Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models

Kiana Mohajeri; Rachita Yadav; Eva D'haene; Philip M Boone; Serkan Erdin; Dadi Gao; Mariana Moyses-Oliveira; Riya Bhavsar; Benjamin B Currall; Kathryn O'Keefe; Nicholas D Burt; Chelsea Lowther; Diane Lucente; Monica Salani; Mathew Larson; Claire Redin; Olga Dudchenko; Erez Lieberman Aiden; Björn Menten; Derek J C Tai; James F Gusella; Sarah Vergult; Michael E Talkowski

doi:10.1016/j.ajhg.2022.09.015

Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models

Am J Hum Genet. 2022 Nov 3;109(11):2049-2067. doi: 10.1016/j.ajhg.2022.09.015. Epub 2022 Oct 24.

Authors

Kiana Mohajeri¹, Rachita Yadav², Eva D'haene³, Philip M Boone⁴, Serkan Erdin⁵, Dadi Gao², Mariana Moyses-Oliveira², Riya Bhavsar⁵, Benjamin B Currall⁵, Kathryn O'Keefe⁵, Nicholas D Burt⁵, Chelsea Lowther², Diane Lucente⁶, Monica Salani⁵, Mathew Larson⁷, Claire Redin⁷, Olga Dudchenko⁸, Erez Lieberman Aiden⁹, Björn Menten³, Derek J C Tai², James F Gusella¹⁰, Sarah Vergult³, Michael E Talkowski¹¹

Affiliations

¹ Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA.
² Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
³ Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
⁴ Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
⁵ Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁶ Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
⁷ Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
⁸ The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, USA.
⁹ The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, USA; UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong, China.
¹⁰ Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
¹¹ Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA. Electronic address: mtalkowski@mgh.harvard.edu.

Abstract

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.

Keywords: CRISPR; MEF2C; TAD; chromatin; genomics; iPSC; induced neurons; neurodevelopmental disorders; topological associating domain; transcriptional regulation.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Genome
Haploinsufficiency
Humans
Induced Pluripotent Stem Cells*
MEF2 Transcription Factors / genetics
Neural Stem Cells*
Neurons
Transcription, Genetic

Substances

MEF2 Transcription Factors
MEF2C protein, human

Abstract

Publication types

MeSH terms

Substances

Grants and funding