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Improved diagnosis of a rare genetic disease using a 3D genome technology
published on 03/10/2024
Genome sequencing is increasingly being used for the investigation of developmental disorders, cancer and also in prenatal screening. While holding great promise for identifying genetic disorders, the use of these techniques has some pitfalls. The enormous volume of generated data makes variant interpretation challenging for clinical geneticists and counsellors. As a consequence, this can increase stress and uncertainty for patients, particularly in the setting of prenatal testing. Therefore, it is vital to provide comprehensive functional information about emerging genetic targets so that clinicians can distinguish pathogenic changes from benign ones and counsel patients accordingly
This study now published in Genome Medicine reveals the clinical application of a novel research technique that allows to distinguish between pathogenic and neutral genetic duplications associated with a rare growth disorder. The research, led by an international team from the Humanitas University in Milan (Italy), the Andalusian Center for Developmental Biology (CABD) in Seville (Spain), and the University Hospital Center of Liège (Belgium), demonstrates how advanced chromatin conformation capture (3C) techniques can refine the diagnosis of X-linked acrogigantism (X-LAG), a severe childhood-onset form of pituitary gigantism caused by abnormal expression of the gene, GPR101.
Giampolo Trivellin, Adrian Daly and Martin Franke, the senior authors from this work.
In 2022, the research team discovered that the underlying cause of X-LAG was due to duplications that disrupted the local 3D architecture of the X chromosome. This disruption affects a chromatin region - called a topologically associating domain (TAD) – at the GPR101 gene, which is separated from nearby genes by a border. The duplication in X-LAG places the normally-insulated gene under control by abnormal ectopic enhancers, forming what is known as a “neo-TAD”. This disorder, called a TADopathy, leads directly to tumoral growth hormone over-secretion and gigantism in affected children.
X-LAG is the only known clinical condition associated with GPR101 duplications, and as it is fully penetrant - meaning that all who carry the duplication develop the disease - the finding of a GPR101 duplication should herald a diagnosis of X-LAG. However, when clinical geneticists who were faced with GPR101 duplications without evidence of gigantism contacted the researchers provoked great surprise. Moreover, these included cases identified during prenatal screening and workup, where a potential diagnosis of X-LAG was considered.
Dr. Adrian Daly, lead author and endocrinologist at the University Hospital Center of Liège, explained the background of the study: “These findings challenged our model of how X-LAG occurs. We immediately saw an opportunity to turn our laboratory research methods into a clinical tool to explain these findings. We wanted to provide our genetics colleagues and parents with medically useful information. The first clue we focused on was the smaller size of the GPR101 duplications in these new cases compared with X-LAG patients.”
The researchers employed 3D genomic techniques, which map the organization of chromatin in the nucleus. The authors compared the 3D chromatin architecture at GPR101 in the new cases to that the researchers had observed in patients with X-LAG. In contrast to X-LAG, where the disrupted TAD border of GPR101 led to a pathogenic neo-TAD, the smaller duplications in the new cases preserved the TAD border and did not form a neo-TAD. Without the involvement of the ectopic enhancers, GPR101 was not over-expressed, thereby explaining why X-LAG did not develop.
Dr. Giampaolo Trivellin, senior author and corresponding researcher at the Humanitas University, emphasized the practical implications of these findings: “This study shows how 3C techniques can be used to aid diagnostic decision making in conditions associated with TAD disruption. By understanding the structural impacts of these duplications, we have shown that we can distinguish pathogenic from neutral GPR101 duplications, allowing for informed clinical decisions and genetic counselling.”
Dr. Martin Franke, senior and corresponding author from the CABD in Seville, concluded, “By applying our toolkit to study the 3D genome in a clinical context, we are opening new avenues for understanding genetic disorders linked to TAD disruption, the so-called TADopathies. The findings of our new research provide a roadmap for interrogating the potential pathogenicity of genetic changes associated with other TADopathies.”
This research provides a proof-of-concept for the use of chromatin mapping as a diagnostic tool, highlighting its potential application in diagnosing other genetic disorders in the future. In addition, it underscores the potential of 3D genome mapping techniques for increasing the accuracy of prenatal screening, thereby improving the mental load for families and streamlining genetic diagnostics.
Daly, A.F., Dunnington, L.A., Rodriguez-Buritica, D.F. et al. Chromatin conformation capture in the clinic: 4C-seq/HiC distinguishes pathogenic from neutral duplications at the GPR101 locus. Genome Med 112 (2024).DOI: https://doi.org/10.1186/s13073-024-01378-5
This press release was written in collaboratio with CSIC Andalucia and CSIC communication departments
