A novel ataxia-telangiectasia mutated autoregulatory feedback mechanism in murine embryonic stem cells

A dynamical systems approach for multiscale synthesis of Alzheimer's pathogenesis

Alzheimer's disease (AD) is a spatially dynamic pathology that implicates a growing volume of multiscale data spanning genetic, cellular, tissue, and organ levels of the organization. These data and bioinformatics analyses provide clear evidence for the interactions within and between these levels. The resulting heterarchy precludes a linear neuron-centric approach and necessitates that the numerous interactions are measured in a way that predicts their impact on the emergent dynamics of the disease. This level of complexity confounds intuition, and we propose a new methodology that uses non-linear dynamical systems modeling to augment intuition and that links with a community-wide participatory platform to co-create and test system-level hypotheses and interventions. In addition to enabling the integration of multiscale knowledge, key benefits include a more rapid innovation cycle and a rational process for prioritization of data campaigns. We argue that such an approach is essential to support the discovery of multilevel-coordinated polypharmaceutical interventions.

Unraveling the mechanistic complexity of Alzheimer's disease through systems biology

Alzheimer's disease (AD) is a complex, multifactorial disease that has reached global epidemic proportions. The challenge remains to fully identify its underlying molecular mechanisms that will enable development of accurate diagnostic tools and therapeutics. Conventional experimental approaches that target individual or small sets of genes or proteins may overlook important parts of the regulatory network, which limits the opportunity of identifying multitarget interventions. Our perspective is that a more complete insight into potential treatment options for AD will only be made possible through studying the disease as a system. We propose an integrative systems biology approach that we argue has been largely untapped in AD research. We present key publications to demonstrate the value of this approach and discuss the potential to intensify research efforts in AD through transdisciplinary collaboration. We highlight challenges and opportunities for significant breakthroughs that could be made if a systems biology approach is fully exploited.

The effect of ataxia-telangiectasia mutated kinase-dependent hyperphosphorylation of checkpoint kinase-2 on oligodeoxynucleotide 7909 containing CpG motifs-enhanced sensitivity to X-rays in human lung adenocarcinoma A549 cells

Objective

The aim of the study reported here was to further investigate the potential effect of ataxia-telangiectasia mutated (ATM) kinase-dependent hyperphosphorylation of checkpoint kinase-2 (Chk2) on radiosensitivity enhanced by oligodeoxynucleotide 7909 containing CpG motifs (CpG ODN7909) in human lung adenocarcinoma A549 cells.

Methods

In vitro A549 cells were randomly separated into control, CpG, X-ray, CpG+ X-ray, ATM kinase-small interfering RNA (siRNA)+CpG+X-ray (ATM-siRNA), and Chk2-siRNA+CpG+X-ray (Chk2-siRNA) groups. siRNAs were adopted to silence the ATM and Chk2 genes. Expression and phosphorylation of ATM kinase and Chk2 were detected by Western blot assay. Cell colonies were observed under inverted phase-contrast microscopy. Cellular survival curves were fitted using a multi-target single-hitting model. Cell cycle and apoptosis were analyzed by flow cytometry.

Results

Expression of ATM kinase and Chk2 was similar among the control, CpG, X-ray, and CpG+X-ray groups. Phosphorylated ATM kinase and Chk2 were significantly increased in the CpG+X-ray group compared with in the X-ray group (t=6.00, P<0.01 and t=3.13, P<0.05, respectively), though these were hardly detected in the control and CpG groups. However, expression of ATM kinase and Chk2 was clearly downregulated in the ATM-siRNA and Chk2-siRNA groups, respectively. Similarly, their phosphorylation levels were also significantly decreased in the ATM-siRNA group (t=14.35, P<0.01 and t=8.46, P<0.01, respectively) and a significant decrease in phosphorylated Chk2 was observed in the Chk2-siRNA group (t=7.28, P<0.01) when compared with the CpG+X-ray group. Further, the number of A549 cells at Gap 2/mitotic phase and the apoptosis rate were clearly increased in the CpG+X-ray group compared with in the other groups (all P<0.05). The multi-target single-hitting model showed that the sensitization enhancement ratio calculated by mean death dose was 1.39 in CpG+X-ray group (vs 1.04 and 1.03 in the ATM-siRNA and Chk2-siRNA groups, respectively).

Conclusion

This study provides the first evidence, as far as we are aware, that CpG ODN7909 can potentiate A549 cell radiosensitivity via increasing ATM kinase-dependent phosphorylation of Chk2, suggesting activation of the ATM kinase/Chk2 signal pathway. However, the mechanism of ATM kinase activation is worth further exploration.

The DNA-damage response to γ-radiation is affected by miR-27a in A549 cells

Perturbations during the cell DNA-Damage Response (DDR) can originate from alteration in the functionality of the microRNA-mediated gene regulation, being microRNAs (miRNAs), small non-coding RNAs that act as post-transcriptional regulators of gene expression. The oncogenic miR-27a is over-expressed in several tumors and, in the present study, we investigated its interaction with ATM, the gene coding for the main kinase of DDR pathway. Experimental validation to confirm miR-27a as a direct regulator of ATM was performed by site-direct mutagenesis of the luciferase reporter vector containing the 3'UTR of ATM gene, and by miRNA oligonucleotide mimics. We then explored the functional miR-27a/ATM interaction under biological conditions, i.e., during the response of A549 cells to ionizing radiation (IR) exposure. To evaluate if miR-27a over-expression affects IR-induced DDR activation in A549 cells we determined cell survival, cell cycle progression and DNA double-strand break (DSB) repair. Our results show that up-regulation of miR-27a promotes cell proliferation of non-irradiated and irradiated cells. Moreover, increased expression of endogenous mature miR-27a in A549 cells affects DBS rejoining kinetics early after irradiation.

Cancer systems biology

Cancer is a complex and heterogeneous disease, not only at a genetic and biochemical level, but also at a tissue, organism, and population level. Multiple data streams, from reductionist biochemistry in vitro to high-throughput "-omics" from clinical material, have been generated with the hope that they encode useful information about phenotype and, ultimately, tumour behaviour in response to drugs. While these data stand alone in terms of the biology they represent, there is the enticing prospect that if incorporated into systems biology models, they can help understand complex systems behaviour and provide a predictive framework as an additional tool in understanding how tumours change and respond to treatment over time. Since these biological data are heterogeneous and frequently qualitative rather than quantitative, at the present time a single systems biology approach is unlikely to be effective; instead, different computational and mathematical approaches should be tailored to different types of data, and to each other, in order to test and re-test hypotheses. In time, these models might converge and result in usable tractable models which accurately represent human cancer. Likewise, biologists and clinicians need to understand what the requirements of systems biology are so that compatible data are produced for computational modelling. In this review, we describe some theoretical approaches (data-driven and process-driven) and experimental methodologies which are being used in cancer research and the clinical context where they might be applied.