User:Elizabeth Y. Choe/Notebook/SynBio in Cancer Research

'''20.109 Research Project Jingxun Chen and Elizabeth Choe Blue group, WF'''

The "Big Picture" Question

 * Our research question: How can the principles of synthetic biology be applied to create effective therapeutics and/or drug delivery systems for cancer treatment?
 * Our starting point is this a review article by Shankar and Pillai. (Mol Biosyst. 2011 Mar 24. [Epub ahead of print]. Translating cancer research by synthetic biology. Shankar S, Pillai MR.)
 * The field of synthetic biology aims to manipulate biological parts into higher-ordered, specified systems. In this review article, the authors explain how this methodology is being used in cancer research. Some of the applications they describe are: using directed evolution to develop enzymes that can be used in detection systems, using modules to create drug delivery systems, and using nucleic acids as drug therapies.

Detailed Questions

 * What are some specific aspects of this field that we could explore?
 * Drug-sensing hydrogels (to fit in with Module 3)
 * Elastin-like polypeptides
 * RNA aptamers that bind to the tumor or deliver therapeutic siRNA (to fit in with Module 1)
 * Programmable E. coli or other bacteria that invade tumors


 * What are some of the problems with the current research? (i.e., what needs to be fixed?)
 * Explore this topic more.

Zooming in on the specific problem

 * Source: A. E. Friedland, T. K. Lu, X. Wang and D. Shi, et al., Synthetic gene networks that count, Science, 2009, 324, 1199–1202
 * Summary: Synthetic genetic counters in E. coli that can count up to three induction events have been made by Friedland et al. in 2009.
 * This counter is called riboregulated transcriptional cascade (RTC) counter
 * One potential application of genetic counters is to couple the induction events to cell cycle and induce cell death after user-defined number of cell cycles. Thus, you could theoreticaly "tell" a therapeutic agent to "die" after a specified time.
 * Our project: implement Friedland's RTC counter in yeast to induce apoptosis after three replicative cycles

To-Do List

 * Select a G1 cdk as induction signal for the RTC counter
 * Select a molecule involved in yeast's apoptotic pathway (Molecule A) as the output of the counter
 * Identify a strong promoter (Promoter X) that is acted upon by enzymes downstream of our G1 cdk
 * Swap the sensing promoter in Friedland's RTC counter with Promoter X
 * Replace the GFP reporter with the gene that synthesize Molecule A
 * Test whether the yeast cells undergo apoptosis after three cycles of replication

Some technical thoughts

 * We will also need to:
 * Find guidelines to choose G1 cdk, Promoter X, and Molecule A
 * Test the constructs piece by piece and as a whole (characterized by transfer functions)
 * Assemble the constructs in yeast
 * Ensure that adding the plasmids don't severely lower cell viability
 * Find a way to measure apoptosis in yeast (should have method publications)
 * Label the yeast cells with biotin that indicate the number of division