Fig. 4: Integrative analysis of the plasma and tumour tissue proteomes in GL261-bearing mice.

a Schematic overview of the laser-capture microdissection (LCM)-coupled LC-MS/MS workflow employed for the proteomics analysis of the brain tissue samples. FFPE-preserved brains (n = 6 biological replicates/time point) were histologically sectioned and stained with haematoxylin and eosin (H&E) to reveal pathological characteristics of the tissue sections. Using a laser capture microscope, a total volume of 0.1 mm³ brain tissue was dissected from the tumour-bearing hemisphere and the ‘non-injected’ lateral hemisphere. Equivalent volumes of brain tissue from the sham injection site and the lateral hemisphere of the same brain were microdissected from sham-injected control mice. Microdissected brain tissue samples were lysed and subjected to S-trap protein digestion prior to their analysis by LC:MS\MS. Created in BioRender. Hadjidemetriou, M. (2025) https://BioRender.com/k25w778. b Volcano plots display the relationship between fold change and significance for the DAPs identified through comparison of healthy and tumour tissues. All proteins with a one-way ANOVA p-value < 0.05 are shown, coloured for upregulation shown in blue and downregulation in black. Any DAPs also identified in sham-injected mice (Supplementary Fig. 3c and Supplementary Data 7–9) were excluded from the lists. DAPs that were common between plasma and brain tissue are highlighted in orange. The full list of DAPs is shown in Supplementary Data 10−12. Venn diagrams illustrate the overlap between the plasma and tumour tissue identified DAPs at D7, D14 and D18 (Full list in Supplementary Data 13). c Dot plot presents the common KEGG pathways identified through independent enrichment analyses of plasma and tumour tissue DAPs at D7, D14 and D18, using a significance threshold of adjusted p-value < 0.05 by one-sided Fisher’s exact test. Pathways are ranked according to the adjusted p-value within each time point. The colour of the dots represents the adjusted p-value, and the size of the dots indicates the gene ratio (genes involved/total number of genes). Source data for Fig. 4c are provided as a Source Data file.