Supplementary Materials and Methods, Figures 1 - 9, Tables 1 - 7 from Molecular Profiling of Patient-Matched Brain and Extracranial Melanoma Metastases Implicates the PI3K Pathway as a Therapeutic Target

Abstract

<p>PDF file - 416KB, Supplementary methods, figures and tables. Fig. S1. Gene expression profiling of patient-matched brain and extracranial metastases. Fig. S2. PTEN gene expression in BM_03 (homozygous copy loss) and EM_03 (one copy loss). Gene expression was measured by microarray. Fig. S3. Quantitative RT-PCR measurement of SGK3, SGSM2, and ELOVL2 expression in five pairs of brain metastases (BM) and extracranial metastases (EM). Fig. S4. Log2 expression levels of RB_pS807_S811 in seven pairs of matched metastases. Fig. S5 Examples of PTEN-absent tumors. PTEN IHC of BM_03 and EM_03 were photographed at 00X magnification. Fig. S6 GSK3/_pS21/S9 IHC staining in 26 pairs of matched brain metastases (BM) and extracranial metastases (EM). Fig. S7. Results of RB_pS807_S811 IHC in 25 pairs of matched brain metastases (BM) and extracranial metastases (EM). Fig. S8. Kaplan-Meier survival analysis of nude mice with BRAF-mutant melanoma brain metastases treated with BKM120 and/or LGX818. Fig. S9. AKT_pS473 level in subcutaneously (sc) and intracranially (ic) implanted melanomas. Table S1. List of clinical samples analyzed. Table S2. Clinical features and genetic aberrations of matched samples analyzed by high-throughput techniques. Table S3. Hotspot mutations analyzed by Sequenom. Table S4. Antibodies used in RPPA analysis. Table S5. Genes with copy number differences (P <0.05) between matched brain metastases (N =10) and extracranial metastases (N =10). Table S6 CNVs in 13 melanoma-related genes in 10 pairs of matched metastases. Table S7. Genes differently expressed between six pairs of matched brain and extracranial metastases (P<0.01).</p>