Integrating methylome and transcriptome signatures expands the molecular classification of the pituitary tumors

Purpose: To explore pituitary tumors by methylome and transcriptome signatures in a heterogeneous ethnic population. 

Design: Retrospective cross-sectional study.

Patients and Methods: Clinicopathological features, methylome, and transcriptome were evaluated in pituitary tumors from 77 patients (61% women, age: 12-72 years)followed due to functioning (FPT: GH-secreting n=18, ACTH-secreting n=14) and non-functioning pituitary tumors (NFPT, n=45) at Ribeirao Preto Medical School, University of Sao Paulo. 

Results: Unsupervised hierarchical clustering analysis (UHCA) of methylome (n=77) and transcriptome (n=65 out of 77) revealed three clusters each: one enriched by FPT, other by NFPT, and another by ACTH-secreting and NFPT. Comparison between each omics-derived cluster identified 3,568 and 5,994 differentially methylated and expressed genes, respectively, which were associated with each other, with tumor clinical presentation, and with 2017 and 2022 WHO classifications. UHCA considering 11 transcripts related to pituitary development/differentiation also supported three clusters: POU1F1-driven somatotroph, TBX19-driven corticotroph, and NR5A1-driven gonadotroph adenomas, with rare exceptions (NR5A1 expressed in few GH-secreting and corticotroph-silent adenomas; POU1F1 in few ACTH-secreting adenomas; and TBX19 in few NFPTs). 

Conclusions: This large heterogenic ethnic Brazilian cohort confirms that integrated methylome and transcriptome signatures classify FPT and NFPT, which are associated with clinical presentation and tumor invasiveness. Moreover, the cluster NFPT/ACTH-secreting adenomas raises interest regarding tumor heterogeneity, supporting the challenge raised by the 2017 and 2022 WHO definitions regarding the discrepancy, in rare cases, between clinical presentation and pituitary lineage markers. Finally, making our data publicly available enables further studies to validate genes/pathways involved in pituitary tumor pathogenesis and prognosis.