3.4 Comparative proteomics for primary and secondary brain tumors
Gliomas and BrMs are the most predominant primary and secondary brain tumors in the human brain with a common trait of various malignancies. We next investigated the proteomic heterogeneity of these two types of brain tumors. These two typical brain tumors are composed of unique cell types, anatomical structures, metabolic constraints, and immune environment [17] , which may explain the tendency of some extracranial cancers to migrate toward the brain and provide new insights into the blood-brain barrier (BBB) changes during tumor metastasis. For comparative proteomic analysis, malignant brain tumors from primary (gliomas, n = 13) and secondary (BrMs, n = 14) brain tumors were utilized.
In total, 352 proteins were statistically different between the cohorts (P < 0.01), of which 93 proteins were upregulated and 259 proteins were downregulated in BrMs versus gliomas (Figure 5A, Figure S4A and Table S3). The 352 DEPs effectively distinguished two types of tumors in unsupervised clustering and PCA based on component 1 (96.1%) and component 2 (1.8%) (Figure 5B and Figure S4B).
We next performed functional enrichment analysis for the upregulated and downregulated proteins, respectively (Figure 5C, Figure S4C and D). To some extent, the general cellular and molecular pathways were similar in both types of malignant brain tumors. However, proteins in some distinct pathways were upregulated in BrMs, such as Golgi vesicle transport, formation of the cornified envelope, and secretion (Figure 5C and Figure S4C). Specific processes involved in gliomas were correlated with cell migration, including regulation of actin cytoskeleton, modulation of chemical synaptic transmission, neuron projection development and so on. Taken together, the proteome-based results clearly illustrated that BrM colonization in the brain depends on tumorigenesis and multiple interactions of metastatic cancer cells with the brain microenvironment, whereas gliomas, as one of the representative primary tumors in the brain, maintain a high tendency to invade. These findings prompted further exploration of candidate biomarkers for distinguishing primary and secondary brain tumors.