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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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A Melanoma Cell State Distinction Influences Sensitivity to MAPK Pathway Inhibitors.
D. J. Konieczkowski, C. M. Johannessen, O. Abudayyeh, J. W. Kim, Z. A. Cooper, A. Piris, D. T. Frederick, M. Barzily-Rokni, R. Straussman, R. Haq, et al. (2014)
Cancer Discovery 4, 816-827
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M. Tinti, K. Dissanayake, S. Synowsky, L. Albergante, and C. MacKintosh (2014)
Open Bio 4, 140029
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