Biology subjects

Binder, M.

Publications and source records attributed to Binder, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Mutation-specific CAR T cells as precision therapy for IGLV3-21R110 expressing high-risk chronic lymphocytic leukemia

The concept of precision cell therapy targeting tumor-specific mutations is appealing but requires surface-exposed neoepitopes, which is a rarity in cancer. B cell receptors (BCR) of mature lymphoid malignancies are exceptional in that they harbor tumor-specific-stereotyped sequences in the form of point mutations that drive self-engagement of the BCR and autologous signaling. Here, we used a BCR light chain neoepitope defined by a characteristic point mutation (IGLV3-21R110) for selective targeting of a poor-risk subset of chronic lymphocytic leukemia (CLL) with chimeric antigen receptor (CAR) T cells. We developed murine and humanized CAR constructs expressed in T cells from healthy donors and CLL patients that eradicated IGLV3-21R110 expressing cell lines and primary CLL cells, but not polyclonal healthy B cells. In vivo experiments confirmed epitope-selective cytolysis in xenograft models using engrafted IGLV3-21R110 expressing cell lines or primary CLL cells. We further demonstrate in two humanized mouse models lack of cytotoxicity towards human B cells. These data provide the basis for novel avenues of resistance-preventive and biomarker-guided cellular targeting of functionally relevant lymphoma driver mutations sparing normal B cells.

cancer biology↗

bioRxiv2023

Field phenotyping reveals the importance of including cultivar-specific per se temperature response in phenology modeling

Predicting plant development, a longstanding goal in plant physiology, involves two interwoven components: continuous growth and the progression of growth stages (phenology). Current models, like thermal time, assume species-level growth responses to temperature. We challenge this assumption, suggesting that cultivar-specific temperature responses significantly affect phenology. To investigate, we collected field-based growth and phenology data in winter wheat and soybean over multiple years. We used diverse models, from linear to neural networks, to assess growth responses to temperature at various trait and covariate levels. Cultivar-specific non-linear models best explained phenology-related cultivar-environment interactions. With cultivar-specific models, additional relations to other stressors than temperature were found. The availability of the presented field phenotyping tools allows incorporating cultivar-specific temperature response functions in future plant physiology studies, which will deepen our understanding of key factors that influence plant development. Consequently, this work has implications for crop breeding and cultivation under adverse climatic conditions.

physiology↗

bioRxiv2023

Enhanced Airway Epithelial Response to SARS-CoV-2 Infection in Children is Critically Tuned by the Cross-Talk Between Immune and Epithelial Cells

To cope with novel virus infections to which no prior adaptive immunity exists, the body strongly relies on the innate immune system. In such cases, including infections with SARS-CoV-2, children tend to fair better than adults. In the context of COVID-19, it became evident that a rapid interferon response at the site of primary infection is key for successful control of the virus and prevention of severe disease. The airway epithelium of children was shown to exhibit a primed state already at homeostasis and to respond particularly well to SARS-CoV-2 infection. However, the underlying mechanism for this priming remained elusive. Here we show that interactions between airway mucosal immune cells and epithelial cells are stronger in children, and via cytokine-mediated signaling lead to IRF-1-dependent upregulation of the viral sensors RIG-I and MDA5. Based on a cellular in vitro model we show that stimulated human peripheral blood mononuclear cells (PBMC) can induce a robust interferon-beta response towards SARS-CoV-2 in a lung epithelial cell line otherwise unresponsive to this virus. This is mediated by type I interferon, interferon-gamma and TNF, and requires induction of both, RIG-I and MDA5. In single cell-analysis of nasal swab samples the same cytokines are found to be elevated in mucosal immune cells of children, correlating with elevated epithelial expression of viral sensors. In vitro analysis of PBMC derived from healthy adolescents and adults confirm that immune cells of younger individuals show increased cytokine production and potential to prime epithelial cells. In co-culture with SARS-CoV-2-infected A549 cells, PBMC from adolescents significantly enhance the antiviral response. Taken together, our study suggests that higher numbers and a more vigorous activity of innate immune cells in the airway mucosa of children tune the set-point of the epithelial antiviral system. This likely is a major contributor to the robust immune response to SARS-CoV-2 in children. Our findings shed light on the molecular underpinnings of the stunning resilience of children towards severe COVID-19, and may propose a novel concept for immunoprophylactic treatments.

immunology↗

bioRxiv2022

Comparison of HAV and HCV infections in vivo and in vitro reveals distinct patterns of innate immune evasion and activation

ObjectiveHepatitis A virus (HAV) infections are considered not to trigger an innate immune response in vivo, in contrast to hepatitis C virus (HCV). This lack of immune induction has been imputed to strong immune counteraction by HAV proteases 3CD and 3ABC. We aimed at elucidating the mechanisms of innate immune induction and counteraction by HAV and HCV in vivo and in vitro. DesignuPA-SCID mice with humanized liver were infected with HAV and HCV. Hepatic cell culture models were used to assess HAV and HCV sensing by TLR3 and RIG-I/MDA5, respectively. Cleavage of the adaptor proteins TRIF and MAVS was analyzed by transient and stable expression of HAV and HCV proteases and virus infection. ResultsWe detected similar levels of Interferon stimulated genes (ISGs) induction in hepatocytes of HAV and HCV infected human liver chimeric mice. In cell culture, HAV induced ISGs exclusively upon sensing by MDA5 and dependent on LGP2. TRIF and MAVS were only partially cleaved by HAV 3ABC and 3CD, not sufficiently to abrogate signalling. In contrast, HCV NS3-4A efficiently degraded MAVS, as previously reported, whereas TRIF was not cleaved. ConclusionsHAV induces an innate immune response in hepatocytes via MDA5/LGP2, with limited control of both pathways by proteolytic cleavage. HCV activates TLR3 and lacks TRIF cleavage, suggesting that this pathway mainly contributes to HCV induced antiviral response in hepatocytes. Our results shed new light on induction and counteraction of innate immunity by HAV and HCV and their potential contribution to clearance and persistence. SIGNIFICANCE OF THIS STUDYO_ST_ABSWhat is already known on this topic?C_ST_ABS-- Despite sharing biological and molecular similarities, HAV infections are always cleared while HCV infections persist in most cases. -- In infected chimpanzees HAV does not trigger a strong innate immune response, as opposed to HCV. This has been imputed to the action of HAV proteases abrogating the signalling pathways. -- Physiological in vitro and in vivo models, based on human hepatocytes, to assess HAV and HCV mechanisms of induction and interference of innate immunity are still missing. What this study adds-- HAV induces an innate immune response in vitro and in vivo, in systems with intact signalling pathways and devoid of adaptive immunity. -- HAV 3ABC and 3CD proteases do not abolish the host innate immune response. -- HCV NS3-4A protease disrupts the RLRs pathways, but cannot cleave TRIF and has no impact on TLR3 response. How this study might affect research, practice or policy-- This study offers a comprehensive, side-by-side investigation on HAV and HCV infections in physiological models which recapitulate a cytokine response in the human liver, and allows a precise assessment of the viral interference related to the function of the respective signalling pathways. -- Our results elucidate mechanisms, so far controversial or poorly investigated, thus contributing to our understanding of HAV clearance and HCV persistence.

immunology↗

bioRxiv2022

Distinct spectral profiles of awake resting EEG in disorders of consciousness - the role of frequency and topography of oscillations

The prolonged disorders of consciousness (PDOC) pose a challenge for an accurate clinical diagnosis, mainly due to patients scarce or ambiguous behavioral responsiveness. Measurement of brain activity can support better diagnosis, independent of motor restrictions. Methods based on spectral analysis of resting-state EEG appear as a promising path, revealing specific changes within the internal brain dynamics in PDOC patients. In this study we used a robust method of resting-state EEG power spectrum parameter extraction to identify distinct spectral properties for different types of PDOC. Sixty patients and 37 healthy volunteers participated in this study. Patient group consisted of 22 unresponsive wakefulness patients, 25 minimally conscious patients and 13 patients emerging from the minimally conscious state. Ten minutes of resting EEG was acquired during wakefulness and transformed into individual power spectra. For each patient, using the spectral decomposition algorithm, we extracted maximum peak frequency within 1-14 Hz range in the centro-parietal region, and the antero-posterior (AP) gradient of the maximal frequency peak. All patients were behaviorally diagnosed using Coma Recovery Scale - Revised (CRS-R). The maximal peak frequency in the 1-14 Hz range successfully predicted both neurobehavioral capacity of patients as indicated by CRS-R total score and PDOC diagnosis. Additionally in patients in whom only one peak within the 1-14 Hz range was observed, the AP gradient significantly contributed to the accuracy of prediction. We have identified three distinct spectral profiles of patients, likely representing separate neurophysiological modes of thalamocortical functioning. Etiology did not have significant influence on the obtained results.

neuroscience↗

bioRxiv2022

Targeting BET Proteins downregulates miR-33a to promote synergy with PIM inhibitors in CMML

Preclinical studies in myeloid neoplasms have demonstrated efficacy of Bromodomain and Extra-Terminal protein inhibitors (BETi). However, BETi demonstrate poor single agent activity in clinical trials. Several studies suggest that combination with other anti-cancer inhibitors may enhance the efficacy of BETi. To nominate BETi combination therapies for myeloid neoplasms, we used a chemical screen with therapies currently in clinical cancer development. We identified PIM inhibitors (PIMi) as therapeutically synergistic with BETi in myeloid leukemia models. Mechanistically, we show that PIM kinase is increased after BETi treatment, and that PIM kinase upregulation is sufficient to induce resistance to BETi and sensitize cells to PIMi. Further, we demonstrate that miR-33a downregulation is the underlying mechanism driving PIM1 upregulation. We also show that GM-CSF hypersensitivity, a hallmark of chronic myelomonocytic leukemia (CMML), represents a molecular signature for sensitivity to combination therapy and credential this using patient-derived xenografts supporting the clinical investigation of this combination.

cancer biology↗

bioRxiv2022

Enhancer deregulation in TET2 Mutant Clonal Hematopoiesis is associated with increased COVID-19 related inflammation severity and mortality

DNMT3A and TET2 are epigenetic regulators commonly mutated in age related clonal hematopoiesis (CH). Despite having opposed epigenetic functions, these mutations are associated with increased all-cause mortality and a low risk for progression to hematological neoplasms. While individual impacts on the epigenome have been described using different model systems, the phenotypic complexity in humans remains to be elucidated. Here we make use of a natural inflammatory response occurring during coronavirus disease 2019 (COVID-19), to understand the association of these mutations with inflammatory morbidity and mortality. We demonstrate the age-independent, negative impact of DNMT3A mutant CH on COVID-19-related cytokine release severity and mortality. Using single cell proteogenomics we show that DNMT3A mutations involve cells of myeloid and lymphoid lineages. Using single cell multiomics sequencing, we identify cell-specific gene expression changes associated with DNMT3A mutations, along with significant epigenomic deregulation affecting enhancer accessibility, resulting in overexpression of IL32, a proinflammatory cytokine that can result in inflammasome activation in monocytes and macrophages. Finally, we show with single cell resolution that the loss of function of DNMT3A is directly associated with increased chromatin accessibility in mutant cells. Together, these data provide a mechanistic insight into the poor inflammatory outcomes seen in DNMT3A mutant CH patients infected with Sars-COV2.

genetics↗

bioRxiv2022

High Resolution Kinetic Characterization and Dynamic Mathematical Modeling of the RIG-I Signaling Pathway and the Antiviral Responses

The pattern recognition receptor RIG-I is essential for the recognition of viral dsRNA and the activation of a cell-autonomous antiviral response. Upon stimulation, RIG-I triggers a signaling cascade leading to the expression of cytokines, most prominently type I and III interferons (IFNs). IFNs are secreted and signal in an auto- and paracrine manner to trigger the expression of a large variety of IFN-stimulated genes, which in concert establish an antiviral state of the cell. While the topology of this pathway has been studied quite intensively, the dynamics, particularly of the RIG-I-mediated IFN induction, is much less understood. Here, we employed electroporation-based transfection to synchronously activate the RIG-I signaling pathway, enabling us to characterize the kinetics and dynamics of cell-intrinsic innate immune signaling to virus infections. By employing an A549 IFNAR1/IFNLR deficient cell line, we could analyze the difference between the primary RIG-I signaling phase and the secondary signaling phase downstream of the IFN receptors. We further used our quantitative data to set up and calibrate a comprehensive dynamic mathematical model of the RIG-I and IFN signaling pathways. This model accurately predicts the kinetics of signaling events downstream of dsRNA recognition by RIG-I as well as the feedback and signal amplification by secreted IFN and JAK/STAT signaling. We have furthermore investigated the impact of various viral immune antagonists on the signaling dynamics experimentally, and we utilized the here described modelling approach to simulate and in silico study these critical virus-host interactions. Our work provides a comprehensive insight into the signaling events occurring early upon virus infection and opens up new avenues to study and disentangle the complexity of the host-virus interface.

immunology↗

bioRxiv2022

Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies

Plus-strand RNA viruses are the largest group of viruses. Many are human pathogens that inflict a socio-economic burden. Interestingly, plus-strand RNA viruses share remarkable similarities in their replication. A hallmark of plus-strand RNA viruses is the remodeling of intracellular membranes to establish replication organelles (so-called "replication factories"), which provide a protected environment for the replicase complex, consisting of the viral genome and proteins necessary for viral RNA synthesis. In the current study, we investigate pan-viral similarities and virus-specific differences in the life cycle of this highly relevant group of viruses. We first measured the kinetics of viral RNA, viral protein, and infectious virus particle production of hepatitis C virus (HCV), dengue virus (DENV), and coxsackievirus B3 (CVB3) in the immuno-compromised Huh7 cell line and thus without perturbations by an intrinsic immune response. Based on these measurements, we developed a detailed mathematical model of the replication of HCV, DENV, and CVB3 and show that only small virus-specific changes in the model were necessary to describe the in vitro dynamics of the different viruses. Our model correctly predicted virus-specific mechanisms such as host cell translation shut off and different kinetics of replication organelles. Further, our model suggests that the ability to suppress or shut down host cell mRNA translation may be a key factor for in vitro replication efficiency which may determine acute self-limited or chronic infection. We further analyzed potential broad-spectrum antiviral treatment options in silico and found that targeting viral RNA translation, especially polyprotein cleavage, and viral RNA synthesis may be the most promising drug targets for all plus-strand RNA viruses. Moreover, we found that targeting only the formation of replicase complexes did not stop the viral replication in vitro early in infection, while inhibiting intracellular trafficking processes may even lead to amplified viral growth. Author summaryPlus-strand RNA viruses comprise a large group of related and medically relevant viruses. The current global pandemic of COVID-19 caused by the SARS-coronavirus-2 as well as the constant spread of diseases such as dengue and chikungunya fever show the necessity of a comprehensive and precise analysis of plus-strand RNA virus infections. Plus-strand RNA viruses share similarities in their life cycle. To understand their within-host replication strategies, we developed a mathematical model that studies pan-viral similarities and virus-specific differences of three plus-strand RNA viruses, namely hepatitis C, dengue, and coxsackievirus. By fitting our model to in vitro data, we found that only small virus-specific variations in the model were required to describe the dynamics of all three viruses. Furthermore, our model predicted that ribosomes involved in viral RNA translation seem to be a key player in plus-strand RNA replication efficiency, which may determine acute or chronic infection outcome. Furthermore, our in-silico drug treatment analysis suggests that targeting viral proteases involved in polyprotein cleavage, in combination with viral RNA replication, may represent promising drug targets with broad-spectrum antiviral activity.

microbiology↗

bioRxiv2022

Rapid hypermutation B cell trajectory recruits previously primed B cells upon third SARS-CoV-2 mRNA vaccination

High antibody affinity against the ancestral SARS-CoV-2 strain seems to be necessary (but not always sufficient) for the control of emerging immune-escape variants. Therefore, aiming at strong B cell somatic hypermutation - not only at high antibody titers - is a priority when utilizing vaccines that are not targeted at individual variants. Here, we developed a next-generation sequencing based SARS-CoV-2 B cell tracking protocol to rapidly determine the level of immunoglobulin somatic hypermutation at distinct points during the immunization period. The percentage of somatically hypermutated B cells in the SARS-CoV-2 specific repertoire was low after the primary vaccination series, evolved further over months and increased steeply after boosting. The third vaccination mobilized not only naive, but also antigen-experienced B cell clones into further rapid somatic hypermutation trajectories indicating increased affinity. Together, the strongly mutated post-booster repertoires and antibodies deriving from this may explain why the booster, but not the primary vaccination series, offers some protection against immune-escape variants such as Omicron B.1.1.529. Brief summaryPriming SARS-CoV-2 vaccinations generate antibodies from low-level matured B cells while the third vaccination strongly boosts somatic hypermutation potentially explaining different protection from immune-escape variants.

immunology↗

bioRxiv2022

Influence of age and cognitive performance on resting-state functional connectivity of dopaminergic and noradrenergic centres

The process of ageing is associated with structural and functional changes in the brain, with a decline in cognitive functions observed as its inevitable symptom, even in the absence of neurodegenerative changes. A body of literature suggests dopamine and noradrenaline as prominent candidate molecules to mediate these effects, however, the knowledge regarding the underlying mechanisms is scarce. To fill this gap, we compared local and distant resting-state functional connectivity patterns of ventral tegmental area, substantia nigra pars compacta and locus coeruleus in healthy young (20-35 years; N = 37) and older adults (55-80 years; N = 27). Additionally, we sought long-range functional connectivity patterns of these structures associated with performance in tasks probing executive, attentional and reward functioning, as well as compared the functional coupling of the left and right substantia nigra. The results showed that each substantia nigra had stronger coupling with ipsilateral cortical and subcortical areas along with contralateral cerebellum, and that strength of functional connections of this structure with angular gyrus and lateral orbitofrontal cortex predicted the visuomotor search abilities. In turn, ageing was associated with increased local synchronisation in the ventral tegmental area, and differences in functional connectivity of the dopaminergic midbrain with numerous cortical and subcortical structures. Locus coeruleus functional coupling showed no differences between the groups and was not associated with any of the behavioural functions. To the best of our knowledge, this work is the first one to report the age-related effects on midbrain local synchronisation and its connectivity with key recipients of dopaminergic innervation, such as striatum, anterior cingulate and insula.

neuroscience↗

bioRxiv2021

Cooperative Effects of RIG-I-like Receptor Signaling and IRF1 on DNA Damage-Induced Cell Death

Properly responding to DNA damage is vital for eukaryotic cells, including the induction of DNA repair, growth arrest and, as a last resort to prevent neoplastic transformation, cell death. Besides being crucial for ensuring homeostasis, the same pathways and mechanisms are at the basis of chemoradiotherapy in cancer treatment, which involves therapeutic induction of DNA damage by chemical or physical (radiological) measures. Apart from typical DNA damage response mediators, the relevance of cell-intrinsic antiviral signaling pathways in response to DNA breaks has recently emerged. Originally known for combatting viruses via expression of antiviral factors including IFNs and establishing of an antiviral state, RIG-I-like receptors (RLRs) were found to be critical for adequate induction of cell death upon the introduction of DNA double-strand breaks. We here show that presence of IRF3 is crucial in this process, most likely through direct activation of pro-apoptotic factors rather than transcriptional induction of canonical downstream components, such as IFNs. Investigating genes reported to be involved in both DNA damage response and antiviral signaling, we demonstrate that IRF1 is an obligatory factor for DNA damage-induced cell death. Interestingly, its regulation does not require activation of RLR signaling, but rather sensing of DNA double strand breaks by ATM and ATR. Hence, even though independently regulated, both RLR signaling and IRF1 are essential for proper induction/execution of intrinsic apoptosis. Our results not only support more broadly developing IRF1 as a biomarker predictive for the effectiveness of chemoradiotherapy, but also suggest investigating a combined pharmacological stimulation of RLR and IRF1 signaling as a potential adjuvant regimen in tumor therapy.

cell biology↗

bioRxiv2020

Identification of a unique TCR repertoire, consistent with a superantigen selection process in Children with Multi-system Inflammatory Syndrome

Multisystem Inflammatory Syndrome in Children (MIS-C), a hyperinflammatory syndrome associated with SARS-CoV-2 infection, shares many clinical features with toxic shock syndrome, which is triggered by bacterial superantigens. The superantigen specificity for binding different V{beta}-chains results in V{beta}-skewing, whereby T cells with specific V{beta}-chains and diverse antigen specificity are overrepresented in the TCR repertoire. Here, we characterized the TCR repertoire of MIS-C patients and found a profound expansion of TCR Beta Variable gene (TRBV)11-2. Furthermore, TRBV11-2 skewing was remarkably correlated with MIS-C severity and serum cytokine levels. Further analysis of TRBJ gene usage and CDR3 length distribution of MIS-C expanding TRBV11-2 clones revealed extensive junctional diversity, indicating a superantigen-mediated selection process for TRBV expansion. In silico modelling indicates that polyacidic residues in TCR V{beta}11-2 engage in strong interactions with the superantigen-like motif of SARS-CoV-2 spike glycoprotein. Overall, our data indicate that the immune response in MIS-C is consistent with superantigenic activation. HighlightsO_LIMultisystem Inflammatory Disease in Children (MIS-C) patients exhibit T cell receptor (TCR) repertoire skewing, with expansion of T cell Receptor Beta Variable gene (TRBV)11-2 C_LIO_LITRBV11-2 skewing correlates with MIS-C severity and cytokine storm C_LIO_LIJ gene/CDR3 diversity in MIS-C patients is compatible with a superantigen selection process C_LIO_LIIn silico modelling indicates TCR V{beta}11-2 engages in CDR3-independent interactions with the polybasic insert P681RRAR in the SAg-like motif of SARS-CoV-2 spike C_LI

immunology↗

bioRxiv2020

SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB

SARS-CoV-2 is a novel virus that has rapidly spread, causing a global pandemic. In the majority of infected patients, SARS-CoV-2 leads to mild disease; however, in a significant proportion of infections, individuals develop severe symptoms that can lead to permanent lung damage or death. These severe cases are often associated with high levels of pro-inflammatory cytokines and low antiviral responses which can lead to systemic complications. We have evaluated transcriptional and cytokine secretion profiles from infected cell cultures and detected a distinct upregulation of inflammatory cytokines that parallels samples taken from infected patients. Building on these observations, we found a specific activation of NF-{kappa}B and a block of IRF3 nuclear translocation in SARS-CoV-2 infected cells. This NF-{kappa}B response is mediated by cGAS-STING activation and could be attenuated through STING targeting drugs. Our results show that SARS-CoV-2 curates a cGAS-STING mediated NF-{kappa}B driven inflammatory immune response in epithelial cells that likely contributes to inflammatory responses seen in patients and might be a target to suppress severe disease symptoms.

microbiology↗

bioRxiv2020

Indoleamine 2,3-dioxygenase-1 expressing aggregate bone marrow dendritic cell populations are associated with systemic T cell compartment changes in chronic myelomonocytic leukemia

Systemic immune tolerance is not well-characterized in chronic myelomonocytic leukemia (CMML). Due to the presence of clonal plasmacytoid dendritic cells (pDC) in CMML, and the established association of lymph node indoleamine 2,3-dioxygenase-1 (IDO1)-positive (+) DC populations (IDC) with systemic immune tolerance in other malignant contexts, we sought to determine the association of IDO1 expression and bone marrow (BM) DC populations with systemic T-cell compartment changes using primary CMML patient samples (BM, plasma, and peripheral blood mononuclear cells) via immunohistochemistry (IHC), liquid chromatography-mass spectrometry (LC-MS), and time-of-flight mass cytometry (CyTOF). Our results highlight that aggregate BM IDC (CD123 and/or CD11c positive) occur in 33% CMML patients at any disease time-point (IHC), correlate with accentuated tryptophan catabolism (LC-MS, increased kynurenine level, median 4.7 versus 3 microM, P=0.049*), systemic regulatory T-cell expansion (CyTOF, %parent cell type, 14.5 versus 4.9%, P=0.04*) and play a role in disease progression, as evidenced by a higher rate of transformation to acute myeloid leukemia (41 versus 13%, P=0.002**), when compared to CMML patients without BM IDC. Our data also highlight a perturbed immune system in CMML with specific systemic immune signatures, particularly type 1, IL-17 producing helper T, CD4 terminal effector and natural killer cell suppression. Key PointsO_LIAggregate IDO1+ dendritic cell populations occur in the CMML bone marrow microenvironment, and their presence correlates with disease progression. C_LIO_LISystemic immune microenvironment signatures in CMML indicate an altered T- and natural killer (NK)-cell balance. Specifically, suppression of type 1 helper T (Th1), IL-17 producing helper T (Th17), CD4 terminal effector and NK cells. C_LIO_LIIDO1+ bone marrow dendritic cell populations in CMML are associated with a T-cell compartment shift towards a regulatory T cell phenotype. C_LI

immunology↗

bioRxiv2020

Identification of Interleukin1β as an Amplifier of Interferon alpha-induced Antiviral Responses

The induction of an interferon-mediated response is the first line of defense against pathogens such as viruses. Yet, the dynamics and extent of interferon alpha (IFN)-induced antiviral genes vary remarkably and comprise three expression clusters: early, intermediate and late. By mathematical modeling based on time-resolved quantitative data, we identified mRNA stability as well as a negative regulatory loop as key mechanisms endogenously controlling the expression dynamics of IFN-induced antiviral genes in hepatocytes. Guided by the mathematical model, we uncovered that this regulatory loop is mediated by the transcription factor IRF2 and showed that knock-down of IRF2 results in enhanced expression of early, intermediate and late IFN-induced antiviral genes. Co-stimulation experiments with different pro-inflammatory cytokines revealed that this amplified expression dynamics of the early, intermediate and late IFN-induced antiviral genes can be mimicked by co-application of IFN and interleukin1 beta (IL1{beta}). Consistently, we found that IL1{beta} enhances IFN-mediated repression of viral replication. Conversely, we observed that in IL1{beta} receptor knock-out mice replication of viruses sensitive to IFN is increased. Thus, IL1{beta} is capable to potentiate IFN-induced antiviral responses and could be exploited to improve antiviral therapies. Author SummaryInnate immune responses contribute to the control of viral infections and the induction of interferon alpha (IFN)-mediated antiviral responses is an important component. However, IFN induces a multitude of antiviral response genes and the expression dynamics of these genes can be classified as early, intermediate and late. Here we show, based on a mathematical modeling approach, that mRNA stability as well as the negative regulator IRF2 control the expression dynamics of IFN-induced antiviral genes. Knock-down of IRF2 resulted in the amplified IFN-mediated induction of the antiviral genes and this amplified expression of antiviral genes could be mimicked by co-stimulation with IFN and IL1{beta}. We observed that co-stimulation with IFN and IL1{beta} enhanced the repression of virus replication and that knock-out of the IL1 receptor in mice resulted in increased replication of a virus sensitive to IFN. In sum, our studies identified IL1{beta} as an important amplifier of IFN-induced antiviral responses.

systems biology↗

bioRxiv2020

Diverse Arctic lake sediment microbiota shape methane emission temperature sensitivity

Northern post-glacial lakes are a significant and increasing source of atmospheric carbon (C), largely through ebullition (bubbling) of microbially-produced methane (CH4) from the sediments1. Ebullitive CH4 flux correlates strongly with temperature, suggesting that solar radiation is the primary driver of these CH4 emissions2. However, here we show that the slope of the temperature-CH4 flux relationship differs spatially, both within and among lakes. Hypothesizing that differences in microbiota could explain this heterogeneity, we compared site-specific CH4 emissions with underlying sediment microbial (metagenomic and amplicon), isotopic, and geochemical data across two post-glacial lakes in Northern Sweden. The temperature-associated increase in CH4 emissions was greater in lake middles--where methanogens were more abundant--than edges, and sediment microbial communities were distinct between lake edges and middles. Although CH4 emissions projections are typically driven by abiotic factors1, regression modeling revealed that microbial abundances, including those of CH4-cycling microorganisms and syntrophs that generate H2 for methanogenesis, can be useful predictors of porewater CH4 concentrations. Our results suggest that deeper lake regions, which currently emit less CH4 than shallower edges, could add substantially to overall CH4 emissions in a warmer Arctic with longer ice-free seasons and that future CH4 emission predictions from northern lakes may be improved by accounting for spatial variations in sediment microbiota.

microbiology↗

bioRxiv2020

The architecture of metabolism maximizes biosynthetic diversity in the largest class of fungi

AbstractO_ST_ABSBackgroundC_ST_ABSEcological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or "specialized" metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales. ResultsHere, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered to be the most phylogenetically diverse class of fungi and are known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation in BGC repertoires is due to non-overlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi. ConclusionsWe project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.

genomics↗