Simultaneous Integration of Multi-omics Data Improves the Identification of Cancer Driver Modules

Cell Systems - Tập 8 - Trang 456-466.e5 - 2019
Dana Silverbush1,2,3, Simona Cristea4,5,6, Gali Yanovich-Arad7, Tamar Geiger7, Niko Beerenwinkel8,9, Roded Sharan3
1Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
2Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
3Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel
4Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
5Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
6Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
7Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
8Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
9SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland

Tài liệu tham khảo

An, 2016, Ncg 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings, Nucleic Acids Res., 44, D992, 10.1093/nar/gkv1123 Babur, 2015, Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations, Genome Biol., 16, 45, 10.1186/s13059-015-0612-6 Cancer Genome Atlas Network, 2012, Comprehensive molecular portraits of human breast tumours, Nature, 490, 61, 10.1038/nature11412 Cancer Genome Atlas Research Network, 2008, Comprehensive genomic characterization defines human glioblastoma genes and core pathways, Nature, 455, 1061, 10.1038/nature07385 Cancer Genome Atlas Research Network, 2011, Integrated genomic analyses of ovarian carcinoma, Nature, 474, 609, 10.1038/nature10166 Cerami, 2012, The cbio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data, Cancer Discov., 2, 401, 10.1158/2159-8290.CD-12-0095 Chen, 2005, Arf-bp1/mule is a critical mediator of the arf tumor suppressor, Cell, 121, 1071, 10.1016/j.cell.2005.03.037 Cheng, 2014, Xpo1 (crm1) inhibition represses stat3 activation to drive a survivin-dependent oncogenic switch in triple-negative breast cancer, Mol. Cancer Ther., 13, 675, 10.1158/1535-7163.MCT-13-0416 Ciriello, 2012, Mutual exclusivity analysis identifies oncogenic network modules, Genome Res., 22, 398, 10.1101/gr.125567.111 Constantinescu, 2016, Timex: a waiting time model for mutually exclusive cancer alterations, Bioinformatics, 32, 968, 10.1093/bioinformatics/btv400 Cristea, 2017, Pathtimex: joint inference of mutually exclusive cancer pathways and their progression dynamics, J. Comput. Biol., 24, 603, 10.1089/cmb.2016.0171 Curtis, 2012, The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups, Nature, 486, 346, 10.1038/nature10983 Davoli, 2013, Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome, Cell, 155, 948, 10.1016/j.cell.2013.10.011 Forbes, 2010, COSMIC (the catalogue of somatic mutations in cancer): a resource to investigate acquired mutations in human cancer, Nucleic Acids Res., 38, D652, 10.1093/nar/gkp995 Fox, 1991, Recombinant nidogen consists of three globular domains and mediates binding of laminin to collagen type iv, EMBO J., 10, 3137, 10.1002/j.1460-2075.1991.tb04875.x Freedman, 1998, Nuclear export is required for degradation of endogenous p53 by mdm2 and human papillomavirus e6, Mol. Cell. Biol., 18, 7288, 10.1128/MCB.18.12.7288 Geiger, 2010, Super-SILAC mix for quantitative proteomics of human tumor tissue, Nat. Methods, 7, 383, 10.1038/nmeth.1446 Gjerdrum, 2010, Axl is an essential epithelial-to-mesenchymal transition-induced regulator of breast cancer metastasis and patient survival, Proc. Natl. Acad. Sci. USA, 107, 1124, 10.1073/pnas.0909333107 Glaab, 2012, EnrichNet: network-based gene set enrichment analysis, Bioinformatics, 28, i451, 10.1093/bioinformatics/bts389 Han, 2015, Trrust: a reference database of human transcriptional regulatory interactions, Sci. Rep., 5, 11432, 10.1038/srep11432 Hanahan, 2000, The hallmarks of cancer, Cell, 100, 57, 10.1016/S0092-8674(00)81683-9 Hofree, 2016, Challenges in identifying cancer genes by analysis of exome sequencing data, Nat. Commun., 7, 12096, 10.1038/ncomms12096 Hollestelle, 2010, Distinct gene mutation profiles among luminal-type and basal-type breast cancer cell lines, Breast Cancer Res. Treat., 121, 53, 10.1007/s10549-009-0460-8 Huret, 2004, An atlas on genes and chromosomes in oncology and haematology, Cell. Mol. Biol., 50, 805 Jerby-Arnon, 2014, Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality, Cell, 158, 1199, 10.1016/j.cell.2014.07.027 Karaayvaz, 2018, Unravelling subclonal heterogeneity and aggressive disease states in tnbc through single-cell rna-seq, Nat. Commun., 9, 3588, 10.1038/s41467-018-06052-0 Karr, 2012, A whole-cell computational model predicts phenotype from genotype, Cell, 150, 389, 10.1016/j.cell.2012.05.044 Kim, 2015, Memcover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types, Bioinformatics, 31, i284, 10.1093/bioinformatics/btv247 Konecny, 2016, Parp inhibitors for BRCA1/2-mutated and sporadic ovarian cancer: current practice and future directions, Br. J. Cancer, 115, 1157, 10.1038/bjc.2016.311 Lee, 2006, Identification of the basement membrane protein nidogen as a candidate ligand for tumor endothelial marker 7 in vitro and in vivo, FEBS Lett., 580, 2253, 10.1016/j.febslet.2006.03.033 Leiserson, 2013, Simultaneous identification of multiple driver pathways in cancer, PLoS Comput. Biol., 9, e1003054, 10.1371/journal.pcbi.1003054 Leiserson, 2015, Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes, Nat. Genet., 47, 106, 10.1038/ng.3168 McCauley, 2012, Preclinical evaluation of selective inhibitors of nuclear export (sine) in basal-like breast cancer (blbc), J. Clin. Oncol., 30, 1055, 10.1200/jco.2012.30.15_suppl.1055 Milanezi, 2008, Egfr/her2 in breast cancer: a biological approach for molecular diagnosis and therapy, Expert Rev. Mol. Diagn., 8, 417, 10.1586/14737159.8.4.417 Ogata, 1999, KEGG: kyoto encyclopedia of genes and genomes, Nucleic Acids Res., 27, 29, 10.1093/nar/27.1.29 Ogiwara, 2012, CBP and p300 histone acetyltransferases contribute to homologous recombination by transcriptionally activating the BRCA1 and RAD51 genes, PLoS One, 7, e52810, 10.1371/journal.pone.0052810 Pao, 2000, CBP/p300 interact with and function as transcriptional coactivators of BRCA1, Proc. Natl. Acad. Sci. USA, 97, 1020, 10.1073/pnas.97.3.1020 Parker, 2009, Supervised risk predictor of breast cancer based on intrinsic subtypes, J. Clin. Oncol., 27, 1160, 10.1200/JCO.2008.18.1370 Paull, 2013, Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE), Bioinformatics, 29, 2757, 10.1093/bioinformatics/btt471 Perou, 2000, Molecular portraits of human breast tumours, Nature, 406, 747, 10.1038/35021093 Pletscher-Frankild, 2015, DISEASES: text mining and data integration of disease-gene associations, Methods, 74, 83, 10.1016/j.ymeth.2014.11.020 Pozniak, 2016, System-wide clinical proteomics of breast cancer reveals global remodeling of tissue homeostasis, Cell Syst., 2, 172, 10.1016/j.cels.2016.02.001 Saal, 2005, PIK3CA mutations correlate with hormone receptors, node metastasis, and ERBB2, and are mutually exclusive with PTEN loss in human breast carcinoma, Cancer Res., 65, 2554, 10.1158/0008-5472-CAN-04-3913 Schaefer, 2012, HIPPIE: integrating protein interaction networks with experiment based quality scores, PLoS One, 7, e31826, 10.1371/journal.pone.0031826 Scholler, 2007, Ca125 in ovarian cancer, Biomark. Med., 1, 513, 10.2217/17520363.1.4.513 Song, 2012, The functions and regulation of the PTEN tumour suppressor, Nat. Rev. Mol. Cell Biol., 13, 283, 10.1038/nrm3330 Sørlie, 2001, Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications, Proc. Natl. Acad. Sci. USA, 98, 10869, 10.1073/pnas.191367098 Subramanian, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl. Acad. Sci. USA, 102, 15545, 10.1073/pnas.0506580102 Turner, 2006, Basal-like breast cancer and the BRCA1 phenotype, Oncogene, 25, 5846, 10.1038/sj.onc.1209876 Turner, 2007, BRCA1 dysfunction in sporadic basal-like breast cancer, Oncogene, 26, 2126, 10.1038/sj.onc.1210014 Tyanova, 2016, Proteomic maps of breast cancer subtypes, Nat. Commun., 7, 10259, 10.1038/ncomms10259 Ulitsky, 2010, Expander: from expression microarrays to networks and functions, Nat. Protoc., 5, 303, 10.1038/nprot.2009.230 2015, UniProt: a hub for protein information, Nucleic Acids Res., 43, D204, 10.1093/nar/gku989 Vandin, 2012, De novo discovery of mutated driver pathways in cancer, Genome Res., 22, 375, 10.1101/gr.120477.111 Vaughan, 2015, Huwe1 ubiquitylates and degrades the rac activator tiam1 promoting cell-cell adhesion disassembly, migration, and invasion, Cell Rep., 10, 88, 10.1016/j.celrep.2014.12.012 Vogelstein, 2013, Cancer genome landscapes, Science, 339, 1546, 10.1126/science.1235122 Wight, 2002, Versican: a versatile extracellular matrix proteoglycan in cell biology, Curr. Opin. Cell Biol., 14, 617, 10.1016/S0955-0674(02)00375-7 Wu, 2015, Comet: a statistical approach to identify combinations of mutually exclusive alterations in cancer, Cancer Res., 75, 1936, 10.1158/1538-7445.AM2015-1936 Zhang, 2008, Axl is a potential target for therapeutic intervention in breast cancer progression, Cancer Res., 68, 1905, 10.1158/0008-5472.CAN-07-2661