Biology subjects

Schroeder, J.

Publications and source records attributed to Schroeder, J..

At least 19 recordsLinked to original sources

bioRxiv2026

CAPRIN1 localizes to CD63-positive MVB-like SARS-CoV-2 egress compartments and limits cytopathic effects

Stress granules (SGs) are cytoplasmic condensates that assemble under cellular stress, including viral infection. The best-characterized evasion strategy in SARS-CoV-2 infection involves the viral nucleocapsid (N) protein hijacking the SG core protein G3BP1, thereby preventing SG assembly. By performing network analysis of N protein interactomes, we identified CAPRIN1 as an underexplored candidate, despite its central role alongside G3BP1 in SG assembly. Here, we provide the first high-resolution spatial and functional data on CAPRIN1 in SARS-CoV-2 infection. Using ultrastructure expansion microscopy (U-ExM), we localized CAPRIN1 and viral egress markers to enlarged, CD63- and LAMP1-positive, multivesicular body (MVB)-like egress compartments, refining the current model of SARS-CoV-2 egress. CAPRIN1 was found on both the limiting membrane of these compartments and within the intraluminal vesicles, a pattern distinct from G3BP1. Knockout of CAPRIN1 increased infection-associated cell death, promoted an aberrant cell-death phenotype, and enhanced syncytia formation. Together, our data reveal distinct activities of CAPRIN1 during infection and identify the egress compartments as MVB-like, raising the possibility that SARS-CoV-2 repurposes more than one cellular pathway for egress.

molecular biology↗

bioRxiv2026

Immune responses to infection modulate peripheral sympathetic neuron functions

The central nervous system interprets inflammatory signals in the body and directs the modulation of inflammatory responses by reflexively engaging peripheral sympathetic neurons1,2. This includes sympathetic neurons that innervate the spleen, which can regulate immune functions3-5 and modulate inflammation6-8. Yet, it is unclear if neuroimmune interactions involve specialised immunoregulatory sympathetic neurons, and if the immune system can reciprocally regulate peripheral sympathetic neurons to control these responses. Using retrograde tracing and single-cell transcriptomics, we find that spleen-innervating neurons are heterogeneous but do not exhibit a distinct transcriptional program indicative of specialisation for immune communication. However, we report that immune responses induced by pathogens can regulate postganglionic sympathetic neuron functions. Cytokines produced by immune cells downregulate expression of the neurotrophin nerve growth factor in spleen mesenchymal cells, leading to organ-specific sympathetic nerve retraction from the spleen. Concurrently, splenic type I interferon signalling induces inflammatory gene expression in neurons and suppresses neuron excitability. Chemogenetic activation of sympathetic neurons demonstrates an impaired anti-inflammatory capacity in the spleen during infection. These results reveal regulation of sympathetic neuronal functions by the immune system, which could support optimal generation of immune responses against pathogens.

immunology↗

bioRxiv2026

High-dimensional multiomics reveals perturbations to IL-6/IL-6R axis and RUNX3 in CD4+ T cells during third trimester pregnancy

ObjectivesCD4+ T cells play key roles in regulating immune responses during pregnancy, therefore we aimed to understand the CD4+ T cell surface proteome and transcriptome during pregnancy. MethodsCD4+ T cells were analysed in blood and decidua from term-pregnancies (>37 weeks), and non-pregnant blood. >350 surface proteins were screened via flow cytometry, and transcriptomes were analysed using single-cell RNA sequencing with >130 CITE-seq barcoded antibodies. ResultsSurface protein screening identified changes to ILT4/CD85d, CD9, IFN-{gamma} receptor {beta}-chain, CX3CR1 and CCR5 in the pregnant blood and decidual CD4+ T cells. CX3CR1 and CCR5 had the highest expression on the effector-memory T cell (TEM) subset in the blood, with expression consistent across subsets in decidua. CD126/IL-6R was lower in pregnant blood and decidual CD4+ T cells, while scRNAseq identified enrichment in the IL-6R signalling pathway in naive CD4+ T cells in pregnant blood. Both sIL-6R and IL-6 concentrations were increased in plasma during pregnancy, suggesting perturbations to the IL-6/IL-6R signalling axis. Meanwhile, decidual CD4+ T cells had increased expression of transcription factor RUNX3 in the CD69+ tissue-resident-like subset. ConclusionsOur findings demonstrate altered molecular expression in CD4+ T cells during pregnancy. This provides important mechanistic insight of their adaptation and regulation during placental development, which may drive placental dysfunction or pregnancy complications including preeclampsia, fetal growth restriction and stillbirth. These new data may inform future studies that focus on determining the significance of differentially- expressed immune features in pregnancy to identify potential targets for immune modulation to treat pregnancy complications and infections.

immunology↗

bioRxiv2026

Defining influenza-specific B cells in vaccine responders, non-responders and influenza breakthrough infections

Although seasonal influenza vaccination programs are effective at a population level, our data from inactivated influenza vaccine (IIV) cohorts in years 2015-2022 reveal that 50-60% of individuals do not seroconvert following immunization. The underlying mechanisms of vaccine non-responsiveness are far from understood. In this study, we sought to define key determinants of optimal B cell immune responses elicited by seasonal influenza vaccination, and to explore why some individuals fail to elicit humoral immunity following immunization. Immune responses associated with seroconversion and vaccine failure from individuals immunized with IIVs were compared at cellular and molecular levels using single-cell transcriptomics. We analyzed HA-specific B cell immunity across vaccine-responders, breakthrough infections and patients hospitalized with acute influenza. Droplet-based single-cell RNA sequencing and VDJ-sequencing of influenza-specific B cells from stored PBMCs was performed using 10x Genomics. Our results show that atypical B cells are the major subset of B cell responses in vaccine non-responders on day 28 post-vaccination. Conversely, individuals who seroconvert had diverse B cell phenotypes. The use of recombinant influenza-specific HA probes allowed us to dissect expression patterns on influenza HA-specific B cells. We found that HA-specific B cells of vaccine non-responders for A/H1N1 and A/H3N2 components displayed elevated atypical-like markers (CD11c, FcRL-5) at baseline, compared to responders. Analysis of differentially expressed genes (DEGs) between responders and non-responders identified differential expression of HLA-DR, CD74, CD83, and CXCR3 genes. We subsequently demonstrated reduced frequencies of HLA-DR-, CD74- and CD83-expressing B cells in patients hospitalized with influenza, compared to healthy participants. Hospitalized influenza patients also had significantly higher proportions of atypical CD21-CD27- B cells. Overall, our data demonstrate an association between elevated frequencies of atypical-like B cells with both lack of seroconversion following immunization and severe influenza infection. These findings broaden our understanding of humoral immunity in influenza vaccination and infection, providing novel insights for vaccination strategies and design.

immunology↗

bioRxiv2025

Mapping prefrontal afferents along development

The medial prefrontal cortex (mPFC) acts as a hub for cognitive, emotional, and social processes, integrating neuronal inputs from numerous brain regions. Knowledge on the processes underlying formation and myelination of prefrontal afferents is essential for a comprehensive understanding of the emergence, maturation, and refinement of mPFC-dependent behaviors. However, despite detailed investigation of long-range projections to the mPFC in the adult brain, little is known about their maturation. Here, we use retrograde labeling, light-sheet imaging, and automatic cell segmentation to quantify afferent projections to the mPFC from neonatal to adult age. We show that densities of ipsi- and contralateral prefrontal afferents change along development from a widespread bilateral distribution at neonatal age to a predominantly ipsilateral organization. Furthermore, myelination of interhemispheric prefrontal afferents starts only after the decline of neonatal contralateral projections and is followed by temporally elevated projection densities from limbic brain regions. Overall, these distinct developmental dynamics of prefrontal afferents might have major implications for the maturation of mPFC-dependent functional and behavioral outputs.

neuroscience↗

bioRxiv2025

Antigen reactivity defines tissue-resident memory and exhausted T cells in tumours

CD8+ T cells are a key weapon in the therapeutic armamentarium against cancer. While CD8+CD103+ T cells with a tissue-resident memory T (TRM) cell phenotype have been favourably correlated with patient prognoses1-6, the tumour microenvironment also contains dysfunctional exhausted T (TEX) cells that exhibit a myriad of TRM-like features, leading to conflation of these two populations. Here, we deconvolute TRM and TEX cells within the intratumoural CD8+CD103+ T cell pool across human cancers, ascribing markers and gene signatures that distinguish these CD8+ populations and enable their functional distinction. We found that while TRM cells exhibit superior functionality and are associated with long-term survival post-tumour resection, they are not associated with responsiveness to immune checkpoint blockade. Deconvolution of the two populations showed that tumour-associated TEX and TRM cells are clonally distinct, with the latter comprising both tumour-independent bystanders and tumour-specific cells segregated from their cognate antigen. Intratumoural TRM cells can be forced towards an exhausted fate when chronic antigen stimulation occurs, arguing that the presence or absence of continuous antigen exposure within the microenvironment is the key distinction between respective tumour-associated TEX and TRM populations. These results suggest unique roles for TRM and TEX cells in tumour control, underscoring the need for distinct strategies to harness these T cell populations in novel cancer therapies.

immunology↗

bioRxiv2025

Examining the genetic and phenotypic correlation between survival and fecundity in a wild bird

There is intraspecific variation in reproduction and survival, which has been hypothesised to be the result of trade-offs in investment. However, we lack compelling evidence that trade- offs drive variation within species, perhaps because genetic trade-offs are masked by environmental variation. We used a long-term dataset of breeding records for a closed population of house sparrows (Passer domesticus) and its associated pedigree to separate the genetic and environmental covariance between fecundity and survival. We measured age-specific changes in reproductive outputs and estimated the heritability of both offspring production and survival in multivariate animal models. Our results show no evidence for survival costs to reproductive output. Nor did we find evidence that individuals fecundity and survival are correlated either the genetic or permanent environment level. Our findings show no evidence that variation in fecundity is driven by the offspring-production/survival trade-off. Instead, our results show that individuals are only somewhat consistent in their reproductive output, and suggest this is a possible mechanism why selection cannot act on individual quality.

evolutionary biology↗

bioRxiv2024

Outcome-Driven Microscopy: Closed-Loop Optogenetic Control of Cell Biology

Smart microscopy is transforming biological imaging by integrating real-time analysis with adaptive acquisition to enhance imaging efficiency. Whereas many emerging implementations are event-driven and focus on on-demand data acquisition to reduce phototoxicity, we here present outcome-driven microscopy, which combines smart microscopy with optogenetics to achieve subcellular spatiotemporal control of biology to predefined outcomes. We validate this approach using light-based control of cell migration and nucleocytoplasmic transport, and demonstrate unprecedented spatiotemporal control over cellular behaviour.

cell biology↗

bioRxiv2024

Vgamma1+ gammadelta T cell-derived IL-4 initiates CD8 T cell immunity

Dendritic cells (DC) are pivotal for initiating adaptive immunity, a process triggered by the activation of DC via pathogen products or damage. Here, we describe an additional layer to this process, essential when pathogen-derived signals alone cannot directly achieve full DC activation. Immunisation with sporozoites from Plasmodium leads to CD8 T cell priming in a complex response that is initiated by a collaboration between conventional type 1 DC (cDC1) and {gamma}{delta} T cells. We unveil a pivotal initiating role for V{gamma}1+ {gamma}{delta} T cells, as they directly supply IL-4 to DC and CD8 T cells. IL-4 synergises with a CD4 T cell-derived CD40L signal to induce IL-12 production by cDC1. Both IL-12 and IL-4 then directly signal CD8 T cells, with synergy between these cytokines driving enhanced IL-12 receptor expression and expansion of responding CD8 T cells. This study reveals a key role for V{gamma}l+ {gamma}{delta} T cells in initiating CD8 T cell immunity to Plasmodium. More broadly, it shows that responses to some pathogens require help from innate-like T cells to pass an initiation threshold and further amplify the response in a process underscored by IL-4 production.

immunology↗

bioRxiv2024

YOLO-Behaviour: A simple, flexible framework to automatically quantify animal behaviours from videos

Manually coding behaviours from videos is essential to study animal behaviour but it is labour-intensive and susceptible to inter-rater bias and reliability issues. Recent developments of computer vision tools enable the automatic quantification of behaviours, supplementing or even replacing manual annotations. However, widespread adoption of these methods is still limited, due to the lack of annotated training datasets and domain-specific knowledge required to optimize these models for animal research. Here, we present YOLO-Behaviour, a flexible framework for identifying visually distinct behaviours from video recordings. The framework is robust, easy to implement, and requires minimal manual annotations as training data. We demonstrate the flexibility of the framework with case studies for event-wise detection in house sparrow nestling provisioning, Siberian jay feeding, human eating behaviours, and frame-wise detections of various behaviours in pigeons, zebras, and giraffes. Our results show that the framework reliably detects behaviours accurately, and retrieve comparable accuracy metrics to manual annotation. However, metrics extracted for event-wise detection were less correlated with manual annotation, and potential reasons for the discrepancy between manual annotation and automatic detection are discussed. To mitigate this problem, the framework can be used as a hybrid approach of first detecting events using the pipeline and then manually confirming the detections, saving annotation time. We provide detailed documentation and guidelines on how to implement the YOLO-Behaviour framework, for researchers to readily train and deploy new models on their own study systems. We anticipate the framework can be another step towards lowering the barrier of entry for applying computer vision methods in animal behaviour.

animal behavior and cognition↗

bioRxiv2024

Damsel: Analysis and visualisation of DamID sequencing in R

SummaryDamID sequencing is a technique to map the genome-wide interaction of a protein with DNA. Damsel is the first Bioconductor package to provide an end to end analysis for DamID sequencing data within R. Damsel performs quantification and testing of significant binding sites along with exploratory and visual analysis. Damsel produces results consistent with previous analysis approaches. Availability and implementationThe R package Damsel is available for install through the Bioconductor project https://bioconductor.org/packages/release/bioc/html/Damsel.html and the code is available on GitHub https://github.com/Oshlack/Damsel/ Contactcaitlin.page@petermac.org Supplementary informationAvailable through the journal.

bioinformatics↗

bioRxiv2023

Plasmacytoid dendritic cells (pDCs) display surface but not membrane-bound IgE across a broad range of total serum IgE levels

IntroductionPlasmacytoid dendritic cells (pDCs) are unique antigen presenting cells that may be implicated in allergic disease because they bind IgE on their surface and modulate important Th1/Th2 cytokine responses. While conducting in vitro experiments using excess omalizumab to capture IgE, we discovered that this immunoglobulin is not readily removed from pDC to the same extent observed for basophils suggesting that a portion of the IgE on pDC is membrane bound. MethodsBasophils and pDC were prepared from leukopacks using established protocols. In order to isolate PBMCs, blood was also drawn from consenting donors with a wide range in total serum IgE levels. B cells and pDCs were identified by flow cytometry by gating on CD19/CD27 and BDCA2/CD123, respectively. Quilizumab, a mouse anti-human monoclonal IgG1 antibody with specificity only for membrane-bound IgE, was used to detect this molecule in both cell types. ResultsWhen used in vitro at 1.5 mg/ml, omalizumab removed [~]80-90% of the IgE expressed by basophils. In contrast, IgE expression decreased only 30-40% on pDC treated likewise. Upon analyzing pDC for membrane-bound IgE, there was no significant difference in number of target-bound cells and mean fluorescence between the mouse isotype control and quilizumab among pDCs (P = 0.125, 0.165). However, the ratio of the proportion of target-bound CD19+27+ B cells compared to other cells was 32:1 for isotype (P < 0.001) and 54:1 for quilizumab (P = 0.015). ConclusionOverall, this study demonstrates that while pDCs express significant levels of Fc{varepsilon}RI that binds IgE to the surface, there is no appreciable amount of membrane-bound IgE noted. The reason for omalizumabs poor ability to remove IgE from pDCs remains unknown.

immunology↗

bioRxiv2023

Metabolism regulates muscle stem cell self-renewal by connecting the microenvironment and histone acetylation

Skeletal muscle contains a resident population of somatic stem cells capable of both self-renewal and differentiation. The signals that regulate this important decision have yet to be fully elucidated. Here we use metabolomics and mass spectrometry imaging (MSI) to identity a state of localized hyperglycaemia following skeletal muscle injury. We show that committed muscle progenitor cells exhibit an enrichment of glycolytic and TCA cycle genes and that extracellular monosaccharide availability regulates intracellular citrate levels and global histone acetylation. Muscle stem cells exposed to a reduced (or altered) monosaccharide environment demonstrate reduced global histone acetylation and transcription of myogenic determination factors (including myod1). Importantly, reduced monosaccharide availability was linked directly to increased rates of asymmetric division and muscle stem cell self-renewal in regenerating skeletal muscle. Our results reveal an important role for the extracellular metabolic environment in the decision to undergo self-renewal or myogenic commitment during skeletal muscle regeneration.

cell biology↗

bioRxiv2023

Liver-specification of human iPSC-derived endothelial cells transplanted into mouse liver

Liver sinusoidal endothelial cells (LSECs) play an important role in liver development, regeneration and pathophysiology, but the differentiation process that generates their unique tissue-specific phenotype is poorly understood and difficult to study as primary cells are only available in limited quantities. To address this, we hypothesised that human induced pluripotent stem cell (hiPSC)-derived endothelial cells (iECs) can produce hiPSC-derived LSECs upon transplantation into the livers of Fah-/-/Rag2-/-/Il2rg-/-mice, and serve as a model to study LSEC specification. Progressive and long-term repopulation of the liver vasculature was observed, as iECs expanded along the sinusoids that run between hepatocytes and increasingly produced human factor VIII, indicating differentiation into LSEC-like cells. To chart the developmental profile associated with LSEC specification, the bulk transcriptome of transplanted cells at time-points between 1 and 12 weeks were compared against primary human adult LSECs, which demonstrated a chronological increase in LSEC markers, LSEC differentiation pathways, and zonation. Bulk transcriptome analysis suggested that the transcription factors NOTCH1, GATA4, and FOS play a central role in LSEC specification, interacting with a network of 27 transcription factors. Novel markers associated with this process include EMCN and CLEC14A. Additionally, single cell transcriptomic analysis demonstrated that transplanted iECs at 4 weeks contain zonal subpopulations with a region-specific phenotype. Collectively, this study confirms that hiPSC can adopt LSEC-like features and provides insight into LSEC specification. This humanised xenograft system can be applied to further interrogate LSEC developmental biology and pathophysiology, bypassing current logistical obstacles associated with primary human LSECs.

cell biology↗

bioRxiv2023

Deep mutational scanning highlights a new role for cytosolic regions in Hrd1 function

Misfolded endoplasmic reticulum proteins are degraded through a process called endoplasmic reticulum associated degradation (ERAD). Soluble, lumenal ERAD targets are recognized, retrotranslocated across the ER membrane, ubiquitinated, extracted from the membrane, and degraded by the proteasome using an ERAD pathway containing a ubiquitin ligase called Hrd1. To determine how Hrd1 mediates these processes, we developed a deep mutational scanning approach to identify residues involved in Hrd1 function, including those exclusively required for lumenal degradation. We identified several regions required for different Hrd1 functions. Most surprisingly, we found two cytosolic regions of Hrd1 required for lumenal ERAD substrate degradation. Using in vivo and in vitro approaches, we defined roles for disordered regions between structural elements that were required for Hrd1s ability to autoubiquitinate and interact with substrate. Our results demonstrate that disordered cytosolic regions promote substrate retrotranslocation by controlling Hrd1 activation and establishing directionality of retrotranslocation for lumenal substrate across the endoplasmic reticulum membrane.

biochemistry↗

bioRxiv2022

Indirect genetic effects improve female extra-pair heritability estimates.

The question of why females engage in extra-pair behaviours is long-standing in evolutionary biology. One suggestion is that these behaviors are maintained through pleiotropic effects on male extra-pair behaviors and lifetime reproductive success (genes controlling extra-pair behaviours are shared between sexes, but only beneficial to one, in this case, males). However, for this to occur extra-pair behaviour must be heritable and positively genetically correlated between sexes. Although previous studies have suggested low heritability with no evidence for between-sex genetic correlations in extra-pair behaviours, indirect genetic effects (those derived from the behaviour of others, IGEs) from the social partner, the influence of the social partners genotype on the phenotype of an individual, have not been considered, despite the potential to uncover hidden heritability. Using data from a closed house sparrow population with a genetic pedigree spanning two decades, we tested the influence of IGEs on heritability and genetic correlation estimates of extra-pair behaviour. We found that the inclusion of IGEs improved model fit for both male and female extra-pair heritability. While IGEs did not change between-sex genetic correlations, we found a reduction in uncertainty in our estimates. Future studies should consider the effect of IGEs on the mechanisms of sex specific extra-pair behaviour.

evolutionary biology↗

bioRxiv2022

Nr6a1 controls axially-restricted body elongation, segmentation, patterning and lineage allocation

The vertebrate main-body axis is laid down during embryonic stages in an anterior-to-posterior (head-to-tail) direction, driven and supplied by posteriorly located progenitors. For the vertebral column, the process of axial progenitor cell expansion that drives elongation, and the process of segmentation which allocates progenitor-descendants into repeating pre-vertebral units, occurs seemingly uninterrupted from the first to the last vertebra. Nonetheless, there is clear developmental and evolutionary support for two discrete modules controlling processes within different axial regions: a trunk and a tail module. Here, we identify Nuclear receptor subfamily 6 group A member 1 (Nr6a1) as a master regulator of elongation, segmentation, patterning and lineage allocation specifically within the trunk region of the mouse. Both gain- and loss-of-function in vivo analyses revealed that the precise level of Nr6a1 acts as a rheostat, expanding or contracting vertebral number of the trunk region autonomously from other axial regions. Moreover, Nr6a1 was found to be required for segmentation, but only for trunk-forming somites, with the timely clearance of Nr6a1 critical in supporting tail formation. In parallel with these morphological outcomes, we reveal Nr6a1 as a novel regulator of global Hox signatures within axial progenitors, preventing the precocious expression of multiple posterior Hox genes as the trunk is being laid down and thus reinforcing that patterning and elongation are coordinated. Finally, our data supports a crucial role for Nr6a1 in regulating gene regulatory networks that guide cell lineage choice of axial progenitors between neural and mesodermal fate. Collectively, these data reveal an axially-restricted role for Nr6a1 in all major cellular and tissue-level events required for vertebral column formation, supporting the view that modulation of Nr6a1 expression level or function is likely to underpin evolutionary changes in axial formulae that exclusively alter the trunk region.

developmental biology↗

bioRxiv2022

Increased opposite sex association is linked with fitness benefits, otherwise sociality is subject to stabilising selection in a wild passerine

Animal sociality, an individuals propensity to associate with others, has fitness consequences through mate choice, for example, directly, by increasing the pool of prospective partners, and indirectly through increased survival, and individuals benefit from both. Annually, fitness consequences are realised through increased mating success and subsequent fecundity. However, it remains unknown whether these consequences translate to life-time fitness. Here, we quantified social associations and their link to fitness annually and over lifetime, using a multi-generational, genetic pedigree. We used social network analysis to calculate variables representing different aspects of an individuals sociality. Sociality showed high within-individual repeatability. We found that birds with more opposite-sex associates had higher annual fitness than those with fewer, but this did not translate to lifetime fitness. Instead, for lifetime fitness, we found evidence for stabilizing selection on opposite-sex sociality, and sociality in general, suggesting that reported benefits are only short-lived in a wild population, and that selection favours an average sociality.

evolutionary biology↗