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Published on: August 23, 2019
Discriminating epigenetic landscapes: multi-omics characterization of benign thyroid nodules versus papillary thyroid
Ping Yang1, Fangning Gao1, Shujia Peng1
1Department of General Surgery, Tangdu Hospital, The Air Force Military Medical University, 569 Xinsi Street, Xi'an, 710038, China.
Background:
Discriminating the epigenetic landscapes of coincidental benign thyroid nodules (particularly follicular adenoma subtypes) from papillary thyroid carcinoma (PTC) remains a critical unresolved challenge, impeding mechanistic insights into their divergent pathogenic trajectories.
Methods:
To address this knowledge gap, we performed integrative multi-omics profiling of histologically paired benign thyroid nodules and PTC lesions from the same patients, synergizing chromatin accessibility mapping (ATAC-seq), whole-exome sequencing, transcriptomics, and ATAC-seq-derived extrachromosomal circular DNA (eccDNA) detection.
Results:
Three pivotal mechanisms emerged from our cross-omics analyses to delineate the benign-malignant dichotomy. First, chromatin architecture interrogation revealed spatially colocalized PTC-specific accessible regions with somatic mutation hotspots, suggesting coordinated interplay between epigenetic remodeling and genomic instability in malignant transformation. Second, we uncovered ARHGEF28 and ARHGEF24 as novel potential benign-specific master regulators, where TEAD4-binding motif enrichment in benign-hyperaccessible chromatin drives their coordinated overexpression, forming a self-reinforcing regulatory loop unique to benign thyroid nodules. Third, eccDNA-centric profiling delineated a different regulatory paradigm: benign thyroid noduless exhibited preferential enrichment of T-cell signaling related elements on eccDNA scaffolds, whereas PTCs eccDNA were enriched in the DNA replication signaling pathways. This multidimensional atlas not only maps lineage-specific regulatory topologies of thyroid neoplasms but also establishes the ARHGEF28/24-TEAD4 axis as potential association with benign lineage.
Conclusions:
By elucidating chromatin-based thresholds of malignant progression, our findings provide a molecular framework for differential diagnosis and mechanistic dissection of transformation checkpoints.
