Cancer: Tilting at windmills?

Molecular Cancer

Volumn 12, Issue 1, 2013, Pages

  Kulkarni, Prakash ^a   Shiraishi, Takumi ^a   Kulkarni, Rahul V ^b  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF MASSACHUSETTS BOSTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTRINSICALLY DISORDERED PROTEIN; PROTEIN; UNCLASSIFIED DRUG;

GENE OVEREXPRESSION; MOLECULAR INTERACTION; NEOPLASM; NOTE; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN MODIFICATION; PROTEIN STRUCTURE;

ANIMALS; HUMANS; INTRINSICALLY DISORDERED PROTEINS; NEOPLASMS; PHENOTYPE; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPS; STOCHASTIC PROCESSES;

EID: 84884474048     PISSN: None     EISSN: 14764598     Source Type: Journal    
DOI: 10.1186/1476-4598-12-108     Document Type: Note

References (31)

1. Vogelstein B, Kinzler KW. Cancer genes and the pathways they control. Nat Med 2004, 10(8):789-99. 10.1038/nm1087, 15286780.
2. Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature 2009, 458(7239):719-24. 10.1038/nature07943, 2821689, 19360079.
3. Soto AM, Sonnenschein C. The somatic mutation theory of cancer: growing problems with the paradigm?. Bioessays 2004, 26(10):1097-107. 10.1002/bies.20087, 15382143.
4. Huang S, Ingber DE. A non-genetic basis for cancer progression and metastasis: self-organizing attractors in cell regulatory networks. Breast Dis 2006, 26:27-54.
5. Shachaf CM, Kopelman AM, Arvanitis C, Karlsson A, Beer S, Mandl S, Bachmann MH, Borowsky AD, Ruebner B, Cardiff RD, Yang Q, Bishop JM, Contag CH, Felsher DW. MYC inactivation uncovers pluripotent differentiation and tumour dormancy in hepatocellular cancer. Nature 2004, 431(7012):1112-7. 10.1038/nature03043, 15475948.
6. Mintz B, Illmensee K. Normal genetically mosaic mice produced from malignant teratocarcinoma cells. Proc Natl Acad Sci U S A 1975, 72(9):3585-9. 10.1073/pnas.72.9.3585, 433040, 1059147.
7. Hochedlinger K, Blelloch R, Brennan C, Yamada Y, Kim M, Chin L, Jaenisch R. Reprogramming of a melanoma genome by nuclear transplantation. Genes Dev 2004, 18(15):1875-85. 10.1101/gad.1213504, 517407, 15289459.
8. Sharma SV, Lee DY, Li B, Quinlan MP, Takahashi F, Maheswaran S, McDermott U, Azizian N, Zou L, Fischbach MA, Wong KK, Brandstetter K, Wittner B, Ramaswamy S, Classon M, Settleman J. A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell 2010, 141(1):69-80. 10.1016/j.cell.2010.02.027, 2851638, 20371346.
9. Allegrucci C, Rushton MD, Dixon JE, Sottile V, Shah M, Kumari R, Watson S, Alberio R, Johnson AD. Epigenetic reprogramming of breast cancer cells with oocyte extracts. Mol Cancer 2011, 10(1):7. 3034708, 21232089.
10. Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, Emili A, Xie XS. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 2010, 329:533-8. 10.1126/science.1188308, 2922915, 20671182.
11. Munsky B, Neuert G, van Oudenaarden A. Using gene expression noise to understand gene regulation. Science 2012, 336:183-7. 10.1126/science.1216379, 3358231, 22499939.
12. Capp JP. Stochastic gene expression, disruption of tissue averaging effects and cancer as a disease of development. Bioessays 2005, 27(12):1277-85. 10.1002/bies.20326, 16299757.
13. Ladbury JE, Arold ST. Noise in cellular signaling pathways: causes and effects. Trends Biochem Sci 2012, 37:173-178. 10.1016/j.tibs.2012.01.001, 3348409, 22341496.
14. Mahmoudabadi G, Rajagopalan K, Getzenberg RH, Hannenhalli S, Rangarajan G, Kulkarni P. Intrinsically disordered proteins and conformational noise: implications in cancer. Cell Cycle 2013, 12(1):26-31. 10.4161/cc.23178, 23255110.
15. Vavouri T, Semple JI, Garcia-Verdugo R, Lehner B. Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity. Cell 2009, 138(1):198-208. 10.1016/j.cell.2009.04.029, 19596244.
16. Uversky VN, Dunker AK. Understanding protein non-folding. Biochim Biophys Acta 1804, 2010:1231-64.
17. Tompa P, Csermely P. The role of structural disorder in the function of RNA and protein chaperones. FASEB J 2004, 18:1169-75. 10.1096/fj.04-1584rev, 15284216.
18. Cumberworth A, Lamour G, Babu MM, Gsponer J. Promiscuity as a functional trait: intrinsically disordered regions as central players of interactomes. Biochem J 2013, 454(3):361-9. 10.1042/BJ20130545, 23988124.
19. Marcotte EM, Tsechansky M. Disorder, promiscuity, and toxic partnerships. Cell 2009, 138:16-18. 10.1016/j.cell.2009.06.024, 2848715, 19596229.
20. Iakoucheva LM, Brown CJ, Lawson JD, Obradović Z, Dunker AK. Intrinsic disorder in cell-signaling and cancer-associated proteins. J Mol Biol 2002, 323(3):573-84. 10.1016/S0022-2836(02)00969-5, 12381310.
21. Rajagopalan K, Mooney SM, Parekh N, Getzenberg RH, Kulkarni P. A majority of the cancer/testis antigens are intrinsically disordered proteins. J Cell Biochem 2011, 112(11):3256-67. 10.1002/jcb.23252, 3214731, 21748782.
22. Eldar A, Elowitz MB. Functional roles for noise in genetic circuits. Nature 2010, 467(7312):167-73. 10.1038/nature09326, 20829787.
23. Yamanaka S. Elite and stochastic models for induced pluripotent stem cell generation. Nature 2009, 460:49-52. 10.1038/nature08180, 19571877.
24. Gupta PB, Fillmore CM, Jiang G, Shapira SD, Tao K, Kuperwasser C, Lander ES. Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells. Cell 2011, 146(4):633-44. 10.1016/j.cell.2011.07.026, 21854987.
25. Kim J, Woo AJ, Chu J, Snow JW, Fujiwara Y, Kim CG, Cantor AB, Orkin SH. A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. Cell 2010, 143(2):313-24. 10.1016/j.cell.2010.09.010, 3018841, 20946988.
26. Lambert G, Estévez-Salmeron L, Oh S, Liao D, Emerson BM, Tlsty TD, Austin RH. An analogy between the evolution of drug resistance in bacterial communities and malignant tissues. Nat Rev Cancer 2011, 11(5):375-82. 10.1038/nrc3039, 3488437, 21508974.
27. Ben-Jacob E, Coffey DS, Levine H. Bacterial survival strategies suggest rethinking cancer cooperativity. Trends Microbiol 2012, 20(9):403-10. 10.1016/j.tim.2012.06.001, 22750098.
28. Sonnenschein S, Soto AM, Rangarajan A, Kulkarni P. Competing views on cancer. J Biosciences 2013, in press.
29. Huang S, Ernberg I, Kauffman S. Cancer attractors: a systems view of tumors from a gene network dynamics and developmental perspective. Semin Cell Dev Biol 2009, 20(7):869-76. 10.1016/j.semcdb.2009.07.003, 2754594, 19595782.
30. Huang S. Tumor progression: chance and necessity in Darwinian and Lamarckian somatic (mutationless) evolution. Prog Biophys Mol Biol 2012, 110(1):69-86. 10.1016/j.pbiomolbio.2012.05.001, 22579660.
31. Mukhtar MS, Carvunis AR, Dreze M, Epple P, Steinbrenner J, Moore J, Tasan M, Galli M, Hao T, Nishimura MT, Pevzner SJ, Donovan SE, Ghamsari L, Santhanam B, Romero V, Poulin MM, Gebreab F, Gutierrez BJ, Tam S, Monachello D, Boxem M, Harbort CJ, McDonald N, Gai L, Chen H, He Y, Vandenhaute J, Roth FP, Hill DE,, et al. European Union Effectoromics Consortium Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science 2011, 333(6042):596-601. 10.1126/science.1203659, 3170753, 21798943, European Union Effectoromics Consortium.