Supplementary Figures and Tables from TFE3 Xp11.2 Translocation Renal Cell Carcinoma Mouse Model Reveals Novel Therapeutic Targets and Identifies GPNMB as a Diagnostic Marker for Human Disease

Supplemental Figure S1. Representative images of TFE3 immunohistochemistry of renal papillae and renal pelvis (a, b), ureters (c, d), and bladders (e, f) from a 10-month-old PRCC-TFE3; KSP-Cre- (a, c, e) mouse and a PRCC-TFE3; KSP-Cre+ (b, d, f) mouse. S2, S3, S4, S5. Supplemental Table S1. (a) List of top 50 significantly upregulated (q-value < 0.05, fold change > 2) genes in kidneys from 4 month old PRCC-TFE3; KSP-Cre+ mice. (b) List of significantly downregulated (q-value < 0.05, fold change < 1/2) genes in kidneys from 4 month old PRCC-TFE3; KSP-Cre+ mice. Supplemental Table S2 (a) List of top 50 significantly upregulated (q-value < 0.05, fold change > 2) genes in kidneys from 7 month old PRCC-TFE3; KSP-Cre+ mice. (b) List of top 50 significantly downregulated (q-value < 0.05, fold change < 1/2) genes in kidneys from 7 month old PRCC-TFE3; KSP-Cre+ mice. Supplemental Fig. S2 Gene Set Enrichment Analysis (GSEA) of microarray data from 4 month old PRCC-TFE3; KSP-Cre+ mouse kidneys (n=4) vs 4 month old PRCC-TFE3; KSP-Cre- mouse kidneys (n=4) (a, b, c, g, h, i) and 7 month old PRCC-TFE3;KSP-Cre+ mouse kidneys (n=4) vs 7 month old PRCC-TFE3; KSP-Cre- mouse kidneys (n=3) (d, e, f, j, k, l). Supplemental Table S3 List of commonly upregulated genes in PRCC-TFE3; KSP-Cre+ mouse kidneys (4 month old and 7 month old) and TFEB overexpressed mouse kidneys (P0 and P14, Calcagni et al. Supplemental Fig. S3 Gene Set Enrichment Analysis (GSEA) of microarray data from 4 month old PRCC-TFE3; KSP-Cre+ mouse kidneys (n=4) vs 4 month old PRCC-TFE3; KSP-Cre- mouse kidneys (n=4) (a) and 7 month old PRCC-TFE3;KSP-Cre+ mouse kidneys (n=4) vs 7 month old PRCC-TFE3; KSP-Cre- mouse kidneys (n=3) (b). Marginal (a) and significant (b) enrichment of genes associated with KRAS activation in kidneys from PRCC-TFE3; KSP-Cre+ mice. Supplemental Fig. S4. The immunohistochemical staining of Tfe3 (a), Gpnmb (b), and Ret (c) on PRCC-TFE3;KSP-Cre- kidneys and PRCC-TFE3;KSP-Cre+ kidneys was semiquantified and scored as (-), (1+) and (2+). Supplemental Fig. S5. Volcano plot of gene expression changes for 4 month-old (a) and 7 month-old (b) PRCC-TFE3; KSP-Cre- kidneys and PRCC-TFE3; KSP-Cre+ kidneys.