Independent Component Analysis Uncovers the Landscape of the Bladder Tumor Transcriptome and Reveals Insights into Luminal and Basal Subtypes

Cell Reports

Volumn 9, Issue 4, 2014, Pages 1235-1245

  Biton, Anne ^a,b,c,o   Bernard Pierrot, Isabelle ^a   Lou, Yinjun ^a,p   Krucker, Clémentine ^a   Chapeaublanc, Elodie ^a   Rubio Pérez, Carlota ^d   López Bigas, Nuria ^d,e   Kamoun, Aurélie ^a   Neuzillet, Yann ^a,f,g   Gestraud, Pierre ^a,b,c   Grieco, Luca ^a,b,c   Rebouissou, Sandra ^a,b   deReyniès, Aurélien ^h   Benhamou, Simone ^i,j   Lebret, Thierry ^f,g   Southgate, Jennifer ^k   Barillot, Emmanuel ^a,b,c   Allory, Yves ^l,m,n   Zinovyev, Andrei ^a,b,c   Radvanyi, François ^a  

^a INSTITUT CURIE   (France)

^b INSERM   (France)

^c PSL RESEARCH UNIVERSITY   (France)

^d UNIVERSITAT POMPEU FABRA   (Spain)

^e INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

^f FOCH HOSPITAL   (France)

^g LABORATOIRE DES SCIENCES DU CLIMAT ET DE L ENVIRONNEMENT   (France)

^h Ligue Nationale Contre le Cancer   (France)

ⁱ INSTITUT GUSTAVE ROUSSY   (France)

^j U946   (France)

^k UNIVERSITY OF YORK   (United Kingdom)

^l HENRI MONDOR HOSPITAL   (France)

^m INSERM U955   (France)

ⁿ FACULTÉ DE MÉDECINE   (France)

^o UNIVERSITY OF CALIFORNIA   (United States)

^p ZHEJIANG UNIVERSITY   (China)

more..

Author keywords

[No Author keywords available]

Indexed keywords

PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; TRANSCRIPTOME;

ARTICLE; BASAL CELL CARCINOMA; BLADDER CANCER; BLADDER TUMOR; CANCER CELL LINE; CELL DIFFERENTIATION; CONTROLLED STUDY; GENE MUTATION; HUMAN; HUMAN TISSUE; INDEPENDENT COMPONENT ANALYSIS; LUMINAL CELL TUMOR; ONCOGENE; PPARG GENE; TUMOR CELL; TUMOR CLASSIFICATION; TUMOR INVASION; TUMOR MICROENVIRONMENT; UROTHELIUM; ALGORITHM; CARCINOGENESIS; CELL SURVIVAL; CLASSIFICATION; DISEASE COURSE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; METABOLISM; MUSCLE; PATHOLOGY; REPRODUCIBILITY; TUMOR GENE;

ALGORITHMS; CARCINOGENESIS; CELL DIFFERENTIATION; CELL SURVIVAL; DATABASES, GENETIC; DISEASE PROGRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; HUMANS; MUSCLES; NEOPLASM INVASIVENESS; PPAR GAMMA; REPRODUCIBILITY OF RESULTS; TRANSCRIPTOME; URINARY BLADDER NEOPLASMS; UROTHELIUM;

EID: 84912071423     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2014.10.035     Document Type: Article

References (35)

1. Bertucci F., Finetti P., Birnbaum D. Basal breast cancer: a complex and deadly molecular subtype. Curr. Mol. Med. 2012, 12:96-110.
2. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012, 487:330-337. Cancer Genome Atlas Network.
3. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 2014, 507:315-322. Cancer Genome Atlas Research Network.
4. Carpentier A.-S., Riva A., Tisseur P., Didier G., Hénaut A. The operons, a criterion to compare the reliability of transcriptome analysis tools: ICA is more reliable than ANOVA, PLS and PCA. Comput. Biol. Chem. 2004, 28:3-10.
5. Cheng W.-Y., Ou Yang T.-H., Anastassiou D. Biomolecular events in cancer revealed by attractor metagenes. PLoS Comput. Biol. 2013, 9:e1002920.
6. Chiappetta P., Roubaud M.C., Torrésani B. Blind source separation and the analysis of microarray data. J.Comput. Biol. 2004, 11:1090-1109.
7. Choi W., Porten S., Kim S., Willis D., Plimack E.R., Hoffman-Censits J., Roth B., Cheng T., Tran M., Lee I.L., et al. Identification of distinct basal and luminal subtypes of muscle-invasive bladder cancer with different sensitivities to frontline chemotherapy. Cancer Cell 2014, 25:152-165.
8. Chung C.H., Parker J.S., Karaca G., Wu J., Funkhouser W.K., Moore D., Butterfoss D., Xiang D., Zanation A., Yin X., et al. Molecular classification of head and neck squamous cell carcinomas using patterns of gene expression. Cancer Cell 2004, 5:489-500.
9. Cline M.S., Smoot M., Cerami E., Kuchinsky A., Landys N., Workman C., Christmas R., Avila-Campilo I., Creech M., Gross B., et al. Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc. 2007, 2:2366-2382.
10. Breast cancer and hormone replacement therapy: collaborative reanalysis of data from 51 epidemiological studies of 52,705 women with breast cancer and 108,411 women without breast cancer. Lancet 1997, 350:1047-1059. Collaborative Group on Hormonal Factors in Breast Cancer.
11. Damrauer J.S., Hoadley K.A., Chism D.D., Fan C., Tiganelli C.J., Wobker S.E., Yeh J.J., Milowsky M.I., Iyer G., Parker J.S., Kim W.Y. Intrinsic subtypes of high-grade bladder cancer reflect the hallmarks of breast cancer biology. Proc. Natl. Acad. Sci. USA 2014, 111:3110-3115.
12. Di Palma S., Simpson R.H.W., Marchiò C., Skálová A., Ungari M., Sandison A., Whitaker S., Parry S., Reis-Filho J.S. Salivary duct carcinomas can be classified into luminal androgen receptor-positive, HER2 and basal-like phenotypes. Histopathology 2012, 61:629-643.
13. Dyrskjøt L., Kruhøffer M., Thykjaer T., Marcussen N., Jensen J.L., Møller K., Ørntoft T.F. Gene expression in the urinary bladder: a common carcinoma insitu gene expression signature exists disregarding histopathological classification. Cancer Res. 2004, 64:4040-4048.
14. Falcon S., Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics 2007, 23:257-258.
15. Ferlay J., Shin H.R., Bray F., Forman D., Mathers C., Parkin D.M. Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int. J. Cancer 2010, 127:2893-2917.
16. Frigyesi A., Veerla S., Lindgren D., Höglund M. Independent component analysis reveals new and biologically significant structures in micro array data. BMC Bioinformatics 2006, 7:290.
17. Himberg J., Hyvärinen A., Esposito F. Validating the independent components of neuroimaging time series via clustering and visualization. Neuroimage 2004, 22:1214-1222.
18. Hyvärinen A. Fast and robust fixed-point algorithms for independent component analysis. IEEE Trans. Neural Netw. 1999, 10:626-634.
19. Jutten C., Hérault J. Blind separation of sources, part I: An adaptive algorithm based on neuromimetic architecture. Signal Process. 1991, 24:1-10.
20. Kim W.J., Kim E.J., Kim S.K., Kim Y.J., Ha Y.S., Jeong P., Kim M.J., Yun S.J., Lee K.M., Moon S.K., et al. Predictive value of progression-related gene classifier in primary non-muscle invasive bladder cancer. Mol. Cancer 2010, 9:3.
21. Kong S.L., Li G., Loh S.L., Sung W.K., Liu E.T. Cellular reprogramming by the conjoint action of ERα, FOXA1, and GATA3 to a ligand-inducible growth state. Mol. Syst. Biol. 2011, 7:526.
22. Lee S.-I., Batzoglou S. Application of independent component analysis to microarrays. Genome Biol. 2003, 4:R76.
23. Liebermeister W. Linear modes of gene expression determined by independent component analysis. Bioinformatics 2002, 18:51-60.
24. Lin D.W., Coleman I.M., Hawley S., Huang C.Y., Dumpit R., Gifford D., Kezele P., Hung H., Knudsen B.S., Kristal A.R., Nelson P.S. Influence of surgical manipulation on prostate gene expression: implications for molecular correlates of treatment effects and disease prognosis. J.Clin. Oncol. 2006, 24:3763-3770.
25. Rebouissou S., Bernard-Pierrot I., de Reyniès A., Lepage M.L., Krucker C., Chapeaublanc E., Hérault A., Kamoun A., Caillault A., Letouzé E., et al. EGFR as a potential therapeutic target for a subset of muscle-invasive bladder cancers presenting a basal-like phenotype. Sci Transl Med 2014, 6:244ra91.
26. Rouveirol C., Stransky N., Hupé P., Rosa P.L., Viara E., Barillot E., Radvanyi F. Computation of recurrent minimal genomic alterations from array-CGH data. Bioinformatics 2006, 22:849-856.
27. Sjödahl G., Lövgren K., Lauss M., Patschan O., Gudjonsson S., Chebil G., Aine M., Eriksson P., Månsson W., Lindgren D., et al. Toward a molecular pathologic classification of urothelial carcinoma. Am. J. Pathol. 2013, 183:681-691.
28. Sørlie T., Perou C.M., Tibshirani R., Aas T., Geisler S., Johnsen H., Hastie T., Eisen M.B., van de Rijn M., Jeffrey S.S., et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl. Acad. Sci. USA 2001, 98:10869-10874.
29. Spruck C.H., Ohneseit P.F., Gonzalez-Zulueta M., Esrig D., Miyao N., Tsai Y.C., Lerner S.P., Schmütte C., Yang A.S., Cote R., et al. Two molecular pathways to transitional cell carcinoma of the bladder. Cancer Res. 1994, 54:784-788.
30. Subramanian A., Tamayo P., Mootha V.K., Mukherjee S., Ebert B.L., Gillette M.A., Paulovich A., Pomeroy S.L., Golub T.R., Lander E.S., Mesirov J.P. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 2005, 102:15545-15550.
31. Teschendorff A.E., Journée M., Absil P.A., Sepulchre R., Caldas C. Elucidating the altered transcriptional programs in breast cancer using independent component analysis. PLoS Comput. Biol. 2007, 3:e161.
32. Turner R.M., Kwok C.S., Chen-Turner C., Maduakor C.A., Singh S., Loke Y.K. Thiazolidinediones and associated risk of bladder cancer: a systematic review and meta-analysis. Br. J. Clin. Pharmacol. 2014, 78:258-273.
33. Vallot C., Stransky N., Bernard-Pierrot I., Hérault A., Zucman-Rossi J., Chapeaublanc E., Vordos D., Laplanche A., Benhamou S., Lebret T., et al. A novel epigenetic phenotype associated with the most aggressive pathway of bladder tumor progression. J.Natl. Cancer Inst. 2011, 103:47-60.
34. Varley C.L., Stahlschmidt J., Lee W.C., Holder J., Diggle C., Selby P.J., Trejdosiewicz L.K., Southgate J. Role of PPARgamma and EGFR signalling in the urothelial terminal differentiation programme. J.Cell Sci. 2004, 117:2029-2036.
35. Wilkerson M.D., Yin X., Hoadley K.A., Liu Y., Hayward M.C., Cabanski C.R., Muldrew K., Miller C.R., Randell S.H., Socinski M.A., et al. Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically important, and correspond to normal cell types. Clin. Cancer Res. 2010, 16:4864-4875.