## 4 Discussion
### Module Key Hub Genes and Their Protein Functions  
#### 4.2.1 Involvement of Hub Genes in Inflammation-Related Pathways Associated with ccRCC  
The identified hub genes were found to be connected in these pathways. KEGG pathway analysis confirmed the involvement of hub genes in RCC, since RCC was obtained in the analysis (Table A1). Upregulated genes _EGFR_, _CD44_, and _SOX2_ in the red module are linked with the HIF-1 signaling pathway. _EGFR_, overexpressed in ccRCC and activated by IL-6 and TNF-\(\alpha\), is less effective as a target due to the lack of mutations or gene amplification [64, 65]. Its membranous expression in RCC tumors [66], compared to its cytoplasmic location in normal kidney tissue, is associated with poorer prognosis and advanced stages [67]. HIF-1 also drives _CD44_[68, 69] upregulation in ccRCC [70, 71, 72] and correlates with poor survival and higher tumor grade [73, 74]. _SOX2_, upregulated by HIF-1, enhances pro-inflammatory signaling and cancer stem cell-like properties, contributing to therapy resistance [75, 76, 77] with poorer overall survival (Figure 8E). In ccRCC, the NF-\(\kappa\)B pathway mediates cytokines and chemokines [78, 79, 80, 55, 81, 82]. Loss of _VHL_ amplifies NF-\(\kappa\)B activation, thus upregulating _BCL2_[14, 79, 80]. _BCL2_ upregulated in the brown and red modules showed that it is associated with better survival and reduced risk of death and recurrence in kidney cancer (Figure 8A), establishing its role as potential marker. Venetoclax, a _BCL2_ inhibitor, was found to be effective in cancers such as leukemia, but continuous use of this agent can lead to drug resistance [83, 84]. _ATM_ enhances NF-\(\kappa\)B, and its expression level could serve as a biomarker for ccRCC [65, 85]. _ATM_ is also involved in resistance to radio- and chemo-therapeutic treatments [65].  
Figure 10: KEGG pathways associated with ccRCC. Arrows indicate that the specific signaling pathways are present at a certain stage.  
Upreguated \(SRC\) was found in the brown and red modules. Studies suggest that targeting \(SRC\) may disrupt pathways in ccRCC [66; 86]. Chemokine can also activate the RAS signaling pathway. Cytokine-based therapies and immune checkpoint inhibitors are being developed to target chemokine signaling to address cancer cells immunity and address their resistance [87; 88; 89; 90; 91]. The Hippo pathway, linked with RCC [52], involves _SMAD3_[53; 92]. SMAD3 activates inflammation and interacts with Hippo effector YAP/TAZ [14; 93]. SMAD3 also showed good survival analysis with reduced risk of death and recurrence (Figure 8D), thus targeting _SMAD3_ in Hippo may effectively inhibit ccRCC [47; 59].  
The MAPK pathway, often activated in cancer [94], upregulates _MAPK1_ and _MAPK8_[95; 96] found in the blue and red modules. The survival analysis also indicated that high levels of _MAPK1_ and _MAPK8_ are associated with better survival outcomes (Figure 8E,F). Research shows that downregulated MYPT1 in ccRCC inhibits _MAPK8_ activation, reducing metastasis [97]. The PI3K-Akt pathway regulates genes such as the upregulated GSK3B found in the red and brown modules. This pathway is frequently dysregulated in RCC since it interacts with the VHL/HIF [98; 99; 100], and a study found that targeting PI3K/Akt, along with its component, with inhibitors like LY294002 and wortmannin reduces inhibit RCC [101]. Overall, these pathways and genes are found to be associated with RCC [17; 100].