Apart from the known PPGL hereditary cases (~40%), there is still a subset of patients showing clinical features of heritability without germline mutations in the susceptibility genes identified so far. This fact strongly suggests the presence of de novo alterations, recessive inheritance, imprinting, or somatic mosaicism involving precursor cells.
In this study, we applied whole-exome sequencing to the germline of a parent-proband trio, a proband presenting multiple (n=7) paragangliomas and no alterations in known PPGL susceptibility genes. Genome-wide methylome analyses of mutated tissues, RNA-Seq of the trio and targeted deep sequencing of a substantial series of tumors were also performed.
Exome sequencing analysis identified a single, novel de novo mutation in a gene involved in epigenetic regulation, affecting a highly conserved residue located close to the aromatic cage in the protein binding site. The mutated tumors and blood tissue from the patient exhibited a unique expression and methylation profile with significant hypermethylation of several target genes (FDR<0.15), providing evidence that the mutation plays an activating role. Targeted deep sequencing revealed the presence of subclonal mutations affecting the same residue in six additional paragangliomas, all of which were head and neck PGLs and exhibited H3K9me3 positive staining. Finally, after increasing the sample set in an international collaboration effort, we were able to find an additional PGL case with a missense activating mutation affecting exactly the same protein domain and exhibiting a similar hypermethylator phenotype to the index case.
The case described herein not only further increases the number of paraganglioma susceptibility genes, but also represents, to the best of our knowledge, the first example of a gain-of-function mutation affecting a methylation gene involved in cancer predisposition.