Biology subjects

Wang, J.-W.

Publications and source records attributed to Wang, J.-W..

15 recordsLinked to original sources

bioRxiv2026

AtlasMap: enabling low-cost, map-style exploration of million-cell single-cell atlases

Interactive visualization is critical for interpreting single-cell atlases, yet existing web-based tools struggle to handle the growing scale of multimillion-cell datasets, often constrained by browser memory limits and rendering latency. Here, we present AtlasMap, a scalable visualization framework that overcomes these bottlenecks through a multi-resolution, tile-based architecture. Unlike conventional systems that transfer cell-level data to the client, AtlasMap employs an offline preprocessing module to generate quadtree-based spatial aggregations stored in compressed Zarr v3 formats. A high-performance Go backend dynamically renders these summaries as PNG tiles, allowing a lightweight frontend to support fluid pan-and-zoom exploration similar to digital geographic maps. Systematic benchmarking against leading tools (including cellxgene and UCSC Cell Browser) demonstrates that AtlasMap decouples visualization performance from dataset size. While point-based approaches incurred prohibitive client-side memory costs or failed entirely at the 11-million-cell scale, AtlasMap maintained sub-second startup latency and a negligible browser footprint (<5 MB). By shifting computational pressure from the browser to an optimized server-side pipeline, AtlasMap enables accessible, high-fidelity exploration of ultra-scale single-cell datasets on standard hardware.

bioinformatics↗

bioRxiv2025

Preliminary Study on the Mechanisms of Cytokinin and Its Receptor Binding Diversity

Cytokinins are key regulators of plant growth and development, directly influencing crop yield. However, the quantitative basis of cytokinin receptor-ligand interactions remain poorly understood. This study aimed to quantitatively assess the binding affinities of cytokinin receptors various cytokinins, including 6-benzylaminopurine (6-BA), N6-isopentenyladenine (2iP), and trans-Zeatin (tZ) and explore cross-species conservation in cytokinin recognition. Microscale Thermophoresis (MST) assays revealed that 6-BA exhibits a higher binding affinity to the CHASE domain of the cytokinin receptor Arabidopsis HK4 (AHK4CD) compared to 2iP. Molecular docking and phylogenetic analyses further confirmed this finding and identified conserved key residues responsible for cytokinin binding across diverse plant species. Intriugingly, despite differences in pocket structure and binding energy, the cytokinin receptor in the bryophyte Marchantia polymorpha retains the capacity to bind cytokinins and respond to exogenous applications. Similarly, one cytokinin receptor in the monocots Oryza sativa exhibits distinct features in its cytokinin-binding pocket while still maintaining its ability to bind cytokinins. Our results thus provide fresh quantitative evidence for cytokinin receptor selectivity and highlight the structural plasticity of cytokinin perception, offering a foundation for designing optimized cytokinins or their receptors in crops.

molecular biology↗

bioRxiv2025

CAPTAIN: A multimodal foundation model pretrained on co-assayed single-cell RNA and protein

Proteins act as the terminal effectors of cellular function, encoding the phenotypic consequences of genomic and transcriptomic programs. Although transcriptomic profiles serve as accessible proxies, they remain incomplete surrogates for the proteomic landscape that ultimately defines cellular phenotypes. Current single-cell foundation models, however, are trained exclusively on transcriptomes, resulting in biased and partial characterizations of cellular states. To address this limitation, we introduce CAPTAIN, a multimodal foundational model pretrained on over four million single cells with concurrently measured transcriptomes and a curated repertoire of 382 surface proteins across diverse human and mouse tissues. Our results show that CAPTAIN learns unified multimodal representations by modeling cross-modality dependencies and capturing the diversity of cellular states across complex biological contexts. CAPTAIN generalizes robustly across both fine-tuning and zero-shot settings, excelling in core downstream tasks such as protein imputation and expansion, cell type annotation, and batch harmonization. Beyond improved accuracy in multi-omics integration, CAPTAIN uncovers previously inaccessible mechanisms of protein-driven intercellular dynamics, including immune interaction patterns linked to COVID-19 severity. CAPTAIN establishes a new paradigm for multimodal single-cell modeling, laying the foundation for comprehensive cellular understanding and virtual cell construction.

bioinformatics↗

bioRxiv2025

FX-Cell: a method for single-cell RNA sequencing on difficult-to-digest and cryopreserved plant samples

Single-cell RNA sequencing (scRNA-seq) in plants requires the isolation of high-quality protoplasts-- cells devoid of cell walls. However, many plant tissues and organs are resistant to enzymatic digestion, posing a significant barrier to advancing single-cell multi-omics research in plants. Furthermore, for many field-grown crops, the lack of immediate laboratory access presents another major challenge for protoplast preparation. To address these limitations, we developed the FX-Cell method and its derivatives, FXcryo-Cell and cryoFX-Cell, to enable scRNA-seq with both difficult-to-digest and cryopreserved plant samples. By optimizing the fixation buffer and minimizing RNA degradation, our approach ensures efficient cell wall digestion at high temperatures while maintaining high-quality single cells, even after long-term storage at -80{degrees}C, and circumvents use of nuclei, which are not representative of the pool of translatable mRNAs. Using these methods, we successfully constructed high-quality cell atlases for rice tiller nodes, rhizomes of wild rice, and maize crown roots grown in field conditions. Moreover, these methods enable the accurate reconstruction of plant acute wounding responses at single-cell resolution. Collectively, these advancements expand the applicability of plant single-cell genomics across a wider range of species and tissues, paving the way for comprehensive Plant Cell Atlases for plant species.

plant biology↗

bioRxiv2024

Immunopipe: A comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline

Single-cell sequencing technologies provide us with information at the level of individual cells. The combination of single-cell RNA-seq and single-cell TCR-seq profiling enables the exploration of cell heterogeneity and T-cell receptor repertoires simultaneously. The integration of both types of data can play a crucial role in enhancing our understanding of T-cell-mediated immunity and, in turn, facilitate the advancement of immunotherapy. Here, we present immunopipe, a comprehensive and flexible pipeline to perform integrated analysis of scRNA-seq and scTCR-seq data. In addition to the command line tool, we provide a user-friendly web interface for pipeline configuration and execution monitoring, benefiting researchers without extensive programming experience. With its comprehensive functionality and ease of use, immunopipe empowers researchers to uncover valuable insights from scRNA-seq and scTCR-seq data, ultimately advancing the understanding of immune responses and immunotherapy development.

bioinformatics↗

bioRxiv2024

Wounding perception by jasmonate-mediated JAZ condensation in plants

Wounding is a common stress experienced by plants, resulting in a quick elicitation of jasmonates (JAs). The widely accepted mechanism of COI1-JAZ coreceptor posits that COI1 directly interacts with the active ligand of JAs, whereas JAZs facilitate to trap the ligand in the binding pocket. Here we show that the multiple JAZs of Arabidopsis undergo phase separation in response to wounding. Taking JAZ1 as an example, we found it is an independent sensor of JA-Ile, the active ligand in most plants. Under basal condition, dispersed JAZ1 interacts with MYC2 to inhibit downstream gene expressions. Upon wounding, JAZ1 binds to JA-Ile and forms condensates, reducing its affinity with MYC2 and tending to recruit COI1 as well as other proteasome related components for quick degradation, thereby accelerating signaling output. Our investigation unveils the underlying mechanism by which JAZ1 regulates swift signaling transduction via phase separation upon the direct perception of JA-Ile.

plant biology↗

bioRxiv2023

Transcriptional reactivation of the tRNASer/tRNATyr gene cluster in Arabidopsis thaliana root tip

Plants retain a repetitious tRNA gene content in their nuclear genome. How important are these individuals, how exactly plants orchestrate their usage, and for what purposes, is poorly understood. Arabidopsis thaliana chromosome 1 holds a cluster of tandemly repeated serine- and tyrosine-decoding tRNA genes (SYY cluster). They intersect with constitutive heterochromatin and are silenced in most parts of the plant. Yet, the natural conditions leading to their transcription remain unknown. Here, we resolve the tissular expression pattern of this cluster along seedling establishment. We show that the root cap columella and few adjacent lateral root cap cells are the main sources of SYY cluster tRNAs. The transcriptional reactivation of the SYY cluster occurs in these tissues although elevated DNA methylation levels. Furthermore, we evidence that these cells are able to accumulate high levels of a transgenic glycoprotein rich in serine, tyrosine, and proline, and that the CRISPR/Cas9 deletion of the SYY cluster alters the phenomenon. Altogether, our work sheds light on pioneering evidence of a developmental and cell-specific expression program for a plant tRNA gene. We provide new perspectives on the role of peculiar tRNA genes in conferring a potential for the high synthesis of glycoproteins in protective tissues of the meristem.

plant biology↗

bioRxiv2023

A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex

De novo DNA methylation in plants relies on transcription elongation of RNA polymerase V (Pol V) along with KTF1 and SPT4, which produces long non-coding RNAs for recruitment and assembly of DNA methylation machinery. Here, we report a cryo-EM structure of the KTF1-bound Pol V transcription elongation complex. The structure reveals conformation of the structure motifs in the active site of Pol V that accounts for its inferior RNA-extension ability. The structure further reveals structural features of Pol V that prevent it from interacting with the general transcription factors of Pol II and Pol IV. The KOW5 domain of KTF1 binds near the RNA exit channel of Pol V, where it provides a scaffold for the proposed recruitment of Argonaute proteins to initiate the assembly of DNA methylation machinery. The structure provides insight into the Pol V transcription elongation and the role of KTF1 during Pol V transcription-coupled DNA methylation.

biochemistry↗

bioRxiv2023

Chloroquine induces eryptosis in P. falciparum-infected red blood cells and the release of extracellular vesicles with a unique protein profile

Malaria is a vector-borne parasitic disease that affects millions worldwide. In order to reach the objective, set by the World Health Organization to decrease the cases by 2030, antimalarial drugs with novel modes of action are required. Previously, a novel mechanism of action of chloroquine (CQ) was reported involving features of programmed cell death in the parasite, mainly characterized by calcium efflux from the digestive vacuole (DV) permeabilization. Increased intracellular calcium induces the suicidal death of erythrocytes also known as eryptosis. This study aimed to identify the hallmarks of eryptosis due to calcium redistribution and the downstream cellular effects during CQ treatment in iRBCs. Plasmodium falciparum 3D7 at mid-late trophozoites were used for the antimalarial drug treatment. Our results revealed increased phosphatidylserine (PS) exposure, cell shrinkage and membrane blebbing, delineating an eryptotic phenotype in the host RBC. Interestingly, the blebs on the surface of the iRBCs released to the extracellular milieu become extracellular vesicles (EVs) which are essential for intercellular communication due to their cargo of proteins, nucleic acids, lipids and metabolites. The proteomic characterization displayed 2 highly enriched protein clusters in EVs from CQ-treated iRBCs, the proteasome and ribosome. We demonstrated that this unique protein cargo is not associated with the parasite growth rate. Additionally, we found that these particular EVs might activate IFN signaling pathways mediated by IL-6 in THP-1-derived macrophages. Our findings shed new insights into a novel drug-induced cell death mechanism that targets the parasite and specific components of the infected host RBC. IMPORTANCEOur previous studies have shown that chloroquine (CQ) treatment in iRBCs triggers Plasmodium falciparum digestive vacuole (DV) membrane permeabilization leading to calcium redistribution. Interestingly, increased intracellular calcium concentration is the main inducer of the suicidal death of red blood cells (RBCs) called eryptosis. The present study shed new insights into a novel CQ-induced cell death mechanism that targets the parasite and the infected host RBC by inducing key phenotypic hallmarks of eryptosis: PS exposure, cell shrinkage and membrane blebbing. Moreover, the proteomic characterization of the blebs released to the extracellular milieu also known as extracellular vesicles (EVs) revealed a cargo highly enriched in ribosomal proteins and proteasome subunits relevant for host-parasite interactions. These findings highlight CQs effect on calcium homeostasis disruption in infected red blood cells (iRBCs) with cellular and immunological consequences of great significance for malaria pathogenesis and potential clinical implications.

cell biology↗

bioRxiv2022

Protection against doxorubicin-induced cardiotoxicity by ergothioneine

Anthracyclines such as doxorubicin remain the first line of treatment for haematological malignancies, and breast cancers. However, the potential risk of cardiac injury by anthracyclines, which may lead to severe myopathy or heart failure, severely limits their application, and remains a challenge to ensuring curative chemotherapy. While the complex interplay between pathological pathways of anthracycline cardiotoxicity is yet to be fully understood, oxidative damage, iron overload-mediated formation of reactive oxygen species (ROS), mitochondrial dysfunction, and inflammation are all believed to be involved. The unique dietary thione, ergothioneine, while not produced in animals and humans, can be avidly absorbed and accumulated in tissues including the heart. Amongst other cytoprotective properties ergothioneine has been shown to scavenge various ROS, decrease proinflammatory mediators, chelate metal cations such as Fe2+, preventing them from partaking in redox activities, and may protect against mitochondrial damage and dysfunction. Moreover, low plasma ergothioneine levels are also strongly correlated to risk of cardiovascular events in humans, suggestive of a cardioprotective role. Taken together this highlights the potential for ergothioneine to counteract anthracycline cardiotoxicity. Here we investigate the potential of ergothioneine supplementation to protect against cardiac dysfunction in mice models of doxorubicin-induced cardiotoxicity and found that it had significant protective effects. Moreover, ergothioneine administration in a mouse breast cancer model did not exacerbate the growth of the tumour and did not interfere with the chemotherapeutic efficacy of doxorubicin. These results suggest that ergothioneine could be a viable co-therapy to alleviate the cardiotoxic effects of anthracyclines in the treatment of cancers.

physiology↗

bioRxiv2021

Degrading intestinal DAF-2 nearly doubles Caenorhabditis elegans lifespan without affecting development or reproduction

Twenty-eight years following the breakthrough discovery that a single-gene mutation of daf-2 can double the lifespan of Caenorhabditis elegans, it remains unclear where this gene, which encodes an insulin/IGF-1 receptor, is expressed and where it acts to regulate aging. Here, by inserting DNA sequences of fluorescent tags into the genomic locus of daf-2 and that of its downstream transcription factor daf-16, we determined that both genes are expressed in most or all tissues from embryos through adulthood, in line with their diverse functions. Using tissue-specific auxin-induced protein degradation, we determined that both DAF-2 and DAF-16 act in the intestine to regulate organismal aging. Strikingly, loss of DAF-2 in the intestine nearly doubled C. elegans lifespan but did not produce the adverse developmental or reproductive phenotypes associated with genetic daf-2 mutants. These findings unify the mechanism of lifespan regulation by genes and that by dietary restriction, and begin to focus anti-aging research on nutrient supply. HighlightsO_LIdaf-2 and daf-16 are expressed in most or all cells of C. elegans using genome editing. C_LIO_LIDAF-2 and DAF-16 both regulate lifespan from the intestine as determined using auxin-induced protein degradation. C_LIO_LIReduced insulin signaling in the intestine nearly doubles C. elegans lifespan without adverse effects on development or reproduction. C_LIO_LILifespan regulation by genes and dietary restriction are unified by intestinal supply of nutrients and metabolism. C_LI

cell biology↗

bioRxiv2020

Computational approach and functional analysis of Pectobacterium carotovorum subsp. carotovorum low-molecular weight bacteriocin Carocin S2

Pectobacterium carotovorum subsp. Carotovorum 3F3 is a gram-negative phyto-parasitic enterobacterium. This strain is a producer of Carocin S2 bacteriocin, which comprises of two proteins of different sizes. Carocin S2K (killer protein) which is responsible for antibiotic resistance and Carocin S2I (immunity protein) which inhibits the antibiotic activity. The present study aimed to predict the structure and functional properties of Carocin S2. Computational approaches utilizing various bioinformatic tools predicted that Carocin S2 is a putative membrane protein having the N-terminal at the extracellular side and the central domain at the coiled-coil region. Carocin S2 was predicted to have three domains, the translocation domains, receptor binding domain and the killer domain. Moreover, the killer domain was calculated to have the catalytic cleft. The in-vivo assays confirmed that for Carocin S2K, bound immunity protein was not a pre-requisite for cell attachment or translocation. The site-directed mutagenesis experiment led us to hypothesized the hydrolysis mechanism of Carocin S2. The predicted structure of Carocin S2K provided a system of understanding on the biochemical and structural function which led to the mechanism of Carocin S2. It revealed that the role of immunity protein to Carocin S2 is not a pre-requisite for translocation pathway. Furthermore, this research led to hypothesized a hydrolytic mechanism of Carocin S2 to target the tRNA.

biochemistry↗

bioRxiv2019

MAGOS: Discovering Subclones in Tumors Sequenced at Standard Depths

Understanding intratumor heterogeneity is critical to designing personalized treatments and improving clinical outcomes of cancers. Such investigations require accurate delineation of the subclonal composition of a tumor, which to date can only be reliably inferred from deep-sequencing data (>300x depth). To enable accurate subclonal discovery in tumors sequenced at standard depths (30-50x), we develop a novel computational method that incorporates an adaptive error model into statistical decomposition of mixed populations, which corrects the mean-variance dependency of sequencing data at the subclonal level. Tested on extensive computer simulations and real-world data, this new method, named model-based adaptive grouping of subclones (MAGOS), consistently outperforms existing methods on minimum sequencing depth, decomposition accuracy and computation efficiency. MAGOS supports subclone analysis using single nucleotide variants and copy number variants from one or more samples of an individual tumor. Applications of MAGOS to whole-exome sequencing data of 331 liver cancer samples discovered a significant association between subclonal diversity and patient overall survival. MAGOS is freely available as an R package at github (https://github.com/liliulab/magos).

bioinformatics↗

bioRxiv2018

In vivo generation of post-infarct mouse cardiac muscle by cardiomyocyte progenitors produced with a reproducible laminin-promoted human stem cell differentiation system

Regeneration of human heart muscle after injury is extremely limited and an unmet clinical need. Despite extensive research, there are no methods for the reproducible generation of clinical quality stem-cell-derived cardiovascular progenitors (CVPs). Here, we identified laminin-221 (LN-221) as the main cardiac laminin, which was produced here as human recombinant protein, and showed that LN-221 promotes differentiation of pluripotent hESCs towards cardiomyocyte lineage and downregulates genes associated with pluripotency and teratoma development. We developed a chemically defined, xeno-free laminin-based cardiomyocyte differentiation protocol to reproducibly generate CVPs that form human muscle in vivo. We assessed the reproducibility of the differentiation protocol using time-course bulk RNA sequencing developed from two different hESC lines. Single-cell RNA sequencing of CVPs derived from two hESC lines further showed high reproducibility and identified three main progenitor subpopulations. These CVPs were transplanted into myocardial infarction mice, where heart function was measured by echocardiogram and human heart muscle bundle formation was identified histologically. This method may provide clinical quality cells for use in regenerative cardiology.

cell biology↗

bioRxiv2017

NFATc2 enhances tumor-initiating phenotypes through the NFATc2/SOX2/ALDH axis in lung adenocarcinoma

Cancers display intratumoral genetic and molecular heterogeneity with tumor initiating cells (TIC) showing enhanced tumor phenotypes. In this study, we show the calcium pathway transcription factor NFATc2 is a novel regulator of lung TIC through the NFATc2/SOX2/ALDH1A1 regulatory axis. In vitro and in vivo cancer cell modeling demonstrated supportive evidences including cell renewal, tumorigenicity at limiting dose, cell motility, resistance to cytotoxic chemotherapy and EGFR targeted therapy. In human lung cancers, high NFATc2 expression predicts poor tumor differentiation, adverse recurrence-free and overall patient survivals. Mechanistic investigations identified NFATc2 response elements in the SOX2 3 enhancer region, and NFATc2/SOX2 coupling upregulates ALDH1A1 by binding to its 5 enhancer. Through this axis, oxidative stresses and reactive oxygen species induced by cancer drug treatment are attenuated, accounting for a mutation-independent mechanism of drug resistance. Targeting this axis provides a novel approach for the long term treatment of lung cancer through TIC elimination.

cancer biology↗