A proteogenomic portrait of lung squamous cell carcinoma.

Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such as LSD1 and EZH2 to target SOX2-overexpressing tumors. Our data support complex regulation of metabolic pathways by crosstalk between post-translational modifications including ubiquitylation. Numerous immune-related proteogenomic observations suggest directions for further investigation. Proteogenomic dissection of CDKN2A mutations argue for more nuanced assessment of RB1 protein expression and phosphorylation before declaring CDK4/6 inhibition unsuccessful. Finally, triangulation between LSCC, LUAD, and HNSCC identified both unique and common therapeutic vulnerabilities. These observations and proteogenomics data resources may guide research into the biology and treatment of LSCC.

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma.

To explore the biology of lung adenocarcinoma (LUAD) and identify new therapeutic opportunities, we performed comprehensive proteogenomic characterization of 110 tumors and 101 matched normal adjacent tissues (NATs) incorporating genomics, epigenomics, deep-scale proteomics, phosphoproteomics, and acetylproteomics. Multi-omics clustering revealed four subgroups defined by key driver mutations, country, and gender. Proteomic and phosphoproteomic data illuminated biology downstream of copy number aberrations, somatic mutations, and fusions and identified therapeutic vulnerabilities associated with driver events involving KRAS, EGFR, and ALK. Immune subtyping revealed a complex landscape, reinforced the association of STK11 with immune-cold behavior, and underscored a potential immunosuppressive role of neutrophil degranulation. Smoking-associated LUADs showed correlation with other environmental exposure signatures and a field effect in NATs. Matched NATs allowed identification of differentially expressed proteins with potential diagnostic and therapeutic utility. This proteogenomics dataset represents a unique public resource for researchers and clinicians seeking to better understand and treat lung adenocarcinomas.

TMT Labeling for the Masses: A Robust and Cost-efficient, In-solution Labeling Approach.

Isobaric stable isotope labeling using, for example, tandem mass tags (TMTs) is increasingly being applied for large-scale proteomic studies. Experiments focusing on proteoform analysis in drug time course or perturbation studies or in large patient cohorts greatly benefit from the reproducible quantification of single peptides across samples. However, such studies often require labeling of hundreds of micrograms of peptides such that the cost for labeling reagents represents a major contribution to the overall cost of an experiment. Here, we describe and evaluate a robust and cost-effective protocol for TMT labeling that reduces the quantity of required labeling reagent by a factor of eight and achieves complete labeling. Under- and overlabeling of peptides derived from complex digests of tissues and cell lines were systematically evaluated using peptide quantities of between 12.5 and 800 µg and TMT-to-peptide ratios (wt/wt) ranging from 8:1 to 1:2 at different TMT and peptide concentrations. When reaction volumes were reduced to maintain TMT and peptide concentrations of at least 10 mm and 2 g/l, respectively, TMT-to-peptide ratios as low as 1:1 (wt/wt) resulted in labeling efficiencies of > 99% and excellent intra- and interlaboratory reproducibility. The utility of the optimized protocol was further demonstrated in a deep-scale proteome and phosphoproteome analysis of patient-derived xenograft tumor tissue benchmarked against the labeling procedure recommended by the TMT vendor. Finally, we discuss the impact of labeling reaction parameters for N-hydroxysuccinimide ester-based chemistry and provide guidance on adopting efficient labeling protocols for different peptide quantities.

Psychosocial burden and out-of-pocket costs in patients with atopic dermatitis in Ireland.

Atopic dermatitis (AD) is one of the most common inflammatory skin diseases in the developed world, affecting 1-3% of the adult population in Europe. This inflammatory disease can have a marked impact on affected individuals, leading to significant impairment in physical wellbeing and quality of life (QoL). The aim of this study was to investigate the psychosocial impact and financial burden of AD on patients in Ireland. To increase our understanding of the psychosocial and financial aspects of AD disease burden in the Irish population, an online survey was designed. The survey was launched by the Irish Skin Foundation, and included questions focusing on disease severity, disease control, psychosocial impact, interrupted sleep, missed work and school days, and financial cost. The survey showed that the impact of AD on QoL was profound. The survey demonstrated that 85% of adults described interrupted sleep, 70% reported social anxiety, 65% avoid exercise and sports, 52% avoid social activities, 52% avoid sexual intimacy and 43% feel they are depressed as a result of their AD. Approximately one-quarter of those surveyed can spend up to €2300 annually on over-the-counter, prescription and alternative treatments. This study has shown the significant impact AD has on patients living in Ireland. It also highlights that out-of-pocket costs for patients is higher compared with previous studies across European countries.

Big Data and diabetes: the applications of Big Data for diabetes care now and in the future.

We review current applications of Big Data in diabetes care and consider the future potential by carrying out a scoping study of the academic literature on Big Data and diabetes care. Healthcare data are being produced at ever-increasing rates, and this information has the potential to transform the provision of diabetes care. Big Data is beginning to have an impact on diabetes care through data research. The use of Big Data for routine clinical care is still a future application. Vast amounts of healthcare data are already being produced, and the key is harnessing these to produce actionable insights. Considerable development work is required to achieve these goals.

Chitosan-Polycaprolactone Core-Shell Microparticles for Sustained Delivery of Bevacizumab.

The current therapy for treating neovascular age-related macular degeneration requires monthly intravitreal injection of angiogenesis inhibitors such as bevacizumab or ranibizumab via a 31-gauge needle to inhibit choroidal neovascularization. However, repeated intravitreal injections are associated with poor patient compliance and potential side effects. Microparticle-based injectable devices have shown great promise to address this issue by sustained delivery of protein therapeutics, but critical barriers remain, including limited loading capacity and steady long-term release without compromising the anti-angiogenic activity of drugs. Addressing these challenges, we developed a unique method for synthesizing biodegradable polymer-based core-shell microparticles with sizes around 10 µm, high physical integrity, and uniform size. Subsequent electrostatic and physical interactions to control protein diffusion were designed for the core-shell microparticles to effectively increase the capacity of drug loading to 25%, reduce burst release by almost 30%, and extend the period of drug release from 3 to 6 months. Remarkably, the microparticles enabled a longer-term drug administration and maintained high drug potency up to 6 months in vitro, representing significant advancement compared to conventional microparticle-based delivery platforms or currently commercialized devices. Additionally, the microparticles presented minimal toxicity to human retinal cells in vitro with over 90% cell viability, and they also exhibited good injection feasibility through 31-gauge needles in an ex vivo porcine eye model. These results warrant further studies to evaluate the clinical potential for treating posterior ophthalmic diseases as well as other conditions or injuries requiring long-term local drug administration.

Enhancing oxygen delivery to ovarian follicles by three different methods markedly improves growth in serum-containing culture medium.

Invitro ovarian follicle culture systems are routinely used to study folliculogenesis and may provide solutions for infertility. Mouse follicles are typically cultured in standard gas-impermeable culture plates under gas phase oxygen concentrations of 5% or 20% (v/v). There is evidence that these conditions may not provide adequate oxygenation for follicles cultured as non-attached intact units in medium supplemented with serum and high levels of FSH. Three different methods of enhancing follicle oxygenation were investigated in this study: increasing the gas phase oxygen concentration, inverting the culture plates and using gas-permeable culture plates. Follicles cultured under 40% O2 were significantly larger (P P P 2 . These effects were associated with reduced secretion of vascular endothelial growth factor (P P P invivo -matured follicles (~500µm in diameter). Such follicular development is not possible under hypoxic conditions.

Statistical challenges posed by uncontrolled master protocols: sensitivity analysis of the vemurafenib study.

Within the evidentiary hierarchy of experimental inquiry, randomized trials are the gold standard. Oncology patients enter clinical studies with diverse lifestyles, treatment pathways, host tissue environments, and competing comorbidities. Randomization attempts to balance prognostic characteristics among study arms, thereby enabling statistical inference of 'average benefit' and attribution to the studied therapies. In contrast, interpretations of uncontrolled trials require additional scrutiny to attempt to place the findings in the context of external evidence. Counter-factual reasoning and speculation across trials may be obscured by the disproportionate enrollment of prognostic subpopulations which may be unknown from publications of trial reports. Recent modifications to the regulatory environment (Food and Drug Administration Safety and Innovation Act) have elevated the importance of non-comparative trials. Moreover, the emergence of recent innovations in precision medicine have yielded trial designs that partition potentially heterogeneous subpopulations into 'statistically exchangeable' cohorts by histologies, or genetic alterations, further elevating the importance of single-cohort analyses. As patient cohorts become ever more refined into smaller targeted subsets, consumers of reports of uncontrolled trials should be further empowered with improvements in reporting practices that better describe the enrolled prognostic subpopulations and importantly their association with study end points. This article demonstrates the issue with a sensitivity analysis of the findings reported in a recent trial that was devised to evaluate the preliminary clinical efficacy of vemurafenib in BRAF V600 mutation-positive nonmelanoma cancers.

Genetic structure and invasion history of the house mouse (Mus musculus domesticus) in Senegal, West Africa: a legacy of colonial and contemporary times.

Knowledge of the genetic make-up and demographic history of invasive populations is critical to understand invasion mechanisms. Commensal rodents are ideal models to study whether complex invasion histories are typical of introductions involving human activities. The house mouse Mus musculus domesticus is a major invasive synanthropic rodent originating from South-West Asia. It has been largely studied in Europe and on several remote islands, but the genetic structure and invasion history of this taxon have been little investigated in several continental areas, including West Africa. In this study, we focussed on invasive populations of M. m. domesticus in Senegal. In this focal area for European settlers, the distribution area and invasion spread of the house mouse is documented by decades of data on commensal rodent communities. Genetic variation at one mitochondrial locus and 16 nuclear microsatellite markers was analysed from individuals sampled in 36 sites distributed across the country. A combination of phylogeographic and population genetics methods showed that there was a single introduction event on the northern coast of Senegal, from an exogenous (probably West European) source, followed by a secondary introduction from northern Senegal into a coastal site further south. The geographic locations of these introduction sites were consistent with the colonial history of Senegal. Overall, the marked microsatellite genetic structure observed in Senegal, even between sites located close together, revealed a complex interplay of different demographic processes occurring during house mouse spatial expansion, including sequential founder effects and stratified dispersal due to human transport along major roads.

Adsorption differences between low coverage enantiomers of alanine on the chiral Cu{421}R surface.

Chiral separation using heterogeneous methods has long been sought after. Chiral metal surfaces have the potential to make it possible to model these systems using small amino acids, the building blocks for proteins. A comparison of submonolayer concentrations of alanine enantiomers adsorbed onto Cu{421}R has revealed a large geometrical differences between the two molecules as compared to the saturated coverage. Large differences were observed in HR-XPS and NEXAFS and complemented by theoretical DFT calculations. At approximately one third of a monolayer a comparison of the C1s XPS signal showed a shift in the methyl group of more than 300 meV indicating that the two enantiomers are in different chemical environments. NEXAFS spectroscopy confirmed the XPS variations and showed large differences in the orientation of the adsorbed molecules. Our DFT results show that the l-enantiomer is energetically the most stable in the {311} microfacet configuration. In contrast to the full monolayer coverage, these lower coverages showed enhanced selectivity.

Corrigendum to: Hypoxia limits mouse follicle growth in vitro.

Ovarian follicle culture is useful for elucidation of factors involved in the regulation of follicular function. We examined the effects of gas phase oxygen concentration, an oil overlay, serum type and medium supplementation with FSH, insulin-transferrin-selenium (ITS) and I-ascorbic acid on cultured preantral mouse follicle growth in a spherical, non-attached follicle culture system. Follicle growth in 5% oxygen was significantly (P<0.01) inferior to growth in 20% oxygen in terms of follicle diameter. This was likely due to hypoxia, as evidenced by significantly (P<0.05) increased follicle secretion of vascular endothelial growth factor (VEGF), a marker of cell hypoxia. Follicular growth was not (P>0.05) affected by an oil overlay, ITS supplementation or serum type. Culture in medium with 5% mouse serum, 1 IU mL-1 FSH, 25 µgmL-1 l-ascorbic acid and 20% oxygen without an oil overlay supported the growth of follicles to a maximum diameter of 380 µm in 6 days. Compared with mature preovulatory mouse follicles in vivo that often have diameters >500 µm within the same time frame, in vitro-grown follicles clearly exhibit limited growth. Thus, adequate oxygenation is an essential factor in the process of optimising follicle growth.

Electronic Properties of High-Quality Epitaxial Topological Dirac Semimetal Thin Films.

Topological Dirac semimetals (TDS) are three-dimensional analogues of graphene, with linear electronic dispersions in three dimensions. Nanoscale confinement of TDSs in thin films is a necessary step toward observing the conventional-to-topological quantum phase transition (QPT) with increasing film thickness, gated devices for electric-field control of topological states, and devices with surface-state-dominated transport phenomena. Thin films can also be interfaced with superconductors (realizing a host for Majorana Fermions) or ferromagnets (realizing Weyl Fermions or T-broken topological states). Here we report structural and electrical characterization of large-area epitaxial thin films of TDS Na3Bi on single crystal Al2O3[0001] substrates. Charge carrier mobilities exceeding 6,000 cm(2)/(V s) and carrier densities below 1 × 10(18) cm(-3) are comparable to the best single crystal values. Perpendicular magnetoresistance at low field shows the perfect weak antilocalization behavior expected for Dirac Fermions in the absence of intervalley scattering. At higher fields up to 0.5 T anomalously large quadratic magnetoresistance is observed, indicating that some aspects of the low field magnetotransport (µB < 1) in this TDS are yet to be explained.

Brain lesions in eclampsia: A series of 39 cases admitted in an Intensive Care Unit.

The aim of this study was to identify the encephalic lesions in the eclampsia occurrences. Within a period of 18 months, computed tomography (CT) of the brain was performed in all patients admitted in intensive care for eclampsia. These CTs were analyzed and intracerebral lesions were identified. Thirty-nine patients were included. We noted 10 cases of ischemic stroke, 9 cases of cerebral edema, and 3 cases of hemorrhagic stroke and subarachnoid hemorrhage. The CT scan came back to normal in 20 eclamptic patients. Overall, delays in obstetric and intensive care and time of completion of the CT were long. CT has allowed highlighting in patients with eclampsia varied intracerebral lesions. The early performance of the CT is therefore essential for a better support of patients.

Highly chromium contaminant tolerant BaO infiltrated La0.6Sr0.4Co0.2Fe0.8O3-δ cathodes for solid oxide fuel cells.

A BaO infiltrated La0.6Sr0.4Co0.2Fe0.8O3-δ (LSCF) cathode shows remarkable tolerance and resistance towards chromium via the formation of BaCrO4 instead of SrCrO4 on the electrode surface, preventing the excess Sr deficiency at the A-site of LSCF perovskite and thus mitigating the Cr poisoning effect.

Hypoxia limits mouse follicle growth in vitro.

Ovarian follicle culture is useful for elucidation of factors involved in the regulation of follicular function. We examined the effects of gas phase oxygen concentration, an oil overlay, serum type and medium supplementation with FSH, insulin-transferrin-selenium (ITS) and l-ascorbic acid on cultured preantral mouse follicle growth in a spherical, non-attached follicle culture system. Follicle growth in 5% oxygen was significantly (P < 0.01) inferior to growth in 20% oxygen in terms of follicle diameter. This was likely due to hypoxia, as evidenced by significantly (P < 0.05) increased follicle secretion of vascular endothelial growth factor (VEGF), a marker of cell hypoxia. Follicular growth was not (P > 0.05) affected by an oil overlay, ITS supplementation or serum type. Culture in medium with 5% mouse serum, 1 IU mL-1 FSH, 25 µg mL-1 l-ascorbic acid and 20% oxygen without an oil overlay supported the growth of follicles to a maximum diameter of 380 µm in 6 days. Compared with mature preovulatory mouse follicles in vivo that often have diameters >500 µm within the same time frame, in vitro-grown follicles clearly exhibit limited growth. Thus, adequate oxygenation is an essential factor in the process of optimising follicle growth.

Phase I study of weekly paclitaxel in combination with pazopanib and lapatinib in advanced solid malignancies.

BACKGROUND: We assessed the maximum tolerated regimen (MTR) and dose-limiting toxicities of pazopanib and lapatinib in combination with weekly paclitaxel, and the effect of pazopanib and lapatinib on paclitaxel pharmacokinetics. METHODS: Patients received intravenous paclitaxel on days 1, 8, and 15 of a 28-day cycle concurrently with daily pazopanib and lapatinib. Dose levels of paclitaxel (mg m(-2))/pazopanib(mg)/lapatinib(mg) were 50/400/1000, 50/800/1000, 80/800/1000, and 80/400/1000. At the MTR, additional patients were enrolled to further evaluate tolerability, and the potential effects of pazopanib and lapatinib, inhibitors of cytochrome P450 (CYP)3A4, on the pharmacokinetics of paclitaxel, a CYP2C8 and CYP3A4 substrate. RESULTS: Twenty-six patients were enrolled. Dose-limiting toxicities at the MTR (80/400/1000) included grade 4 thrombosis and grade 3 aspartate aminotransferase elevation. Other toxicities included diarrhoea, neutropenia, fatigue, and liver enzyme elevations. Coadministration of pazopanib 400 mg and lapatinib 1000 mg increased paclitaxel maximum plasma concentration (38%) and area under the curve (37%) relative to paclitaxel alone. One patient with a salivary gland tumour had a partial response; three patients had stable disease (⩾6 months). CONCLUSIONS: Pazopanib 400 mg per day and lapatinib 1000 mg per day can be combined with paclitaxel 80 mg m(-2) in 28-day cycles. Coadministration of pazopanib and lapatinib, weak inhibitors of CYP2C8 and CYP3A4, had an inhibitory effect on paclitaxel clearance.