Highly restricted deletion of the SNORD116 region is implicated in Prader-Willi Syndrome

Abstract

The SNORD116 locus lies in the 15q11-13 region of paternally expressed genes implicated in Prader-Willi Syndrome (PWS), a complex disease accompanied by obesity and severe neurobehavioural disturbances. Cases of PWS patients with a deletion encompassing the SNORD116 gene cluster, but preserving the expression of flanking genes, have been described. We report a 23-year-old woman who presented clinical criteria of PWS, including the behavioural and nutritional features, obesity, developmental delay and endocrine dysfunctions with hyperghrelinemia. We found a paternally transmitted highly restricted deletion of the SNORD116 gene cluster, the shortest described to date (118 kb). This deletion was also present in the father. This finding in a human case strongly supports the current hypothesis that lack of the paternal SNORD116 gene cluster has a determinant role in the pathogenesis of PWS. Moreover, targeted analysis of the SNORD116 gene cluster, complementary to SNRPN methylation analysis, should be carried out in subjects with a phenotype suggestive of PWS.

Figure 1

Photography of the proband at 23 years.

Figure 2

Characterisation of SNORD116 cluster microdeletion. (a) Schematic physical map of the 15q11.2 region between the SNRPN and UBE3A genes. SnoRNA genes are indicated with bars and other genes with boxes. The paternally expressed genes and the large SNURF-SNRPN transcript (arrow) are labelled in blue and the maternally expressed UBE3A gene with its transcript (arrow) in purple. The bipartite imprinting centre (IC) is indicated by two ovals. The black horizontal bars represent the three previously reported SNORD116 microdeletions (case 1, case 2, case 3) and the present case with the respective genomic positions (hg19). The 15q11.2 region is represented at scale with physical distance in Mb. (b) High-resolution array-CGH of 15q11.2 shows loss of copy number of 333 SNP probes encompassing a segment of ≈116.5 kb. (c) Breakpoint sequence with the 118 159 bp deletion (bold) and the short direct repeat (underlined). (d) Confirmation of the SNORD116 deletion by a PCR assay developed after sequencing of a junction fragment obtained by PCR. The 137-bp fragment resulting in amplification of the breakpoint region is detected in the affected case and in the proband's healthy father. Amplification of exon 16 of CFTR gene (174 bp) is used as a PCR control. (e) Analysis using RT-PCR of fibroblast RNA of SNORD116 and SNRPN expression. PC, present case; C1-2, normal control; (f) Analysis using RT-PCR of lymphocyte RNA of SNORD116 expression. PC, present case; F, father of the present case; M, mother of the present case. RT+, with reverse transcription; RT−, without reverse transcription. Expression of the SNORD116 cluster was negative for RT+ in lymphocytes or fibroblasts of the present case, but it was positive in his father who also carried the 118-kb deletion. On the other hand, SNRPN was normally expressed in the fibroblasts of the present case.