Genetics and Epigenetic Control of Genome Function in Brain Development and Disease
: Epigenetics, Neuroepigenetics, DNA methylation, Chromatin Organization, Genome and Epigenome Editing, CRISPR, MeCP2, CDKL5, Neurexin, Rett Syndrome, Autism, Major Depression
Description of Research
A fundamental question in Genetics and Neuroscience is how the brain executes genetic programs while maintaining the ability to adapt to the environment. The underlying molecular mechanisms are not well understood, but epigenetic regulation, mediated by DNA methylation and chromatin organization, provides an intricate platform bridging genetics and the environment, and allows for the integration of intrinsic and environmental signals into the genome and subsequent translation of the genome into stable yet adaptive functions in the brain. Impaired epigenetic regulation has been implicated in many neurodevelopmental and neuropsychiatric disorders.
The Zhou laboratory is interested in understanding the epigenetic mechanisms that integrate environmental factors with the genetic code to govern brain development and function, elucidating the pathophysiology of specific neurodevelopmental disorders with known genetic causes such as Rett syndrome and CDKL5 deficiency, and illuminating the pathogenesis of selective neuropsychiatric disorders with complex genetic traits such as autism and major depression. We use a variety of cutting-edge genomic technologies, together with cellular and physiological assays in genetically modified mice, to pursue our interests, and aim to ultimately translate our findings into therapeutic development to improve treatment for neurodevelopmental and neuropsychiatric disorders.
1) Defining the stress-induced epigenetic code underlying depressive-like behaviors
The genetic underpinnings of neuropsychiatric disorders are highly complex, involving multifaceted interactions between risk genes and the environment. It is known that environmental factors such as adverse early life events or chronic traumatic experience confer significantly greater susceptibility to psychiatric conditions later in life. However, the pathogenic mechanisms by which environmental factors interact with genetic programs in the nervous system to trigger psychiatric illness remain poorly understood. To gain insights into this process on the molecular level, we have employed both bulk and single-nucleus next-generation sequencing technologies to identify stress-induced epigenetic modifications from individual neuronal cell types and followed up on potential targets using novel genetically modified mice. Using CRISPR-mediated genomic and epigenomic editing techniques, we are prepared to evaluate the causal relationship between stress-induced epigenetic changes and maladaptive behaviors, and to elucidate the key signaling pathways that mediate gene-environment interactions in the brain.
2) Elucidating the molecular basis of Rett Syndrome
Rett Syndrome (RTT) is a neurodevelopmental disorder characterized by developmental regression, motor dysfunction, and cognitive deficits. The majority of RTT cases are associated with mutations on the X-linked gene encoding MeCP2, a methyl-CpG binding protein involved in organizing chromatin and modulating gene expression. To understand the molecular pathogenesis of RTT, we have developed mouse models recapitulating RTT-associated mutations. We found that mice with RTT-associated missense mutations, such as R106W, T158M and T158A, develop RTT-like phenotypes and show deficits in neural circuitry. These mutations decrease the binding of MeCP2 to methylated DNA and concomitantly reduce MeCP2 protein stability, leading to gene expression and cellular morphological changes in a neuronal cell type-specific manner. We have also uncovered cell autonomous and non-cell autonomous functions of MeCP2 in the regulation of gene expression both transcriptionally in the nucleus and post-transcriptionally in the cytoplasm. Given the postulated role of MeCP2 in genome organization, we are prepared to investigate how MeCP2 dysfunction leads to changes in chromatin architecture while gaining molecular insights into the pathogenesis of Rett syndrome.
3) Understanding the pathogenic mechanisms of CDKL5 deficiency
CDKL5 deficiency disorder (CDD) is a disorder caused by genetic defects in the X-linked gene encoding cyclin-dependent kinase-like 5 (CDKL5). Patients with CDKL5 dysfunction show early-onset intractable seizures and severe neurodevelopmental impairment, and are frequently diagnosed with a number of disorders including Infantile Spasms, West Syndrome, Lennox-Gastaut, atypical Rett Syndrome, and autism. To gain insight into the pathogenic mechanisms underlying CDKL5-related disorders, we have developed mouse models in which the CDKL5 gene is ablated or modified. We found that loss of functional CDKL5 disrupts multiple signal transduction pathways, impairs hippocampal event-related potentials, and leads to autistic-like phenotypes in mice. We have employed a genetic strategy to dissect the spatial and temporal contribution of CDKL5 to brain development and function, and have also engineered conditional rescue mouse models to determine the reversibility of CDD-related phenotypes. We are prepared to identify the molecular targets of CDKL5, delineate the optimal time window amenable for treatment, and investigate the neural mechanisms by which CDKL5 dysfunction leads to early onset seizures and cognitive deficits.
4) Exploring the coding and decoding of the methylome in neurons
Cytosine methylation (5mC), mostly at CpG dinucleotides in mammals, is a central epigenetic mark essential for development. Interestingly, neurons have a unique DNA methylation profile, with large amounts of non-CpG DNA methylation (mCH) and hydroxymethylcytosine (5hmC). While we can now profile DNA methylation genome-wide at single-base resolution, how the neuronal methylome is established and maintained, and how the neuron interprets the methylome to affect gene expression and chromatin structure remain poorly understood. Moreover, recent studies have challenged the stability of the methylome in postmitotic neurons and have coupled changes in DNA methylation at specific loci to adaptive behaviors. We are interested in understanding how DNA methylation is coded and decoded genome-wide to help establish and maintain neuronal function across the lifetime. We have generated a variety of in vivo tools to study the functional significance of 5mC and 5hmC in neural development, the role of the methylome in the establishment of neuronal identity, and the molecular mechanisms by which the methylome modulates genome function in the brain.
Experimental Techniques and Themes:
“-Omics” studies using bulk and single-cell next-generation sequencing technologies; Epigenetic remodeling using adapted CRISPR-editing systems; Generation of mouse models using CRISPR or ES cell-based homologous recombination; Mouse behavioral assessment and characterization; Examination of in vivo neuronal connectivity with confocal microscopy; Analysis of neural circuit function with electrophysiology; Biochemical characterization of signaling transduction pathways, and more.
Current Lab Members
Yugong Ho, Senior Research Investigator
Joanna Medina, Postdoctoral Fellow
Xie (Philip) Song, Postdoctoral Fellow
Zijie (Jack) Xia, Postdoctoral Fellow
Daniel Connolly, MD/PhD Student in NGG
Dayne Martinez, MD/PhD Student in NGG
Yaohao Zhang, MS student in Bioengineering
Remy Stuckey, Research Specialist
Zachary Spritzer, Research Specialist
Undergraduate Research Assistants
Sumiya Olsen, Yanjie Zhang, Maria Villela
Darren Goffin (2009-2014), IRSF sponsored postdoctoral Fellow, now Assistant Professor and Lecturer at the University of York; Judy Wang (NGG 2010-2014), Behavioral and Cognitive Neuroscience TG32 Trainee, Winner of Tom Kadesch Prize in Genetic Research, now Director of Business Development at Linus Health; Brian Johnson (CAMB 2010-2016), Trainee of CMB TG32, UNCF/Merck Graduate Science Research Awardee, now Postdoc Fellow at Stanford University; Le Zhang (2010-2011), Postdoc Fellow, now Assistant Professor at Yale University; Kathleen Wood (CAMB 2011-2016), Trainee of Genetics TG32, now Clinical Genomic Scientist at Children's Hospital of Philadelphia; Erina Hara (2011-2012), Postdoc Fellow, now Scientific Research Project Manager at Columbia University Irving Medical Center; Janine Lamonica (2012-2018), IRSF sponsored postdoctoral Fellow, now Senior Research Investigator and Project Lead in the Gene Therapy Program at University of Pennsylvania; Yingtao (Jerry) Zhao (2012-2019), Postdoc Fellow, now Assistant professor at the New York Institute of Technology; Maria Fasolino (NGG 2013-2017), now Scientific Director of the Autism Spectrum Program of Excellence (ASPE) at Penn; Deborah Kwon (2013-2020), Postdoctoral trainee of Neurodevelopmental Disabilities TG32, now Scientist at Biogen; Sheng Tang (NGG MD/PhD 2015-2018), Recipient of NIH/NRSA F30 Fellowship, now Resident Fellow at the Medical Center of Northwestern University; Barbara Terzic (NGG 2015-2020), Recipient of NIH/NRSA F31 Fellowship, Saul Winegrad Awardee for Outstanding Dissertation, now Research Scientist at Spark Therapeutics; Bing Xu (2019-2021), Postdoc Fellow, now Associate Investigator at the First Affiliated Hospital of Shandong First Medical University; Andrew Edmondson (2018-2021), NIH K08 Awardee, now Assistant Professor at Children's Hospital of Philadelphia and University of Pennsylvania.
Research Specialists/Post-Baccalaureate Students
Maria Amorim (2009-2010), Graduate Student at Hospital A.C. Camargo; Megan Allen (2009-2011), Graduate Student at Georgetown University; Nicha Ubol (2011-2012), Nursing Student at Rutgers University; Arith Reyes (2012-2013), Medical Student at the Washington University In St. Louis; Hallene Guo (2014-2015), Medical Student at the University of Maryland; Jun Yeop Lee (2013-2015); Medical Student at Mount Sinai Icahn School of Medicine; Jie Zhou (2018-2019), Graduate Student at the University of Connecticut; George Gardner (2018-2019), Medical Subscriber at the Hospital of the University of Pennsylvania; Joshua Ross (2020-2021), Consultant at Blockfolio; Erin Nugent (2019-2021), Scientist at Carisma Therapeutics.
Arith Reyes (2009-2012); Suzie Hong (2010-2013); Naomi Hachen (2010); Bryan Cam (2011-2012); Serena Zhou (2011-2012); Diana Nwokoye (2013); Olivia Rabe (2013); Hallene Guo (2013-2014); Daniel Bu (2013-2016); Katarina Pance (2016-2017); Zhou Zhou (2017); Hansoo Chang (2017); Katherine Sizov (2016-2018); Nicolas Sarmiento (2016-2019); Christine Liu (2017-2020); Dasha Zaitseva (2018-2021); Isabel Zhang (2019-2021); Dennis Fleysh (2021); Melody Yu (2021); Elana Grajales (2021); Amy Fang (2020-2021); Cadmus Cai (2021-2022); Emily Guo (2019-2022).
Kwon DY, Xu B#, Hu P#, Zhao Y-T, Beagan JA, Nofziger JH, Cui Y, Phillips-Cremins JE, Blendy JA, Wu H, Zhou Z*: Neuronal Yin Yang1 in the prefrontal cortex regulates transcriptional and behavioral responses to chronic stress in mice. Nature Communications 13(1): 55. doi: 10.1038/s41467-021-27571-3, 2022.
Terzic B, Davatolhagh MF, Ho Y, Tang S, Liu Y-T, Xia Z, Cui Y, Fuccillo MV and Zhou Z*: Temporal manipulation of Cdkl5 reveals essential post-developmental functions and reversible CDKL5 deficiency disorder-related deficits. Journal of Clinical Investigation 131(20): e143655, 2021.
Terzic B#, Cui Y#, Edmondson AC#, Tang S, Sarmiento N, Zaitseva D, Marsh ED, Coulter DA and Zhou Z*: X-linked cellular mosaicism underlies age-dependent occurrence of seizure-like events in mouse models of CDKL5 deficiency disorder. Neurobiology of Disease 148: 105176. doi: 10.1016/j.nbd.2020.105176, 2020.
Connolly DR and Zhou Z*: Genomic Insights into MeCP2 Function: A Role for the Maintenance of Chromatin Architecture. Current Opinion in Neurobiology 59: 174-179, 2019.
Lamonica JM and Zhou Z*: Disentangling chromatin architecture to gain insights
into the etiology of brain disorders. Current Opinion in Genetics and Development 55: 76-81, 2019.
Tang S#, Terzic B#, Wang I-T, Sarmiento N, Sizov K, Cui Y, Takano H, Marsh ED, Zhou Z* and Coulter DA* (*co-corresponding author): Altered NMDAR Signaling Underlies Autistic-like Features in Mouse Models of CDKL5 Deficiency Disorder. Nature Communications 10: 2655. doi: 10.1038/s41467-019-10689-w. 2019.
Zhao YT, Kwon DY, Johnson BS, Fasolino M, Lamonica JM, Kim YJ, Zhao BS, He C, Vahedi G, Kim TH and Zhou Z*: Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domains. Genome Research 28(7): 933-942, 2018.
Johnson BS#, Zhao Y#, Fasolino M#, Lamonica JM, Kim YJ, Georgakilas G, Wood KH, Bu D, Cui Y, Goffin D, Vahedi G, Kim TH and Zhou Z*: Biotin tagging of MeCP2 in mice reveals contextual insights into the Rett syndrome transcriptome. Nature Medicine 23(10): 1203-1214, 2017.
Kwon DY, Zhao YT, Lamonica JM and Zhou Z*: Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC. Nature Communications 8: 15315. doi: 10.1038/ncomms15315, 2017.
Lamonica JM, Kwon DY, Goffin D, Fenik P, Johnson BS, Cui Y, Guo H, Veasey S and Zhou Z*: Elevating expression of MeCP2 T158M rescues DNA binding and Rett syndrome–like phenotypes. Journal of Clinical Investigation 127(5): 1889-1904, 2017.
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Last updated: 07/29/2022
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