The average age was 55.8 years in the B1 group, 51.0 years in the B3 group, and 53.8 years in the MTC group. No variations were observed in age or gender (all P > 0.05). Details are provided in Table 1.

In the serum of individuals with thymoma (B1 and B3) and thymic cysts, DEPs were identified by employing TMT-based proteomics to investigate the potential mechanisms underlying thymoma pathogenesis. A collective count of 49 DEPs was screened in the comparison between B1 and MTC (17 upregulated and 32 downregulated), 27 in B3 and MTC (8 upregulated and 19 downregulated), and 38 in B3 and B1 (9 upregulated and 29 downregulated). Figure 1 A-C depicts the volcano plot illustrating the DEPs across the three comparisons. GSTP1, IGHV1-18, F7, ANG, IL13RA1, AMBP, SERPINB3, SRI, SHISA5, and LGALS3BP emerged as the most significantly dysregulated DEPs in the comparison between B1 and MTC. Meanwhile, EPHX4, IL13RA1, PMFBP1, TIMD4, AHCYL1, IGKV4-1, LGALS3BP, PRKCSH, APOF, and F9 exhibited significant dysregulation in the B3 vs. MTC comparison. Additionally, MGAT1, IGF2R, INHBC, BST1, DEFA1, MBL2, AZGP1, AMY1A, APOF, and RNASET2 displayed significant dysregulation in the B3 vs. B1 comparison.(Table 2). After comparisons, 8 DEPs were determined to be differentially expressed in both B1 vs. MTC and B3 vs. MTC (Fig. 1D): IL13RA1 (down), LGALS3BP (up), PRCSH (down), C3 (down), MXRA5 (down), TNN (down), CFHR1 (down), SUN3 (down).

Volcano map of DEPs in B1 vs. MTC, B3 vs. MTC, and B3 vs. B1 comparisons. Note B1 vs. MTC, represents thymic cyst compared with B1 thymoma cancer. B3 vs. MTC, represents thymic cyst compared with B3 thymoma cancer. B3_vs_B1, represents B1 thymoma cancer compared with B3

To find out the biological functions of the DEPs, GO enrichment analysis was conducted. The GO analysis revealed the involvement of these DEPs in diverse fundamental biological processes and the facilitation of numerous molecular functions. Comparison was made between the significantly altered GO terms. The DEPs in B1 vs MTC were predominantly enriched in ‘’astrocyte cell migration’’, ‘’cellular response to organic cyclic compound’’, ‘’antibacterial humoral response’’, ‘’toxic substance binding’’, ‘’pentameric IgM immunoglobulin complex’’, ‘’hexameric IgM immunoglobulin complex’’, ‘’developmental process involved in reproduction’’, ‘’positive regulation of biological process’’, ‘’regulation of sensory perception of pain’’, and ‘’anatomical structure development’’ (Fig. 2A). The DEPs in B3 vs MTC were predominantly enriched in ‘’plasminogen activation’’, ‘’sperm connecting piece’’, ‘’aromatic compound catabolic process’’, ‘’negative regulation of neuron migration’’, ‘’synapse part’’, ‘’endoplasmic reticulum to Golgi vesicle-mediated transport’’, ‘’positive regulation of fibrinolysis’’, ‘’dendritic spine head’’, ‘’lamellipodium assembly involved in ameboidal cell migration’’, and ‘’extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration’’ (Fig. 2B). The DEPs in B3 vs B1 were mainly enriched in ‘’alpha-amylase activity’’, ‘’alpha-amylase activity (releasing maltohexaose)’’, ‘’polysaccharide digestion’’, ‘’heme transport’’, ‘’chloride ion binding’’, ‘’starch metabolic process’’, ‘’sucrose metabolic process’’, ‘’negative regulation of MAP kinase activity’’, ‘’protein O-linked glycosylation’’, and ‘’negative regulation of T cell activation’’ (Fig. 2C).

Furthermore, the KEGG analysis suggested that the DEPs in B1 vs MTC were predominantly enriched in ‘’Metabolism of xenobiotics by cytochrome P450’’, ‘’Chemical carcinogenesis’’, ‘’Hepatocellular carcinoma’’, ‘’Leishmaniasis’’, ‘’Herpes simplex virus 1 infection’’, ‘’Platinum drug resistance’’, ‘’Epstein-Barr virus infection’ ‘Drug metabolism - cytochrome P450’, ‘Fc epsilon RI signaling pathway’, ‘Carbohydrate digestion and absorption’, ‘Chloroalkane and chloroalkene degradation’, ‘Naphthalene degradation’, ‘Degradation of aromatic compounds’, and ‘Chemokine signaling pathway’ (Fig. 3A). The DEPs in B3 vs. MTC were primarily enriched in ‘Complement and coagulation cascades’, ‘Ascorbate and aldarate metabolism’, and ‘Lysine degradation’ (Fig. 3B). The DEPs in B3 vs B1 were mainly enriched in ‘Cholesterol metabolism’ and ‘Steroid biosynthesis’ (Fig. 3C).

The GO analysis of DEPs in B1 vs. MTC (A), B3 vs. MTC (B), and B3 vs. B1 (C) comparisons

The KEGG analysis of DEPs in B1 vs. MTC (A), B3 vs. MTC (B), and B3 vs. B1 (C) comparisons

As per the prediction data from GO and KEGG analyses, the PPI network of DEPs of B1 vs. MTC, B3 vs. MTC, and B3 vs. B1 was constructed. It is shown in Fig. 4A that C3, CR1, AMBP, ALB, APOA1, A2M, PLGLB1, and B2M interacted with each other in the B1 vs. MTC group. F11, F9, SERPINA1, LGALS3BP, APOH, C3, CD55, APOF, and CFHR1 were connected (Fig. 4B). As for B3 vs. B1, AFM, AZGP1, A2M, HPX, SERPINF1, ALB, APOH, SAA4, MBL2, APOB, and HRG closely interacted with each other (Fig. 4C).

The PPI analysis of DEPs in B1 vs. MTC (A), B3 vs. MTC (B), and B3 vs. B1 (C) comparisons

GEPIA was employed to validate some of the critical DEGs (Fig. 5). It was discovered that A2M, C3, LGALS3BP, PMFBP1, and SRI were remarkably upregulated in individuals with thymoma (P < 0.05). CD55 and CR1 were considerably downregulated in thymoma patients. Surprisingly, the dysregulation trend of LGALS3BP is consistent with our study. Afterward, their expression was assessed in other cancers via UALCAN (Fig.  6). Generally, all these genes were significantly dysregulated in thymoma. Moreover, it was found that A2M has a moderate upregulation in almost all cancers except glioblastoma multiforme (GBM), head and neck squamous cell carcinoma (HNSC), and stomach adenocarcinoma (STAD). Despite dysregulation in certain cancers, the expression levels of CR1 and PMFBP1 remained at a superficial level. LGALS3BP exhibited relatively moderate expression in tumors and normal tissues.

The expression level of DEGs in TCGA databases

The expression of A2M, C3, LGALS3BP, PMFBP1, SRI, CD55 and CR1 in pan-cancers