Supplemental Figures

Supplemental Figure 1. Top two canonical pathways clustering the potential

predictive biomarkers. The Ingenuity IPA tool was used to analyze the 194 differentially

expressed probe sets. A) Cytotoxic T lymphocyte

mediated apoptosis of target cells B) Antigen presentation

pathway. Shaded red boxes are the potential marker genes listed

in Supplemental Table 1.

Suppl. Fig 1B. Antigen presentation pathway

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Supplemental Figure 2.

Supplemental Figure 2. Comparison of gene expression profiles of metastatic melanoma tumors from skin versus lymph nodes. Probesets with at least 1.5 fold differential expression in pre-treatment tumors from patients in the CA versus those in the No-CA group were selected. A) Plot of the mean expression values of the selected probesets in tumors originating from skin (x axis) or lymph nodes (y axis) from patients in the No-CA group. B) Plot of the mean expression values of the selected probesets in tumors originating from skin (x axis) or lymph nodes (y axis) from patients in the CA group.

Supplemental Figure 3. Top two canonical pathways clustering the potential early predictive markers. The Ingenuity IPA tool was used to analyze the 470 probesets for genes with increased expression after treatment with ipilimumab.

A) iCOS-iCOSL signaling in T helper cells

B) CTLA4 signaling in cytotoxic T lymphocytes. Shaded red boxes are the potential early predictive marker genes that showed increased expression after ipilimumab treatment, as listed in Supplemental Table 3, Panel A.

Suppl. Fig 3B. T helper cell differentiation

Supplemental Figure 4. Melanocyte development and pigmentation signaling pathway generated by the Ingenuity IPA tool. Shaded green boxes are melanoma-associated genes that showed decreased expression after ipilimumab treatment, as listed in Supplemental Table 3, Panel B.