PGM5P4-AS1 suppresses breast cancer progression and CD8⁺ T cell dysfunction through UPF1-mediated PTK2 mRNA decay

Protein tyrosine kinase 2 (PTK2) is a critical oncogenic that contributes to breast cancer progression and CD8⁺ T cell dysfunction. However, the post-transcriptional regulatory mechanisms of PTK2, particularly those mediated by long non-coding RNAs (lncRNAs), remain incompletely characterized. This study aimed to identify lncRNAs that regulate PTK2 and to elucidate functional and molecular mechanisms of lncRNA in breast cancer. Through mining and analysis of the Cancer Genome Atlas (TCGA) database, we identified a key lncRNA associated with both PTK2 expression levels and patient prognosis, and validated its expression via quantitative real-time polymerase chain reaction (RT-qPCR) in 50 pairs of matched breast cancer tissues and multiple cell lines. Subsequently, the biological functions of PGM5P4-AS1/PTK2 axis were evaluated using gain- and loss-of-function assays in vitro (CCK-8, colony formation, wound healing, Transwell invasion, and Transwell co-culture assays) and in vivo by nude mouse xenograft models. Finally, the molecular mechanisms underlying PGM5P4-AS1-mediated regulation of PTK2 and PGM5P4-AS1 dysregulation in breast cancer were investigated using RNA pull-down, RNA immunoprecipitation (RIP), deletion mapping, chromatin immunoprecipitation (ChIP), dual-luciferase reporter, and actinomycin D stability assays. PGM5P4-AS1 was identified as a critical negative regulator of PTK2. PGM5P4-AS1 was significantly downregulated in breast cancer tissues and cell lines, and low PGM5P4-AS1 expression was markedly associated with reduced overall survival and disease-free survival in breast cancer patients. Functionally, PGM5P4-AS1 suppressed triple negative breast cancer (TNBC) cell proliferation, colony formation, migration, invasion, epithelial-mesenchymal transition (EMT), and alleviated CD8⁺ T cell dysfunction, and these effects were abrogated by PTK2 overexpression. Mechanistically, PGM5P4-AS1, predominantly localized in the cytoplasm, directly interacts with the RNA helicase UPF1 through its 145-377nt region, thereby facilitating the recruitment of UPF1 to PTK2 mRNA and promoting UPF1-dependent PTK2 mRNA decay. Furthermore, the transcription factor TFAP2A, which is aberrantly overexpressed in breast cancer, specifically bound to the -230 to -238 bp region of the PGM5P4-AS1 promoter and recruited histone deacetylase HDAC2, leading to reduced H3K27 acetylation (H3K27ac) and transcriptional repression of PGM5P4-AS1. Our study uncovers that TFAP2A/HDAC2-mediated transcriptional repression of PGM5P4-AS1 alleviates UPF1-dependent PTK2 mRNA decay, thereby promoting TNBC progression and CD8⁺ T cell dysfunction. These findings delineate a novel epigenetic regulatory cascade in TNBC, thereby nominating its targeting as a potential therapeutic strategy and providing a theoretical foundation for developing therapies targeting the PTK2 signaling pathway.