Type-2 diabetes (T2D) and pancreatic cancer (PC) can stimulate each other in a bidirectional manner [10–12]. Therefore, in this study, we attempted to discover shared key genomic biomarkers (sKGBs) and their common mechanisms in the development and progression of both PC and T2D, and associated drug molecules. At first, we identified 52 shared DEGs (sDEGs) that can differentiate both T2D and PC from the control samples by using a statistically robust BRIDGE approach. The PPI network analysis of all sDEGs identified six upregulated sDEGs (GAPDH, CASP1, MYD88, TNFRSF1A, TIMP1, and TNFSF10) as the PC and T2D causing sKGBs (Fig. 3& Table S7) for exploring shared pathogenetic processes and candidate therapeutic agents. To verify the association of sKGBs with both T2D and PC by the independent database, we performed disease-gene enrichment analysis by using the GeneCodis web-tool [34] based DisGeNET database [46] and found their significant (p-value < 0.03 ) association (Table S8). The Random Forest (RF) based prediction model with the expressions of sKGBs can significantly classify both diseases from control samples. This model has a strong predictive ability (AUC > 0.91 and ACC > 0.83) for both diseases, confirming the significance of sKGBs in disease classification (Fig. 4, Table S9). The box-plots analysis with TCGA and GTEx data [31] showed that sKGBs are significantly upregulated in PC compare to the control groups, which supported the upregulation properties of sKGBs (Figure S3). Our proposed sKGBs has also received support as both T2D and PC-causing genes, jointly by some other individual studies (Fig. 7A). Among the sKGBs, Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a versatile protein involved in glycolysis and mRNA stability regulation. It is a potential target for cancer treatment due to its up-regulation in cancer cells [47]. Mutant p53 stabilizes GAPDH, promoting glycolysis in PC cells [48]. GAPDH is also used as a reference gene to assess relative gene expression in PBMCs of individuals with T2D [49]. The CASP1 (Caspase-1) is a key regulator of inflammation and cell death [50] and is overexpressed in the cytoplasm of PC cells, chronic pancreatitis, and tumor-surrounding tissues [51, 52]. The activation of CASP1 controls insulin sensitivity [53] and is involved with chronic inflammation in T2D [54]. The MYD88 gene is involved in immune cell signaling and is essential for inflammation in PC [55, 56]. Hepatocyte-specific deletion of MYD88 affects glucose and lipid metabolism, increasing the risk of developing T2D [57, 58]. The genes TNFRSF1A and TNFSF10 are members of the tumor necrosis factor (TNF) family that are well-known for their roles in promoting fibrosis and inducing apoptosis effects [59]. TNFSF10 promotes cell survival, reduces leukocyte adhesion, and increases glucose levels in T2D [60, 61]. It is also included in a novel risk model consisting of five genes, which is significantly associated with survival in PC patients [62]. TNFRSF1A has shown potential as a blood-based protein biomarker for early-stage PC and may also contribute to insulin resistance and metabolic syndrome [63, 64]. Elevated TIMP1 (Tissue inhibitor of metalloproteinases-1) levels are implicated in the development of T2D through non-liver fibrosis pathways [65], and they are also associated with diabetic retinopathy progression in T2D [66]. It shows prognostic and diagnostic value in PC, correlating with desmoplasia, and tumor cell de-differentiation [67–69].
We explored the shared pathogenetic process of PC and T2D by investigating the sKGBs-set enrichment analysis, an association of sKGBs with the different immune infiltration levels, DNA-methylation, and regulatory analysis of sKGBs with the use of various databases. We employed enrichment analysis of sKGBs-set and explored crucial biological processes (BP), molecular functions (MF) and KEGG pathways that are associated with the development of T2D and PC (Table 2). The significantly enriched T2D and PC- causing crucial BP, MF and KEGG pathways were, NF-kappaB (NF-κB) signaling, cytokine-mediated signaling pathway, regulation of inflammatory response, apoptotic process, and positive regulation of interleukin-1 beta (IL-1β) production, tumor necrosis factor (TNF) binding, Toll-like receptor binding, Lipid and atherosclerosis, and HIF-1 signaling pathway, etc. Among them, NF-κB signaling pathway can be activated by various stimuli, such as cytokines (TNFα, IL-1β, IL-6), growth factors, bacterial and viral products, as well as DNA damage and oncogenic stress within cells. These diverse stimuli ultimately lead to the activation of IκB kinase (IKK), which phosphorylates and degrades IκB. Subsequently, NF-κB translocates to the nucleus, binds to DNA, and activates its target genes. Dysregulation of this pathway has been observed in multiple diseases, including PC and T2D [70–72]. Inflammation triggers the activation and recruitment of immune cells, which produce cytokines that contribute to the initiation and development of PC [73]. Elevated levels of inflammatory factors such as IL-1β, IL-6, and chemokines (released by adipose tissue, liver, and pancreatic islets) can serve as predictive markers for the development of T2D [74–76]. Apoptosis, or programmed cell death, is one of the significant biological process in both PC and T2D. Alterations in the expression and mutations of apoptotic proteins are commonly observed in PC cells, promoting tumor progression [77, 78]. Similarly, apoptosis plays a crucial role in the pathophysiology of T2D, specifically in the loss of β-cell mass [79]. Toll-like receptors (TLRs), a type of pattern recognition receptor, play a crucial role in activating pro-inflammatory pathways and creating a favorable microenvironment for PC growth [80, 81]. TLR2 may have suppressive roles in immune responses and could be implicated in the pathogenesis of immune-related diseases like T2D [82, 83]. Additionally, Dysregulation of lipid metabolism contributes to various metabolic diseases, including PC and T2D [84–86]. The Hypoxia-inducible factor 1 (HIF-1) has an emerged role in PC metastasis [87]. HIF-1α, a subunit of HIF-1, triggers the secretion of the Sonic hedgehog (SHH) ligand, leading to increased activation of Gli proteins and the production of collagen 1 and fibronectin by fibroblasts in PC [88]. In addition to its role in PC, HIFs are implicated in β cell dysfunction and the development of diabetes [89]. Furthermore, we explored survival analysis with the DNA-methylation data. We found that five sKGBs (GAPDH, CASP1, MYD88, TNFRSF1A, and TNFSF10) were significantly (p-value of < 0.05) hypermethylated at different CpG sites (Table 3). These five hypermethylated sKGBs were also involved in the apoptotic process (Table 2). So, it can be said that there is a strong correlation between the survival of apoptotic process and the development and progression of PC by these five hypermethylated sKGBs [90, 91]. We also examined the correlation between the expressions of sKGBs and infiltrates immune cell types in PC. We found that the gene GAPDH has negative and rest five sKGBs have significant positive correlation with the different immune infiltrating cell (Fig. 5 & Table S10). In one study, CASP1 was found to be positively correlated with various immune cell types and associated with a poor prognosis in PC [92]. Also, the GAPDH expression exhibited a negative correlation with immune infiltration, specifically involving cancer-associated fibroblasts, endothelial cells, neutrophil cells [93]. We also identified two important transcription factors (TFAP2A and SP1) and microRNAs (hsa-miR-29c and hsa-miR-22) that regulate the expression of sKGBs and play a crucial role in disease development (Figure S4).
To identify potential drug candidates for the treatment of PC with T2D, we performed molecular docking analysis (Fig. 6& Table S11) and detected eight (out of 327) top-ranked drugs (NVP-BHG712, Irinotecan, Timosaponin AIII, Linsitinib, Gliquidone, Herbacetin, Momordin, and Olaparib) that showed strong binding affinities with the target proteins. We further evaluated the efficacy of the proposed drugs through Drug-Likeness, ADME/T, and DFT analysis. Among the detected eight drugs, six (NVP-BHG712, Irinotecan, Olaparib, Gliquidone, Herbacetin, and Linsitinib) were satisfied at least four parameters of Lipinski's rule of five, indicating their drug-like characteristics (Table S12). The selected six compounds displayed good ADME/T profiles (Table S13), with adequate water solubility, high HIA percentages ranging from 68–99.88%, and no carcinogenic effects. Utilizing DFT, we optimized the FMO of the selected six complexes, including HOMO, LUMO along with the optimized geometry of the metal complexes (Table 4, Figure S5). The studied compound exhibited good chemical stability due to its large energy gap, high ionization potential, low electron affinity, high hardness and low softness. The investigated compound is categorized as a moderate electrophile based on its calculated electrophilicity value [94]. The 3D view of strong binding interactions between top-ranked targets and drugs are given in Table S14. Our proposed candidate drug molecules has also received support as the inhibitors of T2D and PC, jointly by some other independent studies (Fig. 7B). Among the identified candidate drugs, Olaparib and Irinotecan have FDA approval for the treatment of PC with Drug Bank (DB) accession numbers DB09074 and DB00762 respectively [95]. Combining Olaparib with some drugs, including irinotecan, has been reported to play a crucial role in PC treatment [96]. Gliquidone, an FDA-approved anti-diabetic medication in the sulfonylurea class (DB accession numbers DB01251), binds to ATP-sensitive potassium channels in pancreatic beta cells, stimulating insulin release and controlling blood glucose levels [95, 97, 98]. Linsitinib, an investigational cancer drug (DB accession number DB06075), inhibits insulin-like growth factor receptor-1 and has diverse effects on PC growth and metastasis [13, 99]. NVP-BHG712, a kinase inhibitor, has implications in blood circulation, oxygen deficiency, and cancer progression [100]. It is also a specific inhibitor of EphB4 kinase, which may be a therapeutic target for insulin resistance and T2D [101, 102]. NVP-BHG712 has been proposed as a potential therapy for PC [13]. Herbacetin, a natural flavonoid derived from flaxseed, possesses antioxidant, anti-inflammatory, and anticancer properties [103]. Flavonoids, such as Herbacetin, have the potential for diabetes treatment due to their natural properties and no side effects [104, 105]. Molecular docking and metabolomics investigations have demonstrated the efficacy of Herbacetin as a ligand for diabetes treatment [106, 107]. Among the proposed drugs, NVP-BHG712 and Herbacetin are not yet approved and require further evaluation through wet-lab experiments before clinical investigation for the treatment of both T2D and PC.