Analysis of Friedreich's ataxia patient clinical data reveals importance of accurate GAA repeat determination in disease prognosis and gender differences in cardiac measures

Friedreich's ataxia (FRDA) is a rare autosomal recessive inherited neurodegenerative disease which is the result of a triplet repeat expansion in the intronic region of the frataxin FXN gene resulting in depleted frataxin protein expression. Disease onset is usually in childhood and causes progressive damage to the nervous system resulting in progressive disability. This work uses computer aided classification techniques to identify which measures of the disease progression, including accurate determination of the shortest allele repeat length, are the most informative when trying to predict likely disease progression and prognosis. Further we investigate the possibility of a gender difference in the progression of the disease. Our results highlight the importance of accurate determination GAA repeat length in any clinical predictions showing that the number of repeats is the best prognostic tool in FRDA and is strongly linked to the age at onset disease. Further that there are possible gender dependent differences in cardiac measurements recorded from patients of similar age of onset and GAA repeat length.EFACT

A post-mortem survey on end-of-life decisions using a representative sample of death certificates in Flanders, Belgium: research protocol

Background: Reliable studies of the incidence and characteristics of medical end-of-life decisions with a certain or possible life shortening effect (ELDs) are indispensable for an evidence-based medical and societal debate on this issue. This article presents the protocol drafted for the 2007 ELD Study in Flanders, Belgium, and outlines how the main aims and challenges of the study (i.e. making reliable incidence estimates of end-of-life decisions, even rare ones, and describing their characteristics; allowing comparability with past ELD studies; guaranteeing strict anonymity given the sensitive nature of the research topic; and attaining a sufficient response rate) are addressed in a post-mortem survey using a representative sample of death certificates. Study design: Reliable incidence estimates are achievable by using large at random samples of death certificates of deceased persons in Flanders (aged one year or older). This entails the cooperation of the appropriate administrative authorities. To further ensure the reliability of the estimates and descriptions, especially of less prevalent end-of-life decisions (e.g. euthanasia), a stratified sample is drawn. A questionnaire is sent out to the certifying physician of each death sampled. The questionnaire, tested thoroughly and avoiding emotionally charged terms is based largely on questions that have been validated in previous national and European ELD studies. Anonymity of both patient and physician is guaranteed through a rigorous procedure, involving a lawyer as intermediary between responding physicians and researchers. To increase response we follow the Total Design Method (TDM) with a maximum of three follow-up mailings. Also, a non-response survey is conducted to gain insight into the reasons for lack of response. Discussion: The protocol of the 2007 ELD Study in Flanders, Belgium, is appropriate for achieving the objectives of the study; as past studies in Belgium, the Netherlands, and other European countries have shown, strictly anonymous and thorough surveys among physicians using a large, stratified, and representative death certificate sample are most suitable in nationwide studies of incidence and characteristics of end-of-life decisions. There are however also some limitations to the study design

Heterogeneity of Microglial Activation in the Innate Immune Response in the Brain

The immune response in the brain has been widely investigated and while many studies have focused on the proinflammatory cytotoxic response, the brain’s innate immune system demonstrates significant heterogeneity. Microglia, like other tissue macrophages, participate in repair and resolution processes after infection or injury to restore normal tissue homeostasis. This review examines the mechanisms that lead to reduction of self-toxicity and to repair and restructuring of the damaged extracellular matrix in the brain. Part of the resolution process involves switching macrophage functional activation to include reduction of proinflammatory mediators, increased production and release of anti-inflammatory cytokines, and production of cytoactive factors involved in repair and reconstruction of the damaged brain. Two partially overlapping and complimentary functional macrophage states have been identified and are called alternative activation and acquired deactivation. The immunosuppressive and repair processes of each of these states and how alternative activation and acquired deactivation participate in chronic neuroinflammation in the brain are discussed

Combinatorial, additive and dose-dependent drug–microbiome associations

Data availability: The source data for the figures are provided at Zenodo (https://doi.org/10.5281/zenodo.4728981). Raw shotgun sequencing data that support the findings of this study have been deposited at the ENA under accession codes PRJEB41311, PRJEB38742 and PRJEB37249 with public access. Raw spectra for metabolomics have been deposited in the MassIVE database under the accession codes MSV000088043 (UPLC–MS/MS) and MSV000088042 (GC–MS). The metadata on disease groups and drug intake are provided in Supplementary Tables 1–3. The demographic, clinical and phenotype metadata, and processed microbiome and metabolome data for French, German and Danish participants are available at Zenodo (https://doi.org/10.5281/zenodo.4674360).Code availability: The new drug-aware univariate biomarker testing pipeline is available as an R package (metadeconfoundR; Birkner et al., manuscript in preparation) at Github (https://github.com/TillBirkner/metadeconfoundR) and at Zenodo (https://doi.org/10.5281/zenodo.4721078). The latest version (0.1.8) of this package was used to generate the data shown in this publication. The code used for multivariate analysis based on the VpThemAll package is available at Zenodo (https://doi.org/10.5281/zenodo.4719526). The phenotype and drug intake metadata, processed microbiome, and metabolome data and code resources are available for download at Zenodo (https://doi.org/10.5281/zenodo.4674360). The code for reproducing the figures is provided at Zenodo (https://doi.org/10.5281/zenodo.4728981).During the transition from a healthy state to cardiometabolic disease, patients become heavily medicated, which leads to an increasingly aberrant gut microbiome and serum metabolome, and complicates biomarker discovery1,2,3,4,5. Here, through integrated multi-omics analyses of 2,173 European residents from the MetaCardis cohort, we show that the explanatory power of drugs for the variability in both host and gut microbiome features exceeds that of disease. We quantify inferred effects of single medications, their combinations as well as additive effects, and show that the latter shift the metabolome and microbiome towards a healthier state, exemplified in synergistic reduction in serum atherogenic lipoproteins by statins combined with aspirin, or enrichment of intestinal Roseburia by diuretic agents combined with beta-blockers. Several antibiotics exhibit a quantitative relationship between the number of courses prescribed and progression towards a microbiome state that is associated with the severity of cardiometabolic disease. We also report a relationship between cardiometabolic drug dosage, improvement in clinical markers and microbiome composition, supporting direct drug effects. Taken together, our computational framework and resulting resources enable the disentanglement of the effects of drugs and disease on host and microbiome features in multimedicated individuals. Furthermore, the robust signatures identified using our framework provide new hypotheses for drug–host–microbiome interactions in cardiometabolic disease.This work was supported by the European Union’s Seventh Framework Program for research, technological development and demonstration under grant agreement HEALTH-F4-2012-305312 (METACARDIS). Part of this work was also supported by the EMBL, by the Metagenopolis grant ANR-11-DPBS-0001, by the H2020 European Research Council (ERC-AdG-669830) (to P.B.), and by grants from the Deutsche Forschungsgemeinschaft (SFB1365 to S.K.F. and L.M.; and SFB1052/3 A1 MS to M.S. (209933838)). Assistance Publique-Hôpitaux de Paris is the promoter of the clinical investigation (MetaCardis). M.-E.D. is supported by the NIHR Imperial Biomedical Research Centre and by grants from the French National Research Agency (ANR-10-LABX-46 (European Genomics Institute for Diabetes)), from the National Center for Precision Diabetic Medicine – PreciDIAB, which is jointly supported by the French National Agency for Research (ANR-18-IBHU-0001), by the European Union (FEDER), by the Hauts-de-France Regional Council (Agreement 20001891/NP0025517) and by the European Metropolis of Lille (MEL, Agreement 2019_ESR_11) and by Isite ULNE (R-002-20-TALENT-DUMAS), also jointly funded by ANR (ANR-16-IDEX-0004-ULNE), the Hauts-de-France Regional Council (20002845) and by the European Metropolis of Lille (MEL). R.J.A. is a member of the Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Bioscience. The Novo Nordisk Foundation Center for Basic Metabolic Research is an independent research institution at the University of Copenhagen partially funded by an unrestricted donation from the Novo Nordisk Foundation

Combinatorial, additive and dose-dependent drug–microbiome associations

During the transition from a healthy state to cardiometabolic disease, patients become heavily medicated, which leads to an increasingly aberrant gut microbiome and serum metabolome, and complicates biomarker discovery. Here, through integrated multi-omics analyses of 2,173 European residents from the MetaCardis cohort, we show that the explanatory power of drugs for the variability in both host and gut microbiome features exceeds that of disease. We quantify inferred effects of single medications, their combinations as well as additive effects, and show that the latter shift the metabolome and microbiome towards a healthier state, exemplified in synergistic reduction in serum atherogenic lipoproteins by statins combined with aspirin, or enrichment of intestinal Roseburia by diuretic agents combined with beta-blockers. Several antibiotics exhibit a quantitative relationship between the number of courses prescribed and progression towards a microbiome state that is associated with the severity of cardiometabolic disease. We also report a relationship between cardiometabolic drug dosage, improvement in clinical markers and microbiome composition, supporting direct drug effects. Taken together, our computational framework and resulting resources enable the disentanglement of the effects of drugs and disease on host and microbiome features in multimedicated individuals. Furthermore, the robust signatures identified using our framework provide new hypotheses for drug–host–microbiome interactions in cardiometabolic disease

Attitudes and practices of physicians regarding physician-assisted dying in minors

Objective: To investigate attitudes towards physician-assisted death in minors among all physicians involved in the treatment of children dying in Flanders, Belgium over an 18-month period, and how these are related to actual medical end-of-life practices. Design: Anonymous population-based postmortem physician survey. Setting: Flanders, Belgium. Participants: Physicians signing death certificates of all patients aged 1-17 years who died between June 2007 and November 2008. Main outcome measures: Attitudes towards physician-assisted death in minors and actual end-of-life practices in the deaths concerned. Results: 124 physicians for 70.5% of eligible cases (N=149) responded. 69% favour an extension of the Belgian law on euthanasia to include minors, 26.6% think this should be done by establishing clear age limits and 61% think parental consent is required before taking life-shortening decisions. Cluster analysis yielded a cluster (67.7% of physicians) accepting of, and a cluster (32.2% of physicians) reluctant towards physician-assisted death in minors. Controlling for physician specialty and patient characteristics, acceptant physicians were more likely to engage in practices with the intention of shortening a patient's life than were reluctant physicians. Conclusion: A majority of surveyed Flemish physicians appear to accept physician-assisted dying in children under certain circumstances and favour an amendment to the euthanasia law to include minors. The approach favoured is one of assessing decision-making capacity rather than setting arbitrary age limits. These stances, and their connection with actual end-of-life practices, may encourage policy-makers to develop guidelines for medical end-of-life practices in minors that address specific challenges arising in this patient group