Intellectualdisability(ID)affects1-3%ofthepopulation,resultingincognitiveandadaptivebehavioral deficits.ManygenesareassociatedwithID,includingmultiplemutationsinKDM5C,anX-linkedgenewhichwe discoveredtobeahistonedemethylaseadecadeago.Inthepastfundingcycle,wefoundthatKDM5Cpatient mutations reduce both protein stability and catalytic activity. We showed that a mouse Kdm5c knock-out (KO) model recapitulated the cognitive and behavioral deficits seen in human patients. Kdm5c bound primarily at promoters in terminally differentiated mouse neurons to modulate methylation at lysine 4 of histone 3 (H3K4), andKdm5clossaffectedtheexpressionofneuronalgenesintheamygdala.Furtherstudiesofconditionalmouse Kdm5cKOshavesuggestedthatKdm5cpotentiallyplaysaneurodevelopmentalrole.Tostudythefunctionof KDM5Cduringneurodevelopmentinahumanmodel,wehavegeneratedpatient-derivediPScelllinesbearing KDM5C mutations, and isogenic lines with the mutations corrected, both of which can undergo neuronal differentiationinculture.ThesecelllinesprovideanunprecedentedopportunitytoexploretheeffectsofKDM5C inawell-definedandexperimentallyaccessiblehumandevelopmentalsystem. The goals of this work are to obtain a comprehensive molecular and cellular understanding of how KDM5C regulateshumanneurodevelopment.Wewillconducthigh-resolutiontime-courseanalysestodetermineexactly which stages of neuronal differentiation, and which cell types, are compromised by KDM5C mutation. We will investigatethefunctionalityofKDM5C-mutantneuronsbyinterrogatingtheexpressionofsynapticmarkersand electrophysiology.Becausesomeaspectsofbraindevelopment(e.g.formationofmultiplecelltypesandtheir organization)arenotrecapitulatedina2Dculturesystem,wewilluse3Dhumanbrainorganoidsgeneratedfrom mutant and corrected iPS cells to investigate the roles of KDM5C in promoting brain growth, generating the appropriate diversity of neural cell types, and facilitating neuronal network connectivity. Our findings will be validatedinvivoduringembryogenesisofWTandKdm5cKOmice,andthecriticaltimingandlocationofKdm5c activitydeterminedbyexpressingordeletingKdm5cinspecificstages/celltypes.Toinvestigatethemolecular mechanisms of the neuronal differentiation defects in KDM5C mutant cells, we will determine transcriptional profiles of mutant and corrected iPS cells during differentiation in 2D and 3D cultures. Because the critical genomic targets of KDM5C (e.g. promoters, enhancers) during neurodevelopment are unknown, we will map KDM5C binding sites genome-wide during 2D neuronal differentiation, and determine how KDM5C mutations alter the chromatin landscape. Finally, we will use biochemical approaches to identifyKDM5C regulators, and investigatetheireffectsonKDM5Cfunctionandneurodevelopment.Thesestudieswillshedcriticalnewlighton KDM5Cfunctionduringneurodevelopment,andprovideabasisfordesigningtherapeuticstrategiestotreatID.

Public Health Relevance

Intellectualdisability(ID),adevastatingdisease,canbecausedbymutationsinahistone-modifyinggene (KDM5C)thathelpstocontrolhowDNAisorganizedwithinacell,whichultimatelydetermineswhichgenes areturnedonoroff.OurgoalsaretoinvestigatehowKDM5Cpromotesnormalbraindevelopmentusing humanpatient-derivedcellsandmousemodels,andtodeterminehowitinfluencesDNAorganizationtoturn appropriategenesonandoff.ThesestudieswillprovideabasisfordevelopingstrategiestotreatID.

Agency
National Institute of Health (NIH)
Institute
National Institute of Mental Health (NIMH)
Type
Research Project (R01)
Project #
2R01MH096066-06A1
Application #
9522479
Study Section
Molecular Neurogenetics Study Section (MNG)
Program Officer
Panchision, David M
Project Start
2012-08-10
Project End
2023-02-28
Budget Start
2018-06-01
Budget End
2019-02-28
Support Year
6
Fiscal Year
2018
Total Cost
Indirect Cost
Name
Boston Children's Hospital
Department
Type
DUNS #
076593722
City
Boston
State
MA
Country
United States
Zip Code
Iberg-Badeaux, Aimee; Collombet, Samuel; Laurent, Benoit et al. (2017) A Transcription Factor Pulse Can Prime Chromatin for Heritable Transcriptional Memory. Mol Cell Biol 37:
Jambhekar, Ashwini; Anastas, Jamie N; Shi, Yang (2017) Histone Lysine Demethylase Inhibitors. Cold Spring Harb Perspect Med 7:
Murn, Jernej; Shi, Yang (2017) The winding path of protein methylation research: milestones and new frontiers. Nat Rev Mol Cell Biol 18:517-527
Scandaglia, Marilyn; Lopez-Atalaya, Jose P; Medrano-Fernandez, Alejandro et al. (2017) Loss of Kdm5c Causes Spurious Transcription and Prevents the Fine-Tuning of Activity-Regulated Enhancers in Neurons. Cell Rep 21:47-59
Wei, Gengze; Deng, Xinxian; Agarwal, Saurabh et al. (2016) Patient Mutations of the Intellectual Disability Gene KDM5C Downregulate Netrin G2 and Suppress Neurite Growth in Neuro2a Cells. J Mol Neurosci 60:33-45
Iwase, Shigeki; Brookes, Emily; Agarwal, Saurabh et al. (2016) A Mouse Model of X-linked Intellectual Disability Associated with Impaired Removal of Histone Methylation. Cell Rep 14:1000-1009
Murn, Jernej; Teplova, Marianna; Zarnack, Kathi et al. (2016) Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt. Nat Struct Mol Biol 23:16-23
Greer, Eric Lieberman; Blanco, Mario Andres; Gu, Lei et al. (2015) DNA Methylation on N6-Adenine in C. elegans. Cell 161:868-78
Murn, Jernej; Zarnack, Kathi; Yang, Yawei J et al. (2015) Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Genes Dev 29:501-12
Brookes, Emily; Laurent, Benoit; Õunap, Katrin et al. (2015) Mutations in the intellectual disability gene KDM5C reduce protein stability and demethylase activity. Hum Mol Genet 24:2861-72

Showing the most recent 10 out of 22 publications