DNA damage and its processing. relation to human disease

Understanding the effects of Abhraka Bhasma on genotoxicity and its DNA repair potential in mouse model

BACKGROUND

Metal toxicity is of major concern to human health. The metals may modulate molecular mechanisms of various pathways. Rasashastra, the branch of Ayurveda, narrates the properties, unique preparation, processing techniques, and therapeutic uses of minerals. The use of herbal metallic preparations has evoked concern for their potential to produce toxicity, interest in efficacy as therapeutic agents and safety related issues. Abhraka Bhasma, is one such incinerated herbo-metallic preparation of mica, widely used by traditional medicine practitioners. Although there are reports of Abhraka Bhasma on beneficial effects, clear evidence is lacking on the effect of Abhraka Bhasma on genotoxicity and DNA repair.

OBJECTIVE

The present study aims to understand the effects of Abhraka Bhasma on geno toxicity, DNA repair, and other mechanisms in the mice test model.

MATERIAL AND METHODS

The experiments were conducted in in vivo Swiss albino mice. The acute oral toxicity was performed as per the OECD guidelines. The mice were treated with Abhraka Bhasma (120 or 360 mg/kg body weight) for 7 days. They were then challenged with ethyl methanesulfonate and the DNA repair was analyzed.

RESULTS

The data obtained indicated that the Abhraka Bhasma is not a genotoxic and reproductive toxic formulation. The selected higher concentration of Abhraka Bhasma showed a protective role against ethyl methanesulfonate induced chromosomal damages and enhanced constitutive DNA base excision repair in mice.

CONCLUSION

The anti-oxidant, potentiation of DNA repair and hematinic properties of Abhraka Bhasma may be attributed to the synergistic actions of its bioactive components.

Src-mediated phosphorylation of GAPDH regulates its nuclear localization and cellular response to DNA damage

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key enzyme involved in energy metabolism. Recently, GAPDH has been suggested to have extraglycolytic functions in DNA repair, but the underlying mechanism for the GAPDH response to DNA damage remains unclear. Here, we demonstrate that the tyrosine kinase Src is activated under DNA damage stress and phosphorylates GAPDH at Tyr41. This phosphorylation of GAPDH is essential for its nuclear translocation and DNA repair function. Blocking the nuclear import of GAPDH by suppressing Src signaling or through a GAPDH Tyr41 mutation impairs its response to DNA damage. Nuclear GAPDH is recruited to DNA lesions and associates with DNA polymerase β (Pol β) to function in DNA repair. Nuclear GAPDH promotes Pol β polymerase activity and increases base excision repair (BER) efficiency. Furthermore, GAPDH knockdown dramatically decreases BER efficiency and sensitizes cells to DNA damaging agents. Importantly, the knockdown of GAPDH in colon cancer SW480 cells and xenograft models effectively enhances their sensitivity to the chemotherapeutic drug 5-FU. In summary, our findings provide mechanistic insight into the new function of GAPDH in DNA repair and suggest a potential therapeutic target in chemotherapy.

DNA Damage, DNA Repair, Aging, and Neurodegeneration

Aging in mammals is accompanied by a progressive atrophy of tissues and organs, and stochastic damage accumulation to the macromolecules DNA, RNA, proteins, and lipids. The sequence of the human genome represents our genetic blueprint, and accumulating evidence suggests that loss of genomic maintenance may causally contribute to aging. Distinct evidence for a role of imperfect DNA repair in aging is that several premature aging syndromes have underlying genetic DNA repair defects. Accumulation of DNA damage may be particularly prevalent in the central nervous system owing to the low DNA repair capacity in postmitotic brain tissue. It is generally believed that the cumulative effects of the deleterious changes that occur in aging, mostly after the reproductive phase, contribute to species-specific rates of aging. In addition to nuclear DNA damage contributions to aging, there is also abundant evidence for a causative link between mitochondrial DNA damage and the major phenotypes associated with aging. Understanding the mechanistic basis for the association of DNA damage and DNA repair with aging and age-related diseases, such as neurodegeneration, would give insight into contravening age-related diseases and promoting a healthy life span.

Evaluation of the in vivo genotoxic effects of gamma radiation on the peripheral blood leukocytes of head and neck cancer patients undergoing radiotherapy

The present study aimed to evaluate the genotoxic effects of ionizing radiation on non-target cells of Head and Neck Squamous Cell Carcinoma (HNSCC) patients exposed to various cumulative doses of gamma rays during radiotherapy. The ten patients (P1-P10) were treated with cobalt 60 gamma radiation (External Beam Radiotherapy) for a period of five to six weeks with a daily fraction of 2Gy for 5 days each week. The genotoxic effects of radiation (single strand breaks - SSBs) in these patients were analyzed using the alkaline single cell gel electrophoresis (SCGE) technique, with the Olive Tail Moment (OTM) as the critical parameter. A sample of each patient's peripheral blood before starting with radiotherapy (pre-therapy) served as the control, and blood collected at weekly time intervals during the course of the radiotherapy served as treated (10, 20, 30, 40, 50 and 60Gy) samples. In vivo radiosensitivity of these patients, as indicated by SSB's after the cumulative radiation doses at the various times, was assessed using Student's t-test. Significant DNA damage relative to the individual patient's pre-therapy baseline data was observed in all patients. Inter-individual variation of the genotoxic effects was analyzed using two-way ANOVA. The correlation between doses for the means of smoker and non-smoker patients was calculated using the Pearson test. The results of this study may indicate the need to reduce the daily radiotherapy dose further to prevent genotoxic effects on non-target cells, thus improving safety. Furthermore, these results may indicate that the estimation of DNA damage following exposure to a gamma radiation, as measured by the comet assay in whole blood leukocytes, can be used to screen human populations for radiation-induced genetic damage at the molecular level.

Mitochondrial base excision repair assays

Mitochondrial DNA (mtDNA) is constantly exposed to oxidative injury. Due to its location close to the main site of reactive oxygen species, the inner mitochondrial membrane, mtDNA is more susceptible than nuclear DNA to oxidative damage. The accumulation of DNA damage is thought to be particularly deleterious in post-mitotic cells, including neurons, and to play a critical role in the aging process and in a variety of diseases. Thus, efficient mtDNA repair is important for the maintenance of genomic integrity and a healthy life. The base excision repair (BER) mechanism was the first to be described in mitochondria, and consequently it is the best known. This chapter outlines protocols for isolating mitochondria from mammalian cells in culture and from rodent tissues including liver and brain. It also covers the isolation of synaptic mitochondria. BER takes place in four distinct steps, and protocols describing in vitro assays for measuring these enzymatic steps in lysates of isolated mitochondria are included.

Impaired nucleotide excision repair pathway as a possible factor in pathogenesis of head and neck cancer

Tobacco smoking is one of the major risk factors in pathogenesis of head and neck squamous cell carcinomas (HNSCC). Many of the chemical compounds present in tobacco are well-known carcinogens which form adducts with DNA. Cells remove these adducts mainly by the nucleotide excision repair pathway (NER). NER also eliminates a broad spectrum of pyrimidine dimers (CPD) and photo-products (6-4PP) induced by UV-radiation or DNA cross-links after cisplatin anti-cancer treatment. In this study DNA damage and repair was examined in peripheral blood lymphocytes obtained from 20 HNSCC patients and 20 healthy controls as well as HTB-43 larynx and SSC-25 tongue cancer cell lines. DNA repair kinetics in the examined cells after cisplatin or UV-radiation treatment were investigated using alkaline comet assay during 240min of post-treatment incubation. MTT assay was used to analyse cell viability and the Annexin V-FITC kit specific for kinase-3 was employed to determine apoptosis after treating the cells with UV-radiation at dose range from 0.5 to 60J/m(2). NER capability was assessed in vitro with cell extracts by the use of a bacterial plasmid irradiated with UV-light as a substrate for the repair. The results show that lymphocytes from HNSCC patients and HTB-43 or SSC-25 cancer cells were more sensitive to genotoxic treatment with UV-radiation and displayed impaired DNA repair. Also evidenced was a higher rate of apoptosis induction after UV-radiation treatment of lymphocytes from the HNSCC patients and the HTB-43 cancer cells than after treatment of those from healthy donors. Finally, our results showed that there was a significant decrease in NER capacity in HTB-43 or SSC-25 cancer cells as well as in peripheral blood lymphocytes of HNSCC patients compared to controls. In conclusion, we suggest that the impaired NER pathway might be a critical factor in pathogenesis of head and neck cancer.

DNA damage and base excision repair in mitochondria and their role in aging

During the last decades, our knowledge about the processes involved in the aging process has exponentially increased. However, further investigation will be still required to globally understand the complexity of aging. Aging is a multifactorial phenomenon characterized by increased susceptibility to cellular loss and functional decline, where mitochondrial DNA mutations and mitochondrial DNA damage response are thought to play important roles. Due to the proximity of mitochondrial DNA to the main sites of mitochondrial-free radical generation, oxidative stress is a major source of mitochondrial DNA mutations. Mitochondrial DNA repair mechanisms, in particular the base excision repair pathway, constitute an important mechanism for maintenance of mitochondrial DNA integrity. The results reviewed here support that mitochondrial DNA damage plays an important role in aging.

Mitochondrial DNA repair and association with aging--an update

Mitochondrial DNA is constantly exposed to oxidative injury. Due to its location close to the main site of reactive oxygen species, the inner mitochondrial membrane, mtDNA is more susceptible than nuclear DNA to oxidative damage. The accumulation of DNA damage is thought to play a critical role in the aging process and to be particularly deleterious in post-mitotic cells. Thus, DNA repair is an important mechanism for maintenance of genomic integrity. Despite the importance of mitochondria in the aging process, it was thought for many years that mitochondria lacked an enzymatic DNA repair system comparable to that in the nuclear compartment. However, it is now well established that DNA repair actively takes place in mitochondria. Oxidative DNA damage processing, base excision repair mechanisms were the first to be described in these organelles, and consequently the best understood. However, new proteins and novel DNA repair pathways, thought to be exclusively present in the nucleus, have recently been described also to be present in mitochondria. Here we review the main mitochondrial DNA repair pathways and their association with the aging process.

Genetic polymorphisms in DNA base excision repair gene XRCC1 and the risk of squamous cell carcinoma of the head and neck

Background

The genes of base excision repair (BER) pathway have been extensively studied in the association with various human cancers. We performed a case-control study to test the association between two common single nucleotide polymorphisms (SNPs) of XRCC1 gene with human head and neck squamous cell carcinoma (HNSCC).

Methods

The genotype analysis of Arg194Trp and Arg399Gln gene polymorphisms for 92 HNSCC patients and 124 controls of cancer free subjects, in Polish population were performed using the PCR-based restriction fragment length polymorphism (PCR-RFLP) with endonuclease MspI.

Results

No altered risk has been found individually for these SNPs, however haplotypes analysis showed high association with head and neck cancer. The highest frequency, according to wild-type of Arg194Arg and Arg399Arg genotypes, was identified for Arg194Trp-Arg399Arg haplotype (OR, 2.96; 95% CI, 1.01–8.80).

Conclusion

Finally, we identified the combined Arg194Trp-Arg399Arg genotype of base excision repair gene XRCC1 that was associated with HNSCC and may have an impact on identification of a high-risk cancer population.

Role of impaired DNA repair in genotoxic susceptibility of patients with head and neck cancer

DNA repair is critical for genotoxic susceptibility and cancer development. Forty-seven patients with head and neck squamous cell carcinoma (HNSCC) and 38 healthy controls were enrolled in this study. Among the patients, 16 subjects had metastasis of HNSCC. The extent of DNA damage, including oxidative lesions, and efficiency of repair after genotoxic treatment with hydrogen peroxide were examined using the alkaline comet assay. HNSCC cells were sensitive to genotoxic treatment and displayed impaired DNA repair. In particular, lesions caused by hydrogen peroxide were repaired less effectively in cancer cells from patients with metastasis than in cells from healthy controls. We suggest that impaired DNA repair might play a role in genotoxic susceptibility of patients with head and neck cancer. Finally, as a consequence of this finding we have shown that treatment with DNA-reactive drugs could be considered as an effective therapy strategy for head and neck cancer.

Quantification of DNA repair capacity in whole blood of patients with head and neck cancer and healthy donors by comet assay

Comet assay has been used to estimate cancer risk by quantification of DNA damage and repair in response to mutagen challenge. Our goal was to adopt best practices for the alkaline comet assay to measure DNA repair capacity of white blood cells in whole blood of patients with squamous cell carcinoma of the head and neck (HNSCC). The results show that initial damage by 10 Gy of gamma radiation expressed as percent DNA in comet tail was higher in stimulated lymphocytes (61.1+/-11.8) compared to whole blood (43.0+/-12.1) but subsequent repair was similar with comet tail of approximately 20% at 15 min and 13% at 45 min after exposure. Exposure of whole blood embedded in agarose from 5 to 10 Gy gamma radiation was followed by an approximately 70% repair of the DNA damage within 45 min with a faster repair phase in the first 15 min. Variability of the measurement was lower within repeated measurements of the same person compared to measurement of different healthy individuals. The repair during first 15 min was slower (p=0.01) in ex-/non-smokers (41.0+/-2.1%) compared to smokers (50.3+/-2.7%). This phase of repair was also slower (p=0.02) in HNSCC patients (36.8+/-2.1%) compared to controls matched on age and smoking (46.4+/-3.0%). The results of this pilot study suggest that quantification of repair in whole blood following a gamma radiation challenge is feasible. Additional method optimization would be helpful to improve the assay for a large population screening.

Bleomycin-induced double-strand breaks in mitochondrial DNA of Drosophila cells are repaired

Mitochondrial DNA lesions cause numerous human diseases, and it is therefore important to identify the mechanisms whereby the mitochondrion repairs the damage. We have studied in cultured Drosophila cells the repair of bleomycin-induced double-strand breaks (DSBs) in mitochondrial DNA. Our results show that DSBs are repaired as rapidly and effectively in the mitochondria as in the nucleus. DNA repair is complete within 2h following bleomycin treatment, showing that Drosophila mitochondria have an effective system of DSB repair. The mechanism and mitochondrial proteins involved remain to be identified.

Quantification of RNA damage by reverse transcription polymerase chain reactions

RNA damages, such as those generated by nucleic acid-modifying agents, occur randomly in RNA and present challenging problems to organisms. It has been unclear how RNA function would be affected by many forms of RNA damage and how cells are protected against the damage. Elucidation of these mechanisms has been hampered by the lack of sensitive and efficient methodologies detecting damages randomly occurring in RNA, especially for the damage of a specific RNA. In this work, we have developed a method using reverse transcription polymerase chain reactions (RT-PCRs) to determine the level of damage of a specific RNA. The level of damage of the Escherichia coli 16S rRNA caused by oxidative stress was examined. When RNA is treated by H(2)O(2) in vitro, the normalized level of long cDNA is inversely dependent on the dosage of H(2)O(2) as determined by gel-based assay or real-time PCR. Long cDNA was also produced at reduced levels using RNA prepared from H(2)O(2)-treated E. coli cultures compared with RNA from control cultures. Remarkably, the level of cDNA reduction caused by H(2)O(2) treatment depends on the length of cDNA examined, suggesting random occurrences of damage in RNA templates. Approximately 40% of the reduction in cDNA can be detected in each kilobase of RNA from E. coli cultures treated with 0.5 mM H(2)O(2). This method is able to detect any type of damage in RNA-causing termination of reverse transcription and works on specific RNA of interest with high sensitivity.

The essential mechanisms of aging: Irreparable damage accumulation of biochemical side-reactions

Explanations on aging mechanisms have now become unexpectedly complicated. However, it is gradually accepted that 'senescence is a collective consequence of both inheritance and environment'. Based on the achievements of biological and medical research in related fields, we pinpoint in this review that although aging is mainly considered a physiological (non-pathological) process, the biochemical structure of aged organisms is deranged, or 'sick' at the molecular level. The free radical/glycation induced carbonyl stress, the key culprit to form crosslinks, has been identified to cause stable cyclic conjugates of mainly protein-based aggregates implying entropy increase (the Second Law of Thermodynamics) during aging. When combining such key aging processes with age pigment biochemistry, a general picture of aging process can be figured out, as the main clues and results are available. In this review we also propose for the first time that by focusing on 'process' rather than on 'causes' (damages), we can then get a clear view of aging mechanisms. Through rational thinking and critical analysis, we conclude that the accumulation of irreparable damages and alternations caused by spontaneous biological side-reactions seems to be the essential and profound nature of higher animals' aging mechanisms.

Origins of human mitochondrial point mutations as DNA polymerase gamma-mediated errors

Mitochondrial mutational spectra in human cells, tissues and derived tumors for bp 10,030-10,130 are essentially identical, suggesting a predominant mutagenic role for endogenous processes. We hypothesized that errors mediated by mitochondrial DNA polymerase gamma were the primary sources of mutations. Point mutations created in this sequence by human DNA pol gamma in vitro were thus compared to the eighteen mutational hotspots, all single base substitutions, previously found in human tissues. The set of concordant hotspots accounted for 83% of these in vivo mutational events. About half of these mutations are insensitive to prolonged heating of DNA during PCR and half increase proportionally with heating time at 98 degrees C. Primary misincorporation errors and miscopying errors past thermal denaturing products such as deaminated cytosines (uracils) thus appear to be of approximately equal importance. For the sequence studied, these data support the conclusion that, endogenous error mediated by DNA pol gamma constitutes the primary source of mitochondrial point mutations in human tissues.

Mitochondrial DNA maintenance and bioenergetics

Oxidative phosphorylation requires assembly of the protein products of both mitochondrial and of nuclear genomes into functional respiratory complexes. Cellular respiration can be compromised when mitochondrial DNA (mtDNA) sequences are corrupted. Oxidative damage resulting from reactive oxygen species (ROS) produced during respiration is probably a major source of mitochondrial genomic instability leading to respiratory dysfunction. Here, we review mechanisms of mitochondrial ROS production, mtDNA damage and its relationship to mitochondrial dysfunction. We focus particular attention on the roles of mtDNA repair enzymes and processes by which the integrity of the mitochondrial genome is maintained and dysfunction prevented.

Repair of genome destabilizing lesions

Living organisms are constantly exposed to detrimental agents both from the environment (e.g. ionizing radiation, ultraviolet light, natural and synthetic chemicals) and from endogenous metabolic processes (e.g. oxidative and hydrolytic reactions), resulting in modifications of proteins, lipids and DNA. Proteins and lipids are degraded and resynthesized, but the DNA is replicated only during cell division, when DNA damage may result in mutation fixation. Thus the DNA damage generated has the potential to lead to carcinogenesis, cell death, or other genetic disorders in the absence of efficient error-free repair. Because modifications in DNA sequence or structure may be incompatible with its essential role in preservation and transmission of genetic information from generation to generation, exquisitely sensitive DNA repair pathways have evolved to maintain genomic stability and cell viability. This review focuses on the repair and processing of genome destabilizing lesions and helical distortions that differ significantly from the canonical B-form DNA in mammalian cells. In particular, we discuss the introduction and processing of site-specific lesions in mammalian cells with an emphasis on psoralen interstrand crosslinks.

Endogenous DNA damage clusters in human skin, 3-D model, and cultured skin cells

Clustered damages-two or more oxidized bases, abasic sites, or strand breaks on opposing DNA strands within a few helical turns-are formed in DNA by ionizing radiation. Clusters are difficult for cells to repair and thus pose significant challenges to genomic integrity. Although endogenous clusters were found in some permanent human cell lines, it was not known if clusters accumulated in human tissues or primary cells. Using high-sensitivity gel electrophoresis, electronic imaging, and number average length analysis, we determined endogenous cluster levels in DNA from human skin, a 3-D skin model, and primary cultured skin cells. DNA from dermis and epidermis of human skin contained extremely low levels of endogenous clusters (a few per gigabase). However, cultured skin fibroblasts and keratinocytes-whether in monolayer cultures or in 3-D model skin cultures-accumulated oxidized pyrimidine, oxidized purine, and abasic clusters. The levels of endogenous clusters were decreased by growing cells in the presence of selenium or by increasing cellular levels of Fpg protein, presumably by increasing processing of clustered damages. These results imply that the levels of endogenous clusters can be affected by the cells' external environment and their ability to deal with DNA damage.

Effect of DNA damage on PCR amplification efficiency with the relative threshold cycle method

Polymerase stop assays used to quantify DNA damage assume that single lesions are sufficient to block polymerase progression. To test the effect of specific lesions on PCR amplification efficiency, we amplified synthetic 90 base oligonucleotides containing normal or modified DNA bases using real-time PCR and determined the relative threshold cycle amplification efficiency of each template. We found that while the amplification efficiencies of templates containing a single 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) were not significantly perturbed, the presence of a single 8-oxo-7,8-dihydro-2'-deoxyadenosine, abasic site, or a cis-syn thymidine dimer dramatically reduced amplification efficiency. In addition, while templates containing two 8-oxodGs separated by 13 bases amplified as well as the unmodified template, the presence of two tandem 8-oxodGs substantially hindered amplification. From these findings, we conclude that the reduction in polymerase progression is dependent on the type of damage and the relative position of lesions within the template.

Are endogenous clustered DNA damages induced in human cells?

Although clustered DNA damages are induced in cells by ionizing radiation and can be induced artifactually during DNA isolation, it was not known if they are formed in unirradiated cells by normal oxidative metabolism. Using high-sensitivity methods of quantitative gel electrophoresis, electronic imaging, and number average length analysis, we found that two radiosensitive human cell lines (TK6 and WI-L2-NS) accumulated Fpg-oxidized purine clusters and Nth-oxidized pyrimidine clusters but not Nfo-abasic clusters. However, four repair-proficient human lines (MOLT 4, HL-60, WTK1, and 28SC) did not contain significant levels (<5/Gbp) of any cluster type. Cluster levels were independent of p53 status. Measurement of glycosylase levels in 28SC, TK6, and WI-L2-NS cells suggested that depressed hOGG1 and hNth activities in TK6 and WI-L2-NS could be related to oxybase cluster accumulation. Thus, individuals with DNA repair enzyme deficiencies could accumulate potentially cytotoxic and mutagenic clustered DNA damages. The absence of Nfo-detected endogenous clusters in any cells examined suggests that abasic clusters could be a signature of cellular ionizing radiation exposure.

The role of stem cells in aging

The objectives of this review were first to critically review what is known about the effects of aging on stem cells in general, and hematopoietic stem cells in particular. Secondly, evidence is marshalled in support of the hypothesis that aging stem cells play a critical role in determining the effects of aging on organ function, and ultimately on the lifespan of a mammal. Aging has both quantitative and qualitative effects on stem cells. On balance, the qualitative changes are the more important since they affect the self-renewal potential, developmental potential, and interactions with extrinsic signals, including those from stroma. Although hematopoiesis is generally maintained at normal and life-supporting levels during normal aging, diminished function is acutely apparent when old stem cells are subjected to stress. There is ample evidence of diminished self-renewal capacity, restriction of the breadth of developmental potency, and decreased numbers of progeny of old stem cells subjected to hematopoietic demands. The prediction is made that whatever plasticity in developmental potential possessed by a young stem cell is lost during aging. Those parts of the world enjoying an ever-increasing standard of living are also inhabited by an increasingly elderly population. The effects of age on many physiological functions are not well studied or appreciated. A public health challenge to provide increased quality of life for this growing segment of the population requires more attention to the variable of age in experimental studies. Stem cell populations are likely to be a fruitful subject for studies of this type.

Construction and purification of site-specifically modified DNA templates for transcription assays

Chemical and physical agents can alter the structure of DNA by modifying the bases and the phosphate-sugar backbone, consequently compromising both replication and transcription. During transcription elongation, RNA polymerase complexes can stall at a damaged site in DNA and mark the lesion for repair by a subset of proteins that are utilized to execute nucleotide excision repair, a pathway commonly associated with the removal of bulky DNA damage from the genome. This RNA polymerase-induced repair pathway is called transcription-coupled nucleotide excision repair. Although our understanding of DNA lesion effects on transcription elongation and the associated effects of stalled transcription complexes on DNA repair is broadening, the attainment of critical data is somewhat impeded by labor-intensive, time- consuming processes that are required to prepare damaged DNA templates. Here, we describe an approach for building linear DNA templates that contain a single, site-specific DNA lesion and support transcription by human RNA polymerase II. The method is rapid, making use of biotin-avidin interactions and paramagnetic particles to purify the final product. Data are supplied demonstrating that these templates support transcription, and we emphasize the potential versatility of the protocol and compare it with other published methods.