Comprehensive Transcriptional Analysis of Early-Stage Urothelial Carcinoma
Tài liệu tham khảo
Alexandrov, 2013, Signatures of mutational processes in human cancer, Nature, 500, 415, 10.1038/nature12477
Babjuk, 2013, EAU guidelines on non-muscle-invasive urothelial carcinoma of the bladder: update 2013, Eur. Urol., 64, 639, 10.1016/j.eururo.2013.06.003
Birkenkamp-Demtroder, 2016, Genomic alterations in liquid biopsies from patients with bladder cancer, Eur. Urol., 10.1016/j.eururo.2016.01.007
Biton, 2014, Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes, Cell Rep., 9, 1235, 10.1016/j.celrep.2014.10.035
Blaveri, 2005, Bladder cancer outcome and subtype classification by gene expression, Clin. Cancer Res., 11, 4044, 10.1158/1078-0432.CCR-04-2409
Brockdorff, 2013, Noncoding RNA and polycomb recruitment, RNA, 19, 429, 10.1261/rna.037598.112
Cancer Genome Atlas Research Network, 2014, Comprehensive molecular characterization of urothelial bladder carcinoma, Nature, 507, 315, 10.1038/nature12965
Choi, 2014, Intrinsic basal and luminal subtypes of muscle-invasive bladder cancer, Nat. Rev. Urol., 11, 400, 10.1038/nrurol.2014.129
Choi, 2014, Identification of distinct basal and luminal subtypes of muscle-invasive bladder cancer with different sensitivities to frontline chemotherapy, Cancer Cell, 25, 152, 10.1016/j.ccr.2014.01.009
Cingolani, 2012, A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3, Fly (Austin), 6, 80, 10.4161/fly.19695
Damrauer, 2014, Intrinsic subtypes of high-grade bladder cancer reflect the hallmarks of breast cancer biology, Proc. Natl. Acad. Sci. USA, 111, 3110, 10.1073/pnas.1318376111
de Bruin, 2014, Spatial and temporal diversity in genomic instability processes defines lung cancer evolution, Science, 346, 251, 10.1126/science.1253462
Dyrskjot, 2003, Identifying distinct classes of bladder carcinoma using microarrays, Nat. Genet., 33, 90, 10.1038/ng1061
Dyrskjot, 2004, Gene expression in the urinary bladder: a common carcinoma in situ gene expression signature exists disregarding histopathological classification, Cancer Res., 64, 4040, 10.1158/0008-5472.CAN-03-3620
Dyrskjot, 2007, Gene expression signatures predict outcome in non-muscle-invasive bladder carcinoma: a multicenter validation study, Clin. Cancer Res., 13, 3545, 10.1158/1078-0432.CCR-06-2940
Dyrskjot, 2012, Analysis of molecular intra-patient variation and delineation of a prognostic 12-gene signature in non-muscle invasive bladder cancer; technology transfer from microarrays to PCR, Br. J. Cancer, 107, 1392, 10.1038/bjc.2012.412
Ferlay, 2015, Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012, Int. J. Cancer, 136, E359, 10.1002/ijc.29210
Gallego Romero, 2014, RNA-seq: impact of RNA degradation on transcript quantification, BMC Biol., 12, 42, 10.1186/1741-7007-12-42
Gehring, 2015, SomaticSignatures: inferring mutational signatures from single-nucleotide variants, Bioinformatics, 31, 3673, 10.1093/bioinformatics/btv408
Gonzalez-Perez, 2013, IntOGen-mutations identifies cancer drivers across tumor types, Nat. Methods, 10, 1081, 10.1038/nmeth.2642
Han, 2015, The genomic landscape and clinical relevance of a-to-I RNA editing in human cancers, Cancer Cell, 28, 515, 10.1016/j.ccell.2015.08.013
Hong, 2008, Economic impact of tumor markers in bladder cancer surveillance, Urology, 71, 131, 10.1016/j.urology.2007.08.014
Jung, 2014, The role of immunohistochemistry in the diagnosis of flat urothelial lesions: a study using CK20, CK5/6, P53, Cd138, and Her2/Neu, Ann. Diagn. Pathol., 18, 27, 10.1016/j.anndiagpath.2013.10.006
Kim, 2013, TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol., 14, R36, 10.1186/gb-2013-14-4-r36
Kim, 2015, Invasive bladder cancer: genomic insights and therapeutic promise, Clin. Cancer Res., 21, 4514, 10.1158/1078-0432.CCR-14-1215
Lawson, 2015, Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells, Nature, 526, 131, 10.1038/nature15260
Maraver, 2015, NOTCH pathway inactivation promotes bladder cancer progression, J. Clin. Invest., 125, 824, 10.1172/JCI78185
McKenna, 2010, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res., 20, 1297, 10.1101/gr.107524.110
Montes, 2015, The lncRNA MIR31HG regulates p16(INK4A) expression to modulate senescence, Nat. Commun., 6, 6967, 10.1038/ncomms7967
Nie, 2015, Decreased long noncoding RNA MIR31HG is correlated with poor prognosis and contributes to cell proliferation in gastric cancer, Tumour Biol.
Nordentoft, 2014, Mutational context and diverse clonal development in early and late bladder cancer, Cell Rep., 7, 1649, 10.1016/j.celrep.2014.04.038
Patschan, 2015, A molecular pathologic framework for risk stratification of stage T1 urothelial carcinoma, Eur. Urol., 68, 824, 10.1016/j.eururo.2015.02.021
Rampias, 2014, A new tumor suppressor role for the Notch pathway in bladder cancer, Nat. Med., 20, 1199, 10.1038/nm.3678
Rebouissou, 2014, EGFR as a potential therapeutic target for a subset of muscle-invasive bladder cancers presenting a basal-like phenotype, Sci. Transl. Med., 6, 244ra291, 10.1126/scitranslmed.3008970
Roberts, 2013, An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers, Nat. Genet., 45, 970, 10.1038/ng.2702
Rubio-Perez, 2015, In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities, Cancer Cell, 27, 382, 10.1016/j.ccell.2015.02.007
Sanchez-Carbayo, 2006, Defining molecular profiles of poor outcome in patients with invasive bladder cancer using oligonucleotide microarrays, J. Clin. Oncol., 24, 778, 10.1200/JCO.2005.03.2375
Shin, 2014, Hedgehog signaling restrains bladder cancer progression by eliciting stromal production of urothelial differentiation factors, Cancer Cell, 26, 521, 10.1016/j.ccell.2014.09.001
Sieuwerts, 2014, Elevated APOBEC3B correlates with poor outcomes for estrogen-receptor-positive breast cancers, Horm. Cancer, 5, 405, 10.1007/s12672-014-0196-8
Sjodahl, 2012, A molecular taxonomy for urothelial carcinoma, Clin. Cancer Res., 18, 3377, 10.1158/1078-0432.CCR-12-0077-T
Spruck, 1994, Two molecular pathways to transitional cell carcinoma of the bladder, Cancer Res., 54, 784
Swanton, 2015, Apobec enzymes: mutagenic fuel for cancer evolution and heterogeneity, Cancer Discov., 5, 704, 10.1158/2159-8290.CD-15-0344
Tai, 2013, Cytokeratin 15 marks basal epithelia in developing ureters and is upregulated in a subset of urothelial cell carcinomas, PLoS One, 8, e81167, 10.1371/journal.pone.0081167
Thorsen, 2008, Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis, Mol. Cell Proteomics, 7, 1214, 10.1074/mcp.M700590-MCP200
Trapnell, 2010, Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation, Nat. Biotechnol., 28, 511, 10.1038/nbt.1621
van der Horst, 2012, Epithelial plasticity, cancer stem cells, and the tumor-supportive stroma in bladder carcinoma, Mol. Cancer Res., 10, 995, 10.1158/1541-7786.MCR-12-0274
van Rhijn, 2003, Molecular grading of urothelial cell carcinoma with fibroblast growth factor receptor 3 and MIB-1 is superior to pathologic grade for the prediction of clinical outcome, J. Clin. Oncol., 21, 1912, 10.1200/JCO.2003.05.073
Vogelstein, 2013, Cancer genome landscapes, Science, 339, 1546, 10.1126/science.1235122
Volkmer, 2012, Three differentiation states risk-stratify bladder cancer into distinct subtypes, Proc. Natl. Acad. Sci. USA, 109, 2078, 10.1073/pnas.1120605109
Waclaw, 2015, A spatial model predicts that dispersal and cell turnover limit intratumour heterogeneity, Nature, 525, 261, 10.1038/nature14971
West, 2014, The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites, Mol. Cell, 55, 791, 10.1016/j.molcel.2014.07.012
Wilkerson, 2010, ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking, Bioinformatics, 26, 1572, 10.1093/bioinformatics/btq170
Zhang, 2014, EGR1 decreases the malignancy of human non-small cell lung carcinoma by regulating KRT18 expression, Sci. Rep., 4, 5416, 10.1038/srep05416
