Reverse-engineering the genetic circuitry of a cancer cell with predicted intervention in chronic lymphocytic leukemia

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 2, 2013, Pages 459-464

  Vallat, Laurent ^a,b   Kemper, Corey A ^c   Jung, Nicolas ^a   Maumy Bertrand, Myriam ^a   Bertrand, Fréd́eric ^a   Meyer, Nicolas ^d   Pocheville, Arnaud ^e   Fisher III, John W ^c   Gribben, John G ^f   Bahram, Seiamak ^a,b  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b HÔPITAL CIVIL   (France)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d UNIVERSITY HOSPITAL OF STRASBOURG   (France)

^e CNRS   (France)

^f QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

B cell antigen receptor; Lasso penalty; Lymphoproliferative disorder; Predicted intervention; Temporal gene network

Indexed keywords

ARTICLE; CANCER CELL; CELL ACTIVITY; CELL MIGRATION; CELL PROLIFERATION; CHRONIC LYMPHATIC LEUKEMIA; CONTROLLED STUDY; GENE EXPRESSION; GENETIC ENGINEERING; HUMAN; HUMAN CELL; PREDICTION; PRIORITY JOURNAL;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; GENETIC ENGINEERING; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; LEUKEMIA, LYMPHOID; MICROARRAY ANALYSIS; MODELS, BIOLOGICAL; RECEPTORS, ANTIGEN, B-CELL; REGRESSION ANALYSIS; REVERSE GENETICS; RNA INTERFERENCE;

EID: 84872174533     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1211130110     Document Type: Article

References (36)

1. Lee TI, et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298(5594):799-804.
2. Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-312.
3. Yosef N, Regev A (2011) Impulse control: Temporal dynamics in gene transcription. Cell 144(6):886-896.
4. Barabási AL, Oltvai ZN (2004) Network biology: Understanding the cell's functional organization. Nat Rev Genet 5(2):101-113.
5. Kitano H (2002) Systems biology: A brief overview. Science 295(5560):1662-1664.
6. Liu YY, Slotine JJ, Barabási AL (2011) Controllability of complex networks. Nature 473 (7346):167-173.
7. Hecker M, Lambeck S, Toepfer S, van Someren E, Guthke R (2009) Gene regulatory network inference: Data integration in dynamic models-a review. Biosystems 96(1):86-103.
8. Marbach D, et al. (2010) Revealing strengths and weaknesses of methods for gene network inference. Proc Natl Acad Sci USA 107(14):6286-6291.
9. Schäfer J, Strimmer K (2005) An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics 21(6):754-764.
10. Zoppoli P, Morganella S, Ceccarelli M(2010) TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. BMC Bioinformatics 11:154.
11. Gardner TS, di Bernardo D, Lorenz D, Collins JJ (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301(5629):102-105.
12. Vallat LD, Park Y, Li C, Gribben JG (2007) Temporal genetic program following B-cell receptor cross-linking: Altered balance between proliferation and death in healthy and malignant B cells. Blood 109(9):3989-3997.
13. Stevenson FK, Caligaris-Cappio F (2004) Chronic lymphocytic leukemia: Revelations from the B-cell receptor. Blood 103(12):4389-4395.
14. Messmer BT, et al. (2004) Multiple distinct sets of stereotyped antigen receptors indicate a role for antigen in promoting chronic lymphocytic leukemia. J Exp Med 200(4):519-525.
15. Perrot A, et al. (2011) A unique proteomic profile on surface IgM ligation in unmutated chronic lymphocytic leukemia. Blood 118(4):e1-e15.
16. Chiorazzi N, Rai KR, Ferrarini M (2005) Chronic lymphocytic leukemia. N Engl J Med 352(8):804-815.
17. Hamblin TJ, Davis Z, Gardiner A, Oscier DG, Stevenson FK (1999) Unmutated Ig V(H) genes are associated with a more aggressive form of chronic lymphocytic leukemia. Blood 94(6):1848-1854.
18. Herishanu Y, et al. (2011) The lymph node microenvironment promotes B-cell receptor signaling, NF-kappaB activation, and tumor proliferation in chronic lymphocytic leukemia. Blood 117(2):563-574.
19. Guarini A, et al. (2008) BCR ligation induced by IgM stimulation results in gene expression and functional changes only in IgV H unmutated chronic lymphocytic leukemia (CLL) cells. Blood 112(3):782-792.
20. Hao S, Baltimore D (2009) The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules. Nat Immunol 10(3):281-288.
21. Di Camillo B, et al. (2012) Function-based discovery of significant transcriptional temporal patterns in insulin stimulated muscle cells. PLoS ONE 7(3):e32391.
22. Bhowmick D, Davison AC, Goldstein DR, Ruffieux Y (2006) A Laplace mixture model for identification of differential expression in microarray experiments. Biostatistics 7(4):630-641.
23. Califano A (2011) Rewiring makes the difference. Mol Syst Biol 7:463.
24. Christley S, Nie Q, Xie X (2009) Incorporating existing network information into gene network inference. PLoS ONE 4(8):e6799.
25. Long J, Roth M (2008) Synthetic microarray data generation with RANGE and NEMO. Bioinformatics 24(1):132-134.
26. Alon U (2007) Network motifs: Theory and experimental approaches. Nat Rev Genet 8(6):450-461.
27. Weaver DC, et al. (1999) Modeling regulatory networks with weight matrices. Pac Symp Biocomput 4:112-123.
28. Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D (2007) How to infer gene networks from expression profiles. Mol Syst Biol 3:78.
29. Van Rijsbergen CJ (1979) Information Retrieval (Butterworth-Heinemann, London).
30. Huang T, et al. (2010) Using GeneReg to construct time delay gene regulatory networks. BMC Res Notes 3(1):142.
31. Morrissey ER, Juarez MA, Denby KJ, Burroughs NJ (2011) Inferring the time-invariant topology of a nonlinear sparse gene regulatory network using fully Bayesian spline autoregression. Biostatistics 12(4):682-694.
32. Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc Natl Acad Sci USA 98(1):31-36.
33. Huang DW, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37(1):1-13.
34. Mielke P, Berry K (2007) Permutation Methods: A Distance Function Approach (Springer, New York).
35. Ernst J, Nau GJ, Bar-Joseph Z (2005) Clustering short time series gene expression data. Bioinformatics 21(Suppl 1):i159-i168.
36. Margolin AA, et al. (2006) ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7(Suppl 1):S7.