101
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Chen S, Huang V, Xu X, Livingstone J, Soares F, Jeon J, Zeng Y, Hua JT, Petricca J, Guo H, Wang M, Yousif F, Zhang Y, Donmez N, Ahmed M, Volik S, Lapuk A, Chua ML, Heisler LE, Foucal A, Fox NS, Fraser M, Bhandari V, Shiah YJ, Guan J, Li J, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Fradet Y, Têtu B, Liu S, Feng F, Wu X, Shao YW, Komor MA, Sahinalp C, Collins C, Hoogstrate Y, de Jong M, Fijneman RJ, Fei T, Jenster G, van der Kwast T, Bristow RG, Boutros PC, He HH. Widespread and Functional RNA Circularization in Localized Prostate Cancer. Cell 2019; 176:831-843.e22. [DOI: 10.1016/j.cell.2019.01.025] [Citation(s) in RCA: 244] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/19/2018] [Accepted: 01/11/2019] [Indexed: 12/27/2022]
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102
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Das R, Feng FY, Selth LA. Long non-coding RNAs in prostate cancer: Biological and clinical implications. Mol Cell Endocrinol 2019; 480:142-152. [PMID: 30391670 DOI: 10.1016/j.mce.2018.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/12/2018] [Accepted: 10/31/2018] [Indexed: 12/31/2022]
Abstract
Prostate cancer (PCa) is a major health issue in the Western world. Current clinical imperatives for this disease include better stratification of indolent versus aggressive disease to enable improved patient management, as well as the identification of more effective therapies for the prevention and treatment of metastatic and therapy-resistant PCa. The advent of next-generation transcriptomics led to the identification of an important class of molecules, long non-coding RNAs (lncRNAs). LncRNAs have critical functions in normal physiology, but their dysregulation has also been implicated in the development and progression of a variety of cancers, including PCa. Importantly, a subset of lncRNAs are highly prostate-specific, suggesting potential for utility as both biomarkers and therapeutic targets. In this review, we summarise the biology of lncRNAs and their mechanisms of action in the development and progression of prostate cancer. Additionally, we cast a critical eye over the potential for this class of molecules to impact on clinical practice.
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Affiliation(s)
- Rajdeep Das
- Department of Radiation Oncology, University of California San Francisco, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, USA.
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, USA; Department of Urology, University of California San Francisco, USA
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Freemasons Foundation Centre for Men's Health, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia.
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103
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Basiri B, Sutton JM, Hooshfar S, Byrnes CC, Murph MM, Bartlett MG. Direct identification of microribonucleic acid miR-451 from plasma using liquid chromatography mass spectrometry. J Chromatogr A 2019; 1584:97-105. [PMID: 30502920 DOI: 10.1016/j.chroma.2018.11.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/16/2018] [Accepted: 11/15/2018] [Indexed: 12/12/2022]
Abstract
In recent years, small endogenous RNAs have come to the forefront of both basic and translational research. For example, many studies have pointed to the potential role of microRNAs (miRNAs) as disease biomarkers. However, precise quantitative methods for the analysis of miRNAs are still lacking. In this study, we report the first mass spectrometry-based quantitation of miR-451, a circulatory microRNA. Using a highly selective sample preparation method with an average recovery of 83.6% and a novel mobile phase chemistry, we were able to reach an LOQ of 0.5 ng/mL. Because of such high sensitivity, we could detect and quantify the endogenous miR-451 from both human and rat plasma. Considering the increased precision of LC-MS compared to other methods, these results usher in a new era of miRNA biomarker discovery and validation.
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Affiliation(s)
- Babak Basiri
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA 30602-2352, USA
| | - J Michael Sutton
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA 30602-2352, USA
| | - Shirin Hooshfar
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA 30602-2352, USA
| | - Charnel C Byrnes
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA 30602-2352, USA
| | - Mandi M Murph
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA 30602-2352, USA
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA 30602-2352, USA.
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104
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SWI/SNF remains localized to chromatin in the presence of SCHLAP1. Nat Genet 2018; 51:26-29. [PMID: 30510238 PMCID: PMC6339527 DOI: 10.1038/s41588-018-0272-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/05/2018] [Indexed: 12/22/2022]
Abstract
SCHLAP1 is a long-noncoding RNA that is reported to function by depleting the SWI/SNF complex from the genome. We investigated the hypothesis that SCHLAP1 affects only specific compositions of SWI/SNF. Using several assays we found that SWI/SNF is not depleted from the genome by SCHLAP1, and that SWI/SNF is associated with many coding and non-coding RNAs, suggesting SCHLAP1 may function in a SWI/SNF independent manner.
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105
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Wen X, Liu X, Mao YP, Yang XJ, Wang YQ, Zhang PP, Lei Y, Hong XH, He QM, Ma J, Liu N, Li YQ. Long non-coding RNA DANCR stabilizes HIF-1α and promotes metastasis by interacting with NF90/NF45 complex in nasopharyngeal carcinoma. Theranostics 2018; 8:5676-5689. [PMID: 30555573 PMCID: PMC6276287 DOI: 10.7150/thno.28538] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 10/17/2018] [Indexed: 02/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) play an important role in the development and progression of cancers. However, the clinical significances of lncRNAs and their functions and mechanisms in nasopharyngeal carcinoma (NPC) remain largely unclear. Methods: Quantitative RT-PCR was used to determine DANCR expression and Kaplan-Meier curves were used to evaluate its prognostic value. RNA sequencing followed by bioinformatic analysis was performed to determine the potential function of DANCR. In vitro and in vivo experiments were conducted to investigate its biological effects. DANCR-interacting proteins were identified by RNA pull-down assay followed by mass spectrometry and western blotting, and then confirmed by RNA immunoprecipitation (RIP) assays. Results: Our previous microarray analysis identified a metastasis-associated lncRNA DANCR. Here, we found that DANCR was upregulated in NPC, especially in those with lymph lode metastasis, and its upregulation could predict poor survival. We then constructed a prognostic predictive model. RNA sequencing followed by bioinformatic analysis revealed that DANCR was responsible for NPC metastasis and hypoxia phenotype. Functional studies showed that DANCR promoted NPC cell invasion and metastasis in vitro and in vivo. Further investigation suggested that DANCR could increase HIF-1α mRNA stability through interacting with the NF90/NF45 complex. Additionally, overexpression of HIF-1α in DANCR knockdown cells restored its suppressive effects on NPC cell migration and invasion. Conclusions: Taken together, our results suggest that DANCR acts as a prognostic biomarker and increases HIF-1α mRNA stability by interacting with NF90/NF45, leading to metastasis and disease progression of NPC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jun Ma
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, No. 651 Dongfeng Road East, Guangzhou 510060, People's Republic of China
| | - Na Liu
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, No. 651 Dongfeng Road East, Guangzhou 510060, People's Republic of China
| | - Ying-Qin Li
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, No. 651 Dongfeng Road East, Guangzhou 510060, People's Republic of China
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106
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Ali HEA, Lung PY, Sholl AB, Gad SA, Bustamante JJ, Ali HI, Rhim JS, Deep G, Zhang J, Abd Elmageed ZY. Dysregulated gene expression predicts tumor aggressiveness in African-American prostate cancer patients. Sci Rep 2018; 8:16335. [PMID: 30397274 PMCID: PMC6218553 DOI: 10.1038/s41598-018-34637-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 10/22/2018] [Indexed: 12/25/2022] Open
Abstract
Molecular mechanisms underlying the health disparity of prostate cancer (PCa) have not been fully determined. In this study, we applied bioinformatic approach to identify and validate dysregulated genes associated with tumor aggressiveness in African American (AA) compared to Caucasian American (CA) men with PCa. We retrieved and analyzed microarray data from 619 PCa patients, 412 AA and 207 CA, and we validated these genes in tumor tissues and cell lines by Real-Time PCR, Western blot, immunocytochemistry (ICC) and immunohistochemistry (IHC) analyses. We identified 362 differentially expressed genes in AA men and involved in regulating signaling pathways associated with tumor aggressiveness. In PCa tissues and cells, NKX3.1, APPL2, TPD52, LTC4S, ALDH1A3 and AMD1 transcripts were significantly upregulated (p < 0.05) compared to normal cells. IHC confirmed the overexpression of TPD52 (p = 0.0098) and LTC4S (p < 0.0005) in AA compared to CA men. ICC and Western blot analyses additionally corroborated this observation in PCa cells. These findings suggest that dysregulation of transcripts in PCa may drive the disparity of PCa outcomes and provide new insights into development of new therapeutic agents against aggressive tumors. More studies are warranted to investigate the clinical significance of these dysregulated genes in promoting the oncogenic pathways in AA men.
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Affiliation(s)
- Hamdy E A Ali
- Department of Pharmaceutical Sciences, Rangel College of Pharmacy, Texas A&M Health Sciences Center, Kingsville, TX, USA.,Department of Radiobiological Applications, Nuclear Research Center, Atomic Energy Authority, Cairo, Egypt
| | - Pei-Yau Lung
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Andrew B Sholl
- Departments of Pathology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Shaimaa A Gad
- Department of Pharmaceutical Sciences, Rangel College of Pharmacy, Texas A&M Health Sciences Center, Kingsville, TX, USA
| | - Juan J Bustamante
- Department of Pharmaceutical Sciences, Rangel College of Pharmacy, Texas A&M Health Sciences Center, Kingsville, TX, USA
| | - Hamed I Ali
- Department of Pharmaceutical Sciences, Rangel College of Pharmacy, Texas A&M Health Sciences Center, Kingsville, TX, USA
| | - Johng S Rhim
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Gagan Deep
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Zakaria Y Abd Elmageed
- Department of Pharmaceutical Sciences, Rangel College of Pharmacy, Texas A&M Health Sciences Center, Kingsville, TX, USA.
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107
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Udager AM, Tomlins SA. Molecular Biomarkers in the Clinical Management of Prostate Cancer. Cold Spring Harb Perspect Med 2018; 8:a030601. [PMID: 29311125 PMCID: PMC6211380 DOI: 10.1101/cshperspect.a030601] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Prostate cancer, one of the most common noncutaneous malignancies in men, is a heterogeneous disease with variable clinical outcome. Although the majority of patients harbor indolent tumors that are essentially cured by local therapy, subsets of patients present with aggressive disease or recur/progress after primary treatment. With this in mind, modern clinical approaches to prostate cancer emphasize the need to reduce overdiagnosis and overtreatment via personalized medicine. Advances in our understanding of prostate cancer pathogenesis, coupled with recent technologic innovations, have facilitated the development and validation of numerous molecular biomarkers, representing a range of macromolecules assayed from a variety of patient sample types, to help guide the clinical management of prostate cancer, including early detection, diagnosis, prognostication, and targeted therapeutic selection. Herein, we review the current state of the art regarding prostate cancer molecular biomarkers, emphasizing those with demonstrated utility in clinical practice.
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Affiliation(s)
- Aaron M Udager
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109-5054
| | - Scott A Tomlins
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109-5054
- Department of Urology, University of Michigan Medical School, Ann Arbor, Michigan 48109-5948
- Comprehensive Cancer Center, Michigan Medicine, Ann Arbor, Michigan 48109-0944
- Michigan Center for Translational Pathology, Ann Arbor, Michigan 48109-5940
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108
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Zhan F, Shen J, Wang R, Wang L, Dai Y, Zhang Y, Huang X. Role of exosomal small RNA in prostate cancer metastasis. Cancer Manag Res 2018; 10:4029-4038. [PMID: 30319287 PMCID: PMC6167994 DOI: 10.2147/cmar.s170610] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Prostate cancer (PCa) is the second most common cancer in men worldwide. When the disease becomes metastatic, limited treatment strategies exist, and metastatic disease prognoses are difficult to predict. Recently, evidence has emerged, which indicates that small RNAs are detectable in patient fluids, and exosomal small RNA ectopic expression is correlated with the development, progression, and metastasis of human PCa; however, the role of small RNAs in PCa is only partially understood. In this review, we discuss the research status regarding circulating exosomal small RNAs and applications using these small RNAs in PCa particularly looking at metastatic disease. Exosomal small RNAs could be used as potential biomarkers for the early diagnosis, micrometastasis detection, and prognosis of PCa.
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Affiliation(s)
- Fei Zhan
- Department of Gastrointestinal Medical Oncology, Tumor Hospital of Harbin Medical University, Harbin 150081, China,
| | - Jingling Shen
- Department of Histology and Embryology, Harbin Medical University, Harbin 150081, China
| | - Ruitao Wang
- Department of Internal Medicine, Tumor Hospital of Harbin Medical University, Harbin 150081, China
| | - Liang Wang
- Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Yao Dai
- Department of Radiation Oncology, University of Florida, Gainesville, FL, 32610, USA
| | - Yanqiao Zhang
- Department of Gastrointestinal Medical Oncology, Tumor Hospital of Harbin Medical University, Harbin 150081, China,
| | - Xiaoyi Huang
- Biotherapy Center, Tumor Hospital of Harbin Medical University, Harbin 150081, China,
- Center of Translational Medicine, Harbin Medical University, Harbin 150086, China,
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109
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Song X, Xu P, Meng C, Song C, Blackwell TS, Li R, Li H, Zhang J, Lv C. lncITPF Promotes Pulmonary Fibrosis by Targeting hnRNP-L Depending on Its Host Gene ITGBL1. Mol Ther 2018; 27:380-393. [PMID: 30528088 DOI: 10.1016/j.ymthe.2018.08.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/26/2018] [Accepted: 08/31/2018] [Indexed: 01/27/2023] Open
Abstract
The role of long non-coding RNA (lncRNA) in idiopathic pulmonary fibrosis (IPF) is poorly understood. We found a novel lncRNA-ITPF that was upregulated in IPF. Bioinformatics and in vitro translation verified that lncITPF is an actual lncRNA, and its conservation is in evolution. Northern blot and rapid amplification of complementary DNA ends were used to analyze the full-length sequence of lncITPF. RNA fluorescence in situ hybridization and nucleocytoplasmic separation demonstrated that lncITPF was mainly located in the nucleus. RNA sequencing, chromatin immunoprecipitation (ChIP)-qPCR, CRISPR-Cas9 technology, and promoter activity analysis showed that the fibrotic function of lncITPF depends on its host gene integrin β-like 1 (ITGBL1), but they did not share the same promoter and were not co-transcribed. Luciferase activity, pathway inhibitors, and ChIP-qPCR showed that smad2/3 binds to the lncITPF promoter, and TGF-β1-smad2/3 was the upstream inducer of the fibrotic pathway. Furthermore, RNA-protein pull-down, liquid chromatography-mass spectrometry (LC-MS), and protein-RNA immunoprecipitation showed that lncITPF regulated H3 and H4 histone acetylation in the ITGBL1 promoter by targeting heterogeneous nuclear ribonucleoprotein L. Finally, sh-lncITPF was used to evaluate the therapeutic effect of lncITPF. Clinical analysis showed that lncITPF is associated with the clinicopathological features of IPF patients. Our findings provide a therapeutic target or diagnostic biomarker for IPF.
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Affiliation(s)
- Xiaodong Song
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China; Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Pan Xu
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China
| | - Chao Meng
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China
| | - Chenguang Song
- Department of Respiratory Medicine, Zouping Chinese Medicine Hospital, Binzhou 256602, China
| | | | - Rongrong Li
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China
| | - Hongbo Li
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China
| | - Jinjin Zhang
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China; Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China.
| | - Changjun Lv
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China; Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China.
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110
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Unfavorable Pathology, Tissue Biomarkers and Genomic Tests With Clinical Implications in Prostate Cancer Management. Adv Anat Pathol 2018; 25:293-303. [PMID: 29727322 DOI: 10.1097/pap.0000000000000192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Prostate cancer management has traditionally relied upon risk stratification of patients based on Gleason score, pretreatment prostate-specific antigen and clinical tumor stage. However, these factors alone do not adequately reflect the inherent complexity and heterogeneity of prostate cancer. Accurate and individualized risk stratification at the time of diagnosis is instrumental to facilitate clinical decision-making and treatment selection tailored to each patient. The incorporation of tissue and genetic biomarkers into current prostate cancer prediction models may optimize decision-making and improve patient outcomes. In this review we discuss the clinical significance of unfavorable morphologic features such as cribriform architecture and intraductal carcinoma of the prostate, tissue biomarkers and genomic tests and assess their potential use in prostate cancer risk assessment and treatment selection.
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111
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Xu J, Shi A, Long Z, Xu L, Liao G, Deng C, Yan M, Xie A, Luo T, Huang J, Xiao Y, Li X. Capturing functional long non-coding RNAs through integrating large-scale causal relations from gene perturbation experiments. EBioMedicine 2018; 35:369-380. [PMID: 30177244 PMCID: PMC6156711 DOI: 10.1016/j.ebiom.2018.08.050] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/15/2018] [Accepted: 08/22/2018] [Indexed: 02/06/2023] Open
Abstract
Characterizing functions of long noncoding RNAs (lncRNAs) remains a major challenge, mostly due to the lack of lncRNA-involved regulatory relationships. A wide array of genome-wide expression profiles generated by gene perturbation have been widely used to capture causal links between perturbed genes and response genes. Through annotating >600 gene perturbation profiles, over 354,000 causal relationships between perturbed genes and lncRNAs were identified. This large-scale resource of causal relations inspired us to develop a novel computational approach LnCAR for inferring lncRNAs' functions, which showed a higher accuracy than the co-expression based approach. By application of LnCAR to the cancer hallmark processes, we identified 38 lncRNAs involved in distinct carcinogenic processes. The "activating invasion & metastasis" related lncRNAs were strongly associated with metastatic progression in various cancer types and could act as a predictor of cancer metastasis. Meanwhile, the "evading immune destruction" related lncRNAs showed significant associations with immune infiltration of various immune cells and, importantly, can predict response to anti-PD-1 immunotherapy, suggesting their potential roles as biomarkers for immune therapy. Taken together, our approach provides a novel way to systematically reveal functions of lncRNAs, which will be helpful for further experimental exploration and clinical translational research of lncRNAs.
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Affiliation(s)
- Jinyuan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Aiai Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Zhilin Long
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Chunyu Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Aiming Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Tao Luo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China; Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Harbin, Heilongjiang 150086, China.
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China; Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Harbin, Heilongjiang 150086, China.
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112
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113
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Lim MCJ, Baird AM, Aird J, Greene J, Kapoor D, Gray SG, McDermott R, Finn SP. RNAs as Candidate Diagnostic and Prognostic Markers of Prostate Cancer-From Cell Line Models to Liquid Biopsies. Diagnostics (Basel) 2018; 8:E60. [PMID: 30200254 PMCID: PMC6163368 DOI: 10.3390/diagnostics8030060] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 12/19/2022] Open
Abstract
The treatment landscape of prostate cancer has evolved rapidly over the past five years. The explosion in treatment advances has been witnessed in parallel with significant progress in the field of molecular biomarkers. The advent of next-generation sequencing has enabled the molecular profiling of the genomic and transcriptomic architecture of prostate and other cancers. Coupled with this, is a renewed interest in the role of non-coding RNA (ncRNA) in prostate cancer biology. ncRNA consists of several different classes including small non-coding RNA (sncRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). These families are under active investigation, given their essential roles in cancer initiation, development and progression. This review focuses on the evidence for the role of RNAs in prostate cancer, and their use as diagnostic and prognostic markers, and targets for treatment in this disease.
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Affiliation(s)
- Marvin C J Lim
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
- Department of Medical Oncology, Tallaght University Hospital, Dublin D24 NR0A, Ireland.
| | - Anne-Marie Baird
- Cancer and Ageing Research Programme, Queensland University of Technology, Brisbane, QLD 4000, Australia.
- Department of Clinical Medicine, Trinity College Dublin, College Green, Dublin D02 PN40, Ireland.
- Thoracic Oncology Research Group, Labmed Directorate, St. James's Hospital, Dublin 08 W9RT, Ireland.
| | - John Aird
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
| | - John Greene
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
| | - Dhruv Kapoor
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
| | - Steven G Gray
- Department of Clinical Medicine, Trinity College Dublin, College Green, Dublin D02 PN40, Ireland.
- Thoracic Oncology Research Group, Labmed Directorate, St. James's Hospital, Dublin 08 W9RT, Ireland.
- School of Biological Sciences, Dublin Institute of Technology, Dublin D08 NF82, Ireland.
| | - Ray McDermott
- Department of Medical Oncology, Tallaght University Hospital, Dublin D24 NR0A, Ireland.
- Department of Medical Oncology, St. Vincent's University Hospital, Dublin D04 YN26, Ireland.
| | - Stephen P Finn
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
- Department of Histopathology, St. James's Hospital, P.O. Box 580, James's Street, Dublin D08 X4RX, Ireland.
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114
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Zheng Y, Gao Y, Li X, Si S, Xu H, Qi F, Wang J, Cheng G, Hua L, Yang H. Long non-coding RNA NAP1L6 promotes tumor progression and predicts poor prognosis in prostate cancer by targeting Inhibin-β A. Onco Targets Ther 2018; 11:4965-4977. [PMID: 30154665 PMCID: PMC6103656 DOI: 10.2147/ott.s163680] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background/purpose Long non-coding RNAs (lncRNAs) have emerged as key molecules in initiation and progression of prostate cancer (PCa). In this study, we aimed to explore the role of lncRNA NAP1L6 in the development and progression of PCa. Materials and methods We identified that lncRNA NAP1L6 was over-expressed both in PCa tissues and cell lines by gene expression array profiling. The expression level of NAP1L6 in 75 PCa tissues and adjacent tissues was detected by RT-PCR. Next, the correlations between NAP1L6 expression and clinical features of patients with PCa were analyzed by paired t-test or chi-squared test, and its association with patient prognosis was assessed by the Kaplan-Meier method. The effects of NAP1L6 on PC-3 and 22RV1 cells were evaluated by Cell Counting Kit-8 (CCK-8), migration, invasion, and colony formation assays. Further analysis of the results of the microarray was performed to find downstream gene of NAP1L6. Cell function experiments were performed in order to explore the relationship between NAP1L6 and Inhibin-β A (INHBA) and the specific mechanism by which INHBA affects the development of PCa. Results Using microarray analysis, we identified 412 lncRNAs and 1245 mRNAs to be significantly differentially expressed in three PCa samples when compared with adjacent non-tumor tissues (ANTT) (fold-change ≥2.0 or ≤0.5, P<0.05, false discovery rate (FDR) <0.05). NAP1L6 expression was upregulated in PCa tissues and cell lines (both P<0.05) compared with ANTT. Besides, high expression level of NAP1L6 promotes PCa cell proliferation, migration, and invasion (all P<0.05), and is significantly associated with larger tumor diameter, distant metastasis, and shorter survival time (all P<0.05). We found that NAP1L6 promoted the expression of INHBA (P<0.05), and knockdown of NAP1L6 led to the reduction of PCa cell migration, invasion, and proliferation by regulating the expression of INHBA (all P<0.05). Conclusion lncRNA NR6A1 might play an oncogenic role in PCa initiation and progression by regulating the expression of INHBA, and might act as a novel prognostic biomarker for PCa treatment.
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Affiliation(s)
- Yuxiao Zheng
- Department of Urologic Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Yiren Gao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China, ,
| | - Xiao Li
- Department of Urologic Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Shuhui Si
- Research Division of Clinical Pharmacology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Haoxiang Xu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China, ,
| | - Feng Qi
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China, ,
| | - Jun Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China, ,
| | - Gong Cheng
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China, ,
| | - Lixin Hua
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China, ,
| | - Haiwei Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China, ,
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Bao X, Duan J, Yan Y, Ma X, Zhang Y, Wang H, Ni D, Wu S, Peng C, Fan Y, Gao Y, Li X, Chen J, Du Q, Zhang F, Zhang X. Upregulation of long noncoding RNA PVT1 predicts unfavorable prognosis in patients with clear cell renal cell carcinoma. Cancer Biomark 2018; 21:55-63. [PMID: 29081406 DOI: 10.3233/cbm-170251] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Renal cell carcinoma (RCC) is one of the most malignant genitourinary diseases worldwide. Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs in the human genome that are involved in RCC initiation and progression. OBJECTIVE To investigate the expression of PVT1 in ccRCC and evaluate its correlation with clinicopathologic characteristics and patients' survival. METHODS Quantitative real-time PCR was performed to examine PVT1 expression in 129 ccRCC tissue samples and matched adjacent normal tissue samples. The relationship of PVT1 expression with clinicopathologic characteristics and clinical outcome was evaluated. RESULTS We identified the lncRNA PVT1, which was upregulated in clear cell renal cell carcinoma (ccRCC) tissues when compared with corresponding controls. Furthermore, PVT1 expression was positively associated with gender, tumor size, pT stage, TNM stage, and Fuhrman grade. Kaplan-Meier survival analysis showed that patients with high PVT1 expression had shorter disease-free survival (DFS) and overall-survival (OS) than those with low PVT1 expression, and multivariate analysis identified PVT1 as an independent prognostic factor in ccRCC. CONCLUSIONS PVT1 may be an oncogene as well as may promote metastasis in ccRCC and could serve as a potential biomarker to predict the prognosis of ccRCC patients.
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Affiliation(s)
- Xu Bao
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Junyao Duan
- Department of Urology, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing 100700, China.,School of Medicine, Nankai University, Tianjin 300071, China
| | - Yongji Yan
- Department of Urology, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing 100700, China
| | - Xin Ma
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Yu Zhang
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Hanfeng Wang
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Dong Ni
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Shengpan Wu
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Cheng Peng
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Yang Fan
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Yu Gao
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Xintao Li
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Jianwen Chen
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Qingshan Du
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Fan Zhang
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Xu Zhang
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
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Hua JT, Ahmed M, Guo H, Zhang Y, Chen S, Soares F, Lu J, Zhou S, Wang M, Li H, Larson NB, McDonnell SK, Patel PS, Liang Y, Yao CQ, van der Kwast T, Lupien M, Feng FY, Zoubeidi A, Tsao MS, Thibodeau SN, Boutros PC, He HH. Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19. Cell 2018; 174:564-575.e18. [DOI: 10.1016/j.cell.2018.06.014] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/26/2018] [Accepted: 06/06/2018] [Indexed: 11/30/2022]
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Cimadamore A, Gasparrini S, Santoni M, Cheng L, Lopez-Beltran A, Battelli N, Massari F, Giunchi F, Fiorentino M, Scarpelli M, Montironi R. Biomarkers of aggressiveness in genitourinary tumors with emphasis on kidney, bladder, and prostate cancer. Expert Rev Mol Diagn 2018; 18:645-655. [PMID: 29912582 DOI: 10.1080/14737159.2018.1490179] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Over the last decade, the improvement in molecular techniques and the acquisition of genomic information has transformed and increased the quality of patient care and our knowledge of diseases. Areas covered: Protein expression levels in immunohistochemistry and molecular biomarkers are reported for their ability to predict recurrence, progression, development of metastases, or patient survival. In particular, for renal cell carcinoma, we take into consideration the biomarkers applicable to immunohistochemistry and with molecular and genetic analyses. In urothelial carcinoma, there is great interest in the possibility of distinguishing the basal vs. luminal subtypes and to acquire deeper insight into the tumor biology through examining exosomes in urine and biomarkers in the serum. In prostate cancer, single gene expression and multiple gene expression classifiers are reviewed as a tool to distinguish indolent vs. aggressive disease. Expert commentary: The genomic information along with the application of ancillary techniques allow the definition of a neoplasia not only by its morphology but also by its biological signature. This continuous increase in knowledge will result in a better comprehension of oncogenesis, development of targeted therapies and optimizing decision-making processes related to patient care.
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Affiliation(s)
- Alessia Cimadamore
- a Section of Pathological Anatomy, School of Medicine, United Hospitals , Polytechnic University of the Marche Region , Ancona , Italy
| | - Silvia Gasparrini
- a Section of Pathological Anatomy, School of Medicine, United Hospitals , Polytechnic University of the Marche Region , Ancona , Italy
| | | | - Liang Cheng
- c Department of Pathology and Laboratory Medicine , Indiana University School of Medicine , Indianapolis , IN , USA
| | | | | | - Francesco Massari
- e Division of Oncology , S. Orsola-Malpighi Hospital , Bologna , Italy
| | - Francesca Giunchi
- f Laboratory of Oncologic Molecular Pathology , S. Orsola-Malpighi Hospital , Bologna , Italy
| | - Michelangelo Fiorentino
- f Laboratory of Oncologic Molecular Pathology , S. Orsola-Malpighi Hospital , Bologna , Italy
| | - Marina Scarpelli
- a Section of Pathological Anatomy, School of Medicine, United Hospitals , Polytechnic University of the Marche Region , Ancona , Italy
| | - Rodolfo Montironi
- a Section of Pathological Anatomy, School of Medicine, United Hospitals , Polytechnic University of the Marche Region , Ancona , Italy
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Abstract
Over the past few decades there is growing appreciation for the role of chemotherapy in treatment of prostate cancer. Initial successful phase III randomized trials in castration resistant prostate cancer (CRPC) have led to additional successful trials in earlier presentations of disease. Given the established role of radiation in management of locally advanced disease and demonstrated efficacy of taxanes in treatment of prostate cancer, optimal combination of radiation and chemotherapy in this patient population has garnered increased attention. Successful phase III trials in this space have given additional stimulus to further exploring combination therapy with radiation. New directions include assessment of additional chemotherapeutic agents including cabazitaxel and PARP inhibitors as well as personalization of therapy with use of genomic testing and other emerging markers to guide therapeutic decisions.
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Affiliation(s)
- Mark David Hurwitz
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA, USA
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119
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Helsmoortel H, Everaert C, Lumen N, Ost P, Vandesompele J. Detecting long non-coding RNA biomarkers in prostate cancer liquid biopsies: Hype or hope? Noncoding RNA Res 2018; 3:64-74. [PMID: 30159441 PMCID: PMC6096408 DOI: 10.1016/j.ncrna.2018.05.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 05/02/2018] [Accepted: 05/02/2018] [Indexed: 12/22/2022] Open
Abstract
Prostate cancer is a heterogeneous malignancy, with clinical courses widely differing between indolent and aggressive lethal disease. This heterogeneity calls for a more personalized approach towards diagnosis, prognosis, treatment decision, monitoring and follow-up of patients. In this review, we discuss the possibilities and drawbacks of detecting RNA biomarkers in biological fluids to improve disease-specific survival and quality of life. In particular, we examine literature on long non-coding RNAs in blood and urine of prostate cancer patients. We thereby specifically focus on the need for standard operation procedures on many different levels, analytical validation, clinical validation, and assessment of clinical utility. We argue that thorough multi-step validation of putative biomarkers is necessary for successful translation into clinical prostate cancer care. Our recommendations may also prove useful to biomarker research in other cancers.
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Affiliation(s)
- Hetty Helsmoortel
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Celine Everaert
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Nicolaas Lumen
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Urology, Ghent University Hospital, Ghent, Belgium
| | - Piet Ost
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
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120
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Xu J, Lan Y, Yu F, Zhu S, Ran J, Zhu J, Zhang H, Li L, Cheng S, Xiao Y, Li X. Transcriptome analysis reveals a long non-coding RNA signature to improve biochemical recurrence prediction in prostate cancer. Oncotarget 2018; 9:24936-24949. [PMID: 29861844 PMCID: PMC5982764 DOI: 10.18632/oncotarget.25048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/27/2018] [Indexed: 11/25/2022] Open
Abstract
Despite highly successful treatments for localized prostate cancer (PCa), prognostic biomarkers are needed to improve patient management and prognosis. Accumulating evidence suggests that long noncoding RNAs (lncRNAs) are key regulators with biological and clinical significance. By transcriptome analysis, we identified a set of consistently dysregulated lncRNAs in PCa across different datasets and revealed an eight-lncRNA signature that significantly associated with the biochemical recurrence (BCR)-free survival. Based on the signature, patients could be classified into high- and low-risk groups with significantly different survival (HR = 2.19; 95% CI = 1.67-2.88; P < 0.0001). Validations in the validation cohorts and another independent cohort confirmed its prognostic value for recurrence prediction. Multivariable analysis showed that the signature was independent of common clinicopathological features and stratified analysis further revealed its role in elevating risk stratification of current prognostic models. Additionally, the eight-lncRNA signature was able to improve on the CAPRA-S score for the prediction of BCR as well as to reflect the metastatic potential of PCa. Functional characterization suggested that these lncRNAs which showed PCa-specific expression patterns may involve in critical processes in tumorigenesis. Overall, our results demonstrated potential application of lncRNAs as novel independent biomarkers. The eight-lncRNA signature may have clinical potential for facilitating further stratification of more aggressive patients who would benefit from adjuvant therapy.
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Affiliation(s)
- Jinyuan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Fulong Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Shiwei Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Jianrong Ran
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Jiali Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Hongyi Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Lili Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Shujun Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China.,State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Cancer Institute and Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
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Cesnik AJ, Yang B, Truong A, Etheridge T, Spiniello M, Steinbrink MI, Shortreed MR, Frey BL, Jarrard DF, Smith LM. Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers. Transl Oncol 2018; 11:808-814. [PMID: 29723810 PMCID: PMC6154865 DOI: 10.1016/j.tranon.2018.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 01/02/2023] Open
Abstract
INTRODUCTION: The molecular mechanisms underlying aggressive versus indolent disease are not fully understood. Recent research has implicated a class of molecules known as long noncoding RNAs (lncRNAs) in tumorigenesis and progression of cancer. Our objective was to discover lncRNAs that differentiate aggressive and indolent prostate cancers. METHODS: We analyzed paired tumor and normal tissues from six aggressive Gleason score (GS) 8-10 and six indolent GS 6 prostate cancers. Extracted RNA was split for poly(A)+ and ribosomal RNA depletion library preparations, followed byRNA sequencing (RNA-Seq) using an Illumina HiSeq 2000. We developed an RNA-Seq data analysis pipeline to discover and quantify these molecules. Candidate lncRNAs were validated using RT-qPCR on 87 tumor tissue samples: 28 (GS 6), 28 (GS 3+4), 6 (GS 4+3), and 25 (GS 8-10). Statistical correlations between lncRNAs and clinicopathologic variables were tested using ANOVA. RESULTS: The 43 differentially expressed (DE) lncRNAs between aggressive and indolent prostate cancers included 12 annotated and 31 novel lncRNAs. The top six DE lncRNAs were selected based on large, consistent fold-changes in the RNA-Seq results. Three of these candidates passed RT-qPCR validation, including AC009014.3 (P < .001 in tumor tissue) and a newly discovered X-linked lncRNA named XPLAID (P = .049 in tumor tissue and P = .048 in normal tissue). XPLAID and AC009014.3 show promise as prognostic biomarkers. CONCLUSIONS: We discovered several dozen lncRNAs that distinguish aggressive and indolent prostate cancers, of which four were validated using RT-qPCR. The investigation into their biology is ongoing.
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Affiliation(s)
- Anthony J Cesnik
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Bing Yang
- Department of Urology, University of Wisconsin-Madison, Madison, WI, USA; Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA.
| | - Andrew Truong
- Department of Urology, University of Wisconsin-Madison, Madison, WI, USA; Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA.
| | - Tyler Etheridge
- Department of Urology, University of Wisconsin-Madison, Madison, WI, USA; Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA.
| | - Michele Spiniello
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | | | | | - Brian L Frey
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - David F Jarrard
- Department of Urology, University of Wisconsin-Madison, Madison, WI, USA; Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA.
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA; Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
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Montironi R, Zhou M, Magi-Galluzzi C, Epstein JI. Features and Prognostic Significance of Intraductal Carcinoma of the Prostate. Eur Urol Oncol 2018; 1:21-28. [DOI: 10.1016/j.euo.2018.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/04/2018] [Accepted: 03/13/2018] [Indexed: 12/24/2022]
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123
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Arriaga-Canon C, De La Rosa-Velázquez IA, González-Barrios R, Montiel-Manríquez R, Oliva-Rico D, Jiménez-Trejo F, Cortés-González C, Herrera LA. The use of long non-coding RNAs as prognostic biomarkers and therapeutic targets in prostate cancer. Oncotarget 2018; 9:20872-20890. [PMID: 29755696 PMCID: PMC5945524 DOI: 10.18632/oncotarget.25038] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 03/15/2018] [Indexed: 12/16/2022] Open
Abstract
Prostate cancer is the most common cancer in men and the second leading cause of cancer-related deaths. The most used biomarker to detect prostate cancer is Prostate Specific Antigen (PSA), whose levels are measured in serum. However, it has been recently established that molecular markers of cancer should not be based solely on genes and proteins but should also reflect other genomic traits; long non-coding RNAs (lncRNAs) serve this purpose. lncRNAs are transcripts of >200 bases that do not encode proteins and that have been shown to display abnormal expression profiles in different types of cancer. Experimental studies have highlighted lncRNAs as potential biomarkers for prognoses and treatments in patients with different types of cancer, including prostate cancer, where the PCA3 lncRNA is currently used as a diagnostic tool and management strategy. With the development of genomic technologies, particularly next-generation sequencing (NGS), several other lncRNAs have been linked to prostate cancer and are currently under validation for their medical use. In this review, we will discuss different strategies for the discovery of novel lncRNAs that can be evaluated as prognostic biomarkers, the clinical impact of these lncRNAs and how lncRNAs can be used as potential therapeutic targets.
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Affiliation(s)
| | - Inti Alberto De La Rosa-Velázquez
- Universidad Nacional Autónoma de México, Laboratorio de Genómica, CIC-Red de Apoyo a la Investigación, INCMNSZ, Colonia Belisario Domínguez Sección XVI, Delegación Tlalpan C.P.14080, CDMX, Mexico
| | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Tlalpan. C.P. 14080, CDMX, Mexico
| | - Rogelio Montiel-Manríquez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Tlalpan. C.P. 14080, CDMX, Mexico
| | - Diego Oliva-Rico
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Tlalpan. C.P. 14080, CDMX, Mexico
| | | | - Carlo Cortés-González
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Tlalpan. C.P. 14080, CDMX, Mexico
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Tlalpan. C.P. 14080, CDMX, Mexico
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Bijnsdorp IV, van Royen ME, Verhaegh GW, Martens-Uzunova ES. The Non-Coding Transcriptome of Prostate Cancer: Implications for Clinical Practice. Mol Diagn Ther 2018; 21:385-400. [PMID: 28299719 PMCID: PMC5511609 DOI: 10.1007/s40291-017-0271-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Prostate cancer (PCa) is the most common type of cancer and the second leading cause of cancer-related death in men. Despite extensive research, the molecular mechanisms underlying PCa initiation and progression remain unclear, and there is increasing need of better biomarkers that can distinguish indolent from aggressive and life-threatening disease. With the advent of advanced genomic technologies in the last decade, it became apparent that the human genome encodes tens of thousands non-protein-coding RNAs (ncRNAs) with yet to be discovered function. It is clear now that the majority of ncRNAs exhibit highly specific expression patterns restricted to certain tissues and organs or developmental stages and that the expression of many ncRNAs is altered in disease and cancer, including cancer of the prostate. Such ncRNAs can serve as important biomarkers for PCa diagnosis, prognosis, or prediction of therapy response. In this review, we give an overview of the different types of ncRNAs and their function, describe ncRNAs relevant for the diagnosis and prognosis of PCa, and present emerging new aspects of ncRNA research that may contribute to the future utilization of ncRNAs as clinically useful therapeutic targets.
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MESH Headings
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/metabolism
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/urine
- Early Detection of Cancer/methods
- Gene Expression Regulation, Neoplastic
- High-Throughput Nucleotide Sequencing
- Humans
- Male
- Molecular Targeted Therapy
- Precision Medicine
- Prognosis
- Prostatic Neoplasms/diagnosis
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- RNA, Untranslated/blood
- RNA, Untranslated/classification
- RNA, Untranslated/genetics
- RNA, Untranslated/urine
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Affiliation(s)
- Irene V Bijnsdorp
- Department of Urology, VU University Medical Center, Amsterdam, The Netherlands
| | - Martin E van Royen
- Department of Pathology and Erasmus Optical Imaging Centre (OIC), Erasmus Medical Center, Rotterdam, The Netherlands
| | - Gerald W Verhaegh
- Department of Urology, Radboud university medical center, Nijmegen, The Netherlands
| | - Elena S Martens-Uzunova
- Department of Urology, Erasmus Medical Center, Erasmus Cancer Institute, Room Be-362b, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
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125
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Mitobe Y, Takayama KI, Horie-Inoue K, Inoue S. Prostate cancer-associated lncRNAs. Cancer Lett 2018; 418:159-166. [DOI: 10.1016/j.canlet.2018.01.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/19/2017] [Accepted: 01/06/2018] [Indexed: 01/01/2023]
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126
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Interplay between regulation by methylation and noncoding RNAs in cancers. Eur J Cancer Prev 2018; 27:418-424. [PMID: 29557800 DOI: 10.1097/cej.0000000000000433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cancer is one of the most important health problems today; therefore, many researchers are focusing on exploring the mechanisms underlying its development and treatment. The field of cancer epigenetics has flourished in recent decades, and studies have shown that different epigenetic events, such as DNA methylation, histone modification, and noncoding RNA regulation, work together to influence cancer development and progression. In this short review, we summarize the interactions between methylation and noncoding RNAs that affect cancer development.
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Sun T, Du SY, Armenia J, Qu F, Fan J, Wang X, Fei T, Komura K, Liu SX, Lee GSM, Kantoff PW. Expression of lncRNA MIR222HG co-transcribed from the miR-221/222 gene promoter facilitates the development of castration-resistant prostate cancer. Oncogenesis 2018. [PMID: 29540675 PMCID: PMC5852960 DOI: 10.1038/s41389-018-0039-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mechanisms by which non-coding RNAs contribute to the progression of hormone-sensitive prostate cancer (PCa) (HSPC) to castration-resistant PCa (CRPC) remain largely unknown. We previously showed that microRNA-221/222 is up-regulated in CRPC and plays a critical role in modulating androgen receptor function during CRPC development. With further investigation, we characterized a putative promoter region located 23.3 kb upstream of the miR-221/222 gene, and this promoter is differentially activated in CRPC LNCaP-Abl cells, leading to the up-regulation of miR-221/222. Upon promoter activation, a set of polyadenylated long non-coding RNA (lncRNA) MIR222HGs was transcribed from this promoter region. Over-expression of these MIR222HGs increased androgen-independent cell growth and repressed the expression of androgen receptor-regulated dihydrotestosterone (DHT)-induced KLK3, TMPRSS2, and FKBP5 in HSPC LNCaP cells, hallmarks of the CRPC phenotype. Clinically, increased expression of MIR222HG is associated with PCa progression to CRPC. In primary tumors, expression levels of MIR222HG and miR-221/222 inversely correlate with Gleason score and androgen receptor (AR) pathway activity. Interestingly, MIR222HG is Argonaute 2-bound and its expression is Dicer 1-dependent, suggesting its functional association with the RNA-induced silencing complex. Further studies led to the hypothesis that MIR222HG may potentially affect miR-mediated expression silencing, subsequently leading to AR reprogramming. Our study highlights an essential role of a non-coding RNA in CRPC development and that differential activation of a single promoter can up-regulate two different types of non-coding RNAs, miR-221/222 and lncRNA MIR222HG, in CRPC. Additionally, this study reveals a novel function of lncRNAs as a modulator of Argonaute-mediated RNA-induced silencing complex.
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Affiliation(s)
- Tong Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Shin-Yi Du
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Joshua Armenia
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fangfang Qu
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Jingyu Fan
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Xiaodong Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Teng Fei
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Kazumasa Komura
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Shirley X Liu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave, Boston, MA, 02215, USA.
| | - Philip W Kantoff
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave, Boston, MA, 02215, USA. .,Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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128
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Lin D. Commentary on "The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer." Chakravarty D, Sboner A, Nair SS, Giannopoulou E, Li R, Hennig S, Mosquera JM, Pauwels J, Park K, Kossai M, MacDonald TY, Fontugne J, Erho N, Vergara IA, Ghadessi M, Davicioni E, Jenkins RB, Palanisamy N, Chen Z, Nakagawa S, Hirose T, Bander NH, Beltran H, Fox AH, Elemento O, Rubin MA, University of Washington-Urology, Seattle, WA. Nat Commun 2014; 5:5383. Urol Oncol 2018; 34:522. [PMID: 27814882 DOI: 10.1016/j.urolonc.2016.02.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Daniel Lin
- University of Washington-Urology, Seattle, WA.
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129
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Aird J, Baird AM, Lim MC, McDermott R, Finn SP, Gray SG. Carcinogenesis in prostate cancer: The role of long non-coding RNAs. Noncoding RNA Res 2018; 3:29-38. [PMID: 30159437 PMCID: PMC6084828 DOI: 10.1016/j.ncrna.2018.01.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/16/2018] [Indexed: 12/28/2022] Open
Abstract
LncRNAs appear to play a considerable role in tumourigenesis through regulating key processes in cancer cells such as proliferative signalling, replicative immortality, invasion and metastasis, evasion of growth suppressors, induction of angiogenesis and resistance to apoptosis. LncRNAs have been reported to play a role in prostate cancer, particularly in regulating the androgen receptor signalling pathway. In this review article, we summarise the role of 34 lncRNAs in prostate cancer with a particular focus on their role in the androgen receptor signalling pathway and the epithelial to mesenchymal transition pathway.
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Affiliation(s)
- John Aird
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College Dublin, Ireland
| | - Anne-Marie Baird
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College Dublin, Ireland
- Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital, Dublin, Ireland
- Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Marvin C.J. Lim
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College Dublin, Ireland
- Department of Medical Oncology, St. Vincent's University Hospital, Dublin, Ireland
- Department of Medical Oncology, Tallaght Hospital, Dublin, Ireland
| | - Ray McDermott
- Department of Medical Oncology, St. Vincent's University Hospital, Dublin, Ireland
- Department of Medical Oncology, Tallaght Hospital, Dublin, Ireland
| | - Stephen P. Finn
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College Dublin, Ireland
- Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
| | - Steven G. Gray
- Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
- HOPE Directorate, St. James's Hospital, Dublin, Ireland
- Labmed Directorate, St. James's Hospital, Dublin, Ireland
- School of Biological Sciences, Dublin Institute of Technology, Dublin, Ireland
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130
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Innovative methods for biomarker discovery in the evaluation and development of cancer precision therapies. Cancer Metastasis Rev 2018; 37:125-145. [PMID: 29392535 DOI: 10.1007/s10555-017-9710-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The discovery of biomarkers able to detect cancer at an early stage, to evaluate its aggressiveness, and to predict the response to therapy remains a major challenge in clinical oncology and precision medicine. In this review, we summarize recent achievements in the discovery and development of cancer biomarkers. We also highlight emerging innovative methods in biomarker discovery and provide insights into the challenges faced in their evaluation and validation.
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131
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Shen MY, Chen JF, Luo CH, Lee S, Li CH, Yang YL, Tsai YH, Ho BC, Bao LR, Lee TJ, Jan YJ, Zhu YZ, Cheng S, Feng FY, Chen P, Hou S, Agopian V, Hsiao YS, Tseng HR, Posadas EM, Yu HH. Glycan Stimulation Enables Purification of Prostate Cancer Circulating Tumor Cells on PEDOT NanoVelcro Chips for RNA Biomarker Detection. Adv Healthc Mater 2018; 7:10.1002/adhm.201700701. [PMID: 28892262 PMCID: PMC5803304 DOI: 10.1002/adhm.201700701] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/31/2017] [Indexed: 12/30/2022]
Abstract
A glycan-stimulated and poly(3,4-ethylene-dioxythiophene)s (PEDOT)-based nanomaterial platform is fabricated to purify circulating tumor cells (CTCs) from blood samples of prostate cancer (PCa) patients. This new platform, phenylboronic acid (PBA)-grafted PEDOT NanoVelcro, combines the 3D PEDOT nanosubstrate, which greatly enhances CTC capturing efficiency, with a poly(EDOT-PBA-co-EDOT-EG3) interfacial layer, which not only provides high specificity for CTC capture upon antibody conjugation but also enables competitive binding of sorbitol to gently release the captured cells. CTCs purified by this PEDOT NanoVelcro chip provide well-preserved RNA transcripts for the analysis of the expression level of several PCa-specific RNA biomarkers, which may provide clinical insights into the disease.
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Affiliation(s)
- Mo-Yuan Shen
- Smart Organic Material Laboratory, Institute of Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nankang, Taipei, 11529, Taiwan
| | - Jie-Fu Chen
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Los Angeles, CA, 90048, USA
| | - Chun-Hao Luo
- Smart Organic Material Laboratory, Institute of Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nankang, Taipei, 11529, Taiwan
| | - Sangjun Lee
- Department of Molecular and Medical Pharmacology, California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, CA, 90095-1770, USA
| | - Cheng-Hsuan Li
- Smart Organic Material Laboratory, Institute of Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nankang, Taipei, 11529, Taiwan
| | - Yung-Ling Yang
- Smart Organic Material Laboratory, Institute of Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nankang, Taipei, 11529, Taiwan
| | - Yu-Han Tsai
- Smart Organic Material Laboratory, Institute of Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nankang, Taipei, 11529, Taiwan
| | - Bo-Cheng Ho
- Department of Material Engineering, Ming Chi University of Technology, 84 Gungjuan Rd., Taishan Dist., New Taipei City, 24301, Taiwan
| | - Li-Rong Bao
- Department of Molecular and Medical Pharmacology, California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, CA, 90095-1770, USA
| | - Tien-Jung Lee
- Department of Molecular and Medical Pharmacology, California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, CA, 90095-1770, USA
| | - Yu Jen Jan
- Department of Molecular and Medical Pharmacology, California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, CA, 90095-1770, USA
| | - Ya-Zhen Zhu
- Department of Molecular and Medical Pharmacology, California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, CA, 90095-1770, USA
| | - Shirley Cheng
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Los Angeles, CA, 90048, USA
| | - Felix Y Feng
- Departments of Radiation Oncology, Urology, and Medicine, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Shuang Hou
- Liver Transplantation and Hepatobiliary Surgery, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Vatche Agopian
- Liver Transplantation and Hepatobiliary Surgery, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Yu-Sheng Hsiao
- Department of Material Engineering, Ming Chi University of Technology, 84 Gungjuan Rd., Taishan Dist., New Taipei City, 24301, Taiwan
| | - Hsian-Rong Tseng
- Department of Molecular and Medical Pharmacology, California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, CA, 90095-1770, USA
| | - Edwin M Posadas
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Los Angeles, CA, 90048, USA
| | - Hsiao-Hua Yu
- Smart Organic Material Laboratory, Institute of Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nankang, Taipei, 11529, Taiwan
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132
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Xu S, Wang P, You Z, Meng H, Mu G, Bai X, Zhang G, Zhang J, Pang D. The long non-coding RNA EPB41L4A-AS2 inhibits tumor proliferation and is associated with favorable prognoses in breast cancer and other solid tumors. Oncotarget 2018; 7:20704-17. [PMID: 26980733 PMCID: PMC4991486 DOI: 10.18632/oncotarget.8007] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/18/2016] [Indexed: 02/01/2023] Open
Abstract
EPB41L4A-AS2 is a novel long non-coding RNA of unknown function. In this study, we investigated the expression of EPB41L4A-AS2 in breast cancer tissues and evaluated its relationship with the clinicopathological features and prognosis of patients with breast cancer. This entailed conducting a meta-analysis and prognosis validation study using two cohorts from the Gene Expression Omnibus (GEO). In addition, we assessed EPB41L4A-AS2 expression and its relationship with the clinicopathological features of renal and lung cancers using the Cancer Genome Atlas cohort and a GEO dataset. We also clarified the role of EPB41L4A-AS2 expression in mediating cancer cell proliferation in breast, renal, and lung cancer cell lines transfected with an EPB41L4A-AS2 expression vector. We found that high EPB41L4A-AS2 expression is associated with favorable disease outcomes. Gene ontology enrichment analysis revealed that EPB41L4A-AS2 may be involved in processes associated with tumor biology. Finally, overexpression of EPB41L4A-AS2 inhibited tumor cell proliferation in breast, renal, and lung cancer cell lines. Our clinical and in vitro results suggest that EPB41L4A-AS2 inhibits solid tumor formation and that evaluation of this long non-coding RNA may have prognostic value in the clinical management of such malignancies.
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Affiliation(s)
- Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Peiyuan Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Zilong You
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Hongxue Meng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Guannan Mu
- Biotherapy Center, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xianan Bai
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Guangwen Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jinfeng Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
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133
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Chen X, Yang C, Xie S, Cheung E. Long non-coding RNA GAS5 and ZFAS1 are prognostic markers involved in translation targeted by miR-940 in prostate cancer. Oncotarget 2018; 9:1048-1062. [PMID: 29416676 PMCID: PMC5787418 DOI: 10.18632/oncotarget.23254] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/03/2017] [Indexed: 12/30/2022] Open
Abstract
Identification of prognostic biomarkers helps facilitate the prediction of patient outcomes as well as guide treatments. Accumulating evidence now suggests that long non-coding RNAs (lncRNAs) play key roles in tumor progression with diagnostic and prognostic values. However, little is known about the biological functions of lncRNAs and how they contribute to the pathogenesis of cancer. Herein, we performed weighted correlation network analysis (WGCNA) on 380 RNA-seq samples from prostate cancer patients to create networks comprising of microRNAs, lncRNAs, and protein-coding genes. Our analysis revealed expression modules that associated with pathological parameters. More importantly, we identified a gene module that is involved in protein translation and is associated with patient survival. In this gene module, we explored the regulation axis involving GAS5, ZFAS1, and miR-940. We show that GAS5, ZFAS1, and miR-940 are up-regulated in tumors relative to normal prostate tissues, and high expression of either lncRNA is an indicator of poor patient outcome. Finally, we constructed a co-expression network involving GAS5, ZFAS1, and miR-940, as well as the targets of miR-940. Our results show that GAS5 and ZFAS1 are targeted by miR-940 via NAA10 and RPL28. Taken together, co-expression analysis of gene expression profiling from RNA-seq can accelerate the identification and functional characterization of novel prognostic markers in prostate cancer.
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Affiliation(s)
- Xin Chen
- Guangdong Key Laboratory of IoT Information Technology, School of Automation, Guangdong University of Technology, Guangzhou, China
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Chao Yang
- Guangdong Key Laboratory of IoT Information Technology, School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Shengli Xie
- Guangdong Key Laboratory of IoT Information Technology, School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Edwin Cheung
- Faculty of Health Sciences, University of Macau, Macau, China
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134
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Cozar J, Robles-Fernandez I, Martinez-Gonzalez L, Pascual-Geler M, Rodriguez-Martinez A, Serrano M, Lorente J, Alvarez-Cubero M. Genetic markers a landscape in prostate cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 775:1-10. [DOI: 10.1016/j.mrrev.2017.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/21/2017] [Accepted: 11/28/2017] [Indexed: 12/19/2022]
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135
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Xie F, Ling L, van Dam H, Zhou F, Zhang L. TGF-β signaling in cancer metastasis. Acta Biochim Biophys Sin (Shanghai) 2018; 50:121-132. [PMID: 29190313 DOI: 10.1093/abbs/gmx123] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Indexed: 02/06/2023] Open
Abstract
The transforming growth factor (TGF)-β signaling events are well known to control diverse processes and numerous responses, such as cell proliferation, differentiation, apoptosis, and migration. TGF-β signaling plays context-dependent roles in cancer: in pre-malignant cells TGF-β primarily functions as a tumor suppressor, while in the later stages of cancer TGF-β signaling promotes invasion and metastasis. Recent studies have also suggested that the cross-talk between TGF-β signaling and other signaling pathways, such as Hippo, Wnt, EGFR/RAS, and PI3K/AKT pathways, may substantially contribute to our current understanding of TGF-β signaling and cancer. As a result of the wide-ranging effects of TGF-β, blockade of TGF-β and its downstream signaling components provides multiple therapeutic opportunities. Therefore, the outlook for anti-TGF-β signaling therapy for numerous diseases appears bright and will provide valuable information and thinking on the drug molecular design. In this review, we focus on recent insights into the regulation of TGF-β signaling in cancer metastasis which may contribute to the development of novel cancer-targeting therapies.
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Affiliation(s)
- Feng Xie
- Institutes of Biology and Medical Science, Soochow University, Suzhou 215123, China
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Li Ling
- Institutes of Biology and Medical Science, Soochow University, Suzhou 215123, China
| | - Hans van Dam
- Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands, Leiden University Medical Center, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou 215123, China
| | - Long Zhang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
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136
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Cimadamore A, Gasparrini S, Mazzucchelli R, Doria A, Cheng L, Lopez-Beltran A, Santoni M, Scarpelli M, Montironi R. Long Non-coding RNAs in Prostate Cancer with Emphasis on Second Chromosome Locus Associated with Prostate-1 Expression. Front Oncol 2017; 7:305. [PMID: 29312884 PMCID: PMC5732923 DOI: 10.3389/fonc.2017.00305] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/27/2017] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a class of RNA with transcripts longer than 200 nucleotides that lack functional open reading frames. They play various roles in human carcinoma, such as dysregulating gene expression in prostate cancer (PCa), which results in cancer initiation, development, and progression. The non-coding RNA SChLAP1 (second chromosome locus associated with prostate-1) is highly expressed in approximately 25% of PCas with higher prevalence in metastatic compared to localized PCa. Its expression is detectable non-invasively in PCa patient urine samples. Experimental data suggest that targeting SChLAP1 may represent a novel therapeutic application in PCa. This contribution focuses on the role of lncRNAs SChLAP1 expression in PCa diagnosis and prognosis.
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Affiliation(s)
- Alessia Cimadamore
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, Ancona, Italy
| | - Silvia Gasparrini
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, Ancona, Italy
| | - Roberta Mazzucchelli
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, Ancona, Italy
| | - Andrea Doria
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, Ancona, Italy
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Antonio Lopez-Beltran
- Department of Pathology and Surgery, Faculty of Medicine, Universidad de Córdoba, Córdoba, Spain
| | | | - Marina Scarpelli
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, Ancona, Italy
| | - Rodolfo Montironi
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, Ancona, Italy
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137
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A Prostate Cancer “ Nimbosus ”: Genomic Instability and SChLAP1 Dysregulation Underpin Aggression of Intraductal and Cribriform Subpathologies. Eur Urol 2017; 72:665-674. [DOI: 10.1016/j.eururo.2017.04.034] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/27/2017] [Indexed: 11/22/2022]
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138
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Angulo JC, López JI, Ropero S. DNA Methylation and Urological Cancer, a Step Towards Personalized Medicine: Current and Future Prospects. Mol Diagn Ther 2017; 20:531-549. [PMID: 27501813 DOI: 10.1007/s40291-016-0231-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Urologic malignancies are some of the commonest tumors often curable when diagnosed at early stage. However, accurate diagnostic markers and faithful predictors of prognosis are needed to avoid over-diagnosis leading to overtreatment. Many promising exploratory studies have identified epigenetic markers in urinary malignancies based on DNA methylation, histone modification and non-coding ribonucleic acid (ncRNA) expression that epigenetically regulate gene expression. We review and discuss the current state of development and the future potential of epigenetic biomarkers for more accurate and less invasive detection of urological cancer, tumor recurrence and progression of disease serving to establish diagnosis and monitor treatment efficacies. The specific clinical implications of such methylation tests on therapeutic decisions and patient outcome and current limitations are also discussed.
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Affiliation(s)
- Javier C Angulo
- Servicio de Urología, Hospital Universitario de Getafe, Departamento Clínico, Facultad de Ciencias Biomédicas, Universidad Europea de Madrid, Laureate Universities, Hospital Universitario de Getafe, Carretera de Toledo Km 12.5, Getafe, 28905, Madrid, Spain.
| | - Jose I López
- Servicio de Anatomía Patológica, Hospital Universitario de Cruces, Instituto BioCruces,Universidad del País Vasco (UPV-EHU), Bilbao, Spain
| | - Santiago Ropero
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
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139
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Gong X, Siprashvili Z, Eminaga O, Shen Z, Sato Y, Kume H, Homma Y, Ogawa S, Khavari PA, Pollack JR, Brooks JD. Novel lincRNA SLINKY is a prognostic biomarker in kidney cancer. Oncotarget 2017; 8:18657-18669. [PMID: 28423633 PMCID: PMC5386637 DOI: 10.18632/oncotarget.15703] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/24/2017] [Indexed: 01/01/2023] Open
Abstract
Clear cell renal cell carcinomas (ccRCC) show a broad range of clinical behavior, and prognostic biomarkers are needed to stratify patients for appropriate management. We sought to determine whether long intergenic non-coding RNAs (lincRNAs) might predict patient survival. Candidate prognostic lincRNAs were identified by mining The Cancer Genome Atlas (TCGA) transcriptome (RNA-seq) data on 466 ccRCC cases (randomized into discovery and validation sets) annotated for ~21,000 lncRNAs. A previously uncharacterized lincRNA, SLINKY (Survival-predictive LINcRNA in KidneY cancer), was the top-ranked prognostic lincRNA, and validated in an independent University of Tokyo cohort (P=0.004). In multivariable analysis, SLINKY expression predicted overall survival independent of tumor stage and grade [TCGA HR=3.5 (CI, 2.2-5.7), P < 0.001; Tokyo HR=8.4 (CI, 1.8-40.2), P = 0.007], and by decision tree, ROC and decision curve analysis, added independent prognostic value. In ccRCC cell lines, SLINKY knockdown reduced cancer cell proliferation (with cell-cycle G1 arrest) and induced transcriptome changes enriched for cell proliferation and survival processes. Notably, the genes affected by SLINKY knockdown in cell lines were themselves prognostic and correlated with SLINKY expression in the ccRCC patient samples. From a screen for binding partners, we identified direct binding of SLINKY to Heterogeneous Nuclear Ribonucleoprotein K (HNRNPK), whose knockdown recapitulated SLINKY knockdown phenotypes. Thus, SLINKY is a robust prognostic biomarker in ccRCC, where it functions possibly together with HNRNPK in cancer cell proliferation.
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Affiliation(s)
- Xue Gong
- Department of Urology, School of Medicine, Stanford University, Stanford, California, USA.,Department of Pathology, School of Medicine, Stanford University, Stanford, California, USA
| | - Zurab Siprashvili
- Program in Epithelial Biology, School of Medicine, Stanford University, Stanford, California, USA
| | - Okyaz Eminaga
- Department of Urology, School of Medicine, Stanford University, Stanford, California, USA.,Department of Urology, University Hospital Cologne, Cologne, Germany
| | - Zhewei Shen
- Department of Pathology, School of Medicine, Stanford University, Stanford, California, USA
| | - Yusuke Sato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukio Homma
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Paul A Khavari
- Program in Epithelial Biology, School of Medicine, Stanford University, Stanford, California, USA
| | - Jonathan R Pollack
- Department of Pathology, School of Medicine, Stanford University, Stanford, California, USA
| | - James D Brooks
- Department of Urology, School of Medicine, Stanford University, Stanford, California, USA
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140
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Misawa A, Takayama KI, Inoue S. Long non-coding RNAs and prostate cancer. Cancer Sci 2017; 108:2107-2114. [PMID: 28796922 PMCID: PMC5665759 DOI: 10.1111/cas.13352] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 08/07/2017] [Accepted: 08/07/2017] [Indexed: 02/07/2023] Open
Abstract
Long non‐coding RNAs (lncRNAs) are RNA transcripts larger than 200 nucleotides that do not code for proteins the aberrant expression of which has been documented in various types of cancer, including prostate cancer. Lack of appropriate sensitive and specific biomarkers for prostate cancer has led to overdiagnosis and overtreatment, making lncRNAs promising novel biomarkers as well as therapeutic targets for the disease. The present review attempts to summarize the current knowledge of lncRNA expression patterns and mechanisms in prostate cancer, which contribute to carcinogenesis. In particular, we focused on lncRNAs regulated by androgen receptor and expressed in castration‐resistant prostate cancer.
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Affiliation(s)
- Aya Misawa
- Department of Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ken-Ichi Takayama
- Department of Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Functional Biogerontology, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Satoshi Inoue
- Department of Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Functional Biogerontology, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan.,Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
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141
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Ma W, Chen X, Ding L, Ma J, Jing W, Lan T, Sattar H, Wei Y, Zhou F, Yuan Y. The prognostic value of long noncoding RNAs in prostate cancer: a systematic review and meta-analysis. Oncotarget 2017; 8:57755-57765. [PMID: 28915709 PMCID: PMC5593681 DOI: 10.18632/oncotarget.17645] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/25/2017] [Indexed: 12/18/2022] Open
Abstract
The abnormally expressed LncRNAs played irreplaceable roles in the prognosis of prostate cancer (PCa). Therefore, we conducted this systematic review and meta-analysis to summarize the association between the expression of LncRNAs, prognosis and clinicopathology of PCa. 18 eligible studies were recruited into our analysis, including 18 on prognosis and 9 on clinicopathological features. Results indicated that aberrant expression of LncRNAs was significantly associated with biochemical recurrence-free survival (BCR-FS) (HR = 1.55, 95%CI: 1.01-2.37, P < 0.05), recurrence free survival (RSF) (HR = 3.07, 95%CI: 1.07-8.86, P < 0.05) and progression free survival (PFS) (HR = 2.34, 95%CI: 1.94-2.83, P < 0.001) in PCa patients. LncRNAs expression level was correlated with several vital clinical features, like tumor size (HR = 0.52, 95%CI: 0.28-0.95, P = 0.03), distance metastasis (HR = 4.55, 95%CI: 2.26-9.15, P < 0.0001) and histological grade (HR = 6.23, 95% CI: 3.29-11.82, P < 0.00001). Besides, down-regulation of PCAT14 was associated with the prognosis of PCa [over survival (HR = 0.77, 95%CI: 0.63-0.95, P = 0.01), BCR-FS (HR = 0.61, 95%CI: 0.48-0.79, P = 0.0001), prostate cancer-specific survival (HR = 0.64, 95%CI: 0.48-0.85, P = 0.002) and metastasis-free survival (HR = 0.61, 95%CI: 0.50-0.74, P < 0.00001)]. And, the increased SChLAP1 expression could imply the worse BCR-FS (HR = 2.54, 95%CI: 1.82-3.56, P < 0.00001) and correlate with Gleason score (< 7 vs ≥ 7) (OR = 4.11, 95% CI: 1.94-8.70, P = 0.0002). Conclusively, our present work demonstrated that LncRNAs transcription level might be potential prognostic markers in PCa.
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Affiliation(s)
- Weijie Ma
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xi Chen
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lu Ding
- Department of Clinical Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jianhong Ma
- Department of Gynaecology and Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wei Jing
- Department of Clinical Laboratory Medicine and Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Tian Lan
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Haseeb Sattar
- Department of Clinical Pharmacy, Wuhan Union Hospital, Affiliated Hospital, Tongji Medical College, Huazhong University of Science And Technology, Wuhan, China
| | - Yongchang Wei
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fuling Zhou
- Department of Gynaecology and Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yufeng Yuan
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
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142
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Abstract
Molecular biomarkers play little role in the current treatment of metastatic castration-resistant prostate cancer (CRPC). The advent of next-generation sequencing (NGS) has enabled the comprehensive molecular characterization of the genomic and transcriptomic landscape of both untreated primary prostate cancer and CRPC. Recent studies demonstrating the feasibility of interinstitution studies obtaining and NGS profiling of metastatic biopsies, targeted NGS approaches applicable to routine formalin-fixed, paraffin-embedded specimens, and NGS approaches applicable to circulating DNA and circulating tumor cells portend near-term adoption of NGS approaches in the management and treatment of CRPC. Important considerations in the clinical implementation of NGS include interpatient and intrapatient heterogeneity, disease progression to neuroendocrine/small cell prostate carcinoma, and incorporation into clinical trial design to demonstrate clinical utility. We review the recent progress in NGS-based characterization of CRPC to understand disease biology and inform on barriers to widespread clinical adoption.
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143
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Wang L, Song G, Zhang X, Feng T, Pan J, Chen W, Yang M, Bai X, Pang Y, Yu J, Han J, Han B. PADI2-Mediated Citrullination Promotes Prostate Cancer Progression. Cancer Res 2017; 77:5755-5768. [DOI: 10.1158/0008-5472.can-17-0150] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/31/2017] [Accepted: 08/11/2017] [Indexed: 11/16/2022]
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144
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Renganathan A, Felley-Bosco E. Long Noncoding RNAs in Cancer and Therapeutic Potential. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1008:199-222. [DOI: 10.1007/978-981-10-5203-3_7] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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145
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Martignano F, Rossi L, Maugeri A, Gallà V, Conteduca V, De Giorgi U, Casadio V, Schepisi G. Urinary RNA-based biomarkers for prostate cancer detection. Clin Chim Acta 2017; 473:96-105. [PMID: 28807541 DOI: 10.1016/j.cca.2017.08.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/10/2017] [Accepted: 08/10/2017] [Indexed: 12/19/2022]
Abstract
Prostate cancer (PCa) is the commonest malignancy in the male population worldwide. Serum prostate specific antigen (PSA) test is the most important biomarker for the detection, follow-up and therapeutic monitoring of PCa. Defects in PSA specificity have elicited research for new biomarkers to improve early diagnosis and avoid false-positive results. This review evaluates urinary RNA-based biomarkers. Urine is a versatile body fluid for non-invasive biomarker detection in case of urological malignancies. The importance of RNA-based biomarkers has been demonstrated by the current use of PCA3, a long non coding RNA biomarker already approved by the Food and Drugs Administration. Through the years, other urinary RNA biomarkers have been evaluated, including the well-known TMPRSS2:ERG transcript, as well as many messenger RNAs, long non coding RNAs and micro-RNA. Validation of a specific urinary RNA-based marker or an algorithm of different biomarkers levels as diagnostic markers for PCa could be useful to avoid unnecessary prostate biopsies.
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Affiliation(s)
- Filippo Martignano
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, Meldola 47014, Italy
| | - Lorena Rossi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, Meldola 47014, Italy
| | - Antonio Maugeri
- Oncology Pharmacy Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, Meldola 47014, Italy
| | - Valentina Gallà
- Unit of Biostatistics and Clinical Trials, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, Meldola 47014, Italy; University of Florence, Italy
| | - Vincenza Conteduca
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, Meldola 47014, Italy
| | - Ugo De Giorgi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, Meldola 47014, Italy
| | - Valentina Casadio
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, Meldola 47014, Italy.
| | - Giuseppe Schepisi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, Meldola 47014, Italy
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146
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Lu L, Li K, Mao YH, Qu H, Yao B, Zhong WW, Ma B, Wang ZY. Gold-chrysophanol nanoparticles suppress human prostate cancer progression through inactivating AKT expression and inducing apoptosis and ROS generation in vitro and in vivo. Int J Oncol 2017; 51:1089-1103. [PMID: 28849003 PMCID: PMC5592865 DOI: 10.3892/ijo.2017.4095] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/16/2017] [Indexed: 12/12/2022] Open
Abstract
Controlled releasing of regulations remains the most convenient method to deliver various drugs. In the present study, we precipitated gold nanoparticles with chrysophanol. The gold-chrysophanol into poly (DL-lactide-co-glycolide) nanoparticles was loaded and the biological activity of chrysophanol nanoparticles on human LNCap prostate cancer cells, was tested to acquire the sustained releasing property. The circular dichroism spectroscopy indicated that chrysophanol nanoparticles effectively resulted in conformational alterations in DNA and regulated different proteins associated with cell cycle arrest. The reactive oxygen species (ROS), apoptosis, cell cycle, DNA damage, Cyto-c and caspase-3 activity were analyzed, and the expression levels of different anti- and pro-apoptotic were studied using immunoblotting analysis. The cytotoxicity assay suggested that chrysophanol nanoparticles preferentially killed prostate cancer cells in comparison to the normal cells. Chrysophanol nanoparticles reduced histone deacetylases (HDACs) to suppress cell proliferation and induce apoptosis by arresting the cell cycle in sub-G phase. In addition, the cell cycle-related proteins, including p27, CHK1, cyclin D1, CDK1, p-AMP-activated protein kinase (AMPK) and p-protein kinase B (AKT), were regulated by chrysophanol nanoparticles to prevent human prostate cancer cell progression. Chrysophanol nanoparticles induced apoptosis in LNCap cells by promoting p53/ROS crosstalk to prevent proliferation. Pharmacokinetic study in mice indicated that chrysophanol nanoparticle injection showed high bioavailability compared to the free chrysophanol. Also, in vivo study revealed that chrysophanol nanoparticles obviously reduced tumor volume and weight. In conclusion, the data above suggested that chrysophanol nanoparticles might be effective to prevent human prostate cancer progression.
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Affiliation(s)
- Li Lu
- Department of Urology, The Sixth Affliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Ke Li
- Department of Urology, The Third Affliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Yun-Hua Mao
- Department of Urology, The Third Affliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Hu Qu
- Department of Urology, The Sixth Affliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Bing Yao
- Department of Urology, The Sixth Affliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Wen-Wen Zhong
- Department of Urology, The Sixth Affliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Bo Ma
- Department of Urology, The Sixth Affliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Zhong-Yang Wang
- Department of Urology, The Sixth Affliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510655, P.R. China
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147
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Shukla S, Zhang X, Niknafs YS, Xiao L, Mehra R, Cieślik M, Ross A, Schaeffer E, Malik B, Guo S, Freier SM, Bui HH, Siddiqui J, Jing X, Cao X, Dhanasekaran SM, Feng FY, Chinnaiyan AM, Malik R. Identification and Validation of PCAT14 as Prognostic Biomarker in Prostate Cancer. Neoplasia 2017; 18:489-99. [PMID: 27566105 PMCID: PMC5018094 DOI: 10.1016/j.neo.2016.07.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 07/06/2016] [Accepted: 07/06/2016] [Indexed: 12/15/2022] Open
Abstract
Rapid advances in the discovery of long noncoding RNAs (lncRNAs) have identified lineage- and cancer-specific biomarkers that may be relevant in the clinical management of prostate cancer (PCa). Here we assembled and analyzed a large RNA-seq dataset, from 585 patient samples, including benign prostate tissue and both localized and metastatic PCa to discover and validate differentially expressed genes associated with disease aggressiveness. We performed Sample Set Enrichment Analysis (SSEA) and identified genes associated with low versus high Gleason score in the RNA-seq database. Comparing Gleason 6 versus 9+ PCa samples, we identified 99 differentially expressed genes with variable association to Gleason grade as well as robust expression in prostate cancer. The top-ranked novel lncRNA PCAT14, exhibits both cancer and lineage specificity. On multivariate analysis, low PCAT14 expression independently predicts for BPFS (P = .00126), PSS (P = .0385), and MFS (P = .000609), with trends for OS as well (P = .056). An RNA in-situ hybridization (ISH) assay for PCAT14 distinguished benign vs malignant cases, as well as high vs low Gleason disease. PCAT14 is transcriptionally regulated by AR, and endogenous PCAT14 overexpression suppresses cell invasion. Thus, Using RNA-sequencing data we identify PCAT14, a novel prostate cancer and lineage-specific lncRNA. PCAT14 is highly expressed in low grade disease and loss of PCAT14 predicts for disease aggressiveness and recurrence.
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Affiliation(s)
- Sudhanshu Shukla
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, USA; Department of Pathology, University of Michigan, Ann Arbor, USA
| | - Xiang Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, USA; Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Yashar S Niknafs
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, USA
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, USA; Department of Pathology, University of Michigan, Ann Arbor, USA
| | - Rohit Mehra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, USA; Department of Pathology, University of Michigan, Ann Arbor, USA
| | - Marcin Cieślik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, USA; Department of Pathology, University of Michigan, Ann Arbor, USA
| | - Ashley Ross
- James Buchanan Brady Urological Institute, Johns Hopkins University, USA
| | - Edward Schaeffer
- James Buchanan Brady Urological Institute, Johns Hopkins University, USA
| | - Bhavna Malik
- Department of Radiation Oncology, University of Michigan, Ann Arbor, USA
| | | | | | | | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, USA; Department of Pathology, University of Michigan, Ann Arbor, USA
| | - Xiaojun Jing
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, USA; Department of Pathology, University of Michigan, Ann Arbor, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, USA; Department of Pathology, University of Michigan, Ann Arbor, USA
| | - Saravana M Dhanasekaran
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, USA; Department of Pathology, University of Michigan, Ann Arbor, USA
| | - Felix Y Feng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, USA; Department of Radiation Oncology, University of Michigan, Ann Arbor, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, USA; Department of Pathology, University of Michigan, Ann Arbor, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, USA.
| | - Rohit Malik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, USA; Department of Pathology, University of Michigan, Ann Arbor, USA
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148
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Zhang J, Griffith M, Miller CA, Griffith OL, Spencer DH, Walker JR, Magrini V, McGrath SD, Ly A, Helton NM, Trissal M, Link DC, Dang HX, Larson DE, Kulkarni S, Cordes MG, Fronick CC, Fulton RS, Klco JM, Mardis ER, Ley TJ, Wilson RK, Maher CA. Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes. Exp Hematol 2017; 55:19-33. [PMID: 28760689 DOI: 10.1016/j.exphem.2017.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/20/2017] [Accepted: 07/25/2017] [Indexed: 01/29/2023]
Abstract
To detect diverse and novel RNA species comprehensively, we compared deep small RNA and RNA sequencing (RNA-seq) methods applied to a primary acute myeloid leukemia (AML) sample. We were able to discover previously unannotated small RNAs using deep sequencing of a library method using broader insert size selection. We analyzed the long noncoding RNA (lncRNA) landscape in AML by comparing deep sequencing from multiple RNA-seq library construction methods for the sample that we studied and then integrating RNA-seq data from 179 AML cases. This identified lncRNAs that are completely novel, differentially expressed, and associated with specific AML subtypes. Our study revealed the complexity of the noncoding RNA transcriptome through a combined strategy of strand-specific small RNA and total RNA-seq. This dataset will serve as an invaluable resource for future RNA-based analyses.
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Affiliation(s)
- Jin Zhang
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Medicine, Washington University, St. Louis, MO; Siteman Cancer Center, Washington University, St. Louis, MO
| | - Malachi Griffith
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Siteman Cancer Center, Washington University, St. Louis, MO; Department of Genetics, Washington University, St. Louis, MO
| | - Christopher A Miller
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Medicine, Washington University, St. Louis, MO
| | - Obi L Griffith
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Medicine, Washington University, St. Louis, MO; Siteman Cancer Center, Washington University, St. Louis, MO; Department of Genetics, Washington University, St. Louis, MO
| | - David H Spencer
- Department of Medicine, Washington University, St. Louis, MO
| | - Jason R Walker
- The McDonnell Genome Institute, Washington University, St. Louis, MO
| | - Vincent Magrini
- Nationwide Children's Hospital, Institute for Genomic Medicine, Columbus, OH
| | - Sean D McGrath
- Nationwide Children's Hospital, Institute for Genomic Medicine, Columbus, OH
| | - Amy Ly
- The McDonnell Genome Institute, Washington University, St. Louis, MO
| | | | - Maria Trissal
- Department of Medicine, Washington University, St. Louis, MO
| | - Daniel C Link
- Department of Medicine, Washington University, St. Louis, MO
| | - Ha X Dang
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Medicine, Washington University, St. Louis, MO; Siteman Cancer Center, Washington University, St. Louis, MO
| | - David E Larson
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Genetics, Washington University, St. Louis, MO
| | | | - Matthew G Cordes
- The McDonnell Genome Institute, Washington University, St. Louis, MO
| | - Catrina C Fronick
- The McDonnell Genome Institute, Washington University, St. Louis, MO
| | - Robert S Fulton
- The McDonnell Genome Institute, Washington University, St. Louis, MO
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Elaine R Mardis
- Nationwide Children's Hospital, Institute for Genomic Medicine, Columbus, OH
| | - Timothy J Ley
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Medicine, Washington University, St. Louis, MO; Siteman Cancer Center, Washington University, St. Louis, MO; Department of Genetics, Washington University, St. Louis, MO
| | - Richard K Wilson
- Nationwide Children's Hospital, Institute for Genomic Medicine, Columbus, OH
| | - Christopher A Maher
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Medicine, Washington University, St. Louis, MO; Siteman Cancer Center, Washington University, St. Louis, MO; Department of Biomedical Engineering, Washington University, St. Louis, MO.
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149
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Schmitt AM, Chang HY. Long Noncoding RNAs: At the Intersection of Cancer and Chromatin Biology. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026492. [PMID: 28193769 DOI: 10.1101/cshperspect.a026492] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although only 2% of the genome encodes protein, RNA is transcribed from the majority of the genetic sequence, suggesting a massive degree of cellular functionality is programmed in the noncoding genome. The mammalian genome contains tens of thousands of long noncoding RNAs (lncRNAs), many of which occur at disease-associated loci or are specifically expressed in cancer. Although the vast majority of lncRNAs have no known function, recurring molecular mechanisms for lncRNAs are now being observed in chromatin regulation and cancer pathways and emerging technologies are now providing tools to interrogate lncRNA molecular interactions and determine function of these abundant cellular macromolecules.
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Affiliation(s)
- Adam M Schmitt
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305
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150
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Gasparrini S, Cimadamore A, Mazzucchelli R, Scarpelli M, Massari F, Raspollini MR, Galosi AB, Lopez-Beltran A, Cheng L, Montironi R. Pathology and molecular updates in tumors of the prostate: towards a personalized approach. Expert Rev Mol Diagn 2017; 17:781-789. [PMID: 28598696 DOI: 10.1080/14737159.2017.1341314] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION Treatment planning in patients with prostate neoplasms and prostate cancer (PCa) is generally based on the clinical and pathological molecular markers obtained from prostate needle biopsy and/or radical prostatectomy specimens. Area covered: Pathology of prostate neoplasms is evolving rapidly. Emerging trends include new additions to the 2016 World Health Organization (WHO) tumor classification as well as expanded diagnostic utility of biomarkers and molecular testing in tissue specimens, liquid biopsies and urinary samples, with the following purposes: diagnosis, prognosis and prediction. Expert commentary: The new additions to the 2016 WHO tumor classification, which include pathological definition of Intraductal carcinoma of the prostate (IDC-P) and of a new grading system for PCa, as well as identification of molecular markers, such as TMPRSS2-ERG and AR-V7, may pave the way to personalized therapy for patients with prostate tumors.
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Affiliation(s)
- Silvia Gasparrini
- a Section of Pathological Anatomy , Marche Polytechnic University, School of Medicine, United Hospitals , Ancona , Italy
| | - Alessia Cimadamore
- a Section of Pathological Anatomy , Marche Polytechnic University, School of Medicine, United Hospitals , Ancona , Italy
| | - Roberta Mazzucchelli
- a Section of Pathological Anatomy , Marche Polytechnic University, School of Medicine, United Hospitals , Ancona , Italy
| | - Marina Scarpelli
- a Section of Pathological Anatomy , Marche Polytechnic University, School of Medicine, United Hospitals , Ancona , Italy
| | - Francesco Massari
- b Division of Oncology , S. Orsola-Malpighi Hospital , Bologna , Italy
| | | | - Andrea B Galosi
- d Institute of Urology , Marche Polytechnic University, School of Medicine, United Hospitals , Ancona , Italy
| | | | - Liang Cheng
- f Department of Pathology and Laboratory Medicine , Indiana University School of Medicine , Indianapolis , IN , USA
| | - Rodolfo Montironi
- a Section of Pathological Anatomy , Marche Polytechnic University, School of Medicine, United Hospitals , Ancona , Italy
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