Cell Adhesion Molecules Involved in Neurodevelopmental Pathways Implicated in 3p-Deletion Syndrome and Autism Spectrum Disorder

Abstract

Autism spectrum disorder (ASD) is characterized by impaired social interaction, language delay and repetitive or restrictive behaviors. With increasing prevalence, ASD is currently estimated to affect 0.5-2.0% of the global population. However, its etiology remains unclear due to high genetic and phenotypic heterogeneity. Copy number variations (CNVs) are implicated in several forms of syndromic ASD and have been demonstrated to contribute toward ASD development by altering gene dosage and expression. Increasing evidence points toward the p-arm of chromosome 3 (chromosome 3p) as an ASD risk locus. Deletions occurring at chromosome 3p result in 3p-deletion syndrome (Del3p), a rare genetic disorder characterized by developmental delay, intellectual disability, facial dysmorphisms and often, ASD or ASD-associated behaviors. Therefore, we hypothesize that overlapping molecular mechanisms underlie the pathogenesis of Del3p and ASD. To investigate which genes encoded in chromosome 3p could contribute toward Del3p and ASD, we performed a comprehensive literature review and collated reports investigating the phenotypes of individuals with chromosome 3p CNVs. We observe that high frequencies of CNVs occur in the 3p26.3 region, the terminal cytoband of chromosome 3p. This suggests that CNVs disrupting genes encoded within the 3p26.3 region are likely to contribute toward the neurodevelopmental phenotypes observed in individuals affected by Del3p. The 3p26.3 region contains three consecutive genes encoding closely related neuronal immunoglobulin cell adhesion molecules (IgCAMs): Close Homolog of L1 (CHL1), Contactin-6 (CNTN6), and Contactin-4 (CNTN4). CNVs disrupting these neuronal IgCAMs may contribute toward ASD phenotypes as they have been associated with key roles in neurodevelopment. CHL1, CNTN6, and CNTN4 have been observed to promote neurogenesis and neuronal survival, and regulate neuritogenesis and synaptic function. Furthermore, there is evidence that these neuronal IgCAMs possess overlapping interactomes and participate in common signaling pathways regulating axon guidance. Notably, mouse models deficient for these neuronal IgCAMs do not display strong deficits in axonal migration or behavioral phenotypes, which is in contrast to the pronounced defects in neuritogenesis and axon guidance observed in vitro. This suggests that when CHL1, CNTN6, or CNTN4 function is disrupted by CNVs, other neuronal IgCAMs may suppress behavioral phenotypes by compensating for the loss of function.

Keywords: 3p-deletion syndrome; IgCAM; autism spectrum disorder; axon guidance; copy number variation; neurogenesis; synaptic plasticity.

FIGURE 1

Copy number variations alter gene dosage and expression. Copy number variations (CNVs) can manifest as deletions, where segments of DNA are removed (represented in orange), or duplications, where extra copies of a DNA segment are produced (represented in blue). CNVs can vary in size, affecting several exons in a gene, to multiple genes or even cytobands of a chromosome. Created with BioRender.com.

FIGURE 2

The 3p26.3 region encodes three neuronal cell adhesion molecules of the immunoglobulin superfamily. The 3p26.3 region is located at the distal end of the p-arm of chromosome 3. It is the terminal cytoband, lying just before the telomeres and containing three genes (in order from the telomere): Close Homolog of L1 (CHL1), Contactin-6 (CNTN6), and Contactin-4 (CNTN4). Figure adapted from the Ensembl Genome Browser (Yates et al., 2020). Created with BioRender.com.

FIGURE 3

The distribution of CNVs at chromosome 3p mapped by their distal breakpoint. Most deletions and duplications reported at chromosome 3p occur within the 3p26.3 region (380 of 907 CNVs; consisting of 225 deletions and 155 duplications), suggesting genes encoded in this region may be the molecular link between Del3p and ASD. Some studies were unable to provide high-resolution analysis of chromosomal breakpoints, only providing general coordinates (e.g., 3p26 rather than 3p26.1, 3p26.2, or 3p26.3). Additionally, cases of chromosomal translocations involving chromosome 3p have been included within the “Deletion” category for ease of visualization. In cases of inherited CNVs, if the phenotype of the parent is discussed, they have also been included as well. Figure created using GraphPad Prism 8.

FIGURE 4

CHL1, CNTN6, and CNTN4 share similar protein structure. CHL1, CNTN6, and CNTN4 are members of the IgCAM superfamily. These neuronal IgCAMs share similar extracellular domains composed of six Ig domains and five FNIII domains for CHL1, or four FNIII domains for CNTN6 and CNTN4. Whereas CNTN6 and CNTN4 are tethered to the membrane by a GPI anchor, CHL1 has both transmembrane and intracellular domains. Created with BioRender.com.

FIGURE 5

CHL1, CNTN6, and CNTN4 display overlapping expression in the hippocampus and participate in shared signaling pathways. (A) Chl1, Cntn6, and Cntn4 demonstrate region-specific and overlapping expression patterns in the mouse hippocampus. The CA2 and DG only express Cntn4 and Chl1, respectively, while all three neuronal IgCAMs are co-expressed in the CA3, and Chl1 and Cntn4 are co-expressed in the CA1. Data derived from the Allen Brain Atlas (©2015 Allen Institute for Brain Science. Allen Cell Types Database. Available from https://celltypes.brain-map.org/). (B) CHL1, CNTN6, and CNTN4 are capable of homophilic interactions that promote neurite outgrowth. These three neuronal IgCAMs commonly interact with members of the PTPR family – CHL1 interacts with CNTN6 to direct and maintain the correct angle of apical dendrites in cortical pyramidal neurons through PTPRα signaling, and both CNTN6 and CNTN4 are reported to interact with PTPRγ to promote neurite outgrowth. Additionally, CHL1 and CNTN4 interact with APP and enzymes involved in the proteolytic processing of APP – CNTN4 interacts with APP to promote neurite outgrowth and regulate retinal ganglion cell (RGC) axon-target matching in the development of visual pathways, and CHL1 cleavage by BACE1 and ADAM proteins is observed to promote neuronal survival, neurite outgrowth and regulate axonal arborization. Created with BioRender.com.