Novel syndromic neurodevelopmental disorder caused by de novo deletion of CHASERR, a long noncoding RNA

Abstract

Genes encoding long non-coding RNAs (lncRNAs) comprise a large fraction of the human genome, yet haploinsufficiency of a lncRNA has not been shown to cause a Mendelian disease. CHASERR is a highly conserved human lncRNA adjacent to CHD2-a coding gene in which de novo loss-of-function variants cause developmental and epileptic encephalopathy. Here we report three unrelated individuals each harboring an ultra-rare heterozygous de novo deletion in the CHASERR locus. We report similarities in severe developmental delay, facial dysmorphisms, and cerebral dysmyelination in these individuals, distinguishing them from the phenotypic spectrum of CHD2 haploinsufficiency. We demonstrate reduced CHASERR mRNA expression and corresponding increased CHD2 mRNA and protein in whole blood and patient-derived cell lines-specifically increased expression of the CHD2 allele in cis with the CHASERR deletion, as predicted from a prior mouse model of Chaserr haploinsufficiency. We show for the first time that de novo structural variants facilitated by Alu-mediated non-allelic homologous recombination led to deletion of a non-coding element (the lncRNA CHASERR) to cause a rare syndromic neurodevelopmental disorder. We also demonstrate that CHD2 has bidirectional dosage sensitivity in human disease. This work highlights the need to carefully evaluate other lncRNAs, particularly those upstream of genes associated with Mendelian disorders.

Figure 1:. Brain MRI in individuals with CHASERR haploinsufficiency

Brain magnetic resonance imaging (MRI) demonstrates frontal-predominant cortical atrophy with reduced volume of the brainstem (asterisks), and generalized hypomyelination of the corpus callosum and subcortical white matter (arrowheads) (top row), all less apparent in the first year of life (bottom row). T1, T2 = MRI sequence protocols.

Figure 2:. De novo CHASERR deletions and characterization of CHD2 expression

A. Human chromosome 15q26.1, with a 500 kb inset showing a gene-sparse region upstream of the long non-coding RNA gene CHASERR (purple) and its tandem coding gene CHD2 (blue). Arrows = direction of transcription. De novo deletions (red bracketed lines) in Individual 1 (22 kb), Individual 2 (8.4 kb), and Individual 3 (25 kb) overlap the promoter and first three exons of CHASERR. Long read DNA sequencing in Individual 1 identified three de novo single nucleotide variants (SNVs, red dots) in cis with the CHASERR deletion. B. Breakpoint mapping for the deletions in Individuals 1 and 3 shows 40 bp and 20 bp microhomology, respectively, at the junction between two negative-strand oriented SINE/Alu elements (AluSg and AluYb8 for Indiv. 1; AluSx and AluSz for Indiv. 3). Short read genome sequencing in Individual 2 maps the breakpoint near two positive-strand oriented SINE/Alu elements (AluJr, AluSx3), with 8 bp microhomology at the junction. C. Increased CHD2 protein abundance in patient-derived neural precursor cells from Individual 1 (purple) compared to iPSCs from unaffected controls (gray), an individual with CHD2 haploinsufficiency (orange), and CHD2−/− iPSCs (red). CHD2 abundance in haploinsufficient control iPSC lines was 50% relative to wildtype controls. Error bars = ± standard error. * p=0.0009, ** p=0.0024 (t-test). D. RNA-seq from whole blood (WB), cultured fibroblasts (CF), cultured neural precursor cells, and induced pluripotent stem cells from Individual 1, and cultured fibroblasts and whole blood from Individual 2, all show allelic imbalance towards expression of the CHD2 allele in cis with the CHASERR deletion. Control whole blood and cultured fibroblasts from GTEx Consortium participants (black bars) show no allelic imbalance in CHD2. Error bars = 95% confidence interval (assuming binomial distribution).