This is surprising since three of these markers, APOA1, FSH, and TF, are part of the FDA-approved Overa (TM) multi-marker panel (12), which achieved a sensitivity of 91.3% (100% with stage III patients) and a specificity of 69.1%. for 10 out of 12 proteins analyzed, including SPINT2. These findings suggest that in contrast Entecavir hydrate to other entities SPINT2 does not act as a tumor suppressor in HGSC. This is supported by data from the PRECOG and KM-Plotter meta-analysis databases, which point to a tumor-type-specific inverse association of gene expression with survival. Our data also demonstrate that both the PEA and SOMAscan affinity proteomics platforms bear considerable potential for the unbiased discovery of novel disease-associated biomarkers. values were adjusted for multiple hypothesis by the Benjamini-Hochberg method. Spearman correlations were analyzed using Entecavir hydrate the scipy.stats.spearmanr functions with Python. Boxplots were constructed by the seaborn.boxplot function. Functional annotations were performed by PANTHER gene ontology (GO) enrichment analysis (27) (http://www.http://geneontology.org). In case of redundancies in the search results only the term with the highest enrichment and significance (lowest FDR) was included in Tables 1, ?,22. Table 1 Gene ontology term enrichment analysis of biological processes for proteins upregulated in HGSC plasma. 0.05 by U test; ratio OC/N 1 in Table S3). The data for the 30 top proteins (highest significance) are shown in Figure 1. The only protein completely separating OC-plasma and N-plasma samples was WFDC2, consistent with previous findings (8, 9). Other proteins yielding highly significant differences (adjusted 1.5 10?7) between the sample sets were SPINT2 (Serine Peptidase Inhibitor Kunitz Type 2), IL-6 (interleukin 6), MUC16, and PVRL4 (Poliovirus Receptor-Related Protein 4; also known as NECTIN4; Nectin Cell Adhesion Molecule 4). In addition, a number of proteins previously not described in previous studies were also significantly upregulated in OC-plasma, including BCAM, CDH6, DDR1, N2DL-2 (ULBP2), and WISP-1 (CCN4) (Figure 1). Open in a separate window Figure 1 Levels of the top 30 upregulated proteins in OC-plasma (red) vs. N-plasma (blue) based Entecavir hydrate on PEA signals. The dot plots show the results for 20 OC-plasma and 20 N-plasma samples. The indicated 1e-3, ?? 1e-5. We also found 19 proteins present at significantly higher levels (adjusted 0.05) in N-plasma relative to OC-plasma (ratio OC/N 1 in Table S3). We did not follow up on these proteins, as the goal of the present study was the identification of markers upregulated in HGSC patients. Functions of Upregulated Proteins Functional annotation of the proteins upregulated in HGSC plasma by gene ontology (GO) term enrichment analysis identified several biological processes known to be critical for HGSC growth and progression (2), including immune regulation, cell adhesion, cell migration, cell proliferation, cell death and extracellular matrix organization (Table 1). The immune system process group comprised 73 proteins, the metastasis-related groups cell migration and cell adhesion 43 and 41 proteins, respectively (listed below Table 1). The most significant molecular functions associated with upregulated plasma proteins were membrane-receptor-driven pathways triggered by interactions with extracellular matrix (ECM) components and growth factors, such as IGF (insulin-like growth factor), VEGF (vascular endothelial growth factor), TNF (tumor necrosis Entecavir hydrate factor), semaphorins, and PDGF (platelet-derived growth factor), as well as extracellular proteases and their inhibitors. These findings are consistent with our knowledge of progression-driving mechanisms in HGSC. Correlation of Olink, SOMAscan and ELISA Data To assess the validity of the Rabbit Polyclonal to IGF1R results obtained by the antibody-based Olink platform we reanalyzed all samples by the aptamer-based SOMAscan proteomic assay using the 1.3 k panel with 1,305 probes (Table S4). Out of the Entecavir hydrate 157 proteins identified by PEA as upregulated in OC-plasma (see above) 107 were present (by gene names) in the SOMAscan panel. Spearman analysis across all plasma samples revealed a positive median correlation of = 0.62 for these 107 proteins between the platforms (Figure 2A; Table S5), exemplified.