Mutations of the Sonic Hedgehog Pathway Underlie Hypothalamic Hamartoma with Gelastic Epilepsy

Abstract

Hypothalamic hamartoma (HH) with gelastic epilepsy is a well-recognized drug-resistant epilepsy syndrome of early life.(1) Surgical resection allows limited access to the small deep-seated lesions that cause the disease. Here, we report the results of a search for somatic mutations in paired hamartoma- and leukocyte-derived DNA samples from 38 individuals which we conducted by using whole-exome sequencing (WES), chromosomal microarray (CMA), and targeted resequencing (TRS) of candidate genes. Somatic mutations were identified in genes involving regulation of the sonic hedgehog (Shh) pathway in 14/38 individuals (37%). Three individuals had somatic mutations in PRKACA, which encodes a cAMP-dependent protein kinase that acts as a repressor protein in the Shh pathway, and four subjects had somatic mutations in GLI3, an Shh pathway gene associated with HH. In seven other individuals, we identified two recurrent and three single brain-tissue-specific, large copy-number or loss-of-heterozygosity (LOH) variants involving multiple Shh genes, as well as other genes without an obvious biological link to the Shh pathway. The Shh pathway genes in these large somatic lesions include the ligand itself (SHH and IHH), the receptor SMO, and several other Shh downstream pathway members, including CREBBP and GLI2. Taken together, our data implicate perturbation of the Shh pathway in at least 37% of individuals with the HH epilepsy syndrome, consistent with the concept of a developmental pathway brain disease.

Figure 1

Shh Pathway Showing Some of the Proteins Implicated in HH (A) In the presence of SHH, PTCH no longer inhibits SMO from translocating to the membrane, where it inhibits phosphorylation of GLI2 and GLI3 by PKA (PRKACA). Full-length GLI2 and GLI3 translocate to the nucleus and, together with GLI1 and the transcriptional coactivator CREBBP, promote transcription of downstream target genes (B) In the absence of SHH, SMO remains localized to endosomes in the cytoplasm. GLI2 and GLI3 are bound by the SUFU complex and phosphorylated by PKA, leading to their cleavage. The cleaved protein translocates to the nucleus, where it acts to repress target gene transcription. 14 out of 38 individuals with HH had confirmed somatic mutations in the Shh pathway; an additional five individuals had unconfirmed findings in this pathway. Four individuals had confirmed somatic point mutations in GLI3, and an additional individual had a CNV that encompassed this gene. Three individuals had confirmed somatic mutations in PRKACA. Other proteins in the Shh pathway implicated in HH because of their occurrence in CNVs are SHH, SMO, CREBBP, GLI2, and STK36 (or, FU). Not shown on this simplified diagram are IHH, LRP2, LRP5, AKT1, and specific WNT and BMP pathway members that encode proteins in the Shh pathway, or that closely interact with the pathway, and are located within CNVs found in individuals with HH., , ,