Abstract
Structural variants (SVs) that disrupt topologically associating domains can cause disease by rewiring enhancer-promoter interactions. Duplications involving GPR101 are known to cause X-linked acrogigantism (X-LAG) through ectopic GPR101 expression, but not all of these duplications are pathogenic. This presents a diagnostic challenge, especially in the prenatal setting. We evaluated POSTRE, a tool that predicts the regulatory impact of SVs, to distinguish pathogenic from benign GPR101 duplications. We analyzed seven non-pathogenic duplications and 27 known X-LAG-associated duplications. To enable predictions in an X-LAG-relevant tissue, enhancer maps built using H3K27ac ChIP-seq, ATAC-seq, and RNA-seq data derived from human anterior pituitary samples (NIH research protocol 97-CH-0076, Clinicaltrials.gov Identifier NCT00001595, submitted on 11 March 1999) were integrated into POSTRE. POSTRE correctly classified all 34 duplications as benign or pathogenic. In addition, one X-LAG case with mild clinical features (i.e. severe growth hormone hypersecretion without pituitary tumorigenesis) was found to include only 2/5 VGLL1 enhancers, whereas all typical X-LAG cases had ≥4 enhancers duplicated. This suggests that partial enhancer hijacking at VGLL1 could explain the different clinical features in this individual. These findings support the utility of POSTRE to support diagnostic pipelines when interpreting SVs affecting chromatin architecture in pituitary disease and highlight its potential to reduce uncertainty in genetic counseling without requiring chromatin conformation capture assays.
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Data availability
The datasets generated during this study are available at GEO, accession code GSE193113 and at the Humanitas Research Hospital and Humanitas University data repository in Zenodo https://doi.org/10.5281/zenodo.15854045.
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Acknowledgements
The work was supported in part by the following funding sources: Fondazione Telethon, Italy grant no. GGP20130 (to GT, supporting AG); grants from the Fonds d’Investissment pour la Recherche Scientifique 2018-2023 of the Center Hospitalier Universitaire de Liège and grant number FSR-F-2023-FM from the Faculty of Medicine, University of Liège; Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH) Research project Z1A HD008920 (to CAS), USA. The project that gave rise to these results received the support of a fellowship from “La Caixa” Foundation (ID 100010434). The fellowship code is LCF/BQ/PR22/11920006 (to MF). MF further acknowledges support by the Ramón y Cajal 2023 Programme (Grant RYC2023-043037-I), funded by the Spanish Ministry of Science and Innovation (MCIN/AEI/10.13039/501100011033) and co-financed by the European Social Fund Plus (FSE+). VS-G is hired under the Generation D initiative, promoted by Red.es, an organization attached to the Ministry for Digital Transformation and the Civil Service, for the attraction and retention of talent through grants and training contracts, financed by the Recovery, Transformation and Resilience Plan through the European Union's Next Generation funds. .The authors would like to thank the patients and families involved for their interest, generosity and patience. GT and AG also acknowledge Fondazione Humanitas per la Ricerca, the institutional recipient of the Fondazione Telethon’s research grant.
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G.T.: Conceptualization, Investigation, Writing - Original Draft, Writing - Review & Editing, Visualization, Supervision, Funding acquisition; V.S.-G.: Methodology, Software, Formal analysis, Data Curation, Visualization, Writing - Review & Editing; A.G.: Investigation, Writing - Review & Editing; M.P.: Resources, Writing - Review & Editing; CAS: M.P.: Resources, Writing - Review & Editing; D.M.: Resources, Writing - Review & Editing; E.K.: Writing - Review & Editing; A.B.: Writing - Review & Editing; A.G.L.: Writing - Review & Editing; P.P.: Resources, Writing - Review & Editing, Funding acquisition; A.R.-I.: Resources, Writing - Review & Editing; M.F.: Conceptualization, Writing - Original Draft, Writing - Review & Editing; A.F.D.: Conceptualization, Investigation, Writing - Original Draft, Writing - Review & Editing, Supervision.
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AFD, CAS, and GT hold a patent on GPR101 and its function (US Patent No. 10,350,273, Treatment of Hormonal Disorders of Growth). The authors declare no other competing interests.
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Trivellin, G., Sánchez-Gaya, V., Grasso, A. et al. Distinguishing benign from pathogenic duplications involving GPR101 and VGLL1-adjacent enhancers in the clinical setting with the bioinformatic tool POSTRE. npj Genom. Med. (2026). https://doi.org/10.1038/s41525-025-00548-7
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DOI: https://doi.org/10.1038/s41525-025-00548-7
