変異制御研究室

研究室の紹介

発癌は遺伝子異常の蓄積の結果として起こります。次世代シークエンサーを用いた癌ゲノムの網羅的解析により遺伝子異常の配列の組み合わせからその原因により色々なパターンの遺伝子異常が明らかとなり、我々がHIV研究室で研究を続けてきたDNAシトシン脱アミノ化酵素APOBEC3に特徴的な遺伝子異常があることがわかりました。APOBEC3はDNAのシトシンを脱アミノ化してウラシルに置換することで最終的にシトシンからチミンへの遺伝子変異を導入する酵素です。当研究室ではこのAPOBEC3による遺伝子異常の蓄積が血液腫瘍を含む多くの悪性腫瘍で腫瘍のバイオロジーにどう影響するか、研究を続けています。

抗がん剤治療を終えたのち再発する悪性腫瘍は、治療初期の段階で遺伝子変異により治療抵抗性を獲得している腫瘍細胞をわずかに含んでおり、腫瘍のクローン進化が抗がん剤治療の妨げとなっています。APOBEC3による遺伝子変異はパッセンジャー変異だけでなくドライバー変異を含んでおり、腫瘍の性質の変化に影響していると考えられます。APOBEC3の酵素活性を阻害することにより遺伝子変異導入を制御することで一部の腫瘍の高悪性度化、薬剤耐性獲得、遠隔転移などの抑制につながる可能性があると考えられます。

当研究室では、これまでにHIV-1研究室で蓄積した分子生物学的手法にシングルセル解析やCRISPRスクリーニングなどの最新の手法を組み合わせ、京都大学内外の研究室と協力して、多発性骨髄腫や悪性リンパ腫などのリンパ系腫瘍を対象としてシトシン脱アミノ化による変異の導入と腫瘍クローン進化にフォーカスして研究を進めています。最近ではAPOBECだけでなくその他のDNA修飾酵素やその他の薬剤耐性のメカニズムを解析し、薬剤耐性を克服するための新規治療法開発につながるような新たな分子メカニズムを解析しています。

代表的な業績

• Sakurada-Aono M, Sakamoto T, Kobayashi M, Takiuchi Y, Iwai F, Tada K, Sasanuma H, Hirabayashi S, Murakawa Y, Shirakawa K, Sakamoto C, Shindo K, Yasunaga JI, Matsuoka M, Pommier Y, Takeda S, Takaori-Kondo A. HTLV-1 bZIP factor impairs DNA mismatch repair system. Biochem Biophys Res Commun . 2023 May 21;657:43-49. doi: 10.1016/j.bbrc.2023.03.049. Epub 2023 Mar 21. PMID: 36972660
• Kazuma Y, Shirakawa K, Tashiro Y, Yamazaki H, Nomura R, Horisawa Y, Takeuchi S, Stanford E, Konishi Y, Matsui H, Matsumoto T, Tanabe F, Morishita R, Ito S, Takaori-Kondo A. ILF2 enhances the DNA cytosine deaminase activity of tumor mutator APOBEC3B in multiple myeloma cells. Sci Rep . 2022 Feb 10;12(1):2278. doi: 10.1038/s41598-022-06226-3. PMID: 35145187
• Hirabayashi S, Shirakawa K, Horisawa Y, Matsumoto T, Matsui H, Yamazaki H, Sarca AD, Kazuma Y, Nomura R, Konishi Y, Takeuchi S, Stanford E, Kawaji H, Murakawa Y, Takaori-Kondo A. APOBEC3B is preferentially expressed at the G2/M phase of cell cycle. Biochem Biophys Res Commun . 2021 Mar 26;546:178-184. doi: 10.1016/j.bbrc.2021.02.008.
• Takei H, Fukuda H, Pan G, Yamazaki H, Matsumoto T, Kazuma Y, Fujii M, Nakayama S, Kobayashi IS, Shindo K, Yamashita R, Shirakawa K, Takaori-Kondo A, Kobayashi SS. Alternative Splicing of APOBEC3D Generates Functional Diversity and Its Role as a DNA Mutator. Int J Hematol . 2020.
• Matsumoto T, Shirakawa K, Yokoyama M, Fukuda H, Sarca AD, Koyabu S, Yamazaki H, Kazuma Y, Matsui H, Maruyama W, Nagata K, Tanabe F, Kobayashi M, Shindo K, Morishita R, Sato H, Takaori-Kondo A. Protein kinase A inhibits tumor mutator APOBEC3B through phosphorylation. Sci Rep . 2019 Jun 5;9(1):8307. doi: 10.1038/s41598-019-44407-9. PMID: 31165764
• Yamazaki H, Shirakawa K, Matsumoto T, Kazuma Y, Matsui H, Horisawa Y, Stanford E, Sarca AD, Shirakawa R, Shindo K, Takaori-Kondo A. APOBEC3B reporter myeloma cell lines identify DNA damage response pathways leading to APOBEC3B expression.PLoS One . 2020 Jan 8;15(1):e0223463. doi: 10.1371/journal.pone.0223463. eCollection 2020.
• Kawata T, Tada K, Kobayashi M, Sakamoto T, Takiuchi Y, Iwai F, Sakurada M, Hishizawa M, Shirakawa K, Shindo K, Sato H, Takaori-Kondo A. Dual inhibition of the mTORC1 and mTORC2 signaling pathways is a promising therapeutic target for adult T-cell leukemia. Cancer Sci . 2018 Jan;109(1):103-111. doi: 10.1111/cas.13431
• Takiuchi Y, Kobayashi M, Tada K, Iwai F, Sakurada M, Hirabayashi S, Nagata K, Shirakawa K, Shindo K, Yasunaga JI, Murakawa Y, Rajapakse V, Pommier Y, Matsuoka M, Takaori-Kondo A. HTLV-1 bZIP factor suppresses TDP1 expression through inhibition of NRF-1 in adult T-cell leukemia. Sci Rep . 2017 Oct 9;7(1):12849. doi: 10.1038/s41598-017-12924-0.
• Nagata K, Shindo K, Matsui Y, Shirakawa K, Takaori-Kondo A. Critical role of PP2A-B56 family protein degradation in HIV-1 Vif mediated G2 cell cycle arrest. Biochem Biophys Res Commun . 2020 Jun 18;527(1):257-263.
• Yamazaki H, Shirakawa K, Matsumoto T, Kazuma Y, Matsui H, Horisawa Y, Stanford E, Sarca AD, Shirakawa R, Shindo K, Takaori-Kondo A. APOBEC3B reporter myeloma cell lines identify DNA damage response pathways leading to APOBEC3B expression.PLoS One. 2020 Jan 8;15(1):e0223463.
• Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori-Kondo A, Takeuchi O, Carninci P, Katayama S, Hayashizaki Y, Kere J, Kawaji H, Murakawa Y. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat Genet. 2019 Sep;51(9):1369-1379.
• Matsumoto T, Shirakawa K, Yokoyama M, Fukuda H, Sarca AD, Koyabu S, Yamazaki H, Kazuma Y, Matsui H, Maruyama W, Nagata K, Tanabe F, Kobayashi M, Shindo K, Morishita R, Sato H, Takaori-Kondo A. Protein kinase A inhibits tumor mutator APOBEC3B through phosphorylation. Sci Rep. 2019 Jun 5;9(1):8307.
• Fukuda H, Li S, Sardo L, Smith JL, Yamashita K, Sarca AD, Shirakawa K, Standley DM, Takaori-Kondo A, Izumi T. Structural Determinants of the APOBEC3G N-Terminal Domain for HIV-1 RNA Association. Front Cell Infect Microbiol. 2019 May 21;9:129.
• Yamazaki H, Shirakawa K, Matsumoto T, Kobayashi M, Sarca AD, Maruyama W, Kazuma Y, Matsui H, Fukuda H, Shirakawa R, Shindo K, Ri M, Iida S, and Takaori-Kondo AEndogenous APOBEC3B Overexpression Constitutively Generates DNA Substitutions and Deletions in Myeloma Cells.Sci Rep. 2019 May 9;9:7122.
• Eso Y, Uza N, Shirakawa K, Sawada K, Katsuragi K, Matsuura M, Seno H. Choledochoduodenal Fistula during Chemotherapy with Brentuximab Vedotin for Methotrexate-associated Lymphoproliferative Disorder. Intern Med. 2018 Mar 9.
• Kishimoto W, Nishikori M, Arima H, Miyoshi H, Sasaki Y, Kitawaki T, Shirakawa K, Kato T, Imaizumi Y, Ishikawa T, Ohno H, Haga H, Ohshima K, Takaori-Kondo A.Expression of Tim-1 in primary CNS lymphoma.Cancer Med. 2016 Oct 5.
• Maruyama W, Shirakawa K, Matsui H, Matsumoto T, Yamazaki H, Sarca AD, Kazuma Y, Kobayashi M, Shindo K, Takaori-Kondo A. Classical NF-κB pathway is responsible for APOBEC3B expression in cancer cells. Biochem Biophys Res Commun. 2016; 478(3):1466-71.
• Shirakawa K, Wang L, Man N, Maksimoska J, Sorum AW, Lim HW, Lee IS, Shimazu T, Newman JC, Schröder S, Ott M, Marmorstein R, Meier J, Nimer S, Verdin E. Salicylate, diflunisal and their metabolites inhibit CBP/p300 and exhibit anticancer activity.Elife. 2016 May 31;5. pii: e11156.
• Wiley CD, Velarde MC, Lecot P, Liu S, Sarnoski EA, Freund A, Shirakawa K, Lim HW, Davis SS, Ramanathan A, Gerencser AA, Verdin E, Campisi J. Mitochondrial Dysfunction Induces Senescence with a Distinct Secretory Phenotype.Cell Metab. 2016 Feb 9;23(2):303-14.
• Wiley CD, Velarde MC, Lecot P, Liu S, Sarnoski EA, Freund A, Shirakawa K, Lim HW, Davis SS, Ramanathan A, Gerencser AA, Verdin E, Campisi J. Mitochondrial Dysfunction Induces Senescence with a Distinct Secretory Phenotype.Cell Metab. 2016 Feb 9;23(2):303-14.
• Tada K, Kobayashi M, Takiuchi Y, Iwai F, Sakamoto T, Nagata K, Shinohara M, Io K, Shirakawa K, Hishizawa M, Shindo K, Kadowaki N, Hirota K, Yamamoto J, Iwai S, Sasanuma H, Takeda S, Takaori-Kondo A. Abacavir, an anti-HIV-1 drug, targets TDP1-deficient adult T cell leukemia. Sci Adv. 2015 Apr 24;1(3):e1400203.
• Shinohara M, Io K, Shindo K, Matsui M, Sakamoto T, Tada K, Kobayashi M, Kadowaki N, Takaori-Kondo A. APOBEC3B can impair genomic stability by inducing base substitutions in genomic DNA in human cells. Sci Rep. 2012; 2:806.
• Izumi T, Io K, Matsui M, Shirakawa K, Shinohara M, Nagai Y, Kawahara M, Kobayashi M, Kondoh H, Misawa N, Koyanagi Y, Uchiyama T, Takaori-Kondo A. HIV-1 viral infectivity factor interacts with TP53 to induce G2 cell cycle arrest and positively regulate viral replication. Proc Natl Acad Sci U S A. 2010 Nov 30;107(48):20798-803.
• Izumi T, Takaori-Kondo A, Shirakawa K, Higashitsuji H, Itoh K, Io K, Matsui M, Iwai K, Kondoh H, Sato T, Tomonaga M, Ikeda S, Akari H, Koyanagi Y, Fujita J, Uchiyama T. MDM2 is a novel E3 ligase for HIV-1 Vif.Retrovirology. 2009 Jan 7;6:1.
• Shirakawa K, Takaori-kondo A, Yokoyama M, Izumi T, Matsui M, Io K, Sato T, Sato H, Uchiyama T. Phosphorylation of APOBEC3G by protein kinase A regulates its interaction with HIV-1 Vif. Nat Struct Mol Biol. 2008; 15(11):1184-91.
• Izumi T, Shirakawa K, Takaori-Kondo A. Cytidine deaminases as a weapon against retroviruses and a new target for antiviral therapy.Mini Rev Med Chem. 2008 Mar;8(3):231-8. Review.
• Noguchi C, Hiraga N, Mori N, Tsuge M, Imamura M, Takahashi S, Fujimoto Y, Ochi H, Abe H, Maekawa T, Yatsuji H, Shirakawa K, Takaori-Kondo A, Chayama K. Dual effect of APOBEC3G on Hepatitis B virus. J Gen Virol. 2007 Feb;88(Pt 2):432-40.
• Abudu A, Takaori-Kondo A, Izumi T, Shirakawa K, Kobayashi M, Sasada A, Fukunaga K, and Uchiyama T Murine retrovirus escapes from murine APOBEC3 via two distinct novel mechanisms.Current Biolology. 2006 Aug 8;16(15):1565-70.
• Abudu A, Takaori-Kondo A, Izumi T, Shirakawa K, Kobayashi M, Sasada A, Fukunaga K, and Uchiyama T Murine retrovirus escapes from murine APOBEC3 via two distinct novel mechanisms. Current Biolology. 2006 Aug 8;16(15):1565-70.
• Shirakawa K, Takaori-Kondo A, Kobayashi M, Tomonaga M, Izumi T, Fukunaga K, Sasada A, Abudu A, Miyauchi Y, Akari H, Iwai K and Uchiyama T. Ubiquitination of APOBEC3 proteins by the Vif-Cullin5-ElonginB-Elongin C complex.Virology. 2006; 344:263-266.
• Sasada A, Takaori-Kondo A, Shirakawa K, Kobayashi M, Abudu A, Hishizawa M, Imada K, Tanaka Y, Uchiyama T. APOBEC3G targets human T-cell leukemia virus type 1. Retrovirology. 2005 May 19;2(1):32.