Biology subjects

Park, J. M.

Publications and source records attributed to Park, J. M..

16 recordsLinked to original sources

bioRxiv2026

Distinct spatiotemporal immunometabolic remodeling following acute traumatic brain injury

Traumatic brain injury induces profound metabolic reprogramming across neurons, astrocytes, and microglia, yet the spatiotemporal organization of these metabolic responses remains poorly understood. Because pyruvate is uniquely positioned in cerebral metabolism by connecting glycolysis, lactate metabolism, and the tricarboxylic acid cycle, we combined matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging with in vivo administration of isotopically labeled pyruvate and immunohistochemistry to characterize cell-type-wise metabolic remodeling in a controlled cortical impact rat model during the acute and subacute phases of injury. TBI induced distinct spatiotemporal immunometabolic remodeling across neuroglial compartments. Microglia- and macrophage-enriched regions exhibited selective accumulation of citrate, succinate, and itaconate, consistent with inflammatory metabolic rewiring. In contrast, astrocyte enriched regions showed increased glutamine and malate abundance, indicative of altered neuron-astrocyte metabolic coupling such as remodeling of the glutamate-glutamine cycle and enhanced anaplerotic metabolism. These metabolic signatures evolved with distinct regional and temporal distributions, identifying compartmentalized metabolic responses. Notably, labeled isotopologues of selected metabolites, including glutamate and citrate derived from administered pyruvate, changed before the corresponding metabolite pools. Together, these findings describe the spatiotemporal landscape of immunometabolic remodeling following acute TBI, uncover metabolically distinct microglial/macrophage and astrocytic responses during secondary brain injury, and identify candidate metabolic pathways for therapeutic intervention and metabolic imaging.

biochemistry↗

bioRxiv2025

Adaptation of Anaplasma phagocytophilum to the tick vector is controlled by the transcriptional regulator Tr1

Rickettsial pathogens are strictly dependent on the cellular biology of their hosts for survival and replication. Predominantly transmitted by blood-feeding arthropods, these vector-borne pathogens are forced to adapt between the disparate environments of their mammalian host and arthropod vector. To achieve this, the Rickettsial bacteria Anaplasma phagocytophilum undergoes extensive transcriptional reprogramming with over 41% of its genes differentially transcribed between mammals and Ixodes scapularis ticks. How the bacterium orchestrates this dramatic transcriptional reprogramming is not understood. The gene tr1 encodes a Helix-Turn-Helix DNA-binding protein that is exclusively expressed during tick infection. Herein, we show that tr1 is essential for A. phagocytophilum survival in ticks and regulates the transcription of other genes necessary to adapt to the arthropod vector. We demonstrate that Tr1 is a DNA-binding protein and recognizes promotors of tick-specific genes in A. phagocytophilum, including secreted effector ateA, alternate components of type IV secretion system (T4SS), and membrane proteins. Our findings demonstrate that Tr1 is a master regulator of genes that are critical for A. phagocytophilum adaptation to the tick.

microbiology↗

bioRxiv2025

Small-molecule perturbation profiling reveals a mechanistic link between STING signaling and lipid metabolism in macrophages and dendritic cells

The DNA sensor cGAS and the signaling adaptor STING play a key role in the innate immune response to microbial and endogenous DNA in the cytoplasm. The cGAS-STING signaling pathway has evolved to promote immune defense and organismal fitness, yet its dysregulation can lead to chronic inflammation, autoimmunity, and neurodegeneration. Upon sensing double- stranded DNA, cGAS produces a cyclic dinucleotide second messenger that binds to STING in the endoplasmic reticulum. Ligand-bound STING translocates to the Golgi and activates the protein kinase TBK1 and the transcription factor IRF3, resulting in IRF3-driven interferon (IFN) gene transcription. This cascade of molecular events is mechanistically linked to intracellular lipid membrane dynamics and protein lipidation. To explore whether STING signaling is controlled by the availability and metabolic flux of cellular lipids, we screened small-molecule compounds targeting lipid metabolic pathways for their influence on STING agonist-responsive IFN induction. These screens identified inhibitors of the fatty acid synthase FAS and lipases as potent suppressors of STING signaling. An inhibitor of the cholesterol-esterifying enzyme SOAT1 enhanced STING-dependent IFN induction in mouse cells while attenuating it in human cells. Our findings reveal a connection between STING signaling and lipid metabolism and opportunities for expanding the toolbox for treating clinical conditions that arise from aberrant STING activity.

immunology↗

bioRxiv2025

Mechanical environment afforded by engineered polymer hydrogel critically regulates survival of neural stem cells transplanted in the injured spinal cord via Piezo1-mediated mechanotransduction

Neural stem cell (NSC) transplantation is a promising therapeutic approach for spinal cord repair, but poor graft survival remains a critical challenge. Here, we demonstrate that the mechanical properties of the transplantation microenvironment play a crucial role in NSC survival in the injured spinal cord. While our previously engineered imidazole-poly(organophosphazene) (I-5) hydrogel effectively prevented cavity formation by promoting extracellular matrix remodeling, NSCs transplanted with 10% hydrogel exhibited poor survival. Remarkably, increasing the hydrogel concentration to 16%, which created a 5-fold stiffer matrix, significantly enhanced NSC graft survival and synaptic integration. Using in vitro models with controlled substrate stiffness, we found that NSCs on stiffer substrates displayed enhanced adhesion, complex morphology, and increased viability. Importantly, we identified the mechanosensitive ion channel Piezo1 as the key molecular mediator of these stiffness-dependent behaviors. CRISPR/Cas9-mediated Piezo1 gene editing in NSCs significantly reduced graft survival in vivo when transplanted with 16% hydrogel, confirming that Piezo1-mediated mechanotransduction is essential for NSC survival in the injured spinal cord. Our findings reveal a previously unrecognized mechanism governing graft survival in the injured spinal cord and suggest that optimizing the mechanical properties of biomaterial scaffolds or targeting Piezo1-dependent mechanotransduction could substantially improve outcomes of cell-based therapies for neurological disorders.

neuroscience↗

bioRxiv2025

Diploidy confers genomic instability in Schizosaccharomyces pombe

Whole genome duplication, or polyploidy, has been implicated in driving genome instability and tumorigenesis. Recent studies suggest that polyploidy in tumors promotes cancer genome evolution, progression, and chemoresistance resulting in worse prognosis of survival. The mechanisms by which whole genome duplications confer genome instability are not yet fully understood. In this study, we use Schizosaccharomyces pombe (fission yeast) diploids to investigate how whole genome duplication affects genome maintenance and response to stress. We find that S. pombe diploids are sensitive to replication stress and DNA damage, exhibit high levels of loss of heterozygosity, and become dependent on a group of ploidy-specific lethal genes for viability. These findings are observed in other eukaryotic models suggesting conserved consequences of polyploidy. We further investigate ploidy-specific lethal genes by depleting them using an auxin-inducible degron system to elucidate the mechanisms of genome maintenance in diploids. Overall, this work provides new insights on how whole genome duplications lead to genome instability.

molecular biology↗

bioRxiv2024

A pipeline for facile cloning of antibody Fv domains and their expression, purification, and characterization as recombinant His-tagged IgGs

We report a functional pipeline for facile conversion of variable Fv domains, typically discovered in antibody discovery programs, into chimeric monoclonal antibodies (mAbs). Often, in initial screenings, a set of candidate mAbs is produced in small volumes and purified from supernatant for testing. Our pipeline also simplifies purification of mAbs by using an extended histidine tag (His-10) fused to the C-terminus of the light chain. Both the length of the His-10 and its location have been shown to affect the efficacy of mAb purification using an inexpensive nickel-based resin at neutral pH. Our antibody cloning and purification pipeline, when followed together with detection and affinity measurements, can be smoothly incorporated into an antibody discovery workflow.

immunology↗

bioRxiv2023

Mice require proprioception to establish long-term visuospatial memory.

Because the retina moves constantly, the retinotopic representation of the visual world is spatially inaccurate and the brain must transform this spatially inaccurate retinal signal to a spatially accurate signal usable for perception and action. One of the salient discoveries of modern neuroscience is the role of the hippocampus in establishing gaze-independent, long-term visuospatial memories. The rat hippocampus has neurons which report the animals position in space regardless of its angle of gaze. Rats with hippocampal lesions are unable to find the location of an escape platform hidden in a pool of opaque fluid, the Morris Water Maze (MWM) based on the visual aspects of their surrounding environment. Here we show that the representation of proprioception in the dysgranular zone of primary somatosensory cortex is equivalently necessary for mice to learn the location of the hidden platform, presumably because without it they cannot create a long-term gaze-independent visuospatial representation of their environment from the retinal signal. They have no trouble finding the platform when it is marked by a flag, and they have no motor or vestibular deficits.

neuroscience↗

bioRxiv2023

PERK-mediated antioxidant response is key for pathogen persistence in ticks

A crucial phase in the lifecycle of tick-borne pathogens is the time spent colonizing and persisting within the arthropod. Tick immunity is emerging as a key force shaping how transmissible pathogens interact with the vector. How pathogens remain in the tick despite immunological pressure remains unknown. In persistently infected Ixodes scapularis, we found that Borrelia burgdorferi (Lyme disease) and Anaplasma phagocytophilum (granulocytic anaplasmosis) activate a cellular stress pathway mediated by the endoplasmic reticulum receptor PERK and the central regulatory molecule, eIF2. Disabling the PERK pathway through pharmacological inhibition and RNAi significantly decreased microbial numbers. In vivo RNA interference of the PERK pathway not only reduced the number of A. phagocytophilum and B. burgdorferi colonizing larvae after a bloodmeal, but also significantly reduced the number of bacteria that survive the molt. An investigation into PERK pathway-regulated targets revealed that A. phagocytophilum and B. burgdorferi induce activity of the antioxidant response regulator, Nrf2. Tick cells deficient for nrf2 expression or PERK signaling showed accumulation of reactive oxygen and nitrogen species in addition to reduced microbial survival. Supplementation with antioxidants rescued the microbicidal phenotype caused by blocking the PERK pathway. Altogether, our study demonstrates that the Ixodes PERK pathway is activated by transmissible microbes and facilitates persistence in the arthropod by potentiating an Nrf2-regulated antioxidant environment.

microbiology↗

bioRxiv2023

An Anaplasma phagocytophilum T4SS effector, AteA, is essential for tick infection

Pathogens must adapt to disparate environments in permissive host species, a feat that is especially pronounced for vector-borne microbes, which transition between vertebrate hosts and arthropod vectors to complete their lifecycles. Most knowledge about arthropod-vectored bacterial pathogens centers on their life in the mammalian host, where disease occurs. However, disease outbreaks are driven by the arthropod vectors. Adapting to the arthropod is critical for obligate intracellular rickettsial pathogens, as they depend on eukaryotic cells for survival. To manipulate the intracellular environment, these bacteria use Type IV Secretion Systems (T4SS) to deliver effectors into the host cell. To date, few rickettsial T4SS translocated effectors have been identified and have only been examined in the context of mammalian infection. We identified an effector from the tick-borne rickettsial pathogen Anaplasma phagocytophilum, HGE1_02492, as critical for survival in tick cells and acquisition by ticks in vivo. Conversely, HGE1_02492 was dispensable during mammalian cell culture and murine infection. We show HGE1_02492 is translocatable in a T4SS-dependent manner to the host cell cytosol. In eukaryotic cells, the HGE1_02492 localized with cortical actin filaments, which is dependent on multiple sub-domains of the protein. HGE1_02492 is the first arthropod-vector specific T4SS translocated effector identified from a rickettsial pathogen. Moreover, the subcellular target of HGE1_02492 suggests that A. phagocytophilum is manipulating actin to enable arthropod colonization. Based on these findings, we propose the name AteA for Anaplasma (phagocytophilum) tick effector A. Altogether, we show that A. phagocytophilum uses distinct strategies to cycle between mammals and arthropods. ImportanceTicks are the number one vector of pathogens for livestock worldwide and for humans in the US. The biology of tick transmission is an understudied area. Understanding this critical interaction could provide opportunities to affect the course of disease spread. In this study we examined the zoonotic tick-borne agent Anaplasma phagocytophilum and identified a secreted protein, AteA, that is expressed in a tick-specific manner. These secreted proteins, termed effectors, are the first proteins to interact with the host environment. AteA is essential for survival in ticks and appears to interact with cortical actin. Most effector proteins are studied in the context of the mammalian host; however, understanding how this unique set of proteins affect tick transmission is critical to developing interventions.

microbiology↗

bioRxiv2022

AIMP1-derived peptide secreted from hair follicle stem cells activates dermal papilla cells to promote hair growth

Hair follicle stem cells (HFSCs) and dermal papilla cells (DPCs) are crucial in the biogenesis and maintenance of hair follicles (HFs). In this study, a fragment derived from aminoacyl-tRNA synthetase-interacting multifunctional protein1 (AIMP1) was secreted from HFSCs to activate DPCs to maintain hair follicle homeostasis. A histological analysis revealed that AIMP1 levels in hair follicles decreased with hair loss. Hair regrowth in AIMP1-induced mice was faster than that in non-induced mice. Deletion mapping revealed 41 amino acids (TN41, aa 6-46) as the active region of AIMP1. The N-terminal peptide fragment of AIMP1 generated by MMP1 was secreted from Wnt-treated HFSCs to activate DPCs via FGFR2. TN41 activated Akt and ERK, increased {beta}-catenin, and enhanced DPCs activation. TN41 also promoted hair shaft elongation in cultured human hair follicles and improved the hair-inducing activity of cultured DPC spheroids. In summation, the AIMP1 fragment secreted from HFSCs appears to stimulate active hair regrowth through activating DPCs.

cell biology↗

bioRxiv2020

Clonal dynamics in early human embryogenesis inferred from somatic mutation

The trillions of cells that constitute the human body are developed from a fertilized egg through embryogenesis. However, cellular dynamics and developmental outcomes of embryonic cells in humans remain to be largely unknown due to the technical and ethical challenges. Here, we explored whole-genomes of 334 single-cell expanded clones and targeted deep-sequences of 379 bulk tissues obtained from various anatomical locations from seven individuals. Using the discovered 1,688,652 somatic mutations as an intrinsic barcode, we reconstructed cellular phylogenetic trees that provide novel insights into early human embryogenesis. Our findings suggest (1) endogenous mutational rate that is higher in the first cell division of life but decreases to ~1 per cell per cell division later in life, (2) universal unequal contribution of early cells into embryo proper resulting from early cellular bottlenecks that stochastically separate epiblasts from embryonic cells (3) uneven differential outcomes of early cells into three germ layers, left-right and cranio-caudal tissues, (4) emergence of a few ancestral cells that will contribute to the substantial fraction of adult blood cells, and (5) presence of mitochondrial DNA heteroplasmy in the fertilized egg. Our approach additionally provides insights into the age-related mutational processes including UV-mediated mutagenesis and loss of chromosome X or Y in normal somatic cells. Taken together, this study scrutinized somatic mosaicism, clonal architecture, and cellular dynamics in human embryogenesis at an unprecedented level and provides a foundation for future studies to complete cellular phylogenies in human embryogenesis.

genomics↗

bioRxiv2020

Deep and superficial layers of the primary somatosensory cortex are critical for whisker-based texture discrimination in mice

The neocortex, comprised of multiple distinct layers, processes sensory input from the periphery, makes decisions, and executes actions. Despite extensive investigation of cortical anatomy and physiology, the contributions of different cortical layers to sensory guided behaviors remain unknown. Here, we developed a two-alternative forced choice (2AFC) paradigm in which head-fixed mice use a single whisker to either discriminate textures of parametrically varied roughness or detect the same textured surfaces. Lesioning the barrel cortex revealed that 2AFC texture discrimination, but not detection, was cortex-dependent. Paralyzing the whisker pad had little effect on performance, demonstrating that passive can rival active perception and cortical dependence is not movement-related. Transgenic Cre lines were used to target inhibitory opsins to excitatory cortical neurons of specific layers for selective perturbations. Both deep and superficial layers were critical for texture discrimination. We conclude that even basic cortical computations require coordinated transformation of sensory information across layers. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/245381v2_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@16c4d20org.highwire.dtl.DTLVardef@13b8832org.highwire.dtl.DTLVardef@16ac3aborg.highwire.dtl.DTLVardef@5426d8_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2020

Multi-organ signaling mobilizes tumor-associated erythroid cells expressing immune checkpoint molecules

Hematopoietic-derived cells are integral components of the tumor microenvironment and serve as critical mediators of tumor-host interactions. Cells derived from myeloid and lymphoid lineages perform well-established functions linked to cancer development, progression and response to therapy. It is unclear whether erythroid cells exert such host cell functions in cancer, but emerging evidence points to this possibility. Here we show that tumor-promoting environmental stress and tumor-induced physiological disruption trigger renal erythropoietin production and erythropoietin-dependent expansion of splenic erythroid cell populations in mice. These erythroid cells display molecular features indicative of an immature erythroid phenotype and express immune checkpoint molecules. Erythroid cells with similar properties are present in mouse and human tumor tissues. Antibody-mediated erythropoietin blockade or erythroid cell depletion reduces tumor growth. These findings reveal the potential of erythropoietin and erythroid cells as targets for cancer treatment.

cancer biology↗

bioRxiv2020

The Effect of Choline Alphoscerate on Non spatial memory and Neurogenesis in a Rat Model of Dual Stress

Choline alphoscerate (-GPC) is a choline-based compound and acetylcholine precursor commonly found in the brain; it has been known to be effective in treating neuronal injury and increasing the levels of acetylcholine (Ach) and brain-derived neurotrophic factor (BDNF) which in turn enhances memory and cognitive function. This study was designed to establish rat models of dual stress using noise and restraint in order to investigate the effect of -GPC on cognitive function and neurogenesis after dual stress. The rats were randomly divided into four groups as follows: a control group (CG), a control with -GPC group (CDG), a noise-restraint stress group (NRSG), and a noise-restraint stress with -GPC group (NRSDG). Two experimental groups were exposed to the double stress stimuli of noise and restraint, which involved 110dB sound pressure level (SPL) white band noise and restraint at the same time for 3 hours/day for 7 days. While the CG and NRSG received saline, the CDG and NRSDG received -GPC (400mg/kg) orally after stress exposure. The -GPC-treated group showed increased memory function compared to the dual stress group in the novel object recognition test. In analysis of the hippocampus, the -GPC-treated group showed greater Choline acetyltransferase (ChAT) and BDNF expression compared to the dual stress group. The -GPC-treated group showed significantly increased neuroblast expression compared to the dual stress group, which suggests that -GPC enhances BDNF expression and protects the activity of the immature cells at the dentate gyrus. Our results suggest that -GPC treatment can protect cognitive function and neurogenesis in a dual stress model.

neuroscience↗

bioRxiv2020

Anthrax Toxin as a Molecular Platform to Target Nociceptive Neurons and Modulate Pain

Bacterial toxins are able to act on neurons to modulate signaling and function. Here, we find that nociceptive sensory neurons that mediate pain are enriched in the receptor for anthrax toxins, ANTXR2. Anthrax Edema Toxin (ET) induced cAMP and PKA signaling in Nav1.8+ nociceptive neurons and modulated pain in vivo. Peripherally administered ET mediated mechanical allodynia in naive mice and during B. anthracis infection. Intrathecally administered ET produced analgesic effects, potently blocking pain-like behaviors in multiple mouse models of inflammatory and chronic neuropathic pain. Nociceptor-specific ablation of ANTXR2 attenuated ET-induced signaling and analgesia. Modified anthrax toxin successfully delivered exogenous protein cargo into nociceptive neurons, illustrating utility of the anthrax toxin system as a molecular platform to target pain. ET further induced signaling in human iPSC-derived sensory neurons. Our findings highlight novel interactions between a bacterial toxin and nociceptors that may be utilized for developing new pain therapeutics. SUMMARYANTXR2 expression on nociceptive neurons allows selective targeting and modulation of pain by native and engineered anthrax toxins.

neuroscience↗

bioRxiv2018

Human pathogenic bacterium Shigella infects Arabidopsis plants using type-III effectors that suppress conserved MAP kinase signaling

Originality-significance statementIncreased incidence of food-borne disease outbreaks caused by fresh produce contaminated with Escherichia coli O157:H7 and Salmonella spp. has prompted researchers to examine the interaction between these bacteria and various plant species under different environmental conditions. Although studies show that human enteropathogenic bacteria survive both on the surface of and inside plants, little is known about the molecular mechanism underlying plant invasion and colonization. Here, we examined the interaction between the human pathogenic bacterium Shigella and the model plant Arabidopsis. We found that four Shigella spp. strains proliferated successfully in Arabidopsis, causing symptom-like lesions in tissues. Using mutants lacking T3S effectors (i.e., noninvasive human strains), we demonstrated that effectors regulating pathogenesis of shigellosis in humans also play a central role in bacteria-plant interactions. To the best of our knowledge, this is the first study to examine Shigella-mediated virulence and host immune suppression in a plant host at a molecular level.\n\nSummaryAlthough there is debate about whether human intestinal pathogenic bacteria are also plant pathogens, it is clear that these bacteria use plants as an alternative host. Shigella, which infects primates, is reportedly transmitted by fresh vegetables; however, its molecular interactions with plants have not been extensively studied. Here, we show that four Shigella strains, S. boydii (S. b), S. sonnei (S. s), S. flexneri 2a (S. f 2a), and S. flexneri 5a (S. f 5a), proliferated at different levels in Arabidopsis thaliana. Microscopic studies revealed that these bacteria were present inside leaves and damaged plant cells. GFP-labeled S. b, S. f 2a, and S. f 5a entered plants via guard cells, and S. f 2a infiltrated root tissues and colonized roots. Using mutants lacking type III secretion systems (T3SS), we found that T3SS of Shigella that regulate the pathogenesis of shigellosis in humans also play a central role in attachment and multiplication in Arabidopsis. Furthermore, the immunosuppressive activity of two T3S effectors, OspF and OspG, were needed for the proliferation of Shigella in Arabidopsis. These findings demonstrate that Shigella-mediated virulence determinants are expressed, and pathogenic symptoms are observed, in model plants.

microbiology↗