Ales Tichy

Phosphoproteomics: searching for a needle in a haystack.

Most of the cellular processes are regulated by reversible phosphorylation of proteins, which in turn plays a critical role in the regulation of gene expression, cell division, signal transduction, metabolism, differentiation, and apoptosis. Mass spectrometry of phosphopeptides obtained from tryptic protein digests has become a powerful tool for characterization of phosphoproteins involved in these processes. However, there is a general need to significantly enrich the phosphopeptide content to compensate their low abundance, insufficient ionization, and suppression effects of non-phosphorylated peptides. This paper aims to give a comprehensive overview on the methods involved in recent phosphoproteomics. It presents a description of contemporary enrichment techniques with references to particular studies and compares different approaches to characterization of phosphoproteome by mass spectrometry.

To live or let die: Unclear task of autophagy in the radiosensitization battle.

Radiation-induced autophagy is believed to represent a radioprotective mechanism of cancer cells. Thus, its inhibition should support radiation treatment and increase its efficacy. On the other hand, there is evidence that radiation alone or in combination with various chemical agents can induce autophagy that results into increased cell death, especially within transformed apoptosis-resistant cells. In this paper, besides description of autophagic process and its relation to cancer and radiotherapy, we compared two contradictory radiosensitization approaches that employ inhibition and induction of autophagy. In spite of the classical concept based on cytoprotective model, there is a plethora of recently developed inducers of autophagy, which indicates the future trend in radiosensitization via modulation of autophagy. Because contemporary literature is conflicting and inconsistent in this respect, we reviewed the recent studies focused on enhancement of sensitivity of cancer cells toward radiation in regard to autophagy, revealing some striking discrepancies. The deeper the knowledge, the more complex this situation is. To interpret results of various studies correctly one has to take into account the methodology of autophagy assessment and also the fact that radiosensitization might be mediated by other than intrinsic mechanisms related to autophagy. Notwithstanding, targeting autophagy remains an attractive anti-tumor strategy.

Early changes in L-arginine-nitric oxide metabolic pathways in response to the whole-body gamma irradiation of rats

Abstract Purpose: Nitric oxide (NO), a reactive radical, is formed in higher amounts from L-arginine by inducible NO synthase (iNOS) during early response to ionizing radiation presumably as a part of signal transduction pathways. This study investigated the changes in L-arginine-NO metabolic pathways within a 24-hour period after whole-body gamma irradiation of rats with the range of low to supra-lethal doses. Materials and methods: Young adult female Wistar rats received either 0–50 Gy whole-body irradiation or an intraperitoneal injection of bacterial lipopolysaccharide (LPS, 10 mg/kg). Exhaled NO was monitored using chemiluminiscence, nitrite + nitrate (NOx) and L-arginine were assayed by high-performance liquid chromatography, and expression of iNOS was determined using Western blot. Results: Irradiation resulted in a dose-dependent increase of plasma NOx to maximum levels which were 4-fold higher compared to controls (p < 0.001). The NOx levels increased less in the bronchoalveolar lavage fluid (BAL) (1.7-fold, p < 0.001) and liver homogenate (2.5-fold, p < 0.05), respectively, and were dose-independent. Exhaled NO, lung NOx, plasma and BAL L-arginine, and the expression of iNOS in lung and liver tissues of irradiated rats and controls were similar. LPS caused a considerable increase (p < 0.001) in exhaled NO (61-fold), NOx levels (plasma 34-fold, BAL 6-fold, lung 5-fold, liver 4-fold), and in iNOS expression, respectively. Conclusion: In contrast to the LPS treatment of rats, the radiation-induced changes in L-arginine-NO metabolic pathways are modest, particularly in the airways and lungs. Noninvasive measurement of exhaled NO within a 24-h period following the exposure of rats to ionizing radiation has no value for biodosimetry.

Soman poisoning alters p38 MAPK pathway in rat cerebellar Purkinje cells.

The aim of the study was to evaluate the expression of phosphorylated p38 mitogen‐activated protein kinase (p38 MAPK) and MAPK‐activated transcription factors elk‐1, c‐jun and c‐myc in rat cerebellar Purkinje cells after soman poisoning to investigate the pathogenetic mechanism of non‐specific long‐term adverse effects of nerve agents. Male Wistar rats were poisoned by intramuscular administration of soman at a dose 60 µg kg−1 (80% LD50), while control animals were administered physiological saline. Samples were taken 1, 7 and 14 days after poisoning, immunohistochemically stained and p‐p38MAPK, p‐c‐jun, p‐c‐myc, and p‐elk‐1 expressions were measured using computer image analysis. An increased expression of phosphorylated p38 MAPK and c‐myc 14 days after soman poisoning was found, while both activated elk‐1 and c‐jun expression remained unchanged 1, 7 and 14 days after intoxication. Late activation of p38 MAPK and their targets might be the underlying mechanism of chronic neurophysiological adverse effects. Copyright

Enrichment strategies for phosphoproteomics: state-of-the-art

Abstract Protein phosphorylation is a key regulator in many biological processes, such as homeostasis, cellular signaling and communication, transcriptional and translational regulation, and apoptosis. The defects in this tightly controlled reversible post-translational modification have been described to contribute to genesis and progression of various diseases, emphasizing the importance of a systematic research of this phenomenon. Although considerable effort has been devoted to improving the analysis of phosphorylation by mass spectrometry, which is currently the method of choice to study protein phosphorylation, the detection and identification of phosphorylation sites remains challenging because of the low abundance and low ionization efficacy of phosphoproteins in comparison with nonphosphorylated proteins. To overcome this obstacle, different enrichment strategies for phosphorylated peptides/proteins have been established and optimized for subsequent mass spectrometry analysis. In this review, we will give an overview of the methods currently available for the enrichment of phosphorylated proteins and peptides including immunoprecipitation, chemical derivatization and affinity enrichment techniques.

Comparison of Resins for Metal Oxide Affinity Chromatography with Mass Spectrometry Detection for the Determination of Phosphopeptides

Protein phosphorylation is a crucial regulatory mechanism in majority of biological processes. During MS, there is a general need to diminish suppression effect of non-phosphorylated peptides and counterbalance low abundance and insufficient ionization of phosphopeptides. Therefore, selective enrichment of their content in complex mixture has become an indispensable part of any phosphoproteomic study. In this work we employed metal oxide affinity chromatography (MOAC) approach. We have compared “classic” approach of mixing TiO2 and peptides in a microtube with “microcolumns” – commercial tips NuTips (TiO2/ZrO2 1:1) and TopTips® (TiO2, TiO2/ZrO2 1:1, and ZrO2). Selectivity of the given media towards phosphopeptides was tested on a tryptic digest of mixture of bovine proteins: α /β-casein and fetuin (phosphoproteins) with myoglobin and bovine serum albumin (non-phosphorylated proteins) in ratio 1:1:5:5 and 1:1:50:50, respectively. After enrichment, the obtained eluates were analyzed by tandem mass spectrometry (MALDI-TOF/TOF) on ABI 4800 in positive reflectron mode. To each media we applied four different protocols with different composition of loading and washing buffers and we compared efficiency of three displacers (1 M lactic acid, 350 mg/ml DHB, and 0.1 M glutamic acid). In our settings, NuTips® proved as the most efficient media for analysis of low complex samples, since they exhibited the highest phosphoselectivity. Surprisingly, the Titansphere 5 µm particles outperformed mixed TopTips, which against our expectations showed the lowest binding selectivity and reproducibility even after addition of three different displacers.

Validating Baboon Ex Vivo and In Vivo Radiation-Related Gene Expression with Corresponding Human Data

The research for high-throughput diagnostic tests for victims of radio/nuclear incidents remains ongoing. In this context, we have previously identified candidate genes that predict risk of late-occurring hematologic acute radiation syndrome (HARS) in a baboon model. The goal of the current study was to validate these genes after radiation exposure in humans. We also examined ex vivo relative to in vivo measurements in both species and describe dose-response relationships. Eighteen baboons were irradiated in vivo to simulate different patterns of partial- or total-body irradiation (TBI), corresponding to an equivalent dose of 2.5 or 5 Sv. Human in vivo blood samples were obtained from patients exposed to different dose ranges: diagnostic computerized tomography (CT; 0.004–0.018 Sv); radiotherapy for prostate cancer (0.25–0.3 Sv); and TBI of leukemia patients (2 × 1.5 or 2 × 2 Sv, five patients each). Peripheral whole blood of another five baboons and human samples from five healthy donors were cultivated ex vivo and irradiated with 0–4 Sv. RNA was isolated pairwise before and 24 h after irradiation and converted into cDNA. Gene expression of six promising candidate genes found previously by us in a baboon model (WNT3, POU2AF1, CCR7, ARG2, CD177, WLS), as well as three genes commonly used in ex vivo whole blood experiments (FDXR, PCNA, DDB2) was measured using qRT-PCR. We confirmed the six baboon candidate genes in leukemia patients. However, expression for the candidate gene FDXR showed an inverse relationship, as it was downregulated in baboons and upregulated in human samples. Comparisons among the in vivo and ex vivo experiments revealed the same pattern in both species and indicated peripheral blood cells to represent the radiation-responsive targets causing WNT3 and POU2AF1 gene expression changes. CCR7, ARG2, CD177 and WLS appeared to be altered due to radiation-responsive targets other than the whole blood cells. Linear dose-response relationships of FDXR, WNT3 and POU2AF1 using human ex vivo samples corresponded with human in vivo samples, suggesting that ex vivo models for in vivo dose estimates can be used over a wide dose range (0.001–5 Sv for POU2AF1). In summary, we validated six baboon candidate genes in humans, but the FDXR measurements underscored the importance of independent assessments even when candidates from animal models have striking gene sequence homology to humans. Since whole blood cells represented the same radiation-responsive targets for FDXR, WNT3 and POU2AF1 gene expression changes, ex vivo cell culture models can be utilized for in vivo dose estimates over a dose range covering up to 3.5 log scales. These findings might be a step forward in the development of a gene expression-based high-throughput diagnostic test for populations involved in large-scale radio/nuclear incidents.

The first in vivo multiparametric comparison of different radiation exposure biomarkers in human blood

The increasing risk of acute large-scale radiological/nuclear exposures of population underlines the necessity of developing new, rapid and high throughput biodosimetric tools for estimation of received dose and initial triage. We aimed to compare the induction and persistence of different radiation exposure biomarkers in human peripheral blood in vivo. Blood samples of patients with indicated radiotherapy (RT) undergoing partial body irradiation (PBI) were obtained soon before the first treatment and then after 24 h, 48 h, and 5 weeks; i.e. after 1, 2, and 25 fractionated RT procedures. We collected circulating peripheral blood from ten patients with tumor of endometrium (1.8 Gy per fraction) and eight patients with tumor of head and neck (2.0–2.121 Gy per fraction). Incidence of dicentrics and micronuclei was monitored as well as determination of apoptosis and the transcription level of selected radiation-responsive genes. Since mitochondrial DNA (mtDNA) has been reported to be a potential indicator of radiation damage in vitro, we also assessed mtDNA content and deletions by novel multiplex quantitative PCR. Cytogenetic data confirmed linear dose-dependent increase in dicentrics (p < 0.01) and micronuclei (p < 0.001) in peripheral blood mononuclear cells after PBI. Significant up-regulations of five previously identified transcriptional biomarkers of radiation exposure (PHPT1, CCNG1, CDKN1A, GADD45, and SESN1) were also found (p < 0.01). No statistical change in mtDNA deletion levels was detected; however, our data indicate that the total mtDNA content decreased with increasing number of RT fractions. Interestingly, the number of micronuclei appears to correlate with late radiation toxicity (r2 = 0.9025) in endometrial patients suggesting the possibility of predicting the severity of RT-related toxicity by monitoring this parameter. Overall, these data represent, to our best knowledge, the first study providing a multiparametric comparison of radiation biomarkers in human blood in vivo, which have potential for improving biological dosimetry.

Chemical inhibition of DNA repair kinases as a promising tool in oncology.

BACKGROUND DNA repair pathways play a major role in tumour resistance towards chemo- and radiotherapy. Therefore, inhibitors of specific DNA repair pathways might be advantageous when used in combination with DNA-damaging agents, such as ionizing radiation. This review put particular emphasis on the key DNA repair enzymes: DNA-dependent protein kinase (DNA-PK), ataxia-telangiectasia mutated kinase (ATM) and ATM-Rad3-related kinase (ATR) and their specific inhibitors in the context of radio-sensitization. RESULTS We reviewed recent studies on novel and potent inhibitors and found evidence that inhibitors of DNA repair pathways such as small molecule inhibitors could be efficient and selective in tumour cells. Interpretation of recent literature results accompanied with implications for practice and further research are presented. CONCLUSIONS The prospects of targeting DNA repair enzymes to treat cancer are optimistic, but future work will show if this approach has a significant in vivo efficacy, since we are still waiting for the inhibitor which would pass all phases in clinical trials. In spite of the fact that a number of drugs possess interesting synergy of radiotherapy in vitro, the future use will depend on developing compounds with improved solubility and the serum half-life. Normal tissue toxicity leading to a significant increase of radiotherapy efficiency remains a key question that might be answered only by clinical trials.

Novel quinazolin-4-one derivatives as potentiating agents of doxorubicin cytotoxicity

We report the design, synthesis and biological evaluation of 17 novel 8-aryl-2-morpholino-3,4-dihydroquinazoline derivatives based on the standard model of DNA-PK and PI3K inhibitors. Novel compounds are sub-divided into two series where the second series of five derivatives was designed to have a better solubility profile over the first one. A combination of in vitro and in silico techniques suggested a plausible synergistic effect with doxorubicin of the most potent compound 14d on cell proliferation via DNA-PK and poly(ADP-ribose) polymerase-1 (PARP-1) inhibition, while alone having a negligible effect on cell proliferation.