Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis.

Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we perform single-cell transcriptomic and proteomic analyses of peripheral blood and colonic biopsies in healthy controls and patients with UC on VDZ or other therapies. Here we show that VDZ treatment is associated with alterations in circulating and tissue mononuclear phagocyte (MNP) subsets, along with modest shifts in lymphocytes. Spatial multi-omics of formalin-fixed biopsies demonstrates trends towards increased abundance and proximity of MNP and fibroblast subsets in active colitis. Spatial transcriptomics of archived specimens pre-treatment identifies epithelial-, MNP-, and fibroblast-enriched genes related to VDZ responsiveness, highlighting important roles for these subsets in UC.

Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis.

Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we performed single-cell transcriptomic and proteomic analyses of peripheral blood and colonic biopsies in healthy controls and patients with UC on VDZ or other therapies. Here we show that VDZ treatment is associated with alterations in circulating and tissue mononuclear phagocyte (MNP) subsets, along with modest shifts in lymphocytes. Spatial multi-omics of formalin-fixed biopsies demonstrates trends towards increased abundance and proximity of MNP and fibroblast subsets in active colitis. Spatial transcriptomics of archived specimens pre-treatment identifies epithelial-, MNP-, and fibroblast-enriched genes related to VDZ responsiveness, highlighting important roles for these subsets in UC.

DNA from non-viable bacteria biases diversity estimates in the corals Acropora loripes and Pocillopora acuta.

BACKGROUND: Nucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological state of bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles in maintaining health and functioning of the holobiont. However, the coral holobiont contains both dead and living bacteria. The former can be the result of corals feeding on bacteria, rapid swings from hyper- to hypoxic conditions in the coral tissue, the presence of antimicrobial compounds in coral mucus, and an abundance of lytic bacteriophages. RESULTS: By combining propidium monoazide (PMA) treatment with high-throughput sequencing on six coral species (Acropora loripes, A. millepora, A. kenti, Platygyra daedalea, Pocillopora acuta, and Porites lutea) we were able to obtain information on bacterial communities with little noise from non-viable microbial DNA. Metabarcoding of the 16S rRNA gene showed significantly higher community evenness (85%) and species diversity (31%) in untreated compared with PMA-treated tissue for A. loripes only. While PMA-treated coral did not differ significantly from untreated samples in terms of observed number of ASVs, > 30% of ASVs were identified in untreated samples only, suggesting that they originated from cell-free/non-viable DNA. Further, the bacterial community structure was significantly different between PMA-treated and untreated samples for A. loripes and P. acuta indicating that DNA from non-viable microbes can bias community composition data in coral species with low bacterial diversity. CONCLUSIONS: Our study is highly relevant to microbiome studies on coral and other host organisms as it delivers a solution to excluding non-viable DNA in a complex community. These results provide novel insights into the dynamic nature of host-associated microbiomes and underline the importance of applying versatile tools in the analysis of metabarcoding or next-generation sequencing data sets.

Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics.

Juvenile Dermatomyositis (JDM) is one of several childhood-onset autoimmune disorders characterized by a type I interferon response and autoantibodies. Treatment options are limited due to incomplete understanding of how the disease emerges from dysregulated cell states across the immune system. We therefore investigated the blood of JDM patients at different stages of disease activity using single-cell transcriptomics paired with surface protein expression. By immunophenotyping peripheral blood mononuclear cells, we observed skewing of the B cell compartment towards an immature naive state as a hallmark of JDM. Furthermore, we find that these changes in B cells are paralleled by signatures of Th2-mediated inflammation. Additionally, our work identified SIGLEC-1 expression in monocytes as a composite measure of heterogeneous type I interferon activity in disease. We applied network analysis to reveal that hyperactivation of the type I interferon response in all immune populations is coordinated with dysfunctional protein processing and regulation of cell death programming. This analysis separated the ubiquitously expressed type I interferon response into a central hub and revealed previously masked cell states. Together, these findings reveal the coordinated immune dysregulation underpinning JDM and provide novel insight into strategies for restoring balance in immune function.

Single-Cell Multiomics.

Single-cell RNA sequencing methods have led to improved understanding of the heterogeneity and transcriptomic states present in complex biological systems. Recently, the development of novel single-cell technologies for assaying additional modalities, specifically genomic, epigenomic, proteomic, and spatial data, allows for unprecedented insight into cellular biology. While certain technologies collect multiple measurements from the same cells simultaneously, even when modalities are separately assayed in different cells, we can apply novel computational methods to integrate these data. The application of computational integration methods to multimodal paired and unpaired data results in rich information about the identities of the cells present and the interactions between different levels of biology, such as between genetic variation and transcription. In this review, we both discuss the single-cell technologies for measuring these modalities and describe and characterize a variety of computational integration methods for combining the resulting data to leverage multimodal information toward greater biological insight.

Large-scale labeling and assessment of sex bias in publicly available expression data.

BACKGROUND: Women are at more than 1.5-fold higher risk for clinically relevant adverse drug events. While this higher prevalence is partially due to gender-related effects, biological sex differences likely also impact drug response. Publicly available gene expression databases provide a unique opportunity for examining drug response at a cellular level. However, missingness and heterogeneity of metadata prevent large-scale identification of drug exposure studies and limit assessments of sex bias. To address this, we trained organism-specific models to infer sample sex from gene expression data, and used entity normalization to map metadata cell line and drug mentions to existing ontologies. Using this method, we inferred sex labels for 450,371 human and 245,107 mouse microarray and RNA-seq samples from refine.bio. RESULTS: Overall, we find slight female bias (52.1%) in human samples and (62.5%) male bias in mouse samples; this corresponds to a majority of mixed sex studies in humans and single sex studies in mice, split between female-only and male-only (25.8% vs. 18.9% in human and 21.6% vs. 31.1% in mouse, respectively). In drug studies, we find limited evidence for sex-sampling bias overall; however, specific categories of drugs, including human cancer and mouse nervous system drugs, are enriched in female-only and male-only studies, respectively. We leverage our expression-based sex labels to further examine the complexity of cell line sex and assess the frequency of metadata sex label misannotations (2-5%). CONCLUSIONS: Our results demonstrate limited overall sex bias, while highlighting high bias in specific subfields and underscoring the importance of including sex labels to better understand the underlying biology. We make our inferred and normalized labels, along with flags for misannotated samples, publicly available to catalyze the routine use of sex as a study variable in future analyses.

Sex-specific genetic effects across biomarkers.

Sex differences have been shown in laboratory biomarkers; however, the extent to which this is due to genetics is unknown. In this study, we infer sex-specific genetic parameters (heritability and genetic correlation) across 33 quantitative biomarker traits in 181,064 females and 156,135 males from the UK Biobank study. We apply a Bayesian Mixture Model, Sex Effects Mixture Model (SEMM), to Genome-wide Association Study summary statistics in order to (1) estimate the contributions of sex to the genetic variance of these biomarkers and (2) identify variants whose statistical association with these traits is sex-specific. We find that the genetics of most biomarker traits are shared between males and females, with the notable exception of testosterone, where we identify 119 female and 445 male-specific variants. These include protein-altering variants in steroid hormone production genes (POR, UGT2B7). Using the sex-specific variants as genetic instruments for Mendelian randomization, we find evidence for causal links between testosterone levels and height, body mass index, waist and hip circumference, and type 2 diabetes. We also show that sex-specific polygenic risk score models for testosterone outperform a combined model. Overall, these results demonstrate that while sex has a limited role in the genetics of most biomarker traits, sex plays an important role in testosterone genetics.

Gaussian Embedding for Large-scale Gene Set Analysis.

Gene sets, including protein complexes and signaling pathways, have proliferated greatly, in large part as a result of high-throughput biological data. Leveraging gene sets to gain insight into biological discovery requires computational methods for converting them into a useful form for available machine learning models. Here, we study the problem of embedding gene sets as compact features that are compatible with available machine learning codes. We present Set2Gaussian, a novel network-based gene set embedding approach, which represents each gene set as a multivariate Gaussian distribution rather than a single point in the low-dimensional space, according to the proximity of these genes in a protein-protein interaction network. We demonstrate that Set2Gaussian improves gene set member identification, accurately stratifies tumors, and finds concise gene sets for gene set enrichment analysis. We further show how Set2Gaussian allows us to identify a previously unknown clinical prognostic and predictive subnetwork around NEFM in sarcoma, which we validate in independent cohorts.

The utilisation of ion chromatography and tandem mass spectrometry (IC-MS/MS) for the multi-residue simultaneous determination of highly polar anionic pesticides in fruit and vegetables.

A robust and sensitive method utilising a hybrid ion chromatography tandem mass spectrometry system (IC-MS/MS) for the simultaneous determination of nine (9) highly polar anionic pesticides (chlorate, ethephon, fosetyl aluminium, glufosinate, glyphosate, N-acetyl AMPA, N-acetyl glyphosate, perchlorate and phosphonic acid) in fruit and vegetables is described. Mean recoveries (n = 6) at two fortification levels ranged from 83 to 112% with %CVs in the range 3-14%. The linearity range was 0.005-0.4 mg kg-1 and R2 values were >0.99 and the sensitivity of the method allowed (20× or 30×) dilution of samples. Provision of qualitative determination of aminomethylphosphonic acid (AMPA) was also facilitated via minor modification of the chromatographic conditions. Compliance with method validation criteria, survey results from the statutory UK/EU Pesticide Residues in Food 2018 programmes i.e. pea, pineapple, melon and successful z-scores for a UK proficiency testing scheme sample (ethephon in pineapple) demonstrate successful application of this IC-MS/MS method.

C/EBPß LIP and c-Jun synergize to regulate expression of the murine progesterone receptor.

CCAAT/enhancer binding protein ß (C/EBPß) is required for murine mammary ductal morphogenesis and alveologenesis. Progesterone is critical for proliferation and alveologenesis in adult mammary glands, and there is a similar requirement for progesterone receptor isoform B (PRB) in alveologenesis. We examined C/EBPß regulation of PR expression. All three C/EBPß isoforms, including typically inhibitory LIP, transactivated the PR promoter. LIP, particularly, strongly synergized with c-Jun to drive PR transcription. Endogenous C/EBPß and c-Jun stimulated a PR promoter-reporter and these two factors showed promoter occupancy on the endogenous PR gene. Additionally, LIP overexpression elevated endogenous PR protein expression. In pregnancy, both PRB and the relative abundance of LIP among C/EBPß isoforms increase. Consistent with a role in PRB expression, in vivo C/EBPß and PR isoform A expression showed mutually exclusive localization in mammary epithelium, while C/EBPß and PRB largely co-localized. We suggest a critical role for C/EBPß, particularly LIP, in PRB expression.

The impact of a private sector living wage intervention on consumption and cardiovascular disease risk factors in a middle income country.

BACKGROUND: A positive association of socioeconomic position and health is well established in high-income countries. In poorer nations, however, higher income individuals often have more cardiovascular risk factors (including obesity) than do those with less income. Our study goal was to estimate the effects of receiving a living wage (340% higher income) on short-term changes in consumption and cardiovascular risk factors among low-wage workers in a middle-income country. METHODS: This cross-sectional study matched workers at an apparel factory (n=105) in the Dominican Republic with those at a similar factory (n=99) nearby, 15 months after the intervention factory introduced a substantially higher living wage. Statistical matching on non-time varying individual characteristics (childhood health, childhood living conditions, work experience, demographic factors) strengthened causal inference. Primary outcomes were blood pressure (systolic and diastolic), pulse rate, body mass index and waist circumference. Secondary outcomes were dietary consumption and spending on services, consumables and durable goods. RESULTS: Receiving the living wage was associated with increased consumption of protein, dairy, soda and juice and sugars, but not with cardiovascular risk factors. Intervention factory workers spent more on grocery items and household durable goods. CONCLUSIONS: While having a higher income in a middle-income country might be expected to increase obesity and its associated health risks, the current study found no short-term negative associations. There may be possible longer-term negative health consequences of increases in consumption of soda, juice and sugars, however. It is important to consider complementary interventions to support healthy dietary intake in areas with increasing wages.

Maternal Depressive Symptoms and Child Behavior among Mexican Women and Their Children.

Over 50% of mothers in rural Mexico have high depressive symptoms, and their children's health and development are likely to be negatively affected. A critical question is whether children vary in their vulnerability to the effects of high maternal depressive symptoms according to their indigenous ethnicity, maternal education, or household wealth. Our sample included 4442 mothers and 5503 children from an evaluation of Mexico's social welfare program. Maternal depressive symptoms were assessed using the Center for Epidemiologic Studies Depression (CES-D) Scale, and child behavior was measured using an adapted version of the Behavior Problems Index (BPI). Multiple linear regression models were used to explore the associations between maternal depressive symptoms and child behavior problems, and the heterogeneity of associations by indigenous ethnicity, maternal education, and household assets. We found that having greater maternal depressive symptoms was significantly associated with having a child with more behavior problems (ß = 0.114, p < 0.0001, [95% CI 0.101, 0.127]), in adjusted models. In tests of heterogeneity, the association between maternal depressive symptoms and child behavior problems was strongest in households with indigenous ethnicity, low maternal education, or in households with fewer assets. These results strengthen the case for effective mental health interventions in low- and middle-income countries, particularly among the most vulnerable families where mothers and children appear to be at the greatest risk.

Matching Multiple Rigid Domain Decompositions of Proteins.

We describe efficient methods for consistently coloring and visualizing collections of rigid cluster decompositions obtained from variations of a protein structure, and lay the foundation for more complex setups, that may involve different computational and experimental methods. The focus here is on three biological applications: the conceptually simpler problems of visualizing results of dilution and mutation analyses, and the more complex task of matching decompositions of multiple Nucleic Magnetic Resonance (NMR) models of the same protein. Implemented into the KINematics And RIgidity (KINARI) web server application, the improved visualization techniques give useful information about protein folding cores, help examining the effect of mutations on protein flexibility and function, and provide insights into the structural motions of Protein Data Bank proteins solved with solution NMR. These tools have been developed with the goal of improving and validating rigidity analysis as a credible coarse-grained model capturing essential information about a protein's slow motions near the native state.

Does alleviating poverty affect mothers' depressive symptoms? A quasi-experimental investigation of Mexico's Oportunidades programme.

BACKGROUND: Depression is a major cause of disability, particularly among women; poverty heightens the risk for depression. Beyond its direct effects, maternal depression can harm children's health and development. This study aimed to assess the effects of a large-scale anti-poverty programme in Mexico (Oportunidades) on maternal depressive symptoms. METHODS: In 2003, 5050 women living in rural communities who had participated in Oportunidades since its inception were assessed and compared with a group of 1293 women from matched communities, whose families had received no exposure to Oportunidades at the time of assessment but were later enrolled. Self-reported depressive symptoms were measured using the Center for Epidemiologic Studies Depression Scale (CES-D). Ordinary least squares regressions were used to evaluate the treatment effect of programme participation on depression while adjusting for covariates and clustering at the community level. RESULTS: Women in the treatment group had lower depressive symptoms than those in the comparison group (unadjusted mean CES-D scores: 16.9 ± 9.8 vs 18.6 ± 10.2). In multivariable analyses, programme participation was associated with lower depression whilst controlling for maternal age, education and household demographic, ethnicity and socio-economic variables [ß= -1.7 points, 95% confidence interval (95% CI) -2.46 to -0.96, P < 0.001]. Reductions in perceived stress and increases in perceived control were mediators of programme effects on women. CONCLUSIONS: Although Oportunidades did not target maternal mental health directly, we found modest but clinically meaningful effects on depressive symptoms. Our design permits stronger causal inference than observational studies that have linked poverty and depressive symptoms. Our results emphasize that the well-being of individuals is responsive to macro-level economic policies and programmes.

Insulin resistance contributes to aberrant stress responses in the Tg2576 mouse model of Alzheimer's disease.

We previously reported aberrant stress responses and impaired glucose tolerance in transgenic Tg2576 mice, a model of Alzheimer's disease (AD). Here we report that by 8 months of age, Tg2576 mice had lower basal serum insulin concentrations and exhibited a delayed insulin-induced reduction in blood glucose levels relative to wild-type mice. However, the basal levels of blood glucose and percent glycosylated hemoglobin (%HbA1c) were similar between the two groups of mice. While the basal levels of serum corticosterone were similar between Tg2576 and wild-type mice, an overnight fasting caused a greater rise in serum corticosterone levels and an excessive reduction in serum insulin concentrations in the transgenics. At 9 months of age, we began administering Tg2576 mice rosiglitazone, an agonist of peroxisome proliferator-activated receptor-gamma that increases peripheral insulin sensitivity, and after 6 weeks of administration the Tg2576 mice had the same response to insulin and increase in serum corticosterone levels after an overnight fast as did wild-type mice. By 13 months of age, untreated Tg2576 mice had become hyperinsulinemic, in contrast to Tg2576 mice administered rosiglitazone for 4 months where the serum insulin concentrations were maintained at levels observed in wild-type mice. These results provide evidence for a relationship between insulin resistance, impaired regulation of insulin and glucose levels, and aberrant stress responses in Tg2576 mice.