Biology subjects

Jung, J. H.

Publications and source records attributed to Jung, J. H..

9 recordsLinked to original sources

bioRxiv2026

Janus kinase 2 regulates Nurr1 protein stability in dopaminergic neurons of the aging midbrain

The nuclear receptor Nurr1 (NR4A2) is an essential transcription factor that governs the differentiation, maturation, and long-term maintenance of midbrain dopaminergic (mDA) neurons in the substantia nigra. Reduced Nurr1 expression has been closely linked to age-related dopaminergic neuronal loss and the pathogenesis of Parkinsons disease. However, the molecular mechanisms regulating Nurr1 expression and protein stability in the aging midbrain remain poorly understood. Here, we identify Janus kinase 2 (JAK2) as a previously unrecognized regulator of Nurr1 in mDA neurons. In the substantia nigra of aged mice (12-and 18-month-old), JAK2 was robustly expressed in Nurr1-positive mDA neurons, whereas its expression was minimal in young adult mice. In SK-N-BE(2)C neuroblastoma cells, overexpression of JAK2 modestly enhanced Nurr1 transcriptional activity, while the constitutively active mutant JAK2V617F markedly increased it. Notably, this effect was not blocked by pharmacological inhibition of STAT, PI3K, or Akt signaling pathways, indicating that JAK2 regulates Nurr1 independently of canonical JAK/STAT or PI3K/Akt signaling. Mechanistically, JAK2 did not promote tyrosine phosphorylation of Nurr1 but instead physically interacted with Nurr1, leading to enhanced nuclear stability of the Nurr1 protein. Consistent with this mechanism, expression of JAK2V617F increased Nurr1 protein levels without altering its mRNA expression. Functionally, co-expression of JAK2V617F and Nurr1 attenuated oxidative stress-induced cytotoxicity and reduced reactive oxygen species accumulation. Together, these findings reveal a phosphorylation-independent mechanism by which JAK2 stabilizes Nurr1 protein and enhances its transcriptional activity. Our results further suggest that age-associated induction of JAK2 in dopaminergic neurons may promote neuronal resilience by maintaining Nurr1 protein stability during aging.

neuroscience↗

bioRxiv2025

Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells

Primary human myeloid cells are promising candidates for immunotherapy, yet efficient and scalable technologies for genetic engineering and screening in these cells are limited. Here we present a virus-like particle (VLP)-based toolkit that delivers diverse CRISPR genome editing modalities to human monocytes, macrophages, and dendritic cells with high efficiency while preserving viability and innate immune responsiveness. VLP-mediated delivery of ribonucleoprotein payloads supports gene knockout, base editing and epigenetic silencing, and enables site-specific integration of large DNA sequences when combined with AAV donors for homology-directed repair. Leveraging sgRNA delivery via VPX-lentivirus combined with Cas9 protein delivery via engineered virus-like particle (eVLP) treatment ("SLICeVLP"), we performed the first pooled loss-of-function screens in human macrophages. We uncovered regulators of TNF production and CD80 expression in human macrophages, converging on TNFAIP3 as a central regulator of inflammatory polarization. TNFAIP3 ablation promoted a pro-inflammatory cell state that is resistant to suppressive polarization, and augmented cytotoxicity of engineered HER2 CAR-macrophages. Taken together, this technology platform enables unbiased discovery and characterization of functional gene targets in primary human myeloid cells.

immunology↗

bioRxiv2025

Plant age and genotype explain variation in the microbiome of natural Lotus corniculatus populations

In natural populations, plants are associated with a huge diversity of bacteria, fungi and other microbes. There is usually substantial microbiome variation between different plant individuals and populations, and the drivers of this variation are still poorly understood, particularly in wild plants. Here, we were interested in the potential of plant genotype and plant age to explain intraspecific variation in the plant microbiome of Lotus corniculatus. In seven natural populations, we genotyped a total of 168 individuals over four years, determined their ages through growth ring analysis, and then sequenced their root, shoot, flower and seed microbiomes. We found that plant genotypes differed both in the diversity and composition of microbes, and that some microbial taxa were associated with particular plant genotypes. The genotype effects tended to be strongest and most consistent for plant-associated bacteria, with the largest plant genotype differences in the microbiome diversity of flowers and seeds. We found less evidence for an effect of plant age on microbiome diversity: the age of plants explained variation in fungi diversity, and it was associated with the abundance of several microbial taxa. Our study indicates that the genotype of a plant and - to a lesser degree its age - influences the diversity and composition of plant-associated microbiota, even in complex natural environments. ImportanceThe plant microbiome plays a key role in important plant functions such as pathogen resistance, nutrient uptake, and stress tolerance. To fully understand these processes, it is essential to identify the factors that drive microbiome variation. Most research to date has focused on model or crop species under controlled conditions, leaving open questions about the drivers of microbiome diversity and composition in natural populations. In this multi-year field study, we examined how plant genotype and age shape the microbiomes of Lotus corniculatus. We show that the plant genotype strongly influences microbial diversity and composition, while plant age has subtler but still important effects, particularly on fungal communities. To our knowledge, this is the first study to link plant age with microbiome variation in natural populations. These findings demonstrate that plant traits can shape the microbiome even in complex natural environments.

microbiology↗

bioRxiv2024

Placozoan secretory cell types implicated in feeding, innate immunity and regulation of behavior

Placozoa are millimeter-sized, flat, irregularly shaped ciliated animals that crawl on surfaces in warm oceans feeding on biofilms, which they digest externally. They stand out from other animals due to their simple body plans. They lack organs, body cavities, muscles and a nervous system and have only seven broadly defined morphological cell types, each with a unique distribution. Analyses of single cell transcriptomes of four species of placozoans revealed greater diversity of secretory cell types than evident from morphological studies, but the locations of many of these new cell types were unknown and it was unclear which morphological cell types they represent. Furthermore, there were contradictions between the conclusions of previous studies and the single cell RNAseq studies. To address these issues, we used mRNA probes for genes encoding secretory products expressed in different metacells in Trichoplax adhaerens to localize cells in whole mounts and in dissociated cell cultures, where their morphological features could be visualized and identified. The nature and functions of their secretory granules were further investigated with electron microscopic techniques and by imaging secretion in live animals during feeding episodes. We found that two cell types participate in disintegrating prey, one resembling a lytic cell type in mammals and another combining features of zymogen gland cells and enterocytes. We identified secretory epithelial cells expressing glycoproteins or short peptides implicated in defense. We located seven peptidergic cell types and two types of mucocytes. Our findings reveal mechanisms that placozoans use to feed and protect themselves from pathogens and clues about neuropeptidergic signaling. We compare placozoan secretory cell types with cell types in other animal phyla to gain insight about general evolutionary trends in cell type diversification, as well as pathways leading to the emergence of synapomorphies.

evolutionary biology↗

bioRxiv2024

GluN2B-mediated regulation of silent synapses for receptor specification and addiction memory

Psycho-stimulants including cocaine elicit stereotyped, addictive behaviors. Re-emergence of silent synapses containing only NMDA-type glutamate receptors (NMDARs) is a critical mediator of addiction memory and seeking behaviors. Despite the predominant abundance of GluN2B-containing NMDARs in silent synapses, their operational mechanisms are not fully understood. Using conditional depletion/deletion of GluN2B at D1-expressing accumbal medium spiny neurons, we examine the synaptic and behavioral actions that silent synapses incur after repeated exposure to cocaine. GluN2B ablation reduces the proportion of silent synapses, but some of them can persist by substitution to GluN2C, which drives the aberrantly-facilitated synaptic incorporation of calcium-impermeable AMPA-type glutamate receptors (AMPARs). The resultant precocious maturation of silent synapses impairs addiction memory but elevates locomotor activity, which can be normalized by blockade of calcium-impermeable AMPAR trafficking. Collectively, GluN2B supports the competence of cocaine-induced silent synapses for specifying subunit composition of AMPARs, and thereby expression of addition memory and the related behaviors.

neuroscience↗

bioRxiv2023

Discarded sequencing reads uncover natural variation in pest resistance in Thlaspi arvense

Understanding the genomic basis of natural variation in plant pest resistance is an important goal in plant science, but it usually requires large and labour-intensive phenotyping experiments. Here, we explored the possibility that non-target reads from plant DNA sequencing can serve as phenotyping proxies for addressing such questions. We used data from a whole-genome and -epigenome sequencing study of 207 natural lines of field pennycress (Thlaspi arvense) that were grown in a common environment and spontaneously colonized by aphids, mildew and other microbes. We found that the numbers of non-target reads assigned to the pest species differed between populations, had significant SNP-based heritability, and were associated with climate of origin and baseline glucosinolates content. Specifically, pennycress lines from cold and thermally fluctuating habitats, presumably less favorable to aphids, showed higher aphid DNA load, i.e. decreased aphid resistance. Genome-wide association analyses identified genetic variants at known defense genes but also novel genomic regions associated with variation in aphid and mildew DNA load. Moreover, we found several differentially methylated regions associated with pathogen loads, in particular differential methylation at transposons and hypomethylation in the promoter of a gene involved in stomatal closure, likely induced by pathogens. Our study provides first insights into the defense mechanisms of Thlaspi arvense, a rising crop and model species, and demonstrates that non-target whole genome sequencing reads, usually discarded, can be leveraged to estimate intensities of plant biotic interactions. With rapidly increasing numbers of large sequencing datasets worldwide, this approach should have broad application in fundamental and applied research.

evolutionary biology↗

bioRxiv2022

Design of a highly specific glutamine sensor by splitting the glutamine-binding protein

Studies on glutamine (Gln) metabolism have illuminated the vital role of Gln in cellular functions and its potential as a biomarker for disease detection. Despite the increasing interest in Gln metabolism, in-depth evaluations are challenging owing to limitations of conventional Gln-measuring methods. Thus, we developed a ligand-induced dimerization-based sensor for Gln, termed Q-SHINE, by splitting a glutamine binding protein into two separate domains. Q-SHINE enables highly accurate and convenient measurement of Gln concentration in bio-fluid samples, and the detection range is optimal for physiological Gln levels. Genetically encoded Q-SHINE sensors could also visualize intracellular Gln levels and quantify cytoplasmic and mitochondrial Gln change in living cells, which enabled detection of various cell responses to extracellular Gln supplement.

bioengineering↗

bioRxiv2022

High-fidelity optical diffraction tomography of live organisms using non-toxic tunable refractive index media

Optical diffraction tomography (ODT) enables the three-dimensional (3D) refractive index (RI) reconstruction. However, when the RI difference between a sample and a medium increases, effects of light scattering become significant, preventing the acquisition of high-quality and accurate RI reconstructions. Herein, we present a method for high-fidelity ODT by introducing non-toxic RI matching media. Optimally reducing the RI contrast enhances the fidelity and accuracy of 3D RI reconstruction, enabling visualization of the morphology and intra-organization of live biological samples without producing toxic effects. We validate our method using various biological organisms, including C. albicans and C. elegans. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/492426v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@a6b4d4org.highwire.dtl.DTLVardef@a9ec7borg.highwire.dtl.DTLVardef@1e4a795org.highwire.dtl.DTLVardef@b663aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2021

Clinically Validated Model Predicts the Effect of Intratumoral Heterogeneity on Overall Survival for Non-Small Cell Lung Cancer (NSCLC) Patients

PurposeWe demonstrate the importance of considering intratumoral heterogeneity and the development of resistance during fractionated radiotherapy when the same dose of radiation is delivered for all fractions (Fractional Equivalent Dosing FED). Materials and MethodsA mathematical model was developed with the following parameters: a starting population of 1011 non-small cell lung cancer (NSCLC) tumor cells, 48-hour doubling time, and cell death per the linear-quadratic (LQ) model with and {beta} values derived from RSI/{beta}, in a previously described gene expression based model that estimates and {beta}. To incorporate both inter- and intratumor radiation sensitivity, RSI/{beta} output for each patient sample is assumed to represent an average value in a gamma distribution with the bounds set to -50% and +50% of RSI/b. Therefore, we assume that within a given tumor there are subpopulations that have varying radiation sensitivity parameters that are distinct from other tumor samples with a different mean RSI/{beta}. A simulation cohort (SC) comprised of 100 lung cancer patients with available RSI/{beta} (patient specific and {beta} values) was used to investigate 60Gy in 30 fractions with fractionally equivalent dosing (FED). A separate validation cohort (VC) of 57 lung cancer patients treated with radiation with available local control (LC), overall survival (OS), and tumor gene expression was used to clinically validate the model. Cox regression was used to test for significance to predict clinical outcomes as a continuous variable in multivariate analysis (MVA). Finally, the VC was used to compare FED schedules with various altered fractionation schema utilizing a Kruskal-Wallis test. This was examined using the end points of end of treatment log cell count (LCC) and by a parameter described as mean log kill efficiency (LKE) defined as: O_FD O_INLINEFIG[Formula 1]C_INLINEFIGM_FD(1)C_FD ResultsCox regression analysis on LCC for the VC demonstrates that, after incorporation of intratumoral heterogeneity, LCC has a linear correlation with local control (p = 0.002) and overall survival (p =< 0.001). Other suggested treatment schedules labeled as High Intensity Treatment (HIT) with a total 60Gy delivered over 6 weeks have a lower mean LCC and an increased LKE compared to standard of care 60Gy delivered in FED in the VC. ConclusionWe find that LCC is a clinically relevant metric that is correlated with local control and overall survival in NSCLC. We conclude that 60Gy delivered over 6 weeks with altered HIT fractionation leads to an enhancement in tumor control compared to FED when intratumoral heterogeneity is considered.

cancer biology↗