The Contribution of Transcriptomics to Biomarker Development in Systemic Vasculitis and SLE.

A small but increasing number of gene expression based biomarkers are becoming available for routine clinical use, principally in oncology and transplantation. These underscore the potential of gene expression arrays and RNA sequencing for biomarker development, but this potential has not yet been fully realized and most candidates do not progress beyond the initial report. The first part of this review examines the process of gene expression- based biomarker development, highlighting how systematic biases and confounding can significantly skew study outcomes. Adequate validation in an independent cohort remains the single best means of protecting against these concerns. The second part considers gene-expression based biomarkers in Systemic Lupus Erythematosus (SLE) and systemic vasculitis. The type 1 interferon inducible gene signature remains by far the most studied in autoimmune rheumatic disease. While initially presented as an objective, blood-based biomarker of active SLE, subsequent research has shown that it is not specific to SLE and that its association with disease activity is considerably more nuanced than first thought. Nonetheless, it is currently under evaluation in ongoing trials of anti-interferon therapy. Other candidate markers of note include a prognostic CD8+ T-cell gene signature validated in SLE and ANCA-associated vasculitis, and a disease activity biomarker for SLE derived from modules of tightly correlated genes.This is the author accepted manuscript. The final version is available from Bentham Science via http://dx.doi.org/10.2174/138161282166615031313025

Using competency-based education to equip the primary health care workforce to manage chronic disease

The research reported in this paper is a project of the Australian Primary Health Care Research Institute, which is supported by a grant from the Australian Government Department of Health and Ageing under the Primary Health Care Research, Evaluation and Development Strategy

Unbiased Decisions Reduce Regret: Adversarial Domain Adaptation for the Bank Loan Problem

In many real world settings binary classification decisions are made based on limited data in near real-time, e.g. when assessing a loan application. We focus on a class of these problems that share a common feature: the true label is only observed when a data point is assigned a positive label by the principal, e.g. we only find out whether an applicant defaults if we accepted their loan application. As a consequence, the false rejections become self-reinforcing and cause the labelled training set, that is being continuously updated by the model decisions, to accumulate bias. Prior work mitigates this effect by injecting optimism into the model, however this comes at the cost of increased false acceptance rate. We introduce adversarial optimism (AdOpt) to directly address bias in the training set using adversarial domain adaptation. The goal of AdOpt is to learn an unbiased but informative representation of past data, by reducing the distributional shift between the set of accepted data points and all data points seen thus far. AdOpt significantly exceeds state-of-the-art performance on a set of challenging benchmark problems. Our experiments also provide initial evidence that the introduction of adversarial domain adaptation improves fairness in this setting

Peripheral Immune Cell Populations Associated with Cognitive Deficits and Negative Symptoms of Treatment-Resistant Schizophrenia.

BACKGROUND: Hypothetically, psychotic disorders could be caused or conditioned by immunological mechanisms. If so, one might expect there to be peripheral immune system phenotypes that are measurable in blood cells as biomarkers of psychotic states. METHODS: We used multi-parameter flow cytometry of venous blood to quantify and determine the activation state of 73 immune cell subsets for 18 patients with chronic schizophrenia (17 treated with clozapine), and 18 healthy volunteers matched for age, sex, BMI and smoking. We used multivariate methods (partial least squares) to reduce dimensionality and define populations of differentially co-expressed cell counts in the cases compared to controls. RESULTS: Schizophrenia cases had increased relative numbers of NK cells, naïve B cells, CXCR5+ memory T cells and classical monocytes; and decreased numbers of dendritic cells (DC), HLA-DR+ regulatory T-cells (Tregs), and CD4+ memory T cells. Likewise, within the patient group, more severe negative and cognitive symptoms were associated with decreased relative numbers of dendritic cells, HLA-DR+ Tregs, and CD4+ memory T cells. Motivated by the importance of central nervous system dopamine signalling for psychosis, we measured dopamine receptor gene expression in separated CD4+ cells. Expression of the dopamine D3 (DRD3) receptor was significantly increased in clozapine-treated schizophrenia and covaried significantly with differentiated T cell classes in the CD4+ lineage. CONCLUSIONS: Peripheral immune cell populations and dopaminergic signalling are disrupted in clozapine-treated schizophrenia. Immuno-phenotypes may provide peripherally accessible and mechanistically specific biomarkers of residual cognitive and negative symptoms in this treatment-resistant subgroup of patients

Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation.

BACKGROUND: Although numerous investigations have compared gene expression microarray platforms, preprocessing methods and batch correction algorithms using constructed spike-in or dilution datasets, there remains a paucity of studies examining the properties of microarray data using diverse biological samples. Most microarray experiments seek to identify subtle differences between samples with variable background noise, a scenario poorly represented by constructed datasets. Thus, microarray users lack important information regarding the complexities introduced in real-world experimental settings. The recent development of a multiplexed, digital technology for nucleic acid measurement enables counting of individual RNA molecules without amplification and, for the first time, permits such a study. RESULTS: Using a set of human leukocyte subset RNA samples, we compared previously acquired microarray expression values with RNA molecule counts determined by the nCounter Analysis System (NanoString Technologies) in selected genes. We found that gene measurements across samples correlated well between the two platforms, particularly for high-variance genes, while genes deemed unexpressed by the nCounter generally had both low expression and low variance on the microarray. Confirming previous findings from spike-in and dilution datasets, this "gold-standard" comparison demonstrated signal compression that varied dramatically by expression level and, to a lesser extent, by dataset. Most importantly, examination of three different cell types revealed that noise levels differed across tissues. CONCLUSIONS: Microarray measurements generally correlate with relative RNA molecule counts within optimal ranges but suffer from expression-dependent accuracy bias and precision that varies across datasets. We urge microarray users to consider expression-level effects in signal interpretation and to evaluate noise properties in each dataset independently

Leukocyte and serum S100A8/S100A9 expression reflects disease activity in ANCA-associated vasculitis and glomerulonephritis.

Antineutrophil cytoplasm antibody (ANCA)-associated vasculitis (AAV) commonly results in glomerulonephritis, in which neutrophils and monocytes have important roles. The heterodimer calprotectin (S100A8/S100A9, mrp8/14) is a Toll-like receptor-4 ligand found in neutrophils and monocytes and is elevated in inflammatory conditions. By immunohistochemistry of renal biopsies, patients with focal or crescentic glomerular lesions were found to have the highest expression of calprotectin and those with sclerotic the least. Serum levels of calprotectin as measured by ELISA were elevated in patients with active AAV and the levels decreased but did not normalize during remission, suggesting subclinical inflammation. Calprotectin levels in patients with limited systemic disease increased following treatment withdrawal and were significantly elevated in patients who relapsed compared with those who did not. As assessed by flow cytometry, patients with AAV had higher monocyte and neutrophil cell surface calprotectin expression than healthy controls, but this was not associated with augmented mRNA expression in CD14(+) monocytes or CD16(+) neutrophils. Thus, serum calprotectin is a potential disease biomarker in patients with AAV, and may have a role in disease pathogenesis

Leucocyte subset-specific type 1 interferon signatures in SLE and other immune-mediated diseases.

OBJECTIVES: Type 1 interferons (IFN-1) are implicated in the pathogenesis of systemic lupus erythematosus (SLE), but most studies have only reported the effect of IFN-1 on mixed cell populations. We aimed to define modules of IFN-1-associated genes in purified leucocyte populations and use these as a basis for a detailed comparative analysis. METHODS: CD4+ and CD8+ T cells, monocytes and neutrophils were purified from patients with SLE, other immune-mediated diseases and healthy volunteers and gene expression then determined by microarray. Modules of IFN-1-associated genes were defined using weighted gene coexpression network analysis. The composition and expression of these modules was analysed. RESULTS: 1150 of 1288 IFN-1-associated genes were specific to myeloid subsets, compared with 11 genes unique to T cells. IFN-1 genes were more highly expressed in myeloid subsets compared with T cells. A subset of neutrophil samples from healthy volunteers (HV) and conditions not classically associated with IFN-1 signatures displayed increased IFN-1 gene expression, whereas upregulation of IFN-1-associated genes in T cells was restricted to SLE. CONCLUSIONS: Given the broad upregulation of IFN-1 genes in neutrophils including in some HV, investigators reporting IFN-1 signatures on the basis of whole blood samples should be cautious about interpreting this as evidence of bona fide IFN-1-mediated pathology. Instead, specific upregulation of IFN-1-associated genes in T cells may be a useful biomarker and a further mechanism by which elevated IFN-1 contributes to autoimmunity in SLE.SMF holds a Translational Medicine and Therapeutics PhD studentship from the Wellcome Trust and GlaxoSmithKline and has also received funding for this work from the Addenbrooke’s Charitable Trust. KGCS is the Khoo Oon Teik Professor of Nephrology, National University of Singapore. Singapore recruitment was supported by the Khoo Investigator Grant from the Duke-NUS Graduate Medical School, Singapore, and by National Medical Research Council of Singapore grants (NMRC/1164/2008 and IRG07nov089). This work was also supported by UK National Institute of Health Research Cambridge Biomedical Research Centre, the Lupus Research Institute (Distinguished Innovator Award, KGCS), the Medical Research Council UK (programme grant MR/L019027/1) and the Wellcome Trust (programme grant 083650/Z/07/Z and project grant 094227/Z/10/Z). The Cambridge Institute for Medical Research is in receipt of Wellcome Trust Strategic Award 079895.This is the final version of the article. It first appeared from BMJ Group via https://doi.org/10.1136/rmdopen-2015-00018

Large-Scale Stable Isotope Alteration Around the Hydrothermal Carbonate-Replacement Cinco de Mayo Zn-Ag Deposit, Mexico

Carbonate-hosted hydrothermal deposits typically show narrow visible mineralogical and textural alteration halos, which inhibit exploration targeting. In contrast, hydrothermal modification of the country rock’s stable isotope composition usually extends far beyond the limited visible alteration. Hence, stable isotope studies should be an effective tool to aid exploration for carbonate-hosted deposits. Here we present new insight into the development of a large stable isotope alteration halo based on 910 O and C isotope analyses of carbonate veins and hydrothermally altered limestone hosting the Cinco de Mayo Pb-Zn-Ag (Au, Cu) carbonate replacement deposit (CRD), in Chihuahua, Mexico. Our results demonstrate that stable isotope alteration is consistent with reactive, magmatic fluid flow into unaltered limestone and represents a powerful tool for the characterization of these hydrothermal ore systems. Synmineralization veins are texturally and isotopically distinct from those formed during pre- and postmineralization diagenesis and fluid flow and show distinct gradients along the direction of mineralizing fluid flow: this appears to be a promising exploration vectoring tool. Downhole variations in wall-rock isotope values reveal aquifers and aquicludes and outline the principal hydrothermal flow paths. Furthermore, wall-rock δ18OVSMOW systematically decreases toward mineralization from ~23‰ to <17‰ over a distance of ~10 km, providing another vectoring tool. The extent of the stable isotope alteration halo likely reflects the overall fluid volume and areal extent of a fossil hydrothermal system, which may be expected to scale with the mineral endowment. This suggests that constraining the size, shape, and degree of isotopic alteration has direct application to mineral exploration by outlining the system and indicating the potential size of a deposit

NBEAL2 is required for neutrophil and NK cell function and pathogen defense.

Mutations in the human NBEAL2 gene cause gray platelet syndrome (GPS), a bleeding diathesis characterized by a lack of α granules in platelets. The functions of the NBEAL2 protein have not been explored outside platelet biology, but there are reports of increased frequency of infection and abnormal neutrophil morphology in patients with GPS. We therefore investigated the role of NBEAL2 in immunity by analyzing the phenotype of Nbeal2-deficient mice. We found profound abnormalities in the Nbeal2-deficient immune system, particularly in the function of neutrophils and NK cells. Phenotyping of Nbeal2-deficient neutrophils showed a severe reduction in granule contents across all granule subsets. Despite this, Nbeal2-deficient neutrophils had an enhanced phagocyte respiratory burst relative to Nbeal2-expressing neutrophils. This respiratory burst was associated with increased expression of cytosolic components of the NADPH oxidase complex. Nbeal2-deficient NK cells were also dysfunctional and showed reduced degranulation. These abnormalities were associated with increased susceptibility to both bacterial (Staphylococcus aureus) and viral (murine CMV) infection in vivo. These results define an essential role for NBEAL2 in mammalian immunity