The lncRNA PACER Regulates Lung Adenocarcinoma Phenotypes via COX-2 Signaling and RNA Structural Dynamics

Long noncoding RNAs (lncRNAs) are a class of regulatory RNAs with critical roles in cellular homeostasis and disease pathogenesis, including cancer. Dysregulated lncRNA expression in lung adenocarcinoma (LUAD) contributes to oncogenic mechanisms through immune and inflammatory signaling networks, including the arachidonic acid (AA) signaling pathway. Here, we investigate the functional significance of the lncRNA PACER (PTGS2 Antisense NF-κB1 Complex-Mediated Expression Regulator), which modulates cyclooxygenase-2 (COX-2), a key enzyme in the AA pathway. Using stable shRNA-mediated knockdown in A549 LUAD cells, we show that PACER silencing reduces COX-2 expression and impairs cellular proliferation, migration, and invasion. Bioinformatic analysis using LncLOOM revealed conserved motifs across primates and mice, including predicted binding sites for miR-18a-5p, miR-196-5p, miR-1306-5p, and miR-423-3p. To define PACER's structural organization, we performed selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP), generating the first secondary structure determination of PACER. SHAPE-MaP and SuperFold analyses revealed a compact, stabilized 5' domain and a flexible central and 3' region. ΔSHAPE analysis identified multiple sites of differential protection, and Rsample clustering resolved two dominant in vivo conformations, suggesting that PACER adopts a modular architecture with defined structural domains. These structured regions coincide with conserved motifs associated with NF-κB p50 and predicted miRNA binding sites, indicating that PACER function may depend on conformational switching that modulates protein and miRNA accessibility. Together, these findings establish PACER as a regulator of LUAD proliferation and invasion via COX-2 signaling and highlight its potential as a biomarker and therapeutic target in inflammatory cancers.