Biology subjects

Cho, B.

Publications and source records attributed to Cho, B..

17 recordsLinked to original sources

bioRxiv2026

The Oral Microbiome Is a Population-Scale Readout of the Exposome, Age, and Systemic Health

The oral microbiome interfaces humans and the environment and is implicated in diseases from caries to cardiovascular conditions. Yet, few studies systematically interrogate oral taxa associations with the host phenome and exposome in diverse populations. We developed a comprehensive oral microbiome atlas, deploying a Microbiome Association Study (MAS) evaluating relationships between host features including exposome, disease, and physiology and the microbiome in a 10,000-person representative US population. Evaluating demographics, 133 phenotypes, 473 exposures, and 20 disease outcomes across 1,349 taxa yielded >800k relationships and 45,757 FDR-significant associations. Age emerged as a major organizing axis, with genera following non-linear life-course patterns. Oral disease, smoking, and dietary sugar correlated with aciduric and anaerobic taxa, whereas oral health featured oxygen-tolerant Proteobacteria. The exposome and cardiovascular/respiratory disease linked to diverse taxa. These results establish the oral microbiome as a sensitive, population-scale indicator of the exposome, phenome, and systemic health.

microbiology↗

bioRxiv2026

PersonaAI: An Interactive Agentic-AI Framework for Autonomous Hypothesis Generation and Validation in Aging

Elucidating the mechanisms of aging is impeded by its stochastic, multi-scale nature and cellular heterogeneity, challenges that are compounded by the overwhelming volume of biomedical literature and the complexity of genome-wide datasets. To overcome these barriers, we present PersonaAI, an interactive agentic-AI framework that acts as a digital co-scientist. By integrating literature-based reasoning with autonomous in silico validation, PersonaAI synthesizes over 560,000 aging-related publications via retrieval-augmented generation (RAG) to propose mechanistic hypotheses. These hypotheses are subsequently validated by autonomous agents utilizing single-cell RNA-seq data. Using a temporal cutoff strategy restricted to pre-2020 literature, we demonstrate that PersonaAI can generate hypotheses effectively validated by post-2021 discoveries, proving its capacity for inference beyond simple information retrieval. In application, the system identified senescent Cirbp+ hepatocytes as a liver-intrinsic aging program and uncovered a middle-aged, male-specific decline in adipose stem and progenitor cells, driven by vascular niche deterioration and disrupted VEGF-VEGFR signaling. These results establish PersonaAI as a scalable platform that augments human intuition with autonomous data-driven validation, providing a generalizable platform for accelerating discovery in aging biology.

bioinformatics↗

bioRxiv2025

Preference-Based Fine-Tuning of Genomic Sequence Models for Personal Expression Prediction with Data Augmentation

Despite substantial progress in genomic foundation models, accurately predicting inter-individual variation in gene expression from DNA sequence alone remains a major challenge. Current sequence-based models, such as Enformer and Borzoi, trained exclusively on the reference genome, cannot capture the effects of individual-specific regulatory variants. Moreover, the acquisition of paired whole-genome and transcriptome data required for personalized modeling is hindered by privacy and data-sharing constraints. To address this limitation, we integrate genomic data synthesis with established statistical frameworks. Our approach generates thousands of synthetic training samples by simulating genetic variation from the 1000 Genomes Project and assigning pseudo-expression labels using PrediXcan, a validated eQTL-based predictor. Because simulated and real expression values differ in scale and distribution, we introduce a preference-based objective that models relative rather than absolute expression patterns. Fine-tuning Enformer through alternating cycles of real-data regression and synthetic-data preference optimization enables efficient learning from both real and synthesized data. Using the GEUVADIS dataset, our framework outperforms AlphaGenome, PrediXcan, and Enformer fine-tuned without synthesized data, demonstrating that simulation-based integration of population-level regulatory knowledge can effectively mitigate data scarcity and improve cross-individual generalization in sequence-based gene expression prediction. Availability and implementationCode and data are available at https://github.com/pacifiic/augment-finetune-genomics.

bioinformatics↗

bioRxiv2025

Sleep-dependent clearance of brain lipids by peripheral blood cells

Sleep is typically viewed through a brain-centric lens, with little known about the role of the periphery. Here, we identify a sleep function for peripheral macrophage-like cells (hemocytes) in the Drosophila circulation, showing that hemocytes track to the brain during sleep and take up lipids accumulated in cortex glia due to wake-associated oxidative damage. Through a screen of phagocytic receptors expressed in hemocytes, we discovered that knockdown of eater, a member of the Nimrod receptor family, reduces sleep. Loss of eater also disrupts hemocyte adhesion to the brain and lipid uptake, which results in increased brain levels of Acetyl CoA and acetylated proteins, including mitochondrial proteins PGC1 and DRP1. Dysregulation of mitochondria, reflected in high oxidation and reduced NAD+, is accompanied by impaired memory and lifespan. Thus, peripheral blood cells, which we suggest are precursors of mammalian microglia, perform a daily function of sleep to maintain brain function and fitness.

molecular biology↗

bioRxiv2025

Nodal/Smad2 signaling sustains developmental pausing by repressing Pparg-mediated lipid metabolism

Cells and organisms can enter transient dormant states to survive unfavorable conditions during development, physiological adult contexts, and disease. One paradigmatic case of dormancy is diapause, whereby embryos transiently pause development and enter a state of suspended animation. In mammals, diapause occurs pre-implantation at the blastocyst state and involves global growth suppression and metabolic rewiring towards lipid usage as energy source. The molecular regulation of diapause remains poorly understood, including whether it occurs by default or requires active signaling. Here, we identify the Transforming Growth Factor-beta (TGF-{beta}) signaling pathway as an essential driver of transcriptional and metabolic reprogramming in diapause. TGF-{beta} signaling was thought to only be required post-implantation, but we show that the ligand Nodal and its downstream effector Smad2 are essential for the survival of paused embryonic stem cells (ESCs) and blastocysts. Mechanistically, we found that Smad2 represses peroxisome-proliferator activated receptor gamma (Pparg), a transcription factor that is a master regulator of lipid storage, a process incompatible with pausing. Ablation of Pparg in Smad2-deficient ESCs rescues their survival and prevents excess lipid buildup in paused conditions. Our findings establish Nodal/Smad2 signaling as pivotal for sustaining the transcriptional and metabolic programs of embryonic diapause. This crosstalk between TGF-{beta} signaling and the Pparg pathway may be redeployed in other contexts, such as in cancer dormancy and metabolic disorders.

developmental biology↗

bioRxiv2025

Selection of nanobodies against liponanoparticle-embedded membrane proteins by yeast surface display

Single-domain antibodies, known as nanobodies (Nbs), are widely used in structural biology, therapeutics, and as molecular probes in biology and biotechnology. Nbs towards soluble proteins are routinely developed via alpaca immunization or directed evolution in yeast cell-surface display. However, for membrane proteins, the targets are generally detergent-solubilized, and there remains a need for Nb development methods against membrane proteins in a native-like membrane environment. To address this need, we present a protocol for Nb selection via extraction of membrane proteins into amphiphilic polymers such as styrene-maleic acid to produce purified membrane proteins in stable liponanoparticles. Proof of generality is demonstrated by applying the pipeline to four membrane-resident enzymes of differing fold, oligomerization state, and membrane topology (reentrant membrane helix, transmembrane, membrane-associated). Following screening for optimal stabilization into liponanoparticles, Nbs were selected against four target proteins from glycoconjugate biosynthesis pathways. The selected Nbs showed high affinity and selectivity towards their target proteins with KD apparent values ranging from 15 nM to 200 nM, depending on the Nb-protein conjugate. In accordance with their tight binding, various Nb-protein complexes were found to be stable to size-exclusion chromatography purification. The Nbs were also amenable to sortase-mediated ligation, enabling their conversion into molecular probes for the target membrane protein. The ability to select for such high-affinity Nb against membrane proteins in SMALP will facilitate their widespread application in cell biology and biomedical applications.

biochemistry↗

bioRxiv2023

Cell autonomous polarization by the planar cell polarity signaling pathway

As epithelial cells polarize in the tissue plane, the Planar Cell Polarity (PCP) signaling module segregates two distinct molecular subcomplexes to opposite sides of cells. Homodimers of the atypical cadherin Flamingo form bridges linking opposite complexes in neighboring cells, coordinating their direction of polarization. Feedback is required for cell polarization, but whether feedback requires intercellular and/or intracellular pathways is unknown. Using novel tools, we show that cells lacking Flamingo, or bearing a homodimerization-deficient Flamingo, polarize autonomously, indicating that functional PCP subcomplexes form and segregate cell-autonomously. Furthermore, we identify feedback pathways and propose an asymmetry amplifying mechanism that operate cell-autonomously. The intrinsic logic of PCP signaling is therefore more similar to that in single cell systems than was previously recognized.

developmental biology↗

bioRxiv2023

Flamingo participates in multiple models of cell competition

The growth and survival of cells with different fitness, such as those with a proliferative advantage or a deleterious mutation, is controlled through cell competition. During development, cell competition enables healthy cells to eliminate less fit cells that could jeopardize tissue integrity, and facilitates the elimination of pre-malignant cells by healthy cells as a surveillance mechanism to prevent oncogenesis. Malignant cells also benefit from cell competition to promote their expansion. Despite its ubiquitous presence, the mechanisms governing cell competition, particularly those common to developmental competition and tumorigenesis, are poorly understood. Here, we show that in Drosophila, the planar cell polarity (PCP) protein Flamingo (Fmi) is required by winners to maintain their status during cell competition in malignant tumors to overtake healthy tissue, in early pre-malignant cells when they overproliferate among wildtype cells, in healthy cells when they later eliminate pre-malignant cells, and by supercompetitors as they compete to occupy excessive territory within wildtype tissues. "Would-be" winners that lack Fmi are unable to over-proliferate, and instead become losers. We demonstrate that the role of Fmi in cell competition is independent of PCP, and that it uses a distinct mechanism that may more closely resemble one used in other less well-defined functions of Fmi.

developmental biology↗

bioRxiv2023

Protein phosphatase 1 regulates core PCP signaling

AbstractPCP signaling polarizes epithelial cells within the plane of an epithelium. Core PCP signaling components adopt asymmetric subcellular localizations within cells to both polarize and coordinate polarity between cells. Achieving subcellular asymmetry requires additional effectors, including some mediating post-translational modifications of core components. Identification of such proteins is challenging due to pleiotropy. We used mass spectrometry-based proximity labeling proteomics to identify such regulators in the Drosophila wing. We identified the catalytic subunit of Protein Phosphatase1, Pp1-87B, and show that it regulates core protein polarization. Pp1-87B interacts with the core protein Van Gogh and at least one Serine/Threonine kinase, Dco/CKIc, that is known to regulate PCP. Pp1-87B modulates Van Gogh subcellular localization and directs its dephosphorylation in vivo. PNUTS, a Pp1 regulatory subunit, also modulates PCP. While the direct substrate(s) of Pp1-87B in control of PCP is not known, our data support the model that cycling between phosphorylated and unphosphorylated forms of one or more core PCP components may regulate acquisition of asymmetry. Finally, our screen serves as a resource for identifying additional regulators of PCP signaling.

developmental biology↗

bioRxiv2023

An ACE2 decamer viral trap as a durable intervention solution for current and future SARS-CoV

The capacity of SARS-CoV-2 to evolve poses challenges to conventional prevention and treatment options such as vaccination and monoclonal antibodies, as they rely on viral receptor binding domain (RBD) sequences from previous strains. Additionally, animal CoVs, especially those of the SARS family, are now appreciated as a constant pandemic threat. We present here a new antiviral approach featuring inhalation delivery of a recombinant viral trap composed of ten copies of angiotensin-converting enzyme 2 (ACE2) fused to the IgM Fc. This ACE2 decamer viral trap is designed to inhibit SARS-CoV-2 entry function, regardless of viral RBD sequence variations as shown by its high neutralization potency against all known SARS-CoV-2 variants, including Omicron BQ.1, BQ.1.1, XBB.1 and XBB.1.5. In addition, it demonstrates potency against SARS-CoV-1, human NL63, as well as bat and pangolin CoVs. The multivalent trap is effective in both prophylactic and therapeutic settings since a single intranasal dosing confers protection in human ACE2 transgenic mice against viral challenges. Lastly, this molecule is stable at ambient temperature for more than twelve weeks and can sustain physical stress from aerosolization. These results demonstrate the potential of a decameric ACE2 viral trap as an inhalation solution for ACE2-dependent coronaviruses of current and future pandemic concerns.

microbiology↗

bioRxiv2023

S-nitrosylation-mediated unfolded protein response maintains hematopoietic progenitors

The Drosophila lymph gland houses blood progenitors that give rise to myeloid-like blood cells. Initially, blood progenitors proliferate, but later become quiescent to maintain multipotency before differentiation. Despite the identification of various factors involved in multipotency maintenance, the cellular mechanism regulating blood progenitor quiescence remains elusive. Here, we reveal the expression of nitric oxide synthase in blood progenitors, generating nitric oxide for post-translational S-nitrosylation of protein cysteine residues. S-nitrosylation activates the Ire1-Xbp1-mediated unfolded protein response, leading to G2 cell cycle arrest. Specifically, we identify the epidermal growth factor receptor as a target of S-nitrosylation, resulting in its retention within the endoplasmic reticulum and blockade of its receptor function. Collectively, our findings highlight developmentally programmed S-nitrosylation as a critical mechanism that induces protein quality control in blood progenitors, maintaining their undifferentiated state by inhibiting cell cycle progression and rendering them unresponsive to paracrine factors.

developmental biology↗

bioRxiv2023

m6A RNA methylation orchestrates transcriptional dormancy during developmental pausing

Embryos across metazoan lineages can enter reversible states of developmental pausing, or diapause, in response to adverse environmental conditions. The molecular mechanisms that underlie this remarkable dormant state remain largely unknown. Here we show that m6A RNA methylation by Mettl3 is required for developmental pausing in mice by maintaining dormancy of paused embryonic stem cells and blastocysts. Mettl3 enforces transcriptional dormancy via two interconnected mechanisms: i) it promotes global mRNA destabilization and ii) suppresses global nascent transcription by specifically destabilizing the mRNA of the transcriptional amplifier and oncogene N-Myc, which we identify as a critical anti-pausing factor. Our findings reveal Mettl3 as a key orchestrator of the crosstalk between transcriptomic and epitranscriptomic regulation during pausing, with implications for dormancy in stem cells and cancer.

developmental biology↗

bioRxiv2021

Direct acetylation of the conserved threonine of an immune regulator by bacterial effectors activates RPM1-dependent immunity in Arabidopsis

Plant pathogenic bacteria deliver effectors into plant cells to suppress immunity and promote pathogen survival (Buttner, 2016; Deslandes and Rivas, 2012); however, these effectors can be recognised by plant disease resistance (R) proteins to activate innate immunity (Jones and Dangl, 2006; Spoel and Dong, 2012). The bacterial acetyltransferase effectors HopZ5 and AvrBsT trigger immunity in Arabidopsis thaliana genotypes lacking SUPPRESSOR OF AVRBST-ELICITED RESISTANCE 1 (SOBER1) (Choi et al., 2018; Jayaraman et al., 2017). Using an Arabidopsis accession, Tscha-1, that naturally lacks functional SOBER1 but is unable to recognise HopZ5, we demonstrate that RESISTANCE TO P. SYRINGAE PV MACULICOLA 1 (RPM1) and RPM1-INTERACTING PROTEIN 4 (RIN4) are indispensable for HopZ5- or AvrBsT-triggered immunity. Remarkably, T166 of RIN4, the phosphorylation of which is induced by AvrB and AvrRpm1, was directly acetylated by HopZ5 and AvrBsT. Furthermore, we demonstrate that acetylation of RIN4 T166 is required and sufficient for activation of HopZ5- or AvrBsT-triggered defence. Finally, we show that SOBER1 interferes with HopZ5- or AvrBsT-triggered immunity by deacetylating RIN4 T166. Our findings indicate that multiple pathogen effectors with distinct biochemical properties modify a single residue in a guardee protein and activate a plant NLR immune receptor. We have thus elucidated detailed molecular mechanisms underlying the activation and suppression of plant innate immunity triggered by bacterial acetyltransferases.

plant biology↗

bioRxiv2020

Single-cell transcriptome maps of myeloid blood cell lineages in Drosophila

Drosophila lymph gland, the larval hematopoietic organ comprised of prohemocytes and hemocytes, has been a valuable model for understanding mechanisms underlying hematopoiesis and immunity. Three types of mature hemocytes have been characterized in the lymph gland: plasmatocytes, lamellocytes, and crystal cells, which are analogous to vertebrate myeloid cells. Here, we used single-cell RNA sequencing to comprehensively analyze heterogeneity of developing hemocytes in the lymph gland, and discovered novel hemocyte types, stem-like prohemocytes, and intermediate prohemocytes. Additionally, we identified the emergence of the lamellocyte lineage following active cellular immunity caused by wasp infestation. We unraveled similarities and differences between embryonically derived- and larval lymph gland hemocytes. Finally, the comparison of Drosophila lymph gland hemocytes and human immune cells highlights similarities between prohemocytes and hematopoietic stem cell, and between mature hemocytes and myeloid cells across species. Altogether, our study provides detailed insights on the development and evolution of hematopoiesis at single-cell resolution.

developmental biology↗

bioRxiv2019

A single-cell survey of Drosophila blood

Drosophila blood cells, called hemocytes, are classified into plasmatocytes, crystal cells, and lamellocytes based on the expression of a few marker genes and cell morphologies, which are inadequate to classify the complete hemocyte repertoire. Here, we used single-cell RNA sequencing (scRNA-seq) to map hemocytes across different inflammatory conditions in larvae. We resolved plasmatocytes into different states based on the expression of genes involved in cell cycle, antimicrobial response, and metabolism together with the identification of intermediate states. Further, we discovered rare subsets within crystal cells and lamellocytes that express fibroblast growth factor (FGF) ligand branchless and receptor breathless, respectively. We demonstrate that these FGF components are required for mediating effective immune responses against parasitoid wasp eggs, highlighting a novel role for FGF signaling in inter-hemocyte crosstalk. Our scRNA-seq analysis reveals the diversity of hemocytes and provides a rich resource of gene expression profiles for a systems-level understanding of their functions. HighlightsO_LIscRNA-seq of Drosophila blood recovers plasmatocytes, crystal cells, and lamellocytes C_LIO_LIscRNA-seq identifies different plasmatocyte states based on the expression of genes involved in cell cycle regulation, antimicrobial response, and metabolism C_LIO_LIPseudotemporal ordering of single cells identifies crystal cell and lamellocyte intermediate states C_LIO_LIscRNA-seq uncovers a novel role for FGF signaling in inter-hemocyte crosstalk C_LI

immunology↗

bioRxiv2019

Coessential Genetic Networks Reveal the Organization and Constituents of a Dynamic Cellular Stress Response

The interrelated programs essential for cellular fitness in the face of stress are critical to understanding tumorigenesis, neurodegeneration, and aging. However, modelling the combinatorial landscape of stresses experienced by diseased cells is challenging, leaving functional relationships within the global stress response network incompletely understood. Here, we leverage genome-scale fitness screening data from 625 cancer cell lines, each representing a unique biological context, to build a network of "coessential" gene relationships centered around master regulators of the response to proteotoxic, oxidative, hypoxic, and genotoxic stress. This approach organizes the stress response into functional modules, identifies genes connecting distinct modules, and reveals mechanisms underlying cellular dependence on individual modules. As an example of the power of this approach, we discover that the previously unannotated HAPSTR (C16orf72) promotes resilience to diverse stressors as a stress-inducible regulator of the E3 ligase HUWE1. Altogether, we present a broadly applicable framework and interactive tool (http://fireworks.mendillolab.org/) to interrogate biological networks using unbiased genetic screens.

genetics↗

bioRxiv2019

Whole-genome reference panel of 1,781 Northeast Asians improves imputation accuracy of rare and low-frequency variants

Genotype imputation using the reference panel is a cost-effective strategy to fill millions of missing genotypes for the purpose of various genetic analyses. Here, we present the Northeast Asian Reference Database (NARD), including whole-genome sequencing data of 1,781 individuals from Korea, Mongolia, Japan, China, and Hong Kong. NARD provides the genetic diversities of Korean (n=850) and Mongolian (n=386) ancestries that were not present in the 1000 Genomes Project Phase 3 (1KGP3). We combined and re-phased the genotypes from NARD and 1KGP3 to construct a union set of haplotypes. This approach established a robust imputation reference panel for the Northeast Asian populations, which yields the greatest imputation accuracy of rare and low-frequency variants compared with the existing panels. Also, we illustrate that NARD can potentially improve disease variant discovery by reducing pathogenic candidates. Overall, this study provides a decent reference panel for the genetic studies in Northeast Asia.

genomics↗