Biology subjects

Kim, J.

Publications and source records attributed to Kim, J..

At least 109 records · Page 6Linked to original sources

bioRxiv2026

Tau Ablation Rewires Brain Cell Programs in Health and Restores Function in Disease

Tau is a microtubule-associated protein with diverse roles in the healthy brain but contributes to neurodegenerative disorders when dysregulated. Although tau ablation has shown protective effects in several disease models, how its absence confers this protection remain unclear. Here, we performed and analyzed single-nucleus RNA sequencing on cortices of aged tau knockout (Mapt-/-) mice in a wild type background as well as in a vascular amyloid model to evaluate the effect on disease context. Comparisons in a wild type setting revealed that tau ablation induced compensatory remodeling across multiple cell types. Excitatory neurons expanded into a distinct subtype with unique glutamatergic signaling, astrocytes adopted synaptoprotective states, oligodendrocytes upregulated genes supporting connectivity and plasticity, and microglia engaged structural remodeling programs. In contrast, in disease, tau removal not only restored functions disrupted by vascular amyloid pathology, but also generated new phenotypes. Excitatory neurons rewired receptor and postsynaptic signaling, astrocytes and oligodendrocytes recovered wild-type-like gene programs related to neurotransmitter cycling, synaptic support, and myelin integrity, and microglia reprogrammed toward sensing and mounting responses. Together, these findings demonstrate that tau ablation reshapes brain cellular programs in a context-dependent manner, exerting adaptive responses in the otherwise healthy brain while restoring homeostatic functions under vascular amyloid pathology. These results position tau as a key regulator of neuronal-glial network balance and highlight the importance of understanding how tau influences distinct cellular programs within specific disease environments.

neuroscience↗

bioRxiv2026

A multi-omic, spatial, and whole-slide image dataset of lung neuroendocrine tumours from the lungNENomics cohort

Lung neuroendocrine tumours (lung NETs) are rare neoplasms comprising approximately 2% of lung cancers. Recent studies have identified distinct molecular groups based on transcriptome and methylome data, but genomic and morphological features remain underexplored due to limited whole-genome and imaging data. We have generated the largest multi-omic dataset of lung NETs to date (201 participants, for a total of n = 294 tumours), including RNA sequencing, EPIC 850K methylation arrays, and whole-genome sequencing. This multiomic dataset also include multi-regional whole-genome sequencing for 41 participants, allowing for the quantification of intra-tumoural heterogeneity. We additionally generated spatial proteomics (64 participants), spatial transcriptomics (4 participants) and whole-slide histopathology images for 212 cases. This dataset enables a comprehensive characterization of lung NET molecular groups and the identification of group-specific morphological features using deep learning algorithms. All quality control analyses, processed data, and scripts are provided to ensure reproducibility. This dataset is available as a basis for further molecular and morphological analysis of lung NETs, and for future research on multi-scale integration.

bioinformatics↗

bioRxiv2026

Reduction in Hepatic Phosphatidylcholine Biosynthesis Promotes MASH Through Copper Deficiency

Metabolic dysfunction-associated steatohepatitis (MASH) is a progressive liver disease for which the mechanisms linking lipid dysregulation to fibrosis remain poorly defined. Hepatic phosphatidylcholine (PC) content is reduced in MASH, but how this alteration drives disease progression is unclear. Here, we identify a role for copper (Cu) homeostasis as a downstream effector of impaired PC biosynthesis. Using single-nucleus RNA sequencing in complementary genetic and dietary mouse models, we found that reduced hepatic PC is associated with marked depletion of hepatic Cu and a concomitant increase in circulating Cu, indicating disrupted Cu distribution. Mechanistically, PC depletion impaired plasma membrane localization of the high-affinity Cu transporter CTR1 (SLC31A1) in hepatocytes, limiting Cu uptake. In human hepatic stellate cells, Cu promoted fibrogenic activation, whereas suppression of Cu import or pharmacologic inhibition of MAPK signaling attenuated fibronectin deposition. In vivo, liver-directed Cu supplementation restored hepatic Cu levels and reduced steatosis but failed to improve fibrosis. In contrast, pharmacologic Cu chelation with bathocuproinedisulfonic acid (BCS) reduced fibrosis without affecting inflammation. Together, these findings identify Cu redistribution as a consequence of impaired PC biosynthesis and implicate Cu-dependent signaling in stellate cell activation, fibrogenesis and MASH pathogenesis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/723926v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1c2bd52org.highwire.dtl.DTLVardef@1b8295org.highwire.dtl.DTLVardef@1a129dorg.highwire.dtl.DTLVardef@1bc2b87_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2026

Aldoximes serve as auxin precursors and repress phenylpropanoid metabolism in tomato

Aldoximes are amino acid-derived metabolites that serve as precursors of auxins and modulate phenylpropanoid production in Arabidopsis. However, the enzymes responsible for aldoxime production in Solanaceae remain unknown. Here, we report the identification of aldoxime-producing enzymes in tomato (Solanum lycopersicum) and examine how altered aldoxime production affects auxin production and phenylpropanoid metabolism. Through homology-based analysis, we identified five putative CYP79 homologs in tomato, among which SlCYP79DB32 and SlCYP79DB52 exhibited aldoxime-producing activity toward multiple amino acids, including phenylalanine and tryptophan. SlCYP79DB32 and SlCYP79DB52 converted phenylalanine into phenylacetaldoxime (PAOx), whereas only SlCYP79DB52 converted tryptophan into indole-3-acetaldoxime (IAOx). Stable isotope-labeled feeding experiments revealed that IAOx and PAOx can be converted to the auxins indole-3-acetic acid (IAA) and phenylacetic acid (PAA), respectively. Consistently, tomato plants engineered to overproduce IAOx and PAOx accumulated elevated levels of IAA and PAA. These plants also accumulated lower levels of phenylpropanoids. In Brassicaceae plants such as Arabidopsis and Camelina, aldoxime accumulation represses phenylpropanoid production by promoting degradation of phenylalanine ammonia-lyase (PAL). However, aldoxime accumulation did not reduce PAL activity in tomato, suggesting an alternative mechanism in this species. Transcriptome analysis revealed extensive transcriptional reprogramming in aldoxime-overaccumulating tomato plants, including upregulation of stress- and defense-related genes. Despite the observed reduction in phenylpropanoid levels, transcript levels of most phenylpropanoid biosynthetic genes were not decreased, suggesting possible post-transcriptional regulation of this repression. Together, our findings demonstrate that aldoximes can serve as intermediates in auxin biosynthesis in tomato and reveal that aldoxime-mediated repression of phenylpropanoid metabolism extends beyond Brassicaceae.

plant biology↗

bioRxiv2026

Identifying Context-Specific Cell-Cell Interaction Genes Without Ligand-Receptor Databases from Spatial Transcriptomics

Current approaches to inferring cell-cell interactions (CCIs) are largely constrained by predefined ligand-receptor databases, particularly for low-resolution spatial transcriptomics (ST) platforms such as Visium. Due to the difficulties in accurately resolving interacting cells at coarse spatial resolution, other modes of interaction are often overlooked. Low-resolution ST data, however, can serve as an alternative to high-resolution ST, which suffers from low sensitivity, and to image-based ST, which is limited by restricted gene panels. Here, we present CellNeighborEX v2, a database-free framework that directly infers CCI-associated genes from ST data by detecting deviations between observed and expected gene expression at the spot-population level. These deviations are rigorously evaluated through a hybrid statistical framework involving permutation testing and are further refined by considering the abundance of interacting cell-type pairs. Compared with other conventional approaches relying on ligand-receptor databases, CellNeighborEX v2 can capture CCI genes from a broad spectrum of interactions, including both paracrine signaling and contact-dependent communication. Across datasets from hippocampus, liver cancer, colorectal cancer, ovarian cancer, and lymph node infection, CellNeighborEX v2 accurately recapitulated previously identified CCIs. Notably, it uniquely detected interactions absent from existing ligand-receptor databases, enabling detection of context-specific CCIs from Visium data. CellNeighborEX v2 is a tool that expands the analytical spectrum of Visium data and deepens our understanding of the molecular language of intercellular communication.

bioinformatics↗

bioRxiv2026

Phenotypic Analysis of GGDEF/EAL Domain Protein Function in Phytopathogenic Pantoea ananatis

Cyclic diguanosine monophosphate (c-di-GMP) is a ubiquitous bacterial second messenger that regulates diverse cellular processes, including colony morphology, motility, biofilm formation, and virulence. It is synthesized by diguanylate cyclases (DGCs) containing the GGDEF domain and degraded by phosphodiesterases (PDEs) containing the EAL domain. However, studies on the genetic and physiological characteristics of c-di-GMP metabolism in Pantoea ananatis are lacking. In this study, we identified 26 predicted c-di-GMP metabolism-related genes in the P. ananatis PA13 genome: 9 encode GGDEF-only domain proteins, 5 encode dual GGDEF/EAL domain proteins, and 12 encode EAL-only domain proteins. We constructed overexpression strains and mutants of 26 DGC- and PDE-encoding genes, and then assessed their Congo Red binding, mucoid and rugose phenotypes, pellicle formation, and swimming motility. We identified 14 of 26 DGC and PDE proteins that affect phenotype changes. Among the 26 DGC- and PDE-overexpressing strains, 13 exhibited the phenotypic changes described above, with some showing alterations in multiple phenotypes simultaneously. Notably, overexpression of dgcM induced changes across all phenotypes. Among the 26 DGC and PDE mutants, the pdeC mutant increased pellicle formation and Congo red binding, the pdeM mutant reduced the mucoid phenotype, and the pdeS mutant, which shows high similarity to ydiV, an anti-FlhD factor, increased swimming motility. Overexpression strains and mutants of 14 DGC and PDE proteins that exhibited phenotypic changes had higher intracellular c-di-GMP levels than the wild type. This study provides important insight into the role of the c-di-GMP network in the plant pathogen P. ananatis. IMPORTANCEPantoea ananatis is a versatile bacterium that causes significant diseases in various economically important plants. To survive and infect hosts, bacteria use a key signaling molecule called c-di-GMP to switch between swimming freely and forming protective communities known as biofilms. Despite its importance, the specific genes governing this signaling network in P. ananatis remained unknown. In this study, we systematically identified and characterized 26 genes responsible for regulating c-di-GMP levels in P. ananatis PA13. By analyzing mutants and overexpressing these genes, we pinpointed 14 critical factors that control essential behaviors such as motility, pellicle formation, and colony appearance. Notably, we discovered specific genes, such as dgcM and pdeS, that act as master regulators of these traits. This comprehensive functional map of the c-di-GMP network provides essential insights into how this pathogen adapts to its environment, offering potential targets to control plant infections.

microbiology↗

bioRxiv2026

Explicit representation of germline and non-germline residues improves antibody language modeling

Antibodies originate from germline templates and are diversified by somatic hypermutation, producing sequences in which conserved germline residues scaffold structure while rare non-germline (NGL) substitutions refine antigen binding. Current antibody language models (ALMs) treat all residues equivalently and inherit a germline bias that systematically down-weights functionally critical NGL mutations as statistical noise. We introduce PRISM, a germline-aware ALM that explicitly represents germline and nongermline residues as distinct token types over a factorized 53-token vocabulary. PRISM achieves state-of-the-art pseudo-perplexity in hypervariable CDRs and is uniquely positively correlated with experimental binding affinity across three deep mutational scanning landscapes on which all compared ALMs anti-correlate. The dual-vocabulary further enables property-specific controllable generation previously unattainable with entangled ALMs. NGL-directed sampling improves physics-based binding scores while GL-directed sampling preserves stability and solubility. These results establish disentangled germline/non-germline representation as a substantive advance in antibody language modeling.

immunology↗

bioRxiv2026

Graphene Quantum Dots Mitigate Oxidative Stress in Bacteria

Manufacturing and storage processes can expose microbes to oxidative stress, reducing viability and limiting their use in biotechnological applications. Here, we evaluate graphene quantum dots (GQDs) containing hydroxyl and carboxyl groups as protective additives that mitigate peroxide-induced oxidative stress in Escherichia coli. GQDs did not adversely affect bacterial growth under basal conditions and restored growth in the presence of hydrogen peroxide. Using the membrane-partitioning fluorescent probe C11-BODIPY, we found that GQDs reduced peroxide-induced oxidation in bacterial membranes. We further used redox-sensitive roGFP2 probes to monitor intracellular oxidative stress and found that GQDs suppressed intracellular hydrogen peroxide accumulation and attenuated disruption of glutathione redox homeostasis. Together, these results show that GQDs protect bacteria by limiting peroxide-driven oxidative damage at both membrane and intracellular levels. This work supports the potential use of GQDs as protective additives for microbial formulations that are susceptible to oxidative stress.

microbiology↗

bioRxiv2026

Benchmarking and behavioral characterization of LLM agents for protein design

Large language models (LLMs) are increasingly deployed as agents for scientific discovery, but standardized frameworks for evaluating their performance and behavior in scientific workflows are lacking. Protein design provides a demanding test case because modern workflows combine stochastic generative models, structure prediction systems, and physics-based evaluation tools that require extensive candidate exploration and filtering. Here we introduce BioDesignBench, a benchmark of 76 expert-curated protein design tasks spanning antibodies, enzymes, fluorescent proteins, binders, and scaffolds, together with human and non-LLM baselines and behavioral metrics derived from tool-use traces. We evaluate four frontier LLM agents across diverse protein design workflows and find that the strongest agents surpass deterministic hardcoded pipelines but consistently underperform expert practice. Decomposing agent behavior along orthogonal axes of tool coverage and evaluation depth, we localize the gap to evaluation rather than tool selection: agents generally pick appropriate tools but score each candidate against only a narrow set of metrics, rarely compare alternatives, and terminate exploration prematurely. Guided workflows improve tool coverage but not evaluation depth. A compute-matched forced-depth intervention that requires agents to evaluate every candidate across multiple complementary metric categories (structure, interface, physics, and learned affinity) substantially improves performance and rules out generic scaffolding effects, demonstrating that the gap is behavioral rather than a fundamental capability constraint. All evaluations are performed in silico. We release BioDesignBench, open-source reference agents, and a public leaderboard as a community resource for evaluating and improving AI agents for protein engineering.

bioengineering↗

bioRxiv2026

Microglial sTREM2 limits dyskinesia and acts on TrkB to support circuit plasticity

Microglia continuously survey the brain and shape neuronal activity, but their contribution to experience-dependent synaptic plasticity is unclear. Levodopa-induced dyskinesia (LID) is a disabling complication of late-stage Parkinsons disease (PD) that is linked to maladaptive striatal remodeling and is often assumed to reflect detrimental neuroinflammation. Here we identify a dyskinesia-associated microglial gene program in the striatum of PD patients and show that microglia instead act as a protective brake on LID. In a mouse model, microglial depletion exacerbated dyskinesia, whereas microglial repopulation mitigated it. Delivery of AAV expressing soluble TREM2 (sTREM2) similarly reduced LID without impairing the therapeutic benefit of levodopa. Single-nucleus transcriptomics revealed that microglial loss drives extensive remodeling of both direct and indirect spiny projection neurons (SPNs), while repopulation or sTREM2 reverses a large fraction of LID-associated transcriptional changes. Mechanistically, sTREM2 directly engages TrkB and potentiates BDNF-dependent TrkB-ERK signaling, consistent with positive allosteric modulation. Functionally, sTREM2 enhances BDNF-TrkB-dependent hippocampal synaptic plasticity and acutely rebalances striatal dendritic excitability in a compartment- and cell type-specific manner. These findings reveal an unexpected neuroimmune pathway in which microglia restrain maladaptive plasticity via sTREM2-TrkB signaling, with therapeutic implications.

neuroscience↗

bioRxiv2026

Multispecific nanobody degraders co-deplete membrane receptors and enable targeted delivery of diverse payloads

Targeting membrane receptors underlies the success of antibody-drug conjugates (ADCs), yet single-receptor formats can be limited by heterogeneous expression, compensatory signaling, and variable internalization. Here we developed Multivalent Interchangeable Nanobody Degradation System (MINDS), a modular nanobody-Fc chassis that co-engages multiple membrane receptors, promotes their lysosomal co-depletion, and enables delivery of diverse intracellular payloads. As a proof of concept, we generated Tritazumab, a trispecific nanobody-Fc targeting three oncogenic receptors EGFR, cMET, and TfR1. Tritazumab incorporates a high-affinity, non-transferrin-competing anti-TfR1 nanobody that drives efficient uptake and lysosomal trafficking, enabling coordinated depletion of all three receptors. Across non-small cell lung cancer models, Tritazumab achieved rapid and sustained multi-receptor surface loss with picomolar degradation potency, reaching near-maximal depletion within approximately 1.5 hours. Conjugation of Tritazumab to MMAE preserved receptor binding and produced substantially greater antiproliferative activity and improved tumor selectivity relative to clinical ADCs in matched cell models, along with potent in vivo tumor growth inhibition and acceptable tolerability in a xenograft model. Extending the platform beyond cytotoxic payloads, a BRD4 molecular glue conjugate improved the selectivity window by > 100-fold and showed marked in vivo efficacy, while an EZH2-targeting PROTAC conjugate achieved an approximately 1,000-fold increase in intracellular degradation potency relative to the free PROTAC. These findings establish MINDS as a modular multispecific degrader-payload platform that integrates receptor co-depletion to enhance anticancer selectivity and efficacy.

cancer biology↗

bioRxiv2026

Metabolic signals regulate resuscitation speed of antibiotic persister bacteria during infection

All living organisms adjust their metabolism in response to environmental changes. Under unfavorable conditions, organisms enter a state of dormancy by halting metabolism, enabling survival. Dormant bacteria become highly tolerant to antibiotics-a phenomenon called persistence. Here, we demonstrate that selective metabolic reprogramming controls the resuscitation speed of persister after antibiotic exposure. Using multi-omics and in silico modeling, we found that dormant bacteria reprogram metabolic pathways to modulate persister awakening. Accumulation of L-serine and reduction of arginine drive rapid resuscitation. L-serine promotes cysteine biosynthesis and motility while reducing energy metabolism to facilitate rapid resuscitation. In contrast, arginine slows regrowth from dormancy by enhancing ethanol-aldehyde and energy metabolism. L-serine and arginine can, respectively, promote or inhibit the regrowth of antibiotic persister cells in macrophages and mouse models, and regulate the awakening speed of Salmonella, E. coli, and methicillin-resistant Staphylococcus aureus (MRSA). These findings suggest new strategies to target chronic bacterial infections. TeaserL-serine speeds and arginine slows the awakening of antibiotic persisters, revealing targets for chronic infection.

microbiology↗

bioRxiv2026

WISH-barcoding of Salmonella Typhimurium ATCC14028s strains for population dynamics studies in vivo

BackgroundBarcoding of isogenic strains is a powerful approach to assess pathogen population dynamics during infection. Here, we adapted WISH-barcoding to Salmonella Typhimurium ATCC14028s to evaluate its suitability for pooled infection experiments in streptomycin-pretreated mouse models. ResultsWISH-barcoded wild-type pools showed pronounced population instability, characterized by stochastic strain loss and segregation into high- and low-fitness subpopulations. Whole-genome sequencing identified recurrent mutations in the methyltransferase rsmG and loss of the P3 plasmid carrying streptomycin resistance in low-fitness strains; neither was observed in {Delta}invG or {Delta}ssaV pools. We propose that rsmG mutations were enriched during strain construction carried out under streptomycin selection, following loss of the P3 plasmid. Control experiments demonstrated that rsmG mutations and P3 loss are counter-selected in vivo and attenuate gut-luminal colonization in streptomycin-pretreated mice. ConclusionWhile population dynamics experiments with ATCC14028s are feasible in principle, wild-type strains are prone to acquiring fitness-altering mutations during in vitro construction when using the P3 plasmid and streptomycin, highlighting the need for careful pool validation prior to use.

microbiology↗

bioRxiv2026

TFIIIC regulates SMC complex binding and 3D DNA contacts between tRNA genes

Transcription factor IIIC (TFIIIC) is a multi-subunit protein complex that recruits RNA polymerase III (Pol III) to the majority of its target genes. Evolutionarily conserved overlap between TFIIIC binding sites and the structural maintenance of chromosomes (SMC) complexes suggested a role for TFIIIC in SMC regulation and 3D organization of eukaryotic genomes; but the evidence has remained largely correlational due to the essential role of TFIIIC in recruiting RNA Pol III for transcription initiation. Here, we directly tested the function of TFIIIC in SMC complex regulation by using auxin inducible protein degradation in C. elegans. We performed Hi-C and ChIP-seq analyses upon acute depletion of TFTC-3, an essential TFIIIC subunit, and RPC-1, the catalytic subunit of RNA Pol III. Our results showed that TFIIIC is required for the binding of cohesin and condensin complexes to tRNA genes. TFIIIC is also required for increasing 3D contacts between distant tRNA genes located on the same or different chromosomes. Depletion of individual SMC complexes did not significantly reduce the tRNA gene contacts, suggesting redundancy or an independent mechanism of interphase genome organization mediating the 3D contacts between tRNA genes. Together, our study supports an RNA Pol III independent function for TFIIIC in regulating multiple SMC complexes and the 3D organization of tRNA genes.

genomics↗

bioRxiv2026

Leaves in Transition: Single nuclei RNA sequencing provides insights into sorghums juvenile and adult phases

The transition from juvenile to adult phase (JA) is a key developmental process in plants, driven by conserved pathways that shape growth and stress responses. In monocots such as sorghum, this transition influences traits linked to environmental resilience, yet the regulation of micro-anatomical features such as trichomes and bulliform cells remains poorly understood. Here, we use single-nucleus RNA sequencing (snRNA-seq) to generate high-resolution gene expression maps of juvenile and adult sorghum leaves. Contrary to the traditional developmental model, we find that trichomes are present in both juvenile and adult leaves, with stage-dependent differences in gene expression. We also observe that bulliform cells, typically considered adult-specific, are present in juvenile leaves. At the transcriptomic level, cell populations cluster more strongly by developmental stage than by cell type, with juvenile cells grouping with other juvenile cells and adult cells with adult counterparts, indicating a dominant effect of developmental state on gene expression. In addition, we identify enrichment of dhurrin biosynthetic genes in trichome-associated cells as well as elevated expression of aquaporin genes in these cells, pointing to a potential role for trichomes in coordinating defense and water-related processes. Together, these findings refine current models of sorghum development and suggest that key epidermal cells and their associated functions may be established earlier than previously known. Collectively, this study provides a single nucleus resolved framework for understanding how developmental stage shapes gene expression in sorghum leaves.

plant biology↗

bioRxiv2026

Inverse-scattering of absorptive samples via beam propagation

Inverse-scattering methods enable label-free, quantitative visualization of a samples three-dimensional (3D) refractive index (RI), providing intrinsic and volumetric morphological contrast without exogenous labels. This is achieved by developing computational frameworks that reconstruct the samples 3D RI from a series of scattering measurements acquired under different data-capture conditions. Recent advances have demonstrated successful 3D RI reconstructions in multiple-scattering samples using angle-varying illuminations; however, these studies have primarily focused on non-absorptive samples. Here, we extend the multi-slice beam propagation (MSBP) inverse-scattering framework to reconstruct complex-valued RI, encompassing both the samples conventional RI (real part) and absorptivity (imaginary part). We show that reconstructing complex-valued RI makes the inverse problem ill-posed under angle-varying illumination alone, and that incorporating measurement diversity from both angle-varying illumination and sample defocus is necessary to ensure stable and accurate convergence. Experimental demonstrations were conducted on 1) dyed microsphere samples to characterize accuracy of reconstructed RI and absorptivity; and 2) diverse absorptive scattering samples to demonstrate biological utility. These results represent an important step for label-free volumetric imaging in biological tissue, which typically exhibits both scattering and absorption.

bioengineering↗

bioRxiv2026

Genetic Characterization of the TAPBP and Its Haplotypic Association with BF2 in the Chicken Major Histocompatibility Complex

TAPBP is a key chaperone of the peptide-loading complex that facilitates peptide loading onto major histocompatibility complex class I (MHC I) molecules. This study characterized TAPBP alleles in Korean Native Chickens (KNCs), identified novel variants, and evaluated haplotypic associations with BF2. Thirty-six samples representing six KNC lines were genotyped using LEI0258 and the MHC-B SNP panel, and individuals homozygous at both markers were classified into 16 groups. The same samples were subjected to Sanger sequencing of TAPBP exons 3-8. Sequences were assembled and aligned against MHC-B reference haplotypes and the Red Junglefowl reference. Additional comparisons with "tapasin allele" datasets enabled the identification of novel variants. Six novel nucleotide variants were detected across exons 3-6, including one nonsynonymous substitution in exon 4 (D251H). This residue corresponds to position Q265 in human TAPBP and lies adjacent to residues involved in MHC I interaction, suggesting potential functional relevance. Furthermore, TAPBP exhibited high haplotype diversity (Hd = 0.93) and moderate nucleotide diversity ({pi} = 0.00892), with exon 5 showing the highest diversity ({pi} = 0.01). B9 was the most frequent haplotype at the nucleotide level, whereas B6/B24 predominated at the amino acid level. Comparison with BF2 data revealed haplotype-dependent pairing patterns: BF2-B9 consistently matched TAPBP-B9, whereas BF2-B6 was associated with distinct TAPBP nucleotide variants, indicating allelic diversification within a shared haplotypic background. Homozygosity at LEI0258 and the SNP panel corresponded with TAPBP homozygosity, supporting marker-based prediction. These findings highlight potential BF2-TAPBP associations and provide a foundation for understanding variation in MHC I peptide loading.

genetics↗

bioRxiv2026

Investigating the coupled effects of stiffness and stretch on the trabecular meshwork cells using a hydrogel-integrated microfluidic system

Glaucoma is characterized by progressive stiffening of the trabecular meshwork (TM), which elevates intraocular pressure and contributes to tissue dysfunction. Although substrate stiffness and mechanical stimulation both regulate TM homeostasis, their combined effects remain poorly understood. Here, a hydrogel-integrated microfluidic platform is presented that enables simultaneous control of substrate stiffness via tunable gelatin methacryloyl (GelMA) hydrogels and equi-biaxial quasi-static stretch via hydraulic actuation. Finite element analysis validates the applied strain field, and optimized crosslinking ensures structural stability. Primary normal TM (nTM) and glaucomatous TM (gTM) cells cultured under coupled conditions exhibit selective mechanotransduction dysregulation rather than global mechanosensory impairment. While nTM cells dynamically regulate -smooth muscle actin (-SMA), myocilin (MYOC), matrix metalloproteinase-2 (MMP2), and collagen type I (COL1), gTM cells display constitutively elevated -SMA, loss of mechanical regulation of MMP2, and impaired stretch-mediated COL1 suppression, while retaining stiffness-dependent focal adhesion kinase and MYOC sensitivity. Key differences between normal and glaucomatous cells emerge only under combined stiff and stretched conditions, underscoring the importance of coupled mechanical cues in revealing disease-relevant phenotypes. These findings implicate tissue stiffening in selective pathway dysregulation and highlight mechanotransduction-targeted therapeutic strategies.

bioengineering↗