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Objectives: This study assessed associations of three theoretically different occupational class schemes with all-cause and cardiovascular mortality in Norwegian men and women., Study Design: Pooled survey and register data from four Norwegian cohort studies., Methods: We pooled survey data from four general population cohorts (N = 97,469) linked to national mortality registries with follow-up over 45 years. Survival was modelled using accelerated failure time models stratified by sex for three class schemes: The European Socio-Economic Classification (ESeC), The Oslo Register Data Class scheme (ORDC) and The International Socio-Economic Index (ISEI). Main analyses were adjusted for age, birth cohort, and study. Secondary analyses included smoking behaviour as a mediator., Results: During median 27.6 years of observation, 37,488 participants had died (13,243 from cardiovascular disease). Hazard ratios for male all-cause mortality were lowest in the highest occupational class categories ORDC 2: 0.68 (0.65-0.72), ESeC 1: 0.76 (0.73-0.79) and ISEI 5th quintile: 0.80 (0.77-0.82) compared to working class reference categories. Female mortality risks were lowest for Cultural Lower Middle class ORDC 7: 0.84 (0.72-0.98), Small Employers and Self-employed ESeC4: 0.70 (0.50-0.97) and ISEI 5th quintile: 0.79 (0.70-0.90). Patterns for cardiovascular mortality were similar to all-cause mortality. Including smoking behaviour as a mediator attenuated associations, but overall mortality patterns according to occupational class remained unchanged., Conclusion: The results underline that mortality inequalities do not simply consist of higher risks in the most disadvantaged groups. The association of occupational class with mortality is found across different categories of occupational class schemes, illustrating their continued relevance for studying social determinants of health., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The emerging zoonotic West Nile virus (WNV) has serious impact on public health. Thus, understanding the molecular basis of WNV infections in mammalian hosts is important to develop improved diagnostic and treatment strategies. In this context, the role of microRNAs (miRNAs) has been analyzed by several studies under different conditions and with different outcomes. A systematic comparison is therefore necessary. Furthermore, additional information from mRNA target expression data has rarely been taken into account to understand miRNA expression profiles under WNV infections. We conducted a meta-analysis of publicly available miRNA expression data from multiple independent studies, and analyzed them in a harmonized way to increase comparability. In addition, we used gene-set tests on mRNA target expression data to further gain evidence about differentially expressed miRNAs. For this purpose, we also studied the use of target information from different databases. We detected a substantial number of miRNA that emerged as differentially expressed from several miRNA datasets, and from the mRNA target data analysis as well. When using mRNA target data, we found that the targetscan databases provided the most useful information. We demonstrated improved miRNA detection through research synthesis of multiple independent miRNA datasets coupled with mRNA target set testing, leading to the discovery of multiple miRNAs which should be taken into account for further research on the molecular mechanism of WNV infections.

Background: Unsupervised clustering and outlier detection are important in medical research to understand the distributional composition of a collective of patients. A number of clustering methods exist, also for high-dimensional data after dimension reduction. Clustering and outlier detection may, however, become less robust or contradictory if multiple high-dimensional data sets per patient exist. Such a scenario is given when the focus is on 3-D data of multiple organs per patient, and a high-dimensional feature matrix per organ is extracted., Methods: We use principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE) and multiple co-inertia analysis (MCIA) combined with bagplots to study the distribution of multi-organ 3-D data taken by computed tomography scans. After point-set registration of multiple organs from two public data sets, multiple hundred shape features are extracted per organ. While PCA and t-SNE can only be applied to each organ individually, MCIA can project the data of all organs into the same low-dimensional space., Results: MCIA is the only approach, here, with which data of all organs can be projected into the same low-dimensional space. We studied how frequently (i.e., by how many organs) a patient was classified to belong to the inner or outer 50% of the population, or as an outlier. Outliers could only be detected with MCIA and PCA. MCIA and t-SNE were more robust in judging the distributional location of a patient in contrast to PCA., Conclusions: MCIA is more appropriate and robust in judging the distributional location of a patient in the case of multiple high-dimensional data sets per patient. It is still recommendable to apply PCA or t-SNE in parallel to MCIA to study the location of individual organs., (© 2024. The Author(s).)

Objective: The purpose of this study was to identify a panel of biomarkers for distinguishing early stage sepsis patients from non-infected trauma patients., Background: Accurate differentiation between trauma-induced sterile inflammation and real infective sepsis poses a complex life-threatening medical challenge because of their common symptoms albeit diverging clinical implications, namely different therapies. The timely and accurate identification of sepsis in trauma patients is therefore vital to ensure prompt and tailored medical interventions (provision of adequate antimicrobial agents and if possible eradication of infective foci) that can ultimately lead to improved therapeutic management and patient outcome. The adequate withholding of antimicrobials in trauma patients without sepsis is also important in aspects of both patient and environmental perspective., Methods: In this proof-of-concept study, we employed advanced technologies, including Matrix-Assisted Laser Desorption/Ionization (MALDI) and multiplex antibody arrays (MAA) to identify a panel of biomarkers distinguishing actual sepsis from trauma-induced sterile inflammation., Results: By comparing patient groups (controls, infected and non-infected trauma and septic shock patients under mechanical ventilation) at different time points, we uncovered distinct protein patterns associated with early trauma-induced sterile inflammation on the one hand and sepsis on the other hand. SYT13 and IL1F10 emerged as potential early sepsis biomarkers, while reduced levels of A2M were indicative of both trauma-induced inflammation and sepsis conditions. Additionally, higher levels of TREM1 were associated at a later stage in trauma patients. Furthermore, enrichment analyses revealed differences in the inflammatory response between trauma-induced inflammation and sepsis, with proteins related to complement and coagulation cascades being elevated whereas proteins relevant to focal adhesion were diminished in sepsis., Conclusions: Our findings, therefore, suggest that a combination of biomarkers is needed for the development of novel diagnostic approaches deciphering trauma-induced sterile inflammation from actual infective sepsis., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Papareddy, Selle, Partouche, Legros, Rieu, Olinder, Ryden, Bartakova, Holub, Jung, Pottecher and Herwald.)

Immune checkpoint blockade therapy is beneficial and even curative for some cancer patients. However, the majority don't respond to immune therapy. Across different tumor types, pre-existing T cell infiltrates predict response to checkpoint-based immunotherapy. Based on in vitro pharmacological studies, mouse models and analyses of human melanoma patients, we show that the cytokine GDF-15 impairs LFA-1/β2-integrin-mediated adhesion of T cells to activated endothelial cells, which is a pre-requisite of T cell extravasation. In melanoma patients, GDF-15 serum levels strongly correlate with failure of PD-1-based immune checkpoint blockade therapy. Neutralization of GDF-15 improves both T cell trafficking and therapy efficiency in murine tumor models. Thus GDF-15, beside its known role in cancer-related anorexia and cachexia, emerges as a regulator of T cell extravasation into the tumor microenvironment, which provides an even stronger rationale for therapeutic anti-GDF-15 antibody development., (© 2023. The Author(s).)

For research and clinical use of stem cells, a suitable animal model is necessary. Hence, the aim of this study was to compare human-bone-marrow-derived mesenchymal stem cells (hBMSCs) with those from sheep (oBMSCs) and pigs (pBMSCs). The cells from these three species were examined for their self-renewal potential; proliferation potential; adhesion and migration capacity; adipogenic, osteogenic and chondrogenic differentiation potential; and cell morphology. There was no significant difference between hBMSCs and pBMSCs in terms of self-renewal potential or growth potential. The oBMSCs exhibited a significantly higher doubling time than hBMSCs from passage 7. The migration assay showed significant differences between hBMSCs and pBMSCs and oBMSCs-up to 30 min, hBMSCs were faster than both types and after 60 min faster than pBMSCs. In the adhesion assay, hBMSCs were significantly better than oBMSCs and pBMSCs. When differentiating in the direction of osteogenesis, oBMSCs and pBMSCs have shown a clearer osteogenic potential. In all three species, adipogenesis could only be evaluated qualitatively. The chondrogenic differentiation was successful in hBMSCs and pBMSCs in contrast to oBMSCs. It is also important to note that the cell size of pBMSCs was significantly smaller compared to hBMSCs. Finally, it can be concluded that further comparative studies are needed to draw a clear comparison between hBMSCs and pBMSCs/oBMSCs.

Outliers in the training or test set used to fit and evaluate a classifier on transcriptomics data can considerably change the estimated performance of the model. Hence, an either too weak or a too optimistic accuracy is then reported and the estimated model performance cannot be reproduced on independent data. It is then also doubtful whether a classifier qualifies for clinical usage. We estimate classifier performances in simulated gene expression data with artificial outliers and in two real-world datasets. As a new approach, we use two outlier detection methods within a bootstrap procedure to estimate the outlier probability for each sample and evaluate classifiers before and after outlier removal by means of cross-validation. We found that the removal of outliers changed the classification performance notably. For the most part, removing outliers improved the classification results. Taking into account the fact that there are various, sometimes unclear reasons for a sample to be an outlier, we strongly advocate to always report the performance of a transcriptomics classifier with and without outliers in training and test data. This provides a more diverse picture of a classifier's performance and prevents reporting models that later turn out to be not applicable for clinical diagnoses.

Ageing is often accompanied by an increase in bone marrow fat together with reduced bone volume and diseases of the bone such as osteoporosis. As mesenchymal stem cells (MSCs) are capable of forming bone, cartilage and fat tissue, studying these cells is of great importance to understand the underlying mechanisms behind age-related bone diseases. However, inter-donor variation has been found when handling MSCs. Therefore, the aim of this study was to investigate the effects of donor age and sex by comparing in vitro characteristics of human bone marrow-derived MSCs (hBMSCs) from a large donor cohort (n = 175). For this, hBMSCs were analysed for CFU-F capacity, proliferation, differentiation capacity and surface antigen expression under standardized culture conditions. The results demonstrated a significantly reduced CFU-F number for hBMSCs of female compared to male donors. Furthermore, there was a significant decrease in the proliferation rate, adipogenic differentiation potential and cell surface expression of SSEA-4, CD146 and CD274 of hBMSCs with an increase in donor age. Interestingly, all these findings were exclusive to hBMSCs from female donors. Further research should focus on postmenopausal-related effects on hBMSCs, as the results imply a functional loss and immunophenotypic change of hBMSCs particularly in aged women., (© 2022 The Authors. Journal of Cellular and Molecular Medicine published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd.)

Underlying pathomechanisms of osteoporosis are still not fully elucidated. Cell-based therapy approaches pose new possibilities to treat osteoporosis and its complications. The aim of this study was to quantify differences in human bone marrow-derived mesenchymal stem cells (hBMSCs) between healthy donors and those suffering from clinically manifest osteoporosis. Cell samples of seven donors for each group were selected retrospectively from the hBMSC cell bank of the Trauma Department of Hannover Medical School. Cells were evaluated for their adipogenic, osteogenic and chondrogenic differentiation potential, for their proliferation potential and expression of surface antigens. Furthermore, a RT2 Osteoporosis Profiler PCR array, as well as quantitative real-time PCR were carried out to evaluate changes in gene expression. Cultivated hBMSCs from osteoporotic donors showed significantly lower cell surface expression of CD274 (4.98 % ± 2.38 %) than those from the control group (26.03 % ± 13.39 %; p = 0.007), as assessed by flow cytometry. In osteoporotic patients, genes involved in inhibition of the anabolic WNT signalling pathway and those associated with stimulation of bone resorption were significantly upregulated. Apart from these changes, no significant differences were found for the other cell surface antigens, adipogenic, osteogenic and chondrogenic differentiation ability as well as proliferation potential. These findings supported the theory of an influence of CD274 on the regulation of bone metabolism. CD274 might be a promising target for further investigations of the pathogenesis of osteoporosis and of cell-based therapies involving MSCs.

This current cross sectional survey was carried out amongst patients and staff in an acute psychiatric inpatient unit in the very first weeks of the ongoing pandemic outbreak of COVID-19 in Norway. Most patients found the visiting restrictions difficult, many reported that the pandemic made them feel unsafe, affected their sleep and that they feared transmission from other patients. Among staff, almost half were afraid that they would contract the virus, a majority feared they would bring the virus home and infect their family and one third were concerned that the pandemic compromised the treatment provided for the patients., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

Colibactin is a nonribosomal peptide/polyketide hybrid natural product expressed by different members of the Enterobacteriaceae which can be correlated with induction of DNA double-strand breaks and interference with cell cycle progression in eukaryotes. Regulatory features of colibactin expression are only incompletely understood. We used Escherichia coli strain M1/5 as a model to investigate regulation of expression of the colibactin determinant at the transcriptional level and to characterize regulatory elements located within the colibactin pathogenicity island itself. We measured clbR transcription in vitro and observed that cultivation in defined minimal media led to increased colibactin expression relative to rich media. Transcription of clbR directly responds to iron availability. We also characterized structural DNA elements inside the colibactin determinant involved in ClbR-dependent regulation, i.e., ClbR binding sites and a variable number of tandem repeats located upstream of clbR We investigated the impact of clbR overexpression or deletion at the transcriptome and proteome levels. Moreover, we compared global gene regulation under these conditions with that occurring upon overexpression or deletion of clbQ , which affects the flux of colibactin production. Combining the results of the transcriptome and proteome analyses with indirect measurements of colibactin levels by cell culture assays and an approximate quantification of colibactin via the second product of colibactin cleavage from precolibactin, N-myristoyl-d-asparagine, we demonstrate that the variable number of tandem repeats plays a significant regulatory role in colibactin expression. We identify ClbR as the only transcriptional activator known so far that is specific and essential for efficient regulation of colibactin production. IMPORTANCE The nonribosomal peptide/polyketide hybrid colibactin can be considered a bacterial virulence factor involved in extraintestinal infection and also a procarcinogen. Nevertheless, and despite its genotoxic effect, colibactin expression can also inhibit bacterial or tumor growth and correlates with probiotic anti-inflammatory and analgesic properties. Although the biological function of this natural compound has been studied extensively, our understanding of the regulation of colibactin expression is still far from complete. We investigated in detail the role of regulatory elements involved in colibactin expression and in the growth conditions that promote colibactin expression. In this way, our data shed light on the regulatory mechanisms involved in colibactin expression and may support the expression and purification of this interesting nonribosomal peptide/polyketide hybrid for further molecular characterization., (Copyright © 2020 Wallenstein et al.)

The increasing amount of available biological information on the markers can be used to inform the models applied for genomic selection to improve predictions. The objective of this study was to propose a general model for genomic selection using a link function approach within the hierarchical generalized linear model framework (hglm) that can include external information on the markers. These models can be fitted using the well-established hglm package in R. We also present an R package (CodataGS) to fit these models, which is significantly faster than the hglm package. Simulated data were used to validate the proposed model. We tested categorical, continuous and combination models where the external information on the markers was related to 1) the location of the QTL on the genome with varying degree of uncertainty, 2) the relationship of the markers with the QTL calculated as the LD between them, and 3) a combination of both. The proposed models showed improved accuracies from 3.8% up to 23.2% compared to the SNP-BLUP method in a simulated population derived from a base population with 100 individuals. Moreover, the proposed categorical model was tested on a dairy cattle dataset for two traits (Milk Yield and Fat Percentage). These results also showed improved accuracy compared to SNP-BLUP, especially for the Fat% trait. The performance of the proposed models depended on the genetic architecture of the trait, as traits that deviate from the infinitesimal model benefited more from the external information. Also, the gain in accuracy depended on the degree of uncertainty of the external information provided to the model. The usefulness of these type of models is expected to increase with time as more accurate information on the markers becomes available., (Copyright © 2019 Mouresan et al.)

Staphylococcus aureus is a major bacterial pathogen, which causes severe blood and tissue infections that frequently emerge by autoinfection with asymptomatically carried nose and skin populations. However, recent studies report that bloodstream isolates differ systematically from those found in the nose and skin, exhibiting reduced toxicity toward leukocytes. In two patients, an attenuated toxicity bloodstream infection evolved from an asymptomatically carried high-toxicity nasal strain by loss-of-function mutations in the gene encoding the transcription factor repressor of surface proteins (rsp). Here, we report that rsp knockout mutants lead to global transcriptional and proteomic reprofiling, and they exhibit the greatest signal in a genome-wide screen for genes influencing S. aureus survival in human cells. This effect is likely to be mediated in part via SSR42, a long-noncoding RNA. We show that rsp controls SSR42 expression, is induced by hydrogen peroxide, and is required for normal cytotoxicity and hemolytic activity. Rsp inactivation in laboratory- and bacteremia-derived mutants attenuates toxin production, but up-regulates other immune subversion proteins and reduces lethality during experimental infection. Crucially, inactivation of rsp preserves bacterial dissemination, because it affects neither formation of deep abscesses in mice nor survival in human blood. Thus, we have identified a spontaneously evolving, attenuated-cytotoxicity, nonhemolytic S. aureus phenotype, controlled by a pleiotropic transcriptional regulator/noncoding RNA virulence regulatory system, capable of causing S. aureus bloodstream infections. Such a phenotype could promote deep infection with limited early clinical manifestations, raising concerns that bacterial evolution within the human body may contribute to severe infection.

The pathogen Staphylococcus aureus causes a broad range of severe diseases and is feared for its ability to rapidly develop resistance to antibiotic substances. The increasing number of highly resistant S. aureus infections has accelerated the search for alternative treatment options to close the widening gap in anti-S. aureus therapy. This study analyses the humoral immune response to vaccination of Balb/c mice with sublethal doses of live S. aureus. The elicited antibody pattern in the sera of intravenously and intramuscularly vaccinated mice was determined using of a recently developed protein array. We observed a specific antibody response against a broad set of S. aureus antigens which was stronger following i.v. than i.m. vaccination. Intravenous but not intramuscular vaccination protected mice against an intramuscular challenge infection with a high bacterial dose. Vaccine protection was correlated with the strength of the anti-S. aureus antibody response. This study identified novel vaccine candidates by using protein microarrays as an effective tool and showed that successful vaccination against S. aureus relies on the optimal route of administration.

Purpose: The mortality rate of patients with Staphylococcus aureus infections is alarming and urgently demands new strategies to attenuate the course of these infections or to detect them at earlier stages., Experimental Design: To study the adaptive immune response to S. aureus antigens in healthy human volunteers, a protein microarray containing 44 S. aureus proteins was developed using the ArrayStrip platform technology., Results: Testing plasma samples from 15 S. aureus carriers and 15 noncarriers 21 immunogenic S. aureus antigens have been identified. Seven antigens were recognized by antibodies present in at least 60% of the samples, representing the core S. aureus immunome of healthy individuals. S. aureus-specific serum immunoglobulin G (IgG) levels were significantly lower in noncarriers than in carriers specifically anti-IsaA, anti-SACOL0479, and anti-SACOL0480 IgGs were found at lower frequencies and quantities. Twenty-two antigens present on the microarray were encoded by all S. aureus carrier isolates. Nevertheless, the immune system of the carriers was responsive to only eight of them and with different intensities., Conclusion and Clinical Relevance: The established protein microarray allows a broad profiling of the S. aureus-specific antibody response and can be used to identify S. aureus antigens that might serve as vaccines or diagnostic markers., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Isoquinolines (IQs) are natural substances with an antibiotic potential we aim to optimize. Specifically, IQ-238 is a synthetic analog of the novel-type N,C-coupled naphthylisoquinoline (NIQ) alkaloid ancisheynine. Recently, we developed and tested other IQs such as IQ-143. By utilizing genome-wide gene expression data, metabolic network modelling and Voronoi tessalation based data analysis - as well as cytotoxicity measurements, chemical properties calculations and principal component analysis of the NIQs - we show that IQ-238 has strong antibiotic potential for staphylococci and low cytotoxicity against murine or human cells. Compared to IQ-143, systemic effects are less pronounced. Most enzyme activity changes due to IQ-238 are located in the carbohydrate metabolism. Validation includes metabolite measurements on biological replicates. IQ-238 delineates key properties and a chemical space for a good therapeutic window. The combination of analysis methods allows suggestions for further lead development and yields an in-depth look at staphylococcal adaptation and network changes after antibiosis. Results are compared to eukaryotic host cells., (Copyright © 2014 Elsevier GmbH. All rights reserved.)