Identification of the first recurrent PAR1 deletion in Léri-Weill dyschondrosteosis and idiopathic short stature reveals the presence of a novel SHOX enhancer.
BACKGROUND
SHOX, located in the pseudoautosomal region 1 (PAR1) of the sexual chromosomes, encodes a transcription factor implicated in human growth. Defects in SHOX or its enhancers have been observed in ∼60% of Leri-Weill dyschondrosteosis (LWD) patients, a skeletal dysplasia characterised by short stature and/or the characteristic Madelung deformity, and in 2-5% of idiopathic short stature (ISS). To identify the molecular defect in the remaining genetically undiagnosed LWD and ISS patients, this study screened previously unanalysed PAR1 regions in 124 LWD and 576 ISS probands.


METHODS
PAR1 screening was undertaken by multiplex ligation dependent probe amplification (MLPA). Copy number alterations were subsequently confirmed and delimited by locus-specific custom-designed MLPA, array comparative genomic hybridisation (CGH) and breakpoint junction PCR/sequencing.


RESULTS
A recurrent PAR1 deletion downstream of SHOX spanning 47543 bp with identical breakpoints was identified in 19 LWD (15.3%) and 11 ISS (1.9%) probands, from 30 unrelated families. Eight evolutionarily conserved regions (ECRs 1-8) identified within the deleted sequence were evaluated for SHOX regulatory activity by means of chromosome conformation capture (3C) in chicken embryo limbs and luciferase reporter assays in human U2OS osteosarcoma cells. The 3C assay indicated potential SHOX regulatory activity by ECR1, which was subsequently confirmed to act as a SHOX enhancer, operating in an orientation and position independent manner, in human U2OS cells.


CONCLUSIONS
This study has identified the first recurrent PAR1 deletion in LWD and ISS, which results in the loss of a previously uncharacterised SHOX enhancer. The loss of this enhancer may decrease SHOX transcription, resulting in LWD or ISS due to SHOX haploinsufficiency.
Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Spain.
Sara
S
Benito-Sanz
Jose Luis
JL
Royo
Eva
E
Barroso
Beatriz
B
Paumard-Hernández
Ana C
AC
Barreda-Bonis
Pengfei
P
Liu
Ricardo
R
Gracía
James R
JR
Lupski
Ángel
Á
Campos-Barros
José Luis
JL
Gómez-Skarmeta
Karen Elise
KE
Heath
D000818:Animals; D002642:Chick Embryo; D002648:Child; D015331:Cohort Studies; D004742:Enhancer Elements, Genetic; D005121:Extremities / Q000473:pathology; D005260:Female; D018628:Gene Dosage; D005787:Gene Frequency; D006130:Growth Disorders / Q000235:genetics*; D057895:Haploinsufficiency; D018398:Homeodomain Proteins / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D010009:Osteochondrodysplasias / Q000235:genetics*; D010375:Pedigree; D017384:Sequence Deletion / Q000235:genetics*; D012730:Sex Chromosomes / Q000235:genetics* / Q000378:metabolism; D000074122:Short Stature Homeobox Protein; D014157:Transcription Factors / Q000235:genetics
D018398:Homeodomain Proteins; C106071:SHOX protein, human; D000074122:Short Stature Homeobox Protein; D014157:Transcription Factors