scholarly journals Expression of DNA repair and metabolic genes in response to a flavonoid-rich diet

2007 ◽  
Vol 98 (3) ◽  
pp. 525-533 ◽  
Author(s):  
Simonetta Guarrera ◽  
Carlotta Sacerdote ◽  
Laura Fiorini ◽  
Rosa Marsala ◽  
Silvia Polidoro ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Significant Negative Correlation ◽  
Dna Repair Genes ◽  
Metabolic Genes ◽  
Damage Repair ◽  
Flavonoid Intake ◽  
Repair Mechanisms ◽  
Repair Genes

A diet rich in fruit and vegetables can be effective in the reduction of oxidative stress, through the antioxidant effects of phytochemicals and other mechanisms. Protection against the carcinogenic effects of chemicals may also be exerted by an enhancement of detoxification and DNA damage repair mechanisms. To investigate a putative effect of flavonoids, a class of polyphenols, on the regulation of the gene expression of DNA repair and metabolic genes, a 1-month flavonoid-rich diet was administered to thirty healthy male smokers, nine of whom underwent gene expression analysis. We postulated that tobacco smoke is a powerful source of reactive oxygen species. The expression level of twelve genes (APEX, ERCC1, ERCC2, ERCC4, MGMT, OGG1, XPA, XPC, XRCC1, XRCC3, AHR, CYP1A1) was investigated. We found a significant increase (P < 0·001) in flavonoid intake. Urinary phenolic content and anti-mutagenicity did not significantly change after diet, nor was a correlation found between flavonoid intake and urinary phenolic levels or anti-mutagenicity. Phenolic levels showed a significant positive correlation with urinary anti-mutagenicity. AHR levels were significantly reduced after the diet (P = 0·038), whereas the other genes showed a generalized up regulation, significant for XRCC3 gene (P = 0·038). Also in the context of a generalized up regulation of DNA repair genes, we found a non-significant negative correlation between flavonoid intake and the expression of all the DNA repair genes. Larger studies are needed to clarify the possible effects of flavonoids in vivo; our preliminary results could help to better plan new studies on gene expression and diet.

scholarly journals DNA Repair Gene Expression Adjusted by the PCNA Metagene Predicts Survival in Multiple Cancers

2019 ◽  
Author(s):  
Leif Peterson ◽  
Tatiana Kovyrshina
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Gene Selection ◽  
P Value ◽  
Survival Prediction ◽  
Dna Repair Genes ◽  
Repair Gene ◽  
A Genome ◽  
Dna Repair Gene ◽  
Repair Genes

Removal of the proliferation component of gene expression by PCNA adjustment has been addressed in numerous survival prediction studies for breast cancer and all cancers in the TCGA. These studies indicate that widespread co-regulation of proliferation upwardly biases survival prediction when gene selection is performed on a genome-wide basis. In addition, removal of the correlative effects of proliferation does not reduce the random bias associated with survival prediction using random gene selection. Since most cancers become addicted to DNA repair as a result of forced cellular replication, increased oxidation, and repair deficiencies from oncogenic loss or genetic polymorphisms, we pursued an investigation to remove the proliferation component of expression in DNA repair genes to determine survival prediction. This translational hypothesis-driven focus on DNA repair genes is directly amenable to finding new sets of DNA repair genes that could potentially be studied for inhibition therapy. Overall survival (OS) prediction was evaluated in 18 cancers by using normalized RNA-Seq data for 126 DNA repair genes with expression available in TCGA. Transformations for normality and adjustments for age at diagnosis, stage, and PCNA metagene expression were performed for all DNA repair genes. We also analyzed genomic event rates (GER) for somatic mutations, deletions, and amplification in driver genes and DNA repair genes. After performing empirical p-value testing with use of randomly selected gene sets, it was observed that OS could be predicted significantly by sets of DNA repair genes for 61% (11/18) of the cancers. Interestingly, PARP1 was not a significant predictor of survival for any of the 11 cancers. Results from cluster analysis of GERs indicates that the most opportunistic cancers for inhibition therapy may be AML, colorectal, and renal papillary, because of potentially less confounding due to lower GERs for mutations, deletions, and amplifications in DNA repair genes. However, the most opportunistic cancer for inhibition therapy is likely to be AML, since it showed the lowest GERs for mutations, deletions, and amplifications in DNA repair genes. In conclusion, our hypothesis-driven focus to target DNA repair gene expression adjusted for the PCNA metagene as a means of predicting OS in various cancers resulted in statistically significant sets of genes.

scholarly journals Expression of Base Excision DNA Repair Genes Is a Sensitive Biomarker for in Vivo Detection of Chemical-induced Chronic Oxidative Stress

2004 ◽  
Vol 64 (3) ◽  
pp. 1050-1057 ◽  
Author(s):  
Ivan Rusyn ◽  
Shoji Asakura ◽  
Brian Pachkowski ◽  
Blair U. Bradford ◽  
Mikhail F. Denissenko ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Dna Repair ◽  
Dna Repair Genes ◽  
In Vivo Detection ◽  
Chronic Oxidative Stress ◽  
Base Excision ◽  
Base Excision Dna Repair ◽  
Repair Genes

Abstract 4199: Genetic variation in the in vitro genotoxic response to glycidamide and gene expression of DNA repair genes

2011 ◽  
Author(s):  
Marta Pingarilho ◽  
Nuno G. Oliveira ◽  
Célia Martins ◽  
Bruno C. Gomes ◽  
Ana S. Fernandes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Genetic Variation ◽  
Dna Repair Genes ◽  
Repair Genes

scholarly journals The Clinical Significance of DNA Damage Repair Signatures in Clear Cell Renal Cell Carcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Ergang Guo ◽  
Cheng Wu ◽  
Jun Ming ◽  
Wei Zhang ◽  
Linli Zhang ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Dna Damage ◽  
Dna Repair ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Dna Repair Genes ◽  
Cell Renal Cell Carcinoma ◽  
Damage Repair ◽  
Repair Genes

DNA damage repair plays an important role in cancer’s initiation and progression, and in therapeutic resistance. The prognostic potential of damage repair indicators was studied in the case of clear cell renal cell carcinoma (ccRCC). Gene expression profiles of the disease were downloaded from cancer genome databases and gene ontology was applied to the DNA repair-related genes. Twenty-six differentially expressed DNA repair genes were identified, and regression analysis was used to identify those with prognostic potential and to construct a risk model. The model accurately predicted patient outcomes and distinguished among patients with different expression levels of immune evasion genes. The data indicate that DNA repair genes can be valuable for predicting the progression of clear cell renal cell carcinoma and the clinical benefits of immunotherapy.

scholarly journals Genome Instability and DNA Repair in Cancer

2021 ◽  
Author(s):  
Bhaswatee Das ◽  
Bipasha Choudhury ◽  
Aditya Kumar ◽  
Vishwa Jyoti Baruah
Keyword(s):  
Dna Repair ◽  
Genome Instability ◽  
Repair Process ◽  
Repair System ◽  
Dna Repair Genes ◽  
Genomic Locus ◽  
Dna Repair Mechanisms ◽  
Repair Mechanisms ◽  
Or Genes ◽  
Repair Genes

Mutations in genome are essential for evolution but if the frequency of mutation increases it can evince to be detrimental, for a steady maintenance there exist a detailed complex system of surveillance and repair of DNA defects. Therefore, fault in DNA repair processes raises the probability of genomic instability and cancer in organisms. Genome instability encompasses various aspects of mutations from indels to various somatic variants. The chapter tries to present an overview of how cancer puts up several ways to ensure suppression of the fidelity in our DNA repair system. Cancer cells assure failure of efficient DNA repair mechanisms by innumerous ways, by mutation and epigenetic modifications in repair genes themselves or genes controlling their expression and functions, other by some catastrophic events like kataegis, chromothripsis and chromoplexy. These are clustered mutations taking place at a particular genomic locus which deluge the repair process. Cancer generation and evolution is dependent largely on genome instability, so it applies many strategies to overcome one of its basic obstacles that is DNA repair, targeting these DNA repair genes has also demonstrated to be helpful in cancer therapy; but an intricate understanding of recalcitrant process and mechanisms of drug resistant in cancer will further enhance the potential in them.

scholarly journals DNA Repair Gene Expression Adjusted by the PCNA Metagene Predicts Survival in Multiple Cancers

Cancers ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 501 ◽  
Author(s):  
Leif Peterson ◽  
Tatiana Kovyrshina
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Statistical Significance ◽  
Candidate Gene Approach ◽  
Dna Repair Genes ◽  
Repair Gene ◽  
Genome Wide ◽  
A Genome ◽  
Dna Repair Gene ◽  
Repair Genes

Removal of the proliferation component of gene expression by proliferating cell nuclearantigen (PCNA) adjustment via statistical methods has been addressed in numerous survivalprediction studies for breast cancer and all cancers in the Cancer Genome Atlas (TCGA). Thesestudies indicate that the removal of proliferation in gene expression by PCNA adjustment removesthe statistical significance for predicting overall survival (OS) when gene selection is performed ona genome-wide basis. Since cancers become addicted to DNA repair as a result of forced cellularreplication, increased oxidation, and repair deficiencies from oncogenic loss or geneticpolymorphisms, we hypothesized that PCNA adjustment of DNA repair gene expression does notremove statistical significance for OS prediction. The rationale and importance of this translationalhypothesis is that new lists of repair genes which are predictive of OS can be identified to establishnew targets for inhibition therapy. A candidate gene approach was employed using TCGARNA-Seq data for 121 DNA repair genes in 8 molecular pathways to predict OS for 18 cancers.Statistical randomization test results indicate that after PCNA adjustment, OS could be predictedsignificantly by sets of DNA repair genes for 61% (11/18) of the cancers. These findings suggest thatremoval of the proliferation signal in expression by PCNA adjustment does not remove statisticalsignificance for predicting OS. In conclusion, it is likely that previous studies on PCNA adjustmentand survival were biased because genes identified through a genome-wide approach are stronglyco-regulated by proliferation.

Targeting DNA Repair Systems in Antitubercular Drug Development

2019 ◽  
Vol 26 (8) ◽  
pp. 1494-1505 ◽  
Author(s):  
Alina Minias ◽  
Anna Brzostek ◽  
Jarosław Dziadek
Keyword(s):  
Dna Repair ◽  
Protein Crystal ◽  
Model Organisms ◽  
Dna Repair Genes ◽  
Associated Proteins ◽  
Related Proteins ◽  
Repair Genes

Infections with Mycobacterium tuberculosis, the causative agent of tuberculosis, are difficult to treat using currently available chemotherapeutics. Clinicians agree on the urgent need for novel drugs to treat tuberculosis. In this mini review, we summarize data that prompts the consideration of DNA repair-associated proteins as targets for the development of new antitubercular compounds. We discuss data, including gene expression data, that highlight the importance of DNA repair genes during the pathogenic cycle as well as after exposure to antimicrobials currently in use. Specifically, we report experiments on determining the essentiality of DNA repair-related genes. We report the availability of protein crystal structures and summarize discovered protein inhibitors. Further, we describe phenotypes of available gene mutants of M. tuberculosis and model organisms Mycobacterium bovis and Mycobacterium smegmatis. We summarize experiments regarding the role of DNA repair-related proteins in pathogenesis and virulence performed both in vitro and in vivo during the infection of macrophages and animals. We detail the role of DNA repair genes in acquiring mutations, which influence the rate of drug resistance acquisition.

DNA Repair Genes Are Upregulated in Multiple Myeloma (MM) Patients Relapsing after Tandem Transplantation.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 3392-3392
Author(s):  
Guido Tricot ◽  
Fenghuang Zhan ◽  
Yongsheng Huang ◽  
Bart Barlogie ◽  
John Shaughnessy
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Plasma Cells ◽  
Kinase Inhibitor ◽  
Acquired Resistance ◽  
Myeloma Cell ◽  
High Dose ◽  
Dna Repair Genes ◽  
High Dose Melphalan ◽  
Repair Genes

Abstract Background: Repair of DNA interstrand crosslinks (ICLs) is considered the major mechanism by which resistance to high and low dose melphalan emerges (Spanswick et al. Blood2002; 100: 224). Enhanced ICL repair occurs via the Fanconi anemia (FA)/ BRCA pathway in myeloma cell lines (Chen et al. Blood2005; 106: 698). The aim of this study was to evaluate if DNA repair genes were indeed upregulated at relapse when compared to baseline in patients enrolled on our Total Therapy 2 protocol. Methods: We compared 51 paired baseline and relapse bone marrow samples for gene expression profiling of CD138 selected plasma cells using the Affimetrix U133 Plus 2.0 microarray. The microarrays were preprocessed using GCOS 1.1 software and normalized using conventional GCOS 1.1 scaling. Baseline and relapse gene expression was compared using the paired Student t test. Results: More than 30 genes related to DNA repair on the microarray were analyzed. We observed significantly higher expression at relapse of FANCA (p=.003), BRCA 1 (p<.001), CHEK1 (p=.006) and FANCG (p=0.03) (Figure 1). In contrast, FANCD2 was down-regulated at relapse (p=.006), while no significant changes in expression of FANCF or DNA mismatch repair genes were seen. Conclusion: Our data supports the concept that DNA repair genes in the FA/BRCA pathway contribute to acquired resistance to melphalan in patients after high dose melphalan transplants and that inhibition of DNA repair by bortezomib, gemcitabine or the CHEK1 kinase inhibitor UCN-01, may reverse such resistance if added to high dose melphalan. DNA Repair Genes in Paired Relapse Samples (N=51) DNA Repair Genes in Paired Relapse Samples (N=51)

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