Comparison of post-surgical thyroid hormone levels between "reduced" and "unchanged" FT3 patients
Based on our previous report [5], we selected from the group of patients with "reduced" or "unchanged" FT3, 4 patients/group to submit to proteomic analysis. The "reduced" patients were chosen in order to have subjects complaining lower physical and neurocognitive wellbeing after total thyroidectomy. As shown in Table 1, there was no significant difference between post-surgery serum TSH and FT4 levels among groups (by Wilcoxon test for paired data). The mean post-surgical serum FT3 level was significantly (p =0.05) lower in the "reduced" group compared to the "unchanged" (3.4±0.5 pg/ml versus 2.7±0.15 pg/ml) although in the reference range. Age, FT3/FT4 ratio, LT4 dose/day and LT4 dose/kg did not differ between patients with a lower FT3 level after surgery and those in whom FT3 was unchanged. Due to the low number of patients, sex distribution was by chance different in the two groups.
Differential proteomic results
The analyzed dataset enumerated ~1200 protein spots. The unsupervised analysis (data not shown), performed as data quality control, was obtained analyzing the top 100 spots with higher variance intensity through unsupervised heatmap and PCA and the results did not highlight any outliers nor clustering related with any possible covariant disturbances.
However, the comparison emphasized 31 significant differentially abundant spots (DAS) between Reduced FT3 and unchanged FT3 groups (Table S1, Figure 1).
The 31 differential spots are visualizable in the reference gel maps in Figure 2 and Figure S-1.
Peptide Mass Fingerprint identification highlights a characteristic pattern of THRB, APOAI and A1AT protein fragments in FT3 reduced patients
Once performed protein identification by MALDI-ToF mass spectrometer, Mascot Search Results of all differentially abundant spots were reported in Table 2. Interestingly, some identifications highlighted not the full-length protein but a protein fragment. In particular, spots 1Q, 2Q, 3Q, visible only in reduced FT3 samples, were identified by Peptide Mass Fingerprint (PMF) as C-term fragments of thrombin from aa 364 to 622 and corresponding to thrombin heavy chain isoform on UniProt database (Figure 3), demonstrating a possible specific proteolytic process.
Among highly abundant spots in reduced FT3 sera we found spots 4, 11, 12, 21 and 22. All are identified as full-length APOAI, even if spots 11 and 12 showed a mixture with a central fragment of A1AT suggesting a colocalization of these two protein species on the 2DE map (Table 2, Figure 4 and 5). Among low abundant spots in reduced FT3 sera there were spots 24, 14 and 5Q, identified respectively as central, N-terminal and C-terminal fragments of APOAI (Figure 4). Two-dimensional western blot (2D WB) results shown in Figure 4 confirmed the abundance and the distribution of APOAI protein species with a higher abundance of full-length APOAI in spots 4, 11, 12, 21, 22 and a lower abundance of the protein fragments only in spot 24 in FT3 reduced condition.
At the same time, we were interested to validate A1AT proteomic data as well. While the highly abundant spot 15 in reduced FT3 samples was identified as A1AT full-length, spots 11, 12, 24 were identified as a mixture of a central fragments of A1AT and APOAI (Table 2; Figure 5, PMF identification), making impossible to evaluate A1AT abundance for these spots on 2DE. To overcome this problem, we applied a 2D WB approach using A1AT antibodies to validate and quantify A1AT protein pattern (Figure 5). The results corroborated the identification of spots 11 and 12 as A1AT and permitted to highlight differential abundance of A1AT fragments revealing an opposite trend with respect to APOAI. Spot 24 identified by PMF as a mix of APOAI and fragment of A1AT (Table 2; Figure 5, PMF identification), was confirmed by 2DWB also as A1AT (Figure 5) and low abundant in reduced FT3 samples.
PCA and heatmap analysis
The PCA carried on the 31 DASs summarized the 95.6% (PC1:85.2% and PC2:10.4%) of the variance and the two groups clusterized alongside the first component (Figure 6A). In addition, Figure 6B showed the contributions of each significant variant in the first two PCs highlighting spot 11, 12 and 22, identified as APOAI and fragments of A1AT, as the most significant. Similarly, to PCA, the heatmap branching separated the samples in two clusters corresponding to FT3 groups (Figure 6C).
Enrichment analysis
Enrichment analysis by MetaCore permitted the building of the network of molecular interactions related to the identified proteins. Figure 7 shows the protein network where thrombin, alpha1-antitrypsin, APOE, Plasminogen and APOA1 were central functional hubs i.e proteins with a higher number of interactions with respect to the other proteins. Light blue lines in the interactome show the canonical paths delineated in Table S-2 that also reports their relative GO biological processes. Three principal molecular paths such as blood coagulation (yellow), complement system (orange) and lipoprotein particle remodeling (blue) are evident.
Results by process network analysis showed that the inflammation, induced by complement system, Kallikrein-kinin system, IL-6 signaling, protein C signaling and innate inflammatory response, represents the central process where the identified proteins are involved (Table 3). Indeed, all three molecular paths highlighted on the protein network in Figure 7 suggest the activation of different pro-inflammatory ways.
Pathway Maps analysis highlights a strong involvement of the complement, blood coagulation and lipid particle remodeling with the terms “immune response by classical, alternative, lectin induced complement pathways”, “Alternative complement cascade disruption in age-related macular degeneration” and “Complement pathway disruption in thrombotic microangiopathy”, “blood coagulation” and terms such as “lipid metabolism”, “HDL-mediated reverse cholesterol transport” and “HDL dyslipidemia in type 2 diabetes and metabolic syndrome X” (Table 4). Enrichment analysis by GO biological processes in Table S-3, strongly support the involvement of lipoproteins metabolism and remodeling.