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Sci. Signal., 15 May 2012
Vol. 5, Issue 224, p. rs4
[DOI: 10.1126/scisignal.2002612]


MicroSCALE Screening Reveals Genetic Modifiers of Therapeutic Response in Melanoma

Kris C. Wood1,2*, David J. Konieczkowski2,3, Cory M. Johannessen2,3, Jesse S. Boehm2, Pablo Tamayo2, Olga B. Botvinnik2, Jill P. Mesirov2, William C. Hahn2,3, David E. Root2, Levi A. Garraway2,3, and David M. Sabatini1,2,4*

1 Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.
2 Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA.
3 Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA.
4 Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.

Abstract: Cell microarrays are a promising tool for performing large-scale functional genomic screening in mammalian cells at reasonable cost, but owing to technical limitations they have been restricted for use with a narrow range of cell lines and short-term assays. Here, we describe MicroSCALE (Microarrays of Spatially Confined Adhesive Lentiviral Features), a cell microarray–based platform that enables application of this technology to a wide range of cell types and longer-term assays. We used MicroSCALE to uncover kinases that when overexpressed partially desensitized B-RAFV600E–mutant melanoma cells to inhibitors of the mitogen-activated protein kinase kinase kinase (MAPKKK) RAF, the MAPKKs MEK1 and 2 (MEK1/2, mitogen-activated protein kinase kinase 1 and 2), mTOR (mammalian target of rapamycin), or PI3K (phosphatidylinositol 3-kinase). These screens indicated that cells treated with inhibitors acting through common mechanisms were affected by a similar profile of overexpressed proteins. In contrast, screens involving inhibitors acting through distinct mechanisms yielded unique profiles, a finding that has potential relevance for small-molecule target identification and combination drugging studies. Further, by integrating large-scale functional screening results with cancer cell line gene expression and pharmacological sensitivity data, we validated the nuclear factor {kappa}B pathway as a potential mediator of resistance to MAPK pathway inhibitors. The MicroSCALE platform described here may enable new classes of large-scale, resource-efficient screens that were not previously feasible, including those involving combinations of cell lines, perturbations, and assay outputs or those involving limited numbers of cells and limited or expensive reagents.

* To whom correspondence should be addressed. E-mail: kcwood{at} (K.C.W.); sabatini{at} (D.M.S.)

Citation: K. C. Wood, D. J. Konieczkowski, C. M. Johannessen, J. S. Boehm, P. Tamayo, O. B. Botvinnik, J. P. Mesirov, W. C. Hahn, D. E. Root, L. A. Garraway, D. M. Sabatini, MicroSCALE Screening Reveals Genetic Modifiers of Therapeutic Response in Melanoma. Sci. Signal. 5, rs4 (2012).

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Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882