Natural isotope correction improves analysis of protein modification dynamics

Stable isotope labelling in combination with high-resolution mass spectrometry approaches are increasingly used to analyze both metabolite and protein modification dynamics. To enable correct estimation of the resulting dynamics, it is critical to correct the measured values for naturally occurring stable isotopes, a process commonly called isotopologue correction or deconvolution. While the importance of isotopologue correction is well recognized in metabolomics, it has received far less attention in proteomics approaches. Although several tools exist that enable isotopologue correction of mass spectrometry data, the majority is tailored for the analysis of low molecular weight metabolites. We here present PICor which has been developed for isotopologue correction of complex isotope labelling experiments in proteomics or metabolomics and demonstrate the importance of appropriate correction for accurate determination of protein modifications dynamics, using histone acetylation as an example

Automatic vocalisation-based detection of fragile X syndrome and Rett syndrome

Fragile X syndrome (FXS) and Rett syndrome (RTT) are developmental disorders currently not diagnosed before toddlerhood. Even though speech-language deficits are among the key symptoms of both conditions, little is known about infant vocalisation acoustics for an automatic earlier identification of affected individuals. To bridge this gap, we applied intelligent audio analysis methodology to a compact dataset of 4454 home-recorded vocalisations of 3 individuals with FXS and 3 individuals with RTT aged 6 to 11 months, as well as 6 age- and gender-matched typically developing controls (TD). On the basis of a standardised set of 88 acoustic features, we trained linear kernel support vector machines to evaluate the feasibility of automatic classification of (a) FXS vs TD, (b) RTT vs TD, (c) atypical development (FXS+RTT) vs TD, and (d) FXS vs RTT vs TD. In paradigms (a)–(c), all infants were correctly classified; in paradigm (d), 9 of 12 were so. Spectral/cepstral and energy-related features were most relevant for classification across all paradigms. Despite the small sample size, this study reveals new insights into early vocalisation characteristics in FXS and RTT, and provides technical underpinnings for a future earlier identification of affected individuals, enabling earlier intervention and family counselling

PGC-1α Determines Light Damage Susceptibility of the Murine Retina

The peroxisome proliferator-activated receptor γ coactivator 1 (PGC-1) proteins are key regulators of cellular bioenergetics and are accordingly expressed in tissues with a high energetic demand. For example, PGC-1α and PGC-1β control organ function of brown adipose tissue, heart, brain, liver and skeletal muscle. Surprisingly, despite their prominent role in the control of mitochondrial biogenesis and oxidative metabolism, expression and function of the PGC-1 coactivators in the retina, an organ with one of the highest energy demands per tissue weight, are completely unknown. Moreover, the molecular mechanisms that coordinate energy production with repair processes in the damaged retina remain enigmatic. In the present study, we thus investigated the expression and function of the PGC-1 coactivators in the healthy and the damaged retina. We show that PGC-1α and PGC-1β are found at high levels in different structures of the mouse retina, most prominently in the photoreceptors. Furthermore, PGC-1α knockout mice suffer from a striking deterioration in retinal morphology and function upon detrimental light exposure. Gene expression studies revealed dysregulation of all major pathways involved in retinal damage and apoptosis, repair and renewal in the PGC-1α knockouts. The light-induced increase in apoptosis in vivo in the absence of PGC-1α was substantiated in vitro, where overexpression of PGC-1α evoked strong anti-apoptotic effects. Finally, we found that retinal levels of PGC-1 expression are reduced in different mouse models for retinitis pigmentosa. We demonstrate that PGC-1α is a central coordinator of energy production and, importantly, all of the major processes involved in retinal damage and subsequent repair. Together with the observed dysregulation of PGC-1α and PGC-1β in retinitis pigmentosa mouse models, these findings thus imply that PGC-1α might be an attractive target for therapeutic approaches aimed at retinal degeneration diseases

Combined Metabolic and Chemical (CoMetChem) Labeling Using Stable Isotopes—a Strategy to Reveal Site-Specific Histone Acetylation and Deacetylation Rates by LC-MS

[Image: see text] Histone acetylation is an important, reversible post-translational protein modification and a hallmark of epigenetic regulation. However, little is known about the dynamics of this process, due to the lack of analytical methods that can capture site-specific acetylation and deacetylation reactions. We present a new approach that combines metabolic and chemical labeling (CoMetChem) using uniformly 13C-labeled glucose and stable isotope-labeled acetic anhydride. Thereby, chemically equivalent, fully acetylated histone species are generated, enabling accurate relative quantification of site-specific lysine acetylation dynamics in tryptic peptides using high-resolution mass spectrometry. We show that CoMetChem enables site-specific quantification of the incorporation or loss of lysine acetylation over time, allowing the determination of reaction rates for acetylation and deacetylation. Thus, the CoMetChem methodology provides a comprehensive description of site-specific acetylation dynamics

Simple extension of the plane-wave final state in photoemission: Bringing understanding to the photon-energy dependence of two-dimensional materials

Angle-resolved photoemission spectroscopy (ARPES) is a method that measures orbital and band structure contrast through the momentum distribution of photoelectrons. Its simplest interpretation is obtained in the plane-wave approximation, according to which photoelectrons propagate freely to the detector. The photoelectron momentum distribution is then essentially given by the Fourier transform of the real-space orbital. While the plane-wave approximation is remarkably successful in describing the momentum distributions of aromatic compounds, it generally fails to capture kinetic-energy-dependent final-state interference and dichroism effects. Focusing our present study on quasi-freestanding monolayer graphene as the archetypical two-dimensional (2D) material, we observe an exemplary Ekin-dependent modulation of, and a redistribution of spectral weight within, its characteristic horseshoe signature around the K¯ and K¯′ points: both effects indeed cannot be rationalized by the plane-wave final state. Our data are, however, in remarkable agreement with ab initio time-dependent density functional simulations of a freestanding graphene layer and can be explained by a simple extension of the plane-wave final state, permitting the two dipole-allowed partial waves emitted from the C 2pz orbitals to scatter in the potential of their immediate surroundings. Exploiting the absolute photon flux calibration of the Metrology Light Source, this scattered-wave approximation allows us to extract Ekin-dependent amplitudes and phases of both partial waves directly from photoemission data. The scattered-wave approximation thus represents a powerful yet intuitive refinement of the plane-wave final state in photoemission of 2D materials and beyond

Metabolic Activation of Intrahepatic CD8+ T Cells and NKT Cells Causes Nonalcoholic Steatohepatitis and Liver Cancer via Cross-Talk with Hepatocytes

SummaryHepatocellular carcinoma (HCC), the fastest rising cancer in the United States and increasing in Europe, often occurs with nonalcoholic steatohepatitis (NASH). Mechanisms underlying NASH and NASH-induced HCC are largely unknown. We developed a mouse model recapitulating key features of human metabolic syndrome, NASH, and HCC by long-term feeding of a choline-deficient high-fat diet. This induced activated intrahepatic CD8+ T cells, NKT cells, and inflammatory cytokines, similar to NASH patients. CD8+ T cells and NKT cells but not myeloid cells promote NASH and HCC through interactions with hepatocytes. NKT cells primarily cause steatosis via secreted LIGHT, while CD8+ and NKT cells cooperatively induce liver damage. Hepatocellular LTβR and canonical NF-κB signaling facilitate NASH-to-HCC transition, demonstrating that distinct molecular mechanisms determine NASH and HCC development

C6-ceramide synergistically potentiates the anti-tumor effects of histone deacetylase inhibitors via AKT dephosphorylation and α-tubulin hyperacetylation both in vitro and in vivo

Histone deacetylase inhibitors (HDACIs) have shown promising anti-tumor effects for a variety of malignancies, however, many tumors are reportedly resistant to them. In this study, we made a novel discovery that co-administration of HDACIs (Trichostatin A (TSA) and others) and exogenous cell-permeable short-chain ceramide (C6) results in striking increase in cancer cell death and apoptosis in multiple cancer cells. These events are associated with perturbations in diverse cell signaling pathways, including inactivation of Akt/mTOR and increase in α-tubulin acetylation (both in vivo and in vitro). TSA interacts in a highly synergistic manner with C6-ceramide to disrupt HDAC6/protein phosphatase 1 (PP1)/tubulin complex, to induce α-tubulin hyperacetylation, and to release and activate PP1, which then leads to AKT dephosphorylation and eventually causes cancer cell death. Interestingly, TSA itself results in short-term ceramide accumulation, which as a result of metabolic (glycosylation) removal, does not result in evident increase of cancer cell death. However, adding C6-ceramide led to a very pronounced increase in ceramide level and marked increase in cell death. Importantly, the effective synergistic anti-tumor activity of TSA plus C6-ceramide is also seen in in vivo mice xenograft pancreatic and ovarian cancer models, indicating that this regimen (HDACI plus C6-ceramide) may represent a more effective form of therapy against pancreatic and ovarian carcinoma

Routine use of patient reported outcome measures (PROMs) for improving treatment of common mental health disorders in adults

BACKGROUND: Routine outcome monitoring of common mental health disorders (CMHDs), using patient reported outcome measures (PROMs), has been promoted across primary care, psychological therapy and multidisciplinary mental health care settings, but is likely to be costly, given the high prevalence of CMHDs. There has been no systematic review of the use of PROMs in routine outcome monitoring of CMHDs across these three settings. OBJECTIVES: To assess the effects of routine measurement and feedback of the results of PROMs during the management of CMHDs in 1) improving the outcome of CMHDs; and 2) in changing the management of CMHDs. SEARCH METHODS: We searched the Cochrane Depression Anxiety and Neurosis group specialised controlled trials register (CCDANCTR-Studies and CCDANCTR-References), the Oxford University PROMS Bibliography (2002-5), Ovid PsycINFO, Web of Science, The Cochrane Library, and International trial registries, initially to 30 May 2014, and updated to 18 May 2015. SELECTION CRITERIA: We selected cluster and individually randomised controlled trials (RCTs) including participants with CMHDs aged 18 years and over, in which the results of PROMs were fed back to treating clinicians, or both clinicians and patients. We excluded RCTs in child and adolescent treatment settings, and those in which more than 10% of participants had diagnoses of eating disorders, psychoses, substance use disorders, learning disorders or dementia. DATA COLLECTION AND ANALYSIS: At least two authors independently identified eligible trials, assessed trial quality, and extracted data. We conducted meta-analysis across studies, pooling outcome measures which were sufficiently similar to each other to justify pooling. MAIN RESULTS: We included 17 studies involving 8787 participants: nine in multidisciplinary mental health care, six in psychological therapy settings, and two in primary care. Pooling of outcome data to provide a summary estimate of effect across studies was possible only for those studies using the compound Outcome Questionnaire (OQ-45) or Outcome Rating System (ORS) PROMs, which were all conducted in multidisciplinary mental health care or psychological therapy settings, because both primary care studies identified used single symptom outcome measures, which were not directly comparable to the OQ-45 or ORS.Meta-analysis of 12 studies including 3696 participants using these PROMs found no evidence of a difference in outcome in terms of symptoms, between feedback and no-feedback groups (standardised mean difference (SMD) -0.07, 95% confidence interval (CI) -0.16 to 0.01; P value = 0.10). The evidence for this comparison was graded as low quality however, as all included studies were considered at high risk of bias, in most cases due to inadequate blinding of assessors and significant attrition at follow-up.Quality of life was reported in only two studies, social functioning in one, and costs in none. Information on adverse events (thoughts of self-harm or suicide) was collected in one study, but differences between arms were not reported.It was not possible to pool data on changes in drug treatment or referrals as only two studies reported these. Meta-analysis of seven studies including 2608 participants found no evidence of a difference in management of CMHDs between feedback and no-feedback groups, in terms of the number of treatment sessions received (mean difference (MD) -0.02 sessions, 95% CI -0.42 to 0.39; P value = 0.93). However, the evidence for this comparison was also graded as low quality. AUTHORS' CONCLUSIONS: We found insufficient evidence to support the use of routine outcome monitoring using PROMs in the treatment of CMHDs, in terms of improving patient outcomes or in improving management. The findings are subject to considerable uncertainty however, due to the high risk of bias in the large majority of trials meeting the inclusion criteria, which means further research is very likely to have an important impact on the estimate of effect and is likely to change the estimate. More research of better quality is therefore required, particularly in primary care where most CMHDs are treated.Future research should address issues of blinding of assessors and attrition, and measure a range of relevant symptom outcomes, as well as possible harmful effects of monitoring, health-related quality of life, social functioning, and costs. Studies should include people treated with drugs as well as psychological therapies, and should follow them up for longer than six months

Tumor necrosis factor alpha drugs in rheumatoid arthritis: systematic review and metaanalysis of efficacy and safety

Es reproducción del documento publicado en http://dx.doi.org/10.1186/1471-2474-9-52Background: To analyse available evidence on the efficacy and safety of anti-TNF alpha drugs (infliximab, etanercept and adalimumab) for treating rheumatoid arthritis (RA). Methods: We searched systematically for randomised controlled clinical trials on treatment of RA with anti-TNF alpha drugs, followed by a systematic review with metaanalysis. Trials were searched from MEDLINE, EMBASE and Cochrane Library databases. The American College of Rheumatology (ACR) efficacy response criteria were used. Safety parameters provided by the trials were also assessed. Positive and undesired effects were estimated using combined relative risks (RR), number needed to treat (NNT) and number needed to harm (NNH). Heterogeneity was evaluated by Cochrane's Q and I-2 statistics. Results: Thirteen trials (7087 patients) met the inclusion criteria. The combined RR to achieve a therapeutic response to treatment with recommended doses of any anti-TNF alpha drug was 1.81 (95% CI 1.43 - 2.29) with a NNT of 5 (5 - 6) for ACR20. NNT for ACR50 [5 (5 - 6)] and ACR70 [7 (7 - 9)] were similar. Overall therapeutic effects were also similar regardless of the specific anti-TNF alpha drug used and when higher than recommended doses were administered. However, lower than recommended doses elicited low ACR70 responses (NNT 15). Comparison of anti-TNF alpha drugs plus methotrexate (MTX) with MTX alone in patients with insufficient prior responses to MTX showed NNT values of 3 for ACR20, 4 for ACR50 and 8 for ACR70. Comparison of anti-TNF alpha drugs with placebo showed a similar pattern. Comparisons of anti-TNF alpha drugs plus MTX with MTX alone in patients with no previous resistance to MTX showed somewhat lower effects. Etanercept and adalimumab administered as monotherapy showed effects similar to those of MTX. Side effects were more common among patients receiving anti-TNF alpha drugs than controls (overall combined NNH 27). Patients receiving infliximab were more likely to drop out because of side effects (NNH 24) and to suffer severe side effects (NNH 31), infections (NNH 10) and infusion reactions (NNH 9). Patients receiving adalimumab were also more likely to drop out because of side effects (NNH 47) and to suffer injection site reactions (NNH 22). Patients receiving etanercept were less likely to drop out because of side effects (NNH for control versus etanercept 26) but more likely to experience injection site reactions (NNH 5). Conclusion: Anti-TNF alpha drugs are effective in RA patients, with apparently similar results irrespective of the drug administered. Doses other than those recommended are also beneficial. The main factor influencing therapeutic efficacy is the prior response to DMARD treatment. The effect of treatment with etanercept or adalimumab does not differ from that obtained with MTX. The published safety profile for etanercept is superior but the fact that no patients are treated with higher than recommended doses requires explanation