TY - JOUR
T1 - Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models
AU - Mohajeri, Kiana
AU - Yadav, Rachita
AU - D'haene, Eva
AU - Boone, Philip M.
AU - Erdin, Serkan
AU - Gao, Dadi
AU - Moyses-Oliveira, Mariana
AU - Bhavsar, Riya
AU - Currall, Benjamin B.
AU - O'Keefe, Kathryn
AU - Burt, Nicholas D.
AU - Lowther, Chelsea
AU - Lucente, Diane
AU - Salani, Monica
AU - Larson, Mathew
AU - Redin, Claire
AU - Dudchenko, Olga
AU - Aiden, Erez Lieberman
AU - Menten, Björn
AU - Tai, Derek J.C.
AU - Gusella, James F.
AU - Vergult, Sarah
AU - Talkowski, Michael E.
N1 - Funding Information:
We would like to thank Maris Handley and the staff of the Harvard Stem Cell Institute FACS core at Massachusetts General Hospital for helpful discussion and technical assistance with cell sorting for hiPSC clone generation. We would also like to thank Lies Vantomme for excellent technical assistance. This research was supported by grants from the National Institutes of Health: P01GM061354, R01HD096326, R01MH115957, R01MH123155, U01HG011755, R03HD099547, R01NS093200, K08NS117891, and T32GM007748. Support was also provided by the Simons Foundation for Autism Research Initiative, USA (#573206) and by the grants G044615N and 1520518N of the Research Foundation Flanders (FWO). K.M. was supported by the National Science Foundation Graduate Research Fellowship Program (NSF GRFP), USA doctoral fellowship. R.Y. was supported by the Mass General Hospital Fund for Medical Discovery, USA. E.D. and S.V. were respectively supported by a doctoral and postdoctoral fellowship of the Research Foundation Flanders (FWO), Belgium. P.M.B. was supported by 1K08NS117891 and T32GM007748. M.M.O. was supported by the Autism Speaks Postdoctoral Fellowship. Study design: K.M. R.Y. E.D. B.M. J.F.G. S.V. M.E.T. Experiments: K.M. E.D. P.M.B. M.M.O. R.B. B.C. K.O. N.D.B. D.J.C.T. M.S. M.L. Data analysis: K.M. R.Y. E.D. S.E. D.G. C.L. S.V.; Data interpretation: K.M. R.Y. E.D. S.E. S.V. M.E.T.; Manuscript writing: K.M. R.Y. E.D. S.E. J.F.G. S.V. M.E.T. All authors have reviewed and accepted final version of the manuscript. M.E.T. receives research funding and/or reagents from Levo Therapeutics, Microsoft Inc, and Illumina Inc. K.M. initiated employment with Tornado Bio during the writing of this manuscript and is at present an employee of the company. J.F.G. is a founder and member of the scientific advisory board of Triplet Therapeutics, Inc. and has been a paid consultant to Biogen, Inc. Pfizer, Inc. and Wave Biosciences, Inc.
Funding Information:
We would like to thank Maris Handley and the staff of the Harvard Stem Cell Institute FACS core at Massachusetts General Hospital for helpful discussion and technical assistance with cell sorting for hiPSC clone generation. We would also like to thank Lies Vantomme for excellent technical assistance. This research was supported by grants from the National Institutes of Health : P01GM061354 , R01HD096326 , R01MH115957 , R01MH123155 , U01HG011755 , R03HD099547 , R01NS093200 , K08NS117891 , and T32GM007748 . Support was also provided by the Simons Foundation for Autism Research Initiative, USA ( #573206 ) and by the grants G044615N and 1520518N of the Research Foundation Flanders (FWO). K.M. was supported by the National Science Foundation Graduate Research Fellowship Program (NSF GRFP), USA doctoral fellowship. R.Y. was supported by the Mass General Hospital Fund for Medical Discovery, USA. E.D. and S.V. were respectively supported by a doctoral and postdoctoral fellowship of the Research Foundation Flanders (FWO), Belgium. P.M.B . was supported by 1K08NS117891 and T32GM007748 . M.M.O. was supported by the Autism Speaks Postdoctoral Fellowship .
Publisher Copyright:
© 2022 American Society of Human Genetics
PY - 2022/11/3
Y1 - 2022/11/3
N2 - Point mutations and structural variants that directly disrupt the coding sequence of MEF2C have been associated with a spectrum of neurodevelopmental disorders (NDDs). However, the impact of MEF2C haploinsufficiency on neurodevelopmental pathways and synaptic processes is not well understood, nor are the complex mechanisms that govern its regulation. To explore the functional changes associated with structural variants that alter MEF2C expression and/or regulation, we generated an allelic series of 204 isogenic human induced pluripotent stem cell (hiPSC)-derived neural stem cells and glutamatergic induced neurons. These neuronal models harbored CRISPR-engineered mutations that involved direct deletion of MEF2C or deletion of the boundary points for topologically associating domains (TADs) and chromatin loops encompassing MEF2C. Systematic profiling of mutation-specific alterations, contrasted to unedited controls that were exposed to the same guide RNAs for each edit, revealed that deletion of MEF2C caused differential expression of genes associated with neurodevelopmental pathways and synaptic function. We also discovered significant reduction in synaptic activity measured by multielectrode arrays (MEAs) in neuronal cells. By contrast, we observed robust buffering against MEF2C regulatory disruption following deletion of a distal 5q14.3 TAD and loop boundary, whereas homozygous loss of a proximal loop boundary resulted in down-regulation of MEF2C expression and reduced electrophysiological activity on MEA that was comparable to direct gene disruption. Collectively, these studies highlight the considerable functional impact of MEF2C deletion in neuronal cells and systematically characterize the complex interactions that challenge a priori predictions of regulatory consequences from structural variants that disrupt three-dimensional genome organization.
AB - Point mutations and structural variants that directly disrupt the coding sequence of MEF2C have been associated with a spectrum of neurodevelopmental disorders (NDDs). However, the impact of MEF2C haploinsufficiency on neurodevelopmental pathways and synaptic processes is not well understood, nor are the complex mechanisms that govern its regulation. To explore the functional changes associated with structural variants that alter MEF2C expression and/or regulation, we generated an allelic series of 204 isogenic human induced pluripotent stem cell (hiPSC)-derived neural stem cells and glutamatergic induced neurons. These neuronal models harbored CRISPR-engineered mutations that involved direct deletion of MEF2C or deletion of the boundary points for topologically associating domains (TADs) and chromatin loops encompassing MEF2C. Systematic profiling of mutation-specific alterations, contrasted to unedited controls that were exposed to the same guide RNAs for each edit, revealed that deletion of MEF2C caused differential expression of genes associated with neurodevelopmental pathways and synaptic function. We also discovered significant reduction in synaptic activity measured by multielectrode arrays (MEAs) in neuronal cells. By contrast, we observed robust buffering against MEF2C regulatory disruption following deletion of a distal 5q14.3 TAD and loop boundary, whereas homozygous loss of a proximal loop boundary resulted in down-regulation of MEF2C expression and reduced electrophysiological activity on MEA that was comparable to direct gene disruption. Collectively, these studies highlight the considerable functional impact of MEF2C deletion in neuronal cells and systematically characterize the complex interactions that challenge a priori predictions of regulatory consequences from structural variants that disrupt three-dimensional genome organization.
KW - chromatin
KW - CRISPR
KW - genomics
KW - induced neurons
KW - iPSC
KW - MEF2C
KW - neurodevelopmental disorders
KW - TAD
KW - topological associating domain
KW - transcriptional regulation
UR - http://www.scopus.com/inward/record.url?scp=85140968299&partnerID=8YFLogxK
U2 - 10.1016/j.ajhg.2022.09.015
DO - 10.1016/j.ajhg.2022.09.015
M3 - Article
C2 - 36283406
AN - SCOPUS:85140968299
SN - 0002-9297
VL - 109
SP - 2049
EP - 2067
JO - American Journal of Human Genetics
JF - American Journal of Human Genetics
IS - 11
ER -