The DNA Damage Response: Making It Safe to Play with Knives

Histone H2AX phosphorylation on a serine four residues from the carboxyl terminus (producing gammaH2AX) is a sensitive marker for DNA double-strand breaks (DSBs). DSBs may lead to cancer but, paradoxically, are also used to kill cancer cells. Using gammaH2AX detection to determine the extent of DSB induction may help to detect precancerous cells, to stage cancers, to monitor the effectiveness of cancer therapies and to develop novel anticancer drugs.

γH2AX and cancer

DNA double-strand breaks (DSBs) are critical lesions that can result in cell death or a wide variety of genetic alterations including large- or small-scale deletions, loss of heterozygosity, translocations, and chromosome loss. DSBs are repaired by non-homologous end-joining (NHEJ) and homologous recombination (HR), and defects in these pathways cause genome instability and promote tumorigenesis. DSBs arise from endogenous sources including reactive oxygen species generated during cellular metabolism, collapsed replication forks, and nucleases, and from exogenous sources including ionizing radiation and chemicals that directly or indirectly damage DNA and are commonly used in cancer therapy. The DSB repair pathways appear to compete for DSBs, but the balance between them differs widely among species, between different cell types of a single species, and during different cell cycle phases of a single cell type. Here we review the regulatory factors that regulate DSB repair by NHEJ and HR in yeast and higher eukaryotes. These factors include regulated expression and phosphorylation of repair proteins, chromatin modulation of repair factor accessibility, and the availability of homologous repair templates. While most DSB repair proteins appear to function exclusively in NHEJ or HR, a number of proteins influence both pathways, including the MRE11/RAD50/NBS1(XRS2) complex, BRCA1, histone H2AX, PARP-1, RAD18, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and ATM. DNA-PKcs plays a role in mammalian NHEJ, but it also influences HR through a complex regulatory network that may involve crosstalk with ATM, and the regulation of at least 12 proteins involved in HR that are phosphorylated by DNA-PKcs and/or ATM.

/pdf/regulation-of-dna-double-strand-break-repair-pathway-choice-4nmgza2h52.pdf

Regulation of DNA double-strand break repair pathway choice

Recent findings have thrust poly(ADP-ribose) polymerases (PARPs) into the limelight as potential chemotherapeutic targets. To provide a framework for understanding these recent observations, we review what is known about the structures and functions of the family of PARP enzymes, and then outline a series of questions that should be addressed to guide the rational development of PARP inhibitors as anticancer agents.

PARP inhibition: PARP1 and beyond

This 11th edition of the book Modern Nutrition in Health and Disease, featuring the work of more than 190 expert authors and divided into five parts, fully explains and encapsulates the fundamentals of nutrition and its role in contemporary society, from mastering the basic science of nutrient metabolism and function to applying nutritional concepts to combat human disease. Part I comprehensively covers specific dietary components, including major dietary constituents, minerals, vitamins and other Other CABI sites 

Modern Nutrition in Health and Disease

DNA double-strand breaks (DSBs) are extremely dangerous lesions with severe consequences for cell survival and the maintenance of genomic stability. In higher eukaryotic cells, DSBs in chromatin promptly initiate the phosphorylation of the histone H2A variant, H2AX, at Serine 139 to generate gamma-H2AX. This phosphorylation event requires the activation of the phosphatidylinositol-3-OH-kinase-like family of protein kinases, DNA-PKcs, ATM, and ATR, and serves as a landing pad for the accumulation and retention of the central components of the signaling cascade initiated by DNA damage. Regions in chromatin with gamma-H2AX are conveniently detected by immunofluorescence microscopy and serve as beacons of DSBs. This has allowed the development of an assay that has proved particularly useful in the molecular analysis of the processing of DSBs. Here, we first review the role of gamma-H2AX in DNA damage response in the context of chromatin and discuss subsequently the use of this modification as a surrogate marker for mechanistic studies of DSB induction and processing. We conclude with a critical analysis of the strengths and weaknesses of the approach and present some interesting applications of the resulting methodology.

γ-H2AX in recognition and signaling of DNA double-strand breaks in the context of chromatin

DNA double-strand breaks (DSBs) are extremely dangerous lesions with severe consequences for cell survival and the maintenance of genomic stability. In higher eukaryotic cells, DSBs in chromatin promptly initiate the phosphorylation of the histone H2A variant, H2AX, at Serine 139 to generate c-H2AX. This phosphorylation event requires the activation of the phosphatidylinositol-3-OH-kinase-like family of protein kinases, DNA-PKcs, ATM, and ATR, and serves as a landing pad for the accumulation and retention of the central components of the signaling cascade initiated by DNA damage. Regions in chromatin with c-H2AX are conveniently detected by immunofluorescence microscopy and serve as beacons of DSBs. This has allowed the development of an assay that has proved particularly useful in the molecular analysis of the processing of DSBs. Here, we first review the role of c-H2AX in DNA damage response in the context of chromatin and discuss subsequently the use of this modification as a surrogate marker for mechanistic studies of DSB induction and processing. We conclude with a critical analysis of the strengths and weaknesses of the approach and present some interesting applications of the resulting methodology.

http://www.csub.edu/~kszick_miranda/DSB%20chromatin%20review.pdf

SURVEY AND SUMMARY c-H2AX in recognition and signaling of DNA double-strand breaks in the context of chromatin

Poly(ADP-ribose)polymerase 1 (PARP-1) recognizes DNA strand interruptions in vivo and triggers its own modification as well as that of other proteins by the sequential addition of ADP-ribose to form polymers. This modification causes a release of PARP-1 from DNA ends and initiates a variety of responses including DNA repair. While PARP-1 has been firmly implicated in base excision and single strand break repair, its role in the repair of DNA double strand breaks (DSBs) remains unclear. Here, we show that PARP-1, probably together with DNA ligase III, operates in an alternative pathway of non-homologous end joining (NHEJ) that functions as backup to the classical pathway of NHEJ that utilizes DNA-PKcs, Ku, DNA ligase IV, XRCC4, XLF/Cernunnos and Artemis. PARP-1 binds to DNA ends in direct competition with Ku. However, in irradiated cells the higher affinity of Ku for DSBs and an excessive number of other forms of competing DNA lesions limit its contribution to DSB repair. When essential components of the classical pathway of NHEJ are absent, PARP-1 is recruited for DSB repair, particularly in the absence of Ku and non-DSB lesions. This form of DSB repair is sensitive to PARP-1 inhibitors. The results define the function of PARP-1 in DSB repair and characterize a candidate pathway responsible for joining errors causing genomic instability and cancer.

PARP-1 and Ku compete for repair of DNA double strand breaks by distinct NHEJ pathways

Objectives
To investigate the prevalence and associated factors of kidney stones among adults in China.

Subjects and methods
A nationwide cross-sectional survey was conducted among persons aged 18 and older across China from May 2013 to July 2014. Participants underwent urinary tract ultrasonographic examinations, questionnaires, and provided blood and urine samples to analyze. Kidney stones were defined as particles in size of 4 mm or greater. Prevalence was defined as the proportion of participants with kidney stone and binary logistic regression was used to estimate the associated factors.

Results
A total of 12570 individuals (45.2% men) with an average age of 48.8±15.3 (18-96) years were selected and invited to participate in the study. And 9310 (40.7% men) individuals completed the investigation, with a response rate of 74.1%. The prevalence of kidney stones was 6.4% (95% confidence interval (CI):5.9, 6.9), and the age- and sex-adjusted prevalence was 5.8% (95% CI: 5.3, 6.3; 6.5% in men and 5.1% in women). Binary logistic regression analysis showed that male, rural residents, age, family history of urinary stones, concurrent with diabetes mellitus and hyperuricemia, increased consumption of meat, and excessive sweating were all statistical significantly associated with increased risk of kidney stones. By contrast, consumed more tea, legume, and fermented vinegar were statistical significantly associated with decreased risk of kidney stones formation

Conclusion
Kidney stones are common disease among Chinese adults and about one in seventeen adults are affected currently. Some Chinese dietary habits may lower risk of kidney stones formation.

This article is protected by copyright. All rights reserved.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/bju.13828

Wenqi Wu

Papers

γ-H2AX in recognition and signaling of DNA double-strand breaks in the context of chromatin

SURVEY AND SUMMARY c-H2AX in recognition and signaling of DNA double-strand breaks in the context of chromatin

PARP-1 and Ku compete for repair of DNA double strand breaks by distinct NHEJ pathways

Prevalence of kidney stones in China: an ultrasonography based cross-sectional study

Repair of radiation induced DNA double strand breaks by backup NHEJ is enhanced in G2.