Characterization of molecular and cellular phenotypes associated with a heterozygous CNTNAP2 deletion using patient-derived hiPSC neural cells

Abstract

Neurodevelopmental disorders, such as autism spectrum disorders and schizophrenia, are complex disorders with a high degree of heritability. Genetic studies have identified several candidate genes associated with these disorders, including contactin-associated protein-like 2 (CNTNAP2). Traditionally, in animal models or in vitro, CNTNAP2 has been studied by genetic deletion or transcriptional knockdown, which reduces the expression of the entire gene; however, it remains unclear whether the mutations identified in clinical settings are sufficient to alter CNTNAP2 expression in human neurons. Here, using human induced pluripotent stem cells (hiPSCs) derived from two individuals with a large (289 kb) heterozygous deletion in CNTNAP2 (affecting exons 14–15) and discordant clinical outcomes, we have characterized CNTNAP2 expression patterns in hiPSC neural progenitor cells, two independent populations of hiPSC-derived neurons and hiPSC-derived oligodendrocyte precursor cells. First, we observed exon-specific changes in CNTNAP2 expression in both carriers; although the expression of exons 14–15 is significantly decreased, the expression of other exons is upregulated. Second, we observed significant differences in patterns of allele-specific expression in CNTNAP2 carriers that were consistent with the clinical outcome. Third, we observed a robust neural migration phenotype that correlated with diagnosis and exon- and allele-specific CNTNAP2 expression patterns, but not with genotype. In all, our data highlight the importance of considering the nature, location, and regulation of mutated alleles when attempting to connect genome wide association studies to gene function.

When Recessive Genes Mutate to Dominant Gene Action

“…The CNVs and SNVs affecting the transmembrane domain of GRIN1 may very well exert a phenotypic effect by producing completely inactive or 'leaky'NMDA receptors [Lemke et al, 2016]. If, on the other hand, the mutant allele of a gene would suppress the expression of the wild-type allele, as was the case in a patient with an intragenic deletion in the CNTNAP2 gene, significantly less than 50% of wild-type transcript would remain [Lee et al, 2015]. The latter may be the case with the in-frame deletion of CAPN3 [Vissing et al, 2016].…”

Intragenic CNTNAP2 Deletions: A Bridge Too Far

“…In a single case with an inherited intragenic deletion of exons 14 and 15, inducible pluripotent stem cells (iPSC) were generated and induced to neuronal differentiation [Lee et al, 2015]. The deleted allele was preferentially transcribed in the cells derived from the patient, but not in those of the healthy father.…”

Disconnecting CNTNAP2

“…Second, the affected daughter has additional deleterious alleles, which had either arisen de novo or were inherited from her mother, but not from her father. Third, CNTNAP2 alleles with structural deletions may experience incomplete penetrance and variable expressivity as a functional consequence of variable levels of the mutated CNTNAP2 gene being expressed [Lee et al, 2015]. The latter has recently been suggested as a possible contribution to the observed variability among patients with intragenic CNTNAP2 losses [Poot, 2015].…”

“…An association study and a survey of mutations in 2 large cohorts of patients with autism indicated a possible interaction of CNTNAP2 with CNTN6 [Poot, 2014;Mercati et al, 2016]. Yet to what extent and by which mechanism(s) perturbation of these interactions may found that in these cells in their patient the mutated allele was overexpressed, while in the healthy carrier father the full-length transcript was the predominant one [Lee et al, 2015]. The mutated allele would probably be translated into a protein lacking the C-terminal epidermal growth factor-like domain.…”

“…In a case with an inherited heterozygous loss of exons14 and 15 of CNTNAP2 , inducible pluripotent stem cells were generated, which were subsequently made to differentiate into neurons [Lee et al, 2015]. The authors Genomic rearrangements and copy number variations (CNVs) have implicated the contactin-associated protein-like 2 gene (CNTNAP2) in a variety of neurodevelopmental disorders, such as Gilles de la Tourette syndrome, intellectual disability, obsessive compulsive disorder, cortical dysplasia-focal epilepsy syndrome, autism, schizophrenia, Pitt-Hopkins syndrome, and attention deficit hyperactivity disorder [Rodenas-Cuadrado et al, 2014;Poot, 2015].…”