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Knowles JK, Helbig I, Metcalf CS, Lubbers LS, Isom LL, Demarest S, Goldberg EM, George AL, Lerche H, Weckhuysen S, Whittemore V, Berkovic SF, Lowenstein DH. Precision medicine for genetic epilepsy on the horizon: Recent advances, present challenges, and suggestions for continued progress. Epilepsia 2022; 63:2461-2475. [PMID: 35716052 PMCID: PMC9561034 DOI: 10.1111/epi.17332] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 01/18/2023]
Abstract
The genetic basis of many epilepsies is increasingly understood, giving rise to the possibility of precision treatments tailored to specific genetic etiologies. Despite this, current medical therapy for most epilepsies remains imprecise, aimed primarily at empirical seizure reduction rather than targeting specific disease processes. Intellectual and technological leaps in diagnosis over the past 10 years have not yet translated to routine changes in clinical practice. However, the epilepsy community is poised to make impressive gains in precision therapy, with continued innovation in gene discovery, diagnostic ability, and bioinformatics; increased access to genetic testing and counseling; fuller understanding of natural histories; agility and rigor in preclinical research, including strategic use of emerging model systems; and engagement of an evolving group of stakeholders (including patient advocates, governmental resources, and clinicians and scientists in academia and industry). In each of these areas, we highlight notable examples of recent progress, new or persistent challenges, and future directions. The future of precision medicine for genetic epilepsy looks bright if key opportunities on the horizon can be pursued with strategic and coordinated effort.
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Affiliation(s)
- Juliet K. Knowles
- Department of Neurology, Division of Child Neurology, Stanford University School of Medicine, Stanford, California, USA
| | - Ingo Helbig
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Cameron S. Metcalf
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, Utah, USA
| | - Laura S. Lubbers
- Citizens United for Research in Epilepsy, Chicago, Illinois, USA
| | - Lori L. Isom
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Scott Demarest
- Department of Pediatrics and Neurology, University of Colorado, School of Medicine, Aurora, Colorado, USA
| | - Ethan M. Goldberg
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Alfred L. George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Sarah Weckhuysen
- Division of Neurology, University Hospital Antwerp, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Vlaams Instituut voor Biotechnologie Center for Molecular Neurology, Antwerp, Belgium
- Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium
- μNEURO Research Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Vicky Whittemore
- Division of Neuroscience, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Rockville, Maryland, USA
| | - Samuel F. Berkovic
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel H. Lowenstein
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
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Abstract
Autism is a common and complex neurologic disorder whose scientific underpinnings have begun to be established in the past decade. The essence of this breakthrough has been a focus on families, where genetic analyses are strongest, versus large-scale, case-control studies. Autism genetics has progressed in parallel with technology, from analyses of copy number variation to whole-exome sequencing (WES) and whole-genome sequencing (WGS). Gene mutations causing complete loss of function account for perhaps one-third of cases, largely detected through WES. This limitation has increased interest in understanding the regulatory variants of genes that contribute in more subtle ways to the disorder. Strategies combining biochemical analysis of gene regulation, WGS analysis of the noncoding genome, and machine learning have begun to succeed. The emerging picture is that careful control of the amounts of transcription, mRNA, and proteins made by key brain genes-stoichiometry-plays a critical role in defining the clinical features of autism.
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Affiliation(s)
- Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA;
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Dhindsa RS, Zoghbi AW, Krizay DK, Vasavda C, Goldstein DB. A Transcriptome-Based Drug Discovery Paradigm for Neurodevelopmental Disorders. Ann Neurol 2021; 89:199-211. [PMID: 33159466 PMCID: PMC8122510 DOI: 10.1002/ana.25950] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022]
Abstract
Advances in genetic discoveries have created substantial opportunities for precision medicine in neurodevelopmental disorders. Many of the genes implicated in these diseases encode proteins that regulate gene expression, such as chromatin-associated proteins, transcription factors, and RNA-binding proteins. The identification of targeted therapeutics for individuals carrying mutations in these genes remains a challenge, as the encoded proteins can theoretically regulate thousands of downstream targets in a considerable number of cell types. Here, we propose the application of a drug discovery approach originally developed for cancer called "transcriptome reversal" for these neurodevelopmental disorders. This approach attempts to identify compounds that reverse gene-expression signatures associated with disease states. ANN NEUROL 2021;89:199-211.
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Affiliation(s)
- Ryan S. Dhindsa
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Anthony W. Zoghbi
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, USA
- Department of Psychiatry, Columbia University Irving Medical Center, New York, USA; New York State Psychiatric Institute, New York, USA
| | - Daniel K. Krizay
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, USA
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, USA
| | - Chirag Vasavda
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, USA
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, USA
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Berg AT, Gaebler-Spira D, Wilkening G, Zelko F, Knupp K, Dixon-Salazar T, Villas N, Meskis MA, Harwell V, Thompson T, Sims S, Nesbitt G. Nonseizure consequences of Dravet syndrome, KCNQ2-DEE, KCNB1-DEE, Lennox-Gastaut syndrome, ESES: A functional framework. Epilepsy Behav 2020; 111:107287. [PMID: 32759067 DOI: 10.1016/j.yebeh.2020.107287] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 11/28/2022]
Abstract
RATIONALE Developmental epilepsies and encephalopathies (DEEs) are characterized by many severe developmental impairments, which are not well-described. A functional framework could facilitate understanding of their nature and severity and guide the selection instruments to measure improvements in therapeutic trials. METHODS An online survey administered through several parent-organized foundations utilized accepted functional classifications and questionnaires derived from common instruments to determine levels of mobility, fine motor, communication, and feeding functions. Statistical analyses focused on overall levels of function and across-group comparisons adjusted for age. RESULTS From 6/2018 to 2/2020, 252 parents provided information for one or more functional domains. Median age was 7.2 years (interquartile range (IQR): 3.9 to 11.8), and 128 (51%) were females. DEE groups were Dravet syndrome (N = 72), KCNQ2-DEE (N = 80), KCNB1-DEE, (N = 33), Lennox-Gastaut syndrome (LGS; N = 26), electrographic status epilepticus in sleep (ESES; N = 15), and others (N = 26). Overall, functional hand grasp was absent in 48 (20%). Of children ≥2 years old, 60/214 (28%) could not walk independently, 85 (40%) were dependent on someone else for feeding, and 153 (73%) did not effectively communicate with unfamiliar people. Impairments entailing absence or near absence of independent function (profound impairment) were observed in 0, 1, 2, 3, and 4 domains for 58 (25%), 78 (34%), 40 (17%), 33 (14%), and 22 (10%) children, respectively. After adjustment for age, impairment levels varied substantially across DEE group for mobility (p < 0.0001), feeding (p < 0.0001), communication (p < 0.0001), hand grasp (p < 0.0001), and number of profoundly impaired domains (p < 0.0001). Three or four profoundly affected domains were reported in 44% of KCNQ2-DEE participants, followed by LGS (29%), KCNB1-DEE (27%), ESES (7%), and Dravet syndrome (6%). CONCLUSIONS Many children with DEEs experience severe functional impairments, and few children have typical function. As precision therapies will emphasize nonseizures consequences of DEEs, understanding the nature of abilities and impairments will be critical to selecting appropriate outcome measures in therapeutic trials.
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Affiliation(s)
- Anne T Berg
- Division of Neurology, Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago and Department of Pediatrics, Northwestern Feinberg School of Medicine, United States of America.
| | - Deborah Gaebler-Spira
- Shirley Ryan Ability Laboratory, Chicago, IL and Departments Physical Medicine and Rehabilitation and Pediatrics, Northwestern Feinberg School of Medicine, Chicago, IL, United States of America
| | - Greta Wilkening
- Depts. Pediatrics and Neurology, University of Colorado - Anschutz Campus, Aurora, CO, United States of America
| | - Frank Zelko
- Pritzker Department of Psychiatry and Behavioral Health, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States of America
| | - Kelly Knupp
- Depts. Pediatrics and Neurology, University of Colorado - Anschutz Campus, Aurora, CO, United States of America
| | | | - Nicole Villas
- Dravet Syndrome Foundation, Cherry Hill, NJ, United States of America
| | - Mary Anne Meskis
- Dravet Syndrome Foundation, Cherry Hill, NJ, United States of America
| | - Vinez Harwell
- ESES/CSWS/LKS Group, Williamsburg, VA, United States of America
| | - Tina Thompson
- KCNQ2 parent, West Des Moines, IA, United States of America
| | - Scotty Sims
- KCNQ2 Cure Alliance, Denver, CO, United States of America
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Cognitive functions associated with developing prefrontal cortex during adolescence and developmental neuropsychiatric disorders. Neurobiol Dis 2019; 131:104322. [DOI: 10.1016/j.nbd.2018.11.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 09/24/2018] [Accepted: 11/09/2018] [Indexed: 12/30/2022] Open
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Rosch RE, Hunter PR, Baldeweg T, Friston KJ, Meyer MP. Calcium imaging and dynamic causal modelling reveal brain-wide changes in effective connectivity and synaptic dynamics during epileptic seizures. PLoS Comput Biol 2018; 14:e1006375. [PMID: 30138336 PMCID: PMC6124808 DOI: 10.1371/journal.pcbi.1006375] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 09/05/2018] [Accepted: 07/18/2018] [Indexed: 12/31/2022] Open
Abstract
Pathophysiological explanations of epilepsy typically focus on either the micro/mesoscale (e.g. excitation-inhibition imbalance), or on the macroscale (e.g. network architecture). Linking abnormalities across spatial scales remains difficult, partly because of technical limitations in measuring neuronal signatures concurrently at the scales involved. Here we use light sheet imaging of the larval zebrafish brain during acute epileptic seizure induced with pentylenetetrazole. Spectral changes of spontaneous neuronal activity during the seizure are then modelled using neural mass models, allowing Bayesian inference on changes in effective network connectivity and their underlying synaptic dynamics. This dynamic causal modelling of seizures in the zebrafish brain reveals concurrent changes in synaptic coupling at macro- and mesoscale. Fluctuations of both synaptic connection strength and their temporal dynamics are required to explain observed seizure patterns. These findings highlight distinct changes in local (intrinsic) and long-range (extrinsic) synaptic transmission dynamics as a possible seizure pathomechanism and illustrate how our Bayesian model inversion approach can be used to link existing neural mass models of seizure activity and novel experimental methods.
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Affiliation(s)
- Richard E. Rosch
- Wellcome Trust Centre for Neuroimaging, University College London, London, United Kingdom
- Developmental Neurosciences Programme, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Paul R. Hunter
- Department of Developmental Neurobiology & MRC Center for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Torsten Baldeweg
- Developmental Neurosciences Programme, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Karl J. Friston
- Wellcome Trust Centre for Neuroimaging, University College London, London, United Kingdom
| | - Martin P. Meyer
- Department of Developmental Neurobiology & MRC Center for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
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Ho KS, Markham LM, Twede H, Lortz A, Olson LM, Sheng X, Weng C, Wassman ER, Newcomb T, Wassman ER, Carey JC, Battaglia A. A survey of antiepileptic drug responses identifies drugs with potential efficacy for seizure control in Wolf-Hirschhorn syndrome. Epilepsy Behav 2018; 81:55-61. [PMID: 29477837 DOI: 10.1016/j.yebeh.2017.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 12/19/2022]
Abstract
Seizures are present in over 90% of infants and children with Wolf-Hirschhorn syndrome (WHS). When present, they significantly affect quality of life. The goal of this study was to use caregiver reports to describe the comparative efficacies of commonly used antiepileptic medications in a large population of individuals with WHS. A web-based, confidential caregiver survey was developed to capture seizure semiology and a chronologic record of seizure treatments as well as responses to each treatment. Adverse events for each drug were also cataloged. We received 141 complete survey responses (47% response rate) describing the seizures of individuals ranging in age from 4months to 61years (90 females: 51 males). Using the Early Childhood Epilepsy Severity Scale (E-Chess), WHS-associated seizures are demonstrably severe regardless of deletion size. The best-performing antiepileptic drugs (AEDs) for controlling seizures in this cohort were broad spectrum drugs clobazam, levetiracetam, and lamotrigine; whereas, the three commonly used carboxamide class drugs: carbamazepine, phenytoin, and oxcarbazepine, were reported to have little effect on, or even exacerbate, seizures. The carboxamide class drugs, along with phenobarbital and topiramate, were also associated with the highest rate of intolerance due to cooccurrence of adverse events. Levetiracetam, clobazam, and clonazepam demonstrated higher tolerability and comparatively less severe adverse events (Wilcoxon rank sum comparison between performance of levetiracetam and carboxamide class drugs gives a p<0.0001 after multiple comparison adjustment). This is the largest survey to date assessing WHS seizures. This study design is susceptible to possible bias, as the data are largely drawn from caregiver report and investigators had limited access to medical records. Despite this, our data suggest that the genetic etiology of seizures, together with an accurate electroclinical delineation, are important components of drug selection, even in contiguous gene syndromes which may have complex seizure etiologies.
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Affiliation(s)
- Karen S Ho
- Lineagen, Inc., 2677 Parleys Way, Salt Lake City, UT 84109, United States; Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, United States.
| | - Leah M Markham
- Lineagen, Inc., 2677 Parleys Way, Salt Lake City, UT 84109, United States.
| | - Hope Twede
- Lineagen, Inc., 2677 Parleys Way, Salt Lake City, UT 84109, United States.
| | - Amanda Lortz
- 4p- Support Group, 1495 Forest Brooke Way, #262, Delaware, OH 43015, United States.
| | - Lenora M Olson
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, United States.
| | - Xiaoming Sheng
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, United States.
| | - Cindy Weng
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, United States.
| | | | - Tara Newcomb
- Department of Neurology, University of Utah School of Medicine, 175 N Medical Dr, Salt Lake City, UT 84132, United States.
| | - E Robert Wassman
- Lineagen, Inc., 2677 Parleys Way, Salt Lake City, UT 84109, United States.
| | - John C Carey
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, United States.
| | - Agatino Battaglia
- Stella Maris Clinical Research Institute for Child and Adolescent Neuropsychiatry, Pisa, Italy.
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Abstract
For the past three decades, the use of genomics to inform drug discovery and development pipelines has generated both excitement and scepticism. Although earlier efforts successfully identified some new drug targets, the overall clinical efficacy of developed drugs has remained unimpressive, owing in large part to the heterogeneous causes of disease. Recent technological and analytical advances in genomics, however, have now made it possible to rapidly identify and interpret the genetic variation underlying a single patient's disease, thereby providing a window into patient-specific mechanisms that cause or contribute to disease, which could ultimately enable the 'precise' targeting of these mechanisms. Here, we first examine and highlight the successes and limitations of the earlier phases of genomics in drug discovery and development. We then review the current major efforts in precision medicine and discuss the potential broader utility of mechanistically guided treatments going forward.
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Affiliation(s)
- Sarah A Dugger
- Institute for Genomic Medicine, Columbia University Medical Center, Hammer Health Sciences, 1408, 701 West 168th Street, New York, New York 10032, USA
- Department of Genetics & Development, Columbia University Medical Center, Hammer Health Sciences, 1602, 701 West 168th Street, New York, New York 10032, USA
| | - Adam Platt
- AstraZeneca Centre for Genomics Research, Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, UK
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, Hammer Health Sciences, 1408, 701 West 168th Street, New York, New York 10032, USA
- Department of Genetics & Development, Columbia University Medical Center, Hammer Health Sciences, 1602, 701 West 168th Street, New York, New York 10032, USA
- AstraZeneca Centre for Genomics Research, Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, UK
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Delanty N, Cavallleri G. Genomics-Guided Precise Anti-Epileptic Drug Development. Neurochem Res 2017; 42:2084-2088. [DOI: 10.1007/s11064-017-2312-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/23/2017] [Accepted: 05/26/2017] [Indexed: 01/04/2023]
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