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

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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