Elliott H. Sherr, M.D., Ph.D. - US grants

DESCRIPTION (provided by applicant): The corpus callosum, formed between the 8th and 14th weeks of fetal development, is the principal fiber tract that connects the two cerebral hemispheres. Agenesis of the corpus callosum (ACC) has an estimated incidence of 1:4,000 live births. Patients with ACC can have significant developmental disability and seizures and may have cognitive and behavioral impairment such as autism, obsessive compulsive disorder or attention deficit hyperactivity disorder. Callosal anomalies have also been found consistently in drug-naive schizophrenic patients, suggesting that understanding the causes of ACC may have broad implications for understanding other neurobehavioral disorders. The genetic causes for ACC are largely unknown, however, certain cytogenetic loci are repeatedly deleted in ACC patients, suggesting that ACC genes reside in these loci and that missing one copy of the gene can cause ACC. Epidemiological data suggest that 2% of affected individuals have first-degree relatives with ACC, consistent with the possibility that many ACC patients may have de novo causative mutations. This role for gene dosage in ACC is also evident in animal models;deletion of genes involved in callosal formation frequently results in multiple pathfinding defects in the CMS, whereas heterozygous deletion may only result in callosal anomalies. We have undertaken a comprehensive approach to study the clinical, radiographic and genetic features of at least 200 ACC patients and their families. We have begun to test our cohort for chromosomal copy number changes using genomic microarrays. In the first 25 patients, we identified three submicroscopic de novo deletions that correlate with ACC, suggesting that de novo deletions may occur in up to 20% of ACC patients. We hypothesize that some of the remaining 80% will have inactivating point mutations in ACC causative genes contained within one of these intervals. In light of these findings and hypotheses, for this grant we propose to tackle the following Aims: 1. To continue to develop a comprehensive database of clinical, historical and radiologic information on an initial 200 patients with callosal agenesis/dysgenesis. 2. To narrow down previously identified ACC chromosomal intervals and to identify novel ACC intervals utilizing the UCSF 32,000 BAG microarray on 200 ACC patients. 3. To identify inactivating mutations in candidate ACC genes, which are contained in three ACC-associated chromosomal intervals: 2q37.1, 6q27 and 3q13.1.

DESCRIPTION (provided by applicant): Brain malformations are a significant cause of severe developmental disability and seizures. In many cases, less penetrant mutations in the same gene can lead to cognitive and behavior impairment without structural changes, suggesting a broadly applicable role for these genes in brain development and function. We anticipate that discovery of genes involved in these brain malformations will have direct and important implications on our understanding of mental retardation, autism and epilepsy and that this will serve as this first step toward targeted therapies. We propose to focus this grant on Aicardi syndrome (AS). This is a unique disorder of brain and eye development for which the hallmark signs are agenesis of the corpus callosum, chorioretinal lacunae and infantile spasms. These patients also frequently have other brain malformations that include polymicrogyria, subcortical and periventricular heterotopia, cerebral asymmetry, choroid plexus papillomas and cysts, amongst others. Only females and XXY (Klinefelter) males are affected and this sporadid disorder, never occurring twice in one family (with one exception). These constellation of findings suggest that Aicardi syndrome is caused by a de novo mutation on the X chromosome. We propose to search for the causative gene using a microarray platform that will scan DNA from the X chromosome looking for deletions or duplications which may point us to the Aicardi syndrome gene. We also will pursue the cause of AS by pursuing a candidate gene approach. Moreover, many developmental disorders are found to have a broader clinical phenotype once the gene is identified. We plan to capitalize on this potential aspect of AS by sequencing the newly identified AS gene in a large cohort of individuals with agenesis of the corpus callosum, the hallmark cerebral malformation in Aicardi syndrome. PUBLIC HEALTH RELEVANCE: This discovery will ultimately have broad implications on our understanding of how the brain develops and how seizures occur in patients with malformations of brain development. This will also have important implications for our ability to understand and diagnose disorders of brain development both in affected children and in expectant mothers.

DESCRIPTION (provided by applicant): The primary goal of the Epi4K Center Without Walls is to increase understanding of the genetic basis of human epilepsy in order to improve the well-being of patients and family members living with these disorders. This improvement will come in the form of better diagnostics, treatments and cures. To accomplish this goal, Epi4K aims to analyze the exomes and genomes of a large number of well-phenotyped epilepsy patients and families collected by investigators from several major research groups. The specific goals of this project (4 of 7: Epileptic Encephalopathies) are to discover mutations or deletions in genes by mining sequence data from exomes of 500 patients with two severe childhood epileptic encephalopathies. Infantile Spasms (IS) and Lennox Gastaut Syndrome (LGS), to understand how these mutations fit into a broader network of developmental interactions within the brain and to compare the causes of these defined epilepsies with other epileptic encephalopathies (EE) of childhood. Dr. Sherr from UCSF, Dr. Scheffer from the University of Melbourne and Dr. Mefford from the University of Washington will co-direct this project. The discovery of novel genes that lead to IS/LGS and other severe childhood EE in the Epi4K cohorts will further our understanding of epilepsy genetics and lead to a better understanding of epilepsy pathophysiology and to the possibility of better tools for diagnosis and treatment.

Abstract: The corpus callosum ? the largest fiber tract in the human brain, connects and integrates the two cerebral hemispheres. Agenesis of the corpus callosum (ACC) with an incidence of 1 in 2,000 occurs in rare syndromes and in common neurodevelopmental disorders (NDD) including epilepsy, intellectual disability (ID), autism spectrum disorder (ASD), cerebral palsy and schizophrenia. Collectively these affect more than 5% of the population and constitute a major public health concern. Recent evidence including from our team, points to the importance of genetic etiologies. Our whole exome efforts in this grant?s initial submission identified 70 ACC genes that reached genome-wide significance, of which many of which are strong novel candidate genes that need further validation. Based on population estimates, we expect that several hundred additional genes will cause ACC. To discover the full range of ACC genetics and to make progress using model systems, we bring together an outstanding investigative team that has made significant contributions to the biology of ACC. Together we will advance gene discovery, and tackle key questions on CC development. To do so we will: Aim 1: Identify novel de novo genetic causes of ACC and NDD. To do so, we will recruit, obtain clinical data and conduct WES for 1000+ ACC trios from UCSF and collaborators. We will also receive genetic information from 2000+ trios from the two largest commercial exome sequencing laboratories in the US, GeneDx and Invitae. We will also leverage the community?s gene discovery efforts using MatchMaker, and work with the IRC5 (international research consortium for the corpus callosum and cerebral connectivity: www.IRC5.org), which the PI?s co-founded. These combined efforts will ensure robust novel gene discovery. Aim #2: Discover genetic causes of ACC beyond germline de novo coding variants. In addition to gene discovery above, we hypothesize that many ACC cases are caused by mutations in complex genomic regions. We will initially focus on Aicardi syndrome, a highly complex yet distinctive brain malformation disorder. We will conduct short-read deep WGS from affected brain tissue (6 in hand) and other tissues, collaborating with the Broad Mendelian Genome Center, to perform long-read sequencing to resolve complex genomic architecture and other difficult to sequence regions. We will also utilize the same work flow to tackle gene discovery in similarly phenotypically unified conditions in particular focusing on multiplex cases. Aim #3: Engage in functional confirmation and analysis of ACC candidate genes. During our current cycle, we have made significant progress studying the biology C12ORF57. In this proposal, we will advance this directly, by 1. Studying the protein interaction network for C12ORF57 and CAMKIV. We will also study the signaling pathways that link CAMKIV to the transcription factor CREB and to regulation of AMPA receptors, the key glutamatergic receptors for excitatory neural transmission. This work may have critical implications for treatment strategies in epilepsy and possibly disorders of cognition.