Chromatin Conformation Capture in the Clinic: 4C-Seq/HiC Distinguishes Pathogenic From Neutral Duplications at the GPR101 Locus

Authors

Adrian F Daly
Leslie A Dunnington
David F Rodriguez-Buritica
Erica Spiegel
Francesco Brancati
Giovanna Mantovani
Vandana M Rawal
Fabio Rueda Faucz
Hadia Hijazi
Jean-Hubert Caberg
Anna Maria Nardone
Mario Bengala
Paola Fortugno
Giulia Del Sindaco
Marta Ragonese
Helen Gould
Salvatore Cannavò
Patrick Pétrossians
Andrea Lania
James R Lupski
Albert Beckers
Constantine A Stratakis
Brynn Levy
Giampaolo Trivellin
Martin Franke

Publication Date

9-13-2024

Journal

Genome Medicine

Abstract

BACKGROUND: X-linked acrogigantism (X-LAG; MIM: 300942) is a severe form of pituitary gigantism caused by chromosome Xq26.3 duplications involving GPR101. X-LAG-associated duplications disrupt the integrity of the topologically associating domain (TAD) containing GPR101 and lead to the formation of a neo-TAD that drives pituitary GPR101 misexpression and gigantism. As X-LAG is fully penetrant and heritable, duplications involving GPR101 identified on prenatal screening studies, like amniocentesis, can pose an interpretation challenge for medical geneticists and raise important concerns for patients and families. Therefore, providing robust information on the functional genomic impact of such duplications has important research and clinical value with respect to gene regulation and triplosensitivity traits.

METHODS: We employed 4C/HiC-seq as a clinical tool to determine the functional impact of incidentally discovered GPR101 duplications on TAD integrity in three families. After defining duplications and breakpoints around GPR101 by clinical-grade and high-density aCGH, we constructed 4C/HiC chromatin contact maps for our study population and compared them with normal and active (X-LAG) controls.

RESULTS: We showed that duplications involving GPR101 that preserved the centromeric invariant TAD boundary did not generate a pathogenic neo-TAD and that ectopic enhancers were not adopted. This allowed us to discount presumptive/suspected X-LAG diagnoses and GPR101 misexpression, obviating the need for intensive clinical follow-up.

CONCLUSIONS: This study highlights the importance of TAD boundaries and chromatin interactions in determining the functional impact of copy number variants and provides proof-of-concept for using 4C/HiC-seq as a clinical tool to acquire crucial information for genetic counseling and to support clinical decision-making in cases of suspected TADopathies.

Keywords

Humans, Receptors, G-Protein-Coupled, Chromatin, Female, Male, Gene Duplication, Chromosome Duplication, Chromosomes, Human, X, Pedigree

Comments

Supplementary Materials

Data Availability Statement

PMID: 39272130