Dataset Information

Comprehensive constitutional genetic and epigenetic characterization of Lynch-like individuals

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE128068 | GEO | 2019/03/09

REPOSITORIES: GEO

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Project description:Pituicytoma (PITUI), granular cell tumor (GCT), and spindle cell oncocytoma (SCO) are rare tumors of the posterior pituitary lobe. Histologically, they may be challenging to distinguish and have been proposed to represent a histological spectrum of a single entity. We performed targeted next-generation sequencing, DNA methylation profiling, and copy number analysis on 47 tumors (14 PITUI; 12 GCT; 21 SCO) to investigate molecular features and explore possibilities of clinically meaningful tumor subclassification. We detected two main epigenomic subgroups by unsupervised clustering of DNA methylation data, though the overall methylation differences were subtle. The largest group (n=23) contained most PITUIs and a subset of SCOs and was enriched for pathogenic mutations within genes in the MAPK/PI3K pathways (12/17 [71%] of sequenced tumors: FGFR1 (3), HRAS (3), BRAF (2), NF1 (2), CBL (1), MAP2K2 (1), PTEN (1)) and two with TERT promoter mutation. The second group (n=16) contained most GCTs and a subset of SCOs, which mostly lacked identifiable genetic drivers. Outcome analysis demonstrated that the presence of chromosomal imbalances is significantly associated with reduced progression-free survival especially within the combined PITUI and SCO group (p= 0.031). In summary, we observed only subtle DNA methylation differences between posterior pituitary tumors, indicating that these tumors may be best classified as subtypes of a single entity. Nevertheless, our data indicate differences in mutation patterns and clinical outcome. For a clinically meaningful subclassification, we propose a combined histo-molecular approach into three subtypes: One subtype is defined by granular cell histology, has low mutation rates and favorable outcome. The other two subtypes have SCO or PITUI histology but are separated by chromosomal copy number profile into a favorable group (no copy number changes) and a less favorable group (copy number imbalances present). Both of the latter groups have recurrent MAPK alterations that represent potential therapeutic targets.

Dataset Information

Comprehensive constitutional genetic and epigenetic characterization of Lynch-like individuals

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