Alterations in CDH15 and KIRREL3 in patients with mild to severe intellectual disability

Abstract

Cell-adhesion molecules play critical roles in brain development, as well as maintaining synaptic structure, function, and plasticity. Here we have found the disruption of two genes encoding putative cell-adhesion molecules, CDH15 (cadherin superfamily) and KIRREL3 (immunoglobulin superfamily), by a chromosomal translocation t(11;16) in a female patient with intellectual disability (ID). We screened coding regions of these two genes in a cohort of patients with ID and controls and identified four nonsynonymous CDH15 variants and three nonsynonymous KIRREL3 variants that appear rare and unique to ID. These variations altered highly conserved residues and were absent in more than 600 unrelated patients with ID and 800 control individuals. Furthermore, in vivo expression studies showed that three of the CDH15 variations adversely altered its ability to mediate cell-cell adhesion. We also show that in neuronal cells, human KIRREL3 colocalizes and interacts with the synaptic scaffolding protein, CASK, recently implicated in X-linked brain malformation and ID. Taken together, our data suggest that alterations in CDH15 and KIRREL3, either alone or in combination with other factors, could play a role in phenotypic expression of ID in some patients.

Figure 1

Cloning of the t(11;16) Translocation Breakpoints and Identification of the Candidate ID Genes (A) Metaphase spread from the female patient with the t(11;16) translocation showing FISH signals obtained with PAC clone RP4-754F23 (green), with a chromosome 16 centromere-specific alphoid sequence probe (red). The hybridization signals (white arrowheads) on both der(16) and der(11) chromosomes indicate that this PAC clone spans the 16q breakpoint. (B) Genes residing in clone RP4-754F23 are shown. Hybridization of a 1.2 kb probe containing CDH15 exon 2, intron 2, and exon 3 to a Southern blot containing Pst1 restricted DNA from the patient (P) and from a control male (M) and a control female (F). Novel aberrant restriction fragments (1.0 kb, 5.5 kb) corresponding to the two junction fragments were identified in DNA from the patient (arrowheads). Inverse PCR cloning of the 1.0 kb junction fragment and subsequent sequencing identified the chromosome 11 sequence at the t(11;16) translocation. The chromosome 11 breakpoint junction sequence was mapped in intron 1 of the KIRREL3 gene.

Figure 2

Alterations of CDH15 and KIRREL3 (A) An schematic representation of the CDH15 protein is shown, illustrating the four predicted variations (p.V8L, p.R60C, p.R29W, and p.A122V) found in the ID population; the five extracellular cadherin ectodomain repeats (EC) are boxed. A signal peptide (SP) that extends from amino acid 1 to 21 is also indicated. ECD, extracellular domain; TM, transmembrane domain; ICD, cytoplasmic domain. (B) Schematic representation of the domains contained in KIRREL3 illustrating the three variations (p.R40W, p.R336Q, and p.V731F) found in the ID population. Positions of the five immunoglobulin domains (Ig) are indicated. A signal peptide (SP) extends from amino acids 1 to 17. The last four amino acids of the KIRREL3 protein constitute a PDZ (PSD-95, Dlg, and Zo-1) binding domain. The unclassified alterations found in this study and the alterations identified in the 5′- and 3′-untranslated and intronic regions are not indicated.

Figure 3

Expression and Adhesion Function of Wild-Type and Mutant Human CDH15 in Mouse L Cells (A) Western blot analysis of L cells expressing wild-type CDH15 or CDH15 carrying the indicated point variations show similar levels of CDH15 expression (top). Expression at the cell surface is also comparable in all cell types, as shown by biotinylation of cell-surface proteins followed by incubation with avidin beads and western blotting with HA antibody (bottom). WT, L cells expressing wild-type CDH15; L, parental L cells. (B) L cells expressing CDH15 carrying the missense variations found in ID patients lose the ability to form Ca²⁺-dependent aggregates. Two control missense variations made in the same EC1 domain, p.K103R and p.M109T, behave like wild-type L cells. Images of aggregates formed at 3 hr (top) and quantification of aggregation measured as the ratio between aggregates greater than 4 cells and single cells after 3 hr in culture (bottom). Both the visual images and the numerical data reveal loss of Ca²⁺-dependent cell-cell adhesion. EDTA, L cells expressing wild-type CDH15 cultured in the presence of 5 mM EDTA.

Figure 4

Expression of Wild-Type KIRREL3 and Its Interaction with CASK (A) KIRREL3-V5-overexpressing PC12 cells showing localization of KIRREL3 (green) on cell membrane (ii). Nuclei were stained with sytox (red) (i). Staining of KIRREL3 and nucleus were shown simultaneously in (iii). Fluorescence staining was merged with differential interference contrast (DIC) image to illustrate the cells' shape (iv). (B and C) KIRREL3-V5 and GFP-CASK co-overexpressing PC12 cells (B) and HT22 cells (C), expression of KIRREL3 (red) (i) and CASK (green) (ii) are shown. The colocalization was shown as yellow/orange within the region of cell membrane and possibly cytoplasma (iii). DIC image was demonstrated together with the double staining (iv). For each experiment, at least 60 transfected cells were examined. (D) Interaction between KIRREL3 and CASK. Lysates prepared from KIRREL3-V5- and GFP-CASK-overexpressing HEK293H cells were incubated with V5 antibody and subsequently precipitated with magnetic beads. Bound CASK was detected by western blot analysis (top) with the rabbit GFP antibody. KIRREL3-V5 but not LacZ-V5 or CASK itself immobilizes CASK (arrow), suggesting that KIRREL3 and CASK interact in cells. To examine the expression of KIRREL3, the same blot was reprobed with V5 antibody (middle). LacZ-V5 (arrow) and KIRREL3-V5 (arrowhead) were detected as indicated in the respective lanes. Comparable amounts of CASK protein were loaded in each lane (bottom). The co-IP results were verified in three separate experiments. (E) GFP-CASK- and KIRREL3-V5-overexpressing HEK293H cells protein lysate was coimmunoprecipitated with V5 antibody. Immunoblotting with CASK antibody detected endogenous CASK in KIRREL3-V5 immunoprecipitate suggesting endogenous expression of CASK and its interaction with KIRREL3-V5.

Figure 5

Putative Signaling System Likely to Influence Human Cognition Involving Cadherin, KIRREL3, and CASK Variations identified in CDH15 and KIRREL3 are boxed. Previously identified genes with variations in patients with cognitive impairment are shaded in light blue.