Biology subjects

Johnson, M.

Publications and source records attributed to Johnson, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

GPR34 regulation of disease-associated microglial states and responses to physiological stimuli

Expression of the G protein coupled receptor GPR34 is highly enriched in microglia and has been reported to be downregulated in several brain disease contexts, including Alzheimers disease (AD) and multiple sclerosis (MS). GPR34 function is poorly understood, as is its role in regulation of microglial states. Using RNA-sequencing, we find that microglia from Gpr34 knockout (KO) mouse brains exhibited a transcriptomic shift toward disease-associated microglia (DAM) and inflammatory profiles, partially resembling the microglial phenotype seen in 5xFAD AD model mice. Moreover, when Gpr34 KO mice were crossed with 5xFAD mice, the DAM transcriptional profile of microglia and glial pathology were further enhanced beyond the already robust DAM signature driven by 5xFAD alone. This occurred without affecting amyloid plaque burden. Human stem cell-derived microglia (iMGLs) lacking GPR34 showed reduced calcium (Ca{superscript 2}) and phosphorylated ERK (pERK) signaling in response to stimulation with known GPR34 agonists (lyso-phosphatidylserine (lysoPS) and myelin), as well as transcriptomic changes in immune regulation and cell proliferation related pathways. Interestingly, GPR34 KO iMGLs were selectively impaired in phagocytosis of myelin but not amyloid-{beta} (A{beta}) or E. coli, and showed a diminished transcriptional response elicited by myelin. Together, these findings suggest that GPR34 is important for maintaining microglia in a homeostatic state, promotes phagocytosis of and transcriptional response to myelin, and limits microglial activation in neurodegenerative disease conditions.

neuroscience↗

bioRxiv2025

TP53 and RB1 are predictive genetic biomarkers for sensitivity to cytarabine in gliomas

Therapeutic progress in glioma, one of the most lethal human cancers, has been limited by molecular heterogeneity and lack of biomarker-driven drug deployment. Here we used a proprietary large-scale CRISPRi screening in primary patient-derived glioma tumorspheres to identify genetic vulnerabilities and nominate pharmacologically tractable targets. DNA polymerase-linked dependencies emerged as top-ranked hits, which we validated through orthogonal viability assays. Network-based integration of dependency data with drug-target relationships nominated cytarabine, a nucleoside analogue already approved for intrathecal use, as a candidate agent targeting this axis. Dose-response profiling across molecularly diverse glioma models revealed substantial heterogeneity in cytarabine sensitivity (IC50 range: 0.04-9.8 {micro}M). Machine learning analysis of whole-genome sequencing data identified TP53 wild-type and RB1-wild-type status as dominant predictors of response, with double wild-type lines showing three standard deviations (3 s.d.) increased sensitivity compared to altered models. Prospective validation in an independent cohort confirmed that TP53/RB1 genotype stratifies cytarabine activity. These findings establish a mechanistically anchored, biomarker-restricted repurposing opportunity for cytarabine in leptomeningeal glioma, enabling rational prioritisation of an accessible therapy in a molecularly defined patient subset.

cancer biology↗

bioRxiv2025

PROX1 loss in adult mouse Schlemm's canal causes permanent ocular hypertension

Glaucoma is associated with ocular hypertension and lowering intraocular pressure is a key objective of glaucoma therapies. Recent studies have established a role for the Schlemms canal endothelium in this pressure increase and have shown it to have a unique, lymphatic-like, hybrid phenotype. However, the role of these lymphatic phenotypes in the adult canal remains uncertain. Long-term functional studies have been limited by systemic importance of lymphatic genes and lack of Schlemms canal-specific animal models. Here, we designed and validated a strategy using 4OH-tamoxifen-loaded nanocarriers to generate targeted, Schlemms canal specific knockout mice lacking lymphatic phenotypes. Using this system, we selectively deleted Prox1, the master transcription factor governing lymphatic fate. Within four weeks, intraocular pressure significantly increased, and ocular hypertension was maintained for at least 24 weeks. Unlike lymphatic vessels, which degenerate following Prox1 deletion, Schlemms canal reverted to a less functional vein-like phenotype with no change in size or morphology. These results highlight the utility of nanocarriers for tissue-specific genetic recombination and demonstrate that changes in lymphatic phenotypes alter intraocular pressure, providing new targets for glaucoma therapy. Moreover, as we found that PROX1 was downregulated with age in human Schlemms canal, these canal-specific conditional Prox1 knockout mice are a valuable new adult-onset model of ocular hypertension that captures key features of age-related human disease.

physiology↗

bioRxiv2025

Immune transcriptomic differences in paediatric patients with SARS-CoV-2 compared to other lower respiratory tract infections

The clinical severity of SARS-CoV-2 infection in children varies, with asymptomatic or mild illness predominating and a minority developing severe disease. Understanding the immunological responses that underlie severity of disease may guide future development of preventive or therapeutic interventions. This study compared whole blood transcriptomes of healthy children (N=127), children with mild/asymptomatic SARS-CoV-2 infection (N=71) and children hospitalised with severe SARS-COV-2 (N=41), lower respiratory tract illness (LRTI) or LRTI due to Respiratory Syncytial Virus (RSV-LRTI) (N=47) or Pulmonary Tuberculosis (PTB) (N=47). We identified >5000 differentially expressed genes including: OLFM4, IFI27, CBX7, IGF2BP3, OTOF for severe SARS-CoV-2; IFI27, OTOF, SIGLEC1, IFI44L and USP18 for RSV-LRTI, and MMP8, LTF, IGF2BP3, GPR84, CD177, C1QC and DEFA4 for PTB, at false discovery rate (FDR) <0.05. Pathway analysis identified enrichment for neutrophil degranulation, interferon gamma signalling, overexpression of ribosomal proteins and depletion of immune response in severe SARS-CoV-2 compared to healthy (SAR-COV-2 uninfected) children. Weighted Gene Co-expression Network Analysis (WGCNA) identified 10 correlated gene modules shared between LRTI showing similar underlying response mechanisms. Cellular decomposition analysis identified the depletion of 22 cell types in severe SARS-CoV-2, 16 for RSV-LRTI and 21 for PTB compared to healthy SARS-CoV-2 uninfected control children. We identified 82 genes important for discriminating asymptomatic/mild from severe SARS-CoV-2 including CBX7, TRAF1, ZNF324 and CASS4; 93 healthy from severe SARS-CoV-2 including RORC, CBX7, NR3C2, MID2 and ADAMTS2; 110 genes for RSV-LRTI and 95 for PTB children which can be used for future therapeutic targets. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/687132v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@13db618org.highwire.dtl.DTLVardef@7df9e2org.highwire.dtl.DTLVardef@a0a448org.highwire.dtl.DTLVardef@818cef_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Tomato pollen tube integrity is critical for pollen function at high temperature and is controlled by RALF signaling.

Reproductive success at high temperature (HT) depends on the ability of pollen to germinate a pollen tube that delivers sperm for double fertilization. We recently found that Solanum lycopersicum (tomato) cultivars capable of setting fruit at HT produce pollen tubes that continue to grow under heat stress. Our present goal is to define the molecular basis of thermotolerant pollen tube growth using quantitative live imaging, transcriptomic and proteomic profiling, and genetic analysis. We found that pollen tube integrity - the ability to maintain an intact tip during germination and elongation - was the pollen performance parameter that distinguished thermotolerant cultivars. We identified the components of the Rapid Alkalinization Factor (RALF) pollen tube integrity signal transduction pathway in tomato and found that RALF peptides repress germination at control temperature and that signaling is antagonized by HT. Loss of a single RALF peptide changes pollen tube cell wall pectin distribution and enhances pollen tube integrity at HT in thermotolerant Heinz, revealing that RALF signaling regulates thermotolerant pollen tube growth and establishing a molecular framework for improving reproductive heat-resilience in crop plants.

plant biology↗

bioRxiv2025

Butyrate rescues chlorpyrifos-induced social deficits through inhibition of class I histone deacetylases

Chlorpyrifos (CPF) is a widely used organophosphate pesticide effective through inhibiting acetylcholinesterase, which leads to the accumulation of acetylcholine and continuous nerve stimulation. In addition to its well-known acute toxicity, exposure to CPF has also been linked to chronic conditions such as an increasing risk of autism spectrum disorder (ASD) and adverse effects on gut health, including disturbances to the gut microbiome and metabolism. However, the underlying mechanism of CPFs contribution to ASD remains unclear, and the roles of the gut microbiome and gut metabolites in CPF-induced neurodevelopmental toxicity remain elusive. Using a high-throughput social behavior assay, we found that embryonic exposure to CPF induced lasting social deficits in zebrafish. Through a small-scale screen of common health beneficial gut microbiome metabolites, we discovered that butyrate effectively rescued CPF-induced social deficits. RNA sequencing of zebrafish brain tissues revealed that early exposure to CPF induced a lasting suppression of neuronal genes, including many ASD risk genes, and elevated expression of circadian genes. Butyrate partially reversed the suppression of key neuronal genes. Butyrate is a non-selective inhibitor of histone deacetylases (HDACs). Through a series of loss-of-function experiments utilizing CRISPR-Cas9-induced knockouts and selective chemical inhibitors, we found that the class I HDAC, HDAC1, most likely mediates butyrates rescue effect. Metabolomics analysis detected changes in several nitrogen metabolism-related pathways in the zebrafish gut following CPF exposure. Metagenomics analysis revealed an increase in abundance of the denitrifying bacteria Pseudomonas and a reduction in the nitric oxide-sensitive bacteria Aeromonas in the CPF-exposed zebrafish gut microbiome. Our results connect CPF-exposure with changes in the gut microbiome, metabolome, epigenetics, gene expression, and behavior, inspiring a novel hypothesis for the underlying molecular mechanisms of CPF-induced neurodevelopmental toxicity. In the long run, our findings may help elucidate how CPF exposure contributes to autism risk and inspire therapeutic developments.

neuroscience↗

bioRxiv2025

Development of a Synthetic Hydrogel to Foster Microvascularization of an Endometriosis Microphysiological System

The ascent of novel alternative methods (NAMs) in drug development spotlights the dual needs for improved biological fidelity to in vivo along with reproducibility, especially in regulatory applications. The need for pre-clinical models of patient-derived endometriosis lesions motivates development of a vascularizable completely synthetic extracellular matrix (v-CS-ECM) that supports morphogenesis of perfusable microvasculature in a microfluidic device, in the context of relevant lesion cells. This paper describes v-CS-ECM, a peptide-modified polyethylene glycol-based hydrogel crosslinked with a cell-degradable peptide that achieves these dual goals. Vessels form by morphogenesis after the liquid v-CS-ECM precursor, containing endothelial cells and fibroblasts, is injected into the tissue compartment to encapsulate cells. Vessel formation is influenced by ECM biochemical and biophysical properties, source of vascular cells, and microphysiological system (MPS) operating conditions. The v-CS-ECM also supports co-culture of endometrial epithelial organoids (EEOs) and fibroblasts, and formation of microvascularized endometriosis lesion-like structures when all cell types are co-encapsulated in a microfluidic device with constant flow. Hence, v-CS-ECM overcomes limitations of reproducibility and biological function inherent in the fibrin-based ECM typically employed for microvascular morphogenesis, as well as Matrigel for organoid culture, thus offering promise for NAMs evaluating endometriosis drugs in the preclinical setting.

bioengineering↗

bioRxiv2025

A Protein Antibiotic Inhibits the BAM Complex to Kill Without Cell Entry

Many antibiotics are ineffective against Gram-negative pathogens such as Pseudomonas aeruginosa because they cannot penetrate the bacterial outer membrane. Here, we show that protein antibiotics called L-type pyocins kill P. aeruginosa by inhibiting the {beta}-barrel assembly machinery (BAM) complex at the cell surface, halting outer-membrane protein assembly. Using single-particle cryo-electron microscopy, we show that L-type pyocins bind a surface-exposed region of BamA and deploy a C-terminal peptide that competitively inhibits the BAM complex, demonstrating that cell entry is not required for antibiotic activity. We combine genetics, multi-omics and cryo-electron tomography to show that BAM complex inhibition by L-type pyocins or the peptide antibiotic darobactin triggers a multifaceted transcriptomic, proteomic and morphological response. Despite this, BAM inhibition ultimately leads to a catastrophic loss of membrane integrity and cell death. These results validate BAM as a target for antibiotics that do not enter the cell and define an engineerable system for their development.

microbiology↗

bioRxiv2025

Filomicelle-Embedded Composite Hydrogels for Localized Gelation within the Anterior Chamber of the Eye

Nanocarriers hold transformative potential for treating anterior segment eye diseases, yet corneal epithelium impermeability necessitates intraocular injection. Given the discomfort and infection risk, an injectable hydrogel-based depot offers a promising strategy for sustained nanocarrier delivery in intraocular therapy. However, because the aqueous humor is a large, fluid-filled environment, achieving spatially confined gelation remains a key challenge as injected materials rapidly diffuse. Herein, we present a composite hydrogel (C-gel) that enables localized in situ gelation and sustained nanocarrier release within the anterior chamber. This is achieved using poly(ethylene glycol)-b-poly(propylene sulfide) (PEG-b-PPS) filomicelles (FMs), whose filamentous structure confines crosslinking reactions spatially, promoting efficient gel formation. As a result, 90% of the injected polymer is retained within the crosslinked hydrogel matrix. Embedded FMs then undergo oxidation-induced cylinder-to-sphere transitions, facilitating gradual release of micellar nanocarriers. The rheological properties, gelation timing, and microstructure of the C-gel are adjustable, allowing precise control of nanocarrier release dynamics. In vivo evaluation in mice confirmed excellent biocompatibility without inducing intraocular pressure elevation, ocular toxicity, or immune cell infiltration. Sustained release of nanocarriers was observed for over a month under conditions mimicking that of the anterior chamber of the eye, underscoring the potential of C-gels for long-term drug delivery in anterior segment eye diseases therapy.

bioengineering↗

bioRxiv2025

Interacting Hosts with Microbiome Exchange: An Extension of Metacommunity Theory for Discrete Interactions

Microbiomes, which are collections of interacting microbes in an environment, often substantially impact the environmental patches or living hosts that they occupy. In microbiome models, it is important to consider both the local dynamics within an environment and exchanges of microbiomes between environments. One way to incorporate these and other interactions across multiple scales is to employ metacommunity theory. Metacommunity models commonly assume continuous micro-biome dispersal between the environments in which local microbiome dynamics occur. Under this assumption, a single parameter between each pair of environments controls the dispersal rate between those environments. This metacommunity framework is well-suited to abiotic environmental patches, but it fails to capture an essential aspect of the microbiomes of living hosts, which generally do not interact continuously with each other. Instead, living hosts interact with each other in discrete time intervals. In this paper, we develop a modeling framework that encodes such discrete interactions and uses two parameters to separately control the interaction frequencies between hosts and the amount of microbiome exchange during each interaction. We derive analytical approximations of models in our framework in three parameter regimes and prove that they are accurate in those regimes. We compare these approximations to numerical simulations for an illustrative model. We demonstrate that both parameters in our modeling framework are necessary to determine microbiome dynamics. Key features of the dynamics, such as microbiome convergence across hosts, depend sensitively on the interplay between interaction frequency and strength. MSC codes92-10, 92C42, 92D40, 60J76

ecology↗

bioRxiv2025

Artificial Light at Night Disrupts Circadian and Metabolic Gene Expression in the Green Anole Lizard (Anolis carolinensis): A Transcriptomic Analysis

Artificial light at night (ALAN) disrupts natural light-dark cycles, posing ecological challenges for wildlife in urban areas. Here we investigated the effects of ALAN on gene expression in the brain, liver, and skin of green anole lizards (Anolis carolinensis) whose urban populations are increasingly exposed to light pollution. To identify genetic pathways impacted by ALAN exposure we analysed expression of genes associated with circadian and metabolic regulation at midday, midnight and at midnight with artificial light. Differential expression analysis revealed that clock-related genes (PER1, NR1D1, CRY2) were significantly altered in the brain, liver, and skin following ALAN treatment and genes involved in glucagon regulation (GCG) and lipid metabolism (NOCT) were differentially expressed in the liver, indicating metabolic disruptions. Skin exhibited unique responses to ALAN suggesting that repair responses may be altered as genes related to cellular processes, such as wound healing, were upregulated under normal light and dark conditions. Our findings also show that ALAN disrupts core circadian genes, impacting physiological processes including hormone regulation, glucose homeostasis, and potentially reproductive cycles. This study provides the first transcriptomic evidence of the effects of light pollution on green anoles, highlighting the need to preserve natural light cycles in urban habitats. An interactive online database developed for this study allows further exploration of gene expression changes, to promote research on artificial light-polluted environments.

genetics↗

bioRxiv2025

Expression of Non-Visual Opsins in the Green Anole Lizard (Anolis carolinensis)

Extra-retinal photoreception is widely observed across vertebrates, facilitating species-specific regulation of physiological and behavioral responses to diverse photic environments. Yet, the roles of non-visual opsins remain poorly understood, as their distribution and function have not yet been systematically investigated. This study provides the first comprehensive evidence of non-visual opsin expression across the reptile body. Using predicted sequences for extra-retinal photoreceptors, non-visual opsins were confirmed in the brain, eye, testes, liver, and skin. Specifically, OPN3 (encephalopsin) exhibited the highest expression across all tissues, particularly in the testes, corroborating findings in mammals. OPN5 (neuropsin) was detected predominantly in the testes, marking the first such report in reptiles. Moderate expression of OPN4 (melanopsin) in the brain and eye supports its roles in both visual and deep-brain photoreception. In the skin, a distinct pattern of higher opsin expression was observed in the dorsal skin compared to ventral skin. OPN3-3 was most abundant and exhibited a unique expression profile, potentially linking opsins to light-mediated processes influencing chromatophore-driven color changes. Findings from this research provide a critical evolutionary context for understanding the role and conservation of non-visual opsins in reptiles and their relevance to vertebrate lineages, including mammals and birds.

zoology↗

bioRxiv2025

Non-invasive approach for endoluminal biopsy coupled with single-cell proteomics allows for immune characterization of intracranial aneurysms

The immune regulatory mechanisms driving the stability, growth, and rupture of intracranial aneurysms (IAs) remain incompletely understood. In this study, we employ endoluminal biopsy with single-cell proteomics to comprehensively profile the immune landscape of IAs across their pathologic states. Our findings reveal distinct immune signatures associated with aneurysm states. Stable, i.e. non-growing unruptured, IAs exhibit a balanced immune cell composition. Ruptured IAs are marked by significant neutrophil predominance. Notably, we highlight key immune markers in aneurysm instability, offering new insights into immune drivers of aneurysm progression. These findings provide a foundation for immune-targeted, non-invasive therapeutic strategies aimed at targeting IAs and preventing rupture.

physiology↗

bioRxiv2024

Autophagy inhibition induces AML cell death and enhances the efficacy of chemotherapy under hypoxia

Outcomes of relapsed/refractory acute myeloid leukemia (AML) are poor, and strategies to improve outcomes are urgently needed. One important factor promoting relapse and chemoresistance is the ability of AML cells to thrive in vivo within an intrinsically hypoxic bone marrow microenvironment. Here we show that human AML cells exhibit enhanced autophagy, specifically mitophagy (i.e., increased accumulation of mitochondria and decreased mitochondrial membrane potential) under hypoxia. To target this pathway, we investigated the activity of the potent chloroquine-derived autophagy inhibitor, Lys05, on human AML cells, patient samples, and patient derived xenograft models. Inhibition of autophagy by Lys05 in AML cells prevented removal of damaged mitochondria and preferentially enhanced cell death under hypoxia mirroring the marrow microenvironment. Lys05 eradicated human AML cells of all genotypes including p53 mutant cells. Lys05 treatment in primary AML xenografted mice decreased CD34+CD38- human cells and prolonged overall survival. Moreover, Lys05 overcame hypoxia-induced chemoresistance and improved the efficacy of cytarabine, venetoclax, and azacytidine in vitro and in vivo in AML models. Our results demonstrate the importance of autophagy, specifically mitophagy, as a critical survival and chemoresistance mechanism of AML cells under hypoxic marrow conditions. Therapeutic targeting of this pathway in future clinical studies for AML is warranted.

cancer biology↗

bioRxiv2024

Semi-automated high content analysis of pollen performance using TubeTracker

Pollen function is critical for successful plant reproduction and crop productivity and it is important to develop accessible methods to quantitatively analyze pollen performance to enhance reproductive resilience. Here we introduce TubeTracker as a method to quantify key parameters of pollen performance such as, time to pollen grain germination, pollen tube tip velocity and pollen tube survival. TubeTracker integrates manual and automatic image processing routines and the graphical user interface allows the user to interact with the software to make manual corrections of automated steps. TubeTracker does not depend on training data sets required to implement machine learning approaches and thus can be immediately implemented using readily available imaging systems. Furthermore, TubeTracker is an excellent tool to produce the pollen performance data sets necessary to take advantage of emerging AI-based methods to fully automate analysis. We tested TubeTracker and found it to be accurate in measuring pollen tube germination and pollen tube tip elongation across multiple cultivars of tomato. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/624782v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1fc2a63org.highwire.dtl.DTLVardef@42f3a2org.highwire.dtl.DTLVardef@18911d6org.highwire.dtl.DTLVardef@1f236f0_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract Graphical user interface of TubeTracker showing all supported functionalities. C_FIG

plant biology↗

bioRxiv2024

Haploinsufficiency of lysosomal enzyme genes in Alzheimers disease

There is growing evidence suggesting that the lysosome or lysosome dysfunction is associated with Alzheimers disease (AD). Pathway analysis of post mortem brain-derived proteomic data from AD patients shows that the lysosomal system is perturbed relative to similarly aged unaffected controls. However, it is unclear if these changes contributed to the pathogenesis or are a response to the disease. Consistent with the hypothesis that lysosome dysfunction contributes to AD pathogenesis, whole genome sequencing data indicate that heterozygous pathogenic mutations and predicted protein-damaging variants in multiple lysosomal enzyme genes are enriched in AD patients compared to matched controls. Heterozygous loss-of-function mutations in the palmitoyl protein thioesterase-1 (PPT1), -L-iduronidase (IDUA), {beta}-glucuronidase (GUSB), N-acetylglucosaminidase (NAGLU), and galactocerebrosidase (GALC) genes have a gene-dosage effect on A{beta}40 levels in brain interstitial fluid in C57BL/6 mice and significantly increase A{beta} plaque formation in the 5xFAD mouse model of AD, thus providing in vivo validation of the human genetic data. A more detailed analysis of PPT1 heterozygosity in 18-month-old mice revealed changes in -, {beta}-, and {gamma}-secretases that favor an amyloidogenic pathway. Proteomic changes in brain tissue from aged PPT1 heterozygous sheep are consistent with both the mouse data and the potential activation of AD pathways. Finally, CNS-directed, AAV-mediated gene therapy significantly decreased A{beta} plaques, increased life span, and improved behavioral performance in 5xFAD/PPT1+/- mice. Collectively, these data strongly suggest that heterozygosity of multiple lysosomal enzyme genes represent risk factors for AD and may identify precise therapeutic targets for a subset of genetically-defined AD patients. Significance StatementLysosomes play a role in the degradation of aggregation-prone proteins such as amyloid {beta} (A{beta}). Homozygous lysosomal enzyme gene defects result in fatal pediatric lysosomal storage diseases and, historically, carriers were considered normal. However, a human genetic analysis identified deleterious heterozygous variants in multiple lysosomal enzyme genes that are enriched in Alzheimers disease (AD) patients. Those findings were validated in vivo by demonstrating that heterozygous loss-of-function (LoF) mutations in five different lysosomal enzyme genes affect A{beta} processing and exacerbate A{beta} plaque formation. CNS-directed gene therapy ameliorated the effects of a heterozygous LoF mutation in one of those genes in a mouse model of AD. These findings provide insights into the role of lysosomes in AD and have important therapeutic implications.

neuroscience↗

bioRxiv2024

Proteome-wide reverse molecular docking reveals folic acid receptor as a mediator of PFAS-induced neurodevelopmental toxicity

Per- and polyfluoroalkyl substances (PFAS) are a class of long-lasting chemicals with widespread use and environmental persistence that have been increasingly studied for their detrimental impacts to human and animal health. Several major PFAS species are linked to neurodevelopmental toxicity. For example, epidemiological studies have associated prenatal exposure to perfluorooctanoate (PFOA) and perfluorononanoate (PFNA) with autism risk. However, the neurodevelopmental toxicities of major PFAS species have not been systematically evaluated in an animal model, and the molecular mechanisms underlying these toxicities have remained elusive. Using a high-throughput zebrafish social behavioral model, we screened six major PFAS species currently under regulation by the Environmental Protection Agency (EPA), including PFOA, PFNA, perfluorooctane sulfonate (PFOS), perfluorohexanesulfonic acid (PFHxS), perfluorobutane sulfonate (PFBS), and hexafluoropropylene oxide dimer acid ammonium salt (GenX). We found that embryonic exposure to PFNA, PFOA, and PFOS induced social deficits in zebrafish, recapitulating one of the hallmark behavioral deficits in autistic individuals. To uncover protein targets of the six EPA-regulated PFAS, we screened a virtual library containing predicted binding pockets of over 80% of the 3D human proteome through reverse molecular docking. The screen predicts that folate receptor beta (FR-{beta}, encoded by the gene FOLR2) interacts strongly with PFNA, PFOA, and PFOS but to a lesser degree with PFHxS, PFBS, and GenX, correlating positively with their in vivo toxicity. These predictions were validated through in silico molecular docking, in vitro protein binding analysis, and in vivo loss-of-function verification. Furthermore, embryonic co-exposure to folic acid effectively rescued social deficits induced by PFAS. The folate pathway has been implicated in autism, indicating a novel molecular mechanism for PFAS in autism etiology.

pharmacology and toxicology↗

bioRxiv2024

Signatures of selective sweeps in urban and rural white clover populations

Urbanization is increasingly recognized as a powerful force of evolutionary change. However, anthropogenic sources of selection can often be similarly strong and mul{-} tifarious in rural habitats, and whether selection differs in either strength or its targets between habitats is rarely considered. Despite numerous examples of phe{-} notypic differentiation between urban and rural populations, we still lack an un{-} derstanding of the genes enabling adaptation to these contrasting habitats. In this study, we conducted whole genome sequencing of 120 urban, suburban, and rural white clover plants from Toronto, Canada and used these data to identify urban and rural signatures of positive selection. We found evidence for selection in genomic regions involved in abiotic stress tolerance and growth/ development in both urban and rural populations, and clinal change in allele frequencies at SNPs within these regions. Patterns of allele frequency and haplotype differentiation suggest that most sweeps are incomplete and our strongest signals of selective sweeps overlap known large-effect structural variants. These results highlight how both urban and rural habitats are driving ongoing selection in Toronto white clover populations, and mo{-} tivate future work disentangling the genetic architecture of ecologically important phenotypes underlying adaptation to contemporary anthropogenic habitats.

evolutionary biology↗