Methylation-Based Characterization of a New IDH2 Mutation in Sinonasal Undifferentiated Carcinoma

TL;DR

A new IDH2 mutation (R172A) in sinonasal undifferentiated carcinoma is characterized by a hypermethylated profile similar to other known IDH2 mutations.

Contribution

The study reports a novel IDH2 R172A mutation and demonstrates its structural and methylation similarities to other known IDH2 mutations.

Findings

The R172A mutation in IDH2 is associated with a hypermethylated phenotype similar to other IDH2 mutations.

PCA analysis showed the R172A sample clustered closely with other IDH-mutant SNUCs.

Molecular modeling suggests R172A affects the IDH2 active site similarly to other R172 variants.

Abstract

Mutations affecting codon 172 of the isocitrate dehydrogenase 2 (IDH2) gene define a subgroup of sinonasal undifferentiated carcinomas (SNUCs) with a relatively favorable prognosis and a globally hypermethylated phenotype. They are also recurrent (along with IDH1 mutations) in gliomas, acute myeloid leukemia, and intrahepatic cholangiocarcinoma. Commonly reported mutations, all associated with aberrant IDH2 enzymatic activity, include R172K, R172S, R172T, R172G, and R172M. We present a case of SNUC with a never-before-described IDH2 mutation, R172A. Our report compares the methylation pattern of our sample to other cases from the Gene Expression Omnibus database. Hierarchical clustering suggests a strong association between our sample and other IDH-mutant SNUCs and a clear distinction between sinonasal normal tissues and tumors. Principal component analysis (PCA), using 100 principal components explaining 94.5% of the variance, showed the position of our sample to be within 1.02 standard deviation of the other IDH-mutant SNUCs. A molecular modeling analysis of the IDH2 R172A versus other R172 variants provides a structural explanation to how they affect the protein active site. Our findings thus suggest that the R172A mutation in IDH2 confers a gain of function similar to other R172 mutations in IDH2, resulting in a similar hypermethylated profile.

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