Specifically,
protein groups in cluster 1 were relevant to cell development, such as
regulation of cytoskeleton organization, regulation of
protein-containing complex assembly, and supramolecular fiber
organization. Cluster 2 was characterized by ribosome biogenesis for
cell proliferation and immune response to the microenvironment.
Ribosomal proteins (RPs) of the
60S (e.g., RPL3, RPL5, and RPL14) and 40S (e.g., RPS6, RPS8, and RPS16)
were enriched in clusters 2 and 3 (Figure 3C and D). Cell
proliferation-related proteins for pre-mRNA processing (e.g., HNRNPA1,
HNRNPK, and HNRNPL), core spliceosome (e.g., SRSF1, SF3B3, and SFPQ),
and proteasome complex (e.g., PSMC3, PSMA4, and PSMB1) were present in
cluster 2. Moreover, a unit of proteins (ILF2, ILF3, ISG15, and XRCC6)
involved in the modulation of the tumor microenvironment by the
inflammatory was identified. Further, cluster 3 encompassed energy
metabolism and RNA translation for tumorigenesis.
FIGURE 3 Distinct features of BrM proteome
profile. A Unsupervised
clustering of the top 1000
protein features out of 3843 label free quantification (LFQ) proteins
based on their interquartile
range (IQR) in 14 samples of BrMs. Pearson correlation was used for
distance measurement. BGene set enrichment analysis
(GSEA) of proteins in the three clusters. The top 20 annotations of
GO-BP, Reactome, WikiPathways, and KEGG pathways are shown
(Benjamini−Hochberg FDR method, adjusted P < 0.01).C Protein enrichment networks in cluster 2 based on the top
three functional enriched terms (R-HSA-8953854, R-HSA-2262752, and
R-HSA-8953897)
(Benjamini−Hochberg FDR method,
adjusted P < 0.01). D Protein enrichment
networks in cluster 3 based on the top three functional enriched terms
(R-HSA-72766, GO:0006412, and GO:0043043) (Benjamini−Hochberg FDR
method, adjusted P < 0.01).