Cistrome Partitioning Reveals Convergence of Somatic Mutations and Risk Variants on Master Transcription Regulators in Primary Prostate Tumors
Tài liệu tham khảo
Adamo, 2016, The oncogene ERG: a key factor in prostate cancer, Oncogene, 35, 403, 10.1038/onc.2015.109
Ahmadiyeh, 2010, 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC, Proc. Natl. Acad. Sci. U S A, 107, 9742, 10.1073/pnas.0910668107
Ahmed, 2017, Variant Set Enrichment: an R package to identify disease-associated functional genomic regions, BioData Min, 10, 9, 10.1186/s13040-017-0129-5
Al Olama, 2009, Multiple loci on 8q24 associated with prostate cancer susceptibility, Nat. Genet., 41, 1058, 10.1038/ng.452
Amundadottir, 2006, A common variant associated with prostate cancer in European and African populations, Nat. Genet., 38, 652, 10.1038/ng1808
Baca, 2013, Punctuated evolution of prostate cancer genomes, Cell, 153, 666, 10.1016/j.cell.2013.03.021
Bailey, 2015, ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters, Nat. Commun., 2, 6186, 10.1038/ncomms7186
Bailey, 2016, Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer, Nat. Genet., 48, 1260, 10.1038/ng.3650
Barbieri, 2012, Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer, Nat. Genet., 44, 685, 10.1038/ng.2279
Brechka, 2017, HOXB13 mutations and binding partners in prostate development and cancer: function, clinical significance, and future directions, Genes Dis., 4, 75, 10.1016/j.gendis.2017.01.003
Cairns, 1997, Frequent inactivation of PTEN/MMAC1 in primary prostate cancer, Cancer Res., 57, 4997
Cancer Genome Atlas Research Network, 2015, The molecular taxonomy of primary prostate cancer, Cell, 163, 1011, 10.1016/j.cell.2015.10.025
Chen, 2015, Systematic enrichment analysis of potentially functional regions for 103 prostate cancer risk-associated loci, Prostate, 75, 1264, 10.1002/pros.23008
Chen, 2019, Widespread and functional RNA circularization in localized prostate cancer, Cell, 176, 831, 10.1016/j.cell.2019.01.025
Chung, 2011, Association of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility, Cancer Sci., 102, 245, 10.1111/j.1349-7006.2010.01737.x
Copeland, 2018, The androgen receptor malignancy shift in prostate cancer, Prostate, 78, 521, 10.1002/pros.23497
Cowper-Sal-lari, 2012, Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression, Nat. Genet., 44, 1191, 10.1038/ng.2416
Culig, 2014, Androgen receptor signaling in prostate cancer, Cancer Metastasis Rev., 33, 413, 10.1007/s10555-013-9474-0
Dubois-Chevalier, 2018, Organizing combinatorial transcription factor recruitment at cis-regulatory modules, Transcription, 9, 233, 10.1080/21541264.2017.1394424
Dubois-Chevalier, 2017, The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions, Genome Res., 27, 985, 10.1101/gr.217075.116
Economides, 2003, Hoxb13 is required for normal differentiation and secretory function of the ventral prostate, Development, 130, 2061, 10.1242/dev.00432
2011, A user’s guide to the encyclopedia of DNA elements (ENCODE), PLoS Biol., 9, e1001046, 10.1371/journal.pbio.1001046
Ernst, 2011, Mapping and analysis of chromatin state dynamics in nine human cell types, Nature, 473, 43, 10.1038/nature09906
Espiritu, 2018, The evolutionary landscape of localized prostate cancers drives clinical aggression, Cell, 173, 1003, 10.1016/j.cell.2018.03.029
Francis, 2018, SOX9 is a driver of aggressive prostate cancer by promoting invasion, cell fate and cytoskeleton alterations and epithelial to mesenchymal transition, Oncotarget, 9, 7604, 10.18632/oncotarget.24123
Fraser, 2017, Genomic hallmarks of localized, non-indolent prostate cancer, Nature, 541, 359, 10.1038/nature20788
Friedman, 2006, The Foxa family of transcription factors in development and metabolism, Cell. Mol. Life Sci., 63, 2317, 10.1007/s00018-006-6095-6
Gelfman, 2017, Annotating pathogenic non-coding variants in genic regions, Nat. Commun., 8, 236, 10.1038/s41467-017-00141-2
Georgakopoulos-Soares, 2017, MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments, Bioinformatics, 33, 137, 10.1093/bioinformatics/btw584
Gerhardt, 2012, FOXA1 promotes tumor progression in prostate cancer and represents a novel hallmark of castration-resistant prostate cancer, Am. J. Pathol., 180, 848, 10.1016/j.ajpath.2011.10.021
Ghoussaini, 2014, Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation, Nat. Commun., 4, 4999, 10.1038/ncomms5999
Gudmundsson, 2007, Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24, Nat. Genet., 39, 631, 10.1038/ng1999
Guo, 2016, Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer, Nat. Genet., 48, 1142, 10.1038/ng.3637
Hawksworth, 2010, Overexpression of C-MYC oncogene in prostate cancer predicts biochemical recurrence, Prostate Cancer Prostatic Dis., 13, 311, 10.1038/pcan.2010.31
He, 2010, Nucleosome dynamics define transcriptional enhancers, Nat. Genet., 42, 343, 10.1038/ng.545
Heinlein, 2004, Androgen receptor in prostate cancer, Endocr. Rev., 25, 276, 10.1210/er.2002-0032
Heintzman, 2007, Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome, Nat. Genet., 39, 311, 10.1038/ng1966
Heintzman, 2009, Histone modifications at human enhancers reflect global cell-type-specific gene expression, Nature, 459, 108, 10.1038/nature07829
Heinz, 2010, Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities, Mol. Cell, 38, 576, 10.1016/j.molcel.2010.05.004
Horn, 2013, TERT promoter mutations in familial and sporadic melanoma, Science, 339, 959, 10.1126/science.1230062
Hu, 2017, Dynamic maps of UV damage formation and repair for the human genome, Proc. Natl. Acad. Sci. U S A, 114, 6758, 10.1073/pnas.1706522114
Huang, 2013, Highly recurrent TERT promoter mutations in human melanoma, Science, 339, 957, 10.1126/science.1229259
Huang, 2014, A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding, Nat. Genet., 46, 126, 10.1038/ng.2862
Jenkins, 1997, Detection of c-myc oncogene amplification and chromosomal anomalies in metastatic prostatic carcinoma by fluorescence in situ hybridization, Cancer Res., 57, 524
Jozwik, 2012, Pioneer factors in hormone-dependent cancers, Nat. Rev. Cancer, 12, 381, 10.1038/nrc3263
Katainen, 2015, CTCF/cohesin-binding sites are frequently mutated in cancer, Nat. Genet., 47, 818, 10.1038/ng.3335
Kiemeney, 2008, Sequence variant on 8q24 confers susceptibility to urinary bladder cancer, Nat. Genet., 40, 1307, 10.1038/ng.229
Killela, 2013, TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal, Proc. Natl. Acad. Sci. U S A, 110, 6021, 10.1073/pnas.1303607110
Kim, 2016, Chromatin structure–based prediction of recurrent noncoding mutations in cancer, Nat. Genet., 48, 1321, 10.1038/ng.3682
Kim, 2014, HOXB13 downregulates intracellular zinc and increases NF-κB signaling to promote prostate cancer metastasis, Oncogene, 33, 4558, 10.1038/onc.2013.404
Koivisto, 1997, Androgen receptor gene amplification: a possible molecular mechanism for androgen deprivation therapy failure in prostate cancer, Cancer Res., 57, 314
Korhonen, 2009, MOODS: fast search for position weight matrix matches in DNA sequences, Bioinformatics, 25, 3181, 10.1093/bioinformatics/btp554
Kron, 2014, Enhancer alterations in cancer: a source for a cell identity crisis, Genome Med., 6, 77, 10.1186/s13073-014-0077-3
Kron, 2017, TMPRSS2-ERG fusion co-opts master transcription factors and activates NOTCH signaling in primary prostate cancer, Nat. Genet., 49, 1336, 10.1038/ng.3930
Li, 2004, Genotyping with TaqMAMA, Genomics, 83, 311, 10.1016/j.ygeno.2003.08.005
Lin, 2016, Active medulloblastoma enhancers reveal subgroup-specific cellular origins, Nature, 530, 57, 10.1038/nature16546
Liu, 2006, Contrasting effects of phosphatidylinositol- and phosphatidylcholine-specific phospholipase C on apoptosis in cultured endothelial cells, Endothelium, 13, 205, 10.1080/10623320600760423
Lupien, 2009, Cistromics of hormone-dependent cancer, Endocr. Relat. Cancer, 16, 381, 10.1677/ERC-09-0038
Lupien, 2008, FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription, Cell, 132, 958, 10.1016/j.cell.2008.01.018
Lupien, 2010, Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance, Genes Dev., 24, 2219, 10.1101/gad.1944810
Ma, 2016, SOX9 drives WNT pathway activation in prostate cancer, J. Clin. Invest., 126, 1745, 10.1172/JCI78815
Mack, 2018, Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling, Nature, 553, 101, 10.1038/nature25169
McFarland, 2018, Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration, Nat. Commun., 9, 4610, 10.1038/s41467-018-06916-5
Melnikov, 2012, Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay, Nat. Biotechnol., 30, 271, 10.1038/nbt.2137
Melnikov, 2014, Massively parallel reporter assays in cultured mammalian cells, J. Vis. Exp., 90, e51719
Melton, 2015, Recurrent somatic mutations in regulatory regions of human cancer genomes, Nat. Genet., 47, 710, 10.1038/ng.3332
Mularoni, 2016, OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations, Genome Biol., 17, 128, 10.1186/s13059-016-0994-0
Nakagawa, 2013, Prostate cancer genomics by high-throughput technologies: genome-wide association study and sequencing analysis, Endocr. Relat. Cancer, 20, R171, 10.1530/ERC-13-0113
Nault, 2013, High frequency of telomerase reverse-transcriptase promoter somatic mutations in hepatocellular carcinoma and preneoplastic lesions, Nat. Commun., 4, 2218, 10.1038/ncomms3218
Northcott, 2014, Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma, Nature, 511, 428, 10.1038/nature13379
Pasqualucci, 2003, Mutations of the BCL6 proto-oncogene disrupt its negative autoregulation in diffuse large B-cell lymphoma, Blood, 101, 2914, 10.1182/blood-2002-11-3387
Pfeifer, 1992, Binding of transcription factors creates hot spots for UV photoproducts in vivo, Mol. Cell. Biol., 12, 1798, 10.1128/MCB.12.4.1798
Polak, 2015, Cell-of-origin chromatin organization shapes the mutational landscape of cancer, Nature, 518, 360, 10.1038/nature14221
Pomerantz, 2015, The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis, Nat. Genet., 47, 1346, 10.1038/ng.3419
Poulos, 2016, Functional mutations form at CTCF-cohesin binding sites in melanoma due to uneven nucleotide excision repair across the motif, Cell Rep., 17, 2865, 10.1016/j.celrep.2016.11.055
Prensner, 2011, Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression, Nat. Biotechnol., 29, 742, 10.1038/nbt.1914
Quinlan, 2010, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, 26, 841, 10.1093/bioinformatics/btq033
Robinson, 2015, Integrative clinical genomics of advanced prostate cancer, Cell, 161, 1215, 10.1016/j.cell.2015.05.001
Robinson, 2014, Elevated levels of FOXA1 facilitate androgen receptor chromatin binding resulting in a CRPC-like phenotype, Oncogene, 33, 5666, 10.1038/onc.2013.508
Sabarinathan, 2016, Nucleotide excision repair is impaired by binding of transcription factors to DNA, Nature, 532, 264, 10.1038/nature17661
Sallari, 2017, Convergence of dispersed regulatory mutations predicts driver genes in prostate cancer, BioRxiv
Schones, 2008, Dynamic regulation of nucleosome positioning in the human genome, Cell, 132, 887, 10.1016/j.cell.2008.02.022
Schumacher, 2018, Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci, Nat. Genet., 50, 928, 10.1038/s41588-018-0142-8
Severson, 2018, Characterizing steroid hormone receptor chromatin binding landscapes in male and female breast cancer, Nat. Commun., 9, 482, 10.1038/s41467-018-02856-2
Shin, 2009, CEAS: cis-regulatory element annotation system, Bioinformatics, 25, 2605, 10.1093/bioinformatics/btp479
Stelloo, 2018, Endogenous androgen receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis, Oncogene, 37, 313, 10.1038/onc.2017.330
Taplin, 1995, Mutation of the androgen-receptor gene in metastatic androgen-independent prostate cancer, N. Engl. J. Med., 332, 1393, 10.1056/NEJM199505253322101
Thomsen, 2010, SOX9 elevation in the prostate promotes proliferation and cooperates with PTEN loss to drive tumor formation, Cancer Res., 70, 979, 10.1158/0008-5472.CAN-09-2370
Tomlins, 2005, Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer, Science, 310, 644, 10.1126/science.1117679
Tomlinson, 2007, A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21, Nat. Genet., 39, 984, 10.1038/ng2085
Ulirsch, 2016, Systematic functional dissection of common genetic variation affecting red blood cell traits, Cell, 165, 1530, 10.1016/j.cell.2016.04.048
Umer, 2016, A significant regulatory mutation burden at a high-affinity position of the CTCF motif in gastrointestinal cancers, Hum. Mutat., 37, 904, 10.1002/humu.23014
Valouev, 2011, Determinants of nucleosome organization in primary human cells, Nature, 474, 516, 10.1038/nature10002
Vinagre, 2013, Frequency of TERT promoter mutations in human cancers, Nat. Commun., 4, 2185, 10.1038/ncomms3185
Wang, 2007, SOX9 is expressed in normal prostate basal cells and regulates androgen receptor expression in prostate cancer cells, Cancer Res., 67, 528, 10.1158/0008-5472.CAN-06-1672
Wang, 2008, SOX9 is expressed in human fetal prostate epithelium and enhances prostate cancer invasion, Cancer Res., 68, 1625, 10.1158/0008-5472.CAN-07-5915
Ward, 2012, HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants, Nucleic Acids Res., 40, D930, 10.1093/nar/gkr917
Wasserman, 2010, An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer, Genome Res., 20, 1191, 10.1101/gr.105361.110
Weinhold, 2014, Genome-wide analysis of noncoding regulatory mutations in cancer, Nat. Genet., 46, 1160, 10.1038/ng.3101
Weirauch, 2014, Determination and inference of eukaryotic transcription factor sequence specificity, Cell, 158, 1431, 10.1016/j.cell.2014.08.009
Xu, 2017, Long non-coding RNA PCAT-1 contributes to tumorigenesis by regulating FSCN1 via miR-145-5p in prostate cancer, Biomed. Pharmacother., 95, 1112, 10.1016/j.biopha.2017.09.019
Zabalza, 2015, HOXB13 overexpression is an independent predictor of early PSA recurrence in prostate cancer treated by radical prostatectomy, Oncotarget, 6, 12822, 10.18632/oncotarget.3431
Zhang, 2018, A global transcriptional network connecting noncoding mutations to changes in tumor gene expression, Nat. Genet., 50, 613, 10.1038/s41588-018-0091-2
Zhang, 2012, Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus, Genome Res., 22, 1437, 10.1101/gr.135665.111
Zhang, 2014, Laying a solid foundation for Manhattan – “setting the functional basis for the post-GWAS era, Trends Genet., 30, 140, 10.1016/j.tig.2014.02.006
Zhang, 2008, Model-based analysis of ChIP-seq (MACS), Genome Biol., 9, R137, 10.1186/gb-2008-9-9-r137
Zhou, 2016, Emergence of the noncoding cancer genome: a target of genetic and epigenetic alterations, Cancer Discov., 6, 1215, 10.1158/2159-8290.CD-16-0745