Biology subjects

Wheeler, K.

Publications and source records attributed to Wheeler, K..

9 recordsLinked to original sources

bioRxiv2026

Early-Life Wildfire Smoke Exposure Is Associated with Long-Term Systemic Immune Remodeling and Epigenetic Reprogramming

Wildfire smoke is an escalating global public health threat exposing millions of people, including children, to hazardous air pollution each year. Although wildfire smoke toxicants have been linked to a range of adverse health outcomes, including immune dysregulation, the long-term consequences of real-world pediatric wildfire smoke exposure on health and development remain largely unknown. To investigate the persistent effects of early-life exposure on immune health, here we leveraged a cohort of rhesus macaques that experienced nine consecutive days of hazardous wildfire smoke exposure in infancy during the 2020 Oregon Labor Day wildfires. By integrating ex vivo immune stimulations, multiplex cytokine profiling, single-cell transcriptomics, and genome-wide DNA methylation profiling, we identified persistent immunological consequences across molecular and functional levels. We found that a single severe postnatal exposure, in the first three months of life, was associated with persistent change in the innate immune response, including reduced pro-inflammatory cytokine response to a bacterial endotoxin, with subtle but consistent transcriptional changes in myeloid cells, particularly among males. Wildfire smoke exposure was also associated with changes in proportion of B and T/NK cells, and within the T/NK cell compartment, exposed animals exhibited an expansion of cytotoxic cells. Consistent with this, CD8+ T cells displayed extensive transcriptional remodeling and shifted toward more differentiated effector states, with the greatest differentiation observed in animals exposed at the youngest ages. Genome-wide DNA methylation profiling identified smoke-associated methylation changes consistent with acceleration of epigenetic aging, as well as persistent epigenetic alterations impacting genes involved in oxidative stress responses, innate immunity, T cell differentiation, and hematopoiesis. These findings demonstrate that a single severe wildfire smoke exposure during a critical developmental window is associated with extensive immune and epigenetic remodeling that persist years after exposure, providing new insight into the long-term biological consequences of early-life wildfire smoke exposure.

immunology↗

bioRxiv2025

TNFα and Endothelial IL-1 Receptor Signaling Drive Peritubular Capillary Regression and Fibrosis in Obstructive Kidney Injury

Capillary regression destabilizes tissue homeostasis and contributes to chronic organ dysfunction, yet the inflammatory pathways that drive pathological vessel loss remain incompletely defined. We previously identified the inflammatory cytokines TNF and IL-1 as conserved mediators of physiological vessel regression in the neonatal mouse eye, but whether these cytokines contribute to pathological capillary regression in adult mice is unknown. In this study, we investigated the capillary regression that occurs along with inflammation in murine kidneys following irreversible unilateral ureteral obstruction (UUO) surgical challenge. Mice lacking genes encoding global TNF, the endothelial IL-1 receptor IL-1R1, or both (double knockout, DKO) were examined at 10 days after UUO surgery. While loss of the individual genes did not affect peritubular capillary (PTC) regression, PTC regression was significantly reduced in DKO mice. This reduction in PTC regression correlated with less expression of the tubular epithelial injury marker KIM-1. DKO kidneys also displayed less fibrosis by Picrosirius Red and Massons trichrome staining. These findings demonstrate that TNF and endothelial IL-1R1 cooperatively drive pathological capillary regression in the irreversible UUO model of chronic kidney injury and that preservation of PTCs correlates with less renal tubular injury and fibrosis at 10 days after injury. NEW & NOTEWORTHYPathological PTC regression drives progressive kidney injury, but its inflammatory triggers are unclear. Using the UUO model, this study identifies cooperative TNF and endothelial IL-1R1 signaling as key drivers of capillary loss. While deletion of either pathway alone was insufficient, combined loss preserved PTCs, reduced tubular injury, and attenuated fibrosis. These findings highlight synergistic inflammatory signaling in microvascular loss and suggest dual targeting may help preserve PTC integrity in chronic kidney disease.

pathology↗

bioRxiv2025

European ash pangenome reveals widespread structural variation and a diverse genetic basis for low ash dieback susceptibility

European Ash (Fraxinus excelsior) is a keystone forest tree species, whose populations are being decimated by ash dieback disease (ADB). Uncovering the genetic basis of low susceptibility to this devastating disease relies on a comprehensive understanding of genetic variation present in F. excelsior. A linear reference genome from a single individual cannot contain the total sequence variability within a species, including its genic regions; a pangenome more fully captures total sequence content. In this study, we developed a F. excelsior pangenome reference using a new chromosomal-level phased linear reference genome, and de novo assemblies and long-read data from a geographically diverse set of fifty F. excelsior samples, with particular focus on individuals showing low ADB susceptibility. We identified 362,965 structural variants (SVs) present in more than three individuals, including 174Mb of sequence absent from the linear reference genome (22% of the linear reference size). We demonstrated that failing to explicitly link SVs with gene sequences can lead to substantial overestimation of dispensable genes (those that vary in their presence/absence between individuals) due to variability in the annotation process. Controlling for this reduced the fraction of the genome estimated as dispensable from 35.9% to 8.7%, identifying 3,412 high-confidence dispensable genes, including 141 annotated with gene ontology terms associated with defence response. We used the pangenome to analyse existing genomic data from over 1,200 individuals to identify loci associated with reduced susceptibility to ADB. This revealed 220 single nucleotide polymorphisms (SNPs) showing allele frequency shifts between healthy and highly damaged pools of individuals that are broadly consistent across the mainly UK seed sources sampled, explicitly demonstrating the existence of a shared genetic component to low ADB susceptibility.

genomics↗

bioRxiv2025

MvfR shapes Pseudomonas aeruginosa Interactions in Polymicrobial Contexts: Implications for Targeted Quorum Sensing Inhibition

Infections often occur in complex niches consisting of multiple bacteria. Despite the in-creasing awareness, there is a fundamental gap in understanding which interactions govern mi-crobial community composition. Pseudomonas aeruginosa is frequently isolated from monomicrobi-al and polymicrobial human infections. This pathogen forms polymicrobial infections with other ESKAPEE pathogens and defies eradication by conventional therapies. By analyzing the competi-tion within cocultures of P. aeruginosa and representative secondary pathogens that commonly co-infect patients, we demonstrate the antagonism of P. aeruginosa against other ESKAPEE pathogens and the contribution of this pathogens multiple quorum sensing (QS) systems in these interac-tions. QS is a highly conserved bacterial cell-to-cell communication mechanism that coordinates collective gene expressions at the population level, and it is also involved in P. aeruginosa virulence. Using a collection of P. aeruginosa QS mutants of the three major systems, LasR/LasI, MvfR/PqsABCDE, and RhlR/RhlI and mutants of several QS-regulated functions, we reveal that MvfR and, to a lesser extent, LasR and RhlR control competition between P. aeruginosa and other microbes, possibly through their positive impact on pyoverdine, pyochelin, and phenazine genes. We show that MvfR inhibition alters competitive interspecies interactions and preserves the coex- istence of P. aeruginosa with ESKAPEE pathogens tested while disarming the pathogens ability to form biofilm and adhere to lung epithelial cells. Our results highlight the role of MvfR inhibition in modulating microbial competitive interactions across multiple species, while simultaneously atten-uating virulence traits. These findings reveal the complexity and importance of QS in interspecies interactions and underscore the impact of the anti-virulence approach in microbial ecology and its importance for treating polymicrobial infections.

microbiology↗

bioRxiv2023

Epigenetic Regulation of Endothelial Extracellular Matrix Components is Critical for Murine Lung Development

BackgroundThe chromatin remodeling enzymes BRG1 (brahma-related gene 1) and CHD4 (chromodomain helicase DNA binding protein 4) independently regulate transcription of genes critical for vascular development, but their coordinated impact on vessels in late- stage embryos has not been explored. MethodsIn this study we genetically deleted endothelial Brg1 and Chd4 in mixed background mice (Brg1fl/fl;Chd4fl/fl;VE-Cadherin-Cre+), and littermates that were negative for Cre recombinase were used as controls. Perinatal lung tissue was analyzed by immunostaining, immunoblots, and flow cytometry. Quantitative reverse transcription PCR was used to determine gene expression, and chromatin immunoprecipitation revealed gene targets of BRG1 and CHD4 in cultured endothelial cells (ECs). ResultsWe found that Brg1/Chd4 double mutants died soon after birth with small and compact lungs. Despite having normal cellular composition, distal air sacs of the mutant lungs displayed diminished ECM (extracellular matrix) components and TGF{beta} (transforming growth factor beta) signaling, which typically promotes matrix synthesis. Transcripts for collagen- and elastin-related genes and the TGF{beta} ligand Tgfb1 were decreased in mutant lung ECs, but genetic deletion of endothelial Tgfb1 failed to recapitulate the small lungs and ECM defects seen in Brg1/Chd4 mutants. We instead found several ECM genes to be direct targets of BRG1 and CHD4 in cultured ECs. ConclusionsCollectively, our data highlight essential roles for ECs in promoting ECM deposition at late stages of embryonic lung development. Moreover, this endothelial ECM production is epigenetically regulated. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/552718v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@210be1org.highwire.dtl.DTLVardef@192ee2dorg.highwire.dtl.DTLVardef@1530595org.highwire.dtl.DTLVardef@1938529_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIGenetic deletion of the chromatin remodeling enzymes BRG1 and CHD4 in endothelial cells of late-stage mouse embryos (Brg1/Chd4-ECdko) results in small and compact lungs at birth. C_LIO_LIMutant embryos display reduced collagen IV deposition, dysregulated elastin fibers, and diminished TGF{beta}1 in the distal air sacs. C_LIO_LIOur combined in vitro and in vivo analyses indicate that BRG1 and CHD4 epigenetically regulate collagen IV- and elastin-related gene expression in embryonic ECs to promote proper lung development. C_LI

developmental biology↗

bioRxiv2023

Moderate intensity aerobic exercise in 6-OHDA-lesioned rats alleviates established motor deficits and reduces neurofilament light and glial fibrillary acidic protein serum levels without increased striatal dopamine or tyrosine hydroxylase protein

BackgroundAlleviation of motor impairment by aerobic exercise (AE) in Parkinsons disease (PD) points to a CNS response that could be targeted by therapeutic approaches, but recovery of striatal dopamine (DA) or tyrosine hydroxylase (TH) has been inconsistent in rodent studies. ObjectiveTo increase translation of AE, 3 components were implemented into AE design to determine if recovery of established motor impairment, concomitant with >80% striatal DA and TH loss, was possible. We also evaluated if serum levels of neurofilament light (NfL) and glial fibrillary acidic protein (GFAP), blood-based biomarkers of disease severity in human PD, were affected. MethodsWe used a 6-OHDA hemiparkinson rat model featuring progressive nigrostriatal neuron loss over 28 days, with impaired forelimb use 7 days post-lesion, and hypokinesia onset 21 days post-lesion. After establishing forelimb use deficits, moderate intensity AE began 1-3 days later, 3x per week, for 40 min/session. Motor assessments were conducted weekly for 3 wks, followed by determination of striatal DA, TH protein and mRNA, and NfL and GFAP serum levels. ResultsSeven days after 6-OHDA lesion, recovery of depolarization-stimulated extracellular DA and DA tissue content was <10%, representing severity of DA loss in human PD, concomitant with 50% reduction in forelimb use. Despite severe DA loss, recovery of forelimb use deficits and alleviation of hypokinesia progression began after 2 weeks of AE and was maintained. Increased NfLand GFAP levels from lesion were reduced by AE. Despite these AE-driven changes, striatal DA tissue and TH protein levels were unaffected. ConclusionsThis proof-of-concept study shows AE, using exercise parameters within the capabilities most PD patients, promotes recovery of established motor deficits in a rodent PD model, concomitant with reduced levels of blood-based biomarkers associated with PD severity, without commensurate increase in striatal DA or TH protein.

neuroscience↗

bioRxiv2023

Persistent biofluid small molecule alterations induced by Trypanosoma cruzi infection are not restored by antiparasitic treatment

Table of contents graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/543565v1_figu1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@10c3a0aorg.highwire.dtl.DTLVardef@1b69d6dorg.highwire.dtl.DTLVardef@199867org.highwire.dtl.DTLVardef@64b20b_HPS_FORMAT_FIGEXP M_FIG C_FIG Chagas Disease (CD), caused by Trypanosoma cruzi (T. cruzi) protozoa, is a complicated parasitic illness with inadequate medical measures for diagnosing infection and monitoring treatment success. To address this gap, we analyzed changes in the metabolome of T. cruzi-infected mice via liquid chromatography tandem mass spectrometry analysis of clinically-accessible biofluids: saliva, urine, and plasma. Urine was the most indicative of infection status, across mouse and parasite genotypes. Metabolites perturbed by infection in the urine include kynurenate, acylcarnitines, and threonylcarbamoyladenosine. Based on these results, we sought to implement urine as a tool for assessment of CD treatment success. Strikingly, it was found that mice with parasite clearance following benznidazole antiparasitic treatment had comparable overall urine metabolome to mice that failed to clear parasites. These results match with clinical trial data in which benznidazole treatment did not improve patient outcomes in late-stage disease. Overall, this study provides insights into new small molecule-based CD diagnostic methods and a new approach to assess functional treatment response.

microbiology↗

bioRxiv2023

Cytokine-Mediated Degradation of the Transcription Factor ERG Impacts the Pulmonary Vascular Response to Systemic Inflammatory Challenge

BackgroundDuring infectious diseases, pro-inflammatory cytokines transiently destabilize interactions between adjacent vascular endothelial cells (ECs) to facilitate the passage of immune molecules and cells into tissues. However, in the lung the resulting vascular hyperpermeability can lead to organ dysfunction. Previous work identified the transcription factor ERG as a master regulator of endothelial homeostasis. Here we investigate whether the sensitivity of pulmonary blood vessels to cytokine-induced destabilization is due to organotypic mechanisms affecting the ability of endothelial ERG to protect lung ECs from inflammatory injury. MethodsCytokine-dependent ubiquitination and proteasomal degradation of ERG was analyzed in cultured Human Umbilical Vein ECs (HUVECs). Systemic administration of TNF or the bacterial cell wall component lipopolysaccharide (LPS) was used to cause a widespread inflammatory challenge in mice; ERG protein levels were assessed by immunoprecipitation, immunoblot, and immunofluorescence. Murine Erg deletion was genetically induced in ECs (Ergfl/fl;Cdh5(PAC)CreERT2), and multiple organs were analyzed by histology, immunostaining, and electron microscopy. ResultsIn vitro, TNF promoted the ubiquitination and degradation of ERG in HUVECs, which was blocked by the proteasomal inhibitor MG132. In vivo, systemic administration of TNF or LPS resulted in a rapid and substantial degradation of ERG within lung ECs, but not ECs of the retina, heart, liver, or kidney. Pulmonary ERG was also downregulated in a murine model of influenza infection. Ergfl/fl;Cdh5(PAC)-CreERT2 mice spontaneously recapitulated aspects of inflammatory challenges, including lung-predominant vascular hyperpermeability, immune cell recruitment, and fibrosis. These phenotypes were associated with a lung-specific decrease in the expression of Tek, a gene target of ERG previously implicated in maintaining pulmonary vascular stability during inflammation. ConclusionsCollectively, our data highlight a unique role for ERG in pulmonary vascular function. We propose that cytokine-induced ERG degradation and subsequent transcriptional changes in lung ECs play critical roles in the destabilization of pulmonary blood vessels during infectious diseases.

cell biology↗

bioRxiv2022

Visual Perception of 3D Space and Shape In Time - Part IV: 3D Shape Recognition by 3D Rotation

Human vision has a remarkable ability to recognize complex 3D objects such as faces that appear at any size and 3D orientations at any 3D location. If we initially memorize a face only with a normalized size upfront at the object center, the direct comparison between the one-sized memory and an incoming new image would demand tremendous mental frame translations in 7D. How can we perform such a demanding task so promptly as we experience it in our daily lives? This paper specifically addresses the recognition of human faces with arbitrary 3D orientation in the [Roll, Yaw, Pitch] axes. According to our new model of NHT (Neural Holography Tomography), space is represented by time utilizing the phase of the alpha brainwave. This principle should be applicable to any mental rotation in 3D; thus, it predicts that extra time is required to perceive a rotated face to revolve it back to upright by the constant-speed alpha wave. To assess this hypothesis, we designed a reaction time (RT) experiment, where participants were first asked to memorize sets of upright unfamiliar faces. Following the memorization phase, similar stimuli with a wide range of rotating faces in 3D were presented, and RTs were recorded. As expected, the memorized upfront face was the fastest RT. The excess of the RT was observed proportional to the rotating angle in all [Roll, Yaw, Pitch] axes. Roll had the flattest slope, whereas upper Pitch was the steepest. We suspect that Roll is the swiftest mental operation because it can be conducted by the linear frame translation on the log-polar retinotopy of the visual cortex.

neuroscience↗