Targeting the synthetic lethal relationship between FOCAD and TUT7 represents a potential therapeutic opportunity for TUT4/7 small molecule inhibitors in cancer.

Targeting synthetic lethal interactions between genes has emerged as a promising strategy for cancer therapy. This study explores the intricate interplay between terminal uridyltransferase 4 (TUT4) and terminal uridyltransferase 7 (TUT7), the 3'-5' exoribonuclease DIS3L2, and the SKI complex-interacting factor Focadhesin (FOCAD) in the context of cancer vulnerability. Using CRISPR and public functional genomics data, we show impairment of cell proliferation upon knockout of TUT7 or DIS3L2, but not TUT4, on cancer cells with FOCAD loss. Moreover, we report the characterization of the first potent and selective TUT4/7 inhibitors that substantially reduce uridylation and demonstrate in vitro and in vivo antiproliferative activity specifically in FOCAD-deleted cancer. FOCAD deficiency post-transcriptionally disrupts the stability of the SKI complex, whose role is to safeguard cells against aberrant RNA. Re-introduction of FOCAD restores the SKI complex and makes these cells less sensitive to TUT4/7 inhibitors, indicating that TUT7 dependency is FOCAD loss-driven. We propose a model where, in absence of FOCAD, TUT7 and DIS3L2 function as a salvage mechanism that degrades aberrant RNA, and genetic or pharmacological inhibition of this pathway leads to cell death. Our findings underscore the significance of FOCAD loss as a genetic driver of TUT7 vulnerability and provide insights into the potential utility of TUT4/7 inhibitors for cancer treatment.

Lack of evidence for low-LET radiation induced bystander response in normal human fibroblasts and colon carcinoma cells.

PURPOSE: To investigate radiation-induced bystander responses and to determine the role of gap junction intercellular communication and the radiation environment in propagating this response. MATERIALS AND METHODS: We used medium transfer and targeted irradiation to examine radiation-induced bystander effects in primary human fibroblast (AG01522) and human colon carcinoma (RKO36) cells. We examined the effect of variables such as gap junction intercellular communication, linear energy transfer (LET), and the role of the radiation environment in non-targeted responses. Endpoints included clonogenic survival, micronucleus formation and foci formation at histone 2AX over doses ranging from 10-100 cGy. RESULTS: The results showed no evidence of a low-LET radiation-induced bystander response for the endpoints of clonogenic survival and induction of DNA damage. Nor did we see evidence of a high-LET, Fe ion radiation (1 GeV/n) induced bystander effect. However, direct comparison for 3.2 MeV alpha-particle exposures showed a statistically significant medium transfer bystander effect for this high-LET radiation. CONCLUSIONS: From our results, it is evident that there are many confounding factors influencing bystander responses as reported in the literature. Our observations reflect the inherent variability in biological systems and the difficulties in extrapolating from in vitro models to radiation risks in humans.

Therapeutic doses of hydroxyurea cause telomere dysfunction and reduce TRF2 binding to telomeres.

Hydroxyurea (HU) is a chemotherapeutic agent commonly used for various malignancies and hematological disorders, including chronic myelogenous leukemia and sickle cell anemia. We show here that chronic, low-level treatment with HU induces a variety of defects in telomere replication and maintenance. HU treatment preferentially decreased the rate of telomere DNA synthesis and altered the cell cycle timing of telomere replication. HU reduced the expression levels of telomere repeat RNA (TERRA). In some cells, HU caused a rapid loss of telomere restriction fragment length. Chromatin immunoprecipitation (ChIP) assay indicated that telomere repeat binding factors TRF1 and TRF2 dissociate from telomere DNA after HU treatment. TRF2 protein purified from HU treated cells showed a modest reduction in DNA binding activity and a change in isoelectric point as measured by 2D gel electrophoresis. However, chronic low level HU treatment did not evoke a DNA replication checkpoint response, suggesting that the mechanism of action is distinct from the well-characterized S-phase checkpoint pathway. We conclude that therapeutic doses of HU preferentially effects telomere replication and maintenance, through a mechanism that may involve the direct modification of TRF2. These findings provide new insight into the potential mechanisms of action of HU at telomeres and in cancer chemotherapies.

Epstein-Barr virus episome stability is coupled to a delay in replication timing.

The temporal regulation of DNA replication is thought to be important for chromosome organization and genome stability. We show here that Epstein-Barr virus (EBV) genomes replicate in mid- to late S phase and that agents that accelerate replication timing of EBV reduce viral genome stability. Hydroxyurea (HU) treatment, which is known to eliminate EBV episomes, shifted EBV replication to earlier times in the cell cycle. HU treatment correlated with hyperacetylation of histone H3 and loss of telomere repeat factor 2 (TRF2) binding at the EBV origin of plasmid replication (OriP). Deletion of TRF2 binding sites within OriP or short hairpin RNA depletion of TRF2 advanced the replication timing of OriP-containing plasmids. Inhibitors of class I histone deacetylases (HDACs) increased histone acetylation at OriP, advanced the replication timing of EBV, and reduced EBV genome copy number. We also show that HDAC1 and -2 form a stable complex with TRF2 at OriP and that HU treatment inhibits HDAC activity. We propose that the TRF2-HDAC complex enhances EBV episome stability by providing a checkpoint that delays replication initiation at OriP.

Lack of consensus gene expression changes associated with radiation-induced chromosomal instability.

The relatively high frequency with which ionizing radiation induces genomic instability suggests that a gene mutation occurring after irradiation is an unlikely cause of the phenotype. To search for mechanism(s) of initiation and perpetuation of this instability phenotype, gene expression profiles of clones exhibiting delayed chromosomal instability were analyzed. Microarray analysis using two pools of isogenic radiation-induced chromosomally unstable clones compared to an irradiated but chromosomally stable clone uncovered a set of 68 differentially expressed genes using two methods of analysis. Unexpectedly, all 68 genes were under-expressed relative to the chromosomally stable reference clone. Further analysis of the candidates placed the differentially expressed genes into pathways implicating differential MAP kinase signaling, ubiquitin/proteasome function, DNA repair, cell cycle control, lipid signaling, nucleotide metabolism, and other potentially disrupted pathways. Validation studies using northern and western blotting, and functional assays concluded that although differences in some of these pathways exist, no single gene or molecular pathway was found to be differentially regulated in all of the chromosomally unstable clones tested. Inferred from these data is that there are multiple potential molecular pathways and/or events that maintain the unstable phenotype, and no single expression pattern is linked to instability in the unstable clones analyzed.

Differential induction and activation of NF-kappaB transcription complexes in radiation-induced chromosomally unstable cell lines.

Radiation-induced genomic instability is a delayed effect of ionizing radiation that may contribute to radiation carcinogenesis. Prior microarray studies investigating gene expression changes in genomically unstable cell lines isolated after radiation exposure uncovered the differential expression of the NF-kappaB p105 mRNA. In this study, the functionality of the NF-kappaB pathway was examined to determine its role in regulating gene expression changes after oxidative stress in chromosomally stable and unstable human-hamster hybrid clones. Basal DNA-binding activity assays showed no significant differences between the clones; however, further experiments established differences in NF-kappaB induction in three chromosomally unstable clones after acute hydrogen peroxide treatment. A second assay was used to confirm this differential activity in the chromosomally unstable clones by studying reporter gene activation after treatment with hydrogen peroxide. Yet an initial upstream analysis of the pathway revealed no significant increase in the level of IkappaBalpha inhibitor protein in the unstable clones. Downstream tests analyzing the induction of the antiapoptotic target protein Bcl-2 found variable induction among the stable and unstable clones. These differences did not translate to a reduction in clonogenic survival after acute exposure to oxidative stress, as the irradiated but chromosomally stable clone displayed the most sensitivity. Due to its role in regulating a diverse set of cellular functions, including responses to oxidative stress, alterations in the NF-kappaB pathway in chromosomally unstable clones may regulate the differential physiology of a subset of chromosomally unstable clones and could contribute to the perpetuation of the phenotype. However, a specific role for defective induction and activation of this pathway remains unidentified.

Radiation-induced chromosomal instability and gene expression profiling: searching for clues to initiation and perpetuation.

Radiation-induced genomic instability (RIGI) manifests in the progeny of cells surviving ionizing radiation (IR), and can be measured using such endpoints as delayed mutation, micronuclei formation, and chromosomal instability. The frequency of RIGI is relatively high, exceeding the gene mutation rate of IR by orders of magnitude, leading to conjecture that a gene mutation is not the cause of the phenotype. We have started to explore whether differential gene expression patterns are associated with the instability phenotype, in order to shed light on its initiation and perpetuation. Using GM10115 human-hamster hybrid-derived chromosomally stable and radiation-induced unstable clones, gene expression patterns were analyzed using microarray analysis. Two methods were used to find differentially expressed genes, and all candidate genes identified by these methods were under-expressed relative to the chromosomally stable reference sample. Among this set differentially expressed genes identified were two candidates with a relationship to the ubiquitin/proteasome pathway. While follow-up gene expression analyses have confirmed the under-expression of these two genes in some of our chromosomally unstable clones, preliminary functional studies have been unable to demonstrate a link to instability. It is anticipated that as we apply this technology to the study of radiation-induced genomic instability, clues to its onset will be revealed, ultimately contributing to a greater understanding of the mechanisms of radiation carcinogenesis.

Gene expression profiling after irradiation: clues to understanding acute and persistent responses?

Ionizing radiation (IR) is an ever-present hazard to humans primarily due to its mutagenic, carcinogenic, and cell killing ability. In addition to causing DNA damage, irradiation initiates a plethora of signal transduction cascades responsible for maintaining cellular homeostasis and promoting interactions with neighboring cells. Large-scale changes in gene expression have also been found after irradiation, and microarrays have helped discern these subsequent transcriptional alterations. While some studies have focused on low dose-rate experiments, others have analyzed the gene expression response of IR compared to other DNA damaging agents. Very few genes have been found to be consistently up-regulated by IR, but that set includes GADD45, CDKN1A, and genes associated with the nucleotide excision repair pathway. Overall, the immediate transcriptional responses to IR have implications for DNA repair, cell cycle arrest, growth control, and cell signaling. Additionally, there is a substantial p53-independent component to the transcriptional profile that could be exploited to increase the effectiveness of radiotherapy. Initial characterizations of the persistent responses to IR yielded a completely different profile than observed immediately after exposure. This profile is ephemeral, shifting even over the course of one set of experiments. Microarray analysis of radiation responses has also been applied to clinical response to radiotherapy, identifying genes linked to radio-sensitivity and resistance in B-cell chronic lymphoid leukemia and cervical cancer. Overall, these large-scale gene expression studies have added to the understanding of the complicated biological responses to IR, and when combined with other data sets will yield a complete picture of the short and long-term consequences of radiation.

Review of radiation-induced bystander effects.

It is now apparent that the target for the biological effects of ionizing radiation (IR) is not solely the irradiated cell(s), but also includes the surrounding cells/tissue as well. Radiation-induced bystander effects (BSEs) are defined by the presence of the biological effects of radiation in cells that were not themselves in the field of irradiation. Decreased plating efficiency, increased sister chromatid exchanges, oncogenic transformation, among other endpoints have been used to describe the BSE. Two primary means have been established for the transmission of the bystander signal; one is mediated by gap-junction intracellular communication, and the other is initiated through the secretion of factors from irradiated cells. While the basis for these phenomena have been established in cell culture systems, there is also evidence for their presence in vivo. This in vivo effect may contribute to increased tumor cell killing, and may also play a role in the abscopal effects of radiation, where radiation responses are seen in areas separated from the irradiated tissue. Although the precise molecular components and mechanisms remain unknown, their discovery will shed new light on the role of the BSEs in radiation risk assessment, and clinical radiotherapy in the clinic.

Radiation-induced genomic instability and its implications for radiation carcinogenesis.

Radiation-induced genomic instability is characterized by an increased rate of genetic alterations including cytogenetic rearrangements, mutations, gene amplifications, transformation and cell death in the progeny of irradiated cells multiple generations after the initial insult. Chromosomal rearrangements are the best-characterized end point of radiation-induced genomic instability, and many of the rearrangements described are similar to those found in human cancers. Chromosome breakage syndromes are defined by chromosome instability, and individuals with these diseases are cancer prone. Consequently, chromosomal instability as a phenotype may underlie some fraction of those changes leading to cancer. Here we attempt to relate current knowledge regarding radiation-induced chromosome instability with the emerging molecular information on the chromosome breakage syndromes. The goal is to understand how genetic and epigenetic factors might influence the onset of chromosome instability and the role of chromosomal instability in carcinogenesis.

16S rDNA sequence analysis of environmental Bdellovibrio-and-like organisms (BALO) reveals extensive diversity.

Bdellovibrio-and-like organisms (BALO) are Gram-negative, predatory bacteria that inhabit terrestrial, freshwater and salt-water environments. Historically, these organisms have been classified together despite documented genetic differences between isolates. The genetic diversity of these microbes was assessed by sequencing the 16S rRNA gene. Primers that selectively amplify predator 16S rDNA, and not contaminating prey DNA, were utilized to study 17 freshwater and terrestrial and nine salt-water BALO isolates. When the 16S rDNA sequences were compared with representatives of other bacterial classes, 25 of the 26 BALO isolates clustered into two groups. One group, supported 100% by bootstrap analysis, included all of the Bdellovibrio bacteriovorus isolates. Each member of this group was isolated from either a freshwater or terrestrial source. The genetic distance between these isolates was less than 12%. The other group, supported 94% by bootstrap analysis, includes Bacteriovorax starrii, Bacteriovorax stolpii and the salt-water isolates. The salt-water isolates form a subgroup (83% by bootstrap) and differ within the subgroup by less than 110%. This observation implies that the salt-water isolates arose from Bacteriovorax progenitors. The difference between isolates in different clades is over 17%, a quantity similar to differences between bacterial species in different classes. However, both the Bdellovibrio and Bacteriovorax clades were closest to other representatives of the delta-Proteobacteria using maximum-likelihood. One freshwater isolate, James Island, was distinct from all other BALO (> 19%), but differed from Pseudomonas putida, a member of the gamma-Proteobacteria, by only 3%. Thus, by 16S rDNA sequence analysis, the BALO appear to have multiple origins, contrary to the unified taxonomic grouping based on morphology and natural history. These observations are consistent with the need to review and revise the taxonomy of these organisms.