Although epilepsy has a large genetic contribution, causative genes are not known for most epilepsy patients. And while epilepsy can be inherited in families, it is more commonly 'sporadic'or spontaneous, without a clear family history, and causes of sporadic epilepsy cases are mostly unknown. Since the cause of epilepsy often directs the choice of treatments, categorizing patients is of great importance therapeutically. Many epilepsy syndromes appear to involve 'somatic'mutations, in which a subpopulation of brain cells shows a mutation not shared by all cells of the body, because the mutation occurred during mitosis of somatic cells of the embryo after fertilization. Our lab and other have reported on somatic mutations is several genes known to cause epilepsy, however until now, technological limitations have prevented a systematic search for somatic mutations in epilepsy. Whole genome or whole exome sequencing will not identify somatic mutations unless the study is designed to detect them: responsible mutations may not be present in most blood cells, but would instead be limited to cells in the brain. Even relevant mutations limited to neurons may be missed by bulk brain sequencing because 1] neurons are surrounded by glial cells with distinct embryological origins, and with whom they would not be expected to share mutations, and 2] neurons themselves are derived from two embryological origins, with pyramidal neurons derived from cortical proliferative regions, and inhibitory nonpyramidal neurons migrating into cortex from distant subcortical regions, so that bulk sequencing of postmortem brain tissue may also not detect mutations limited to specific neuronal populations. We have recently developed technology that allows sorting of single or small numbers of cerebral cortical neuronal nuclei, and amplification of their genomes in quantities sufficient for any next-generation sequencing. We are proposing to use this technology to examine cortical neurons from postmortem brains or cortical resections from epilepsy patients in order to 1) perform a systematic assessment of copy number variation (CNV) in cerebral neurons;and 2) perform whole exome sequencing to identify mutations in known epilepsy genes. Comparison of single neuron sequence to that from other cells of the body could then determine how frequently spontaneous mutations occur in cortical neurons, and identify and catalogue these mutations. Our proposed study thus enables a systematic analysis of all mechanisms of somatic mutation in the epileptic human brain.

Public Health Relevance

Epilepsy is a major health problem, with lifetime risk of a seizure being 3%. Our work challenges major paradigms about epilepsy causation that suggest that epilepsy can be a 'complex trait'due to multiple interacting genetic mutations, and instead suggests that epilepsy can be caused by developmental genetic anomalies that occur in only some of the neurons of the brain. Our work will not only improve the specificity of epilepsy diagnosis, but also promises to provide a new paradigm for considering epilepsy treatment.

Agency
National Institute of Health (NIH)
Institute
National Institute of Neurological Disorders and Stroke (NINDS)
Type
Research Project (R01)
Project #
1R01NS079277-01
Application #
8333652
Study Section
Special Emphasis Panel (ZNS1-SRB-B (32))
Program Officer
Fureman, Brandy E
Project Start
2012-04-01
Project End
2015-12-31
Budget Start
2012-04-01
Budget End
2012-12-31
Support Year
1
Fiscal Year
2012
Total Cost
$348,000
Indirect Cost
$148,000
Name
Children's Hospital Boston
Department
Type
DUNS #
076593722
City
Boston
State
MA
Country
United States
Zip Code
02115
Woodworth, Mollie B; Girskis, Kelly M; Walsh, Christopher A (2017) Building a lineage from single cells: genetic techniques for cell lineage tracking. Nat Rev Genet 18:230-244
D'Gama, Alissa M; Woodworth, Mollie B; Hossain, Amer A et al. (2017) Somatic Mutations Activating the mTOR Pathway in Dorsal Telencephalic Progenitors Cause a Continuum of Cortical Dysplasias. Cell Rep 21:3754-3766
Evrony, Gilad D; Lee, Eunjung; Park, Peter J et al. (2016) Resolving rates of mutation in the brain using single-neuron genomics. Elife 5:
Lodato, Michael A; Woodworth, Mollie B; Lee, Semin et al. (2015) Somatic mutation in single human neurons tracks developmental and transcriptional history. Science 350:94-98
Jamuar, Saumya S; Walsh, Christopher A (2015) Genomic variants and variations in malformations of cortical development. Pediatr Clin North Am 62:571-85
Evrony, Gilad D; Lee, Eunjung; Mehta, Bhaven K et al. (2015) Cell lineage analysis in human brain using endogenous retroelements. Neuron 85:49-59
D'Gama, Alissa M; Geng, Ying; Couto, Javier A et al. (2015) Mammalian target of rapamycin pathway mutations cause hemimegalencephaly and focal cortical dysplasia. Ann Neurol 77:720-5
Cai, Xuyu; Evrony, Gilad D; Lehmann, Hillel S et al. (2014) Single-cell, genome-wide sequencing identifies clonal somatic copy-number variation in the human brain. Cell Rep 8:1280-9
Jamuar, Saumya S; Lam, Anh-Thu N; Kircher, Martin et al. (2014) Somatic mutations in cerebral cortical malformations. N Engl J Med 371:733-43
Jamuar, Saumya S; Walsh, Christopher A (2014) Somatic mutations in cerebral cortical malformations. N Engl J Med 371:2038

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