Biology subjects

Cho, W.

Publications and source records attributed to Cho, W..

At least 19 recordsLinked to original sources

bioRxiv2026

Haplotype-resolved genetic mapping using selfed progeny enables simultaneous genome assembly validation and trait dissection in a heterozygous plant

Genetic linkage maps are essential for genome analysis and molecular breeding, but developing suitable mapping populations remains challenging in many plant species. Approaches requiring inbred parental lines are particularly difficult to implement in plants with long generation times or severe inbreeding depression. We developed haplotype-resolved genetic mapping (HRGM) to construct linkage maps from a single heterozygous individual and its selfed progeny without requiring inbred parental lines. HRGM combines haplotype-resolved unitig assemblies from the S0 parent with genotype data from its S1 progeny, using sequence differences between the two haplotypes to define phased SNP markers. Application to Cynanchum wilfordii generated a high-density genetic map comprising 8,147 SNP markers consolidated into 464 bins across 11 linkage groups, spanning 786.4 cM. The map enabled the detection of two loci associated with root development. Recombination patterns derived from the S1 population showed strong concordance with the chromosome-scale genome assembly and exhibited recombination suppression in putative centromeric regions. HRGM integrates recombination-based genome assembly validation and trait mapping within a single framework. By using one generation of selfed progeny and obtaining linkage-phase information directly from phased assemblies, it simplifies mapping population development and extends the utility of genomic resources for genetic analysis and molecular breeding, particularly in species where selfed progeny can be obtained but conventional mapping populations are difficult to establish.

genomics↗

bioRxiv2026

Reelin coordinates neuronal positioning and Müller glia scaffold maturation during retinal development

Reelin is a secreted extracellular matrix protein that regulates neuronal migration and layer formation in the developing brain, yet its role in retinal development remains incompletely defined. Here, we investigated Reelin function in retinal lamination using wild-type and Reeler (Reln-/-) mice, combining stage-resolved RNA in situ hybridization, immunohistochemistry, and single-nucleus RNA sequencing. We show that Reln is dynamically expressed in ganglion cell layer and inner nuclear layer neurons during retinal development and persists in discrete adult neuronal populations. Loss of Reelin leads to widespread defects in retinal organization affecting both neurons and Muller glia. In Reln-/- retinas, Muller glia exhibit reduced Glul positive extensions, indicating impaired glial scaffold maturation. Early-born neuronal populations are also disrupted, with altered spatial organization markers associated with retinal ganglion cell differentiation within the ganglion cell layer at postnatal day 9. Horizontal cells are significantly reduced with dorsal-predominant vulnerability, while cone photoreceptors are generated in normal numbers but show incomplete positioning within the outer nuclear layer. Together, these findings identify Reelin as a key regulator of retinal lamination that coordinates neuronal positioning with Muller glia morphogenesis, extending its canonical role in brain development to the vertebrate retina.

developmental biology↗

bioRxiv2026

Stress granule fusion is a mitochondria-coordinated process for stress adaptation

Stress granules are cytoplasmic membraneless organelles assembled during stress to maintain cellular homeostasis. Although fusion is a hallmark of liquid-like behavior of these condensates, whether this process carries functional significance beyond its physical coalescence remains unclear. Here, we show that stress granule fusion is facilitated by mitochondrial dynamics and membrane potential. Intact mitochondria actively associate with stress granules, facilitating fusion and maturation. In contrast, loss of mitochondrial membrane potential, along with disrupted mitochondrial structure or motility, weakens these interactions and reduces fusion frequency. We find that impaired fusion leads to the accumulation of immature granules that retain fewer sequestered components, which correlates with premature cell death. Remarkably, restoring mitochondrial membrane potential rescues granule fusion and enlargement, and is accompanied by increased cell viability and a corresponding increase in granule-associated apoptotic factors. These results demonstrate that stress granule fusion is actively coordinated by mitochondria rather than driven solely by passive coalescence, reshaping how condensate dynamics are understood to integrate with organelle function during cellular stress response.

cell biology↗

bioRxiv2026

Site-specific cholesterol depletion therapy for gastric cancer

Altered cholesterol metabolism is a recognized hallmark of cancer, but systemic modulation has not yet delivered significant clinical results. Accumulating evidence shows that cholesterol plays distinct roles across diverse cellular membranes, suggesting that site-specific modulation may produce superior therapeutic outcomes. Cholesterol is associated with gastric cancer (GC), but the mechanistic link is complex and no effective cholesterol-targeted therapy has been developed. Here, we report that cholesterol levels in GC cells are site-specifically elevated in the inner leaflet of the plasma membrane (IPM). This elevated IPM cholesterol constitutively activates Wnt-{beta}-catenin signaling to drive cell survival and proliferation. Mechanistically, Niemann-Pick C1-like 1 (NPC1L1), which is highly expressed in GC patient tissues and cell lines, acts as a cholesterol flippase to raise IPM cholesterol levels, facilitating ligand-independent {beta}-catenin signalosome formation. Ezetimibe, a clinically approved NPC1L1 inhibitor, blocks this flippase activity, lowers IPM cholesterol levels, and suppresses {beta}-catenin signaling. Ezetimibe treatment induces apoptosis in GC cells while sparing normal primary gastric epithelial cells, which exhibit low levels of NPC1L1 and IPM cholesterol. Collectively, these results suggest that site-specific modulation of cellular cholesterol is a viable approach to developing safe and effective therapies for cancers linked to local cholesterol elevation.

biochemistry↗

bioRxiv2026

Programmable synthetic cytokine receptors polarize macrophages to user-defined functional states

Technology that precisely controls macrophage polarization to distinct functional states would deepen our understanding of macrophage biology and enable the development of new macrophage cell therapies. Here, we use a synthetic cytokine receptor (SCR) platform with a programmable signaling domain to control the polarization of primary human macrophages. SCRs containing signaling motifs from the interferon-gamma (IFN-{gamma}) or Interleukin-10 (IL-10) receptors mimic key features of pro-inflammatory or anti-inflammatory polarization, respectively. Random recombination of nine distinct signaling motifs to create new SCR signaling domains generates a diverse landscape of synthetic macrophage states with varied expression of inflammatory markers (CD80, CD40) and anti-inflammatory markers (CD163, CD206), and varied phagocytic capacity. SCRs programmed with multiple YLxQ motifs increase macrophage phagocytosis of E. coli and chimeric antigen receptor (CAR)-macrophage phagocytosis of cancer cells in mice, reducing tumor burden by 30-fold. The motif-dependent polarization is well-described by a two-state model, enabling quantitative prediction of macrophage polarization state from SCR signaling domain composition. Leveraging this model, we design an SCR that simultaneously enhances phagocytosis and maintains a macrophage pro-inflammatory state. Together, these findings establish a framework for synthetic programming of macrophage polarization states, with potential applications in cancer immunotherapy and other disease contexts.

synthetic biology↗

bioRxiv2026

Whole-brain protein profiling using organ-scale multiplexed immunolabeling and image co-registration

Proteins are major drivers of biological functions. Single-cell, organ-scale multiplexed protein imaging can reveal high-dimensional molecular and structural features of individual cells and their interactions, enabling an in-depth understanding of complex biological systems. However, achieving such imaging has remained elusive due to hurdles in multiplexed immunolabeling (mIF) of intact organs and integrative image analysis. Here, we present 3D CYCLIC, an organ-scale multiplexed immunolabeling technique, and TACTIC, a single-cell-level, organ-scale image co-registration algorithm. 3D CYCLIC combines ultrafast, versatile 3D immunolabeling with a cleavable crosslinker that preserves signals by protecting bound antibodies during optical clearing while enabling their detachment for subsequent rounds of immunolabeling. TACTIC uses deep warping networks coupled with a propagation-based cell-pair search to co-register individual cells across whole-brain images acquired from multiple rounds of 3D CYCLIC labeling. 3D CYCLIC enabled 6-plex protein profiling of a mouse brain hemisphere, with images that can be combined with TACTIC for integrative analysis. 3D CYCLIC and TACTIC are versatile techniques and will therefore enable a holistic, unbiased understanding of diverse organs.

neuroscience↗

bioRxiv2025

A continuous landscape of signaling encodes a corresponding landscape of CAR T cell phenotype

Cytokine signaling is critical to the function of natural immune cells and engineered immune cell therapies such as chimeric antigen receptor (CAR) T cells. It remains unclear how the limited set of signal transducers and activators of transcription (STATs) and other proteins activated by these cytokine receptors can encode the observed diversity of immune cell phenotypes. To understand how signaling downstream of cytokines control immune cell phenotype, we sought to map the structure of Janus kinase (JAK)/STAT signaling domains to cell signaling and resulting CAR T cell function. We recombined 14 signaling motifs to construct a library of [~]30,000 constitutively active synthetic cytokine receptors (SCRs) with intracellular domains composed of novel signaling motif combinations that activate different signaling cascades. We experimentally tested [~]450 SCRs which generated a range of CAR T cell memory, cytotoxicity, and proliferation. SCRs with pSTAT1 and 3 signaling generated effector memory CAR T cells, while SCRs with strong pSTAT5 generated effector CAR T cells with potent anti-tumor activity. To map the structure-signaling-phenotype landscape we trained models to predict signaling and CAR T cell phenotype that result from varied motif combinations. From neural network predictions we identified features, including strong STAT5 and Shc signaling, that promote unsafe autonomous CAR T cell proliferation. Models also revealed a trade-off between memory and cytotoxicity, with a Pareto front encoded by a continuous change in signaling. These results demonstrate that recombination of a limited set of signaling motifs creates a continuous spectrum of signaling that encodes a corresponding spectrum of cell phenotype. This work synthetically expands the combinatorial space of JAK/STAT signaling and provides a foundation for rational design of CAR T cells with improved cytotoxicity, memory, and safety profiles. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/658149v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@cc1498org.highwire.dtl.DTLVardef@5c2864org.highwire.dtl.DTLVardef@5fc8b3org.highwire.dtl.DTLVardef@719f8f_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

The visual system of the longest-living vertebrate, the Greenland shark

The Greenland shark (Somniosus microcephalus) is the longest-living vertebrate and inhabits the extremely dim and cold waters of the Arctic deep sea. This has led to speculations that it may have lost functional vision. Here, we present genomic, transcriptomic, histological and functional evidence that the Greenland shark retains an intact visual system well-adapted for life in dim light. Histology and in vitro opsin expression revealed visual adaptations typical of deep-sea species, including densely packed, elongated rods and a short-wavelength shift in rod visual pigment sensitivity. RNAscope confirmed the presence of essential visual cell types, such as rods, Muller glia, and bipolar, amacrine, and ganglion cells. Moreover, despite being centuries old, the examined specimens showed no signs of retinal degeneration. Using whole genome and retinal RNA-sequencing, we further show that dim-light (rod-based) vision genes are intact and robustly expressed, while many bright-light (cone-based) vision genes have become pseudogenized and/or are no longer expressed. Finally, our data suggest that efficient DNA repair mechanisms may contribute to the long-term preservation of retinal function over centuries in the Greenland shark.

evolutionary biology↗

bioRxiv2025

Combining model-based and data-driven models: an application to synthetic biology resource competition

This work explores the integration of machine learning (ML) and mechanistic models (MM). While ML has demonstrated remarkable success in data-driven modeling across engineering, biology, and other scientific fields, MM remain essential for their interpretability and capacity to extrapolate beyond observed conditions based on established principles such as chemical kinetics and physiological processes. However, MM can be labor-intensive to construct and often rely on simplifying assumptions that may not fully capture real-world complexity. It is thus desirable to combine MM and ML approaches so as to enable more robust predictions, enhanced system insights, and improved handling of sparse or noisy data. A key challenge when doing so is ensuring that ML components do not disregard mechanistic information, potentially leading to overfitting or reduced interpretability. To address that challenge, this paper introduces the idea of Partially Uncertain Model Structures (PUMS) and investigates conditions that discourage the ML components from ignoring mechanistic constraints. This work also introduces the concept of embedded Physics-Informed Neural Networks (ePINNs), which consist of two loss-sharing neural networks that seamlessly blend ML and MM components. This work arose in the study of the context problem in synthetic biology. Engineered genetic circuits may exhibit unexpected behavior in living cells due to resource sharing. To illustrate the advantages of the ePINNs approach, this paper applies the framework to a gene network model subject to resource competition, demonstrating the effectiveness of this hybrid modeling approach in capturing complex system interactions while maintaining physical consistency.

systems biology↗

bioRxiv2025

Cholesterol efflux protein, ABCA1, supports anti-cancer functions of myeloid immune cells

Although immune therapy has seen significant advances, the majority of breast and other solid tumors do not respond or quickly develop de novo resistance. One factor driving resistance is highly immune suppressive myeloid cells (MCs) such as macrophages. Previous work has established clinical links between cholesterol and cancer outcome, and that MC function can be regulated through disruption in cholesterol metabolism. Thus, we screened for proteins that were expressed in MCs, involved in cholesterol homeostasis and whose expression was associated with survival; we identify the cholesterol efflux protein ABCA1. Preclinical studies revealed that ABCA1 activity resulted in increased anti-cancer functions of macrophages: enhanced tumor infiltration, decreased angiogenic potential, reduced efferocytosis, and improved support of CD8+ T cell activity. Mechanistically, different AKT isoforms are involved, through both PI3K dependent and independent mechanisms. Assessment of human blood and breast tumors revealed correlations between ABCA1 in macrophages and angiogenic potential, VEGFA, and CD8 T cell abundance and activity, highlighting the clinical relevance of our findings. The culmination of the effects of ABCA1 on MC function were demonstrated through increased tumor growth and metastasis in mice with MC specific knockout of ABCA1. Therefore, modulating ABCA1 activity within MCs may represent a novel approach to immune therapy.

cancer biology↗

bioRxiv2025

Noncanonical PI(4,5)P2 coordinates lysosome positioning through cholesterol trafficking

In p53-deficient cancers, targeting cholesterol metabolism has emerged as a promising therapeutic approach, given that p53 loss dysregulates sterol regulatory element-binding protein 2 (SREBP-2) pathways, thereby enhancing cholesterol biosynthesis. While cholesterol synthesis inhibitors such as statins have shown initial success, their efficacy is often compromised by the development of acquired resistance. Consequently, new strategies are being explored to disrupt cholesterol homeostasis more comprehensively by inhibiting its synthesis and intracellular transport. In this study, we investigate a previously underexplored function of PI5P4Ks, which catalyzes the conversion of PI(5)P to PI(4,5)P2 at intracellular membranes. Our findings reveal that PI5P4Ks play a key role in facilitating lysosomal cholesterol transport, regulating lysosome positioning, and sustaining growth signaling via the mTOR pathway. While PI5P4Ks have previously been implicated in mTOR signaling and tumor proliferation in p53-deficient contexts, this work elucidates an upstream mechanism that unifies these earlier observations.

cell biology↗

bioRxiv2024

Ocular hypertension impairs axonal transport in the optic nerve head leading to neurodegeneration in a novel Cre-inducible mouse model of myocilin glaucoma.

Elevation of intraocular pressure (IOP) due to trabecular meshwork (TM) dysfunction, leading to neurodegeneration, is the pathological hallmark of primary open-angle glaucoma (POAG). Impaired axonal transport is an early and critical feature of glaucomatous neurodegeneration. However, a robust mouse model that replicates these human POAG features accurately has been lacking. We report the development and characterization of a novel Cre-inducible mouse model expressing a DsRed-tagged Y437H mutant of human myocilin (Tg.CreMYOCY437H). A single intravitreal injection of HAd5-Cre induced selective MYOC expression in the TM, causing TM dysfunction, reducing outflow facility, and progressively elevating IOP in Tg.CreMYOCY437H mice. Sustained IOP elevation resulted in significant retinal ganglion cell (RGC) loss and progressive axonal degeneration in Cre-induced Tg.CreMYOCY437H mice. Notably, impaired anterograde axonal transport was observed at the optic nerve head before RGC degeneration, independent of age, indicating that impaired axonal transport contributes to RGC degeneration in Tg.CreMYOCY437H mice. In contrast, axonal transport remained intact in ocular hypertensive mice injected with microbeads, despite significant RGC loss. Our findings indicate that Cre-inducible Tg.CreMYOCY437Hmice replicate all glaucoma phenotypes, providing an ideal model for studying early events of TM dysfunction and neuronal loss in POAG.

neuroscience↗

bioRxiv2024

Polyunsaturated Fatty Acid - mediated Cellular Rejuvenation for Reversing Age-related Vision Decline

The retina is uniquely enriched in polyunsaturated fatty acids (PUFAs), which are primarily localized in cell membranes, where they govern membrane biophysical properties such as diffusion, permeability, domain formation, and curvature generation. During aging, alterations in lipid metabolism lead to reduced content of very long-chain PUFAs (VLC-PUFAs) in the retina, and this decline is associated with normal age-related visual decline and pathological age-related macular degeneration (AMD). ELOVL2 (Elongation of very-long-chain fatty acids-like 2) encodes a transmembrane protein that produces precursors to docosahexaenoic acid (DHA) and VLC-PUFAs, and methylation level of its promoter is currently the best predictor of chronological age. Here, we show that mice lacking ELOVL2-specific enzymatic activity (Elovl2C234W) have impaired contrast sensitivity and slower rod response recovery following bright light exposure. Intravitreal supplementation with the direct product of ELOVL2, 24:5n-3, in aged animals significantly improved visual function and reduced accumulation of ApoE, HTRA1 and complement proteins in sub-RPE deposits. At the molecular level, the gene expression pattern observed in retinas supplemented with 24:5n-3 exhibited a partial rejuvenation profile, including decreased expression of aging-related genes and a transcriptomic signature of younger retina. Finally, we present the first human genetic data showing significant association of several variants in the human ELOVL2 locus with the onset of intermediate AMD, underlying the translational significance of our findings. In sum, our study identifies novel therapeutic opportunities and defines ELOVL2 as a promising target for interventions aimed at preventing age-related vision loss.

molecular biology↗

bioRxiv2023

PI(3,5)P2 Controls the Signaling Activity of Class I PI3K

3-Phosphoinositides are ubiquitous cellular lipids that play pivotal regulatory roles in health and disease. Among 3-phosphoinositides, phosphatidylinositol-3,5-bisphosphate (PI(3,5)P2) remains the least understood species in terms of its spatiotemporal dynamics and physiological function due to the lack of a specific sensor that allows spatiotemporally resolved quantitative imaging of PI(3,5)P2. Using a newly developed ratiometric PI(3,5)P2 sensor engineered from the C-terminal SH2 domain of Class I phosphoinositide 3-kinases (PI3K)-p85 subunit we demonstrate that a unique pool of PI(3,5)P2 is generated on lysosomes and late endosomes in response to growth factor stimulation. This PI(3,5)P2, the formation of which is mediated sequentially by Class II PI3KC2{beta} and PIKfyve, plays a crucial role in terminating the activity of growth factor-stimulated Class I PI3K, one of the most frequently mutated proteins in cancer, via specific interaction with its regulatory p85 subunit. A small molecule inhibitor of p85-PI(3,5)P2 binding specifically blocks the feedback inhibition of Class I PI3K by PI(3,5)P2 and thus serves as a PI3K activator that promotes neurite growth. Furthermore, cancer-causing mutations of the Class I PI3K-p85 subunit inhibit p85-PI(3,5)P2 interaction and thereby induce sustained activation of Class I PI3K. Our results unravel a hitherto unknown spatiotemporally specific regulatory function of PI(3,5)P2 that links Class I and II PI3Ks and modulates the magnitude of PI3K-mediated growth factor signaling. These results also suggest new therapeutic possibilities for treating cancer patients with p85 mutations and promoting wound healing and tissue regeneration.

biochemistry↗

bioRxiv2022

Noncovalent antibody catenation on a target surface drastically increases the antigen-binding avidity

Immunoglobulin G (IgG) antibodies are widely used for diagnosis and therapy. Given the unique dimeric structure of IgG, we hypothesized that, by genetically fusing a homodimeric protein (catenator) to the C-terminus of IgG, reversible catenation of antibody molecules could be induced on a surface where target antigen molecules are abundant, and that it could be an effective way to greatly enhance the antigen-binding avidity. A thermodynamic simulation shows that quite low homodimerization affinity of a catenator, e.g. dissociation constant of 100 M, can enhance nanomolar antigen-binding avidity to a picomolar level, and that the fold enhancement sharply depends on the density of the antigen. In a proof-of-concept experiment where antigen molecules are immobilized on a biosensor tip, C-terminal fusion of a weakly homodimerizing protein to two different antibodies enhanced the antigen-binding avidity by at least 210 to 5,120 folds from the intrinsic binding avidity. Thus, the homodimerization-induced antibody catenation would be a simple, powerful and general approach to improve many antibody applications, including the detection of scarce biomarkers and targeted anticancer therapies.

biophysics↗

bioRxiv2022

Accelerated aging induced by stress in experimental murine ocular hypertension.

Aging, a universal process that affects all cells in an organism, is a major risk factor for a group of neuropathies called glaucoma, where elevated intraocular pressure is one of the known stresses affecting the tissue. Our understanding of molecular impact of aging on response to stress in retina is very limited, therefore we developed a new mouse model to approach this question experimentally. Here we show that susceptibility to response to stress increases with age and is primed on epigenetic level. We demonstrate that program activated by hypertension is similar to natural aging, and that one of the earliest pathways activated upon stress is senescence. Finally, we show that multiple instances of pressure elevation cause accelerated aging of young retina as measured on transcriptional and epigenetic level. Our work emphasizes the importance of early diagnosis and prevention as well as age-specific management of age-related eye-diseases, including glaucoma.

molecular biology↗

bioRxiv2020

Ultra-Fast Homomorphic Encryption Models enable Secure Outsourcing of Genotype Imputation

ABSTRACTGenotype imputation is a fundamental step in genomic data analysis such as GWAS, where missing variant genotypes are predicted using the existing genotypes of nearby ‘tag’ variants. Imputation greatly decreases the genotyping cost and provides high-quality estimates of common variant genotypes. As population panels increase, e.g., the TOPMED Project, genotype imputation is becoming more accurate, but it requires high computational power. Although researchers can outsource genotype imputation, privacy concerns may prohibit genetic data sharing with an untrusted imputation service. To address this problem, we developed the first fully secure genotype imputation by utilizing ultra-fast homomorphic encryption (HE) techniques that can evaluate millions of imputation models in seconds. In HE-based methods, the genotype data is end-to-end encrypted, i.e., encrypted in transit, at rest, and, most importantly, in analysis, and can be decrypted only by the data owner. We compared secure imputation with three other state-of-the-art non-secure methods under different settings. We found that HE-based methods provide full genetic data security with comparable or slightly lower accuracy. In addition, HE-based methods have time and memory requirements that are comparable and even lower than the non-secure methods. We provide five different implementations and workflows that make use of three cutting-edge HE schemes (BFV, CKKS, TFHE) developed by the top contestants of the iDASH19 Genome Privacy Challenge. Our results provide strong evidence that HE-based methods can practically perform resource-intensive computations for high throughput genetic data analysis. In addition, the publicly available codebases provide a reference for the development of secure genomic data analysis methods.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗

bioRxiv2019

Hedgehog pathway activation through conformational blockade of the Patched sterol conduit

Activation of the Hedgehog pathway may have therapeutic value for improved bone healing, taste receptor cell regeneration, and alleviation of colitis or other conditions. Systemic pathway activation, however, may be detrimental and therapeutic application has been difficult for lack of agents amenable to tissue targeting. We have developed a novel agonist, a conformation-specific nanobody against the Hedgehog receptor Patched1. This nanobody potently activates the Hedgehog pathway in vitro and in vivo by stabilizing an alternative conformation of a Patched1 \"switch helix\", as revealed by cryo-EM structure determination. Although this conformation likely constitutes part of the transport cycle, nanobody-trapping disrupts the cycle and prevents substrate movement through the Patched1 sterol conduit. Our conformation-selective nanobody approach provides a new route to the development of transporter-related pharmacologic agents and may be generally applicable to the study of other transporters.

biophysics↗