Page 87 - EJMO-9-3

Eurasian Journal of
Medicine and Oncology Mapping breast cancer PPI networks for targets

Table 4. The spatial allocation of growth‑related proteins Table 8 highlights that proteins successfully targeted by
within the BCPIN zones drugs are predominantly found in zones 1 – 3, accounting
for 9.09%, 5.04%, and 1.26%, respectively. This distribution
Zone Protein count Growth proteins (%) Total suggests that proteins within the core may be promising
1 374 28 (7.48) 234 drug targets.
2 4496 156 (3.46)
3 2918 45 (1.54) 3.3. MAPK signaling and apoptosis in core zones as
4 249 5 (2) drug targets
5 27 0 (0) Table 9 shows the distribution of MAPK signaling
Abbreviation: BCPIN: Breast cancer protein-protein interaction components, positive/negative regulation of signaling, and
network. apoptosis-related proteins within BCPIN. These pathways
are concentrated in the central zones, reinforcing their
Table 5. The spatial allocation of cell cycle proteins within potential as therapeutic targets.
the BCPIN zones
3.4. Functional specialization in core zones
Zone Protein count Cell cycle proteins (%) Total
According to pathway enrichment analysis, functional
1 374 73 (19.50) 570
2 4496 431 (9.58) specialization was identified in the core zones of BCPIN
(Table 10). Zone 1 is enriched in signaling regulation,
3 2918 64 (2.2) immune system function, apoptosis, gene expression, and
4 249 2 (0.80) p53/Notch signaling. Zone 2 displays similar enrichment
5 27 0 (0) but to a lesser degree, while zones 3 and 4 exhibit minimal
Abbreviation: BCPIN: Breast cancer protein-protein interaction pathway enrichment. These findings suggest that the
network. central zones play a critical role in cancer progression and
may offer novel therapeutic targets.
Table 6. The spatial allocation of suppressor proteins within
the BCPIN zones 3.5. Pathway and function enrichment analysis for
essential proteins for cancer cell survival
Zone Protein count Suppressor proteins (%) Total
1 374 14 (3.74) 59 Genes that are vital for the existence of an organism
2 4496 42 (0.93) are referred to as essential genes. The genes used in this
3 2918 3 (0.10) analysis have been found critical for cancer cell’s survival
in different environments. 35,36 At least 8% of the genes in
4 249 0 (0) each zone are essential and are in pathways critical for
5 27 0 (0) cancer development and progression (Table 11).
Abbreviation: BCPIN: Breast cancer protein-protein interaction
network. 3.6. Disease pathways in core zones
With the intent of finding out the central zones of BCIPN
Table 7. The spatial allocation of oncogene proteins within
the BCPIN zones of biological significance, we mapped them to proteins
in the KEGG pathways. Using this enriched analysis of
37
Zone Protein count Oncogene proteins (%) Total zones, we found that the majority of proteins involved in
1 374 15 (4.01) 48 the pathways of cancer are concentrated in zones close to
2 4496 32 (0.71) the center (Figure 3).
3 2918 1 (0.3) Among these are p53, BRCA1, and BRCA2
4 249 0 (0) proteins, which are well documented as associated
38
5 27 0 (0) with hereditary breast and ovarian cancer. For
Abbreviation: BCPIN: Breast cancer protein-protein interaction zone 2, enriched analysis showed 102, 344, and 172
network. proteins in pathways of breast cancer, cancer, and
MAPK, respectively. Amidst them are ATM, CDH1,
Table 7 displays the allocation of oncogenic proteins, PTEN, BARD1, and CHEK2 proteins that are known
highlighting their prevalence in the network’s core. predisposition genes. 39,40

Volume 9 Issue 3 (2025) 79 doi: 10.36922/ejmo.8208