Defining new criteria for selection of cell-based intestinal models using publicly available databases

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Christensen, Jon ^a   El Gebali, Sara ^b   Natoli, Manuela ^c   Sengstag, Thierry ^d   Delorenzi, Mauro ^e,f   Bentz, Susanne ^b   Bouzourene, Hanifa ^g   Rumbo, Martin ^h   Felsani, Armando ^c   Siissalo, Sanna ⁱ   Hirvonen, Jouni ⁱ   Vila, Maya R ^j   Saletti, Piercarlo ^k   Aguet, Michel ^f   Anderle, Pascale ^b,e,f  

^a UNIVERSITY OF FREIBURG   (Germany)

^b UNIVERSITY OF BERN   (Switzerland)

^c CNR   (Italy)

^d RIKEN YOKOHAMA INSTITUTE   (Japan)

^e SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^f EPFL   (Switzerland)

^g LAUSANNE UNIVERSITY HOSPITAL   (Switzerland)

^h FACULTAD DE CIENCIAS EXACTAS   (Argentina)

ⁱ UNIVERSITY OF HELSINKI   (Finland)

^j LEITAT TECHNOLOGICAL CENTER   (Spain)

^k REGIONAL HOSPITAL OF LUGANO   (Switzerland)

more..

Author keywords

Cell lines; Chemosensitivity; Colon cancer; Epithelial mesenchymal transition; Genomic profiling; Intestine; Malignant traits

Indexed keywords

CARRIER PROTEIN; ANTINEOPLASTIC AGENT;

ARTICLE; BIOLOGICAL MODEL; CANCER PATIENT; CANCER RECURRENCE; CANCER RESISTANCE; CANCER SURVIVAL; CARCINOMA CELL; CELL ACTIVITY; CELL ASSAY; CELL DIFFERENTIATION; CELL LINE; CELL MIGRATION; CELL PROLIFERATION; CELL STRAIN; CELL STRAIN CACO 2; CELL STRAIN HT29; CELL STRAIN SW480; CELL STRAIN T84; CHEMOSENSITIVITY; CLASSIFICATION; COLON CARCINOMA; CONTROLLED STUDY; DATA BASE; DRUG ABSORPTION; DRUG RESEARCH; DRUG RESPONSE; EPITHELIAL MESENCHYMAL TRANSITION; GENE EXPRESSION PROFILING; HIGH RISK POPULATION; HUMAN; HUMAN CELL; INTESTINE EPITHELIUM CELL; NUCLEOTIDE SEQUENCE; OVERALL SURVIVAL; PHENOTYPE; PRACTICE GUIDELINE; PROTEIN EXPRESSION; SCORING SYSTEM; SMALL INTESTINE ABSORPTION; TUMOR MODEL; COLON TUMOR; CYTOLOGY; DRUG EFFECT; DRUG RESISTANCE; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; INTESTINE MUCOSA; METABOLISM; PRINCIPAL COMPONENT ANALYSIS; TUMOR CELL LINE;

ANTINEOPLASTIC AGENTS; CACO-2 CELLS; CELL DIFFERENTIATION; CELL LINE, TUMOR; COLONIC NEOPLASMS; DATABASES, GENETIC; DRUG RESISTANCE, NEOPLASM; EPITHELIAL-MESENCHYMAL TRANSITION; GENE EXPRESSION REGULATION, NEOPLASTIC; HT29 CELLS; HUMANS; INTESTINAL MUCOSA; MODELS, BIOLOGICAL; PRINCIPAL COMPONENT ANALYSIS;

EID: 84862585776     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-274     Document Type: Article

References (58)

1. Markowitz SD, Bertagnolli MM. Molecular origins of cancer: Molecular basis of colorectal cancer. N Engl J Med 2009, 361(25):2449-2460. 10.1056/NEJMra0804588, 2843693, 20018966.
2. Gayet J, Zhou XP, Duval A, Rolland S, Hoang JM, Cottu P, Hamelin R. Extensive characterization of genetic alterations in a series of human colorectal cancer cell lines. Oncogene 2001, 20(36):5025-5032. 10.1038/sj.onc.1204611, 11526487.
3. Oliveira C, Pinto M, Duval A, Brennetot C, Domingo E, Espin E, Armengol M, Yamamoto H, Hamelin R, Seruca R, et al. BRAF mutations characterize colon but not gastric cancer with mismatch repair deficiency. Oncogene 2003, 22(57):9192-9196. 10.1038/sj.onc.1207061, 14668801.
4. Rosin-Arbesfeld R, Cliffe A, Brabletz T, Bienz M. Nuclear export of the APC tumour suppressor controls beta-catenin function in transcription. EMBO J 2003, 22(5):1101-1113. 10.1093/emboj/cdg105, 150338, 12606575.
5. van Erk MJ, Krul CA, Caldenhoven E, Stierum RH, Peters WH, Woutersen RA, van Ommen B. Expression profiling of colon cancer cell lines and colon biopsies: towards a screening system for potential cancer-preventive compounds. Eur J Cancer Prev 2005, 14(5):439-457. 10.1097/01.cej.0000174781.51883.21, 16175049.
6. Cespedes MV, Espina C, Garcia-Cabezas MA, Trias M, Boluda A, Gomez del Pulgar MT, Sancho FJ, Nistal M, Lacal JC, Mangues R. Orthotopic microinjection of human colon cancer cells in nude mice induces tumor foci in all clinically relevant metastatic sites. Am J Pathol 2007, 170(3):1077-1085. 10.2353/ajpath.2007.060773, 1864873, 17322390.
7. Chantret I, Barbat A, Dussaulx E, Brattain MG, Zweibaum A. Epithelial polarity, villin expression, and enterocytic differentiation of cultured human colon carcinoma cells: a survey of twenty cell lines. Cancer Res 1988, 48(7):1936-1942.
8. Flatmark K, Maelandsmo GM, Martinsen M, Rasmussen H, Fodstad O. Twelve colorectal cancer cell lines exhibit highly variable growth and metastatic capacities in an orthotopic model in nude mice. Eur J Cancer 2004, 40(10):1593-1598. 10.1016/j.ejca.2004.02.023, 15196545.
9. Thiery JP, Sleeman JP. Complex networks orchestrate epithelial-mesenchymal transitions. Nat Rev Mol Cell Biol 2006, 7(2):131-142. 10.1038/nrm1835, 16493418.
10. Mani SA, Guo W, Liao MJ, Eaton EN, Ayyanan A, Zhou AY, Brooks M, Reinhard F, Zhang CC, Shipitsin M, et al. The epithelial-mesenchymal transition generates cells with properties of stem cells. Cell 2008, 133(4):704-715. 10.1016/j.cell.2008.03.027, 2728032, 18485877.
11. Gupta PB, Onder TT, Jiang G, Tao K, Kuperwasser C, Weinberg RA, Lander ES. Identification of selective inhibitors of cancer stem cells by high-throughput screening. Cell 2009, 138(4):645-659. 10.1016/j.cell.2009.06.034, 19682730.
12. Singh A, Settleman J. EMT, cancer stem cells and drug resistance: an emerging axis of evil in the war on cancer. Oncogene 2010, 29(34):4741-4751. 10.1038/onc.2010.215, 3176718, 20531305.
13. Loboda A, Nebozhyn MV, Watters JW, Buser CA, Shaw PM, Huang PS, Van't Veer L, Tollenaar RA, Jackson DB, Agrawal D, et al. EMT is the dominant program in human colon cancer. BMC Med Genet 2011, 4:9.
14. Oh SC, Park YY, Park ES, Lim JY, Kim SM, Kim SB, Kim J, Kim SC, Chu IS, Smith JJ, et al. Prognostic gene expression signature associated with two molecularly distinct subtypes of colorectal cancer. Gut 2011,
15. Sharma SV, Haber DA, Settleman J. Cell line-based platforms to evaluate the therapeutic efficacy of candidate anticancer agents. Nat Rev Cancer 2010, 10(4):241-253. 10.1038/nrc2820, 20300105.
16. Shoemaker RH. The NCI60 human tumour cell line anticancer drug screen. Nat Rev Cancer 2006, 6(10):813-823. 10.1038/nrc1951, 16990858.
17. Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, et al. A gene expression database for the molecular pharmacology of cancer. Nat Genet 2000, 24(3):236-244. 10.1038/73439, 10700175.
18. Arango D, Mariadason JM, Wilson AJ, Yang W, Corner GA, Nicholas C, Aranes MJ, Augenlicht LH. c-Myc overexpression sensitises colon cancer cells to camptothecin-induced apoptosis. Br J Cancer 2003, 89(9):1757-1765. 10.1038/sj.bjc.6601338, 2394410, 14583781.
19. Augenlicht LH, Velcich A, Klampfer L, Huang J, Corner G, Aranes M, Laboisse C, Rigas B, Lipkin M, Yang K, et al. Application of gene expression profiling to colon cell maturation, transformation and chemoprevention. J Nutr 2003, 133(7 Suppl):2410S-2416S.
20. Boyer J, Allen WL, McLean EG, Wilson PM, McCulla A, Moore S, Longley DB, Caldas C, Johnston PG. Pharmacogenomic identification of novel determinants of response to chemotherapy in colon cancer. Cancer Res 2006, 66(5):2765-2777. 10.1158/0008-5472.CAN-05-2693, 16510598.
21. Hoshino H, Miyoshi N, Nagai K, Tomimaru Y, Nagano H, Sekimoto M, Doki Y, Mori M, Ishii H. Epithelial-mesenchymal transition with expression of SNAI1-induced chemoresistance in colorectal cancer. Biochem Biophys Res Commun 2009, 390(3):1061-1065. 10.1016/j.bbrc.2009.10.117, 19861116.
22. Jung JJ, Jeung HC, Lee JO, Kim TS, Chung HC, Rha SY. Putative chemosensitivity predictive genes in colorectal cancer cell lines for anticancer agents. Oncol Rep 2007, 18(3):593-599.
23. Mariadason JM, Arango D, Augenlicht LH. Customizing chemotherapy for colon cancer: the potential of gene expression profiling. Drug Resist Updat 2004, 7(3):209-218. 10.1016/j.drup.2004.05.001, 15296862.
24. Sabbah M, Emami S, Redeuilh G, Julien S, Prevost G, Zimber A, Ouelaa R, Bracke M, De Wever O, Gespach C. Molecular signature and therapeutic perspective of the epithelial-to-mesenchymal transitions in epithelial cancers. Drug Resist Updat 2008, 11(4-5):123-151.
25. Spitzner M, Emons G, Kramer F, Gaedcke J, Rave-Frank M, Scharf JG, Burfeind P, Becker H, Beissbarth T, Ghadimi BM, et al. A gene expression signature for chemoradiosensitivity of colorectal cancer cells. Int J Radiat Oncol Biol Phys 2010, 78(4):1184-1192. 10.1016/j.ijrobp.2010.06.023, 20970032.
26. Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, et al. Chemosensitivity prediction by transcriptional profiling. Proc Natl Acad Sci U S A 2001, 98(19):10787-10792. 10.1073/pnas.191368598, 58553, 11553813.
27. Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, Fevr T, Clark L, Bayani N, Coppe JP, Tong F, et al. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 2006, 10(6):515-527. 10.1016/j.ccr.2006.10.008, 2730521, 17157791.
28. Vermeulen L, De Sousa EMF, van der Heijden M, Cameron K, de Jong JH, Borovski T, Tuynman JB, Todaro M, Merz C, Rodermond H, et al. Wnt activity defines colon cancer stem cells and is regulated by the microenvironment. Nat Cell Biol 2010, 12(5):468-476. 10.1038/ncb2048, 20418870.
29. Deka J, Wiedemann N, Anderle P, Murphy-Seiler F, Bultinck J, Eyckerman S, Stehle JC, Andre S, Vilain N, Zilian O, et al. Bcl9/Bcl9l are critical for Wnt-mediated regulation of stem cell traits in colon epithelium and adenocarcinomas. Cancer Res 2010, 70(16):6619-6628. 10.1158/0008-5472.CAN-10-0148, 20682801.
30. Merlos-Suarez A, Barriga FM, Jung P, Iglesias M, Cespedes MV, Rossell D, Sevillano M, Hernando-Momblona X, da Silva-Diz V, Munoz P. The Intestinal Stem Cell Signature Identifies Colorectal Cancer Stem Cells and Predicts Disease Relapse. Cell Stem Cell 2011, 8(5):511-524. 10.1016/j.stem.2011.02.020, 21419747.
31. Guo RJ, Suh ER, Lynch JP. The role of Cdx proteins in intestinal development and cancer. Cancer Biol Ther 2004, 3(7):593-601. 10.4161/cbt.3.7.913, 15136761.
32. Artursson P, Palm K, Luthman K. Caco-2 monolayers in experimental and theoretical predictions of drug transport. Adv Drug Deliv Rev 2001, 46(1-3):27-43.
33. Fleet JC, Wang L, Vitek O, Craig BA, Edenberg HJ. Gene expression profiling of Caco-2 BBe cells suggests a role for specific signaling pathways during intestinal differentiation. Physiol Genomics 2003, 13(1):57-68.
34. Mariadason JM, Bordonaro M, Aslam F, Shi L, Kuraguchi M, Velcich A, Augenlicht LH. Down-regulation of beta-catenin TCF signaling is linked to colonic epithelial cell differentiation. Cancer Res 2001, 61(8):3465-3471.
35. Pshezhetsky AV, Fedjaev M, Ashmarina L, Mazur A, Budman L, Sinnett D, Labuda D, Beaulieu JF, Menard D, Nifant'ev I, et al. Subcellular proteomics of cell differentiation: quantitative analysis of the plasma membrane proteome of Caco-2 cells. Proteomics 2007, 7(13):2201-2215. 10.1002/pmic.200600956, 17549793.
36. Saaf AM, Halbleib JM, Chen X, Yuen ST, Leung SY, Nelson WJ, Brown PO. Parallels between global transcriptional programs of polarizing Caco-2 intestinal epithelial cells in vitro and gene expression programs in normal colon and colon cancer. Mol Biol Cell 2007, 18(11):4245-4260. 10.1091/mbc.E07-04-0309, 2043540, 17699589.
37. Hayeshi R, Hilgendorf C, Artursson P, Augustijns P, Brodin B, Dehertogh P, Fisher K, Fossati L, Hovenkamp E, Korjamo T, et al. Comparison of drug transporter gene expression and functionality in Caco-2 cells from 10 different laboratories. Eur J Pharm Sci 2008, 35(5):383-396. 10.1016/j.ejps.2008.08.004, 18782614.
38. Anderle P, Rakhmanova V, Woodford K, Zerangue N, Sadee W. Messenger RNA expression of transporter and ion channel genes in undifferentiated and differentiated Caco-2 cells compared to human intestines. Pharm Res 2003, 20(1):3-15. 10.1023/A:1022282221530, 12608530.
39. Calcagno AM, Ludwig JA, Fostel JM, Gottesman MM, Ambudkar SV. Comparison of drug transporter levels in normal colon, colon cancer, and Caco-2 cells: impact on drug disposition and discovery. Mol Pharm 2006, 3(1):87-93. 10.1021/mp050090k, 16686373.
40. Tremblay E, Auclair J, Delvin E, Levy E, Menard D, Pshezhetsky AV, Rivard N, Seidman EG, Sinnett D, Vachon PH, et al. Gene expression profiles of normal proliferating and differentiating human intestinal epithelial cells: a comparison with the Caco-2 cell model. J Cell Biochem 2006, 99(4):1175-1186. 10.1002/jcb.21015, 16795037.
41. Anderle P, Nielsen CU. Transporters in the gastrointestinal tract. Drug Bioavailability: The Future of Integrative Metabolism 2008, Wiley VCH, , Waterbeemd H, Testa B.
42. Mellor HR, Callaghan R. Resistance to chemotherapy in cancer: a complex and integrated cellular response. Pharmacology 2008, 81(4):275-300. 10.1159/000115967, 18259091.
43. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011, 144(5):646-674. 10.1016/j.cell.2011.02.013, 21376230.
44. de Vries JE, Dinjens WN, De Bruyne GK, Verspaget HW, van der Linden EP, de Bruine AP, Mareel MM, Bosman FT, ten Kate J. In vivo and in vitro invasion in relation to phenotypic characteristics of human colorectal carcinoma cells. Br J Cancer 1995, 71(2):271-277. 10.1038/bjc.1995.55, 2033572, 7841040.
45. Press B, Di Grandi D. Permeability for intestinal absorption: Caco-2 assay and related issues. Curr Drug Metab 2008, 9(9):893-900. 10.2174/138920008786485119, 18991586.
46. Sambuy Y, De Angelis I, Ranaldi G, Scarino ML, Stammati A, Zucco F. The Caco-2 cell line as a model of the intestinal barrier: influence of cell and culture-related factors on Caco-2 cell functional characteristics. Cell Biol Toxicol 2005, 21(1):1-26. 10.1007/s10565-005-0085-6, 15868485.
47. Sun H, Chow EC, Liu S, Du Y, Pang KS. The Caco-2 cell monolayer: usefulness and limitations. Expert Opin Drug Metab Toxicol 2008, 4(4):395-411. 10.1517/17425255.4.4.395, 18433344.
48. Alison MR, Lim SM, Nicholson LJ. Cancer stem cells: problems for therapy?. J Pathol 2011, 223(2):147-161.
49. Zhou BB, Zhang H, Damelin M, Geles KG, Grindley JC, Dirks PB. Tumour-initiating cells: challenges and opportunities for anticancer drug discovery. Nat Rev Drug Discov 2009, 8(10):806-823. 10.1038/nrd2137, 19794444.
50. Farmer P, Bonnefoi H, Anderle P, Cameron D, Wirapati P, Becette V, Andre S, Piccart M, Campone M, Brain E, et al. A stroma-related gene signature predicts resistance to neoadjuvant chemotherapy in breast cancer. Nat Med 2009, 15(1):68-74. 10.1038/nm.1908, 19122658.
51. Natoli M, Leoni BD, D'Agnano I, D'Onofrio M, Brandi R, Arisi I, Zucco F, Felsani A. Cell growing density affects the structural and functional properties of Caco-2 differentiated monolayer. J Cell Physiol 2011, 226(6):1531-1543. 10.1002/jcp.22487, 20945374.
52. Pfister TD, Reinhold WC, Agama K, Gupta S, Khin SA, Kinders RJ, Parchment RE, Tomaszewski JE, Doroshow JH, Pommier Y. Topoisomerase I levels in the NCI-60 cancer cell line panel determined by validated ELISA and microarray analysis and correlation with indenoisoquinoline sensitivity. Mol Cancer Ther 2009, 8(7):1878-1884. 10.1158/1535-7163.MCT-09-0016, 2728499, 19584232.
53. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005, 102(43):15545-15550. 10.1073/pnas.0506580102, 1239896, 16199517.
54. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 1998, 95(25):14863-14868. 10.1073/pnas.95.25.14863, 24541, 9843981.
55. Verzi MP, Shin H, He HH, Sulahian R, Meyer CA, Montgomery RK, Fleet JC, Brown M, Liu XS, Shivdasani RA. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev Cell 2010, 19(5):713-726. 10.1016/j.devcel.2010.10.006, 3001591, 21074721.
56. Gassler N, Newrzella D, Bohm C, Lyer S, Li L, Sorgenfrei O, van Laer L, Sido B, Mollenhauer J, Poustka A, et al. Molecular characterisation of non-absorptive and absorptive enterocytes in human small intestine. Gut 2006, 55(8):1084-1089. 1856251, 16556670.
57. van der Flier LG, van Gijn ME, Hatzis P, Kujala P, Haegebarth A, Stange DE, Begthel H, van den Born M, Guryev V, Oving I, et al. Transcription factor achaete scute-like 2 controls intestinal stem cell fate. Cell 2009, 136(5):903-912. 10.1016/j.cell.2009.01.031, 19269367.
58. Fritzmann J, Morkel M, Besser D, Budczies J, Kosel F, Brembeck FH, Stein U, Fichtner I, Schlag PM, Birchmeier W. A colorectal cancer expression profile that includes transforming growth factor beta inhibitor BAMBI predicts metastatic potential. Gastroenterology 2009, 137(1):165-175. 10.1053/j.gastro.2009.03.041, 19328798.