A small molecule SMAC mimic LBW242 potentiates TRAIL- and anticancer drug-mediated cell death of ovarian cancer cells

Background

Ovarian cancer remains a leading cause of death in women and development of new therapies is essential. Second mitochondria derived activator of caspase (SMAC) has been described to sensitize for apoptosis. We have explored the pro-apoptotic activity of LBW242, a mimic of SMAC/DIABLO, on ovarian cancer cell lines (A2780 cells and its chemoresistant derivative A2780/ADR, SKOV3 and HEY cells) and in primary ovarian cancer cells. The effects of LBW242 on ovarian cancer cell lines and primary ovarian cancer cells was determined by cell proliferation, apoptosis and biochemical assays.

Principal Findings

LBW242 added alone elicited only a moderate pro-apoptotic effect; however, it strongly synergizes with tumor necrosis factor-related apoptosis inducing ligand (TRAIL) or anticancer drugs in inducing apoptosis of both ovarian cancer cell lines and primary ovarian cancer cells. Mechanistic studies show that LBW242-induced apoptosis in ovarian cancer cells is associated with activation of caspase-8. In line with this mechanism, c-FLIP overexpression inhibits LBW242-mediated apoptosis.

Conclusion

LBW242 sensitizes ovarian cancer cells to the antitumor effects of TRAIL and anticancer drugs commonly used in clinic. These observations suggest that the SMAC/DIABLO mimic LBW242 could be of value for the development of experimental strategies for treatment of ovarian cancer.     

CUX2 Protein Functions as an Accessory Factor in the Repair of Oxidative DNA Damage

CUX1 and CUX2 proteins are characterized by the presence of three highly similar regions called Cut repeats 1, 2, and 3. Although CUX1 is ubiquitously expressed, CUX2 plays an important role in the specification of neuronal cells and continues to be expressed in postmitotic neurons. Cut repeats from the CUX1 protein were recently shown to stimulate 8-oxoguanine DNA glycosylase 1 (OGG1), an enzyme that removes oxidized purines from DNA and introduces a single strand break through its apurinic/apyrimidinic lyase activity to initiate base excision repair. Here, we investigated whether CUX2 plays a similar role in the repair of oxidative DNA damage. Cux2 knockdown in embryonic cortical neurons increased levels of oxidative DNA damage. In vitro, Cut repeats from CUX2 increased the binding of OGG1 to 7,8-dihydro-8-oxoguanine-containing DNA and stimulated both the glycosylase and apurinic/apyrimidinic lyase activities of OGG1. Genetic inactivation in mouse embryo fibroblasts or CUX2 knockdown in HCC38 cells delayed DNA repair and increased DNA damage. Conversely, ectopic expression of Cut repeats from CUX2 accelerated DNA repair and reduced levels of oxidative DNA damage. These results demonstrate that CUX2 functions as an accessory factor that stimulates the repair of oxidative DNA damage. Neurons produce a high level of reactive oxygen species because of their dependence on aerobic oxidation of glucose as their source of energy. Our results suggest that the persistent expression of CUX2 in postmitotic neurons contributes to the maintenance of genome integrity through its stimulation of oxidative DNA damage repair.     

Differential modification of seawater carbonate chemistry by major coral reef benthic communities

Ocean acidification (OA) resulting from uptake of anthropogenic CO₂ may negatively affect coral reefs by causing decreased rates of biogenic calcification and increased rates of CaCO₃ dissolution and bioerosion. However, in addition to the gradual decrease in seawater pH and Ω _a resulting from anthropogenic activities, seawater carbonate chemistry in these coastal ecosystems is also strongly influenced by the benthic metabolism which can either exacerbate or alleviate OA through net community calcification (NCC = calcification – CaCO₃ dissolution) and net community organic carbon production (NCP = primary production ? respiration). Therefore, to project OA on coral reefs, it is necessary to understand how different benthic communities modify the reef seawater carbonate chemistry. In this study, we used flow-through mesocosms to investigate the modification of seawater carbonate chemistry by benthic metabolism of five distinct reef communities [carbonate sand, crustose coralline algae (CCA), corals, fleshy algae, and a mixed community] under ambient and acidified conditions during summer and winter. The results showed that different communities had distinct influences on carbonate chemistry related to the relative importance of NCC and NCP. Sand, CCA, and corals exerted relatively small influences on seawater pH and Ω _a over diel cycles due to closely balanced NCC and NCP rates, whereas fleshy algae and mixed communities strongly elevated daytime pH and Ω _a due to high NCP rates. Interestingly, the influence on seawater pH at night was relatively small and quite similar across communities. NCC and NCP rates were not significantly affected by short-term acidification, but larger diel variability in pH was observed due to decreased seawater buffering capacity. Except for corals, increased net dissolution was observed at night for all communities under OA, partially buffering against nighttime acidification. Thus, algal-dominated areas of coral reefs and increased net CaCO₃ dissolution may partially counteract reductions in seawater pH associated with anthropogenic OA at the local scale.     

Mixed acid-base disorders, hydroelectrolyte imbalance and lactate production in hypercapnic respiratory failure: the role of noninvasive ventilation

Background

Hypercapnic Chronic Obstructive Pulmonary Disease (COPD) exacerbation in patients with comorbidities and multidrug therapy is complicated by mixed acid-base, hydro-electrolyte and lactate disorders. Aim of this study was to determine the relationships of these disorders with the requirement for and duration of noninvasive ventilation (NIV) when treating hypercapnic respiratory failure.

Methods

Sixty-seven consecutive patients who were hospitalized for hypercapnic COPD exacerbation had their clinical condition, respiratory function, blood chemistry, arterial blood gases, blood lactate and volemic state assessed. Heart and respiratory rates, pH, PaO₂ and PaCO₂ and blood lactate were checked at the 1st, 2nd, 6th and 24th hours after starting NIV.

Results

Nine patients were transferred to the intensive care unit. NIV was performed in 11/17 (64.7%) mixed respiratory acidosis–metabolic alkalosis, 10/36 (27.8%) respiratory acidosis and 3/5 (60%) mixed respiratory-metabolic acidosis patients (p = 0.026), with durations of 45.1±9.8, 36.2±8.9 and 53.3±4.1 hours, respectively (p = 0.016). The duration of ventilation was associated with higher blood lactate (p<0.001), lower pH (p = 0.016), lower serum sodium (p = 0.014) and lower chloride (p = 0.038). Hyponatremia without hypervolemic hypochloremia occurred in 11 respiratory acidosis patients. Hypovolemic hyponatremia with hypochloremia and hypokalemia occurred in 10 mixed respiratory acidosis–metabolic alkalosis patients, and euvolemic hypochloremia occurred in the other 7 patients with this mixed acid-base disorder.

Conclusions

Mixed acid-base and lactate disorders during hypercapnic COPD exacerbations predict the need for and longer duration of NIV. The combination of mixed acid-base disorders and hydro-electrolyte disturbances should be further investigated.     

Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen

Bone samples from several vertebrates were collected from the Ziegler Reservoir fossil site, in Snowmass Village, Colorado, and processed for proteomics analysis. The specimens come from Pleistocene megafauna Bison latifrons, dating back ∼120,000 years. Proteomics analysis using a simplified sample preparation procedure and tandem mass spectrometry (MS/MS) was applied to obtain protein identifications. Several bioinformatics resources were used to obtain peptide identifications based on sequence homology to extant species with annotated genomes. With the exception of soil sample controls, all samples resulted in confident peptide identifications that mapped to type I collagen. In addition, we analyzed a specimen from the extinct B. latifrons that yielded peptide identifications mapping to over 33 bovine proteins. Our analysis resulted in extensive fibrillar collagen sequence coverage, including the identification of posttranslational modifications. Hydroxylysine glucosylgalactosylation, a modification thought to be involved in collagen fiber formation and bone mineralization, was identified for the first time in an ancient protein dataset. Meta-analysis of data from other studies indicates that this modification may be common in well-preserved prehistoric samples. Additional peptide sequences from extracellular matrix (ECM) and non-ECM proteins have also been identified for the first time in ancient tissue samples. These data provide a framework for analyzing ancient protein signatures in well-preserved fossil specimens, while also contributing novel insights into the molecular basis of organic matter preservation. As such, this analysis has unearthed common posttranslational modifications of collagen that may assist in its preservation over time. The data are available via ProteomeXchange with identifier PXD001827.During the last decade, paleontology and taphonomy (the study of decaying organisms over time and the fossilization processes) have begun to overlap with the field of proteomics to shed new light on preserved organic matter in fossilized bones (1–4). These bones represent a time capsule of ancient biomolecules, owing to their natural resistance to post mortem decay arising from a unique combination of mechanical, structural, and chemical properties (4–7).Although bones can be cursorily described as a composite of collagen (protein) and hydroxyapatite (mineral), fossilized bones undergo three distinct diagenesis pathways: (i) chemical deterioration of the organic phase; (ii) chemical deterioration of the mineral phase; and (iii) (micro)biological attack of the composite (6). In addition, the rate of these degradation pathways are affected by temperature, as higher burial temperatures have been shown to accelerate these processes (6, 8). Though relatively unusual, the first of these three pathways results in a slower deterioration process, which is more generally mitigated under (6) specific environmental constraints, such as geochemical stability (stable temperature and acidity) that promote bone mineral preservation. Importantly, slower deterioration results in more preserved biological materials that are more amenable to downstream analytical assays. One example of this is the controversial case of bone and soft-tissue preservation from the Cretaceous/Tertiary boundary (9–22). In light of these and other studies of ancient biomolecules, paleontological models have proposed that organic biomolecules in ancient samples, such as collagen sequences from the 80 million-year-(my)-old Campanian hadrosaur, Brachylophosaurus canadensis (16) or 68-my-old Tyrannosaurus rex, might be protected by the microenvironment within bones. Such spaces are believed to form a protective shelter that is able to reduce the effects of diagenetic events. In addition to collagen, preserved biomolecules include blood proteins, cellular lipids, and DNA (4, 5). While the maximum estimated lifespan of DNA in bones is ∼20,000 years (ky) at 10 °C, bone proteins have an even longer lifespan, making them an exceptional target for analysis to gain relevant insights into fossilized samples (6). Indeed, the survival of collagen, which is considered to be the most abundant bone protein, is estimated to be in the range 340 ky at 20 °C. Similarly, osteocalcin, the second-most abundant bone protein, can persist for ≈45 ky at 20 °C, thus opening an unprecedented analytical window to study extremely old samples (2, 4, 23).Although ancient DNA amplification and sequencing can yield interesting clues and potential artifacts from contaminating agents (7, 24–28), the improved preservation of ancient proteins provides access to a reservoir of otherwise unavailable genetic information for phylogenetic inference (25, 29, 30). In particular, mass spectrometry (MS)-based screening of species-specific collagen peptides has recently been used as a low-cost, rapid alternative to DNA sequencing for taxonomic attribution of morphologically unidentifiable small bone fragments and teeth stemming from diverse archeological contexts (25, 31–33).For over five decades, researchers have presented biochemical evidence for the existence of preserved protein material from ancient bone samples (34–36). One of the first direct measurements was by amino acid analysis, which showed that the compositional profile of ancient samples was consistent with collagens in modern bone samples (37–39). Preservation of organic biomolecules, either from bone, dentin, antlers, or ivory, has been investigated by radiolabeled ¹⁴C fossil dating (40) to provide an avenue of delineating evolutionary divergence from extant species (3, 41, 42). It is also important to note that these parameters primarily depend on ancient bone collagen as the levels remain largely unchanged (a high percentage of collagen is retained, as gleaned by laboratory experiments on bone taphonomy (6)). Additionally, antibody-based immunostaining methods have given indirect evidence of intact peptide amide bonds (43–45) to aid some of the first evidence of protein other than collagen and osteocalcin in ancient mammoth (43) and human specimens (46).In the past, mass spectrometry has been used to obtain MS signals consistent with modern osteocalcin samples (2, 47), and eventually postsource decay peptide fragmentation was used to confirm the identification of osteocalcin in fossil hominids dating back ∼75 ky (48). More recently, modern “bottom-up” proteomic methods were applied to mastodon and T. rex samples (10), complementing immunohistochemistry evidence (13, 17). The results hinted at the potential of identifying peptides from proteolytic digest of well-preserved bone samples. This work also highlighted the importance of minimizing sources of protein contamination and adhering to data publication guidelines (20, 21). In the past few years, a very well-preserved juvenile mammoth referred to as Lyuba was discovered in the Siberian permafrost and analyzed using high-resolution tandem mass spectrometry (29). This study was followed with a report by Wadsworth and Buckley (30) describing the analysis of proteins from 19 bovine bone samples spanning 4 ky to 1.5 my. Both of these groups reported the identification of additional collagen and noncollagen proteins.Recently, a series of large extinct mammal bones were unearthed at a reservoir near Snowmass Village, Colorado, USA (49, 50). The finding was made during a construction project at the Ziegler Reservoir, a fossil site that was originally a lake formed at an elevation of ∼2,705 m during the Bull Lake glaciations ∼140 ky ago (49, 51). The original lake area was ∼5 hectares in size with a total catchment of ∼14 hectares and lacked a direct water flow inlet or outlet. This closed drainage basin established a relatively unique environment that resulted in the exceptional preservation of plant material, insects (52), and vertebrate bones (49). In particular, a cranial specimen from extinct Bison latifrons was unearthed from the Biostratigraphic Zone/Marine Oxygen Isotope Stage (MIS) 5d, which dates back to ∼120 ky (53, 54).Here, we describe the use of paleoproteomics, for the identification of protein remnants with a focus on a particularly unique B. latifrons cranial specimen found at the Ziegler site. We developed a simplified sample processing approach that allows for analysis of low milligram quantities of ancient samples for peptide identification. Our method avoids the extensive demineralization steps of traditional protocols and utilizes an acid labile detergent to allow for efficient extraction and digestion without the need for additional sample cleanup steps. This approach was applied to a specimen from B. latifrons that displayed visual and mechanical properties consistent with the meninges, a fibrous tissue that lines the cranial cavity. Bioinformatics analysis revealed the presence of a recurring glycosylation signature in well-preserved collagens. In particular, the presence of glycosylated hydroxylysine residues was identified as a unique feature of bone fossil collagen, as gleaned through meta-analyses of raw data from previous reports on woolly mammoth (Mammuthus primigenius) and bovine samples (29, 30). The results from these meta-analyses indicate a common, unique feature of collagen that coincides with, and possibly contributes to its preservation.     

Protein aggregation and amyloid fibril formation by an SH3 domain probed by limited proteolysis

The SH3 domains are small protein modules of 60-85 amino acid residues that are found in many proteins involved in intracellular signal transduction. The SH3 domain of the p85alpha subunit of bovine phosphatidylinositol 3'-kinase (PI3-SH3) under acidic solution adopts a compact denatured state from which amyloid fibrils are readily formed. This aggregation process has been found to be modulated substantially by solution conditions. Here, we have analyzed the conformational features of the native and acid denatured states of PI3-SH3 by limited proteolysis experiments using proteinase K and pepsin, respectively. Moreover, we have analyzed the propensity of PI3-SH3 to be hydrolyzed by pepsin at different stages in the process of aggregation and amyloid formation at pH 1.2 and 2.0 and compared the sites of proteolysis under these conditions with the conformational features of both native and aggregated PI3-SH3. The results demonstrate that the denatured state of PI3-SH3 formed at low pH is relatively resistant to proteolysis, indicating that it is partially folded. The long loop connecting beta-strands b and c in the native protein is the region in this structure most susceptible to proteolysis. Remarkably, aggregates of PI3-SH3 that are formed initially from this denatured state in acid solution display enhanced susceptibility to proteolysis of the long loop, suggesting that the protein becomes more unfolded in the early stages of aggregation. By contrast, the more defined amyloid fibrils that are formed over longer periods of time are completely resistant to proteolysis. We suggest that the protein aggregates formed initially are relatively dynamic species that are able readily to reorganize their interactions to enable formation of very well ordered fibrillar structures. In addition, the disordered and non-native character of the polypeptide chains in the early aggregates could be important in determining the high cytotoxicity that has been revealed in previous studies of these species.     

Liquid chromatography-mass spectrometry assay for quantitation of ifosfamide and its N-deschloroethylated metabolites in rat microsomal medium

A specific and sensitive quantitative assay has been developed using high performance liquid chromatography-electrospray ionization mass spectrometry (HPLC-ESI-MS) for the simultaneous quantitation of the antitumor drug ifosfamide (IFM) and its two metabolites, N2-deschloroethylifosfamide (N2-DCE-IFM) and N3-deschloroethylifosfamide (N3-DCE-IFM) in microsomal medium. The analytes and the internal standard (cyclophosphamide) were isolated by ethylacetate extraction from rat liver microsomes. They were analysed on a Nucleosil C18 HD column (125 mm x 4 mm, 5 microm) using a step gradient with the mobile phase (2 mM ammonium formate and methanol). The HPLC-ESI-MS method used selected ion monitoring of ions m/z 199.1 Th and m/z 261.1 Th and was validated in the concentrations ranges of 100-5000 ng/mL for IFM and 50-2500 ng/mL for its N-deschloroethylated metabolites (DCE-IFM) with good accuracy and precision (CV less than 15%). The low limits of quantitation (LLOQ) were found at 50 ng/mL for N-deschloroethylated metabolites and at 100 ng/mL for the parent drug (IFM). The method was applied for the determination of ifosfamide and its N-deschloroethylated metabolites in rat microsomal incubations.     

Complex evolutionary history of a Neotropical lowland forest bird (Lepidothrix coronata) and its implications for historical hypotheses of the origin of Neotropical avian diversity

Here we apply a combination of phylogeographic and historical demographic analyses to the study of mtDNA sequence variation within the Blue-crowned Manakin (Lepidothrix coronata), a widespread Neotropical bird. A high degree of phylogeographic structure allowed us to demonstrate that several vicariant events, including Andean uplift, the formation of riverine barriers, and climatically induced vegetational shifts, as well as a non-vicariant process, range expansion, have all acted, at varying spatial and temporal scales, to influence genetic structure within L. coronata, suggesting that current historical hypotheses of the origin of Neotropical avian diversity that focus on single vicariant mechanisms may be overly simplistic. Our data also support an origin (>2 mybp) that is substantially older than the late Pleistocene for the genetic structure within this species and indicate that phylogeographic patterns within the species are not concordant with plumage-based subspecific taxonomy. These data add to a growing body of evidence suggesting that the origin of several Neotropical avian species may have occurred in the mid-Pliocene, thus, geological arguments surrounding putative Pleistocene vicariant events, while interesting in their own right, may have little relevance to Neotropical avian diversification at the species level.     

Evaluation of the anti-inflammatory and antinociceptive properties of p-cymene in mice

We attempted to identify the antinociceptive and anti-inflammatory actions of the monoterpene p-cymene. Firstly, behavioural screening was carried out to verify the influence of p-cymene [25, 50, and 100 mg/kg intraperitoneal (i.p.)] on the central nervous system (CNS) activity. The antinociceptive activity of p-cymene was evaluated by the acetic acid-induced writhing response, formalin, and hot-plate test, respectively. The leukocyte migration induced by injection of carrageenan was used to assess the anti-inflammatory activity. p-Cymene showed depressant activity on CNS after 4 h of treatment and also a possible action on the autonomous nervous system (ANS), mainly at the dose of 100 mg/kg (i.p.). It was found that p-cymene (50 and 100 mg/kg, i.p.) significantly (p < 0.05) reduced the writhing responses induced by acetic acid. p-Cymene also decreased the licking time in the first and second phase, respectively, of the formalin test. The results of the hot-plate test showed that all doses of p-cymene increased significantly the latency time of the response to the thermal stimulus in both licking and jumping parameters. In addition, there was a significantly (p < 0.05) decreased leukocyte migration at all doses of p-cymene. The experimental data demonstrate that p-cymene possesses antinociceptive and anti-inflammatory activities.