551
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Huang L, Damle SS, Booten S, Singh P, Sabripour M, Hsu J, Jo M, Katz M, Watt A, Hart CE, Freier SM, Monia BP, Guo S. Partial Hepatectomy Induced Long Noncoding RNA Inhibits Hepatocyte Proliferation during Liver Regeneration. PLoS One 2015. [PMID: 26207833 PMCID: PMC4514479 DOI: 10.1371/journal.pone.0132798] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Liver regeneration after partial hepatectomy (PHx) is a complex and well-orchestrated biological process in which synchronized cell proliferation is induced in response to the loss of liver mass. To define long noncoding RNAs (lncRNAs) that participate in the regulation of liver regeneration, we performed microarray analysis and identified more than 400 lncRNAs exhibiting significantly altered expression. Of these, one lncRNA, LncPHx2 (Long noncoding RNA induced by PHx 2), was highly upregulated during liver regeneration. Depletion of LncPHx2 during liver regeneration using antisense oligonucleotides led to a transient increase in hepatocyte proliferation and more rapid liver regeneration. Gene expression analysis showed that LncPHx2 depletion resulted in upregulation of mRNAs encoding proteins known to promote cell proliferation, including MCM components, DNA polymerases, histone proteins, and transcription factors. LncPHx2 interacts with the mRNAs of MCM components, making it a candidate to regulate the expression of MCMs and other genes post-transcriptionally. Collectively, our data demonstrate that LncPHx2 is a key lncRNA that participates in a negative feedback loop modulating hepatocyte proliferation through RNA-RNA interactions.
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Affiliation(s)
- Lulu Huang
- Department of Antisense Drug Discovery, Isis Pharmaceuticals Inc., Carlsbad, CA, 92010, United States of America
| | - Sagar S. Damle
- Department of Antisense Drug Discovery, Isis Pharmaceuticals Inc., Carlsbad, CA, 92010, United States of America
| | - Sheri Booten
- Department of Antisense Drug Discovery, Isis Pharmaceuticals Inc., Carlsbad, CA, 92010, United States of America
| | - Priyam Singh
- Department of Antisense Drug Discovery, Isis Pharmaceuticals Inc., Carlsbad, CA, 92010, United States of America
| | - Mahyar Sabripour
- Department of Antisense Drug Discovery, Isis Pharmaceuticals Inc., Carlsbad, CA, 92010, United States of America
| | - Jeff Hsu
- Department of Antisense Drug Discovery, Isis Pharmaceuticals Inc., Carlsbad, CA, 92010, United States of America
| | - Minji Jo
- Department of Antisense Drug Discovery, Isis Pharmaceuticals Inc., Carlsbad, CA, 92010, United States of America
| | - Melanie Katz
- Department of Antisense Drug Discovery, Isis Pharmaceuticals Inc., Carlsbad, CA, 92010, United States of America
| | - Andy Watt
- Department of Antisense Drug Discovery, Isis Pharmaceuticals Inc., Carlsbad, CA, 92010, United States of America
| | - Christopher E. Hart
- Department of Antisense Drug Discovery, Isis Pharmaceuticals Inc., Carlsbad, CA, 92010, United States of America
| | - Susan M. Freier
- Department of Antisense Drug Discovery, Isis Pharmaceuticals Inc., Carlsbad, CA, 92010, United States of America
| | - Brett P. Monia
- Department of Antisense Drug Discovery, Isis Pharmaceuticals Inc., Carlsbad, CA, 92010, United States of America
| | - Shuling Guo
- Department of Antisense Drug Discovery, Isis Pharmaceuticals Inc., Carlsbad, CA, 92010, United States of America
- * E-mail:
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552
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Xing D, Liang JQ, Li Y, Lu J, Jia HB, Xu LY, Ma XL. Identification of long noncoding RNA associated with osteoarthritis in humans. Orthop Surg 2015; 6:288-93. [PMID: 25430712 DOI: 10.1111/os.12147] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 10/20/2014] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVE Long noncoding RNAs (lncRNAs) are an important class of genes involved in various biological functions; however, knowledge about lncRNAs in osteoarthritis (OA) is limited. Therefore, the present study aimed to identify which lncRNAs are expressed in OA versus normal cartilage. METHODS To identify lncRNAs specifically expressed in OA cartilage, expression of lncRNAs in OA cartilage was compared with that in normal cartilage using microarray analysis. The identified differences in expression of lncRNAs were validated by real time polymerase chain reaction (RT-PCR). Furthermore, expression of several key mRNAs associated with OA, including those for matrix metalloproteinase (MMP)-9, MMP-13, bone morphogenetic protein (BMP)-2, COL2A1 and ADAMTS5, was investigated by RT-PCR in OA and normal cartilage. RESULTS Microarray analysis identified 121 lncRNAs that were up- or down-regulated in OA compared with normal tissue, 73 being upregulated and 48 downregulated compared with normal cartilage. Twenty-one of the above differently expressed lncRNAs were up-regulated twofold. Expression of six lncRNAs, including HOTAIR, GAS5, PMS2L2, RP11-445H22.4, H19 and CTD-2574D22.4, was up-regulated in OA compared with normal tissue as validated by RT-PCR after microarray analysis. Expression of mRNA for MMP-9, MMP-13, BMP-2, and ADAMTS5 in OA was significantly greater than in normal cartilage. However, expression of mRNA for COL2A1 was lower in OA than in normal cartilage. CONCLUSION The differently expressed lncRNAs may be associated with the pathogenesis of OA. Further functional studies are critical to confirming the function of lncRNAs in OA and to exploring new potential targets for therapy.
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Affiliation(s)
- Dan Xing
- Department of Orthopaedics, Tianjin Hospital, Tianjin, China
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553
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Expanding the p53 regulatory network: LncRNAs take up the challenge. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015. [PMID: 26196323 DOI: 10.1016/j.bbagrm.2015.07.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Long noncoding RNAs (lncRNAs) are rapidly emerging as important regulators of gene expression in a wide variety of physiological and pathological cellular processes. In particular, a number of studies revealed that some lncRNAs participate in the p53 pathway, the unquestioned protagonist of tumor suppressor response. Indeed, several lncRNAs are not only part of the large pool of genes coordinated by p53 transcription factor, but are also required by p53 to fine-tune its response and to fully accomplish its tumor suppressor program. In this review we will discuss the current and fast growing knowledge about the contribution of lncRNAs to the complexity of the p53 network, the different mechanisms by which they affect gene regulation in this context, and their involvement in cancer. The incipient impact of lncRNAs in the p53 biological response may encourage the development of therapies and diagnostic methods focused on these noncoding molecules. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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554
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Sand LGL, Szuhai K, Hogendoorn PCW. Sequencing Overview of Ewing Sarcoma: A Journey across Genomic, Epigenomic and Transcriptomic Landscapes. Int J Mol Sci 2015; 16:16176-215. [PMID: 26193259 PMCID: PMC4519945 DOI: 10.3390/ijms160716176] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/03/2015] [Accepted: 07/07/2015] [Indexed: 12/17/2022] Open
Abstract
Ewing sarcoma is an aggressive neoplasm occurring predominantly in adolescent Caucasians. At the genome level, a pathognomonic EWSR1-ETS translocation is present. The resulting fusion protein acts as a molecular driver in the tumor development and interferes, amongst others, with endogenous transcription and splicing. The Ewing sarcoma cell shows a poorly differentiated, stem-cell like phenotype. Consequently, the cellular origin of Ewing sarcoma is still a hot discussed topic. To further characterize Ewing sarcoma and to further elucidate the role of EWSR1-ETS fusion protein multiple genome, epigenome and transcriptome level studies were performed. In this review, the data from these studies were combined into a comprehensive overview. Presently, classical morphological predictive markers are used in the clinic and the therapy is dominantly based on systemic chemotherapy in combination with surgical interventions. Using sequencing, novel predictive markers and candidates for immuno- and targeted therapy were identified which were summarized in this review.
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Affiliation(s)
- Laurens G L Sand
- Department of Pathology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.
| | - Karoly Szuhai
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.
| | - Pancras C W Hogendoorn
- Department of Pathology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.
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555
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Eckel-Passow JE, Lachance DH, Molinaro AM, Walsh KM, Decker PA, Sicotte H, Pekmezci M, Rice T, Kosel ML, Smirnov IV, Sarkar G, Caron AA, Kollmeyer TM, Praska CE, Chada AR, Halder C, Hansen HM, McCoy LS, Bracci PM, Marshall R, Zheng S, Reis GF, Pico AR, O'Neill BP, Buckner JC, Giannini C, Huse JT, Perry A, Tihan T, Berger MS, Chang SM, Prados MD, Wiemels J, Wiencke JK, Wrensch MR, Jenkins RB. Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors. N Engl J Med 2015; 372:2499-508. [PMID: 26061753 PMCID: PMC4489704 DOI: 10.1056/nejmoa1407279] [Citation(s) in RCA: 1422] [Impact Index Per Article: 158.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND The prediction of clinical behavior, response to therapy, and outcome of infiltrative glioma is challenging. On the basis of previous studies of tumor biology, we defined five glioma molecular groups with the use of three alterations: mutations in the TERT promoter, mutations in IDH, and codeletion of chromosome arms 1p and 19q (1p/19q codeletion). We tested the hypothesis that within groups based on these features, tumors would have similar clinical variables, acquired somatic alterations, and germline variants. METHODS We scored tumors as negative or positive for each of these markers in 1087 gliomas and compared acquired alterations and patient characteristics among the five primary molecular groups. Using 11,590 controls, we assessed associations between these groups and known glioma germline variants. RESULTS Among 615 grade II or III gliomas, 29% had all three alterations (i.e., were triple-positive), 5% had TERT and IDH mutations, 45% had only IDH mutations, 7% were triple-negative, and 10% had only TERT mutations; 5% had other combinations. Among 472 grade IV gliomas, less than 1% were triple-positive, 2% had TERT and IDH mutations, 7% had only IDH mutations, 17% were triple-negative, and 74% had only TERT mutations. The mean age at diagnosis was lowest (37 years) among patients who had gliomas with only IDH mutations and was highest (59 years) among patients who had gliomas with only TERT mutations. The molecular groups were independently associated with overall survival among patients with grade II or III gliomas but not among patients with grade IV gliomas. The molecular groups were associated with specific germline variants. CONCLUSIONS Gliomas were classified into five principal groups on the basis of three tumor markers. The groups had different ages at onset, overall survival, and associations with germline variants, which implies that they are characterized by distinct mechanisms of pathogenesis. (Funded by the National Institutes of Health and others.).
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Affiliation(s)
- Jeanette E Eckel-Passow
- From the Departments of Health Sciences Research (J.E.E.-P., P.A.D., H.S., M.L.K.), Laboratory Medicine and Pathology (D.H.L., G.S., A.A.C., T.M.K., C.E.P., A.R.C., C.H., C.G., R.B.J.), Neurology (D.H.L., B.P.O.), and Oncology (J.C.B.), Mayo Clinic, Rochester, MN; the Departments of Neurological Surgery (A.M.M., K.M.W., T.R., I.V.S., H.M.H., L.S.M., S.Z., A.P., M.S.B., S.M.C., M.D.P., J.K.W., M.R.W.), Epidemiology and Biostatistics (A.M.M., P.M.B., J.W., J.K.W., M.R.W.) and Pathology (M.P., R.M., G.F.R., A.P., T.T.) and the Institute of Human Genetics (J.W., J.K.W., M.R.W.), University of California, San Francisco, and the Bioinformatics Core, Gladstone Institutes (A.R.P.) - all in San Francisco; and the Department of Pathology and Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York (J.T.H.)
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556
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Hezroni H, Koppstein D, Schwartz MG, Avrutin A, Bartel DP, Ulitsky I. Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. Cell Rep 2015; 11:1110-22. [PMID: 25959816 DOI: 10.1016/j.celrep.2015.04.023] [Citation(s) in RCA: 457] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 03/02/2015] [Accepted: 04/09/2015] [Indexed: 12/15/2022] Open
Abstract
The inability to predict long noncoding RNAs from genomic sequence has impeded the use of comparative genomics for studying their biology. Here, we develop methods that use RNA sequencing (RNA-seq) data to annotate the transcriptomes of 16 vertebrates and the echinoid sea urchin, uncovering thousands of previously unannotated genes, most of which produce long intervening noncoding RNAs (lincRNAs). Although in each species, >70% of lincRNAs cannot be traced to homologs in species that diverged >50 million years ago, thousands of human lincRNAs have homologs with similar expression patterns in other species. These homologs share short, 5'-biased patches of sequence conservation nested in exonic architectures that have been extensively rewired, in part by transposable element exonization. Thus, over a thousand human lincRNAs are likely to have conserved functions in mammals, and hundreds beyond mammals, but those functions require only short patches of specific sequences and can tolerate major changes in gene architecture.
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Affiliation(s)
- Hadas Hezroni
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Koppstein
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Alexandra Avrutin
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David P Bartel
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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557
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Yung MK, Lo KW, Yip CW, Chung GTY, Tong CYK, Cheung PFY, Cheung TT, Poon RTP, So S, Fan ST, Cheung ST. Copy number gain of granulin-epithelin precursor (GEP) at chromosome 17q21 associates with overexpression in human liver cancer. BMC Cancer 2015; 15:264. [PMID: 25885205 PMCID: PMC4403714 DOI: 10.1186/s12885-015-1294-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 03/31/2015] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Granulin-epithelin precursor (GEP), a secretory growth factor, demonstrated overexpression in various human cancers, however, mechanism remain elusive. Primary liver cancer, hepatocellular carcinoma (HCC), ranks the second in cancer-related death globally. GEP controlled growth, invasion, metastasis and chemo-resistance in liver cancer. Noted that GEP gene locates at 17q21 and the region has been frequently reported to be amplified in subset of HCC. The study aims to investigate if copy number gain would associate with GEP overexpression. METHODS Quantitative Microsatellite Analysis (QuMA) was used to quantify the GEP DNA copy number, and fluorescent in situ hybridization (FISH) was performed to consolidate the amplification status. GEP gene copy number, mRNA expression level and clinico-pathological features were analyzed. RESULTS GEP DNA copy number determined by QuMA corroborated well with the FISH data, and the gene copy number correlated with the expression levels (n = 60, r = 0.331, P = 0.010). Gain of GEP copy number was observed in 20% (12/60) HCC and associated with hepatitis B virus infection status (P = 0.015). In HCC with increased GEP copy number, tight association between GEP DNA and mRNA levels were observed (n = 12, r = 0.664, P = 0.019). CONCLUSIONS Gain of the GEP gene copy number was observed in 20% HCC and the frequency comparable to literatures reported on the chromosome region 17q. Increased gene copy number contributed to GEP overexpression in subset of HCC.
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Affiliation(s)
- Man Kuen Yung
- Department of Surgery, The University of Hong Kong, Hong Kong, China.
| | - Kwok Wai Lo
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Chi Wai Yip
- Department of Surgery, The University of Hong Kong, Hong Kong, China. .,Centre for Cancer Research, The University of Hong Kong, Hong Kong, China.
| | - Grace T Y Chung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Carol Y K Tong
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Phyllis F Y Cheung
- Department of Surgery, The University of Hong Kong, Hong Kong, China. .,Centre for Cancer Research, The University of Hong Kong, Hong Kong, China.
| | - Tan To Cheung
- Department of Surgery, The University of Hong Kong, Hong Kong, China. .,Department of Surgery, Queen Mary Hospital, Hong Kong, China.
| | - Ronnie T P Poon
- Department of Surgery, The University of Hong Kong, Hong Kong, China. .,Centre for Cancer Research, The University of Hong Kong, Hong Kong, China. .,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China.
| | - Samuel So
- Department of Surgery, Stanford University, Stanford, USA.
| | - Sheung Tat Fan
- Department of Surgery, The University of Hong Kong, Hong Kong, China. .,Centre for Cancer Research, The University of Hong Kong, Hong Kong, China. .,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China.
| | - Siu Tim Cheung
- Department of Surgery, The University of Hong Kong, Hong Kong, China. .,Centre for Cancer Research, The University of Hong Kong, Hong Kong, China. .,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China. .,Department of Surgery, The University of Hong Kong, L9-55, Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Hong Kong, China.
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558
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PAX5 is a tumor suppressor in mouse mutagenesis models of acute lymphoblastic leukemia. Blood 2015; 125:3609-17. [PMID: 25855603 DOI: 10.1182/blood-2015-02-626127] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 03/31/2015] [Indexed: 12/13/2022] Open
Abstract
Alterations of genes encoding transcriptional regulators of lymphoid development are a hallmark of B-progenitor acute lymphoblastic leukemia (B-ALL) and most commonly involve PAX5, encoding the DNA-binding transcription factor paired-box 5. The majority of PAX5 alterations in ALL are heterozygous, and key PAX5 target genes are expressed in leukemic cells, suggesting that PAX5 may be a haploinsufficient tumor suppressor. To examine the role of PAX5 alterations in leukemogenesis, we performed mutagenesis screens of mice heterozygous for a loss-of-function Pax5 allele. Both chemical and retroviral mutagenesis resulted in a significantly increased penetrance and reduced latency of leukemia, with a shift to B-lymphoid lineage. Genomic profiling identified a high frequency of secondary genomic mutations, deletions, and retroviral insertions targeting B-lymphoid development, including Pax5, and additional genes and pathways mutated in ALL, including tumor suppressors, Ras, and Janus kinase-signal transducer and activator of transcription signaling. These results show that in contrast to simple Pax5 haploinsufficiency, multiple sequential alterations targeting lymphoid development are central to leukemogenesis and contribute to the arrest in lymphoid maturation characteristic of ALL. This cross-species analysis also validates the importance of concomitant alterations of multiple cellular growth, signaling, and tumor suppression pathways in the pathogenesis of B-ALL.
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559
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Tseng YY, Bagchi A. The PVT1-MYC duet in cancer. Mol Cell Oncol 2015; 2:e974467. [PMID: 27308428 PMCID: PMC4904896 DOI: 10.4161/23723556.2014.974467] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 06/06/2023]
Abstract
Gain of 8q24, harboring the avian myelocytomatosis viral oncogene homolog (MYC), is a frequent mutation in cancers. Although MYC is the usual suspect in these cancers, the role of other co-gained loci remains mostly unknown. We have recently found that MYC partners with the adjacent long non-coding RNA (lncRNA) plasmacytoma variant translocation 1 (PVT1), which stabilizes MYC protein and potentiates its activity.
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Affiliation(s)
- Yuen-Yi Tseng
- Department of Genetics; Cell Biology and Development; University of Minnesota, Twin Cities; Minneapolis, MN, USA
| | - Anindya Bagchi
- Department of Genetics; Cell Biology and Development; University of Minnesota, Twin Cities; Minneapolis, MN, USA
- Masonic Cancer Center; University of Minnesota, Twin Cities; Minneapolis, MN, USA
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560
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PVT1: a rising star among oncogenic long noncoding RNAs. BIOMED RESEARCH INTERNATIONAL 2015; 2015:304208. [PMID: 25883951 PMCID: PMC4391155 DOI: 10.1155/2015/304208] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/12/2015] [Indexed: 12/13/2022]
Abstract
It is becoming increasingly clear that short and long noncoding RNAs critically participate in the regulation of cell growth, differentiation, and (mis)function. However, while the functional characterization of short non-coding RNAs has been reaching maturity, there is still a paucity of well characterized long noncoding RNAs, even though large studies in recent years are rapidly increasing the number of annotated ones. The long noncoding RNA PVT1 is encoded by a gene that has been long known since it resides in the well-known cancer risk region 8q24. However, a couple of accidental concurrent conditions have slowed down the study of this gene, that is, a preconception on the primacy of the protein-coding over noncoding RNAs and the prevalent interest in its neighbor MYC oncogene. Recent studies have brought PVT1 under the spotlight suggesting interesting models of functioning, such as competing endogenous RNA activity and regulation of protein stability of important oncogenes, primarily of the MYC oncogene. Despite some advancements in modelling the PVT1 role in cancer, there are many questions that remain unanswered concerning the precise molecular mechanisms underlying its functioning.
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561
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Mallory AC, Shkumatava A. LncRNAs in vertebrates: advances and challenges. Biochimie 2015; 117:3-14. [PMID: 25812751 DOI: 10.1016/j.biochi.2015.03.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/17/2015] [Indexed: 01/06/2023]
Abstract
Beyond the handful of classic and well-characterized long noncoding RNAs (lncRNAs), more recently, hundreds of thousands of lncRNAs have been identified in multiple species including bacteria, plants and vertebrates, and the number of newly annotated lncRNAs continues to increase as more transcriptomes are analyzed. In vertebrates, the expression of many lncRNAs is highly regulated, displaying discrete temporal and spatial expression patterns, suggesting roles in a wide range of developmental processes and setting them apart from classic housekeeping ncRNAs. In addition, the deregulation of a subset of these lncRNAs has been linked to the development of several diseases, including cancers, as well as developmental anomalies. However, the majority of vertebrate lncRNA functions remain enigmatic. As such, a major task at hand is to decipher the biological roles of lncRNAs and uncover the regulatory networks upon which they impinge. This review focuses on our emerging understanding of lncRNAs in vertebrate animals, highlighting some recent advances in their functional analyses across several species and emphasizing the current challenges researchers face to characterize lncRNAs and identify their in vivo functions.
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Affiliation(s)
- Allison C Mallory
- Institut Curie, 26 Rue d'Ulm, 75248 Paris Cedex 05, France; CNRS UMR3215, 75248 Paris Cedex 05, France; INSERM U934, 75248 Paris Cedex 05, France.
| | - Alena Shkumatava
- Institut Curie, 26 Rue d'Ulm, 75248 Paris Cedex 05, France; CNRS UMR3215, 75248 Paris Cedex 05, France; INSERM U934, 75248 Paris Cedex 05, France.
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562
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Kasak L, Rull K, Vaas P, Teesalu P, Laan M. Extensive load of somatic CNVs in the human placenta. Sci Rep 2015; 5:8342. [PMID: 25666259 PMCID: PMC4914949 DOI: 10.1038/srep08342] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/15/2015] [Indexed: 11/09/2022] Open
Abstract
Placenta is a temporary, but indispensable organ in mammalian pregnancy. From its basic nature, it exhibits highly invasive tumour-like properties facilitating effective implantation through trophoblast cell proliferation and migration, and a critical role in pregnancy success. We hypothesized that similarly to cancer, somatic genomic rearrangements are promoted in the support of placental function. Here we present the first profiling of copy number variations (CNVs) in human placental genomes, showing an extensive load of somatic CNVs, especially duplications and suggesting that this phenomenon may be critical for normal gestation. Placental somatic CNVs were significantly enriched in genes involved in cell adhesion, immunity, embryonic development and cell cycle. Overrepresentation of imprinted genes in somatic duplications suggests that amplified gene copies may represent an alternative mechanism to support parent-of-origin specific gene expression. Placentas from pregnancy complications exhibited significantly altered CNV profile compared to normal gestations, indicative to the clinical implications of the study.
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Affiliation(s)
- Laura Kasak
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia
| | - Kristiina Rull
- 1] Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia [2] Department of Obstetrics and Gynaecology, University of Tartu, Puusepa St. 8, Tartu 51014, Estonia [3] Women's Clinic of Tartu University Hospital, Puusepa St. 8, Tartu 51014, Estonia
| | - Pille Vaas
- 1] Department of Obstetrics and Gynaecology, University of Tartu, Puusepa St. 8, Tartu 51014, Estonia [2] Women's Clinic of Tartu University Hospital, Puusepa St. 8, Tartu 51014, Estonia
| | - Pille Teesalu
- 1] Department of Obstetrics and Gynaecology, University of Tartu, Puusepa St. 8, Tartu 51014, Estonia [2] Women's Clinic of Tartu University Hospital, Puusepa St. 8, Tartu 51014, Estonia
| | - Maris Laan
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia
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563
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Ling H, Vincent K, Pichler M, Fodde R, Berindan-Neagoe I, Slack FJ, Calin GA. Junk DNA and the long non-coding RNA twist in cancer genetics. Oncogene 2015; 34:5003-11. [PMID: 25619839 PMCID: PMC4552604 DOI: 10.1038/onc.2014.456] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/03/2014] [Accepted: 12/04/2014] [Indexed: 02/07/2023]
Abstract
The central dogma of molecular biology states that the flow of genetic information moves from DNA to RNA to protein. However, in the last decade this dogma has been challenged by new findings on non-coding RNAs (ncRNAs) such as microRNAs (miRNAs). More recently, long non-coding RNAs (lncRNAs) have attracted much attention due to their large number and biological significance. Many lncRNAs have been identified as mapping to regulatory elements including gene promoters and enhancers, ultraconserved regions, and intergenic regions of protein-coding genes. Yet, the biological function and molecular mechanisms of lncRNA in human diseases in general and cancer in particular remain largely unknown. Data from the literature suggest that lncRNA, often via interaction with proteins, functions in specific genomic loci or use their own transcription loci for regulatory activity. In this review, we summarize recent findings supporting the importance of DNA loci in lncRNA function, and the underlying molecular mechanisms via cis or trans regulation, and discuss their implications in cancer. In addition, we use the 8q24 genomic locus, a region containing interactive SNPs, DNA regulatory elements and lncRNAs, as an example to illustrate how single nucleotide polymorphism (SNP) located within lncRNAs may be functionally associated with the individual’s susceptibility to cancer.
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Affiliation(s)
- H Ling
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - K Vincent
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - M Pichler
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - R Fodde
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - I Berindan-Neagoe
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA.,Department of Immunology and Research Center for Functional Genomics, Biomedicine and Translational Medicine University of Medicine and Pharmacy 'I. Hatieganu', Cluj-Napoca, Romania.,Department of Functional Genomics, The Oncology Institute Ion Chiricuta, Cluj-Napoca, Romania
| | - F J Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard medical School, Boston, MA, USA
| | - G A Calin
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
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564
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Sun T, Ye H, Wu CL, Lee GSM, Kantoff PW. Emerging players in prostate cancer: long non-coding RNAs. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2014; 2:294-299. [PMID: 25606575 PMCID: PMC4297325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/09/2014] [Indexed: 06/04/2023]
Abstract
Recent observations of novel long non-coding RNAs (lncRNAs) have considerably altered our understanding of cell biology. The role of lncRNAs as tumor suppressors or oncogenes has been extensively studied. Over-expression of oncogenic lncRNAs promotes tumor-cell proliferation and metastasis through chromatin looping and distal engagement with the androgen receptor, anti-sense gene regulation, alternative splicing, and impeding DNA repair. Prostate cancer is the most common type of cancer and frequent cause of cancer-related mortality in men worldwide. Unraveling the molecular and biological processes that contribute to prostate cancer development and progression is a challenging task. In prostate cancer, aberrant expression of lncRNAs has been associated with disease progression. In this review, we highlight the emerging impact of lncRNAs in prostate cancer research, with a particular focus on the mechanisms and functions of lncRNAs. Increased research on lncRNAs will lead to a greater understanding of prostate cancercinogenesis and progression and may lead to novel clinical applications. LncRNAs have great potential to become new biomarkers for detection, prognostication and prediction in prostate cancer.
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Affiliation(s)
- Tong Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical SchoolUSA
| | - Huihui Ye
- Department of Pathology, Beth-Israel Deaconess Medical Center, Harvard Medical SchoolUSA
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Harvard Medical SchoolUSA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical SchoolUSA
| | - Philip W Kantoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical SchoolUSA
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565
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Abstract
Frequently amplified regions of the cancer genome contain well-known oncogenes. In this issue of Cancer Cell, Hu and colleagues discover that FAL1, a long noncoding RNA is encoded in one of these regions. FAL1 acts as an oncogene by stabilizing BMI1, which results in the repression of CDKN1A expression.
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Affiliation(s)
- Alejandro Athie
- Center for Applied Medical Research, University of Navarra, 331008 Pamplona, Spain
| | - Maite Huarte
- Center for Applied Medical Research, University of Navarra, 331008 Pamplona, Spain.
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566
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Abstract
New findings bring to light a previously unappreciated mechanism involved in the regulation of the oncoprotein MYC. Interesting observations find that the long noncoding RNA (lncRNA) PVT1 is active in controlling levels of MYC through regulation of MYC protein stability.
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