Institute of Development, Aging and Cancer, Tohoku University

About

Div. Dynamic Proteome in Aging and Cancer

Professor Akira YASUI, PhD
Senior Assistant Professor Shin-ichiro KANNO, MD
Assistant Professor Ayako UI, PhD
Collaborative Researcher Mikiko HOSHI
Project Researcher Reiko WATANABE
Technical assistant Kumiko KONDO
Secretarial Assistant Izumi CHIBA

Background of Our Research
DNA damage can be caused by both cell-intrinsic sources, such as reactive oxygen species, and a variety of extrinsic factors, including ultraviolet light, ionizing radiation (IR) and radiomimetic chemicals. If DNA damage is left unrepaired, it may cause cell death and genomic instability, leading to mutation and chromosome rearrangement, and predisposition to cancer. Cell death by DNA damage may cause early aging (Figure 1). Understanding of the mechanisms of DNA damage response is important for the prevention of cancer and cancer therapy.

 Figure 1

Strategy of Our Research
We want to elucidate the mechanisms of DNA damage repair in living human cells by identifying proteins in real time under microscope and by determining protein complexes at DNA damage site with mass spectrometry. By combining each results of live cell analysis and proteomics, we are able to understand how cells respond to various types of DNA damage and the roles of proteins and protein complexes in DNA damage repair.
Although only several DNA repair pathways are present in human cell, there are several hundreds of proteins involved in cellular resistance to DNA damage (Figure 2), indicating that the mechanisms of damage response within cell are quite complicated. This is partly due to the chromatin structure surrounding DNA, which plays important roles in the repair processes within cell.

 Figure 2

In order to understand how cells respond to DNA damage, we developed various types of cellular micro irradiation system, which enable us to produce various types of DNA damage and visualize proteins accumulating at the site of DNA damage in real time. Since proteins works in general as complexes within cell, we determine protein complexes working at the damage site (Figure 3). We combined the live cell analysis and the proteome analysis, a number of novel proteins and protein complexes have been already identified (see references of our publications). We want to utilize our findings for cancer prevention and cancer therapy.

 Figure 3


Recent Publications (2002-2011)

  1. Li S, Kanno S, Watanabe R, Ogiwara H, Kohno T, Watanabe G, Yasui A, and Lieber MR. Polynucleotide kinase and aprataxin-like forkhead-associated protein (PALF) acts as both a single-stranded DNA endonuclease and a single-stranded DNA 3' exonuclease and can participate in DNA end joining in a biochemical system. J Biol Chem. 2011 Oct 21;286(42):36368-77.
  2. Wei, L. Lan L, Yasui A, Tanaka K, Saijo M, Matsuzawa A, Kashiwagi R, Maseki E, Hu Y, Parvin JD, Ishioka C, and Chiba N. BRCA1 contributes to transcription-coupled repair of DNA damage through polyubiquitination and degradation of Cockayne syndrome B protein. Cancer Sci. 2011, Oct.
  3. Zlatanou A, Despras E, Braz-Petta T, Boubakour-Azzouz I, Pouvelle C, Stewart GS, Nakajima S, Yasui A, Ishchenko AA, Kannouche PL. The hMsh2-hMsh6 complex acts in concert with monoubiquitinated PCNA and Pol η in response to oxidative DNA damage in human cells. Mol Cell. 2011 Aug 19;43(4):649-62.
  4. Lan L, Ui A, Nakajima S, Hatakeyama K, Hoshi M, Watanabe R, Janicki SM, Ogiwara H, Kohno T, Kanno SI, and Yasui A. The ACF1 complex is required for DNA double-strand break repair in human cells. Mol Cell 40, 976-987, 2010.
  5. Ogiwara H, Ui A, Otsuka A, Satoh H, Yokomi I, Nakajima S, Yasui A, Yokota J, and Kohno T, Histone acetylation by p300 at double-strand break sites facilitates SWI/SNF chromatin remodeling and the recruitment of non-homologous end joining factors. Oncogene, 18, 2135-2146, 2011.
  6. Horibata K, Saijo M, Bay MN, Lan L, Kuraoka I, Brook PJ, Honma M, Nohmi T, Yasui A, and Tanaka K. Mutant Cockayne syndrome group B protein inhibits repair of DNA topoisomerase I-DNA covalent complex. Genes Cells, 16, 101-114, 2011.
  7. Itoh G, Kanno SI, Uchida KS, Chiba S, Sugino S, Watanabe K, Mizuno K, Yasui A, Hirota T, and Tanaka K. CAMP (C13orf8, ZNF828) is a novel regulator of kinetochore-microtubule attachment. EMBO J. 30, 130-144, 2011.
  8. Isogai S, Kanno S, Ariyoshi M, Tochio H, Ito Y, Yasui A, and Shirakawa M. Solution structure of a zinc-finger domain that binds to poly-ADP-ribose. Genes Cells 15, 101-110, 2010.
  9. Asagoshi K, Liu Y, Masaoka A, Lan L, Prasad R, Horton JK, Brown AR, Wang XH, Bdour HM, Sobol RW, Taylor JS, Yasui A, and Wilson SH. DNA polymerase beta-dependent long patch base excision repair in living cells. DNA Repair, 9, 109-119, 2010.
  10. Yasui A, Lan L, Nakajima S, Hatakeyama K, Zehui H, and Kanno SI. Repair of DNA strand breaks in living human cells and implications for cancer therapy. In “Extended Abstracts for the 40th International Symposium of the Princess Takamatsu Cancer Research Fund”, 68-73, 2010.
  11. Mori H, Ouchida R, Hijikata A, Kitamura H, Ohara O, Li Y, Gao X, Yasui A, Lloyd RS, and Wang JY. Deficiency of the oxidative damage-specific DNA glycosylase NEIL1 leads to reduced germinal center B cell expansion. DNA Repair (Amst). 8,1328-1332, 2009
  12. Ziv O, Geacintov N, Nakajima S, Yasui A, and Livneh Z. DNA polymerase zeta cooperates with polymerases kappa and iota in translesion DNA synthesis across pyrimidine photodimers in cells from XPV patients. Proc Natl Acad Sci U S A. 106, 11552-11557, 2009
  13. Minami Y, Kasukawa T, Kakazu Y, Iigo M, Sugimoto M, Ikeda S, Yasui A, van der Horst GT, Soga T, and Ueda HR. Measurement of internal body time by blood metabolomics. Proc Natl Acad Sci U S A. 106, 9890-9895, 2009
  14. Wei L, Lan L, Hong Z, Yasui A, Ishioka C, and Chiba N. Rapid recruitment of BRCA1 to DNA double-strand breaks is dependent on its association with Ku80. Mol Cell Biol. 28, 7380-7393, 2008.
  15. Hong Z, Jiang J, Hashiguchi K, Hoshi M, Lan L, and Yasui A. Recruitment of mismatch repair proteins to the site of DNA damage in human cells. J. Cell Sci. 121, 3146-3154, 2008.
  16. Niimi A, Brown S, Sabbioneda S, Kannouche P, Scott, A, Yasui A, Green CM, and Lehmann AR. Regulation of proliferating cell nuclear antigen ubiquitination in mammalian cells. Proc. Natl. Acad. Sci. USA, 105, 16125-16130, 2008
  17. Petta TB, Nakajima S, Zlatanou A, Despras E, Sarasin A, Yasui A, and Kannouche P. Human DNA polymerase iota protects cells against oxidative stress. EMBO J. 27, 2883-2895, 2008.
  18. Hong Z, Jiang J, Lan L, Nakajima S, Kanno S, Koseki H, and Yasui A. A polycomb group protein, PHF1, is involved in the response to DNA double-strand breaks in human cell. Nucleic Acids Res. 36, 2937-2947, 2008.
  19. Honma S, Yasuda T, Yasui A, van der Horst GT, and Honma K. Circadian behavioral rhythms in Cry1/Cry2 double-deficient mice induced by methamphetamine. J Biol Rhythms. 23, 91-94, 2008.
  20. Prasad R, Liu Y, Deterding LJ, Poltoratsky VP, Kedar PS, Horton JK, Kanno SI, Asagoshi K, Hou EW, Khodyreva SN, Lavrik OI, Tomer KB, Yasui A, and Wilson SH. HMGB1 is a co-factor in mammalian base excision repair. Mol. Cell, 27, 829-841, 2007.
  21. Friedberg EC, Hanaoka F, Tanaka K, Wilson S, and Yasui A. The 3rd Japan-US DNA Repair Meeting, Sendai, Japan, May 7-11, 2007. DNA Repair, 6, 1545-1555, 2007.
  22. Kamath-Loeb AS, Li L, Nakajima S, Yasui A, and Loeb LL. The Werner syndrome protein interacts functionally with translesion DNA synthesis. Proc. Natl. Acad. Sci. USA., 104, 10394-10399, 2007.
  23. Kanno S, Kuzuoka H, Sasao S, Hong Z, Lan L, Nakajima S, and Yasui A. A novel human AP endonuclease with conserved zinc-finger-like motifs involved in DNA strand break responses, EMBO J. 26, 2094-2103, 2007.
  24. Hashiguchi K, Matsumoto Y, and Yasui A. Recruitment of DNA repair synthesis machinery to sites of DNA damage/repair in living cells. Nucleic Acids Res. 35, 2913-2923, 2007.
  25. Hirano M, Yamamoto A, Mori T, Lan L, Iwamoto TA, Aoki M, Shimada K, Furiya Y, Kariya S, Asai H, Yasui A, Nishiwaki T, Imoto K, Kobayashi N, Kiriyama T, Nagata T, Konishi N, Itoyama Y, and Ueno S. DNA single-strand break repair is impaired in aprataxin-related ataxia. Ann Neurol. 61,162-174, 2007.
  26. Saberi A, Hochegger H, Szuts D, Lan L, Yasui A, Sale JE, Taniguchi Y, Murakawa Y, Zeng W, Yokomori K, Helleday T, Teraoka H, Arakawa H, Buerstedde JM, and Takeda S. RAD18 and poly(ADP-ribose) polymerase independently suppress the access of nonhomologous end joining to double-strand breaks and facilitate homologous recombination-mediated repair. Mol Cell Biol. 27, 2562-2571, 2007.
  27. Nakajima S, Lan L, Kanno S, Usami N, Kobayashi K, Mori M, Shiomi T, and Yasui A. Replication-dependent and −independent responses of RAD18 to DNA damage in human cells. J. Biol. Chem. 281, 34687-34695, 2006.
  28. Jans J, Garinis GA, Schul W, van Oudenaren A, Moorhouse M, Smid M, Sert YG, van der Veide A, Rijksen Y, de Gruijl FR, van der Spek PL, Yasui A, Hoeijmakers JH, Leenen PJ, and van der Horst GT. Differential role of basal keratinocytes in UV-induced immunosuppression and skin cancer. Mol Cell Biol. 26, 8515-8526, 2006.
  29. Yoshimura M, Kohzaki M, Nakamura J, Asagoshi K, Sonoda E, Hou E, Prasad R, Wilson SH, Tano K, Yasui A, Lan L, Seki M, Wood RD, Arakawa H, Buerstedde JM, Hochegger H, Okada T, Hiraoka M, and Takeda S. Vertebrate PolQ cells against oxidative DNA damage through base excision repair and translesion DNA synthesis. Mol Cell, 24, 115-125, 2006.
  30. Karmakar P, Seki M, Kanamori M, Hashiguchi K, Ohtsuki M, Murata E, Inoue E, Tada S, Lan L, Yasui A, and Enomoto T. BLM is an early responder to DNA double-strand breaks. Biochem. Biophys. Res. Commun. 348, 62-69, 2006.
  31. Hirano M, Furuya Y, Asai H, Yasui A, and Ueno S. ALADINI482S causes selective failure of nuclear protein import and hypersensitivity to oxidative stress in triple A syndrome. Proc. Natl Acad. Sci. USA. 103, 2298-2303, 2006.
  32. Lan L, Nakajima S, Komatsu K, Nussenzweig A, Shimamoto A, Oshima J, and Yasui A. Accumulation of Werner protein at DNA double-strand breaks in human cells. J. Cell Sci. 118, 4153-4162, 2005.
  33. Takao M, and Yasui A. DNA repair initiated by glycosylases in the nucleus and mitochondria of mammalian cells; how our cells respond to a flood of oxidative DNA damage. J. Dermat. Sci. Suppl. 1, S9-S19, 2005.
  34. Lo H-L, Nakajima S, Ma L, Walter B, Yasui A, Ethell DW, and Owen LB. Differential biologic effects of CPD and 6-4PP UV-induced DNA damage on the induction of apoptosis and cell-cycle arrest. BMC Cancer, 5, 135-143, 2005.
  35. Hamdi M, Kool J, Cornelissen-Steijger P, Carlotti F, Popeijus HE, van der Burgt C, Janssen JM, Yasui A, Hoeben RC, Terleth C, Mullenders LH, and van Dam H. DNA damage in transcribed genes induces apoptosis via the JNK pathway and the JNK-phosphatase MKP-1. Oncogene, 24, 7135-7144, 2005.
  36. Braithwaite EK, Kedar PS, Lan L., Polosina YY, Asagoshi K, Poltoratsky V, Horton JK, Miller H, Teebor GW, Yasui A, and Wilson SH. DNA polymerase l protect mouse fibroblasts against oxidative DNA damage and is recruited to sites of DNA damage/repair. J. Biol. Chem. 280, 31641-31647. 2005.
  37. Okano S, Lan L, Tomkinson AE, and Yasui A. Translocation of XRCC1 and DNA ligase IIIa from centrosomes to chromosomes in response to DNA damage in mitotic human cells. Nucleic Acids Res. 33, 422-429, 2005.
  38. Moser J, Volker M, Kool H, Alekseev S, Vrieling H, Yasui A, van Zeelad AA, and Mullender LH. The UV-damaged DNA binding protein mediates efficient targeting of the nucleotide excision repair complex to UV-induced photo lesions. DNA Repair, 4, 571-582, 2005.
  39. Wilson TM, Vaisman A, Martomo SA, Sullivan P, Lan L, Hanaoka F, Yasui A, Woodgate R, and Gearhart PJ. MSH2-MSH6 stimulates DNA polymerase h, suggesting a role for A-T mutation in immunoglobulin genes. J. Exp. Med. 201, 637-645, 2005.
  40. Jans J, Schul W, Sert Y-G, Rijksen Y, Rebel H, Eker APM, Nakajima S, van Steeg H, de Gruijl FR, Yasui A, Hoeijmakers JHJ, van der Horst GTJ. Powerful skin cancer protection by a CPD-photolyase transgene. Curr. Biology, 15, 1-20, 2005.
  41. Zhang QM, Yonekura S, Takao M, Yasui A, Sugiyama H, and Yonei S. DNA glycosylase activities for thymine residues oxidized in the methyl group are functions of the hNEIL1 and hNTH1 enzymes in human cells. DNA Repair, 4, 71-79, 2005.
  42. Nakajima S, Lan L, Kanno S, Takao M, Yamamoto K, Eker APM, and Yasui A. UV-induced DNA damage and tolerance for survival of nucleotide excision repair-deficient human cells. J. Biol. Chem. 279, 46674-46677, 2004.
  43. Lan L, Nakajima S, Oohata Y, Takao M, Okano S, Masutani M, Wilson SH, and Yasui A. In situ analysis of repair processes for oxidative DNA damage in mammalian cells. Proc. Natl. Acad. Sci. USA, 101, 13738-13743, 2004.
  44. Lan L. Hayashi, T, Rokshana M. R, Nakajima S, Kanno S, Takao M, Matsunaga T, Yoshino M, Ichikawa M, te Riele H, Tsuchiya S, Tanaka K, and Yasui A. Functional and physical Interactions between ERCC1 and MSH2 complexes for resistance to cis-diamminedichloroplatinum(II) in mammalian cells. DNA Repair 3. 135-143, 2004.
  45. Fitch ME, Nakajima S, Yasui A, and Ford JM. In vivo recruitment of XPC to UV-induced cyclobutane pyrimidine dimmers by the DDB2 gene product. J. Biol. Chem. 278, 46906-46910, 2003
  46. Okano S, Lan L, Caldecot K, Mori T, and Yasui A. Spatial and temporal assembly of the proteins involved in repair of single-strand breaks in human cells. Mol. Cell. Biol. 23. 3974-3981, 2003.
  47. Takahashi H, Umeda N, Tsutumi Y, Fukumura R, Ohkaze H, Sujino M, van der Horst, G, Yasui A, Inoue ST, Fujimori A, Ohhata T, Araki R, and Abe M. Mouse dexamethasone-induced RAS protein 1 gene is expressed in a circadian rhythmic manner in the suprachiasmatic nucleus. Mol. Brain Res. 110, 1-6, 2003.
  48. Friedberg EC, Hanaoka F, Tanaka K, Wilson SH, and Yasui A. Report on the First US-Japan DNA Repair Meeting. Sendai, Japan, October 27-31, 2002. DNA Repair, 2, 639-652, 2003.
  49. Takao M, Kanno S, Kobayashi K, Zhang QM, Yonei S, van der Horst G, and Yasui A. A back-up glycosylase in Nth1-knockout mice is a functional Nei (endonuclease VIII) homologue. J. Biol. Chem. 277, 42205-42213, 2002.
  50. Chigancas V, Batista LF, Brumatti G, Amarante-Mendes GP, Yasui A, and Menck CF. Photorepair of RNA polymerase arrest and apoptosis after ultraviolet irradiation in normal and XPB deficient rodent cells. Cell Death Differ. 9, 1099-1107, 2002.
  51. Oster H, Yasui A, van der Horst GTJ, and Albrecht U. Disruption of mCry2 restores circadian rhythmicity in mPer2 mutant mice. Genes Dev. 16, 2633-2638, 2002.
  52. Albus H, Bonnefont X, Chaves I, Yasui A, Doczy J, van der Horst GT, and Meijer JH. Cryptochrome-deficient mice lack circadian electrical activity in the suprachiasmatic nuclei. Curr Biol. 9, 1130-1133, 2002.
  53. Schul W, Jans J, Rijksen YMA, Klemann HM, Eker APM, de Wit J, Nikaido O, Nakajima S, Yasui A, Hoeijmakers JHJ, and van der Horst GTJ. Enhanced repair of cyclobutane pyrimidine dimers and improved UV resistance in photolyase transgenic mice. EMBO J. 21, 4719-4729, 2002.
  54. Miiyabe I, Zhang QM, Kino K, Sugiyama H, Takao M, Yasui A, and Yonei S. Identification of 5-formyluracil DNA glycosylase activity of human hNTH1 protein. Nucleic Acids Res. 30, 3454-3463, 2002.
  55. Takao M, Kanno S, Shiromoto T, Hasegawa R, Ide H, Iikeda S, Sarker AH, Seki S, Xing JZ, Le XC, Weinfeld M Kobayashi K, Miyazaki J, Muijtjens M, Hoeijmakers JHJ, van der Horst G, and Yasui. A. Novel nuclear and mitochondrial glycosylases revealed by disruption of the mouse Nth1 gene encoding an endonuclease III homologue for repair of thymine glycol. EMBO J. 21. 3486-3493, 2002

Page Top