Exploring the molecular and functional cellular response to hydrazine via transcriptomics and DNA repair mutant cell lines.

Hydrazine is a rodent carcinogen and is classified as a probable human carcinogen by IARC. Though hydrazine is positive in both in vitro and in vivo DNA strand break (comet) assays, hydrazine was reported to be negative in an in vitro mutation Muta Mouse lung epithelial cell (FE1) test, as well as in a regulatory-compliant, in vivo Big Blue mouse mutation test. In this article, mechanistic studies explored the cellular response to hydrazine. When tested in a regulatory-compliant mouse lymphoma assay, hydrazine yielded unusual, weakly positive results. This prompted an investigation into the transcriptional response to hydrazine in FE1 cells via RNA sequencing. Amongst the changes identified was a dose-dependent increase in G2/M DNA damage checkpoint activation associated genes. Flow cytometric experiments in FE1 cells revealed that hydrazine exposure led to S-phase cell cycle arrest. Clonogenic assays in a variety of cell lines harboring key DNA repair protein deficiencies indicated that hydrazine could sensitize cells lacking homology dependent repair proteins (Brca2 and Fancg). Lastly, hprt assays with hydrazine were conducted to determine whether a lack of DNA repair could lead to mutagenicity. However, no robust, dose-dependent induction of mutations was noted. The transcriptional and cell cycle response to hydrazine, coupled with functional investigations of DNA repair-deficient cell lines support the inconsistencies noted in the genetic toxicology regulatory battery. In summary, while hydrazine may be genotoxic, transcriptional and functional processes involved in cell cycle regulation and DNA repair appear to play a nuanced role in mediating the mutagenic potential.

Weak silica nanomaterial-induced genotoxicity can be explained by indirect DNA damage as shown by the OGG1-modified comet assay and genomic analysis.

In a previous study, 15-nm silica nanoparticles (NPs) caused small increases in DNA damage in liver as measured in the in vivo comet and micronucleus assays after intravenous administration to rats at their maximum tolerated dose, a worst-case exposure scenario. Histopathological examination supported a particle-induced, tissue damage-mediated inflammatory response. This study used a targeted approach to provide insight into the mode of action (MoA) by examining transcriptional regulation of genes in liver in a time and dose-dependent manner at 1, 2, 4, 8 and 24 h after intravenous administration of 15-nm silica NPs. DNA damage was assessed using the standard comet assay and hOGG1 glycosylase-modified comet assay that also measures oxidative DNA damage. Potassium bromate, an IARC Class 2B carcinogen that specifically operates via an oxidative stress MoA, was used as a positive control for the hOGG1 comet assay and gave a strong signal in its main target organ, the kidney, while showing less activity in liver. Treatment of rats with silica NPs at 50 mg/kg body weight (bw) caused small, statistically insignificant increases in DNA damage in liver measured by the standard comet assay, while a statistically significant increase was observed at 4 h with the hOGG1 comet assay, consistent with a MoA involving reactive oxygen species. Histopathology showed liver damage and neutrophil involvement while genomic analysis and response pattern of key genes involved in inflammation and oxidative stress supported a tissue damage-mediated inflammatory response involving the complement system for removing/phagocytising damaged cells. No changes were observed for histopathology or gene array for the low-dose (5 mg/kg bw) silica NPs. The results of this study confirm our hypothesis that the weak DNA damage observed by silica NPs occurs secondary to inflammation/immune response, indicating that a threshold can be applied in the risk assessment of these materials.

Silica nanoparticles administered at the maximum tolerated dose induce genotoxic effects through an inflammatory reaction while gold nanoparticles do not.

While the collection of genotoxicity data and insights into potential mechanisms of action for nano-sized particulate materials (NPs) are steadily increasing, there is great uncertainty whether current standard assays are suitable to appropriately characterize potential risks. We investigated the effects of NPs in an in vivo Comet/micronucleus (MN) combination assay and in an in vitro MN assay performed with human blood. We also incorporated additional endpoints into the in vivo study in an effort to delineate primary from secondary mechanisms. Amorphous silica NPs (15 and 55 nm) were chosen for their known reactivity, while gold nano/microparticles (2, 20, and 200 nm) were selected for their wide size range and lower reactivity. DNA damage in liver, lung and blood cells and micronuclei in circulating reticulocytes were measured after 3 consecutive intravenous injections to male Wistar rats at 48, 24 and 4h before sacrifice. Gold nano/microparticles were negative for MN induction in vitro and in vivo, and for the induction of DNA damage in all tissues. Silica particles, however, caused a small but reproducible increase in DNA damage and micronucleated reticulocytes when tested at their maximum tolerated dose (MTD). No genotoxic effects were observed at lower doses, and the in vitro MN assay was also negative. We hypothesize that silica NPs initiate secondary genotoxic effects through release of inflammatory cell-derived oxidants, similar to that described for crystalline silica (quartz). Such a mechanism is supported by the occurrence of increased neutrophilic infiltration, necrosis, and apoptotic cells in the liver, and induction of inflammatory markers TNF-α and IL-6 in plasma at the MTDs. These results were fairly consistent between silica NPs and the quartz control, thereby strengthening the argument that silica NPs may act in a similar, thresholded manner. The observed profile is supportive of a secondary genotoxicity mechanism that is driven by inflammation.

A novel locus for disseminated superficial actinic porokeratosis maps to chromosome 16q24.1-24.3.

Disseminated superficial actinic porokeratosis (DSAP) is an uncommon autosomal dominant keratinization disorder with genetic heterogeneity characterized by multiple superficial keratotic lesions surrounded by a slightly raised keratotic border. Thus far, there have been three susceptible loci determined for DSAP and one locus for disseminated superficial porokeratosis (DSP), i.e. 12q23.2-24.1, 15q25.1-26.1, 1p31.3-p31.1 and 18p11.3. Moreover, the locus for porokeratosis palmaris plantaris et disseminata (PPPD) was mapped to 12q24.1-24.2, which overlapped with the first DSAP locus. Following the exclusion of these known loci in a four-generation Chinese DSAP family, we performed a genome-wide linkage analysis and identified a new locus on chromosome 16q24.1-24.3. The maximum two-point LOD score of 3.73 was obtained with the marker D16S3074 at a recombination fraction θ of 0.00. Haplotype analysis defined the critical 17.4-cM region for DSAP between D16S3091 and D16S413. This is regarded to be the forth locus for DSAP (DSAP4). ATP2C1 was sequenced as a candidate gene, however, no mutation was found. Further investigation for the genetic basis of DSAP is under way.

Inhibition of poly(ADP-ribose) polymerase down-regulates BRCA1 and RAD51 in a pathway mediated by E2F4 and p130.

Inhibitors of poly(ADP-ribose) polymerase (PARP) are in clinical trials for cancer therapy, on the basis of the role of PARP in recruitment of base excision repair (BER) factors to sites of DNA damage. Here we show that PARP inhibition to block BER is toxic to hypoxic cancer cells, in which homology-dependent repair (HDR) is known to be down-regulated. However, we also report the unexpected finding that disruption of PARP, itself, either via chemical PARP inhibitors or siRNAs targeted to PARP-1, can inhibit HDR by suppressing expression of BRCA1 and RAD51, key factors in HDR of DNA breaks. Mechanistically, PARP inhibition was found to cause increased occupancy of the BRCA1 and RAD51 promoters by repressive E2F4/p130 complexes, a pathway prevented by expression of HPV E7, which disrupts p130 activity, or by siRNAs to knock down p130 expression. Functionally, disruption of p130 by E7 expression or by siRNA knockdown also reverses the cytotoxicity and radiosensitivity associated with PARP inhibition, suggesting that the down-regulation of BRCA1 and RAD51 is central to these effects. Direct measurement of HDR using a GFP-based assay demonstrates reduced HDR in cells treated with PARP inhibitors. This work identifies a mechanism by which PARP regulates DNA repair and suggests new strategies for combination cancer therapies.

Reassessment of microarray expression data of porokeratosis by quantitative real-time polymerase chain reaction.

BACKGROUND: Porokeratosis (PK) is a heterogeneous group of keratinization disorders that exhibit similarities with psoriasis at both the clinical and molecular levels. METHODS: The transcript levels of keratin (KRT) 6A, 16, 17, S100A7, A8, A9, p53 and three candidate genes (i.e. SART3, SSH1 and ARPC3) were reassessed in pairwise lesional and uninvolved skin from nine patients with PK by real-time quantitative polymerase chain reaction (RTQ-PCR). RESULTS: The results of RTQ-PCR confirmed that KRT6A, 16, S100A7, A8 and A9 (p = 0.008) were mostly up-regulated in the lesional skin when compared with uninvolved skin. Different from the microarray data, there was no significant difference observed in KRT17 expression patterns between lesional and normal-appearing skin (p = 0.066). No statistical difference was observed in p53 and three candidate genes' expression patterns between lesional and uninvolved skin. CONCLUSIONS: In the present study, 9 of the 10 gene expression measured by RTQ-PCR in PK were statistically comparable to microarray data. KRT6A was identified as specific biomarker for porokeratotic keratinocytes, as it was the most significantly up-regulated gene in the nine patient samples.

Emerging roles of microRNAs in the molecular responses to hypoxia.

Recent studies have established that the regulation of microRNAs (miRs) is a feature of the hypoxic response. In this review, we discuss the role of hypoxia-regulated miRs, with an emphasis on miR-210 and miR-373, and anticipate directions for clinical applications. The induction of miR-210 and miR-373 is dependent upon hypoxia inducible factor (HIF), and their up-regulation has been detected in a variety of solid tumors. Both miRs have been associated with adverse prognosis and metastatic potential. The increased expression of miR-210 is linked to an in vivo hypoxic signature. MiR-210 also participates in endothelial and neuronal cells' response to oxygen deprivation and may possess a role in the regulation of angiogenesis. A variety of miR-210 and miR-373 targets that may be relevant to hypoxia have been validated or proposed. Very recently, targets of these miRs that are implicated in DNA repair have been identified, thus establishing an additional link between the hypoxic tumor microenvironment and DNA damage. Extending beyond cancer biology, some of miR-210 targets are likely involved in the regulation of angiogenesis, and neuronal cell survival. Inactivation of miRs affected by hypoxia presents a promising therapeutic strategy in the case of difficult-to-treat cancers, as well as in other non-cancer-related diseases.

MicroRNA regulation of DNA repair gene expression in hypoxic stress.

Genetic instability is a hallmark of cancer; the hypoxic tumor microenvironment has been implicated as a cause of this phenomenon. MicroRNAs (miR) are small nonprotein coding RNAs that can regulate various cellular pathways. We report here that two miRs, miR-210 and miR-373, are up-regulated in a hypoxia-inducible factor-1alpha-dependent manner in hypoxic cells. Bioinformatics analyses suggested that these miRs could regulate factors implicated in DNA repair pathways. Forced expression of miR-210 was found to suppress the levels of RAD52, which is a key factor in homology-dependent repair (HDR); the forced expression of miR-373 led to a reduction in the nucleotide excision repair (NER) protein, RAD23B, as well as in RAD52. Consistent with these results, both RAD52 and RAD23B were found to be down-regulated in hypoxia, but in both cases, the hypoxia-induced down-regulation could be partially reversed by antisense inhibition of miR-210 and miR-373. Importantly, luciferase reporter assays indicated that miR-210 is capable of interacting with the 3' untranslated region (UTR) of RAD52 and that miR-373 can act on the 3' UTR of RAD23B. These results indicate that hypoxia-inducible miR-210 and miR-373 play roles in modulating the expression levels of key proteins involved in the HDR and NER pathways, providing new mechanistic insight into the effect of hypoxia on DNA repair and genetic instability in cancer.

Gene expression profiling of porokeratosis.

BACKGROUND: Porokeratosis (PK) represents a heterogeneous group of disorders of keratinization and has a wide variety of clinical manifestations. PK may exhibit similarities with psoriasis at both clinical and molecular levels. The genetic basis and pathogenesis for PK remain elusive. METHODS: We studied the transcriptional profiles of three pairwise lesional and uninvolved skin biopsies from patients with different subtypes of PK using the Illumina BeadArray platform. RESULTS: A total of 37 upregulated genes were identified in our study, including wound-induced keratins, S100 calcium-binding protein genes involved in epidermal differentiation, as well as genes involved in mediating intercellular communication and the immune response. To our knowledge, this is the first study that characterizes the immune profile of PK lesions. CONCLUSIONS: Here, we report that keratinocytes (KCs)-harboring lesions have activated and overexpressed wound-induced keratin genes, which appear to be coregulated with other genes involved in mediating epidermal differentiation, intercellular communication and immunity. This study, from the perspective of gene profiling, supports that gene misregulation in PK mimics that of psoriasis. Our data indicate that the genes implicated in the T-cell-mediated immune response pathway and activation of KCs play a key role in the pathogenesis of PK.

Regulation of CD20 expression by radiation-induced changes in intracellular redox status.

Increasing the levels of CD20 expression in cells that harbor low CD20 levels may enhance their responsiveness to CD20-specific antibody therapies. Here, we examined the regulation of CD20 expression after treatment with 0.5-2.0 Gy X-irradiation and hydrogen peroxide (H(2)O(2)), in the presence or absence of known antioxidants, in the Burkitt lymphoma cell lines Daudi and Raji. Irradiation of cells enhanced cell-surface CD20 expression; the kinetics and extent of this change were cell-type specific and time-dependent. The kinetics of reactive oxygen species generation and changes in mitochondrial membrane potential after irradiation were also correlated with changes in CD20 expression. Raji and Daudi cells treated with H(2)O(2) showed a 2-to 2.5-fold increase in CD20 expression at 12 and 20 h, respectively. Buthionine sulfoximine, which depletes glutathione, also increased surface CD20, whereas antioxidants, such as PEG-catalase, PEG-SOD, vitamin C, and amifostine, decreased CD20 expression induced by radiation or H(2)O(2). The antioxidant-mediated decrease in CD20 expression induced by radiation or H(2)O(2) suggests a mechanism involving redox regulation. These results demonstrate the critical role of radiation-induced oxidative stress in CD20 expression and may have implications for defining and improving the efficacy of CD20-targeted antibody therapy and radioimmunotherapy.

E2F4 function in G2: maintaining G2-arrest to prevent mitotic entry with damaged DNA.

Mammalian cells undergo cell cycle arrest in response to DNA damage through multiple checkpoint mechanisms. One such checkpoint pathway maintains genomic integrity by delaying mitotic progression in response to genotoxic stress. Transition though the G2 phase and entry into mitosis is considered to be regulated primarily by cyclin B1 and its associated catalytically active partner Cdk1. While not necessary for its initiation, the p130 and Rb-dependent target genes have emerged as being important for stable maintenance of a G2 arrest. It was recently demonstrated that by interacting with p130, E2F4 is present in the nuclei and plays a key role in the maintenance of this stable G2 arrest. Increased E2F4 levels and its translocation to the nucleus following genotoxic stress result in downregulation of many mitotic genes and as a result promote a G0-like state. Irradiation of E2F4-depleted cells leads to enhanced cellular DNA double-strand breaks that may be measured by comet assays. It also results in cell death that is characterized by caspase activation, sub-G1 and sub-G2 DNA content, and decreased clonogenic cell survival. Here we review these recent findings and discuss the mechanisms of G2 phase checkpoint activation and maintenance with a particular focus on E2F4.

Regulation of DNA repair in hypoxic cancer cells.

Emerging evidence indicates that the tumor microenvironmental stress of hypoxia can induce genetic instability in cancer cells. We and others have found that the expression levels of key genes within the DNA mismatch repair (MMR) and homologous recombination (HR) pathways are coordinately repressed by hypoxia. These decreases are associated with functional impairments in both MMR and HR repair under hypoxic conditions, and thus they represent a possible mechanistic explanation for the observed phenomenon of hypoxia-induced genetic instability. In parallel, studies also indicate that several DNA damage response factors are activated in response to hypoxia and subsequent reoxygenation, including ATM/ATR, Chkl/Chk2 and BRCA1. Taken together, these findings reveal that hypoxia induces a unique cellular stress response involving an initial, acute DNA damage response to hypoxia and reoxygenation, followed by a chronic response to prolonged hypoxia in which selected DNA repair pathways are coordinately suppressed. In this review, we discuss these pathways and the possible mechanisms involved, as well as the consequences for genetic instability and tumor progression within the tumor microenvironment.

Increased expression of p130 in Alzheimer disease.

A number of recent findings support the notion of mechanistic parallels between Alzheimer disease (AD) and oncogenic processes, specifically, that neurons in AD, like cancer cells, display aberrant mitotic cell cycle re-entry. However, the mechanism that drives postmitotic neurons to reenter cell cycle remains elusive. In this study, we focused on the retinoblastoma-related protein p130 in AD. p130 is a transcriptional regulator that complexes with E2F4/5 in the nucleus and suppresses genes that regulate entry into the cell cycle. Interestingly, our results show that there are increases in p130 in cytoplasm of susceptible pyramidal neurons as well as neuroglia, often surrounding senile plaques, and within Hirano bodies in AD. By marked contrast, p130 is found at background levels in non-diseased, age-matched controls. Our data suggest that, despite its upregulation, the aberrant localization of p130 to the neuronal cytoplasm facilitates neuronal cell cycle re-entry in AD.

Apoptosis assays.

A large number of methods devoted to the identification of apoptotic cells and the analysis of the morphological, biochemical, and molecular changes that take place during this universal biological process have been developed. Apoptotic cells are recognized on the basis of their reduced DNA content and morphological changes that include nuclear condensation and which can be detected by flow cytometry (sub-G1 DNA content), Trypan Blue, or Hoechst staining. Changes in plasma membrane composition and function are detected by the appearance of phosphatidylserine on the plasma membrane, which reacts with Annexin V-fluorochrome conjugates. Combined with propidium iodide (PI) staining, this method can distinguish between the early and late apoptotic events. The best-recognized biochemical hallmarks of apoptosis are the activation of cysteine proteases (caspases), condensation of chromatin, and fragmentation of genomic DNA into nucleosomal fragments. Recognized by a variety of assays, activated caspases cleave many cellular proteins and the resulting fragments may serve as apoptosis markers. Finally, the mitochondria and the Bcl-2 family proteins play an important role in this process that can be recognized by translocation of apoptogenic factors, such as Bax and cytochrome c, in and out of mitochondria.

p53 binding to target sites is dynamically regulated before and after ionizing radiation-mediated DNA damage.

Although radiation therapy has been an important modality for cancer treatment, the molecular mechanisms underlying the overall genomic response of mammalian cells to radiation are not well characterized. The success of radiation therapy using ionizing radiation relies upon the regulation of both the cell cycle and apoptosis, as conferred by the activation of DNA damage-responsive genes. To better understand the key players involved in this response, expression-profiling experiments were performed using custom-made cDNA microarrays. In MOLT-4 lymphoma tumor cells, the induction of target gene products following irradiation supports a major role for p53 as a transcriptional activator, but also invokes questions regarding conditional transcription regulation following irradiation. Using chromatin immunoprecipitation (ChIP), p53 binding to chromatin was examined following irradiation using primers that are specific for p53 binding sites in target genes. PCR analysis indicates dynamic target gene binding. Thus, at 8 hours following radiation treatment, the p21 and puma promoter sites were characterized by relative increases in chromatin precipitation, while the bax promoter site was not. Because the binding of p53 to these sites only changed modestly following radiation, other studies were conducted to characterize the presence of constitutive binding to putative p53 DNA binding sites in several other genes.

Opposing roles of E2Fs in cell proliferation and death.

Progression through the cell cycle is dependent upon the temporal and spatial regulation of the various members of the E2F family of transcription factors. Two of these members, E2F1 and E2F4 have opposing roles in cell cycle progression, which were defined over a decade ago. While E2F1 is an activator of cell cycle progression, E2F4 functions as a transcriptional repressor. Recent data indicate that these transcription factors also play a role in the cellular response to DNA damage. In the case of E2F1, its overexpression leads to apoptosis. In contrast, the decreased expression of E2F4, in response to siRNA-mediated knockdown or to certain therapeutic agents, induces apoptosis. Conversely, increased levels of E2F4 may confer resistance to apoptosis-inducing therapies used in the clinic. The balance between the activities of these two proteins in tumor cells is of great interest. Directed control of E2F1 and E2F4 action may lead to better diagnosis of disease and improved therapeutic modalities.