|Year : 2016 | Volume
| Issue : 4 | Page : 568-574
Long noncoding RNAs in prostate cancer: overview and clinical implications
Bhavna Malik1, Felix Y Feng2
1 Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
2 Department of Radiation Oncology, Urology, and Medicine, University of California at San Francisco; Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, USA
|Date of Web Publication||12-Apr-2016|
Dr. Felix Y Feng
Department of Radiation Oncology, Urology, and Medicine, University of California at San Francisco; Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco
Source of Support: None, Conflict of Interest: None
Prostate cancer is the second most common cause of cancer mortality among men in the United States. While many prostate cancers are indolent, an important subset of patients experiences disease recurrence after conventional therapy and progresses to castration-resistant prostate cancer (CRPC), which is currently incurable. Thus, there is a critical need to identify biomarkers that will distinguish indolent from aggressive disease, as well as novel therapeutic targets for the prevention or treatment of CRPC. In recent years, long noncoding RNAs (lncRNAs) have emerged as an important class of biological molecules. LncRNAs are polyadenylated RNA species that share many similarities with protein-coding genes despite the fact that they are noncoding (not translated into proteins). They are usually transcribed by RNA polymerase II and exhibit the same epigenetic signatures as protein-coding genes. LncRNAs have also been implicated in the development and progression of variety of cancers, including prostate cancer. While a large number of lncRNAs exhibit tissue- and cancer-specific expression, their utility as diagnostic and prognostic biomarkers is just starting to be explored. In this review, we highlight recent findings on the functional role and molecular mechanisms of lncRNAs in the progression of prostate cancer and evaluate their use as potential biomarkers and therapeutic targets.
Keywords: biomarker; long noncoding RNAs (lncRNAs); prostate cancer
|How to cite this article:|
Malik B, Feng FY. Long noncoding RNAs in prostate cancer: overview and clinical implications. Asian J Androl 2016;18:568-74
|How to cite this URL:|
Malik B, Feng FY. Long noncoding RNAs in prostate cancer: overview and clinical implications. Asian J Androl [serial online] 2016 [cited 2019 Oct 16];18:568-74. Available from: http://www.ajandrology.com/text.asp?2016/18/4/568/177123 - DOI: 10.4103/1008-682X.177123
| Introduction|| |
In the past decade, numerous studies have helped unravel the molecular and biological processes that contribute to prostate cancer (PCa) development. With the advent of whole genome- and exome-sequencing, scientists have deciphered various genomic alterations contributing to PCa pathogenesis. , The loss of one copy of the tumor suppressor PTEN has been found in approximately 60% of men with PCa.  Mutations in p53, BRCA1 and BRCA2, and loss of RB have also been reported in smaller proportions of PCa cases. ,, Moreover, chromosomal rearrangements such as TMPRSS2-ETS gene family fusions have been found frequently in Caucasian PCa cohorts.  In addition to mutations and chromosomal translocations, epigenetic alterations have also been associated with PCa. For instance, hypermethylation at the promoter regions of PTEN, RB, and CDH1 is associated with advanced PCa. 
However, while the majority of these previous studies has focused on protein-coding genes, recent studies have suggested that only 2% of the genome is comprised of protein-coding genes.  Strikingly, the vast majority of the genome (around 70%) is actively transcribed, meaning that the majority of the human transcriptome is comprised of noncoding RNAs (ncRNAs), genes that are transcribed into RNA but not translated into protein.  NcRNAs are classified by their size as small ncRNAs (<200 bp) or long ncRNAs (>200 bp).  One particular class of small ncRNAs, microRNAs (miRNAs), has been extensively studied in the literature. MiRNAs negatively regulate the protein expression of a gene via binding to the 3' untranslated region of the target gene mRNA.  As opposed to miRNAs, long noncoding RNAs (lncRNAs) are much less studied. LncRNAs are further categorized as intergenic, intronic, exonic, antisense, or overlapping based on the genomic location relative to a protein-coding gene, as shown in [Figure 1]. , The significance of lncRNAs in cancers is rapidly gaining attention because of recent studies discovering tens of thousands of novel, unannotated lncRNAs. ,
|Figure 1: Classification of long noncoding RNAs. Long noncoding RNAs (lncRNAs) are categorized as exonic, intronic, intergenic, antisense, or overlapping based on their genomic location relative to a protein-coding gene. Exonic lncRNAs share exons with a protein-coding gene. Intronic lncRNAs are transcribed within the introns of a protein-coding gene. Intergenic lncRNAs are transcribed within the regions between two protein-coding genes. Antisense lncRNAs are located on the opposite strand from a protein-coding gene. Overlapping lncRNAs are transcripts that contain a protein-coding gene within its intron.|
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In the past, a major hurdle in lncRNA research was the inability of conventionally utilized microarrays to detect lncRNA expression due to the lack of lncRNA-directed probes, hence limiting our understanding of the role of lncRNAs in prostate cancer. However, recent advances in transcriptome sequencing (RNASeq) technologies have allowed the study of gene expression in an unbiased manner, resulting in the discovery of thousands of novel RNA species including lncRNAs. One initial study identified 121 lncRNAs, termed as PCATs (prostate cancer-associated noncoding transcripts), using ab initio computational approaches on RNASeq data from 102 prostate cancer tissue samples.  The expression pattern of these 121 lncRNAs distinguished benign, localized, and metastatic prostate samples.  More recently, a significant effort has been made both by our group and others to discover a landscape of lncRNAs in the human transcriptome using bioinformatics-based approaches. This study employed RNAseq data from 25 independent studies comprising over 7000 RNAseq libraries from tumors, normal tissues, and cell lines.  Over 50 000 lncRNAs were identified, of which 79% were novel or unannotated, thus quadrupling the number of known lncRNAs.  Importantly, about 8000 lncRNAs were characterized to be lineage- or cancer-specific, suggesting that lncRNAs are very attractive as potential biomarkers or therapeutic targets.
| Potential Mechanisms and Functions Of LncRNAs|| |
LncRNAs are nonprotein-coding genes characterized by several features. While the majority of lncRNAs is polyadenylated and transcribed by RNA polymerase II, a significant subset is nonpolyadenylated and transcribed by RNA polymerase III. As other transcribed genes, lncRNAs harbor epigenetic marks, such as trimethylation of histone 3 lysine 4 (H3K4me3) at the promoter region and trimethylation of histone 3 lysine 36 (H3K36me3) throughout the body of the gene.  Moreover, lncRNAs exhibit frequent splicing of multiple exons and are expressed in a cell- and tissue-specific manner. ,,
Similar to protein-coding genes, lncRNAs vary considerably in function. The function of lncRNAs often relates to the transcriptional regulation of genes leading to differential mRNA processing. There are different ways by which lncRNAs function to regulate target gene expression, as shown in [Figure 2]. The most common mode of gene regulation involves an epigenetic mechanism that typically results in transcriptional repression by coupling with chromatin-remodeling or histone-modifying protein complexes.  Among all the chromatin remodeling complexes, the most common protein partners for lncRNAs are Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2). LncRNAs serve as scaffolds that mediate the recruitment of these Polycomb Repressive Complexes to certain genomic regions to guide transcriptional regulation.
|Figure 2: Functions of long noncoding RNAs. Long noncoding RNAs (lncRNAs) regulate target gene expression in a variety of approaches, including the following: (1) LncRNAs can interact with transcriptional activators, thereby leading to target gene activation. (2) LncRNAs may mediate transcriptional repression either by directly affecting tumor suppressor signaling or by acting as decoy to keep transcriptional activators away from chromatin. (3) LncRNAs transcribed from gene enhancers (eRNAs) may regulate signaling by recruiting lineage-specific complexes. (4) LncRNAs may serve as scaffolding proteins by recruiting chromatin remodeling complexes, including PRC1 and PRC2. (5) LncRNAs may regulate RNA splicing either by interacting with splicing factors or by binding the splicing junctions of pre-mRNA. (6) LncRNAs may serve as molecular sponges by harboring binding sites for miRNAs and titrating them away from their mRNA targets. eRNA: enhancer RNA, GTF: general transcription factors, LncRNA: long noncoding RNA, mRNA: messenger RNA, miRNA: microRNA, Pol II: RNA polymerase II, PRC2: polycomb repressive complex 2, TF: transcription factors, UTR: untranslated region.|
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In addition to transcriptional regulation by epigenetic changes, lncRNAs are also known to be involved in mRNA processing, including mRNA stability, splicing, and translation ([Figure 2]). These posttranscriptional RNA modifications, including alternative splicing, involve the assembly of RNA-processing factors containing nuclear domains at certain genomic sites.  Moreover, lncRNAs can function as decoys or molecular sponges for miRNAs that target protein-coding mRNAs. In this way, lncRNAs sequester miRNAs to regulate gene expression indirectly.  Furthermore, emerging evidence suggests a role for certain lncRNAs, termed enhancer RNAs (eRNAs), in gene regulation via influencing the activity of gene enhancers. These eRNAs are transcribed from gene enhancers, and can cooperate with lineage-specific complexes, such as FOXA1 and AR, to facilitate hormone signaling pathways. 
Mechanistically, lncRNAs can be characterized as cis- and trans-regulators of gene expression based on whether they target genes that are local or distant, respectively, from their genomic location. For example, lncRNAs have been shown to regulate gene expression in both cis- and trans-based approaches by facilitating the recruitment of PRC2 complexes to local and distant genes. , Taken together, it is clear that the mechanisms by which lncRNAs regulate gene expression are quite complex, with further investigation necessary to more clearly decipher the role of lncRNAs.
Through the functions highlighted in [Figure 2], lncRNAs can function as oncogenes or tumor suppressors by modulating physiological and pathological processes, including cell growth and differentiation, stem cell reprogramming, and disease progression. Many lncRNAs have been shown to be either up- or down-regulated in various cancers, including prostate cancer, and are associated with disease progression. In fact, using high-throughput approaches to interrogate RNA expression in over a thousand prostate cancer patients treated with prostatectomy, a recent study from our group demonstrated that among all protein-coding genes and lncRNAs annotated at the time of the study, the lncRNA SChLAP1 was the top overexpressed gene in cancers that subsequently metastasized versus those that did not.  The finding that the prognostic value of lncRNAs may rival or outperform that of top protein-coding genes has significant implications for clinical biomarker development in prostate cancer. Below, we highlight several lncRNAs that have been implicated in prostate carcinogenesis or progression.
| Prostate Cancer-Associated LncRNAs|| |
Since the initial discovery of lncRNAs such as XIST and H19, there have been dramatic advances in the high-throughput technologies, thereby enabling the discovery of RNA transcripts in an unbiased manner. ,,,,,, Since then, many lncRNAs have been linked to tumorigenesis, either as oncogenes or tumor suppressors. While the underlying mechanism of many of these lncRNAs remains to be elucidated, it is clear that lncRNAs contribute to dysregulation of gene expression in prostate cancer, which then results in cancer initiation, development, and progression. 
One of the first lncRNAs discovered to be highly upregulated in prostate cancer (PCa) was Prostate Cancer Antigen 3 (PCA3), which was initially discovered via expression profiling of PCa samples.  PCA3 was shown to be significantly overexpressed in PCa versus adjacent noncancerous prostate tissues in 95% of radical prostatectomy specimens.  Extensive analysis of the genomic loci of PCA3 (Chr9q21-22) demonstrated no open reading frame for this gene, consistent with a noncoding RNA transcript.  A preclinical study suggested that knockdown of PCA3 hinders PCa cell viability and alters the expression of AR target genes.  More recently, it was reported that PCA3 is antisense to the tumor-suppressive protein-coding gene PRUNE2 and downregulates the expression of PRUNE2 via RNA editing mediated by a supramolecular complex containing adenosine deaminase acting on RNA (ADAR) family members.  Following the discovery of PCA3, other lncRNAs including Prostate Cancer-associated ncRNA Transcript 1 (PCAT1) and Second Chromosome Locus Associated with Prostate-1 (SChLAP1) were found to be differentially expressed in prostate cancer versus nonneoplastic prostate tissues. ,
PCAT1 was discovered as a prostate cancer-associated intergenic ncRNA in a cohort of 102 prostate tissues and cell lines via high-throughput RNAseq studies.  PCAT1 is highly prostate-specific and is remarkably upregulated in a subset of localized and metastatic prostate cancer tissues compared to adjacent nonneoplastic prostate tissues.  The mechanisms by which PCAT1 contributes to prostate carcinogenesis and progression have been studied in a series of preclinical studies. , First, PCAT1 represses BRCA2, a DNA repair gene critical to homologous recombination, by regulating its 3' untranslated region (UTR). This repression leads to a functional deficiency in homologous recombination, resulting in sensitivity to PARP1 inhibitors and radiation.  Second, PCAT1 also promotes prostate cell proliferation through the upregulation of c-Myc.  Collectively, these data suggest that PCAT1 contributes to disease progression via two complementary approaches: one where PCAT1 represses BRCA2 to create deficiencies in DNA damage repair to promote carcinogenesis and another where PCAT1 facilitates prostate cell proliferation via regulating c-Myc. Given that DNA repair defects and unchecked proliferation represent two of the hallmarks of cancer, PCAT1 may represent a prostate cancer biomarker that may hold value as both a biomarker prognostic of outcome but also predictive of response to particular therapies.
SChLAP1 was discovered as a highly expressed intergenic lncRNA associated with aggressive disease in subset of prostate cancer patients via cancer outlier profile analysis (COPA).  As described earlier, SChLAP1 is notable for being one of the genes most enriched in expression in prostate cancers that will metastasize compared to those that do not.  SChLAP1 expression has been shown to be an independent predictor of aggressive prostate cancer when accounting for standard clinicopathological factors, with high SChLAP1 expression associated with biochemical recurrence, metastatic progression, and prostate cancer-specific mortality.  SChLAP1 also significantly promotes cancer cell proliferation, invasion, and metastasis in vitro and in vivo. Mechanistically, SChLAP1 facilitates aggressive phenotypes associated with cancer by antagonizing the tumor suppressive SWI/SNF (Switch/Sucrose Nonfermenting) chromatin remodeling complex. The multiprotein SWI/SNF complex regulates gene transcription by physically moving nucleosomes at the gene promoters.  SChLAP1 has been shown to interact with SNF5, a key component of SWI/SNF complex, and impairs the genomic binding of SNF5, thereby antagonizing the tumor suppressive function of SWI/SNF complex.  SChLAP1 is currently developed as a prognostic biomarker using an RNA in situ hybridization assay. ,
Recent studies have also identified that lncRNAs may interact with the androgen receptor (AR), a well-known driver of prostate cancer. Two lncRNAs, PCGEM1 and PRNCR1, have been proposed to be highly upregulated in primary prostate cancer versus normal prostate epithelium. , In laboratory studies, increased cell proliferation and colony formation were observed with overexpression of PCGEM1, along with attenuated apoptotic response.  In addition, the knockdown of PRNCR1 resulted in decreased cell viability.  These lncRNAs have been reported to bind AR and enhance AR-mediated gene activation programs. , However, this area requires further study as the second study could not confirm the role of PCGEM1 and PRNCR1 in prostate cancer progression and AR signaling.  In addition, another recent publication demonstrated the upregulation of PCGEM1 but not PRNCR1 in AR+/androgen-dependent PCa xenograft models.  In addition to its potential AR-associated roles, PCGEM1 may regulate tumor metabolism via c-Myc activation, by interacting physically with c-Myc and enhancing its chromatin recruitment and transactivation activity. 
Several other lncRNAs have also been implicated as mediators or modulators of AR signaling. One study suggested that reciprocal regulation between the lncRNA PlncRNA-1 and AR contributes to oncogenic phenotypes in vitro.  Another androgen responsive lncRNA, C-terminal binding protein 1-antisense (CTBP1-AS), was demonstrated to promote both androgen-dependent and castration-resistant tumor growth by directly repressing the expression of its antisense gene CTBP1, a known AR corepressor.  More recently, a novel lncRNA cluster DRAIC/PCAT29 has been shown to inhibit cancer cell migration and invasion. , Mechanistically, the expression of DRAIC is repressed by binding of AR to the DRAIC locus but is induced by binding of FOXA1 and NKX3-1 to the same locus as AR. Together, these studies suggest that as the expressions of FOXA1 and NKX3-1 decrease with prostate cancer progression, there is decreased expression of the tumor suppressive DRAIC/PCAT29 lncRNAs, leading to aggressive phenotypes. ,
Outside of AR, lncRNAs have been demonstrated to be involved in mediating the function of other potential prostate cancer drivers. The estrogen receptor alpha (ERα) is expressed in subsets of PCa, independent of AR status, and may be associated with aggressive disease. Chakravarty et al. developed an ERα-specific noncoding transcriptome signature, and used this signature to identify Nuclear Enriched Abundant Transcript 1 (NEAT1) as the most significantly overexpressed ERα-regulated lncRNA in PCa.  This group also demonstrated that PCa cells with high expression of NEAT1 are resistant to androgen receptor antagonists.  Another group identified 145 previously unannotated lncRNAs associated with castration-resistant prostate cancer (CRPC) and characterized one of these, PCAT5, as a regulatory target of the transcription factor ERG, which is activated in 50% of all prostate cancers.  Furthermore, by profiling androgen-dependent versus androgen-independent cell lines, another team recently identified Linc00963 as a lncRNA which regulates the epidermal growth factor receptor signaling pathway to promote cell growth, migration, and invasion. 
Another intriguing lncRNA in prostate cancer biology is Antisense Noncoding RNA in the INK4 Locus (ANRIL), which has been shown to have an important role in cancer biology and is one of the best studied natural antisense transcript genes. It is an antisense transcript overlapping the tumor suppressor INK4b-ARF-INK4a gene cluster and is one of the most frequently altered lncRNAs in cancer.  There is either homozygous deletion or transcriptional silencing of the ANRIL gene cluster in almost 40% of human cancers.  The INK4b-ARF-INK4a gene cluster plays an important role in stress-induced apoptosis, cell cycle inhibition, and senescence, and the expression of this gene cluster has been shown to be repressed by the expression of ANRIL. ,, The expression of ANRIL is higher in preneoplastic prostate epithelial tissues compared to untransformed prostate epithelial tissues. In addition, there are higher levels of ANRIL in prostate cancer relative to normal prostate epithelial cells with a corresponding decrease in the expression of INK4a.  In coordination with the PRC1 and PRC2 complexes, ANRIL leads to the transcriptional silencing of INK4b-ARF-INK4a locus via directly binding to INK4b transcripts. Moreover, in ANRIL knockdown studies, reduced levels of histone H3 lysine K27 methylation (H3K27me) has been reported at the INK4b-ARF-INK4a locus.  In addition, the role of ANRIL has also been studied in DNA damage response. Upon DNA damage, the expression of ANRIL is induced by E2F1 transcription factor in an ATM-dependent manner.  Further, the elevated ANRIL expression suppresses the expression of INK4b-ARF-INK4a locus. Thus, ANRIL could represent an interesting therapeutic target to sensitize cancers to DNA damaging drugs.
In prostate cancer, the lncRNA Metastasis-associated Lung Adenocarcinoma Transcript 1 (MALAT1) is involved in mRNA splicing and is highly upregulated. MALAT1 is an intergenic lncRNA on chromosome locus 11q13.1 that is thought to regulate gene expression through mRNA splicing and editing.  MALAT1 is primarily located in nuclear speckles and overexpressed in a variety of human cancers, including prostate cancer, and has been linked to poor prognosis. ,,, Moreover, knockdown of MALAT1 in prostate cancer cell lines abrogates cell growth, migration and invasion, and induced G0/G1 cell cycle arrest. Therapeutically, MALAT1 has been targeted in prostate cancer xenografts with intratumoral delivery of MALAT1 siRNA, resulting in significant reduction in tumor growth and metastasis. 
In contrast to the many oncogenic lncRNAs, fewer have been reported as tumor suppressor lncRNAs in prostate cancer. Growth Arrest-Specific Transcript 5 (GAS5) is a lncRNA that is highly upregulated in normal prostate epithelial cells but decreases in expression in prostate cancer cell lines. GAS5 manifests multiple isoforms that constitute approximately 12 exons. Mechanistically, GAS5 promotes cell apoptosis by antagonizing glucocorticoid receptor (GR) signaling axis in breast cancer. Similarly in prostate cancer, GAS5 is suspected to regulate androgen receptor-mediated signaling to prevent the progression to metastatic castration-resistant disease.  Another lncRNA, Maternally Expressed Gene 3 (MEG3) has been shown to be downregulated in prostate cancer cell lines and primary tumors compared to normal tissues. MEG3 is proposed to induce apoptosis in both p53 dependent and independent manners. ,
Our understanding of the potential roles of long noncoding RNAs in prostate cancer is starting to develop. However, given the discovery of >40 000 novel lncRNAs on recent transcriptome sequencing studies, it is also clear that much additional research needs to be performed in this area, to understand the molecular mechanisms underlying these genes. In addition, given that many of these lncRNAs are highly tissue- or lineage-specific, there is a clear need to pursue top candidates as potential biomarkers and therapeutic targets. In the following section, we discuss the potential clinical significance of lncRNAs in prostate cancer.
| Opportunities to Utilize Lncrnas in the Clinical Management of Prostate Cancer|| |
In the clinical management of prostate cancer, there is a critical need to better tailor therapy based on individual tumor characteristics. To improve the personalization of therapy for patients, two goals need to be achieved: (1) the identification of biomarkers to distinguish indolent from aggressive disease, in the context of diagnosis or work-up of localized disease and (2) the discovery of novel prostate cancer drivers, which can serve as new therapeutic targets in subsets of patients. Therefore, lncRNAs have the potential to contribute toward both of these goals.
As potential prostate cancer diagnostic and prognostic biomarkers, lncRNAs exhibit several ideal qualities. First, certain lncRNAs are expressed at extremely high levels in subsets of cancers and exhibit outlier profiles,  which facilitates their detection in both tissue and bodily fluids. Second, significant subsets of lncRNAs are extremely specific for a particular cancer, considering that a recent study discovered approximately 8000 novel lncRNAs which are extremely cancer- or lineage-specific. , A number of these lncRNAs are specific for prostate cancer,  and this specificity is an ideal trait for a potential noninvasive biomarker. Finally, lncRNAs represent a vastly unexplored area of cancer biology, and given that they outnumber protein-coding genes,  there are likely many clinically relevant lncRNA biomarkers that are, to date, uncharacterized.
Up to now, the best-studied lncRNA biomarker is PCA3, which has been explored extensively as a urinary biomarker. Following the initial discovery and characterization of PCA3 as a highly overexpressed lncRNA specific to prostate cancer,  a clinical assay was developed and introduced for the detection of urinary PCA3 levels. This assay, named the Progensa PCA3 assay,  required urine specimens to be obtained after digital rectal examination (3 strokes to each lobe), and quantified PCA3 transcript expression based on transcription-mediated amplification and hybridization, and normalized PCA3 levels based on prostate-specific antigen (PSA) transcript levels. Early studies demonstrated that the PCA3 test improved the ability to diagnose prostate cancer, with a univariable AUC of 0.69 (compared to an AUC of 0.55 for PSA) that increased to 0.75 in a multivariable model with other clinical factors.  PCA3 was demonstrated to be independent of PSA levels, prostate volume, or age.  Based on these findings and others, the Food and Drug Administration approved the PCA3 assay for use as a diagnostic test in men with a previous negative biopsy. , Subsequent studies have focused on identifying the optimal cut-off score of PCA3 in the context of clinical use. A meta-analysis from Luo et al. evaluated the performance of threshold scores ranging from 20 to 35 and concluded that a cut-off of 20 was superior to 35 in the repeat biopsy setting, with a sensitivity of 93% and a specificity of 64%.  In the context of the National Cancer Institute Early Detection Research Network validation trial, Wei et al. confirmed that PCA3 scores <20 were associated with an extremely low rate of high-grade cancers on repeat biopsy.  In more recent years, studies have investigated the PCA3 test in the setting of initial (rather than repeat) biopsy and have compared the PCA3 to other assays. Overall, these studies have suggested that in limited cohorts, PCA3 may not perform as well compared to other diagnostic tests, such as multi-parametric MRI or the Prostate Health Index test.  These results indicate that while PCA3 may outperform PSA, further studies need to be performed to define the optimal clinical settings for its use.
While the PCA3 assay is designed to diagnose prostate cancer, its utility as a prognostic biomarker is much more limited as it can detect both higher-grade and lower-grade disease.  A more promising prognostic urine biomarker is SChLAP1, which has been readily detected in urine sediments through qPCR.  Since SChLAP1 was identified as the top overexpressed gene enriched in prostate cancer tissue samples (n > 1000) from high-risk patients who eventually experienced metastatic progression versus those who did not,  SChLAP1 may better predict for lethal disease than other candidate genes. Preliminary studies suggest that urinary SChLAP1 expression also exhibits outlier profiles and predicts for more aggressive disease.  In addition to its potential as a urine biomarker, tissue-based assays for SChLAP1 are also being developed with SChLAP1 expression currently available on the clinically used Decipher array,  and there are also ongoing efforts to validate an RNA in situ hybridization assay for SChLAP1 as well. ,
In addition to serving as potential prognostic biomarkers (i.e., biomarkers associated with poor outcomes independent of treatment), lncRNAs may also serve as biomarkers which specifically predict response or resistance to particular therapies. The ERα-regulated lncRNA NEAT1 has been reported to confer resistance to anti-androgen therapies in laboratory models,  additional studies are necessary to determine if this finding validates in clinical samples. More recently, PARP1 inhibition has been identified as a promising therapeutic approach in patients with castration-resistant prostate cancers harboring alterations in DNA repair genes.  Given preclinical findings that the lncRNA PCAT1 confers defects in homologous recombination in vitro and sensitivity to PARP1 inhibitors in vivo,  PCAT1 represents a promising biomarker of response to PARP1 inhibition although this finding needs to be further assessed in clinical samples as well.
Ultimately, the "holy grail" in utilizing lncRNAs to personalize therapy will entail the development of successful strategies to target lncRNAs clinically. Currently, RNA interference approaches, with small interfering RNAs (siRNAs), small hairpin RNAs (shRNAs), miRNAs, and antisense oligonucleotides (ASOs), represent a promising strategy for targeting lncRNAs. Within in vivo models, targeting SChLAP1 with shRNA-based approaches decreases metastases in a tail-vein injection model.  In addition, intratumoral delivery of therapeutic siRNAs directed against MALAT-1 delays xenograft growth in castrated mice.  ASOs have been developed against MALAT-1 and demonstrated to be effective in lung cancer xenograft models, supporting the investigation of ASOs in prostate cancer models as well. While RNA interference strategies have shown promise in preclinical models of prostate and other cancers, there are several challenges that must be overcome in the clinical application of these approaches. These issues include optimizing delivery systems for appropriate dosing/distribution and ensuring stability of RNA targeting agents among other issues. To date, a number of siRNA- and ASO-based agents are assessed in both early and late clinical trials for various disease and cancer indications. , Further research is necessary to determine if these RNA-targeting strategies can be successfully applied to prostate cancer lncRNAs.
| Summary|| |
Recent advances in RNAseq technologies, combined with large-scale efforts to sequence patient samples, have drastically enhanced the discovery of disease-associated lncRNAs.  While several prostate cancer lncRNAs promote aggressive phenotypes in preclinical models and are associated with disease progression in clinical cohorts, the underlying mechanisms of these oncogenic lncRNAs need to be further investigated. It is clear that lncRNAs are very promising as diagnostic, prognostic, and predictive biomarkers in prostate cancer. Only time will tell if prostate cancer lncRNAs can be successfully targeted therapeutically, but this area of research holds tremendous potential.
| Competing Financial Interest|| |
| Acknowledgments|| |
We would like to acknowledge Rohit Malik and Joseph R Evans for helpful discussions, and Steven Kronenberg and Kari Wilder-Romans for technical assistance.
| References|| |
Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, et al.
The genomic complexity of primary human prostate cancer. Nature
2011; 470: 214-20.
Grasso CS, Wu YM, Robinson DR, Cao X, Dhanasekaran SM, et al.
The mutational landscape of lethal castration-resistant prostate cancer. Nature
2012; 487: 239-43.
Phin S, Moore MW, Cotter PD. Genomic rearrangements of PTEN in prostate cancer. Front Oncol
2013; 3: 240.
Castro E, Goh C, Olmos D, Saunders E, Leongamornlert D, et al.
Germline BRCA mutations are associated with higher risk of nodal involvement, distant metastasis, and poor survival outcomes in prostate cancer. J Clin Oncol
2013; 31: 1748-57.
Ecke TH, Schlechte HH, Schiemenz K, Sachs MD, Lenk SV, et al.
TP53 gene mutations in prostate cancer progression. Anticancer Res
2010; 30: 1579-86.
Sharma A, Yeow WS, Ertel A, Coleman I, Clegg N, et al.
The retinoblastoma tumor suppressor controls androgen signaling and human prostate cancer progression. J Clin Invest
2010; 120: 4478-92.
Gasi Tandefelt D, Boormans J, Hermans K, Trapman J. ETS fusion genes in prostate cancer. Endocr Relat Cancer
2014; 21: R143-52.
Friedlander TW, Roy R, Tomlins SA, Ngo VT, Kobayashi Y, et al.
Common structural and epigenetic changes in the genome of castration-resistant prostate cancer. Cancer Res
2012; 72: 616-25.
Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature
2012; 489: 57-74.
Gibb EA, Brown CJ, Lam WL. The functional role of long non-coding RNA in human carcinomas. Mol Cancer
2011; 10: 38.
Esteller M. Non-coding RNAs in human disease. Nat Rev Genet
2011; 12: 861-74.
Gibb EA, Vucic EA, Enfield KS, Stewart GL, Lonergan KM, et al.
Human cancer long non-coding RNA transcriptomes. PLoS One
2011; 6: e25915.
Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell
2009; 136: 629-41.
Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, et al.
The landscape of long noncoding RNAs in the human transcriptome. Nat Genet
2015; 47: 199-208.
Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, et al.
Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol
2011; 29: 742-9.
Guttman M, Amit I, Garber M, French C, Lin MF, et al.
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature
2009; 458: 223-7.
Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, et al.
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev
2011; 25: 1915-27.
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, et al.
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res
2012; 22: 1775-89.
Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, et al.
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature
2010; 464: 1071-6.
Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, et al.
The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell
2010; 39: 925-38.
Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, et al
. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature
2010; 465: 1033-8.
Wang D, Garcia-Bassets I, Benner C, Li W, Su X, et al.
Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature
2011; 474: 390-4.
Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, et al.
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell
2007; 129: 1311-23.
Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science
2008; 322: 750-6.
Prensner JR, Zhao S, Erho N, Schipper M, Iyer MK, et al.
RNA biomarkers associated with metastatic progression in prostate cancer: a multi-institutional high-throughput analysis of SChLAP1. Lancet Oncol
2014; 15: 1469-80.
Bartolomei MS, Zemel S, Tilghman SM. Parental imprinting of the mouse H19 gene. Nature
1991; 351: 153-5.
Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M, et al
. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature
1991; 349: 38-44.
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, et al.
The transcriptional landscape of the mammalian genome. Science
2005; 309: 1559-63.
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, et al.
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science
2005; 308: 1149-54.
Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, et al. Ab initio
reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol
2010; 28: 503-10.
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al.
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol
2010; 28: 511-5.
Bussemakers MJ, van Bokhoven A, Verhaegh GW, Smit FP, Karthaus HF, et al.
DD3: a new prostate-specific gene, highly overexpressed in prostate cancer. Cancer Res
1999; 59: 5975-9.
Ferreira LB, Palumbo A, de Mello KD, Sternberg C, Caetano MS, et al.
PCA3 noncoding RNA is involved in the control of prostate-cancer cell survival and modulates androgen receptor signaling. BMC Cancer
2012; 12: 507.
Salameh A, Lee AK, Cardo-Vila M, Nunes DN, Efstathiou E, et al.
PRUNE2 is a human prostate cancer suppressor regulated by the intronic long noncoding RNA PCA3. Proc Natl Acad Sci U S A
2015; 112: 8403-8.
Prensner JR, Iyer MK, Sahu A, Asangani IA, Cao Q, et al.
The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet
2013; 45: 1392-8.
Prensner JR, Chen W, Iyer MK, Cao Q, Ma T, et al.
PCAT-1, a long noncoding RNA, regulates BRCA2 and controls homologous recombination in cancer. Cancer Res
2014; 74: 1651-60.
Prensner JR, Chen W, Han S, Iyer MK, Cao Q, et al.
The long non-coding RNA PCAT-1 promotes prostate cancer cell proliferation through cMyc. Neoplasia
2014; 16: 900-8.
Roberts CW, Orkin SH. The SWI/SNF complex - Chromatin and cancer. Nat Rev Cancer
2004; 4: 133-42.
Bottcher R, Hoogland AM, Dits N, Verhoef EI, Kweldam C, et al.
Novel long non-coding RNAs are specific diagnostic and prognostic markers for prostate cancer. Oncotarget
2015; 6: 4036-50.
Mehra R, Shi Y, Udager AM, Prensner JR, Sahu A, et al
. A novel RNA in situ
hybridization assay for the long noncoding RNA SChLAP1 predicts poor clinical outcome after radical prostatectomy in clinically localized prostate cancer. Neoplasia
2014; 16: 1121-7.
Srikantan V, Zou Z, Petrovics G, Xu L, Augustus M, et al.
PCGEM1, a prostate-specific gene, is overexpressed in prostate cancer. Proc Natl Acad Sci U S A
2000; 97: 12216-21.
Yang L, Lin C, Jin C, Yang JC, Tanasa B, et al.
lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs. Nature
2013; 500: 598-602.
Petrovics G, Zhang W, Makarem M, Street JP, Connelly R, et al.
Elevated expression of PCGEM1, a prostate-specific gene with cell growth-promoting function, is associated with high-risk prostate cancer patients. Oncogene
2004; 23: 605-11.
Chung S, Nakagawa H, Uemura M, Piao L, Ashikawa K, et al.
Association of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility. Cancer Sci
2011; 102: 245-52.
Prensner JR, Sahu A, Iyer MK, Malik R, Chandler B, et al.
The IncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer. Oncotarget
2014; 5: 1434-8.
Parolia A, Crea F, Xue H, Wang Y, Mo F, et al.
The long non-coding RNA PCGEM1 is regulated by androgen receptor activity in vivo
. Mol Cancer
2015; 14: 46.
Hung CL, Wang LY, Yu YL, Chen HW, Srivastava S, et al
. A long noncoding RNA connects c-Myc to tumor metabolism. Proc Natl Acad Sci U S A
2014; 111: 18697-702.
Cui Z, Ren S, Lu J, Wang F, Xu W, et al.
The prostate cancer-up-regulated long noncoding RNA PlncRNA-1 modulates apoptosis and proliferation through reciprocal regulation of androgen receptor. Urol Oncol
2013; 31: 1117-23.
Takayama K, Horie-Inoue K, Katayama S, Suzuki T, Tsutsumi S, et al.
Androgen-responsive long noncoding RNA CTBP1-AS promotes prostate cancer. EMBO J
2013; 32: 1665-80.
Malik R, Patel L, Prensner JR, Shi Y, Iyer MK, et al.
The lncRNA PCAT29 inhibits oncogenic phenotypes in prostate cancer. Mol Cancer Res
2014; 12: 1081-7.
Sakurai K, Reon BJ, Anaya J, Dutta A. The lncRNA DRAIC/PCAT29 locus constitutes a tumor-suppressive nexus. Mol Cancer Res
2015; 13: 828-38.
Chakravarty D, Sboner A, Nair SS, Giannopoulou E, Li R, et al.
The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer. Nat Commun
2014; 5: 5383.
Ylipaa A, Kivinummi K, Kohvakka A, Annala M, Latonen L, et al.
Transcriptome sequencing reveals PCAT5 as a novel ERG-regulated long noncoding RNA in prostate cancer. Cancer Res
2015; 75: 4026-31.
Wang L, Han S, Jin G, Zhou X, Li M, et al.
Linc00963: a novel, long non-coding RNA involved in the transition of prostate cancer from androgen-dependence to androgen-independence. Int J Oncol
2014; 44: 2041-9.
Pasmant E, Laurendeau I, Heron D, Vidaud M, Vidaud D, et al.
Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF. Cancer Res
2007; 67: 3963-9.
Tano K, Akimitsu N. Long non-coding RNAs in cancer progression. Front Genet
2012; 3: 219.
El Messaoudi-Aubert S, Nicholls J, Maertens GN, Brookes S, Bernstein E, et al.
Role for the MOV10 RNA helicase in polycomb-mediated repression of the INK4a tumor suppressor. Nat Struct Mol Biol
2010; 17: 862-8.
Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, et al.
Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature
2008; 451: 202-6.
Yap KL, Li S, Munoz-Cabello AM, Raguz S, Zeng L, et al.
Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell
2010; 38: 662-74.
Wan G, Mathur R, Hu X, Liu Y, Zhang X, et al.
Long non-coding RNA ANRIL (CDKN2B-AS) is induced by the ATM-E2F1 signaling pathway. Cell Signal
2013; 25: 1086-95.
Wilusz JE, Freier SM, Spector DL. 3′ end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell
2008; 135: 919-32.
Bernard D, Prasanth KV, Tripathi V, Colasse S, Nakamura T, et al
. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J
2010; 29: 3082-93.
Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, et al
. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics
2007; 8: 39.
Ji P, Diederichs S, Wang W, Boing S, Metzger R, et al.
MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene
2003; 22: 8031-41.
Ren S, Liu Y, Xu W, Sun Y, Lu J, et al.
Long noncoding RNA MALAT-1 is a new potential therapeutic target for castration resistant prostate cancer. J Urol
2013; 190: 2278-87.
Mourtada-Maarabouni M, Pickard MR, Hedge VL, Farzaneh F, Williams GT. GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene
2009; 28: 195-208.
Zhou Y, Zhang X, Klibanski A. MEG3 noncoding RNA: a tumor suppressor. J Mol Endocrinol
2012; 48: R45-53.
Zhou Y, Zhong Y, Wang Y, Zhang X, Batista DL, et al.
Activation of p53 by MEG3 non-coding RNA. J Biol Chem
2007; 282: 24731-42.
Groskopf J, Aubin SM, Deras IL, Blase A, Bodrug S, et al.
APTIMA PCA3 molecular urine test: development of a method to aid in the diagnosis of prostate cancer. Clin Chem
2006; 52: 1089-95.
Deras IL, Aubin SM, Blase A, Day JR, Koo S, et al.
PCA3: a molecular urine assay for predicting prostate biopsy outcome. J Urol
2008; 179: 1587-92.
Chun FK, de la Taille A, van Poppel H, Marberger M, Stenzl A, et al.
Prostate cancer gene 3 (PCA3): development and internal validation of a novel biopsy nomogram. Eur Urol
2009; 56: 659-67.
Haese A, de la Taille A, van Poppel H, Marberger M, Stenzl A, et al.
Clinical utility of the PCA3 urine assay in European men scheduled for repeat biopsy. Eur Urol
2008; 54: 1081-8.
Hessels D, Schalken JA. The use of PCA3 in the diagnosis of prostate cancer. Nat Rev Urol
2009; 6: 255-61.
Luo Y, Gou X, Huang P, Mou C. The PCA3 test for guiding repeat biopsy of prostate cancer and its cut-off score: a systematic review and meta-analysis. Asian J Androl
2014; 16: 487-92.
Wei JT, Feng Z, Partin AW, Brown E, Thompson I, et al.
Can urinary PCA3 supplement PSA in the early detection of prostate cancer? J Clin Oncol
2014; 32: 4066-72.
Tosoian JJ, Ross AE, Sokoll LJ, Partin AW, Pavlovich CP. Urinary biomarkers for prostate cancer. Urol Clin North Am
2016; 43: 17-38.
Mehra R, Udager AM, Ahearn TU, Cao X, Feng FY, et al.
Overexpression of the long non-coding RNA SChLAP1 independently predicts lethal prostate cancer. Eur Urol
2015; S0302-2838(15)01211-7. [Doi: 10.1016/j.eururo.2015.12.003] [Epub ahead of print].
Mateo J, Carreira S, Sandhu S, Miranda S, Mossop H, et al.
DNA-repair defects and olaparib in metastatic prostate cancer. N Engl J Med
2015; 373: 1697-708.
McClorey G, Wood MJ. An overview of the clinical application of antisense oligonucleotides for RNA-targeting therapies. Curr Opin Pharmacol
2015; 24: 52-8.
Ozcan G, Ozpolat B, Coleman RL, Sood AK, Lopez-Berestein G. Preclinical and clinical development of siRNA-based therapeutics. Adv Drug Deliv Rev
2015; 87: 108-19.
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