EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery

MOTIVATION

Automated chromatin segmentation based on ChIP-seq (chromatin immunoprecipitation followed by sequencing) data reveals insights into the epigenetic regulation of chromatin accessibility. Existing segmentation methods are constrained by simplifying modeling assumptions, which may have a negative impact on the segmentation quality.

RESULTS

We introduce EpiSegMix, a novel segmentation method based on a hidden Markov model with flexible read count distribution types and state duration modeling, allowing for a more flexible modeling of both histone signals and segment lengths. In a comparison with existing tools, ChromHMM, Segway, and EpiCSeg, we show that EpiSegMix is more predictive of cell biology, such as gene expression. Its flexible framework enables it to fit an accurate probabilistic model, which has the potential to increase the biological interpretability of chromatin states.

AVAILABILITY AND IMPLEMENTATION

Source code: https://gitlab.com/rahmannlab/episegmix.

Enhanced medullary and extramedullary granulopoiesis sustain the inflammatory response in lupus nephritis

OBJECTIVES

In SLE, deregulation of haematopoiesis is characterised by inflammatory priming and myeloid skewing of haematopoietic stem and progenitor cells (HSPCs). We sought to investigate the role of extramedullary haematopoiesis (EMH) as a key player for tissue injury in systemic autoimmune disorders.

METHODS

Transcriptomic analysis of bone marrow (BM)-derived HSPCs from patients with SLE and NZBW/F1 lupus-prone mice was performed in combination with DNA methylation profile. Trained immunity (TI) was induced through β-glucan administration to the NZBW/F1 lupus-prone model. Disease activity was assessed through lupus nephritis (LN) histological grading. Colony-forming unit assay and adoptive cell transfer were used to assess HSPCs functionalities.

RESULTS

Transcriptomic analysis shows that splenic HSPCs carry a higher inflammatory potential compared with their BM counterparts. Further induction of TI, through β-glucan administration, exacerbates splenic EMH, accentuates myeloid skewing and worsens LN. Methylomic analysis of BM-derived HSPCs demonstrates myeloid skewing which is in part driven by epigenetic tinkering. Importantly, transcriptomic analysis of human SLE BM-derived HSPCs demonstrates similar findings to those observed in diseased mice.

CONCLUSIONS

These data support a key role of granulocytes derived from primed HSPCs both at medullary and extramedullary sites in the pathogenesis of LN. EMH and TI contribute to SLE by sustaining the systemic inflammatory response and increasing the risk for flare.

Mutual Regulation of Transcriptomes between Murine Pneumocytes and Fibroblasts Mediates Alveolar Regeneration in Air-Liquid Interface Cultures

Alveolar type 2 and club cells are part of the stem cell niche of the lung and their differentiation is required for pulmonary homeostasis and tissue regeneration. A disturbed crosstalk between fibroblasts and epithelial cells contributes to the loss of lung structure in chronic lung diseases. Therefore, it is important to understand how fibroblasts and lung epithelial cells interact during regeneration. Here, we analyzed the interaction of fibroblasts and the alveolar epithelium modeled in air-liquid interface cultures. Single-cell transcriptomics showed that cocultivation with fibroblasts leads to increased expression of type 2 markers in pneumocytes, activation of regulons associated with the maintenance of alveolar type 2 cells (e.g., Etv5), and transdifferentiation of club cells toward pneumocytes. This was accompanied by an intensified transepithelial barrier. Vice versa, the activation of NF-κB pathways and the CEBPB regulon and the expression of IL-6 and other differentiation factors (e.g., fibroblast growth factors) were increased in fibroblasts cocultured with epithelial cells. Recombinant IL-6 enhanced epithelial barrier formation. Therefore, in our coculture model, regulatory loops were identified by which lung epithelial cells mediate regeneration and differentiation of the alveolar epithelium in a cooperative manner with the mesenchymal compartment.

Molecular control of endurance training adaptation in male mouse skeletal muscle

Skeletal muscle has an enormous plastic potential to adapt to various external and internal perturbations. Although morphological changes in endurance-trained muscles are well described, the molecular underpinnings of training adaptation are poorly understood. We therefore aimed to elucidate the molecular signature of muscles of trained male mice and unravel the training status-dependent responses to an acute bout of exercise. Our results reveal that, even though at baseline an unexpectedly low number of genes define the trained muscle, training status substantially affects the transcriptional response to an acute challenge, both quantitatively and qualitatively, in part associated with epigenetic modifications. Finally, transiently activated factors such as the peroxisome proliferator-activated receptor-γ coactivator 1α are indispensable for normal training adaptation. Together, these results provide a molecular framework of the temporal and training status-dependent exercise response that underpins muscle plasticity in training.

Age-Associated Changes in Endothelial Transcriptome and Epigenetic Landscapes Correlate With Elevated Risk of Cerebral Microbleeds

Background Stroke is a leading global cause of human death and disability, with advanced aging associated with elevated incidences of stroke. Despite high mortality and morbidity of stroke, the mechanisms leading to blood-brain barrier dysfunction and development of stroke with age are poorly understood. In the vasculature of brain, endothelial cells (ECs) constitute the core component of the blood-brain barrier and provide a physical barrier composed of tight junctions, adherens junctions, and basement membrane. Methods and Results We show, in mice, the incidents of intracerebral bleeding increases with age. After isolating an enriched population of cerebral ECs from murine brains at 2, 6, 12, 18, and 24 months, we studied age-associated changes in gene expression. The study reveals age-dependent dysregulation of 1388 genes, including many involved in the maintenance of the blood-brain barrier and vascular integrity. We also investigated age-dependent changes on the levels of CpG methylation and accessible chromatin in cerebral ECs. Our study reveals correlations between age-dependent changes in chromatin structure and gene expression, whereas the dynamics of DNA methylation changes are different. Conclusions We find significant age-dependent downregulation of the Aplnr gene along with age-dependent reduction in chromatin accessibility of promoter region of the Aplnr gene in cerebral ECs. Aplnr is associated with positive regulation of vasodilation and is implicated in vascular health. Altogether, our data suggest a potential role of the apelinergic axis involving the ligand apelin and its receptor to be critical in maintenance of the blood-brain barrier and vascular integrity.

Alterations in the hepatocyte epigenetic landscape in steatosis

Fatty liver disease or the accumulation of fat in the liver, has been reported to affect the global population. This comes with an increased risk for the development of fibrosis, cirrhosis, and hepatocellular carcinoma. Yet, little is known about the effects of a diet containing high fat and alcohol towards epigenetic aging, with respect to changes in transcriptional and epigenomic profiles. In this study, we took up a multi-omics approach and integrated gene expression, methylation signals, and chromatin signals to study the epigenomic effects of a high-fat and alcohol-containing diet on mouse hepatocytes. We identified four relevant gene network clusters that were associated with relevant pathways that promote steatosis. Using a machine learning approach, we predict specific transcription factors that might be responsible to modulate the functionally relevant clusters. Finally, we discover four additional CpG loci and validate aging-related differential CpG methylation. Differential CpG methylation linked to aging showed minimal overlap with altered methylation in steatosis.

A Monoclonal Human Alveolar Epithelial Cell Line ("Arlo") with Pronounced Barrier Function for Studying Drug Permeability and Viral Infections

In the development of orally inhaled drug products preclinical animal models regularly fail to predict pharmacological as well as toxicological responses in humans. Models based on human cells and tissues are potential alternatives to animal experimentation allowing for the isolation of essential processes of human biology and making them accessible in vitro. Here, the generation of a novel monoclonal cell line "Arlo," derived from the polyclonal human alveolar epithelium lentivirus immortalized cell line hAELVi via single-cell printing, and its characterization as a model for the human alveolar epithelium as well as a building block for future complex in vitro models is described. "Arlo" is systematically compared in vitro to primary human alveolar epithelial cells (hAEpCs) as well as to the polyclonal hAELVi cell line. "Arlo" cells show enhanced barrier properties with high transepithelial electrical resistance (TEER) of ≈3000 Ω cm2 and a potential difference (PD) of ≈30 mV under air-liquid interface (ALI) conditions, that can be modulated. The cells grow in a polarized monolayer and express genes relevant to barrier integrity as well as homeostasis as is observed in hAEpCs. Successful productive infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a proof-of-principle study offers an additional, attractive application of "Arlo" beyond biopharmaceutical experimentation.

Green room temperature synthesis of silver-gold alloy nanoparticles

Metallic alloy nanoparticles (NPs) exhibit interesting optical, electrical and catalytic properties, dependent on their size, shape and composition. In particular, silver-gold alloy NPs are widely applied as model systems to better understand the syntheses and formation (kinetics) of alloy NPs, as the two elements are fully miscible. Our study targets product design via environmentally friendly synthesis conditions. We use dextran as the reducing and stabilizing agent for the synthesis of homogeneous silver-gold alloy NPs at room temperature. Our approach is a one-pot, low temperature, reaction-controlled, green and scalable synthesis route of well-controlled composition and narrow particle size distribution. The composition over a broad range of molar gold contents is confirmed by scanning transmission electron microscopy-energy-dispersive X-ray spectroscopy (STEM-EDX) measurements and auxiliary inductively coupled plasma-optical emission spectroscopy measurements (ICP-OES). The distributions of the resulting particles in size and composition are obtained from multi-wavelength analytical ultracentrifugation using the optical back coupling method and further confirmed by high-pressure liquid chromatography. Finally, we provide insight into the reaction kinetics during the synthesis, discuss the reaction mechanism and demonstrate possibilities for scale-up by a factor of more than 250 by increasing the reactor volume and NP concentration.

Hypomorphic RAG deficiency: impact of disease burden on survival and thymic recovery argues for early diagnosis and HSCT

Patients with hypomorphic mutations in the RAG1 or RAG2 gene present with either Omenn syndrome or atypical combined immunodeficiency with a wide phenotypic range. Hematopoietic stem cell transplantation (HSCT) is potentially curative, but data are scarce. We report on a worldwide cohort of 60 patients with hypomorphic RAG variants who underwent HSCT, 78% of whom experienced infections (29% active at HSCT), 72% had autoimmunity, and 18% had granulomas pretransplant. These complications are frequently associated with organ damage. Eight individuals (13%) were diagnosed by newborn screening or family history. HSCT was performed at a median of 3.4 years (range 0.3-42.9 years) from matched unrelated donors, matched sibling or matched family donors, or mismatched donors in 48%, 22%, and 30% of the patients, respectively. Grafts were T-cell depleted in 15 cases (25%). Overall survival at 1 and 4 years was 77.5% and 67.5% (median follow-up of 39 months). Infection was the main cause of death. In univariable analysis, active infection, organ damage pre-HSCT, T-cell depletion of the graft, and transplant from a mismatched family donor were predictive of worse outcome, whereas organ damage and T-cell depletion remained significant in multivariable analysis (hazard ratio [HR] = 6.01, HR = 8.46, respectively). All patients diagnosed by newborn screening or family history survived. Cumulative incidences of acute and chronic graft-versus-host disease were 35% and 22%, respectively. Cumulative incidences of new-onset autoimmunity was 15%. Immune reconstitution, particularly recovery of naïve CD4+ T cells, was faster and more robust in patients transplanted before 3.5 years of age, and without organ damage. These findings support the indication for early transplantation.

Transfer of blocker-based qPCR reactions for DNA methylation analysis into a microfluidic LoC system using thermal modeling

Changes in the DNA methylation landscape are associated with many diseases like cancer. Therefore, DNA methylation analysis is of great interest for molecular diagnostics and can be applied, e.g., for minimally invasive diagnostics in liquid biopsy samples like blood plasma. Sensitive detection of local de novo methylation, which occurs in various cancer types, can be achieved with quantitative HeavyMethyl-PCR using oligonucleotides that block the amplification of unmethylated DNA. A transfer of these quantitative PCRs (qPCRs) into point-of-care (PoC) devices like microfluidic Lab-on-Chip (LoC) cartridges can be challenging as LoC systems show significantly different thermal properties than qPCR cyclers. We demonstrate how an adequate thermal model of the specific LoC system can help us to identify a suitable thermal profile, even for complex HeavyMethyl qPCRs, with reduced experimental effort. Using a simulation-based approach, we demonstrate a proof-of-principle for the successful LoC transfer of colorectal SEPT9/ACTB-qPCR from Epi Procolon® colorectal carcinoma test, by avoidance of oligonucleotide interactions.

Increased chromatin accessibility facilitates intron retention in specific cell differentiation states

Dynamic intron retention (IR) in vertebrate cells is of widespread biological importance. Aberrant IR is associated with numerous human diseases including several cancers. Despite consistent reports demonstrating that intrinsic sequence features can help introns evade splicing, conflicting findings about cell type- or condition-specific IR regulation by trans-regulatory and epigenetic mechanisms demand an unbiased and systematic analysis of IR in a controlled experimental setting. We integrated matched mRNA sequencing (mRNA-Seq), whole-genome bisulfite sequencing (WGBS), nucleosome occupancy methylome sequencing (NOMe-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) data from primary human myeloid and lymphoid cells. Using these multi-omics data and machine learning, we trained two complementary models to determine the role of epigenetic factors in the regulation of IR in cells of the innate immune system. We show that increased chromatin accessibility, as revealed by nucleosome-free regions, contributes substantially to the retention of introns in a cell-specific manner. We also confirm that intrinsic characteristics of introns are key for them to evade splicing. This study suggests an important role for chromatin architecture in IR regulation. With an increasing appreciation that pathogenic alterations are linked to RNA processing, our findings may provide useful insights for the development of novel therapeutic approaches that target aberrant splicing.

Identification of an FXR-modulated liver-intestine hybrid state in iPSC-derived hepatocyte-like cells

BACKGROUND & AIMS

Pluripotent stem cell (PSC)-derived hepatocyte-like cells (HLC) have enormous potential as a replacement for primary hepatocytes in drug screening, toxicology and cell replacement therapy, but their genome-wide expression patterns differ strongly from primary human hepatocytes (PHH).

METHODS

We differentiated human induced pluripotent stem cells (hiPSC) via definitive endoderm to HLC and characterized the cells by single-cell and bulk RNA-seq, with complementary epigenetic analyses. We then compared HLC to PHH and publicly available data on human fetal hepatocytes (FH) ex vivo; we performed bioinformatics-guided interventions to improve HLC differentiation via lentiviral transduction of the nuclear receptor FXR and agonist exposure.

RESULTS

Single-cell RNA-seq revealed that transcriptomes of individual HLC display a hybrid state, where hepatocyte-associated genes are expressed in concert with genes that are not expressed in PHH - mostly intestinal genes - within the same cell. Bulk-level overrepresentation analysis, as well as regulon analysis at the single-cell level, identified sets of regulatory factors discriminating HLC, FH, and PHH, hinting at a central role for the nuclear receptor FXR in the functional maturation of HLC. Combined FXR expression plus agonist exposure enhanced the expression of hepatocyte-associated genes and increased the ability of bile canalicular secretion as well as lipid droplet formation, thereby increasing HLCs' similarity to PHH. The undesired non-liver gene expression was reproducibly decreased, although only by a moderate degree.

CONCLUSION

In contrast to physiological hepatocyte precursor cells and mature hepatocytes, HLC co-express liver and hybrid genes in the same cell. Targeted modification of the FXR gene regulatory network improves their differentiation by suppressing intestinal traits whilst inducing hepatocyte features.

LAY SUMMARY

Generation of human hepatocytes from stem cells represents an active research field but its success is hampered by the fact that the stem cell-derived 'hepatocytes' still show major differences to hepatocytes obtained from a liver. Here, we identified an important reason for the difference, specifically that the stem cell-derived 'hepatocyte' represents a hybrid cell with features of hepatocytes and intestinal cells. We show that a specific protein (FXR) suppresses intestinal and induces liver features, thus bringing the stem cell-derived cells closer to hepatocytes derived from human livers.

Differences in circulating cardiac troponin I and T in acute and chronic cardiac disease

Background

Clinical practice and guidelines assume that cardiac troponin I (cTnI) and cTnT are interchangeable, reflecting identical pathophysiological processes. However, it is unknown if cTnI and cTnT really are equivalent measures in different pathophysiological settings.

Purpose

To highlight potential differences in the release of cTnI and cTnT.

Methods

Large pooled cohort analysis including extensively characterized individuals, stratified into three groups: no cardiac disease (normal aging), chronic cardiac disease, and acute cardiac disease. Circulating cTnI and cTnT concentrations were measured blinded to clinical data using high-sensitivity assays (hs-cTnI-Architect, hs-cTnT-Elecsys) and their ratio calculated. Findings were validated using a second hs-cTnI assay (hs-cTnI-Clarity).

Results

Among 8719 individuals, 29% female, 10% had no known cardiac disease, 71% chronic cardiac disease, and 20% acute cardiac disease. Baseline characteristics including renal function were comparable between individuals with chronic and acute cardiac disease. Normal aging (without cardiac disease) was associated with a disproportional increase in cTnT versus cTnI (low cTnI/cTnT ratio, median 0.50, IQR 0.38–0.68). Although older, patients with chronic cardiac disease had a slightly higher cTnI/cTnT ratio (median 0.53, IQR 0.37–0.79, p<0.05). In contrast, in patients with acute cardiac disease, cTnI concentrations were disproportionally elevated compared to cTnT concentrations, resulting in a cTnI/cTnT ratio of 1.96 (IQR 0.93–4.73, p<0.001). Internal validation using a second hs-cTnI assay confirmed these findings.

Conclusion

These findings suggest relevant differences in the release of cTnI and cTnT with a greater release of cTnT versus cTnI in normal aging and a disproportional increase in cTnI versus cTnT in acute cardiac disease.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): Swiss National Science Foundation

Detrimental effects of intense vasodilation in women with acute heart failure: novel insights from a prospective randomized controlled trial

Background

Guidelines recommend evaluating the risk/benefit ratio of novel therapies individually in women and men, as the pathophysiology and the response to treatment may differ according to sex. Among patients with acute heart failure (AHF), a strategy of intensive vasodilation, compared with usual care, overall did provide comparable outcomes. However, sex-specific differences in heart failure pathophysiology and the effect of the strategy in women with AHF remained unclear.

Purpose

To characterize sex-specific differences in heart failure pathophysiology and to evaluate the effect of a strategy that emphasized early intensive and sustained vasodilation in women with AHF.

Methods

In a randomized, open-label blinded-end-point trial patients hospitalized for AHF were enrolled in 10 hospitals in Switzerland, Bulgaria, Germany, Brazil, and Spain. Inclusion criteria were AHF expressed by acute dyspnea and increased plasma concentrations of natriuretic peptides, systolic blood pressure ≥100 mmHg, and a plan for treatment in a general ward. Patients were randomized 1:1 to a strategy of early intensive and sustained vasodilation throughout the hospitalization or usual care. The primary end point was a composite of all-cause mortality or rehospitalization for AHF at 180 days. The subgroup analysis according to sex was predefined.

Results

Among 781 patients who completed the trial, 288 (36.9%) were women. Women were significantly older, had a higher systolic blood pressure at presentation and a more common history of diastolic dysfunction (all ps<0.05), whereas men had a significantly higher body surface area, a more common history of ischemic heart disease and a significant lower left ventricular ejection fraction (all ps<0.05). The primary end point, a composite of all-cause mortality or rehospitalization for AHF at 180 days, occurred in 53 female patients (37.9%) in the intervention group (including 28 deaths [20.0%]) and in 35 female patients (23.6%) in the usual care group (including 22 deaths [14.9%]) (absolute difference for the primary end point, 14.3%; adjusted hazard ratio, 1.62 [95% CI, 1.05–2.50]; P=0.03).

Conclusion

Among women with AHF, a strategy of early intensive and sustained vasodilation, compared with usual care, had a detrimental effect on a composite outcome of all-cause mortality and AHF rehospitalization at 180 days.

Funding Acknowledgement

Type of funding sources: Public hospital(s). Main funding source(s): University Hospital Basel

Prognostic value of a disease-specific health-related quality score in acute heart failure

Background

Despite the striking therapeutic progress made in the treatment of heart failure (HF), rehospitalization rate and mortality remain a major and often unpredictable problem. Previous studies have shown the prognostic value of Kansas City Cardiomyopathy Questionnaire (KCCQ), a score assessing disease-specific health-related quality of life in stable chronic HF patients. Recently, a large study including 4898 patients with acute HF (AHF) enrolled in China reported the incremental predictive ability of KCCQ for a composite outcome of death and rehospitalization. However, these findings were not yet confirmed. In order to address this unmet need, the aim of this study was to examine the prognostic value of KCCQ in another AHF cohort.

Purpose

To validate the prognostic value of the KCCQ in AHF.

Methods

Goal-directed AfterLoad Reduction in Acute Congestive Cardiac Decompensation Study (GALACTIC) was a prospective, multicenter (n=10), randomized, interventional controlled trial enrolling adult patients presenting with AHF. KCCQ was assessed shortly after admission. We focused on the prognostic value of the short version KCCQ-12, explored the association with the composite of all-cause mortality and AHF rehospitalization within 30- and 180-day follow-up and compared it to the original score. Patients were grouped into quartiles according their KCCQ: high-risk (0–<25), moderate- to high-risk (25–<50), low- to moderate-risk (50–<75) and low-risk group (75–100). Cumulative incidence of assessed endpoints was displayed in Kaplan-Meier curves. Covariate adjustments were made using Cox regression. Prognostic accuracy over N-terminal pro-B-type natriuretic peptide (NT-proBNP) was evaluated by time-dependent area under the curve.

Results

Among 781 patients, 419 (median age 78, 35% female, 32% new onset of HF) had a complete set of variables to calculate KCCQ. Follow-up was available in all patients up to 180 days. 29 (7%) and 122 (29%) patients died or were rehospitalized for AHF within 30- and 180-days, respectively. Median KCCQ-12 was 37.5 with 25% of patients attaining the high- and 8% the low-risk group. After adjustment, each 10-point decrease in the KCCQ was associated with a 10% increase in 180-day risk regardless of new onset or acute decompensated chronic HF, age, sex, comorbidities, systolic blood pressure, creatinine, NT-proBNP and sodium levels. The prognostic ability for a 30-day risk was not significant. Using the same adjustments, a 10-point decrease in the original KCCQ was significant for a 20% and a 11% increase in risk for the short- and long-term composite outcome. The prognostic accuracy of KCCQ was comparable to NT-proBNP.

Conclusions

Health status, measured by the KCCQ-12 among patients with AHF, is significantly associated with a long-term composite outcome of all-cause mortality and AHF rehospitalization. The original KCCQ overall score is an independent predictor for both, the 30- and 180-day composite outcome.

Funding Acknowledgement

Type of funding sources: Public grant(s) – EU funding. Main funding source(s): European Union, the Swiss National Science Foundation

Using high-sensitivity cardiac troponin for the exclusion of inducible myocardial ischemia in patients without previously known coronary artery disease

Background

The rapid and safe exclusion of functionally relevant coronary artery disease (CAD) is a crucial, yet unmet clinical need. High-sensitivity cardiac troponin (hs-cTn) may be an attractive strategy, particularly in patients without previously known CAD.

Purpose

To derive and internally validate optimal rule-out cutoffs for an early and safe exclusion of functionally relevant CAD in symptomatic patients without previously known CAD.

Methods

In an ongoing single-center, prospective, cohort study, we enrolled consecutive patients without previously known CAD that were referred with symptoms possibly related to functionally relevant CAD. Cardiac troponin concentrations were measured at presentation using two high-sensitivity assays (Elecsys hs-cTnT and Architect hs-cTnI). Presence of functionally relevant CAD was adjudicated by 2 independent cardiologists, blinded to hs-cTn measurements, using MPI-SPECT/CT in all patients, as well as coronary angiography and fractional flow reserve measurements, whenever available. The primary diagnostic outcome was safety for early rule-out of functionally relevant CAD, quantified by sensitivity and the negative predictive value (NPV). The co-primary prognostic outcomes were cumulative incidences of cardiovascular death and all-cause death after 5 years. A NPV ≥90% and sensitivity ≥90% were predefined as acceptable performance criteria. The derived cutoffs were further evaluated in pre-specified subgroups. Internal validity was assessed with a bootstrapping procedure for a realistic estimate in similar future patients. Cumulative incidence curves stratified by the presence of functionally relevant CAD and hs-cTn concentrations below and above the derived cutoffs were constructed.

Results

Among 2111 eligible patients, 498 (23.6%) had a final diagnosis of functionally relevant CAD. Median age was 68 years and 938 (44.4%) were female. For ruling out functionally relevant CAD, a hs-cTnT concentration <5 ng/L resulted in a sensitivity of 90.8% (95% CI: 87.9–93.0%) and a NPV of 90.2% (95% CI: 87.1–92.5), triaging 468 (22.2%) patients towards rule-out. Similarly, a hs-cTnI concentration <2 ng/L resulted in a sensitivity of 91.6% (95% CI: 88.8–93.7%) and a NPV of 90.0% (95% CI: 86.8–92.6), triaging 422 (20.0%) patients. Internal validation showed robustness of these findings. The diagnostic performance of the derived cutoffs did not significantly vary across the subgroups. Hs-cTn concentrations above the derived cutoffs were associated with a substantially higher cumulative event rate of cardiovascular death (hs-cTnT: 7.0% vs. 0.8%; hs-cTnI: 6.6% vs. 1.2%) and all-cause death (hs-cTnT: 14.3% vs. 2.4%; hs-cTnI: 13.1% vs. 4.4%) during 5-years follow-up (log rank p<0.001 for all).

Conclusion

In symptomatic patients without previously known CAD, very low hs-cTn concentrations may generally allow to safely and effectively exclude functionally relevant CAD.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Swiss National Science FoundationSwiss Heart Foundation

Multidimensional characterization of noble metal alloy nanoparticles by multiwavelength analytical ultracentrifugation

In this study, we introduce a method for the simultaneous retrieval of two-dimensional size-composition distributions of noble metal Ag-Au alloy nanoparticles utilizing an analytical ultracentrifuge equipped with a multiwavelength extinction detector (MWL-AUC). MWL-AUC is used to measure coupled optical and sedimentation properties of the particles. The optical response of the nanoparticles is calculated using Mie's theory, where the particles' complex refractive index is corrected due to the effect of reduced mean free path of electrons. Using a combined analysis of the hydrodynamic and spectral data captured by MWL-AUC, the size and composition of the alloy particles is retrieved. Our method is validated through the analysis of synthetic data and by the very good agreement between experimental scanning transmission electron microscopy and our AUC data. The presented comprehensive characterization approach contributes to improved synthesis, scale-up and production of particulate systems as it provides a simple, fast and direct method to determine noble metal alloy nanoparticle size and composition distributions simultaneously.

Determination of specific and non-specific protein-protein interactions for beta-lactoglobulin by analytical ultracentrifugation and membrane osmometry experiments

Protein-protein interactions are essential for the understanding of biological processes. Specific protein aggregation is an important aspect for many biological systems. In particular, electrostatic interactions play the key role for protein-protein interactions, as many amino acids have pH-dependent charge states. Moreover, protein dissociation is directly related to the solution pH, ionic strength, temperature and protein concentration. The subtle interplay between different specific and non-specific interactions is demonstrated for beta-lactoglobulin (BLG) with a focus on low salt concentrations, thus mimicking technically relevant processing conditions. BLG is a well-characterized model system, proven to attain its monomer-dimer equilibrium strongly dependent upon the pH of the solution. In this manuscript, we present a unique combination of analytical ultracentrifugation and membrane osmometry experiments, which quantifies specific and non-specific interactions, i.e. in terms of the dimer dissociation constants and the second osmotic virial coefficient, at pH 3 and 7 and sodium chloride concentrations of 10 mM and 100 mM. This provides direct insight to protein-protein interactions for a system with a concentration-dependent monomer-dimer equilibrium. Moreover, using a coarse-grained extended DLVO model in combination with molecular dynamics simulations, we quantify non-specific monomer-monomer, monomer-dimer and dimer-dimer interactions as well as the binding free energy of BLG dimerization from theoretical calculations. The experimentally determined interactions are shown to be mainly governed by electrostatic interactions and further agree with free energy calculations. Our experimental protocol aims to determine non-specific and specific interactions for a dynamically interacting system and provides an understanding of protein-protein interactions for BLG at low salt concentrations.

Transcriptional and Epigenetic Consequences of DMSO Treatment on HepaRG Cells

Dimethyl sulfoxide (DMSO) is used to sustain or favor hepatocyte differentiation in vitro. Thus, DMSO is used in the differentiation protocol of the HepaRG cells that present the closest drug-metabolizing enzyme activities to primary human hepatocytes in culture. The aim of our study is to clarify its influence on liver-specific gene expression. For that purpose, we performed a large-scale analysis (gene expression and histone modification) to determine the global role of DMSO exposure during the differentiation process of the HepaRG cells. The addition of DMSO drives the upregulation of genes mainly regulated by PXR and PPARα whereas genes not affected by this addition are regulated by HNF1α, HNF4α, and PPARα. DMSO-differentiated-HepaRG cells show a differential expression for genes regulated by histone acetylation, while differentiated-HepaRG cells without DMSO show gene signatures associated with histone deacetylases. In addition, we observed an interplay between cytoskeleton organization and EMC remodeling with hepatocyte maturation.

Detailed stratified GWAS analysis for severe COVID-19 in four European populations

Given the highly variable clinical phenotype of Coronavirus disease 2019 (COVID-19), a deeper analysis of the host genetic contribution to severe COVID-19 is important to improve our understanding of underlying disease mechanisms. Here, we describe an extended genome-wide association meta-analysis of a well-characterized cohort of 3255 COVID-19 patients with respiratory failure and 12 488 population controls from Italy, Spain, Norway and Germany/Austria, including stratified analyses based on age, sex and disease severity, as well as targeted analyses of chromosome Y haplotypes, the human leukocyte antigen region and the SARS-CoV-2 peptidome. By inversion imputation, we traced a reported association at 17q21.31 to a ~0.9-Mb inversion polymorphism that creates two highly differentiated haplotypes and characterized the potential effects of the inversion in detail. Our data, together with the 5th release of summary statistics from the COVID-19 Host Genetics Initiative including non-Caucasian individuals, also identified a new locus at 19q13.33, including NAPSA, a gene which is expressed primarily in alveolar cells responsible for gas exchange in the lung.

DNA Methylation Biomarkers in Colorectal Cancer: Clinical Applications for Precision Medicine

Colorectal cancer (CRC) is the second leading cause of cancer death worldwide that is attributed to gradual long-term accumulation of both genetic and epigenetic changes. To reduce the mortality rate of CRC and to improve treatment efficacy, it will be important to develop accurate noninvasive diagnostic tests for screening, acute, and personalized diagnosis. Epigenetic changes such as DNA methylation play an important role in the development and progression of CRC. Over the last decade, a panel of DNA methylation markers has been reported showing a high accuracy and reproducibility in various semi-invasive or noninvasive biosamples. Research to obtain comprehensive panels of markers allowing a highly sensitive and differentiating diagnosis of CRC is ongoing. Moreover, the epigenetic alterations for cancer therapy, as a precision medicine strategy will increase their therapeutic potential over time. Here, we discuss the current state of DNA methylation-based biomarkers and their impact on CRC diagnosis. We emphasize the need to further identify and stratify methylation-biomarkers and to develop robust and effective detection methods that are applicable for a routine clinical setting of CRC diagnostics particularly at the early stage of the disease.

OP0038 VITAMIN D AND MARINE n-3 FATTY ACID SUPPLEMENTATION FOR PREVENTION OF AUTOIMMUNE DISEASE IN THE VITAL RANDOMIZED CONTROLLED TRIAL: OUTCOMES OVER 7 YEARS

Background

Strong biologic rationale supports both vitamin D and marine omega-3 (n-3) fatty acids for prevention of autoimmune disease (AD). Within the randomized, double-blind, placebo-controlled VITamin D and OmegA-3 TriaL (VITAL), we tested the effects of these supplements on AD incidence. We previously reported results after 5.3 years of randomized follow-up showing overall protective effects for vitamin D on AD incidence (HR 0.78, 95% CI 0.61-0.99) and suggestive results for n-3 fatty acids (HR 0.85, 95%CI 0.67-1.08)1.

Objectives

We aimed to test effects of these supplements with two more years of post-intervention follow-up in VITAL.

Methods

VITAL enrolled and randomized men and women (age ≥50 and ≥55 years, respectively) in a 2-by-2 factorial design to vitamin D3 (2000 IU/d) and/or n-3 fatty acids (1000 mg/d) or placebo and followed for median 5.3 years. Here, we followed participants for another 2 years of observation to assess for sustained effects. Incident AD diagnoses were reported by participants annually and confirmed by medical record review by expert physicians using existing classification criteria. The primary endpoint was total incident AD, including rheumatoid arthritis (RA), polymyalgia rheumatica (PMR), autoimmune thyroid disease (AITD), psoriasis, and all others. Pre-specified secondary endpoints included individual common AD; and probable AD. Cox models calcuated hazard ratios (HR) for incident ADs.

Results

Of 25,871 participants randomized, 71% self-reported non-Hispanic Whites, 20% Black, 9% other racial/ethnic groups, 51% women, mean age was 67.1 years. During 7.5 years median follow-up, confirmed AD was diagnosed in 156 participants in vitamin D arm vs 198 in vitamin D placebo arm, HR 0.79 (0.64-0.97). Incident AD was confirmed in 167 participants in n-3 fatty acid arm and 187 in n-3 fatty acid placebo arm, HR 0.89 (0.72-1.10). For vitamin D, HRs trended toward reduction for RA 0.67 (0.37- 1.21), PMR 0.69 (0.46-1.03) and psoriasis 0.57 (0.33-0.99). For n-3 fatty acids, HRs trended toward reduction for RA 0.55 (0.30-1.10) and AITD 0.61 (0.33-1.12). Vitamin D’s effect on AD incidence was stronger in those with body mass index (BMI) < 25 (HR 0.65, 0.44-0.96) than ≥ 25 kg/m2 (p interaction 0.01).

Conclusion

Supplementation for 5.3 years with 2000 IU/day vitamin D (compared to placebo), followed by 2 years of observational follow-up, significantly reduced overall incident AD by 21% in older adults. HRs for RA, PMR and psoriasis trended toward reduction with vitamin D, with stronger effect in those with normal BMI. Supplementation with 1000 mg/day n-3 fatty acids did not significantly reduce total AD.

References

[1]Hahn J et al, BMJ, 2022 Jan 26;376: e066452.

Table 1.

Hazard Ratios for Primary and Secondary Endpoints, by Randomized Assignment to Vitamin D/Placebo (Left), N-3 Fatty Acids/Placebo (Right)a

EndpointVitamin D3(N=12,927)Placebo (N=12,944)Hazard Ratio (95% CI)pN-3 Fatty Acids (N=12,933)Placebo (N=12,938)Hazard Ratio (95% CI)pPrimary: Confirmed AD1561980.79 (0.64-0.97)0.031671870.89 (0.72-1.10)0.27Secondary:Confirmed + probable AD2653210.83 (0.70-0.97)0.022713150.86 (0.73-1.01)0.06Excluding subjects with any pre-randomization AD Confirmed AD1271620. 79 (0.62-0.99)0.041411480.95 (0.75-1.20)0.66 Confirmed + probable AD2112700. 78 (0.65-0.94)0.0072322490.93 (0.78-1.11)0.41Excluding first 2 years follow-up Confirmed AD861300.66 (0.50-0.87)0.0031041120.92 (0.71-1.21)0.56 Confirmed + probable AD1472050.72 (0.58-0.89)0.0021721800.95 (0.77-1.17)0.63Individual ADb RA18270.67 (0.37-1.21)0.1816290.55 (0.30-1.01)0.06 PMR39570.69 (0.46-1.03)0.0746500.92 (0.61-1.37)0.67 AITD27181.50 (0.82-2.71)0.1917280.61 (0.33-1.12)0.11 Psoriasis20350.57 (0.33-0.99)0.0534211.62 (0.94-2.79)0.08

aAnalyses from Cox regression models controlled for age, sex, race, and other (n-3 fatty acid or vitamin D) randomization group bConfirmed AD.

Figure 1.

Disclosure of Interests

Karen Costenbader Consultant of: Astra Zeneca, Glaxo Smith Kline, Neutrolis, Grant/research support from: Merck, Exagen, Gilead, Nancy Cook: None declared, I-min Lee: None declared, Jill Hahn: None declared, Joseph Walter: None declared, Vadim Bubes: None declared, Gregory Kotler: None declared, Nicole Yang: None declared, Sonia Friedman: None declared, Erik Alexander: None declared, JoAnn Manson: None declared.

Effects of Resistant Starch on Symptoms, Fecal Markers, and Gut Microbiota in Parkinson's Disease - The RESISTA-PD Trial

The composition of the gut microbiota is linked to multiple diseases, including Parkinson's disease (PD). Abundance of bacteria producing short-chain fatty acids (SCFAs) and fecal SCFA concentrations are reduced in PD. SCFAs exert various beneficial functions in humans. In the interventional, monocentric, open-label clinical trial "Effects of Resistant Starch on Bowel Habits, Short Chain Fatty Acids and Gut Microbiota in Parkinson'sDisease" (RESISTA-PD; ID: NCT02784145), we aimed at altering fecal SCFAs by an 8-week prebiotic intervention with resistant starch (RS). We enrolled 87 subjects in three study-arms: 32 PD patients received RS (PD + RS), 30 control subjects received RS, and 25 PD patients received solely dietary instructions. We performed paired-end 100 bp length metagenomic sequencing of fecal samples using the BGISEQ platform at an average of 9.9 GB. RS was well-tolerated. In the PD + RS group, fecal butyrate concentrations increased significantly, and fecal calprotectin concentrations dropped significantly after 8 weeks of RS intervention. Clinically, we observed a reduction in non-motor symptom load in the PD + RS group. The reference-based analysis of metagenomes highlighted stable alpha-diversity and beta-diversity across the three groups, including bacteria producing SCFAs. Reference-free analysis suggested punctual, yet pronounced differences in the metagenomic signature in the PD + RS group. RESISTA-PD highlights that a prebiotic treatment with RS is safe and well-tolerated in PD. The stable alpha-diversity and beta-diversity alongside altered fecal butyrate and calprotectin concentrations call for long-term studies, also investigating whether RS is able to modify the clinical course of PD.

A comprehensive approach for genome-wide efficiency profiling of DNA modifying enzymes

A precise understanding of DNA methylation dynamics is of great importance for a variety of biological processes including cellular reprogramming and differentiation. To date, complex integration of multiple and distinct genome-wide datasets is required to realize this task. We present GwEEP (genome-wide epigenetic efficiency profiling) a versatile approach to infer dynamic efficiencies of DNA modifying enzymes. GwEEP relies on genome-wide hairpin datasets, which are translated by a hidden Markov model into quantitative enzyme efficiencies with reported confidence around the estimates. GwEEP predicts de novo and maintenance methylation efficiencies of Dnmts and furthermore the hydroxylation efficiency of Tets. Its design also allows capturing further oxidation processes given available data. We show that GwEEP predicts accurately the epigenetic changes of ESCs following a Serum-to-2i shift and applied to Tet TKO cells confirms the hypothesized mutual interference between Dnmts and Tets.

Resident memory CD4+ T lymphocytes mobilize from bone marrow to contribute to a systemic secondary immune reaction

Resident memory T lymphocytes (T_RM ) of epithelial tissues and the bone marrow protect their host tissue. To what extent these cells are mobilized and contribute to systemic immune reactions is less clear. Here we show that in secondary immune reactions to the measles-mumps-rubella (MMR) vaccine, CD4⁺ T_RM are mobilized into the blood within 16 to 48 hours after immunization in humans. This mobilization of T_RM is cognate: T_RM recognizing other antigens are not mobilized, unless they cross-react with the vaccine. We also demonstrate through methylome analyses that T_RM are mobilized from the bone marrow. These mobilized cells make significant contribution to the systemic immune reaction, as evidenced by their T-cell receptor Vβ clonotypes represented among the newly generated circulating memory T-cells, 14 days after vaccination. Thus, T_RM of the bone marrow confer not only local, but also systemic immune memory. This article is protected by copyright. All rights reserved.

Bisulfite profiling of the MGMT promoter and comparison with routine testing in glioblastoma diagnostics

Background

Promoter methylation of the DNA repair gene O⁶-methylguanine-DNA methyltransferase (MGMT) is an acknowledged predictive epigenetic marker in glioblastoma multiforme and anaplastic astrocytoma. Patients with methylated CpGs in the MGMT promoter benefit from treatment with alkylating agents, such as temozolomide, and show an improved overall survival and progression-free interval. A precise determination of MGMT promoter methylation is of importance for diagnostic decisions. We experienced that different methods show partially divergent results in a daily routine. For an integrated neuropathological diagnosis of malignant gliomas, we therefore currently apply a combination of methylation-specific PCR assays and pyrosequencing.

Results

To better rationalize the variation across assays, we compared these standard techniques and assays to deep bisulfite sequencing results in a cohort of 80 malignant astrocytomas. Our deep analysis covers 49 CpG sites of the expanded MGMT promoter, including exon 1, parts of intron 1 and a region upstream of the transcription start site (TSS). We observed that deep sequencing data are in general in agreement with CpG-specific pyrosequencing, while the most widely used MSP assays published by Esteller et al. (N Engl J Med 343(19):1350–1354, 2000. 10.1056/NEJM200011093431901) and Felsberg et al. (Clin Cancer Res 15(21):6683–6693, 2009. 10.1158/1078-0432.CCR-08-2801) resulted in partially discordant results in 22 tumors (27.5%). Local deep bisulfite sequencing (LDBS) revealed that CpGs located in exon 1 are suited best to discriminate methylated from unmethylated samples. Based on LDBS data, we propose an optimized MSP primer pair with 83% and 85% concordance to pyrosequencing and LDBS data. A hitherto neglected region upstream of the TSS, with an overall higher methylation compared to exon 1 and intron 1 of MGMT, is also able to discriminate the methylation status.

Conclusion

Our integrated analysis allows to evaluate and redefine co-methylation domains within the MGMT promoter and to rationalize the practical impact on assays used in daily routine diagnostics.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13148-022-01244-4.

Strong Expansion of Human Regulatory T Cells for Adoptive Cell Therapy Results in Epigenetic Changes Which May Impact Their Survival and Function

Adoptive transfer of regulatory T cells (Treg) is a promising new therapeutic option to treat detrimental inflammatory conditions after transplantation and during autoimmune disease. To reach sufficient cell yield for treatment, ex vivo isolated autologous or allogenic Tregs need to be expanded extensively in vitro during manufacturing of the Treg product. However, repetitive cycles of restimulation and prolonged culture have been shown to impact T cell phenotypes, functionality and fitness. It is therefore critical to scrutinize the molecular changes which occur during T cell product generation, and reexamine current manufacturing practices. We performed genome-wide DNA methylation profiling of cells throughout the manufacturing process of a polyclonal Treg product that has proven safety and hints of therapeutic efficacy in kidney transplant patients. We found progressive DNA methylation changes over the duration of culture, which were donor-independent and reproducible between manufacturing runs. Differentially methylated regions (DMRs) in the final products were significantly enriched at promoters and enhancers of genes implicated in T cell activation. Additionally, significant hypomethylation did also occur in promoters of genes implicated in functional exhaustion in conventional T cells, some of which, however, have been reported to strengthen immunosuppressive effector function in Tregs. At the same time, a set of reported Treg-specific demethylated regions increased methylation levels with culture, indicating a possible destabilization of Treg identity during manufacturing, which was independent of the purity of the starting material. Together, our results indicate that the repetitive TCR-mediated stimulation lead to epigenetic changes that might impact functionality of Treg products in multiple ways, by possibly shifting to an effector Treg phenotype with enhanced functional activity or by risking destabilization of Treg identity and impaired TCR activation. Our analyses also illustrate the value of epigenetic profiling for the evaluation of T cell product manufacturing pipelines, which might open new avenues for the improvement of current adoptive Treg therapies with relevance for conventional effector T cell products.

Derivation and validation of a novel 3-hour pathway for the observe-zone of the ESC 0/1h-algorithm

Background

The latest non-ST elevation myocardial infarction (NSTEMI) guidelines from the European Society of Cardiology (ESC) recommend a 3h cardiac troponin determination in patients triaged to the observe-zone of the ESC 0/1h-algorithm; however, no specific cut-off for further triage is endorsed.

Purpose

To derive and internally, as well as externally, validate a novel 3-hour pathway for the observe-zone of the ESC 0/1h-algorithm.

Methods

In an ongoing multicentre international diagnostic study, we prospectively enrolled unselected patients presenting to the emergency department with symptoms suggestive of myocardial infarction (MI). Final diagnoses were centrally adjudicated by two independent cardiologists applying the 4th universal definition of MI, based on complete cardiac work-up including cardiac imaging, serial high sensitivity cardiac troponin T (hs-cTnT) sampling and 90-day follow-up information. High sensitivity-cTnT concentrations were measured at presentation and after 1 and 3 hours. The primary outcome was safety, quantified by the sensitivity and NPV for early rule out of NSTEMI. External validation was performed in an independent multicentre international study.

Results

Among 2076 eligible patients, application of the ESC 0/1h-algorithm triaged 1512 patients (72.8%) to either rule-out or rule-in of NSTEMI, remaining 564 patients (27.2%) in the observe-zone (adjudicated NSTEMI prevalence 120/564 patients, 21.3%). The novel derived 3h-pathway for the observe-zone patients ruled-out NSTEMI with a 3h hs-cTnT concentration &lt;15 ng/L and a 0/3h-hs-cTnT absolute change &lt;4 ng/L, triaging 138 patients (25%) towards rule-out, resulting in a sensitivity of 99.2% (95% CI 96.0–99.9) and a NPV of 99.3% (95% CI 95.4–99.9). A 0/3h-hs-cTnT absolute change ≥6 ng/L ruled-in 63 patients (11.2%), resulting in a specificity of 98% (95% CI 96.2–98.9) and a PPV of 85.7% (95% CI75.0–92.3). The novel 3h-pathway reduced the number of patients in the observe zone by 36%, and the number of T1MI by 50% (Figure 1). Findings were confirmed in both internal and external validation.

Conclusions

A novel derived pathway combining a 3h hs-cTnT concentration &lt;15 ng/L and a 0/3h absolute change &lt;4 ng/L allowed to very safely rule-out NSTEMI in patients remaining in the observe-zone of the ESC 0/1h-algorithm.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): The Swiss Heart FoundationThe Swiss National Science Foundation Figure 1

Discordance in prognostic ability between physician assessed NYHA classification and self-reported health status in patients with acute heart failure

Background

Especially in patients with acute heart failure (AHF) the NYHA classification remains of uncertain representation of patients' actual health state. Alternatively, patient's subjective well-being, in terms of health-related quality of life (HRQL), showed to have an excellent prognostic ability in out clinic patients with chronic heart failure.

Objectives

It is unknown whether HRQL instruments can assess a more reliable prognostication in patients hospitalized due to AHF than the NYHA classification.

Methods

Goal Directed Afterload Reduction in Acute Congestive Cardiac Decompensation Study (GALACTIC) was a multicenter, randomized, open-label blinded-end-point trial that emphasized early intensive and sustained vasodilation in adult patients hospitalized due to AHF with NYHA functional class III/IV, however provided neutral findings. HRQL was assessed by the generic EQ-5D-3L which is a 3-leveled 5-item instrument and the disease-specific Kansas City Cardiomyopathy Questionnaire (KCCQ). Unadjusted and adjusted Cox regression models were performed after patients were grouped into low (EQ-5D −0.074&lt;0.25; KCCQ 0&lt;25), moderately low (0.25&lt;0.5; 25&lt;50), moderately high (0.5&lt;0.75; 50&lt;75) and high HRQL (0.75–1.0; 75–100).

Results

781 patients were enrolled in 10 centres in 5 countries over 2 continents among which 536 (69%) patientshad completed theEQ-5D and 419 (54%) the KCCQ shortly after admission. Within 180 days of follow-up69 (13%) and 54 (13%) patients died and 151 (28%) and 122 (29%) died or were rehospitalized due to AHF, respectively. Cumulative incidence as well as HRs in patients grouped according to NYHA (n=536) indicated a comparable or significantly lower risk in patients with NYHA IV: e.g. for the combined outcome HR 1.07 (95% CI 0.777–1.473) and aHR 0.463 (95% CI 0.245–0.875). Whereas HRs in patients grouped according to both, EQ-5D (n=536) and KCCQ (n=419), increased from the group with highest to the group with the lowest HRQL: e.g. aHR for moderately high 1.11 (95% CI 0.718–1.715), for moderately low 1.721 (95% CI 1.102–2.688) and for low EQ-5D index 1.891 (95% CI 1.136–3.149) referenced to high HRQL (EQ-5D index 0.75–1.0).

Conclusions

These findings corroborate and extend previous work suggesting that NYHA classification poorly discriminates AHF patients' prognosis and challenge its' extensive application. HRQL might be a possible alternative to easily assess these patients' heath state.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Swiss National Science Foundation, the Swiss Heart Foundation A. 180-day mortality; B. composite outcome

Prolactin-sensitive olfactory sensory neurons regulate male preference in female mice by modulating responses to chemosensory cues

Chemosensory cues detected in the nose need to be integrated with the hormonal status to trigger appropriate behaviors, but the neural circuits linking the olfactory and the endocrine system are insufficiently understood. Here, we characterize olfactory sensory neurons in the murine nose that respond to the pituitary hormone prolactin. Deletion of prolactin receptor in these cells results in impaired detection of social odors and blunts male preference in females. The prolactin-responsive olfactory sensory neurons exhibit a distinctive projection pattern to the brain that is similar across different individuals and express a limited subset of chemosensory receptors. Prolactin modulates the responses within these neurons to discrete chemosensory cues contained in male urine, providing a mechanism by which the hormonal status can be directly linked with distinct olfactory cues to generate appropriate behavioral responses.

Dysregulation of cholesterol homeostasis in human lung cancer tissue and tumour-associated macrophages

Background

Based on reports on elevated cholesterol levels in cancer cells, strategies to lower cholesterol synthesis have been suggested as an antitumour strategy. However, cholesterol depletion has also been shown to induce tumour-promoting actions in tumour-associated macrophages (TAMs).

Methods

We performed lipidomic and transcriptomic analyses of human lung cancer material. To assess whether the TAM phenotype is shaped by secreted factors produced by tumour cells, primary human monocyte-derived macrophages were polarized towards a TAM-like phenotype using tumour cell-conditioned medium.

Findings

Lipidomic analysis of lung adenocarcinoma (n=29) and adjacent non-tumour tissues (n=22) revealed a significant accumulation of free cholesterol and cholesteryl esters within the tumour tissue. In contrast, cholesterol levels were reduced in TAMs isolated from lung adenocarcinoma tissues when compared with alveolar macrophages (AMs) obtained from adjacent non-tumour tissues. Bulk-RNA-Seq revealed that genes involved in cholesterol biosynthesis and metabolism were downregulated in TAMs, while cholesterol efflux transporters were upregulated. In vitro polarized TAM-like macrophages showed an attenuated lipogenic gene expression signature and exhibited lower cholesterol levels compared with non-polarized macrophages. A genome-wide comparison by bulk RNA-Seq confirmed a high similarity of ex vivo TAMs and in vitro TAM-like macrophages. Modulation of intracellular cholesterol levels by either starving, cholesterol depletion, or efflux transporter inhibition indicated that cholesterol distinctly shapes macrophage gene expression.

Interpretation

Our data show an opposite dysregulation of cholesterol homeostasis in tumour tissue vs. TAMs. Polarization of in vitro differentiated macrophages by tumour cell-conditioned medium recapitulates key features of ex vivo TAMs.

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR

Background

Understanding the influence of genetic variants on DNA methylation is fundamental for the interpretation of epigenomic data in the context of disease. There is a need for systematic approaches not only for determining methylation quantitative trait loci (methQTL), but also for discriminating general from cell type-specific effects.

Results

Here, we present a two-step computational framework MAGAR (https://bioconductor.org/packages/MAGAR), which fully supports the identification of methQTLs from matched genotyping and DNA methylation data, and additionally allows for illuminating cell type-specific methQTL effects. In a pilot analysis, we apply MAGAR on data in four tissues (ileum, rectum, T cells, B cells) from healthy individuals and demonstrate the discrimination of common from cell type-specific methQTLs. We experimentally validate both types of methQTLs in an independent data set comprising additional cell types and tissues. Finally, we validate selected methQTLs located in the PON1, ZNF155, and NRG2 genes by ultra-deep local sequencing. In line with previous reports, we find cell type-specific methQTLs to be preferentially located in enhancer elements.

Conclusions

Our analysis demonstrates that a systematic analysis of methQTLs provides important new insights on the influences of genetic variants to cell type-specific epigenomic variation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13072-021-00415-6.

Prenatal exposure to endocrine disrupting chemicals is associated with altered DNA methylation in cord blood

Prenatal exposure to endocrine disrupting chemicals can interfere with development, and has been associated with social-cognitive functioning and adverse health outcomes later in life. Exposure-associated changes of DNA methylation (DNAm) patterns have been suggested as a possible mediator of this relationship. This study investigated whether prenatal low-dose exposure to polychlorinated biphenyls (PCBs) and polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) is associated with altered DNAm patterns across the genome in a Western urban-industrial population. In 142 mother-infant pairs from the Duisburg Birth Cohort Study, PCBs and PCDD/Fs levels were quantified from maternal blood during late pregnancy and associated with DNAm levels in cord blood using the Illumina EPIC beadchip. The epigenome-wide association studies (EWAS) identified 32 significantly differentially methylated positions (DMPs) and eight differentially methylated regions (DMRs) associated with six congeners of PCB and PCDD in females or males (FDRs < 0.05). DMPs and DMRs mapped to genes involved in neurodevelopment, gene regulation, and immune functioning. Weighted gene correlation network analysis (WGCNA) showed 31 co-methylated modules (FDRs < 0.05) associated with one congener of PCDF levels in females. Results of both analytical strategies indicate that prenatal exposure to PCBs and PCDD/Fs is associated with altered DNAm of genes involved in neurodevelopment, gene expression and immune functioning. DNAm and gene expression levels of several of these genes were previously associated with EDC exposure in rodent models. Follow-up studies will clarify whether these epigenetic changes might contribute to the origin for adverse mental and health outcomes.

Early standardized clinical judgement for syncope diagnosis in the emergency department

BACKGROUND

The diagnosis of cardiac syncope remains a challenge in the emergency department (ED).

OBJECTIVE

Assessing the diagnostic accuracy of the early standardized clinical judgement (ESCJ) including a standardized syncope-specific case report form (CRF) in comparison with a recommended multivariable diagnostic score.

METHODS

In a prospective international observational multicentre study, diagnostic accuracy for cardiac syncope of ESCJ by the ED physician amongst patients ≥ 40 years presenting with syncope to the ED was directly compared with that of the Evaluation of Guidelines in Syncope Study (EGSYS) diagnostic score. Cardiac syncope was centrally adjudicated independently of the ESCJ or conducted workup by two ED specialists based on all information available up to 1-year follow-up. Secondary aims included direct comparison with high-sensitivity cardiac troponin I (hs-cTnI) and B-type natriuretic peptide (BNP) concentrations and a Lasso regression to identify variables contributing most to ESCJ.

RESULTS

Cardiac syncope was adjudicated in 252/1494 patients (15.2%). The diagnostic accuracy of ESCJ for cardiac syncope as quantified by the area under the curve (AUC) was 0.87 (95% CI: 0.84-0.89), and higher compared with the EGSYS diagnostic score (0.73 (95% CI: 0.70-0.76)), hs-cTnI (0.77 (95% CI: 0.73-0.80)) and BNP (0.77 (95% CI: 0.74-0.80)), all P < 0.001. Both biomarkers (alone or in combination) on top of the ESCJ significantly improved diagnostic accuracy.

CONCLUSION

ESCJ including a standardized syncope-specific CRF has very high diagnostic accuracy and outperforms the EGSYS score, hs-cTnI and BNP.

Epigenomic and transcriptional profiling identifies impaired glyoxylate detoxification in NAFLD as a risk factor for hyperoxaluria

Epigenetic modifications (e.g. DNA methylation) in NAFLD and their contribution to disease progression and extrahepatic complications are poorly explored. Here, we use an integrated epigenome and transcriptome analysis of mouse NAFLD hepatocytes and identify alterations in glyoxylate metabolism, a pathway relevant in kidney damage via oxalate release-a harmful waste product and kidney stone-promoting factor. Downregulation and hypermethylation of alanine-glyoxylate aminotransferase (Agxt), which detoxifies glyoxylate, preventing excessive oxalate accumulation, is accompanied by increased oxalate formation after metabolism of the precursor hydroxyproline. Viral-mediated Agxt transfer or inhibiting hydroxyproline catabolism rescues excessive oxalate release. In human steatotic hepatocytes, AGXT is also downregulated and hypermethylated, and in NAFLD adolescents, steatosis severity correlates with urinary oxalate excretion. Thus, this work identifies a reduced capacity of the steatotic liver to detoxify glyoxylate, triggering elevated oxalate, and provides a mechanistic explanation for the increased risk of kidney stones and chronic kidney disease in NAFLD patients.

Rapid Base-Specific Calling of SARS-CoV-2 Variants of Concern Using Combined RT-PCR Melting Curve Screening and SIRPH Technology

Background

The emergence of novel variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands fast and reliable detection of such variants in local populations.

Methods

Here we present a cost-efficient and fast workflow combining a prescreening of SARS-CoV-2-positive samples using reverse transcription polymerase chain reaction melting curve analysis with multiplexed IP-RP-HPLC-based single nucleotide primer extensions.

Results

The entire workflow from positive SARS-CoV-2 testing to base-specific identification of variants requires about 24 hours.

Conclusions

We applied the sensitive method to monitor local variant of concern outbreaks in SARS-CoV-2-positive samples collected in a confined region of Germany.

DNA methylation-based prediction of response to immune checkpoint inhibition in metastatic melanoma

Background

Therapies based on targeting immune checkpoints have revolutionized the treatment of metastatic melanoma in recent years. Still, biomarkers predicting long-term therapy responses are lacking.

Methods

A novel approach of reference-free deconvolution of large-scale DNA methylation data enabled us to develop a machine learning classifier based on CpG sites, specific for latent methylation components (LMC), that allowed for patient allocation to prognostic clusters. DNA methylation data were processed using reference-free analyses (MeDeCom) and reference-based computational tumor deconvolution (MethylCIBERSORT, LUMP).

Results

We provide evidence that DNA methylation signatures of tumor tissue from cutaneous metastases are predictive for therapy response to immune checkpoint inhibition in patients with stage IV metastatic melanoma.

Conclusions

These results demonstrate that LMC-based segregation of large-scale DNA methylation data is a promising tool for classifier development and treatment response estimation in cancer patients under targeted immunotherapy.

Dnmt1 has de novo activity targeted to transposable elements

DNA methylation plays a critical role during development, particularly in repressing retrotransposons. The mammalian methylation landscape is dependent on the combined activities of the canonical maintenance enzyme Dnmt1 and the de novo Dnmts, 3a and 3b. Here, we demonstrate that Dnmt1 displays de novo methylation activity in vitro and in vivo with specific retrotransposon targeting. We used whole-genome bisulfite and long-read Nanopore sequencing in genetically engineered methylation-depleted mouse embryonic stem cells to provide an in-depth assessment and quantification of this activity. Utilizing additional knockout lines and molecular characterization, we show that the de novo methylation activity of Dnmt1 depends on Uhrf1, and its genomic recruitment overlaps with regions that enrich for Uhrf1, Trim28 and H3K9 trimethylation. Our data demonstrate that Dnmt1 can catalyze DNA methylation in both a de novo and maintenance context, especially at retrotransposons, where this mechanism may provide additional stability for long-term repression and epigenetic propagation throughout development.