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. The resulting 2550 phenotypic profiles revealed distinct drug responses and the cellular activity landscapes derived from deep (phospho)proteomes (9-10,000 proteins and 10-27,000 phosphorylation sites per cell line) enabled several lines of analysis. For instance, connecting the (phospho)proteomic data with drug responses revealed known and novel mechanisms of action (MoAs) of KIs and identified markers of drug sensitivity or resistance. All data is publicly accessible via an interactive web application that enables exploration of this rich molecular resource for a better understanding of active signalling pathways in sarcoma cells, identifying treatment response predictors and revealing novel MoA of clinical KIs.

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 neighborhood social deprivation. METHODS: All incident 18-85-year-old patients starting dialysis in France between January 1, 2017 and December 31, 2019 were included. Three outcomes were assessed: (i) access to the KT waiting list after dialysis start, (ii) KT access after waitlisting, and (iii) KT access after dialysis start. Cox and Fine and Gray models were used. Gender-EDI and gender-age interactions were tested and analyses were performed among strata if required. RESULTS: 29,395 patients were included (35% of women). After adjusting for social deprivation and comorbidities, women were less likely to be waitlisted at 1 (adjHR: 0.91 [0.87-0.96]) and 3 years (adjHR: 0.87 [0.84-0.91]) post-dialysis initiation. This disparity concerned mainly ≥60-year-old women (adjHR: 0.76 [0.71-0.82] at 1 year and 0.75 [0.71-0.81] at 3 years). Access to KT, after 2 years of waitlisting was similar between genders. Access to KT was similar between genders at 3 years after dialysis start, but decreased for women after 4 years (adjHR: 0.93 [0.88-0.99]) and longer follow-up (adjHR: 0.90 [0.85-0.96]). CONCLUSIONS: In France, women are less likely to be waitlisted and undergo kidney transplantation. This is driven by the ≥60-year-old group and is not explained by comorbidities or social deprivation level.

Experience of Chronic Kidney Disease and Perceptions of Transplantation by Sex.

Importance: The pathway to kidney transplantation (KT) begins with the patient's acceptance of this surgical procedure after discussion with the nephrologist. The patients' perceptions of the disease and of KT may influence their willingness to undergo transplantation. Objective: To describe patients' experiences of kidney disease and their perceptions of KT and the nephrologists' perceptions of the patient experience. Design, Setting, and Participants: This qualitative study collected data through semistructured interviews with patients with chronic kidney disease and nephrologists in the Bretagne, Île-de-France and Normandie regions, France. Researchers involved in the study in each region purposely selected 99 patients with chronic kidney disease who initiated dialysis in 2021, based on their age, sex, dialysis facility ownership, and also 45 nephrologists, based on their sex and years of experience. Data analysis was performed from January to October 2023. Main Outcomes and Measures: Themes were identified using inductive thematic analysis. Specific characteristics of men and women as well as the nephrologist's views for each theme were described. Results: This study included 42 men and 57 women (56 [57%] aged 60 years or older) who started dialysis in 2021 and 45 nephrologists (23 women and 22 men). Six major themes were identified: (1) burden of chronic kidney disease on patients and their families, (2) health care professional-patient relationship and other factors that modulate chronic kidney disease acceptance, (3) dialysis perceived as a restrictive treatment, (4) patients' representation of the kidney graft, (5) role of past experiences in KT perception, and (6) dualistic perception of KT. In some cases, women and nephrologists indicated that women's perceptions and experiences were different than men's; for example, the disease's psychological impact and the living donor KT refusal were mainly reported by 8 women. Conclusions and Relevance: Patients' past experience of chronic kidney disease in general and of KT in particular, as well as their relationship with their family and nephrologist, were substantial determinants of KT perception in this qualitative study. Targeted policies on these different factors might help to improve access to KT, and more research is needed to understand whether there are sex-based disparities.

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. This comprehensive dataset serves as a resource for the investigation of the molecular mechanisms underlying KDACi action in cells and can be interactively explored online in ProteomicsDB.

Multiple air pollutant exposure is associated with higher risk of all-cause mortality in dialysis patients: a French registry-based nationwide study.

Background: Little is known about the effect of combined exposure to different air pollutants on mortality in dialysis patients. This study aimed to investigate the association of multiple exposures to air pollutants with all-cause and cause-specific death in dialysis patients. Materials and methods: This registry-based nationwide cohort study included 90,373 adult kidney failure patients initiating maintenance dialysis between 2012 and 2020 identified from the French REIN registry. Estimated mean annual municipality levels of PM2.5, PM10, and NO2 between 2009 and 2020 were combined in different composite air pollution scores to estimate each participant's exposure at the residential place one to 3 years before dialysis initiation. Adjusted cause-specific Cox proportional hazard models were used to estimate hazard ratios (HRs) per interquartile range (IQR) greater air pollution score. Effect measure modification was assessed for age, sex, dialysis care model, and baseline comorbidities. Results: Higher levels of the main air pollution score were associated with a greater rate of all-cause deaths (HR, 1.082 [95% confidence interval (CI), 1.057-1.104] per IQR increase), regardless of the exposure lag. This association was also confirmed in cause-specific analyses, most markedly for infectious mortality (HR, 1.686 [95% CI, 1.470-1.933]). Sensitivity analyses with alternative composite air pollution scores showed consistent findings. Subgroup analyses revealed a significantly stronger association among women and fewer comorbid patients. Discussion: Long-term multiple air pollutant exposure is associated with all-cause and cause-specific mortality among patients receiving maintenance dialysis, suggesting that air pollution may be a significant contributor to the increasing trend of CKD-attributable mortality worldwide.

Social Deprivation and Incidence of Pediatric Kidney Failure in France.

Introduction: Approximately 8 per million children and young adults aged < 20 years initiate kidney replacement therapy (KRT) per year in France. We hypothesize that social deprivation could be a determinant of childhood-onset kidney failure. The objective of this study was to estimate the incidence of pediatric KRT in France according to the level of social deprivation. Methods: All patients < 20 years who initiated KRT from 2010 to 2015 in metropolitan France were included. Data were collected from the comprehensive French registry of KRT French Renal Epidemiology and Information network (REIN). We used a validated ecological index to assess social deprivation, the 2011 French version of the European Deprivation Index (EDI). We estimated the age standardized incidence rates according to the quintiles of EDI using direct standardization and incidence rate ratio using Poisson regression. Results: We included 672 children with kidney failure (58.6% males, 30.7% with glomerular or vascular disease, 43.3% starting KRT between 11 and 17 years). 38.8% were from the most deprived areas (quintile 5 of EDI). The age standardized incidence rate increased with quintile of EDI, from 5.45 (95% confidence interval [CI] = 4.25-6.64) per million children per year in the least deprived quintile to 8.46 (95% CI = 7.41-9.51) in the most deprived quintile of EDI (incidence rates ratio Q5 vs. Q1 1.53-fold; 95% CI = 1.18-2.01). Conclusion: This study showed that even in a country with a universal health care system, there is a strong association between the incidence of pediatric KRT and social deprivation showing that social health inequalities appear from KRT initiation. This study highlights the need to look further into social inequalities in the earliest stage of chronic kidney disease (CKD).