251
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Secondary structure impacts patterns of selection in human lncRNAs. BMC Biol 2016; 14:60. [PMID: 27457204 PMCID: PMC4960838 DOI: 10.1186/s12915-016-0283-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/04/2016] [Indexed: 02/04/2023] Open
Abstract
Background Metazoans transcribe many long non-coding RNAs (lncRNAs) that are poorly conserved and whose function remains unknown. This has raised the questions of what fraction of the predicted lncRNAs is actually functional, and whether selection can effectively constrain lncRNAs in species with small effective population sizes such as human populations. Results Here we evaluate signatures of selection in human lncRNAs using inter-specific data and intra-specific comparisons from five major populations, as well as by assessing relationships between sequence variation and predictions of secondary structure. In all analyses we included a reference of functionally characterized lncRNAs. Altogether, our results show compelling evidence of recent purifying selection acting on both characterized and predicted lncRNAs. We found that RNA secondary structure constrains sequence variation in lncRNAs, so that polymorphisms are depleted in paired regions with low accessibility and tend to be neutral with respect to structural stability. Conclusions Important implications of our results are that secondary structure plays a role in the functionality of lncRNAs, and that the set of predicted lncRNAs contains a large fraction of functional ones that may play key roles that remain to be discovered. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0283-0) contains supplementary material, which is available to authorized users.
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252
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Nitsche A, Stadler PF. Evolutionary clues in lncRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27436689 DOI: 10.1002/wrna.1376] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/06/2016] [Accepted: 06/09/2016] [Indexed: 12/13/2022]
Abstract
The diversity of long non-coding RNAs (lncRNAs) in the human transcriptome is in stark contrast to the sparse exploration of their functions concomitant with their conservation and evolution. The pervasive transcription of the largely non-coding human genome makes the evolutionary age and conservation patterns of lncRNAs to a topic of interest. Yet it is a fairly unexplored field and not that easy to determine as for protein-coding genes. Although there are a few experimentally studied cases, which are conserved at the sequence level, most lncRNAs exhibit weak or untraceable primary sequence conservation. Recent studies shed light on the interspecies conservation of secondary structures among lncRNA homologs by using diverse computational methods. This highlights the importance of structure on functionality of lncRNAs as opposed to the poor impact of primary sequence changes. Further clues in the evolution of lncRNAs are given by selective constraints on non-coding gene structures (e.g., promoters or splice sites) as well as the conservation of prevalent spatio-temporal expression patterns. However, a rapid evolutionary turnover is observable throughout the heterogeneous group of lncRNAs. This still gives rise to questions about its functional meaning. WIREs RNA 2017, 8:e1376. doi: 10.1002/wrna.1376 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Anne Nitsche
- Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany.,Institute de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Cedex, France
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology - IZI, Leipzig, Germany.,Center for Non-Coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.,Department of Theoretical Chemistry, University of Vienna, Wien, Austria.,Santa Fe Institute, Santa Fe, NM, USA
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253
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Serghiou S, Kyriakopoulou A, Ioannidis JPA. Long noncoding RNAs as novel predictors of survival in human cancer: a systematic review and meta-analysis. Mol Cancer 2016; 15:50. [PMID: 27352941 PMCID: PMC4924330 DOI: 10.1186/s12943-016-0535-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/14/2016] [Indexed: 12/23/2022] Open
Abstract
Background Expression of various long noncoding RNAs (lncRNAs) may affect cancer prognosis. Here, we aim to gather and examine all evidence on the potential role of lncRNAs as novel predictors of survival in human cancer. Methods We systematically searched through PubMed, to identify all published studies reporting on the association between any individual lncRNA or group of lncRNAs with prognosis in human cancer (death or other clinical outcomes). Where appropriate, we then performed quantitative synthesis of those results using meta-analytic methods to identify the true effect size of lncRNAs on cancer prognosis. The reliability of those results was then examined using measures of heterogeneity and testing for selective reporting biases. Results Three hundred ninety-two studies were screened to eventually identify 111 eligible studies on 127 datasets. In total, these represented 16,754 independent participants pertaining to 53 individual and 6 grouped lncRNAs within a total of 19 cancer sites. Overall, 83 % of the studies we identified addressed overall survival and 32 % of the studies addressed recurrence-free survival. For overall survival, 96 % (88/92) of studies identified a statistically significant association of lncRNA expression to prognosis. Meta-analysis of 6 out of 7 lncRNAs for which three or more studies were available, identified statistically significant associations with overall survival. The lncRNA HOTAIR was by far the most broadly studied lncRNA (n = 29; of 111 studies) and featured a summary hazard ratio (HR) of 2.22 (95 % confidence interval (CI), 1.86–2.65) with modest heterogeneity (I2 = 49 %; 95 % CI, 14–79 %). Prominent excess significance was demonstrated across all meta-analyses (p-value = 0.0003), raising the possibility of substantial selective reporting biases. Conclusions Multiple lncRNAs have been shown to be strongly associated with prognosis in diverse cancers, but substantial bias cannot be excluded in this field and larger studies are needed to understand whether these prognostic information may eventually be useful. Electronic supplementary material The online version of this article (doi:10.1186/s12943-016-0535-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stylianos Serghiou
- St. John's Hospital, Livingston, EH54 6PP, UK.,College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | | | - John P A Ioannidis
- Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine Stanford, Stanford, CA, 94305, USA. .,Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Statistics, Stanford University School of Humanities and Sciences, Stanford, CA, 94305, USA. .,Meta-Research Innovation Center at Stanford (METRICS), Stanford University, 1265 Welch Rd, MSOB X306, Stanford, CA, 94305, USA.
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254
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Liu J, Cheng G, Yang H, Deng X, Qin C, Hua L, Yin C. Reciprocal regulation of long noncoding RNAs THBS4‑003 and THBS4 control migration and invasion in prostate cancer cell lines. Mol Med Rep 2016; 14:1451-8. [PMID: 27357608 PMCID: PMC4940078 DOI: 10.3892/mmr.2016.5443] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 02/18/2016] [Indexed: 01/21/2023] Open
Abstract
Increasing evidence implicates long noncoding RNAs (lncRNAs), a class of noncoding RNAs >200 nucleotides in length, in the development of cancer. However, the mechanism underlying the effects of lncRNAs in prostate cancer (PCa) remains to be elucidated. The present study aimed to investigate the role of lncRNA-THBS4-003 in the pathogensis of PCa. In the present study, a microarray containing 8,277 lncRNA probes and 32,207 mRNA probes were used to identify dysregulated mRNAs in three patients with PCa, and reverse transcription-quantitative polymerase chain reaction was used to determine the expression levels of thrombospondin 4 (THBS4) and lncRNA-THBS4-003 in 46 primary PCa and adjacent non-tumor tissue samples. The expression levels of THBS4 were determined in six samples of PCa and adjacent non-tumor tissues using Western blot analysis. The effects of forced THBS4 knockdown and lncRNA-THBS4-003 knockdown in the two PCa cell lines, DU145 and PC-3, were evaluated using cell migration and invasion assays, as well as using Western blot analysis. Of the 40,484 probes in the microarray, 354 were significantly upregulated (P<0.05; fold-change >2). The most significantly upregulated mRNA was THBS4. The expression levels of THBS4 and lncRNA-THBS4-003 in the 46 primary PCa samples was significantly higher, compared with that in the adjacent non-tumor tissue samples. Patients with Gleason scores >7 exhibited higher expression levels of lncRNA-THBS4-003, compared with patients with lower scores. Knockdown of THBS4 or lncRNA-THBS4-003 significantly reduced the migratory and invasive abilities of the PCa cells in vitro, and decreased the expression levels of p38 and matrix metal-loproteinase (MMP)-9. These findings suggested that the reciprocal regulation of lncRNA-THBS4-003 and THBS4 contributed to the pathogenesis of PCa. Therefore silencing lncRNA-THBS4-003 or THBS4 may inhibit PCa cell migration and invasion, and regulate the levels of MMP-9 through the mitogen-activated protein kinase signaling pathway.
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Affiliation(s)
- Jinliang Liu
- State Key Laboratory of Reproductive Medicine, Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Gong Cheng
- State Key Laboratory of Reproductive Medicine, Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Haiwei Yang
- State Key Laboratory of Reproductive Medicine, Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Xiaheng Deng
- State Key Laboratory of Reproductive Medicine, Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Chao Qin
- State Key Laboratory of Reproductive Medicine, Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Lixin Hua
- State Key Laboratory of Reproductive Medicine, Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Changjun Yin
- State Key Laboratory of Reproductive Medicine, Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
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255
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Warnefors M, Hartmann B, Thomsen S, Alonso CR. Combinatorial Gene Regulatory Functions Underlie Ultraconserved Elements in Drosophila. Mol Biol Evol 2016; 33:2294-306. [PMID: 27247329 PMCID: PMC4989106 DOI: 10.1093/molbev/msw101] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ultraconserved elements (UCEs) are discrete genomic elements conserved across large evolutionary distances. Although UCEs have been linked to multiple facets of mammalian gene regulation their extreme evolutionary conservation remains largely unexplained. Here, we apply a computational approach to investigate this question in Drosophila, exploring the molecular functions of more than 1,500 UCEs shared across the genomes of 12 Drosophila species. Our data indicate that Drosophila UCEs are hubs for gene regulatory functions and suggest that UCE sequence invariance originates from their combinatorial roles in gene control. We also note that the gene regulatory roles of intronic and intergenic UCEs (iUCEs) are distinct from those found in exonic UCEs (eUCEs). In iUCEs, transcription factor (TF) and epigenetic factor binding data strongly support iUCE roles in transcriptional and epigenetic regulation. In contrast, analyses of eUCEs indicate that they are two orders of magnitude more likely than the expected to simultaneously include protein-coding sequence, TF-binding sites, splice sites, and RNA editing sites but have reduced roles in transcriptional or epigenetic regulation. Furthermore, we use a Drosophila cell culture system and transgenic Drosophila embryos to validate the notion of UCE combinatorial regulatory roles using an eUCE within the Hox gene Ultrabithorax and show that its protein-coding region also contains alternative splicing regulatory information. Taken together our experiments indicate that UCEs emerge as a result of combinatorial gene regulatory roles and highlight common features in mammalian and insect UCEs implying that similar processes might underlie ultraconservation in diverse animal taxa.
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Affiliation(s)
- Maria Warnefors
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Britta Hartmann
- Institute of Human Genetics, Freiburg, Germany BIOSS Centre for Biological Signaling Studies, University Medical Center Freiburg, Freiburg, Germany
| | - Stefan Thomsen
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Claudio R Alonso
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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256
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Abstract
Neuroblastoma is a disease that affects infants and despite intense multimodal therapy, high-risk patients have low survival rates (<50%). In recent years long noncoding RNAs (lncRNAs) have become the cutting edge of cancer research with inroads made in understanding their roles in multiple cancer types, including prostate and breast cancers. The roles of lncRNAs in neuroblastoma have just begun to be elucidated. This review summarises where we are with regards to lncRNAs in neuroblastoma. The known mechanistic roles of lncRNAs during neuroblastoma pathogenesis are discussed, as well as the relationship between lncRNA expression and the differentiation capacity of neuroblastoma cells. We speculate about the use of some of these lncRNAs, such as those mapping to the 6p22 hotspot, as biomarkers for neuroblastoma prognosis and treatment. This novel way of thinking about both neuroblastoma and lncRNAs brings a new perspective to the prognosis and treatment of high-risk patients.
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257
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Saus E, Brunet-Vega A, Iraola-Guzmán S, Pegueroles C, Gabaldón T, Pericay C. Long Non-Coding RNAs As Potential Novel Prognostic Biomarkers in Colorectal Cancer. Front Genet 2016; 7:54. [PMID: 27148353 PMCID: PMC4828582 DOI: 10.3389/fgene.2016.00054] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/21/2016] [Indexed: 01/27/2023] Open
Abstract
Colorectal cancer (CRC) is the fourth most common cause of death worldwide. Surgery is usually the first line of treatment for patients with CRC but many tumors with similar histopathological features show significantly different clinical outcomes. The discovery of robust prognostic biomarkers in patients with CRC is imperative to achieve more effective treatment strategies and improve patient's care. Recent progress in next generation sequencing methods and transcriptome analysis has revealed that a much larger part of the genome is transcribed into RNA than previously assumed. Collectively referred to as non-coding RNAs (ncRNAs), some of these RNA molecules such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been shown to be altered and to play critical roles in tumor biology. This discovery leads to exciting possibilities for personalized cancer diagnosis, and therapy. Many lncRNAs are tissue and cancer-type specific and have already revealed to be useful as prognostic markers. In this review, we focus on recent findings concerning aberrant expression of lncRNAs in CRC tumors and emphasize their prognostic potential in CRC. Further studies focused on the mechanisms of action of lncRNAs will contribute to the development of novel biomarkers for diagnosis and disease progression.
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Affiliation(s)
- Ester Saus
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain
| | - Anna Brunet-Vega
- Department of Oncology Research, Parc Taulí Foundation, Corporació Sanitària Parc Taulí - University Institute - UAB Barcelona Sabadell, Spain
| | - Susana Iraola-Guzmán
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain
| | - Cinta Pegueroles
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain; Institució Catalana de Recerca i Estudis AvançatsBarcelona, Spain
| | - Carles Pericay
- Department of Oncology Research, Parc Taulí Foundation, Corporació Sanitària Parc Taulí - University Institute - UAB BarcelonaSabadell, Spain; Oncology Service, Hospital de Sabadell, Corporació Sanitària Parc Taulí - University Institute - UAB BarcelonaSabadell, Spain
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258
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Schmitt AM, Chang HY. Long Noncoding RNAs in Cancer Pathways. Cancer Cell 2016; 29:452-463. [PMID: 27070700 PMCID: PMC4831138 DOI: 10.1016/j.ccell.2016.03.010] [Citation(s) in RCA: 2288] [Impact Index Per Article: 286.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/01/2016] [Accepted: 03/14/2016] [Indexed: 12/16/2022]
Abstract
Genome-wide cancer mutation analyses are revealing an extensive landscape of functional mutations within the noncoding genome, with profound effects on the expression of long noncoding RNAs (lncRNAs). While the exquisite regulation of lncRNA transcription can provide signals of malignant transformation, we now understand that lncRNAs drive many important cancer phenotypes through their interactions with other cellular macromolecules including DNA, protein, and RNA. Recent advancements in surveying lncRNA molecular mechanisms are now providing the tools to functionally annotate these cancer-associated transcripts, making these molecules attractive targets for therapeutic intervention in the fight against cancer.
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Affiliation(s)
- Adam M Schmitt
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA.
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259
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Ultraconserved region-containing Transformer 2β4 controls senescence of colon cancer cells. Oncogenesis 2016; 5:e213. [PMID: 27043659 PMCID: PMC4848834 DOI: 10.1038/oncsis.2016.18] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/08/2016] [Accepted: 01/28/2016] [Indexed: 01/23/2023] Open
Abstract
Ultraconserved regions (UCRs) are >200 bp genomic segments with perfect human-to-rodent sequence identity. Transcribed UCRs constitute a new category of noncoding RNAs whose functions remain poorly understood. The human transformer 2β (TRA2B) gene contains a 419-bp UCR spanning the 276-bp exon 2 and its neighboring introns. TRA2B exon 2 has premature stop codons, whereas an exon 2-containing splice variant (TRA2β4) was expressed preferentially in the nuclei of human colon cancer cells. TRA2β4 knockdown p53-independently stimulated CDKN1A transcription and increased p21, resulting in the appearance of senescent cells. Biotin pull-down and RNA immunoprecipitation assays revealed that TRA2β4 interacted with Sp1 through a Sp1-binding sequence (485-GGGG-488) in a stem-loop structure of exon 2. Mutation of this sequence (485-AAGG-488) disrupted the stem-loop structure, blocked the interaction with Sp1 and increased CDKN1A transcription. Overexpression of TRA2β4 significantly decreased CDKN1A mRNA levels and accelerated cell growth, but the introduction of the mutation in the Sp1-binding sequence completely canceled these effects. Taken together, TRA2β4 may sequester Sp1 from occupying promoters of target genes including CDKN1A, promoting cell growth by interrupting the senescence-related gene expression program. This novel function of TRA2β4 may uncover an oncogenic function of transcribed UCRs.
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260
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Bao BY, Lin VC, Yu CC, Yin HL, Chang TY, Lu TL, Lee HZ, Pao JB, Huang CY, Huang SP. Genetic variants in ultraconserved regions associate with prostate cancer recurrence and survival. Sci Rep 2016; 6:22124. [PMID: 26902966 PMCID: PMC4763269 DOI: 10.1038/srep22124] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/08/2016] [Indexed: 12/20/2022] Open
Abstract
Ultraconserved regions (UCRs) are DNA segments of longer than 200 bp in length that are completely conserved between human, rat, and mouse genomes. Recent studies have shown that UCRs are frequently located at fragile sites involved in cancers, and their levels of transcription can be altered during human tumorigenesis. We systematically evaluated 14 common single-nucleotide polymorphisms (SNPs) within UCRs in three cohorts of prostate cancer patients, to test the hypothesis that these UCR SNPs might influence clinical outcomes. Examination using multivariate analysis adjusted for known clinicopathologic factors found association between rs8004379 and recurrence in localized disease [hazard ratio (HR) 0.61, 95% confidence interval (CI) 0.41–0.91, P = 0.015], which was confirmed in the replication set (HR 0.70, 95% CI 0.51–0.96, P = 0.027). Remarkably, a consistent association of rs8004379 with a decreased risk for prostate cancer-specific mortality was also observed in the advanced prostate cancer patient group (HR 0.48, 95% CI 0.32–0.70, P < 0.001). Additional in silico analysis suggests that rs8004379 tends to affect NPAS3 expression, which in turn was found to be correlated with patient prognosis. In conclusion, our findings suggest that SNPs within UCRs may be valuable prognostic biomarkers for assessing prostate cancer treatment response and survival.
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Affiliation(s)
- Bo-Ying Bao
- Department of Pharmacy, China Medical University, Taichung, Taiwan.,Sex Hormone Research Center, China Medical University Hospital, Taichung, Taiwan.,Department of Nursing, Asia University, Taichung, Taiwan
| | - Victor C Lin
- Department of Urology, E-Da Hospital, Kaohsiung, Taiwan.,School of Medicine for International Students, I-Shou University, Kaohsiung, Taiwan
| | - Chia-Cheng Yu
- Division of Urology, Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Pharmacy, Tajen University, Pingtung, Taiwan
| | - Hsin-Ling Yin
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Pathology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ta-Yuan Chang
- Department of Occupational Safety and Health, China Medical University, Taichung, Taiwan
| | - Te-Ling Lu
- Department of Pharmacy, China Medical University, Taichung, Taiwan
| | - Hong-Zin Lee
- Department of Pharmacy, China Medical University, Taichung, Taiwan
| | - Jiunn-Bey Pao
- Department of Pharmacy, Linsen Chinese Medicine Branch, Taipei City Hospital, Taipei, Taiwan
| | - Chao-Yuan Huang
- Department of Urology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shu-Pin Huang
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Urology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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261
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Ge M, Li A, Wang M. A Bipartite Network-based Method for Prediction of Long Non-coding RNA-protein Interactions. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:62-71. [PMID: 26917505 PMCID: PMC4792848 DOI: 10.1016/j.gpb.2016.01.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/04/2016] [Accepted: 01/06/2016] [Indexed: 01/08/2023]
Abstract
As one large class of non-coding RNAs (ncRNAs), long ncRNAs (lncRNAs) have gained considerable attention in recent years. Mutations and dysfunction of lncRNAs have been implicated in human disorders. Many lncRNAs exert their effects through interactions with the corresponding RNA-binding proteins. Several computational approaches have been developed, but only few are able to perform the prediction of these interactions from a network-based point of view. Here, we introduce a computational method named lncRNA–protein bipartite network inference (LPBNI). LPBNI aims to identify potential lncRNA–interacting proteins, by making full use of the known lncRNA–protein interactions. Leave-one-out cross validation (LOOCV) test shows that LPBNI significantly outperforms other network-based methods, including random walk (RWR) and protein-based collaborative filtering (ProCF). Furthermore, a case study was performed to demonstrate the performance of LPBNI using real data in predicting potential lncRNA–interacting proteins.
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Affiliation(s)
- Mengqu Ge
- School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China
| | - Ao Li
- School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China; Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China.
| | - Minghui Wang
- School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China; Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China
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262
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Abstract
It is increasingly evident that many of the genomic mutations in cancer reside inside regions that do not encode proteins. However, these regions are often transcribed into long noncoding RNAs (lncRNAs). The recent application of next-generation sequencing to a growing number of cancer transcriptomes has indeed revealed thousands of lncRNAs whose aberrant expression is associated with different cancer types. Among the few that have been functionally characterized, several have been linked to malignant transformation. Notably, these lncRNAs have key roles in gene regulation and thus affect various aspects of cellular homeostasis, including proliferation, survival, migration or genomic stability. This review aims to summarize current knowledge of lncRNAs from the cancer perspective. It discusses the strategies that led to the identification of cancer-related lncRNAs and the methodologies and challenges involving the study of these molecules, as well as the imminent applications of these findings to the clinic.
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263
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Linc-ROR induces epithelial-mesenchymal transition and contributes to drug resistance and invasion of breast cancer cells. Tumour Biol 2016; 37:10861-70. [DOI: 10.1007/s13277-016-4909-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/22/2016] [Indexed: 10/22/2022] Open
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264
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Khurana E, Fu Y, Chakravarty D, Demichelis F, Rubin MA, Gerstein M. Role of non-coding sequence variants in cancer. Nat Rev Genet 2016; 17:93-108. [PMID: 26781813 DOI: 10.1038/nrg.2015.17] [Citation(s) in RCA: 319] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Patients with cancer carry somatic sequence variants in their tumour in addition to the germline variants in their inherited genome. Although variants in protein-coding regions have received the most attention, numerous studies have noted the importance of non-coding variants in cancer. Moreover, the overwhelming majority of variants, both somatic and germline, occur in non-coding portions of the genome. We review the current understanding of non-coding variants in cancer, including the great diversity of the mutation types--from single nucleotide variants to large genomic rearrangements--and the wide range of mechanisms by which they affect gene expression to promote tumorigenesis, such as disrupting transcription factor-binding sites or functions of non-coding RNAs. We highlight specific case studies of somatic and germline variants, and discuss how non-coding variants can be interpreted on a large-scale through computational and experimental methods.
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Affiliation(s)
- Ekta Khurana
- Meyer Cancer Center, Weill Cornell Medical College, New York, New York 10065, USA.,Institute for Precision Medicine, Weill Cornell Medical College, New York, New York 10065, USA.,Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA
| | - Yao Fu
- Bina Technologies, Roche Sequencing, Redwood City, California 94065, USA
| | - Dimple Chakravarty
- Institute for Precision Medicine, Weill Cornell Medical College, New York, New York 10065, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Francesca Demichelis
- Institute for Precision Medicine, Weill Cornell Medical College, New York, New York 10065, USA.,Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York 10021, USA.,Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Mark A Rubin
- Meyer Cancer Center, Weill Cornell Medical College, New York, New York 10065, USA.,Institute for Precision Medicine, Weill Cornell Medical College, New York, New York 10065, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.,Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA
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265
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Abstract
Accumulating evidence has shown the presence of cancer stem cells in a wide spectrum of human cancers, which have the ability to self-renew and differentiate, thus leading to tumorigenesis, proliferation, cancer dissemination, drug resistance, and tumor relapse. Cancer cell plasticity allows tumor to invade and grow at primary or distant sites. Epithelial-mesenchymal transition (EMT) is the most important mechanism of cancer cell plasticity and cancer stem cells. Substantial evidence has supported a noncoding RNA network, especially miRNA, in regulating cancer cell plasticity and cancer stem cell biology. Besides, lncRNA is also found to participate in cancer development. Understanding the mechanisms of these processes might be valuable for developing accurate targeted therapies to tackle cancer progression and cancer stem cells.
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266
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Zhang X, Lopez-Berestein G, Sood AK, Calin GA. Profiling Long Noncoding RNA Expression Using Custom-Designed Microarray. Methods Mol Biol 2016; 1402:33-41. [PMID: 26721482 DOI: 10.1007/978-1-4939-3378-5_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Long noncoding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. The abnormal expression of lncRNAs has been implicated in a range of many human diseases, including cancer. But only a small number of functional lncRNAs have been well characterized to date. lncRNA expression profiling may help to identify useful molecular biomarkers and targets for novel therapeutic approaches in the future. In this chapter, we describe a highly efficient lncRNA expression profiling method using a custom-designed microarray.
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Affiliation(s)
- Xinna Zhang
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA.
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Gabriel Lopez-Berestein
- Center for RNA Interference andNon-coding RNAs, The University of Texas MD Anderson Cancer Center (MDACC), 1515 Holcombe Blvd., Houston, TX, 77030, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center (MDACC), 1515 Holcombe Blvd., Houston, TX, 77030, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, USA
| | - George A Calin
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of GynecologicOncology and ReproductiveMedicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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267
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Abstract
Long noncoding RNAs (lncRNAs) are noncoding transcripts usually longer than 200 nts that have recently emerged as one of the largest and significantly diverse RNA families. The biological role and functions of lncRNAs are still mostly uncharacterized. Their target-mimetic, sponge/decoy function on microRNAs was recently uncovered. miRNAs are a class of noncoding RNA species (~22 nts) that play a central role in posttranscriptional regulation of protein coding genes by mRNA cleavage, direct translational repression and/or mRNA destabilization. LncRNAs can act as miRNA sponges, reducing their regulatory effect on mRNAs. This function introduces an extra layer of complexity in the miRNA-target interaction network. This chapter focuses on the study of miRNA-lncRNA interactions with either in silico or experimentally supported analyses. The proposed methodologies can be appropriately adapted in order to become the backbone of advanced multistep functional miRNA analyses.
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Affiliation(s)
- Maria D Paraskevopoulou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, Volos, Greece.
| | - Artemis G Hatzigeorgiou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, Volos, Greece.
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268
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Gumireddy K, Yan J, Huang Q. Isolation of Protein Complexes Associated with Long Noncoding RNAs. Methods Mol Biol 2016; 1402:27-32. [PMID: 26721481 DOI: 10.1007/978-1-4939-3378-5_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) are a new class of regulatory genes that play critical roles in various processes ranging from normal development to human diseases. Recent studies have shown that protein complexes are required for the functions of lncRNAs. The identification of these proteins which are associated with lncRNAs is critical for the understanding of molecular mechanisms of lncRNAs in gene regulation and their functions. In this chapter, we describe a method to isolate proteins associated with lncRNAs. This procedure involves fusion protein maltose-binding protein (MBP) fused to MS2-binding protein to pull down the proteins associated with lncRNA and the identification of these proteins by mass spectrometry.
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Affiliation(s)
| | - Jinchun Yan
- University of Washington Medical Center, 1959 N.E. Pacific Street, Seattle, WA, 98195, USA
| | - Qihong Huang
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA.
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269
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Predicting Long Noncoding RNA and Protein Interactions Using Heterogeneous Network Model. BIOMED RESEARCH INTERNATIONAL 2015; 2015:671950. [PMID: 26839884 PMCID: PMC4709602 DOI: 10.1155/2015/671950] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 11/16/2015] [Accepted: 12/01/2015] [Indexed: 12/11/2022]
Abstract
Recent study shows that long noncoding RNAs (lncRNAs) are participating in diverse biological processes and complex diseases. However, at present the functions of lncRNAs are still rarely known. In this study, we propose a network-based computational method, which is called lncRNA-protein interaction prediction based on Heterogeneous Network Model (LPIHN), to predict the potential lncRNA-protein interactions. First, we construct a heterogeneous network by integrating the lncRNA-lncRNA similarity network, lncRNA-protein interaction network, and protein-protein interaction (PPI) network. Then, a random walk with restart is implemented on the heterogeneous network to infer novel lncRNA-protein interactions. The leave-one-out cross validation test shows that our approach can achieve an AUC value of 96.0%. Some lncRNA-protein interactions predicted by our method have been confirmed in recent research or database, indicating the efficiency of LPIHN to predict novel lncRNA-protein interactions.
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270
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Wang X, Chen K, Guo G, Chen JL. Noncoding RNAs and their functional involvement in regulation of chronic myeloid leukemia. Brief Funct Genomics 2015; 15:239-48. [PMID: 26647283 DOI: 10.1093/bfgp/elv059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Noncoding RNAs (ncRNAs) comprise multiple classes of transcripts that have no protein-coding ability but play critical roles as RNA regulators in various cellular processes. To date, the well-studied ncRNAs are microRNAs (miRs) that generally act as regulators of gene expression through binding to target mRNAs. Recent advances in high-throughput sequencing technologies have led to the discovery of thousands of unannotated noncoding transcripts, especially long noncoding RNAs (lncRNAs). These lncRNAs are being increasingly recognized as key regulators in diverse biological processes via a variety of mechanisms. Aberrant expression of miRs and lncRNAs has been shown to be associated with many human diseases and cancers. Increasing ncRNAs have been identified as biomarkers for patient prognosis and potential therapeutic agents for cancers. Furthermore, it is worth noting that progresses have been made in understanding the functional involvement of ncRNAs in Bcr-Abl-induced chronic myeloid leukemia (CML). Here, we highlight the pathogenesis of CML, functional significance of miRs and lncRNAs in regulation of CML development and involved mechanisms underlying their action.
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271
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Goto K, Ishikawa S, Honma R, Tanimoto K, Sakamoto N, Sentani K, Oue N, Teishima J, Matsubara A, Yasui W. The transcribed-ultraconserved regions in prostate and gastric cancer: DNA hypermethylation and microRNA-associated regulation. Oncogene 2015; 35:3598-606. [PMID: 26640143 DOI: 10.1038/onc.2015.445] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 09/18/2015] [Accepted: 10/05/2015] [Indexed: 12/24/2022]
Abstract
The transcribed-ultraconserved regions (T-UCRs) are a novel class of non-coding RNAs, which are absolutely conserved (100%) between the orthologous regions of the human, rat and mouse genomes. Previous studies have described that several T-UCRs show differential expressions in cancers and might be involved in cancer development. We investigated the transcriptional levels of representative 26 T-UCRs and determined the regions that were differently expressed in prostate cancer (PCa) and gastric cancer (GC). A quantitative reverse transcription-polymerase chain reaction analysis revealed the downregulation of Uc.158+A expression by a DNA methylation-associated mechanism, which was restored by 5-Aza-dC (5-aza-2'-deoxycytidine) treatment. Bisulfite genomic sequencing using cell lines and tissue samples demonstrated cancer-specific CpG hypermethylation in both GC and PCa. However, Uc.416+A was only overexpressed in GC and we identified an miR-153 binding site in the possible regulatory region of Uc.416+A using online databases. Along with a forced expression or knockdown of miR-153 in MKN-74 GC cells, the transcriptional levels of Uc.416+A were significantly disturbed. A luciferase reporter gene assay supported the direct regulation of Uc.416+A expression by miR-153. Furthermore, Uc.416+A was associated with cell growth through the regulation of IGFBP6 (insulin-like growth factor-binding protein 6) in GC. These findings suggest an oncogenic role of Uc.416+A in GC, which suggests that our approach would provide new insights into functional studies of T-UCRs in cancer biology.
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Affiliation(s)
- K Goto
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan.,Department of Urology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - S Ishikawa
- School of Medicine, Hiroshima University, Hiroshima, Japan
| | - R Honma
- School of Medicine, Hiroshima University, Hiroshima, Japan
| | - K Tanimoto
- Department of Radiation Medicine, Hiroshima University Research Institute for Radiation Biology and Medicine, Hiroshima Japan
| | - N Sakamoto
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - K Sentani
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - N Oue
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - J Teishima
- Department of Urology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - A Matsubara
- Department of Urology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - W Yasui
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
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272
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Chen X. KATZLDA: KATZ measure for the lncRNA-disease association prediction. Sci Rep 2015; 5:16840. [PMID: 26577439 PMCID: PMC4649494 DOI: 10.1038/srep16840] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/21/2015] [Indexed: 12/28/2022] Open
Abstract
Accumulating experimental studies have demonstrated important associations between alterations and dysregulations of lncRNAs and the development and progression of various complex human diseases. Developing effective computational models to integrate vast amount of heterogeneous biological data for the identification of potential disease-lncRNA associations has become a hot topic in the fields of human complex diseases and lncRNAs, which could benefit lncRNA biomarker detection for disease diagnosis, treatment, and prevention. Considering the limitations in previous computational methods, the model of KATZ measure for LncRNA-Disease Association prediction (KATZLDA) was developed to uncover potential lncRNA-disease associations by integrating known lncRNA-disease associations, lncRNA expression profiles, lncRNA functional similarity, disease semantic similarity, and Gaussian interaction profile kernel similarity. KATZLDA could work for diseases without known related lncRNAs and lncRNAs without known associated diseases. KATZLDA obtained reliable AUCs of 7175, 0.7886, 0.7719 in the local and global leave-one-out cross validation and 5-fold cross validation, respectively, significantly improving previous classical methods. Furthermore, case studies of colon, gastric, and renal cancer were implemented and 60% of top 10 predictions have been confirmed by recent biological experiments. It is anticipated that KATZLDA could be an important resource with potential values for biomedical researches.
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Affiliation(s)
- Xing Chen
- National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, 100190, China.,Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
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273
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Chen L, Kang C. miRNA interventions serve as 'magic bullets' in the reversal of glioblastoma hallmarks. Oncotarget 2015; 6:38628-42. [PMID: 26439688 PMCID: PMC4770725 DOI: 10.18632/oncotarget.5926] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 09/06/2015] [Indexed: 01/04/2023] Open
Abstract
microRNAs (miRNAs) are no longer deemed small pieces of RNA "trash" in the human transcriptome but are considered to be master regulators of gene expression that are critical in maintaining cellular homeostasis post-transcriptionally. The concept triggers great interest in studying miRNA dysregulations in human diseases, especially in cancers. Glioblastoma (GBM) has long been the leading cause of the high mortality and morbidity of CNS tumors in adults, which is a consequence of the lack of strategies to reverse the hallmark features of GBM (e.g., borderless expansion and diffuse infiltration). In the past decade, dissecting the molecular architecture of GBM has led to a better understanding of the molecular basis of the hallmarks, generating many promising pharmacological protein targets. However, few clinical responses have been highlighted, suggesting the demand for new therapeutic strategies and targets. In this review, we systemically summarize the context-dependently validated miRNAs with one or more functional targets in the development of GBM hallmarks and review the current miRNA-targeting strategies. We note that only a few miRNA-based therapeutics are trialed for clinical significance, and none of them is tailored to GBM, thereby urging us to bring miRNA therapeutics to the front line either alone or in combination.
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Affiliation(s)
- Luyue Chen
- Laboratory of Neuro-Oncology, Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Chunsheng Kang
- Laboratory of Neuro-Oncology, Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
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274
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Xu TP, Liu XX, Xia R, Yin L, Kong R, Chen WM, Huang MD, Shu YQ. SP1-induced upregulation of the long noncoding RNA TINCR regulates cell proliferation and apoptosis by affecting KLF2 mRNA stability in gastric cancer. Oncogene 2015; 34:5648-61. [PMID: 25728677 DOI: 10.1038/onc.2015.18] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 01/14/2015] [Accepted: 01/16/2015] [Indexed: 12/25/2022]
Abstract
The long noncoding RNA TINCR shows aberrant expression in human squamous carcinomas. However, its expression and function in gastric cancer remain unclear. We report that TINCR is strongly upregulated in human gastric carcinoma (GC), where it was found to contribute to oncogenesis and cancer progression. We also revealed that TINCR overexpression is induced by nuclear transcription factor SP1. Silencing TINCR expression inhibited cell proliferation, colony formation, tumorigenicity and apoptosis promotion, whereas TINCR overexpression promoted cell growth, as documented in the SGC7901 and BGC823 cell lines. Mechanistic analyses indicated that TINCR could bind to STAU1 (staufen1) protein, and influence KLF2 mRNA stability and expression, then KLF2 regulated cyclin-dependent kinase genes CDKN1A/P21 and CDKN2B/P15 transcription and expression, thereby affecting the proliferation and apoptosis of GC cells. Together, our findings suggest that TINCR contributes to the oncogenic potential of GC and may constitute a potential therapeutic target in this disease.
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Affiliation(s)
- T-P Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - X-X Liu
- Department of Gastrointestinal Surgery, Northern Jiangsu People's Hospital, Clinical Medical School, Yangzhou University, Yangzhou, People's Republic of China
| | - R Xia
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - L Yin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - R Kong
- Clinical Medical Examination Center, Northern Jiangsu People's Hospital, Clinical Medical School, Yangzhou University, Yangzhou, People's Republic of China
| | - W-M Chen
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - M-D Huang
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, People's Republic of China
| | - Y-Q Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
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275
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YANG XIAODONG, XU HONGTAO, XU XIAOHUI, RU GAN, LIU WEI, ZHU JUNJIA, WU YONGYOU, ZHAO KUI, WU YONG, XING CHUNGEN, ZHANG SHUYU, CAO JIANPING, LI MING. Knockdown of long non-coding RNA HOTAIR inhibits proliferation and invasiveness and improves radiosensitivity in colorectal cancer. Oncol Rep 2015; 35:479-87. [DOI: 10.3892/or.2015.4397] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/12/2015] [Indexed: 11/06/2022] Open
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276
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Yan X, Hu Z, Feng Y, Hu X, Yuan J, Zhao SD, Zhang Y, Yang L, Shan W, He Q, Fan L, Kandalaft LE, Tanyi JL, Li C, Yuan CX, Zhang D, Yuan H, Hua K, Lu Y, Katsaros D, Huang Q, Montone K, Fan Y, Coukos G, Boyd J, Sood AK, Rebbeck T, Mills GB, Dang CV, Zhang L. Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers. Cancer Cell 2015; 28:529-540. [PMID: 26461095 PMCID: PMC4777353 DOI: 10.1016/j.ccell.2015.09.006] [Citation(s) in RCA: 515] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 07/23/2015] [Accepted: 09/15/2015] [Indexed: 12/14/2022]
Abstract
The discovery of long non-coding RNA (lncRNA) has dramatically altered our understanding of cancer. Here, we describe a comprehensive analysis of lncRNA alterations at transcriptional, genomic, and epigenetic levels in 5,037 human tumor specimens across 13 cancer types from The Cancer Genome Atlas. Our results suggest that the expression and dysregulation of lncRNAs are highly cancer type specific compared with protein-coding genes. Using the integrative data generated by this analysis, we present a clinically guided small interfering RNA screening strategy and a co-expression analysis approach to identify cancer driver lncRNAs and predict their functions. This provides a resource for investigating lncRNAs in cancer and lays the groundwork for the development of new diagnostics and treatments.
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Affiliation(s)
- Xiaohui Yan
- Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
| | - Zhongyi Hu
- Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Feng
- Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaowen Hu
- Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jiao Yuan
- Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sihai D Zhao
- Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
| | - Youyou Zhang
- Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lu Yang
- Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; West China Medical School, Sichuan University, Chengdu 610041, China
| | - Weiwei Shan
- Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
| | - Qun He
- Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lingling Fan
- Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
| | - Lana E Kandalaft
- Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Ludwig Center for Cancer Research and Department of Oncology, University of Lausanne, Lausanne 1007, Switzerland
| | - Janos L Tanyi
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chunsheng Li
- Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chao-Xing Yuan
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dongmei Zhang
- Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; West China Medical School, Sichuan University, Chengdu 610041, China
| | - Huiqing Yuan
- Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan 250012, China
| | - Keqin Hua
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
| | - Yiling Lu
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Dionyssios Katsaros
- Department of Surgical Sciences, Gynecologic Oncology, Azienda Ospedaliero - Universitaria Citta della Salute, Turin 10126, Italy
| | | | - Kathleen Montone
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Fan
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - George Coukos
- Ludwig Center for Cancer Research and Department of Oncology, University of Lausanne, Lausanne 1007, Switzerland
| | - Jeff Boyd
- Cancer Genome Institute, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Anil K Sood
- Department of Gynecologic Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Center for RNA Interference and Non-Coding RNA, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Timothy Rebbeck
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Chi V Dang
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Lin Zhang
- Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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277
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Pan Y, Liu R, Terpstra E, Wang Y, Qiao F, Wang J, Tong Y, Pan B. Dysregulation and Diagnostic Potential of microRNA in Alzheimer’s Disease. J Alzheimers Dis 2015; 49:1-12. [DOI: 10.3233/jad-150451] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoqian Pan
- Department of Veterinary Pathology, College of Animal Sciences, Henan Institute of Science and Technology, Xinxiang, China
| | - Ruizhu Liu
- China-Japan Union Hospital Jilin University, Changchun, Jilin, China
| | - Erin Terpstra
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA
| | - Yanqing Wang
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA
| | - Fangfang Qiao
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA
| | - Jin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Lab of Agrobiotechnology, Key Lab of Animal Epidemiology and Zoonosis, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bo Pan
- Department of Veterinary Pathology, College of Animal Sciences, Henan Institute of Science and Technology, Xinxiang, China
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Lab of Agrobiotechnology, Key Lab of Animal Epidemiology and Zoonosis, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
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278
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Abstract
Colorectal cancer (CRC) is a leading cause of cancer deaths worldwide. One of the fundamental processes driving the initiation and progression of CRC is the accumulation of a variety of genetic and epigenetic changes in colonic epithelial cells. Over the past decade, major advances have been made in our understanding of cancer epigenetics, particularly regarding aberrant DNA methylation, microRNA (miRNA) and noncoding RNA deregulation, and alterations in histone modification states. Assessment of the colon cancer "epigenome" has revealed that virtually all CRCs have aberrantly methylated genes and altered miRNA expression. The average CRC methylome has hundreds to thousands of abnormally methylated genes and dozens of altered miRNAs. As with gene mutations in the cancer genome, a subset of these epigenetic alterations, called driver events, are presumed to have a functional role in CRC. In addition, the advances in our understanding of epigenetic alterations in CRC have led to these alterations being developed as clinical biomarkers for diagnostic, prognostic, and therapeutic applications. Progress in this field suggests that these epigenetic alterations will be commonly used in the near future to direct the prevention and treatment of CRC.
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Affiliation(s)
- Yoshinaga Okugawa
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, TX, 75246-2017, USA
| | - William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA,Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ajay Goel
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, Texas.
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279
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Abstract
Non-coding RNAs have gained increasing attention, as their physiological and pathological functions are being gradually uncovered. MicroRNAs are the most well-studied ncRNAs, which play essential roles in translational repression and mRNA degradation. In contrast, long non-coding RNAs are distinguished from other small/short non-coding RNAs by length and regulate chromatin remodeling, gene transcription and posttranscriptional modifications. Recently, circular RNAs have emerged as endogenous, abundant, conserved and stable in mammalian cells. It has been demonstrated that circular RNAs can function as miRNA sponges. Other possible biological functions of circular RNAs are still under investigation. In this review, the biogenesis and biological functions of the three major types of ncRNAs, including miRNAs, lncRNAs and circRNAs, are overviewed. In addition, the role of ncRNAs in human diseases and potential clinical applications of ncRNAs are discussed.
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Affiliation(s)
- Nan Wu
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Burton B Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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280
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Jayakodi M, Jung JW, Park D, Ahn YJ, Lee SC, Shin SY, Shin C, Yang TJ, Kwon HW. Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera. BMC Genomics 2015; 16:680. [PMID: 26341079 PMCID: PMC4559890 DOI: 10.1186/s12864-015-1868-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 08/19/2015] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins. Recently, lncRNAs have gained special attention for their roles in various biological process and diseases. RESULTS In an attempt to identify long intergenic non-coding RNAs (lincRNAs) and their possible involvement in honey bee development and diseases, we analyzed RNA-seq datasets generated from Asian honey bee (Apis cerana) and western honey bee (Apis mellifera). We identified 2470 lincRNAs with an average length of 1011 bp from A. cerana and 1514 lincRNAs with an average length of 790 bp in A. mellifera. Comparative analysis revealed that 5 % of the total lincRNAs derived from both species are unique in each species. Our comparative digital gene expression analysis revealed a high degree of tissue-specific expression among the seven major tissues of honey bee, different from mRNA expression patterns. A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues. Importantly, we identified 11 lincRNAs that are specifically regulated upon viral infection in honey bees, and 10 of them appear to play roles during infection with various viruses. CONCLUSIONS This study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee.
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Affiliation(s)
- Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Je Won Jung
- WCU Biomodulation Major, Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Doori Park
- WCU Biomodulation Major, Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Young-Joon Ahn
- WCU Biomodulation Major, Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Sang-Yoon Shin
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Chanseok Shin
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Hyung Wook Kwon
- WCU Biomodulation Major, Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
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281
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Upregulated expression of long non-coding RNA LINC00982 regulates cell proliferation and its clinical relevance in patients with gastric cancer. Tumour Biol 2015; 37:1983-93. [PMID: 26334618 DOI: 10.1007/s13277-015-3979-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 08/24/2015] [Indexed: 12/14/2022] Open
Abstract
Emerging evidences indicate that dysregulated long non-coding RNAs (lncRNAs) are implicated in cancer tumorigenesis and progression and might be used as diagnosis and prognosis biomarker or potential therapeutic targets. Therefore, identification of cancer-associated lncRNAs and investigation of their biological functions and molecular mechanisms are important for understanding the development and progression of cancer. In this study, we identified a novel lncRNA LINC00982, whose expression was downregulated in tumor tissues in 106 patients with gastric cancer (GC) compared with those in the adjacent normal tissues (P < 0.001). Furthermore, decreased LINC00982 expression was negatively correlated with invasion depth (P < 0.001), advanced TNM stage (P = 0.004), and regional lymph node metastasis (P = 0.005). LINC00982 levels were robust in differentiating gastric cancer tissues from controls [area under the curve (AUC) = 0.742; 95 % confidence interval (CI) = 0.678-0.800, P < 0.01]. Kaplan-Meier analysis demonstrated that decreased LINC00982 expression contributed to poor overall survival (P < 0.01) and disease-free survival (P < 0.01) of patients. A multivariate survival analysis also indicated that LINC00982 could be an independent prognostic marker. The levels of LINC00982 in gastric juice from gastric patients were significantly lower than those from normal subjects (P = 0.026). Furthermore, knockdown of LINC00982 expression by small interfering RNA (siRNA) could promote cell proliferation and cell cycle progression, while ectopic expression of LINC00982 inhibited cell proliferation and rendered cell cycle arrest in GC cells partly via regulating P15 and P16 protein expressions. Our findings present that decreased lncRNA LINC00982 could be identified as a poor prognostic biomarker in GC and regulate cell proliferation.
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282
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Chen X. Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA. Sci Rep 2015; 5:13186. [PMID: 26278472 PMCID: PMC4538606 DOI: 10.1038/srep13186] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/22/2015] [Indexed: 12/16/2022] Open
Abstract
Accumulating experimental studies have indicated that lncRNAs play important roles in various critical biological process and their alterations and dysregulations have been associated with many important complex diseases. Developing effective computational models to predict potential disease-lncRNA association could benefit not only the understanding of disease mechanism at lncRNA level, but also the detection of disease biomarkers for disease diagnosis, treatment, prognosis and prevention. However, known experimentally confirmed disease-lncRNA associations are still very limited. In this study, a novel model of HyperGeometric distribution for LncRNA-Disease Association inference (HGLDA) was developed to predict lncRNA-disease associations by integrating miRNA-disease associations and lncRNA-miRNA interactions. Although HGLDA didn't rely on any known disease-lncRNA associations, it still obtained an AUC of 0.7621 in the leave-one-out cross validation. Furthermore, 19 predicted associations for breast cancer, lung cancer, and colorectal cancer were verified by biological experimental studies. Furthermore, the model of LncRNA Functional Similarity Calculation based on the information of MiRNA (LFSCM) was developed to calculate lncRNA functional similarity on a large scale by integrating disease semantic similarity, miRNA-disease associations, and miRNA-lncRNA interactions. It is anticipated that HGLDA and LFSCM could be effective biological tools for biomedical research.
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Affiliation(s)
- Xing Chen
- National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, 100190, China
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
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283
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Long Non-Coding RNAs: The Key Players in Glioma Pathogenesis. Cancers (Basel) 2015; 7:1406-24. [PMID: 26230711 PMCID: PMC4586776 DOI: 10.3390/cancers7030843] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/22/2015] [Accepted: 07/23/2015] [Indexed: 01/17/2023] Open
Abstract
Long non-coding RNAs (LncRNAs) represent a novel class of RNAs with no functional protein-coding ability, yet it has become increasingly clear that interactions between lncRNAs with other molecules are responsible for important gene regulatory functions in various contexts. Given their relatively high expressions in the brain, lncRNAs are now thought to play important roles in normal brain development as well as diverse disease processes including gliomagenesis. Intriguingly, certain lncRNAs are closely associated with the initiation, differentiation, progression, recurrence and stem-like characteristics in glioma, and may therefore be exploited for the purposes of sub-classification, diagnosis and prognosis. LncRNAs may also serve as potential therapeutic targets as well as a novel biomarkers in the treatment of glioma. In this article, the functional aspects of lncRNAs, particularly within the central nervous system (CNS), will be briefly discussed, followed by highlights of the important roles of lncRNAs in mediating critical steps during glioma development. In addition, the key lncRNA players and their possible mechanistic pathways associated with gliomagenesis will be addressed.
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284
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Zhou J, Lai PBS, Tsui SKW. Identification of a non-coding KLF4 transcript generated from intron retention and downregulated in human hepatocellular carcinoma. Int J Oncol 2015; 47:1554-62. [PMID: 26238073 DOI: 10.3892/ijo.2015.3104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 06/29/2015] [Indexed: 11/06/2022] Open
Abstract
The Krüppel-like factor 4 (KLF4) gene is related to various biological processes including stem cell reprogramming and tumorigenesis. In this study, we identified and characterized a non-coding transcript of KLF4, which was designated KLF4‑003, in human liver tissue samples. KLF4‑003 was identified in a number of cell lines by reverse transcription PCR and DNA sequencing. Its expression levels were determined in 54 pairs of human hepatocellular carcinoma (HCC) tissues and a number of HCC cell lines by real-time PCR (RT-PCR). Methylation status of KLF4‑003 CpG islands was determined by bisulfite sequencing. The regulatory effect of KLF4‑003 CpG islands hypermethylation in Hep3B cells was then validated by the 5-aza-dC demethylation treatment, followed by RT-PCR analysis. Receiver operating characteristic (ROC) curve was created to evaluate the diagnostic value for differentiating between HCC cancer and benign diseases. The association study between KLF4‑003 expression level and clinical traits of HCC patients was performed with SPSS. We found that KLF4‑003 was downregulated in 46 out of 54 HCC samples compared with their adjunct normal tissues. The reduced KLF4‑003 expression was significantly associated with HCC recurrence (P=0.045) in the follow-up of 31 HCC patients. Significant differences were detected between the methylation status of HCC specimens and their adjacent normal controls. Demethylation treatment significantly rescued the expression of KLF4‑003 in Hep3B cells. Such observation indicated that the CpG island hypermethylation was at least partially responsible for the downregulation of KLF4‑003 in HCC. The area under ROC curve for the prediction of HCC reached 0.803 (95% CI=0.719-0.886, P<0.001). Our results suggested that the expression of KLF4‑003 was epigenetically regulated by methylation status of a KLF4‑003 CpG island in HCC. The differential expression of KLF4‑003 might play an important role in HCC development and might serve as a potential biomarker for the diagnosis of HCC.
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Affiliation(s)
- Junwei Zhou
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Paul Bo-San Lai
- Department of Surgery, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
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285
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Abstract
A long ncRNA (lncRNA) prostate cancer non-coding RNA 1 (PRNCR1) in the 8q24 has been reported to be upregulated in prostate cancer with a function of activating androgen receptor (AR). AR plays a key role in the gender disparity, cell migration, and invasion of gastric cancer (GC). We hypothesized that single nucleotide polymorphisms (SNPs) in the lncRNA PRNCR1 may be related to the risk of GC. We conducted a case-control study to investigate the association between SNPs in the lncRNA PRNCR1 and the risk of GC. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay was used to determine the genotypes of 613 subjects including 219 cases with GC and 394 controls. We found that patients with the rs13252298AG genotype displayed a 1.50-fold increased risk of GC (AG vs. AA, 95 % confidence interval (CI) = 1.05-2.12, p = 0.02). Interestingly, the rs7007694CT and CC and the rs1456315GG genotypes displayed a decreased risk of GC (rs7007694CT vs. TT, odds ratio (OR) = 0.68, 95 % CI = 0.48-0.97, p = 0.03; rs7007694CC vs. TT, OR = 0.36, 95 % CI = 0.13-0.97, p = 0.04; rs1456315GG vs. AA, OR = 0.30, 95 % CI = 0.13-0.70, p = 0.004, respectively). Our results suggest that SNPs in the lncRNA PRNCR1 may be a biomarker for the etiology of GC.
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286
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Vilborg A, Passarelli MC, Yario TA, Tycowski KT, Steitz JA. Widespread Inducible Transcription Downstream of Human Genes. Mol Cell 2015; 59:449-61. [PMID: 26190259 DOI: 10.1016/j.molcel.2015.06.016] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 04/29/2015] [Accepted: 06/10/2015] [Indexed: 01/09/2023]
Abstract
Pervasive transcription of the human genome generates RNAs whose mode of formation and functions are largely uncharacterized. Here, we combine RNA-seq with detailed mechanistic studies to describe a transcript type derived from protein-coding genes. The resulting RNAs, which we call DoGs for downstream of gene containing transcripts, possess long non-coding regions (often >45 kb) and remain chromatin bound. DoGs are inducible by osmotic stress through an IP3 receptor signaling-dependent pathway, indicating active regulation. DoG levels are increased by decreased termination of the upstream transcript, a previously undescribed mechanism for rapid transcript induction. Relative depletion of polyA signals in DoG regions correlates with increased levels of DoGs after osmotic stress. We detect DoG transcription in several human cell lines and provide evidence for thousands of DoGs genome wide.
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Affiliation(s)
- Anna Vilborg
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Maria C Passarelli
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Therese A Yario
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.
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287
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Zhou Y, Wu K, Jiang J, Huang J, Zhang P, Zhu Y, Hu G, Lang J, Shi Y, Hu L, Huang T, Kong X. Integrative analysis reveals enhanced regulatory effects of human long intergenic non-coding RNAs in lung adenocarcinoma. J Genet Genomics 2015; 42:423-36. [PMID: 26336799 DOI: 10.1016/j.jgg.2015.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/29/2015] [Accepted: 07/02/2015] [Indexed: 12/24/2022]
Abstract
Although there is an accumulating appreciation of the key roles that long intergenic non-coding RNAs (lincRNAs) play in diverse cellular processes, our knowledge of how lincRNAs function in cancer remains sparse. Here, we present a comprehensive landscape of RNA-seq transcriptome profiles of lung adenocarcinomas and their paired normal counterparts to unravel gene regulation rules of lincRNAs. Consistent with previous findings of co-expression between neighboring protein-coding genes, lincRNAs were typically co-expressed with their neighboring genes, which was found in both cancerous and normal tissues. By building a mathematical model based on correlated gene expression, we distinguished an additional subset of lincRNAs termed "regulatory lincRNAs", representing their dominant roles in gene regulation. The number of regulatory lincRNAs was significantly higher in cancerous compared to normal tissues, and most of them positively regulated protein-coding genes in trans. Functional validation, using knockdown, determined that regulatory lincRNA, GAS5, affected its predicted protein-coding targets. Moreover, we discovered hundreds of differentially expressed regulatory lincRNAs with inclusion of some cancer-associated lincRNAs. Our integrated analysis reveals enhanced regulatory effects of lincRNAs and provides a resource for the study of regulatory lincRNAs that play critical roles in lung adenocarcinoma.
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Affiliation(s)
- You Zhou
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Kai Wu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Jianping Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinfei Huang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Peiwei Zhang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Yufei Zhu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Guohong Hu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Jingyu Lang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Yufang Shi
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Landian Hu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Tao Huang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China.
| | - Xiangyin Kong
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China.
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288
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Liz J, Esteller M. lncRNAs and microRNAs with a role in cancer development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:169-76. [PMID: 26149773 DOI: 10.1016/j.bbagrm.2015.06.015] [Citation(s) in RCA: 410] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/03/2015] [Accepted: 06/30/2015] [Indexed: 12/12/2022]
Abstract
Most diseases, including human cancer, are frequently associated with an altered transcription pattern. The alteration of the transcriptome is not restricted to the production of aberrant levels of protein-coding RNAs, but also refers to the dysregulation of the expression of the multiple noncoding members that comprise the human genome. Unexpectedly, recent RNA-seq data of the human transcriptome have revealed that less than 2% of the genome encodes protein-coding transcripts, even though the vast majority of the genome is actively transcribed into non-coding RNAs (ncRNAs) under different conditions. In this review, we present an updated version of the mechanistic aspects of some long non-coding RNAs (lncRNAs) that play critical roles in human cancer. Most importantly, we focus on the interplay between lncRNAs and microRNAs, and the importance of such interactions during the tumorigenic process, providing new insight into the regulatory mechanisms underlying several ncRNA classes of importance in cancer, particularly transcribed ultraconserved regions (T-UCRs). This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Julia Liz
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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289
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Cajigas I, Leib DE, Cochrane J, Luo H, Swyter KR, Chen S, Clark BS, Thompson J, Yates JR, Kingston RE, Kohtz JD. Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling. Development 2015; 142:2641-52. [PMID: 26138476 DOI: 10.1242/dev.126318] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 06/09/2015] [Indexed: 01/12/2023]
Abstract
Transcription-regulating long non-coding RNAs (lncRNAs) have the potential to control the site-specific expression of thousands of target genes. Previously, we showed that Evf2, the first described ultraconserved lncRNA, increases the association of transcriptional activators (DLX homeodomain proteins) with key DNA enhancers but represses gene expression. In this report, mass spectrometry shows that the Evf2-DLX1 ribonucleoprotein (RNP) contains the SWI/SNF-related chromatin remodelers Brahma-related gene 1 (BRG1, SMARCA4) and Brahma-associated factor (BAF170, SMARCC2) in the developing mouse forebrain. Evf2 RNA colocalizes with BRG1 in nuclear clouds and increases BRG1 association with key DNA regulatory enhancers in the developing forebrain. While BRG1 directly interacts with DLX1 and Evf2 through distinct binding sites, Evf2 directly inhibits BRG1 ATPase and chromatin remodeling activities. In vitro studies show that both RNA-BRG1 binding and RNA inhibition of BRG1 ATPase/remodeling activity are promiscuous, suggesting that context is a crucial factor in RNA-dependent chromatin remodeling inhibition. Together, these experiments support a model in which RNAs convert an active enhancer to a repressed enhancer by directly inhibiting chromatin remodeling activity, and address the apparent paradox of RNA-mediated stabilization of transcriptional activators at enhancers with a repressive outcome. The importance of BRG1/RNA and BRG1/homeodomain interactions in neurodevelopmental disorders is underscored by the finding that mutations in Coffin-Siris syndrome, a human intellectual disability disorder, localize to the BRG1 RNA-binding and DLX1-binding domains.
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Affiliation(s)
- Ivelisse Cajigas
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - David E Leib
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Jesse Cochrane
- Department of Molecular Biology, Harvard University, Boston, MA 02114, USA
| | - Hao Luo
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Kelsey R Swyter
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Sean Chen
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Brian S Clark
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | | | - John R Yates
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert E Kingston
- Department of Molecular Biology, Harvard University, Boston, MA 02114, USA
| | - Jhumku D Kohtz
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
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290
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Lopez JP, Diallo A, Cruceanu C, Fiori LM, Laboissiere S, Guillet I, Fontaine J, Ragoussis J, Benes V, Turecki G, Ernst C. Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing. BMC Med Genomics 2015; 8:35. [PMID: 26130076 PMCID: PMC4487992 DOI: 10.1186/s12920-015-0109-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/16/2015] [Indexed: 02/08/2023] Open
Abstract
Background Small ncRNAs (sncRNAs) offer great hope as biomarkers of disease and response to treatment. This has been highlighted in the context of several medical conditions such as cancer, liver disease, cardiovascular disease, and central nervous system disorders, among many others. Here we assessed several steps involved in the development of an ncRNA biomarker discovery pipeline, ranging from sample preparation to bioinformatic processing of small RNA sequencing data. Methods A total of 45 biological samples were included in the present study. All libraries were prepared using the Illumina TruSeq Small RNA protocol and sequenced using the HiSeq2500 or MiSeq Illumina sequencers. Small RNA sequencing data was validated using qRT-PCR. At each stage, we evaluated the pros and cons of different techniques that may be suitable for different experimental designs. Evaluation methods included quality of data output in relation to hands-on laboratory time, cost, and efficiency of processing. Results Our results show that good quality sequencing libraries can be prepared from small amounts of total RNA and that varying degradation levels in the samples do not have a significant effect on the overall quantification of sncRNAs via NGS. In addition, we describe the strengths and limitations of three commercially available library preparation methods: (1) Novex TBE PAGE gel; (2) Pippin Prep automated gel system; and (3) AMPure XP beads. We describe our bioinformatics pipeline, provide recommendations for sequencing coverage, and describe in detail the expression and distribution of all sncRNAs in four human tissues: whole-blood, brain, heart and liver. Conclusions Ultimately this study provides tools and outcome metrics that will aid researchers and clinicians in choosing an appropriate and effective high-throughput sequencing quantification method for various study designs, and overall generating valuable information that can contribute to our understanding of small ncRNAs as potential biomarkers and mediators of biological functions and disease. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0109-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Pablo Lopez
- McGill Group for Suicide Studies (MGSS), Douglas Mental Health University Institute, McGill University, Frank B Common Pavilion, Room F-2101.2, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada. .,Department of Human Genetics, McGill University, Montreal, QC, Canada.
| | - Alpha Diallo
- McGill Group for Suicide Studies (MGSS), Douglas Mental Health University Institute, McGill University, Frank B Common Pavilion, Room F-2101.2, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada.
| | - Cristiana Cruceanu
- McGill Group for Suicide Studies (MGSS), Douglas Mental Health University Institute, McGill University, Frank B Common Pavilion, Room F-2101.2, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada. .,Department of Human Genetics, McGill University, Montreal, QC, Canada.
| | - Laura M Fiori
- McGill Group for Suicide Studies (MGSS), Douglas Mental Health University Institute, McGill University, Frank B Common Pavilion, Room F-2101.2, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada.
| | - Sylvie Laboissiere
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.
| | - Isabelle Guillet
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.
| | - Joelle Fontaine
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.
| | - Vladimir Benes
- European Molecular Biology Laboratory (EMBL), Genomics Core Facility, Heidelberg, Germany.
| | - Gustavo Turecki
- McGill Group for Suicide Studies (MGSS), Douglas Mental Health University Institute, McGill University, Frank B Common Pavilion, Room F-2101.2, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada. .,Department of Human Genetics, McGill University, Montreal, QC, Canada.
| | - Carl Ernst
- McGill Group for Suicide Studies (MGSS), Douglas Mental Health University Institute, McGill University, Frank B Common Pavilion, Room F-2101.2, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada. .,Department of Human Genetics, McGill University, Montreal, QC, Canada.
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291
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Sciamanna I, Gualtieri A, Piazza PF, Spadafora C. Regulatory roles of LINE-1-encoded reverse transcriptase in cancer onset and progression. Oncotarget 2015; 5:8039-51. [PMID: 25478632 PMCID: PMC4226666 DOI: 10.18632/oncotarget.2504] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
LINE-1 retrotransposons encode the reverse transcriptase (RT) enzyme, required for their own mobility, the expression of which is inhibited in differentiated tissues while being active in tumors. Experimental evidence indicate that the inhibition of LINE-1-derived RT restores differentiation in cancer cells, inhibits tumor progression and yields globally reprogrammed transcription profiles. Newly emerging data suggest that LINE-1-encoded RT modulates the biogenesis of miRNAs, by governing the balance between the production of regulatory double-stranded RNAs and RNA:DNA hybrid molecules, with a direct impact on global gene expression. Abnormally high RT activity unbalances the transcriptome in cancer cells, while RT inhibition restores ‘normal’ miRNA profiles and their regulatory networks. This RT-dependent mechanism can target the myriad of transcripts - both coding and non-coding, sense and antisense - in eukaryotic transcriptomes, with a profound impact on cell fates. LINE-1-encoded RT emerges therefore as a key regulator of a previously unrecognized mechanism in tumorigenesis
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292
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Fatima R, Akhade VS, Pal D, Rao SMR. Long noncoding RNAs in development and cancer: potential biomarkers and therapeutic targets. MOLECULAR AND CELLULAR THERAPIES 2015; 3:5. [PMID: 26082843 PMCID: PMC4469312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/19/2015] [Indexed: 11/21/2023]
Abstract
Long noncoding RNAs are emerging as key players in various fundamental biological processes. We highlight the varied molecular mechanisms by which lncRNAs modulate gene expression in diverse cellular contexts and their role in early mammalian development in this review. Furthermore, it is being increasingly recognized that altered expression of lncRNAs is specifically associated with tumorigenesis, tumor progression and metastasis. We discuss various lncRNAs implicated in different cancer types with a focus on their clinical applications as potential biomarkers and therapeutic targets in the pathology of diverse cancers.
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Affiliation(s)
- Roshan Fatima
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Vijay Suresh Akhade
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Debosree Pal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Satyanarayana MR Rao
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
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293
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Fatima R, Akhade VS, Pal D, Rao SM. Long noncoding RNAs in development and cancer: potential biomarkers and therapeutic targets. MOLECULAR AND CELLULAR THERAPIES 2015; 3:5. [PMID: 26082843 PMCID: PMC4469312 DOI: 10.1186/s40591-015-0042-6] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/19/2015] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs are emerging as key players in various fundamental biological processes. We highlight the varied molecular mechanisms by which lncRNAs modulate gene expression in diverse cellular contexts and their role in early mammalian development in this review. Furthermore, it is being increasingly recognized that altered expression of lncRNAs is specifically associated with tumorigenesis, tumor progression and metastasis. We discuss various lncRNAs implicated in different cancer types with a focus on their clinical applications as potential biomarkers and therapeutic targets in the pathology of diverse cancers.
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Affiliation(s)
- Roshan Fatima
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Vijay Suresh Akhade
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Debosree Pal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Satyanarayana Mr Rao
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
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294
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Chen X, Yan CC, Luo C, Ji W, Zhang Y, Dai Q. Constructing lncRNA functional similarity network based on lncRNA-disease associations and disease semantic similarity. Sci Rep 2015; 5:11338. [PMID: 26061969 PMCID: PMC4462156 DOI: 10.1038/srep11338] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/21/2015] [Indexed: 12/28/2022] Open
Abstract
Increasing evidence has indicated that plenty of lncRNAs play important roles in many critical biological processes. Developing powerful computational models to construct lncRNA functional similarity network based on heterogeneous biological datasets is one of the most important and popular topics in the fields of both lncRNAs and complex diseases. Functional similarity network consturction could benefit the model development for both lncRNA function inference and lncRNA-disease association identification. However, little effort has been attempted to analysis and calculate lncRNA functional similarity on a large scale. In this study, based on the assumption that functionally similar lncRNAs tend to be associated with similar diseases, we developed two novel lncRNA functional similarity calculation models (LNCSIM). LNCSIM was evaluated by introducing similarity scores into the model of Laplacian Regularized Least Squares for LncRNA–Disease Association (LRLSLDA) for lncRNA-disease association prediction. As a result, new predictive models improved the performance of LRLSLDA in the leave-one-out cross validation of various known lncRNA-disease associations datasets. Furthermore, some of the predictive results for colorectal cancer and lung cancer were verified by independent biological experimental studies. It is anticipated that LNCSIM could be a useful and important biological tool for human disease diagnosis, treatment, and prevention.
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Affiliation(s)
- Xing Chen
- 1] National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, 100190, China [2] Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | | | - Cai Luo
- Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Wen Ji
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yongdong Zhang
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, 100084, China
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295
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Lee B, Mazar J, Aftab MN, Qi F, Shelley J, Li JL, Govindarajan S, Valerio F, Rivera I, Thurn T, Tran TA, Kameh D, Patel V, Perera RJ. Long noncoding RNAs as putative biomarkers for prostate cancer detection. J Mol Diagn 2015; 16:615-26. [PMID: 25307116 DOI: 10.1016/j.jmoldx.2014.06.009] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 05/29/2014] [Accepted: 06/03/2014] [Indexed: 12/16/2022] Open
Abstract
Prostate cancer is one of the leading causes of mortality among US males. There is an urgent unmet need to develop sensitive and specific biomarkers for the early detection of prostate cancer to reduce overtreatment and accompanying morbidity. We identified a group of differentially expressed long noncoding RNAs in prostate cancer cell lines and patient samples and further characterized six long noncoding RNAs (AK024556, XLOC_007697, LOC100287482, XLOC_005327, XLOC_008559, and XLOC_009911) in prostatic adenocarcinoma tissue samples (Gleason score >6.0) and compared them with matched normal (healthy) tissues. Interestingly, these markers were also successfully detected in patient urine samples and were found to be up-regulated when compared with normal (healthy) urine. AK024556 (SPRY4-IT1) was highly up-regulated in human prostate cancer cell line PC3 but not in LNCaP, and siRNA knockdown of SPRY4-IT1 in PC3 cells inhibited cell proliferation and invasion and increased cell apoptosis. Chromogenic in situ hybridization assay was developed to detect long noncoding RNAs in primary prostatic adenocarcinoma tissue samples, paving the way for clinical diagnostics. We believe that these results will set the stage for more extensive studies to develop novel long noncoding RNA-based diagnostic assays for early prostate cancer detection and will help to distinguish benign prostate cancer from precancerous lesions.
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296
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Ghidini M, Braconi C. Non-Coding RNAs in Primary Liver Cancer. Front Med (Lausanne) 2015; 2:36. [PMID: 26131450 PMCID: PMC4469108 DOI: 10.3389/fmed.2015.00036] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/19/2015] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a primary malignancy of the liver with poor prognosis and limited therapeutic options. Over the past few years, many studies have evaluated the role of non-coding RNAs (ncRNAs) in hepatocarcinogenesis and tumor progression. ncRNAs were shown to have diagnostic, prognostic, and therapeutic potential in HCC. In this manuscript, we review the latest major discoveries concerning microRNAs and long ncRNAs in HCC pathogenesis, and discuss the potentials and the limitations for their use in clinical practice.
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Affiliation(s)
- Michele Ghidini
- Division of Cancer Therapeutics, The Institute of Cancer Research , London , UK ; Cancer Center, Humanitas Clinical and Research Center , Milano , Italy
| | - Chiara Braconi
- Division of Cancer Therapeutics, The Institute of Cancer Research , London , UK ; The Royal Marsden NHS Foundation Trust , London , UK
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297
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Zhou Y, Wang M, Wu J, Jie Z, Chang S, Shuang T. The clinicopathological significance of miR-1307 in chemotherapy resistant epithelial ovarian cancer. J Ovarian Res 2015; 8:23. [PMID: 25887170 PMCID: PMC4449560 DOI: 10.1186/s13048-015-0143-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/12/2015] [Indexed: 01/29/2023] Open
Abstract
Background We aimed to examine the expression of miR-1307 in chemosensitive and chemoresistant epithelial ovarian cancer tissues and cell lines and to analyze the clinicopathological significance of miR-1307 in ovarian cancer. Methods MicroRNA microarray was used to screen differentially expressed microRNAs between the chemosensitive and chemoresistant epithelial ovarian cancer tissues. RT-PCR was used to validate the candidate microRNA. The potential target genes and their enriched biological pathways of microRNA were also analyzed. Dual Luciferase Reporter Gene Assay was conducted to validate the regulation of miRNA-1307 on the 3’-UTR of DAPK3. Results miRNA-1307 was up-regulated in the chemoresistant epithelial ovarian cancer tissues compared to the chemosensitive counterparts. The up-regulation of miRNA-1307 was not associated with menopause, tumor differentiation state, clinical stage, and lymph node metastasis of ovarian cancer. Gene ontology analysis of miR-1307 candidate target genes indicated that miR-1307 candidate target genes were enriched in the processes of cell proliferation and differentiation, nucleotide synthesis and metabolism, and lymphocytes activation. Conclusion Our results suggest that miRNA-1307 may play a role in the development of chemoresistance in ovarian cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13048-015-0143-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yingying Zhou
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, 36 Sanhao Street, Shenyang, Liaoning, 110004, P.R. China.
| | - Min Wang
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, 36 Sanhao Street, Shenyang, Liaoning, 110004, P.R. China.
| | - Jianlei Wu
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, 36 Sanhao Street, Shenyang, Liaoning, 110004, P.R. China.
| | - Zhihui Jie
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, 36 Sanhao Street, Shenyang, Liaoning, 110004, P.R. China.
| | - Shuang Chang
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, 36 Sanhao Street, Shenyang, Liaoning, 110004, P.R. China.
| | - Ting Shuang
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, 36 Sanhao Street, Shenyang, Liaoning, 110004, P.R. China.
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298
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Ma Y, Ma W, Huang L, Feng D, Cai B. Long non-coding RNAs, a new important regulator of cardiovascular physiology and pathology. Int J Cardiol 2015; 188:105-10. [PMID: 25917923 DOI: 10.1016/j.ijcard.2015.04.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/30/2015] [Accepted: 04/02/2015] [Indexed: 01/23/2023]
Abstract
LncRNAs were previously considered to be the 'noise' of gene transcription having no biological functions, but now it has become evident that lncRNAs function as modulators of gene expression network. LncRNAs may regulate diverse gene expression levels which were roughly summarized to epigenetic, transcriptional and post-transcriptional levels. It has been clarified that some lncRNAs were expressed differentially in cardiovascular diseases, and aberrant changes of those lncRNAs were involved in the development of heart disorders. The role of lncRNAs in this process transcended the tradition of protein regulatory platform to be the orchestrator of cardiac sophisticated governing system of heart development, adaptation and pathological reaction. This review summarizes recent advances in the study of functions and mechanisms of lncRNAs in cardiovascular physiology and pathology. The regulatory roles of lncRNAs in cardiovascular diseases provide new strategy for interventional therapy of heart diseases.
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Affiliation(s)
- Yidi Ma
- Department of Pharmacology, Harbin Medical University, Harbin 150081, China
| | - Wenya Ma
- Department of Pharmacology, Harbin Medical University, Harbin 150081, China
| | - Lina Huang
- Department of Pharmacology, Harbin Medical University, Harbin 150081, China
| | - Dan Feng
- Department of Pharmacology, Harbin Medical University, Harbin 150081, China
| | - Benzhi Cai
- Department of Pharmacology, Harbin Medical University, Harbin 150081, China.
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299
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Hu G, Yang T, Zheng J, Dai J, Nan A, Lai Y, Zhang Y, Yang C, Jiang Y. Functional role and mechanism of lncRNA LOC728228 in malignant 16HBE cells transformed by anti-benzopyrene-trans-7,8-dihydrodiol-9,10-epoxide. Mol Carcinog 2015; 54 Suppl 1:E192-204. [PMID: 25820656 DOI: 10.1002/mc.22314] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 02/11/2015] [Accepted: 02/21/2015] [Indexed: 11/09/2022]
Abstract
Lung cancer is a major health problem, and is considered one of the deadliest cancers in humans. It is refractory to current treatments, and the mechanisms of lung cancer are unknown. Long noncoding RNAs (lncRNAs) are involved in various biological processes and human diseases. However, the exact functional roles and mechanisms of lncRNAs are largely unclear. In this study, we attempted to identify lung-cancer-related lncRNAs. We found changes in lncRNA expression in the anti-benzo(a) pyrene-7,8-diol-9,10-epoxide (anti-BPDE)-transformed human bronchial epithelial cell line (16HBE-T cells) using microarrays and qRT-PCR. Of these lncRNAs, LOC728228 was upregulated relative to its expression in control untransformed16HBE (16HBE-N) cells. LOC728228 knockdown inhibited cell proliferation, caused G0/G1-phase cell-cycle arrest, reduced cellular migration, suppressed colony formation in vitro, and inhibited tumor growth in a nude mouse xenograft model. LOC728228 knockdown also suppressed cyclin D1 expression, and the depletion of cyclin D1 induced G0/G1-phase cell-cycle arrest and inhibited cell proliferation, thus influencing the malignant potential of cancer cells. In summary, our results suggest that lncRNA LOC728228 has an oncogene-like function and plays a vital role in human lung cancer.
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Affiliation(s)
- Gongcheng Hu
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, 510182, PR China
| | - Ti Yang
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, 510182, PR China
| | - Jingli Zheng
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, 510182, PR China
| | - Jiabing Dai
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, 510182, PR China
| | - Aruo Nan
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, 510182, PR China
| | - Yandong Lai
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, 510182, PR China
| | - Yajie Zhang
- Department of Pathology, Guangzhou Medical University, Guangzhou, 510182, PR China
| | - Chengfeng Yang
- Department of Physiology and Center for Integrative Toxicology, Michigan State University, East Lansing, Michigan, 48824
| | - Yiguo Jiang
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, 510182, PR China
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300
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Abstract
In recent years, long non-coding RNAs (lncRNAs) are emerging as either oncogenes or tumor suppressor genes. Recent evidences suggest that lncRNAs play a very important role in digestive system carcinomas. However, the biological function of lncRNAs in the vast majority of digestive system carcinomas remains unclear. Recently, increasing studies has begun to explore their molecular mechanisms and regulatory networks that they are implicated in tumorigenesis. In this review, we highlight the emerging functional role of lncRNAs in digestive system carcinomas. It is becoming clear that lncRNAs will be exciting and potentially useful for diagnosis and treatment of digestive system carcinomas, some of these lncRNAs might function as both diagnostic markers and the treatment targets of digestive system carcinomas.
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