Laura J. Niedernhofer, MD, PhD

Genomic DNA is damaged tens of thousands of times per day in every cell. This damage occurs as a consequence of environmental insults and because electrophilic genotoxins are generated endogenously as by-products of metabolism. Maintaining the integrity of the genetic code is essential for the viability and proper functioning of cells. The fact that DNA repair mechanisms are amongst the most evolutionarily conserved of pathways also testifies to the importance of genome maintenance. Genetic diseases in which DNA repair mechanisms are affected reveal the biological consequences of DNA damage. We identified a single gene (XPF) that when mutated in humans can lead to a profound risk of cancer or rapidly accelerated aging. We modeled this in the mouse to create an experimental system in which study the relationship between DNA damage, cancer and aging. 

1. The first goal of our research is to discover what types of DNA damage are responsible for spontaneous cancer and rapid aging in our DNA repair-deficient mouse model. We hypothesize that DNA lesions that simultaneously affect both strands of DNA (e.g., DNA interstrand crosslinks and double-strand breaks) and which therefore are particularly cytotoxic contribute to aging, while lesions affecting only one strand of DNA (e.g., oxidative lesions and chemical adducts) lead to mutations and contribute to cancer. This hypothesis is being tested by systematically exposing XPF-deficient mice and cells derived from them to genotoxins that induce various types of DNA lesions to determine which exacerbate the cancer or aging phenotypes and to measure endpoints such as apoptosis and mutation frequency. This led to the identification of a novel function of the XPF-ERCC1 DNA repair complex in the repair of double-strand breaks. Once we’ve identified the class of DNA lesion that promotes cancer and aging in our mouse model, it will permit us to take a targeted approach toward identifying the endogenous lesions that are responsible for spontaneous disease in these animals, which will be pertinent to human health. 
2. The second goal of our research is to identify means to attenuate DNA damage in vivo. Although endogenous DNA damage is undoubtedly responsible for cancer and aging in XPF-deficient mice, we hypothesize that it is possible to reduce this endogenous damage and therefore disease through dietary changes, nutraceuticals or anti-inflammatories. To test this hypothesis, we are exposing the XPF-deficient mice to diets with variable fat content, anti-oxidants and inhibitors of NF-κB to determine if any will delay cancer and progeroid symptoms and extend lifespan. Preliminary data indicate that diets depleted of polyunsaturated fats extend life, whereas diets rich in these fats reduce lifespan and accelerate aging. Polyunsaturated fats derived from vegetable oils are currently recommended by the FDA as a healthy alternative to saturated fats derived from animals. However polyunsaturated fats are prone to peroxidation in vivo, which is a major source of endogenous genotoxins. Future work is aimed at identifying the DNA lesions induced by dietary fats and the identification of anti-oxidants that prevent lipid peroxidation in vivo. 
3. The third aim of our research is discover the mechanism of DNA interstrand crosslink repair in mammalian cells. This is one mechanism of DNA repair that remains ill-defined. We are using cells with well-defined genetic mutations that are hypersensitive to crosslink damage to study the mechanism. This has led to novel understanding of how the Fanconi anemia proteins interact with XPF-ERCC1 repair complex, both implicated in the repair of crosslinks. Future work is aimed at developing a method to create crosslink lesions in only a fraction of a cell nucleus using photo-activated crosslinking agents and laser scissors. This technique will be used to track the order in which DNA repair proteins accumulate at the sites of crosslink damage. 
4. The fourth aim of our research is to determine if measuring levels of either ERCC1 or XPF is prognostic in human cancer. There are numerous reports that ERCC1 is overexpressed in a variety of human tumors causing increased DNA repair, resistance to chemotherapy and correlating poor prognosis. We recently demonstrated that the antibody used in the majority of these studies is not specific for ERCC1. Current work is aimed at identifying the antigen recognized by this protein, evaluating the specificity of other ERCC1 and XPF antibodies and testing specific antibodies for their prognostic value in human cancer
5. The fifth aim of our research is to discover novel functions of the ERCC1-XPF. Orthologs of this nuclease are implicated in the repair of abasic sites, topoisomerase-I induced DNA lesions and DNA double-strand breaks, in addition to its well established and highly conserved functions in nucleotide excision repair and the repair of DNA interstrand crosslinks. Cells and mice deficient in ERCC1-XPF are hypersensitive to ionizing radiation. Furthermore, irradiated cells accumulate γ-H2AX foci, chromatid fragments and radial structures, all hallmarks of unrepaired DSBs. This work will be submitted shortly for publication. Preliminary data indicate that ERCC1-XPF deficient cells are also hypersensitive to camptothecin, a topI poison, and folate free media that induces AP sites. Thus we are pursuing the hypothesis that mammalian ERCC1-XPF functions in the same repertoire of DNA repair pathways as the yeast ortholog RAD10-RAD1.

As of July 1, 2012, Dr. Niedernhofer will be continuing her research at The Scripps Institute in Juniper, FL. We wish her the best of luck in all of her future endeavors.