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Updated: Jan 9, 2026
Methyl-binding DNA capture Sequencing for Patient Tissues
Published on: October 31, 2016
DNA methylation profiling predicts postsurgical regrowth in SF1-lineage nonfunctioning pituitary neuroendocrine
Morten Winkler Møller1,2, Grayson A Herrgott3, Marianne Skovsager Andersen4
1Department of Neurosurgery, Odense University Hospital (M.W.M., B.H., C.B.P., F.R.P.).
Background:
Nonfunctioning pituitary neuroendocrine tumors (NFPitNETs) account for ∼30-35% of PitNETs; ∼75% arise from the SF1 lineage. Recurrence remains common despite resection (∼30% in 10 years), and routine histopathology/IHC has limited value in predicting recurrence risk. This study evaluated whether DNA methylation profiling improves recurrence risk stratification.
Materials And Methods:
Genome-wide tissue methylation (Illumina EPIC v1, 850K) was analyzed in 117 retrospective NFPitNETs with clinical and imaging follow-up. Unsupervised consensus clustering defined methylation-based subgroups, followed by supervised differential methylation analysis to identify cluster-specific differentially methylated probes (DMPs). A classifier was trained using these signatures, with predicted subgroup memberships correlated with regrowth and progression-free survival (PFS). To ensure reliable estimations, longitudinal mixed-effects models were restricted to the interval of model stability (∼9 years), reflecting cohort follow-up. External validation was performed in 3 independent cohorts.
Results:
Five clusters (k1-k5) emerged: 4 SF1-positive-predominant (k1, k2, k3, and k5) and 1 TPIT/PIT1-enriched NFPitNETs (k4). Among the 562 DMPs, many mapped to genes regulating cell-cycle and immune pathways. Compared with k1-k2, k3, k4, and k5 possessed significantly higher recurrence risk. Within SF1-lineage tumors, k3 exhibited postoperative tumor-volume expansion beginning at ∼6 years. The methylation-based classifier achieved ∼97% accuracy in assigning clusters and maintained prognostic separation across independent cohorts.
Conclusions:
DNA methylation profiling identifies biologically and clinically distinct NFPitNET subgroups, particularly within the SF1 lineage, and may enhance prediction of recurrence risk. Prospective validation and demonstration of clinical utility are warranted to support integration into precision management workflows.
