Soichiro Yamada

image of Soichiro Yamada

Associate Professor

Departments

Biomedical Engineering (Grad)

Offices and Labs

GBSF 2317
5307547251
GBSF 2216
5307527828

Profile Introduction

Our laboratory is interested in how mammalian cells touch, feel and work together to form multi-cellular tissues and organs. Cell-to-cell interactions are mediated by cell adhesion molecules and the cytoskeleton, and carefully regulated. Since abnormal cell adhesion is common in diseases like cancer, understanding of cell adhesion should lead to novel treatments. Using biophysical and cell biological approaches, we are trying to tease out the mechanisms involved in the regulation of cell adhesion. One approach is to analyze cell interactions in a physiologically relevant three-dimensional matrix using a live-cell confocal microscope system (see our movies on Youtube). In addition, we are analyzing the regulation of cell adhesion strength using microfabricated force sensor and atomic force microscopy. Currently, our focus is on how cancer cells interact with each other to regulate their migration through surrounding extracellular matrix and neighboring cells. Our unique experimental approaches provide new perspectives on how proteins assemble to generate physical and dynamic cell adhesions essential for morphogenesis and metastasis.

Degrees

2006 Postdoc Cell Biology Stanford University
2001 PhD Chemical Engineering The Johns Hopkins University
1996 BS Chemical Engineering Rutgers University

Research Interests

Mechano-transduction of cells

We are interested in how cells generate and respond to mechanical forces. Using multi-faceted approaches that include biochemistry, live-cell imaging, micro-fabrication, 3D matrix, traction force analysis, and atomic force microscopy, we are trying to tease out mechanisms by which cells sense and regulate forces. Examples of our approaches are shown in our youtube page. 

Membrane fusion at adhesive contacts

We recently found that, when membrane protrusions of epithelial or endothelial cells fold and touch their own plasma membrane, these self-contacts are eliminated by membrane fusion. Since two adhering cells rarely fuse, our observation implies that cells have an ability to discriminate self from neighboring membranes despite the identical surface chemistry of both self and cell-cell junctions. We know that this self-recognition process, at least initially, depends on cadherins, and is possibly regulated by mechanical factors. 

 

Awards

Hellman Family New Faculty Award, 2008
Beckman Young Investigator Award, 2009
NIH EUREKA R01, 2010

Department and Center Affiliations

UC Davis Cancer Center

ProfessionalSocieties

American Society for Cell Biology
Biomedical Engineering Society

CBS Grad Group Affiliations

Biochemistry, Molecular, Cellular and Developmental Biology

Specialties / Focus

Biochemistry, Molecular, Cellular and Developmental Biology
  • Cell Biology
  • Developmental Biology
  • Cancer Biology
  • Cell Division and the Cytoskeleton
  • Cellular Responses to Toxins and Stress
  • Organelle and Membrane Biology
  • Biochemistry
  • Differentiation, Morphogenesis and Wound Healing

Graduate Groups not Housed in CBS

Biomedical Engineering

Courses

BIM 102 Cellular Dynamics (Fall)
BIM 202 Cell and Molecular Biology for Engineers (Fall)
BIM 222 Cytoskeletal Mechanics (Fall)

Publications

2/15/2017 1:18:02 PM
  • Renner DJ, Ewald ML, Kim T, Yamada S. (2017) Biochemical analysis of force-sensitive responses using a large-scale cell stretch device. Cell adhesion & migration :1-10.
  • Lee E, Ewald ML, Sedarous M, Kim T, Weyers BW, Truong RH, Yamada S. (2016) Deletion of the cytoplasmic domain of N-cadherin reduces, but does not eliminate, traction force-transmission. Biochemical and biophysical research communications 478(4):1640-6.
  • Lee JK, Hu JC, Yamada S, Athanasiou KA. (2016) Initiation of Chondrocyte Self-Assembly Requires an Intact Cytoskeletal Network. Tissue engineering. Part A 22(3-4):318-25.
  • Sumida GM, Yamada S. (2015) Rho GTPases and the downstream effectors actin-related protein 2/3 (Arp2/3) complex and myosin II induce membrane fusion at self-contacts. The Journal of biological chemistry 290(6):3238-47.
  • Ueda S, Blee AM, Macway KG, Renner DJ, Yamada S. (2015) Force dependent biotinylation of myosin IIA by α-catenin tagged with a promiscuous biotin ligase. PloS one 10(3):e0122886.
  • Sumida, G. M. and Yamada, S. Self-contact elimination by membrane fusion. Proc Natl Acad Sci U S A. 110:18958, 2013

  • Jorrisch, M., Shih, W., and Yamada, S. Myosin IIA deficient cells migrate efficiently despite reduced traction forces at cell periphery. Biol Open 2:368, 2013

  • Cui, Y. and Yamada, S. N-cadherin dependent collective cell invasion of prostate cancer cells is regulated by the N-terminus of alpha-catenin. PLoS One 8:e55069, 2013

  • Shih, W., Yamada, S. N-cadherin as a key regulator of collective cell migration in a 3D environment. Cell Adh Migr. 6:513, 2012

  • Steele, A., Sumida, G., and Yamada, S. Tandem LIM sequences do not enhance force sensitive accumulation. Biochem Biophys Res Commun. 422:653, 2012

  • Shih, W., Yamada, S. N-cadherin-mediated cell-cell adhesion promotes cell migration in a three-dimensional matrix. J Cell Sci, 125:3661, 2012

  • Li, L., Hartley, R., Reissc, B., Sun, Y., Pu, J., Hoang, T., Yamada, S., Jiangb, J., Zhao, M. E-cadherin plays an essential role in collective directional migration of large epithelial sheets. Cell Mol Life Sci. 69:2779, 2012

  • Shih, W., Yamada, S. Live-cell imaging of migrating cells expressing fluorescently-tagged proteins in a three-dimensional matrix. J. Vis. Exp. (58), e3589, DOI: 10.3791/3589, 2011

  • Sumida, G. M., Tomita, T., Shih, W., Yamada, S. Myosin II activity dependent and independent vinculin recruitment to the sites of E-cadherin mediated cell-cell adhesion. BMC Cell Biol. 12:48, 2011

  • Uemura, A., Nguyen, T-N., Steele A. N., Yamada, S. The LIM domain of zyxin is sufficient for force-induced accumulation during cell migration. Biophys J. 101:1069, 2011

  • Ounkomol C, Yamada S, Heinrich V. (2010) Single-cell adhesion tests against functionalized microspheres arrayed on AFM cantilevers confirm heterophilic E- and N-cadherin binding. Biophys J. 99(12):L100-2.
  • Nguyen TN, Uemura A, Shih W, Yamada S. (2010) Zyxin-mediated actin assembly is required for efficient wound closure. J Biol Chem. 285(46):35439-45.
  • Shih W, Yamada S. (2010) Myosin IIA dependent retrograde flow drives 3D cell migration. Biophys J. 98(8):L29-31.
  • Pokutta S, Drees F, Yamada S, Nelson WJ, Weis WI. (2008) Biochemical and structural analysis of alpha-catenin in cell-cell contacts. Biochem Soc Trans. 36(Pt 2):141-7
  • Yamada, S. and Nelson, W. J. Localized RhoA activation regulates actomyosin contraction and compaction of epithelial cell-cell adhesion (2007) J Cell Biol. 178:517-27
  • Yamada, S. and Nelson, W. J. Synapses: sites of cell recognition, adhesion, and functional specification. (2007) Annu Rev Biochem. 76:267-94
  • Drees, F. Pokutta, S. Yamada, S. Nelson, W. J. and Weis, W. I. (2005) Alpha-catenin is a molecular switch that binds E-cadherin/beta-catenin and regulates actin filament assembly. Cell 123:903
  • Yamada, S. Pokutta, S. Drees, F. Weis, W. I. and Nelson, W. J. (2005) Deconstructing the cadherin-catenin-actin complex. Cell 123:889