bioRxiv Science⌕ Search

Biology subjects

Han, Y.

Publications and source records attributed to Han, Y..

At least 91 records · Page 5Linked to original sources
bioRxiv2025

Infants who develop BPD have an airway endotype defined by vimentin expression and ciliary loss

RationaleBronchopulmonary Dysplasia (BPD) results from abnormal lung development after preterm birth, with structural deficits at every respiratory tree level. BPD with lower airway disease is emerging as a clinically significant phenotype with increased mortality, and there is a significant knowledge gap in the molecular mechanisms whereby preterm birth disrupts normal airway development. ObjectivesTo develop a human model of lower airway disease after preterm birth and to characterize a molecular endotype of evolving BPD (eBPD) at baseline and in response to injury. MethodsWe used a combination of an ex vivo organotypic Airway Epithelial Cell (AEC models) and well-characterized pathologic and transcriptomic patient samples for quantitative immunohistochemistry and RNA sequencing analyses. Measurements and Main ResultsCompared to AECs from healthy patients, eBPD- derived AECs have a molecular endotype of reduced proliferation, impaired differentiation to ciliated epithelium, and an expanded vimentin-positive population with a transcriptional shift toward stromal cell-associated genes. With hyperoxia exposure, eBPD-derived AECs exhibited a pronounced vimentin response ex vivo, which parallels the increased vimentin expression of airway cells observed in lung tissue from human infants with BPD. ConclusionsIn this organotypic model of neonatal airway differentiation, we find that infants with eBPD have impaired differentiation, increased expression of vimentin, and concomitant loss of cilia, with an exaggerated increase in vimentin expression after hyperoxia injury, findings that mimic the effects of prematurity in airway cells in human patients. These data provide a foundation for future mechanistic studies interrogating the role of intermediate filaments in epithelial differentiation and repair.

cell biology↗
bioRxiv2025

SpatialZoomer: multi-scale feature analysis of spatial transcriptomics

Single-cell resolution spatial transcriptomics (ST) provides a great opportunity to explore the complex cellular contents in different tissues. In this study, we introduce SpatialZoomer, a spectral graph-based method that applies a set of low-pass filters to efficiently extract spatial molecular features from ST data at multiple resolutions or scales, including the single cell scale, the niche scale with dozens of closely interacting cells, and the domain scale with spatially-organized cell contents. The corresponding "critical" scales can be automatically identified by partitioning a cross-scale similarity map. Results show that SpatialZoomer can identify disease-progression signals at specific scales in Alzheimers Disease, and spatial context dependent cell subtypes in tumor microenvironment. The extracted multi-scale features also uncovered spatially heterogeneous niches in cancer. SpatialZoomer also takes advantage of high computational efficiency and low hardware requirements.

bioinformatics↗
bioRxiv2025

Versatile HIV Rev-dependent reporter cell system for stringent and sensitive quantification of viral reservoirs, neutralizing antibodies, and restriction factors

Detecting and measuring HIV reservoirs, neutralizing antibodies, and restriction factors are important for HIV cure research and the development of new therapeutics and vaccines. Here we describe the development and validation of several HIV Rev-dependent indicator cell lines for these purposes. These reporter cells come from different T-lymphoblast cell lines, including MOLT-4-R5, SupT1-R5, CEM-SS, A3R5, and from the adherent TZM cell platform based on HeLa clone JC53. These cells express CD4, CXCR4, and various levels of CCR5. We compared these cell lines for responsiveness to both X4 and R5-tropic viruses, and confirmed that reporter expression in these cells is not affected by stimulation from mitogens but is responsive to HIV Tat and Rev, reducing non-specific reporter induction from the leaky LTR promoter. To validate the sensitivity of the Rev-dependent reporter cell systems, we conducted a viral dilution assay with three primary HIV-1 clade C swarms from an adult in Malawi. We also validated the systems for quantifying antibody neutralization and screening restriction factors; these systems are also sensitive for viral outgrowth assays for quantifying viral reservoirs in clinical and basic research settings. Given that the systems can measure HIV accurately in complex environments with mitogens or other substances, they can be used for versatile applications, such as quantifying latent reservoirs, testing inhibitory compounds, conducting neutralizing antibody assays, and identifying new restriction factors.

microbiology↗
bioRxiv2025

Protected areas show substantial and increasing risk of wildfire globally

Protected area coverage is set to expand in response to climate change and the biodiversity crisis, but we lack assessments of wildfire incidence in protected areas. Here we quantify bigeographical variation in global patterns of burned area in protected areas. During the twenty-first century, wildfires have burned 2 billion hectares of protected areas - an area the size of Russia and India combined - and, while protected areas only cover 19.2% of semi-natural ecosystems, they concentrate 28.5% of the area burned annually. Wildfire in protected areas increased significantly between 2001-2024 (+0.46% yr-1), even after taking into account increases in protected area (+0.27% yr-1), pointing to a disproportional impact of fire on protected areas under increasingly severe fire weather. This pattern showed marked variation across biomes, with the largest disproportionate increases occurring in fire-prone biomes (e.g. Mediterranean and dry tropical forests, tropical grasslands and xeric shrublands). There were important exceptions to this general trend, and protected area fire was lower than expected in biomes where fire activity is naturally limited by moisture (e.g. tropical rainforests or montane grasslands). Wildfires are important for the health of many ecosystems, and such values of burned area will not always mean a negative outcome. Amidst concerted efforts to expand protected area coverage such as the Global Biodiversity Framework, our results highlight the need for new management strategies that address the globally increasing impacts of burned area across protected areas under unabated climate change.

ecology↗
bioRxiv2025

Single-nucleus transcriptome analyses uncover a dynamic transcriptional landscape of soybean roots in response to soybean cyst nematode infection

Soybean cyst nematode (SCN, Heterodera glycines) causes substantial yield losses by inducing the formation of specialized feeding structure called syncytia, which arise from extensive reprogramming of host root cells. Despite their pivotal role in SCN parasitism, the molecular mechanisms governing syncytium formation and function remain poorly understood, largely due to the technique challenges in precisely isolating these rare cell types. Here, we employed single-nucleus RNA sequencing (snRNA-seq) to generate a comprehensive, high-resolution transcriptomic atlas of SCN-infected soybean roots, comparing two resistant cultivars (PI 88788 and Forrest) with a susceptible cultivar (Williams 82) across multiple infection stages. By leveraging the well-characterized syncytium marker GmSNAP18, we successfully identified and transcriptionally profiled syncytial cells, and validate the spatial expression of known SCN-resistant genes. Our analyses revealed strong induction of resistance-associated genes specifically enriched in syncytia from resistant cultivars. Functional validation further demonstrated that overexpression of three novel candidate genes significantly suppressed SCN development. Pseudotime trajectory analyses traced syncytium development back to procambial cell origins, uncovering distinct, cultivar-specific developmental pathways. Collectively, this work provides a foundational single cell transcriptomic resource, advances our understanding of syncytial biology and SCN resistance mechanisms, and identifies promising molecular targets for engineering nematode-resistant soybean varieties.

plant biology↗
bioRxiv2025

Socially regulated developmental plasticity in the color pattern of an anemonefish

Understanding the developmental basis of phenotypic plasticity is key to unraveling the origins of biodiversity. In coral reef fishes, color pattern changes during ontogeny can serve adaptive functions, yet the mechanisms and ecological contexts shaping these transitions remain largely unknown. Here, we investigated color pattern development in the tomato anemonefish (Amphiprion frenatus), which exhibits transient posterior white barring during early juvenile stages. We demonstrated that the timing of bar loss is plastic and modulated by the social environment, where juveniles cohabiting with adult conspecifics exhibited bar loss [~]24 days earlier than those isolated from adults. Through transcriptomic profiling, we identified gene expression changes implicating apoptosis- and autophagy-related pathways, as well as alterations in chromatophore development. Moreover, shifts in the expression of multiple thyroid hormone marker genes highlighted the potential neuroendocrinal integration of social cues that promoted bar loss. Ultrastructural analyses via transmission electron microscopy and in-situ assays indicated massive apoptosis of iridophores and associated dermal remodeling during the white-to-orange transition. The pharmacological inhibition of caspases delayed bar loss, confirming the functional role of programmed cell death. Behavioral trials revealed that adults responded differently to juveniles with/without the posterior bar, suggesting a role of transient barring in conflict avoidance during recruitment. Lastly, our evolutionary reconstruction of this plastic trait suggests that colony size is an important factor promoting this ontogenetic switch throughout anemonefishes. Our results provide compelling evidence for socially mediated plasticity in color pattern ontogeny with ecological and evolutionary implications for communication and species diversification in reef fishes.

developmental biology↗
bioRxiv2025

TMEM63 proteins act as mechanically-activated cholesterol modulated lipid scramblases contributing to membrane mechano-resilience

OSCA/TMEM63 mechanosensitive ion channels play critical physiological roles in plants and animals. These channels bear structural homology to the dual functional TMEM16 family, and OSCA1.2 was recently shown to form a lipid-lined ion conduction pathway in the open state. This raised the question of whether members of the OSCA/TMEM63 family may also function as mechanically activated lipid scramblases. Using a combination of in vitro and cellular assays with computational techniques, we show that phospholipids can be translocated through the open pores of OSCA1.1/1.2/2.2 and TMEM63A/B proteins, suggesting a dual ion channel and lipid scramblase function for members of this protein family. We characterize the effects of mutating key groove lining residues demonstrating that different residues form bottlenecks for lipids and ions respectively and show that cholesterol inhibits lipid scrambling by stabilizing the closed state and slowing translocation through the open pore. We show that lipid scrambling in TMEM63 proteins can be activated by mechanical forces in the membrane, making these the first identified mechanically activated lipid scramblases. Finally, we demonstrate that this activity is important for the mechanically induced morphological remodeling of biological membranes and the resilience of cells to high mechanical forces.

biophysics↗
bioRxiv2025

Resolving synaptic events using subsynaptically targeted GCaMP8 variants

While genetically encoded Ca2+ indicators are valuable for visualizing neural activity, their speed and sensitivity have had limited performance when compared to chemical dyes and electrophysiology, particularly at synaptic compartments. We addressed these limitations by engineering a suite of next-generation GCaMP8-based indicators, targeted to presynaptic boutons, active zones, and postsynaptic compartments at the Drosophila neuromuscular junction. We first validated these sensors to be superior to previous versions and synthetic dyes. Next, we developed a Python-based analysis program, CaFire, which enables the automated quantification of evoked and spontaneous Ca{superscript 2} signals. Using CaFire, we show a ratiometric presynaptic GCaMP8m sensor accurately captures physiologically-relevant presynaptic Ca2+ changes with superior sensitivity and similar kinetics compared to chemical dyes. Moreover, we test the ability of an active zone-targeted, ratiometric GCaMP8m sensor to report differences in Ca{superscript 2} between release sites. Finally, a newly engineered postsynaptic GCaMP8m, positioned near glutamate receptors, detects quantal events with temporal and signal resolution comparable to electrophysiological recordings. These next generation indicators and analytical methods demonstrate that GCaMP8 sensors, targeted to synaptic compartments, can now achieve the speed and sensitivity necessary to resolve Ca2+ dynamics at levels previously only attainable with chemical dyes or electrophysiology.

neuroscience↗
bioRxiv2025

Population-specific brain charts reveal Chinese-Western differences in neurodevelopmental trajectories

Human brain charts provide unprecedented opportunities for decoding neurodevelopmental milestones and establishing clinical benchmarks for precision brain medicine 1-7. However, current lifespan brain charts are primarily derived from European and North American cohorts, with Asian populations severely underrepresented. Here, we present the first population-specific brain charts for China, developed through the Chinese Lifespan Brain Mapping Consortium (Phase I) using neuroimaging data from 43,037 participants (aged 0-100 years) across 384 sites nationwide. We establish the lifespan normative trajectories for 296 structural brain phenotypes, encompassing global, subcortical, and cortical measures. Cross-population comparisons with Western brain charts (based on data from 56,339 participants aged 0-100 years) reveal distinct neurodevelopmental patterns in the Chinese population, including prolonged cortical and subcortical maturation, accelerated cerebellar growth, and earlier development of sensorimotor regions relative to paralimbic regions. Crucially, these Chinese-specific charts outperform Western-derived models in predicting healthy brain phenotypes and detecting pathological deviations in Chinese clinical cohorts. These findings highlight the urgent need for diverse, population-representative brain charts to advance equitable precision neuroscience and improve clinical validity across populations.

neuroscience↗
bioRxiv2025

Divergent MIC of Clarithromycin and Azithromycin Against Clinical Isolates of Mycobacterium abscessus Complex

Current treatment guidelines for Mycobacterium abscessus complex (MAB) infections recommend macrolides (clarithromycin/CAM and azithromycin/AZM) as cornerstone therapies, considering them clinically interchangeable without distinction. This study evaluated the comparative in vitro activity of clarithromycin (CAM) and azithromycin (AZM) against 146 clinical isolates of Mycobacterium abscessus complex organisms. MIC distributions revealed significantly higher resistance to AZM (94.5% resistant at [&ge;]8 g/mL) compared to CAM (77.4% resistant at [&ge;]8 g/mL), with only 4.8% of isolates susceptible to both drugs. Notably, 26 strains (17.8% of total) showed AZM resistance despite being non-resistant to CAM (MIC <8 g/mL) among 146 clinical isolates. Among the 33 CAM-non-resistant isolates (including susceptible and intermediate strains), 78.8% (26/33) were AZM-resistant, demonstrating frequent discordance in susceptibility profiles. These findings contrast with current treatment guidelines that recommend using CAM and AZM interchangeably without distinction. Subspecies analysis showed three distinct susceptibility profiles: isolates susceptible to both antibiotics (n=3, M. massiliense), isolates resistant to both antibiotics (n=3, M. massiliense), and M. bolletii with CAM-susceptible/AZM-resistant phenotypes (n=2). This differential resistance pattern suggests that while both drugs face substantial resistance challenges, CAM retains meaningful activity against certain strains that are AZM-resistant-particularly in M. bolletii. These findings indicate that AZM and CAM should not be used interchangeably to treat MAB infections and emphasize the need to prioritize CAM over AZM in treatment regimens.

microbiology↗
bioRxiv2025

The decameric repeat (DR) of PSGL-1 functions as a basic antiviral unit in restricting HIV-1 infectivity

PSGL-1 (P-selectin glycoprotein ligand-1) is a dimeric, mucin-like surface glycoprotein that interacts with selectins on the endothelium, facilitating leukocyte tethering and rolling during transmigration. Previous studies have demonstrated that PSGL-1 acts as an HIV restriction factor, blocking HIV infectivity by hindering particle attachment to target cells. A large part of PSGL-1s extracellular region consists of a mucin-like domain, characterized by decameric repeats (DR), which comprise 14 to 16 DR tandems. Each DR is composed of 10 consensus amino acids (-A-T/M-E-A-Q-T-T-X-P/L-A/T-) and is notably rich in O-glycosylated threonines (30%) and prolines (10%). A proposed function of the DR is to elongate the protein backbone needed for selectin binding. However, the precise role of DR in PSGL-1s antiviral mechanisms has yet to be fully elucidated. In this study, we performed DR deletion mutagenesis and molecular modeling, systematically deleting from one DR to all DRs, and quantified their effects on PSGL-1s antiviral functions. Here, we demonstrate that DR is necessary for PSGL-1s antiviral activity. Deleting DR did not affect virion incorporation of PSGL-1, but diminished PSGL-1s ability to hinder virion attachment to target cells. We also discovered that individual single DR mutants retained 3.5 to 18% of the antiviral activity exhibited by full-length PSGL-1, and the basic antiviral activity of DR is cumulative; increasing the number of DRs correlates with heightened antiviral activity. Additionally, the intrinsic anti-HIV capability of DR was found to be transferrable; inserting the DR domain into the extracellular Ig-like domain of CD2 permitted the hybrid CD2-DR molecules to partially acquire the anti-HIV properties of PSGL-1. Further molecular modeling utilizing all-atom replica exchange molecular dynamics simulations highlighted a structure-function relationship between the anti-HIV potency of DR and the elongation of the DR backbone, as measured by DR backbone dihedral angles ({varphi}) and the radial distributions of peptide atom number density (rmax). These results collectively suggest that DR serves as an essential antiviral unit within the framework of PSGL-1s restriction mechanism against HIV.

immunology↗
bioRxiv2025

Development and application of a genotyping by target sequencing SNP array panel in Salix suchowensis

Salix suchowensis is an important species of Salix, known for its rapid growth property and wide application in environmental construction, ecological restoration, wicker production, and biomass energy production. Due to its significance as a sustainable biological resource, S. suchowensis has been the centre of intensive breeding. However, rapid improvement of growth and biomass has been hindered by a lack of genomic resources. To address this limitation, we designed a genotyping by target sequencing SNP array panel to facilitate efficient genotyping. Using whole-genome resequencing data, a total of 39,076 SNPs were selected for the array panel, consisting of trait-associated SNPs, intragenic SNPs, and intergenic SNPs. This panel was validated by genotyping 550 new samples, demonstrating high call rates and effective capture of the population structure. Genome-wide association analysis identified 72 SNPs associated with plant height and ground diameter. Additionally, the array panel shows a high potential for genomic selection, with high prediction accuracy for various traits. These results highlight the efficiency of this panel in capturing genomic variations that are highly valuable for future genetic research and breeding applications.

genetics↗
bioRxiv2025

Divergent Minimum Inhibitory Concentrations of Clarithromycin and Azithromycin Against Clinical Isolates of Mycobacterium abscessus Complex

Current treatment guidelines for Mycobacterium abscessus complex (MAB) infections recommend macrolides (clarithromycin/CAM and azithromycin/AZM) as cornerstone therapies, considering them clinically interchangeable without distinction. This study evaluated the comparative in vitro activity of clarithromycin (CAM) and azithromycin (AZM) against 146 clinical isolates of Mycobacterium abscessus complex organisms. MIC distributions revealed significantly higher resistance to AZM (94.5% resistant at [&ge;]8 g/mL) compared to CAM (77.4% resistant at [&ge;]8 g/mL), with only 4.8% of isolates susceptible to both drugs. Notably, 26 strains (17.8% of total) showed AZM resistance despite being non-resistant to CAM (MIC <8 g/mL) among 146 clinical isolates. Among the 33 CAM-non-resistant isolates (including susceptible and intermediate strains), 78.8% (26/33) were AZM-resistant, demonstrating frequent discordance in susceptibility profiles. These findings contrast with current treatment guidelines that recommend using CAM and AZM interchangeably without distinction. Subspecies analysis showed three distinct susceptibility profiles: isolates susceptible to both antibiotics (n=3, M. massiliense), isolates resistant to both antibiotics (n=3, M. massiliense), and M. bolletii with CAM-susceptible/AZM-resistant phenotypes (n=2). This differential resistance pattern suggests that while both drugs face substantial resistance challenges, CAM retains meaningful activity against certain strains that are AZM-resistant--particularly in M. bolletii. These findings indicate that AZM and CAM should not be used interchangeably to treat MAB infections and emphasize the need to prioritize CAM over AZM in treatment regimens.

microbiology↗
bioRxiv2025

Towards individualized deep brain stimulation: A stereoencephalography-based workflow for unbiased neurostimulation target identification

ObjectivesDeep brain stimulation (DBS) is increasingly being used to treat a variety of neuropsychiatric conditions, many of which exhibit idiosyncratic symptom presentations and neural correlates across individuals. Thus, we have utilized inpatient stereoelectroencephalography (sEEG) to identify personalized therapeutic stimulation sites for chronic implantation of DBS. Informed by our experience, we have developed a statistics-driven framework for stimulation testing to identify therapeutic targets. Materials and MethodsFourteen participants (major depressive disorder = 6, chronic pain = 6, obsessive-compulsive disorder = 2) underwent inpatient testing using sEEG and symptom monitoring to identify personalized stimulation targets for subsequent DBS implantation. We present a structured approach to this sEEG testing, integrating a Stimulation Testing Decision Tree with power analysis and effect size considerations to inform adequately powered results to detect therapeutic stimulation sites with statistical rigor. ResultsEffect sizes (Hedges g) of stimulation-induced symptom score changes ranged from -1.5 to +2.39. The standard deviation of sham trial responses was a strong predictor of stimulation response variability, as confirmed by a leave-one-out cross-validated linear regression (R2 = 0.67, permutation p<0.001). Thus, early sham trial data could be used to estimate the variability of stimulation responses for power analysis calculations. We show that approximately 10 sham trials were needed to robustly estimate sham variability. Power analysis (using a paired-t test) showed that for effect sizes [&ge;] 1.1, roughly 10 trials should be used per stimulation site for sufficiently powered results. ConclusionsThe presented workflow is adaptable to multiple indications and is specifically designed to overcome key challenges experienced during stimulation site testing. Through incorporating sham trials, effect size calculations, and tolerability testing, the described approach can be used to identify personalized and clinically efficacious stimulation sites.

neuroscience↗
bioRxiv2025

Metagenomic-scale analysis of the predicted protein structure universe

Protein structure prediction breakthroughs, AlphaFold2 and ESMfold, have led to an unprecedented influx of computationally derived structures. The AlphaFold Protein Structure Database provides over 200 million predictions, while the ESM Metagenomic Atlas (ESMatlas) includes over 600 million predictions from uncultured microbes. We combine these into AFESM, an 820-million-entry dataset, and cluster them using a scalable pipeline based on sequence and structure similarity, yielding 5.12 million non-singleton structural clusters. We identify common ancestors and biomes for these clusters to explore their environmental diversity and specificity, and we investigate their structural novelties. From non-singleton clusters unique to ESMatlas, we identified 12 novel domain folds, repredicting a subset ([~]45%) of low-quality domains with ColabFold yielded 33 additional novel folds. This underscores the importance of prediction quality in structural novelty discovery. We also identified 11,941 previously unseen domain combinations, highlighting the untapped structural diversity and importance of metagenomic data for illuminating underexplored regions of the protein structural universe. An interactive webserver and data are available at afesm.foldseek.com.

bioinformatics↗
bioRxiv2025

Niche Macrophages Recycle Iron to Tumor Cells and Foster Erythroblast Mimicry to Promote Bone Metastasis and Anemia

Bone marrow is both a primary site for blood cell production and a fertile niche for metastatic cancer cell growth, notably in breast cancer. Although anemia is common among patients with bone metastasis, the mechanistic link between metastatic colonization and disrupted erythropoiesis remains poorly understood. Using in vivo niche labeling and single-cell RNA sequencing, we identified a specialized population of VCAM1+CD163+CCR3+ macrophages enriched in the bone metastatic niche. These macrophages, typically essential for erythropoiesis in healthy bone marrow, are co- opted by tumor cells to support their growth through iron acquisition. The hijacking of these macrophages by tumor cells reduces iron availability for erythroblasts, impairing erythropoiesis and contributing to anemia. With increased iron supply, tumor cells further adapt by mimicking erythroblasts, producing hemoglobin under GATA1 regulation in response to hypoxic stress. Notably, macrophages with similar iron- regulating features were found in human bone metastases across multiple cancer types, and elevated HBB expression in breast cancer correlates with increased risk of bone metastasis. These findings establish iron-recycling macrophages as essential regulators within the metastatic bone niche, revealing novel insights into the interplay between immune modulation, metal metabolism and tumor cell plasticity in driving metastatic progression and anemia.

cancer biology↗
bioRxiv2025

TUCL-Seq for miRNA single molecule sequencing

MicroRNAs (miRNAs) are pivotal regulatory molecules in gene expression, and their precise quantification is essential for elucidating their roles in diverse biological processes. This research paper introduces a pioneering workflow for the single molecule sequencing (SMS) of miRNA, integrating advanced miRNA sample preparation with SMS sequencing. Central to our approach is TUCL-Seq, which is an automated, on-chip miRNA library preparation method designed to streamline the sequencing process. This innovative approach incorporates the addition of sequencing adaptor to RNA samples in solution, and converts it to cDNA on a sequencing flow cell for sequencing. Coupled with single molecule sequencing instrument and base-call software, our workflow significantly reduces sample-to-result time, and decreases the need for manual interventions compared to traditional SMS and next-generation sequencing methods. We demonstrate the efficacy of TUCL-Seq by accurately quantifying synthetic miRNA samples with a 24-hour workflow, showcasing its potential for high-throughput miRNA profiling. Our findings highlight the promise of this integrated workflow for advancing miRNA research and applications in diagnostics and therapeutics.

biochemistry↗