Multi-Transcriptomics Analysis Identifies NNAT as a Key Molecule Driving the Invasive Phenotype Across All Lineages of Pituitary Adenomas

Abstract Background Although histologically benign, invasive pituitary adenomas exhibit malignant-like biological behavior, characterized by local invasiveness and high proliferative activity. Clinical management remains challenging due to the absence of effective targeted therapies, difficulties with surgical resection, and high risks of postoperative residual disease and recurrence. Precise therapeutic targets are urgently needed. Methods To investigate molecular mechanisms underlying pituitary adenoma invasion and identify potential therapeutic targets, we collected 216 whole transcriptome sequencing datasets representing all pituitary adenoma lineages, along with several single-cell transcriptome datasets. The Scissor algorithm was utilized to identify invasion-associated cell subpopulations. Single-cell weighted gene co-expression network analysis delineated the underlying gene regulatory network. Differential gene expression and pathway enrichment analyses explored NNAT–MAPK contributions to pituitary adenoma invasion. Findings were validated through in vitro and in vivo experiments (quantitative polymerase chain reaction, CCK-8, colony formation, Transwell assays, western blotting, immunohistochemistry, and multiplex immunofluorescence). Results Multi-transcriptomics analysis comprehensively characterized the transcriptomic landscape of invasive pituitary adenomas and revealed active RNA interactions within these tumors, particularly between mRNAs and long non-coding RNAs. Specific cell subpopulations associated with invasiveness were confirmed at the single-cell level. Analysis of phenotype-associated gene regulatory networks within these subpopulations identified the NNAT–MAPK–p38 axis, which promotes epithelial–mesenchymal transition in pituitary adenoma cells and drives invasion. Conclusion These findings enhance understanding of the mechanisms underlying pituitary adenoma invasiveness and identify NNAT as a candidate for targeted therapy development, offering potential precision treatment strategies for patients resistant to conventional therapies or experiencing recurrent disease after surgery.