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Kohvakka A, Sattari M, Nättinen J, Aapola U, Gregorová P, Tammela TLJ, Uusitalo H, Sarin LP, Visakorpi T, Latonen L. Long noncoding RNA EPCART regulates translation through PI3K/AKT/mTOR pathway and PDCD4 in prostate cancer. Cancer Gene Ther 2024:10.1038/s41417-024-00822-3. [PMID: 39147845 DOI: 10.1038/s41417-024-00822-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/29/2024] [Accepted: 08/08/2024] [Indexed: 08/17/2024]
Abstract
While hundreds of cancer-associated long noncoding RNAs (lncRNAs) have been discovered, their functional role in cancer cells is still largely a mystery. An increasing number of lncRNAs are recognized to function in the cytoplasm, e.g., as modulators of translation. Here, we investigated the detailed molecular identity and functional role of EPCART, a lncRNA we previously discovered to be a potential oncogene in prostate cancer (PCa). First, we interrogated the transcript structure of EPCART and then confirmed EPCART to be a non-peptide-coding lncRNA using in silico methods. Pathway analysis of differentially expressed protein-coding genes in EPCART knockout cells implied that EPCART modulates the translational machinery of PCa cells. EPCART was also largely located in the cytoplasm and at the sites of translation. With quantitative proteome analysis on EPCART knockout cells we discovered PDCD4, an inhibitor of protein translation, to be increased by EPCART reduction. Further studies indicated that the inhibitory effect of EPCART silencing on translation was mediated by reduced activation of AKT and inhibition of the mTORC1 pathway. Together, our findings identify EPCART as a translation-associated lncRNA that functions via modulation of the PI3K/AKT/mTORC1 pathway in PCa cells. Furthermore, we provide evidence for the prognostic potential of PDCD4 in PCa tumors in connection with EPCART.
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Affiliation(s)
- Annika Kohvakka
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, 33520, Tampere, Finland
| | - Mina Sattari
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, 33520, Tampere, Finland
| | - Janika Nättinen
- Eye and Vision Research Group, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland
| | - Ulla Aapola
- Eye and Vision Research Group, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland
| | - Pavlína Gregorová
- RNAcious Laboratory, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Teuvo L J Tammela
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, 33520, Tampere, Finland
- Department of Urology, Tampere University Hospital, Tampere, Finland
| | - Hannu Uusitalo
- Eye and Vision Research Group, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland
- Tays Eye Centre, Tampere University Hospital, 33520, Tampere, Finland
| | - L Peter Sarin
- RNAcious Laboratory, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- HiLIFE Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, 33520, Tampere, Finland.
- Fimlab Laboratories Ltd, Tampere University Hospital, 00014, Tampere, Finland.
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, 70211, Kuopio, Finland.
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2
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van Riet J, Saha C, Strepis N, Brouwer RWW, Martens-Uzunova ES, van de Geer WS, Swagemakers SMA, Stubbs A, Halimi Y, Voogd S, Tanmoy AM, Komor MA, Hoogstrate Y, Janssen B, Fijneman RJA, Niknafs YS, Chinnaiyan AM, van IJcken WFJ, van der Spek PJ, Jenster G, Louwen R. CRISPRs in the human genome are differentially expressed between malignant and normal adjacent to tumor tissue. Commun Biol 2022; 5:338. [PMID: 35396392 PMCID: PMC8993844 DOI: 10.1038/s42003-022-03249-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/09/2022] [Indexed: 11/09/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) have been identified in bacteria, archaea and mitochondria of plants, but not in eukaryotes. Here, we report the discovery of 12,572 putative CRISPRs randomly distributed across the human chromosomes, which we termed hCRISPRs. By using available transcriptome datasets, we demonstrate that hCRISPRs are distinctively expressed as small non-coding RNAs (sncRNAs) in cell lines and human tissues. Moreover, expression patterns thereof enabled us to distinguish normal from malignant tissues. In prostate cancer, we confirmed the differential hCRISPR expression between normal adjacent and malignant primary prostate tissue by RT-qPCR and demonstrate that the SHERLOCK and DETECTR dipstick tools are suitable to detect these sncRNAs. We anticipate that the discovery of CRISPRs in the human genome can be further exploited for diagnostic purposes in cancer and other medical conditions, which certainly will lead to the development of point-of-care tests based on the differential expression of the hCRISPRs.
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Affiliation(s)
- Job van Riet
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Chinmoy Saha
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Nikolaos Strepis
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rutger W W Brouwer
- Center for Biomics, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Elena S Martens-Uzunova
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Wesley S van de Geer
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Sigrid M A Swagemakers
- Clinical Bioinformatics, Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Andrew Stubbs
- Clinical Bioinformatics, Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Yassir Halimi
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Sanne Voogd
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Arif Mohammad Tanmoy
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
- Child Health Research Foundation, 23/2 SEL Huq Skypark, Block-B, Khilji Rd, Dhaka, 1207, Bangladesh
| | - Malgorzata A Komor
- Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Youri Hoogstrate
- Department of Neurology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | | | - Remond J A Fijneman
- Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Yashar S Niknafs
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Peter J van der Spek
- Clinical Bioinformatics, Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rogier Louwen
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.
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3
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Hidden clues in prostate cancer - Lessons learned from clinical and pre-clinical approaches on diagnosis and risk stratification. Cancer Lett 2022; 524:182-192. [PMID: 34687792 DOI: 10.1016/j.canlet.2021.10.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/17/2021] [Accepted: 10/13/2021] [Indexed: 12/18/2022]
Abstract
The heterogeneity of prostate cancer is evident at clinical, morphological and molecular levels. To aid clinical decision making, a three-tiered system for risk stratification is used to designate low-, intermediate-, and high-risk of disease progression. Intermediate-risk prostate cancers are the most frequently diagnosed, and even with common diagnostic features, can exhibit vastly different clinical progression. Thus, improved risk stratification methods are needed to better predict patient outcomes. Here, we provide an overview of the improvements in diagnosis/prognosis arising from advances in pathology reporting of prostate cancer, which can improve risk stratification, especially for patients with intermediate-risk disease. This review discusses updates to pathology reporting of morphological growth patterns, and proposes the utility of integrating prognostic biomarkers or innovative imaging techniques to enhance clinical decision-making. To complement clinical studies, experimental approaches using patient-derived tumors have highlighted important cellular and morphological features associated with aggressive disease that may impact treatment response. The intersection of urology, pathology and scientific disciplines is required to work towards a common goal of understanding disease pathogenesis, improving the stratification of patients with intermediate-risk disease and subsequently defining optimal treatment strategies using precision-based approaches.
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Genomic Features and Clinical Implications of Intraductal Carcinoma of the Prostate. Int J Mol Sci 2021; 22:ijms222313125. [PMID: 34884926 PMCID: PMC8658449 DOI: 10.3390/ijms222313125] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 01/29/2023] Open
Abstract
Intraductal carcinoma of the prostate (IDC-P) is a rare and unique form of aggressive prostate carcinoma, which is characterized by an expansile proliferation of malignant prostatic epithelial cells within prostatic ducts or acini and the preservation of basal cell layers around the involved glands. The vast majority of IDC-P tumors result from adjacent high-grade invasive cancer via the retrograde spreading of tumor cells into normal prostatic ducts or acini. A subset of IDC-P tumors is rarely derived from the de novo intraductal proliferation of premalignant cells. The presence of IDC-P in biopsy or surgical specimens is significantly associated with aggressive pathologic features, such as high Gleason grade, large tumor volume, and advanced tumor stage, and with poor clinical courses, including earlier biochemical recurrence, distant metastasis, and worse survival outcomes. These architectural and behavioral features of IDC-P may be driven by specific molecular properties. Notably, IDC-P possesses distinct genomic profiles, including higher rates of TMPRSS2–ERG gene fusions and PTEN loss, increased percentage of genomic instability, and higher prevalence of germline BRCA2 mutations. Considering that IDC-P tumors are usually resistant to conventional therapies for prostate cancer, further studies should be performed to develop optimal therapeutic strategies based on distinct genomic features, such as treatment with immune checkpoint blockades or poly (adenosine diphosphate–ribose) polymerase inhibitors for patients harboring increased genomic instability or BRCA2 mutations, as well as genetic counseling with genetic testing. Patient-derived xenografts and tumor organoid models can be the promising in vitro platforms for investigating the molecular features of IDC-P tumor.
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Bacolod MD, Barany F. A Unified Transcriptional, Pharmacogenomic, and Gene Dependency Approach to Decipher the Biology, Diagnostic Markers, and Therapeutic Targets Associated with Prostate Cancer Metastasis. Cancers (Basel) 2021; 13:cancers13205158. [PMID: 34680307 PMCID: PMC8534121 DOI: 10.3390/cancers13205158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 01/18/2023] Open
Abstract
Simple Summary This manuscript demonstrates how integrated bioinformatic and statistical reanalysis of publicly available genomic datasets can be utilized to identify molecular pathways and biomarkers that may be clinically relevant to metastatic prostate cancer (mPrCa) progression. The most notable observation is that the transition from primary prostate cancer to mPrCa is characterized by upregulation of processes associated with DNA replication, metastasis, and events regulated by the serine/threonine kinase PLK1. Moreover, our analysis also identified over-expressed genes that may be exploited for potential targeted therapeutics and minimally invasive diagnostics and monitoring of mPrCa. The primary data analyzed were two transcriptional datasets for tissues derived from normal prostate, primary prostate cancer, and mPrCa. Also incorporated in the analysis were the transcriptional, gene dependency, and drug response data for hundreds of cell lines, including those derived from prostate cancer tissues. Abstract Our understanding of metastatic prostate cancer (mPrCa) has dramatically advanced during the genomics era. Nonetheless, many aspects of the disease may still be uncovered through reanalysis of public datasets. We integrated the expression datasets for 209 PrCa tissues (metastasis, primary, normal) with expression, gene dependency (GD) (from CRISPR/cas9 screen), and drug viability data for hundreds of cancer lines (including PrCa). Comparative statistical and pathways analyses and functional annotations (available inhibitors, protein localization) revealed relevant pathways and potential (and previously reported) protein markers for minimally invasive mPrCa diagnostics. The transition from localized to mPrCa involved the upregulation of DNA replication, mitosis, and PLK1-mediated events. Genes highly upregulated in mPrCa and with very high average GD (~1) are potential therapeutic targets. We showed that fostamatinib (which can target PLK1 and other over-expressed serine/threonine kinases such as AURKA, MELK, NEK2, and TTK) is more active against cancer lines with more pronounced signatures of invasion (e.g., extracellular matrix organization/degradation). Furthermore, we identified surface-bound (e.g., ADAM15, CD276, ABCC5, CD36, NRP1, SCARB1) and likely secreted proteins (e.g., APLN, ANGPT2, CTHRC1, ADAM12) that are potential mPrCa diagnostic markers. Overall, we demonstrated that comprehensive analyses of public genomics data could reveal potentially clinically relevant information regarding mPrCa.
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6
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Samaržija I. Site-Specific and Common Prostate Cancer Metastasis Genes as Suggested by Meta-Analysis of Gene Expression Data. Life (Basel) 2021; 11:life11070636. [PMID: 34209195 PMCID: PMC8304581 DOI: 10.3390/life11070636] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/19/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
Anticancer therapies mainly target primary tumor growth and little attention is given to the events driving metastasis formation. Metastatic prostate cancer, in comparison to localized disease, has a much worse prognosis. In the work presented here, groups of genes that are common to prostate cancer metastatic cells from bones, lymph nodes, and liver and those that are site-specific were delineated. The purpose of the study was to dissect potential markers and targets of anticancer therapies considering the common characteristics and differences in transcriptional programs of metastatic cells from different secondary sites. To that end, a meta-analysis of gene expression data of prostate cancer datasets from the GEO database was conducted. Genes with differential expression in all metastatic sites analyzed belong to the class of filaments, focal adhesion, and androgen receptor signaling. Bone metastases undergo the largest transcriptional changes that are highly enriched for the term of the chemokine signaling pathway, while lymph node metastasis show perturbation in signaling cascades. Liver metastases change the expression of genes in a way that is reminiscent of processes that take place in the target organ. Survival analysis for the common hub genes revealed involvements in prostate cancer prognosis and suggested potential biomarkers.
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Affiliation(s)
- Ivana Samaržija
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia;
- Laboratory for Cell Biology and Signalling, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
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7
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Lawrence MG, Porter LH, Clouston D, Murphy DG, Frydenberg M, Taylor RA, Risbridger GP. Knowing what's growing: Why ductal and intraductal prostate cancer matter. Sci Transl Med 2021; 12:12/533/eaaz0152. [PMID: 32132214 DOI: 10.1126/scitranslmed.aaz0152] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/16/2020] [Indexed: 12/12/2022]
Abstract
Prostate cancer is a common malignancy, but only some tumors are lethal. Accurately identifying these tumors will improve clinical practice and instruct research. Aggressive cancers often have distinctive pathologies, including intraductal carcinoma of the prostate (IDC-P) and ductal adenocarcinoma. Here, we review the importance of these pathologies because they are often overlooked, especially in genomics and preclinical testing. Pathology, genomics, and patient-derived models show that IDC-P and ductal adenocarcinoma accompany multiple markers of poor prognosis. Consequently, "knowing what is growing" will help translate preclinical research to pinpoint and treat high-risk prostate cancer in the clinic.
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Affiliation(s)
- Mitchell G Lawrence
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Laura H Porter
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | | | - Declan G Murphy
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia.,Division of Cancer Surgery, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC 3000, Australia.,Epworth HealthCare, Melbourne, VIC 3000, Australia
| | - Mark Frydenberg
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia.,Australian Urology Associates, Melbourne, VIC 3000, Australia.,Department of Urology, Cabrini Health, Malvern, VIC 3144, Australia
| | - Renea A Taylor
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia.,Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Physiology, Monash University, Clayton, VIC 3800, Australia
| | - Gail P Risbridger
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia. .,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
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8
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Shang M, Lim SB, Jiang K, Yap YS, Khoo BL, Han J, Lim CT. Microfluidic studies of hydrostatic pressure-enhanced doxorubicin resistance in human breast cancer cells. LAB ON A CHIP 2021; 21:746-754. [PMID: 33502419 DOI: 10.1039/d0lc01103g] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Acquired multidrug resistance in tumors is a big challenge in cancer therapy. As an important physical stimulus in the tumor microenvironment, elevated interstitial fluid pressure has been reported to inhibit drug delivery and promote metastasis in solid tumors. However, the direct influence of this fluid pressure on anticancer drug resistance remains unclear. Here, we develop a pressurized in vitro circulating tumor cell (CTC) culture platform for anticancer drug screening. By using human breast cancer cell line MCF-7 and MDA-MB-231, we find that doxorubicin resistance can be increased by up to 2.5 times under 30 mmHg culture condition, through ABCC1 overexpression that reduces intracellular doxorubicin concentration. A similar chemoresistance change is also observed in clinical metastatic circulating tumor cells samples. These findings provide a new insight into the chemoresistance mechanism of metastatic human breast cancer cells and elucidate the significance of abnormal hydrostatic pressure in cancer progression.
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Affiliation(s)
- Menglin Shang
- Critical Analytics for Manufacturing Personalized-Medicine (CAMP) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore and Department of Biomedical Engineering, National University of Singapore, Singapore.
| | - Su Bin Lim
- The Johns Hopkins University School of Medicine, Baltimore, USA
| | - Kuan Jiang
- Department of Biomedical Engineering, National University of Singapore, Singapore.
| | - Yoon Sim Yap
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Bee Luan Khoo
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong
| | - Jongyoon Han
- Critical Analytics for Manufacturing Personalized-Medicine (CAMP) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore and Department of Electrical Engineering and Computer Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA and Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Chwee Teck Lim
- Critical Analytics for Manufacturing Personalized-Medicine (CAMP) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore and Department of Biomedical Engineering, National University of Singapore, Singapore. and Institute for Health Innovation and Technology, 14 Medical Drive, Singapore and Mechanobiology Institute, National University of Singapore, Singapore
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9
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van Leenders GJLH, Verhoef EI, Hollemans E. Prostate cancer growth patterns beyond the Gleason score: entering a new era of comprehensive tumour grading. Histopathology 2020; 77:850-861. [PMID: 32683729 PMCID: PMC7756302 DOI: 10.1111/his.14214] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/18/2022]
Abstract
The Gleason grading system is one of the most important factors in clinical decision‐making for prostate cancer patients, and is entirely based on the classification of tumour growth patterns. In recent years it has become clear that some individual growth patterns themselves have independent prognostic value, and could be used for better personalised risk stratification. In this review we summarise recent literature on the clinicopathological value and molecular characteristics of individual prostate cancer growth patterns, and show how these, most particularly cribriform architecture, could alter treatment decisions for prostate cancer patients.
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Affiliation(s)
| | - Esther I Verhoef
- Department of Pathology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
| | - Eva Hollemans
- Department of Pathology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
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10
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Kohvakka A, Sattari M, Shcherban A, Annala M, Urbanucci A, Kesseli J, Tammela TLJ, Kivinummi K, Latonen L, Nykter M, Visakorpi T. AR and ERG drive the expression of prostate cancer specific long noncoding RNAs. Oncogene 2020; 39:5241-5251. [PMID: 32555329 DOI: 10.1038/s41388-020-1365-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/25/2020] [Accepted: 06/08/2020] [Indexed: 01/04/2023]
Abstract
Long noncoding RNAs (lncRNAs) play pivotal roles in cancer development and progression, and some function in a highly cancer-specific manner. However, whether the cause of their expression is an outcome of a specific regulatory mechanism or nonspecific transcription induced by genome reorganization in cancer remains largely unknown. Here, we investigated a group of lncRNAs that we previously identified to be aberrantly expressed in prostate cancer (PC), called TPCATs. Our high-throughput real-time PCR experiments were integrated with publicly available RNA-seq and ChIP-seq data and revealed that the expression of a subset of TPCATs is driven by PC-specific transcription factors (TFs), especially androgen receptor (AR) and ETS-related gene (ERG). Our in vitro validations confirmed that AR and ERG regulated a subset of TPCATs, most notably for EPCART. Knockout of EPCART was found to reduce migration and proliferation of the PC cells in vitro. The high expression of EPCART and two other TPCATs (TPCAT-3-174133 and TPCAT-18-31849) were also associated with the biochemical recurrence of PC in prostatectomy patients and were independent prognostic markers. Our findings suggest that the expression of numerous PC-associated lncRNAs is driven by PC-specific mechanisms and not by random cellular events that occur during cancer development. Furthermore, we report three prospective prognostic markers for the early detection of advanced PC and show EPCART to be a functionally relevant lncRNA in PC.
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Affiliation(s)
- Annika Kohvakka
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Mina Sattari
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Anastasia Shcherban
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Matti Annala
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Juha Kesseli
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Teuvo L J Tammela
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Department of Urology, Tampere University Hospital, Tampere, Finland
| | - Kati Kivinummi
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland. .,Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland.
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11
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Wang K, Sun H, Sun T, Qu H, Xie Q, Lv H, Hu B. Long non-coding RNA AFAP1-AS1 promotes proliferation and invasion in prostate cancer via targeting miR-512-3p. Gene 2019; 726:144169. [PMID: 31669642 DOI: 10.1016/j.gene.2019.144169] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/27/2019] [Accepted: 10/11/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND (OBJECTIVE) In the development of tumor therapy, the role of long non-coding RNA actin filagenin 1 antisense RNA 1 (1ncRNA AFAP1-AS1) is quite significant, but the actual role of AFAP1-AS1 in the treatment of prostate cancer has not been determined. In view of this, the author took AFAP1-AS1 as the research object to design an experimental study, and conducted an in-depth exploration of the pathogenesis of prostate cancer. METHODS RT-qPCR was used to detect the expression of AFAP1-AS1 and miR-512-3p in prostate cancer tissues and cell lines. Perforation, flow cytometry and CCK-8 were used to detect the effects of cell proliferation, migration and invasion of mir-512-3p and a AFAP1-AS1. And the luciferase reporter gene was used to detect the downstream target gene of AFAP1-AS1, and the expression of CDK4, CDK6 and CCND1 protein was detected by Western blot. RESULTS AFAP1-AS1 is highly expressed in prostate cancer tissues and cell lines. The expression level of AFAP1-AS1 is correlated with histological grade and distant metastasis. The overall level of patients with high expression of AFAP1-AS1 is low, and their survival rate is relatively low. Silencing AFAP1-AS1 can significantly increase the proliferation and migration of prostate cancer cells. AFAP1-AS1 silencing induces cell cycle arrest at G0/G1 phase. The downstream target of AFAP1-AS1 was mir-512-3p. The role of AFAP1-AS1 in the progression of prostate cancer cells was mediated by mir-512-3p. CONCLUSION AFAP1-AS1 regulates miR-512-3p, so as to realize the regulation effect on the proliferation, invasion and migration of prostate cancer cells, and thereby promote the occurrence and development of prostate cancer, so as to provide the corresponding program for the treatment of prostate cancer. Abberivation: ADPC, androgen-dependent prostate cancer; CRPC, castrated prostate cancer; RNA1 AFAP1-Asl, Actin fiber-associated protein 1-anti-RNA1; miRNAs, MicroRNAs.
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Affiliation(s)
- Kai Wang
- Urology Department, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, Shengyang City, Liaoning Province 110044, PR China
| | - Hao Sun
- Urology Department, China Medical University, Cancer Hospital of China Medical University, Shengyang City, Liaoning Province 110044, PR China
| | - Tao Sun
- Urology Department, Dalian Medical University, Dalian Medical University Clinical Oncology College, Shengyang City, Liaoning Province 110044, PR China
| | - Hongchen Qu
- Urology Department, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, Shengyang City, Liaoning Province 110044, PR China
| | - Qingpeng Xie
- Urology Department, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, Shengyang City, Liaoning Province 110044, PR China
| | - Hang Lv
- Urology Department, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, Shengyang City, Liaoning Province 110044, PR China
| | - Bin Hu
- Urology Department, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, Shengyang City, Liaoning Province 110044, PR China.
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12
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LncRNA NRON down-regulates lncRNA snaR and inhibits cancer cell proliferation in TNBC. Biosci Rep 2019; 39:BSR20190468. [PMID: 30996114 PMCID: PMC6522729 DOI: 10.1042/bsr20190468] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 03/26/2019] [Accepted: 04/07/2019] [Indexed: 12/17/2022] Open
Abstract
NRON mediates the degradation of tat protein to participate in HIV-1 infection. Interestingly, our study observed the down-regulation of NRON in triple-negative breast cancer (TNBC) tissues compared with paired adjacent healthy tissues. In contrast, lncRNA snaR was up-regulated in TNBC tissues and was inversely correlated with NRON. Expression levels of snaR increased, while expression levels of NRON decreased along with the increase of clinical stages. The snaR overexpression resulted in promoted cancer cell proliferation but did not significantly affect NRON expression. NRON overexpression inhibited cancer cell proliferation and down-regulated snaR. The snaR overexpression reduced the effects of NRON overexpression. We therefore conclude that NRON may down-regulate lncRNA snaR to inhibit cancer cell proliferation in TNBC.
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13
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Rombaut D, Chiu HS, Decaesteker B, Everaert C, Yigit N, Peltier A, Janoueix-Lerosey I, Bartenhagen C, Fischer M, Roberts S, D'Haene N, De Preter K, Speleman F, Denecker G, Sumazin P, Vandesompele J, Lefever S, Mestdagh P. Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes. Sci Rep 2019; 9:5685. [PMID: 30952905 PMCID: PMC6451017 DOI: 10.1038/s41598-019-42107-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/20/2019] [Indexed: 12/13/2022] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) are emerging as integral components of signaling pathways in various cancer types. In neuroblastoma, only a handful of lincRNAs are known as upstream regulators or downstream effectors of oncogenes. Here, we exploit RNA sequencing data of primary neuroblastoma tumors, neuroblast precursor cells, neuroblastoma cell lines and various cellular perturbation model systems to define the neuroblastoma lincRNome and map lincRNAs up- and downstream of neuroblastoma driver genes MYCN, ALK and PHOX2B. Each of these driver genes controls the expression of a particular subset of lincRNAs, several of which are associated with poor survival and are differentially expressed in neuroblastoma tumors compared to neuroblasts. By integrating RNA sequencing data from both primary tumor tissue and cancer cell lines, we demonstrate that several of these lincRNAs are expressed in stromal cells. Deconvolution of primary tumor gene expression data revealed a strong association between stromal cell composition and driver gene status, resulting in differential expression of these lincRNAs. We also explored lincRNAs that putatively act upstream of neuroblastoma driver genes, either as presumed modulators of driver gene activity, or as modulators of effectors regulating driver gene expression. This analysis revealed strong associations between the neuroblastoma lincRNAs MIAT and MEG3 and MYCN and PHOX2B activity or expression. Together, our results provide a comprehensive catalogue of the neuroblastoma lincRNome, highlighting lincRNAs up- and downstream of key neuroblastoma driver genes. This catalogue forms a solid basis for further functional validation of candidate neuroblastoma lincRNAs.
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Affiliation(s)
- Dries Rombaut
- Center for Medical Genetics, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Hua-Sheng Chiu
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Bieke Decaesteker
- Center for Medical Genetics, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Celine Everaert
- Center for Medical Genetics, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Nurten Yigit
- Center for Medical Genetics, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Agathe Peltier
- Institut Curie, PSL Research University, Inserm U830, Equipe Labellisée contre le Cancer, F-75005, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, F-75005, Paris, France
| | - Isabelle Janoueix-Lerosey
- Institut Curie, PSL Research University, Inserm U830, Equipe Labellisée contre le Cancer, F-75005, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, F-75005, Paris, France
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, 50937, Cologne, Germany
| | - Matthias Fischer
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany.,Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, 50937, Cologne, Germany
| | - Stephen Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicky D'Haene
- Hôpital Erasme, Cliniques Universitaires de Bruxelles, Bruxelles, 1070, Belgium
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Geertrui Denecker
- Center for Medical Genetics, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Pavel Sumazin
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Steve Lefever
- Center for Medical Genetics, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Pieter Mestdagh
- Center for Medical Genetics, Ghent University, Ghent, 9000, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium.
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14
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Wang Z, Qin B. Prognostic and clinicopathological significance of long noncoding RNA CTD-2510F5.4 in gastric cancer. Gastric Cancer 2019; 22:692-704. [PMID: 30560474 PMCID: PMC6570689 DOI: 10.1007/s10120-018-00911-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 12/02/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Compelling studies have demonstrated the correlation between aberrant expressed lncRNAs and human cancers, and revealed promise of these lncRNAs as biomarkers in predicting patients' survival and outcome. METHODS We downloaded the RNA-seq data from the Cancer Genome Atlas, and screened out DEGs and DELs between gastric cancer tissues and normal gastric tissues. By bioinformatics analysis, we identified CTD-2510F5.4 was a malignant phenotype associated lncRNA. The expression levels of CTD-2510F5.4 in tissues were detected by ISH, and the relationships between CTD-2510F5.4 expression and clinicopathological characteristics were analyzed by statistical analysis. RESULTS By bioinformatics analysis and functional analysis, we identified CTD-2510F5.4 was a malignant phenotype associated lncRNA of gastric cancer that potentially regulated cell cycle and apoptosis. CTD-2510F5.4 expression was significantly higher in gastric cancers, and was correlated with pathological grade, vascular or nerve invasion, AJCC TNM stage and OS. Moreover, gastric cancer patients with high CTD-2510F5.4 expression showed significantly shorter MST. High CTD-2510F5.4 expression was a independent risk factor for gastric cancers at pathological grade < III and without vascular or nerve invasion. CONCLUSIONS We identified CTD-2510F5.4 was a malignant phenotype associated lncRNA potentially involved in the pathogenesis of gastric cancer. Our data also supported the clinical potential of CTD-2510F5.4 being a diagnostic and prognostic biomarker for gastric cancer.
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Affiliation(s)
- Zhe Wang
- Medical Oncology Department of Gastrointestinal Cancer (1), Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, NO.44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning, People's Republic of China
| | - Baoli Qin
- Medical Oncology Department of Gastrointestinal Cancer (1), Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, NO.44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning, People's Republic of China.
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15
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Rodríguez-Blanco G, Zeneyedpour L, Duijvesz D, Hoogland AM, Verhoef EI, Kweldam CF, Burgers PC, Smitt PS, Bangma CH, Jenster G, van Leenders GJLH, Dekker LJM, Luider TM. Tissue proteomics outlines AGR2 AND LOX5 as markers for biochemical recurrence of prostate cancer. Oncotarget 2018; 9:36444-36456. [PMID: 30559929 PMCID: PMC6284859 DOI: 10.18632/oncotarget.26342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/21/2018] [Indexed: 12/22/2022] Open
Abstract
Although many patients are cured from prostate cancer (PCa) by surgery only, there are still patients who will experience rising prostate-specific antigen (PSA) levels after surgery, a condition known as biochemical recurrence (BCR). Novel protein prognostic markers in PCa tissue might enable finding better treatment for those patients experiencing BCR with a high chance of metastasis. In this study, we aimed to identify altered proteins in prostate cancer tissue, and to evaluate their potential role as prognostic markers. We used two proteomics strategies to analyse 34 prostate tumours (PCa) and 33 normal adjacent prostate (NAP) tissues. An independent cohort of 481 samples was used to evaluate the expression of three proteins: AGR2, FASN and LOX5 as prognostic markers of the disease. Tissue microarray immunohistochemical staining indicated that a low percentage of positive tumour cells for AGR2 (HR (95% CI) = 0.61 (0.43-0.93)), and a low percentage of positive tumour cells for LOX5 expression (HR (95% CI) = 2.53 (1.23-5.22)) are predictors of BCR after RP. In contrast, FASN expression had no prognostic value for PCa.
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Affiliation(s)
| | - Lona Zeneyedpour
- Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Diederick Duijvesz
- Department of Urology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - A Marije Hoogland
- Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Esther I Verhoef
- Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - Peter C Burgers
- Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - Chris H Bangma
- Department of Urology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - Lennard J M Dekker
- Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
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16
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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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17
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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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18
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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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19
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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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20
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Zhang Y, Kong Z, Zhang Y, Huang W, Wu H, Wan X, Li Y. Increased expression of long non-coding RNA GLIDR in prostate cancer. Cancer Biomark 2018; 19:145-150. [PMID: 28211799 DOI: 10.3233/cbm-160166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Prostate cancer (PCa) was one of the most common cancers in males in China. Long non-coding RNAs (lncRNA), a class of non-coding RNAs with more than 200 nucleotides, played key roles in the progression of prostate cancer. GLIDR, a novel long intergenic ncRNA, was found to be upregulated in tumors compared to normal tissues by using publically databases. In the clinical validation cohort, our results showed GLIDR was significantly up-regulated in prostate cancer samples and cell lines. To explore the potential functions of the GLIDR, we constructed gene co-expression networks and applied GO analysis. Our analysis revealed that GLIDR was involved in the regulation of translational elongation, transcription, rRNA processing, RNA splicing, signal transduction, and cell adhesion. Furthermore, a GLIDR-mediated ceRNA network in prostate cancer was also identified. We believed that this study still provided some clues in exploring new therapeutic and prognostic targets for prostate cancer.
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Affiliation(s)
- Yingyi Zhang
- Department of Oncology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China.,State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China
| | - Zhe Kong
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China.,State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China
| | - Yalong Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China
| | - Wenhua Huang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China
| | - Hai Wu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China
| | - Xuechao Wan
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China
| | - Yao Li
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China
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21
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Böttcher R, Dulla K, van Strijp D, Dits N, Verhoef EI, Baillie GS, van Leenders GJLH, Houslay MD, Jenster G, Hoffmann R. Human PDE4D isoform composition is deregulated in primary prostate cancer and indicative for disease progression and development of distant metastases. Oncotarget 2018; 7:70669-70684. [PMID: 27683107 PMCID: PMC5342582 DOI: 10.18632/oncotarget.12204] [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: 02/03/2016] [Accepted: 09/12/2016] [Indexed: 02/07/2023] Open
Abstract
Phosphodiesterase 4D7 was recently shown to be specifically over-expressed in localized prostate cancer, raising the question as to which regulatory mechanisms are involved and whether other isoforms of this gene family (PDE4D) are affected under the same conditions.We investigated PDE4D isoform composition in prostatic tissues using a total of seven independent expression datasets and also included data on DNA methylation, copy number and AR and ERG binding in PDE4D promoters to gain insight into their effect on PDE4D transcription.We show that expression of PDE4D isoforms is consistently altered in primary human prostate cancer compared to benign tissue, with PDE4D7 being up-regulated while PDE4D5 and PDE4D9 are down-regulated. Disease progression is marked by an overall down-regulation of long PDE4D isoforms, while short isoforms (PDE4D1/2) appear to be relatively unaffected. While these alterations seem to be independent of copy number alterations in the PDE4D locus and driven by AR and ERG binding, we also observed increased DNA methylation in the promoter region of PDE4D5, indicating a long lasting alteration of the isoform composition in prostate cancer tissues.We propose two independent metrics that may serve as diagnostic and prognostic markers for prostate disease: (PDE4D7 - PDE4D5) provides an effective means for distinguishing PCa from normal adjacent prostate, whereas PDE4D1/2 - (PDE4D5 + PDE4D7 + PDE4D9) offers strong prognostic potential to detect aggressive forms of PCa and is associated with metastasis free survival. Overall, our findings highlight the relevance of PDE4D as prostate cancer biomarker and potential drug target.
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Affiliation(s)
- René Böttcher
- Department of Urology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Bioinformatics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Kalyan Dulla
- Department of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven, The Netherlands
| | - Dianne van Strijp
- Department of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven, The Netherlands
| | - Natasja Dits
- Department of Urology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Esther I Verhoef
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - George S Baillie
- Institute of Cardiovascular and Medical Science, University of Glasgow, Glasgow, Scotland, UK
| | | | - Miles D Houslay
- Institute of Pharmaceutical Science, King's College London, London, UK
| | - Guido Jenster
- Department of Urology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ralf Hoffmann
- Department of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven, The Netherlands.,Institute of Cardiovascular and Medical Science, University of Glasgow, Glasgow, Scotland, UK
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22
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Fotouhi Ghiam A, Taeb S, Huang X, Huang V, Ray J, Scarcello S, Hoey C, Jahangiri S, Fokas E, Loblaw A, Bristow RG, Vesprini D, Boutros P, Liu SK. Long non-coding RNA urothelial carcinoma associated 1 (UCA1) mediates radiation response in prostate cancer. Oncotarget 2018; 8:4668-4689. [PMID: 27902466 PMCID: PMC5354863 DOI: 10.18632/oncotarget.13576] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 11/06/2016] [Indexed: 01/23/2023] Open
Abstract
Radioresistance remains a significant obstacle in the treatment of Prostate Cancer (PCa). To simulate the clinical scenario of irradiation resistance (IRR), we created DU145-IRR PCa cell lines by treatment with 2 Gy daily IR for 59 fractions. DU145-IRR cells acquired an aggressive phenotype as evidenced by increased clonogenic survival, tumorigenic potential and invasiveness. We performed transcriptome profiling to discover dysregulated genes in DU145-IRR cells and identified the long non-coding RNA (lncRNA), Urothelial carcinoma-associated 1 (UCA1). We first investigated the role of UCA1 in radiation response and found that UCA1 abundance was significantly higher in DU145-IRR cells compared to control cells. UCA1 siRNA-knockdown reversed the aggressive phenotype and significantly increased sensitivity to IR. UCA1 depletion inhibited growth, induced cell cycle arrest at the G2/M transition and decreased activation of the pro-survival Akt pathway. We then studied the clinical significance of UCA1 expression in two independent cohorts of PCa patients: MSKCC (130 patients) and CPC-GENE (209 patients). UCA1 over-expression was associated with decreased 5-year disease-free survival in MSKCC patients (HR = 2.9; p = 0.007) and a trend toward lower biochemical recurrence-free survival in CPC-GENE patients (HR = 2.7; p = 0.05). We showed for the first time that UCA1 depletion induces radiosensitivity, decreases proliferative capacity and disrupts cell cycle progression, which may occur through altered Akt signaling and induced cell cycle arrest at the G2/M transition. Our results indicate that UCA1 might have prognostic value in PCa and be a potential therapeutic target.
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Affiliation(s)
- Alireza Fotouhi Ghiam
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, Canada
| | - Samira Taeb
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Xiaoyong Huang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Vincent Huang
- Ontario Institute for Cancer Research, University of Toronto, Toronto, Canada
| | - Jessica Ray
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Seville Scarcello
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Christianne Hoey
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Sahar Jahangiri
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Emmanouil Fokas
- Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Andrew Loblaw
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, Canada
| | - Robert G Bristow
- Department of Radiation Oncology, University of Toronto, Toronto, Canada.,Ontario Institute for Cancer Research, University of Toronto, Toronto, Canada
| | - Danny Vesprini
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, Canada
| | - Paul Boutros
- Ontario Institute for Cancer Research, University of Toronto, Toronto, Canada.,Department of Medical Biophysics, University of Toronto,, Toronto, Canada
| | - Stanley K Liu
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
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23
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Böttcher R, Kweldam CF, Livingstone J, Lalonde E, Yamaguchi TN, Huang V, Yousif F, Fraser M, Bristow RG, van der Kwast T, Boutros PC, Jenster G, van Leenders GJLH. Cribriform and intraductal prostate cancer are associated with increased genomic instability and distinct genomic alterations. BMC Cancer 2018; 18:8. [PMID: 29295717 PMCID: PMC5751811 DOI: 10.1186/s12885-017-3976-z] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 12/21/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Invasive cribriform and intraductal carcinoma (CR/IDC) is associated with adverse outcome of prostate cancer patients. The aim of this study was to determine the molecular aberrations associated with CR/IDC in primary prostate cancer, focusing on genomic instability and somatic copy number alterations (CNA). METHODS Whole-slide images of The Cancer Genome Atlas Project (TCGA, N = 260) and the Canadian Prostate Cancer Genome Network (CPC-GENE, N = 199) radical prostatectomy datasets were reviewed for Gleason score (GS) and presence of CR/IDC. Genomic instability was assessed by calculating the percentage of genome altered (PGA). Somatic copy number alterations (CNA) were determined using Fisher-Boschloo tests and logistic regression. Primary analysis were performed on TCGA (N = 260) as discovery and CPC-GENE (N = 199) as validation set. RESULTS CR/IDC growth was present in 80/260 (31%) TCGA and 76/199 (38%) CPC-GENE cases. Patients with CR/IDC and ≥ GS 7 had significantly higher PGA than men without this pattern in both TCGA (2.2 fold; p = 0.0003) and CPC-GENE (1.7 fold; p = 0.004) cohorts. CR/IDC growth was associated with deletions of 8p, 16q, 10q23, 13q22, 17p13, 21q22, and amplification of 8q24. CNAs comprised a total of 1299 gene deletions and 369 amplifications in the TCGA dataset, of which 474 and 328 events were independently validated, respectively. Several of the affected genes were known to be associated with aggressive prostate cancer such as loss of PTEN, CDH1, BCAR1 and gain of MYC. Point mutations in TP53, SPOP and FOXA1were also associated with CR/IDC, but occurred less frequently than CNAs. CONCLUSIONS CR/IDC growth is associated with increased genomic instability clustering to genetic regions involved in aggressive prostate cancer. Therefore, CR/IDC is a pathologic substrate for progressive molecular tumour derangement.
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Affiliation(s)
- René Böttcher
- Department of Urology, Erasmus MC, Rotterdam, the Netherlands
| | - Charlotte F. Kweldam
- Department of Pathology, Erasmus University Medical Center, Josephine Nefkens Institute building, Be-222, P.O. Box 2040, Rotterdam, 3000 CA The Netherlands
| | - Julie Livingstone
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON Canada
| | - Emilie Lalonde
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Takafumi N. Yamaguchi
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON Canada
| | - Vincent Huang
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON Canada
| | - Fouad Yousif
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON Canada
| | - Michael Fraser
- Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON Canada
| | - Robert G. Bristow
- Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
- Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON Canada
| | - Theodorus van der Kwast
- Department of Pathology and Laboratory Medicine, Toronto General Hospital, University Health Network, Toronto, ON Canada
| | - Paul C. Boutros
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON Canada
| | - Guido Jenster
- Department of Urology, Erasmus MC, Rotterdam, the Netherlands
| | - Geert J. L. H. van Leenders
- Department of Pathology, Erasmus University Medical Center, Josephine Nefkens Institute building, Be-222, P.O. Box 2040, Rotterdam, 3000 CA The Netherlands
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24
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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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25
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Long non-coding RNA00544 serves as a potential novel predictive and prognostic marker for HR+ HER2- subtype breast cancer. Sci Rep 2017; 7:12382. [PMID: 28959047 PMCID: PMC5620366 DOI: 10.1038/s41598-017-11066-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/28/2017] [Indexed: 12/31/2022] Open
Abstract
Luminal breast cancers (BC) account for majority of breast cancer. Due to its heterogeneity and the development of treatment resistance, luminal BC patients can vary substantially. Long noncoding RNAs (lncRNAs), as we known, is involved in breast cancer progression. Here, we aim to identify the lncRNAs which are involved in the particular type luminal BC progression. By Gene Chips analysis, we found a novel lncRNA00544, which was highly expressed in the metastatic axillary nodes compared with corresponding luminal BC tissues (fold change = 2.26, P = 0.043). This result was confirmed in luminal BC cell lines (p = 0.0113) and 49 paired breast cancer samples compared with in corresponding controls (p = 0.011). Furthermore, Kaplan-Meier survival curves of 373 breast cancer patients indicated that disease-free survival was significantly poor in breast cancer patients with high lncRNA00544 expression (p < 0.001). Univariate and multivariate Cox regression analyses showed that lncRNA00544 was a significant independent prognostic biomarker in luminal BC patients. Further analysis showed that the prognosis of high lncRNA00544 expression in breast cancer patients was actually related to HR + HER2- subtype. Together, our studies indicate that lncRNA00544 may represent a novel predictive and prognostic indicator in luminal BC patients.
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26
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Ginkgo biloba extract EGb 761-induced upregulation of LincRNA-p21 inhibits colorectal cancer metastasis by associating with EZH2. Oncotarget 2017; 8:91614-91627. [PMID: 29207671 PMCID: PMC5710951 DOI: 10.18632/oncotarget.21345] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 07/26/2017] [Indexed: 12/31/2022] Open
Abstract
EGb 761, the standard ginkgo biloba extract, is frequently prescribed in traditional Chinese medicine. Currently, there is no research focusing on its role in human colorectal cancer progression. In our study, we determined the anti-metastatic effect of EGb 761 on colorectal cancer cells and further explored the potential underlying regulatory mechanism. The cell migration and invasion assay indicated that EGb 761 treatment of colorectal cancer cells induced inhibition of cell migration and invasion ability in a concentration-dependent manner. To further explore the underlying regulatory mechanisms that may account for these findings, we performed quantitative real-time PCR (RT-qPCR), western blotting and immunoprecipitation analysis. The results showed that EGb 761 induced upregulation of LincRNA-p21 expression in a dose- and time-dependent manner. Overexpression of LincRNA-p21 also suppressed colorectal cancer cell metastasis. Furthermore, EGb 761 as well as LincRNA-p21 inhibited the expression of extracellular matrix protein, fibronectin. More importantly, RNA immunoprecipitation (RIP) and Chromatin immunoprecipitation (ChIP) assays showed that LincRNA-p21 directly interacted with EZH2, and this interaction suppressed the expression of fibronectin. Finally, the gain and loss function assay revealed that EGb 761 inhibited migration, invasion and fibronctin expression by the LincRNA-p21/EZH2 pathway in colorectal cancer cells. Hence, EGb 761 may be a promising treatment regimen for colorectal cancer and restoration of LincRNA-p21 levels may be helpful for enhancing the anti-cancer effect of EGb 761.
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27
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Abstract
Prostate cancer is the second most common cause of cancer mortality among men in the United States. While many prostate cancers are indolent, an important subset of patients experiences disease recurrence after conventional therapy and progresses to castration-resistant prostate cancer (CRPC), which is currently incurable. Thus, there is a critical need to identify biomarkers that will distinguish indolent from aggressive disease, as well as novel therapeutic targets for the prevention or treatment of CRPC. In recent years, long noncoding RNAs (lncRNAs) have emerged as an important class of biological molecules. LncRNAs are polyadenylated RNA species that share many similarities with protein-coding genes despite the fact that they are noncoding (not translated into proteins). They are usually transcribed by RNA polymerase II and exhibit the same epigenetic signatures as protein-coding genes. LncRNAs have also been implicated in the development and progression of variety of cancers, including prostate cancer. While a large number of lncRNAs exhibit tissue- and cancer-specific expression, their utility as diagnostic and prognostic biomarkers is just starting to be explored. In this review, we highlight recent findings on the functional role and molecular mechanisms of lncRNAs in the progression of prostate cancer and evaluate their use as potential biomarkers and therapeutic targets.
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Affiliation(s)
- Bhavna Malik
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - Felix Y Feng
- Department of Radiation Oncology, Urology, and Medicine, University of California at San Francisco; Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, USA
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28
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Liao M, Li B, Zhang S, Liu Q, Liao W, Xie W, Zhang Y. Relationship between LINC00341 expression and cancer prognosis. Oncotarget 2017; 8:15283-15293. [PMID: 28146429 PMCID: PMC5362486 DOI: 10.18632/oncotarget.14843] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/17/2017] [Indexed: 12/13/2022] Open
Abstract
LINC00341 is a novel long intergenic non-protein coding RNA with unknown functions. In our report, we investigated LINC00341 expression and its prognostic value in cancer patients. DNA over-methylation triggered low expression of LINC00341 and that was associated with poor prognosis in cancers. A meta-analysis further confirmed that high expression of LINC00341 was associated with a better prognosis in cancer patients. Both gene set enrichment analysis and meta-analysis showed that LINC00341 inhibited cancer metastasis. Finally, a large-scale multicentre analysis supported a prognostic value of LINC00341 in cancers.
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Affiliation(s)
- Meijian Liao
- School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China
| | - Bing Li
- School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China
| | - Shikuan Zhang
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China
| | - Qing Liu
- School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China
| | - Weijie Liao
- School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China
| | - Weidong Xie
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China
- Open FIESTA Center, Tsinghua University, Shenzhen 518055, P.R. China
| | - Yaou Zhang
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China
- Open FIESTA Center, Tsinghua University, Shenzhen 518055, P.R. China
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29
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Wan X, Huang W, Yang S, Zhang Y, Pu H, Fu F, Huang Y, Wu H, Li T, Li Y. Identification of androgen-responsive lncRNAs as diagnostic and prognostic markers for prostate cancer. Oncotarget 2016; 7:60503-60518. [PMID: 27556357 PMCID: PMC5312399 DOI: 10.18632/oncotarget.11391] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 07/26/2016] [Indexed: 12/26/2022] Open
Abstract
Prostate cancer (PCa) is a leading cause of mortality among males. Long non-coding RNAs (lncRNAs) are subclass of noncoding RNAs that may act as biomarkers and therapeutic targets. In this study, we firstly conducted analysis of global lncRNA expression patterns by using our own cohort (GSE73397) and two public available gene expression datasets: The Cancer Genome Atlas (TCGA) and GSE55909. Next, we performed microarray to observe genome-wide lncRNAs' expressions under dihydrotestosterone (DHT) stimulation in LNCaP cells (GSE72866), and overlapped the result with ChIPBase data to predict androgen-responsive lncRNAs with ARE. Combined the two results, a total of 44 androgen-responsive lncRNAs with ARE were found to be over-expressed in PCa samples. Ten lncRNAs were selected for further validation by examining their expressions in LNCaP cells under DHT stimulation, and in PCa samples and cell lines. Among them, RP1-4514.2, LINC01138, SUZ12P1 and KLKP1 were validated as directly AR-targeted lncRNAs by ChIP-PCR. Then we conducted a bioinformatic analysis to identify lncRNAs as putative prognostic and therapeutic targets by using TCGA data. Three androgen-responsive lncRNAs, LINC01138, SUZ12P1 and SNHG1 showed association with gleason score and pT-stage. The biological functions of LINC01138 and SUZ12P1 were also evaluated, both lncRNAs promoted the proliferation and inhibited apoptosis of PCa. These results provide potent information for exploring potential biomarkers and therapeutic targets for prostate cancer, especially for castration-resistant PCa.
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Affiliation(s)
- Xuechao Wan
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center Of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Wenhua Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center Of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Shu Yang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center Of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Yalong Zhang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center Of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Honglei Pu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center Of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Fangqiu Fu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center Of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Yan Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center Of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Hai Wu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center Of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Tao Li
- Department of Urology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200433, PR China
| | - Yao Li
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center Of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
- Key Laboratory of Reproduction Regulation of NPFPC, Fudan University, Shanghai 200433, PR China
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30
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Zhang Y, Zhang P, Wan X, Su X, Kong Z, Zhai Q, Xiang X, Li L, Li Y. Downregulation of long non-coding RNA HCG11 predicts a poor prognosis in prostate cancer. Biomed Pharmacother 2016; 83:936-941. [PMID: 27522256 DOI: 10.1016/j.biopha.2016.08.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/20/2016] [Accepted: 08/05/2016] [Indexed: 11/29/2022] Open
Abstract
Long non-coding RNAs (lncRNA) have been reported as key regulators in the progression and metastasis of prostate cancer (PCa). In this study, we found that the expression levels of HCG11 in PCa tissues were significantly lower than those in non-tumor tissues in publically available databases and in human PCa samples. Our results showed the expression levels of HCG11 in patients with PCa were associated with the age, Lymph Node Status (LN status), preoperative PSA level, Gleason score, and biochemical recurrence (BCR). Kaplan-Meier analysis indicated that downregulation of HCG11 expression in tissues was associated with poor survival of PCa patients. GO and KEGG pathway analysis were applied to explore the potential roles of HCG11. Moreover, a HCG11 mediated ceRNA network was built using co-expression relationships of the differentially expressed mRNAs and miRNAs. We believed that this study will provide a potential new therapeutic and prognostic target for prostate cancer.
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Affiliation(s)
- Yalong Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, 200433, People's Republic of China
| | - Pu Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, 200433, People's Republic of China
| | - Xuechao Wan
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, 200433, People's Republic of China
| | - Xinya Su
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, 200433, People's Republic of China
| | - Zhe Kong
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, 200433, People's Republic of China
| | - Qiaoli Zhai
- Center of Translational Medicine, Central Hospital of Zibo, Zibo, 255036, People's Republic of China
| | - Xinxin Xiang
- Center of Translational Medicine, Central Hospital of Zibo, Zibo, 255036, People's Republic of China
| | - Liang Li
- Center of Translational Medicine, Central Hospital of Zibo, Zibo, 255036, People's Republic of China.
| | - Yao Li
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, 200433, People's Republic of China.
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31
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Schmitt AM, Chang HY. Long Noncoding RNAs in Cancer Pathways. Cancer Cell 2016; 29:452-463. [PMID: 27070700 PMCID: PMC4831138 DOI: 10.1016/j.ccell.2016.03.010] [Citation(s) in RCA: 2306] [Impact Index Per Article: 288.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/01/2016] [Accepted: 03/14/2016] [Indexed: 12/16/2022]
Abstract
Genome-wide cancer mutation analyses are revealing an extensive landscape of functional mutations within the noncoding genome, with profound effects on the expression of long noncoding RNAs (lncRNAs). While the exquisite regulation of lncRNA transcription can provide signals of malignant transformation, we now understand that lncRNAs drive many important cancer phenotypes through their interactions with other cellular macromolecules including DNA, protein, and RNA. Recent advancements in surveying lncRNA molecular mechanisms are now providing the tools to functionally annotate these cancer-associated transcripts, making these molecules attractive targets for therapeutic intervention in the fight against cancer.
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Affiliation(s)
- Adam M Schmitt
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA.
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32
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Zhang A, Zhang J, Kaipainen A, Lucas JM, Yang H. Long non-coding RNA: A newly deciphered "code" in prostate cancer. Cancer Lett 2016; 375:323-330. [PMID: 26965999 DOI: 10.1016/j.canlet.2016.03.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/02/2016] [Accepted: 03/02/2016] [Indexed: 01/03/2023]
Abstract
As one of the most frequently diagnosed cancers in males, the development and progression of prostate cancer remains an open area of research. The role of lncRNAs in prostate cancer is an emerging field of study. In this review, we summarize what is currently known about lncRNAs in prostate cancer while focusing on a few key lncRNAs. PCA3 was the first lncRNA identified in prostate cancer and has been shown to be expressed in a majority of prostate cancer cases. It may act in both an androgen dependent and independent fashion and has clinical utility as a biomarker. Other lncRNAs are known to interact directly with the androgen receptor pathway including PlncRNA-1, HOTAIR, PRNCR1 and PCGEM1. Additionally, lncRNAs have been shown to interfere with tumor suppressors, DNA break repair, transcription and alternate RNA splicing. While only in its infancy, an understanding of the role of lncRNAs in prostate cancer development should present ample opportunities for the discovery of new cancer biomarkers and therapeutic targets.
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Affiliation(s)
- Ailin Zhang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jiawei Zhang
- School of Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Arja Kaipainen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jared M Lucas
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Hong Yang
- Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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33
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Böttcher R, Henderson DJP, Dulla K, van Strijp D, Waanders LF, Tevz G, Lehman ML, Merkle D, van Leenders GJLH, Baillie GS, Jenster G, Houslay MD, Hoffmann R. Human phosphodiesterase 4D7 (PDE4D7) expression is increased in TMPRSS2-ERG-positive primary prostate cancer and independently adds to a reduced risk of post-surgical disease progression. Br J Cancer 2016; 113:1502-11. [PMID: 26575822 PMCID: PMC4815894 DOI: 10.1038/bjc.2015.335] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/14/2015] [Accepted: 08/20/2015] [Indexed: 02/07/2023] Open
Abstract
Background: There is an acute need to uncover biomarkers that reflect the molecular pathologies, underpinning prostate cancer progression and poor patient outcome. We have previously demonstrated that in prostate cancer cell lines PDE4D7 is downregulated in advanced cases of the disease. To investigate further the prognostic power of PDE4D7 expression during prostate cancer progression and assess how downregulation of this PDE isoform may affect disease outcome, we have examined PDE4D7 expression in physiologically relevant primary human samples. Methods: About 1405 patient samples across 8 publically available qPCR, Affymetrix Exon 1.0 ST arrays and RNA sequencing data sets were screened for PDE4D7 expression. The TMPRSS2-ERG gene rearrangement status of patient samples was determined by transformation of the exon array and RNA seq expression data to robust z-scores followed by the application of a threshold >3 to define a positive TMPRSS2-ERG gene fusion event in a tumour sample. Results: We demonstrate that PDE4D7 expression positively correlates with primary tumour development. We also show a positive association with the highly prostate cancer-specific gene rearrangement between TMPRSS2 and the ETS transcription factor family member ERG. In addition, we find that in primary TMPRSS2-ERG-positive tumours PDE4D7 expression is significantly positively correlated with low-grade disease and a reduced likelihood of progression after primary treatment. Conversely, PDE4D7 transcript levels become significantly decreased in castration resistant prostate cancer (CRPC). Conclusions: We further characterise and add physiological relevance to PDE4D7 as a novel marker that is associated with the development and progression of prostate tumours. We propose that the assessment of PDE4D7 levels may provide a novel, independent predictor of post-surgical disease progression.
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Affiliation(s)
- R Böttcher
- Department of Urology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - D J P Henderson
- Institute of Cardiovascular and Medical Science, University of Glasgow, Glasgow G12 8TA, Scotland
| | - K Dulla
- Departments of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven 5656 AE, The Netherlands
| | - D van Strijp
- Departments of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven 5656 AE, The Netherlands
| | - L F Waanders
- Departments of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven 5656 AE, The Netherlands
| | - G Tevz
- Departments of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven 5656 AE, The Netherlands.,Australian Prostate Cancer Research Centre-Institute of Health and Biomedical Innovation, University of Technology, and Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - M L Lehman
- Australian Prostate Cancer Research Centre-Institute of Health and Biomedical Innovation, University of Technology, and Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - D Merkle
- Departments of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven 5656 AE, The Netherlands
| | - G J L H van Leenders
- Department of Pathology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - G S Baillie
- Institute of Cardiovascular and Medical Science, University of Glasgow, Glasgow G12 8TA, Scotland
| | - G Jenster
- Department of Urology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - M D Houslay
- Institute of Pharmaceutical Science, King's College London, London WC2R 2LS, UK
| | - R Hoffmann
- Institute of Cardiovascular and Medical Science, University of Glasgow, Glasgow G12 8TA, Scotland.,Departments of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven 5656 AE, The Netherlands
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34
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Mehra R, Udager AM, Ahearn TU, Cao X, Feng FY, Loda M, Petimar JS, Kantoff P, Mucci LA, Chinnaiyan AM. Overexpression of the Long Non-coding RNA SChLAP1 Independently Predicts Lethal Prostate Cancer. Eur Urol 2015; 70:549-552. [PMID: 26724257 DOI: 10.1016/j.eururo.2015.12.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 12/04/2015] [Indexed: 11/26/2022]
Abstract
The long noncoding RNA SChLAP1 is overexpressed in a subset of prostate cancers (PCa), and high SChLAP1 expression by in situ hybridization (ISH) independently predicts biochemical recurrence after radical prostatectomy. Importantly, although biochemical recurrence is a significant clinical outcome, it is not a validated surrogate for PCa-related mortality. Thus, we evaluated the association between SChLAP1 expression and development of lethal PCa in a large cohort of American men with PCa and long-term follow-up. SChLAP1 ISH was performed on tissue microarrays containing representative formalin-fixed, paraffin-embedded PCa tissue from all patients and scored using a semiquantitative method (ISH score range 0-400). Hazard ratios (HRs) for the association between SChLAP1 expression and time to development of lethal PCa were estimated using multivariable Cox regression analysis. Of the 937 patients evaluated, 89 (9.5%) had high SChLAP1 expression (ISH score ≥100), which in patients treated with radical prostatectomy was strongly associated with development of lethal PCa independent of age, Gleason score, pathologic stage, and PTEN status (HR 2.2, 95% confidence interval 1.1-4.1). These results suggest that SChLAP1 may be a useful tissue-based biomarker for identifying PCa patients at higher risk of lethal progression. PATIENT SUMMARY We examined expression of the RNA molecule SChLAP1 in a large group of prostate cancer patients with long-term follow-up and found that patients with high SChLAP1 expression had a significantly higher chance of developing lethal disease.
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Affiliation(s)
- Rohit Mehra
- Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Health System, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Ann Arbor, MI, USA.
| | - Aaron M Udager
- Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA
| | - Thomas U Ahearn
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Felix Y Feng
- Comprehensive Cancer Center, University of Michigan Health System, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Ann Arbor, MI, USA; Department of Radiation Oncology, University of Michigan Health System, Ann Arbor, MI, USA
| | - Massimo Loda
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joshua S Petimar
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Philip Kantoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Health System, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Ann Arbor, MI, USA; Howard Hughes Medical Institute, Ann Arbor, MI, USA.
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35
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Kontos CK, Adamopoulos PG, Scorilas A. Prognostic and predictive biomarkers in prostate cancer. Expert Rev Mol Diagn 2015; 15:1567-76. [PMID: 26548550 DOI: 10.1586/14737159.2015.1110022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Prostate cancer (PCa) is one of the leading causes of cancer death among males, especially in more developed countries. Diagnosis is often achieved at an early stage of the disease with prostate biopsy, following a screening test showing elevated serum levels of prostate-specific antigen or a positive digital rectal examination. Early detection of PCa has led to a substantial decline in the number of metastatic patients. However, the prostate-specific antigen screening test has proved to be a double-edged sword so far, as it also accounts for PCa overdiagnosis. Due to the variability of PCa features, accurate prognosis of PCa patients is very important for determining treatment options. Therefore, this review focuses on the most promising prognostic and predictive biomarkers in PCa, which are likely to play a pivotal role, alone or in panels, in the personalized medicine era that has recently emerged.
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Affiliation(s)
- Christos K Kontos
- a Department of Biochemistry and Molecular Biology , University of Athens , Athens , Greece
| | | | - Andreas Scorilas
- a Department of Biochemistry and Molecular Biology , University of Athens , Athens , Greece
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36
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Sahu A, Singhal U, Chinnaiyan AM. Long noncoding RNAs in cancer: from function to translation. Trends Cancer 2015; 1:93-109. [PMID: 26693181 DOI: 10.1016/j.trecan.2015.08.010] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While our understanding of the molecular mechanisms underlying cancer has significantly improved, most of our knowledge focuses on protein-coding genes that make up a fraction of the genome. Recent studies have uncovered thousands of long noncoding RNAs (lncRNAs) that populate the cancer genome. A subset of these molecules shows striking cancer- and lineage-specific expression patterns, suggesting they may be potential drivers of cancer biology and have utility as clinical biomarkers. Here, we discuss emerging modalities of lncRNA biology and their interplay with cancer-associated concepts, including epigenetic regulation, DNA damage and cell cycle control, microRNA silencing, signal transduction pathways, and hormone-driven disease. Additionally, we highlight the translational impact of lncRNAs, tools for their mechanistic investigation, and directions for future lncRNA research.
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Affiliation(s)
- Anirban Sahu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan USA. ; Department of Pathology, University of Michigan, Ann Arbor, Michigan USA
| | - Udit Singhal
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan USA. ; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan USA. ; Department of Pathology, University of Michigan, Ann Arbor, Michigan USA. ; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan USA. ; Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan USA. ; Department of Urology, University of Michigan, Ann Arbor, Michigan USA
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