Proteomic analyses identify targets, pathways, and cellular consequences of oncogenic KRAS signaling.

Mutations that activate the small GTPase KRAS are a frequent genetic alteration in cancer, and drug discovery efforts have led to inhibitors that block KRAS activity. We sought to better understand oncogenic KRAS signaling and the cytostatic effects of drugs that target this system. We performed proteomic analyses to investigate changes in protein abundance and posttranslational modifications in inhibitor-treated human KRAS-mutant pancreatic (KRAS G12C and G12D) and lung cancer (KRAS G12C) cells.

Proteomic Diversity in Bacteria: Insights and Implications for Bacterial Identification.

Mass spectrometry-based proteomics has revolutionized bacterial identification and elucidated many molecular mechanisms underlying bacterial growth, community formation, and drug resistance. However, most research has been focused on a few model bacteria, overlooking bacterial diversity. In this study, we present the most extensive bacterial proteomic resource to date, covering 303 species, 119 genera, and five phyla with over 636,000 unique expressed proteins, confirming the existence of over 38,700 hypothetical proteins.

Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response.

The DNA-damaging agent Gemcitabine (GEM) is a first-line treatment for pancreatic cancer, but chemoresistance is frequently observed. Several clinical trials investigate the efficacy of GEM in combination with targeted drugs, including kinase inhibitors, but the experimental evidence for such rationale is often unclear. Here, we phenotypically screened 13 human pancreatic adenocarcinoma (PDAC) cell lines against GEM in combination with 146 clinical inhibitors and observed strong synergy for the ATR kinase inhibitor Elimusertib in most cell lines.

PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways.

Post-translational modifications (PTMs) play pivotal roles in regulating cellular signaling, fine-tuning protein function, and orchestrating complex biological processes. Despite their importance, the lack of comprehensive tools for studying PTMs from a pathway-centric perspective has limited our ability to understand how PTMs modulate cellular pathways on a molecular level. Here, we present PTMNavigator, a tool integrated into the ProteomicsDB platform that offers an interactive interface for researchers to overlay experimental PTM data with pathway diagrams.

A convergent mixed methods to study registration on kidney transplantation waiting list refusal by women and men on dialysis in France.

Not all patients on dialysis want to be registered on the kidney transplantation (KT) waiting list and undergo transplantation. The aim of this convergent mixed methods study was to determine the features of patients refusing to be registered on the KT waiting list and the reasons. Quantitative data on all 2017-2019 incident 18-85-year-old dialysis patients, eligible for KT, were extracted from the REIN registry in France.

High-fidelity color characterization in virtual reality across head mounted displays, game engines, and materials.

We present a comprehensive colorimetric analysis of three head mounted displays (HMDs) - HTC Vive Pro Eye, Pimax 8K X DMAS, and Varjo Aero - focusing on their color calibration and uniformity across different game engines (Unity and Unreal) and for different materials/shaders. We developed a robust methodology combining hardware and software tools, including spectroradiometry and imaging colorimetry, to characterize and calibrate these HMDs for accurate color reproduction. The study showcases substantial advancements in colorimetric accuracy, with a reduction in the average deltaE00 of 90 or more across all tested HMDs and conditions.

Parallel ecological and evolutionary responses to selection in a natural bacterial community.

Evolution can occur over ecological timescales, suggesting a potentially important role for rapid evolution in shaping community trait distributions. However, evidence of concordant eco-evolutionary dynamics often comes from in vitro studies of highly simplified communities, and measures of ecological and evolutionary dynamics are rarely directly comparable. Here, we quantified how ecological species sorting and rapid evolution simultaneously shape community trait distributions by tracking within- and between-species changes in a key trait in a complex bacterial community.

Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics.

Lysine deacetylase inhibitors (KDACis) are approved drugs for cutaneous T cell lymphoma (CTCL), peripheral T cell lymphoma (PTCL), and multiple myeloma, but many aspects of their cellular mechanism of action (MoA) and substantial toxicity are not well understood. To shed more light on how KDACis elicit cellular responses, we systematically measured dose-dependent changes in acetylation, phosphorylation, and protein expression in response to 21 clinical and pre-clinical KDACis. The resulting 862,000 dose-response curves revealed, for instance, limited cellular specificity of histone deacetylase (HDAC) 1, 2, 3, and 6 inhibitors; strong cross-talk between acetylation and phosphorylation pathways; localization of most drug-responsive acetylation sites to intrinsically disordered regions (IDRs); an underappreciated role of acetylation in protein structure; and a shift in EP300 protein abundance between the cytoplasm and the nucleus.

Lower access to kidney transplantation for women in France is not explained by comorbidities and social deprivation.

Background: Access to kidney transplantation (KT) remains challenging for patients with end-stage kidney disease. This study assessed women's access to KT in France by considering comorbidities and neighbourhood social deprivation.

Methods: All incident patients 18-85 years old starting dialysis in France between 1 January 2017 and 31 December 2019 were included.

Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics.

Kinase inhibitors (KIs) are important cancer drugs but often feature polypharmacology that is molecularly not understood. This disconnect is particularly apparent in cancer entities such as sarcomas for which the oncogenic drivers are often not clear. To investigate more systematically how the cellular proteotypes of sarcoma cells shape their response to molecularly targeted drugs, we profiled the proteomes and phosphoproteomes of 17 sarcoma cell lines and screened the same against 150 cancer drugs.

CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose-response curves.

Dose-response curves are key metrics in pharmacology and biology to assess phenotypic or molecular actions of bioactive compounds in a quantitative fashion. Yet, it is often unclear whether or not a measured response significantly differs from a curve without regulation, particularly in high-throughput applications or unstable assays. Treating potency and effect size estimates from random and true curves with the same level of confidence can lead to incorrect hypotheses and issues in training machine learning models.

[Health care provision].

On the occasion of the 20th anniversary of the REIN (French Renal Epidemiology and Information Network), a summary work on the contributions of the French national ESKD register was carried out. On the issue of healthcare provision, the following key messages were retained. France offers diversified, local healthcare that adapts to the patients’ needs with several additional players (public, university, lucrative private, solidarity private).

Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes.

Bacteria are the most abundant and diverse organisms among the kingdoms of life. Due to this excessive variance, finding a unified, comprehensive, and safe workflow for quantitative bacterial proteomics is challenging. In this study, we have systematically evaluated and optimized sample preparation, mass spectrometric data acquisition, and data analysis strategies in bacterial proteomics.

The ecology of scale: impact of volume on coalescence and function in methanogenic communities.

Engineered ecosystems span multiple volume scales, from a nano-scale to thousands of cubic metres. Even the largest industrial systems are tested in pilot scale facilities. But does scale affect outcomes? Here we look at comparing different size laboratory anaerobic fermentors to see if and how the volume of the community affects the outcome of community coalescence (combining multiple communities) on community composition and function.

Decrypting drug actions and protein modifications by dose- and time-resolved proteomics.

Although most cancer drugs modulate the activities of cellular pathways by changing posttranslational modifications (PTMs), little is known regarding the extent and the time- and dose-response characteristics of drug-regulated PTMs. In this work, we introduce a proteomic assay called decryptM that quantifies drug-PTM modulation for thousands of PTMs in cells to shed light on target engagement and drug mechanism of action. Examples range from detecting DNA damage by chemotherapeutics, to identifying drug-specific PTM signatures of kinase inhibitors, to demonstrating that rituximab kills CD20-positive B cells by overactivating B cell receptor signaling.

Women's Access to Kidney Transplantation in France: A Mixed Methods Research Protocol.

Kidney transplantation is the best renal replacement therapy (medically and economically) for eligible patients with end-stage kidney disease. Studies in some French regions and in other countries suggest a lower access to the kidney transplant waiting listing and also to kidney transplantation, once waitlisted, for women. Using a mixed methods approach, this study aims to precisely understand these potential sex disparities and their causes.

Functional representation of the network organisation of dialysis activities in France: A novel level for assessing quality of care.

To assess quality of care, groups of care units that cared for the same patients at various stages of end-stage renal disease, might be more appropriate than the centre level. These groups constitute "communities" that need to be delineated to evaluate their practices and outcomes. In this article, we describe the use of an agglomerative (Fast Greedy) and a divisive (Edge Betweenness) method to describe dialysis activities in France.

The new French kidney allocation system for donations after brain death: Rationale, implementation, and evaluation.

In recent decades, the allocation policies of many countries have moved from center-based to patient-based approaches. The new French kidney allocation system (KAS) of donations after brain death for adult recipients, implemented in 2015, was principally designed to introduce a unified allocation score (UAS) to be applied locally for one kidney and nationally for the other and to replace regional borders by a new geographical model. The new KAS balances dialysis duration and waiting time to compensate for listing delays and provides more effective longevity matching between donors and recipients with better HLA and age matching.

Mass spectrometry-based draft of the mouse proteome.

The laboratory mouse ranks among the most important experimental systems for biomedical research and molecular reference maps of such models are essential informational tools. Here, we present a quantitative draft of the mouse proteome and phosphoproteome constructed from 41 healthy tissues and several lines of analyses exemplify which insights can be gleaned from the data. For instance, tissue- and cell-type resolved profiles provide protein evidence for the expression of 17,000 genes, thousands of isoforms and 50,000 phosphorylation sites in vivo.

France's New Lung Transplant Allocation System: Combining Equity With Proximity by Optimizing Geographic Boundaries Through the Supply/Demand Ratio.

A new lung allocation system was introduced in France in September 2020. It aimed to reduce geographic disparities in lung allocation while maintaining proximity. In the previous two-tiered priority-based system, grafts not allocated through national high-urgency status were offered to transplant centres according to geographic criteria.

Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides.

The prediction of fragment ion intensities and retention time of peptides has gained significant attention over the past few years. However, the progress shown in the accurate prediction of such properties focused primarily on unlabeled peptides. Tandem mass tags (TMT) are chemical peptide labels that are coupled to free amine groups usually after protein digestion to enable the multiplexed analysis of multiple samples in bottom-up mass spectrometry.