Genes mapped at the genomic loci 11q13.4-q24.3 interval are associated with cell adhesion and inflammation pathways
To investigate the association between CNAs in Ch11q and COX-2 protein expression, we selected the cytobands with CNAs in the following genomic loci of three patients in Group 2: 11q13.4-q25 (Pat15 and Pat20), and 11q12.1-q25 (Pat42), with a common interval among all three patients at 11q13.4-q24.3 (Figure 3A). Identification of the genes mapped in the common interval revealed a total of 409 protein-coding genes and 34 miRNAs (Supplemental Tables S1, S2 and S3). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis (DIANA-miRPath v.3) associated 14 of the miRNAs with glycosphingolipid, fatty acid, and steroid hormone biosynthesis and cell adhesion molecules (Supplemental Table S4). Using TarBase v.7.0 miRNA target prediction analysis, 39 targets were predicted to be regulated by these miRNAs.
The list composed of the 409 protein-coding genes, the 39 miRNA targets, and the 30 inflammation-related genes 17, 30 was used to generate a PPI network. It resulted in a network with 469 nodes and 476 edges (Figure 4A), with a PPI enrichment p-value of 1.0e-16, which indicates that proteins in the network present more mutual interactions than expected. Surprisingly, no direct connection was found betweenPTGS2 and Ch11q-related genes. Thus, indirect relationship analysis was performed by applying the degree, betweenness, and eigenvector centrality. Ninety-two out of the 469 nodes were of more topological relevance in the network: 29 hubs, 6 bottlenecks, 14 switches, and 30 HBS (Figure 4). Besides, gene ontologies (GO) analysis revealed cell adhesion, transcription, DNA repair, and inflammation as the main biological processes related to these genes. Clustering and GOs analysis led to identifying five clusters (Figure 4B; Supplemental Table S5). Cluster 1 is associated with the regulation of cytokine production, immune system process, apoptosis, cell proliferation, programmed cell death, and the mutual interaction of metalloproteinases (MMPs), which is involved in the collagen metabolic process. Cell and biological adhesion were the only processes associated with Clusters 2 and 4. ThePTGS2 gene is an HBS node found only in cluster 3, where its interaction with other genes of the PGE2 and other inflammatory pathways is evident, as well as its indirect interaction with CLPB(chromosome location Ch11q13.4), a gene involved in the cellular heat response. In cluster 5, several genes were identified related to the neurological system process, in addition to a connection of interleukin 6 (IL-6 ), IL-6 receptor (IL-6R ), and signal transducer and activator of transcription 3 (STAT3 ), involved in IL-6-mediated signaling pathway. The CLPB gene, together with PTGES3 andPTGER1, are common HBS between Clusters 3 and 5. Likewise, other HBS nodes, such as the ones involving IL-1β and CEBPB , intersect between Clusters 1 and 3, while EP300 and STAT3are common HBS to Clusters 1, 3, and 5. Altogether, this analysis led to identifying nodes of biological relevance that interconnect clusters with different profiles of gene interactions, progressing toward understanding the correlation of COX-2 expression and aberrations in Ch11q.