Network effects of the neuropsychiatric 15q13.3 microdeletion on the transcriptome and epigenome in human induced neurons

Abstract

Heterozygous deletions in the 15q13.3 region are associated with several neuropsychiatric disorders including autism, schizophrenia, and attention deficit hyperactivity disorder. Several genes within the 15q13.3 deletion region may play a role in neuronal dysfunction, based on association studies in humans and functional studies in mice, but the intermediate molecular mechanisms remain unknown.We analyzed the genome-wide effects of the 15q13.3 microdeletion on the transcriptome and epigenome. Induced pluripotent stem cell (iPSC) lines from three patients with the typical heterozygous 15q13.3 microdeletion and three sex-matched controls were generated and converted into induced neurons (iNs) using the neurogenin-2 induction method. We analyzed genome-wide gene expression using RNA-Seq, genome-wide DNA methylation using SeqCap-Epi, and genome-wide chromatin accessibility using ATAC-Seq, in both iPSCs and iNs. In both cell types, gene copy number change within the 15q13.3 microdeletion was accompanied by significantly decreased gene expression and no compensatory changes in DNA methylation or chromatin accessibility, supporting the model that haploinsufficiency of genes within the deleted region drives the disorder. Further, we observed global effects of the deletion on the transcriptome and epigenome, with the effects being cell type specific and occurring at discrete loci. Several genes and pathways associated with neuropsychiatric disorders and neuronal development were significantly altered, including Wnt signaling, ribosome biogenesis, DNA binding, and clustered protocadherins. This molecular systems analysis of a large neuropsychiatric microdeletion can also be applied to other brain relevant chromosomal aberrations to further our etiological understanding of neuropsychiatric disorders. IntroductionThe neuropsychiatric 15q13.3 microdeletion (OMIM 612001) is a heterozygous deletion of approximately 1.5-2 Mb at coordinates 30.5 Mb to 32.5 Mb on chromosome 15 (hg19) [1]. The deletion breakpoints lie within two regions of segmental duplications, which likely mediate the creation of the recurrent microdeletion via non-allelic homologous recombination [2]. The 15q13.3 microdeletion has an estimated prevalence of 1 in 40,000 individuals, and was first reported in 2008, in nine individuals with mental retardation, seizures, and mild facial dysmorphism [3]. Since then, several other phenotypes have been associated with this copy number variant (CNV), including autism spectrum disorder, schizophrenia, mood disorders, attention deficit hyperactivity disorder, hypotonia, and cardiac defects [1,4,5].The most common form of the 15q13.3 microdeletion, which is the subject of our study, results in the heterozygous loss of seven protein-coding genes (CHRNA7, FAN1, TRPM1, KLF13, OTUD7A, MTMR10, ARHGAP11B) and one microRNA (MIR211) [4]. Several of these genes have previously been investigated as candidates for having a role in the neuropsychiatric symptoms associated with the CNV. The most frequently proposed candidate gene is C...

Meta-analyses of genome wide association studies in lines of laying hens divergently selected for feather pecking using imputed sequence level genotypes

“…disorder [26]. Furthermore, we found three intronvariants in LRP1B (lowest p-value 8.392 × 10 − 10 ) to be significantly associated with the trait FPD.…”

“…In proximity to KCHN8 we discovered five significant variants (lowest p-value 7.451 × 10 − 10 ). KCNH8 was identified in the context of the neuropsychiatric 15q13.3 microdeletion which is associated with several neuropsychiatric disorders including autism, schizophrenia, and attention deficit hyperactivity disorder [ 26 ]. Furthermore, we found three intron-variants in LRP1B (lowest p -value 8.392 × 10 − 10 ) to be significantly associated with the trait FPD.…”

“…We identified several significant genomic variants associated with the trait FPD, that mostly affect genes that have been previously associated with psychiatric and neurological disorders. Among them SPATS2L , ZEB2 , and KCHN8 , all of which have been identified in schizophrenia studies [ 12 – 17 , 24 , 26 ]. Furthermore, the genes ZEB2 and MRPL13 , which are affected by significantly associated variants, respond to nicotine treatment [ 25 , 30 ].…”

Impaired OTUD7A-dependent Ankyrin regulation mediates neuronal dysfunction in mouse and human models of the 15q13.3 microdeletion syndrome

“…Recent transcriptomic studies of the 15q13.3 microdeletion have implicated a wide array of potentially affected pathways 29,31,102 . However, changes in the transcriptome do not always align with changes to the proteome.…”

“…Cortical excitatory and inhibitory neurons have both been implicated 26,[28][29][30] , but how dysfunction of either of these cell types occurs at the molecular level is not understood. Human studies on 15q13.3 microdeletion iPSCs have identified transcriptional alterations in developing cortical neural cells, but the functional consequences remain unknow 31 . Previous work has identified several candidate genes in the locus contributing to the clinical phenotype including Cholinergic Receptor Nicotinic Alpha 7 Subunit (CHRNA7), Fanconi-associated nuclease 1 (FAN1) and Ovarian tumor domain containing protein 7A (OTUD7A) 18,21,30,[32][33][34][35][36] .…”