Interplay between oncogene-induced DNA damage response and heterochromatin in senescence and cancer

Two major mechanisms have been causally implicated in the establishment of cellular senescence: the activation of the DNA damage response (DDR) pathway and the formation of senescence-associated heterochromatic foci (SAHF). Here we show that in human fibroblasts resistant to premature p16(INK4a) induction, SAHF are preferentially formed following oncogene activation but are not detected during replicative cellular senescence or on exposure to a variety of senescence-inducing stimuli. Oncogene-induced SAHF formation depends on DNA replication and ATR (ataxia telangiectasia and Rad3-related). Inactivation of ATM (ataxia telangiectasia mutated) or p53 allows the proliferation of oncogene-expressing cells that retain increased heterochromatin induction. In human cancers, levels of heterochromatin markers are higher than in normal tissues, and are independent of the proliferative index or stage of the tumours. Pharmacological and genetic perturbation of heterochromatin in oncogene-expressing cells increase DDR signalling and lead to apoptosis. In vivo, a histone deacetylase inhibitor (HDACi) causes heterochromatin relaxation, increased DDR, apoptosis and tumour regression. These results indicate that heterochromatin induced by oncogenic stress restrains DDR and suggest that the use of chromatin-modifying drugs in cancer therapies may benefit from the study of chromatin and DDR status of tumours.     

The tick salivary protein sialostatin L inhibits the Th9-derived production of the asthma-promoting cytokine IL-9 and is effective in the prevention of experimental asthma

Ticks developed a multitude of different immune evasion strategies to obtain a blood meal. Sialostatin L is an immunosuppressive cysteine protease inhibitor present in the saliva of the hard tick Ixodes scapularis. In this study, we demonstrate that sialostatin L strongly inhibits the production of IL-9 by Th9 cells. Because we could show recently that Th9-derived IL-9 is essentially involved in the induction of asthma symptoms, sialostatin L was used for the treatment of experimental asthma. Application of sialostatin L in a model of experimental asthma almost completely abrogated airway hyperresponsiveness and eosinophilia. Our data suggest that sialostatin L can prevent experimental asthma, most likely by inhibiting the IL-9 production of Th9 cells. Thus, alternative to IL-9 neutralization sialostatin L provides the basis for the development of innovative therapeutic strategies to treat asthma.     

Analysis of the urine proteome via a combination of multi-dimensional approaches

Urine is a biological fluid that is non-invasively and easily harvested, and exhibits high stability from the proteomics point of view. At the downside, the overall low protein content of urine as well as the presence of low- and high-abundance proteins underscores the need for protein enrichment. As a continuation of previous efforts towards the comprehensive characterization of the urine proteome, the current study targeted the mining of urine proteins through the combined application of different protein separation methodologies, specifically, liquid chromatography and preparative electrophoresis along with 1D gel electrophoresis and protein identification by mass spectrometry. In order to enhance comparison and integration of different experimental data sets, the "standard" urine sample developed within the European Kidney and Urine Proteomics (EuroKUP) COST Action, was employed. As a contribution to the existing knowledge, we focused on maintaining and providing information about experimental mass of the identified proteins as well as information pertaining to their relative abundance--as allowed by technical limitations--thus providing an initial view of different isoforms representation and facilitating their future characterization. The difficulties in comparing proteome mining data sets become once more evident, underscoring the need for adopting standardized ways for data reporting as well as for potential new approaches for data analysis involving a thorough investigation of received information at the peptide level.     

Comparison of physiological and post-endovascular aneurysm repair infrarenal blood flow

Endovascular aneurysm repair (EVAR) of abdominal aortic aneurysms results in redirection of blood through the deployed endograft (EG). Even though EVAR is clinically effective, the absolute flow restoration is not warranted. Our purpose was to compare the physiological with the post-EVAR infrarenal flow conditions. We developed patient-specific models based on computed tomography data of five healthy volunteers and ten patients treated with the Endurant^® stent-graft system. Wall shear stress (WSS), helicity, pressure and velocity fields were calculated using computational fluid dynamics. The results showed a decrease of peak WSS on the part of the EG that resides in the iliac arteries, compared to the physiological value (p = 0.01). At the abdominal part, the average helicity seems to increase after EVAR, while at the iliac arteries part, the intensity of helical flow seems physiological. Pressure drop and peak velocity in the iliac arteries part are lower than the physiological values (p = 0.04). The comparison revealed that most hemodynamic properties converge to normal levels at the abdominal part whereas statistically significant variations were observed in the iliac arteries part. The delineation of the differences between physiological and postoperative flow data could pave the way for the improvement of EG designs.     

Molecular size determination of a membrane protein in surfactants by light scattering

The molecular size of an outer surface protein from the photosynthetic bacterium Chlorobium tepidum was studied by dynamic light scattering (DLS) and HPLC gel filtration. For that purpose, the membrane protein was isolated and studied in four different nonionic surfactants, namely t-octylphenoxypolyethenoxyethanol (Triton X-100), (methyl-6-O-(N)-heptyl-carbamoyl)-alpha-D-glucopyranoside (Hecameg), dodecyl-beta-D-maltoside (DDM) and n-octyl-oligo-oxyethylene (Octyl-POE). The protein was isolated by solubilization of the membranes with Triton X-100. The final purification step was a gel filtration, which was also used for surfactant exchange. Light scattering reveals the simultaneous presence of particles of different sizes in the 3-6 and 20-110 nm range, respectively. The smaller size is related to the hydrodynamic radius of the individual protein/surfactant complexes, whereas the larger size is associated with the presence of complex aggregates.     

Comparative proteomic analysis of hypertrophic chondrocytes in osteoarthritis

Background

Osteoarthritis (OA) is a multi-factorial disease leading progressively to loss of articular cartilage and subsequently to loss of joint function. While hypertrophy of chondrocytes is a physiological process implicated in the longitudinal growth of long bones, hypertrophy-like alterations in chondrocytes play a major role in OA. We performed a quantitative proteomic analysis in osteoarthritic and normal chondrocytes followed by functional analyses to investigate proteome changes and molecular pathways involved in OA pathogenesis.

Methods

Chondrocytes were isolated from articular cartilage of ten patients with primary OA undergoing knee replacement surgery and six normal donors undergoing fracture repair surgery without history of joint disease and no OA clinical manifestations. We analyzed the proteome of chondrocytes using high resolution mass spectrometry and quantified it by label-free quantification and western blot analysis. We also used WebGestalt, a web-based enrichment tool for the functional annotation and pathway analysis of the differentially synthesized proteins, using the Wikipathways database. ClueGO, a Cytoscape plug-in, is also used to compare groups of proteins and to visualize the functionally organized Gene Ontology (GO) terms and pathways in the form of dynamical network structures.

Results

The proteomic analysis led to the identification of a total of ~2400 proteins. 269 of them showed differential synthesis levels between the two groups. Using functional annotation, we found that proteins belonging to pathways associated with regulation of the actin cytoskeleton, EGF/EGFR, TGF-β, MAPK signaling, integrin-mediated cell adhesion, and lipid metabolism were significantly enriched in the OA samples (p ≤10⁻⁵). We also observed that the proteins GSTP1, PLS3, MYOF, HSD17B12, PRDX2, APCS, PLA2G2A SERPINH1/HSP47 and MVP, show distinct synthesis levels, characteristic for OA or control chondrocytes.

Conclusion

In this study we compared the quantitative changes in proteins synthesized in osteoarthritic compared to normal chondrocytes. We identified several pathways and proteins to be associated with OA chondrocytes. This study provides evidence for further testing on the molecular mechanism of the disease and also propose proteins as candidate markers of OA chondrocyte phenotype.

Electronic supplementary material

The online version of this article (doi:10.1186/s12014-015-9085-6) contains supplementary material, which is available to authorized users.     

Breast cancer: the upgraded role of HER-3 and HER-4

Breast cancer is the most common cancer in women and the ErbB receptor family holds crucial role in its pathogenesis. Among them, epidermal growth factor receptor and HER-2 are the most studied members and their overexpression has been associated with aggressive clinical behaviour. These data were further strengthened by the clinical success of trastuzumab, a monoclonal antibody against HER-2 in breast cancer patients with HER-2 overexpression and/or amplification. However, trastuzumab failure in some patients may partly be attributed to co-expression of other ErbB receptors. Herein, we provide updated views regarding the role of HER-3 and HER-4 in breast cancer. Accumulated evidence implies that these receptors should be considered more than heterodimerisation partners. Their expression profile might be useful in predicting responsiveness to current treatment options, while new strategies targeting their ligands and downstream effectors are being developed.     

Genome-wide proteomics of Natronomonas pharaonis

The aerobic, haloalkaliphilic archaeon Natronomonas pharaonis is able to survive in salt-saturated lakes of pH 11. According to genome analysis, the theoretical proteome consists of 2843 proteins. To reach further conclusions about its cellular physiology, the cytosolic protein inventory of Nmn. pharaonis has been analyzed using MS/MS on an ESI-Q-TOF mass spectrometer coupled on-line with a nanoLC system. The efficiency of this shotgun approach is illustrated by the identification of 929 proteins of which 886 are soluble proteins representing 41% of the cytosolic proteome. Cell lysis under denaturing conditions in water with subsequent separation by SDS-PAGE prior to nanoLC-MS/MS resulted in identification of 700 proteins. The same number (but a different subset) of proteins was identified upon cell lysis under native conditions followed by size fractionation (retaining protein complexes) prior to SDS-PAGE. Additional size fractionation reduced sample complexity and increased identification reliability. The set of identified proteins covers about 60% of the cytosolic proteins involved in metabolism and genetic information processing. Many of the identified proteins illustrate the high genetic variability among the halophilic archaea.     

Selective modulation of the erythropoietic and tissue-protective effects of erythropoietin: time to reach the full therapeutic potential of erythropoietin

Erythropoietin (EPO) has been used clinically both as an erythropoietic stimulating agent in the treatment of anemia and as a tissue-protective agent in diverse clinical settings including stroke, multiple sclerosis, acute myocardial infarction and others. However, use of EPO or EPO-analogues leads to simultaneous targeting of both the erythropoietic and tissue-protective properties of EPO, and this strategy has been associated with several problems. Specifically, the benefit of correction of cancer-related anemia can be offset by the tissue-protective effects of EPO, which may lead to stimulation of cancer cell proliferation. Conversely, the benefit of tissue-protection in patients with stroke or myocardial infarction can be offset by adverse effects associated with the erythropoietic effects of EPO such as elevation of red blood cell mass, hypertension and prothrombotic phenomena. The finding that the erythropoietic and tissue-protective properties of EPO are conferred via two distinct receptor systems raises the interesting possibility of discovering novel drugs that selectively stimulate either the erythropoietic or the tissue-protective activities of EPO. This article reviews the current status of the clinical use of EPO and EPO-analogues in the treatment of cancer-related anemia and for tissue protection, outlines the distinct molecular biology of the tissue-protective and erythropoietic effects of EPO and discusses strategies of selective targeting of these activities with the goal of exploiting the full therapeutic potential of EPO.