SummaryBackgroundBirt-Hogg-Dubé (BHD) syndrome, caused by germline alteration of folliculin(FLCN)gene, develops hybrid oncocytic/chromophobe tumour (HOCT) and chromophobe renal cell carcinoma (ChRCC), whereas sporadic ChRCC does not harborFLCNalteration. To date, molecular characteristics of these similar histological types of tumours have been incompletely elucidated.MethodsTo elucidate renal tumourigenesis of BHD-associated renal tumours and sporadic renal tumours, we conducted whole genome sequencing (WGS) and RNA-sequencing (RNA-seq) of sixteen BHD-associated renal tumours from nine unrelated BHD patients, twenty-one sporadic ChRCCs and seven sporadic oncocytomas. We then compared somatic mutation profiles withFLCNvariants and RNA expression profiles between BHD-associated renal tumours and sporadic renal tumours.FindingsRNA-seq analysis revealed that BHD-associated renal tumours and sporadic renal tumours have totally different expression profiles. Sporadic ChRCCs were clustered into two distinct clusters characterized byL1CAMandFOXI1expressions, molecular markers for renal tubule subclasses. Increased mitochondrial DNA (mtDNA) copy number with fewer variants was observed in BHD-associated renal tumours compared to sporadic ChRCCs. Cell-of-origin analysis using WGS data demonstrated that BHD-associated renal tumours and sporadic ChRCCs may arise from different cells of origin and second hitFLCNalterations may occur in early third decade of life in BHD patients.InterpretationThese data further our understanding of renal tumourigenesis of these two different types of renal tumours with similar histology.FundingThis study was supported by10.13039/501100001691JSPSKAKENHI Grants,10.13039/501100006264RIKENinternal grant, and the Intramural Research Program of the10.13039/100000002National Institutes of Health(10.13039/100000002NIH),10.13039/100000054National Cancer Institute(NCI),Center for Cancer Research.