SETD2 Regulates the Methylation of Translation Elongation Factor eEF1A1 in Clear Cell Renal Cell Carcinoma1

Abstract

BACKGROUND: SET domain-containing protein 2 (SETD2) is commonly mutated in renal cell carcinoma. SETD2 methylates histone H3 as well as a growing list of non-histone proteins. OBJECTIVE: Initially, we sought to explore SETD2-dependent changes in lysine methylation of proteins in proximal renal tubule cells. Subsequently, we focused on changes in lysine methylation of the translation elongation factor eEF1A1. METHODS: To accomplish these objectives, we initially performed a systems-wide analysis of protein lysine-methylation and expression in wild type (WT) and SETD2-knock out (KO) kidney cells and later focused our studies on eEF1A1 as well as the expression of lysine methyltransferases that regulate its lysine methylation. RESULTS: We observed decreased lysine methylation of the translation elongation factor eEF1A1. EEF1AKMT2 and EEF1AKMT3 are known to methylate eEF1A1, and we show here that their expression is dependent on SET-domain function of SETD2. Globally, we observe differential expression of hundreds of proteins in WT versus SETD2-KO cells, including increased expression of many involved in protein translation. Finally, we observe decreased progression free survival and loss of EEF1AKMT2 gene expression in SETD2-mutated tumors predicted to have loss of function of the SET domain. CONCLUSION: Overall, these data suggest that SETD2-mutated ccRCC, via loss of enzymatic function of the SET domain, displays dysregulation of protein translation as a potentially important component of the transformed phenotype.

Methylation of elongation factor 1A by yeast Efm4 or human eEF1A-KMT2 involves a beta-hairpin recognition motif and crosstalks with phosphorylation

“…Deciphering how these unique methyltransferases recognize and methylate eEF1A will be important for understanding how they can be targeted therapeutically. This is important as differential expression of eEF1A methyltransferases is associated with cancer progression ( 61 , 62 , 63 , 64 ). For example, increased eEF1A K55 methylation by overexpression of METTL13 plays a central role in the development of lung and pancreatic cancers ( 63 ).…”

“…For example, increased eEF1A K55 methylation by overexpression of METTL13 plays a central role in the development of lung and pancreatic cancers ( 63 ). Conversely, reduced expression of eEF1A-KMT2 is correlated with decreased survival in patients with renal cell carcinoma ( 62 ), while lower expression of eEF1A-KMT3 in gastric cancer is associated with poor prognosis ( 61 ). Separate to cancer, a decrease in eEF1A methylation levels in muscle tissue may be associated with aging ( 65 ).…”

Histone methyltransferase SETD2: An epigenetic driver in clear cell renal cell carcinoma

“…A recent study reported that SETD2 could indirectly methylate non-histone substrates, loss of SETD2 increases protein translation-related gene expression and decreases eEF1A1 K165me3 and K318me1 in ccRCC, but SETD2 is associated with eEF1A1 methylation indirectly, SET domain of SETD2 regulated the expression of EEF1AKMT2 and EEF1AKMT3, EEF1AKMT3 methylates eEF1A1 on lysine 165 and EEF1AKMT2 methylates eEF1A1 on lysine 318 ( 109 ). Finally, the discovery of SETD2 for non-histone substrates is particularly crucial for a more in-depth understanding of its biological role ( Figure 2 ).…”