Albiglutide and cardiovascular outcomes in patients with type 2 diabetes and cardiovascular disease (Harmony Outcomes): a double-blind, randomised placebo-controlled trial

Background: Glucagon-like peptide 1 receptor agonists differ in chemical structure, duration of action, and in their effects on clinical outcomes. The cardiovascular effects of once-weekly albiglutide in type 2 diabetes are unknown. We aimed to determine the safety and efficacy of albiglutide in preventing cardiovascular death, myocardial infarction, or stroke. Methods: We did a double-blind, randomised, placebo-controlled trial in 610 sites across 28 countries. We randomly assigned patients aged 40 years and older with type 2 diabetes and cardiovascular disease (at a 1:1 ratio) to groups that either received a subcutaneous injection of albiglutide (30–50 mg, based on glycaemic response and tolerability) or of a matched volume of placebo once a week, in addition to their standard care. Investigators used an interactive voice or web response system to obtain treatment assignment, and patients and all study investigators were masked to their treatment allocation. We hypothesised that albiglutide would be non-inferior to placebo for the primary outcome of the first occurrence of cardiovascular death, myocardial infarction, or stroke, which was assessed in the intention-to-treat population. If non-inferiority was confirmed by an upper limit of the 95% CI for a hazard ratio of less than 1·30, closed testing for superiority was prespecified. This study is registered with ClinicalTrials.gov, number NCT02465515. Findings: Patients were screened between July 1, 2015, and Nov 24, 2016. 10 793 patients were screened and 9463 participants were enrolled and randomly assigned to groups: 4731 patients were assigned to receive albiglutide and 4732 patients to receive placebo. On Nov 8, 2017, it was determined that 611 primary endpoints and a median follow-up of at least 1·5 years had accrued, and participants returned for a final visit and discontinuation from study treatment; the last patient visit was on March 12, 2018. These 9463 patients, the intention-to-treat population, were evaluated for a median duration of 1·6 years and were assessed for the primary outcome. The primary composite outcome occurred in 338 (7%) of 4731 patients at an incidence rate of 4·6 events per 100 person-years in the albiglutide group and in 428 (9%) of 4732 patients at an incidence rate of 5·9 events per 100 person-years in the placebo group (hazard ratio 0·78, 95% CI 0·68–0·90), which indicated that albiglutide was superior to placebo (p<0·0001 for non-inferiority; p=0·0006 for superiority). The incidence of acute pancreatitis (ten patients in the albiglutide group and seven patients in the placebo group), pancreatic cancer (six patients in the albiglutide group and five patients in the placebo group), medullary thyroid carcinoma (zero patients in both groups), and other serious adverse events did not differ between the two groups. There were three (<1%) deaths in the placebo group that were assessed by investigators, who were masked to study drug assignment, to be treatment-related and two (<1%) deaths in the albiglutide group. Interpretation: In patients with type 2 diabetes and cardiovascular disease, albiglutide was superior to placebo with respect to major adverse cardiovascular events. Evidence-based glucagon-like peptide 1 receptor agonists should therefore be considered as part of a comprehensive strategy to reduce the risk of cardiovascular events in patients with type 2 diabetes. Funding: GlaxoSmithKline

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

A literature review and database of how the primary KIT/PDGFRA variant of a gastrointestinal stromal tumour predicts for sensitivity to imatinib

It is well recognized that the primary KIT or PDGFRA variant of a gastrointestinal stromal tumour (GIST) can predict sensitivity to imatinib. However, these data are currently spread across a wide range of publications and have not been collated as one reference. A broad-ranging literature search was therefore performed to assemble such a database which should help optimize imatinib-based management of GIST patients henceforth. Having excluded wild type GISTs and results for imatinib used as adjuvant therapy, 79 publications (dated August 2001 to March 2022) underwent data extraction. These data on imatinib sensitivity were either derived from in vitro studies, predicted by in silico analysis or based on in vivo clinical patient response. Data interpretation carried some caveats: there was a potential for replication of patient-derived data between older and new publications; only predicted protein sequences were presented; the criteria used to record clinical response were not uniform across all publications; and imatinib dosage could vary between different clinical publications. However, these data showed broad agreement of imatinib sensitivity amongst similar subtypes of KIT or PDGFRA variant. There was also agreement between in vivo versus in vitro/in silico derived sensitivity data for most variants when both data types were available.</p

Vesicle transport in chloroplasts with emphasis on Rab proteins

Chloroplasts perform photosynthesis using PSI and PSII during its light-dependent phase. Inside the chloroplast there is a membrane called thylakoid. The thylakoid membranes are an internal system of interconnected membranes that carry out the light reactions of photosynthesis. The thylakoid membranes do not produce their own lipids or proteins, so they are mainly transported from the envelope to the thylakoid for maintenance of e.g. the photosynthetic apparatus. An aqueous stroma made hinder between the envelope and thylakoid for the lipids to move between the two compartments. Vesicle transport is suggested to transport lipids to thylakoids supported by biochemical and ultra-structural data. Proteins could potentially also be transported by vesicles as cargo but this is not supported yet experimentally. However, proteins targeted to thylakoids are mediated by four pathways so far identified but it has been proposed that a vesicle transport could exist for proteins targeted to thylakoids as well similar to the cytosolic vesicle transport system. This thesis revealed similarity of vesicle transport inside the chloroplast to the cytosolic system. A novel Rab protein CPRabA5E (CP= chloroplast localized) was shown in Arabidopsis to be chloroplast localized and characterized to be important for thylakoid structure, plant development, and oxidative stress response. Moreover, CPRabA5e complemented the yeast homologues being involved in vesicle transport, and the cprabA5e mutants were affected for vesicle formation in the chloroplasts. Another Rab (CPRabF1) was also identified inside the chloroplast and could possibly play a role in vesicle transport. Interestingly, CPRabF1 has previously been characterized for its involvement in vesicle transport in the cytosol and thus its localization in chloroplasts might indicate dual targeting of CPRabF1. No phenotype was observed despite usage of several applied factors e.g. high light and osmotic stress. A previous bioinformatics study predicted several Rab related proteins inside chloroplasts linked to a suggested COPII vesicle transport system. We analyzed the gene expression for the Rab related genes at several developmental stages covering the life span of Arabidopsis e.g. from seedlings to senescence. The data indicated a rather homogenous expression pattern among the genes studied being around 20-60% expressed for all developmental stages except for senescence were the expression pattern was more discrete. At senescence chloroplast degradation occurs indicating less need for vesicle components. The idea of a COPII vesicle system inside chloroplast raised the question of a COPI or clathrin coated vesicle (CCV) system in chloroplasts. Through a bioinformatics approach we found several homologues of cytosolic COPI and CCV related vesicle transport components inside chloroplast. However, many of them already had a clear function other than vesicle transport or were having an unknown function. Moreover, many necessary subunits to build a functional COPI and CCV system were not even identified to be chloroplast localized and so we concluded that vesicle transport in chloroplast do not have strong similarities with a COPI or CCV system, rather being more linked to a COPII system as recently suggested

Involvement of the Electrophilic Isothiocyanate Sulforaphane in Arabidopsis Local Defense Responses

Plants defend themselves against microbial pathogens through a range of highly sophisticated and integrated molecular systems. Recognition of pathogen-secreted effector proteins often triggers the hypersensitive response (HR), a complex multicellular defense reaction where programmed cell death (PCD) of cells surrounding the primary site of infection is a prominent feature. Even though the HR was described almost a century ago, cell to cell factors acting at the local level generating the full defense reaction has remained obscure. In this study, we sought to identify diffusible molecules produced during the HR that could induce cell death in naïve tissue. We found that 4-methylsulfinylbutyl isothiocyanate (sulforaphane) is released by Arabidopsis thaliana leaf tissue undergoing HR, and that this compound induces cell death as well as prime defense in naïve tissue. Two different mutants impaired in the pathogen-induced accumulation of sulforaphane displayed attenuated PCD upon bacterial and oomycete effector recognition as well as decreased resistance to several isolates of the plant pathogen Hyaloperonospora arabidopsidis. Treatment with sulforaphane provided protection against a virulent H. arabidopsidis isolate. Glucosinolate breakdown products are recognized as antifeeding compounds towards insects and recently also as intracellular signaling and bacteriostatic molecules in Arabidopsis. The data presented herein indicate that these compounds also trigger local defense responses in Arabidopsis tissue