Both Rare and De Novo Copy Number Variants Are Prevalent in Agenesis of the Corpus Callosum but Not in Cerebellar Hypoplasia or Polymicrogyria

Abstract

Agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and polymicrogyria (PMG) are severe congenital brain malformations with largely undiscovered causes. We conducted a large-scale chromosomal copy number variation (CNV) discovery effort in 255 ACC, 220 CBLH, and 147 PMG patients, and 2,349 controls. Compared to controls, significantly more ACC, but unexpectedly not CBLH or PMG patients, had rare genic CNVs over one megabase (p = 1.48×10−3; odds ratio [OR] = 3.19; 95% confidence interval [CI] = 1.89–5.39). Rare genic CNVs were those that impacted at least one gene in less than 1% of the combined population of patients and controls. Compared to controls, significantly more ACC but not CBLH or PMG patients had rare CNVs impacting over 20 genes (p = 0.01; OR = 2.95; 95% CI = 1.69–5.18). Independent qPCR confirmation showed that 9.4% of ACC patients had de novo CNVs. These, in comparison to inherited CNVs, preferentially overlapped de novo CNVs previously observed in patients with autism spectrum disorders (p = 3.06×10−4; OR = 7.55; 95% CI = 2.40–23.72). Interestingly, numerous reports have shown a reduced corpus callosum area in autistic patients, and diminished social and executive function in many ACC patients. We also confirmed and refined previously known CNVs, including significantly narrowing the 8p23.1-p11.1 duplication present in 2% of our current ACC cohort. We found six novel CNVs, each in a single patient, that are likely deleterious: deletions of 1p31.3-p31.1, 1q31.2-q31.3, 5q23.1, and 15q11.2-q13.1; and duplications of 2q11.2-q13 and 11p14.3-p14.2. One ACC patient with microcephaly had a paternally inherited deletion of 16p13.11 that included NDE1. Exome sequencing identified a recessive maternally inherited nonsense mutation in the non-deleted allele of NDE1, revealing the complexity of ACC genetics. This is the first systematic study of CNVs in congenital brain malformations, and shows a much higher prevalence of large gene-rich CNVs in ACC than in CBLH and PMG.

Astroglial-Mediated Remodeling of the Interhemispheric Midline Is Required for the Formation of the Corpus Callosum

“…Additionally, we demonstrate that Fgf8 is a crucial ligand signaling upstream of the Mapk pathway to induce astroglial differentiation via the pro-astrogliogenic transcription factors Nfia and Nfib. Taken together, our findings elucidate a key cellular mechanism that reconciles the relationship between delayed astroglial development and callosal agenesis, and are consistent with previous observations following mouse or human mutations in either Fgf signaling genes or Nfi genes (Barton et al, 1995; Chen et al, 2011; Dode and Hardelin, 2009; Dode et al, 2003; Ji et al, 2014; Koehler et al, 2010; Lajeunie et al, 1999; Li et al, 2012; Lu et al, 2007; McCabe et al, 2011; Piper et al, 2009a; Rao et al, 2014; Raybaud and Di Rocco, 2007; Sajan et al, 2013; Shu et al, 2003a; Sivasankaran et al, 1997; Smith et al, 2006; Steele-Perkins et al, 2005; Stewart et al, 2016; Tokumaru et al, 1996; Wilkie et al, 1995). …”

“…Since human individuals with NFIA haploinsufficiency, as well as Nfia and Nfib knockout mice, exhibit callosal malformations (Chen et al, 2011; Lu et al, 2007; Piper et al, 2009a; Sajan et al, 2013; Shu et al, 2003a; Steele-Perkins et al, 2005), we sought to investigate whether Nfi transcription factors regulate callosal development via astroglial IHF remodeling. Examination of two cases of human NFIA and NFIB haploinsufficiency using structural MRI revealed that these individuals display abnormal retention of the IHF associated with callosal agenesis (Figure 6E).…”

“…Sherr, Barkovich, Dobyns, Reardon and colleagues obtained consent for patients and families to participate, and clinical T1-weighted or T2-weighted brain MRI scans were obtained and systematically reviewed. Genetic information on two individuals with either NFIA or NFIB haploinsufficiency was obtained through both clinical and research-based array comparative genomic hybridization studies, for which the assembled cohort has been previously reported (Sajan et al, 2013; identification numbers: LR01-282 and 1127-0). For the correlative analysis of IHF remodeling defects, patients with complete agenesis of the corpus callosum, without additional cortical malformations, were selected for evaluation.…”

Array‐based molecular karyotyping in 115 VATER/VACTERL and VATER/VACTERL‐like patients identifies disease‐causing copy number variations

“…Because none of these tissues belong to the classic VATER/VACTERL organ systems, its involvement in expression of VATER/VACTERL phenotypes in human seems unlikely. However, recently, Sajan et al () identified an overlapping deletion on chromosomal region 5q23.1 in a patient with cerebellar hypoplasia. Therefore, it cannot be excluded, that the here‐observed deletion of chromosomal region 5q23.1 contributed to the expression of the VATER/VACTERL‐like phenotype in Patient 5.…”

Developmental neurogenetics and multimodal neuroimaging of sex differences in autism

“…Chromosome Xp22.3 deletion has been discovered in a boy with cerebral cortical heterotopias and mental retardation (van Steensel, Vreeburg et al 2008). While chromosome 8p21.1-q11.23 is linked to basal ganglia calcification (Dai, Gao et al 2010), 8p23.1-p11.1 duplications as well as 1p31.3-p31.1 deletions have been observed in patients with corpus callosum agenesis (Sajan, Fernandez et al 2013). Duplication of 15q has also been found in those with hippocampal dysplasia and heterotopias, hippocampal sclerosis and malformation, corpus callosum hypoplasia and thinning, as well as greater pericerebral spaces (Boronat, Mehan et al 2015).…”