3.3 Glioma subtypes correlate with respective protein patterns
Although the heterogeneity of gliomas has been described in terms of histochemistry and prognosis [2, 4], the understanding of low- and high-grade gliomas remains rudimentary to date, and there is no effective diagnostic method based on proteins [25, 26]. In response to the poor diagnostic outcomes in different subtypes of gliomas, we next focused on resolving protein pattern differences among gliomas. Firstly, integrated proteomic analysis of different grades of glioma showed independent and well-separated clusters. Low-grade gliomas (WHO grade II and III) exhibited a close correlation and differed from grade IV gliomas (Figure 4A). Complementarily, gliosarcoma (GSM), a rare form of grade IV gliomas (2%) that has both sarcomatous and malignant glial components [17], was found as a relatively separate entity in principal component analysis (PCA) and even had a closer relationship with grade III glioma when using Pearson correlation (Figure S3A and B). However, in GBMs, no separate clustering betweenIDH1 mutation (IV-Mut) and wild type (IV-WT) was observed.
To compare the proteome differences between low- and high-grade gliomas, we grouped WHO grades II and III tumors into a single consolidated low-grade group (II/III-Mut) and compared it to GBMs with IDH1 mutation (IV-Mut). In total, 36 proteins were aberrantly expressed in IV-Mut versus II/III-Mut (P< 0.05), of which 25 proteins were upregulated and 11 proteins were downregulated (Figure 4B and Figure S3B and C). Of note, the downregulated proteins in IV-Mut were associated with poor survival, whereas upregulated proteins were associated with the immune response.
IDH1/2mutant GBMs are distinct from wild-type GBMs with respect to molecular and clinical features, including prognosis [27, 28]. We next elucidated the proteomic differences between IV-Mut and IV-WT GBMs, which accounted for 66 upregulated proteins and 10 downregulated proteins (Figure S3E). To further investigate these differentially expressed proteins (DEPs), gene set enrichment analysis (GSEA) was performed (Figure 4C). Tumor invasion-related processes (e.g., Rho GTPase cycle, cellular amino acid metabolic process, membrane trafficking, and ferroptosis) were predominately upregulated in IV-Mut. Intriguingly, ferroptosis, a newly discovered form of cell death, is not only correlated with cell migration but also represents a better prognosis in IV-Mut versus IV-WT [29, 30].