Saha Pritha, Ravanan Palaniyandi, Talwar Priti
Apoptosis and Cell Survival Research Laboratory, 412G Pearl Research Park, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
Functional Genomics Laboratory, Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, 610005, India.
Biol Direct. 2025 Jun 11;20(1):68. doi: 10.1186/s13062-025-00654-7.
As members of the nuclear receptor (NR) family of transcription factors, peroxisome proliferator-activated receptors (PPARs) regulate essential cellular processes, including lipid metabolism, glucose uptake, cell proliferation, and programmed cell death through ligand-mediated activation. Within the PPAR subfamilies, PPAR-γ (PPARG) is crucial to the development of fat cells, sensitivity to insulin, apoptosis, and metastasis. Furthermore, it demonstrates properties that counteract fibrosis and inflammation, thus establishing itself as a notable target for therapeutic interventions against conditions such as type 2 diabetes and cancer. PPARG is reported to be a promising target for patients diagnosed with colorectal cancer (CRC). Globally, colorectal cancer ranks as the third most prevalent malignancy and is responsible for approximately 10% of all cancer mortalities, and PPARG is significantly expressed in 70% of the sporadic CRC. In individuals with CRC, the precise function of PPARG remains not entirely comprehended and elucidation of the PPARG transcriptional regulation in CRC seems promising.
This study integrates RNA-seq and ChIP-seq reads to analyze the effects of Rosiglitazone on HT-29 colon cancer cells. Peak calling analysis from ChIP-seq data identified 14,000 to 34,000 binding sites for PPARG across different experimental conditions. RNA-seq analysis highlighted significant differential gene expression in Rosiglitazone-treated cells, with 4362 and 6780 genes significantly regulated at 24 and 48 h, respectively. The correlation of these datasets with PPRE-associated kinases resulted in the identification of 18 differentially expressed genes (DEGs), followed by subsequent analysis of gene ontology, pathway enrichment, and protein-protein interactions, culminating in the elucidation of seven hub genes (PTK2, HGS, CDK8, PRPF6, PRKDC, PRKCZ, MET). Further these hub genes correlated with CRC progression and patient survival. Validation using independent GEO datasets (GSE113513 and GSE210693) and gene effect scores derived from CRISPR knockout screens further supported the functional impact of these hub genes. Disease ontology and mutational analyses implicated the hub genes in various cancers, including CRC. Moreover, miRNA analysis identified 37 experimentally validated miRNAs potentially modulating hub gene expression.
These findings advance our understanding of PPARG's regulatory network and underscore its potential as a therapeutic target, establishing a robust framework for future research in PPARG-related pathways.
作为核受体（NR）转录因子家族的成员，过氧化物酶体增殖物激活受体（PPARs）通过配体介导的激活作用调节包括脂质代谢、葡萄糖摄取、细胞增殖和程序性细胞死亡在内的重要细胞过程。在PPAR亚家族中，PPAR-γ（PPARG）对脂肪细胞的发育、胰岛素敏感性、细胞凋亡和转移至关重要。此外，它还具有对抗纤维化和炎症的特性，因此成为针对2型糖尿病和癌症等疾病进行治疗干预的显著靶点。据报道，PPARG是诊断为结直肠癌（CRC）患者的一个有前景的靶点。在全球范围内，结直肠癌是第三大最常见的恶性肿瘤，约占所有癌症死亡人数的10%，并且在70%的散发性CRC中PPARG有显著表达。在CRC患者中，PPARG的确切功能仍未完全理解，阐明CRC中PPARG的转录调控似乎很有前景。
本研究整合了RNA测序和染色质免疫沉淀测序（ChIP-seq）读数，以分析罗格列酮对HT-29结肠癌细胞的影响。ChIP-seq数据的峰检测分析在不同实验条件下确定了PPARG的14,000至34,000个结合位点。RNA测序分析突出了罗格列酮处理细胞中显著的差异基因表达，分别在24小时和48小时有4362个和6780个基因受到显著调控。这些数据集与PPRE相关激酶的相关性导致鉴定出18个差异表达基因（DEGs），随后进行基因本体论、通路富集和蛋白质-蛋白质相互作用分析，最终阐明了7个核心基因（PTK2、HGS、CDK8、PRPF6、PRKDC、PRKCZ、MET）。此外，这些核心基因与CRC进展和患者生存相关。使用独立的基因表达综合数据库（GEO）数据集（GSE113513和GSE210693）以及来自CRISPR基因敲除筛选的基因效应评分进行验证，进一步支持了这些核心基因的功能影响。疾病本体论和突变分析表明这些核心基因与包括CRC在内的各种癌症有关。此外，miRNA分析鉴定出37个经实验验证的可能调节核心基因表达的miRNA。
这些发现推进了我们对PPARG调控网络的理解，并强调了其作为治疗靶点的潜力，为未来PPARG相关通路的研究建立了一个强大的框架。
