Transcriptomic profiling of PTX4 overexpression in THP-1 cells

Our study demonstrated that PTX4 is silenced by promoter hypermethylation in adverse-risk AML patients, and patients with lower PTX4 expression exhibit significantly reduced overall survival. Methylation-specific PCR confirmed PTX4 promoter methylation in multiple AML cell lines including THP-1, and treatment with the demethylating agent 5-azacytidine restored PTX4 expression. To elucidate the molecular mechanisms by which PTX4 exerts its tumor suppressive function, we performed RNA-sequencing analysis of THP-1 cells with stable PTX4 overexpression compared to empty vector controls. Total RNA was extracted from three biological replicates each of THP-1-EV and THP-1-PTX4-OE cells using the RNeasy mini kit (Qiagen). RNA library construction and sequencing were performed by Novogene Singapore using the Illumina NovaSeq 6000 platform with paired-end sequencing. Raw reads were quality-assessed using FastQC v0.11.5, followed by adapter trimming and alignment to the human reference genome (GRCh38/hg38). Pathway analysis demonstrated that PTX4 suppresses oncogenic programs including NF-κB signaling, IL-17 signaling, and Toll-like receptor pathways, while enhancing T cell receptor signaling and MAPK pathways. This dataset provides molecular insights into PTX4-mediated tumor suppression in AML and supports its potential as a therapeutic target through demethylating agents.