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Transcription Factors as Detection and Diagnostic Biomarkers in Cancer

  • W. L. GohEmail author
  • E. Assah
  • X. T. Zheng
  • D. P. Lane
  • F. J. Ghadessy
  • Y. N. Tan
Chapter

Abstract

The survival of cellular life depends on the accurate and coordinated maintenance of biological processes at the single-cell level such as cell-cycle progression, differentiation, metabolism, development, and programmed cell death (Rudel and Sommer 2003; Hanahan and Weinberg 2011; DeBerardinis and Thompson 2012). Consequently, simultaneous regulation of complex intracellular programs is heavily reliant on the precision of gene expression at the transcriptional level. Eukaryotic gene expression begins typically with the assembly of transcription-related protein complexes and cofactors on DNA before genetic information is transcribed into messenger RNA molecules, through the recruitment of RNA polymerase and cofactors, allowing for downstream protein translation (Lee and Young 2000). Sequence-specific DNA-binding transcription factors (TFs) are an integral part of the transcriptional machinery that regulate gene expression rates through the recognition and binding to precise DNA motifs (enhancer regions or response elements) resulting in either transcriptional activation or repression (Robertson et al. 2006) through further interaction with co-regulators and histone modifiers (HATs, HDACs) (Schaefer et al. 2011). Whole-genome studies have predicted 2000–3000 TFs in the human genome (Babu et al. 2004; Kummerfeld and Teichmann 2006; Venter et al. 2001), and bioinformatics, transcriptome analysis estimates that TFs account for ~8–10% of human genes expressed (Messina et al. 2004; Kummerfeld and Teichmann 2006).

References

  1. Andre F, Bachelot T, Commo F, Campone M, Arnedos M, Dieras V, Lacroix-Triki M, Lacroix L, Cohen P, Gentien D, Adelaide J, Dalenc F, Goncalves A, Levy C, Ferrero JM, Bonneterre J, Lefeuvre C, Jimenez M, Filleron T, Bonnefoi H (2014) Comparative genomic hybridisation array and DNA sequencing to direct treatment of metastatic breast cancer: a multicentre, prospective trial (SAFIR01/UNICANCER). Lancet Oncol 15:267–274PubMedCrossRefGoogle Scholar
  2. Ascenzi P, Bocedi A, Marino M (2006) Structure-function relationship of estrogen receptor alpha and beta: impact on human health. Mol Asp Med 27:299–402CrossRefGoogle Scholar
  3. Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA (2004) Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 14:283–291PubMedCrossRefGoogle Scholar
  4. Balagurumoorthy P, Sakamoto H, Lewis MS, Zambrano N, Clore GM, Gronenborn AM, Appella E, Harrington RE (1995) Four p53 DNA-binding domain peptides bind natural p53-response elements and bend the DNA. Proc Natl Acad Sci U S A 92:8591–8595PubMedPubMedCentralCrossRefGoogle Scholar
  5. Beckerman R, Prives C (2010) Transcriptional regulation by p53. Cold Spring Harb Perspect Biol 2:a000935PubMedPubMedCentralCrossRefGoogle Scholar
  6. Beishline K, Azizkhan-Clifford J (2015) Sp1 and the ‘hallmarks of cancer’. FEBS J 282:224–258PubMedCrossRefGoogle Scholar
  7. Belyi VA, Ak P, Markert E, Wang H, Hu W, Puzio-Kuter A, Levine AJ (2010) The origins and evolution of the p53 family of genes. Cold Spring Harb Perspect Biol 2:a001198PubMedPubMedCentralCrossRefGoogle Scholar
  8. Bieging KT, Mello SS, Attardi LD (2014) Unravelling mechanisms of p53-mediated tumour suppression. Nat Rev Cancer 14:359–370PubMedPubMedCentralCrossRefGoogle Scholar
  9. Blackwood EM, Eisenman RN (1991) Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding complex with Myc. Science 251:1211–1217PubMedCrossRefGoogle Scholar
  10. Boutell et al (2004) Proteomics 4(7):1950–1958Google Scholar
  11. Brenowitz M, Senear DF, Shea MA, Ackers GK (1986) Quantitative DNase footprint titration: a method for studying protein-DNA interactions. Methods Enzymol 130:132–181PubMedCrossRefGoogle Scholar
  12. Bullock AN, Fersht AR (2001) Rescuing the function of mutant p53. Nat Rev Cancer 1:68–76PubMedCrossRefGoogle Scholar
  13. Cai Q, Yan L, Xu Y (2015) Anoikis resistance is a critical feature of highly aggressive ovarian cancer cells. Oncogene 34:3315–3324PubMedCrossRefGoogle Scholar
  14. Chang GS, Chen XA, Park B, Rhee HS, Li P, Han KH, Mishra T, Chan-Salis KY, Li Y, Hardison RC, Wang Y, Pugh BF (2014) A comprehensive and high-resolution genome-wide response of p53 to stress. Cell Rep 8:514–527PubMedPubMedCentralCrossRefGoogle Scholar
  15. Chen FE, Huang DB, Chen YQ, Ghosh G (1998) Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA. Nature 391:410–413PubMedCrossRefGoogle Scholar
  16. Cheng Q, Chen J (2010) Mechanism of p53 stabilization by ATM after DNA damage. Cell Cycle 9:472–478PubMedPubMedCentralCrossRefGoogle Scholar
  17. Chin PL, Momand J, Pfeifer GP (1997) In vivo evidence for binding of p53 to consensus binding sites in the p21 and GADD45 genes in response to ionizing radiation. Oncogene 15:87–99PubMedCrossRefGoogle Scholar
  18. Cho Y, Gorina S, Jeffrey PD, Pavletich NP (1994) Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science 265:346–355PubMedCrossRefGoogle Scholar
  19. Ciriello et al (2015) Cell 8;163(2):506–519. doi: 10.1016/j.cell.2015.09.033
  20. DeBerardinis RJ, Thompson CB (2012) Cellular metabolism and disease: what do metabolic outliers teach us? Cell 148:1132–1144PubMedPubMedCentralCrossRefGoogle Scholar
  21. Dornan D, Hupp TR (2001) Inhibition of p53-dependent transcription by BOX-I phospho-peptide mimetics that bind to p300. EMBO Rep 2:139–144PubMedPubMedCentralCrossRefGoogle Scholar
  22. Eferl R, Wagner EF (2003) AP-1: a double-edged sword in tumorigenesis. Nat Rev Cancer 3:859–868PubMedCrossRefGoogle Scholar
  23. el-Deiry WS, Kern SE, Pietenpol JA, Kinzler KW, Vogelstein B (1992) Definition of a consensus binding site for p53. Nat Genet 1:45–49PubMedCrossRefGoogle Scholar
  24. el-Deiry WS, Tokino T, Velculescu VE, Levy DB, Parsons R, Trent JM, Lin D, Mercer WE, Kinzler KW, Vogelstein B (1993) WAF1, a potential mediator of p53 tumor suppression. Cell 75:817–825PubMedCrossRefGoogle Scholar
  25. Fan D, Liu SY, van Hasselt CA, Vlantis AC, Ng EK, Zhang H, Dong Y, Ng SK, Chu R, Chan AB, Du J, Wei W, Liu X, Liu Z, Xing M, Chen GG (2015) Estrogen receptor alpha induces prosurvival autophagy in papillary thyroid cancer via stimulating reactive oxygen species and extracellular signal regulated kinases. J Clin Endocrinol Metab 100:E561–E571PubMedCrossRefGoogle Scholar
  26. Fang X, Li JJ, Tan W (2000) Using molecular beacons to probe molecular interactions between lactate dehydrogenase and single-stranded DNA. Anal Chem 72:3280–3285PubMedCrossRefGoogle Scholar
  27. Fried MG (1989) Measurement of protein-DNA interaction parameters by electrophoresis mobility shift assay. Electrophoresis 10:366–376PubMedCrossRefGoogle Scholar
  28. Friedler A, Veprintsev DB, Freund SM, von Glos KI, Fersht AR (2005) Modulation of binding of DNA to the C-terminal domain of p53 by acetylation. Structure 13:629–636PubMedCrossRefGoogle Scholar
  29. Galas DJ, Schmitz A (1978) DNAase footprinting a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res 5:3157–3170PubMedPubMedCentralCrossRefGoogle Scholar
  30. Garner MM, Revzin A (1981) A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res 9:3047–3060PubMedPubMedCentralCrossRefGoogle Scholar
  31. Geng J, Goh WLP, Zhang C, Lane D, Liu B, Ghadessy FJ, Tan YN (2015) A highly sensitive fluoresce light-up probe for real-time detection of endogenous protein target and its antagonism in live cells. J Mater Chem B 3:5933–5937CrossRefGoogle Scholar
  32. Giannetti A, Citti L, Domenici C, Tedeschi L, Baldini F, Wabuyele MB, Vo-Dinh T (2006) FRET-based protein–DNA binding assay for detection of active NF-κB. Sensors Actuators B Chem 113:649–654CrossRefGoogle Scholar
  33. Gilmore TD (2006) Introduction to NF-kappaB: players, pathways, perspectives. Oncogene 25:6680–6684PubMedCrossRefGoogle Scholar
  34. Goh W, Lane D, Ghadessy F (2010) Development of a novel multiplex in vitro binding assay to profile p53-DNA interactions. Cell Cycle 9:3030–3038PubMedCrossRefGoogle Scholar
  35. Goh WL, Lee MY, Joseph TL, Quah ST, Brown CJ, Verma C, Brenner S, Ghadessy FJ, Teo YN (2014) Molecular rotors as conditionally fluorescent labels for rapid detection of biomolecular interactions. J Am Chem Soc 136:6159–6162PubMedCrossRefGoogle Scholar
  36. Gorodetsky AA, Ebrahim A, Barton JK (2008) Electrical detection of TATA binding protein at DNA-modified microelectrodes. J Am Chem Soc 130:2924–2925PubMedPubMedCentralCrossRefGoogle Scholar
  37. Grabowski ZR, Rotkiewicz K, Rettig W (2003) Structural changes accompanying intramolecular electron transfer: focus on twisted intramolecular charge-transfer states and structures. Chem Rev 103:3899–4032PubMedCrossRefGoogle Scholar
  38. Han SH, Kim SK, Park K, Yi SY, Park H-J, Lyu H-K, Kim M, Chung BH (2010) Detection of mutant p53 using field-effect transistor biosensor. Anal Chim Acta 665:79–83PubMedCrossRefGoogle Scholar
  39. Hanada R, Hanada T, Sigl V, Schramek D, Penninger JM (2011) RANKL/RANK-beyond bones. J Mol Med (Berl) 89:647–656CrossRefGoogle Scholar
  40. Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144:646–674PubMedCrossRefGoogle Scholar
  41. Hayden MS, Ghosh S (2012) NF-kappaB, the first quarter-century: remarkable progress and outstanding questions. Genes Dev 26:203–234PubMedPubMedCentralCrossRefGoogle Scholar
  42. Heinlein CA, Chang C (2004) Androgen receptor in prostate cancer. Endocr Rev 25:276–308PubMedCrossRefGoogle Scholar
  43. Hermeking H, Lengauer C, Polyak K, He TC, Zhang L, Thiagalingam S, Kinzler KW, Vogelstein B (1997) 14-3-3 sigma is a p53-regulated inhibitor of G2/M progression. Mol Cell 1:3–11PubMedCrossRefGoogle Scholar
  44. Heyduk T, Heyduk E (2002) Molecular beacons for detecting DNA binding proteins. Nat Biotechnol 20:171–176PubMedCrossRefGoogle Scholar
  45. Hibino E, Inoue R, Sugiyama M, Kuwahara J, Matsuzaki K, Hoshino M (2016) Interaction between intrinsically disordered regions in transcription factors Sp1 and TAF4. Protein Sci 25:2006–2017PubMedPubMedCentralCrossRefGoogle Scholar
  46. Hoesel B, Schmid JA (2013) The complexity of NF-kappaB signaling in inflammation and cancer. Mol Cancer 12:86PubMedPubMedCentralCrossRefGoogle Scholar
  47. Huber MA, Azoitei N, Baumann B, Grunert S, Sommer A, Pehamberger H, Kraut N, Beug H, Wirth T (2004) NF-kappaB is essential for epithelial-mesenchymal transition and metastasis in a model of breast cancer progression. J Clin Invest 114:569–581PubMedPubMedCentralCrossRefGoogle Scholar
  48. Hupp TR, Meek DW, Midgley CA, Lane DP (1992) Regulation of the specific DNA binding function of p53. Cell 71:875–886PubMedCrossRefGoogle Scholar
  49. Iwanicki MP, Chen HY, Iavarone C, Zervantonakis IK, Muranen T, Novak M, Ince TA, Drapkin R, Brugge JS (2016) Mutant p53 regulates ovarian cancer transformed phenotypes through autocrine matrix deposition. JCI Insight 1:e86829PubMedPubMedCentralCrossRefGoogle Scholar
  50. Jacobs MD, Harrison SC (1998) Structure of an IkappaBalpha/NF-kappaB complex. Cell 95:749–758PubMedCrossRefGoogle Scholar
  51. Jacque E, Tchenio T, Piton G, Romeo PH, Baud V (2005) RelA repression of RelB activity induces selective gene activation downstream of TNF receptors. Proc Natl Acad Sci U S A 102:14635–14640PubMedPubMedCentralCrossRefGoogle Scholar
  52. Jagelska E, Brazda V, Pospisilova S, Vojtesek B, Palecek E (2002) New ELISA technique for analysis of p53 protein/DNA binding properties. J Immunol Methods 267:227–235PubMedCrossRefGoogle Scholar
  53. Jares-Erijman EA, Jovin TM (2003) FRET imaging. Nat Biotechnol 21:1387–1395PubMedCrossRefGoogle Scholar
  54. Jerry DJ, Dunphy KA, Hagen MJ (2010) Estrogens, regulation of p53 and breast cancer risk: a balancing act. Cell Mol Life Sci 67:1017–1023PubMedCrossRefGoogle Scholar
  55. Ji H, Wu G, Zhan X, Nolan A, Koh C, De Marzo A, Doan HM, Fan J, Cheadle C, Fallahi M, Cleveland JL, Dang CV, Zeller KI (2011) Cell-type independent MYC target genes reveal a primordial signature involved in biomass accumulation. PLoS One 6:e26057PubMedPubMedCentralCrossRefGoogle Scholar
  56. Joerger AC, Fersht AR (2007) Structure-function-rescue: the diverse nature of common p53 cancer mutants. Oncogene 26:2226–2242PubMedCrossRefGoogle Scholar
  57. Joerger AC, Fersht AR (2010) The tumor suppressor p53: from structures to drug discovery. Cold Spring Harb Perspect Biol 2:a000919PubMedPubMedCentralCrossRefGoogle Scholar
  58. Jordan JJ, Menendez D, Inga A, Noureddine M, Bell DA, Resnick MA (2008) Noncanonical DNA motifs as transactivation targets by wild type and mutant p53. PLoS Genet 4:e1000104PubMedPubMedCentralCrossRefGoogle Scholar
  59. Karin M, Ben-Neriah Y (2000) Phosphorylation meets ubiquitination: the control of NF-[kappa]B activity. Annu Rev Immunol 18:621–663PubMedCrossRefGoogle Scholar
  60. Khoury MP, Bourdon JC (2011) p53 isoforms: an intracellular microprocessor? Genes Cancer 2:453–465PubMedPubMedCentralCrossRefGoogle Scholar
  61. Kuiper GG, Enmark E, Pelto-Huikko M, Nilsson S, Gustafsson JA (1996) Cloning of a novel receptor expressed in rat prostate and ovary. Proc Natl Acad Sci U S A 93:5925–5930PubMedPubMedCentralCrossRefGoogle Scholar
  62. Kummerfeld SK, Teichmann SA (2006) DBD: a transcription factor prediction database. Nucleic Acids Res 34:D74–D81PubMedCrossRefGoogle Scholar
  63. Kussie PH, Gorina S, Marechal V, Elenbaas B, Moreau J, Levine AJ, Pavletich NP (1996) Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274:948–953PubMedCrossRefGoogle Scholar
  64. Kyewski B, Klein L (2006) A central role for central tolerance. Annu Rev Immunol 24:571–606PubMedCrossRefGoogle Scholar
  65. Lambert PF, Kashanchi F, Radonovich MF, Shiekhattar R, Brady JN (1998) Phosphorylation of p53 serine 15 increases interaction with CBP. J Biol Chem 273:33048–33053PubMedCrossRefGoogle Scholar
  66. Lane DP (1992) Cancer. p53, guardian of the genome. Nature 358:15–16PubMedCrossRefGoogle Scholar
  67. Langer A, Hampel PA, Kaiser W, Knezevic J, Welte T, Villa V, Maruyama M, Svejda M, Jähner S, Fischer F, Strasser R, Rant U (2013) Protein analysis by time-resolved measurements with an electro-switchable DNA chip. Nat Commun 4:2099PubMedPubMedCentralCrossRefGoogle Scholar
  68. Laptenko O, Shiff I, Freed-Pastor W, Zupnick A, Mattia M, Freulich E, Shamir I, Kadouri N, Kahan T, Manfredi J, Simon I, Prives C (2015) The p53 C terminus controls site-specific DNA binding and promotes structural changes within the central DNA binding domain. Mol Cell 57:1034–1046PubMedCrossRefGoogle Scholar
  69. Laptenko O, Tong DR, Manfredi J, Prives C (2016) The tail that wags the dog: how the disordered C-terminal domain controls the transcriptional activities of the p53 tumor-suppressor protein. Trends Biochem Sci 41:1022–1034PubMedCrossRefGoogle Scholar
  70. Le Romancer M, Poulard C, Cohen P, Sentis S, Renoir JM, Corbo L (2011) Cracking the estrogen receptor's posttranslational code in breast tumors. Endocr Rev 32:597–622PubMedCrossRefGoogle Scholar
  71. Lee TI, Young RA (2000) Transcription of eukaryotic protein-coding genes. Annu Rev Genet 34:77–137PubMedCrossRefGoogle Scholar
  72. Lee TI, Young RA (2013) Transcriptional regulation and its misregulation in disease. Cell 152:1237–1251PubMedPubMedCentralCrossRefGoogle Scholar
  73. Lequin RM (2005) Enzyme immunoassay (EIA)/enzyme-linked immunosorbent assay (ELISA). Clin Chem 51:2415–2418PubMedCrossRefGoogle Scholar
  74. Liang J, Shang Y (2013) Estrogen and cancer. Annu Rev Physiol 75:225–240PubMedCrossRefGoogle Scholar
  75. Licht JD (2001) AML1 and the AML1-ETO fusion protein in the pathogenesis of t(8;21) AML. Oncogene 20:5660–5679PubMedCrossRefGoogle Scholar
  76. Lin CY, Loven J, Rahl PB, Paranal RM, Burge CB, Bradner JE, Lee TI, Young RA (2012) Transcriptional amplification in tumor cells with elevated c-Myc. Cell 151:56–67PubMedPubMedCentralCrossRefGoogle Scholar
  77. Liou GY, Storz P (2010) Reactive oxygen species in cancer. Free Radic Res 44:479–496PubMedCrossRefGoogle Scholar
  78. Liu J, Cao Z, Lu Y (2009) Functional nucleic acid sensors. Chem Rev 109:1948–1998PubMedPubMedCentralCrossRefGoogle Scholar
  79. Liu JJ, Song XR, Wang YW, Chen GN, Yang HH (2012) A graphene oxide (GO)-based molecular beacon for DNA-binding transcription factor detection. Nanoscale 4:3655–3659PubMedCrossRefGoogle Scholar
  80. Liu X, Ouyang L, Cai X, Huang Y, Feng X, Fan Q, Huang W (2013) An ultrasensitive label-free biosensor for assaying of sequence-specific DNA-binding protein based on amplifying fluorescent conjugated polymer. Biosens Bioelectron 41:218–224PubMedCrossRefGoogle Scholar
  81. Lohrum MA, Woods DB, Ludwig RL, Balint E, Vousden KH (2001) C-terminal ubiquitination of p53 contributes to nuclear export. Mol Cell Biol 21:8521–8532PubMedPubMedCentralCrossRefGoogle Scholar
  82. Lu X, Liu DP, Xu Y (2013) The gain of function of p53 cancer mutant in promoting mammary tumorigenesis. Oncogene 32:2900–2906PubMedCrossRefGoogle Scholar
  83. Lukasik SM, Zhang L, Corpora T, Tomanicek S, Li Y, Kundu M, Hartman K, Liu PP, Laue TM, Biltonen RL, Speck NA, Bushweller JH (2002) Altered affinity of CBF beta-SMMHC for Runx1 explains its role in leukemogenesis. Nat Struct Biol 9(9):674PubMedCrossRefGoogle Scholar
  84. Ma F, Yang Y, Zhang CY (2014) Ultrasensitive detection of transcription factors using transcription-mediated isothermally exponential amplification-induced chemiluminescence. Anal Chem 86:6006–6011PubMedCrossRefGoogle Scholar
  85. Maestro MA, Cardalda C, Boj SF, Luco RF, Servitja JM, Ferrer J (2007) Distinct roles of HNF1beta, HNF1alpha, and HNF4alpha in regulating pancreas development, beta-cell function and growth. Endocr Dev 12:33–45PubMedCrossRefGoogle Scholar
  86. Malkin D (2011) Li-fraumeni syndrome. Genes Cancer 2:475–484PubMedPubMedCentralCrossRefGoogle Scholar
  87. Mantovani F, Banks L (2001) The human papillomavirus E6 protein and its contribution to malignant progression. Oncogene 20:7874–7887PubMedCrossRefGoogle Scholar
  88. Martinez, LA. Mutant p53 and ETS2, a Tale of Reciprocity. Front Oncol 6, 35 (2016).Google Scholar
  89. May MJ, Ghosh S (1997) Rel/NF-kappa B and I kappa B proteins: an overview. Semin Cancer Biol 8:63–73PubMedCrossRefGoogle Scholar
  90. Meek DW, Anderson CW (2009) Posttranslational modification of p53: cooperative integrators of function. Cold Spring Harb Perspect Biol 1:a000950PubMedPubMedCentralCrossRefGoogle Scholar
  91. Menendez D, Inga A, Resnick MA (2009) The expanding universe of p53 targets. Nat Rev Cancer 9:724–737PubMedCrossRefGoogle Scholar
  92. Mermod N, O'Neill EA, Kelly TJ, Tjian R (1989) The proline-rich transcriptional activator of CTF/NF-I is distinct from the replication and DNA binding domain. Cell 58:741–753PubMedCrossRefGoogle Scholar
  93. Messina DN, Glasscock J, Gish W, Lovett M (2004) An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression. Genome Res 14:2041–2047PubMedPubMedCentralCrossRefGoogle Scholar
  94. Meyer N, Penn LZ (2008) Reflecting on 25 years with MYC. Nat Rev Cancer 8:976–990PubMedCrossRefGoogle Scholar
  95. Milde-Langosch K (2005) The Fos family of transcription factors and their role in tumourigenesis. Eur J Cancer 41:2449–2461PubMedCrossRefGoogle Scholar
  96. Miyashita T, Reed JC (1995) Tumor suppressor p53 is a direct transcriptional activator of the human bax gene. Cell 80:293–299PubMedCrossRefGoogle Scholar
  97. Mognol GP, Carneiro FR, Robbs BK, Faget DV, Viola JP (2016) Cell cycle and apoptosis regulation by NFAT transcription factors: new roles for an old player. Cell Death Dis 7:e2199PubMedPubMedCentralCrossRefGoogle Scholar
  98. Nakano K, Vousden KH (2001) PUMA, a novel proapoptotic gene, is induced by p53. Mol Cell 7:683–694PubMedCrossRefGoogle Scholar
  99. Narod (2011) Nat Rev Clin Oncol 8(11):669–676Google Scholar
  100. Nolan E, Vaillant F, Branstetter D, Pal B, Giner G, Whitehead L, Lok SW, Mann GB, Rohrbach K, Huang LY, Soriano R, Smyth GK, Dougall WC, Visvader JE, Lindeman GJ (2016) RANK ligand as a potential target for breast cancer prevention in BRCA1-mutation carriers. Nat Med 22:933–939PubMedCrossRefGoogle Scholar
  101. Noureddine MA, Menendez D, Campbell MR, Bandele OJ, Horvath MM, Wang X, Pittman GS, Chorley BN, Resnick MA, Bell DA (2009) Probing the functional impact of sequence variation on p53-DNA interactions using a novel microsphere assay for protein-DNA binding with human cell extracts. PLoS Genet 5:e1000462PubMedPubMedCentralCrossRefGoogle Scholar
  102. Oberlander S, Xie T, Chandrachud U, Gal S (2010) Scintillation proximity assay for total p53 protein as an alternative to ELISA. J Immunol Methods 360:173–177PubMedPubMedCentralCrossRefGoogle Scholar
  103. Okuda M, Araki K, Ohtani K, Nishimura Y (2016) The interaction mode of the acidic region of the cell cycle transcription factor DP1 with TFIIH. J Mol Biol 428:4993–5006PubMedCrossRefGoogle Scholar
  104. Ong HJ, Siau JW, Zhang JB, Hong M, Flotow H, Ghadessy F (2012) Analysis of p53 binding to DNA by fluorescence imaging microscopy. Micron 43:996–1000PubMedCrossRefGoogle Scholar
  105. Peh WY, Reimhult E, Teh HF, Thomsen JS, Su X (2007) Understanding ligand binding effects on the conformation of estrogen receptor α-DNA complexes: a combinational quartz crystal microbalance with dissipation and surface plasmon resonance study. Biophys J 92:4415–4423PubMedPubMedCentralCrossRefGoogle Scholar
  106. Piskacek S, Gregor M, Nemethova M, Grabner M, Kovarik P, Piskacek M (2007) Nine-amino-acid transactivation domain: establishment and prediction utilities. Genomics 89:756–768PubMedCrossRefGoogle Scholar
  107. Powell et al (2014) Cancer Discov 4(4):405–414Google Scholar
  108. Proft T (2010) Sortase-mediated protein ligation: an emerging biotechnology tool for protein modification and immobilisation. Biotechnol Lett 32:1–10PubMedCrossRefGoogle Scholar
  109. Ravikumar Y, Nadarajan SP, Yoo TH, Lee CS, Yun H (2015) Unnatural amino acid mutagenesis-based enzyme engineering. Trends Biotechnol 33:462–470PubMedCrossRefGoogle Scholar
  110. Rayburn E, Zhang R, He J, Wang H (2005) MDM2 and human malignancies: expression, clinical pathology, prognostic markers, and implications for chemotherapy. Curr Cancer Drug Targets 5:27–41PubMedCrossRefGoogle Scholar
  111. Reed M, Woelker B, Wang P, Wang Y, Anderson ME, Tegtmeyer P (1995) The C-terminal domain of p53 recognizes DNA damaged by ionizing radiation. Proc Natl Acad Sci U S A 92:9455–9459PubMedPubMedCentralCrossRefGoogle Scholar
  112. Riley T, Sontag E, Chen P, Levine A (2008) Transcriptional control of human p53-regulated genes. Nat Rev Mol Cell Biol 9:402–412PubMedCrossRefGoogle Scholar
  113. Robertson G, Bilenky M, Lin K, He A, Yuen W, Dagpinar M, Varhol R, Teague K, Griffith OL, Zhang X, Pan Y, Hassel M, Sleumer MC, Pan W, Pleasance ED, Chuang M, Hao H, Li YY, Robertson N, Fjell C, Li B, Montgomery SB, Astakhova T, Zhou J, Sander J, Siddiqui AS, Jones SJ (2006) cisRED: a database system for genome-scale computational discovery of regulatory elements. Nucleic Acids Res 34:D68–D73PubMedCrossRefGoogle Scholar
  114. Rudel D, Sommer RJ (2003) The evolution of developmental mechanisms. Dev Biol 264:15–37PubMedCrossRefGoogle Scholar
  115. Sammons MA, Zhu J, Drake AM, Berger SL (2015) TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity. Genome Res 25:179–188PubMedPubMedCentralCrossRefGoogle Scholar
  116. Sanda T, Lawton LN, Barrasa MI, Fan ZP, Kohlhammer H, Gutierrez A, Ma W, Tatarek J, Ahn Y, Kelliher MA, Jamieson CH, Staudt LM, Young RA, Look AT (2012) Core transcriptional regulatory circuit controlled by the TAL1 complex in human T cell acute lymphoblastic leukemia. Cancer Cell 22:209–221PubMedPubMedCentralCrossRefGoogle Scholar
  117. Sasaki CY, Barberi TJ, Ghosh P, Longo DL (2005) Phosphorylation of RelA/p65 on serine 536 defines an I{kappa}B{alpha}-independent NF-{kappa}B pathway. J Biol Chem 280:34538–34547PubMedCrossRefGoogle Scholar
  118. Schaefer U, Schmeier S, Bajic VB (2011) TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Res 39:D106–D110PubMedCrossRefGoogle Scholar
  119. Seow N, Tan YN, Yung L-YL, Su X (2015) DNA-directed assembly of Nanogold dimers: a unique dynamic light scattering sensing probe for transcription factor detection. Sci Rep 5:18293PubMedPubMedCentralCrossRefGoogle Scholar
  120. Sha L, Zhang X, Wang G (2016) A label-free and enzyme-free ultra-sensitive transcription factors biosensor using DNA-templated copper nanoparticles as fluorescent indicator and hairpin DNA cascade reaction as signal amplifier. Biosens Bioelectron 82:85–92PubMedCrossRefGoogle Scholar
  121. Shang Y (2007) Hormones and cancer. Cell Res 17:277–279PubMedCrossRefGoogle Scholar
  122. Smeenk L, van Heeringen SJ, Koeppel M, van Driel MA, Bartels SJ, Akkers RC, Denissov S, Stunnenberg HG, Lohrum M (2008) Characterization of genome-wide p53-binding sites upon stress response. Nucleic Acids Res 36:3639–3654PubMedPubMedCentralCrossRefGoogle Scholar
  123. Solomon H, Buganim Y, Kogan-Sakin I, Pomeraniec L, Assia Y, Madar S, Goldstein I, Brosh R, Kalo E, Beatus T, Goldfinger N, Rotter V (2012) Various p53 mutant proteins differently regulate the Ras circuit to induce a cancer-related gene signature. J Cell Sci 125:3144–3152PubMedCrossRefGoogle Scholar
  124. Song H, Hollstein M, Xu Y (2007) p53 gain-of-function cancer mutants induce genetic instability by inactivating ATM. Nat Cell Biol 9:573–580PubMedCrossRefGoogle Scholar
  125. Squires A, Atas E, Meller A (2015) Nanopore sensing of individual transcription factors bound to DNA. Sci Rep 5:11643PubMedPubMedCentralCrossRefGoogle Scholar
  126. Stender JD, Kim K, Charn TH, Komm B, Chang KC, Kraus WL, Benner C, Glass CK, Katzenellenbogen BS (2010) Genome-wide analysis of estrogen receptor alpha DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation. Mol Cell Biol 30:3943–3955PubMedPubMedCentralCrossRefGoogle Scholar
  127. Stojanovic MN, Kolpashchikov DM (2004) Modular aptameric sensors. J Am Chem Soc 126:9266–9270PubMedCrossRefGoogle Scholar
  128. Strom A, Hartman J, Foster JS, Kietz S, Wimalasena J, Gustafsson JA (2004) Estrogen receptor beta inhibits 17beta-estradiol-stimulated proliferation of the breast cancer cell line T47D. Proc Natl Acad Sci U S A 101:1566–1571PubMedPubMedCentralCrossRefGoogle Scholar
  129. Su X, Lin C-Y, O'Shea SJ, Teh HF, Peh WY, Thomsen JS (2006) Combinational application of surface plasmon resonance spectroscopy and quartz crystal microbalance for studying nuclear hormone receptor-response element interactions. Anal Chem 78:5552–5558PubMedCrossRefGoogle Scholar
  130. Swedenborg E, Power KA, Cai W, Pongratz I, Ruegg J (2009) Regulation of estrogen receptor beta activity and implications in health and disease. Cell Mol Life Sci 66:3873–3894PubMedCrossRefGoogle Scholar
  131. Tan YN, Lai A, Su X (2014) Interrogating cooperative interactions of transcription factors with composite DNA elements using gold nanoparticles. Sci Adv Mater 6:1460–1466CrossRefGoogle Scholar
  132. Tan YN, Lee KH, Su X (2011) Study of single-stranded DNA binding protein–nucleic acids interactions using unmodified gold nanoparticles and its application for detection of single nucleotide polymorphisms. Anal Chem 83:4251–4257PubMedCrossRefGoogle Scholar
  133. Tan YN, Lee KH, Su X (2013) A study of DNA design dependency of segmented DNA-induced gold nanoparticle aggregation towards versatile bioassay development. RSC Adv 3:21604–21612CrossRefGoogle Scholar
  134. Tan YN, Su X, Liu ET, Thomsen JS (2010a) Gold-nanoparticle-based assay for instantaneous detection of nuclear hormone receptor− response elements interactions. Anal Chem 82:2759–2765PubMedCrossRefGoogle Scholar
  135. Tan YN, Su X, Zhu Y, Lee JY (2010b) Sensing of transcription factor through controlled-assembly of metal nanoparticles modified with segmented DNA elements. ACS Nano 4:5101–5110PubMedCrossRefGoogle Scholar
  136. Tebaldi T, Zaccara S, Alessandrini F, Bisio A, Ciribilli Y, Inga A (2015) Whole-genome cartography of p53 response elements ranked on transactivation potential. BMC Genomics 16:464PubMedPubMedCentralCrossRefGoogle Scholar
  137. Thanos CD, Bowie JU (1999) p53 family members p63 and p73 are SAM domain-containing proteins. Protein Sci 8:1708–1710PubMedPubMedCentralCrossRefGoogle Scholar
  138. Thaxton CS, Georganopoulou DG, Mirkin CA (2006) Gold nanoparticle probes for the detection of nucleic acid targets. Clin Chim Acta 363:120–126PubMedCrossRefGoogle Scholar
  139. Thomas C, Gustafsson JA (2011) The different roles of ER subtypes in cancer biology and therapy. Nat Rev Cancer 11:597–608PubMedCrossRefGoogle Scholar
  140. Tyagi S (2009) Imaging intracellular RNA distribution and dynamics in living cells. Nat Methods 6:331–338PubMedCrossRefGoogle Scholar
  141. Vallee-Belisle A, Bonham AJ, Reich NO, Ricci F, Plaxco KW (2011) Transcription factor beacons for the quantitative detection of DNA binding activity. J Am Chem Soc 133:13836–13839PubMedCrossRefGoogle Scholar
  142. Vallée-Bélisle A, Plaxco KW (2010) Structure-switching biosensors: inspired by nature. Curr Opin Struct Biol 20:518–526PubMedPubMedCentralCrossRefGoogle Scholar
  143. Vang R, Levine DA, Soslow RA, Zaloudek C, Shih Ie M, Kurman RJ (2016) Molecular alterations of TP53 are a defining feature of ovarian high-grade serous carcinoma: a Rereview of cases lacking TP53 mutations in the cancer genome atlas ovarian study. Int J Gynecol Pathol 35:48–55PubMedPubMedCentralCrossRefGoogle Scholar
  144. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM (2009) A census of human transcription factors: function, expression and evolution. Nat Rev Genet 10:252–263PubMedCrossRefGoogle Scholar
  145. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C et al (2001) The sequence of the human genome. Science 291:1304–1351PubMedCrossRefGoogle Scholar
  146. Verma IM, Stevenson JK, Schwarz EM, Van Antwerp D, Miyamoto S (1995) Rel/NF-kappa B/I kappa B family: intimate tales of association and dissociation. Genes Dev 9:2723–2735PubMedCrossRefGoogle Scholar
  147. Vogelstein B, Lane D, Levine AJ (2000) Surfing the p53 network. Nature 408:307–310PubMedCrossRefGoogle Scholar
  148. Vousden KH, Lane DP (2007) p53 in health and disease. Nat Rev Mol Cell Biol 8:275–283PubMedCrossRefGoogle Scholar
  149. Wan F, Lenardo MJ (2009) Specification of DNA binding activity of NF-kappaB proteins. Cold Spring Harb Perspect Biol 1:a000067PubMedPubMedCentralCrossRefGoogle Scholar
  150. Wang B, Xiao Z, Ren EC (2009a) Redefining the p53 response element. Proc Natl Acad Sci U S A 106:14373–14378PubMedPubMedCentralCrossRefGoogle Scholar
  151. Wang K, Tang Z, Yang CJ, Kim Y, Fang X, Li W, Wu Y, Medley CD, Cao Z, Li J (2009b) Molecular engineering of DNA: molecular beacons. Angew Chem Int Ed 48:856–870CrossRefGoogle Scholar
  152. Wang Y, Zhu X, Wu M, Xia N, Wang J, Zhou F (2009c) Simultaneous and label-free determination of wild-type and mutant p53 at a single surface plasmon resonance chip preimmobilized with consensus DNA and monoclonal antibody. Anal Chem 81:8441–8446PubMedCrossRefGoogle Scholar
  153. Weinberg RL, Veprintsev DB, Bycroft M, Fersht AR (2005) Comparative binding of p53 to its promoter and DNA recognition elements. J Mol Biol 348:589–596PubMedCrossRefGoogle Scholar
  154. Xie TX, Xia Z, Zhang N, Gong W, Huang S (2010) Constitutive NF-kappaB activity regulates the expression of VEGF and IL-8 and tumor angiogenesis of human glioblastoma. Oncol Rep 23:725–732PubMedCrossRefGoogle Scholar
  155. Zeron-Medina J, Wang X, Repapi E, Campbell MR, Su D, Castro-Giner F, Davies B, Peterse EF, Sacilotto N, Walker GJ, Terzian T, Tomlinson IP, Box NF, Meinshausen N, De Val S, Bell DA, Bond GL (2013) A polymorphic p53 response element in KIT ligand influences cancer risk and has undergone natural selection. Cell 155:410–422PubMedPubMedCentralCrossRefGoogle Scholar
  156. Zhang K, Wang K, Zhu X, Xie M (2016) Sensitive detection of transcription factors in cell nuclear extracts by using a molecular beacons based amplification strategy. Biosens Bioelectron 77:264–269PubMedCrossRefGoogle Scholar
  157. Zhang Y, Hu J, Zhang C-y (2012) Sensitive detection of transcription factors by isothermal exponential amplification-based colorimetric assay. Anal Chem 84:9544–9549PubMedCrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  • W. L. Goh
    • 1
    Email author
  • E. Assah
    • 2
  • X. T. Zheng
    • 2
  • D. P. Lane
    • 1
  • F. J. Ghadessy
    • 1
  • Y. N. Tan
    • 2
  1. 1.p53 Laboratory, Biomedical Sciences Institute, Agency of Science, Technology and Research, A*STARSingaporeSingapore
  2. 2.Institute of Materials Research and Engineering (IMRE), Agency of Science, Technology and Research, A*STARSingaporeSingapore

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