Biology subjects

Jang, J.

Publications and source records attributed to Jang, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Multichromatic Dynamic Control of Multi-Membered Microbial Consortia Compositions for Chemical Production

Engineered microbial consortia offer a promising strategy for chemical production by distributing specialized functions among microbial strains, reducing metabolic burden, facilitating modular pathway optimization, reducing toxicity, and increasing strain stability. However, differences in growth rates can destabilize population composition, compromising productivity and limiting their applicability. Here, we developed a multichromatic optogenetic Toxin-Antitoxin (optogeneticTA) platform for dynamic control of Escherichia coli consortia of up to four members using blue, red, and near-infrared light and darkness. By varying light intensities or pulses, we precisely program and dynamically modulate the population composition of two-, three-, and four-membered consortia. We further developed a modular mathematical framework that captures and predicts population dynamics of these optogenetically controlled co-cultures. Applying dynamic control to a two-membered engineered consortium increased phenol production by ~69% relative to unregulated consortia. These results establish a programmable platform for stabilizing and dynamically optimizing microbial consortia, with potential applications across microbial biomanufacturing.

synthetic biology↗

bioRxiv2026

PredHLM: quantitative and interpretable prediction of metabolic half-life in human liver microsomes

MotivationHuman liver microsome (HLM)-based metabolic stability assays are fundamental in early drug discovery, shaping pharmacokinetic profiles and oral bioavailability. However, these experimental assays are labor-intensive and time-consuming, limiting their application in large-scale virtual screening. Computational models can prioritize compounds at scale, yet most are classification-based, leaving quantitative and interpretable prediction of HLM half-life limited. ResultsIn this study, we developed a quantitative machine learning model for the direct prediction of HLM half-life (T1/2) by integrating 11,790 compounds combining in-house and curated public data. Among various combinations of molecular features and learning algorithms, the XGBoost model with RDKit 2D descriptors achieved the best predictive performance, with an RMSE of 0.507 and an R2 of 0.431 on an independent test set. Shapley Additive Explanations (SHAP) analysis identified lipophilicity and known metabolic soft-spot features as the primary contributors to the predictions. These results suggest that this quantitative approach provides a practical framework for defining metabolic stability margins, thereby supporting rapid Go/No-go decisions in preclinical drug discovery. AvailabilityThe source code, data, and trained model are available at https://github.com/joshua-416/PredHLM. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/736062v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@7d94c1org.highwire.dtl.DTLVardef@b13e71org.highwire.dtl.DTLVardef@7aa684org.highwire.dtl.DTLVardef@4a2668_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Synaptic Plasticity as a Function of the Temporal Derivative

A major outstanding question in neuroscience is whether the neocortex uses the same powerful learning algorithm as current AI models: error backpropagation. One way this could be accomplished is as a function of the temporal derivative (i.e., differences in neural activity states over time), which can closely approximate the backpropagated error gradient. We tested the hypothesis that the direction of synaptic plasticity is a function of the temporal derivative in synaptic activity over the course of a 200 ms (5 Hz) theta cycle. Using mouse hippocampal slices, we drove presynaptic activity across the two 100 ms halves of a 200 ms window at either 25 Hz or 50 Hz, combined with corresponding low and high magnitudes of postsynaptic depolarization, testing all four 2x2 combinations of these low and high activity levels, while measuring the resulting effects on synaptic efficacy (as measured by EPSP amplitude to standard test probes). Consistent with the computational hypothesis, a positive temporal derivative (low to high) resulted in LTP (increased synaptic strength), while a negative temporal derivative (high to low) resulted in LTD. Critically, both no-change conditions (stable low or high across 200 ms) resulted in no net synaptic change, even though the high no-change condition had the highest overall synaptic activity levels. Possible biochemical mechanisms that could support these results are discussed.

neuroscience↗

bioRxiv2026

Spatiotemporal Transcriptomic Dissection Uncovers Age-Dependent Deceleration of Esophageal Cell Differentiation

Precise orchestration of stem and progenitor cells is essential for tissue homeostasis and regeneration but becomes dysregulated during aging. Despite the known markers, the age-related dynamics of esophageal epithelial cell lineages remain unclear. Using single-cell single cell transcriptomics, we analyzed human esophageal epithelia across different age groups. We identified two stem cell populations: quiescent (qeSCs) and proliferative (peSCs) esophageal stem cells. qeSCs from young donors showed higher WNT10A expression and Wnt signaling activity. Analysis of cell lineage trajectories combined with cell plastic potentials showed stronger connectivity between peSCs and differentiated cells in younger tissues, indicating more efficient and rapid epithelial turnover and homeostatic maintenance. Cell-cell interaction analysis further demonstrated that NOTCH signaling is more prominent within peSCs and qeSCs in younger esophagi, whereas in older tissues, NOTCH activity is preferentially retained in differentiated cells. Additionally, the inflammatory signaling, Interleukin-1 pathway, is more active in younger esophagi but is largely restricted to differentiated cells. Our findings suggest that age-related decline in esophageal homeostasis is primarily driven by impaired differentiation dynamics rather than by alterations in stem cell self-renewal capacity.

cell biology↗

bioRxiv2026

A functional triangle relationship of topoisomerase IIβ, BARD1, and ERK2 in immediate early gene transcription

Immediate early genes (IEGs) encode master transcription factors, including EGR1, FOS, JUN, and MYC genes that drive robust transcription in the G1 phase of cell cycle. Our previous studies indicate that topoisomerase II{beta} (TOP2B) critically regulates IEG transcription and that the activities of TOP2B are dynamically controlled through post-translational modifications by BRCA1-BARD1 and ERKs. Here, we show that two E2 enzymes, UBCH5b and UBC13/MMS2, differentiate the effects and functions of TOP2B ubiquitination by BRCA1-BARD1. Comprehensive transcriptomics, proteomics, and biochemical and molecular cellular analyses revealed a close relationship between BARD1 and key mitogen-activated protein kinase pathway genes and identified activated ERK2 as a novel kinase that phosphorylates BARD1 at S391, a previously reported mitotic phosphorylation site, whose genetic mutation has been linked to tumorigenesis. Mechanistically, the catalytic activity of ERK2 stimulates TOP2B ubiquitination mediated by BRCA1-BARD1 in complex with UBCH5b and UBC13/MMS2, which controls the binding and function of TOP2B and BARD1 for transcriptional activation at representative IEGs. Taken together, our data propose that there is a functional regulatory circuit involving TOP2B, BARD1, and ERK2, three key transcriptional activators for IEG transcription, in which the gene association and catalytic activity of TOP2B are regulated through E2-differentiated ubiquitination by BRCA1-BARD1 and the phosphorylation of BARD1 by ERK2 for productive transcription.

molecular biology↗

bioRxiv2026

Serial vaccination expands and refines human CD4+ T cell memory

CD4+ T cells coordinate protective immunity against pathogens. However, a major unresolved question is how human CD4+ T cell memory is established and evolves following primary and repeated vaccination. Using COVID-19 mRNA vaccination as a model, we tracked 50 distinct antigen-specific populations directly ex vivo with peptide-MHC class II tetramers in eight SARS-CoV-2-naive individuals from pre-vaccine baseline through memory time points after three mRNA doses. Our findings identify the primary vaccine series as the main driver of memory pool size. It leverages pre-existing memory while preferentially recruiting high-avidity T cells, establishing an immunodominance hierarchy dominated by a small subset of precursors. Booster vaccination refines both the magnitude and quality of T cell memory. It increases select populations and enhances differentiation of subdominant CD4+ T cells. Populations that did not become more abundant after boosting retained their polyfunctional potential. Beyond establishing memory to the ancestral spike, vaccinations broadened responses by recruiting cross-reactive T cells recognizing viral variants. Collectively, these findings reveal how human CD4+ T cell memory evolves through sequential immunizations to generate a functionally diverse and broadly responsive memory repertoire against future viral challenges.

immunology↗

bioRxiv2026

Spiperone targets HBV cccDNA via ER stress induced innate immune activation and epigenetic silencing

Chronic hepatitis B persists due to the stability of nuclear covalently closed circular DNA (cccDNA), which maintains viral transcription despite prolonged antiviral therapy, highlighting the need for strategies that suppress cccDNA via host-targeted mechanisms. Here, we identify Spiperone, a clinically approved compound, as a repurposed anti-HBV candidate with strong translational potential. Spiperone robustly reduced HBsAg, HBeAg, viral DNA, and pgRNA across HepG2.2.15, HBV-infected HepG2-NTCP-C4 and HepaRG cells, and multiple in vivo models, including HBV transgenic, hydrodynamic injection, and AAV- HBV1.04x models. Notably, intrahepatic cccDNA was significantly diminished. In combination, Spiperone potentiated tenofovir activity, exhibiting synergistic effects, while both intraperitoneal and oral administration reduced antigenemia and viremia. Mechanistically, Spiperone activated the PERK-eIF2-ATF4 arm of the ER stress response, coupled with mitochondrial perturbation and cytosolic release of oxidized mitochondrial DNA, leading to activation of IFI16-STING-IRF3 signaling. This cascade induced type I interferon (IFN-I) and interferon-stimulated genes. ChIP-qPCR further demonstrated reduced enrichment of activating histone marks on cccDNA, consistent with transcriptional repression. Collectively, these findings position Spiperone as a host-directed antiviral that converges ER stress-linked innate immunity and epigenetic repression to suppress cccDNA, supporting its advancement in combination strategies toward a functional cure for chronic HBV infection.

microbiology↗

bioRxiv2026

NFATc3 enhances DREAM complex-driven tumorigenesis

The nuclear factor of activated T cells (NFAT) transcription factors, activated by calcium-calcineurin signaling, regulate various cellular processes, including cell differentiation, angiogenesis, and immune cell activation. Nonetheless, their roles in tumor cells remain largely undefined. The dimerization partner, RB-like, E2F, and multi-vulval class B (DREAM) complex orchestrates cell quiescence and proliferation. Pharmacological mimicry of DREAM-activated transcriptional signatures identified two calcium signaling inhibitors that suppressed lung adenocarcinoma (LUAD) cell proliferation. Among the five NFAT members, NFATc3/NFAT4 was predominantly expressed in LUAD cells and required for both LUAD cell proliferation and DREAM target gene transactivation. NFATc3 was enriched at DREAM target promoters and associated with the DREAM complex, possibly via LIN9, a scaffolding protein of the Multi-Vulva class B (MuvB) core proteins. These findings reveal an unexpected role for NFATc3 in promoting DREAM target gene transactivation and suggest the calcium-NFATc3 axis as a molecular target in LUAD, enriched by DREAM complex activation.

molecular biology↗

bioRxiv2026

YAP activation reverses aging-related visual dysfunction caused by impaired cell-matrix adhesion

Cellular senescence of retinal pigment epithelium (RPE) cells drives age-related visual decline, particularly in the pathology of age-related macular degeneration (AMD). While genome-wide association studies (GWAS) have identified genetic risk factors underlying AMD, the molecular mechanisms governing RPE senescence remain unclear. Here, single-cell RNA sequencing of young and old mouse RPE revealed dysregulated cell-matrix adhesion as a key feature of senescence, consistent with transcriptional changes in AMD patients. Hydrogel-based experiments confirmed that impaired integrin-mediated adhesion induces RPE senescence. Yes-associated protein 1 (YAP), a crucial mechanotransducer, mediated the protective effects of cell-matrix adhesion, and its activation alone reversed aging phenotypes in senescent RPE cells. Notably, treatment with TRULI, a small-molecule YAP activator, significantly improved visual function in AMD and naturally aged mice. These findings highlight the integrin-YAP mechanotransduction pathway as a fundamental regulator of RPE senescence and a potential therapeutic target for AMD.

physiology↗

bioRxiv2025

MechanoMR microparticle (M3) sensors reveal dynamic stress loading as a driver of epithelial-mesenchymal transition

The dynamic mechanical response of tissues underlies their physiological function, yet direct, quantitative measurement of tissue stress in vivo has remained a major challenge. Here, we introduce the mechanoMR microparticle (M3, "M-cube") sensor, a hybrid soft-matter/nanoparticle probe that integrates directly into tissue mechanical networks while transducing local stress into quantitative magnetic resonance (MR) readouts with single-particle resolution. We demonstrate the utility of this platform across diverse model systems, including tumor spheroids, Xenopus embryos, and mouse xenografts, where the M3 sensor enables noninvasive, spatiotemporally resolved mapping of tissue stress dynamics during cancer development. Using this approach, we reveal that epithelial-mesenchymal transition (EMT) is accompanied by distinctive stress-remodeling patterns observable in vivo. Strikingly, we find that abrupt stress increases, rather than cumulative or peak stress magnitude, are the key determinants of EMT induction in cancer cells within the tumor microenvironment. Transcriptomic profiling under controlled stress-loading dynamics shows that sustained yet gradual stress escalation activates cytoprotective antioxidation pathways (e.g., FOXO/AMPK) that reinforce epithelial stability, whereas acute stress surges overwhelm these defense mechanisms, predisposing cells toward mesenchymal reprogramming. These findings establish the M3 sensor as a broadly applicable technology for linking dynamic mechanical cues to cell-state transitions in development, homeostasis, and disease.

bioengineering↗

bioRxiv2025

Novel therapy for gastric cancer peritoneal dissemination using genetically modified dental pulp cells and astatine-211

Peritoneal dissemination of gastric cancer is a terminal stage with limited treatment options and a five-year survival rate below 10%. To develop a more effective treatment, we created a new approach that uses genetically engineered human dental pulp cells (DPCs) that express the sodium/iodide symporter (NIS). These cells (NIS-DPCs) deliver astatine-211 (At-211) directly to tumor sites. When injected intraperitoneally into a mouse model of gastric cancer dissemination, DPCs, which were isolated and expanded, showed strong tumor-homing ability. Chemotaxis mediated by the CXCR4/SDF-1 axis has been reported to play a role in this accumulation. In addition to histological analysis, fluorescent imaging confirmed the selective accumulation of NIS-DPCs within tumor lesions. Introducing the NIS gene markedly increased SLC5A5 expression, enabling efficient At-211 uptake. To avoid nonspecific binding, sodium At-211 was utilized. High-resolution alpha-particle imaging visualized alpha-ray emission specifically from NIS-DPCs, confirming the radionuclides intracellular retention. In vivo, the sequential administration of NIS-DPCs, followed by Na[At-211], resulted in the pronounced regression of peritoneal tumors and a significant extension of survival compared to controls. The therapeutic mechanism involves three coordinated steps: tumor-directed migration of NIS-DPCs, At-211 uptake via NIS transporters, and localized alpha-particle-mediated cytotoxicity. This study introduces the novel concept of cell-based alpha-radiotherapy, which integrates regenerative and nuclear medicine. Due to the well-documented safety profile of DPCs in human clinical trials (J-REPAIR, jRCT1080224505), the NIS-DPC platform emerges as a promising approach for the precise, localized irradiation of disseminated gastric cancer and other challenging malignancies.

cancer biology↗

bioRxiv2025

Red-light-only control of protein-protein interactions using a cyanobacteriochrome (UNICYCL)

Most optogenetic tools are controlled by blue light. Red-light responsive tools enable multiwavelength applications and allow greater biological tissue penetration with reduced toxicity. Current red-light tools are primarily based on phytochromes, large dimeric proteins with a structurally complex mode of interaction with their binding partners. Here we introduce a small red-light-only responsive system composed of a GA domain (6 kDa) that binds to a CBCR GAF domain (17 kDa) with a Kd [~]1-5 {micro}M to form a 1:1 complex in the dark. Red light causes dissociation of the complex by causing a >25-fold decrease in binding affinity. The CBCR GAF domain reverts to the dark state with a half-life of [~]1 min and the complex reforms. Structural analysis using NMR measurements combined with molecular docking and dynamics simulations shows that the binder interacts with the GAF domain and senses isomerization of the bilin chromophore at a site that overlaps the critical tongue domain of phytochromes. This system provides a small, simple red-light-only optogenetic tool that can operate to control protein-protein interactions in vitro and in living cells.

biochemistry↗

bioRxiv2025

Comparative single-cell transcriptomics of orthotopic and subcutaneous gastric tumors reveal immune and stromal heterogeneity

Preclinical cancer models often use subcutaneous (SC) implantation, which fails to recapitulate the native tumor microenvironment (TME) of orthotopic (ORT) sites. To resolve these differences, we used single-cell RNA sequencing (scRNA-seq) on paired SC and ORT implants of the CKP syngeneic gastric cancer model. Histopathological differences were minimal, but scRNA-seq revealed profound TME divergence. ORT tumors displayed robust stromal activation, coordinated fibroblast and endothelial signaling, and an immune compartment marked by higher T/NK cell activation and IgA-biased B cell plasma programs, reflecting a physiological mucosal environment. In contrast, SC tumors had higher overall T cell infiltration but showed markedly increased CD8+ T cell exhaustion and an enriched oxidative tumor program. Our findings provide critical guidance: SC models are optimal for high-throughput and exhaustion-focused assays, whereas ORT models are indispensable for studying organ-specific immune and stromal biology with translational fidelity.

cancer biology↗

bioRxiv2025

NAC promotes co-translational folding at the ribosomal tunnel exit

The nascent polypeptide-associated complex (NAC) coordinates enzymatic modifications and membrane targeting of nascent chains during translation. While NACs function as a dynamic hub for other factors is well-established, its direct role in co-translational folding is unclear. By proteome-wide profiling NAC co-translational interactions in human cells, we found that NAC recognizes emerging segments enriched in hydrophobicity and -helical propensity, within folded domains of cytonuclear proteins. Single-molecule and structural analyses reveal that NAC, via its {beta}-barrel domain, dynamically interacts with nascent chains at the ribosomal tunnel exit and is capable of promoting on-pathway folding. Compartment-specific nascent chain interactions of NAC further elucidate its role in targeting to the endoplasmic reticulum and mitochondrial membrane protein biogenesis. Together, these findings show that NAC acts as a bona fide co-translational chaperone that facilitates early protein folding at the ribosomal tunnel exit, expanding its functional repertoire in protein biogenesis.

biochemistry↗

bioRxiv2025

Cancer systems immunology reveals myeloid - T cell interactions and B cell activation mediate response to checkpoint inhibition in metastatic breast cancer

Sensitization of the immune-suppressed tumor microenvironment (TME) of breast cancer by histone deacetylase inhibition shows promise, but the mechanisms of sensitization are unknown. We investigated the TME of breast-to-lung metastases by combining experimental and clinical data with theory. Knowledge-guided subclustering of single-cell RNA-sequencing data and cell circuits analysis identified 39 cell states and salient interactions, of which myeloid, T cell and B cell subpopulations were most affected by treatment. Using functional immunologic assays, we verified that inhibition of the ICAM pathway partially recapitulated treatment effects. Mathematical modeling of tumor-immune dynamics confirmed that tumor reduction required simultaneous modulation of multiple TME interactions. We found evidence that treatment affected anti-tumor antibody production. Analysis of patient biopsies via spatial proteomics corroborated preclinical findings: in responders we observed increased B cell activation, mature tertiary lymphoid structures, and increased CD8+ T cell--macrophage distances with treatment. Overall, this study provides a framework for the discovery of cell-cell interactions that govern responses in complex TMEs. Statement of significanceThis study provides a framework for the discovery of cell-cell interactions that control responses in complex TMEs. We not only identify impactful tumor immunologic interactions that facilitate sensitization of the metastatic TME but also demonstrate how interdisciplinary data integration fuels cancer systems immunology to accelerate discovery of mechanisms of successful immunotherapeutic response in breast cancers and other previously unresponsive solid tumor types.

cancer biology↗

bioRxiv2025

SMARCA4 is essential for early-stage tumor development but its loss promotes late-stage cancer progression in small-cell lung cancer

SMARCA4 and other components of the SWI/SNF chromatin remodeling complex have been implicated in various cancers. Yet, its role in small cell lung cancer (SCLC) tumorigenesis remains poorly understood. Genetically engineered mouse models (GEMMs) of SCLC revealed that deletion of Smarca4 significantly decreased tumor development in this model. Pharmacological inhibition of SMARCA4 decreased the proliferation of preneoplastic neuroendocrine (NE) cells. These effects coincided with reduced expression of the lineage-specific transcription factor, ASCL1, suggesting that disruption of the SMARCA4-ASCL1 axis impairs tumor development. However, Smarca4-deficient tumors, albeit smaller than controls, displayed features associated with malignant progression, including variant histology and the loss of NE differentiation. This prompted us to test the functional role of SMARCA4 in established tumor cells that recapitulate late-stage disease. Intriguingly, whilst Smarca4 knockdown in tumor cells failed to affect their proliferative capacity in vitro, Smarca4 knockdown tumors exhibited enhanced growth following subcutaneous transplantation in athymic nude mice. Interestingly, SMARCA4 knockdown significantly reduced expression and cell-surface display of PVR, a ligand for activating natural killer (NK) cells. These results led to an idea that the enhanced tumor formation was partly owing to altered tumor-NK cell interactions mediated by the SMARCA4-PVR axis in tumor cells. These findings suggest that SMARCA4 plays a temporally distinct role in SCLC, supporting early tumorigenesis but potentially functioning as a tumor suppressor in the later stages. The dramatic differences observed when targeting SMARCA4 in distinct disease states emphasize a need to acknowledge how differences in the timing of alterations can drastically alter tumor evolution.

cancer biology↗

bioRxiv2025

Siderophores can alter the population dynamics of fungal-bacterial communities by inhibiting specialized metabolism

Siderophores are microbial metabolites with a strong affinity for Fe(III) ions, in addition to other roles beyond iron acquisition. In this study, we propose that bacillibactin, a siderophore produced by the bacterium Bacillus subtilis, provides an advantage to its producer by inhibiting the specialized metabolism of antagonistic Penicillium fungi. Metabolome and transcriptome analyses indicate that iron deficiency caused by bacillibactin plays a critical role in downregulating the specialized metabolism of competing Penicillium species. Since many specialized metabolites of Penicillium spp. have antibacterial properties, we hypothesize that bacillibactin cross-protects other bacteria during fungal-bacterial community interactions. A tripartite coculture model demonstrated that bacillibactin production influences community dynamics by reducing the growth of specialized metabolite-producing Penicillium species, thereby facilitating the colonization of B. subtilis and other co-inhabiting bacterial species.

microbiology↗

bioRxiv2025

SCassist: An AI Based Workflow Assistant for Single-Cell Analysis

SummarySingle-cell RNA sequencing (scRNA-seq) data analysis often involves complex iterative workflow, requiring significant expertise and time. To navigate this complexity, we have developed SCassist, an R package that leverages the power of the large language models (LLMs) to guide and enhance scRNA-seq analysis. SCassist integrates LLMs into key workflow steps, to analyze user data and provide relevant recommendations for filtering, normalization and clustering parameters. It also provides LLM guided insightful interpretations of variable features and principal components, along with cell type annotations and enrichment analysis. SCassist provides intelligent assistance using popular LLMs like Googles Gemini, OpenAIs GPT and Metas Llama3, making scRNA-seq analysis accessible to researchers at all levels. Availability and implementationThe SCassist package, along with the detailed tutorials, is available at GitHub. https://github.com/NIH-NEI/SCassist

bioinformatics↗