A homozygous SP7/OSX mutation causes osteogenesis and dentinogenesis imperfecta with craniofacial anomalies

Abstract

Osteogenesis imperfecta (OI) is a heterogeneous spectrum of hereditary genetic disorders that cause bone fragility, through various quantitative and qualitative defects of type 1 collagen, a triple helix composed of two α1 and one α2 chains encoded by COL1A1 and COL1A2, respectively. The main extra-skeletal manifestations of OI include blue sclerae, opalescent teeth, and hearing impairment. Moreover, multiple genes involved in osteoblast maturation and type 1 collagen biosynthesis are now known to cause recessive forms of OI. In this study a multiplex consanguineous family of two affected males with OI was recruited for genetic screening. To determine the causative, pathogenic variant(s), genomic DNA from two affected family members were analyzed using whole exome sequencing, autozygosity mapping, and then validated with Sanger sequencing. The analysis led to the mapping of a homozygous variant previously reported in SP7/OSX, a gene encoding for Osterix, a transcription factor that activates a repertoire of genes involved in osteoblast and osteocyte differentiation and function. The identified variant (c.946C > T; p.Arg316Cys) in exon 2 of SP7/OSX results in a pathogenic amino acid change in two affected male siblings and develops OI, dentinogenesis imperfecta, and craniofacial anomaly. On the basis of the findings of the present study, SP7/OSX:c. 946C > T is a rare homozygous variant causing OI with extra-skeletal features in inbred Arab populations.

Keywords: SP7/OSX gene; conductive hearing loss; consanguinity; craniofacial anomalies; dentinogenesis imperfecta; osteogenesis imperfecta.

Graphical Abstract

Figure 1

Genetic linkage of 22-autosomal chromosomes of Family KU-49. Figure 1A shows the pedigree of Family KU-49, which has two affected male siblings with OI (KU-49.IV-2 and KU-49.IV-3). Figure 1B is the Agile Multi Ideogram for the two affected male siblings that indicates a significate shared IBD interval at chromosome 12, highlighted by a red arrow. The ideogram is representing the linkage scan as circular axis for the KU-49.IV-2 and KU-49.IV-3 OI individuals belonging to the same family in one group. In multiplex families: the exclusive regions of homozygosity (ROH) shared between the affected relatives are displayed as navy-blue bars. The homozygous regions that are not shared among affected relatives are displayed as light blue bars. As seen from the initial linkage scan the two patients have shared IBD intervals (navy blue bars) at chr:11, chr:12 and chr:13. The two affected siblings have only one exclusive shared IBD at chr: 12 across the SP7/OSX locus indicated by a red arrow. In the ideogram the linkage scan is presented from the ideogram edge (first circus: KU-49.IV-3) towards the centre (last circus: KU-49.IV-2). The alignment is solely controlled by the software. Figure 1C Multiple linkage analysis at chromosome 12 for the two affected siblings that performed using AgileVCFMapper software. The shared IBD interval at chr: 12 was estimated to be (41,454,063-65,805,469). The physical location of SP7/OSX is at Chr12: 53,326,575-53,336,354 (within the estimated IBD interval) and highlighted by the red asterisk. As seen, each row represents the genotypes for chromosome 12 for one OI individual. The concordant autozygous shared and common alleles represented as (blue lines); concordant autozygous rare alleles that most likely harbouring rare pathogenic variants represented as (black lines); homozygous discordant alleles represented as (yellow lines).

Figure 2

SP7/OSX variants chromatographs for the members of family KU-49. The figure represents the sequences for the healthy subject, the parents (KU-49.III-1 and KU-49.III-2), and the two OI patients (KU-49.IV-2 and the KU-49.IV-3), respectively. The two affected siblings KU-49.IV-2 and KU-49.IV-3 carry a homozygous missense variant (c.946C > T; p.Arg316Cys) in exon 2 of SP7/OSX that results in an arginine to cysteine amino acid change. This variant has no RS number to date. Segregation analysis demonstrate that the parents, KU-49.III-1 and KU-49.III-2, are heterozygous carriers for this variant consistent with the fact that this variant is segregated with OI phenotype in this family compared with the healthy subject that carries the two normal wild–type alleles. The MedPred = 0.81, which indicates the variant is very damaging.

Figure 3

Main radiological findings for the two affected siblings KU-49.IV-2 and KU-49.IV-3. (A) Lateral radiograph of the skull of the KU-49.IV-3 patient demonstrates type III dental malocclusion with mandibular prognathism (line arrow) and wormian bones (block arrow) with occipital protuberance. (B) Radiograph of the proximal right femur of the KU-49.IV-3 patient shows an insuffiency spiral fracture, which was managed gamma nails. (C) Radiograph of the right leg of the KU-49.IV-3 patient demonstrating a healing fracture of the tibia with intramedullary fixation nails in situ. (D) Radiograph of the forearm of the KU-49.IV-3 patient shows undertublation of the meatacarals (block arrows) with healing fractures demonstrated in the ulna (chevrons). (E) Radiograph of the leg of the KU-49.IV-3 patient show undertublation of the tibia (block arrows), with healing fractures demonstrated tibia (chevrons). (F) Knees radiograph of the KU-49.IV-2 patient shows diffuse osteopenia with genu valgum deformity with lower leg bending outwards with respect to the long axis of the femur.

Figure 4

Intraoral photographs and dental radiographs confirming the two patients have dentinogenesis imperfecta and craniofacial anomalies: panoramic and cephalometric radiographs for the two affected siblings: (A) KU-49.IV-2 and (B) KU-49.IV-3. The clinical evaluation was clearly explained in the results section.

Figure 5

Hight resolution CT scan of the petrous bones for KU-49.IV-3 patient. It shows ill–defined lucency (focal demineralization) in the region of the fissula ante fenestrum bilaterally (arrows). Cochlea and the ossicles are spared. Findings consistent with bilateral otosclerosis (fenestral type): (A) right and (B) left.