Xeroderma Pigmentosum (XP) is a rare autosomal recessive disorder characterized by defects in Nucleotide Excision Repair (NER) or translesion synthesis. XP patients have an extremely high risk of skin cancer (1,000-fold increase) and an elevated incidence of internal tumors, including leukemia and gynecological and brain cancers (34-fold increase). However, the somatic mutagenesis mechanisms underlying this cancer predisposition remain incompletely understood from a genomic perspective.

We assembled a unique cohort of skin tumors (n=39) from five XP subgroups with the highest cancer susceptibility (XP-A, XP-C, XP-D, XP-E, XP-V) and internal cancers (n=23) from XP-C patients, including leukemia, ovarian, pancreatic, thyroid tumors, and others. Whole-genome sequencing and detailed bioinformatic analyses were performed to characterize their mutational landscapes in comparison with sporadic cancers. In vitro (XP-C, XP-V) and in vivo (XP-C) mutation accumulation models were developed to investigate mechanisms mutagenesis in XP.

An ultra-mutated tumor phenotype was observed in skin tumors with impaired GG-NER (XP-E: 350 mut/Mb, XP-C: 162 mut/Mb) and TLS (XP-V: 248 mut/Mb). Mutational profiles of XP skin tumors with NER defects were dominated by C>T mutations, with each XP group exhibiting distinct trinucleotide context features. XP-A and XP-D tumors, with combined GG-NER and TC-NER defects, showed a uniform mutation distribution across chromatin compartments, indicating that NER modulates genome-wide mutation rate heterogeneity. XP-V skin tumors, characterized by TLS polymerase eta deficiency, exhibited a unique mutational profile with a high frequency of TG>TT mutations (28%), absent in sporadic skin cancers. These mutations likely arise from error-prone bypass of rare photolesions in TpA and TpG contexts in the absence of polymerase eta. In internal tumors, XP-C cancers displayed a 21-fold increase in mutation rates compared to sporadic, tissue-matched counterparts. The mutational signature of XP-C internal tumors was consistent across different cancer types but markedly distinct from sporadic cancers. Mutations showed strong transcriptional bias, suggesting an association with unidentified endogenous bulky purine DNA lesions. To validate our findings, we sequenced hematopoietic stem cells from XPC knockout (KO) mice and observed a significant age-dependent increase in mutagenesis. The mutational signature in XPC KO mice resembled that of XP-C internal cancers, reinforcing our hypothesis.

The increased cancer susceptibility in XP patients is driven by an excess of unrepaired DNA lesions on the untranscribed strand, defective translesion synthesis, and impaired repair of endogenous oxidative DNA damage. These factors contribute to the elevated mutation burden and distinct mutational landscapes observed in both skin and internal tumors of XP patients.