. In addition, increased NEAT1 expression level was associated with poor differentiation, metastasis, invasion, as well as TNM staging. High NEAT1 expression was associated with shorter disease‐free survival and overall survival in CRC patients. Importantly, Cox's proportional hazards analysis demonstrated that high NEAT1 expression served as an independent marker of poor prognosis, suggesting NEAT1 might serve as a prognostic marker for CRC.40 Another study showed that whole‐blood NEAT1 levels were significantly higher in CRC patients than in normal controls, demonstrating a high distinguishing accuracy. Functionally, knockdown of NEAT1‐1 decreased cell proliferation and invasion in vitro while knockdown of NEAT1‐2 increased cell growth. Furthermore, high expression of NEAT1‐1 was associated with poorer overall survival, whereas NEAT1‐2 was associated with better overall survival. These results suggested that expression of NEAT1, in particular the variant NEAT1‐1, might serve as a novel biomarker for diagnosis and prognostication of patients with CRC.41

2.5. Hepatocellular cancer

The epidemiology of hepatocellular carcinoma (HCC) is under dynamic change. In some Asian countries, HCC incidence is decreasing because of reduced consumption of aflatoxin B1‐contaminated food and infant immunization against hepatitis B virus. However, HCC incidence is rising in many Western countries as a result of prevalent chronic hepatitis C virus infection.42 Currently, there is no effective systemic therapy for HCC.

Guo and colleagues evaluated the expression and function of NEAT1 in HCC. They showed that NEAT1 expression was higher in HCC tissues as compared with the adjacent non‐cancerous tissues. Moreover, high NEAT1 expression was significantly associated with advanced TNM stages, metastasis, number of tumour nodes and the infiltration of tumour cells. NEAT1 expression was also positively associated with the expression of several genes, including MDTH, NM23 and MALAT1. These findings indicated that NEAT1 might be useful as a prognostic marker in HCC.43 A recent study further demonstrated that NEAT1 is recurrently mutated in HCC.44

2.6. Breast cancer

Breast cancer is the leading cause of cancer death in women and its incidence rates are increasing. Breast cancer is divided into four major molecular subtypes (ie, luminal A, luminal B, triple negative/basal‐like and HER2 type) in most studies and its heterogeneity poses clinical challenges to its diagnosis and treatment.45

Aberrant activation of hypoxia‐inducible factor and its downstream transcriptional responses is common in breast cancer and may contribute to stem cell phenotpye,46 epithelial mesenchymal transition47 and bone metastasis.48 Choudhry and colleagues demonstrated that NEAT1 was among the most hypoxia‐induced lncRNAs in MCF‐7 breast cancer cells.49 Further study demonstrated that induction of F11R (also known as junctional adhesion molecule 1, JAM1) upon hypoxia was dependent on NEAT1. In this regard, increased NEAT1 expression in hypoxia promoted cell proliferation and clonogenic survival as well as decreased apoptosis. High expression of NEAT1 was also correlated with shorter survival in patients with breast cancer, suggesting that NEAT1 could play a central role in HIF‐mediated transcriptional regulation and the hypoxia‐induced phenotypic changes in breast cancer.50

2.7. Ovarian cancer

Ovarian carcinoma is a heterogeneous group of neoplasms with the serous, endometrioid, clear cell and mucinous tumours as the four most common subtypes.51 NEAT1 was significantly upregulated in Stage III serous ovarian carcinoma as compared with the normal human ovary.52 Pils and colleagues performed genome‐wide expression analysis in leucocytes isolated from 44 epithelial ovarian cancer patients and 19 normal controls. They identified 13 differentially expressed genes, including NEAT1. They concluded that NEAT1, in combination of 12 remaining genes and 6 plasma proteins, might discriminate patients with epithelial ovarian cancer from normal controls with a sensitivity of 95.6% and a specificity of 99.6%. These results indicated that NEAT1 might be used as a diagnostic biomarker for ovarian cancer.53

2.8. Prostate cancer

Prostate cancer is one of the most common types of cancer in men with about one man in seven diagnosed with it during his lifetime. However, most prostate cancers develop very slowly and might never cause any symptoms. Advancements in surgery, hormone therapy and radiotherapy also improve the survival of patients with prostate cancer. The progression of prostate cancer is tightly linked to the androgen receptor. Chakravarty and colleagues reported that NEAT1 was the most upregulated lncRNA in prostate cancer. NEAT1 expression was also associated with prostate cancer progression in two large clinical cohorts. Importantly, high NEAT1 expression rendered prostate cancer cells resistant to androgen receptor antagonists.21 These results suggested that androgen receptor antagonists in combination with NEAT1 target might exert synergistic anti‐cancer effects in prostate cancer.

2.9. Glioma

Glioma is the most lethal primary central nervous system tumour. NEAT1 expression was significantly upregulated in glioma tissues as compared with adjacent non‐tumourous tissues. High NEAT1 expression was also independently associated with shortened overall survival and tumour recurrence as well as larger tumour size and WHO grade. Moreover, high NEAT1 expression in patients with stage III‐IV glioma indicated poor prognosis. NEAT1 might be a novel prognostic biomarker for patients with glioma.54

2.10. Acute promyelocytic leukaemia

Acute promyelocytic leukaemia (APL) is the M3 subtype of acute myelogenous leukaemia with aberrant accumulation of promyelocytes as its hallmark. Aberrant chromosomal reciprocal translocation t(15;17) resulting from fusion of promyelocytic leukaemia (PML) gene with the retinoic acid receptor α (RARα) gene is key to APL pathogenesis.1 PML‐RARα oncoprotein leads to blockade of leucocyte differentiation at the promyelocytic stage. NEAT1 expression level was significantly lower in de novo APL samples than healthy subjects. Furthermore, NEAT1 expression was decreased by PML‐RARα. To this end, NEAT1 expression was significantly upregulated during all‐trans retinoic acid‐induced APL cell line NB4 cell differentiation, in which inhibition of NEAT1 blocked the pro‐differentiation effect of ATRA.22 These findings indicated that aberrant NEAT1 downregulation contributes to blockade of differentiation in APL. These data were shown in the Table 1.

Table 1.

NEAT1 expression in different types of malignancies

	Cancer type	Expression	Role	Reference
1	Lung cancer	Upregulated	Oncogene	31, 32, 33, 34
2	Esophageal cancer	Upregulated	Oncogene	19
3	Laryngeal cancer	Upregulated	Oncogene	37
4	Colorectal cancer	Upregulated	Oncogene	40, 41
5	Hepatocellular cancer	Upregulated	Oncogene	43
6	Prostate cancer	Upregulated	Oncogene	21
7	Breast cancer	Upregulated	Oncogene	50
8	Ovarian cancer	Upregulated	Oncogene	53
9	Acute leukemia	Downregulated	Tumor suppressor	22
10	Glioma	Upregulated	Oncogene	54

3. Conclusion and future perspectives

Since its discovery, NEAT1 have been widely investigated in various human malignancies. NEAT1 is upregulated and plays an oncogenic role in most, if not all, types of solid tumour. The mechanism by which NEAT1 mediates its actions is complex and involves multiple factors, including sponging of tumour‐suppressive microRNAs (Figure  2). However, in acute promyelocytic leukaemia, NEAT1 expression is downregulated and functions as a tumour suppressor by promoting leucocyte differentiation. Such discrepancy might be caused by distinct gene expression backgrounds in solid tumours and haematological malignancies. In this regard, further efforts should be put forth to understand downstream mechanism of NEAT1 dysregulation by transcriptome‐wide approaches, such as RNA sequencing and expression array. Pertinent to clinical practice, NEAT1 might serve as an independent prognostic marker whose upregulation foreshadows a poor clinical outcome. Nevertheless, the mechanisms underlying the aberrant upregulation and function of NEAT1 in most cancer types remain largely undefined. Importantly, most studies did not include an independent cohort for validation. The chemical stability of NEAT1 in biological samples (eg, serum) is also unclear. In future studies, the diagnostic and prognostic performance of NEAT1 should be evaluated head‐to‐head with existing clinicopathological and serological markers in larger cohorts in order to accelerate its clinical utilization. Further studies need to investigate the role of NEAT1 in more cancers such as osteosarcoma and cutaneous squamous cell carcinoma.

Figure 2.

Proposed oncogenic action of NEAT1 in solid tumours. NEAT1 acts as a competing endogenous lncRNA to sponge tumour‐suppressive microRNAs to mediate its pro‐tumourigenic action

Conflicts of Interest

The authors declare no competing financial interests.

Yu X, Li Z, Zheng H, Chan MTV, and Wu WKK. NEAT1: A novel cancer‐related long non‐coding RNA . Cell Prolif. 2017;50:e12329. 10.1111/cpr.12329