#1193 Tracking kidney cancer initiation via somatic mutation analysis of pre-cancer cells from Von Hippel Lindau cancer predisposition syndrome
Authors: Margaria Jean Piero , Pipitone Giovanni Battista , Larcher Alessandro , Faienza Sipontina , Rowe Isaline , Corea Francesca , DI Stefano Gianfranco , Capitanio Umberto , Carrera Paola , Salonia Andrea , Boletta Alessandra , Franco Irene 
Published: May 2024

Background and Aims

Somatic mutations promote the transition from a normal cell to a cancer clone. Little is known about the factors that promote mutation in normal tissues, but whole genome sequencing of pre-cancer cells, followed by mutational pattern analyses, is a revolutionary tool to understand somatic mutation mechanisms active during an individual's lifetime. In the kidney, we have shown that normal kidney tubule epithelial cells (TEC) derived from damaged PT display an excess of somatic mutations and a peculiar enrichment of mutations in exons and highly transcribed DNA compared to other cell types [1]. However, the direct contribution of this PT-specific mutational process to carcinogenesis needs further demonstration.

Here, we have analyzed normal TEC that are genetically predisposed to evolve into clear cell renal cell carcinoma (ccRCC), as they harbor a germline heterozygous mutation in the tumor suppressor Von Hippel Lindau, VHL. Using this genetic model of tumor predisposition, we have tracked the PT-specific mutational process from normal cells to overt ccRCC. This study sheds light on the etiology of this mutational process, as well as its causative role in ccRCC.

Method

We detected somatic mutations in single genomes from normal kidney TEC from 8 control individuals and 7 VHL-disease patients in the age range 24-70. Different from our previous study [1], we isolated kidney tubule cells from the urine. Multiple TECs per individual were subjected to in vitro clonal expansion, followed by whole genome sequencing (WGS), a golden-standard method to obtain high confidence somatic mutation data. We analyzed concomitant somatic mutation- and gene expression-data from 58 clones, and expression data from 154 TEC clones.

Results

First, we compared our newly generated dataset (TECs obtained from urines) with our previous dataset (TECs obtained from kidney biopsies). QPCR measurements of marker gene expression and somatic mutational pattern analyses showed that the same two populations could be clonally expanded from both urines and kidney biopsies. One population expressed markers of proximal tubule (AQP1, SLC17A3) and tubule damage (VCAM1, KIM1), and showed an excess of somatic single base substitutions (SBSs). This TEC population was defined: VCAM1-PT cells.

We characterized the types of SBSs that are more frequently found in VCAM1-PT genomes. The mutation spectrum was different from that induced by exposure to common mutagens, e.g. aristolochic acid, reactive oxygen species and tobacco. Normal cells, including TEC, fat and blood progenitors, showed mutation depletion in highly transcribed genes, in agreement with more efficient repair. Instead, VCAM1-PT cells showed an enrichment of specific SBS types, distinct from those induced by another transcription-coupled mutational process described in the liver. In vitro exposure of TECs to the alkylating agent ENU recapitulates some features of the spectrum of mutations observed in vivo, suggesting that VCAM1-PT cells might fail to repair damage induced by endogenous alkylating agents.

The VCAM1-PT-specific mutational signature was observed in ccRCC, but not found in a variety of non-kidney cell-types and cancers. Importantly, the impact of the mutational signature was more evident in VCAM1-PT genomes from VHL-disease patients compared to similar samples from control individuals. Moreover, VCAM1-PT cells were more common (8-fold increase, chi squared test P = .026) in the urines of VHL-disease patients than in the urines of controls.

Conclusion

Our data show that TECs derived from damaged PTs are subjected to a specific somatic mutation process during adult life. The process is a distinctive feature of kidney cancer (ccRCC) genomes, and is more evident in patients affected by VHL-cancer predisposition syndrome. These data suggest that heterozygous loss of VHL facilitates a PT-specific, somatic mutation process involved in cancer initiation.