Leveraging the TCGA papillary RCC (KIRP) cohort35,53, mRNA expression levels of PAX2 and PAX8 were significantly decreased in TFE3 fusion-RCC cases, compared to ccRCC (Fig. 6I), while expression levels of related family members PAX5 and PAX6 remained unaltered (Supplementary Fig. 8G), though sample numbers were too small to examine the effects of specific fusions on PAX8 and PAX2 expression. Here, TFE3 is linked to nonpapillary renal cell carcinoma.