A novel small molecule inhibitor of the DNA repair protein Ku70/80

Non-Homologous End-Joining (NHEJ) is the predominant pathway for the repair of DNA double strand breaks (DSBs) in human cells. The NHEJ pathway is frequently upregulated in several solid cancers as a compensatory mechanism for a separate DSB repair defect or for innate genomic instability, making this pathway a powerful target for synthetic lethality approaches. In addition, NHEJ reduces the efficacy of cancer treatment modalities which rely on the introduction of DSBs, like radiation therapy or genotoxic chemotherapy. Consequently, inhibition of the NHEJ pathway can modulate a radiation- or chemo-refractory disease presentation. The Ku70/80 heterodimer protein plays a pivotal role in the NHEJ process. It possesses a ring-shaped structure with high affinity for DSBs and serves as the first responder and central scaffold around which the rest of the repair complex is assembled. Because of this central position, the Ku70/80 dimer is a logical target for the disruption of the entire NHEJ pathway. Surprisingly, specific inhibitors of the Ku70/80 heterodimer are currently not available. We here describe an in silico, pocket-based drug discovery methodology utilizing the crystal structure of the Ku70/80 heterodimer. We identified a novel putative small molecule binding pocket and selected several potential inhibitors by computational screening. Subsequent biological screening resulted in the first identification of a compound with confirmed Ku-inhibitory activity in the low micro-molar range, capable of disrupting the binding of Ku70/80 to DNA substrates and impairing Ku-dependent activation of another NHEJ factor, the DNA-PK_CS kinase. Importantly, this compound synergistically sensitized human cell lines to radiation treatment, indicating a clear potential to diminish DSB repair. The chemical scaffold we here describe can be utilized as a lead-generating platform for the design and development of a novel class of anti-cancer agents.     

The effect of treatment delay on time-to-recovery in the presence of unobserved heterogeneity

We study the effect of delaying treatment in the presence of (unobserved) heterogeneity. In a homogeneous population and assuming a proportional treatment effect, a treatment delay period will result in notably lower cumulative recovery percentages. We show in theoretical scenarios using frailty models that if the population is heterogeneous, the effect of a delay period is much smaller. This can be explained by the selection process that is induced by the frailty. Patient groups that start treatment later have already undergone more selection. The marginal hazard ratio for the treatment will act differently in such a more homogeneous patient group. We further discuss modeling approaches for estimating the effect of treatment delay in the presence of heterogeneity, and compare their performance in a simulation study. The conventional Cox model that fails to account for heterogeneity overestimates the effect of treatment delay. Including interaction terms between treatment and starting time of treatment or between treatment and follow up time gave no improvement. Estimating a frailty term can improve the estimation, but is sensitive to misspecification of the frailty distribution. Therefore, multiple frailty distributions should be used and the results should be compared using the Akaike Information Criterion. Non-parametric estimation of the cumulative recovery percentages can be considered if the dataset contains sufficient long term follow up for each of the delay strategies. The methods are demonstrated on a motivating application evaluating the effect of delaying the start of treatment with assisted reproductive techniques on time-to-pregnancy in couples with unexplained subfertility.     

Effets de la chimiothérapie sur le métabolisme cérébral des patients traités pour un lymphome de Hodgkin : étude préliminaire rétrospective de 37 patients

ObjectiveThe main aim of this study was to evaluate the effect of chemotherapy on brain metabolism among patients with Hodgkin's disease (HD) treated by ABVD or BEACOPP.Materials and methodsThirty-seven patients with histologically proved HD were included. Among the 37 patients, 25 had PET after 2 cycles, 22 had PET after 4 cycles and 22 had PET after 6 cycles of chemotherapy. Fifteen patients received ABVD, 12 received BEACOPP, 10 received both successively. The brain metabolism was analyzed thanks to Statistical Parametric Mapping (SPM).ResultsWe found hypometabolic areas in bilateral anterior cingulate cortex and left inferior frontal and insular cortex after 2 cycles chemotherapy and hypometabolic areas in the left anterior cingulate cortex, in the left inferior frontal and insular cortex and finally in the left temporal lobe after 6 cycles of chemotherapy.ConclusionThis study showed the emergence of cortical metabolic abnormalities after two cycles persisting after 6 cycles. The kind of chemotherapy could have a part in the emergence of these troubles.     

An ecological resilience perspective on cancer: Insights from a toy model

In this paper we propose an ecological resilience point of view on cancer. This view is based on the analysis of a simple ODE model for the interactions between cancer and normal cells. The model presents two regimes for tumor growth. In the first, cancer arises due to three reasons: a partial corruption of the functions that avoid the growth of mutated cells, an aggressive phenotype of tumor cells and exposure to external carcinogenic factors. In this case, treatments may be effective if they drive the system to the basin of attraction of the cancer cure state. In the second regime, cancer arises because the repair system is intrinsically corrupted. In this case, the complete cure is not possible since the cancer cure state is no more stable, but tumor recurrence may be delayed if treatment is prolongued. We review three indicators of the resilience of a stable equilibrium, related with size and shape of its basin of attraction: latitude, precariousness and resistance. A novel method to calculate these indicators is proposed. This method is simpler and more efficient than those currently used, and may be easily applied to other population dynamics models. We apply this method to the model and investigate how these indicators behave with parameters changes. Finally, we present some simulations to illustrate how the resilience analysis can be applied to validated models in order to obtain indicators for personalized cancer treatments.     

Activation of Leishmania (Leishmania) amazonensis arginase at low temperature by binuclear Mn center formation of the immobilized enzyme on a Ni resin

In Leishmania, arginase is responsible for the production of ornithine, a precursor of polyamines required for proliferation of the parasite. In this work, the activation kinetics of immobilized arginase enzyme from L. (L.) amazonensis were studied by varying the concentration of Mn²⁺ applied to the nickel column at 23 °C. The intensity of the binding of the enzyme to the Ni²⁺ resin was directly proportional to the concentration of Mn²⁺. Conformational changes of the enzyme may occur when the enzyme interacts with immobilized Ni²⁺, allowing the following to occur: (1) entrance of Mn²⁺ and formation of the metal bridge; (2) stabilization and activation of the enzyme at 23 °C; and (3) an increase in the affinity of the enzyme to Ni²⁺ after the Mn²⁺ activation step. The conformational alterations can be summarized as follows: the interaction with the Ni²⁺ simulates thermal heating in the artificial activation by opening a channel for Mn²⁺ to enter.     

Proteasome inhibition prevents cell death induced by the chemotherapeutic agent cisplatin downstream of DNA damage

Cisplatin is a highly effective chemotherapeutic drug acting as a DNA-damaging agent that induces apoptosis of rapidly proliferating cells. Unfortunately, cellular resistance still occurs. Mutations in p53 in a large fraction of tumor cells contribute to defects in apoptotic pathways and drug resistance. To uncover new strategies to eliminate tumors through a p53-independent pathway, we established a simplified model devoid of p53 to study cisplatin-induced regulated cell death, using the yeast Saccharomyces cerevisiae. We previously showed that cisplatin induces an active form of cell death accompanied by DNA condensation and fragmentation/degradation, but no significant mitochondrial dysfunction. We further demonstrated that proteasome inhibition, either with MG132 or genetically, increased resistance to cisplatin. In this study, we sought to determine how proteasome inhibition is important for cisplatin resistance by analyzing how it affects several phenotypes associated with the DNA damage response. We found MG132 does not seem to affect the activation of the DNA damage response or increase damage tolerance. Moreover, central modulators of the DNA damage response are not required for cisplatin resistance imparted by MG132. These results suggest the proteasome is involved in modulation of cisplatin toxicity downstream of DNA damage. Proteasome inhibitors can sensitize tumor cells to cisplatin, but protect others from cisplatin-induced cell death. Elucidation of this mechanism will therefore aid in the development of new strategies to increase the efficacy of chemotherapy.     

Drugging the R-loop interactome: RNA-DNA hybrid binding proteins as targets for cancer therapy

Unravelling the origin of genetic alterations from point mutations to chromosomal rearrangements was greatly enhanced by the discovery of RNA-DNA hybrids (R-loops) that behave as hotspots of genomic instability in a variety of organisms. Current models suggest that uncontrolled R-loops are a hazard to genome integrity, therefore, identifying proteins that are involved in recognising and signalling R-loop structures are of key importance. Herein we analysed key RNA-DNA hybrid binding proteins in humans taking advantage of large-scale gene expression, survival rate, and drug-sensitivity data from cancer genomics databases. We show that expression of RNA-DNA hybrid binding proteins in various cancer types is associated with survival and may have contrasting outcomes in responding to therapeutic treatments. Based on the revealed pharmacogenomic landscape of human RNA-DNA hybrid binding proteins, we propose that R-loops and R-loop binding proteins are potentially relevant new epigenetic markers and therapeutic targets in multiple cancers.