Detection of PKD1 and PKD2 Somatic Variants in Autosomal Dominant Polycystic Kidney Cyst Epithelial Cells by Whole-Genome Sequencing

Significance Statement Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in PKD1 and PKD2 (PKD1/2) in renal tubular epithelium. PKD1/2 somatic mutations were previously implicated in cyst formation, but studies of this second-hit model in ADPKD had significant technical limitations. Comprehensive analysis of renal cyst epithelium by whole-genome sequencing identified pathogenic inactivating somatic mutations of PKD1/2 in all 24 patients and in 93% of their 90 cysts. Short variant mutations occurred in 77% of cysts, and another 18% acquired chromosomal loss of heterozygosity encompassing PKD1/2, frequently at chromosomal fragile sites or in regions comprising chromosome microdeletion diseases/syndromes. These findings support a cellular recessive mechanism for renal cystogenesis in ADPKD caused by inactivating germline and somatic variants of PKD1/2. Background Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder characterized by the development of multiple cysts in the kidneys. It is often caused by pathogenic mutations in PKD1 and PKD2 genes that encode polycystin proteins. Although the molecular mechanisms for cystogenesis are not established, concurrent inactivating germline and somatic mutations in PKD1 and PKD2 have been previously observed in renal tubular epithelium (RTE). Methods To further investigate the cellular recessive mechanism of cystogenesis in RTE, we conducted whole-genome DNA sequencing analysis to identify germline variants and somatic alterations in RTE of 90 unique kidney cysts obtained during nephrectomy from 24 unrelated participants. Results Kidney cysts were overall genomically stable, with low burdens of somatic short mutations or large-scale structural alterations. Pathogenic somatic ?second hit? alterations disrupting PKD1 or PKD2 were identified in 93% of the cysts. Of these, 77% of cysts acquired short mutations in PKD1 or PKD2; specifically, 60% resulted in protein truncations (nonsense, frameshift, or splice site) and 17% caused non-truncating mutations (missense, in-frame insertions, or deletions). Another 18% of cysts acquired somatic chromosomal loss of heterozygosity (LOH) events encompassing PKD1 or PKD2 ranging from 2.6 to 81.3 Mb. 14% of these cysts harbored copy number neutral LOH events, while the other 3% had hemizygous chromosomal deletions. LOH events frequently occurred at chromosomal fragile sites, or in regions comprising chromosome microdeletion diseases/syndromes. Almost all somatic ?second hit? alterations occurred at the same germline mutated PKD1/2 gene. Conclusions These findings further support a cellular recessive mechanism for cystogenesis in ADPKD primarily caused by inactivating germline and somatic variants of PKD1 or PKD2 genes in kidney cyst epithelium.