CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells.
CHD8(chromodomain helicase DNA-binding protein 8), which codes for a member of the CHD family of ATP-dependent chromatin-remodeling factors, is one of the most commonly mutated genes in autism spectrum disorders (ASD) identified in exome-sequencing studies. Loss of function mutations in the gene have also been found in schizophrenia (SZ) and intellectual disabilities and influence cancer cell proliferation. We previously reported an RNA-seq analysis carried out on neural progenitor cells (NPCs) and monolayer neurons derived from induced pluripotent stem (iPS) cells that were heterozygous forCHD8knockout (KO) alleles generated using CRISPR-Cas9 gene editing. A significant number of ASD and SZ candidate genes were among those that were differentially expressed in a comparison of heterozygous KO lines (CHD8+/-) vs isogenic controls (CHD8+/-), including the SZ and bipolar disorder (BD) candidate geneTCF4, which was markedly upregulated inCHD8+/-neuronal cells.



In the current study, RNA-seq was carried out onCHD8+/-and isogenic control (CHD8+/+) cerebral organoids, which are 3-dimensional structures derived from iPS cells that model the developing human telencephalon.



TCF4expression was, again, significantly upregulated. Pathway analysis carried out on differentially expressed genes (DEGs) revealed an enrichment of genes involved in neurogenesis, neuronal differentiation, forebrain development, Wnt/β-catenin signaling, and axonal guidance, similar to our previous study on NPCs and monolayer neurons. There was also significant overlap in ourCHD8+/-DEGs with those found in a transcriptome analysis carried out by another group using cerebral organoids derived from a family with idiopathic ASD. Remarkably, the top DEG in our respective studies was the non-coding RNADLX6-AS1, which was markedly upregulated in both studies;DLX6-AS1regulates the expression of members of theDLX(distal-less homeobox) gene family.DLX1was also upregulated in both studies.DLXgenes code for transcription factors that play a key role in GABAergic interneuron differentiation. Significant overlap was also found in a transcriptome study carried out by another group using iPS cell-derived neurons from patients with BD, a condition characterized by dysregulated WNT/β-catenin signaling in a subgroup of affected individuals.



Overall, the findings show that distinct ASD, SZ, and BD candidate genes converge on common molecular targets-an important consideration for developing novel therapeutics in genetically heterogeneous complex traits.
Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA.
Ping
P
Wang
Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey.
Ryan
R
Mokhtari
Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey.
Erika
E
Pedrosa
Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey.
Michael
M
Kirschenbaum
Erciyes University School of Medicine, Kayseri, Turkey.
Can
C
Bayrak
Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA.|Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA.|Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA.
Deyou
D
Zheng
Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA.|Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey.|Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA.|Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA.
Herbert M
HM
Lachman
D000067877:Autism Spectrum Disorder / Q000235:genetics; D001714:Bipolar Disorder / Q000235:genetics; D064113:CRISPR-Cas Systems; D002454:Cell Differentiation; D002478:Cells, Cultured; D004268:DNA-Binding Proteins / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D055786:Gene Knockout Techniques; D053263:Gene Regulatory Networks; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000166:cytology*; D001523:Mental Disorders / Q000235:genetics*; D009154:Mutation; D009940:Organoids / Q000166:cytology*; D012559:Schizophrenia / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D013687:Telencephalon / Q000166:cytology*; D014157:Transcription Factors / Q000235:genetics*
C523331:CHD8 protein, human; D004268:DNA-Binding Proteins; D014157:Transcription Factors
Autism; Beta-catenin; Bipolar disorder; Cancer; DLX6-AS1; Distal-less homeobox; Gabaergic; HMGA2; Schizophrenia; TCF4; Wnt; ZNF132