Measuring Nucleotide Excision Repair in Human Populations

Principal Investigator:
Laura Niedernhofer, Ph.D.

Project Number: U01 ES029603

Nucleotide excision repair (NER) is a DNA repair mechanism that recognizes and removes bulky, helix-distorting lesions from the nuclear genome. Key substrates for NER are lesions induced by ultraviolet (UV) radiation upon environmental exposure to sunlight and a subset of oxidative DNA lesions produced endogenously. This is dramatically illustrated by patients with xeroderma pigmentosum (XP), a disease caused by inherited defects in NER. XP patients have a 10,000-fold increased risk of skin cancer and early onset neurodegeneration. XP is heterogeneous, ranging from mild to profoundly debilitating. XP severity is proportional to the extent to which NER is disrupted. This suggests that subtle defects in NER, due to, for example, polymorphisms in NER genes, might modestly but significantly impact one’s risk of skin cancer. Since skin cancer affects 20% of Americans and is preventable (by avoiding environmental exposure to UV), identifying those at risk could have a tremendous impact on the health of Americans and healthcare costs. The greatest barrier to identifying those at risk is the lack of an assay to measure NER that is rapid, inexpensive and applicable to samples safely and easily collected from patients. NER occurs in a series of steps involving the recognition of a site of DNA damage, unwinding the DNA locally, excision of a single-stranded oligonucleotide containing the lesion, and templated DNA synthesis to fill the residual gap. NER is the only way that UV-induced photolesions are removed from the genome in human cells. Therefore, NER is measured by the detection and quantification of UV-induced DNA synthesis outside of the S-phase of the cell cycle, or unscheduled DNA synthesis (UDS). Historically, UDS measurement required the use of radioactively-labeled nucleosides and/or specialized equipment. Project researchers developed a method to measure NER that employs the thymidine analog 5-ethynyl-2'-deoxyuridine and Click-iT chemistry for fluorescent detection of UDS by flow cytometry. This can be applied to peripheral blood cells for rapid measurement of NER requiring minimally invasive sample collection. UDS in XP patients ranges from <10% to 50%. Nothing is known about the health implications of having a UDS between 50-100%, or how to define 100% NER capacity. This project aims to correct these gaps in knowledge through optimization of its functional assay and proof-of concept pilot human studies. The assay will be applied to existing cohorts of patients seen at the University of Miami Skin Cancer Clinics, the NIH Undiagnosed Diseases Program or enrolled in the University of Maryland Amish Longevity Study, to interrogate associations between NER capacity and high risk of skin cancer, early onset neurodegeneration, and within family pedigrees, respectively. This project will yield an NER assay applicable to larger population studies aimed at testing associations between NER capacity, environmental exposures and disease risk, and begin to define “normal” NER capacity. The assay could have a significant impact on how risk of squamous cell or basal cell carcinoma of the skin, melanoma, lung or head and neck cancer, neurodegeneration, and resistance to cancer chemotherapy is identified and managed.