Identification of the first PAR1 deletion encompassing upstream SHOX enhancers in a family with idiopathic short stature

Abstract

Short stature homeobox-containing gene, MIM 312865 (SHOX) is located within the pseudoautosomal region 1 (PAR1) of the sex chromosomes. Mutations in SHOX or its downstream transcriptional regulatory elements represent the underlying molecular defect in ~60% of Léri-Weill dyschondrosteosis (LWD) and ~5-15% of idiopathic short stature (ISS) patients. Recently, three novel enhancer elements have been identified upstream of SHOX but to date, no PAR1 deletions upstream of SHOX have been observed that only encompass these enhancers in LWD or ISS patients. We set out to search for genetic alterations of the upstream SHOX regulatory elements in 63 LWD and 100 ISS patients with no known alteration in SHOX or the downstream enhancer regions using a specifically designed MLPA assay, which covers the PAR1 upstream of SHOX. An upstream SHOX deletion was identified in an ISS proband and her affected father. The deletion was confirmed and delimited by array-CGH, to extend ~286 kb. The deletion included two of the upstream SHOX enhancers without affecting SHOX. The 13.3-year-old proband had proportionate short stature with normal GH and IGF-I levels. In conclusion, we have identified the first PAR1 deletion encompassing only the upstream SHOX transcription regulatory elements in a family with ISS. The loss of these elements may result in SHOX haploinsufficiency because of decreased SHOX transcription. Therefore, this upstream region should be included in the routine analysis of PAR1 in patients with LWD, LMD and ISS.

Figure 1

Schematic representation of the genomic location and approximate extensions of the observed upstream SHOX deletion. The approximate coordinates are according to chromosome X, NCBI assembly GRCh37 with the upstream enhancers indicated as CNE2, 3 and 5. The MLPA probes are indicated by grey boxes. ^*Two genes/loci that are included in both the commercial and the upstream MLPA assays but the binding sequences are different ▴, the presence of a heterozygous deletion. The deletion size range is indicated adjacent to each individual. The deletion detected in a patient with brachymesomelic dysplasia with Peters anomaly of the eye is also shown. The extension limits were determined according to the reported array and PCR data. Black solid lines indicate deleted sequences, white lines indicate the presence of two copies while hashed lines indicate non-informative areas. The diagram is not drawn to scale.

Figure 2

Characterization of the upstream SHOX deletion by fine-tiling Y chromosome aCGH (Nimblegen Y chromosome-specific array). Fluorescence log2 intensity ratios of test to reference are shown for each oligonucleotide from telomere to centromere across the short arm of the Y chromosome. Sequence coordinates are taken from the Y chromosome assembly (NCBI assembly GRCh36). The log2 ratio data are shown in the NimbleGen SignalMap data viewer and each point indicates the midpoint of a 300 bp window average, which has been calculated from 1–15 probes. The deletion extensions are indicated by the line marked with an asterisk (^*) and correspond from ∼124349 to ∼409949 (Y chromosome, NCBI assembly CRCh36), which corresponds to ∼134349–439949 on the chromosome Y, NCBI assembly GRCh37 (∼184349–489949 on the chromosome X, NCBI assembly GRCh37 for cross referencing with Figure 1).