Kathy Y. Wei
Department of Bioengineering,
- kywei [at] stanford [dot] edu
- Curriculum Vitae:
- NDSEG Fellowship, NSF GRFP
Manipulating and re-programming cells from the inside out.
A yeast-based rapid prototype platform for gene-control elements in mammalian cells
Wei KY, Chen YY, Smolke CD. 17 Jan 2013. Biotech. Bioeng.
Programming genetic circuits in mammalian cells requires flexible, tunable,
and user-tailored gene-control systems. However, most existing control systems
are either mechanistically specific for microbial organisms or must be
laboriously re-engineered to function in mammalian cells. Here, we demonstrate a
ribozyme-based device platform that can be directly transported from yeast to
mammalian cells in a ‘plug-and-play’ manner. Ribozyme switches previously
prototyped in yeast are shown to regulate gene expression in a predictable,
ligand-responsive manner in human HEK 293, HeLa, and U2OS cell lines without any
change to device sequence nor further optimization. We observe strong
correlations of device performance between yeast and all mammalian cell lines
tested (R2 = 0.63-0.97). Our unique device architecture can therefore act as a
rapid prototyping platform (RPP) based on a yeast chassis, providing a
well-developed and genetically tractable system that supports rapid and
high-throughput screens for generating gene-controllers with a broad range of
functions in mammalian cells.
Synthetic biology: advancing the design of diverse genetic systems
Wang Y-H*, Wei KY*, Smolke CD. 2013. AR Chem. Biomol. Eng.
A main objective of synthetic biology is to make the process of
designing genetically-encoded biological systems more systematic, predictable, robust,
scalable, and efficient. The examples of genetic systems in the field vary widely in terms
of operating hosts, compositional approaches, and network complexity, ranging from a simple
genetic switch to search-and-destroy systems. While significant advances in synthesis
capabilities support the potential for the implementation of pathway- and genome-scale
programs, several design challenges currently restrict the scale of systems that can be
reasonably designed and implemented. Synthetic biology offers much promise in developing
systems to address challenges faced in manufacturing, the environment and sustainability,
and health and medicine, but the realization of this potential is currently limited by the
diversity of available parts and effective design frameworks. As researchers make progress
in bridging this design gap, advances in the field hint at ever more diverse applications
for biological systems.
*These authors contributed equally to this work
A Small Molecule Inducible MicroRNA Based Cell Cycle Controller
Dept. of Bioengineering, Stanford University, Jun 2010-present
Mentor: Dr. Christina Smolke
In order to enable the engineering of cellular function in living organisms,
it is necessary to develop tools that are both genetically encoded and capable of regulating
endogenous protein levels in response to user-specified molecular signals. The goal of this project
is to engineer a set of microRNA regulatory networks with integrated modular ligand sensors for the
reversible arrest of living mammalian cell populations in G0/1, S, G2, and M. Unlike currently
available small molecule inhibitors of the cell cycle that broadly disrupt cell function,
a switchable microRNA platform allows inducible cell cycle arrest through regulation of specific
endogenous gene targets with potentially any small molecule effector by modular replacement of
the microRNA targeting sequence or aptamer-based sensing region. We have identified promising RNAi
targets for G0/1 arrest in a human cell line, measuring over 76% knockdown of mRNA levels by qRT-PCR
and accumulation of over 92% of cells in G0/1 by flow cytometry. We can quantitatively measured
mature microRNA and target mRNA levels by qRT-PCR, as well as target protein levels and cell cycle
distribution by flow cytometry, providing a detailed picture of the changes in gene expression
that lead to a measurable phenotypic change. More broadly, these ligand-responsive microRNAs
represent a general class of synthetic biology tools that can be adapted for sophisticated
control of complex cellular processes in higher organisms.
Funding: NDSEG, NSF GRFP
Stem Cell and Tissue Engineering
Dept. of Bioengineering, Stanford University, Spr 2010
Mentor: Dr. Fang Yang
Utilizing natural properties of stem cells and advantages
of biomaterials to develop a modular therapeutic platform for the treatment of
malignant brain tumors. Funding: NDSEG
Engineering microRNAs for the Manipulation of Mammalian Cells
Dept. of Bioengineering, Stanford University, Win 2010
Mentor: Dr. Christina Smolke, Yvonne Chen
MicroRNAs are non-coding RNAs that repress translation of their target protein.
Projects include: 1) engineering miRNAs capable of responding to the
presence specific nuclear proteins and 2) elucidating the characteristics
of inter-miRNA spacers that allows efficient processing of multiple miRNAs.
Regulated Flux Balance Analysis of Host-Pathogen Interactions
Dept. of Bioengineering, Stanford University, Aut 2009
Mentor: Dr. Markus Covert
Host-pathogen systems emerge from the intricate interactions between
two organisms and result in more extensive networks than suggested by
studying the host or pathogen separately. Bacteriophage lambda infection
of E. coli is an is 1) a classic host-pathogen model and 2) relevant to
other systems. The process of incorporating a lambda phage component into
an regulated flux balance analysis (rFBA) model of E. coli to accurately reflect
phage impact on host E. coli metabolism will provide insight into phage
impact on E. coli metabolism, regulation between the
host and pathogen, and the nature of the ‘objective function’ for FBA models
involving multiple entities.
University of Washington
Rational Design of an Oligoarginine Based
Gene Delivery Vehicle Targeted to Hepatocarcinoma
Dept. of Bioengineering, University of Washington, 2008-2009
Mentors: Dr. Suzie Pun, Dr. Rob Burke
Liver cancer is one of the three deadliest cancers in the world and current treatments involve significant damage to healthy tissue.
Gene therapy, which aims to replace defective genes inside cells in order to
treat diseases, holds promise for treating liver cancer because of the various pathways it can exploit.
Non-viral materials have the potential to overcome safety and scalability limitations of viral vectors.
This project was to design, construct, and test novel peptide-based materials
specifically targeted to hepatocarcinoma for use as systemically administered gene therapy vectors.
The peptide material consists of a nonaarginine DNA condensing component linked to a
hepatocarcinoma-specific binding peptide (seq: FQHPSFI) to form an anticancer “nanopod” protects and guides the DNA therapeutic.
Funding: Barry M. Goldwater Foundation
MOLECULAR SWISS ARMY KNIFE: Designing Multifunctional
Non-viral Vehicles for Gene Delivery to Neurons
Dept. of Bioengineering, University of Washington, 2007-2008
Mentors: Dr. Suzie Pun, Dr. Jamie Bergen
Gene therapy promises to treat neurological disorders,
such as Alzheimer's and Huntington’s disease, that currently have limited or
no available treatment.
The particular non-viral vehicles used in this experiment are polyplexes,
or polymer/DNA complexes.
The major challenge faced by these materials is the inefficiency of polyplexes at
overcoming barriers to gene delivery, especially in non-dividing cell types such as neurons.
Intracellular barriers to nuclear delivery of foreign DNA include targeting,
uptake, endosomal escape, retrograde transport, and nuclear localization.
This project focuses on attaching peptide ligands that target barriers to the surface
of polyplexes to increase DNA delivery efficiency.
Specifically, a peptide ligand based on the human papillomavirus minor capsid protein L2,
which is hypothesized to have endosomal escape as well as retrograde transport capabilities,
was conjugated to polyethylenimine.
Funding: Amgen Foundation, Mary Gates Endowment
HIFU Reflection Lesion Characterization
Vaezy Laboratory, Dept. of Bioengineering, University of Washington, 2005
Mentors: Dr. Shahram Vaezy, Dr. Jinfei Yu
High Intensity Focused Ultrasound (HIFU) is a medical therapy modality for non-invasive,
capable of extracorporeal treatment of internal bleeding and tumors.
The energy delivered by a HIFU transducer can be amplified by reflecting the ultrasound beam
from post-focal regions back towards the focus.
We studied the volume of the lesions produced in turkey breast, by HIFU,
with and without an ultrasound reflector in order to more fully understand
how to utilize the reflections.
Funding: NASA SURP
Stanford University ● Sep 2009-present
Department of Bioengineering, PhD Program
Stanford University ● Sep 2009-Jun 2011
Masters in Bioegineering
University of Washington ● Sep 2005-Jun 2009
BS in Bioengineering with Honors, Summa Cum Laude
BS in Computer Science and Engineering, Summa Cum Laude
Awards and Fellowships
2009||NSF GRFP Fellow,
Barry M. Goldwater Scholar, 2008
UW College of Engineering Dean's Medal for Academic Excellence, 2009
UW Outstanding Senior in Computer Science and Engineering, 2008-2009
Last Updated: Feb 2013
© 2010-2013 Kathy Y. Wei