Fig. 3.

GSEA analysis results. Enrichment plots of normal melanocytes versus UM cells for the WP_AMPACTIVATED_PROTEIN_KINASE_AMPK_SIGNALING (NES: 1.05) (a) and REACTOME_ENERGY_DEPENDENT_REGULATION_OF_MTOR_BY_LKB1_AMPK (NES: 1.06) (c) gene sets are shown. Genes involved in AMPK signaling and energy-dependent regulation of mTOR by LKB1-AMPK were downregulated in UM cells compared with normal melanocyte cells. Gene expression data were acquired from NCBI Gene Expression Omnibus (GSE176345) and GSEA was performed as described previously [53]. Genes that contribute to the enrichment results within each gene set are shown in blue-pink O’grams of altered AMPK signaling and energy-dependent regulation of mTOR by LKB1-AMPK in (b) and (d), respectively. These GSEA results are consistent with our KEGG findings concerning AMPK signaling pathway gene expressions of UM and normal melanocyte cells. b, d Normal melanocyte cell population was enriched for expression of PRKAA1, which is a gene that encodes AMPK (i.e., third and first rows in blue-pink O’grams, respectively). d On the other hand, expressions of late endosomal/lysosomal adaptor and MAPK and mTOR activator (LAMTOR) 1, 2, 4, and 3 genes were upregulated in UM cells. LAMTOR is a scaffold protein complex that senses nutrients such as amino acids and lipids while integrating growth factor signaling [72]. LAMTOR1 functions as an anchor for the remaining LAMTOR subunits [73–77]. LAMTOR was also reported to activate mTORC1 signaling [78]. e The graph shows that patients with low AMPK level had significantly higher tumor mutational burden (TMB). f The “24-AMPK-gene set” scores of the patient samples. g The “24-AMPK-gene set” scores of the UM patients with or without metastasis. GSEA, Gene Set Enrichment Analysis; NES, normalized enrichment score; PRKAA1, protein kinase AMP-activated alpha 1 catalytic subunit; UM, uveal melanoma; LKB1, liver kinase B1; mTORC1, mTOR complex 1.