Article (Scientific journals)
Delineation of functionally essential protein regions for 242 neurodevelopmental genes
Iqbal, Sumaiya; Brünger, Tobias; Pérez-Palma, Eduardo et al.
2023In Brain: a Journal of Neurology, 146 (2), p. 519-533
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Keywords :
Neurodevelopmental diseases; genetics; bioinformatics
Abstract :
[en] Neurodevelopmental disorders (NDDs), including severe pediatric epilepsy, autism, and intellectual disabilities are heterogeneous conditions in which clinical genetic testing can often identify a pathogenic variant. For many of them, genetic therapies will be tested in this or the coming years in clinical trials. In contrast to first-generation symptomatic treatments, the new disease-modifying precision medicines require a genetic test-informed diagnosis before a patient can be enrolled in a clinical trial. However, even in 2022, most identified genetic variants in NDD genes are ‘Variants of Uncertain Significance’. To safely enroll patients in precision medicine clinical trials, it is important to increase our knowledge about which regions in NDD-associated proteins can ‘tolerate’ missense variants and which ones are ‘essential’ and will cause a NDD when mutated. In addition, knowledge about functionally indispensable regions in the three-dimensional (3D) structure context of proteins can also provide insights into the molecular mechanisms of disease variants. We developed a novel consensus approach that overlays evolutionary, and population based genomic scores to identify 3D essential sites (Essential3D) on protein structures. After extensive benchmarking of AlphaFold predicted and experimentally solved protein structures, we generated the currently largest expert curated protein structure set for 242 NDDs and identified 14,377 Essential3D sites across 189 gene disorders associated proteins. We demonstrate that the consensus annotation of Essential3D sites improves prioritization of disease mutations over single annotations. The identified Essential3D sites were enriched for functional features such as intermembrane regions or active sites and discovered key inter-molecule interactions in protein complexes that were otherwise not annotated. Using the currently largest autism, developmental disorders, and epilepsies exome sequencing studies including >360,000 NDD patients and population controls, we found that missense variants at Essential3D sites are 8-fold enriched in patients. In summary, we developed a comprehensive protein structure set for 242 neurodevelopmental disorders and identified 14,377 Essential3D sites in these. All data are available at https://es-ndd.broadinstitute.org for interactive visual inspection to enhance variant interpretation and development of mechanistic hypotheses for 242 NDDs genes. The provided resources will enhance clinical variant interpretation and in silico drug target development for NDD-associated genes and encoded proteins.
Research center :
- Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
Disciplines :
Neurology
Genetics & genetic processes
Author, co-author :
Iqbal, Sumaiya
Brünger, Tobias
Pérez-Palma, Eduardo
Macnee, Marie
Brunklaus, Andreas
Daly, Mark J.
Campbell, Arthur J.
Hoksza, David
May, Patrick  ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core
Lal, Dennis
External co-authors :
yes
Language :
English
Title :
Delineation of functionally essential protein regions for 242 neurodevelopmental genes
Publication date :
February 2023
Journal title :
Brain: a Journal of Neurology
ISSN :
1460-2156
Publisher :
Oxford University Press, Oxford, United Kingdom
Volume :
146
Issue :
2
Pages :
519-533
Peer reviewed :
Peer Reviewed verified by ORBi
Focus Area :
Systems Biomedicine
FnR Project :
FNR16394868 - Epileptogenesis Of Genetic Epilepsies, 2021 (01/10/2021-...) - Alexander Skupin
Funders :
FNR - Fonds National de la Recherche [LU]
DFG - Deutsche Forschungsgemeinschaft [DE]
BMBF - Bundesministerium für Bildung und Forschung [DE]
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