Subtypes of primary colorectal tumors correlate with response to targeted treatment in colorectal cell lines

BMC Medical Genomics

Lodewyk FA Wessels²  Tim French⁴  George Orphanides³  Denis Alferez Castro³  Kerry Heathcote³  Sara Davenport³  Sarah Runswick⁴  Susie Weston⁴  Alison Pritchard³  Gael McWalter⁴  Christine M Chresta³  Garry Beran³  Andreas Schlicker¹ 

[1] Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands;Department of Molecular Carcinogenesis, Plesmanlaan 121, Amsterdam, 1066CX, The Netherlands;Oncology iMed, AstraZeneca R&D, Alderley Park, Macclesfield, United Kingdom;Personalised Healthcare and Biomarkers Group, AstraZeneca R&D, Alderley Park, Macclesfield, United Kingdom

关键词: Targeted therapy;    Cell lines;    Tumor subtyping;    Colorectal cancer;   

Others  :  1121214
DOI  :  10.1186/1755-8794-5-66

 received in 2012-09-19, accepted in 2012-12-17,  发布年份 2012

【 摘 要 】

Background

Colorectal cancer (CRC) is a heterogeneous and biologically poorly understood disease. To tailor CRC treatment, it is essential to first model this heterogeneity by defining subtypes of patients with homogeneous biological and clinical characteristics and second match these subtypes to cell lines for which extensive pharmacological data is available, thus linking targeted therapies to patients most likely to respond to treatment.

Methods

We applied a new unsupervised, iterative approach to stratify CRC tumor samples into subtypes based on genome-wide mRNA expression data. By applying this stratification to several CRC cell line panels and integrating pharmacological response data, we generated hypotheses regarding the targeted treatment of different subtypes.

Results

In agreement with earlier studies, the two dominant CRC subtypes are highly correlated with a gene expression signature of epithelial-mesenchymal-transition (EMT). Notably, further dividing these two subtypes using iNMF (iterative Non-negative Matrix Factorization) revealed five subtypes that exhibit activation of specific signaling pathways, and show significant differences in clinical and molecular characteristics. Importantly, we were able to validate the stratification on independent, published datasets comprising over 1600 samples. Application of this stratification to four CRC cell line panels comprising 74 different cell lines, showed that the tumor subtypes are well represented in available CRC cell line panels. Pharmacological response data for targeted inhibitors of SRC, WNT, GSK3b, aurora kinase, PI3 kinase, and mTOR, showed significant differences in sensitivity across cell lines assigned to different subtypes. Importantly, some of these differences in sensitivity were in concordance with high expression of the targets or activation of the corresponding pathways in primary tumor samples of the same subtype.

Conclusions

The stratification presented here is robust, captures important features of CRC, and offers valuable insight into functional differences between CRC subtypes. By matching the identified subtypes to cell line panels that have been pharmacologically characterized, it opens up new possibilities for the development and application of targeted therapies for defined CRC patient sub-populations.

【 授权许可】

   
2012 Schlicker et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D: Global cancer statistics. CA Cancer J Clin 2011, 61:69-90.
• [2]Tomeo CA, Colditz GA, Willett WC, Giovannucci E, Platz E, Rockhill B, Dart H, Hunter DJ: Harvard report on cancer prevention. Volume 3: prevention of colon cancer in the united states. Cancer Causes Control 1999, 10:167-180.
• [3]Fearon ER: Molecular genetics of colorectal cancer. Annu Rev Pathol 2011, 6:479-507.
• [4]Saif MW, Chu E: Biology of colorectal cancer. Cancer J 2010, 16:196-201.
• [5]Issa J-P: Colon cancer: it’s CIN or CIMP. Clin Cancer Res 2008, 14:5939-5940.
• [6]Sanchez JA, Krumroy L, Plummer S, Aung P, Merkulova A, Skacel M, DeJulius KL, Manilich E, Church JM, Casey G, Kalady MF: Genetic and epigenetic classifications define clinical phenotypes and determine patient outcomes in colorectal cancer. Br J Surg 2009, 96:1196-1204.
• [7]Markowitz SD, Bertagnolli MM: Molecular origins of cancer: molecular basis of colorectal cancer. N Engl J Med 2009, 361:2449-2460.
• [8]Iacopetta B, Grieu F, Amanuel B: Microsatellite instability in colorectal cancer. Asia Pac J Clin Oncol 2010, 6:260-269.
• [9]van Engeland M, Derks S, Smits KM, Meijer GA, Herman JG: Colorectal cancer epigenetics: complex simplicity. J Clin Oncol 2011, 29:1382-1391.
• [10]Chibaudel B, Tournigand C, André T, Larsen AK, de Gramont A: Targeted therapies as adjuvant treatment for early-stage colorectal cancer: first impressions and clinical questions. Clin Colorectal Cancer 2010, 9:269-273.
• [11]Cutsem EV, Köhne C-H, Láng I, Folprecht G, Nowacki MP, Cascinu S, Shchepotin I, Maurel J, Cunningham D, Tejpar S, Schlichting M, Zubel A, Celik I, Rougier P, Ciardiello F: Cetuximab plus irinotecan, fluorouracil, and leucovorin as first-line treatment for metastatic colorectal cancer: updated analysis of overall survival according to tumor KRAS and BRAF mutation status. J Clin Oncol 2011, 29:2011-2019.
• [12]Molinari F, Felicioni L, Buscarino M, Dosso SD, Buttitta F, Malatesta S, Movilia A, Luoni M, Boldorini R, Alabiso O, Girlando S, Soini B, Spitale A, Nicolantonio FD, Saletti P, Crippa S, Mazzucchelli L, Marchetti A, Bardelli A, Frattini M: Increased detection sensitivity for KRAS mutations enhances the prediction of anti-EGFR monoclonal antibody resistance in metastatic colorectal cancer. Clin Cancer Res 2011, 17:4901-4914.
• [13]Sullivan KM, Kozuch PS: Impact of KRAS mutations on management of colorectal carcinoma. Patholog Res Int 2011, 2011:219309.
• [14]Prahallad A, Sun C, Huang S, Di Nicolantonio F, Salazar R, Zecchin D, Beijersbergen RL, Bardelli A, Bernards R: Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR. Nature 2012, 483:100-103.
• [15]Dry JR, Pavey S, Pratilas CA, Harbron C, Runswick S, Hodgson D, Chresta C, McCormack R, Byrne N, Cockerill M, Graham A, Beran G, Cassidy A, Haggerty C, Brown H, Ellison G, Dering J, Taylor BS, Stark M, Bonazzi V, Ravishankar S, Packer L, Xing F, Solit DB, Finn RS, Rosen N, Hayward NK, French T, Smith PD: Transcriptional pathway signatures predict MEK addiction and response to selumetinib (AZD6244). Cancer Res 2010, 70:2264-2273.
• [16]Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J, Liu Q, Iorio F, Surdez D, Chen L, Milano RJ, Bignell GR, Tam AT, Davies H, Stevenson JA, Barthorpe S, Lutz SR, Kogera F, Lawrence K, McLaren-Douglas A, Mitropoulos X, Mironenko T, Thi H, Richardson L, Zhou W, Jewitt F, Zhang T, O’Brien P, Boisvert JL, Price S, Hur W, Yang W, Deng X, Butler A, Choi HG, Chang JW, Baselga J, Stamenkovic I, Engelman JA, Sharma SV, Delattre O, Saez-Rodriguez J, Gray NS, Settleman J, Futreal PA, Haber DA, Stratton MR, Ramaswamy S, McDermott U, Benes CH: Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 2012, 483:570-575.
• [17]Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P Jr, De Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA: The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012, 483:603-607.
• [18]Arango D, Laiho P, Kokko A, Alhopuro P, Sammalkorpi H, Salovaara R, Nicorici D, Hautaniemi S, Alazzouzi H, Mecklin J-P, Järvinen H, Hemminki A, Astola J, Schwartz S Jr, Aaltonen LA: Gene-expression profiling predicts recurrence in Dukes’ C colorectal cancer. Gastroenterology 2005, 129:874-884.
• [19]Barrier A, Boelle P-Y, Roser F, Gregg J, Tse C, Brault D, Lacaine F, Houry S, Huguier M, Franc B, Flahault A, Lemoine A, Dudoit S: Stage II colon cancer prognosis prediction by tumor gene expression profiling. J Clin Oncol 2006, 24:4685-4691.
• [20]Eschrich S, Yang I, Bloom G, Kwong KY, Boulware D, Cantor A, Coppola D, Kruhøffer M, Aaltonen L, Orntoft TF, Quackenbush J, Yeatman TJ: Molecular staging for survival prediction of colorectal cancer patients. J Clin Oncol 2005, 23:3526-3535.
• [21]Garman KS, Acharya CR, Edelman E, Grade M, Gaedcke J, Sud S, Barry W, Diehl AM, Provenzale D, Ginsburg GS, Ghadimi BM, Ried T, Nevins JR, Mukherjee S, Hsu D, Potti A: A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities. Proc Natl Acad Sci USA 2008, 105:19432-19437.
• [22]Lin Y-H, Friederichs J, Black MA, Mages J, Rosenberg R, Guilford PJ, Phillips V, Thompson-Fawcett M, Kasabov N, Toro T, Merrie AE, van Rij A, Yoon H-S, McCall JL, Siewert JR, Holzmann B, Reeve AE: Multiple gene expression classifiers from different array platforms predict poor prognosis of colorectal cancer. Clin Cancer Res 2007, 13:498-507.
• [23]O’Connell MJ, Lavery I, Yothers G, Paik S, Clark-Langone KM, Lopatin M, Watson D, Baehner FL, Shak S, Baker J, Cowens JW, Wolmark N: Relationship between tumor gene expression and recurrence in four independent studies of patients with stage II/III colon cancer treated with surgery alone or surgery plus adjuvant fluorouracil plus leucovorin. J Clin Oncol 2010, 28:3937-3944.
• [24]Salazar R, Roepman P, Capella G, Moreno V, Simon I, Dreezen C, Lopez-Doriga A, Santos C, Marijnen C, Westerga J, Bruin S, Kerr D, Kuppen P, van de Velde C, Morreau H, Velthuysen LV, Glas AM, Veer LJV, Tollenaar R: Gene expression signature to improve prognosis prediction of stage II and III colorectal cancer. J Clin Oncol 2011, 29:17-24.
• [25]Wang Y, Jatkoe T, Zhang Y, Mutch MG, Talantov D, Jiang J, McLeod HL, Atkins D: Gene expression profiles and molecular markers to predict recurrence of Dukes’ B colon cancer. J Clin Oncol 2004, 22:1564-1571.
• [26]Jorissen RN, Gibbs P, Christie M, Prakash S, Lipton L, Desai J, Kerr D, Aaltonen LA, Arango D, Kruhøffer M, Orntoft TF, Andersen CL, Gruidl M, Kamath VP, Eschrich S, Yeatman TJ, Sieber OM: Metastasis-associated gene expression changes predict poor outcomes in patients with dukes stage B and C colorectal cancer. Clin Cancer Res 2009, 15:7642-7651.
• [27]Birkenkamp-Demtroder K, Christensen LL, Olesen SH, Frederiksen CM, Laiho P, Aaltonen LA, Laurberg S, Sørensen FB, Hagemann R, ØRntoft TF: Gene expression in colorectal cancer. Cancer Res 2002, 62:4352-4363.
• [28]Frederiksen CM, Knudsen S, Laurberg S, Ørntoft TF: Classification of Dukes’ B and C colorectal cancers using expression arrays. J Cancer Res Clin Oncol 2003, 129:263-271.
• [29]Bertucci F, Salas S, Eysteries S, Nasser V, Finetti P, Ginestier C, Charafe-Jauffret E, Loriod B, Bachelart L, Montfort J, Victorero G, Viret F, Ollendorff V, Fert V, Giovaninni M, Delpero J-R, Nguyen C, Viens P, Monges G, Birnbaum D, Houlgatte R: Gene expression profiling of colon cancer by DNA microarrays and correlation with histoclinical parameters. Oncogene 2004, 23:1377-1391.
• [30]Kleivi K, Lind GE, Diep CB, Meling GI, Brandal LT, Nesland JM, Myklebost O, Rognum TO, Giercksky K-E, Skotheim RI, Lothe RA: Gene expression profiles of primary colorectal carcinomas, liver metastases, and carcinomatoses. Mol Cancer 2007, 6:2. BioMed Central Full Text
• [31]Kwong KY, Bloom GC, Yang I, Boulware D, Coppola D, Haseman J, Chen E, McGrath A, Makusky AJ, Taylor J, Steiner S, Zhou J, Yeatman TJ, Quackenbush J: Synchronous global assessment of gene and protein expression in colorectal cancer progression. Genomics 2005, 86:142-158.
• [32]Loboda A, Nebozhyn MV, Watters JW, Buser CA, Shaw PM, Huang PS, Veer LV, Tollenaar RAEM, Jackson DB, Agrawal D, Dai H, Yeatman TJ: EMT is the dominant program in human colon cancer. BMC Med Genomics 2011, 4:9.
• [33]Oh SC, Park Y-Y, Park ES, Lim JY, Kim SM, Kim S-B, Kim J, Kim SC, Chu I-S, Smith JJ, Beauchamp RD, Yeatman TJ, Kopetz S, Lee J-S: Prognostic gene expression signature associated with two molecularly distinct subtypes of colorectal cancer. Gut 2012, 61:1291-1298.
• [34]Perez-Villamil B, Romera-Lopez A, Hernandez-Prieto S, Lopez-Campos G, Calles A, Lopez-Asenjo J-A, Sanz-Ortega J, Fernandez-Perez C, Sastre J, Alfonso R, Caldes T, Martin-Sanchez F, Diaz-Rubio E: Colon cancer molecular subtypes identified by expression profiling and associated to stroma, mucinous type and different clinical behavior. BMC Cancer 2012, 12:260. BioMed Central Full Text
• [35]Wagner KW, Punnoose EA, Januario T, Lawrence DA, Pitti RM, Lancaster K, Lee D, von Goetz M, Yee SF, Totpal K, Huw L, Katta V, Cavet G, Hymowitz SG, Amler L, Ashkenazi A: Death-receptor O-glycosylation controls tumor-cell sensitivity to the proapoptotic ligand Apo2L/TRAIL. Nat Med 2007, 13:1070-1077.
• [36]Greshock J, Bachman KE, Degenhardt YY, Jing J, Wen YH, Eastman S, McNeil E, Moy C, Wegrzyn R, Auger K, Hardwicke MA, Wooster R: Molecular target class is predictive of in vitro response profile. Cancer Res 2010, 70:3677-3686.
• [37]Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80. BioMed Central Full Text
• [38]Gautier L, Cope L, Bolstad BM, Irizarry RA: affy–analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20:307-315.
• [39]Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012, 40:D109-D114.
• [40]Warren P, Taylor D, Martini PGV, Jackson J, Bienkowska J: PANP - a New Method of Gene Detection on Oligonucleotide Expression Arrays. Proc. 7th IEEE Int. Conf. Bioinformatics and Bioengineering BIBE 2007 2007, 108-115.
• [41]Smith JJ, Deane NG, Wu F, Merchant NB, Zhang B, Jiang A, Lu P, Johnson JC, Schmidt C, Bailey CE, Eschrich S, Kis C, Levy S, Washington MK, Heslin MJ, Coffey RJ, Yeatman TJ, Shyr Y, Beauchamp RD: Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer. Gastroenterology 2010, 138:958-968.
• [42]de Sousa E, Melo F, Colak S, Buikhuisen J, Koster J, Cameron K, de Jong JH, Tuynman JB, Prasetyanti PR, Fessler E, van den Bergh SP, Rodermond H, Dekker E, van der Loos CM, Pals ST, van de Vijver MJ, Versteeg R, Richel DJ, Vermeulen L, Medema JP: Methylation of cancer-stem-cell-associated Wnt target genes predicts poor prognosis in colorectal cancer patients. Cell Stem Cell 2011, 9:476-485.
• [43]Gaujoux R, Seoighe C: A flexible R package for nonnegative matrix factorization. BMC Bioinforma 2010, 11:367. BioMed Central Full Text
• [44]Taube JH, Herschkowitz JI, Komurov K, Zhou AY, Gupta S, Yang J, Hartwell K, Onder TT, Gupta PB, Evans KW, Hollier BG, Ram PT, Lander ES, Rosen JM, Weinberg RA, Mani SA: Core epithelial-to-mesenchymal transition interactome gene-expression signature is associated with claudin-low and metaplastic breast cancer subtypes. Proc Natl Acad Sci USA 2010, 107:15449-15454.
• [45]Parikh JR, Klinger B, Xia Y, Marto JA, Blüthgen N: Discovering causal signaling pathways through gene-expression patterns. Nucleic Acids Res 2010, 38(Suppl):W109-W117.
• [46]Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005, 102:15545-15550.
• [47]Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH: PID: the pathway interaction database. Nucleic Acids Res 2009, 37:D674-D679.
• [48]Ramírez F, Lawyer G, Albrecht M: Novel search method for the discovery of functional relationships. Bioinformatics 2012, 28:269-276.
• [49]Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 2000, 25:25-29.
• [50]The Cancer Genome Atlas Network: Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012, 487:330-337.
• [51]Seshagiri S, Stawiski EW, Durinck S, Modrusan Z, Storm EE, Conboy CB, Chaudhuri S, Guan Y, Janakiraman V, Jaiswal BS, Guillory J, Ha C, Dijkgraaf GJP, Stinson J, Gnad F, Huntley MA, Degenhardt JD, Haverty PM, Bourgon R, Wang W, Koeppen H, Gentleman R, Starr TK, Zhang Z, Largaespada DA, Wu TD, de Sauvage FJ: Recurrent R-spondin fusions in colon cancer. Nature 2012, 488:660-664.
• [52]March HN, Rust AG, Wright NA, ten Hoeve J, de Ridder J, Eldridge M, van der Weyden L, Berns A, Gadiot J, Uren A, Kemp R, Arends MJ, Wessels LFA, Winton DJ, Adams DJ: Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis. Nat Genet 2011, 43:1202-1209.
• [53]Starr TK, Allaei R, Silverstein KAT, Staggs RA, Sarver AL, Bergemann TL, Gupta M, O’Sullivan MG, Matise I, Dupuy AJ, Collier LS, Powers S, Oberg AL, Asmann YW, Thibodeau SN, Tessarollo L, Copeland NG, Jenkins NA, Cormier RT, Largaespada DA: A transposon-based genetic screen in mice identifies genes altered in colorectal cancer. Science 2009, 323:1747-1750.
• [54]Santilli G, Aronow BJ, Sala A: Essential requirement of apolipoprotein J (clusterin) signaling for IkappaB expression and regulation of NF-kappaB activity. J Biol Chem 2003, 278:38214-38219.
• [55]Zhang H, Kim JK, Edwards CA, Xu Z, Taichman R, Wang C-Y: Clusterin inhibits apoptosis by interacting with activated Bax. Nat Cell Biol 2005, 7:909-915.
• [56]Wu K, Yang Y, Wang C, Davoli MA, D’Amico M, Li A, Cveklova K, Kozmik Z, Lisanti MP, Russell RG, Cvekl A, Pestell RG: DACH1 inhibits transforming growth factor-beta signaling through binding Smad4. J Biol Chem 2003, 278:51673-51684.
• [57]Smyrk TC, Watson P, Kaul K, Lynch HT: Tumor-infiltrating lymphocytes are a marker for microsatellite instability in colorectal carcinoma. Cancer 2001, 91:2417-2422.
• [58]Gao R-N, Neutel CI, Wai E: Gender differences in colorectal cancer incidence, mortality, hospitalizations and surgical procedures in Canada. J Public Health 2008, 30:194-201.
• [59]Bufill JA: Colorectal cancer: evidence for distinct genetic categories based on proximal or distal tumor location. Ann Intern Med 1990, 113:779-788.
• [60]Auman JT, McLeod HL: Colorectal cancer cell lines lack the molecular heterogeneity of clinical colorectal tumors. Clin Colorectal Cancer 2010, 9:40-47.