Leveraging amino acid conservation, genetic variation in health and disease and gene expression to gain insight into pathomechanisms in the superfamily of voltage-gated sodium and calcium channels

• Applicant: Dr. Henrike Heyne
• Subject Area: Human Genetics ; Molecular Biology and Physiology of Neurons and Glial Cells
• Term: from 2017 to 2019
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 374360668

• Final Report Year: 2019

Final Report Abstract

I successfully completed my 2-year research fellowship at Mark Daly’s lab at the Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA and Stanley Center for Psychiatric Research, Broad Institute of M.I.T and Harvard, Cambridge, MA, USA. I reached all main goals of the two research proposals. In the first project, we meta-analysed large cohorts of individuals with severe early onset epilepsy. We first performed a meta-analysis of exome-wide de novo variants (DNVs) on 1942 individuals with neurodevelopmental disorders (NDD) and epilepsy. We found a markedly overlapping genetic spectrum of epileptic encephalopathy (EE) and NDDs with unspecified epilepsy challenging commonly used clinical labels. We found 33 genes enriched for DNV in NDDs with epilepsy and reported three new disease genes: SNAP25, GABRB2 and CACNA1E. When comparing NDDs with and without epilepsy, we found missense DNVs, DNVs in specific genes, age of recruitment, and severity of intellectual disability to be associated with epilepsy. We show that our results should significantly improve yield in current genetic testing. We further showed that 5% (84/1,587) of DNV in NDDs with epilepsy were in genes with therapeutic consequences (CEBM criteria) emphasizing the potential therapeutic benefit of accurate genetic diagnosis in NDDs with epilepsy. In the second project of the first proposal, we analysed epilepsy related gene panels in collaboration with two private diagnostic companies in 6994 individuals with severe epilepsy with a suspected monogenic cause. We found genes with highest frequencies of ultra-rare variants in NDD and epilepsy, concordant with two other large epilepsy cohorts we investigated, which could help prioritise genes to maximise yield for genetic testing under limited resources. We also pointed out which genes with low evidence for true disease-association or very few ultra-rare variants could be omitted from future panels. Malfunctions of voltage-gated sodium and calcium channels (SCN and CACNA1 genes) have been associated with severe neurologic, psychiatric, cardiac and other diseases. The goal of my second project proposal was to jointly analyze the superfamily of voltage-gated sodium and calcium channels to identify sites where amino acids are more conserved and compare those with protein features and genetic variant data. Using those data, we further developed a statistical model that can predict functional effects of genetic variants in these channels. Functional effects of ion channel variants are frequently grouped into gain or loss of ion channel function (GOF or LOF, respectively), often corresponding to clinical disease outcomes and differences in drug response. Experimental studies of channel however usually focus only on a few variants at a time. Based on known gene disease mechanisms, we inferred LOF and GOF of disease causing variants from phenotypes of variant carriers. We trained a machine learning model on the sequence- and structure-based protein features to predict LOF or GOF of missense variants. We then successfully validated the GOF versus LOF prediction on 87 functionally tested variants in SCN1/2/8A and CACNA1I and in exome-wide data from > 100.000 cases and controls. This approach may ultimately help acute decision-making in clinical settings when treatment decisions must be made before functional work can be done. Our method may also be useful to help stratify drug trial cohorts (two new drugs reducing SCN8A function are currently in Phase I clinical trials). Our method may also be used to partition functional effects of missense variants for which disease associations and/or mechanisms have not yet been elucidated.

Publications

• „De Novo Variants In Neurodevelopmental Disorders With Epilepsy“, Nature Genetics, 2018
  H. O. Heyne […] M. Daly, I. Helbig, D. Lal, J. Lemke
  
• “Insights into Protein Structural, Physicochemical, and Functional Impacts of Missense Variations in 1,330 Disease-associated Human Genes”, bioRxiv, 2019
  S. Iqbal, J. Jespersen, E. Perez-Palma, P. May, D. Hoksza, H. O. Heyne […] M. Daly, A. Campbell, D. Lal
  
• “Paternal-age-related de novo mutations and risk for five disorders“, Nature Communications, 2019
  J. Taylor, J-C Debost, S. Morton, E. M. Wigdor, H. O. Heyne […] M. Daly, Elise Robinson
  
• “Predicting Functional Effects of Missense Variants in Voltage-Gated Sodium and Calcium Channels”, bioRxiv, 2019
  H. O. Heyne […] M. Daly
  
• „Targeted gene sequencing in 6994 individuals with neurodevelopmental disorder with epilepsy“, Genetics in Medicine, 2019
  H. O. Heyne […] M. Daly, I. Helbig, S. Biskup, Y. Weber, J. Lemke