Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time.
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Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time.
Powered by AI, Base by Base offers a new way to learn on the go. Special thanks to authors who publish under CC BY 4.0, making open-access science faster to share and easier to explore.
189: DNA methylation patterns facilitate tracing the origin of neuroendocrine neoplasms
Base by Base
14 minutes 22 seconds
4 days ago
189: DNA methylation patterns facilitate tracing the origin of neuroendocrine neoplasms
️ Episode 189: DNA methylation patterns facilitate tracing the origin of neuroendocrine neoplasms
In this episode of PaperCast Base by Base, we explore how genome-wide DNA methylation profiling can pinpoint the organ of origin for neuroendocrine neoplasms (NEN), with a special focus on lesions detected in the liver and long-debated “primary hepatic NEN”.
Study Highlights:Using two independent cohorts totaling 212 NEN tissues, the authors profiled methylation patterns and visualized them with dimensionality-reduction approaches, revealing distinct clusters for most organ sites. Hepatic NEN without a detectable extrahepatic primary did not form a unique liver-specific cluster and instead colocalized with extrahepatic subtypes, frequently showing foregut-like methylation signatures. A latent methylation component–based Random Forest classifier achieved high accuracy in predicting organ site from biopsy material and suggested that many presumed primary hepatic NEN are likely misclassified metastases of unknown primary. Copy-number analyses supported organ‑site–specific patterns and further differentiated grades and subtypes, including NET versus NEC.
Conclusion:Methylome profiling offers a practical path to identify the primary site in neuroendocrine neoplasms—including liver-detected cases—supporting more precise diagnosis and treatment selection in real-world pathology workflows.
Reference:Goeppert B, Charbel A, Toth R, et al. DNA methylation patterns facilitate tracing the origin of neuroendocrine neoplasms. Nature Communications. 2025;16:9477. https://doi.org/10.1038/s41467-025-65227-8
License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/
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Base by Base
Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time.
Powered by AI, Base by Base offers a new way to learn on the go. Special thanks to authors who publish under CC BY 4.0, making open-access science faster to share and easier to explore.
