Microarrays of small molecules embedded in biodegradable polymers for use in mammalian cell-based screens

doi:10.1073/pnas.0404425101

Microarrays of small molecules embedded in biodegradable polymers for use in mammalian cell-based screens

^*Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142; and ^‡Departments of Biological Sciences and Chemistry, Columbia University, Fairchild Center MC2406, 1212 Amsterdam Avenue, New York, NY 10027

Edited by Tony Hunter, The Salk Institute for Biological Studies, La Jolla, CA, and approved September 27, 2004 (received for review June 21, 2004)

Abstract

We developed a microarray-based system for screening small molecules in mammalian cells. This system is compatible with image-based screens and requires fewer than 100 cells per compound. Each compound is impregnated in a 200-μm-diameter disc composed of biodegradable poly-(d),(l)-lactide/glycolide copolymer. Cells are seeded on top of these discs, and compounds slowly diffuse out, affecting proximal cells. In contrast with microtiter-based screening, this system does not involve the use of wells or walls between each compound-treated group of cells. We demonstrate detection of the effects of a single compound in a large microarray, that diverse compounds can be released in this format, and that extended release over several days is feasible. We performed a small synthetic lethal screen and identified a compound (macbecin II) that has reduced activity in cells with RNA interference-mediated decrease in the expression of tuberous sclerosis 2. Thus, we have developed a microarray-based screening system for testing the effects of small molecules on mammalian cells by using an imaging-based readout. This method will be useful to those performing small-molecule screens to discover new chemical tools and potential therapeutic agents.

Footnotes

↵ † To whom correspondence may be addressed. E-mail: sabatini{at}wi.mit.edu or stockwell{at}biology.columbia.edu.
Author contributions: D.M.S. and B.R.S. designed research; S.N.B., D.M.S., and B.R.S. performed research; S.N.B., D.M.S., and B.R.S. analyzed data; and S.N.B., D.M.S., and B.R.S. wrote the paper.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: PLGA, poly-(d),(l)-lactide/glycolide copolymer; PAO, phenylarsine oxide; PTX, podophyllotoxin; siRNA, small interfering RNA; ROI, region of interest; CPA, cells per area; RT, room temperature; TSC2, tuberous sclerosis complex gene 2; mTOR, mammalian target of rapamycin.