{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE316nnn/GSE316513/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Homo sapiens"],"gds_type":["Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE316513"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptomic profiling of PTX4 overexpression in THP-1 cells","description":"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.","dates":{"publication":"2026/06/01"},"accession":"GSE316513","cross_references":{"GSM":["GSM9455117","GSM9455116","GSM9455115","GSM9455119","GSM9455118","GSM9455120"],"GPL":["24676"],"GSE":["316513"],"taxon":["Homo sapiens"]}}