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Evaluation of the causal effect of fibrinogen on incident coronary heart disease via Mendelian randomization

BackgroundFibrinogen is an essential hemostatic factor and cardiovascular disease risk factor. Early attempts at evaluating the causal effect of fibrinogen on coronary heart disease (CHD) and myocardial infraction (MI) using Mendelian randomization (MR) used single variant approaches, and did not take advantage of recent genome-wide association studies (GWAS) or multi-variant, pleiotropy robust MR methodologies.\n\nMethods and FindingsWe evaluated evidence for a causal effect of fibrinogen on both CHD and MI using MR. We used both an allele score approach and pleiotropy robust MR models. The allele score was composed of 38 fibrinogen-associated variants from recent GWAS. Initial analyses using the allele score incorporated data from 11 European-ancestry prospective cohorts to examine incidence CHD and MI. We also applied 2 sample MR methods with data from a prevalent CHD and MI GWAS. Results are given in terms of the hazard ratio (HR) or odds ratio (OR), depending on the study design, and associated 95% confidence interval (CI).\n\nIn single variant analyses no causal effect of fibrinogen on CHD or MI was observed. In multi-variant analyses using incidence CHD cases and the allele score approach, the estimated causal effect (HR) of a 1 g/L higher fibrinogen concentration was 1.62 (CI = 1.12, 2.36) when using incident cases and the allele score approach. In 2 sample MR analyses that accounted for pleiotropy, the causal estimate (OR) was reduced to 1.18 (CI = 0.98, 1.42) and 1.09 (CI = 0.89, 1.33) in the 2 most precise (smallest CI) models, out of 4 models evaluated. In the 2 sample MR analyses for MI, there was only very weak evidence of a causal effect in only 1 out of 4 models.\n\nConclusionsA small causal effect of fibrinogen on CHD is observed using multi-variant MR approaches which account for pleiotropy, but not single variant MR approaches. Taken together, results indicate that even with large sample sizes and multi-variant approaches MR analyses still cannot exclude the null when estimating the causal effect of fibrinogen on CHD, but that any potential causal effect is likely to be much smaller than observed in epidemiological studies.\n\nAuthor SummaryInitial Mendelian Randomization (MR) analyses of the causal effect of fibrinogen on coronary heart disease (CHD) utilized single variants and did not take advantage of modern, multivariant approaches. This manuscript provides an important update to these initial analyses by incorporating larger sample sizes and employing multiple, modern multi-variant MR approaches to account for pleiotropy. We used incident cases to perform a MR study of the causal effect of fibrinogen on incident CHD and the nested outcome of myocardial infarction (MI) using an allele score approach. Then using data from a case-control genome-wide association study for CHD and MI we performed two sample MR analyses with multiple, pleiotropy robust approaches. Overall, the results indicated that associations between fibrinogen and CHD in observational studies are likely upwardly biased from any underlying causal effect. Single variant MR approaches show little evidence of a causal effect of fibrinogen on CHD or MI. Multi-variant MR analyses of fibrinogen on CHD indicate there may be a small positive effect, however this result needs to be interpreted carefully as the 95% confidence intervals were still consistent with a null effect. Multi-variant MR approaches did not suggest evidence of even a small causal effect of fibrinogen on MI.

genetics

Old fibroblasts secrete inflammatory cytokines that drive variability in reprogramming efficiency and may affect wound healing between old individuals

Age-associated chronic inflammation (inflammaging) has emerged as a central hallmark of aging1-3, but its impact on specific cells is still largely unknown. Fibroblasts are present in all tissues and contribute to wound healing4-6. They are also the cell type that is mostly used for induced pluripotent stem cell (iPSC) reprogramming7 - a process that has implications for regenerative medicine and rejuvenation strategies8-17. Here we show that primary fibroblasts from old mice secrete inflammatory cytokines and that there is an increased variability in reprogramming efficiency between fibroblast cultures from old individuals. Individual-to-individual variability is emerging as a key feature of old age18-21, which could reflect distinct aging trajectories, but the underlying causes remain unknown. To identify drivers of this variability, we perform a multi-omic assessment of young and old fibroblast cultures with different reprogramming efficiency. This approach, coupled with single cell transcriptomics, reveals that old fibroblast cultures are heterogeneous and show a greater proportion of activated fibroblasts that secrete inflammatory cytokines, which correlates with reprogramming efficiency. We experimentally validate that activated fibroblasts express inflammatory cytokines in vivo and that their presence is linked to enhanced reprogramming efficiency in culture. Conditioned-media swapping experiments show that extrinsic factors secreted by activated fibroblasts are more critical than intrinsic factors for the individual-to-individual variability in reprogramming efficiency, and we identify TNF as a key inflammatory cytokine underlying this variability. Interestingly, old mice also exhibit variability in wound healing efficiency in vivo and old wounds show an increased subpopulation of activated fibroblasts with a unique TNF signature. Our study shows that a switch in fibroblast composition, and the ratio of inflammatory cytokines they secrete, drives variability in reprogramming in vitro and may influence wound healing in vivo. These findings could help identify personalized strategies to improve iPSC generation and wound healing in older individuals.

cell biology

Loss of the Heparan Sulfate Proteoglycan Glypican5 facilitates long range Shh signaling.

As a morphogen, Sonic Hedgehog (Shh) mediates signaling at a distance from its sites of synthesis. After secretion, Shh must traverse a distance through the extracellular matrix (ECM) to reach the target cells and activate the Hh response. Extracellular matrix proteins, in particular the Heparan Sulfate Proteoglycans (HSPGs) of the Glypican family have both negative and positive effects on non-cell autonomous Shh signaling, all attributed to their ability to bind Shh. Using mouse embryonic stem cell-derived mosaic tissues with compartments that lack the glycosyltransferases Exostosin1 (Ext1) and Exostosin2 (Ext2), or the HSPG core protein Glypican5 we show that cells surrounded by a mutated extracellular matrix are highly proficient distributing Shh. In contrast, cells that lack Ext1 function poorly secrete Shh. Our results confirm earlier observations that HSPGs can have both positive (Shh export) and negative influences (Shh distribution), and are supporting a model in which Shh presented on the cell surface in the context of HSPGs preferentially distributes into ECM that lacks HSPGs, possibly due to the absence of Shh sequestering molecules.

cell biology

Discordant perturbations of transcriptome and epigenome landscapes highlight dual roles of proinflammatory players in normal and IL1B-compromised OPC maturation trajectory in a prenatal model of diffuse white matter injury

Inflammatory insults accompanying prematurity provokes diffuse white matter injury (DWMI) which is associated with increased risk of neurodevelopmental disorders: pre-term infants have a 10 to 18-fold increased risk of developing autism spectrum disorders, compared to term infants. DWMI is due to maturation arrest in oligodendrocyte precursor cells (OPCs). Using integrated genome-wide approaches in a validated mouse perinatal model of DWMI, induced by systemic- and neuro-inflammation based on repeated interleukin-1B administrations, we show that neuroinflammation induces limited epigenomic disturbances in OPCs. In contrast, we unravel marked transcriptomic alterations of genes of the immune/inflammatory pathways, which are expressed in unstressed OPCs and physiologically downregulated along OPC maturation. Consistently, we observe that transcription factors of the inflammatory pathways occupy DNA both in unstressed and inflamed OPCs. Thus, rather than altering genome-wide chromatin accessibility, neuroinflammation takes advantage of open chromatin regions and deeply counteracts the stage-dependent downregulation of these active transcriptional programs. Therefore, our study opens new avenues for the future development of targeted approaches to protect preterm brains. Highlights{circ} Limited epigenomic impact of inflammation on OPC maturation blockade {circ}Major transcriptomic disturbances take advantage of a primed epigenetic landscape {circ}Proinflammatory genes are active in OPCs and downregulated upon maturation {circ}Neuroinflammation counteracts both this downregulation and maturation in OPCs

developmental biology

GRID - Genomics of Rare Immune Disorders: a highly sensitive and specific diagnostic gene panel for patients with primary immunodeficiencies

Primary Immune disorders affect 15,000 new patients every year in Europe. Genetic tests are usually performed on a single or very limited number of genes leaving the majority of patients without a genetic diagnosis. We designed, optimised and validated a new clinical diagnostic platform called GRID, Genomics of Rare Immune Disorders, to screen in parallel 279 genes, including 2015 IUIS genes, known to be causative of Primary Immune disorders (PID). Validation to clinical standard using more than 58,000 variants in 176 PID patients shows an excellent sensitivity, specificity. The customised and automated bioinformatics pipeline prioritises and reports pertinent Single Nucleotide Variants (SNVs), INsertions and DELetions (INDELs) as well as Copy Number Variants (CNVs). An example of the clinical utility of the GRID panel, is represented by a patient initially diagnosed with X-linked agammaglobulinemia due to a missense variant in the BTK gene with severe inflammatory bowel disease. GRID results identified two additional compound heterozygous variants in IL17RC, potentially driving the altered phenotype.

genomics

Novel DNA methylation sites of glucose and insulin homeostasis: an integrative cross-omics analysis

Despite existing reports on differential DNA methylation in type 2 diabetes (T2D) and obesity, our understanding of the functional relevance of the phenomenon remains limited. Because obesity is the main risk factor for T2D and a driver of methylation from previous study, we aimed to explore the effect of DNA methylation in the early phases of T2D pathology while accounting for body mass index (BMI). We performed a blood-based epigenome-wide association study (EWAS) of fasting glucose and insulin among 4,808 non-diabetic European individuals and replicated the findings in an independent sample consisting of 11,750 non-diabetic subjects. We integrated blood-based in silico cross-omics databases comprising genomics, epigenomics and transcriptomics collected by BIOS project of the Biobanking and BioMolecular resources Research Infrastructure of the Netherlands (BBMRI-NL), the Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC), the DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) consortium, and the tissue-specific Genotype-Tissue Expression (GTEx) project. We identified and replicated nine novel differentially methylated sites in whole blood (P-value < 1.27 x 10-7): sites in LETM1, RBM20, IRS2, MAN2A2 genes and 1q25.3 region were associated with fasting insulin; sites in FCRL6, SLAMF1, APOBEC3H genes and 15q26.1 region were associated with fasting glucose. The association between SLAMF1, APOBEC3H and 15q26.1 methylation sites and glucose emerged only when accounted for BMI. Follow-up in silico cross-omics analyses indicate that the cis-acting meQTLs near SLAMF1 and SLAMF1 expression are involved in glucose level regulation. Moreover, our data suggest that differential methylation in FCRL6 may affect glucose level and the risk of T2D by regulating FCLR6 expression in the liver. In conclusion, the present study provided nine new DNA methylation sites associated with glycemia homeostasis and also provided new insights of glycemia related loci into the genetics, epigenetics and transcriptomics pathways based on the integration of cross-omics data in silico.

genomics

Spatial updating of attention across eye movements: A neuro-computational approach

While scanning our environment, the retinal image changes with every saccade. Nevertheless, the visual system anticipates where an attended target will be next and attention is updated to the new location. Recently, two different types of perisaccadic attentional updates were discovered: Predictive remapping of attention before saccade onset (Rolfs, Jonikaitis, Deubel, & Cavanagh, 2011) as well as lingering of attention after saccade (Golomb, Chun, & Mazer, 2008; Golomb, Pulido, Albrecht, Chun, & Mazer, 2010). We here propose a neurocomputational model located in LIP based on a previous model of perisaccadic space perception (Ziesche & Hamker, 2011, 2014). Our model can account for both types of updating of attention at a neural systems level. The lingering effect originates from the late updating of the proprioceptive eye position signal and the remapping from the early corollary discharge signal. We put these results in relationship to predictive remapping of receptive fields and show that both phenomena arise from the same simple, recurrent neural circuit. Thus, together with the previously published results, the model provides a comprehensive framework to discuss multiple experimental observations that occur around saccades.

neuroscience

The intrinsic and regulated proteomes of barley seeds in response to fungal infection

Barley is an important cereal grain used for beer brewing, animal feed, and human food consumption. Fungal disease can impact barley production, as it causes substantial yield loss and lowers seed quality. We used sequential window acquisition of all theoretical ions mass spectrometry (SWATH-MS) to measure and quantify the relative abundance of proteins within seeds of different barley varieties under various fungal pathogen burdens. Fungal burden in the leaves and stems of barley resulted in changes to the seed proteome. However, these changes were minimal and showed substantial variation among barley samples infected with different pathogens. The limited effect of intrinsic disease resistance on the seed proteome is consistent with the main mediators of disease resistance being present in the leaves and stems of the plant. The seeds of barley varieties accredited for use as malt had higher levels of proteins associated with starch synthesis and beer quality. The proteomic workflows developed and implemented here have potential application in quality control, breeding and processing of barley, and other agricultural products.

biochemistry

Loss Of Kat2a Enhances Transcriptional Noise And Depletes Acute Myeloid Leukemia Stem-Like Cells

Acute Myeloid Leukemia (AML) is an aggressive hematological malignancy with abnormal progenitor self-renewal and defective myelo-monocytic differentiation. Its pathogenesis comprises subversion of transcriptional regulation, through mutation and by hijacking normal chromatin regulation. Kat2a is a histone acetyltransferase central to promoter activity that we recently associated with stability of pluripotency networks, and identified as a genetic vulnerability in AML. Through combined chromatin profiling and single-cell transcriptomics, we demonstrate that Kat2a contributes to leukemia propagation through homogeneity of transcriptional programs and preservation of leukemia stem-like cells. Kat2a loss reduces transcriptional bursting frequency in a subset of gene promoters, generating enhanced variability of transcript levels but minimal effects on mean gene expression. Destabilization of target programs shifts cellular equilibrium out of self-renewal towards differentiation. We propose that control of transcriptional variability is central to leukemia stem-like cell propagation, and establish a paradigm exploitable in different tumors and at distinct stages of cancer evolution.

cancer biology

Distinct neural mechanisms and temporal constraints govern a cascade of audiotactile interactions

Asynchrony is a critical cue informing the brain whether sensory signals are caused by a common source and should be integrated or segregated. It is unclear how the brain binds audiotactile signals into behavioural benefits depending on their asynchrony. Participants actively responded (psychophysics) or passively attended (electroencephalogrpahy) to noise bursts, taps-to-the-face, and their audiotactile (AT) combinations at seven audiotactile asynchronies: 0, {+/-}20, {+/-}70, and {+/-}500ms. Observers were faster at detecting AT than unisensory stimuli, maximally for synchronous stimulation and declining within a [&le;]70ms temporal integration window. We observed AT interactions for (1) near-synchronous stimuli within a [&le;]20ms temporal integration window for evoked response potentials (ERPs) at 110ms and [~]400ms, (2) specifically {+/-}70ms asynchronies, across the P200 ERP and theta-band inter-trial coherence (ITC) and power at [~]200ms, with a frontocentral topography, and (3) beta-band power across several asynchronies. Our results suggest that early AT interactions for ERP and theta-band ITC and power mediate behavioural response facilitation within a [&le;]70ms temporal integration window, but beta-band power reflects AT interactions that are less relevant for behaviour. This diversity of temporal profiles and constraints demonstrates how audiotactile integration unfolds in a cascade of interactions to generate behavioural benefits.

neuroscience

Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

Perennial grasses are promising feedstocks for biofuel production. The phyllosphere (aerial surfaces) of these cellulosic crops provide a sizable surface area of microbial habitation. Leaf microbial communities may benefit the host plant, have consequence for biomass deconstruction, and interact with foliar pathogens. Here, we characterized the origins, diversity, and assembly of bacterial and archaeal communities of two perennial cellulosic feedstocks: switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus x giganteus). We used 16S rRNA gene sequencing to assess microbiome structure on leaves and soils, following crop phenology every three weeks from pre-emergence through senescence for one miscanthus growing season and two consecutive switchgrass seasons. We found abundant and persistent core leaf taxa that originated in soil but were adapted for life on the leaf, rather than vagabonds that randomly disperse from air or soil. Seasonal and host-specific assembly suggested a functional relationship between the phyllosphere microbiomes and plants. This foundational knowledge advances goals to leverage native microbiomes to promote crop wellness and productivity in the field, and specifically in support of biofuels agriculture.

microbiology

Authorship inflation and author gender in pulmonology research.

IntroductionHonorary authorship and equal gender representation are two pressing matters in scientific research. Honorary authorship is the inclusion of authors who do not meet the criteria established by the International Committee of Medical Journal Editors (ICMJE) authorship guidelines. The inclusion of honorary authors in the medical literature has led to an increase of the number of authors on studies and a decrease in single author studies in various fields.\n\nMethodsOur primary objective was to assess authorship trends in two major pulmonology journals (selected on the basis of Google Scholar rankings): Thorax and American Journal of Respiratory and Critical Care Medicine. We reviewed all articles published in both journals in the years 1994, 2004, and 2014 using Web of Science and extracted data such as number of authors and gender of the first and last authors.\n\nResultsThe total number of authors steadily increased from 1994 to 2014. The median number of authors grew from about four in 1994 to nearly seven in 2014, which is approximately a 75% increase. When we compiled all the data, we found the percentage of female authors from both journals had increased from 17% to 29.9% during the study period.\n\nDiscussionWe found an increase in the average number of authors on pulmonology publications between 1994 and 2014 as well as an increase in the number of females with a lead or main author position. This may be due to a variety of factors, such as increased team science. However, our data in conjunction with data from other areas of medicine, indicate that honorary authorship may be contributing to the trends we identified.

scientific communication and education

CopySwitch - in vivo optimization of gene copy numbers for heterologous gene expression in Bacillus subtilis

1.The Gram-positive bacterium Bacillus subtilis has long been used as a host for production and secretion of industrially relevant enzymes like amylases and proteases. It is imperative for optimal efficiency, to balance protein yield and correct folding. Gene copy numbers are an important tuning valve for the optimization of heterologous gene expression. While some genes are best expressed from many gene copies, for other genes, medium or even single copy numbers are the only way to avoid formation of inclusion bodies, toxic gene dosage effects or achieve desired levels for metabolic engineering. In order to provide a simple and robust method to address above-mentioned issues in the Gram-positive bacterium Bacillus subtilis, we have developed an automatable system for the tuning of heterologous gene expression based on the hosts intrinsic natural competence and homologous recombination capabilities. By supplying our reporter strains with a linearized, low copy number plasmid containing homology regions left and right of the reporter genes and an antibiotic resistance marker, we could show an up to 3.6-fold higher gfp (green fluorescent protein) expression and up to 1.3-fold higher mPLC (mature phospholipase C) expression after successful recombination and thus circularization of our plasmid. Furthermore, the plasmid-borne gfp expression seems to be more stable, since over the whole cultivation period the share of fluorescent cells compared to all measured cells is consistently higher.

bioengineering

Multi-Method Molecular Characterisation of Human Dust-Mite-associated Allergic Asthma

Asthma is a chronic inflammatory disorder of the airways. Disease presentation varies greatly in terms of cause, development, severity, and response to medication, and thus the condition has been subdivided into a number of asthma phenotypes. There is still an unmet need for the identification of phenotype-specific markers and accompanying molecular tools that facilitate the classification of asthma phenotype. To this end, we utilised a range of molecular tools to characterise a well-defined group of adults with poorly controlled asthma associated with house dust mite (HDM) allergy, relative to non-asthmatic control subjects. Circulating messenger RNA (mRNA) and microRNA (miRNA) were sequenced and quantified, and a differential expression analysis of the two RNA populations performed to determine how gene expression and regulation varied in the disease state. Further, a number of circulating proteins (IL-4, 5, 10, 17A, Eotaxin, GM-CSF, IFNy, MCP-1, TARC, TNFa, Total IgE, and Endotoxin) were quantified to determine whether the protein profiles differed significantly dependent on disease state. Finally, assessment of the circulating \"blood microbiome\" was performed using 16S rRNA amplification and sequencing. Asthmatic subjects displayed a range of significant alterations to circulating gene expression and regulation, relative to healthy control subjects, that may influence systemic immune activity. Notably, several circulating mRNAs were detected in the plasma in a condition-specific manner, and many more were found to be expressed at altered levels. Proteomic analysis revealed increased levels of inflammatory proteins within the serum, and decreased levels of the bacterial endotoxin protein in the asthma state. Comparison of blood microbiome composition revealed a significant increase in the Firmicutes phylum with asthma that was associated with a concomitant reduction in the Proteobacteria phylum. This study provides a valuable insight into the systemic changes evident in the HDM-associated asthma, identifies a range of molecules that are present in the circulation in a condition-specific manner (with clear biomarker potential), and highlights a range of hypotheses for further study.

molecular biology

Focusing on what matters: Modulation of the human hippocampus by relational attention

Hippocampal episodic memory is fundamentally relational, consisting of links between events and the spatial and temporal contexts in which they occurred. Such relations are also important over much shorter time periods, during online visual perception. For example, how do we assess the relative spatial positions of objects, their temporal order, or the relationship between their features? Here, we investigate the role of the hippocampus in such online relational processing by manipulating visual attention to different kinds of relations in a dynamic display. While undergoing high-resolution fMRI, participants viewed two images in rapid succession on each trial and performed one of three relational tasks, judging the images relative: spatial positions, temporal onsets, or sizes. As a control, they sometimes also judged whether one image was tilted, irrespective of the other; this served as a baseline item task with no demands on relational processing. All hippocampal regions of interest (CA1, CA2/3/DG, subiculum) showed reliable deactivation when participants attended to relational vs. item information. Attention to temporal relations was associated with more robust deactivation than the other conditions. One possible interpretation of such deactivation is that it reflects hippocampal disengagement. If true, there should be reduced information content and noisier, less reliable patterns of activity in the hippocampus for the temporal vs. other tasks. Instead, analyses of multivariate activity patterns revealed more stable hippocampal representations in the temporal task. Additional analyses showed that this increased pattern similarity was not simply a reflection of the lower univariate activity. Thus, the hippocampus differentiates between relational and item processing even during online visual perception, and its representations of temporal relations in particular are robust and stable. Together, these findings suggest that the relational computations of the hippocampus, known to be important for memory, extend beyond this purpose, enabling the rapid online extraction of relational information in visual perception.

neuroscience

Explaining heritable variance in human character

Personality is moderately heritable (around 40%), across a variety of measures [1]. Non-linear genetic influences (subsumed by the influence of the \"dominance\" factor in the heritability literature) likely play a large role in the genetics of personality [2], even more so than for other phenotypes. Zwir and colleagues [3] sought to identify sets of SNPs that, through both additive and interactive effects, explain the previously observed heritability of personality. The abstract reported identification of a set of SNPs that \"explained nearly all the heritability expected for character in each sample (50 to 58%).\" This reported effect size is extraordinary. The papers Supplemental Materials reveal how such an estimate occurred.\n\nThe variance explained in character by the identified SNPs are the R2 values from regression models in which polygenic scores were fit and evaluated within each of three samples (Finnish, ...

genetics

On Parameter Interpretability of Phenomenological-Based Semiphysical Models

Empirical and phenomenological based models are used to represent biological and physiological processes. Phenomenological models are derived from the knowledge of the mechanisms that underlie the behaviour of the system under study, while empirical models are derived from analysis of data to quantify relationships between variables of interest. For studying biological systems, the phenomenological modeling approach offers the great advantage of having a structure with variables and parameters with physical meaning that enhance the interpretability of the model and its further used for decision making. The interpretability property of models, however, remains a vague concept. In this study, we tackled the interpretability property for parameters of phenomenological-based models. To our knowledge, this property has not been deeply discussed, perhaps by the implicit assumption that interpretability is inherent to the phenomenological-based models. We propose a conceptual framework to address the parameter interpretability and its implications for parameter identifiability. We use as battle horse a simple but relevant model representing the enzymatic degradation of {beta}-casein by a Lactococcus lactis bacterium.

bioengineering

Conformational states control Lck switching between free and confined diffusion modes in T cells

T cell receptor (TCR) phosphorylation by Lck is an essential step in T cell activation. It is known the conformational states of Lck control enzymatic activity; however, the underlying principles of how Lck finds its substrate in the plasma membrane remain elusive. Here, single-particle tracking is paired with photoactivatable localization microscopy (sptPALM) to observe the diffusive modes of Lck in the plasma membrane. Individual Lck molecules switched between free and confined diffusion in resting and stimulated T cells. Conformational state, but not partitioning into membrane domains, caused Lck confinement as open conformation Lck was more confined than closed. Further confinement of kinase-dead versions of Lck suggests that Lck interacts with open active Lck to cause confinement, irrespectively of kinase activity. Our data supports a model that confined diffusion of open Lck results in high local phosphorylation rates and closed Lck diffuses freely to enable wide-range scanning of the plasma membrane.

immunology