Identification of PPREs and PPRE associated genes in the human genome: insights into related kinases and disease implications

Abstract

Introduction: "Peroxisome Proliferator-Activated Receptors" (PPARs) belong to the class of transcription factors (TF) identified as Nuclear Receptors (NR). Upon activation by peroxisome proliferators (PPs), PPARs modulate a diverse range of genes, consequently regulating intra-cellular lipid metabolism, glucose uptake, apoptosis, and cell proliferation. Subsequent to the heterodimerization of Retinoid X Receptors (RXR) with PPARs induced by the binding of activators to PPARs, facilitates the binding of the resulting complex to Peroxisome Proliferator-Activated Receptors Response Elements (PPRE), with a consensus sequence 5'AGGTCANAGGTCA-3', and regulate the transcription of the targeted genes.

Methods: A comprehensive screening of PPRE within the whole human genome was performed using the Genome Workbench and UCSC Genome Browser to find the associated genes. Subsequently, the kinase subset was isolated from the extracted list of PPRE-related genes. Functional enrichment of the kinases was performed using FunRich, ToppGene, and ShinyGO. Network analysis and enrichment studies were then further performed using NDEx to elucidate these identified kinases' connections and significance. Additionally, the disease association of the PPRE kinases was analyzed using DisGeNET data in R studio and the COSMIC dataset.

Results: A comprehensive analysis of 1002 PPRE sequences within the human genome (T2T), yielded the identification of 660 associated genes, including 29 kinases. The engagement of these kinases in various biological pathways, such as apoptosis, platelet activation, and cytokine pathways, revealed from the functional enrichment analysis, illuminates the multifaceted role of PPAR in the regulation of cellular homeostasis and biological processes. Network analysis reveals the kinases interact with approximately 5.56% of the Human Integrated Protein-Protein Interaction rEference (HIPPIE) network. Disease association analysis using DisGeNET and COSMIC datasets revealed the significant roles of these kinases in cellular processes and disease modulation.

Discussion: This study elucidates the regulatory role of PPAR-associated genes and their association with numerous biological pathways. The involvement of the kinases with disease-related pathways highlights new potential for the development of therapeutic strategies designed for disease management and intervention.

Keywords: UCSC genome browser; genome workbench; kinase; network analysis; peroxisome proliferator activated receptor response element; protein protein interaction.

Figure 1

PPARs are ligand-induced transcription factors of nuclear hormone receptor superfamily. PPAR binds to the 13bp conserved sequence, PPRE as a conjugate with the RXR, and can recruit coactivator or corepressor proteins to mediate the gene expression of lipid metabolism, glucose homeostasis, inflammation, and apoptosis regulators. (PPARs, “Peroxisome proliferator-activated receptors”; PPRE, PPAR response element; RXR, “Retinoid X Receptor”).

Figure 2

The overall workflow of the study is represented as a flowchart.

Figure 3

High confidence interactions (confidence score ≥ 0.7) of the PPRE-associated kinases with human PPI (HIPPIE- Human Scored Interactions database) revealed their ability to regulate 5.56% of human PPI. The query kinases are highlighted: green- PPRE-associated kinases; red- hub genes (kinases) within the network.

Figure 4

Distributional analysis of key proteins across human tissues. (A) 85.7% of genes are expressed in plasma and testis and 82.1% of the genes are predominantly expressed in the lung. The genes are also significantly expressed in liver, human umbilical vein endothelial cells (HUVEC), liver, and kidney. (B) Heatmap of gene expression levels across various fetal and adult tissues, as well as specific cell types (Green represents lower expression, red indicates higher expression): PRKDC is highly expressed in all tissues except platelets, and KALRN is significantly expressed in adult heart and platelets. HGS and PRPF6 show relatively higher expression in adult gallbladder and prostate. In the lung, a significant expression of PRPF6 is observed. In contrast, genes like FAM47E, CERKL, SIK3, PFKFB4, MAP3K6, AKAP14 and MOB3C exhibit low expression in most tissues. Noteworthy patterns include MYLK2 being highly expressed in the adult heart, adult gallbladder, esophagus and colon, while PDK2 and STK24 are strongly expressed in the adult kidney, and STK24 additionally in the esophagus, colon, urinary bladder, prostate, and platelets. HGS is also strongly expressed in the adult frontal cortex, spinal cord, gallbladder, kidney, colon, urinary bladder, prostate and PRPF6 is highly expressed in adult testis, lung, adrenal gland, gallbladder, pancreas esophagus, colon, prostate and placenta. Lastly, SPEG is highly expressed in adult heart and gallbladder, and PTK2 is in adult colon, urinary bladder and platelets.

Figure 5

(A) Protein domain analysis of the key proteins reveals serine/threonine kinase domain and coiled-coil region is ubiquitously present in our query hits. Other protein domains like Tyrosine kinase C, FN3, IGc2, and SH3 domains are also observed among the kinases. (B) PPARG (46.2%), PPARA (26.9%), SP1 (53.8%), and HNF4A (46.2%) are predominant transcription factors regulating PPRE kinases.

Figure 6

Gene ontology analysis and functional enrichment of the hits. (A) GO: BP analysis of hits reveals the high association of the genes with protein phosphorylation and tyrosine kinase signaling pathway. (B) GO: MF analysis of the hits exhibits ATP binding activity, adenyl ribonucleotide binding activity, and phosphotransferase activity. (C) Molecular function analysis using FunRich reveals 37% of the genes are associated with protein serine/threonine kinase activity and 11.1% possess lipid kinase activity.

Figure 7

FunRich analysis of biological pathways of the key Proteins. The kinases are highly significant in mediating VEGFR, IL-3, PDGF, GMCSF, IL-5, IFN-γ, and TGF-β pathways. The hits are also associated with apoptosis, platelet activation, CDC42 signaling pathway.

Figure 8

Disease association of the hits. (A) A heatmap of top GDA>0.3 was created using R studio. Based on GDA score a significant association of MET with liver and papillary liver cell carcinoma is observed. (B) FunRich analysis of the COSMIC dataset reveals the somatic mutations of the hits to be highly associated with cancer of the large intestine, lung, central nervous system, kidney, liver, breast, ovary, pancreas, urinary tract, and thyroid.