All publications

A list of all publications of current staff.

2024

• Nakamura Y, Shimada IS, Maroofian R, Falabella M, Zaki MS, Fujimoto M, Sato E, Takase H, Aoki S, Miyauchi A, Koshimizu E, Miyatake S, Arioka Y, Honda M, Higashi T, Miya F, Okubo Y, Ogawa I, Scardamaglia A, Miryounesi M, Alijanpour S, Ahmadabadi F, Herkenrath P, Dafsari HS, Velmans C, Al Balwi M, Vitobello A, Denommé-Pichon AS, Jeanne M, Civit A, Abdel-Hamid MS, Naderi H, Darvish H, Bakhtiari S, Kruer MC, Carroll CJ, Ghayoor Karimiani E, Khailany RA, Abdulqadir TA, Ozaslan M, Bauer P, Zifarelli G, Seifi T, Zamani M, Al Alam C, Alvi JR, Sultan T, Efthymiou S, Pope SAS, Haginoya K, Matsunaga T, Osaka H, Matsumoto N, Ozaki N, Ohkawa Y, Oki S, Tsunoda T, Pitceathly RDS, Taketomi Y, Houlden H, Murakami M, Kato Y, Saitoh S.
  Biallelic null variants in PNPLA8 cause microcephaly by reducing the number of basal radial glia.
  Brain, 2024 Nov 4;147(11):3949-3967.

• Earwood R, Ninomiya H, Wang H, Shimada IS, Stroud M, Perez D, Uuganbayar U, Yamada C, Akiyama-Miyoshi T, Stefanovic B, Kato Y.
  The binding of LARP6 and DNAAF6 in biomolecular condensates influences ciliogenesis of multiciliated cells.
  Journal of Biological Chemistry, 2024 Jun;300(6):107373.

2022

• Kojima R, Hassan E, Ozawa F, Yamada-Namikawa C, Ogawa S, Mase S, Goto S, Nishikawa R, Inagaki H, Kato Y, Sugiura-Ogasawara M.
  Abnormal accumulation of OFD1 in endometrial cancer with poor prognosis inhibits ciliogenesis.
  Oncology Letters, 2022 May 17;24(1):214.

• Shimada IS, Kato Y.
  Ciliary signaling in stem cells in health and disease: Hedgehog pathway and beyond.
  Seminars in Cell and Developmental Biology, 2022 Apr 21;S1084-9521(22)00135-5.

• Hassan E, Kojima R, Ozawa F, Yoshihara H, Goto S, Kitaori T, Inagaki H, Kato Y, Sugiura-Ogasawara M.
  Abnormal ciliogenesis in decidual stromal cells in recurrent miscarriage.
  Journal of Reproductive Immunology, 2022 Mar;150:103486.

2021

• Shi W, Sheng X, Dorr KM, Hutton JE, Emerson JI, Davies HA, Andrade TD, Wasson LK, Greco TM, Hashimoto Y, Federspiel JD, Robbe ZL, Chen X, Arnold AP, Cristea IM, Conlon FL.
  Cardiac proteomics reveals sex chromosome-dependent differences between males and females that arise prior to gonad formation.
  Developmental Cell, 2021 Nov 8;56(21):3019-3034.e7.

2020

• Shirane M, Shoji H, Hashimoto Y, Katagiri H, Kobayashi S, Manabe T, Miyakawa T, Nakayama KI.
  Protrudin-deficient mice manifest depression-like behavior with abnormalities in activity, attention, and cued fear-conditioning.
  Molecular Brain, Nov 10;13(1):146.

• Kinoshita N, Hashimoto Y, Yasue N, Suzuki M, Cristea IM, Ueno N.
  Mechanical Stress Regulates Epithelial Tissue Integrity and Stiffness through the FGFR/Erk2 Signaling Pathway during Embryogenesis.
  Cell Reports, 2020 Mar 17;30(11):3875-3888.

• Ninomiya H, Intoh A, Ishimine H, Onuma Y, Ito Y, Michiue T, Tazaki A, Kato M.
  Application of a human mesoderm tissue elongation system in vitro derived from human induced pluripotent stem cells to risk assessment for teratogenic chemicals.
  Chemosphere, 2020 Feb 07;250:126124.

• Hashimoto Y, Sheng X, Murray LA, Cristea IM.
  Temporal dynamics of protein complex formation and dissociation during human cytomegalovirus infection.
  Nature Communications, 2020 Feb 10;11(1):806.

2019

• Goshima T, Habara M, Maeda K, Hanaki S, Kato Y, Shimada M.
  Calcineurin regulates cyclin D1 stability through dephosphorylation at T286.
  Scientific Reports, 2019 Sep 4;9(1):12779.

• Shimada IS, Somatilaka BN, Hwang SH, Anderson AG, Shelton JM, Rajaram V, Konopka G, Mukhopadhyay S.
  Derepression of sonic hedgehog signaling upon Gpr161 deletion unravels forebrain and ventricular abnormalities.
  Developmental Biology, 2019 Jun 1;450(1):47-62.

• Hashimoto Y, Kinoshita N, Greco TM, Federspiel JD, Jean Beltran PM, Ueno N, Cristea IM.
  Mechanical Force Induces Phosphorylation-Mediated Signaling that Underlies Tissue Response and Robustness in Xenopus Embryos.
  Cell Systems, 2019 Mar 27;8(3):226-241.e7

• Hashimoto Y, Greco TM, Cristea IM.
  Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology.
  Advancements of Mass Spectrometry in Biomedical Research, 2019;1140:143-154

• Itoh M, Dai H, Horike SI, Gonzalez J, Kitami Y, Meguro-Horike M, Kuki I, Shimakawa S, Yoshinaga H, Ota Y, Okazaki T, Maegaki Y, Nabatame S, Okazaki S, Kawawaki H, Ueno N, Goto YI, Kato Y.
  Biallelic KARS pathogenic variants cause an early-onset progressive leukodystrophy.
  Brain, 2019 Mar 1;142(3):560-573.

2018

• Jean Beltran PM, Cook KC, Hashimoto Y, Galitzine C, Murray LA, Vitek O, Cristea IM.
  Infection-Induced Peroxisome Biogenesis Is a Metabolic Strategy for Herpesvirus Replication.
  Cell Host & Microbe, 2018 Oct 10;24(4):526-541.e7

• Li X, Ohgami N, Yajima I, Xu H, Iida M, Oshino R, Ninomiya H, Shen D, Ahsan N, Akhand AA, Kato M.
  Arsenic level in toenails is associated with hearing loss in humans.
  PloS one, 2018 Jul 5;13(7):e0198743

• Ninomiya H, Ohgami N, Oshino R, Kato M, Ohgami K, Li X, Shen D, Iida M, Yajima I, Angelidis CE, Adachi H, Katsuno M, Sobue G, Kato M.
  Increased expression level of Hsp70 in the inner ears of mice by exposure to low frequency noise.
  Hearing research, 2018 Jun;363 49-54.

• Hashimoto Y, Shirane M, Nakayama KI.
  TMEM55B contributes to lysosomal homeostasis and amino acid-induced mTORC1 activation.
  Genes to Cells, 2018 Jun;23(6):418-434

• Yoshinaga M, Ninomiya H, Al Hossain MMA, Sudo M, Akhand AA, Ahsan N, Alim MA, Khalequzzaman M, Iida M, Yajima I, Ohgami N, Kato M.
  A comprehensive study including monitoring, assessment of health effects and development of a remediation method for chromium pollution.
  Chemosphere, 2018 Jun;201:667-675.

• Shimada IS, Hwang SH, Somatilaka BN, Wang X, Skowron P, Kim J, Kim M, Shelton JM, Rajaram V, Xuan Z, Taylor MD, Mukhopadhyay S.
  Basal Suppression of the Sonic Hedgehog Pathway by the G-Protein-Coupled Receptor Gpr161 Restricts Medulloblastoma Pathogenesis.
  Cell Reports, 2018 Jan 30;22(5):1169-1184.

2017

• Kumasaka MY, Yajima I, Ohgami N, Ninomiya H, Iida M, Li X, Oshino R, Tanihata H, Yoshinaga M, Kato M.
  Manganese-Mediated Decrease in Levels of c-RET and Tyrosine Hydroxylase Expression In Vitro.
  Neurotoxicity research, 2017 Nov;32(4):661-670

• Shimada IS, Acar M, Burgess RJ, Zhao Z, Morrison SJ.
  Prdm16 is required for the maintenance of neural stem cells in the postnatal forebrain and their differentiation into ependymal cells.
  Genes & development, 2017 Jun;31(11):1134-1146

• Shimada IS, Badgandi H, Somatilaka BN, Mukhopadhyay S.
  Using Primary Neurosphere Cultures to Study Primary Cilia.
  Journal of visualized experiments : JoVE, 2017 Apr;(122)

• Manojlovic Z, Earwood R, Kato A, Perez D, Cabrera OA, Didier R, Megraw TL, Stefanovic B, Kato Y.
  La-related protein 6 controls ciliated cell differentiation.
  Cilia, 2017 Mar 23;6:4.

• Badgandi HB, Hwang SH, Shimada IS, Loriot E, Mukhopadhyay S.
  Tubby family proteins are adapters for ciliary trafficking of integral membrane proteins.
  The Journal of cell biology, 2017 Mar;216(3):743-760

• Ohgami N, Oshino R, Ninomiya H, Li X, Kato M.
  Impairments of Inner Ears Caused by Physical Environmental Stresses.
  Nihon Eiseigaku Zasshi, 2017;72(1):38-42

• Ohgami N, Oshino R, Ninomiya H, Li X, Kato M, Yajima I, Kato M.
  Risk Assessment of Neonatal Exposure to Low Frequency Noise Based on Balance in Mice.
  Frontiers in behavioral neuroscience, 2017 Feb 22;11:30

• Shimada IS, Mukhopadhyay S.
  G-protein-coupled receptor signaling and neural tube closure defects.
  Birth defects research, 2017 Jan;109(2):129-139

• Mukhopadhyay S, Badgandi HB, Hwang SH, Somatilaka B, Shimada IS, Pal K.
  Trafficking to the primary cilium membrane.
  Molecular biology of the cell, 2017 Jan;28(2):233-239

2016

• Ilmiawati C, Thang ND, Iida M, Maeda M, Ohnuma S, Yajima I, Ohgami N, Oshino R, Al Hossain MM, Ninomiya H, Kato M.
  Limited effectiveness of household sand filters for removal of arsenic from well water in North Vietnam.
  Journal of water and health, 2016 Dec;14(6):1032-1040

• Yue R, Zhou BO, Shimada IS, Zhao Z, Morrison SJ.
  Leptin Receptor Promotes Adipogenesis and Reduces Osteogenesis by Regulating Mesenchymal Stromal Cells in Adult Bone Marrow.
  Cell stem cell, 2016 Jun;18(6):782-796

• Kato M, Ninomiya H, Maeda M, Ilmiawati C, Al Hossain MM, Yoshinaga M, Ohgami N.
  Reply to the commentary "To Gorelenkova Miller and Mieyal (2015): Sulfhydryl-mediated redox signaling in inflammation: role in neurodegenerative diseases" by Mieyal JJ.
  Archives of toxicology, 2016 Jun;90(6):1523-4

• Kato M, Ninomiya H, Maeda M, Tanaka N, Ilmiawati C, Yoshinaga M.
  Commentary to Gorelenkova Miller and Mieyal (2015): sulfhydryl-mediated redox signaling in inflammation: role in neurodegenerative diseases.
  Archives of toxicology, 2016 Apr;90(4):1017-8

2015

• LeComte MD, Shimada IS, Sherwin C, Spees JL.
  Notch1-STAT3-ETBR signaling axis controls reactive astrocyte proliferation after brain injury.
  Proc. Natl. Acad. Sci. USA, 2015 Jul;112(28):8726-8731

• Tözser J, Earwood R, Kato A, Brown J, Tanaka K, Didier R, Megraw TL, Blum M, Kato Y.
  TGF-β Signaling Regulates the Differentiation of Motile Cilia.
  Cell reports, 2015 Mar;11(7):1000-1007

• Ninomiya H, Mizuno K, Terada R, Miura T, Ohnuma K, Takahashi S, Asashima M, Michiue T.
  Improved efficiency of definitive endoderm induction from human induced pluripotent stem cells in feeder and serum-free culture system.
  In vitro cellular & developmental biology, 2015 Jan;51(1):1-8

2014

• Manojlovic Z, Earwood R, Kato A, Stefanovic B, Kato Y.
  RFX7 is required for the formation of cilia in the neural tube.
  Mechanisms of development, 2014 May;132:28-37

• Hashimoto Y, Shirane M, Matsuzaki F, Saita S, Ohnishi T, Nakayama KI.
  Protrudin regulates endoplasmic reticulum morphology and function associated with the pathogenesis of hereditary spastic paraplegia.
  Journal of Biological Chemistry, 2014 May 9;289(19):12946-61

• Tanaka K, Kato A, Angelocci C, Watanabe M, Kato Y.
  A potential molecular pathogenesis of cardiac/laterality defects in Oculo-Facio-Cardio-Dental syndrome.
  Developmental biology, 2014 Mar;387(1):28-36

• Ohnishi T, Shirane M, Hashimoto Y, Saita S, Nakayama KI.
  Identification and characterization of a neuron-specific isoform of protrudin.
  Genes to Cells, 2014 Feb;19(2):97-111

2012

• Xu Y, Xu C, Kato A, Tempel W, Abreu JG, Bian C, Hu Y, Hu D, Zhao B, Cerovina T, Diao J, Wu F, He HH, Cui Q, Clark E, Ma C, Barbara A, Veenstra GJ, Xu G, Kaiser UB, Liu XS, Sugrue SP, He X, Min J, Kato Y, Shi YG.
  Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development.
  Cell, 2012 Dec;151(6):1200-1213

• Shimada IS, LeComte MD, Granger JC, Quinlan NJ, Spees JL.
  Self-renewal and differentiation of reactive astrocyte-derived neural stem/progenitor cells isolated from the cortical peri-infarct area after stroke.
  The Journal of neuroscience : the official journal of the Society for Neuroscience, 2012 Jun;32(23):7926-7940

• Ninomiya H, David R, Damm EW, Fagotto F, Niessen CM, Winklbauer R.
  Cadherin-dependent differential cell adhesion in Xenopus causes cell sorting in vitro but not in the embryo.
  Journal of cell science, 2012 Apr 15;125(Pt 8):1877-83

2011

• Kato Y.
  The multiple roles of Notch signaling during left-right patterning.
  Cell Mol. Life Sci., 2011;68:2555-2567

• Shimada IS, Borders A, Aronshtam A, Spees JL.
  Proliferating reactive astrocytes are regulated by Notch-1 in the peri-infarct area after stroke.
  Stroke, 2011 Nov;42(11):3231-3237

• Bakondi B, Shimada IS, Peterson BM, Spees JL.
  SDF-1α secreted by human CD133-derived multipotent stromal cells promotes neural progenitor cell survival through CXCR7.
  Stem cells and development, 2011 Jun;20(6):1021-1029

• Luu O, David R, Ninomiya H, Winklbauer R.
  Large-scale mechanical properties of Xenopus embryonic epithelium.
  Proc. Natl. Acad. Sci. USA, 2011 Mar 8;108(10):4000-5

• Shimada IS, Spees JL.
  Stem and progenitor cells for neurological repair: minor issues, major hurdles, and exciting opportunities for paracrine-based therapeutics.
  Journal of cellular biochemistry, 2011 Feb;112(2):374-380

2010

• Shimada IS, Peterson BM, Spees JL.
  Isolation of locally derived stem/progenitor cells from the peri-infarct area that do not migrate from the lateral ventricle after cortical stroke.
  Stroke, 2010 Sep;41(9):e552-60

• Sakano D, Kato A, Parikh N, McKnight K, Terry D, Stefanovic B, Kato Y.
  BCL6 canalizes Notch-dependent transcription, excluding Mastermind-like1 from selected target genes during left-right patterning.
  Developmental cell, 2010 Mar;18(3):450-462

2009

• Bakondi B, Shimada IS, Perry A, Munoz JR, Ylostalo J, Howard AB, Gregory CA, Spees JL.
  CD133 identifies a human bone marrow stem/progenitor cell sub-population with a repertoire of secreted factors that protect against stroke.
  Molecular therapy : the journal of the American Society of Gene Therapy, 2009 Nov;17(11):1938-1947

• David R, Ninomiya H, Winklbauer R, Neumann AW.
  Tissue surface tension measurement by rigorous axisymmetric drop shape analysis.
  Colloids and surfaces. B, Biointerfaces, 2009 Sep 1;72(2):236-40

• Koide Y, Kiyota T, Tonganunt M, Pinkaew D, Liu Z, Kato Y, Hutadilok-Towatana N, Phongdara A, Fujise K.
  Embryonic lethality of fortilin-null mutant mice by BMP-pathway overactivation.
  Biochimica et biophysica acta, 2009 May;1790(5):326-338

• Kalantarian A, Ninomiya H, Saad SM, David R, Winklbauer R, Neumann AW.
  Axisymmetric drop shape analysis for estimating the surface tension of cell aggregates by centrifugation.
  Biophysical journal, 2009 Feb 18;96(4):1606-16

2008

• Kiyota T, Kato A, Altmann CR, Kato Y.
  The POU homeobox protein Oct-1 regulates radial glia formation downstream of Notch signaling.
  Developmental biology, 2008 Mar;315(2):579-592

• Ninomiya H, Winklbauer R.
  Epithelial coating controls mesenchymal shape change through tissue-positioning effects and reduction of surface-minimizing tension.
  Nature cell biology, 2008 Jan;10(1):61-9

• Petersen LF, Ninomiya H, Winklbauer R.
  Regulation of convergent extension by non-canonical Wnt signaling in the Xenopus embryo.
  Methods in molecular biology, 2008;469:477-84

2007

• Kiyota T, Kato A, Kato Y.
  Ets-1 regulates radial glia formation during vertebrate embryogenesis.
  Organogenesis, 2007 Oct;3(2):93-101

2006

• Zhang W, Chen X, Kato Y, Evans PM, Yuan S, Yang J, Rychahou PG, Yang VW, He X, Evers BM, Liu C.
  Novel cross talk of Kruppel-like factor 4 and beta-catenin regulates normal intestinal homeostasis and tumor repression.
  Molecular and cellular biology, 2006 Mar;26(6):2055-2064

2004

• Nakaya MA, Habas R, Biris K, Dunty WC Jr, Kato Y, He X, Yamaguchi TP.
  Identification and comparative expression analyses of Daam genes in mouse and Xenopus.
  Gene expression patterns : GEP, 2004 Nov;5(1):97-105

• Fraley GS, Scarlett JM, Shimada I, Teklemichael DN, Acohido BV, Clifton DK, Steiner RA.
  Effects of diabetes and insulin on the expression of galanin-like peptide in the hypothalamus of the rat.
  Diabetes, 2004 May;53(5):1237-1242

2003

• Kusakabe T, Mishima S, Shimada I, Kitajima Y, Tsuda M.
  Structure, expression, and cluster organization of genes encoding gonadotropin-releasing hormone receptors found in the neural complex of the ascidian Ciona intestinalis.
  Gene, 2003 Dec;322:77-84

• Ninomiya H, Elinson RP, Winklbauer R.
  Antero-posterior tissue polarity links mesoderm convergent extension to axial patterning.
  Nature, 2004 Jul 15;430(6997):364-7

• Fraley GS, Shimada I, Baumgartner JW, Clifton DK, Steiner RA.
  Differential patterns of Fos induction in the hypothalamus of the rat following central injections of galanin-like peptide and galanin.
  Endocrinology, 2003 Apr;144(4):1143-1146

• Elinson RP, Ninomiya H.
  Parallel microtubules and other conserved elements of dorsal axial specification in the direct developing frog, Eleutherodactylus coqui.
  Development genes and evolution, 2003 Feb;213(1):28-34

2002

• Kato Y, Habas R, Katsuyama Y, Näär AM, He X.
  A component of the ARC/Mediator complex required for TGF beta/Nodal signalling.
  Nature, 2002 Aug;418(6898):641-646

2001

• Ninomiya H, Zhang Q, Elinson RP.
  Mesoderm formation in Eleutherodactylus coqui: body patterning in a frog with a large egg.
  Developmental biology, 2001 Aug 1;236(1):109-23

• Habas R, Kato Y, He X.
  Wnt/Frizzled activation of Rho regulates vertebrate gastrulation and requires a novel Formin homology protein Daam1.
  Cell, 2001;107:843-854

2000

• Inagaki H, Kato Y, Hamajima N, Nonaka M, Sasaki M, Eimoto T.
  Differential expression of dihydropyrimidinase-related protein genes in developing and adult enteric nervous system.
  Histochem. Cell Biol., 2000;113:37-41

• Tamai K, Semenov M, Kato Y, Spokony R, Liu C, Katsuyama Y, Hess F, Saint-Jeannet JP, He X.
  LDL-receptor-related proteins in Wnt signal transduction.
  Nature, 2000;407:530-535

1999

• Ninomiya H, Takahashi S, Tanegashima K, Yokota C, Asashima M.
  Endoderm differentiation and inductive effect of activin-treated ectoderm in Xenopus.
  Development, growth & differentiation, 1999 Aug;41(4):391-400

• Liu C, Kato Y, Zhang Z, Do VM, Yankner BA, He X.
  beta-Trcp couples beta-catenin phosphorylation-degradation and regulates Xenopus axis formation.
  Proc. Natl. Acad. Sci. USA, 1999;96:6273-6278

• Kato Y, Shi Y, He X.
  Neuralization of the Xenopus embryo by inhibition of p300/ CREB-binding protein function.
  J. Neurosci, 1999;19:9364-9373

1998

• Ninomiya H, Ariizumi T, Asashima M.
  Activin-treated ectoderm has complete organizing center activity in Cynops embryos.
  Development, growth & differentiation, 1998 Apr;40(2):199-208

• Kato Y, Hamajima N, Inagaki H, Okamura N, Koji T, Sasaki M, Nonaka M.
  Post-meiotic expression of the mouse dihydropyrimidinase-related protein 3 (DRP-3) gene during spermiogenesis.
  Mol. Reprod. Dev., 1998;51:105-111

1997

• Uochi T, Takahashi S, Ninomiya H, Fukui A, Asashima M.
  The Na+,K+-ATPase alpha subunit requires gastrulation in the Xenopus embryo.
  Development, growth & differentiation, 1997 Oct;39(5):571-80

• Nonaka M, Namikawa C, Kato Y, Sasaki M, Salter-Cid L, Flajnik MF.
  Major histocompatibility complex gene mapping in the amphibian Xenopus implies a primordial organization.
  Proc. Natl. Acad. Sci. USA, 1997;94:5789-5791

1996

• Mo R, Kato Y, Nonaka M, Nakayama K, Takahashi M.
  Fourth component of Xenopus laevis complement: cDNA cloning and linkage analysis of the frog MHC.
  Immunogenetics, 1996;43:360-369

1995

• Kato Y, Salter-Cid L, Flajnik MF, Namikawa C, Sasaki M, Nonaka M.
  Duplication of the MHC-linked Xenopus complement factor B gene.
  Immunogenetics, 1995;42:196-203

• Namikawa C, Salter-Cid L, Flajnik MF, Kato Y, Nonaka M, Sasaki M.
  Isolation of Xenopus LMP-7 homologues. Striking allelic diversity and linkage to MHC.
  J. Immunol., 1995;155:1964-1971

1994

• Kato Y, Salter-Cid L, Flajnik MF, Kasahara M, Namikawa C, Sasaki M, Nonaka M.
  Isolation of the Xenopus complement factor B complementary DNA and linkage of the gene to the frog MHC.
  J. Immunol., 1994;53:4546-4554