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Volumn 3, Issue , 2013, Pages

RNA sequencing of cancer reveals novel splicing alterations

Author keywords

[No Author keywords available]

Indexed keywords

ISOPROTEIN; RNA; TUMOR PROTEIN;

EID: 84877768911     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep01689     Document Type: Article
Times cited : (150)

References (54)
  • 2
    • 52949096470 scopus 로고    scopus 로고
    • Genetic predisposition to breast cancer: Past, present, and future
    • Turnbull, C. & Rahman, N. Genetic predisposition to breast cancer: past, present, and future. Annu Rev Genomics Hum Genet 9, 321-345 (2008).
    • (2008) Annu Rev Genomics Hum Genet , vol.9 , pp. 321-345
    • Turnbull, C.1    Rahman, N.2
  • 3
    • 84858295021 scopus 로고    scopus 로고
    • BRCA1 testing should be offered to individuals with triplenegative breast cancer diagnosed below 50 years
    • Robertson, L. et al. BRCA1 testing should be offered to individuals with triplenegative breast cancer diagnosed below 50 years. Br J Cancer 106, 1234-1238.
    • Br J Cancer , vol.106 , pp. 1234-1238
    • Robertson, L.1
  • 5
    • 84859786122 scopus 로고    scopus 로고
    • Transcriptomic landscape of breast cancers through mRNA sequencing
    • Eswaran, J. et al. Transcriptomic landscape of breast cancers through mRNA sequencing. Sci Rep 2, 264 (2012).
    • (2012) Sci Rep , vol.2 , pp. 264
    • Eswaran, J.1
  • 6
    • 84861527388 scopus 로고    scopus 로고
    • The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
    • Curtis, C. et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486, 346-352.
    • Nature , vol.486 , pp. 346-352
    • Curtis, C.1
  • 7
    • 84855539848 scopus 로고    scopus 로고
    • Targeted RNA sequencing reveals the deep complexity of the human transcriptome
    • Mercer, T. R. et al. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol 30, 99-104 (2012).
    • (2012) Nat Biotechnol , vol.30 , pp. 99-104
    • Mercer, T.R.1
  • 8
    • 24644519490 scopus 로고    scopus 로고
    • The transcriptional landscape of the mammalian genome
    • Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559-1563 (2005).
    • (2005) Science , vol.309 , pp. 1559-1563
    • Carninci, P.1
  • 9
    • 33747322165 scopus 로고    scopus 로고
    • Taggingmammalian transcription complexity
    • Carninci, P. Taggingmammalian transcription complexity. Trends Genet 22, 501-510 (2006).
    • (2006) Trends Genet , vol.22 , pp. 501-510
    • Carninci, P.1
  • 10
    • 34347405524 scopus 로고    scopus 로고
    • Promoting transcriptome diversity
    • DOI 10.1101/gr.6499807
    • Strausberg, R. L. & Levy, S. Promoting transcriptome diversity. Genome Res 17, 965-968 (2007). (Pubitemid 47026343)
    • (2007) Genome Research , vol.17 , Issue.7 , pp. 965-968
    • Strausberg, R.L.1    Levy, S.2
  • 11
    • 21644451890 scopus 로고    scopus 로고
    • Why do humans have so few genes
    • DOI 10.1126/science.309.5731.80
    • Pennisi, E. Why do humans have so few genes? Science 309, 80 (2005). (Pubitemid 40934960)
    • (2005) Science , vol.309 , Issue.5731 , pp. 80
    • Pennisi, E.1
  • 12
    • 12344291073 scopus 로고    scopus 로고
    • Dark matter in the genome: Evidence of widespread transcription detected by microarray tiling experiments
    • DOI 10.1016/j.tig.2004.12.009, PII S0168952504003373
    • Johnson, J. M., Edwards, S., Shoemaker, D. & Schadt, E. E. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet 21, 93-102 (2005). (Pubitemid 40127353)
    • (2005) Trends in Genetics , vol.21 , Issue.2 , pp. 93-102
    • Johnson, J.M.1    Edwards, S.2    Shoemaker, D.3    Schadt, E.E.4
  • 14
    • 50849145126 scopus 로고    scopus 로고
    • Tissue-specific splicing factor gene expression signatures
    • Grosso, A. R. et al. Tissue-specific splicing factor gene expression signatures. Nucleic Acids Res 36, 4823-4832 (2008).
    • (2008) Nucleic Acids Res , vol.36 , pp. 4823-4832
    • Grosso, A.R.1
  • 15
    • 18344364099 scopus 로고    scopus 로고
    • Understanding alternative splicing: Towards a cellular code
    • DOI 10.1038/nrm1645
    • Matlin, A. J., Clark, F. & Smith, C.W. Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 6, 386-398 (2005). (Pubitemid 40637856)
    • (2005) Nature Reviews Molecular Cell Biology , vol.6 , Issue.5 , pp. 386-398
    • Matlin, A.J.1    Clark, F.2    Smith, C.W.J.3
  • 16
    • 58149163446 scopus 로고    scopus 로고
    • Tissue-specific genetic control of splicing: Implications for the study of complex traits
    • Heinzen, E. L. et al. Tissue-specific genetic control of splicing: implications for the study of complex traits. PLoS Biol 6, e1 (2008).
    • (2008) PLoS Biol , vol.6
    • Heinzen, E.L.1
  • 17
    • 0032435862 scopus 로고    scopus 로고
    • Alternative splicing of pre-mRNA: Developmental consequences and mechanisms of regulation
    • DOI 10.1146/annurev.genet.32.1.279
    • Lopez, A. J. Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation. Annu Rev Genet 32, 279-305 (1998). (Pubitemid 29045315)
    • (1998) Annual Review of Genetics , vol.32 , pp. 279-305
    • Lopez, A.J.1
  • 21
    • 80052322960 scopus 로고    scopus 로고
    • An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype
    • Shapiro, I. M. et al. An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype. PLoS Genet 7, e1002218 (2011).
    • (2011) PLoS Genet , vol.7
    • Shapiro, I.M.1
  • 23
    • 0043136678 scopus 로고    scopus 로고
    • Alternative splicing disrupts a nuclear localization signal in spleen tyrosine kinase that is required for invasion suppression in breast cancer
    • Wang, L. et al. Alternative splicing disrupts a nuclear localization signal in spleen tyrosine kinase that is required for invasion suppression in breast cancer. Cancer Res 63, 4724-4730 (2003). (Pubitemid 36951053)
    • (2003) Cancer Research , vol.63 , Issue.15 , pp. 4724-4730
    • Wang, L.1    Duke, L.2    Zhang, P.S.3    Arlinghaus, R.B.4    Symmans, W.F.5    Sahin, A.6    Mendez, R.7    Dai, J.L.8
  • 24
    • 4444351219 scopus 로고    scopus 로고
    • Regulation of human p53 activity and cell localization by alternative splicing
    • DOI 10.1128/MCB.24.18.7987-7997.2004
    • Ghosh, A., Stewart, D. & Matlashewski, G. Regulation of human p53 activity and cell localization by alternative splicing. Mol Cell Biol 24, 7987-7997 (2004). (Pubitemid 39167449)
    • (2004) Molecular and Cellular Biology , vol.24 , Issue.18 , pp. 7987-7997
    • Ghosh, A.1    Stewart, D.2    Matlashewski, G.3
  • 27
    • 51449112388 scopus 로고    scopus 로고
    • Genetic regulation of MUC1 alternative splicing in human tissues
    • Ng, W., Loh, A. X., Teixeira, A. S., Pereira, S. P. & Swallow, D. M. Genetic regulation of MUC1 alternative splicing in human tissues. Br J Cancer 99, 978-985 (2008).
    • (2008) Br J Cancer , vol.99 , pp. 978-985
    • Ng, W.1    Loh, A.X.2    Teixeira, A.S.3    Pereira, S.P.4    Swallow, D.M.5
  • 28
    • 77955463831 scopus 로고    scopus 로고
    • Exon-level microarray analyses identify alternative splicing programs in breast cancer
    • Lapuk, A. et al. Exon-level microarray analyses identify alternative splicing programs in breast cancer. Mol Cancer Res 8, 961-974 (2010).
    • (2010) Mol Cancer Res , vol.8 , pp. 961-974
    • Lapuk, A.1
  • 29
    • 77957307409 scopus 로고    scopus 로고
    • Alternative splicing and breast cancer
    • Dutertre, M., Vagner, S. & Auboeuf, D. Alternative splicing and breast cancer. RNA Biol 7, 403-411 (2010).
    • (2010) RNA Biol , vol.7 , pp. 403-411
    • Dutertre, M.1    Vagner, S.2    Auboeuf, D.3
  • 30
    • 78650827356 scopus 로고    scopus 로고
    • Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts
    • Ferreira, E. N. et al. Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts. BMC Genomics 11 Suppl 5, S4.
    • BMC Genomics , vol.11 , Issue.SUPPL. 5
    • Ferreira, E.N.1
  • 31
    • 3042642783 scopus 로고    scopus 로고
    • Splice variants as cancer biomarkers
    • DOI 10.1016/j.clinbiochem.2004.05.015, PII S0009912004001377
    • Brinkman, B. M. Splice variants as cancer biomarkers. Clin Biochem 37, 584-594 (2004). (Pubitemid 38845021)
    • (2004) Clinical Biochemistry , vol.37 , Issue.7 , pp. 584-594
    • Brinkman, B.M.N.1
  • 32
    • 78650058951 scopus 로고    scopus 로고
    • Gene expression profiling of human breast tissue samples using SAGE-Seq
    • Wu, Z. J. et al. Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res 20, 1730-1739.
    • Genome Res , vol.20 , pp. 1730-1739
    • Wu, Z.J.1
  • 34
    • 79957842166 scopus 로고    scopus 로고
    • Computational methods for transcriptome annotation and quantification using RNA-seq
    • Garber, M.,Grabherr, M. G.,Guttman, M. & Trapnell, C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 8, 469-477 (2011).
    • (2011) Nat Methods , vol.8 , pp. 469-477
    • Garber, M.1    Grabherr, M.G.2    Guttman, M.3    Trapnell, C.4
  • 35
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7, 562-578 (2012).
    • (2012) Nat Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1
  • 36
    • 80051941094 scopus 로고    scopus 로고
    • Identification of novel transcripts in annotated genomes using RNA-Seq
    • Roberts, A., Pimentel, H., Trapnell, C. & Pachter, L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 27, 2325-2329 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 2325-2329
    • Roberts, A.1    Pimentel, H.2    Trapnell, C.3    Pachter, L.4
  • 37
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28, 511-515 (2010).
    • (2010) Nat Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1
  • 38
    • 84860385776 scopus 로고    scopus 로고
    • MATS: A Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data
    • Shen, S. et al. MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res 40, e61 (2012).
    • (2012) Nucleic Acids Res , vol.40
    • Shen, S.1
  • 39
    • 7444220147 scopus 로고    scopus 로고
    • Aberrant and alternative splicing in cancer
    • DOI 10.1158/0008-5472.CAN-04-1910
    • Venables, J. P. Aberrant and alternative splicing in cancer. Cancer Res 64, 7647-7654 (2004). (Pubitemid 39446889)
    • (2004) Cancer Research , vol.64 , Issue.21 , pp. 7647-7654
    • Venables, J.P.1
  • 41
    • 56749164864 scopus 로고    scopus 로고
    • Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines
    • Castle, J. C. et al. Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet 40, 1416-1425 (2008).
    • (2008) Nat Genet , vol.40 , pp. 1416-1425
    • Castle, J.C.1
  • 42
    • 0030257584 scopus 로고    scopus 로고
    • P53-Dependent repression of cdk4 synthesis in transforming growth factor-β-induced G1 cell cycle arrest
    • Ewen, M. E. p53-dependent repression of cdk4 synthesis in transforming growth factor-beta-induced G1 cell cycle arrest. J Lab Clin Med 128, 355-360 (1996). (Pubitemid 27506921)
    • (1996) Journal of Laboratory and Clinical Medicine , vol.128 , Issue.4 , pp. 355-360
    • Ewen, M.E.1
  • 43
    • 0033756586 scopus 로고    scopus 로고
    • P53 binds selectively to the 5' untranslated region of cdk4, an RNA element necessary and sufficient for transforming growth factor beta-and p53-mediated translational inhibition of cdk4
    • Miller, S. J., Suthiphongchai, T., Zambetti, G. P. & Ewen, M. E. p53 binds selectively to the 5' untranslated region of cdk4, an RNA element necessary and sufficient for transforming growth factor beta-and p53-mediated translational inhibition of cdk4. Mol Cell Biol 20, 8420-8431 (2000).
    • (2000) Mol Cell Biol , vol.20 , pp. 8420-8431
    • Miller, S.J.1    Suthiphongchai, T.2    Zambetti, G.P.3    Ewen, M.E.4
  • 44
    • 45749126026 scopus 로고    scopus 로고
    • C. elegans La-related protein, LARP-1, localizes to germline P bodies and attenuates Ras-MAPK signaling during oogenesis
    • DOI 10.1261/rna.1066008
    • Nykamp, K., Lee, M. H. & Kimble, J. C. elegans La-related protein, LARP-1, localizes to germline P bodies and attenuates Ras-MAPK signaling during oogenesis. RNA 14, 1378-1389 (2008). (Pubitemid 351872194)
    • (2008) RNA , vol.14 , Issue.7 , pp. 1378-1389
    • Nykamp, K.1    Lee, M.-H.2    Kimble, J.3
  • 45
    • 77956513137 scopus 로고    scopus 로고
    • The RNA binding protein Larp1 regulates cell division, apoptosis and cell migration
    • Burrows, C. et al. The RNA binding protein Larp1 regulates cell division, apoptosis and cell migration. Nucleic Acids Res 38, 5542-5553.
    • Nucleic Acids Res , vol.38 , pp. 5542-5553
    • Burrows, C.1
  • 46
    • 33947203621 scopus 로고    scopus 로고
    • PHLPP and a Second Isoform, PHLPP2, Differentially Attenuate the Amplitude of Akt Signaling by Regulating Distinct Akt Isoforms
    • DOI 10.1016/j.molcel.2007.02.017, PII S1097276507001177
    • Brognard, J., Sierecki, E., Gao, T. & Newton, A. C. PHLPP and a second isoform, PHLPP2, differentially attenuate the amplitude of Akt signaling by regulating distinct Akt isoforms. Mol Cell 25, 917-931 (2007). (Pubitemid 46436532)
    • (2007) Molecular Cell , vol.25 , Issue.6 , pp. 917-931
    • Brognard, J.1    Sierecki, E.2    Gao, T.3    Newton, A.C.4
  • 47
    • 77958043359 scopus 로고    scopus 로고
    • Adducins regulate remodeling of apical junctions in human epithelial cells
    • Naydenov, N. G. & Ivanov, A. I. Adducins regulate remodeling of apical junctions in human epithelial cells. Mol Biol Cell 21, 3506-3517.
    • Mol Biol Cell , vol.21 , pp. 3506-3517
    • Naydenov, N.G.1    Ivanov, A.I.2
  • 48
    • 63149156942 scopus 로고    scopus 로고
    • Exonic expression profiling of breast cancer and benign lesions: A retrospective analysis
    • Andre, F. et al. Exonic expression profiling of breast cancer and benign lesions: a retrospective analysis. Lancet Oncol 10, 381-390 (2009).
    • (2009) Lancet Oncol , vol.10 , pp. 381-390
    • Andre, F.1
  • 49
    • 77957772409 scopus 로고    scopus 로고
    • Exon-level transcriptome profiling in murine breast cancer reveals splicing changes specific to tumors with different metastatic abilities
    • Bemmo, A. et al. Exon-level transcriptome profiling in murine breast cancer reveals splicing changes specific to tumors with different metastatic abilities. PLoS One 5, e11981.
    • PLoS One , vol.5
    • Bemmo, A.1
  • 50
    • 76249100558 scopus 로고    scopus 로고
    • Exon-based clustering of murine breast tumor transcriptomes reveals alternative exons whose expression is associated with metastasis
    • Dutertre, M. et al. Exon-based clustering of murine breast tumor transcriptomes reveals alternative exons whose expression is associated with metastasis. Cancer Res 70, 896-905.
    • Cancer Res , vol.70 , pp. 896-905
    • Dutertre, M.1
  • 51
    • 0035844238 scopus 로고    scopus 로고
    • Modification of alternative splicing of Bcl-x pre-mRNA in prostate and breast cancer cells
    • Mercatante, D. R., Bortner, C. D., Cidlowski, J. A. & Kole, R. Modification of alternative splicing of Bcl-x pre-mRNA in prostate and breast cancer cells. analysis of apoptosis and cell death. J Biol Chem 276, 16411-16417 (2001).
    • (2001) J Biol Chem , vol.276 , pp. 16411-16417
    • Mercatante, D.R.1    Bortner, C.D.2    Cidlowski, J.A.3    Kole, R.4
  • 52
    • 84863725803 scopus 로고    scopus 로고
    • Progression of ductal carcinoma in situ to invasive breast cancer is associated with gene expression programs of EMT and myoepithelia
    • Knudsen, E. S. et al. Progression of ductal carcinoma in situ to invasive breast cancer is associated with gene expression programs of EMT and myoepithelia. Breast Cancer Res Treat 133, 1009-1024.
    • Breast Cancer Res Treat , vol.133 , pp. 1009-1024
    • Knudsen, E.S.1
  • 53
    • 0035266249 scopus 로고    scopus 로고
    • 1
    • Zhou, J., Gurates, B., Yang, S., Sebastian, S. & Bulun, S. E. Malignant breast epithelial cells stimulate aromatase expression via promoter II in human adipose fibroblasts: an epithelial-stromal interaction in breast tumors mediated by CCAAT/enhancer binding protein beta. Cancer Res 61, 2328-2334 (2001). (Pubitemid 32692067)
    • (2001) Cancer Research , vol.61 , Issue.5 , pp. 2328-2334
    • Zhou, J.1    Gurates, B.2    Yang, S.3    Sebastian, S.4    Bulun, S.E.5
  • 54
    • 79960889611 scopus 로고    scopus 로고
    • Changes in aromatase (CYP19) gene promoter usage in nonsmall cell lung cancer
    • Demura, M. et al. Changes in aromatase (CYP19) gene promoter usage in nonsmall cell lung cancer. Lung Cancer 73, 289-293 (2011).
    • (2011) Lung Cancer , vol.73 , pp. 289-293
    • Demura, M.1


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