Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients

Cell - Tập 161 Số 4 - Trang 933-945 - 2015
Marc van de Wetering1,2, Hayley E. Francies3, Joshua M. Francis4,5, Gergana Bounova6, Francesco Iorio7, Apollo Pronk8, Winan J. van Houdt8, Joost van Gorp9, Amaro Taylor‐Weiner5, Lennart Kester2, Anne McLaren-Douglas3, Joyce Blokker1,2, Sridevi Jaksani1,2, Sina Bartfeld2, Richard Volckman10, Peter van Sluis10, Vivian Li11, Sara Seepo5, Chandra Sekhar Pedamallu4,5, Kristian Cibulskis5, Scott L. Carter4,5, Aaron McKenna5, Michael S. Lawrence5, Lee Lichtenstein5, Chip Stewart5, Jan Köster10, Rogier Versteeg10, Alexander van Oudenaarden2, Julio Sáez-Rodríguez7, Robert G.J. Vries1,2, Gad Getz4,5, Lodewyk F.A. Wessels6, Michael R. Stratton3, Ultan McDermott3, Matthew Meyerson4,5, Mathew J. Garnett3, Hans Clevers1,2
1Foundation Hubrecht Organoid Technology (HUB), 3584 CT Utrecht, the Netherlands
2Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Cancer Genomics and University Medical Center, 3584 CT Utrecht, the Netherlands
3Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
4Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115 USA
5The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
6Computational Cancer Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
7European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
8Department of Surgery, Diakonessenhuis, 3582 KE Utrecht, the Netherlands
9Department of Pathology, Diakonessenhuis, 3582 KE Utrecht, the Netherlands
10Department of Oncogenomics, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
11Division of Stem Cell Biology and Developmental Genetics, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK

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Tài liệu tham khảo

Barker, 2007, Identification of stem cells in small intestine and colon by marker gene Lgr5, Nature, 449, 1003, 10.1038/nature06196

Barretina, 2012, The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity, Nature, 483, 603, 10.1038/nature11003

Bass, 2011, Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion, Nat. Genet., 43, 964, 10.1038/ng.936

Boland, 2010, Microsatellite instability in colorectal cancer, Gastroenterology, 138, 2073, 10.1053/j.gastro.2009.12.064

Burrell, 2013, The causes and consequences of genetic heterogeneity in cancer evolution, Nature, 501, 338, 10.1038/nature12625

2012, Comprehensive molecular characterization of human colon and rectal cancer, Nature, 487, 330, 10.1038/nature11252

Carmon, 2011, R-spondins function as ligands of the orphan receptors LGR4 and LGR5 to regulate Wnt/beta-catenin signaling, Proc. Natl. Acad. Sci. USA, 108, 11452, 10.1073/pnas.1106083108

Carter, 2012, Absolute quantification of somatic DNA alterations in human cancer, Nat. Biotechnol., 30, 413, 10.1038/nbt.2203

Centenera, 2013, Ex vivo culture of human prostate tissue and drug development, Nat. Rev. Urol., 10, 483, 10.1038/nrurol.2013.126

Chen, 2009, Small molecule-mediated disruption of Wnt-dependent signaling in tissue regeneration and cancer, Nat. Chem. Biol., 5, 100, 10.1038/nchembio.137

Chiang, 2009, High-resolution mapping of copy-number alterations with massively parallel sequencing, Nat. Methods, 6, 99, 10.1038/nmeth.1276

Cibulskis, 2013, Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples, Nat. Biotechnol., 31, 213, 10.1038/nbt.2514

de Lau, 2011, Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling, Nature, 476, 293, 10.1038/nature10337

de Lau, 2014, The R-spondin/Lgr5/Rnf43 module: regulator of Wnt signal strength, Genes Dev., 28, 305, 10.1101/gad.235473.113

De Roock, 2010, Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: a retrospective consortium analysis, Lancet Oncol., 11, 753, 10.1016/S1470-2045(10)70130-3

DePristo, 2011, A framework for variation discovery and genotyping using next-generation DNA sequencing data, Nat. Genet., 43, 491, 10.1038/ng.806

Di Nicolantonio, 2008, Wild-type BRAF is required for response to panitumumab or cetuximab in metastatic colorectal cancer, J. Clin. Oncol., 26, 5705, 10.1200/JCO.2008.18.0786

Eirew, 2015, Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution, Nature, 518, 422, 10.1038/nature13952

Fearon, 2011, Molecular genetics of colorectal cancer, Annu. Rev. Pathol., 6, 479, 10.1146/annurev-pathol-011110-130235

Fearon, 1990, A genetic model for colorectal tumorigenesis, Cell, 61, 759, 10.1016/0092-8674(90)90186-I

Fisher, 2011, A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries, Genome Biol., 12, R1, 10.1186/gb-2011-12-1-r1

Futreal, 2004, A census of human cancer genes, Nat. Rev. Cancer, 4, 177, 10.1038/nrc1299

Garnett, 2012, Systematic identification of genomic markers of drug sensitivity in cancer cells, Nature, 483, 570, 10.1038/nature11005

Garraway, 2013, Lessons from the cancer genome, Cell, 153, 17, 10.1016/j.cell.2013.03.002

Giannakis, 2014, RNF43 is frequently mutated in colorectal and endometrial cancers, Nat. Genet., 46, 1264, 10.1038/ng.3127

Hao, 2012, ZNRF3 promotes Wnt receptor turnover in an R-spondin-sensitive manner, Nature, 485, 195, 10.1038/nature11019

Haramis, 2004, De novo crypt formation and juvenile polyposis on BMP inhibition in mouse intestine, Science, 303, 1684, 10.1126/science.1093587

Imielinski, 2012, Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing, Cell, 150, 1107, 10.1016/j.cell.2012.08.029

Ivanov, 2007, Identifying candidate colon cancer tumor suppressor genes using inhibition of nonsense-mediated mRNA decay in colon cancer cells, Oncogene, 26, 2873, 10.1038/sj.onc.1210098

Jiao, 2014, Whole-exome sequencing of pancreatic neoplasms with acinar differentiation, J. Pathol., 232, 428, 10.1002/path.4310

Jin, 2010, Patient-derived human tumour tissue xenografts in immunodeficient mice: a systematic review, Clin. Transl. Oncol., 12, 473, 10.1007/s12094-010-0540-6

Kadowaki, 1996, The segment polarity gene porcupine encodes a putative multitransmembrane protein involved in Wingless processing, Genes Dev., 10, 3116, 10.1101/gad.10.24.3116

Kim, 2005, Mitogenic influence of human R-spondin1 on the intestinal epithelium, Science, 309, 1256, 10.1126/science.1112521

Koo, 2012, Tumour suppressor RNF43 is a stem-cell E3 ligase that induces endocytosis of Wnt receptors, Nature, 488, 665, 10.1038/nature11308

Korinek, 1998, Depletion of epithelial stem-cell compartments in the small intestine of mice lacking Tcf-4, Nat. Genet., 19, 379, 10.1038/1270

Kuhnert, 2004, Essential requirement for Wnt signaling in proliferation of adult small intestine and colon revealed by adenoviral expression of Dickkopf-1, Proc. Natl. Acad. Sci. USA, 101, 266, 10.1073/pnas.2536800100

Landau, 2013, Evolution and impact of subclonal mutations in chronic lymphocytic leukemia, Cell, 152, 714, 10.1016/j.cell.2013.01.019

Lawrence, 2014, Discovery and saturation analysis of cancer genes across 21 tumour types, Nature, 505, 495, 10.1038/nature12912

Lengauer, 1997, Genetic instability in colorectal cancers, Nature, 386, 623, 10.1038/386623a0

Liu, 2012, ROCK inhibitor and feeder cells induce the conditional reprogramming of epithelial cells, Am. J. Pathol., 180, 599, 10.1016/j.ajpath.2011.10.036

Ojesina, 2014, Landscape of genomic alterations in cervical carcinomas, Nature, 506, 371, 10.1038/nature12881

Pinto, 2003, Canonical Wnt signals are essential for homeostasis of the intestinal epithelium, Genes Dev., 17, 1709, 10.1101/gad.267103

Ryland, 2013, RNF43 is a tumour suppressor gene mutated in mucinous tumours of the ovary, J. Pathol., 229, 469, 10.1002/path.4134

Sadanandam, 2013, A colorectal cancer classification system that associates cellular phenotype and responses to therapy, Nat. Med., 19, 619, 10.1038/nm.3175

Sato, 2009, Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche, Nature, 459, 262, 10.1038/nature07935

Sato, 2011, Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett’s epithelium, Gastroenterology, 141, 1762, 10.1053/j.gastro.2011.07.050

Seshagiri, 2012, Recurrent R-spondin fusions in colon cancer, Nature, 488, 660, 10.1038/nature11282

Takahashi, 2002, Isolation of a novel human gene, APCDD1, as a direct target of the beta-Catenin/T-cell factor 4 complex with probable involvement in colorectal carcinogenesis, Cancer Res., 62, 5651

Tentler, 2012, Patient-derived tumour xenografts as models for oncology drug development, Nat. Rev. Clin. Oncol., 9, 338, 10.1038/nrclinonc.2012.61

Vassilev, 2004, In vivo activation of the p53 pathway by small-molecule antagonists of MDM2, Science, 303, 844, 10.1126/science.1092472

Vecchione, 2014, Optimization of anti-EGFR treatment of advanced colorectal cancer, Curr. Colorectal Cancer Rep., 10, 263, 10.1007/s11888-014-0232-7

Vogelstein, 2013, Cancer genome landscapes, Science, 339, 1546, 10.1126/science.1235122

Wang, 2014, Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer, Nat. Genet., 46, 573, 10.1038/ng.2983

Wong, 2012, Lrig1 controls intestinal stem-cell homeostasis by negative regulation of ErbB signalling, Nat. Cell Biol., 14, 401, 10.1038/ncb2464

Hashimshony, 2012, CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification, Cell Rep., 2, 666, 10.1016/j.celrep.2012.08.003

Johnson, 2007, Adjusting batch effects in microarray expression data using empirical Bayes methods, Biostatistics, 8, 118, 10.1093/biostatistics/kxj037

Li, 2010, Fast and accurate long-read alignment with Burrows-Wheeler transform, Bioinformatics, 26, 589, 10.1093/bioinformatics/btp698

Mermel, 2011, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biol., 12, R41, 10.1186/gb-2011-12-4-r41

Meyer, 2013, The UCSC Genome Browser database: extensions and updates 2013, Nucleic Acids Res., 41, D64, 10.1093/nar/gks1048

Olshen, 2004, Circular binary segmentation for the analysis of array-based DNA copy number data, Biostatistics, 5, 557, 10.1093/biostatistics/kxh008

Robinson, 2011, Integrative genomics viewer, Nat. Biotechnol., 29, 24, 10.1038/nbt.1754