Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers

Genome Biology

Volumn 9, Issue 7, 2008, Pages

  Naxerova, Kamila ^a   Bult, Carol J ^b   Peaston, Anne ^b   Fancher, Karen ^b   Knowles, Barbara B ^b   Kasif, Simon ^a,c   Kohane, Isaac S ^a  

^a HARVARD MIT DIVISION OF HEALTH SCIENCES AND TECHNOLOGY   (United States)

^b JACKSON LABORATORY   (United States)

^c Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; ABC TRANSPORTER B; APOLIPOPROTEIN C1; CHAPERONIN; CYCLIN B2; CYCLIN DEPENDENT KINASE 2; CYCLINE; DYSTROBREVIN; GUANOSINE TRIPHOSPHATASE ACTIVATING PROTEIN; HELICASE; HELICASE LYMPHOID SPECIFIC; HISTONE H2AX; INTERLEUKIN 7 RECEPTOR; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1C; MATRILYSIN; NUDIX HYDROLASE; PROTEASOME; PROTEASOME BETA 8; PROTEIN CCT3; PROTEIN CCT7; RAC GUANOSINE TRIPHOSPHATASE ACTIVATING PROTEIN 1; RIBONUCLEOTIDE REDUCTASE; RIBONUCLEOTIDE REDUCTASE M1; THYMIDINE PHOSPHATE; THYMIDYLATE KINASE; TRANSPORTER ASSOCIATED WITH ANTIGEN PROCESSING 1; UNCOUPLING PROTEIN 2; URACIL DNA GLYCOSIDASE;

ARTICLE; CANCER GENETICS; CARCINOGENESIS; DEVELOPMENTAL GENETICS; DEVELOPMENTAL STAGE; FETUS LUNG; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETIC HETEROGENEITY; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; LUNG DEVELOPMENT; NEOPLASM; NONHUMAN; QUANTITATIVE ANALYSIS; TIME SERIES ANALYSIS; TISSUE DIFFERENTIATION; TISSUE SPECIFICITY; UPREGULATION; ANIMAL; CELL PROLIFERATION; CLASSIFICATION; GENETICS; MOUSE; PRENATAL DEVELOPMENT;

MURINAE;

ANIMALS; CELL PROLIFERATION; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MICE; NEOPLASMS;

EID: 48549094872     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-7-r108     Document Type: Article

References (45)

1. Virchow RLK Cellular Pathology Berlin 1859.
2. Hartwell KA Muir B Reinhardt F Carpenter AE Sgroi DC Weinberg RA The Spemann organizer gene, Goosecoid, promotes tumor metastasis. Proc Natl Acad Sci USA 2006, 103:18969-18974. 1748161 17142318 10.1073/ pnas.0608636103
3. Sparmann A van Lohuizen M Polycomb silencers control cell fate, development and cancer. Nat Rev Cancer 2006, 6:846-856. 10.1038/nrc1991 17060944
4. Liu S Dontu G Mantle ID Patel S Ahn NS Jackson KW Suri P Wicha MS Hedgehog signaling and Bmi-1 regulate self-renewal of normal and malignant human mammary stem cells. Cancer Res 2006, 66:6063-6071. 10.1158/0008-5472.CAN-06-0054 16778178
5. Borczuk AC Gorenstein L Walter KL Assaad AA Wang L Powell CA Non-small-cell lung cancer molecular signatures recapitulate lung developmental pathways. Am J Pathol 2003, 163:1949-1960. 1892411 14578194
6. Liu H Kho AT Kohane IS Sun Y Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development. PLoS Med 2006, 3:e232. 1483910 16800721 10.1371/ journal.pmed.0030232
7. Coulouarn C Derambure C Lefebvre G Daveau R Hiron M Scotte M Francois A Daveau M Salier JP Global gene repression in hepatocellular carcinoma and fetal liver, and suppression of dudulin-2 mRNA as a possible marker for the cirrhosis-to-tumor transition. J Hepatol 2005, 42:860-869. 10.1016/j.jhep.2005.01.027 15885357
8. Dekel B Metsuyanim S Schmidt-Ott KM Fridman E Jacob-Hirsch J Simon A Pinthus J Mor Y Barasch J Amariglio N Reisner Y Kaminski N Rechavi G Multiple imprinted and stemness genes provide a link between normal and tumor progenitor cells of the developing human kidney. Cancer Res 2006, 66:6040-6049. 10.1158/0008-5472.CAN-05-4528 16778176
9. Hu M Shivdasani RA Overlapping gene expression in fetal mouse intestine development and human colorectal cancer. Cancer Res 2005, 65:8715-8722. 10.1158/0008-5472.CAN-05-0700 16204040
10. Kaiser S Park YK Franklin JL Halberg RB Yu M Jessen WJ Freudenberg J Chen X Haigis K Jegga AG Kong S Sakthivel B Xu H Reichling T Azhar M Boivin GP Roberts RB Bissahoyo AC Gonzales F Bloom GC Eschrich S Carter SL Aronow JE Kleimeyer J Kleimeyer M Ramaswamy V Settle SH Boone B Levy S Graff JM Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer. Genome Biol 2007, 8:R131. 2323222 17615082 10.1186/gb-2007-8-7-r131
11. Kho AT Zhao Q Cai Z Butte AJ Kim JY Pomeroy SL Rowitch DH Kohane IS Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev 2004, 18:629-640. 387239 15075291 10.1101/gad.1182504
12. Liu R Wang X Chen GY Dalerba P Gurney A Hoey T Sherlock G Lewicki J Shedden K Clarke MF The prognostic role of a gene signature from tumorigenic breast-cancer cells. N Engl J Med 2007, 356:217-226. 10.1056/ NEJMoa063994 17229949
13. Garraway LA Sellers WR Lineage dependency and lineage-survival oncogenes in human cancer. Nat Rev Cancer 2006, 6:593-602. 10.1038/nrc1947 16862190
14. Berek JS Interval debulking of ovarian cancer - an interim measure. N Engl J Med 1995, 332:675-677. 10.1056/NEJM199503093321010 7845434
15. Oda T Takahashi A Miyao N Yanase M Masumori N Itoh N Sato MA Kon S Tsukamoto T Cell proliferation, apoptosis, angiogenesis and growth rate of incidentally found renal cell carcinoma. Int J Urol 2003, 10:13-18. 10.1046/j.1442-2042.2003.00558.x 12534920
16. Fujimoto N Sugita A Terasawa Y Kato M Observations on the growth rate of renal cell carcinoma. Int J Urol 1995, 2:71-76. 10.1111/ j.1442-2042.1995.tb00427.x 7553291
17. Riesco-Eizaguirre G Santisteban P New insights in thyroid follicular cell biology and its impact in thyroid cancer therapy. Endocr Relat Cancer 2007, 14:957-977. 10.1677/ERC-07-0085 18045949
18. Schmid HP McNeal JE Stamey TA Clinical observations on the doubling time of prostate cancer. Eur Urol 1993, 23(Suppl 2):60-63. 7685704
19. Whitfield ML Sherlock G Saldanha AJ Murray JI Ball CA Alexander KE Matese JC Perou CM Hurt MM Brown PO Botstein D Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell 2002, 13:1977-2000. 117619 12058064 10.1091/ mbc.02-02-0030.
20. Jaroudi S SenGupta S DNA repair in mammalian embryos. Mutat Res 2007, 635:53-77. 10.1016/j.mrrev.2006.09.002 17141556
21. Karnoub AE Weinberg RA Chemokine networks and breast cancer metastasis. Breast Dis 2007, 26:75-85.
22. Yusuf F Rehimi R Morosan-Puopolo G Dai F Zhang X Brand-Saberi B Inhibitors of CXCR4 affect the migration and fate of CXCR4+ progenitors in the developing limb of chick embryos. Dev Dyn 2006, 235:3007-3015. 10.1002/dvdy.20951 16958136
23. Karnoub AE Dash AB Vo AP Sullivan A Brooks MW Bell GW Richardson AL Polyak K Tubo R Weinberg RA Mesenchymal stem cells within tumour stroma promote breast cancer metastasis. Nature 2007, 449:557-563. 10.1038/ nature06188 17914389
24. 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. 1239896 16199517 10.1073/pnas.0506580102
25. Iyer VR Eisen MB Ross DT Schuler G Moore T Lee JC Trent JM Staudt LM Hudson J Jr Boguski MS Lashkari D Shalon D Botstein D Brown PO The transcriptional program in the response of human fibroblasts to serum. Science 1999, 283:83-87. 10.1126/science.283.5398.83 9872747
26. Yu P Huang B Shen M Lau C Chan E Michel J Xiong Y Payan DG Luo Y p15(PAF), a novel PCNA associated factor with increased expression in tumor tissues. Oncogene 2001, 20:484-489. 10.1038/sj.onc.1204113 11313979
27. Kufe D Pollock R Weichselbaum R Bast R Gansler T Holland J Frei E Cancer Medicine Hamilton, Canada: BC Decker Inc. 2003.
28. Andäng M Hjerling-Leffler J Moliner A Lundgren TK Castelo-Branco G Nanou E Pozas E Bryja V Halliez S Nishimaru H Wilbertz J Arenas E Koltzenburg M Charnay P El Manira A Ibañez CF Ernfors P Histone H2AX-dependent GABA(A) receptor regulation of stem cell proliferation. Nature 2008, 451:460-464. 10.1038/nature06488 18185516
29. Lu J Getz G Miska EA Alvarez-Saavedra E Lamb J Peck D Sweet-Cordero A Ebert BL Mak RH Ferrando AA Downing JR Jacks T Horvitz HR Golub TR MicroRNA expression profiles classify human cancers. Nature 2005, 435:834-838. 10.1038/nature03702 15944708
30. Potten CS Barthel D Li YQ Ohlrich R Matthé B Loeffler M Proliferation in murine epidermis after minor mechanical stimulation. Part 1. Sustained increase in keratinocyte production and migration. Cell Prolif 2000, 33:231-246. 10.1046/j.1365-2184.2000.00178.x 11041204
31. Darby IA Hewitson TD Fibroblast differentiation in wound healing and fibrosis. Int Rev Cytol 2007, 257:143-179. 10.1016/S0074-7696(07)57004-X 17280897
32. Reynolds LP Killilea SD Redmer DA Angiogenesis in the female reproductive system. FASEB J 1992, 6:886-892. 1371260
33. Otu HH Naxerova K Ho K Can H Nesbitt N Libermann TA Karp SJ Restoration of liver mass after injury requires proliferative and not embryonic transcriptional patterns. J Biol Chem 2007, 282:11197-11204. 10.1074/ jbc.M608441200 17227769
34. Dvorak HF Tumors: Wounds that do not heal. Similarities between tumor stroma generation and wound healing. N Engl J Med 1986, 315:1650-1659. 3537791
35. Stearman RS Dwyer-Nield L Grady MC Malkinson AM Geraci MW A macrophage gene expression signature defines a field effect in the lung tumor microenvironment. Cancer Res 2008, 68:34-43. 10.1158/ 0008-5472.CAN-07-0988 18172294
36. Irizarry RA Hobbs B Collin F Beazer-Barclay YD Antonellis KJ Scherf U Speed TP Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264. 10.1093/biostatistics/4.2.249 12925520
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 JY Zhang J Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80. 545600 15461798 10.1186/gb-2004-5-10-r80
38. The R Project for Statistical Computing http://www.r-project.org/
39. Tusher VG Tibshirani R Chu G Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98:5116-5121. 33173 11309499 10.1073/pnas.091062498
40. strucchange http://cran.r-project.org/web/packages/strucchange/
41. Identification of Genes Periodically Expressed in the Human Cell Cycle and Their Expression in Tumors http://genome-www.stanford.edu/ Human-CellCycle/Hela/
42. Bioconductor http://www.bioconductor.org
43. C2 Gene Sets http://www.broad.mit.edu/gsea/msigdb/ genesets.jsp?collection=C2
44. Macrobiology at the Children's Hospital Informatics Program http://www.chip.org/macrobiology/
45. Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/