文部科学省 科学研究費補助金 学術変革領域研究 (A) 2023〜2027年度
FY2023-2027 MEXT KAKENHI Grant-in-Aid for Transformative Research Area (A)
Achievements
multimodal.ecm[at]gmail.com (Please replace [at] with @)
75) AP2A1 modulates cell states between senescence and rejuvenation
Chantachotikul P, Liu S, Furukawa K, and Deguchi S
Cell. Signal., 127:111616 (2025)
74) Collagen fiber and cellular dynamics of axolotl skin with aging
Shima C, Ohashi A, Furukawa S, Yamamoto S, Kashmoto R, and Satoh A
73) Dorsoventral patterning beyond the gastrulation stage: Interpretation of early dorsoventral cues and modular development mediated by zic1/zic4
Kawanishi T and Takeda H
Cells Dev., 204012 (2025) (in press)
72) Electrical Conduction Mechanism of Gels and Films Formed by Self-Assembled Elastin-Like Polypeptide Nanofibers: Implications for Tissue Regeneration
Shibata R, Islam MZ, Takahashi R, Nakaya M, Onoe J, Sugawara-Narutaki A
ACS Appl. Nano Mater., 8(10):5141–5148 (2025).
71) Stiff extracellular matrix activates the transcription factor ATF5 to promote proliferation of cancer cells
Ishihara S, Enomoto A, Sakai A, Iida T, Tange S, Kioka N, Nukuda A, Ichikawa Nagasato A, Yasuda M, Tokino T, Haga H
70) Biomechanical properties of regenerated digital flexor tendon in immature newt following complete transection
Masuda-Otsuka Y, Kamiya T, Suzuki D, Hayashi T, Kim J, Matsumoto T and Maeda E
Bio-Med. Mater. Eng., in press.
69) Cell position-based evaluation of mechanical features of cells in multicellular systems
Koyama H, Ito AM, Okumura H, Otani T, Nakamura K, and Fujimori T
J. Theor. Biol., 607 (7):112070 (2025)
68) Impacts of Structural Properties of Myosin II Filaments on Force Generation
Ding S, Chou P-E, Deguchi S, and Kim T
67) Keratinocyte-driven dermal collagen formation in the axolotl skin
Ohashi A, Sakamoto H., Kuroda J., Kondo Y.,Kamei Y., Nonaka S., Furukawa S., Yamamoto S., and Satoh A.,
Nat. Commun., 16(1):1757 (2025)
66) Endogenous chondroitin extends lifespan by inhibiting VHA-7-mediated tubular lysosome formation
Shibata Y, Tanaka Y, Mori S, Mizutani K, Sasakura H, Morioka Y, Takeuchi K
Sci. Rep., 14(1):29651-29662 (2024)
65) miR-PAIR: microRNA-protein analysis of integrative relationship for the identification of significantly working miRNAs
Akai M, Maeda Y, Kawami M, Yumoto R, Takano M, Uchida Y
Biochim. Biophys. Acta - Gen. Subj., 1869(2):130746(2025).
64) Regulation of swelling behaviour while preserving bulk modulus in hydrogels via surface grafting
Nishimoto T, Akimoto A M, Enomoto T, Lin C-H, Luo S-C, and Yoshida R
Soft Matter, 21:356-360 (2025)
63) Isolation method of brain microvessels from small frozen human brain tissue for blood-brain barrier protein expression analysis
Ogata S, Ito S, Masuda T, and Ohtsuki S
Fluids Barriers CNS, 21(1):106 (2024)
62) Fibrillin-1 G234D mutation in the hybrid1 domain causes tight skin associated with dysregulated elastogenesis and increased collagen cross-linking in mice
Hossain AS, Clarin M, Kimura K, Biggin G, Taga Y, Uto K, Yamagishi A, Motoyama E, Narenmandula, Mizuno K, Nakamura C, Asano K, Ohtsuki S, Nakamura T, Kanki S, Baldock C, Raja E, and Yanagisawa H
Matrix Biol., 135:24-38 (2025)
61) An actin bracket-induced elastoplastic transition determines epithelial folding irreversibility
Teranishi A, Mori M, Ichiki R, Toda S, Shioi G, and Okuda S
60) Self-organized patterning of peristaltic waves by suppressive actions in a developing gut
Kawamura K, Kato S, Utsunomiya S, Takahashi Y, and Inaba M
Front. Cell Dev. Biol., 13: 1529975 (2025).
59) Survivability and life support in sealed mini-ecosystems with simulated planetary soils
Sato T, Abe K, Koseki J, Seto M, Yokoyama J, Akashi T, Terada M, Kadowaki K, Yoshida S, Yamashiki YA, Shimamura T
58) An eGFP-Col4a2 mouse model reveals basement membrane dynamics underlying hair follicle morphogenesis
Wuergezhen D, Gindroz E, Morita R, Hashimoto K, Abe T, Kiyonari H, Fujiwara H
J. Cell Biol., 224(2):e202404003 (2025).
57) Evolutionary changes leading to efficient glymphatic circulation in the mammalian brain
Kameya N, Sakai I, Saito K, Hamabe-Horiike T, Shinmyo Y, Nakada M, Okuda S, and Kawasaki H
56) Progressive Amyloid-β Accumulation in the Brain leads to Altered Protein Expressions in the Liver and Kidneys of APP knock-in Mice
Ito S, Iwata Y, Otsuka M, Kaneko Y, Ogata S, Yagi R, Uemura T, Masuda T, Saito T, Saido T, and Ohtsuki S
J. Pharm. Sci., 3549(24)00503-3 (2025)
55) LineageVAE: reconstructing historical cell states and transcriptomes toward unobserved progenitors
Majima K, Kojima Y, Minoura K, Abe K, Hirose H, Shimamura T
Bioinfomatics, 40(10):btae520 (2024)
54) A Direct Approach for Living Biomembrane Printing on a Nanoparticle
Mizuta R, Kanao E, Ukyo K, Kuwada S, Sawada SI, Ishihama Y, and Sasaki Y
Nano Lett., 24(41):12907–12914 (2024).
53) Functional analysis of regenerated digit in newt following complete amputation at proximal interphalangeal joint
Kasahara T, Teramoto M, Agata K, Kim J, Matsumoto T, and Maeda E
J. Biomech. Sci. Eng., 20 (2): 24-00276 (2025).
52) Polysaccharide-Based Coacervate Microgel Bearing Cationic Peptides That Achieve Dynamic Cell-Membrane Structure Alteration and Facile Cytosolic Infusion of IgGs
Michibata J, Kawaguchi Y, Hirose H, Eguchi A, Deguchi S, Takayama K, and Futaki S
Bioconjugate Chem., 35(12):1888–1899 (2024).
51) Histological and gene-expression analyses of pyloric sphincter formation during stomach metamorphosis in Xenopus laevis
Nagura K, Ikeda T, Hasebe T, Satou-Kobayashi Y, Udagawa S, Shigenobu S, Ishizuya-Oka A, Taira M
Dev. Biol., 517:100-116 (2025).
50) Ex vivo SIM-AFM measurements reveal the spatial correlation of stiffness and molecular distributions in 3D living tissue
Shioka I, Morita R, Yagasaki R, Wuergezhen D, Yamashita T, Fujiwara H, Okuda S
Acta Biomater., 189:351-365 (2024)
49) Fgf8 contributes to the pathogenesis of Nager syndrome
1 Ulhaq Z.S., You M.S., Yabe T., Takada S., Chen J.K., Ogino Y., Jiang Y.J., Tse W.K.F.
Int. J. Biol. Macromol., 280:135692(2024).
48) DeepKINET: a deep generative model for estimating single-cell RNA splicing and degradation rates
Mizukoshi C, Kojima Y, Nomura S, Hayashi S, Abe K, Shimamura T
Genome Biol., 25(1):229 (2024)
47) Extracellular Vesicles Comprising Carborane Prepared by a Host Exchanging Reaction as a Boron Carrier for Boron Neutron Capture Therapy
Kawasaki R, Oshige A, Kono N, Yamana K, Hirano H, Miura Y, Sato K, Yasuhara K, Yamada Y, and Ikeda A
ACS Appl. Mater. Interfaces, 16(36):47137–47149 (2024)
46) Twisted cell flow facilitates three-dimensional somite morphogenesis in zebrafish
Kametani H, Tong Y, Shimada A, Takeda H, Sushida T, Akiyama M, Kawanishi T
Cells Dev., 180:203969 (2024).
45) Diffusion model predicts the geometry of actin cytoskeleton from cell morphology
Li H, Liu S, Deguchi S, Matsunaga M
PLoS Comput. Biol., 20(8):e1012312 (2024)
44) Dynamic duo: Cell-extracellular matrix interactions in hair follicle development and regeneration
Fujiwara H
43) The gut contractile organoid: a novel model for studying the gut motility regulated by coordinating signals between interstitial cells of Cajal and smooth muscles
Yagasaki R, Nakamura R, Shikaya Y, Tadokoro R, Hao R, Wang Z, Eiraku M, Inaba M, and Takahashi Y
42) Effective mechanical potential of cell–cell interaction in tissues harboring cavity and in cell sheet toward morphogenesis
Koyama H, Okumura H, Otani T, Ito AM, Nakamura K, Kato K, and Fujimori T
Front. Cell Dev. Biol., 12:1414601 (2024)
41) Improving Proteomic Identification Using Narrow Isolation Windows with Zeno SWATH Data-Independent Acquisition
Gu K, Kumabe H, Yamamoto T, Tashiro N, Masuda T, Ito S, and Ohtsuki S
J. Proteome Res., 23(8):3484-349 (2024)
40) Intracellular Macromolecular Crowding within Individual Stress Fibers Analyzed by Fluorescence Correlation Spectroscopy
Buenaventura A, Saito T, Kanao T, Matsunaga D, Matsui TS, and Deguchi S
39) Application of cysteinyl prolyl ester for the synthesis of cyclic peptides containing an RGD sequence and their biological activity measurement
Yamada A, Takei T, Kawakami T, Taniguchi Y, Sekiguchi K, and Hojo H
Front. Chem., 12:1391678 (2024).
38) Transporter Protein Expression of Corneal Epithelium in Rabbit and Porcine: Evaluation of Models for Ocular Drug Transport Study
Ramsay E, Montaser AB, Niitsu K, Urtti A, Auriola S, Huttunen KM, Uchida Y, Kidron H, Terasaki T
Mol. Pharm., 21(7):3204-3217(2024).
37) Abemaciclib-induced epithelial-mesenchymal transition mediated by cyclin-dependent kinase 4/6 independent of cell cycle arrest pathway
Yoshimori T, Kawami M, Kumagai Y, Futatsugi S, Yumoto R, Uchida Y, Takano M
Int. J. Biochem. Cell Biol., 172:106601(2024).
36) Endogenous chondroitin extends the lifespan and healthspan in C. elegans
Saijo S , Nagoshi N, Kawai M, Kitagawa N, Suematsu Y, Ozaki M, Shinozaki M, Shibata S, Takeuchi K, Nakamura M, Yuzaki M, Okano H
Sci. Rep., 14(1):4813-4822 (2024)
35) ZNT5-6 and ZNT7 play an integral role in protein N-glycosylation by supplying Zn2+ to Golgi α-mannosidase II
Yuasa H, Morino N, Wagatsuma T, Munekane M, Ueda S, Matsunaga M, Uchida Y, Katayama T, Katoh T, Kambe T
34) Human-induced pluripotent stem cell-derived neural stem/progenitor cell ex vivo gene therapy with synaptic organizer CPTX for spinal cord injury
Saijo S , Nagoshi N, Kawai M, Kitagawa N, Suematsu Y, Ozaki M, Shinozaki M, Shibata S, Takeuchi K, Nakamura M, Yuzaki M, Okano H
Stem Cell Rep., 19(3):383-398 (2024).
33) Oncogenic Kras induces spatiotemporally specific tissue deformation through converting pulsatile into sustained ERK activation
Xin T, Gallini S, Wei H, Gonzalez DG, Matte-Martone C, Machida H, Fujiwara H, Pasolli HA, Suozzi KC, Gonzalez LE, Regot S, Greco V
Nat. Cell Biol., 26(6):859-867 (2024).
32) Heparan sulfate chain-conjugated laminin-E8 fragments advance paraxial mesodermal differentiation followed by high myogenic induction from hiPSCs
Zhao M, Taniguchi Y, Shimono C, Jonuchi T, Cheng Y, Shimizu Y, Nalbandian M, Yamamoto T, Nakagawa M, Sekiguchi K, and Sakurai H
31) Spatial and single-cell colocalisation analysis reveals MDK-mediated immunosuppressive environment with regulatory T cells in colorectal carcinogenesis
Hashimoto M, Kojima Y, Sakamoto T, Ozato Y, Nakano Y, Abe T, Hosoda K, Saito H, Higuchi S, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Hata T, Nagayama S, Kagawa K, Goto Y, Utou M, Gamachi A, Imamura K, Kuze Y, Zenkoh J, Suzuki A, Takahashi K, Niida A, Hirose H, Hayashi S, Koseki J, Fukuchi S, Murakami K, Yoshizumi T, Kadomatsu K, Tobo T, Oda Y, Uemura M, Eguchi H, Doki Y, Mori M, Oshima M, Shibata T, Suzuki Y, Shimamura T, Mimori K
EBioMedicine, 103:105102 (2024)
30) Enveloped Viral Replica Equipped with Spike Protein Derived from SARS-CoV-2
Furukawa H, Nakamura S, Mizuta R, Sakamoto K, Inaba H, Sawada SI, and Matsuura K
ACS Synth. Biol., 60(10):1123-1131(2024).
29) Spatial cell fate manipulation of human pluripotent stem cells by controlling the microenvironment using photocurable hydrogel
Wang Z, Numada A, Wagai F, Oda Y, Ohgushi M, Maki K, Adachi T, and Eiraku M
28) Tumor endothelial cell-derived Sfrp1 supports the maintenance of cancer stem cells via Wnt signaling
Hayashi Y, Hashimoto M, Takaoka K, Takemoto T, Takakura N, and Kidoya H.
In Vitro Cell Dev Biol Anim, 60(10):1123-1131(2024).
27) Brain-derived endothelial cells are neuroprotective in a chronic cerebral hypoperfusion mouse model
Matsui Y, Muramatsu F, Nakamura H, Noda Y, Matsumoto K, Kishima H, and Takakura N
26) Improvement of the Green-Red Förster Resonance Energy Transfer-Based Ca2+ Indicator by Using the Green Fluorescent Protein, Gamillus, with a Trans Chromophore as the Donor
Matsuda T, Sakai S, Okazaki KI, and Nagai T
ACS Sens., 9(4):1743-1748 (2024).
25) Deficiency of mastl, a mitotic regulator, results in cell detachment from developing tissues of zebrafish embryos
Utsumi H., Yabe T, Koshida S., Yamashita A., and Takada S.
Front. Cell Dev. Biol., 12:1375655 (2024)
24) In vitro induction of patterned branchial arch-like aggregate from human pluripotent stem cells
Seto Y, Ogihara R, Takizawa K, and Eiraku M
23) Numerical assessment of the applicability of geometry-based force inference on homogeneous and heterogeneous cells
Miyasaka S, Izumi K, Okuda S and Miki Y
PLOS ONE, 19(4):e0299016 (2024).
22) The humidity responsiveness of a poly(N-isopropylacrylamide) gel using a PEG/water mixed solution as the solvent
Makita R, Akimoto A, Enomoto T, Nishimoto T, Li X, Shibayama M, Yoshida R
Polymer J., 56, 639-642 (2024)
21) Soluble Frizzled-related proteins promote exosome-mediated Wnt re-secretion.
Tran THN, Takada R, Elena Krayukhina E, Maruno T, Mii Y, Uchiyama S, and Takada S
20) Single-cell colocalization analysis using a deep generative model
Kojima Y, Mii S, Hayashi S, Hirose H, Ishikawa M, Akiyama M, Enomoto A, Shimamura T
19) Asymmetric response emerges between creation and disintegration of force-bearing subcellular structures as revealed by percolation analysis
Ueda Y, Matsunaga D, Deguchi S
Integr. Biol. , 16:zyae012 (2024)
18) Dissection of N-deacetylase and N-sulfotransferase activities of NDST1 and their effects on Wnt8 distribution and signaling in Xenopus embryos
Suzuki M, Takada S, and Mii Y
Dev. Growth. Differ., 66(3), 248-255 (2024).
17) Simultaneous binding of bFGF to both FGFR and integrin maintains properties of primed human induced pluripotent stem cells
Cheng YS, Taniguchi Y, Yunoki Y, Masai S, Nogi M, Doi H, Sekiguchi K, and Nakagawa M
16) Discovery of Transcription Factors Involved in the Maintenance of Resident Vascular Endothelial Stem Cell Properties
Konishi H, Rahmawati FN, Okamoto N, Akuta K, Inukai K, Jia W, Muramatsu F, and Takakura N
15) Gap junction-mediated contraction of myoepithelial cells induces the peristaltic transport of sweat in human eccrine glands
Nakashima K, Kato H, Kurata R, Luo Q, Hayakawa T, Okada F, Fujita F, Nakagawa Y, Tanemura A, Murota H, Katayama I, and Sekiguchi K
14) Efficient selection of knocked-in pluripotent stem cells using a dual cassette cellular elimination system.
Nakade K, Tsukamoto S, Nakashima K, An Y, Sato I, Li J, Shimoda Y, Hemmi Y, Miwa Y, and Hayashi Y
Cell Rep. methods,3:100662 (2023)
13) Proteomic alterations in the brain and blood–brain barrier during brain Aβ accumulation in an APP knock-in mouse model of Alzheimer’s disease
Ito S, Yagi R, Ogata S, Masuda T, Saito T, Saido T, and Ohtsuki S
Fluids Barriers CNS, 20(1):66 (2023)
12) Laminin fragments conjugated with perlecan’s growth factor-binding domain differentiate human induced pluripotent stem cells into skin-derived precursor cells
Sugiyama‐Nakagiri Y, Yamashita S, Taniguchi Y, Shimono C, and Sekiguchi K
11) Hypoxia activates SREBP2 through Golgi disassembly in bone marrow-derived monocytes for enhanced tumor growth
Nakahara R, Aki S, Sugaya M, Hirose H, Kato M, Maeda K, Sakamoto DM, Kojima Y, Nishida M, Ando R, Muramatsu M, Pan M, Tsuchida R, Matsumura Y, Yanai H, Takano H, Yao R, Sando S, Shibuya M, Sakai J, Kodama T, Kidoya H, Shimamura T, Osawa T.
EMBO J., 42(22):e114032.(2023)
10) Rapid and Highly Efficient Purification of Extracellular Vesicles Enabled by a TiO2 Hybridized Spongy-like Polymer
Kanao E, Ishida K, Mizuta R, Li Y, Imami K, Tanigawa T, Sasaki Y, Akiyoshi K, Adachi J, Otsuka K, Ishihama Y, and Kubo T*
Anal. Chem.,95, 38, 14502 (2023)
9) Apelin provides an alternative function to estrogen in regulating lymphatic vascular integrity
Sawane M, Gantumur E, Muramatsu F, Kidoya H, Takakura N, Kajiya K.
J. Dermatol. Sci., 111(3):124-127(2024)
8) Aging impairs the ability of vascular endothelial stem cells to generate endothelial cells in mice
Shimizu S, Iba T, Naito H, Rahmawati FN, Konishi H, Jia W, Muramatsu F, and Takakura N
Angiogenesis,26:567-580 (2023).
7) UNMF: a unified nonnegative matrix factorization for multi-dimensional omics data
Abe K and Shimamura T
Brief. Bioinform.,24:bbad253 (2023)
6) Polydom/SVEP1 binds to Tie1 and promotes migration of lymphatic endothelial cells
Sato-Nishiuchi R, Doiguchi M, Morooka N, and Sekiguchi K
J. Cell Biol., 222:e202208047 (2023).
5) Development of a method for isolating brain capillaries from a single neonatal mouse brain and comparison of proteomic profiles between neonatal and adult brain capillaries
Hamada Y, Ogata S, Masuda T, Ito S, and Ohtsuki S
Fluids Barriers CNS, 20:50 (2023).
4) Optogenetic control of gut movements reveals peristaltic wave-mediated induction of cloacal contractions and reactivation of impaired gut motility
Shikaya Y, Inaba M, Tadokoro R, Utsunomiya S, and Takahashi Y
Front. Physiol., Sec. Developmental Physiology, 14:1175951 (2023)
3) Topological data analysis of protein structure and inter/intra-molecular interaction changes attributable to amino acid mutations
Koseki J, Hayashi S, Kojima Y, Hirose H, and Shimamura T
Comput. Struct. Biotechnol. J.,21:2950 (2023).
2) Surface Glycan Profiling of Extracellular Vesicles by Lectin Microarray and Glycoengineering for Control of Cellular Interactions
Shimoda A and Akiyoshi K
1) Visualization of basement membranes by a nidogen-based fluorescent reporter in mice
Futaki S, Horomoto A, Shimono C, Norioka N, Taniguchi Y, Hamaoka H, Kaneko M, Shigeta M, Abe T, Sekiguchi K, and Kondo Y