Geodesic
Analysis of the Growth Control Network Specific for Human Lung Adenocarcinoma Cells
G. Pinna1 ; A. Zinovyev2, 3, 4 ; N. Araujo1 ; N. Morozova1 ; A. Harel-Bellan1
1 CNRS FRE 3377, CEA Saclay, Gif-sur-Yvette, F-91191 and Universite Paris-Sud, Gif-sur-Yvette, F-91191, France
2 Institut Curie, 26 rue d’Ulm, Paris, France
3 INSERM, U900, F-75248 Paris, France
4 Mines ParisTech, Centre for Computational Biology, F-77300 Fontainebleau, France
Mathematical modelling of natural phenomena, Tome 7 (2012) no. 1, pp. 337-368.

Voir la notice de l'article provenant de la source EDP Sciences

Many cancer-associated genes and pathways remain to be identified in order to clarify the molecular mechanisms underlying cancer progression. In this area, genome-wide loss-of-function screens appear to be powerful biological tools, allowing the accumulation of large amounts of data. However, this approach currently lacks analytical tools to exploit the data with maximum efficiency, for which systems biology methods analyzing complex cellular networks may be extremely helpful. In this article we report such a systems biology strategy based on the construction of a Network for a biological process and specific for a given cell system (cell type). The networks are created from genome-wide loss-of-function screen datasets. We also propose tools to analyze network properties. As one of the tools, we suggest a mathematical model for discrimination between two distinct cell processes that may be affected by knocking down the activity of a gene, i. e., a decreased cell number may be caused by arrested cell proliferation or enhanced cell death. Next we show how this discrimination between the two cell processes helps to construct two corresponding subnetworks. Finally, we demonstrate an application of the proposed strategy to the identification and characterization of putative novel genes and pathways significant for the control of lung cancer cell growth, based on the results of a genome-wide proliferation/viability loss-of-function screen of human lung adenocarcinoma cells.
DOI : 10.1051/mmnp/20127115

G. Pinna 1 ; A. Zinovyev 2, 3, 4 ; N. Araujo 1 ; N. Morozova 1 ; A. Harel-Bellan 1

1 CNRS FRE 3377, CEA Saclay, Gif-sur-Yvette, F-91191 and Universite Paris-Sud, Gif-sur-Yvette, F-91191, France
2 Institut Curie, 26 rue d’Ulm, Paris, France
3 INSERM, U900, F-75248 Paris, France
4 Mines ParisTech, Centre for Computational Biology, F-77300 Fontainebleau, France 
@article{MMNP_2012_7_1_a14,
     author = {G. Pinna and A. Zinovyev and N. Araujo and N. Morozova and A. Harel-Bellan},
     title = {Analysis of the {Growth} {Control} {Network} {Specific} for {Human} {Lung} {Adenocarcinoma} {Cells}},
     journal = {Mathematical modelling of natural phenomena},
     pages = {337--368},
     publisher = {mathdoc},
     volume = {7},
     number = {1},
     year = {2012},
     doi = {10.1051/mmnp/20127115},
     language = {en},
     url = {http://geodesic.mathdoc.fr/articles/10.1051/mmnp/20127115/}
}
TY  - JOUR
AU  - G. Pinna
AU  - A. Zinovyev
AU  - N. Araujo
AU  - N. Morozova
AU  - A. Harel-Bellan
TI  - Analysis of the Growth Control Network Specific for Human Lung Adenocarcinoma Cells
JO  - Mathematical modelling of natural phenomena
PY  - 2012
SP  - 337
EP  - 368
VL  - 7
IS  - 1
PB  - mathdoc
UR  - http://geodesic.mathdoc.fr/articles/10.1051/mmnp/20127115/
DO  - 10.1051/mmnp/20127115
LA  - en
ID  - MMNP_2012_7_1_a14
ER  - 
%0 Journal Article
%A G. Pinna
%A A. Zinovyev
%A N. Araujo
%A N. Morozova
%A A. Harel-Bellan
%T Analysis of the Growth Control Network Specific for Human Lung Adenocarcinoma Cells
%J Mathematical modelling of natural phenomena
%D 2012
%P 337-368
%V 7
%N 1
%I mathdoc
%U http://geodesic.mathdoc.fr/articles/10.1051/mmnp/20127115/
%R 10.1051/mmnp/20127115
%G en
%F MMNP_2012_7_1_a14
G. Pinna; A. Zinovyev; N. Araujo; N. Morozova; A. Harel-Bellan. Analysis of the Growth Control Network Specific for Human Lung Adenocarcinoma Cells. Mathematical modelling of natural phenomena, Tome 7 (2012) no. 1, pp. 337-368. doi : 10.1051/mmnp/20127115. http://geodesic.mathdoc.fr/articles/10.1051/mmnp/20127115/

[1] C.J. Creighton, J.L. Bromberg-White, D.E. Misek, D.J. Monsma, F. Brichory, R. Kuick, T.J. Giordano, W. Gao, G.S. Omenn, C.P. Webb, S.M. Hanash Mol Cancer Res. 2005 119 29

[2] Y. Murakami Oncogene 2002 6936 48

[3] Y. Jiang, L. Cui, T.A. Yie, W.N. Rom, H. Cheng, K.M. Tchou-Wong Inhibition of anchorage-independent growth and lung metastasis of A549 lung carcinoma cells by IkappaBbeta Oncogene 2001 2254 63

[4] M. Soda Identification of the transforming EML4-ALK fusion gene in non-small cell lung cancer Nature 2007 561 566

[5] R. Kittler, L. Pelletier, A.K. Heninger, M. Slabicki, M. Theis, L. Miroslaw, I. Poser, S. Lawo, H. Grabner, K. Kozak, J. Wagner, V. Surendranath, C. Richter, W. Bowen, A.L. Jackson, B. Habermann, A.A. Hyman, F. Buchholz Genome-scale RNAi profiling of cell division in human tissue culture cells Nat Cell Biol. 2007 1401 12

[6] M.A. Pujana, J.D. Han, L.M. Starita, K.N. Stevens, M. Tewari, J.S. Ahn, G. Rennert, V. Moreno, T. Kirchhoff, B. Gold, V. Assmann, W.M. Elshamy, J.F. Rual, D. Levine, L.S. Rozek, R.S. Gelman, K.C. Gunsalus, R.A. Greenberg, B. Sobhian, N. Bertin, K. Venkatesan, N. Ayivi-Guedehoussou, X. Sole, P. Hernindez, C. Lazaro, K.L. Nathanson, B.L. Weber, M.E. Cusick, D.E. Hill, K. Offit, D.M. Livingston, S.B. Gruber, J.D. Parvin, M. Vidal Network modeling links breast cancer susceptibility and centrosome dysfunction Nat Genet. 2007 1338 49

[7] M. Vidal A biological atlas of functional maps Cell 2001 333 339

[8] E. Segal, N. Friedman, D. Koller, A. Regev A module map showing conditional activity of expression modules in cancer Nat Genet. 2004 1090 1098

[9] A. Beyer, S. Bandyopadhyay, T. Ideker Nat Rev Genet. 2007 699 710

[10] T. Haberichter, B. Mädge, R.A. Christopher, N. Yoshioka, A. Dhiman, R. Miller, R. Gendelman, S.V. Aksenov, I.G. Khalil, S.F. Dowdy Mol Syst Biol. 2007

[11] O. Sahin, C. Löbke, U. Korf, H. Appelhans, Sültmann H, Poustka A, Wiemann S, Arlt D Combinatorial RNAi for quantitative protein network analysis Proc Natl Acad Sci U S A. 2007 6579 84

[12] A. Bankhead, I. Sach, C. Ni, N. Lemeur, M. Kruger, M. Ferrer, R. Gentleman, C. Rohl BMC Syst Biol. 2009

[13] B. Lehner, C. Crombie, J. Tischler, A. Fortunato, A.G. Fraser Nat Genet. 2006 896 903

[14] M. Mukherji, R. Bell, L. Supekova, Y. Wang, A.P. Orth, S. Batalov, L. Miraglia, D. Huesken, J. Lange, C. Martin, S. Sahasrabudhe, M. Reinhardt, F. Natt, J. Hall, C. Mickanin, M. Labow, S.K. Chanda, C.Y. Cho, P.G. Schultz PNAS 2006 14819 14824

[15] M.H. Beers, Lung Carcinoma. In The Merck manual of diagnosis and therapy (R.S. Porter, and T.V. Jones, editors). Rahway : Merck Co., Inc. (2008), 2992.

[16] A. Jemal J Natl Cancer Inst 2008 1672 1694

[17] R.K. Kancha, N. Von Bubnoff, C. Peschel, J. Duyster Clin Cancer Res. 2009 460 467

[18] C.T. Miller, G. Chen, T.G. Gharib, H. Wang, D.G. Thomas, D.E. Misek, T.J. Giordano, J. Yee, M.B. Orringer, S.M. Hanash, D.G. Beer Oncogene 2003 7950 7957

[19] A. Zinovyev, E. Viara, L. Calzone, E. Barillot Bioinformatics 2008 876 877

[20] H. Shigematsu, A.F. Gazdar Int J Cancer 2006 257 262

[21] C. Mascaux, N. Iannino, B. Martin, M. Paesmans, T. Berghmans, M. Dusart, A. Haller, P. Lothaire, A.P. Meert, S. Noel, J.J. Lafitte, J.P. Sculier Br J Cancer. 2005 131 139

[22] M. Smoot, K. Ono, J. Ruscheinski, P.-L. Wang, T. Ideker Bioinformatics 2011 431 432

[23] Y.M. Chook, G. Blobel Curr Opin Struct Biol. 2001 703 715

[24] B. Lü, J. Xu, Y. Zhu, H. Zhang, M. Lai Clin Chim Acta. 2007 42 47

[25] J.W. Park, Y.S. Bae Biochem Biophys Res Commun 1999 475 481

Cité par Sources :