Copy-Number Variation Contributes to the Mutational Load of Bardet-Biedl Syndrome

Abstract

Bardet-Biedl syndrome (BBS) is a defining ciliopathy, notable for extensive allelic and genetic heterogeneity, almost all of which has been identified through sequencing. Recent data have suggested that copy-number variants (CNVs) also contribute to BBS. We used a custom oligonucleotide array comparative genomic hybridization (aCGH) covering 20 genes that encode intraflagellar transport (IFT) components and 74 ciliopathy loci to screen 92 unrelated individuals with BBS, irrespective of their known mutational burden. We identified 17 individuals with exon-disruptive CNVs (18.5%), including 13 different deletions in eight BBS genes (BBS1, BBS2, ARL6/BBS3, BBS4, BBS5, BBS7, BBS9, and NPHP1) and a deletion and a duplication in other ciliopathy-associated genes (ALMS1 and NPHP4, respectively). By contrast, we found a single heterozygous exon-disruptive event in a BBS-associated gene (BBS9) in 229 control subjects. Superimposing these data with resequencing revealed CNVs to (1) be sufficient to cause disease, (2) Mendelize heterozygous deleterious alleles, and (3) contribute oligogenic alleles by combining point mutations and exonic CNVs in multiple genes. Finally, we report a deletion and a splice site mutation in IFT74, inherited under a recessive paradigm, defining a candidate BBS locus. Our data suggest that CNVs contribute pathogenic alleles to a substantial fraction of BBS-affected individuals and highlight how either deletions or point mutations in discrete splice isoforms can induce hypomorphic mutations in genes otherwise intolerant to deleterious variation. Our data also suggest that CNV analyses and resequencing studies unbiased for previous mutational burden is necessary to delineate the complexity of disease architecture.

Keywords: ciliopathy; mechanism of rearrangements; oligogenic disease; zebrafish model.

Figure 1

Schematic of Non-recurrent Exon-Disruptive CNVs Identified in BBS-Affected Case Subjects (A) Three heterozygous BBS1 deletions were identified in trans with deleterious point mutations. (B–D) A single homozygous BBS2 deletion (B); two homozygous ARL6/BBS3 deletions (C); and three homozygous BBS4 deletions (D) were identified in BBS-affected case subjects. (E) A heterozygous deletion was detected in BBS5; no other deleterious variant was detected in trans, suggesting that it is a second-site contributor in this individual. (F) A heterozygous single-exon deletion in BBS7 was identified in trans with a pathogenic SNV. (G) A heterozygous ALMS1 deletion was detected in a BBS pedigree harboring a homozygous BBS4 exon 5–6 deletion (see D). (H) Identification of a complex duplication encompassing the NPHP4 locus. Chromosomal locations are indicated in red (top of each panel); genes, horizontal black lines; exons, vertical black bars (if different transcript isoforms exist, all putative exons are shown); CNVs, horizontal bars (blue, homozygous deletion; green, heterozygous deletion; red, duplication); SNVs, black stars. Repeat elements are shown for Alu-mediated CNVs in the relevant panels.

Figure 2

Pedigrees and Segregation Data of Primary Causal BBS Gene CNVs in Our Cohort Segregation analysis results indicate that CNVs can either be sufficient to cause disease (D–I; blue coloring) or Mendelize heterozygous deleterious alleles (A–C, J; green coloring). Squares, males; circles, females; black symbols, individuals affected with BBS; double lines, consanguinity.

Figure 3

IFT74 Is a Candidate BBS Locus (A) Chromosomal location of human IFT74 on chromosome 9p21 is indicated with a vertical red bar. (B) Schematic of two IFT74 transcript variants (long, GenBank: NM_025103.2; short, NM_001099224.1) with alternate 3′ exon usage. Horizontal line, gene locus; vertical black bars, exons; black star, paternally inherited point mutation; green bar, heterozygous deletion. (C) aCGH plot indicates a heterozygous deletion of ∼20 kb encompassing exons 14–19 of the long transcript. (D) Enlarged view of the CNV- and SNV-bearing region of IFT74 (corresponds to the dashed blue box in B) and location of AluSz and AluY repeat elements. (E) BBS pedigree AR672 and segregation of the paternally inherited c.1685−1G>T splice variant and maternally inherited exon 14–19 deletion. (F) Breakpoint characterization of the IFT74 deletion. The junction sequence and corresponding reference location is highlighted in blue and microhomology is shown in red. (G) Chromatogram corresponding to the microhomology region shown in (F).

Figure 4

In Vivo Knockdown or Genome Editing of ift74 Results in Gastrulation Defects and Renal Phenotypes in Zebrafish (A) Representative live images of ift74 morphant zebrafish embryos at the mid-somitic stage (top, lateral; bottom, dorsal) display gastrulation defects typical of IFT and other ciliary gene suppression models. (B and C) In vivo complementation studies indicate that the short IFT74 transcript is a hypomorphic allele; n = 39–86 embryos/injection batch; masked scoring, repeated at least twice; statistical significance was determined using a χ² test to compare injected batches versus controls; ^∗p < 0.0001; NS, not significant; WT, wild-type. (D) Fixed 4 day post fertilization larvae were immunostained with anti-Na⁺/K⁺ ATPase antibody to mark renal tubules, representative images are shown for each of the ift74 morphant and mutant models; green dashed boxes indicate region of inset; blue lines indicates the location of the renal tubule diameter measured on lateral images. (E) Quantification of renal phenotypes in larvae injected with 50 pg guide RNA alone; 50 pg guide RNA/200 pg CAS9 protein; 9 ng ift74 sb1 or 9 ng ift74 sb2 MO demonstrate an increased diameter of the proximal convoluted tubule in comparison to controls; n = 23–54 per condition, repeated; statistical significance was determined by a Student’s t test to compare injected batches versus controls. NS, not significant; ^∗∗∗∗p < 0.0001. Error bars represent standard error of the mean (SEM).

Figure 5

Segregation and In Vivo Analysis of Oligogenic BBS Loci Demonstrate Epistatic Effects AR883-03 harbors a heterozygous BBS5 CNV that is a likely second-site contributor to disease caused by mutation at the primary causal locus BBS10. (A) Pedigree and segregation of each BBS gene variant (CNV or SNV; separate pedigrees for each gene) with the primary locus harboring causal variants shown on the far left. Gene name color indicates heterozygous deletion CNV (magenta) or point mutation (gray). (B) Bar chart indicates in vivo assessment of bbs gene interaction by the comparison of either single-gene or pairwise injection of sub-effective doses of MOs and phenotypic scoring of zebrafish embryo batches at the mid-somitic stage. Objective scoring criteria correspond to images shown in Figure 4A and demonstrate an epistatic effect in the double-MO batch. See Table S5 for embryo counts and additional examples. (C) A second phenotypic readout, area of proximal convoluted tubule measured at 4 days post fertilization, demonstrates epistatic effects of bbs gene interaction. Fixed larvae were immunostained with anti-Na⁺/K⁺ ATPase antibody; green dashed box indicates region of inset; blue dashed line indicates the region of the proximal convoluted tubule measured on lateral images. (D) Quantification of renal phenotypes in single or double MO-injected larvae demonstrate a progressive reduction in the size of the proximal convoluted tubule; n = 34–46 per condition, repeated; statistical significance was determined by a Student’s t test to compare injected batches versus controls. NS, not significant; ^∗∗p < 0.01. Error bars represent standard error of the mean (SEM).

Figure 6

Genetic Architecture of BBS Gene Variation in 17 BBS-Affected Case Subjects Harboring CNVs Each slice of the pie chart represents one BBS-affected case subject and the primary BBS locus harboring causal variants is indicated with gene names and colors (homozygous CNV, blue; compound heterozygous CNV + SNV, green; homozygous or compound heterozygous SNV, gray). Circles overlapping each slice represent the additional mutational burden in each BBS-affected case subject (CNV, magenta; SNV, gray). 5/17 individuals (29%) harbor no additional BBS gene variants outside their primary causal driver; 12/17 individuals (71%) have 1–4 additional heterozygous deleterious variants in BBS1-16, IFT27/BBS19, or NPHP1. Asterisk (^∗) indicates duplication CNV.