5-Hydroxymethylcytosine-mediated active demethylation is required for mammalian neuronal differentiation and function.

Although high levels of 5-hydroxymethylcytosine (5hmC) accumulate in mammalian neurons, our knowledge of its roles in terminal differentiation or as an intermediate in active DNA demethylation is incomplete. We report high-resolution mapping of DNA methylation and hydroxymethylation, chromatin accessibility, and histone marks in developing postmitotic Purkinje cells (PCs) in Mus musculus. Our data reveal new relationships between PC transcriptional and epigenetic programs, and identify a class of genes that lose both 5-methylcytosine (5mC) and 5hmC during terminal differentiation. Deletion of the 5hmC writers Tet1, Tet2, and Tet3 from postmitotic PCs prevents loss of 5mC and 5hmC in regulatory domains and gene bodies, and hinders transcriptional and epigenetic developmental transitions. Our data demonstrate that Tet-mediated active DNA demethylation occurs in vivo, and that acquisition of the precise molecular properties of adult PCs require continued oxidation of 5mC to 5hmC during the final phases of differentiation.

At birth, the mammalian brain contains tens of billions of neurons. Although the number does not increase much as the animal grows, there are many dramatic changes to their size and structure. These changes allow the neurons to communicate with one another, develop into networks, and learn the tasks of the adult brain. One way that these changes occur is by the accumulation of chemical marks on each neuron's DNA that help dictate which genes switch on, and which turn off. One of the most common ways that DNA can be marked is through the addition of a chemical group called a methyl group to one of the four DNA bases, cytosine. This process is called methylation. When methylation occurs, cytosine becomes 5-methylcytosine, or 5mC for short. In 2009, researchers found another modification present in the DNA in the brain: 5-hydroxymethylcytosine, or 5hmC. This modification appears when a group of proteins called the Tet hydroxylases turn 5mC into 5hmC. Converting 5mC to 5hmC normally helps cells remove marks on their DNA before they divide and expand. This is important because the newly generated cells need to be able to accumulate their own methylation marks to perform their roles properly. However, neurons in the brain accumulate 5hmC after birth, when the cells are no longer dividing, indicating that 5hmC may be required for the neurons to mature. Stoyanova et al. set out to determine whether mouse neurons need 5hmC to get their adult characteristics by tracking the chemical changes that occur in DNA from birth to adulthood. Some of the mice they tested produced 5hmC normally, while others lacked the genes necessary to make the Tet proteins in a specific class of neurons, preventing them from converting 5mC to 5hmC as they differentiate. The results reveal that neurons do not mature properly if 5hmC is not produced continuously following the first week of life. This is because neurons need to have the right genes switched on and off to differentiate correctly, and this only happens when 5hmC accumulates in some genes, while 5hmC and 5mC are removed from others. The data highlight the role of the Tet proteins, which convert 5mC into 5hmC, in preparing the marks for removal and demonstrate that active removal of these marks is essential for neuronal differentiation. Given the role of 5hmC in the development of neurons, it is possible that problems in this system could contribute to brain disorders. Further studies aimed at understanding how cells control 5hmC levels could lead to new ways to improve brain health. Research has also shown that if dividing cells lose the ability to make 5hmC, they can become cancerous. Future work could explain more about how and why this happens.

MeCP2 nuclear dynamics in live neurons results from low and high affinity chromatin interactions.

Methyl-CpG-binding-Protein 2 (MeCP2) is an abundant nuclear protein highly enriched in neurons. Here we report live-cell single-molecule imaging studies of the kinetic features of mouse MeCP2 at high spatial-temporal resolution. MeCP2 displays dynamic features that are distinct from both highly mobile transcription factors and immobile histones. Stable binding of MeCP2 in living neurons requires its methyl-binding domain and is sensitive to DNA modification levels. Diffusion of unbound MeCP2 is strongly constrained by weak, transient interactions mediated primarily by its AT-hook domains, and varies with the level of chromatin compaction and cell type. These findings extend previous studies of the role of the MeCP2 MBD in high affinity DNA binding to living neurons, and identify a new role for its AT-hooks domains as critical determinants of its kinetic behavior. They suggest that limited nuclear diffusion of MeCP2 in live neurons contributes to its local impact on chromatin structure and gene expression.

Species and cell-type properties of classically defined human and rodent neurons and glia.

Determination of the molecular properties of genetically targeted cell types has led to fundamental insights into mouse brain function and dysfunction. Here, we report an efficient strategy for precise exploration of gene expression and epigenetic events in specific cell types in a range of species, including postmortem human brain. We demonstrate that classically defined, homologous neuronal and glial cell types differ between rodent and human by the expression of hundreds of orthologous, cell specific genes. Confirmation that these genes are differentially active was obtained using epigenetic mapping and immunofluorescence localization. Studies of sixteen human postmortem brains revealed gender specific transcriptional differences, cell-specific molecular responses to aging, and the induction of a shared, robust response to an unknown external event evident in three donor samples. Our data establish a comprehensive approach for analysis of molecular events associated with specific circuits and cell types in a wide variety of human conditions.

Influence of Carnicor, Venofer, and Sevelamer on the levels of genotoxic damage in end-stage renal disease patients.

End-stage renal disease (ESRD) patients present high levels of phosphorus and calcium products in serum, which contribute to the development of vascular calcification and cardiovascular disease, and to low iron stores and carnitine deficiency. For these reasons, ESRD patients are generally supplemented with different medicines. Some of the most common treatments include the use of Carnicor, Venofer, and Sevelamer drugs. Carnicor is used as a source of L-carnitine, acting as antioxidant and neuroprotector. Venofer is used to reduce the deficit of iron. Sevelamer is used to treat hyperphosphatemia. To determine the potential harmful genotoxic effects of these drugs, a group of 214 patients included in a hemodialysis program with different intakes of Carnicor, Venofer, and Sevelamer were evaluated. The levels of basal and oxidative DNA damage, as well as chromosomal damage, were measured in all individuals using the comet and the micronucleus assays, respectively. Our results indicate that Carnicor administration was associated with low but significant increases in the frequency of basal DNA damage and micronuclei. Environ. Mol. Mutagen. 59:302-311, 2018. © 2018 Wiley Periodicals, Inc.

Genomic damage as a biomarker of chronic kidney disease status.

Patients suffering from chronic kidney disease (CKD) exhibit a high incidence of cancer and cardiovascular diseases, as well as high levels of genomic damage. To confirm the association of CKD with genomic damage we have carried out the largest study to date addressing this issue, using a total of 602 subjects (187 controls, 206 pre-dialysis CKD patients and 209 CKD patients in hemodialysis). DNA oxidative damage was measured in all individuals using the comet assay. Our results indicate that CKD patients have significantly higher levels of DNA damage than controls, but no significant differences were observed between pre-hemodialysis (pre-HD) and hemodialysis (HD) patients. When oxidative damage was measured, no differences were observed between patients and controls, although HD patients showed significantly higher levels of oxidative damage than pre-HD patients. In addition, a positive relationship was demonstrated between genomic damage and all-cause mortality. Our study confirms that genomic damage can be predictive of prognosis in CKD patients, with high levels of DNA damage indicating a poor prognosis in HD patients.

Time in hemodialysis modulates the levels of genetic damage in hemodialysis patients.

It is assumed that hemodialysis treatment can diminish the levels of genetic damage in circulating lymphocytes by cleaning the blood of uremic toxins that cause oxidative stress. However, the hemodialysis process by itself may also induce genomic damage by producing reactive oxygen species (ROS). We conducted a follow-up study in a group of 70 hemodialysis patients followed for a mean time of 15 months. We investigated the effect of exposure time in hemodialysis on the levels of genetic damage in peripheral blood lymphocytes using the micronucleus assay. In addition, genetic damage after in vitro irradiation with 0.5 Gy was also analyzed to evaluate changes in radiosensitivity. Our results showed that, at the end of the study, there was a decrease in both the basal levels of genetic damage (9.9 ± 1.0 vs. 7.6 ± 0.7) and radiosensitivity values (38.5 ± 3.0 vs. 27.6 ± 2.4). We conclude that hemodialysis procedures may act as an ameliorating factor reducing the genetic damage present in chronic kidney disease patients.

Base excision repair capacity in chronic renal failure patients undergoing hemodialysis treatment.

The aim of this study was to determine if the differences observed in the levels of DNA damage in a group of patients suffering from chronic renal failure are due to differences in the repair capability. DNA damage was initially measured with the comet assay in 106 hemodialysis patients. A selected group of 21 patients representing high (ten patients) and low (11 patients) levels of DNA damage were obtained for determination of base excision repair capacity. This was measured in an in vitro assay where protein extracts from lymphocytes were incubated with a substrate of DNA containing 8-oxoguanine, and the rate of incision was measured with the comet assay. Patients with high levels of genomic damage showed, as an average, significantly lower repair capacity (12·73 ± 1·84) in comparison with patients with low levels of genomic damage (18·13 ± 1·13). Nevertheless, the correlation coefficient between repair ability and levels of genomic damage was found to be only close to the significance value (r:-0·423, p: 0·056). Although DNA damage was clearly related to time on hemodialysis, base excision repair capacity was not. This is one of the few studies providing information on the repair capacity of chronic renal failure patients undergoing hemodialysis. As a summary, our results would indicate that DNA damage levels are in part associated to the repair capacity of the patients, and this repair capacity is not associated with the duration of hemodialysis treatment.

Genomic damage as an independent predictor marker of mortality in hemodialysis patients.

AIM: Hemodialysis (HD) patients present an enhanced mortality. Since oxidative DNA damage can be considered a biomarker of genomic instability our aim was to evaluate the influence of this genetic biomarker in all-cause mortality in a group of HD patients followed for 4 years. MATERIAL AND METHODS: 123 chronic HD patients were included. Overall genomic damage was analyzed using the Comet assay. Oxidative DNA damage was measured using the Comet assay complemented with the use of Endo-III and FPG enzymes. Follow-up was carried out from January 2007 to July 2011. RESULTS: Selected HD patients had a mean age of 62 ± 15 years. During the follow-up 36% of patients died (48% due to cardiovascular disease) and 23% were transplanted. Older patients, with high CRP levels, low levels of cholesterol-HDL and albumin, and higher genetic damage at the beginning of the study showed an increased risk for mortality. Multivariate analysis showed that only genomic damage, age and CRP were independently associated with mortality. CONCLUSIONS: Our study shows for the first time that, in HD patients, the presence of high levels of genomic damage is a strong predictor of all-cause mortality. This association remains significant after adjustment for relevant covariates.

Genomic instability in chronic renal failure patients.

Patients suffering chronic renal failure (CRF) exhibit a high incidence of cancer, as well as high levels of genetic damage. We hypothesized that these patients show genomic instability as measured by increased radiosensitivity to the induction of genetic damage. The background levels of genetic damage and the net genetic damage after in vitro irradiation with 0.5 Gy were analyzed using the micronucleus assay in peripheral blood lymphocytes of 174 CRF patients and 53 controls. The net radiation-induced genetic damage was significantly higher in CRF patients with respect to controls. Among CRF patients, the levels of genetic damage were higher in those with prior incidence of cancer than in those without cancer; in addition, those CRF patients undergoing hemodialysis presented with higher levels of genetic damage than those in the advanced Stages (4-5) of the pathology. A positive association was observed between basal and net micronucleus frequency among CFR patients. However, no association was found between net genetic damage and parameters linked to the different stages of the pathology, such as urine creatinine levels and glomerular filtration rate. Our results indicate that CRF patients show increased radiosensitivity and that the degree of radiosensitivity is associated with the progression of the pathological stage of the disease.

Chromium-induced genotoxicity and interference in human lymphoblastoid cell (TK6) repair processes.

Two model chromium (Cr) compounds, one hexavalent (sodium chromate) and one trivalent (chromium chloride), were investigated in a human lymphoblastoid cell line (TK6) to increase our knowledge regarding Cr-induced genotoxicity mechanisms. Both selected compounds were genotoxic using the comet assay, although the percentage of DNA in tail obtained after treatment with Cr(VI) was significantly higher than that obtained with Cr(III), at the higher concentrations tested. To determine the nature of the induced damage, enzymes recognizing oxidized bases were used. Treatments with formamidopyrimidine (FPG) and endonuclease III (EndoIII) displayed a greater degree of DNA damage, indicating that the induction of oxidized bases accounts for an important proportion of the damage induced by Cr compounds. In addition, the kinetic repair studies showed that generated DNA damage is removed in approximately 8 h, with the damage induced by Cr(III) being removed/repaired more rapidly than damage produced by Cr(VI). To detect Cr interferences with the repair process, a post-treatment was applied after exposure to 2 Gy gamma radiation. Post-treatment significantly delayed the repair kinetics of DNA damage induced by radiation. This interference effect induced by Cr(VI) was more pronounced. In conclusion, evidence indicates that a high proportion of the Cr-induced DNA damage is correlated with oxidative damage, and that both Cr compounds interfere with repair mechanisms involved in repair of DNA damage induced by gamma radiation.

Genetic damage in chronic renal failure patients is associated with the glomerular filtration rate index.

Chronic renal failure (CRF) patients are considered to present genomic instability and, as a consequence, elevated levels of genetic damage. An open question is whether this damage is related to the stage of the pathology. To determine the background levels of genetic damage, a large population of 258 Caucasian adults (201 CRF patients and 57 controls) was analysed using the micronucleus (MN) assay. The frequency of MN in CRF patients was significantly higher than in controls and correlated with the progression of the disease, according to the glomerular filtration rate. In addition, a significant association was observed between genetic damage and serum creatinine levels. Genetic damage, measured as frequency of MN, increases when renal function decreases. The fact that an increased level of MN is already observed in patients' Stage 2 seems to indicate a genetic predisposition on these patients. Nevertheless, part of the observed damage can be attributed to the uraemic state itself.

Oxidative DNA damage in chronic renal failure patients.

BACKGROUND: Chronic renal failure (CRF) patients present a high incidence of cardiovascular pathologies and cancer. This has been attributed to the existence of genomic instability in these patients, and consequently they should present elevated levels of genetic damage. METHODS: To determine the background levels of genetic damage and its specific levels of oxidative damage, a large population of 253 CRF patients (77 in dialysis) was analysed using the comet assay. The percentage of DNA in the tail was used as a measure of basal genetic damage. In addition, the use of endo III and FPG enzymes allowed us to determine the levels of specific oxidative damage in DNA bases. RESULTS: This is the first study that uses endo III and FPG enzymes to measure oxidative damage in CRF patients. Overall genetic damage, as well as specific oxidative damage, was higher in dialysis patients than in the CRF patients with different stages of uraemic state; genetic damage increased when serum creatinine levels increased. Genomic damage in dialysis patients decreased in those patients submitted to dialysis for a long time. CONCLUSIONS: Genetic damage increases when renal function decreases, being maximum in haemodialysis patients. Although part of the observed damage can be attributed to the uraemic state itself, other individual genetic factors can influence a state of genomic instability responsible for the observed genomic damage.