Abstract A11: Serum cell-free DNA methylome-based signatures distinguish pituitary tumor from other neoplasias and by clinicopathologic features

Background: Several reports have indicated that distinct epigenomic patterns of pituitary tumor (PT) tissue, specifically DNA methylation, distinguish these tumors according to their functionality and could be involved in their pathogenesis. Thus far, molecular diagnosis and classification systems that guide clinical management of these tumors rely on the tissue profiling obtained by invasive surgical approaches (e.g., excision). However, increasing evidence showed that CNS tumors release cell material into the circulation, despite the existence of the blood-brain barrier, creating an opportunity for molecular profiling using a liquid biopsy. Although the pituitary portal system and the invasion of the cavernous system by PT may facilitate the spillage of tumor cell material into the bloodstream, until now liquid biopsy has not been described in pituitary tumors. Considering the stability, the cell specificity, and the reported role of DNA methylation in PT, we investigated the feasibility to detect and define PT-specific methylation-based signatures in the serum of patients harboring these tumors. Methods and Findings: In order to identify PT-specific methylation-based signatures in the serum of patients with PT, we conducted unsupervised and supervised analysis of the methylome profile of paired serum cfDNA (EPIC array) and/or tissue from 13 patients with pituitary macroadenomas (9 males; median age: 62; 9 nonfunctioning/4 functioning, 6 invasive/7 noninvasive), 4 controls serum (nontumor and healthy), and patients with other CNS tumors or conditions (114 gliomas, 6 meningiomas, 1 brain metastasis, 1 colloid cyst, 6 radiation necrosis). Serum PT-tissue-specific methylation was also used as input into a machine learning algorithm to generate a PT score, which was tested in an independent cohort. Unsupervised and supervised analysis indicated that the serum methylome from patients harboring PT was distinct from controls and other CNS diseases. A generated PT score using the 37 identified PT tissue-specific methylation probes was able to distinguish serum from patients harboring PT from other CNS tumors. Serum-derived PT function-specific DMP also distinguished PT according to functional status. Serum-derived invasive-specific DMPs were less prominent to define invasive status in an independent cohort of PT, most probably due to the limited number of cases. Conclusion: This is the first study to show the feasibility of profiling methylome in the serum of patients with PT using cfDNA. In addition, we identified unique methylation signatures that distinguished PT from other CNS tumors and according to distinct PT subtypes. These results underpin the potential role of methylation profile and liquid biopsy as a noninvasive approach to assess clinically relevant molecular features that can be used as diagnostic, prognostic, and surveillance in patients with PT. Citation Format: Michael Wells, Karam Asmaro, Jack Rock, Thais Sabedot, Maritza Mosella, Tathiane Malta, Kevin Nelson, James Snyder, Steven Kalkanis, Ana Valeria Castro, Houtan Noushmehr. Serum cell-free DNA methylome-based signatures distinguish pituitary tumor from other neoplasias and by clinicopathologic features [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A11.