Construction of a computable network model for DNA damage, autophagy, cell death, and senescence

Bioinformatics and Biology Insights

Volumn 7, Issue , 2013, Pages 97-117

  Gebel, Stephan ^a   Lichtner, Rosemarie B ^a   Frushour, Brian ^c   Schlage, Walter K ^a   Hoang, Vy ^c   Talikka, Marja ^b   Hengstermann, Arnd ^a   Mathis, Carole ^b   Veljkovic, Emilija ^b   Peck, Michael ^b   Peitsch, Manuel C ^b   Deehan, Renee ^c   Hoeng, Julia ^b   Westra, Jurjen W ^c  

^a Philip Morris Research Laboratories GmbH   (Germany)

^b PHILIP MORRIS PRODUCTS S A   (Switzerland)

^c Selventa   (United States)

Author keywords

Apoptosis; Autophagy; Biological expression language (BEL); Computable; Dna damage; Necroptosis; Network model; Senescence

Indexed keywords

APOPTOSIS; ARTICLE; AUTOPHAGY; CELL AGING; CELL FATE; CELL STRESS; COMPUTER PROGRAM; DNA DAMAGE; ENVIRONMENTAL EXPOSURE; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; NECROPTOSIS; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; SYSTEMS BIOLOGY;

EID: 84874921123     PISSN: 11779322     EISSN: None     Source Type: Journal    
DOI: 10.4137/BBI.S11154     Document Type: Article

References (69)

1. Mahadevan B, Snyder RD, Waters MD, et al. Genetic toxicology in the 21st century: reflections and future directions. Environ Mol Mutagen. Jun 2011;52(5):339-54.
2. Stephens ML, Barrow C, Andersen ME, et al. Accelerating the development of 21st-century toxicology: outcome of a Human Toxicology Project Consortium workshop. Toxicol Sci. 2012;125(2):327-34.
3. Schlage WK, Westra JW, Gebel S, et al. A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue. BMC Syst Biol. 5 2011;5:168.
4. Westra JW, Schlage WK, Frushour BP, et al. Construction of a computable cell proliferation network focused on non-diseased lung cells. BMC Syst Biol. 2011;5:105.
5. Kuper H, Adami HO, Boffetta P. Tobacco use, cancer causation and public health impact. J Intern Med. 2002;251(6):455-66.
6. Ris C. US EPA health assessment for diesel engine exhaust: a review. Inhal Toxicol. 2007;19 Suppl 1:229-39.
7. Budinger GR, Mutlu GM. Update in environmental and occupational medicine 2010. Am J Respir Crit Care Med. 2011;183(12):1614-9.
8. Courtois-Cox S, Genther Williams SM, Reczek EE, et al. A negative feedback signaling network underlies oncogene-induced senescence. Cancer Cell. 2006;10(6):459-72.
9. Zhang JY, Wang Y, Prakash C. Xenobiotic-metabolizing enzymes in human lung. Curr Drug Metab. 2006;7(8):939-48.
10. Ron D, Walter P. Signal integration in the endoplasmic reticulum unfolded protein response. Nat Rev Mol Cell Biol. 2007;8(7):519-29.
11. Vicencio JM, Galluzzi L, Tajeddine N, et al. Senescence, apoptosis or autophagy? When a damaged cell must decide its path-a mini-review. Gerontology. 2008;54(2):92-9.
12. Langerak P, Russell P. Regulatory networks integrating cell cycle control with DNA damage checkpoints and double-strand break repair. Philos Trans R Soc Lond B Biol Sci. 2011;366(1584):3562-71.
13. Ulukaya E, Acilan C, Yilmaz Y. Apoptosis: why and how does it occur in biology? Cell Biochem Funct. 2011;29(6):468-80.
14. Kroemer G, Galluzzi L, Vandenabeele P, et al. Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009. Cell Death Differ. 2009;16(1):3-11.
15. Vandenabeele P, Galluzzi L, Vanden Berghe T, Kroemer G. Molecular mechanisms of necroptosis: an ordered cellular explosion. Nat Rev Mol Cell Biol. 2010;11(10):700-14.
16. Cho S, Hwang ES. Fluorescence-based detection and quantification of features of cellular senescence. Methods Cell Biol. 2011;103:149-88.
17. Ryter SW, Nakahira K, Haspel JA, Choi AM. Autophagy in pulmonary diseases. Annu Rev Physiol. 2012;74:377-401.
18. Kroemer G, Marino G, Levine B. Autophagy and the integrated stress response. Mol Cell. 2010;40(2):280-93.
19. Marino G, Madeo F, Kroemer G. Autophagy for tissue homeostasis and neuroprotection. Curr Opin Cell Biol. 2011;23(2):198-206.
20. Campisi J, d'Adda di Fagagna F. Cellular senescence: when bad things happen to good cells. Nat Rev Mol Cell Biol. 2007;8:729-40.
21. Rodier F, Campisi J. Four faces of cellular senescence. J Cell Biol. 2011; 192(4):547-56.
22. Nyunoya T, Monick MM, Klingelhutz A, Yarovinsky TO, Cagley JR, Hunninghake GW. Cigarette smoke induces cellular senescence. Am J Respir Cell Mol Biol. 2006;35(6):681-8.
23. Kim HP, Wang X, Chen ZH, et al. Autophagic proteins regulate cigarette smoke-induced apoptosis: protective role of heme oxygenase-1. Autophagy. 2008;4(7):887-95.
24. Nyunoya T, Monick MM, Klingelhutz AL, et al. Cigarette smoke induces cellular senescence via Werner's syndrome protein down-regulation. Am J Respir Crit Care Med. 2009;179(4):279-87.
25. Sdralia ND, Patmanidi AL, Velentzas AD, et al. The mode of lymphoblastoid cell death in response to gas phase cigarette smoke is dose-dependent. Respir Res. 2009;10(1):82.
26. Zhao H, Albino AP, Jorgensen E, Traganos F, Darzynkiewicz Z. DNA damage response induced by tobacco smoke in normal human bronchial epithelial and A549 pulmonary adenocarcinoma cells assessed by laser scanning cytometry. Cytometry A. 2009;75(10):840-7.
27. Chen ZH, Lam HC, Jin Y, et al. Autophagy protein microtubule-associated protein 1 light chain-3B (LC3B) activates extrinsic apoptosis during cigarette smoke-induced emphysema. Proc Natl Acad Sci U S A. 2010;107(44): 18880-5.
28. Elias ST, Diniz J, Almeida RS, et al. Cytotoxic effect of tobacco extracts on human oral squamous cell carcinoma cell-line. Oral Oncol. 2010;46(12): 869-73.
29. Jorgensen ED, Zhao H, Traganos F, Albino AP, Darzynkiewicz Z. DNA damage response induced by exposure of human lung adenocarcinoma cells to smoke from tobacco- and nicotine-free cigarettes. Cell Cycle. 2010;9(11): 2170-6.
30. Leone A, Landini L, Leone A. What is tobacco smoke? Sociocultural dimensions of the association with cardiovascular risk. Curr Pharm Des. 2010;16(23):2510-7.
31. Ryter SW, Choi AM. Autophagy in the lung. Proc Am Thorac Soc. 2010;7(1): 13-21.
32. Haspel JA, Choi AM. Autophagy: A Core Cellular Process with Emerging Links to Pulmonary Disease. Am J Respir Crit Care Med. 2011;184(11): 1237-46.
33. Shapiro SD. Merging personalized medicine and biology of aging in chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2011;184(8): 864-6.
34. Liu H, Knabb JR, Spike BT, Macleod KF. Elevated poly-(ADP-ribose)-polymerase activity sensitizes retinoblastoma-deficient cells to DNA damage-induced necrosis. Mol Cancer Res. 2009;7(7):1099-109.
35. Garinis GA, Uittenboogaard LM, Stachelscheid H, et al. Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity. Nat Cell Biol. 2009;11(5):604-15.
36. Pazolli E, Luo X, Brehm S, et al. Senescent stromal-derived osteopontin promotes preneoplastic cell growth. Cancer Res. 2009;69(3):1230-9.
37. Narita M, Young AR, Arakawa S, et al. Spatial coupling of mTOR and autophagy augments secretory phenotypes. Science. 2011;332(6032): 966-70.
38. Carpentier J, Luyckx AS, Lefebvre PJ. Influence of metformin on arginine-induced glucagon secretion in human diabetes. Diabete Metab. 1975;1:23-8.
39. Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4(2):249-64.
40. Gentleman RC, Carey VJ, Bates DM, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80.
41. Du P, Kibbe WA, Lin SM. nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays. Biol Direct. 2007; 2:16.
42. R Development Core Team. R: A Language and Environment for Statistical Computing; 2007.
43. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article 3.
44. Selventa. Reverse Causal Reasoning Methods Whitepaper; 2010.
45. Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498-504.
46. Zhu J, Woods D, McMahon M, Bishop JM. Senescence of human fibroblasts induced by oncogenic Raf. Genes Dev. 1998;12(19):2997-3007.
47. Wei S, Wei S, Sedivy JM. Expression of catalytically active telomerase does not prevent premature senescence caused by overexpression of oncogenic Ha-Ras in normal human fibroblasts. Cancer Res. 1999;59(7): 1539-43.
48. Batsi C, Markopoulou S, Vartholomatos G, et al. Chronic NF-kappaB activation delays RasV12-induced premature senescence of human fibroblasts by suppressing the DNA damage checkpoint response. Mech Ageing Dev. 2009;130(7):409-19.
49. Freund A, Orjalo AV, Desprez PY, Campisi J. Inflammatory networks during cellular senescence: causes and consequences. Trends Mol Med. 2010;16(5): 238-46.
50. Sun P, Yoshizuka N, New L, et al. PRAK is essential for ras-induced senescence and tumor suppression. Cell. 2007;128(2):295-308.
51. Li H, Wang W, Liu X, Paulson KE, Yee AS, Zhang X. Transcriptional factor HBP1 targets P16(INK4A), upregulating its expression and consequently is involved in Ras-induced premature senescence. Oncogene. 2010;29(36): 5083-94.
52. Sharpless NE. Ink4a/Arf links senescence and aging. Exp Gerontol. 2004; 39(11-12):1751-9.
53. Chai J, Charboneau AL, Betz BL, Weissman BE. Loss of the hSNF5 gene concomitantly inactivates p21CIP/WAF1 and p16INK4a activity associated with replicative senescence in A204 rhabdoid tumor cells. Cancer Res. 2005;65(22):10192-8.
54. Wu J, Xue L, Weng M, et al. Sp1 is essential for p16 expression in human diploid fibroblasts during senescence. PLoS One. 2007;2(1):e164.
55. Gan Q, Huang J, Zhou R, et al. PPAR{gamma} accelerates cellular senescence by inducing p16INK4{alpha} expression in human diploid fibroblasts. J Cell Sci. 2008;121(Pt 13):2235-45.
56. Wang X, Feng Y, Xu L, et al. YY1 restrained cell senescence through repressing the transcription of p16. Biochim Biophys Acta. 2008;(10)1783: 1876-83.
57. Lanigan F, Geraghty JG, Bracken AP. Transcriptional regulation of cellular senescence. Oncogene. 2011;30(26):2901-11.
58. Bracken AP, Kleine-Kohlbrecher D, Dietrich N, et al. The Polycomb group proteins bind throughout the INK4A-ARF locus and are disassociated in senescent cells. Genes Dev. 2007;21(5):525-30.
59. Wang SW, Lee JK, Ku CC, et al. Jun Dimerization Protein 2 in Oxygen Restriction; Control of Senescence. Curr Pharm Des. 2011;17(22):2278-89.
60. Cobrinik D. Pocket proteins and cell cycle control. Oncogene. 2005;24(17): 2796-809.
61. Croonquist PA, Linden MA, Zhao F, Van Ness BG. Gene profiling of a myeloma cell line reveals similarities and unique signatures among IL-6 response, N-ras-activating mutations, and coculture with bone marrow stromal cells. Blood. 2003;102(7):2581-92.
62. Tsuyama N, Danjoh I, Otsuyama K, et al. IL-6-induced Bcl6 variant 2 supports IL-6-dependent myeloma cell proliferation and survival through STAT3. Biochem Biophys Res Commun. 2005;337(1):201-8.
63. Coppe JP, Patil CK, Rodier F, et al. A human-like senescence-associated secretory phenotype is conserved in mouse cells dependent on physiological oxygen. PLoS One. 2010;5(2):e9188.
64. Freund A, Patil CK, Campisi J. p38MAPK is a novel DNA damage response-independent regulator of the senescence-associated secretory phenotype. EMBO J. 2011;30(8):1536-48.
65. Behrends C, Sowa ME, Gygi SP, Harper JW. Network organization of the human autophagy system. Nature. 2010;466(7302):68-76.
66. Caron E, Ghosh S, Matsuoka Y, et al. A comprehensive map of the mTOR signaling network. Mol Syst Biol. 2010;6:453.
67. Passos JF, Nelson G, Wang C, et al. Feedback between p21 and reactive oxygen production is necessary for cell senescence. Mol Syst Biol. 2010;6: 347.
68. Plant N. Can systems toxicology identify common biomarkers of non-genotoxic carcinogenesis? Toxicology. 2008;254(3):164-9.
69. Kienhuis AS, Bessems JG, Pennings JL, et al. Application of toxicogenomics in hepatic systems toxicology for risk assessment: acetaminophen as a case study. Toxicol Appl Pharmacol. 2011;250(2):96-107.