Tumour-associated antigenic peptides are present in the HLA class I ligandome of cancer cell line derived extracellular vesicles

Funding: Breast Cancer Now (Grant Number(s): 2018JulPR1086), Wellcome Trust (GrantNumber(s): 105621/Z/14/Z), Melville Charitable Trust.The recent success of monoclonal antibody checkpoint inhibitor therapies that enhance the ability of CD8+ T cells to detect cancer-related antigenic peptides has refocused the need to fully understand the repertoire of peptides being presented to the immune system. Whilst the peptide ligandome presented by cell surface human leucocyte antigen class I (HLA-I) molecules on cancer cells has been studied extensively, the ligandome of extracellular vesicles (EVs) remains poorly defined. Here we report the HLA-I ligandome of both the cell surface and EVs from eight breast cancer cell lines (MCF7, MDA-MB-231, MDA-MB-361, MDA-MB-415, MDA-MB-453, HCC 1806, HCC 1395, and HCC 1954), and additionally the melanoma cell line ESTDAB-056 and the multiple myeloma line RPMI 8226. Utilising HLA-I immunoisolation and mass spectrometry, we detected a total of 6574 peptides from the cell surface and 2461 peptides from the EVs of the cell lines studied. Within the EV HLA-I ligandome, we identified 150 peptides derived from tumour associated antigenic proteins, of which 19 peptides have been shown to elicit T cell responses in previous studies. Our data thus shows the prevalence of clinically relevant tumour-associated antigenic peptides in the HLA-I ligandome presented on EV.Publisher PDFPeer reviewe

Effects of personal characteristics on serum CA125, mesothelin, and HE4 levels in healthy postmenopausal women at high-risk for ovarian cancer.

OBJECTIVE: To evaluate if serum levels of candidate ovarian cancer biomarkers vary with individual characteristics of healthy women who are likely candidates for an ovarian cancer screening program. METHODS: We analyzed serum CA125, mesothelin, and HE4 levels in a sample of 155 healthy postmenopausal women at increased risk for developing ovarian cancer based on personal and family cancer history. Information on reproductive, family and medical histories, lifestyle factors, and anthropometry was collected by self-report. Twenty-two factors were examined using univariate and multiple linear regression models for the three biomarker levels. RESULTS: In the multivariate models, CA125 levels were significantly higher in women who had used talcum powder (P = 0.02) and were lower in women who were parous (P = 0.05). Mesothelin levels were significantly higher in older women (P = 0.01) and lower in heavier women (P = 0.03). HE4 levels were higher in older women (P = 0.001) and in women who began menstruating at an older age (P = 0.03). CONCLUSIONS: CA125, mesothelin, and HE4 levels in healthy, postmenopausal women at increased risk for ovarian cancer are significantly associated with a few ovarian cancer risk factors. Since the effects of these personal characteristics on these serum markers are not large, their incorporation in screening algorithms may be unnecessary. This is true especially if a longitudinal algorithm is used because the marker level at the previous screen reflects personal characteristics such as age, body mass index, and age of menarche. Understanding the influence of personal factors on levels of novel early detection markers in healthy, unaffected women may have clinical utility in interpreting biomarker levels

Ground Support Software for Spaceborne Instrumentation

ION is a system of ground support software for the ion and neutral mass spectrometer (INMS) instrument aboard the Cassini spacecraft. By incorporating commercial off-the-shelf database, Web server, and Java application components, ION offers considerably more ground-support-service capability than was available previously. A member of the team that operates the INMS or a scientist who uses the data collected by the INMS can gain access to most of the services provided by ION via a standard pointand click hyperlink interface generated by almost any Web-browser program running in almost any operating system on almost any computer. Data are stored in one central location in a relational database in a non-proprietary format, are accessible in many combinations and formats, and can be combined with data from other instruments and spacecraft. The use of the Java programming language as a system-interface language offers numerous capabilities for object-oriented programming and for making the database accessible to participants using a variety of computer hardware and software

Gut Microbiome Dysbiosis in Antibiotic-Treated COVID-19 Patients is Associated with Microbial Translocation and Bacteremia

Although microbial populations in the gut microbiome are associated with COVID-19 severity, a causal impact on patient health has not been established. Here we provide evidence that gut microbiome dysbiosis is associated with translocation of bacteria into the blood during COVID-19, causing life-threatening secondary infections. We first demonstrate SARS-CoV-2 infection induces gut microbiome dysbiosis in mice, which correlated with alterations to Paneth cells and goblet cells, and markers of barrier permeability. Samples collected from 96 COVID-19 patients at two different clinical sites also revealed substantial gut microbiome dysbiosis, including blooms of opportunistic pathogenic bacterial genera known to include antimicrobial-resistant species. Analysis of blood culture results testing for secondary microbial bloodstream infections with paired microbiome data indicates that bacteria may translocate from the gut into the systemic circulation of COVID-19 patients. These results are consistent with a direct role for gut microbiome dysbiosis in enabling dangerous secondary infections during COVID-19

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

Development and validation of outcome prediction models for aneurysmal subarachnoid haemorrhage:the SAHIT multinational cohort study

Objective To develop and validate a set of practical prediction tools that reliably estimate the outcome of subarachnoid haemorrhage from ruptured intracranial aneurysms (SAH). Design Cohort study with logistic regression analysis to combine predictors and treatment modality. Setting Subarachnoid Haemorrhage International Trialists' (SAHIT) data repository, including randomised clinical trials, prospective observational studies, and hospital registries. Participants Researchers collaborated to pool datasets of prospective observational studies, hospital registries, and randomised clinical trials of SAH from multiple geographical regions to develop and validate clinical predicti

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

Schizophrenia-associated somatic copy-number variants from 12,834 cases reveal recurrent NRXN1 and ABCB11 disruptions

While germline copy-number variants (CNVs) contribute to schizophrenia (SCZ) risk, the contribution of somatic CNVs (sCNVs)—present in some but not all cells—remains unknown. We identified sCNVs using blood-derived genotype arrays from 12,834 SCZ cases and 11,648 controls, filtering sCNVs at loci recurrently mutated in clonal blood disorders. Likely early-developmental sCNVs were more common in cases (0.91%) than controls (0.51%, p = 2.68e−4), with recurrent somatic deletions of exons 1–5 of the NRXN1 gene in five SCZ cases. Hi-C maps revealed ectopic, allele-specific loops forming between a potential cryptic promoter and non-coding cis-regulatory elements upon 5′ deletions in NRXN1. We also observed recurrent intragenic deletions of ABCB11, encoding a transporter implicated in anti-psychotic response, in five treatment-resistant SCZ cases and showed that ABCB11 is specifically enriched in neurons forming mesocortical and mesolimbic dopaminergic projections. Our results indicate potential roles of sCNVs in SCZ risk

The Role of the Tbx5 Paralogues during Pectoral Fin Development in Zebrafish

The transcription factor Tbx5 is necessary for development of the forelimb and closely linked with the evolution of this limb. Loss of just one copy of TBX5 in humans is associated with Holt-Oram Syndrome (HOS), which manifests as defects in both the forelimb and the heart. In zebrafish, tbx5 was duplicated during the teleost specific whole-genome duplication, and zebrafish therefore have two copies of tbx5: tbx5a and tbx5b. In the pectoral fins of wildtype embryos, the cells of the fin field migrate away from the somites along the mediolateral (ML) axis and converge along the anterio-posterior (AP) axis. Tbx5a regulates the AP convergence of these cells during fin field migration by controlling expression of fgf24 in a subset of the fin field cues. Therefore, loss of Tbx5a results in embryos lacking pectoral fins. Tbx5b-deficient embryos form small pectoral fins, through unknown mechanisms. In this dissertation, I aim to characterize the role of tbx5b during zebrafish development, particularly during pectoral fin development, and compare to the known functions of tbx5a. These comparisons will provide insight into the fate of duplicated genes in the zebrafish. All previous work on the role of tbx5b has been performed in Tbx5b-deficient embryos generated via morpholino. In order to confirm that the morpholino accurately recapitulates the mutant phenotype, I first created and characterized a mutant for tbx5b. The tbx5b -/- embryos phenocopy the previously described Tbx5b-deficient embryos in both the heart and the pectoral fin defects. Further analysis of tbx5b -/- pectoral fins reveals that in addition to the small size when compared to same-stage wildtype fins, tbx5b -/- pectoral fins lack some anterior structures of the fin, which is similar to the limb defects seen in HOS patients. In order to identify the different transcriptional networks of embryos deficient in the tbx5 paralogues, whole-embryo RNA sequencing was performed in wildtype embryos and embryos lacking the tbx5 paralogues during the stages of pectoral fin development. Loss of the tbx5 paralogues, in particular tbx5b, resulted in changes to gene expression in the intermediate mesoderm, the somites, and the yolk syncytial layer, which may be sources of signaling cues during the migration processes of the cells of the fin field, due to their proximity to the migrating cells. Furthermore, loss of the tbx5 paralogues produced morphological changes in both the vasculature and the somites. To understand how loss of tbx5b could result in a small fin, I performed cell tracking analysis in the fin field of Tbx5b-deficient embryos and compared this data to previously collected data on the dynamics of the cells of the fin field in both wildtype and Tbx5a- deficient embryos. Normal fin field migration involves both an AP convergence movement and a ML migration. In Tbx5a-deficient embryos, the signaling molecule Fgf24 is no longer present, resulting in a lack of AP convergence, although ML migration is unaffected. In Tbx5b-deficient embryos, there are mild defects in AP convergence, likely due to a decrease in the levels of fgf24 expression. The anterior cells are most strongly affected by loss of Tbx5b, which may explain the anterior defects seen in Tbx5b-deficient fins. Additionally, in Tbx5b-deficient embryos, there is no net ML migration of the fin field. Furthermore, the double-deficient embryos display defects in both AP convergence and ML migration. Overall, this dissertation expands the knowledge on the role of the tbx5 paralogues in zebrafish during migration of the cells of the fin field. Loss of the tbx5 paralogues results in changes in surrounding tissues, illustrating the complex interactions and signaling that occur between tissues. Likewise, tissues such as the intermediate mesoderm and yolk syn- cytial layer have the ability to impact the development of the fin. Additionally, both tbx5 paralogues regulate the migration of the cells of the fin field, with tbx5a primarily respon- sible for regulating AP convergence and tbx5b primarily responsible for regulating the ML migration movements. The genetic association of these movements along orthogonal axes suggests that subfunctionalization of these movements has occured. Furthermore, this data suggests that in tetrapods, the ancestral Tbx5 regulates both migration movements, such that loss of Tbx5 would result in cells that fail to migrate, therefore explaining the lack of forelimb in Tbx5-deficient tetrapods