MicroSCALE Screening Reveals Genetic Modifiers of Therapeutic Response in Melanoma

Kris C. Wood,* David J. Konieczkowski, Cory M. Johannessen, Jesse S. Boehm, Pablo Tamayo, Olga B. Botvinnik, Jill P. Mesirov, William C. Hahn, David E. Root, Levi A. Garraway, David M. Sabatini*

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

This PDF file includes:

• Fig. S1. Strategy for restricting cell adhesion to printed features.
• Fig. S2. Requirement for purification and concentration of lentiviruses before microarray printing.
• Fig. S3. High-throughput lentivirus concentration using polyelectrolyte complexation.
• Fig. S4. Puromycin selection of infected cells on MicroSCALE features.
• Fig. S5. Quantification of cell number on MicroSCALE features using a DNA microarray scanner.
• Fig. S6. Printing and infections with ORF-expressing lentiviruses containing inserts of varying sizes.
• Fig. S7. Modifier screening pipeline.
• Fig. S8. Percentage of the total validated hits identified in a screen with six replicate arrays as a function of the number of replicate (drug-treated) microarrays used.
• Fig. S9. Sensitivity of A375 and MDA-MB-453 cells to targeted inhibitors.
• Fig. S10. Confirmation of hits identified in primary screens.
• Fig. S11. GI₅₀ concentrations for B-RAF^V600–mutant melanoma cell lines treated with MAPK inhibitors.
• Fig. S12. Effect of IKBKB overexpression on sensitivity to inhibitors of the MAPK pathway and the mTOR and PI3K pathway.
• Fig. S13. Comparison of resistance to PLX4720 conferred by overexpression of IKBKB, exogenous TNFα, or overexpression of C-RAF.
• Fig. S14. Phosphorylation of RelA and ERK in response to NF-κB pathway manipulations and PLX4720 treatment in SkMel28 cells.
• Fig. S15. Effects of TNFα on PLX4720-induced apoptosis and cell cycle arrest in Colo679 cells.
• Table S1. Examples of cell lines compatible with MicroSCALE screening.
• Table S2. Examples of cell lines incompatible with MicroSCALE screening.
• Table S3. Constructs present on Kinome ORF MicroSCALEs.
• Table S5. Materials requirements and throughput estimates for kinome-scale drug modifier screens in MicroSCALE and 384-well formats.

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Other Supplementary Material for this manuscript includes the following:

• Table S4 (Microsoft Excel format). Results of a PLX4720 modifier screen in A375 cells.

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© 2012 American Association for the Advancement of Science