Biology subjects

Retter, A.

Publications and source records attributed to Retter, A..

4 recordsLinked to original sources

bioRxiv2026

Cytokine-induced Chromatin Accessibility in Whole Blood Neutrophils Links to Sepsis Transcriptional 1 States

BackgroundNeutrophils play an important role in the immune system and sense environmental perturbations including pathogens. Upon pathogen detection, neutrophils extrude their chromatin, forming neutrophil extracellular traps (NETs) trapping and removing pathogens. Previous studies have shown that controlled chromatin decondensation occurs during NET formation, reflecting NET inducing pathways, and the cellular environment. While NET inducing stimuli like phorbol 12-myristate 13-acetate (PMA) is commonly used to study NET formation, it bypassing regulatory mechanisms, limiting insights. MethodsWe used the Assay for Transposase-Accessible Chromatin with sequencing (ATAC-Seq) to profile chromatin accessibility in neutrophils stimulated in whole blood with PMA and physiologically relevant inflammatory factors (NFs), including TNF-, GM-CSF, fMLP, C5a, and IL-1{beta}, alone and in combination. Chromatin responses were compared across conditions and integrated with publicly available transcriptomic sepsis cohorts. ResultsWe found that NF stimulation induced stimulus specific chromatin accessibility programs distinct from PMA. Individual NFs increased specific transcription factor (TF) motif enrichments in a stimulus dependent manner, with GM-CSF increasing STATs, TNF- increasing NF-{kappa}B, C5a/fMLP increasing AP-1, and Combined with a cooperative response including CEBP. Integration with sepsis transcriptomic datasets revealed that promoter accessibility changes within NF stimulations correspond to transcriptional states associated with sepsis disease severity, highlighting the upstream regulatory programs linked to clinical outcomes. ConclusionsThese findings demonstrate that NF stimulation in whole blood reveals chromatin accessibility programs in neutrophils that correlate with disease severity in sepsis. This approach provides a framework for linking cytokine driven neutrophil regulation to heterogenous inflammatory states in sepsis and other NET-associated diseases.

immunology↗

bioRxiv2025

Chromatin Changes Associated with Neutrophil Extracellular Trap (NET) Formation in Whole Blood Reflect Complex Immune Signaling

BackgroundNeutrophils are key players in innate immunity, forming neutrophil extracellular traps (NETs) to defend against infections. However, excess NET formation is implicated in inflammatory conditions such as sepsis and immunothrombosis. Studying NET formation in isolated neutrophils provides important mechanistic insights but does not reflect the complexity of immune interactions in whole blood, limiting our understanding of neutrophil responses. MethodsThis study investigates chromatin accessibility changes using Assay for Transposase-Accessible Chromatin with sequencing (ATAC-Seq) during phorbol 12-myristate 13-acetate (PMA) induced NET formation in whole blood. We compared chromatin accessibility patterns in neutrophils following PMA treatment in isolation and whole blood to assess the impact of other immune cells and signaling environment. ResultsWhole blood PMA stimulation elicited consistent chromatin accessibility changes across donors, demonstrating organized chromatin decondensation during NET formation. The chromatin response was characterized by increased accessibility in genomic regions enriched for immune-specific pathways, highlighting the role of immune cell interactions in NET formation. Differentially accessible regions (DARs) present following PMA induction in whole blood and isolated neutrophils showed greater association with NET-related and inflammatory transcription factors, while DARs specific to isolated neutrophils showed fewer relevant motifs. Pathway analysis indicated that whole blood responses involved more robust activation of immune-specific pathways, such as interleukin and cytokine signaling, compared to isolated neutrophils. ConclusionsOur findings underscore the importance of studying NET formation within a whole blood environment to capture the complexity of neutrophil responses and immune cell interactions. This understanding is crucial for identifying effective therapeutic targets in NET-associated inflammatory diseases.

immunology↗

bioRxiv2023

Novel rapid high-throughput method of NETosis Induction and Inhibition with physiological triggers and inhibitors

Neutrophils, the most abundant white blood cells in humans, play pivotal roles in innate immunity, rapidly migrating to sites of infection and inflammation to phagocytose, neutralize, and eliminate invading pathogens. Neutrophil Extracellular Trap (NET) formation in response to pathogens is increasingly recognized as an essential rapid innate immune response, but when dysregulated contributes to pathogenesis of sepsis and immunothrombotic disease. Current models of NETosis are limited, routinely employing non-physiological triggers that can bypass natural NET regulatory pathways. Models utilizing isolated neutrophils and immortalized cell lines, do not reflect the complex biology underlying neutrophil activation and NETosis, that occurs in whole-blood. Here we describe a novel, high-throughput ex-vivo whole blood induced NETosis model using combinatorial pooling of native NETosis inducing factors in a more biologically relevant Synthetic-Sepsis model. We found different combinations of factors evoked distinct neutrophil responses in the rate of NET generation and/or magnitude of NETosis. Despite inter-donor variability, similar sets of pro-inflammatory molecules induced consistent responses across donors. We found at least three biological triggers were necessary to induce NETosis in our system including either TNF- or LT-. To our knowledge, we report the first human ex-vivo model utilizing naturally occurring molecules to induce NETosis in whole blood. This approach could be used for drug screening and, importantly, inadvertent activators of NETosis. These findings emphasize the importance of investigating neutrophil physiology in a biologically relevant context to enable a better understanding of disease pathology, risk factors, and therapeutic targets, potentially, providing novel strategies for disease intervention and treatment. EssentialsO_LINETosis is a vital immune response, but dysregulation leads to disastrous health outcomes. C_LIO_LICurrent NETosis models dont reflect the complex endogenous signaling that occurs in whole blood C_LIO_LINetosis induction stimuli differs between isolated neutrophils and whole blood. C_LIO_LIA minimum of three physiological factors are required to induce NETosis in whole blood. C_LI

immunology↗

bioRxiv2023

What mycologists should talk about when they are talking about the International Code of Nomenclature for algae, fungi, and plants

Fungal metabarcoding of substrates such as soil, wood, and water are uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside of the ambit of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of the mycological community - that "the code" works fine and that these complications will somehow sort themselves out given enough time and a following wind - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. However, the present authors fear that no waves of change will be lapping the shores of mycology for the foreseeable future, leaving the overwhelming majority of extant fungi without formal names and thus scientific and environmental agency. It is not clear to us who benefits from that, but neither fungi nor mycology are likely to be on the winning side.

scientific communication and education↗