Gene expression perturbation in vitro - A growing case for three-dimensional (3D) culture systems

Seminars in Cancer Biology

Volumn 15, Issue 5 SPEC. ISS., 2005, Pages 405-412

  Birgersdotter, Anna ^a   Sandberg, Rickard ^a,b   Ernberg, Ingemar ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

3 D cell culture; Cancer cell lines; Global gene expression; Transcriptome; Tumor stroma

Indexed keywords

DNA; FOCAL ADHESION KINASE; PROTEIN; RIBOSOME PROTEIN; TRANSCRIPTOME;

CANCER CELL CULTURE; CANCER MODEL; CELL ADHESION; CELL GROWTH; CELL IMMORTALIZATION; CELL INTERACTION; CELL PROLIFERATION; DNA MICROARRAY; DNA REPLICATION; EXTRACELLULAR MATRIX; FOCAL ADHESION; GENE EXPRESSION PROFILING; GENOTYPE PHENOTYPE CORRELATION; GLYCOLYSIS; MICROTUBULE ASSEMBLY; NONHUMAN; PROTEIN MODIFICATION; QUANTITATIVE ANALYSIS; REVIEW; STROMA CELL; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; TUMOR GROWTH; UPREGULATION;

EID: 23744472983     PISSN: 1044579X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.semcancer.2005.06.009     Document Type: Review

References (52)

1. A. Carrel On the permanent life of tissues outside of the organism J Exp Med 15 1912 516 528
2. K.E. Sanford, W.R. Earle, and G.D. Likely The growth in vitro of single isolated tissue cells J Natl Cancer Inst 9 3 1948 229 246
3. H. Eagle Nutrition needs of mammalian cells in tissue culture Science 122 3168 1955 501 504
4. D. Hanahan, and R.A. Weinberg The hallmarks of cancer Cell 100 1 2000 57 70
5. A.V. Roschke, G. Tonon, K.S. Gehlhaus, N. McTyre, K.J. Bussey, and S. Lababidi Karyotypic complexity of the NCI-60 drug-screening panel Cancer Res 63 24 2003 8634 8647
6. D.T. Ross, U. Scherf, M.B. Eisen, C.M. Perou, C. Rees, and P. Spellman Systematic variation in gene expression patterns in human cancer cell lines Nat Genet 24 3 2000 227 235
7. J.M. Irish, R. Hovland, P.O. Krutzik, O.D. Perez, O. Bruserud, and B.T. Gjertsen Single cell profiling of potentiated phospho-protein networks in cancer cells Cell 118 2 2004 217 228
8. J.R. Masters Human cancer cell lines: fact and fantasy Nat Rev Mol Cell Biol 1 3 2000 233 236
9. T. Jacks, and R.A. Weinberg Taking the study of cancer cell survival to a new dimension Cell 111 7 2002 923 925
10. U. Alon, N. Barkai, D.A. Notterman, K. Gish, S. Ybarra, and D. Mack Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays Proc Natl Acad Sci USA 96 12 1999 6745 6750
11. C.M. Perou, S.S. Jeffrey, M. van de Rijn, C.A. Rees, M.B. Eisen, and D.T. Ross Distinctive gene expression patterns in human mammary epithelial cells and breast cancers Proc Natl Acad Sci USA 96 16 1999 9212 9217
12. A.A. Alizadeh, M.B. Eisen, R.E. Davis, C. Ma, I.S. Lossos, and A. Rosenwald Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling Nature 403 6769 2000 503 511
13. C. Virtanen, Y. Ishikawa, D. Honjoh, M. Kimura, M. Shimane, and T. Miyoshi Integrated classification of lung tumors and cell lines by expression profiling Proc Natl Acad Sci USA 99 19 2002 12357 12362
14. M.E. Schaner, D.T. Ross, G. Ciaravino, T. Sorlie, O. Troyanskaya, and M. Diehn Gene expression patterns in ovarian carcinomas Mol Biol Cell 14 11 2003 4376 4386
15. J.B. Welsh, L.M. Sapinoso, A.I. Su, S.G. Kern, J. Wang-Rodriguez, and C.A. Moskaluk Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer Cancer Res 61 16 2001 5974 5978
16. Sandberg R, Ernberg I. The molecular portrait of in vitro growth by meta-analysis of gene expression profiles. Genome Biol, in press.
17. C. Creighton, R. Kuick, D.E. Misek, D.S. Rickman, F.M. Brichory, and J.M. Rouillard Profiling of pathway-specific changes in gene expression following growth of human cancer cell lines transplanted into mice Genome Biol 4 7 2003 R46
18. S.H. Dairkee, Y. Ji, Y. Ben, D.H. Moore, Z. Meng, and S.S. Jeffrey A molecular 'signature' of primary breast cancer cultures; patterns resembling tumor tissue BMC Genomics 5 1 2004 47
19. W.D. Stein, T. Litman, T. Fojo, and S.E. Bates A serial analysis of Gene Expression (SAGE) database analysis of chemosensitivity: comparing solid tumors with cell lines and comparing solid tumors from different tissue origins Cancer Res 64 8 2004 2805 2816
20. K.A. Beningo, M. Dembo, and Y.L. Wang Responses of fibroblasts to anchorage of dorsal extracellular matrix receptors Proc Natl Acad Sci USA 101 52 2004 18024 18029
21. E. Cukierman, R. Pankov, D.R. Stevens, and K.M. Yamada Taking cell-matrix adhesions to the third dimension Science 294 5547 2001 1708 1712
22. S. Li, J. Lao, B.P. Chen, Y.S. Li, Y. Zhao, and J. Chu Genomic analysis of smooth muscle cells in 3-dimensional collagen matrix FASEB J 17 1 2003 97 99
23. H. Liu, D.C. Radisky, F. Wang, and M.J. Bissell Polarity and proliferation are controlled by distinct signaling pathways downstream of PI3-kinase in breast epithelial tumor cells J Cell Biol 164 4 2004 603 612
24. V.M. Weaver, O.W. Petersen, F. Wang, C.A. Larabell, P. Briand, and C. Damsky Reversion of the malignant phenotype of human breast cells in three-dimensional culture and in vivo by integrin blocking antibodies J Cell Biol 137 1 1997 231 245
25. F. Wang, V.M. Weaver, O.W. Petersen, C.A. Larabell, S. Dedhar, and P. Briand Reciprocal interactions between beta1-integrin and epidermal growth factor receptor in three-dimensional basement membrane breast cultures: a different perspective in epithelial biology Proc Natl Acad Sci USA 95 25 1998 14821 14826
26. K. Wolf, I. Mazo, H. Leung, K. Engelke, U.H. von Andrian, and E.I. Deryugina Compensation mechanism in tumor cell migration: mesenchymal-amoeboid transition after blocking of pericellular proteolysis J Cell Biol 160 2 2003 267 277
27. S. Ghosh, G.C. Spagnoli, I. Martin, S. Ploegert, P. Demougin, and M. Heberer Three-dimensional culture of melanoma cells profoundly affects gene expression profile: a high density oligonucleotide array study J Cell Physiol 2005
28. A.I. Su, T. Wiltshire, S. Batalov, H. Lapp, K.A. Ching, and D. Block A gene atlas of the mouse and human protein-encoding transcriptomes Proc Natl Acad Sci USA 101 16 2004 6062 6067
29. A.I. Su, M.P. Cooke, K.A. Ching, Y. Hakak, J.R. Walker, and T. Wiltshire Large-scale analysis of the human and mouse transcriptomes Proc Natl Acad Sci USA 99 7 2002 4465 4470
30. J. Fogh, J.M. Fogh, and T. Orfeo One hundred and twenty-seven cultured human tumor cell lines producing tumors in nude mice J Natl Cancer Inst 59 1 1977 221 226
31. I.I. Wistuba, C. Behrens, S. Milchgrub, S. Syed, M. Ahmadian, and A.K. Virmani Comparison of features of human breast cancer cell lines and their corresponding tumors Clin Cancer Res 4 12 1998 2931 2938
32. I.I. Wistuba, D. Bryant, C. Behrens, S. Milchgrub, A.K. Virmani, and R. Ashfaq Comparison of features of human lung cancer cell lines and their corresponding tumors Clin Cancer Res 5 5 1999 991 1000
33. H.G. Drexler, W.G. Dirks, Y. Matsuo, and R.A. MacLeod False leukemia-lymphoma cell lines: an update on over 500 cell lines Leukemia 17 2 2003 416 426
34. J. Masters False cell lines Carcinogenesis 23 2 2002 371
35. R. Sandberg, and I. Ernberg Assessment of tumor characteristic gene expression in cell lines using a Tissue Similarity Index Proc Natl Acad Sci USA 102 6 2005 2052 2057
36. Cheng JD, Weiner LM. Tumors and their microenvironments: tilling the soil. Commentary re: Scott AM et al. A Phase I dose-escalation study of sibrotuzumab in patients with advanced or metastatic fibroblast activation protein-positive cancer. Clin Cancer Res 2003;9:1639-47.
37. Clin Cancer Res 2003;9(5):1590-5.
38. J.L. Camps, S.M. Chang, T.C. Hsu, M.R. Reeman, S.J. Hong, and H.E. Zhau Fibroblast-mediated acceleration of human epithelial tumor growth in vivo Proc Natl Acad Sci USA 87 1 1990 75 79
39. E.F. Adams, C.J. Newton, H. Braunsberg, N. Shaikh, M. Ghilchik, and V.H. James Effects of human breast fibroblasts on growth and 17 beta-estradiol dehydrogenase activity of MCF-7 cells in culture Breast Cancer Res Treat 11 2 1988 165 172
40. C. Yazhou, S. Wenlv, Z. Weidong, and W. Licun Clinicopathological significance of stromal myofibroblasts in invasive ductal carcinoma of the breast Tumour Biol 25 5-6 2004 290 295
41. A.M. Scott, G. Wiseman, S. Welt, A. Adjei, F.T. Lee, W. Hopkins, and C.R. Divgi A Phase I dose-escalation study of sibrotuzumab in patients with advanced or metastatic fibroblast activation protein-positive cancer Clin Cancer Res 9 5 2003 1639 1647
42. J. Folkman Tumor angiogenesis: therapeutic implications N Engl J Med 285 21 1971 1182 1186
43. L.M. Coussens, and Z. Werb Inflammation and cancer Nature 420 6917 2002 860 867
44. R.D. Leek, C.E. Lewis, R. Whitehouse, M. Greenall, J. Clarke, and A.L. Harris Association of macrophage infiltration with angiogenesis and prognosis in invasive breast carcinoma Cancer Res 56 20 1996 4625 4629
45. L. Shunyakov, C.K. Ryan, D.M. Sahasrabudhe, and A.A. Khorana The influence of host response on colorectal cancer prognosis Clin Colorectal Cancer 4 1 2004 38 45
46. N.A. Marshall, L.E. Christie, L.R. Munro, D.J. Culligan, P.W. Johnston, and R.N. Barker Immunosuppressive regulatory T cells are abundant in the reactive lymphocytes of Hodgkin lymphoma Blood 103 5 2004 1755 1762
47. D. Molin, A. Edstrom, I. Glimelius, B. Glimelius, G. Nilsson, and C. Sundstrom Mast cell infiltration correlates with poor prognosis in Hodgkin's lymphoma Br J Haematol 119 1 2002 122 124
48. L.M. Coussens, W.W. Raymond, G. Bergers, M. Laig-Webster, O. Behrendtsen, and Z. Werb Inflammatory mast cells up-regulate angiogenesis during squamous epithelial carcinogenesis Genes Dev 13 11 1999 1382 1397
49. K.W. Kinzler, and B. Vogelstein Landscaping the cancer terrain Science 280 1998 1036 1037
50. K. Takaku, M. Oshima, H. Miyoshi, M. Matsui, M.F. Seldin, and M.M. Taketo Intestinal tumorigenesis in compound mutant mice of both Dpc4 (Smad4) and Apc genes Cell 92 5 1998 645 656
51. M. Chatterjee, D. Honemann, S. Lentzsch, K. Bommert, C. Sers, and P. Herrmann In the presence of bone marrow stromal cells human multiple myeloma cells become independent of the IL-6/gp130/STAT3 pathway Blood 100 9 2002 3311 3318
52. M.M. Mueller, and N.E. Fusenig Friends or foes - bipolar effects of the tumour stroma in cancer Nat Rev Cancer 4 11 2004 839 849