In silico analysis reveals distinct changes in markers of epithelial to mesenchymal transition in glioma subtypes

Nives Pećina-Šlaus; Alja Zottel; Željko Škripek; Borna Puljko; Fran Dumančić; Anja Bukovac; Ivana Jovčevska; Anja Kafka

doi:10.17305/bb.2025.12598

Authors

Nives Pećina-Šlaus Department of Biology, School of Medicine, University of Zagreb, Zagreb, Croatia; Laboratory of Neuro-oncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Zagreb, Croatia
Alja Zottel Center for Functional Genomics and Biochips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
Željko Škripek Department of Biology, School of Medicine, University of Zagreb, Zagreb, Croatia https://orcid.org/0009-0008-4212-8893
Borna Puljko Laboratory for molecular neurobiology and neurochemistry, Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia; Department of Chemistry and Biochemistry, School of Medicine, University of Zagreb, Zagreb, Croatia https://orcid.org/0000-0003-4198-3982
Fran Dumančić Department of Biology, School of Medicine, University of Zagreb, Zagreb, Croatia; Laboratory of Neuro-oncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Zagreb, Croatia
Anja Bukovac Department of Biology, School of Medicine, University of Zagreb, Zagreb, Croatia; Laboratory of Neuro-oncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Zagreb, Croatia
Ivana Jovčevska Center for Functional Genomics and Biochips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia https://orcid.org/0000-0002-0418-2986
Anja Kafka Department of Biology, School of Medicine, University of Zagreb, Zagreb, Croatia; Laboratory of Neuro-oncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Zagreb, Croatia

DOI:

https://doi.org/10.17305/bb.2025.12598

Keywords:

Glioma, EMT marker, NOTCH1, SOX2, progression, WHO grade, cBioPortal, GlioVis, qRT-PCR

Abstract

Epithelial to mesenchymal transition (EMT) plays a critical role in tumor progression and metastasis, including in gliomas. To examine and interpret data on major genes involved in EMT and associate their changes with low-grade (LGG) and/or high-grade (HGG) gliomas, data from the cBioPortal—a publicly available database for tumor genomics and transcriptomics, were collected for 13 genes: CDH1, CDH2, CTNNB1, LEF1, NOTCH1, SNAI1, SNAI2, SOX2, TJP1/ZO1, TWIST1, VIM, ZEB1, and ZEB2. The dataset included mutations, copy number alterations (CNA), and changes in transcript levels reported for each gene. The genes were additionally validated by gene expression on the GlioVis portal, STRING protein network analysis, survival analysis, and experimentally with qRT-PCR. Glioblastoma and diffuse glioma harbored changes in all 13 analyzed genes, while anaplastic oligodendroglioma and anaplastic astrocytoma in 46.15%, oligodendroglioma in 23.08%, and oligoastrocytoma in 15.38%. NOTCH1 and SOX2 were most affected by changes. The NOTCH1 gene was statistically more frequently changed compared to CDH1, CTNNB1, and ZEB1 (p < 0.05). The virtual study showed that alterations in NOTCH1 and LEF1 were associated with LGG, while alterations in CDH1, CTNNB1, TJP1, TWIST1, SOX2, VIM, ZEB1, and ZEB2 were associated with HGG. Differential expression analysis stratified for IDH1 mutations showed that IDH1-mutant glioblastoma had significantly lower CDH2, LEF1 and SNAI1 expression, and higher ZEB1. Gene expression in different glioblastoma subtypes showed that the TJP1/ZO1 gene was associated with the classical subtype, while ZEB2 was associated with the proneural subtype. qRT-PCR confirmed GlioVis mRNA expression data for NOTCH1, SOX2, CDH1, CTNNB1, TJP1/ZO-1, VIM, TWIST1, and partially for SNAI1 (SNAIL), SNAI2, and CDH2. Our study shows consistent changes in genes involved in EMT in gliomas of different grades. Additional research is needed to confirm the knowledge brought by this study.