Genome-wide molecular effects of the neuropsychiatric 16p11 CNVs in an iPSC-to-iN neuronal model

Abstract

Copy number variants (CNVs), either deletions or duplications, at the 16p11.2 locus in the human genome are known to increase the risk for autism spectrum disorders (ASD), schizophrenia, and for several other developmental conditions. Here, we investigate the global effects on gene expression and DNA methylation using a 16p11.2 CNV patientderived induced pluripotent stem cell (iPSC) to induced neuron (iN) cell model system.This approach revealed genome-wide and cell-type specific alterations to both gene expression and DNA methylation patterns and also yielded specific leads on genes potentially contributing to some of the known 16p11.2 patient phenotypes. PCSK9 is identified as a possible contributing factor to the symptoms seen in carriers of the 16p11.2 CNVs. The protocadherin (PCDH) gene family is found to have altered DNA methylation patterns in the CNV patient samples. The iPSC lines used for this study are available through a repository as a resource for research into the molecular etiology of the clinical phenotypes of 16p11.2 CNVs and into that of neuropsychiatric and neurodevelopmental disorders in general.

Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes

“…The motivation behind our approach is that in 16p11.2 and 22q11.2 CNV carriers, variation in gene copy number is expected to lead to variation in RNA copy number (with possible downstream effects on protein product). Expression measurements in mouse or human cell lines carrying 16p11.2 and 22q11.2 deletions and duplications confirm that for nearly all genes, duplication carriers have increased expression of individual CNV genes compared to controls and deletion carriers have reduced expression compared to controls [44][45][46][47][48][49]. As the breakpoints of these CNVs do not disrupt the coding regions of individual genes, we believe that the variation in expression of one or more of the genes is the cause of pathogenicity.…”

“…In order to find genes at copy number variant loci driving brain-related disorders, we performed an association analysis between imputed gene expression levels and five traits: ASD, bipolar disorder, schizophrenia, body mass index, and IQ. It has been observed that the 16p11.2 and 22q11.2 copy number variants affect expression of nearby genes, so we included genes flanking the CNV locus by 200kb in both directions [44,45,66]. Overall, we tested 83 coding and noncoding genes at or near 22q11.2 and 46 genes at or near 16p11.2 for which a predictive model was available (S2 Table, S1 Fig).…”

Combinations of genes at the 16p11.2 and 22q11.2 CNVs contribute to neurobehavioral traits

“…Data in humans and mice suggest that the expression of 16p11.2 and 22q11.2 CNV genes is consistently upregulated/downregulated in duplication/deletion carriers [17][18][19][20]. From this observation, we can propose that gene expression dysregulation (and potential downstream protein expression) is likely to be a pathophysiological mechanism of CNV-associated traits.…”

Complete and haplotype-specific sequence assembly of segmental duplication-mediated genome rearrangements using CRISPR-targeted ultra-long read sequencing (CTLR-Seq)

“…Due to their strong associations with neuropsychiatric disorders, the 22q11.2 and 16p11.2 CNVs serve as key points of entry for the investigations of molecular etiologies of neurodevelopmental disorders (Blumenthal et al, 2014;Migliavacca et al, 2015;Deshpande et al, 2017;Ward et al, 2020 (Fig 1), which consist of >100 kb segmental duplications (SegDup) with >99% similarity to each other (Bailey et al, 2002). The duplicated sequences between BP4/5 are placed in direct (non-inverted) orientation which act as substrates for rearrangement creating either deletion or duplication (Bailey et al, 2002;Zufferey et al, 2012).…”

“…Similar to 22q11DS (Malhotra and Sebat, 2012; Kirov, 2015; Deshpande and Weiss, 2018), the 16p11.2 CNVs are also associated with broad developmental consequences including speech/language delay, intellectual disability, developmental delay, and ADHD; ~50% of either deletion or duplication carriers have at least one psychiatric diagnosis (Ghebranious et al, 2007; Green Snyder et al, 2016; Steinman et al, 2016; Bernier et al, 2017; Niarchou et al, 2019). Due to their strong associations with neuropsychiatric disorders, the 22q11.2 and 16p11.2 CNVs serve as key points of entry for the investigations of molecular etiologies of neurodevelopmental disorders (Blumenthal et al, 2014; Migliavacca et al, 2015; Deshpande et al, 2017; Ward et al, 2020).…”