Epigenomic and transcriptomic characterization of cutaneous squamous cell carcinoma (cSCC) in xeroderma pigmentosum (XP)

• Applicant: Dr. Manuel Rodríguez Paredes
• Subject Area: Dermatology ; General Genetics and Functional Genome Biology
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 499597103

Xeroderma pigmentosum (XP) is a rare genetic disease typically caused by an autosomal recessive mutation in any of the genes of the nucleotide excision repair (NER) system. Furthermore, a small group of patients (those from complementation group V, XP-V) present mutations in the POLH gene, which encodes the DNA polymerase η responsible for error-free translesional synthesis past DNA photoproducts. Since these factors are responsible for repairing DNA damage caused by UV radiation, the effects of this disease are especially manifested in skin areas exposed to sunlight, where XP patients often show very early in life a strong sensitivity to light, hyperpigmentation, signs of premature aging and different kinds of skin tumors. DNA methylation is an epigenetic modification that occurs mainly in CpG dinucleotides and that, through the control of chromatin accessibility and gene expression, determines both cellular states and identity. Previous work showed that DNA methylation profiles in normal (non-XP) epidermal keratinocytes undergo photoaging-related changes in skin areas exposed to sunlight. Furthermore, it is known that these changes are maintained during the development of non-melanoma skin cancer (NMSC), which is also mainly produced by sun exposure. However, the effects of UV radiation on the methylome of XP-derived NMSC tumors, which constitute the main cause of death in patients with this disease, remain unknown. In this project we will use Infinium MethylationEPIC BeadChip microarrays, the gold standard for DNA methylation studies, as well as RNA sequencing (RNA-seq) to analyze and integrate for the first time the methylomes and transcriptomes of sun-exposed and NMSC epidermal samples from XP-V patients. Different comparisons between these datasets and others generated from non-XP individuals will allow us to investigate the epigenomic deregulation associated with the disease, deepen our understanding of the effects of the extrinsic aging caused by UV radiation and evaluate its influence on the development of NMSC. Importantly, our analyses will also allow us to identify and characterize the transcriptomic differences between non-XP NMSC tumors and those particularly aggressive from XP patients. Differentially expressed markers that ultimately confer increased proliferation or invasion capabilities to XP tumors will finally be determined by CRISPR inactivation (CRISPRi)- and CRISPR activation (CRISPRa)-based candidate gene testing approaches on a cSCC model cell line.

• DFG Programme: Research Grants