In Silico cancer cell versus stroma cellularity index computed from species-specific human and mouse transcriptome of xenograft models: Towards accurate stroma targeting therapy assessment

BMC Medical Genomics

Volumn 7, Issue SUPPL.1, 2014, Pages

  Yang, Xinan ^a,d   Huang, Yong ^a   Lee, Younghee ^a   Gardeux, Vincent ^b,c,f   Achour, Ikbel ^b,f   Regan, Kelly ^b   Rebman, Ellen ^b   Li, Haiquan ^b,f   Lussier, Yves A ^a,b,e,f  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^c UNIVERSITÉ DE CERGY PONTOISE   (France)

^d UNIVERSITY OF CHICAGO   (United States)

^e UNIVERSITY OF CHICAGO   (United States)

^f UNIVERSITY OF ARIZONA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ANIMAL CELL; ARTICLE; BIOINFORMATICS; CANCER CELL; CELLULAR PARAMETERS; CELLULARITY INDEX; COMPUTER MODEL; COMPUTER PREDICTION; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; CROSS HYBRIDIZATION; DATA ANALYSIS; GENE EXPRESSION; GENETIC ALGORITHM; GOLD STANDARD; HUMAN; HUMAN AND MOUSE MICROARRAY ANALYSIS; HUMAN CELL; IN VITRO STUDY; INTERMETHOD COMPARISON; INTERSPECIFIC HYBRIDIZATION; LASER CAPTURE MICRODISSECTION; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; STROMA CELL; THEORETICAL STUDY; TRANSCRIPTOMICS; TUMOR XENOGRAFT; VALIDATION STUDY; ANIMAL; CELL TRANSFORMATION; COMPARATIVE STUDY; DNA MICROARRAY; DRUG SCREENING; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; METABOLISM; MOLECULAR GENETICS; MOLECULARLY TARGETED THERAPY; NEOPLASMS; NUCLEIC ACID HYBRIDIZATION; PATHOLOGY; PROCEDURES; REPRODUCIBILITY; SPECIES DIFFERENCE; TUMOR MICROENVIRONMENT;

MESSENGER RNA;

ANIMALS; CELL TRANSFORMATION, NEOPLASTIC; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; MICE; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR TARGETED THERAPY; NEOPLASMS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; SPECIES SPECIFICITY; STROMAL CELLS; TUMOR MICROENVIRONMENT; XENOGRAFT MODEL ANTITUMOR ASSAYS;

EID: 84900429502     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-7-S1-S2     Document Type: Article

References (35)

1. The fibroblastic coconspirator in cancer progression. Egeblad M, E. LL, Cold Spring Harb Symp Quant Biol 2005 70 383 388 10.1101/sqb.2005.70.007 16869775 (Pubitemid 44124893)
2. Modifying the soil to affect the seed: role of stromal-derived matrix metalloproteinases in cancer progression. Jodele S, Blavier L, Yoon JM, DeClerck YA, Cancer metastasis reviews 2006 25 1 35 43 10.1007/s10555-006-7887-8 16680570 (Pubitemid 43723980)
3. Cathepsin B and tumor proteolysis: contribution of the tumor microenvironment. Sloane BF, Yan S, Podgorski I, Linebaugh BE, Cher ML, Mai J, Cavallo-Medved D, Sameni M, Dosescu J, Moin K, Seminars in cancer biology 2005 15 2 149 157 10.1016/j.semcancer.2004.08.001 15652460 (Pubitemid 40126246)
4. Tumour microenvironment-opinion: validating matrix metalloproteinases as drug targets and anti-targets for cancer therapy. Overall CM, Kleifeld O, Nature reviews Cancer 2006 6 3 227 239 10.1038/nrc1821 16498445 (Pubitemid 43292566)
5. Gene expression signatures of morphologically normal breast tissue identify basal-like tumors. Finak G, Sadekova S, Pepin F, Hallett M, Meterissian S, Halwani F, Khetani K, Souleimanova M, Zabolotny B, Omeroglu A, Park M, Breast cancer research: BCR 2006 8 5 58 10.1186/bcr1608 17054791 (Pubitemid 44804003)
6. Stromal gene expression predicts clinical outcome in breast cancer. Finak G, Bertos N, Pepin F, Sadekova S, Souleimanova M, Zhao H, Chen H, Omeroglu G, Meterissian S, Omeroglu A, Hallett M, Park M, Nature medicine 2008 14 5 518 527 10.1038/nm1764 18438415 (Pubitemid 351655218)
7. The tumour microenvironment as a target for chemoprevention. Albini A, Sporn MB, Nature reviews Cancer 2007 7 2 139 147 17218951 (Pubitemid 46160989)
8. CD34+ fibrocytes: morphology, histogenesis and function. Barth PJ, Westhoff CC, Current stem cell research & therapy 2007 2 3 221 227 10.2174/157488807781696249 18220905 (Pubitemid 47496606)
9. Stroma-derived three-dimensional matrices are necessary and sufficient to promote desmoplastic differentiation of normal fibroblasts. Amatangelo MD, Bassi DE, Klein-Szanto AJ, Cukierman E, The American journal of pathology 2005 167 2 475 488 10.1016/S0002-9440(10)62991-4 16049333 (Pubitemid 43026103)
10. Exploring the tumour environment: cancer-associated fibroblasts as targets in cancer therapy. Micke P, Ostman A, Expert opinion on therapeutic targets 2005 9 6 1217 1233 10.1517/14728222.9.6.1217 16300472 (Pubitemid 41762875)
11. Laser capture microdissection. Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, Weiss RA, Liotta LA, Science 1996 274 5289 998 1001 10.1126/science.274.5289.998 8875945 (Pubitemid 26398425)
12. HIN-1, a putative cytokine highly expressed in normal but not cancerous mammary epithelial cells. Krop IE, Sgroi D, Porter DA, Lunetta KL, LeVangie R, Seth P, Kaelin CM, Rhei E, Bosenberg M, Schnitt S, Marks JR, Pagon Z, Belina D, Razumovic J, Polyak K, Proc Natl Acad Sci USA 2001 98 17 9796 9801 10.1073/pnas.171138398 11481438 (Pubitemid 32769383)
13. Evidence of high incidence of EGFRvIII expression and coexpression with EGFR in human invasive breast cancer by laser capture microdissection and immunohistochemical analysis. Ge H, Gong X, Tang CK, Int J Cancer 2002 98 3 357 361 10.1002/ijc.10224 11920586 (Pubitemid 34188678)
14. Detection of gene amplification in intraductal and infiltrating breast cancer by laser-assisted microdissection and quantitative real-time PCR. Glockner S, Lehmann U, Wilke N, Kleeberger W, Langer F, Kreipe H, Pathobiology: journal of immunopathology, molecular and cellular biology 2000 68 4-5 173 179 10.1159/000055920 11279343 (Pubitemid 32247252)
15. Expressions of cytochrome P450, UDP-glucuronosyltranferase, and transporter genes in monolayer carcinoma cells change in subcutaneous tumors grown as xenografts in immunodeficient nude mice. Sugawara M, Okamoto K, Kadowaki T, Kusano K, Fukamizu A, Yoshimura T, Drug metabolism and disposition: the biological fate of chemicals 2010 38 3 526 533 10.1124/dmd.109.030668 20007293
16. Hu/Mu ProtIn oligonucleotide microarray: dual-species array for profiling protease and protease inhibitor gene expression in tumors and their microenvironment. Schwartz DR, Moin K, Yao B, Matrisian LM, Coussens LM, Bugge T, Fingleton B, Acuff H, Sinnamon M, Nassar H, Platts AE, Krawetz SA, Linebaugh BE, Sloane BF, Mol Cancer Res 2007 5 5 443 454 10.1158/1541-7786.MCR-06-0337 17510311 (Pubitemid 46903953)
17. Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. Yang X, Lee Y, Huang Y, Chen JL, Xing RH, Lussier YA, BMC bioinformatics 2010 11 Suppl 9 11 10.1186/1471-2105-11-S9-S11 21044358
18. The CLIP-CHIP™: A Focused Oligonucleotide Microarray Platform for Transcriptome Analysis of the Complete Human and Murine Cancer Degradomes. Schwartz DR, Moin K, Weber E, Sloane BF, The Cancer Degradome. D E, G H-H, F B, BF S 2008 17 35
19. Comprehensive viral oligonucleotide probe design using conserved protein regions. Jabado OJ, Liu Y, Conlan S, Quan PL, Hegyi H, Lussier Y, Briese T, Palacios G, Lipkin WI, Nucleic acids research 2008 36 1 3 18079152
20. Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays. Liu Y, Sam L, Li J, Lussier YA, BMC bioinformatics 2009 10 Suppl 2 11 10.1186/1471-2105-10-S2-S11 19208186
21. Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Palacios G, Quan PL, Jabado OJ, Conlan S, Hirschberg DL, Liu Y, Zhai J, Renwick N, Hui J, Hegyi H, Grolla A, Strong JE, Towner JS, Geisbert TW, Jahrling PB, Buchen-Osmond C, Ellerbrok H, Sanchez-Seco MP, Lussier Y, Formenty P, Nichol MS, Feldmann H, Briese T, Lipkin WI, Emerg Infect Dis 2007 13 1 73 81 10.3201/eid1301.060837 17370518 (Pubitemid 46057840)
22. Evidence based selection of housekeeping genes. de Jonge HJ, Fehrmann RS, de Bont ES, Hofstra RM, Gerbens F, Kamps WA, de Vries EG, van der Zee AG, te Meerman GJ, ter Elst A, PloS one 2007 2 9 898 10.1371/journal.pone.0000898 17878933 (Pubitemid 351425878)
23. A scaling normalization method for differential expression analysis of RNA-seq data. Robinson MD, Oshlack A, Genome Biol 2010 11 3 25 10.1186/gb-2010-11-3-r25 20196867
24. Basic local alignment search tool. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, Journal of molecular biology 1990 215 3 403 410 10.1016/S0022-2836(05)80360-2 2231712
25. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M, Bioinformatics 2002 18 Suppl 1 96 104 10.1093/bioinformatics/18.suppl-1.S96 12169536
26. Using GOstats to test gene lists for GO term association. Falcon S, Gentleman R, Bioinformatics 2007 23 2 257 258 10.1093/bioinformatics/btl567 17098774 (Pubitemid 46189622)
27. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Benjamini Y, Hochberg Y, Journal of the Royal Statistical Society Series B (Methodological) 2005 57 289 300
28. Improving gene set analysis of microarray data by SAM-GS. Dinu I, Potter JD, Mueller T, Liu Q, Adewale AJ, Jhangri GS, Einecke G, Famulski KS, Halloran P, Yasui Y, BMC bioinformatics 2007 8 242 10.1186/1471-2105-8-242 17612399 (Pubitemid 47163143)
29. Stromal cells are active contributors to tumorigenesis. Weinberg R, The Biology of Cancer. 2007 548 551
30. Characterization of a novel breast carcinoma xenograft and cell line derived from a BRCA1 germ-line mutation carrier. Johannsson OT, Staff S, Vallon-Christersson J, Kytola S, Gudjonsson T, Rennstam K, Hedenfalk IA, Adeyinka A, Kjellen E, Wennerberg J, Baldetorp B, Petersen OW, Olsson H, Oredsson S, Isola J, Borg A, Laboratory investigation; a journal of technical methods and pathology 2003 83 3 387 396 10.1097/01.LAB.0000060030.10652.8C 12649339 (Pubitemid 36351000)
31. Gene expression profiling of human colon xenograft tumors following treatment with SU11248, a multitargeted tyrosine kinase inhibitor. Morimoto AM, Tan N, West K, McArthur G, Toner GC, Manning WC, Smolich BD, Cherrington JM, Oncogene 2004 23 8 1618 1626 10.1038/sj.onc.1207268 14985702 (Pubitemid 38406525)
32. STAT1 pathway mediates amplification of metastatic potential and resistance to therapy. Khodarev NN, Roach P, Pitroda SP, Golden DW, Bhayani M, Shao MY, Darga TE, Beveridge MG, Sood RF, Sutton HG, Beckett MA, Mauceri HJ, Posner MC, Weichselbaum RR, PloS one 2009 4 6 5821 10.1371/journal.pone.0005821 19503789
33. Evolution of the androgen receptor pathway during progression of prostate cancer. Hendriksen PJ, Dits NF, Kokame K, Veldhoven A, van Weerden WM, Bangma CH, Trapman J, Jenster G, Cancer research 2006 66 10 5012 5020 10.1158/0008-5472.CAN-05-3082 16707422 (Pubitemid 43844921)
34. Molecular determinants of resistance to antiandrogen therapy. Chen CD, Welsbie DS, Tran C, Baek SH, Chen R, Vessella R, Rosenfeld MG, Sawyers CL, Nature medicine 2004 10 1 33 39 10.1038/nm972 14702632 (Pubitemid 38524696)
35. High frequencies of leukemia stem cells in poor-outcome childhood precursor-B acute lymphoblastic leukemias. Morisot S, Wayne AS, Bohana-Kashtan O, Kaplan IM, Gocke CD, Hildreth R, Stetler-Stevenson M, Walker RL, Davis S, Meltzer PS, Wheelan SJ, Brown P, Jones RJ, Shultz LD, Civin CI, Leukemia 2010 20739953