Biology subjects

Han, E.

Publications and source records attributed to Han, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Structural proteomics reveals a coagulation-complement accessibility signature of macrovascular invasion in hepatocellular carcinoma

Macrovascular invasion (MVI) and extrahepatic spread (EHS) define the most aggressive, treatment-refractory hepatocellular carcinoma (HCC), yet blood-based markers that report the underlying protein-network biology are lacking. Conventional proteomics measures protein abundance but not the conformational and protein-protein-interaction (PPI) states that govern function. We applied covalent proteome painting (CPP)--a dimethylation-based accessibility assay that reads out binding-site openness--to matched tumor and serum, reasoning that intravascular tumor dissemination remodels plasma protein complexes in a manner detectable as changes in accessibility. Eight treatment-native HCC patients were profiled by CPP using matched FFPE tumor and top-14- depleted serum on a Q Exactive Orbitrap HF. The 85 tumor-serum common proteins defined an 81-protein targeted panel, validated by multiple-reaction-monitoring (MRM) mass spectrometry with heavy stable-isotope-standard peptides (296 peptides; 3,717 light/heavy transition pairs) in 22 FFPE tumors and 22 matched sera. Accessibility was the light/heavy ratio (high, open; low, closed). We assessed differential accessibility, serum-tissue translatability, pathway enrichment, and biomarker/survival performance. Aggressive disease showed broadly decreased protein accessibility. MVI-associated changes were directionally concordant between tumor and serum (Spearman {rho}=0.21; 59% concordant), driven by coagulation and complement proteins (FGG, CTSD, LBP, C4BPA); the EHS axis did not translate. Decreased-accessibility proteins were enriched for complement-coagulation cascades and IGF/IGFBP transport. A six-protein serum accessibility signature discriminated MVI (leave-one-out cross-validated AUC 0.80; best single markers ceruloplasmin 0.83 and haemoglobin- 0.77), and MVI status trended with shorter overall survival (log-rank p=0.06). Accessibility-based serum proteomics captures MVI-associated protein-complex remodeling that abundance assays miss, nominating a coagulation/complement-anchored serum signature for vascular-invasive HCC that warrants prospective validation.

systems biology↗

bioRxiv2026

A targeted plasma-proteomic axis separates autoimmune thyroid disease from growth-hormone deficiency

Targeted mass spectrometry (multiple-reaction monitoring, MRM) enables reproducible, multiplexed quantification of plasma proteins, but whether a fixed targeted panel can resolve endocrine disorders with overlapping systemic features is unknown. We analyzed a 256-protein targeted panel (1,894 peptides; 3,790 transitions) quantified in 57 participants spanning autoimmune thyroid disease (Hashimotos thyroiditis, n=7; Graves disease, n=5) and growth-hormone deficiency (GHD; partial, n=26; complete, n=19). Protein abundances were obtained by transition summation, log2 transformation, and per-sample median normalization. We applied unsupervised analysis (PCA, PERMANOVA), differential expression (limma), an ordered severity-trend test, and leave-one-out cross-validated classification with feature selection performed strictly inside each fold. All 256 proteins were quantified in every sample (median inter-sample r=0.875). PC1 (36% variance) separated autoimmune thyroid disease from GHD (p=0.016), whereas the global four-group structure was not significant (PERMANOVA p=0.17). No protein reached FDR<0.05, but the autoimmune-versus-GHD contrast was strongly enriched for low p-values (26 proteins at p<0.05; binomial p=5.4x10-4). The signal was biologically coherent: immunoglobulin/B-cell-receptor proteins, including CD79A, were lower, whereas proteasome subunits (PSMC5, PSMC3) and the NF-{kappa}B subunit RELA were higher in autoimmune disease. A cross-validated classifier separated the two classes (AUC 0.72; permutation p=0.05; eight proteins selected in all folds), whereas GHD severity was not predictable (AUC 0.31). A fixed 256-protein targeted panel reproducibly captures an immunoglobulin/B-cell-receptor and proteasome/NF-{kappa}B axis that distinguishes autoimmune thyroid disease from GHD but cannot resolve within-class severity.

systems biology↗

bioRxiv2026

Sex and race shape serum protein biomarkers and bias diagnostic reference intervals

Clinical protein biomarkers--whether measured by FDA-cleared in-vitro diagnostic (IVD) assays or deployed as laboratory-developed tests (LDTs)--are routinely interpreted against fixed, population-agnostic reference intervals. Whether the baseline serum concentrations of these proteins differ systematically by sex and by self-reported race in healthy individuals has not been tested across a broad clinical panel on a single standardized platform. Using scheduled multiple reaction monitoring - mass spectrometry (MRM-MS) with stable-isotope-labelled internal standards, we quantified 87 proteins (39 FDA-cleared analytes; 48 LDT/research markers) in 60 healthy, age-matched donors balanced across three races (White, Hispanic, Black) and both sexes. Sex was a pervasive axis of variation: donors separated by sex in unsupervised multivariate space (PERMANOVA p = 0.020) but not by race (p = 0.14). Three FDA-target proteins differed by sex at FDR q < 0.05--sex hormone-binding globulin, haemoglobin- and albumin--with directions preserved within every race. Race differences were real but protein-specific, exemplified by ancestry-associated CD14. Critically, applying a single pooled 95% reference interval mis-flagged as many as [~]25% of a demographic subgroup as abnormal, versus the 5% expected. Demographic context should therefore be incorporated into reference intervals and decision thresholds for protein-based diagnostics.

molecular biology↗

bioRxiv2026

A targeted mass-spectrometry plasma proteome for simultaneous multi-disease screening

Population health screening is fragmented across dozens of single-condition assays. We asked whether one targeted mass-spectrometry measurement of the plasma proteome could screen simultaneously for many common diseases. Using multiple-reaction-monitoring LC-MS/MS, we quantified 126 proteins (509 peptides) directly in crude plasma from 490 individuals spanning 16 diseases (eight cancers, three inflammatory or renal conditions, and five metabolic and lifestyle disorders) plus age- and sex-matched controls, each protein referenced to a stable-isotope-labelled internal standard. Proteome variation was organised primarily by disease rather than demographics. Cross-validated classifiers detected each disease against matched controls with a mean AUROC of 0.979, a 17-way model identified the specific disease at roughly ten times chance, and a 20-protein subset reproduced full-panel performance. We show that these within-cohort estimates are optimistic upper bounds because each disease was acquired as a separate case-control batch without independent validation. We quantify this, establishing analytical feasibility and defining the validation required for translation.

molecular biology↗

bioRxiv2026

Age-dependent Structural Reorganization of the Human Plasma Proteome

Aging is characterized by progressive physiological decline, yet the molecular mechanisms underlying these changes remain incompletely understood. Although extensive work has examined age-related alterations in protein abundance, the age-dependent structural reorganization of proteins and their interaction networks remains largely unexplored. Here, we quantitatively characterize the structural dynamics of plasma proteins across healthy adult aging and identify age-dependent accessibility patterns that may serve as candidate structural biomarkers. We employed Covalent Protein Painting (CPP) coupled with multiple reaction monitoring (MRM)-based LC-MS/MS to analyze plasma from 24 healthy individuals spanning four age groups (20s to 50s, n = 6 per group). Lysine surface accessibility changes were analyzed using cosine similarity trajectory matching and limma-based linear modeling. The intersection of the two approaches defined five reproducible age-dependent trajectories encompassing 27 proteins and 57 peptides. Integrating STRING/Cytoscape network analysis with AlphaFold3 multimer complex prediction localized several CPP-detected peptides to within [~]5 [A] of predicted protein-protein interaction interfaces (KNG1, C3; REN, ALB; and ALB, FGB), suggesting that age-associated accessibility changes are organized at interaction interfaces rather than occurring as isolated local events. Our findings indicate that the human plasma proteome undergoes coordinated, network-level changes in structural accessibility during adult aging, providing a framework for structure-based biomarker discovery. Because CPP signal reflects both conformational accessibility and protein abundance, and because the cohort is modest and cross-sectional, the trajectories reported here are framed as hypothesis-generating and are interpreted with these constraints made explicit throughout.

molecular biology↗

bioRxiv2026

Sequence determinants of efficient exon 44 skipping in Duchenne muscular dystrophy define design principles for steric-blocking antisense oligonucleotides

Duchenne muscular dystrophy (DMD) is caused by mutations in the DMD gene that disrupt the reading frame and abolish expression of functional dystrophin protein. Antisense oligonucleotides (ASO) can restore production of partially functional dystrophins by inducing exon skipping to restore the reading frame of dystrophin transcripts. While exon skipping is an FDA approved therapeutic strategy, there are currently no approved therapies for patients amenable to exon 44 skipping (8% of DMD patients). Here, we carried out a discovery campaign to identify phosphorothioate (PS) ASOs that efficiently induce exon 44 skipping and to define key sequence and chemistry features associated with activity. A tiling and micro-tiling approach with 18mer fully PS and 2-O-methoxyethyl (2MOE) modified ASOs in patient-derived myotubes identified five exonic target regions that promote skipping. ASO activity was strongly correlated across skeletal muscle and iPSC-derived cardiomyocytes, indicating similar exon 44 splicing regulation across cell types. Optimization studies showed that for 2MOE PS ASOs, 16-20mers were generally most active, while longer ASOs often had reduced activity due in part to impaired productive uptake into cells. Swapping out 2MOE modifications at both terminal positions for locked nucleic acids (LNAs) rarely improved activity and could also reduce it. Finally, promising candidates were tested in a humanized mouse model with an exon 44 skippable deletion, where one ASO outperformed others, inducing dose-dependent exon 44 skipping and dystrophin restoration in mouse models. These findings define practical design rules for exon 44-targeted ASOs and provide a foundation for therapeutic development.

molecular biology↗

bioRxiv2026

Generalisable tissue-wide molecular reconstruction from histology

Spatial transcriptomics technologies measure gene expression within intact tissues but remain difficult to scale across large tissue sections and patient cohorts. Consequently, many studies rely on tissue microarrays (TMAs) or sparse spatial profiling designs, where molecular measurements are available for only limited tissue regions and are often generated using heterogeneous gene panels. Existing H&E to spatial gene expression prediction methods remain challenged by sparse molecular measurements, partially overlapping gene panels and tissue-wide reconstruction across heterogeneous spatial datasets. Here, we present GHIST+, a framework for tissue-wide reconstruction of single-cell molecular states from H&E histology. GHIST+ integrates cellular morphology, local tissue context and shared tissue representations to extend sparse molecular measurements into tissue-wide molecular maps across heterogeneous spatial datasets. Across multiple cancer types and GTEx breast tissues, GHIST+ reconstructs biologically meaningful tissue-wide molecular organisation from sparse TMA-derived measurements while preserving spatial tissue structure, cell-type organisation and age-associated tissue states across cancer and non-cancer settings. GHIST+ establishes a scalable framework for transforming sparse spatial profiling experiments into tissue-wide molecular maps, enabling cohort-scale molecular reconstruction from routine histology under heterogeneous spatial transcriptomic settings.

bioinformatics↗

bioRxiv2026

Transformers Outperform ConvNets for Root Segmentation: A Systematic Comparison Across Nine Datasets

Root segmentation is a fundamental yet challenging task in image-based plant phenotyping. We present the first systematic comparison of Transformer and Convolutional Neural Network (ConvNet) architectures for root segmentation, evaluating 21 architectures across nine diverse datasets and comparing pre-trained models to training from scratch. Transformer-based models significantly outperform ConvNets for segmentation accuracy and root-diameter agreement. Pre-training significantly improves mean Dice from 0.623 to 0.666 (p = 3.3 x 10-10). We also find that Transformers benefit more from pre-training than ConvNets, with Dice improvements of +0.072 versus +0.022 (p = 3.7 x 10-4), supporting the hypothesis that fine-tuned Transformers transfer more effectively across large domain gaps. Among evaluated models, MobileSAM achieved the highest Dice score while maintaining computational efficiency. Dataset choice explained far more performance variance (70.9%) than model architecture (6.7%), suggesting that data curation matters more than model selection.

plant biology↗

bioRxiv2025

Essential Resources for Curated Immune Markers and Antibody Panels in Cytometry Analysis

The immune system, fundamental to numerous biological research fields, is increasingly investigated at single-cell resolution using high-dimensional flow cytometry and mass cytometry technologies. These approaches require comprehensive immunomarker information and carefully designed antibody panels that address the technical challenges of isotopic and spectral overlap inherent in metal/fluorescent-labeled antibodies. While immune cell markers have been extensively characterized and systematically catalogued, antibody panel information remains fragmented across the literature. To bridge this critical gap, we present ImapDB (Immune cell Marker and Panel Database), a novel Python-based graphical user interface that consolidates curated information on cell markers and antibody panels. ImapDB integrates data from commercial guidebooks, peer-reviewed literature, and validated research sources, currently focusing on normal human immune cell states. The database encompasses 127 distinct immune cell subtypes with over 350 validated markers and includes 45 commercial and 23 custom research antibody panels. Available on GitHub (https://github.com/kimlab-cnu/Cell_Marker_GUI), ImapDB serves as a centralized repository designed to streamline immune profiling assays and enhance research efficiency.

bioinformatics↗

bioRxiv2025

In Silico Design of APOE ε4 Interaction Inhibitor Peptides for Alzheimer's Disease

BackgroundProtein-protein interactions (PPIs) are essential for cellular functions, and their aberrant formation contributes to neurodegenerative diseases. Alzheimers disease (AD), characterized by its complex pathogenesis, poses an increasing societal burden with population aging. The APOE {varepsilon}4 allele represents the strongest genetic risk factor for late-onset AD, yet its pathological mechanisms remain incompletely understood. MethodsWe employed artificial intelligence-driven peptide design to elucidate the pathological interaction between APOE {varepsilon}4 and amyloid precursor protein (APP). Using advanced AI algorithms, we identified critical binding interfaces and designed mimetic peptides targeting the APOE {varepsilon}4-APP interaction site. Peptide efficacy was evaluated through comprehensive molecular dynamics simulations. ResultsOur analysis revealed key residues mediating APOE {varepsilon}4-APP binding. The designed inhibitory peptides demonstrated stable interaction with target sites, favorable binding energetics, and sustained structural integrity throughout simulations. Lead candidate effectively disrupted APOE {varepsilon}4- APP complex formation in silico. ConclusionThis study presents a novel AI-powered approach for developing PPI-targeted therapeutics against AD. Our computationally validated peptide inhibitors offer promising therapeutic candidates that warrant experimental validation. These findings demonstrate the potential of integrating artificial intelligence with structural biology for accelerating drug discovery in neurodegenerative diseases.

bioinformatics↗

bioRxiv2025

COVID-19 in Space: Possible Health Risks and Preparedness Guidelines

Background The COVID-19 pandemic of 2020 resulted in over 705 million infections and more than 7 million deaths worldwide. The virus primarily spreads through aerosol droplets released during breathing, coughing, or sneezing, leading to symptoms ranging from mild fever and cough to severe outcomes, including death. Given the high risk associated with COVID-19, understanding its behaviour in diverse geographical and environmental conditions is critical. Space exploration and tourism represent an emerging industry, projected to reach a market value of $1.8 trillion. With numerous space missions planned by space agencies such as NASA, SpaceX, and ISRO, it is vital to address potential health risks for astronauts and space tourists. ObjectiveWith the expansion of human exploration into space, there is an urgent need to assess the risks posed by COVID-19 in extraterrestrial environments. This study reviews existing literature on airborne infections in space, identifies key knowledge gaps, and enhances preparedness for potential COVID-19 outbreaks during space missions. MethodsA systematic literature review was conducted to identify studies examining airborne infectious diseases in space and their health effects under microgravity. Databases searched included PubMed and NASAs Open Data Portal. To compare these findings with Earth-based data, additional systematic reviews were performed to analyze the known effects of these diseases on Earth, using Pathogen Safety Data Sheets. A separate systematic review was conducted using PubMed to explore similarities between COVID-19 and the selected airborne infectious diseases. Using a comparative approach, disease effects observed on Earth and in space were analyzed to predict COVID-19s potential behavior in microgravity. Existing guidelines for managing airborne diseases in space and on Earth were reviewed and compared to develop a set of preparedness recommendations for COVID-19 in space. ResultsThe airborne infectious diseases occurring in space found in this study include Aspergillus fumigatus, Beauveria bassiana, Epstein-Barr Virus (EBV), Escherichia coli, Klebsiella pneumoniae infections, Pseudomonas aeruginosa, Roseolovirus (Human Herpesvirus 6 & 7), Salmonella Typhimurium infection, Serratia marcescens infection, Staphylococcus aureus, Staphylococcus epidermidis, and Varicella-Zoster Virus (VZV). The relationship between the aforementioned diseases and COVID-19 was used in regard to theorizing the effects of COVID-19 in space. Six Tentative effects of COVID-19 in a microgravity environment could be theorized in this study. Along with that, recommendations to improve the current space travel health guidelines have also been referred to. ConclusionThe results of this study will change the course of human space exploration by assisting in the protection of space travelers and guiding the development of new designs for spacecraft that include extra safety features.

microbiology↗

bioRxiv2025

Five seasons with DeepRootLab: A unique facility for easier deep root research in the field

Deep-rooted crops accessing water and nutrients from deep soil layers enhance the resource base for crop production. However, studying these roots in field conditions is labor-intensive, limiting research scope. We established a field root research facility with 48 plots for replicated experiments. The facility includes 144 six-meter-long minirhizotron tubes and an AI-based pipeline for rapid root trait analysis. We also attempted to install access-tubes and customized ingrowth-core production for less-invasive root activity determination. Our study revealed significant differences in deep root density among species, particularly at depths of 2.5 to 4.5 meters, over five years. The less invasive studies using ingrowth-cores reached depths of 4.2 meters. Nutrient tracer 15N analysis showed marked differences in deep root activity among crop species. TDR sensors indicated varying water depletion in deeper soil layers, influenced by crop species and root growth patterns. We established a field facility for studying deep root growth and function, demonstrating its effectiveness in analyzing diverse deep-rooted plant species. This facility provides an ideal platform for conducting meaningful research in deep soil layers, yielding statistically and biologically significant results for agricultural applications.

plant biology↗

bioRxiv2024

Modulatory Effects of M3 Muscarinic Acetylcholine Receptor on Inflammatory Profiles of Human Memory T Helper Cells

Memory T helper (Th) cells, generated after immunogenic challenge, are crucial in directing the adaptive immune response. Muscarinic ACh receptor (mAChR) subtypes expressed by immune cells can be stimulated with acetylcholine or muscarinic-selective drug oxotremorine-M. Cholinergic signaling can influence immune cells, but it is not known how cholinergic stimuli regulate memory Th cells. This study focused on the role of mAChRs, specifically the M3 muscarinic ACh receptor (M3R), in the cytokine profile and NF-{kappa}B p65 activity of primary human memory Th cells. Memory Th cells (CD3+CD4+CD45RA-CD45RO+) were isolated from healthy participants peripheral blood. Cell culture was performed with anti-CD3/anti-CD28/anti-CD2 reagent, oxotremorine-M (M1R-M5R agonist), atropine (M1R-M5R antagonist), and J104129 (M3R-selective antagonist). MR1-MR5 genes CHRM1-CHRM5 were measured with RT-qPCR. Protein expression of M3R and phosphorylated NF-{kappa}B p65 were quantified by Western blot. The secretion of IFN-{gamma}, IL-17A, and IL-4 was assessed by ELISA and intracellular cytokine staining flow cytometry. CHRM3, encoding M3R, was knocked out using CRISPR-Cas9 gene targeting. Memory Th cells expressed all five mAChR subtypes. Oxotremorine-M increased IFN-{gamma} and IL-17A while reducing IL-4 in an atropine-sensitive manner. Stimulation of mAChRs in cells with CHRM3-knockout or M3R blockade prevented increases in IFN-{gamma} and IL-17A but continued to inhibit IL-4. mAChR stimulation enhanced NF-{kappa}B p65 activity without affecting cell proliferation, viability, or M3R expression. This investigation demonstrates that muscarinic signaling increases the pro-inflammatory profile of memory Th cells, including NF-{kappa}B p65, IFN-{gamma}, and IL-17A, with a reduction in IL-4. Focusing on M3R blockers could modulate adaptive immune responses and alleviate immune-related conditions.

immunology↗

bioRxiv2024

β2-Adrenergic Biased Agonist Inhibits the Development of Th17 and the Response of Memory Th17 Cells in an NF-κB-Dependent Manner.

IntroductionAdrenergic receptors regulate metabolic, cardiovascular and immunological functions in response to the sympathetic nervous system. The effect of {beta}2-adrenergic receptor (AR) as a high-expression receptor on different subpopulations of T cells is complex and varies depending on the type of ligand and context. While traditional {beta}2-AR agonists generally suppress T cells, they potentially enhance IL-17A production by Th17 cells. The effects of pharmacological drugs that count as biased agonists of AR like nebivolol are not completely understood. We investigated the impact of nebivolol on human memory CD4+ T (Th1, Th2, Th17) cells and polarized naive Th17 cells highlighting its potential for IL-17A suppression via a non-canonical {beta}2AR cell-signaling pathway. MethodsThe effects of nebivolol were tested on healthy human peripheral blood mononuclear cells, purified memory Th cells, and polarized naive Th17 cells activated with antiCD3/antiCD28/antiCD2 ImmunoCult reagent. IFN-{gamma}, IL-4, and IL-17A which are primarily derived from Th1, Th2, and Th17 cells respectively, were quantified by ELISA and flow cytometry. IL-10 was measured by ELISA. Gene expression of RORC, ADRB1, ADRB2, and ADRB3 was evaluated by qPCR. The ADRB2 gene was knocked out in memory Th cells using CRISPR/Cas9. Protein expression of phosphorylated-serine133-CREB and phosphorylated-NF-{kappa}B p65 was assessed by Western blot. Proliferation was assessed by fluorescent dye loading and flow cytometry. ResultsNebivolol treatment decreased IL-17A and IFN-{gamma} secretion by activated-memory Th cells and elevated IL-4 levels. Nebivolol reduced the proportion of IL-17A+ Th cells and downregulated RORC expression. Unlike the {beta}2-AR agonist terbutaline, nebivolol inhibited the shift of naive CD4+ T cells towards the Th17 phenotype. IL-10 and proliferation index remained unchanged. Nebivolol-treated {beta}2-knockout memory Th cells showed significant inhibition of {beta}2AR-mediated signaling, evidenced by the absence of IL-17A suppression compared to controls. Phosphorylation of the NF-{kappa}B p65 subunit was inhibited by nebivolol, but CREB phosphorylation was not changed, suggesting a selective transcriptional control. ConclusionsThe findings demonstrate that nebivolol acts through a {beta}2-AR-mediated signaling pathway, as a distinctive anti-inflammatory agent capable of selectively shifting Th17 cells and suppressing phosphorylation of NF-{kappa}B. This highlights nebivolols potential for therapeutic interventions in chronic autoimmune conditions with elevated IL-17A levels.

immunology↗

bioRxiv2024

GABAergic interneurons contribute to the fatal seizure phenotype of CLN2 disease mice

GABAergic interneuron deficits have been implicated in the epileptogenesis of multiple neurological diseases. While epileptic seizures are a key clinical hallmark of CLN2 disease, a childhood-onset neurodegenerative lysosomal storage disorder caused by a deficiency of tripeptidyl peptidase 1 (TPP1), the etiology of these seizures remains elusive. Given that Cln2R207X/R207X mice display fatal spontaneous seizures and an early loss of several cortical interneuron populations, we hypothesized that those two events might be causally related. To address this hypothesis, we first generated an inducible transgenic mouse expressing lysosomal membrane-tethered TPP1 (TPP1LAMP1) on the Cln2R207X/R207X genetic background to study the cell-autonomous effects of cell-type-specific TPP1 deficiency. We crossed the TPP1LAMP1 mice with Vgat-Cre mice to introduce interneuron-specific TPP1 deficiency. Vgat-Cre; TPP1LAMP1 mice displayed storage material accumulation in several interneuron populations both in cortex and striatum, and increased susceptibility to die after PTZ-induced seizures. Secondly, to test the role of GABAergic interneuron activity in seizure progression, we selectively activated these cells in Cln2R207X/R207X mice using Designer Receptor Exclusively Activated by Designer Drugs (DREADDs) in in Vgat-Cre: Cln2R207X/R207X mice. EEG monitoring revealed that DREADD-mediated activation of interneurons via chronic deschloroclozapine administration accelerated the onset of spontaneous seizures and seizure-associated death in Vgat-Cre: Cln2R207X/R207X mice, suggesting that modulating interneuron activity can exert influence over epileptiform abnormalities in CLN2 disease. Taken together, these results provide new mechanistic insights into the underlying etiology of seizures and premature death that characterize CLN2 disease.

neuroscience↗

bioRxiv2024

Importin-β specific nuclear transport defects recapitulate phenotypic and transcriptional alterations seen in neurodegeneration

Defects in Nucleocytoplasmic transport have been implicated as an important neurodegenerative pathway in ALS/FTD. Here, we show that a NemfR86S mutation results in the disruption of NCT both in vitro and in vivo. These disruptions are specific to Importin-{beta} nuclear import, and result in the nuclear loss and cytoplasmic gain of NEMF, Importin-{beta}, and TDP-43. We show that a transient nuclear import block is capable of inducing the mis-localization of TDP-43 and is associated with altered transcriptional expression of ALS, FTD, and AD/ARD genes. Taken together, these findings show that disrupted Importin-{beta} nuclear import, whether through genetic forms such as Nemf mutations, or through pharmacological inhibition, is the primary driver of TDP-43 pathology, disease-related transcriptional alterations, and neurodegeneration.

neuroscience↗

bioRxiv2024

Functionally distinct subdomains of dopamine in the hippocampus

Numerous studies have identified dopamine signaling in the hippocampus as necessary for certain types of learning and memory. Since dopamine in the striatum is strongly tied to rewards, dopamine in the hippocampus is thought to reinforce reward learning. Despite the critical influence of dopamine on hippocampal function, little is known about dopamine release in the hippocampus or the specific ways dopamine can influence hippocampal function. Based on the functional complexity of hippocampal circuitry, we hypothesized the existence of multiple dopamine signaling domains. Using optical dopamine sensors, two-photon imaging, and head-fixed behaviors, we identified two functionally and spatially distinct dopamine domains in the hippocampus. The "superficial" domain (cell somata and apical dendrites) showed reward-related dopamine transients early in Pavlovian conditioning but were replaced by "deep" domain transients (basal dendritic layer) with experience. These two domains also play distinct roles in a hippocampal-dependent, goal-directed virtual reality task where mice use exploratory licks to discover the location of a hidden reward zone. Here, positive dopamine ramps appeared in the superficial domain as mice approached the reward zone, similar to those seen in the striatum. At the same time, the deep domain showed strong reward-related transients. These results reveal small-scale, anatomically segregated, dopamine domains in the hippocampus. Furthermore dopamine domain activity had temporal-specificity for different phases of behavior. Finally, the subcellular scale of dopamine domains suggests specialized postsynaptic pathways for processing and integrating functionally distinct dopaminergic influences.

neuroscience↗

bioRxiv2023

Integrin-like adhesin CglD confers traction and stabilizes bacterial focal adhesions involved in myxobacterial gliding motility

AO_SCPLOWBSTRACTC_SCPLOWIntegrins are crucial for eukaryotic cell attachment and motility within the extracellular matrix (ECM) via focal-adhesion formation, with their evolutionary emergence important for the development of multicellularity. Intriguingly, single gliding cells of the predatory deltaproteobacterium Myxococcus xanthus form bacterial focal-adhesion (bFA) sites; therein, helically-trafficked motors become immobilized at anchored locations through Glt apparatus association with cell-surface integrin I-domain-like adhesin CglB. Using traction-force, bead-force, and total internal reflection-fluorescence microscopies combined with biochemical approaches, we herein identify the von Willebrand A domain-containing cell-surface lipoprotein CglD to be a {beta}-integrin-like outer-membrane lipoprotein that functionally associates with and anchors the trans-envelope Glt-CglB gliding apparatus, stabilizing and efficiently anchoring this assembly at bFAs. Calcium dependence governs CglD importance, consistent with its integrated ECM eukaryotic cartilage oligomeric matrix protein domains. CglD thus confers mechanosensory and mechanotransductory capabilities to the gliding apparatus, helping explain bFA-mediated trans-envelope force transduction, from inner-membrane-embedded motors to the cell surface.

microbiology↗