Biology subjects

Fowler, J.

Publications and source records attributed to Fowler, J..

12 recordsLinked to original sources

bioRxiv2026

A global signature of microbiome resilience to climate stress

As climate change accelerates, the microbial communities sustaining organisms and ecosystems worldwide face an uncertain future, with some proving resilient to stress while others collapse, yet no generalizable framework exists to distinguish the two beforehand. Using amplicon sequencing data from ~29,000 microbiomes, we constructed over 440 matched network pairs spanning three of the most pressing stressors: drought, warming, and salinity. We show that keystone microbes with high connectivity, functional redundancy, and metabolic flexibility, are disproportionately likely to survive stress, and that baseline network and functional properties predict community-level structural and functional stability even as taxonomic composition shifts stochastically. These relationships held across the diverse hosts, ecosystems, and regions we tested. Because these properties can be derived from standard, low-cost sequencing collected before disturbance occurs, our findings turn baseline microbiome data into an early-warning system for identifying which communities are most vulnerable to climate stress.

systems biology↗

bioRxiv2026

Distinct transcriptional states of draining lymph node T cells following influenza vaccination in individuals with underrepresented ancestries

The transcriptional and cell repertoire changes of lymph node (LN) T cells following influenza vaccination have been under-investigated across different ethnicities. Draining (dLN) and non-draining (ndLN) axillary LN cells from 17 participants with genotypically varied African or Asian ancestry (ISRCTN13657999) were collected by fine needle aspiration (FNA) before, 5 days and 42 days after adjuvanted influenza vaccination and analysed by single-cell RNA-sequencing (scRNA-seq). The early dLN transcriptional profile and cellular dynamics were distinct from the ndLN; BACH2 expressing T cells were highly induced, exhibiting stem-like and unique quiescence signatures. Proliferating T follicular helper cells (Tfh) were enriched in dLN and Th1-like Tfh predominated with highly induced transcriptional changes. The BACH2+ T cell state and Th1-like Tfh cells, transcriptionally distinct from germinal centre (GC) T cells, were co-localised with LAMP3+ dendritic cells in the T cell zone of publicly available LN datasets, a region that was also distinct from GC Tfh niches. Together, these findings indicate that the induction of a robust, proliferative, and transcriptionally diverse Tfh response, alongside a discrete subset of BACH2+ T cells, represents a marked feature of the early T cell zone immune response to adjuvanted influenza vaccine in the dLN.

immunology↗

bioRxiv2026

ABERRANT HIPPOCAMPAL NEUROGENESIS IS A CONSERVED RESPONSE TO STROKE IN MICE: A MULTI-CENTER MULTIMODEL STUDY

BackgroundAdult hippocampal neurogenesis is markedly altered after cerebral ischemia. Although stroke increases the production of newborn neurons, many of these cells display aberrant morphological and positional features that impair their functional integration and contribute to long-term cognitive decline. Given the clinical heterogeneity of ischemic stroke and the persistent translational failures of preclinical approaches relying on single-model studies it remains unknown whether post-stroke neurogenic alterations are conserved across different experimental paradigms. This study aimed to define common and model-specific features of hippocampal neurogenesis across complementary focal ischemia models. MethodsWe performed a multi-center, multimodel analysis within the STROKE-IMPaCT consortium using permanent and transient middle cerebral artery occlusion (MCAO) paradigms (MCAO via ligation or cauterization under normoxic (dMCAO) or hypoxic conditions (dMCAO+Hypoxia); and filament-based tMCAO across six international sites. Brains from adult C57BL/6J mice were collected 3 days, 7 days, or 2 months after ischemia, sham, or naive conditions. Hippocampal cell proliferation (Ki67) and neuroblast density (DCX) were quantified, and the morphological maturation of newborn neurons was evaluated using high-resolution analyses of dendritic architecture and somatodendritic polarity. All analyses were performed blind to experimental group. ResultsAcross all stroke models, ischemia induced a robust bilateral increase in hippocampal cell proliferation, most pronounced at 3 days and still elevated at 7 days, with levels returning to baseline by 2 months. Neuroblast density was similarly increased at 7 days, particularly in the ipsilateral hippocampus, but normalized by 2 months. Despite recovery in cell number, long-term morphological analysis revealed a consistent reduction in apical dendrite length and a higher proportion of neurons exhibiting aberrant features including ectopic localization, multipolar or inverted polarity, and abnormal lateral growth across all models. These abnormalities were observed both when pooling data across sites and when analyzing each model or center individually. ConclusionsIschemia induces an early, transient increase in hippocampal neurogenesis across diverse stroke paradigms, but the newborn neurons generated after stroke consistently display maladaptive morphological features. These cross-model, cross-site abnormalities indicate that aberrant hippocampal neurogenesis represents a robust hallmark of post-stroke pathology within the investigated species, independent of ischemia type or surgical approach, despite known differences in the spatial distribution of primary injury across experimental stroke models. Our findings support the concept that maladaptive neurogenesis may contribute to chronic post-stroke cognitive impairment and underscore the need to consider the quality not only the quantity of newborn neurons when developing therapeutic strategies.

animal behavior and cognition↗

bioRxiv2025

Determination of α-Synuclein Protein Interactions by μMap Photo-proximity Labeling

Fibrillar aggregates of the natively disordered protein -synuclein (S) are hallmarks of Parkinsons disease and related neurodegenerative disorders termed synucleinopathies. Here, we used micromap ({micro}Map) photo-proximity labeling to determine the interactomes of S monomers and fibrils in mouse brain lysate to better understand both the loss of healthy function and gain of toxic function aspects of synucleinopathies. Several S variants were synthesized and characterized, showing that the small size (1 kDa) of the Ir catalyst attached through a Cys-maleimide linkage makes it minimally-perturbing to S, with a narrow labeling radius that allows one to identify interactome differences between different regions of S. Monomer and fibril interactomes were compared to each other and to previous proximity labeling data sets for validation and several examples of further investigations are demonstrated, including Western blotting, super-resolution microscopy, and {micro}Map in primary neurons.

biochemistry↗

bioRxiv2025

CD300LG is a receptor for triglyceride-rich lipoproteins that facilitates postprandial lipid clearance

Circulating triglycerides are principally transported by triglyceride-rich lipoprotein particles (TRLs) including very-low-density-lipoproteins (VLDL) and chylomicrons and require the activity of lipoprotein lipase for appropriate lipid processing and cellular uptake. Despite known genetic links between CD300LG variants and altered lipid profiles, the functional role of CD300LG in lipid metabolism remains unclear. In this study, we identify CD300LG as a crucial receptor for TRLs. Human genetic analyses reveal that reduced CD300LG protein levels are causally linked with CAD risk and increased number, diameter, and TAG concentration of TRLs. In mice, CD300LG deficiency results in postprandial hypertriglyceridemia independent of changes in VLDL secretion, intestinal lipid absorption, or lipoprotein lipase activity. Mechanistically, CD300LG acts as a receptor for TRLs through a direct interaction with ApoA4 to facilitate TRL clearance at the microvascular endothelium. These findings elucidate new functions for both CD300LG and ApoA4 and advance our general understanding of triglyceride metabolism.

physiology↗

bioRxiv2025

CMG2 interaction with actin is required for growth factor-induced chemotaxis in endothelial cells.

Capillary morphogenesis gene 2 (CMG2/ANTXR2) is a cell surface receptor that contributes to corneal angiogenesis and is essential for orienting endothelial cell chemotaxis in growth factor gradients. However, the mechanism by which CMG2 transmits signals to orient endothelial cells is unknown. Here, we use affinity proteomics to identify proteins that interact with CMG2. This led us to investigate CMG2 interaction with F-actin in the context of serum and individual growth factors (bFGF/PDGF/VEGF) in both primary and immortalized endothelial cells. We also measured different matrix-protein-mediated changes in chemotaxis. We find that CMG2 function is matrix dependent, and that CMG2-actin interaction is required for serum- and growth-factor-induced chemotaxis. Inhibiting chemotaxis with CMG2 antagonists (collagen 6, penta-galloyl-glucose, or anthrax toxin protective antigen; PA) leads to the release of actin cytoskeleton from CMG2. Furthermore, CMG2 co-localizes with actin at the leading edge during live migration. This colocalization is disrupted by PA, which also disrupts directional movement. Finally, we demonstrate that the conserved actin binding domain of CMG2 directly binds to F-actin in vitro where it bundles F-actin, suggesting a mechanism by which it enables directional migration.

molecular biology↗

bioRxiv2025

How to quantify immigration from community abundance data using the Neutral Community Model

Biological communities are connected through dispersal, which regulates diversity across local and regional scales. However, dispersal is difficult to measure directly, limiting what is known about dispersals impact on species composition in complex communities. One method to measure dispersal employs the Neutral Community Model (NCM) to quantify how a local community is influenced by the immigration of individuals from a larger source community. Conveniently, the immigration rate NTm of the NCM can be fit from biological sequence abundance datasets, which are plentiful. Yet it is neither known if these estimated values reflect the ground truth, nor what sampling effort is required to yield accurate estimates. In this study we introduce two inference methods, a variance-based and a Dirichlet-Multinomial Log-Likelihood (DM-LL) method, to complement the established occupancy-based inference method. In simulations of communities that resemble activated sludge microbiomes, all inference methods were capable of estimating NTm within 10% of ground-truth, with the variance-based and DM-LL methods requiring less sampling effort. Accurate inferences require read depths greater than NTm in each sample. The three methods agree in their inferred NTm in simulations of communities experiencing weak non-neutral effects (e.g., selection), and in applications to an empirical dataset from wastewater activated sludge. Based on these findings, we propose practical sampling and methodological guidelines for quantifying immigration between highly diverse, complex communities using the NCM.

ecology↗

bioRxiv2024

Early regional lymph node activation drives influenza vaccine responses in an ancestrally diverse cohort

Early in vivo dynamics of human immune-cell activation across regionally activated lymphoid tissue sites upon immunisation are poorly characterised in ancestrally diverse individuals. Here, we profiled draining and non-draining axillary lymph nodes (dLNs and ndLNs) by ultrasound-guided fine-needle aspiration (FNA) in 13 Black and Asian ancestry individuals, before and 3-7 days after vaccination with adjuvanted influenza vaccine. Draining but not ndLNs rapidly increased in size post-vaccination, by day 3, with distinct cellular dynamics determined through single cell multiomics. Dissecting LN cellular diversity into 42 lymphoid and non-lymphoid cell states, post-vaccination cell abundance changes were observed across all LNs, but dLNs were specifically characterised by CD4+ T follicular helper (CD4+ Tfh) cell expansion. Gene expression analysis revealed a dLN post-vaccination hub of multicellular activity defined by CD4+ Tfh signalling, cross-compartmental activation, translation, and enhanced antigen-presentation capacity. Thus, robust responses to intramuscular immunisation transcending ancestral inter-individual variation are elicited through temporal, anatomical and cellular lymphatic co-ordination with implications for vaccine design in ancestrally diverse populations. SummaryIn this study of ancestrally diverse young adults, the temporarily co-ordinated response to an adjuvanted influenza vaccine at lymph nodes local to (draining) and distal from (non-draining) the injection site, reveals early regulation of cellular kinetics and anatomical hierarchy of the innate and adaptive immune responses.

immunology↗

bioRxiv2024

DNMT3AR882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency

Genetic mutations are being thoroughly mapped in human cancers, yet a fundamental question in cancer biology is whether such mutations are functionally required for cancer initiation, maintenance of established cancer, or both. Here, we study this question in the context of human acute myeloid leukemia (AML), where DNMT3AR882 missense mutations often arise early, in pre-leukemic clonal hematopoiesis, and corrupt the DNA methylation landscape to initiate leukemia. We developed CRISPR-based methods to directly correct DNMT3AR882 mutations in leukemic cells obtained from patients. Surprisingly, DNMT3AR882 mutations were largely dispensable for disease maintenance. Replacing DNMT3AR882 mutants with wild-type DNMT3A did not impair the ability of AML cells to engraft in vivo, and minimally altered DNA methylation. Taken together, DNMT3AR882 mutations are initially necessary for AML initiation, but are largely dispensable for disease maintenance. The notion that initiating oncogenes differ from those that maintain cancer has important implications for cancer evolution and therapy. STATEMENT OF SIGNIFICANCEUnderstanding which driver mutations are required for cancer initiation, maintenance, or both phases remains poorly understood. Here, we uncover that highly prevalent pre-leukemic DNMT3A mutations are only required during disease initiation, but become dispensable after leukemic transformation, uncovering the context-specific role of this driver mutation with important therapeutic implications.

cancer biology↗

bioRxiv2022

Astrocyte-Oligodendrocyte interaction regulates central nervous system regeneration

Failed regeneration of myelin around neuronal axons following central nervous system damage contributes to nerve dysfunction and clinical decline in various neurological conditions, for which there is an unmet therapeutic demand1,2. Here, we show that interaction between glial cells - astrocytes and mature myelin-forming oligodendrocytes - is a critical determinant of remyelination. Astrocytes support the survival of regenerating oligodendrocytes, via downregulation of the Nrf2 pathway associated with increased astrocytic cholesterol biosynthesis pathway activation. Remyelination fails following sustained astrocytic Nrf2 activation yet is restored by either cholesterol biosynthesis/efflux stimulation, or Nrf2 inhibition using the existing therapeutic Luteolin. We identify that astrocyte-oligodendrocyte interaction regulates remyelination, and reveal a drug strategy for central nervous system regeneration centred on targeting this interaction.

neuroscience↗

bioRxiv2019

DNA and RNA-SIP reveal Nitrospira spp. as key drivers of nitrification in groundwater-fed biofilters

Nitrification, the oxidative process converting ammonia to nitrite and nitrate, is driven by microbes and plays a central role in the global nitrogen cycle. Our earlier metagenomics, amoA-amplicon, and amoA-qPCR based investigations of groundwater-fed biofilters indicated a consistently high abundance of comammox Nitrospira, and we hypothesized that these non-classical nitrifiers drive ammonia-N oxidation. Hence, we used DNA and RNA stable isotope probing (SIP) coupled with 16S rRNA amplicon sequencing to identify the active members in the biofilter community when subject to a continuous supply of NH4+ or NO2- in the presence of 13C-HCO3- (labelled) or 12C-HCO3- (unlabelled). Allylthiourea (ATU) and sodium chlorate were added to inhibit autotrophic ammonia- and nitrite-oxidizing bacteria, respectively. Our results confirmed that lineage II Nitrospira dominated ammonium oxidation in the biofilter community. A total of 78 (8 in RNA-SIP and 70 in DNA-SIP) and 96 (25 in RNA-SIP and 71 in DNA-SIP) Nitrospira phylotypes (at 99% 16S rRNA sequence similarity) were identified as complete ammonia- and nitrite-oxidizing, respectively. We also detected significant HCO3- uptake by Acidobacteria subgroup10, Pedomicrobium, Rhizobactera, and Acidovorax under conditions that favoured ammonium oxidation. Canonical Nitrospira alone drove nitrite oxidation in the biofilter community, and activity of archaeal ammonia oxidizing taxa was not detected in the SIP fractions. This study provides the first in-situ evidence of ammonia oxidation by comammox Nitrospira in an ecologically relevant complex microbiome.

physiology↗

bioRxiv2019

Pan cancer patterns of allelic imbalance from chromosomal aberrations in 33 tumor types

Somatic copy number alterations (SCNAs), including deletions and duplications, serve as hallmarks of tumorigenesis. SCNAs may span entire chromosomes and typically result in deviations from an expected one-to-one ratio of alleles at heterozygous loci, leading to allelic imbalance (AI). The Cancer Genome Atlas (TCGA) reports SCNAs identified using a circular binary segmentation (CBS) algorithm, providing segment mean copy number estimates from Affymetrix single-nucleotide polymorphism DNA microarray total (log R ratio) intensities, but not allele-specific (\"B allele\") intensities that inform of AI. Here we seek to provide a TCGA-wide description of AI in tumor genomes, including AI induced by SCNAs and copy-neutral loss-of-heterozygosity (cnLOH), using a powerful haplotype-based method applied to allele-specific intensities. We present AI summaries for all 33 tumor sites and propose an automated adjustment procedure to improve calibration of existing SCNA calls in TCGA for tumors with high levels of aneuploidy where baseline intensities were difficult to establish without annotation of AI. Overall, 94% of tumor samples exhibited AI. Recurrent events included deletions of 17p, 9q, 3p, amplifications of 8q, 1q, 7p as well as mixed event types on 8p and 13q. The AI-based approach identified frequent cnLOH on 17p across multiple tumor sites, with additional site-specific cnLOH patterns. Our findings support the exploration of additional methods for robust automated inference procedures and to aid empirical discoveries across TCGA.

genomics↗