Supplementary Tables S1-S10 shows: 1) All the coding region variants (missense, premature stop codon, frameshift) of 21 sequenced somatotropinomas that passed the somatic filtering. 2) Results of correlation tests between genetic instability (GI%) and clinical variables. 3) Differentially expressed transcripts (FDR {less than or equal to} 5%, FC -2 {greater than or equal to} x {greater than or equal to} 2) in CA- and CS-tumors. 4) Significantly enriched canonical pathways carried out from differentially expressed genes (FDR < 5% and |FC|>2; CA- vs CS-tumors). 5) Immunostaining intensities of total- and phosphorylated-RB1 in CA- and CS-tumors. 6) CpG quality statistics. 7) Replication timing and CpG methylation. 8) Differentially methylated regions (DMRs) between Gsp+ versus Gsp- tumors, and nearby genes. 9) Integration of DMRs with matched transcriptomes by expression quantitative trait methylation (eQTM) analysis (at 5% FDR). 10) The complete list of significantly (p< 0.05) enriched cis-eQTM pathways.
ARTICLE ABSTRACT
Somatic driver mechanisms of pituitary adenoma pathogenesis have remained incompletely characterized; apart from mutations in the stimulatory Gα protein (Gαs encoded by GNAS) causing activated cAMP synthesis, pathogenic variants are rarely found in growth hormone–secreting pituitary tumors (somatotropinomas). The purpose of the current work was to clarify how genetic and epigenetic alterations contribute to the development of somatotropinomas by conducting an integrated copy number alteration, whole-genome and bisulfite sequencing, and transcriptome analysis of 21 tumors. Somatic mutation burden was low, but somatotropinomas formed two subtypes associated with distinct aneuploidy rates and unique transcription profiles. Tumors with recurrent chromosome aneuploidy (CA) were GNAS mutation negative (Gsp−). The chromosome stable (CS) –group contained Gsp+ somatotropinomas and two totally aneuploidy-free Gsp− tumors. Genes related to the mitotic G1–S-checkpoint transition were differentially expressed in CA- and CS-tumors, indicating difference in mitotic progression. Also, pituitary tumor transforming gene 1 (PTTG1), a regulator of sister chromatid segregation, showed abundant expression in CA-tumors. Moreover, somatotropinomas displayed distinct Gsp genotype–specific methylation profiles and expression quantitative methylation (eQTM) analysis revealed that inhibitory Gα (Gαi) signaling is activated in Gsp+ tumors. These findings suggest that aneuploidy through modulated driver pathways may be a causative mechanism for tumorigenesis in Gsp− somatotropinomas, whereas Gsp+ tumors with constitutively activated cAMP synthesis seem to be characterized by DNA methylation activated Gαi signaling.
These findings provide valuable new information about subtype-specific pituitary tumorigenesis and may help to elucidate the mechanisms of aneuploidy also in other tumor types.
