Keough-Hesburgh Chair in Electrical Engineering and Biological Sciences at the University of Notre Dame
University of Notre Dame
"Biomedical nanotechnology for cancer diagnosis and therapy"
We are using “live cell lithography” to create in vitro three-dimensional microenvironments conducive to engrafting tumor cells, i.e. a metastatic niche, that reproduces the structure and mRNA expression observed in micro-metastases extracted from breast cancer patients, and then determine the effect of the microenvironment on the metastatic potential. By controlling the architecture of the tissue, the cell-type and position, as well as the flow and gradients of soluble signals, growth factors (GF) and nutrients we will discover the factors triggering metastasis with single cell resolution.
Another project involves the detection of proteins secreted from cells which can mediate intercellular communication and so affect gene expression. These proteins comprise a complex and sparse set of molecules referred to as the ‘secretome’. We are testing the feasibility of using a nanopore for analysis and manipulation of the secretome. Our results will extend the frontier of secretomics towards single molecule analysis with single cell resolution, offering an unprecedented probe of tissue heterogeneity. We hypothesize that the exquisite control over the electrostatic potential available in a silicon device—specifically, a nanopore in a dielectric membrane—can be exploited to trap and identify proteins, and even manipulate the secretome through cell transfection. We expect to use the potential in a nanopore to directly manipulate protein electrostatics, forcing it to denature. The corresponding forces will then be used to identify the protein. Furthermore, we expect that control over the electrostatic potential in a pore could be used to manipulate the secretome of a cell positioned close enough to the pore through transfection of nucleic acids via electroporation, so that the same device could be used to analyze and manipulate the secretome at the same time.
Nelson E, Li H, Timp G, "Direct, Concurrent Measurements of the Forces and Currents Affecting DNA in a Nanopore with Comparable Topography" ACS Nano, 2014, 8 (6), pp 5484–5493, doi:10.1021/nn405331t.
Kurz V, Tanaka T, Timp G, "Single Cell Transfection with Single Molecule Resolution Using a Synthetic Nanopore" Nanoletters, 2014. 14 (2), pp 604–611, doi: 10.1021/nl403789z.
Kurz V, Nelson EM, Shim J, Timp G, "Direct Visualization of Single-Molecule Translocations through Synthetic Nanopores Comparable in Size to a Molecule" ACS Nano, 2013, 7 (5), pp 4057–4069, doi: 10.1021/nn400182s.
E.M. Nelson, V. Kurz, J. Shim, W. Timp and G. Timp, "Using a nanopore for single molecule detection and single cell transfection" Analyst RSC, 2012, Issue 137, pp 3020–3027, doi: 10.1039/C2AN35571J.
Kurz V, Nelson EM, Perry N, Timp W, Timp G, "Epigenetic Memory Emerging from Integrated Transcription Bursts", Biophys. J. 2013, 105(6) pp 1526-32, doi: 10.1016/j.bpj.2013.08.010.
Dong Z, Kennedy E, Hokmabadi M, and Timp G, "Discriminating Residue Substitutions in a Single Protein Molecule Using a Sub-nanopore" ACS Nano, published online 24 May 2017. doi: 10.1021/acsnano.6b08452. Link to publication.
Kennedy E, Dong Z, Tennant C, and Timp G, "Reading the primary structure of a protein with 0.07 nm3 resolution using a subnanometre-diameter pore" Nature Nanotechnology, published online 25 July 2016. doi: 10.1038/NNANO.2016.120. Link to publication.
Eisenstein M, "Teaching nanopores to speak protein" Nature Methods 13, 715 (2016) doi: 10.1038/nmeth.3988. Link to publication.
Kolmogorov M, Kennedy E, Dong Z, Timp G, Pevzner P, "Single-Molecule Protein Identification by Sub-Nanopore Sensors" PLOS Computational Biology doi: https://doi.org/10.1371/hournal.pcbi.1005356. Link to publication.