Allele-Specific Biased Expression of the CNTN6 Gene in iPS Cell-Derived Neurons from a Patient with Intellectual Disability and 3p26.3 Microduplication Involving the CNTN6 Gene

Abstract

Copy number variations (CNVs) of the human CNTN6 gene caused by megabase-scale microdeletions or microduplications in the 3p26.3 region are often the cause of neurodevelopmental disorders, including intellectual disability and developmental delay. Surprisingly, patients with different copy numbers of this gene display notable overlapping of neuropsychiatric symptoms. The complexity of the study of human neuropathologies is associated with the inaccessibility of brain material. This problem can be overcome through the use of reprogramming technologies that permit the generation of induced pluripotent stem (iPS) cells from fibroblasts and their subsequent in vitro differentiation into neurons. We obtained a set of iPS cell lines derived from a patient carrier of the CNTN6 gene duplication and from two healthy donors. All iPS cell lines displayed the characteristics of pluripotent cells. Some iPS cell lines derived from the patient and from healthy donors were differentiated in vitro by exogenous expression of the Ngn2 transcription factor or by spontaneous neural differentiation of iPS cells through the neural rosette stage. The obtained neurons showed the characteristics of mature neurons as judged by the presence of neuronal markers and by their electrophysiological characteristics. Analysis of allele-specific expression of the CNTN6 gene in these neuronal cells by droplet digital PCR demonstrated that the level of expression of the duplicated allele was significantly reduced compared to that of the wild-type allele. Importantly, according to the sequencing data, both copies of the CNTN6 gene, which were approximately 1 Mb in size, showed no any additional structural rearrangements.

Quantitative prediction of enhancer-promoter interactions

“…Currently, both experimental data describing 3D-genome alterations for known rearrangements and tools modeling spatial landscape of novel variants are limited. In the same time, others 20,21,29,30 and we 31 have recently reported novel variations with unexpected pathological phenotype, which might be explained, at least partially, by changes of chromatin organization 32,33 . Future development and validation of models predicting chromatin contacts in rearranged genome is essential for better understanding of biomedical consequences of these rearrangements.…”

Time origin and structural analysis of the induced CRISPR/cas9 megabase-sized deletions and duplications involving the Cntn6 gene in mice

“…Among these founders, we identified two mosaic animals carrying a 2,274 kb duplication involving the same gene. These mice may be useful experimental models for neurodevelopmental disorders since they contain similar chromosomal rearrangements affecting the CNTN6 gene in human 26–29 . For this reason, it is important to estimate level of unpredicted DNA changes accompanying the rearrangements.…”

Quantitative prediction of enhancer–promoter interactions

“…Currently, both the experimental data describing 3D genome alterations associated with known rearrangements and tools modeling the spatial landscape of novel variants are limited. At the same time, we (Gridina et al 2018) and others (Lupiáñez et al 2015;Franke et al 2016;Redin et al 2017;Zepeda-Mendoza et al 2017) have recently reported novel variations with unexpected pathological phenotypes, which might be explained, at least partially, by changes of chromatin organization (Fishman et al 2018;Spielmann et al 2018). Future development and validation of models predicting chromatin contacts in a rearranged genome is essential for a better understanding of the biological consequences of these rearrangements.…”