Nucleotide excision repair gene polymorphisms, meat intake and colon cancer risk

Much of the DNA damage from colon cancer-related carcinogens, including heterocyclic amines (HCA) and polycyclic aromatic hydrocarbons (PAH) from red meat cooked at high temperature, are repaired by the nucleotide excision repair (NER) pathway. Thus, we examined whether NER non-synonymous single nucleotide polymorphisms (nsSNPs) modified the association between red meat intake and colon cancer risk

Characterisation of the mycobacterial NER system reveals novel functions of uvrD1 helicase

In this study, we investigated the role of the nucleotide excision repair (NER) pathway in mycobacterial DNA repair. Mycobacterium smegmatis lacking the NER excinuclease component uvrB, the helicase uvrD1 and a double knock-out lacking both proteins were constructed and their sensitivity to a series of DNA damaging agents wa analysed. As anticipated, the mycobacterial NER system was shown to be involved in the processing of bulky DNA adducts and inter-strand cross-links. In addition, it could be shown to exert a protective effect against oxidising and nitrosating agents. Interestingly, inactivation of uvrB and uvrD1 significantly increased marker integration frequencies in gene conversion assays. This implies that in mycobacteria, which lack the postreplicative mismatch repair system, NER, and particularly the UvrD1 helicase, is involved in the processing of a subset of recombination-associated mismatches

Chromatin remodeling in the UV-induced DNA damage response

__Abstract__ DNA damage interferes with transcription and replication, causing cell death, chromosomal aberrations or mutations, eventually leading to aging and tumorigenesis (Hoeijmakers, 2009). The integrity of DNA is protected by a network of DNA repair and associated signalling pathways, collectively called the DNA damage response (DDR) (Jackson & Bartek, 2009). Chromatin poses a barrier for DNA repair and as such plays a critical role in controlling DDR efficiency. Chromatin is modified to regulate access of repair proteins to DNA and needs also to be restored to its original configuration afterwards. Chromatin also serves as an optimal regulation platform for DNA repair by mediating signalling events, providing docking sites for signaling proteins and controlling their activity. The work that we describe in this thesis is focused on the role of chromatin remodelling in DDR, specifically the Nucleotide Excision Repair (NER) pathway

Paracrine Regulation of Melanocyte Genomic Stability: A Focus on Nucleotide Excision Repair

UV radiation is a major environmental risk factor for the development of melanoma by causing DNA damage and mutations. Resistance to UV damage is largely determined by the capacity of melanocytes to respond to UV injury by repairing mutagenic photolesions. The nucleotide excision repair (NER) pathway is the major mechanism by which cells correct UV photodamage. This multistep process involves the basic steps of damage recognition, isolation, localized strand unwinding, assembly of a repair complex, excision of the damage‐containing strand 3′ and 5′ to the photolesion, synthesis of a sequence‐appropriate replacement strand, and finally ligation to restore continuity of genomic DNA. In melanocytes, the efficiency of NER is regulated by several hormonal pathways including the melanocortin and endothelin signaling pathways. Elucidating molecular mechanisms by which melanocyte DNA repair is regulated offers the possibility of developing novel melanoma‐preventive strategies to reduce UV mutagenesis, especially in UV‐sensitive melanoma‐prone individuals

Adverse Effects of Trichothiodystrophy DNA Repair and Transcription Gene Abnormalities on Human Fetal Development

The effects of DNA repair and transcription genes in human prenatal life have never been studied. Trichothiodystrophy (TTD) is a rare (affected frequency of 10^-6^) recessive disorder caused by mutations in genes involved in the nucleotide excision repair (NER) pathway and in transcription. Based on our clinical observations, we conducted a genetic epidemiologic study to investigate gestational outcomes associated with TTD. We compared pregnancies resulting in TTD-affected offspring (N=24) with respect to abnormalities in their antenatal and neonatal periods to pregnancies resulting in their unaffected siblings (N=18), accounting for correlation, and to population reference values. Significantly higher incidence of several severe gestational complications was noted in TTD-affected pregnancies. Gestational complications were noted in nearly all pregnancies resulting in TTD-affected offspring with _XPD_ and _TTDN1_, but not _TTD-A_, gene mutations. Abnormal placental development may explain the constellation of observed complications; therefore, we hypothesize that some TTD genes play an important role in normal placental and fetal development. We investigated this hypothesis by analyzing the expression patterns of TTD genes. Expression of _TTDA_ was strongly negatively correlated (r=-0.7,P<0.0001) with gestational age, while _XPD, XPB_ and _TTDN1_ were consistently expressed from 14 to 40 weeks gestation. *Conclusion:* Our results indicate an important role for _XPD, XPB_ and _TTDN1_ gene products during normal human placental and fetal development

NUCLEOTIDE EXCISION REPAIR: IMPACTS OF ENVIRONMENTAL CARCINOGENS AND ITS ROLE IN CANCER SUSCEPTIBILITY IN APPALACHIAN KENTUCKY

Lung cancer is a particularly devastating disease, accounting for the most deaths among all cancer types in the United States. Despite a reduction in the country’s smoking rates, cigarette smoking remains the number one risk factor for lung cancer. Additionally arsenic exposure, which occurs primarily through contaminated drinking water in the U.S., is associated with increased lung cancer incidence. The nucleotide excision repair (NER) pathway is critical for maintenance of genomic fidelity, removing DNA lesions that could otherwise promote DNA mutations and drive carcinogenesis. Tobacco smoking introduces significant amounts of DNA damage and produces characteristic DNA mutations found in lung cancers of smokers, and arsenic increases lung cancer risk in smokers beyond the risk of smoking along. The contributions of these chemicals to DNA damage and cancer have been well documented, but few studies have examined their effects on DNA repair pathways, particularly the nucleotide excision repair (NER) pathway. Arsenic, while not directly mutagenic, promotes the carcinogenicity of other compounds including agents that produce DNA damage that is repaired by the NER pathway. In this dissertation I investigated the effects of cigarette smoke condensate (CSC, a whole-smoke tobacco surrogate) and arsenic on NER. I observed that CSC or arsenic treatment inhibited NER as measured by a slot-blot assay using UV-induced photolesions as model substrates to measure NER. The abundance of Xeroderma Pigmentosum complementation group C (XPC), a critical NER protein, was significantly reduced in all lines treated with either chemical, while XPA protein was unaffected. CSC and arsenic also affected RNA levels of certain NER genes. Finally, proteasome-regulated XPC turnover was affected by CSC and arsenic treatment, suggesting a potential mechanism for XPC protein inhibition. The observed impairment of NER by CSC is critically important in tobacco cancer etiology – CSC introduces DNA damage, some of which is repaired exclusively by NER, and CSC inhibits the NER pathway as well, providing a two-sided assault on cellular genetic fidelity. I then adapted the NER assay to measure repair in lymphocytes isolated from human subjects of a study investigating the high incidence of lung cancer in Appalachian Kentucky. I observed an age-dependent decline in NER efficiency that was modulated by subject smoking status and a reduced NER efficiency among current smokers in the lung cancer patient population compared to control subjects in the youngest age group, suggesting individual DNA repair capacity measured with this repair assay may be a biomarker for lung cancer susceptibility

Evaluation of mitochondrial functions of XPC protein deficient cells, involved in nucleotide excision repair (NER) pathway

Orientadores: Nadja Cristhina de Souza Pinto, Anibal Eugenio VercesiTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências MédicasResumo: Xeroderma Pigmentosum (XP) é uma doença rara, autossômica recessiva, caracterizada por fotossensibilidade, mudanças pigmentares, envelhecimento precoce da pele e incidência elevada de neoplasias de pele. XP é causada por mutações em, pelo menos oito genes, que caracterizam sete diferentes grupos de complementação genética (XP-A a XP-G) e um tipo variante (XP-V). Mutações em cada em dos genes envolvidos resultam em diferentes graus de severidade da doença, principalmente quanto ao comprometimento neurológico. Pacientes XP-C apresentam mutações no gene Xpc, que resultam, geralmente, em proteínas truncadas e instáveis. XPC é uma proteína envolvida na via de reparo de DNA por excisão de nucleotídeos (NER) e sua função é reconhecer a lesão na fita de DNA e dar início ao reparo. Recentemente, a participação indireta de XPC no reparo por excisão de bases (BER) foi sugerida, através de sua interação física e funcional com a DNA glicosilase OGG1. Uma vez que OGG1 é essencial para a remoção de purinas oxidadas do DNA mitocondrial, nós hipotetizamos que o DNAmt, e consequentemente a função mitocondrial, estariam comprometidas em células deficientes em XPC. Desta forma, este trabalho se propôs a investigar alterações bioenergéticas mitocondrias em células obtidas de pacientes XP-C. Nossos resultados revelaram que linhagens celulares XP-C apresentavam menor função mitocondrial, apesar de não apresentarem alterações no número de cópias de DNAmt. O consumo de oxigênio pelo complexo I estava significativamente diminuído em células XP-C quando comparado à células controle, enquanto que o consumo de O2 via os complexos II, III e IV foi maior em células XP-C. A capacidade de captar cálcio também se mostrou alterada nas células XP-C, uma vez que essa célula era incapaz de captar e reter concentrações fisiológicas desse íon. A produção de espécies reativas de oxigênio foi significativamente maior em células XP-C comparadas a células controle. Em acordo, a atividade das enzimas antioxidantes superóxido dismutase e glutationa peroxidase foi menor em células XP-C, indicando um desbalanço redox nessas células. A análise da expressão de genes relacionados à biogênese mitocondrial revelou que um regulador transcricional fundamental, o coativador PGC1?, estava significativamente reduzido em células XP-C transformadas e primárias. Resultados de Western blotting e imunofluorescência revelaram que as alterações bioenergéticas e genômicas observadas em células XP-C eram via sinalização e não por efeito direto, uma vez que nas condições experimentais utilizadas neste trabalho, XPC não está presente na mitocôndria. Nossos resultados demonstram, pela primeira vez, que a proteína XPC exerce um papel indireto na manutenção da integridade funcional da mitocôndria, provavelmente através de seu papel no controle da expressão de genes envolvidos na biogênese mitocondrialAbstract: Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder characterized by photosensitivity, pigmentary changes, premature skin aging and increased incidence of skin cancer. XP is caused by mutations in at least eight genes, which characterize seven different genetic complementation groups (XP-A to XP-G) and variant type (XP-V). Mutations in each gene result in varying degrees of severity, mostly regarding the presence or not of neurodegeneration. XP-C is caused by mutations in the Xpc gene, resulting, mostly, in a truncated and unstable protein. The XPC protein is involved in the nucleotide excision repair pathway (NER), where it functions as a damage recognition factor. Recently, a role for XPC in the base excision repair (BER) pathway has been proposed, through its physical and fucntional interaction with the DNA glycosylase OGG1. Since OGG1 has a major function in repairing oxidized purines in the mitochondrial DNA (mtDNA), we hypothesized that XPC played a role in maitaining mtDNA integrity, and consequently, mitochondrial function. Thus, this study proposes to investigate mitocondrial function in XP-C cell. Our results showed that XP-C cells had less mitochondrial function, although without changes in mtDNA copy number. Oxygen consumption through complex I was lower in XP-C cells compared to control cells, while respiration through complexes II, III and IV was higher in XP-C cells. Calcium uptake and retention by mitochondria was also decreased in XP-C cells, as these cells were unable to retain even physiological spikes in calcium concentration. Reactive oxygen species production was significantly higher in XPC cells compared to controls. In agreement to that, the activity of the antioxidant enzymes superoxide dismutase and glutathione peroxidase was significatly decreased in XP-C cells, indicating that these cells are under a severe redox signaling inbalance. The analysis of the expression of genes related to mitochondrial biogenesis revealed that the key transcriptional regulator PGC1? was significantly lower in both transformed and primary XP-C cells. The results of Western blotting and imunofluorescence revealed that the bioenergetic impairment observed in XP-C cells is likely the result of changes in expression and signaling pathwyas, since, under the experimental conditions used here, XPC is not present in mitochondria. Our results indicate, for the first time, that XPC plays an important role in mitochondrial maintenace, likely via its role in transcription regulation of mitochondrial biogenesisDoutoradoFisiopatologia MédicaDoutora em Ciência

Role of the XPA protein in the NER pathway: A perspective on the function of structural disorder in macromolecular assembly

Lack of structure is often an essential functional feature of protein domains. The coordination of macromolecular assemblies in DNA repair pathways is yet another task disordered protein regions are highly implicated in. Here I review the available experimental and computational data and within this context discuss the functional role of structure and disorder in one of the essential scaffolding proteins in the nucleotide excision repair (NER) pathway, namely Xeroderma pigmentosum complementation group A (XPA). From the analysis of the current knowledge, in addition to protein–protein docking and secondary structure prediction results presented for the first time herein, a mechanistic framework emerges, where XPA builds the NER pre-incision complex in a modular fashion, as “beads on a string”, where the protein–protein interaction “beads”, or modules, are interconnected by disordered link regions. This architecture is ideal to avoid the expected steric hindrance constraints of the DNA expanded bubble. Finally, the role of the XPA structural disorder in binding affinity modulation and in the sequential binding of NER core factors in the pre-incision complex is also discussed