Exploration of the Key Proteins in the Normal-Adenoma-Carcinoma Sequence of Colorectal Cancer Evolution Using In-Depth Quantitative Proteomics

Figure 3

Integrating transcriptomic datasets and proteomic profiles to identify hub proteins in the N-A-C sequence. (a) Venn diagram showing the intersection of upregulated DEPs in the N-C process (UpDEPs-N-C), upregulated DEPs in the N-A process (UpDEPs-N-A), and upregulated DEGs of GSE 117606 and GSE 50114 in the N-A process. A total of 45 intersected genes in the four datasets were identified. (b) The protein-protein interaction (PPI) network of the 45 intersected proteins which could contribute to a connection in the N-A process. The MCODE1 cluster is circled in red and the seed protein (RRP12) is highlighted (MCODE criteria: degree cutoff = 2, node score cutoff ≥ 0.2, K-core ≥ 3, and max. depth from seed = 100; MCODE1 score = 7.231). (c) The primary enrichment of biological processes and pathways in MCODE1 of N-A process. (d) Venn diagram showing the intersection of UpDEPs-N-C, upregulated DEPs in the A-C process (UpDEPs-A-C), and upregulated DEGs of GSE 117606 and GSE 50115 in the A-C process. A total of 29 intersected genes in the four datasets were identified. (e) The protein-protein interaction (PPI) network of the 45 intersected proteins which could contribute to a connection in the A-C process. The MCODE1 and MCODE2 clusters are circled in red and green, respectively. The seed (MCODE1: IGFBP7; MCODE2: CDK1) and hinge protein (SERPINH1) are highlighted (MCODE criteria: degree cutoff = 2, node score cutoff ≥ 0.2, K-core ≥ 3, and max. depth from seed = 100; MCODE1 score = 3.25 and MCODE2 score = 2.222). (f) The primary enrichment of biological processes and pathways in MCODE1 and MCODE2 of the A-C process. (g) Six algorithms (MCC, Degree, EPC, MNC, Bottleneck, and Radiality) were used to analyze and rank the hub proteins of the PPI network in the N-A and A-C processes using the “cytoHubba” plugin. The ranking of RRP12, SERPINH1, CDK1, and IGFBP7 is visualized in a heatmap. Only top five hub proteins in each algorithm are colored as shown in the bar. If the protein was not ranked among the top five, the corresponding column would be gray. Only RRP12 and SERPINH1 were verified among the top five hub proteins using the six algorithms. The rank ranges of RRP12 and SERPINH1 were 3–5 and 1–2, respectively. (h) The variation in the expression of RRP12 and SERPINH1 in the N-A-C sequence was validated using an external dataset reported by Wisniewski et al. based on the criteria of value < 0.05 and log2 FC ratio > 0.3, RRP12 was significantly upregulated in the N-A and N-C processes, and SERPINH1 was significantly upregulated in the A-C and N-C processes. There were no significant differences in the expression of RRP12 in the A-C process and that of SERPINH1 in the N-A process.

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