Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification

British Journal of Cancer

Volumn 100, Issue 9, 2009, Pages 1452-1464

  Smith, M J ^a   Culhane, A C ^b,c   Donovan, M ^a   Coffey, J C ^a   Barry, B D ^a   Kelly, M A ^a   Higgins, D G ^d   Wang, J H ^a   Kirwan, W O ^a   Cotter, T G ^a   Redmond, H P ^a,e  

^a UNIVERSITY COLLEGE CORK   (Ireland)

^b DANA FARBER CANCER INSTITUTE   (United States)

^c HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^d UNIVERSITY COLLEGE DUBLIN   (Ireland)

^e University College Cork and INFANT Centre   (Ireland)

Author keywords

Colorectal cancer; Fluorescence activated cell sorting; Gene expression microarray analysis; Humans

Indexed keywords

OLIGONUCLEOTIDE; RNA; ALPHA 2(I) COLLAGEN; CELL ADHESION MOLECULE; COLLAGEN; COLLAGEN TYPE 6; POSTN PROTEIN, HUMAN; TISSUE INHIBITOR OF METALLOPROTEINASE 2;

ADULT; AGED; ARTICLE; CELL POPULATION; CELL SUSPENSION; CLINICAL ASSESSMENT; COLORECTAL CANCER; COLORECTAL CARCINOMA; COLORECTAL TUMOR; CONTROLLED STUDY; FEMALE; FLUORESCENCE ACTIVATED CELL SORTING; GENE EXPRESSION; GENE OVEREXPRESSION; GENETIC ANALYSIS; HUMAN; HUMAN CELL; HUMAN TISSUE; MALE; MICROARRAY ANALYSIS; PARENCHYMA; PRIORITY JOURNAL; RNA HYBRIDIZATION; STROMA; TUMOR BIOPSY; TUMOR GENE; BIOPSY; CELL SEPARATION; DNA MICROARRAY; FLOW CYTOMETRY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; PATHOLOGY; STROMA CELL;

BIOPSY; CELL ADHESION MOLECULES; CELL SEPARATION; COLLAGEN; COLLAGEN TYPE VI; COLORECTAL NEOPLASMS; FLOW CYTOMETRY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, NEOPLASM; STROMAL CELLS; TISSUE INHIBITOR OF METALLOPROTEINASE-2;

EID: 65549144626     PISSN: 00070920     EISSN: 15321827     Source Type: Journal    
DOI: 10.1038/sj.bjc.6604931     Document Type: Article

References (55)

1. Ach RA- Floore A, Curry B, Lazar V, Glas AM, Pover R, Tsalenko A, Ripoche H, Cardoso F, d'Assignies MS, Bruhn L, Van't Veer LJ (2007) Robust interlaboratory reproducibility of a gene expression signature measurement consistent with the needs of a new generation of diagnostic tools. BMC Genomics 8: 148
2. Afanasyeva M, Georgakopoulos D, Belardi DF, Ramsundar AC, Barin JG, Kass DA, Rose NR (2004) Quantitative analysis of myocardial inflammation by flow cytometry in murine autoimmune myocarditis: correlation with cardiac function. Am J Pathol 164: 807-815
3. Allen C, Hogg N (1985) Monocytes and other infiltrating cells in human colorectal tumours identified by monoclonal antibodies. Immunology 55: 289-299
4. Allen C, Hogg N (1987) Elevation of infiltrating mononuclear phagocytes in human colorectal tumors. J Natl Cancer Inst 78: 465-470
5. Birkenkamp-Demtroder K, Christensen LL, Olesen SH, Frederiksen CM, Laiho P, Aaltonen LA, Laurberg S, Sorensen FB, Hagemann R, TF OR (2002) Gene expression in colorectal cancer. Cancer Res 62: 4352-4363
6. Bittner M, Meltzer P, Chen Y, Jiang Y, Seftor E, Hendrix M, Radmacher M, Simon R, Yakhini Z, Ben-Dor A, Sampas N, Dougherty E, Wang E, Marincola F, Gooden C, Lueders J, Glatfelter A, Pollock P, Carpten J, Gillanders E, Leja D, Dietrich K, Beaudry C, Berens M, Alberts D, Sondak V (2000) Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 406: 536-540
7. Breitling R, Armengaud P, Amtmann A, Herzyk P (2004) Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett 573: 83-92
8. Butte A (2002) The use and analysis of microarray data. Nat Rev Drug Discov 1: 951-960
9. Cardoso F, Van't Veer L, Rutgers E, Loi S, Mook S, Piccart-Gebhart MJ (2008) Clinical application of the 70-gene profile: the MINDACT trial. Clin Oncol 26: 729-735
10. Chang JC, Wooten EC, Tsimelzon A, Hilsenbeck SG, Gutierrez MC, Elledge R, Mohsin S, Osborne CK, Chamness GC, Allred DC, O'Connell P (2003) Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer. Lancet 362: 362-369
11. Culhane AC, Thioulouse J, Perriere G, Higgins DG (2005) MADE4: an R package for multivariate analysis of gene expression data. Bioinformatics 21: 2789-2790
12. Curtin JF, Cotter TG (2004) JNK regulates HIPK3 expression and promotes resistance to Fas-mediated apoptosis in DU 145 prostate carcinoma cells. JBM Chem 279: 17090-17100
13. de Bruin EC, van de Pas S, Lips EH, van Eijk R, van der Zee MM, Lombaerts M, van Wezel T, Marijnen CA, van Krieken JH, Medema JP, van de Velde CJ, Eilers PH, Peltenburg LT (2005) Macrodissection versus microdissection of rectal carcinoma: minor influence of stroma cells to tumor cell gene expression profiles. BMC Genomics 6: 142
14. Delarue FL, Adnane J, Joshi B, Blaskovich MA, Wang DA, Hawker J, Bizouarn F, Ohkanda J, Zhu K, Hamilton AD, Chellappan S, Sebti SM (2007) Farnesyltransferase and geranylgeranyltransferase I inhibitors upregulate RhoB expression by HDACl dissociation, HAT association and histone acetylation of the RhoB promoter. Oncogene 26: 633-640
15. Dennis Jr G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biol 4: P3
16. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sei USA 95: 14863-14868
17. Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, Weiss RA, Liotta LA (1996) Laser capture microdissection. Science 274:998-1001
18. Fellenberg K, Hauser NC, Brors B, Neutzner A, Hoheisel JD, Vingron M (2001) Correspondence analysis applied to microarray data. Proc Natl Acad Sei USA 98: 10781-10786
19. Fukino K, Shen L, Patocs A, Mutter GL, Eng C (2007) Genomic instability within tumor stroma and clinicopathological characteristics of sporadic primary invasive breast carcinoma. JAMA 297: 2103-2111
20. 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 JY, Zhang J (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80
21. Gershon D (2004) Microarrays go mainstream. Nat Methods 1: 263-270
22. Glas AM, Floore A, Delahaye LJ, Witteveen AT, Pover RC, Bakx N, LahtiDomenici JS, Bruinsma TJ, Warmoes MO, Bernards R, Wessels LF, Van't Veer LJ (2006) Converting a breast cancer microarray signature into a high-throughput diagnostic test. BMC Genomics 7: 278
23. Guo J, Xiao B, Zhang X, Jin Z, Chen J, Qin L, Mao X, Shen G, Chen H, Liu Z (2004) Combined use of positive and negative immunomagnetic isolation followed by real-time RT-PCR for detection of the circulating tumor cells in patients with colorectal cancers. J MoI Med 82: 768-774
24. Hofmann WK, de Vos S, Elashoff D, Gschaidmeier H, Hoelzer D, Koeffler HP, Ottmann OG (2002) Relation between resistance of Philadelphiachromosome- positive acute lymphoblastic leukaemia to the tyrosine kinase inhibitor STI571 and gene-expression profiles: a gene-expression study. Lancet 359: 481 -486
25. Huang E, Cheng SH, Dressman H, Pittman J, Tsou MH, Horng CF, BiId A, Iversen ES, Liao M, Chen CM, West M, Nevins JR, Huang AT (2003) Gene expression predictors of breast cancer outcomes. Lancet 361: 1590-1596
26. Iizuka N, Oka M, Yamada-Okabe H, Nishida M, Maeda Y, Mori N, Takao T, Tamesa T, Tangoku A, Tabuchi H, Hamada K, Nakayama H, Ishitsuka H, Miyamoto T, Hirabayashi A, Uchimura S, Hamamoto Y (2003) Oligonucleotide microarray for prediction of early intrahepatic recurrence of hepatocellular carcinoma after curative resection. Lancet 361: 923-929
27. Jarvis JN, Centola M (2005) Gene-expression profiling: time for clinical application? Lancet 365: 199-200
28. Jeffery IB, Higgins DG, Culhane AC (2006) Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics 7: 359
29. 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 (2005) Synchronous global assessment of gene and protein expression in colorectal cancer progression. Genomics 86: 142-158
30. Latza U, Niedobitek G, Schwarting R, Nekarda H, Stein H (1990) Ber-EP4: new monoclonal antibody which distinguishes epithelia from mesotheM. J Clin Pathol 43: 213-219
31. Li C, Hung Wong W (2001) Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol 2: RESEARCH0032
32. Liu ET (2007) Stromal effects in breast cancer. N Engl J Med 357: 2537-2538
33. Liu S, Wang H, Currie BM, Molinolo A, Leung HJ, Moayeri M, Basile JR, Alfano RW, Gutkind JS, Frankel AE, Bugge TH, Leppla SH (2008) Matrix metalloproteinase-activated anthrax lethal toxin demonstrates high potency in targeting tumor vasculature. J Biol Chem 283: 529-540
34. Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, Bassett Jr DE, Hartwell LH, Brown PO, Friend SH (1998) Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med 4: 1293-1301
35. Michel C, Desdouets C, Sacre-Salem B, Gautier JC, Roberts R, Boitier E (2003) Liver gene expression profiles of rats treated with clofibric acid: comparison of whole liver and laser capture microdissected liver. Am J Pathol 163:2191-2199
36. Moyers JS, Bilan PJ, Zhu J, Kahn CR (1997) Rad and Rad-related GTPases interact with calmodulin and calmodulin-dependent protein kinase II. J Biol Chem 272: 11832-11839
37. Nyengaard JR (1999) Stereologic methods and their application in kidney research. J Am Soc Nephrol 10: 1100-1123
38. Patocs A, Zhang L, Xu Y, Weber F, Caldes T, Mutter GL, Platzer P, Eng C (2007) Breast-cancer stromal cells with TP53 mutations and nodal metastases. N Engl JMed 357: 2543-2551
39. Ramaswamy S, Ross KN, Lander ES, Golub TR (2003) A molecular signature of metastasis in primary solid tumors. Nat Genet 33: 49-54
40. Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov JP, Poggio T, Gerald W, Loda M, Lander ES, Golub TR (2001) Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sei USA 98: 15149-15154
41. Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 24: 227-235
42. Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, Lightfoot S, Menzel W, Granzow M, Ragg T (2006) The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC MoI Biol 7: 3
43. Seibenhener ML, Geetha T, Wooten MW (2007) Sequestosome l/p62 - more than just a scaffold. FEBS Lett 581: 175-179
44. Selaru FM, Xu Y, Yin J, Zou T, Liu TC, Mori Y, Abraham JM, Sato F, Wang S, Twigg C, Olaru A, Shustova V, Leytin A, Hytiroglou P, Shibata D, Harpaz N, Meltzer SJ (2002) Artificial neural networks distinguish among subtypes of neoplastic colorectal lesions. Gastroenterology 122: 606-613
45. Shipp MA, Ross KN, Tamayo P, Weng AP, Kutok JL, Aguiar RC, Gaasenbeek M, Angelo M, Reich M, Pinkus GS, Ray TS, Koval MA, Last KW, Norton A, Lister TA, Mesirov J, Neuberg DS, Lander ES, Aster JC, Golub TR (2002) Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med 8:68-74
46. Smith MJ, Coffey JC, Wang JH, Cotter TG, Redmond HP (2003) Gene expression profiling in biliary atresia. Lancet 361: 971-972;
47. Sugiyama Y, Sugiyama K, Hirai Y, Akiyama F, Hasumi K (2002) Microdissection is essential for gene expression profiling of clinically resected cancer tissues. Am J Clin Pathol 117: 109-116
48. Suzuki A, Nakauchi H, Taniguchi H (2004) Prospective isolation of multipotent pancreatic progenitors using flow-cytometric cell sorting. Diabetes 53: 2143-2152
49. van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415:530-536
50. van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, van der Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R (2002) A geneexpression signature as a predictor of survival in breast cancer. N Engl J Med 347: 1999-2009
51. Vider BZ, Zimber A, Hirsch D, Estlein D, Chastre E, Prevot S, Gespach C, Yaniv A, Gazit A (1997) Human colorectal carcinogenesis is associated with deregulation of homeobox gene expression. Biochem Biophys Res Commun 232: 742-748
52. Waguri N, Suda T, Nomoto M, Kawai H, Mita Y, Kuroiwa T, Igarashi M, Kobayashi M, Fukuhara Y, Aoyagi Y (2003) Sensitive and specific detection of circulating cancer cells in patients with hepatocellular carcinoma; detection of human telomerase reverse transcriptase messenger RNA after immunomagnetic separation. Clin Cancer Res 9: 3004-3011
53. Wang Y, Jatkoe T, Zhang Y, Mutch MG, Talantov D, Jiang J, McLeod HL, Atkins D (2004) Gene expression profiles and molecular markers to predict recurrence of Dukes' B colon cancer. J Clin Oncol 22: 1564-1571
54. Winegarden N (2003) Microarrays in cancer: moving from hype to clinical reality. Lancet 362: 1428
55. Zigeuner RE, Riesenberg R, Pohla H, Hofstetter A, Oberneder R (2000) Immunomagnetic cell enrichment detects more disseminated cancer cells than immunocytochemistry in vitro. J Urol 164: 1834-1837