To better understand the mechanisms underlying proteasome addiction in Ewing and other sarcomas, we systematically performed Kaplan Meier analyses of the impacts of expression level of each of the 377 human E3 ubiquitin ligases on overall survival (OS) and recurrence free survival (RFS) of sarcoma patients. We identified 102 E3 ligases whose high-level expression is associated with shortened OS, suggesting that these E3 ligases mediate proteasome addiction. Thirteen of these shorten OS by >40 months. Nineteen of the 102 E3 ligases whose increased expression is associated with reduced OS also show correlation between increased expression and reduced RFS. Among these, nine reduce median RFS by 56-75 months. Somewhat unexpectedly, we found 73 E3 ligases whose overexpression significantly extended patient OS, with 18 of these extending OS by >40 months. Elevated expression of 21 of these 73 E3 ligases significantly extends RFS as well, and 20 of these extend median RFS by 48.8-72.1 months. Using UbiBrowser 2.0, we identified known and putative substrates unique to the 13 E3 ligases whose elevated expression shortens OS by >40 months and the 18 E3 ligases whose elevated expression extends OS by >40 months. Enrichment analyses of these two substrate sets using Reactome revealed largely non-overlapping functions. The E3 ligases whose elevated expression shorten OS uniquely targeted functions related to the cell cycle, cell cell communication, disease, cellular responses to stimuli, DNA repair, metabolism of proteins, chromatin organization, DNA replication, reproduction, developmental biology, and gene expression. The E3 ligases whose elevated expression extend OS uniquely targeted functions related to extracellular matrix organization and the neuronal system. Both sets of E3 ligases targeted functions related to immune system, signal transduction, and vesicle mediated transport. Detailed analyses of functions uniquely targeted by each set of ligases are expected to reveal candidate therapeutic targets with greater therapeutic index than the proteasome.
Elucidation of mechanisms underlying proteasome addiction in sarcomas
I will be presenting work initiated by Waldorf undergraduate Zack Bender during spring semester of 2025 at "The Tumor Ecosystem: From Bench to Clinic and Back" in Houston, TX, Nov. 19-21. We have shown that only a very small percentage of E3 ubiquitin ligases contribute to proteasome addiction.