DNA Methylation-based Signatures Classify Sporadic Pituitary Tumors According to Clinicopathological Features
Authors: Mosella Maritza S. , Sabedot Thais S. , Silva Tiago C. , Malta Tathiane M. , Segato Felipe D. , Asmaro Karam P. , Wells Michael , Mukherjee Abir , Poisson Laila M. , Snyder James , deCarvalho Ana C. , Walbert T Tobias , Aho Todd , Kalkanis Steven , Elias Paula C. , Antonini Sonir R. , Rock Jack , Noushmehr Houtan , Castro Margaret , Castro Ana Valeria 
Published: April 2020

Background

Distinct genome-wide methylation patterns have consistently clustered pituitary neuroendocrine tumors (PT) into molecular groups associated with specific clinicopathological features. Here we aim to identify, characterize and validate the methylation signatures that objectively classify PT into those molecular groups.

Methods

Combiningin-houseand publicly available data, we conducted an analysis of the methylome profile of a comprehensive cohort of 177 tumor and 20 non-tumor specimens from the pituitary gland. We also retrieved methylome data from an independent pituitary tumor (PT) cohort (N=86) to validate our findings.

Results

We identified three methylation clusters associated with functional status and adenohypophyseal cell lineages using an unsupervised approach. We also identified signatures based on differentially methylated CpG probes (DMP), some of which overlapped with pituitary-specific transcription factors genes (SF1 and Tpit), that significantly distinguished pairs of clusters related to functional status and adenohypophyseal cell lineage. These findings were reproduced in an independent cohort, validating these methylation signatures. The DMPs were mainly annotated in enhancer regions associated with pathways and genes involved in cell identity and tumorigenesis.

Conclusions

We identified and validated methylation signatures that distinguished PT by distinct functional status and adenohypophyseal cell lineages. These signatures, annotated in enhancer regions, indicate the importance of these elements in pituitary tumorigenesis. They also provide an unbiased approach to classify pituitary tumors according to the most recent classification recommended by the WHO 2017 using methylation profiling.

Key-points

Distinct methylation landscapes define PT groups with specific functional status/subtypes and adenohypophyseal lineages subtypes.

Methylation abnormalities in each cluster mainly occur in CpG annotated in distal regions overlapping predicted enhancers regions associated with pathways and genes involved in cell identity and tumorigenesis.

DNA methylation signatures provide an unbiased approach to classify PT.

Importance of the study

This study harnessed the largest methylome data to date from a comprehensive cohort of pituitary specimens obtained from four different institutions. We identified and validated methylation signatures that distinguished pituitary tumors into molecular groups that reflect the functionality and adenohypophyseal cell lineages of these tumors. These signatures, mainly located in enhancers, are associated with pathways and genes involved in cell identity and tumorigenesis. Our results show that methylome profiling provides an objective approach to classify PT according to the most recent classification of PT recommended by the 2017 WHO.