Publications

BioRxiv (preprint):

Poetsch I, Ebner P, Deszcz L, Bachtrog I, Stephani M, Gómez Díaz C, Dagdas Y, Ikeda F. The anti-apoptosis ubiquitin E3 ligase XIAP promotes autophagosome-lysosome fusion during autophagy. bioRxiv 291294; doi: https://www.biorxiv.org/content/10.1101/291294v1

Research articles and reviews from the Ikeda Lab:

2024

2023

PMID: 36939198 Review.

FEBS Journal Editorial Team, Ikeda F. Editor Profile: Fumiyo Ikeda. FEBS J. 2023 Feb13. doi:10.1111/febs.16733. Online ahead of print.
PMID: 36781398

2022

2021

Gomez-Diaz C, Jonsson G, Schodl K, Deszcz L, Bestehorn A, Eislmayr K, Almagro J, Kavirayani A, Seida M, Fennell LM, Hagelkruys A, Kovarik P, Penninger JM, Ikeda F. The ubiquitin ligase HOIL-1L regulates immune responses by interacting with linear ubiquitin chains. iScience 2021 Oct 8;24(11):103241. doi: 10.1016/j.isci.2021.103241. eCollection 2021 Nov 19.
PMID: 34755089, bioRxiv link

Rodriguez Carvajal A, Grishkovskaya I, Gomez Diaz C, Vogel A, Sonn-Segev A, Kushwah MS, Schodl K, Deszcz L, Orban-Nemeth Z, Sakamoto S, Mechtler K, Kukura P, Clausen T, Haselbach D, Ikeda F. The linear ubiquitin chain assembly complex LUBAC generates heterotypic ubiquitin chains. eLife. 2021 Jun 18;10:e60660. doi: 10.7554/eLife.60660.
PMID: 34142657, bioRxiv link

Klionsky DJ et al., Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 2021 Jan;17(1):1-382. doi: 10.1080/15548627.2020.1797280.
PMID: 33634751

2020

Ikeda F. Ubiquitin conjugating enzymes in the regulation of the autophagy-dependent degradation pathway. Matrix Biol. 2021 Jun;100-101:23-29. doi: 10.1016/j.matbio.2020.11.004. Epub 2020 Dec 2.
PMID: 33276077 Review.

Licchesi JDF, Laman H, Ikeda F and Bolanos-Garcia VM. Editorial: E3 Ubiquitin Ligases: From Structure to Physiology. Front Physiol. 2020 Nov 26;11:621053. doi: 10.3389/fphys.2020.621053. eCollection 2020.
PMID: 33329070.

Fennell LM, Gomez Diaz C, Deszcz L, Kavirayani A, Hoffmann D, Yanagitani K, Schleiffer A, Mechtler K, Hagelkruys A, Penninger J, Ikeda F. Site-specific ubiquitination of the E3 ligase HOIP regulates apoptosis and immune signaling. EMBO J. 2020 Dec 15;39(24):e103303. doi: 10.15252/embj.2019103303. Epub 2020 Nov 20.
PMID: 33215740, bioRxiv link
Press release (in Japanese): link
the NEWS page of the Kyushu Univ webstie (in English). link
the NEWS page of the EMBO Journal website. link

Ikeda F. Diverse ubiquitin codes in the regulation of inflammatory signaling. Proc Jpn Acad Ser B Phys Biol Sci. 2020;96(9):431-439. doi: 10.2183/pjab.96.032.
PMID: 33177297

Ikeda F. Mitophagy is induced by short ubiquitin chains on mitochondria. J Cell Biol. 2020 Sep 7;219(9):e202008031. doi: 10.1083/jcb.202008031.
PMID: 32858748

Stephani M, Picchianti L, Gajic A, Beveridge R, Skarwan E, Sanchez de Medina Hernandez V, Mohseni A, Clavel M, Zeng Y, Naumann C, Matuszkiewicz M, Turco E, Loefke C, Li B, Dürnberger G, Schutzbier M, Chen HT, Abdrakhmanov A, Savova A, Chia KS, Djamei A, Schaffner I, Abel S, Jiang L, Mechtler K, Ikeda F, Martens S, Clausen T, Dagdas Y. A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress. Elife. 2020 Aug 27;9:e58396. doi: 10.7554/eLife.58396.
PMID: 32851973

Kogler M, Tortola L, Negri GL, Leopoldi A, El-Naggar AM, Mereiter S, Gomez Diaz C, Nitsch R, Tortora D, Kavirayani AM, Gapp BV, Rao S, Uribesalgo I, Hoffmann D, Cikes D, Novatchkova M, Williams DA, Trent JM, Ikeda F, Daugaard M, Hagelkruys A, Sorensen PH, Penninger JM. HACE1 Prevents Lung Carcinogenesis via Inhibition of RAC-family GTPases. Cancer Res. 2020 May 4;canres.2270.2019. doi: 10.1158/0008-5472.CAN-19-2270.
PMID: 32366477

Meschede J, Šadić M, Furthmann N, Miedema T, Sehr DA, Müller-Rischart AK, Bader V, Berlemann LA, Pilsl A, Schlierf A, Barkovits K, Kachholz B, Rittinger K, Ikeda F, Marcus K, Schaefer L, Tatzelt J, Winklhofer KF. The parkin-coregulated gene product PACRG promotes TNF signaling by stabilizing LUBAC. Sci Signal. 2020 Feb 4;13(617). pii: eaav1256. doi: 10.1126/scisignal.aav1256.
PMID: 32019898

2019

Gómez-Díaz C, Ikeda F. Roles of ubiquitin in autophagy and cell death. Semin Cell Dev Biol. 2019 Sep;93:125-135. doi: 10.1016/j.semcdb.2018.09.004. Epub 2018 Sep 10. PMID: 30195063 Review.

2018

Fennell LM, Rahighi S, Ikeda F. Linear ubiquitin chain-binding domains. FEBSJ. 2018 Aug;285(15):2746-2761. doi: 10.1111/febs.14478. Epub 2018 Apr 30. Review.
PMID: 29679476

Ebner P, Poetsch I, Deszcz L, Hoffmann T, Zuber J, Ikeda F. The IAP family member BRUCE regulates autophagosome-lysosome fusion. Nat Commun. 2018 Feb 9;9(1):599. doi: 10.1038/s41467-018-02823-x.
PMID: 29426817

Ikeda F. The anti-apoptotic ubiquitin conjugating enzyme BIRC6/BRUCE regulates autophagosome-lysosome fusion. Autophagy. 2018;14(7):1283-1284. doi:10.1080/15548627.2018.1471311. Epub 2018 Jul 20.
PMID: 29929453

2017

Ebner P, Versteeg GA, Ikeda F. Ubiquitin enzymes in the regulation of immune responses. Crit Rev Biochem Mol Biol. 2017 Aug;52(4):425-460. doi: 10.1080/10409238.2017.1325829. Epub 2017 May 19. Review.
PMID: 28524749

Rittinger K, Ikeda F. Linear ubiquitin chains: enzymes, mechanisms and biology. Open Biol. 2017 Apr;7(4). pii: 170026. doi: 10.1098/rsob.170026. Review.
PMID: 28446710

2016

Asaoka T, Almagro J, Ehrhardt C, Tsai I, Schleiffer A, Deszcz L, Junttila S, Ringrose L, Mechtler K, Kavirayani A, Gyenesei A, Hofmann K, Duchek P, Rittinger K, Ikeda F. Linear ubiquitination by LUBEL has a role in Drosophila heat stress response. EMBO Rep. 2016 Nov;17(11):1624-1640. Epub 2016 Oct 4.
PMID: 27702987

Wirnsberger G, Zwolanek F, Asaoka T, Kozieradzki I, Tortola L, Wimmer RA, Kavirayani A, Fresser F, Baier G, Langdon WY, Ikeda F, Kuchler K, Penninger JM. Inhibition of CBLB protects from lethal Candida albicans sepsis. Nat Med. 2016 Aug;22(8):915-23. doi: 10.1038/nm.4134. Epub 2016 Jul 18.
PMID: 27428901

Tortola L, Nitsch R, Bertrand MJM, Kogler M, Redouane Y, Kozieradzki I, Uribesalgo I, Fennell LM, Daugaard M, Klug H, Wirnsberger G, Wimmer R, Perlot T, Sarao R, Rao S, Hanada T, Takahashi N, Kernbauer E, Demiröz D, Lang M, Superti-Furga G, Decker T, Pichler A, Ikeda F, Kroemer G, Vandenabeele P, Sorensen PH, Penninger JM. The Tumor Suppressor Hace1 Is a Critical Regulator of TNFR1-Mediated Cell Fate. Cell Rep. 2016 May 17;15(7):1481-1492. doi: 10.1016/j.celrep.2016.04.032. Epub 2016 May 5. Erratum in: Cell Rep. 2016 Sep 20;16(12 ):3414.
PMID: 27160902

Nastase MV, Zeng-Brouwers J, Frey H, Hsieh LT, Poluzzi C, Beckmann J, Schroeder N, Pfeilschifter J, Lopez-Mosqueda J, Mersmann J, Ikeda F, Iozzo RV, Dikic I, Schaefer L. An Essential Role for SHARPIN in the Regulation of Caspase 1 Activity in Sepsis. Am J Pathol. 2016 May;186(5):1206-20. doi: 10.1016/j.ajpath.2015.12.026. Epub 2016 Mar 8.
PMID: 26968342

2015

Ikeda F. Linear ubiquitination signals in adaptive immune responses. Immunol Rev. 2015 Jul;266(1):222-36. doi: 10.1111/imr.12300. Review.
PMID: 26085218

Asaoka T, Ikeda F. New Insights into the Role of Ubiquitin Networks in the Regulation of Antiapoptosis Pathways. Int Rev Cell Mol Biol. 2015;318:121-58. doi: 10.1016/bs.ircmb.2015.05.003. Epub 2015 Jun 17. Review.
PMID: 26315885

2014

Kumari S, Redouane Y, Lopez-Mosqueda J, Shiraishi R, Romanowska M, Lutzmayer S, Kuiper J, Martinez C, Dikic I, Pasparakis M, Ikeda F. Sharpin prevents skin inflammation by inhibiting TNFR1-induced keratinocyte apoptosis. Elife. 2014 Dec 2;3. doi: 10.7554/eLife.03422.
PMID: 25443631

Paolino M, Choidas A, Wallner S, Pranjic B, Uribesalgo I, Loeser S, Jamieson AM, Langdon WY, Ikeda F, Fededa JP, Cronin SJ, Nitsch R, Schultz-Fademrecht C, Eickhoff J, Menninger S, Unger A, Torka R, Gruber T, Hinterleitner R, Baier G, Wolf D, Ullrich A, Klebl BM, Penninger JM. The E3 ligase Cbl-b and TAM receptors regulate cancer metastasis via natural killer cells. Nature. 2014 Mar 27;507(7493):508-12. doi: 10.1038/nature12998. Epub 2014 Feb 19.
PMID: 24553136

2013

Ikeda F, Lahav G. Signal transduction and signaling networks. Mol Biol Cell. 2013 Mar;24(6):676. doi: 10.1091/mbc.E12-12-0877.
PMID: 23486400

2012

Ikeda F. Fumiyo Ikeda: ubiquitin lines up for action. Interview by Caitlin Sedwick. J Cell Biol. 2012 Oct 29;199(3):405-6. doi: 10.1083/jcb.1993pi.
PMID: 23109664

Past research (from the postdoc and PhD labs):

Ikeda

2012

Kensche T, Tokunaga F, Ikeda F, Goto E, Iwai K, Dikic I. Analysis of nuclear factor-κB (NF-κB) essential modulator (NEMO) binding to linear and lysine-linked ubiquitin chains and its role in the activation of NF-κB. J Biol Chem. 2012 Jul 6;287(28):23626-34. doi: 10.1074/jbc.M112.347195. Epub 2012 May 17.
PMID: 22605335

2011

Ikeda F, Deribe YL, Skånland SS, Stieglitz B, Grabbe C, Franz-Wachtel M, van Wijk SJ, Goswami P, Nagy V, Terzic J, Tokunaga F, Androulidaki A, Nakagawa T, Pasparakis M, Iwai K, Sundberg JP, Schaefer L, Rittinger K, Macek B, Dikic I. SHARPIN forms a linear ubiquitin ligase complex regulating NF-κB activity and apoptosis. Nature. 2011 Mar 31;471(7340):637-41. doi: 10.1038/nature09814.
PMID: 21455181

Ikeda F, Rahighi S, Wakatsuki S, Dikic I. Selective binding of linear ubiquitin chains to NEMO in NF-kappaB activation. Adv Exp Med Biol. 2011;691:107-14. doi: 10.1007/978-1-4419-6612-4_11.
PMID: 21153314

2010

Ikeda F, Crosetto N, Dikic I. What determines the specificity and outcomes of ubiquitin signaling? Cell. 2010 Nov 24;143(5):677-81. doi: 10.1016/j.cell.2010.10.026.
PMID: 21111228.

Matsubara T, Ikeda F, Hata K, Nakanishi M, Okada M, Yasuda H, Nishimura R, Yoneda T. Cbp recruitment of Csk into lipid rafts is critical to c-Src kinase activity and bone resorption in osteoclasts. J Bone Miner Res. 2010 May;25(5):1068-76. doi: 10.1359/jbmr.091039.
PMID: 19874196

2009

Rahighi S, Ikeda F, Kawasaki M, Akutsu M, Suzuki N, Kato R, Kensche T, Uejima T, Bloor S, Komander D, Randow F, Wakatsuki S, Dikic I. Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation. Cell. 2009 Mar 20;136(6):1098-109. doi: 10.1016/j.cell.2009.03.007.
PMID: 19303852

2008

Hata K, Nishimura R, Muramatsu S, Matsuda A, Matsubara T, Amano K, Ikeda F, Harley VR, Yoneda T. Paraspeckle protein p54nrb links Sox9-mediated transcription with RNA processing during chondrogenesis in mice. J Clin Invest. 2008 Sep;118(9):3098-108. doi: 10.1172/JCI31373.
PMID: 18677406

Ikeda F, Dikic I. Atypical ubiquitin chains: new molecular signals. ‘Protein Modifications: Beyond the Usual Suspects’ review series. EMBO Rep. 2008 Jun;9(6):536-42. doi: 10.1038/embor.2008.93. Review.
PMID: 18516089

Ikeda F, Matsubara T, Tsurukai T, Hata K, Nishimura R, Yoneda T. JNK/c-Jun signaling mediates an anti-apoptotic effect of RANKL in osteoclasts. J Bone Miner Res. 2008 Jun;23(6):907-14. doi: 10.1359/jbmr.080211.
PMID: 18251700

Wagner S, Carpentier I, Rogov V, Kreike M, Ikeda F, Löhr F, Wu CJ, Ashwell JD, Dötsch V, Dikic I, Beyaert R. Ubiquitin binding mediates the NF-kappaB inhibitory potential of ABIN proteins. Oncogene. 2008 Jun 12;27(26):3739-45. doi: 10.1038/sj.onc.1211042. Epub 2008 Jan 21.
PMID: 18212736

Iha H, Peloponese JM, Verstrepen L, Zapart G, Ikeda F, Smith CD, Starost MF, Yedavalli V, Heyninck K, Dikic I, Beyaert R, Jeang KT. Inflammatory cardiac valvulitis in TAX1BP1-deficient mice through selective NF-kappaB activation. EMBO J. 2008 Feb 20;27(4):629-41. doi: 10.1038/emboj.2008.5. Epub 2008 Jan 31.
PMID: 18239685

Nishimura R, Hata K, Ikeda F, Ichida F, Shimoyama A, Matsubara T, Wada M, Amano K, Yoneda T. Signal transduction and transcriptional regulation during mesenchymal cell differentiation. J Bone Miner Metab. 2008;26(3):203-12. doi:10.1007/s00774-007-0824-2. Epub 2008 May 11. Review.
PMID: 18470659.

2007

Terzic J, Marinovic-Terzic I, Ikeda F, Dikic I. Ubiquitin signals in the NF-kappaB pathway. Biochem Soc Trans. 2007 Nov;35(Pt 5):942-5. Review.
PMID: 17956251

Ikeda F, Hecker CM, Rozenknop A, Nordmeier RD, Rogov V, Hofmann K, Akira S, Dötsch V, Dikic I. Involvement of the ubiquitin-like domain of TBK1/IKK-i kinases in regulation of IFN-inducible genes. EMBO J. 2007 Jul 25;26(14):3451-62. Epub 2007 Jun 28.
PMID: 17599067

Shimoyama A, Wada M, Ikeda F, Hata K, Matsubara T, Nifuji A, Noda M, Amano K, Yamaguchi A, Nishimura R, Yoneda T. Ihh/Gli2 signaling promotes osteoblast differentiation by regulating Runx2 expression and function. Mol Biol Cell. 2007 Jul;18(7):2411-8. Epub 2007 Apr 18.
PMID: 17442891

2006

Ikeda F, Nishimura R, Matsubara T, Hata K, Reddy SV, Yoneda T. Activation of NFAT signal in vivo leads to osteopenia associated with increased osteoclastogenesis and bone-resorbing activity. J Immunol. 2006 Aug 15;177(4):2384-90.
PMID: 16888000

Ikeda F, Dikic I. CYLD in ubiquitin signaling and tumor pathogenesis. Cell. 2006 May 19;125(4):643-5.
PMID: 16713556

Matsubara T, Myoui A, Ikeda F, Hata K, Yoshikawa H, Nishimura R, Yoneda T. Critical role of cortactin in actin ring formation and osteoclastic bone resorption. J Bone Miner Metab. 2006;24(5):368-72.
PMID: 16937268

2005

Hiraga T, Hata K, Ikeda F, Kitagaki J, Fujimoto-Ouchi K, Tanaka Y, Yoneda T. Preferential inhibition of bone metastases by 5′-deoxy-5-fluorouridine and capecitabine in the 4T1/luc mouse breast cancer model. Oncol Rep. 2005 Sep;14(3):695-9.
PMID: 16077977

Hata K, Nishimura R, Ueda M, Ikeda F, Matsubara T, Ichida F, Hisada K, Nokubi T, Yamaguchi A, Yoneda T. A CCAAT/enhancer binding protein beta isoform, liver-enriched inhibitory protein, regulates commitment of osteoblasts and adipocytes. Mol Cell Biol. 2005 Mar;25(5):1971-9.
PMID: 15713650

2004

Ichida F, Nishimura R, Hata K, Matsubara T, Ikeda F, Hisada K, Yatani H, Cao X, Komori T, Yamaguchi A, Yoneda T. Reciprocal roles of MSX2 in regulation of osteoblast and adipocyte differentiation. J Biol Chem. 2004 Aug 6;279(32):34015-22. Epub 2004 Jun 1.
PMID: 15175325

Ikeda F, Nishimura R, Matsubara T, Tanaka S, Inoue J, Reddy SV, Hata K, Yamashita K, Hiraga T, Watanabe T, Kukita T, Yoshioka K, Rao A, Yoneda T. Critical roles of c-Jun signaling in regulation of NFAT family and RANKL-regulated osteoclast differentiation. J Clin Invest. 2004 Aug;114(4):475-84.
PMID: 15314684

2003

Hiraga T, Ueda A, Tamura D, Hata K, Ikeda F, Williams PJ, Yoneda T. Effects of oral UFT combined with or without zoledronic acid on bone metastasis in the 4T1/luc mouse breast cancer. Int J Cancer. 2003 Oct 10;106(6):973-9.
PMID: 12918079

Nishimura R, Hata K, Ikeda F, Matsubara T, Yamashita K, Ichida F, Yoneda T. The role of Smads in BMP signaling. Front Biosci. 2003 May 1;8:s275-84. Review.
PMID: 12700068

Hata K, Nishimura R, Ikeda F, Yamashita K, Matsubara T, Nokubi T, Yoneda T. Differential roles of Smad1 and p38 kinase in regulation of peroxisome proliferator-activating receptor gamma during bone morphogenetic protein 2-induced adipogenesis. Mol Biol Cell. 2003 Feb;14(2):545-55.
PMID: 12589053

2002

Nishimura R, Hata K, Harris SE, Ikeda F, Yoneda T. Core-binding factor alpha 1 (Cbfa1) induces osteoblastic differentiation of C2C12 cells without interactions with Smad1 and Smad5. Bone. 2002 Aug;31(2):303-12.
PMID: 12151083

Yanagitani (see also Google scholar)

Sogawa A, Komori R, Yanagitani K#, Ohfurudono M, Tsuru A, Kadoi K, Kimata Y, Yoshida H, Kohno K#. Signal sequence-triage is activated by translocon obstruction sensed by an ER stress sensor IRE1α. Cell Struct Funct. 2023 Sep 28. doi: 10.1247/csf.23072.

Yanagitani K, Juszkiewicz S, Hegde RS. UBE2O is a quality control factor for orphans of multiprotein complexes. Science. 2017 Aug 4;357(6350):472-475. doi:10.1126/science.aan0178.

Kanda S, Yanagitani K, Yokota Y, Esaki Y, Kohno K. Autonomous translational pausing is required for XBP1u mRNA recruitment to the ER via the SRP pathway. Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):E5886-E5895. Epub 2016 Sep 20.

Shinya S, Kadokura H, Imagawa Y, Inoue M, Yanagitani K, Kohno K. Reconstitution and characterization of the unconventional splicing of XBP1u mRNA in vitro. Nucleic Acids Res. 2011 Jul;39(12):5245-54. doi: 10.1093/nar/gkr132. Epub 2011 Mar 11.

Yanagitani K, Kimata Y, Kadokura H, Kohno K. Translational pausing ensures membrane targeting and cytoplasmic splicing of XBP1u mRNA. Science. 2011 Feb 4;331(6017):586-9. doi: 10.1126/science.1197142. Epub 2011 Jan 13.

Yanagitani K, Imagawa Y, Iwawaki T, Hosoda A, Saito M, Kimata Y, Kohno K. Cotranslational targeting of XBP1 protein to the membrane promotes cytoplasmic splicing of its own mRNA. Mol Cell. 2009 Apr 24;34(2):191-200. doi: 10.1016/j.molcel.2009.02.033.