REVIEW Molecular & Cellular Oncology 1:3, e963469; October 1, 2014; © 2014 Taylor & Francis Group, LLC
Long noncoding RNAs in prostate cancer: mechanisms and applications Chunlai Li1, Liuqing Yang1,2,*, and Chunru Lin1,2,* 1
Department of Molecular and Cellular Oncology; The University of Texas MD Anderson Cancer Center; Houston, TX, 77030, USA; 2Program in Cancer Biology; The University of Texas Graduate School of Biomedical Sciences at Houston; Houston, TX, 77030, USA
Keywords: biomarker, epigenetic modification, long noncoding RNAs (lncRNAs), metastasis, prostate cancer, regulatory mechanism, therapeutic target Abbreviations: ANRIL, antisense lncRNA of the INK4 locus; AR, androgen receptor; CBP, CREB-binding protein; CBX7, chromobox homolog 7; CCND1, cyclin D1; ceRNAs, competing endogenous RNAs; CHART, capture hybridization analysis of RNA targets; ChIRP, chromatin isolation by RNA purification; CRPC, castration-resistant prostate cancer; CTBP1, C-terminal binding protein 1; DHT, 5a-dihydrotestosterone; DOX, doxorubicin; DSBs, double-stranded DNA breaks; EMT, epithelial-mesenchymal transition; eRNAs, enhancer RNAs; FDA, the Food and Drug Administration; GAS5, growth arrest-specific 5; HR, homologous recombination; lncRNAs, long ncRNAs; MALAT1, metastasis associated in lung adenocarcinoma transcript 1; mRNAs, messenger RNAs; ncRNAs, noncoding RNAs; PAR-CLIP, photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation; PCa, prostate cancer; PCA3, prostate cancer antigen 3; PCAT1, prostate cancer-associated transcript 1; PCGEM1, prostate cancer gene expression marker 1; PRC, polycomb repressive complex; PRNCR1, prostate cancer noncoding RNA 1; RDE, RNA destabilizing elements; RIP-Seq, RNA immunoprecipitation sequencing; SChLAP1, second chromosome locus associated with prostate-1; snoRNAs, small nucleolar RNAs; SNPs, single nucleotide polymorphisms; SR, serine/arginine-rich; TERC, telomerase RNA component; TLS, translocated in liposarcoma; T-UCRs, transcribed UCRs; UCR, ultra-conserved genomic regions; XIST, X inactive specific transcript; ZFN, zinc finger nucleases
A large proportion of the control of gene expression in humans is mediated by noncoding elements in the genome. Long noncoding RNAs (lncRNAs) have emerged as a new class of pivotal regulatory components, orchestrating extensive cellular processes and connections. LncRNAs play various roles from chromatin modification to alternative splicing and posttranscriptional processing and are involved in almost all aspects of eukaryotic regulation. LncRNA-based mechanisms modulate cell fates during development, and their dysregulation underscores many human disorders, especially cancer, through chromosomal translocation, deletion, and nucleotide expansions. Recent studies demonstrate that multiple prostate cancer risk loci are associated with lncRNAs and that ectopic expression of these transcripts triggers a cascade of cellular events driving tumor initiation and progression. The recent increased rate of discovery of lncRNAs has been leveraged for application in clinical strategies such as novel biomarkers and therapeutic targets. Despite this potential, many issues remain to be addressed in this fast-growing field.
Introduction Recent whole-genome sequence assessments and transcriptomic analyses of model organisms have challenged the conventional *Correspondence to: Liuqing Yang; Email: [email protected]; Chunru Lin; Email: [email protected] Submitted: 06/30/2014; Revised: 08/04/2014; Accepted: 08/12/2014 http://dx.doi.org/10.4161/23723548.2014.963469
www.landesbioscience.com
belief that a limited number of protein-coding genes form the basis of architectural complexity and phenotypic diversity in the evolution of metazoans. In humans, approximately 1.5% of the genome is protein coding whereas over 80% appears to participate in biochemical activities that may be functionally important.1,2 At least 70% of the human genome is actively transcribed as a versatile group of RNA transcripts that have no protein coding potential, termed noncoding RNAs (ncRNAs), many of which are conserved throughout the eukaryotic kingdoms. Based on transcript size, the long ncRNAs (lncRNAs) are currently defined as transcripts of greater than 200 nucleotides that share many features of mRNA.3,4 LncRNAs have been discovered within the introns of protein-coding genes, in intergenic regions, and antisense to protein-coding genes.4 Within the past 4 years, the number of discovered human lncRNA genes has increased from 6,000 to over 13,870.5,6 It is likely that hundreds of thousands of lncRNAs have yet to be identified because lncRNAs arising from overlapping protein-encoding loci remain to be analyzed, and 15% of the human genome has yet to be annotated.6 Many of the lncRNAs identified to date show specific spatial and temporal patterns of expression, indicating that lncRNA expression is finely regulated and functionally crucial.4 Although only a minority of lncRNAs has been characterized in detail, it is clear that lncRNAs participate in diverse biological processes and operate through a variety of mechanisms. LncRNAs have been implicated in multiple processes, including chromosome dosage compensation, genomic imprinting, embryonic development, control of stem cell pluripotency, cell proliferation, cell differentiation, apoptosis, cell cycle control, regulation of epithelial-mesenchymal transition (EMT) and synaptic plasticity,
Molecular & Cellular Oncology
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Table 1. Publically available long noncoding RNA databases Name ChIPBase Functional RNAdb GENCODE lncRNA db LNCipedia LncRNABase LncRNADisease lncRNome NcRNA Database ncRNAimprint NONCODE NPInter NRED Rfam
Description
URLs
Expression/transcriptional regulation profiles of ncRNAs Functional ncRNA catalog, microarray information Human lncRNA catalog Eukaryotic functional lncRNAs Human lncRNA sequences and structures miRNA–lncRNA interactions and association with cancer lncRNA and disease association database Searchable human lncRNA database Multiple kingdoms Mammalian imprinted ncRNAs Experiment-based, multiple kingdoms ncRNA interactions lncRNA expression database ncRNA structures, sequence alignments, multiple kingdoms
http://deepbase.sysu.edu.cn/chipbase/ http://www.ncrna.org/frnadb/ http://www.gencodegenes.org/ http://www.lncrnadb.org/ http://www.lncipedia.org http://starbase.sysu.edu.cn/mirLncRNA.php http://cmbi.bjmu.edu.cn/lncrnadisease http://genome.igib.res.in/lncRNome/ http://biobases.ibch.poznan.pl/ncRNA/ http://rnaqueen.sysu.edu.cn/ncRNAimprint/ http://www.noncode.org/ http://www.bioinfo.org/NPInter/ http://jsm-research.imb.uq.edu.au/nred/ http://rfam.xfam.org/
and nuclear and cytoplasmic trafficking.7-13 In the past decade the number of publications related to lncRNAs has increased exponentially and dozens of publically available lncRNA databases have been created (Table 1). Some of these databases (e.g., NONCODE and LncRNADisease) list lncRNAs that have been experimentally validated and exhibit associations with human carcinomas. Prostate cancer ranks second both in terms of cancer prevalence and cancer-related deaths in men in the United States. It is estimated that nearly 233,000 men will be diagnosed with prostate cancer in 2014 in the United States, while nearly 29,480 men will die of prostate cancer (http://www.cancer.org/cancer/ prostatecancer/). Despite extensive research, our understanding of the molecular basis of cancer development remains largely deficient. Substantial progress in unveiling the comprehensive genetic regulation of cancer impels us to reconsider the crucial role of non–protein-coding elements within the human genome. Here, we review recent advances in our understanding of a variety of lncRNAs in prostate cancer, the gene regulatory mechanisms of lncRNA-promoted tumorigenesis, and highlight the potential implications of these RNA species as novel biomarkers and therapeutic targets in prostate cancer.
Long Noncoding RNAs in Prostate Cancer Like protein-coding genes, lncRNAs can function as oncogenic and tumor suppressor genes, thus affecting one or more of the cancer hallmarks.14 Recent studies indicate that lncRNAs function as master regulators of cancer development by sustaining tumor cell proliferation, evading growth suppressors, enabling replicative immortality, stimulating angiogenesis, and promoting invasion and metastasis. The first suggestion that not all long RNA transcripts are mRNAs that pass information from DNA to protein came more than 20 years ago with the discovery of the gene for the paternally imprinted maternally expressed transcript H19, which encodes a fetal-specific lncRNA that is deregulated in embryonic and adult tumors.8,15 Shortly after, the identification of the X inactive specific transcript (XIST) suggested a
e963469-2
Refs 72 73 6 74 75 76 77 78 79 80 81 82 83 84
nuclear structural and cis-limited gene regulatory function for ncRNAs.7,16,17 The idea that lncRNAs may exhibit cancerspecific expression was strengthened by the discovery of the lncRNA prostate cancer antigen 3 (PCA3, also known as DD3), which is specifically overexpressed in malignant prostate tissue.18 Another of the earliest lncRNAs discovered in prostate cancer (PCa) was prostate cancer gene expression marker 1 (PCGEM1), a prostate-specific noncoding RNA whose expression correlated with tumorigenesis. 19 Later findings demonstrated that PCGEM1 overexpression in LNCaP and NIH3T3 cells promoted cell proliferation and colony formation, and that increased expression levels were associated with high-risk PCa patients.20 Genetic variations in the PCGEM1 locus may contribute to individual susceptibility to PCa in Chinese men.21 However, additional functional analyses are required to elucidate the detailed mechanism underlying these observed associations. The lncRNA and small nucleolar RNA (snoRNA) host gene, tumor suppressor growth arrest-specific 5 (GAS5), hosts 10 different snoRNAs in its introns.22 Interestingly, some, but not all, of the GAS5-encoded snoRNAs are upregulated during the progression of PCa, suggesting that separate mechanisms control the post-transcriptional levels of these RNA products even though they are derived from the same precursor transcript.23 Downregulation of GAS5 expression has been associated with the progression of LNCaP cells to castration-resistant PCa cells in an in vivo model.24 More recently, high levels of GAS5 expression were found to promote basal apoptosis and enhance the response to a range of apoptotic stimuli, whereas low levels of expression had no detectable effect on basal survival but markedly attenuated the induction of programmed cell death in response to physical and chemical stimuli.25 A notable example of oncogenic lncRNAs is metastasis associated in lung adenocarcinoma transcript 1 (MALAT1), which was originally shown to be overexpressed in non-small cell lung cancer.26 Subsequent studies in various neoplasms have linked increased MALAT1 expression with multiple metastatic carcinomas including hepatocellular carcinoma, breast cancer, pancreatic cancer, colon cancer, and prostate cancer.27
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Table 2. Long noncoding RNAs with known or putative involvement in prostate cancer LncRNA name ANRIL CBR3-AS1 CDKN1A-AS CTBP1-AS GAS5 LINC00963 LOC728606 MALAT1 ncRNACCND1 PCA3 PCAT1 PCGEM1 PRNCR1 PTENP1 PVT1 SChLAP1 XIST
Alias CDKN2B-AS1 PlncRNA-1 p21-AS PCAT10 SNHG2 PCAT18 HCN, NEAT2 ncRNAcyclin D1 DD3 LINC00071 PCAT8 PTEN-rs, psiPTEN LINC00079 PCAT11, LINC00913 SXI1, LINC00001
Genbank Accession No
Cytology
Length
Function
NR_003529 NR_038892 Bx332409 NR_104331 NR_002578 NR_038955 NR_024259 NR_002819
9p21.3 21q22.12 6p21.2 4p16.3 1q25.1 9q34 18q11.2 11q13.1 11q13.3 9q21.22 8q24.21 2q32.2 8q24.21 9p13.3 8q24.21 2q31.3 Xq13.2
»3.8 kb 1.6 kb »1.0 kb 3.9 kb > 0.6 kb 2.1 kb 2.6 kb 8.7 kb »0.3 kb 3.7 kb 2.0 kb 1.6 kb 12.7 kb 3.9 kb 1.7 kb 1.4 kb 19.3 kb
Oncogene Oncogene Oncogene Oncogene Tumor suppressor Metastasis Metastasis Metastasis Tumor suppressor Diagnostic marker Oncogene Oncogene Oncogene Tumor suppressor Oncogene Metastasis Methylation signature
NR_015342 NR_045262 NR_002769 NR_109833 NR_023917 NR_003367 NR_104319 NR_001564
In addition, some noncoding transcripts are derived from ultraconserved genomic regions (UCRs);28 these transcribed UCRs (T-UCRs) can be altered at the genomic level in human cancer.29 In PCa, some ucRNAs demonstrate altered expression associated with the Gleason score and extraprostatic extension. The transcription of several ucRNAs in PCa cells is controlled by epigenetic mechanisms and/or androgens and correlates negatively with microRNA (miRNA) expression. Analysis of ucRNA targets in PCa has identified more than 1,000 possible ucRNA– mRNA interactions, with enrichment of ucRNA targets in pathways related to calcium binding and RAS signaling.30 Recent advances in transcriptomic sequencing have led to the discovery of many new lncRNAs associated with prostate malignancies31,32 and have allowed re-evaluation of other known cancer-associated lncRNAs whose functions have remained unknown for decades (Table 2). Taken together, these findings highlight the importance of lncRNAs in cancer processes and provide a better understanding of the impact that lncRNAs will have in comprehending the regulation of gene expression in cancer, especially in relation to the diagnosis and treatment of cancer.
Functional Mechanisms of Long Noncoding RNAs in Prostate Tumorigenesis The relevance of lncRNAs in gene regulation has been extensively unveiled during the last decade. Nevertheless, our knowledge of how lncRNAs act in the cell and the roles that they might play in cancer is still very limited. Recently, it has become more obvious that lncRNAs play an important role in regulating gene expression at various levels, including chromatin modification, transcription, and post-transcriptional processing. A significant role of lncRNAs is recruiting protein complexes for the regulation of chromatin states. A number of these transcripts may function in cis, acting on genes adjacent to the site of RNA synthesis. The INK4b/ARF/INK4a locus encodes 3 tumor suppressor genes that have been linked to various types of
www.landesbioscience.com
Refs 33,34 61 85 42 24,25 86 62 26,87 41 18,88 31,35 19,20,39 37,39 45 89 36 90
cancers. Expression of an antisense transcript, antisense lncRNA of the INK4 locus (ANRIL), which is located within this gene cluster33 and overlaps 2 exons of p15/CDKN2B, correlates with INK4b epigenetic silencing.10 A subsequent study characterized the mechanism by which the lncRNA ANRIL mediates INK4a transcriptional repression in cis: ANRIL was shown to interact with the Pc/Chromobox 7 (CBX7) protein within the polycomb repressive complex 1 (PRC1), repress the INK4b/ARF/INK4a locus, and control senescence.34 Elevated levels of both CBX7 and ANRIL are found in PCa tissues and are closely correlated with reduced INK4a levels.34 Another lncRNA, prostate cancer-associated transcript 1 (PCAT1), is upregulated in a subset of metastatic tumors and promotes cell proliferation in vitro through transcriptional regulation of its target genes. The expression of PCAT1 and EZH2 within PRC2 has been shown to be mutually antagonistic; knockdown or inhibition of EZH2 leads to the reactivation of PCAT1 and downregulation of target genes.31 In addition, PCAT1 was found to repress the BRCA2 tumor suppressor gene leading to downstream impairment of homologous recombination (HR), thus demonstrating a role for lncRNAs in the regulation of double-stranded DNA breaks (DSBs) in PCa.35 More recently, second chromosome locus associated with prostate-1 (SChLAP1) was found to be abundantly expressed in a subset of PCa, and was shown to mechanically antagonize SWI/SNF5mediated regulation of gene expression and genomic binding and coordinate cancer cell invasion in vitro and metastatic spread in vivo.36 LncRNAs can also activate gene expression by recruiting protein factors. Prostate cancer noncoding RNA 1 (PRNCR1, also known as PCAT8), is upregulated in the precursor lesion prostatic intraepithelial neoplasia and is positively associated with the viability of PCa cells.37 Overexpression of PCGEM1 results in attenuated induction of p53 and p21Waf1/Cip1 by doxorubicin (DOX), and resistance to apoptosis in LNCaP PCa cells but not in androgen-independent variants of LNCaP.38 Yang et al. recently demonstrated that PRNCR1 and PCGEM1 successively
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interact with the androgen receptor (AR) bound at DNAenhancer regions in a ligand-dependent fashion and facilitate chromosomal looping between AR-bound enhancers and the promoter sequences of androgen-responsive genes.39 The use of genome-wide transcriptome analysis in conjunction with GRO-seq has also uncovered divergent transcription of relatively short (
Long noncoding RNAs in prostate cancer: mechanisms and applications Chunlai Li1, Liuqing Yang1,2,*, and Chunru Lin1,2,* 1
Department of Molecular and Cellular Oncology; The University of Texas MD Anderson Cancer Center; Houston, TX, 77030, USA; 2Program in Cancer Biology; The University of Texas Graduate School of Biomedical Sciences at Houston; Houston, TX, 77030, USA
Keywords: biomarker, epigenetic modification, long noncoding RNAs (lncRNAs), metastasis, prostate cancer, regulatory mechanism, therapeutic target Abbreviations: ANRIL, antisense lncRNA of the INK4 locus; AR, androgen receptor; CBP, CREB-binding protein; CBX7, chromobox homolog 7; CCND1, cyclin D1; ceRNAs, competing endogenous RNAs; CHART, capture hybridization analysis of RNA targets; ChIRP, chromatin isolation by RNA purification; CRPC, castration-resistant prostate cancer; CTBP1, C-terminal binding protein 1; DHT, 5a-dihydrotestosterone; DOX, doxorubicin; DSBs, double-stranded DNA breaks; EMT, epithelial-mesenchymal transition; eRNAs, enhancer RNAs; FDA, the Food and Drug Administration; GAS5, growth arrest-specific 5; HR, homologous recombination; lncRNAs, long ncRNAs; MALAT1, metastasis associated in lung adenocarcinoma transcript 1; mRNAs, messenger RNAs; ncRNAs, noncoding RNAs; PAR-CLIP, photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation; PCa, prostate cancer; PCA3, prostate cancer antigen 3; PCAT1, prostate cancer-associated transcript 1; PCGEM1, prostate cancer gene expression marker 1; PRC, polycomb repressive complex; PRNCR1, prostate cancer noncoding RNA 1; RDE, RNA destabilizing elements; RIP-Seq, RNA immunoprecipitation sequencing; SChLAP1, second chromosome locus associated with prostate-1; snoRNAs, small nucleolar RNAs; SNPs, single nucleotide polymorphisms; SR, serine/arginine-rich; TERC, telomerase RNA component; TLS, translocated in liposarcoma; T-UCRs, transcribed UCRs; UCR, ultra-conserved genomic regions; XIST, X inactive specific transcript; ZFN, zinc finger nucleases
A large proportion of the control of gene expression in humans is mediated by noncoding elements in the genome. Long noncoding RNAs (lncRNAs) have emerged as a new class of pivotal regulatory components, orchestrating extensive cellular processes and connections. LncRNAs play various roles from chromatin modification to alternative splicing and posttranscriptional processing and are involved in almost all aspects of eukaryotic regulation. LncRNA-based mechanisms modulate cell fates during development, and their dysregulation underscores many human disorders, especially cancer, through chromosomal translocation, deletion, and nucleotide expansions. Recent studies demonstrate that multiple prostate cancer risk loci are associated with lncRNAs and that ectopic expression of these transcripts triggers a cascade of cellular events driving tumor initiation and progression. The recent increased rate of discovery of lncRNAs has been leveraged for application in clinical strategies such as novel biomarkers and therapeutic targets. Despite this potential, many issues remain to be addressed in this fast-growing field.
Introduction Recent whole-genome sequence assessments and transcriptomic analyses of model organisms have challenged the conventional *Correspondence to: Liuqing Yang; Email: [email protected]; Chunru Lin; Email: [email protected] Submitted: 06/30/2014; Revised: 08/04/2014; Accepted: 08/12/2014 http://dx.doi.org/10.4161/23723548.2014.963469
www.landesbioscience.com
belief that a limited number of protein-coding genes form the basis of architectural complexity and phenotypic diversity in the evolution of metazoans. In humans, approximately 1.5% of the genome is protein coding whereas over 80% appears to participate in biochemical activities that may be functionally important.1,2 At least 70% of the human genome is actively transcribed as a versatile group of RNA transcripts that have no protein coding potential, termed noncoding RNAs (ncRNAs), many of which are conserved throughout the eukaryotic kingdoms. Based on transcript size, the long ncRNAs (lncRNAs) are currently defined as transcripts of greater than 200 nucleotides that share many features of mRNA.3,4 LncRNAs have been discovered within the introns of protein-coding genes, in intergenic regions, and antisense to protein-coding genes.4 Within the past 4 years, the number of discovered human lncRNA genes has increased from 6,000 to over 13,870.5,6 It is likely that hundreds of thousands of lncRNAs have yet to be identified because lncRNAs arising from overlapping protein-encoding loci remain to be analyzed, and 15% of the human genome has yet to be annotated.6 Many of the lncRNAs identified to date show specific spatial and temporal patterns of expression, indicating that lncRNA expression is finely regulated and functionally crucial.4 Although only a minority of lncRNAs has been characterized in detail, it is clear that lncRNAs participate in diverse biological processes and operate through a variety of mechanisms. LncRNAs have been implicated in multiple processes, including chromosome dosage compensation, genomic imprinting, embryonic development, control of stem cell pluripotency, cell proliferation, cell differentiation, apoptosis, cell cycle control, regulation of epithelial-mesenchymal transition (EMT) and synaptic plasticity,
Molecular & Cellular Oncology
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Table 1. Publically available long noncoding RNA databases Name ChIPBase Functional RNAdb GENCODE lncRNA db LNCipedia LncRNABase LncRNADisease lncRNome NcRNA Database ncRNAimprint NONCODE NPInter NRED Rfam
Description
URLs
Expression/transcriptional regulation profiles of ncRNAs Functional ncRNA catalog, microarray information Human lncRNA catalog Eukaryotic functional lncRNAs Human lncRNA sequences and structures miRNA–lncRNA interactions and association with cancer lncRNA and disease association database Searchable human lncRNA database Multiple kingdoms Mammalian imprinted ncRNAs Experiment-based, multiple kingdoms ncRNA interactions lncRNA expression database ncRNA structures, sequence alignments, multiple kingdoms
http://deepbase.sysu.edu.cn/chipbase/ http://www.ncrna.org/frnadb/ http://www.gencodegenes.org/ http://www.lncrnadb.org/ http://www.lncipedia.org http://starbase.sysu.edu.cn/mirLncRNA.php http://cmbi.bjmu.edu.cn/lncrnadisease http://genome.igib.res.in/lncRNome/ http://biobases.ibch.poznan.pl/ncRNA/ http://rnaqueen.sysu.edu.cn/ncRNAimprint/ http://www.noncode.org/ http://www.bioinfo.org/NPInter/ http://jsm-research.imb.uq.edu.au/nred/ http://rfam.xfam.org/
and nuclear and cytoplasmic trafficking.7-13 In the past decade the number of publications related to lncRNAs has increased exponentially and dozens of publically available lncRNA databases have been created (Table 1). Some of these databases (e.g., NONCODE and LncRNADisease) list lncRNAs that have been experimentally validated and exhibit associations with human carcinomas. Prostate cancer ranks second both in terms of cancer prevalence and cancer-related deaths in men in the United States. It is estimated that nearly 233,000 men will be diagnosed with prostate cancer in 2014 in the United States, while nearly 29,480 men will die of prostate cancer (http://www.cancer.org/cancer/ prostatecancer/). Despite extensive research, our understanding of the molecular basis of cancer development remains largely deficient. Substantial progress in unveiling the comprehensive genetic regulation of cancer impels us to reconsider the crucial role of non–protein-coding elements within the human genome. Here, we review recent advances in our understanding of a variety of lncRNAs in prostate cancer, the gene regulatory mechanisms of lncRNA-promoted tumorigenesis, and highlight the potential implications of these RNA species as novel biomarkers and therapeutic targets in prostate cancer.
Long Noncoding RNAs in Prostate Cancer Like protein-coding genes, lncRNAs can function as oncogenic and tumor suppressor genes, thus affecting one or more of the cancer hallmarks.14 Recent studies indicate that lncRNAs function as master regulators of cancer development by sustaining tumor cell proliferation, evading growth suppressors, enabling replicative immortality, stimulating angiogenesis, and promoting invasion and metastasis. The first suggestion that not all long RNA transcripts are mRNAs that pass information from DNA to protein came more than 20 years ago with the discovery of the gene for the paternally imprinted maternally expressed transcript H19, which encodes a fetal-specific lncRNA that is deregulated in embryonic and adult tumors.8,15 Shortly after, the identification of the X inactive specific transcript (XIST) suggested a
e963469-2
Refs 72 73 6 74 75 76 77 78 79 80 81 82 83 84
nuclear structural and cis-limited gene regulatory function for ncRNAs.7,16,17 The idea that lncRNAs may exhibit cancerspecific expression was strengthened by the discovery of the lncRNA prostate cancer antigen 3 (PCA3, also known as DD3), which is specifically overexpressed in malignant prostate tissue.18 Another of the earliest lncRNAs discovered in prostate cancer (PCa) was prostate cancer gene expression marker 1 (PCGEM1), a prostate-specific noncoding RNA whose expression correlated with tumorigenesis. 19 Later findings demonstrated that PCGEM1 overexpression in LNCaP and NIH3T3 cells promoted cell proliferation and colony formation, and that increased expression levels were associated with high-risk PCa patients.20 Genetic variations in the PCGEM1 locus may contribute to individual susceptibility to PCa in Chinese men.21 However, additional functional analyses are required to elucidate the detailed mechanism underlying these observed associations. The lncRNA and small nucleolar RNA (snoRNA) host gene, tumor suppressor growth arrest-specific 5 (GAS5), hosts 10 different snoRNAs in its introns.22 Interestingly, some, but not all, of the GAS5-encoded snoRNAs are upregulated during the progression of PCa, suggesting that separate mechanisms control the post-transcriptional levels of these RNA products even though they are derived from the same precursor transcript.23 Downregulation of GAS5 expression has been associated with the progression of LNCaP cells to castration-resistant PCa cells in an in vivo model.24 More recently, high levels of GAS5 expression were found to promote basal apoptosis and enhance the response to a range of apoptotic stimuli, whereas low levels of expression had no detectable effect on basal survival but markedly attenuated the induction of programmed cell death in response to physical and chemical stimuli.25 A notable example of oncogenic lncRNAs is metastasis associated in lung adenocarcinoma transcript 1 (MALAT1), which was originally shown to be overexpressed in non-small cell lung cancer.26 Subsequent studies in various neoplasms have linked increased MALAT1 expression with multiple metastatic carcinomas including hepatocellular carcinoma, breast cancer, pancreatic cancer, colon cancer, and prostate cancer.27
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Table 2. Long noncoding RNAs with known or putative involvement in prostate cancer LncRNA name ANRIL CBR3-AS1 CDKN1A-AS CTBP1-AS GAS5 LINC00963 LOC728606 MALAT1 ncRNACCND1 PCA3 PCAT1 PCGEM1 PRNCR1 PTENP1 PVT1 SChLAP1 XIST
Alias CDKN2B-AS1 PlncRNA-1 p21-AS PCAT10 SNHG2 PCAT18 HCN, NEAT2 ncRNAcyclin D1 DD3 LINC00071 PCAT8 PTEN-rs, psiPTEN LINC00079 PCAT11, LINC00913 SXI1, LINC00001
Genbank Accession No
Cytology
Length
Function
NR_003529 NR_038892 Bx332409 NR_104331 NR_002578 NR_038955 NR_024259 NR_002819
9p21.3 21q22.12 6p21.2 4p16.3 1q25.1 9q34 18q11.2 11q13.1 11q13.3 9q21.22 8q24.21 2q32.2 8q24.21 9p13.3 8q24.21 2q31.3 Xq13.2
»3.8 kb 1.6 kb »1.0 kb 3.9 kb > 0.6 kb 2.1 kb 2.6 kb 8.7 kb »0.3 kb 3.7 kb 2.0 kb 1.6 kb 12.7 kb 3.9 kb 1.7 kb 1.4 kb 19.3 kb
Oncogene Oncogene Oncogene Oncogene Tumor suppressor Metastasis Metastasis Metastasis Tumor suppressor Diagnostic marker Oncogene Oncogene Oncogene Tumor suppressor Oncogene Metastasis Methylation signature
NR_015342 NR_045262 NR_002769 NR_109833 NR_023917 NR_003367 NR_104319 NR_001564
In addition, some noncoding transcripts are derived from ultraconserved genomic regions (UCRs);28 these transcribed UCRs (T-UCRs) can be altered at the genomic level in human cancer.29 In PCa, some ucRNAs demonstrate altered expression associated with the Gleason score and extraprostatic extension. The transcription of several ucRNAs in PCa cells is controlled by epigenetic mechanisms and/or androgens and correlates negatively with microRNA (miRNA) expression. Analysis of ucRNA targets in PCa has identified more than 1,000 possible ucRNA– mRNA interactions, with enrichment of ucRNA targets in pathways related to calcium binding and RAS signaling.30 Recent advances in transcriptomic sequencing have led to the discovery of many new lncRNAs associated with prostate malignancies31,32 and have allowed re-evaluation of other known cancer-associated lncRNAs whose functions have remained unknown for decades (Table 2). Taken together, these findings highlight the importance of lncRNAs in cancer processes and provide a better understanding of the impact that lncRNAs will have in comprehending the regulation of gene expression in cancer, especially in relation to the diagnosis and treatment of cancer.
Functional Mechanisms of Long Noncoding RNAs in Prostate Tumorigenesis The relevance of lncRNAs in gene regulation has been extensively unveiled during the last decade. Nevertheless, our knowledge of how lncRNAs act in the cell and the roles that they might play in cancer is still very limited. Recently, it has become more obvious that lncRNAs play an important role in regulating gene expression at various levels, including chromatin modification, transcription, and post-transcriptional processing. A significant role of lncRNAs is recruiting protein complexes for the regulation of chromatin states. A number of these transcripts may function in cis, acting on genes adjacent to the site of RNA synthesis. The INK4b/ARF/INK4a locus encodes 3 tumor suppressor genes that have been linked to various types of
www.landesbioscience.com
Refs 33,34 61 85 42 24,25 86 62 26,87 41 18,88 31,35 19,20,39 37,39 45 89 36 90
cancers. Expression of an antisense transcript, antisense lncRNA of the INK4 locus (ANRIL), which is located within this gene cluster33 and overlaps 2 exons of p15/CDKN2B, correlates with INK4b epigenetic silencing.10 A subsequent study characterized the mechanism by which the lncRNA ANRIL mediates INK4a transcriptional repression in cis: ANRIL was shown to interact with the Pc/Chromobox 7 (CBX7) protein within the polycomb repressive complex 1 (PRC1), repress the INK4b/ARF/INK4a locus, and control senescence.34 Elevated levels of both CBX7 and ANRIL are found in PCa tissues and are closely correlated with reduced INK4a levels.34 Another lncRNA, prostate cancer-associated transcript 1 (PCAT1), is upregulated in a subset of metastatic tumors and promotes cell proliferation in vitro through transcriptional regulation of its target genes. The expression of PCAT1 and EZH2 within PRC2 has been shown to be mutually antagonistic; knockdown or inhibition of EZH2 leads to the reactivation of PCAT1 and downregulation of target genes.31 In addition, PCAT1 was found to repress the BRCA2 tumor suppressor gene leading to downstream impairment of homologous recombination (HR), thus demonstrating a role for lncRNAs in the regulation of double-stranded DNA breaks (DSBs) in PCa.35 More recently, second chromosome locus associated with prostate-1 (SChLAP1) was found to be abundantly expressed in a subset of PCa, and was shown to mechanically antagonize SWI/SNF5mediated regulation of gene expression and genomic binding and coordinate cancer cell invasion in vitro and metastatic spread in vivo.36 LncRNAs can also activate gene expression by recruiting protein factors. Prostate cancer noncoding RNA 1 (PRNCR1, also known as PCAT8), is upregulated in the precursor lesion prostatic intraepithelial neoplasia and is positively associated with the viability of PCa cells.37 Overexpression of PCGEM1 results in attenuated induction of p53 and p21Waf1/Cip1 by doxorubicin (DOX), and resistance to apoptosis in LNCaP PCa cells but not in androgen-independent variants of LNCaP.38 Yang et al. recently demonstrated that PRNCR1 and PCGEM1 successively
Molecular & Cellular Oncology
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interact with the androgen receptor (AR) bound at DNAenhancer regions in a ligand-dependent fashion and facilitate chromosomal looping between AR-bound enhancers and the promoter sequences of androgen-responsive genes.39 The use of genome-wide transcriptome analysis in conjunction with GRO-seq has also uncovered divergent transcription of relatively short (
