headshot of Keisuke Ishihara

Keisuke Ishihara

Assistant Professor
ISHIHARA@pitt.edu
Google Scholar Bioengineering Department

overview

My group takes a synthetic approach to study how cells form tissues. “Synthetic” embodies the experimental creation of states of physical organization and gene expression that push a multicellular system to all possible extremes. The synthetic approach allows us to discover novel regulatory molecules, dormant genetic programs, and general physical principles, which we will critically evaluate as next generation strategies for organ engineering. My group will quantitatively capture 3D tissue morphogenesis through imaging, computation, and molecular profiling. We will use this knowledge to develop genetic and chemical tools to engineer in vitro tissues such as human brain organoids and cardiac organoids.

about

PhD in Systems Biology, Harvard University, 2016

BSE in Chemical Engineering, Princeton University, 2010

Bragulat-Teixidor, H., Ishihara, K., Szücs, G.M., & Otsuka, S. (2024). The endoplasmic reticulum connects to the nucleus by constricted junctions that mature after mitosis. EMBO Rep, 25(7), 3137-3159.Springer Nature. doi: 10.1038/s44319-024-00175-w.

Krammer, T., Stuart, H.T., Gromberg, E., Ishihara, K., Cislo, D., Melchionda, M., Becerril Perez, F., Wang, J., Costantini, E., Lehr, S., Arbanas, L., Hörmann, A., Neumüller, R.A., Elvassore, N., Siggia, E., Briscoe, J., Kicheva, A., & Tanaka, E.M. (2024). Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Dev Cell, 59(15), 1940-1953.e10.Elsevier. doi: 10.1016/j.devcel.2024.04.021.

Bragulat-Teixidor, H., Ishihara, K., Szücs, G.M., & Otsuka, S. (2023). The endoplasmic reticulum connects to the nucleus by constricted junctions that mature after open mitosis in mammalian cells. 2023.01.31.526419.Cold Spring Harbor Laboratory. doi: 10.1101/2023.01.31.526419.

Ishihara, K., Mukherjee, A., Gromberg, E., Brugués, J., Tanaka, E.M., & Jülicher, F. (2023). Topological morphogenesis of neuroepithelial organoids. Nat Phys, 19(2), 177-183.Springer Nature. doi: 10.1038/s41567-022-01822-6.

Krammer, T., Stuart, H.T., Gromberg, E., Ishihara, K., Melchionda, M., Wang, J., Costantini, E., Lehr, S., Cislo, D., Arbanas, L., Hörmann, A., Neumüller, R.A., Elvassore, N., Siggia, E., Briscoe, J., Kicheva, A., & Tanaka, E.M. (2023). Neural tube organoids self-organise floorplate through BMP-mediated cluster competition. 2023.06.25.546258.Cold Spring Harbor Laboratory. doi: 10.1101/2023.06.25.546258.

Ishihara, K., Decker, F., Caldas, P., Pelletier, J.F., Loose, M., Brugués, J., & Mitchison, T.J. (2021). Spatial variation of microtubule depolymerization in large asters. In Surrey, T. (Ed.). Mol Biol Cell, 32(9), 869-879.American Society for Cell Biology (ASCB). doi: 10.1091/mbc.E20-11-0723.

Ishihara, K., Mukherjee, A., Gromberg, E., Brugués, J., Tanaka, E.M., & Jülicher, F. (2021). Topological morphogenesis of neuroepithelial organoids. 2021.08.08.455385.Cold Spring Harbor Laboratory. doi: 10.1101/2021.08.08.455385.

Quail, T., Golfier, S., Elsner, M., Ishihara, K., Murugesan, V., Renger, R., Julicher, F., & Brugues, J. (2021). Force generation by protein-DNA co-condensation. NATURE PHYSICS, 17(9), 1007-+.Springer Nature. doi: 10.1038/s41567-021-01285-1.

Ishihara, K., Decker, F., Caldas, P., Pelletier, J.F., Loose, M., Brugués, J., & Mitchison, T.J. (2020). Spatial Variation of Microtubule Depolymerization in Large Asters Suggests Regulation by MAP Depletion. 2020.06.26.172783.Cold Spring Harbor Laboratory. doi: 10.1101/2020.06.26.172783.

Ishihara, K., George, A.B., Cornelius, R., & Korolev, K.S. (2020). Traveling fronts in self-replicating persistent random walks with multiple internal states. NEW JOURNAL OF PHYSICS, 22(8), 083034.IOP Publishing. doi: 10.1088/1367-2630/aba219.

Ishihara, K., George, A.B., Cornelius, R., & Korolev, K.S. (2020). Traveling fronts in self-replicating persistent random walks with multiple internal states. 2020.04.15.042895.Cold Spring Harbor Laboratory. doi: 10.1101/2020.04.15.042895.

Quail, T., Golfier, S., Elsner, M., Ishihara, K., Murugesan, V., Renger, R., Jülicher, F., & Brugués, J. (2020). Force generation by protein-DNA co-condensation. 2020.09.17.302299.Cold Spring Harbor Laboratory. doi: 10.1101/2020.09.17.302299.

Rieckhoff, E.M., Berndt, F., Elsner, M., Golfier, S., Decker, F., Ishihara, K., & Brugués, J. (2020). Spindle Scaling Is Governed by Cell Boundary Regulation of Microtubule Nucleation. Curr Biol, 30(24), 4973-4983.e10.Elsevier. doi: 10.1016/j.cub.2020.10.093.

Rieckhoff, E.M., Ishihara, K., & Brugués, J. (2019). How to tune spindle size relative to cell size?. Curr Opin Cell Biol, 60, 139-144.Elsevier. doi: 10.1016/j.ceb.2019.06.007.

Ishihara, K., & Tanaka, E.M. (2018). Spontaneous symmetry breaking and pattern formation of organoids. Current Opinion in Systems Biology, 11, 123-128.Elsevier. doi: 10.1016/j.coisb.2018.06.002.

Ishihara, K., Ranga, A., Lutolf, M.P., Tanaka, E.M., & Meinhardt, A. (2017). Reconstitution of a Patterned Neural Tube from Single Mouse Embryonic Stem Cells. In Organ Regeneration. 1597, (pp. 43-55).Springer Nature. doi: 10.1007/978-1-4939-6949-4_4.

Ishihara, K., Korolev, K.S., & Mitchison, T.J. (2016). Physical basis of large microtubule aster growth. Elife, 5, e19145.eLife. doi: 10.7554/eLife.19145.

Ishihara, K., Korolev, K.S., & Mitchison, T.J. (2016). Physical Basis of Large Microtubule Aster Growth. 055939.Cold Spring Harbor Laboratory. doi: 10.1101/055939.

Mitchison, T.J., Ishihara, K., Nguyen, P., & Wühr, M. (2015). Size Scaling of Microtubule Assemblies in Early Xenopus Embryos. Cold Spring Harb Perspect Biol, 7(10), a019182.Cold Spring Harbor Laboratory. doi: 10.1101/cshperspect.a019182.

Wühr, M., Güttler, T., Peshkin, L., McAlister, G.C., Sonnett, M., Ishihara, K., Groen, A.C., Presler, M., Erickson, B.K., Mitchison, T.J., Kirschner, M.W., & Gygi, S.P. (2015). The Nuclear Proteome of a Vertebrate. Curr Biol, 25(20), 2663-2671.Elsevier. doi: 10.1016/j.cub.2015.08.047.

Field, C.M., Nguyen, P.A., Ishihara, K., Groen, A.C., & Mitchison, T.J. (2014). Xenopus egg cytoplasm with intact actin. Methods Enzymol, 540, 399-415.Elsevier. doi: 10.1016/B978-0-12-397924-7.00022-4.

Groen, A.C., Ngyuen, P.A., Field, C.M., Ishihara, K., & Mitchison, T.J. (2014). Glycogen-supplemented mitotic cytosol for analyzing Xenopus egg microtubule organization. Methods Enzymol, 540, 417-433.Elsevier. doi: 10.1016/B978-0-12-397924-7.00023-6.

Ishihara, K., Nguyen, P.A., Groen, A.C., Field, C.M., & Mitchison, T.J. (2014). Microtubule nucleation remote from centrosomes may explain how asters span large cells. Proc Natl Acad Sci U S A, 111(50), 17715-17722.Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1418796111.

Ishihara, K., Nguyen, P.A., Wühr, M., Groen, A.C., Field, C.M., & Mitchison, T.J. (2014). Organization of early frog embryos by chemical waves emanating from centrosomes. Philos Trans R Soc Lond B Biol Sci, 369(1650), 20130454.The Royal Society. doi: 10.1098/rstb.2013.0454.

Nguyen, P.A., Groen, A.C., Loose, M., Ishihara, K., Wühr, M., Field, C.M., & Mitchison, T.J. (2014). Spatial organization of cytokinesis signaling reconstituted in a cell-free system. Science, 346(6206), 244-247.American Association for the Advancement of Science (AAAS). doi: 10.1126/science.1256773.

Kim, Y., Iagovitina, A., Ishihara, K., Fitzgerald, K.M., Deplancke, B., Papatsenko, D., & Shvartsman, S.Y. (2013). Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo. Chaos, 23(2), 025105.AIP Publishing. doi: 10.1063/1.4808157.

Petry, S., Groen, A.C., Ishihara, K., Mitchison, T.J., & Vale, R.D. (2013). Branching microtubule nucleation in Xenopus egg extracts mediated by augmin and TPX2. Cell, 152(4), 768-777.Elsevier. doi: 10.1016/j.cell.2012.12.044.

Mitchison, T., Wühr, M., Nguyen, P., Ishihara, K., Groen, A., & Field, C.M. (2012). Growth, interaction, and positioning of microtubule asters in extremely large vertebrate embryo cells. Cytoskeleton (Hoboken), 69(10), 738-750.Wiley. doi: 10.1002/cm.21050.

Nguyen, P.A., Ishihara, K., Wühr, M., & Mitchison, T.J. (2012). Pronuclear migration: no attachment? No union, but a futile cycle!. Curr Biol, 22(10), R409-R411.Elsevier. doi: 10.1016/j.cub.2012.03.062.