Single-Cell Transcriptome Profiling Reveals Cellular Programs Associated with Growth and Clinical Behavior in Nonfunctioning Pituitary Neuroendocrine Tumors

Introduction: Nonfunctioning pituitary neuroendocrine tumors (NF-PitNETs) are the most common pituitary tumors requiring surgery. Although hormonally silent, they often cause mass effects, recur and may grow aggressively. Current pathology and imaging fail to predict which tumors will progress, and no medical therapies exist. Single-cell technologies now enable high-resolution analysis of tumor biology and may reveal molecular predictors of clinical behavior. Aims: We aimed to define the cellular programs that drive growth potential and clinical silence in NF-PitNETs using single-cell profiling, and to establish a foundation for prognostic tools and therapeutic targets. Methods: Single-nucleus RNA-seq was performed on eight fresh frozen NF-PitNETs (4 invasive, 4 noninvasive; 7 SF1 positive, 1 TPIT positive macroadenomas). Single-nucleus transcriptome data from non-tumor pituitary was retrieved from public repositories. Tumor and non-tumor compartments were separated using copy number inference and established lineage markers. Clustering and subsequent gene-based expression program analyses uncovered programs linked to invasiveness, recurrence, proliferative indices, and radiographic mass effect. Results: Analysis revealed four conserved gene expression programs associated with clinical features. Excitability and developmental plasticity programs were frequent but uncoupled from secretion, explaining clinical silence. Tumors enriched for enhanced developmental and adhesion mechanisms were associated with higher proliferative indices and invasiveness, consistent with more aggressive growth. The silent corticotroph tumor separated clearly from normal pituitary tissue and from all gonadotroph tumors which clustered together. In addition to presenting secretory pathways with lack of excitability signals explaining its nonfunctioning status, it presented a distinct program enrichment with focus in adhesion dynamics which could predispose to growth ability, although at diagnosis the tumor was still noninvasive (Knosp grade 1). Discussion/Conclusion: NF-PitNETs, while silent, are biologically active and shaped by transcriptional programs which align with growth propensity and secretory ability. These programs carry prognostic potential which are invisible to conventional pathology. These results provide an initial framework for linking tumor biology to clinical behavior, which future studies may refine into prognostic tools and therapeutic targets. Publication History Article published online: 27 February 2026 © 2026. Thieme. All rights reserved. Georg Thieme Verlag KG Oswald-Hesse-Straße 50, 70469 Stuttgart, Germany