Genomic evolution and heterogeneity of von Hippel-Lindau (VHL)-associated clear cell renal cell carcinoma revealed by multi-region whole-genome sequencing

Intra-tumor heterogeneity (ITH) of somatic mutations is a hallmark of sporadic clear cell renal cell carcinoma (ccRCC). In contrast, the extent and nature of ITH in hereditary (VHL-associated) ccRCC remain poorly characterised, primarily due to the rarity of these tumors. This study aims to comprehensively characterise this heterogeneity and elucidate its evolutionary dynamics and biological relevance. To investigate intra- and inter-tumor heterogeneity in VHL-associated ccRCC, we performed multi-region whole-genome sequencing (WGS) of 23 primary tumor biopsies obtained from four spatially distinct regions of six small (≤3 cm) renal tumors across two patients carrying pathogenic germline VHL mutations. Somatic single-nucleotide variants (SNVs) and copy number alterations (CNAs) were analysed to reconstruct the genomic histories of these tumors. We found that all tumors were clonally independent, each harboring distinct sets of somatic variants and chromosomal copy number alterations, including the characteristic chromosome 3p loss. Within individual tumors, copy number profiles were homogeneous across regions, suggesting early acquisition of these events. Subclonal diversification of somatic SNVs was detected in all tumors. Notably, in one patient, two of the three analysed tumors displayed pronounced ITH, with most mutations being unique to a single region. Moreover, markedly distinct patient-specific molecular profiles emerged, characterised by divergent driver events and copy number landscapes that correlated with differences in their clinical grades. Although preliminary, these findings provide new insights into the genomic heterogeneity of VHL-associated ccRCC, advancing our understanding of how inherited kidney cancers develop and diversify, and potentially informing improved clinical management of patients with VHL disease.