Biology subjects

Miao, K.

Publications and source records attributed to Miao, K..

11 recordsLinked to original sources

bioRxiv2026

Loss of DNA Demethylase Enhances Arsenic Resistance Via Reducing of PIN2 Antisense Long Noncoding RNA

DNA methylation dynamics regulate diverse plant stress responses, but the mechanisms governing arsenic (As) tolerance through epigenetic pathways remain largely unknown. Here we report that Arabidopsis mutants lacking the DNA demethylase, REPRESSOR OF SILENCING (ROS1), show substantially enhanced As resistance. Integrating transcriptome and methylome data, we found that PIN-FORMED 2 (PIN2), encoding an auxin efflux carrier that also transports As out of cells, represents a key ROS1 target. In ros1, we observed increased methylation in the last exon of PIN2, a region functioning as the promoter for an antisense long non-coding RNA (lncRNA). Hypermethylation of the promoter suppresses the antisense lncRNA, which follows reduction of sense PIN2 transcription. As a result, PIN2 expression increases in ros1 mutants during As exposure, enhancing As tolerance. Analysis of ros1 pin2 double mutants confirmed that PIN2 acts downstream of ROS1 in As tolerance. Our study demonstrates an epigenetic pathway in which ROS1 regulates As tolerance by controlling PIN2 expression through antisense lncRNA-mediated transcriptional interference, offering new epigenetic strategies using plants in heavy metal contaminated environments.

plant biology↗

bioRxiv2026

Organoids reveal niche-specific mechanotransduction-guided human cortical patterning and cell fate acquisition

The highly dynamic mechanical environment of the developing cerebral cortex has the potential to encode information vital for neuronal differentiation. Changes in local biophysical properties have been implicated in processes ranging from the maintenance of neural progenitors to long-range axon guidance. However, whether cortical mechanics influence cellular organisation and specification during neurogenesis remains largely unexplored. Here, we leverage a 3D mosaic organoid model of human cortical development, in which we selectively disrupt a key component of nuclear mechanosensing, the LINC complex, decoupling cells from their mechanical environment. We show that LINC-decoupling alters nuclear morphology in a compartment-specific manner, driving preferential exclusion from the germinal zone and concomitant premature differentiation. Excluded cells exhibit a biased spatial distribution in the cortical plate and altered fate allocation, with loss of intermediate progenitors and upper-layer neuron populations. Combining this approach with single-cell transcriptomic profiling, we reveal a signature of impaired ERK activation and density sensing in LINC-decoupled cells. Furthermore, we show that altered density sensing contributes to mislocalisation of the nuclear envelope protein emerin and disruption of histone mark deposition during differentiation. Taken together, our findings illustrate how the dynamic mechanical environment of a complex tissue can dictate cell fate and pattern formation during development.

developmental biology↗

bioRxiv2026

Targeted extracellular degradation of LRP8 promotes ferroptosis in cancer cells

Tumor reliance on antioxidant defenses creates a vulnerability to ferroptosis, yet strategies to therapeutically disable these systems remain limited. Here, we identify targeted degradation of the selenium uptake receptor LRP8 as an effective approach to decrease the abundance of the ferroptosis-protective enzyme glutathione peroxidase 4 (GPX4). Using bispecific cytokine receptor-targeting chimeras (KineTACs) that couple LRP8 to cytokine receptor internalization pathways, we selectively direct LRP8 to the lysosome for degradation. LRP8 degradation reduces the abundance of several selenoproteins, including GPX4, lowering the cellular threshold for lipid peroxidation and sensitizing cancer cells to ferroptosis. These findings establish receptor-mediated selenium uptake as a critical, targetable node in ferroptosis resistance and demonstrate that extracellular protein degradation can be leveraged to reprogram intracellular translational dependencies in cancer cells. More broadly, this work provides a framework for exploiting nutrient acquisition pathways to overcome therapy resistance.

bioengineering↗

bioRxiv2026

Targeted shedding of extracellular membrane proteins by induced protease recruitment

Extracellular targeted protein degradation has emerged as a promising therapeutic modality to eliminate proteins of interest (POIs) at the cell surface, by using bifunctional molecules to recruit natural recycling receptors or membrane-bound E3 ligases that redirect POIs to the lysosome. Another natural mechanism involves extracellular proteases that cleave and shed extracellular domains. Here, we exploit this endogenous mechanism by engineering bispecific antibody Shedders, that recruit a classic sheddase ADAM10 to POIs, inducing selective ectodomain shedding. We first targeted the immune checkpoint receptor LAG-3 and observed robust depletion of surface LAG-3 accompanied by accumulation of soluble LAG-3 fragments in both engineered cell lines and primary human T cells. Using biochemical and imaging assays, we confirmed that this antibody-induced shedding is restricted to extracellular protease activity and occurs independently of lysosomal trafficking. Notably, induced shedding of LAG-3 on activated primary T cells partially alleviated inhibitory signaling and reinvigorated IFN{gamma} secretion. We extended the scope of induced shedding by developing Shedders that recognize synthetic epitope-tags that enabling rapid assessment of substrate compatibility across diverse targets. Using this platform, we identified multiple immune modulatory cell-surface receptors, including IL6R, CD62L and MIC-A that can be targeted for shedding. In summary, this work establishes a new paradigm for targeted extracellular proteolysis and expands the toolkit for studying extracellular proteolysis with potential therapeutic benefit.

bioengineering↗

bioRxiv2025

Low-density lipoprotein receptor-targeting chimeras for membrane protein degradation and enhanced drug delivery

Antibody-based therapeutics encompass diverse modalities for targeting tumor cells. Among these, antibody-drug conjugates (ADCs) and extracellular targeted protein degradation (eTPD) specifically depend on efficient lysosomal trafficking for activity. However, many tumor antigens exhibit poor internalization, limiting ADC effectiveness. To address this, we developed low-density lipoprotein receptor-targeting chimeras (LIPTACs), leveraging the constitutive endocytic and recycling activity of the LDLR to enhance lysosomal delivery. LIPTACs enable efficient and selective degradation of diverse extracellular membrane proteins. Additionally, by coupling LIPTACs with cytotoxic payloads to generate degrader-drug conjugates, we can achieve superior intracellular delivery and enhanced cytotoxicity compared to conventional ADCs. The dual modality addresses key challenges of inadequate internalization in conventional ADCs and cytotoxic potency for current eTPD strategies. Our findings demonstrate that LDLR-mediated trafficking can enhance eTPD and ADCs, providing a hybrid blueprint for developing next-generation antibody therapeutics with broader utility and improved efficacy in cancer treatment.

bioengineering↗

bioRxiv2025

GFP-Free Live-Neuron Quantitative Imaging Reveals Compartmentalization and Growth Dynamics of PolyQ Aggregates

Huntingtons Disease (HD), the most prevalent polyglutamine (polyQ) neurodegenerative disorder, features brain aggregates induced by mutant huntingtin (mHtt) proteins harboring expanded polyQ tracts. Despite extensive efforts, molecular mechanisms of polyQ aggregates remain elusive. Here we establish quantitative stimulated Raman scattering imaging of polyQ aggregates (q-aggSRS) for non-invasive investigations in live neuronal co-cultures using deuterated glutamine labeling. Q-aggSRS allows for specific visualization by targeting the distinct Raman peak from carbon-deuterium bonds, eliminating the need for bulky GFP tagging. Coupled with analysis from aggregate-tailored expansion microscopy, newly designed two-color imaging, and pulse-chase visualization, we comprehensively quantified the mHtt and non-mHtt proteins within the same aggregates across varying sizes, cell types, mHtt constructs, and subcellular locations. Our findings demonstrate a two-phase aggregate growth model with a distinct core-shell spatial organization, reveal significant heterogeneity in nucleus/cytoplasm compartmentalization specific to neurons, and identify previously unrecognized "gel-like" aggregates specifically in neuronal nuclei. These insights should advance our understanding of native polyQ aggregates and our proposed interaction coefficients may offer new quantitative parameters for developing effective HD therapies.

biophysics↗

bioRxiv2024

Host-derived Lactobacillus plantarum alleviates hyperuricemia by improving gut microbial community and hydrolase-mediated degradation of purine nucleosides

AbstractGut microbiota has been considered to be associated with the development of hyperuricemia (HUA) and gout. Some prebiotics from different sources had the potential alleviation function in HUA. However, whether host-derived potential probiotics, like Lactobacillus, from the gut of HUA animals could prevent the development of HUA is still uncertain. In this study, we established a HUA geese model and isolated a Lactobacillus plantarum strain, SQ001, from the cecum of HUA geese. Nucleoside co-culture and metabolomics analyses revealed that L. plantarum SQ001 is involved in the absorption and hydrolysis of nucleosides. Whole genome analysis showed there are four genes related with nucleosides hydrolysis in L. plantarum SQ001. The function of iunH, a nucleoside hydrolase gene, was further confirmed by heterologous expression and knockout assays. Oral administration of L. plantarum SQ001 in HUA geese models upregulated the Lactobacillus abundance and reduced serum uric acid (UA) levels. Likewise, in mouse models, L. plantarum SQ001 increased the L. plantarum abundance and lowered serum UA levels by reducing hepatic UA synthesis protein XO and renal UA reabsorption protein GLUT9 expression, while increasing renal UA excretion protein ABCG2 expression. Our findings demonstrated that host-derived probiotics from geese could alleviate gut microbe dysbiosis and HUA in its host and mouse model. This study provides insights into the potential probiotic role of Lactobacillus plantarum in HUA or gout therapy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/606206v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@698e7eorg.highwire.dtl.DTLVardef@a2091org.highwire.dtl.DTLVardef@e0348aorg.highwire.dtl.DTLVardef@19958ad_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Cortical gradient perturbation in attention deficit hyperactivity disorder correlates with neurotransmitter-, cell type-specific and chromosome- transcriptomic signatures

Neurofunctional dysregulations in spatially discrete areas or isolated pathways have been suggested as neural markers for attention deficit hyperactivity disorder (ADHD). However, multiscale perspectives into the neurobiological underpins of ADHD spanning multiple biological systems remain sparse. This points to the need of multi-levels of analysis encompassing brain functional organization and its correlation with molecular and cell-specific transcriptional signatures are stressed. Here, we capitalized on diffusion mapping embedding model to derive the functional connectome gradient, and deployed multivariate partial least square (PLS) method to uncover the enrichment of neurotransmitomic, cellular and chromosomal connectome-transcriptional signatures of ADHD. Compared to typical control, ADHD children presented connectopic cortical perturbations in lateral orbito-frontal and superior temporal regions, which had also been validated in another independent sample. This gradient-derived variants in ADHD further aligned spatially with distributions of GABAA/BZ and 5-HT2A receptors and co-varied with genetic transcriptional expression. Cognitive decoding and gene-expression annotation showed the correlates of these variants in memory, emotional regulation and spatial attention. Moreover, the gradient-derived transcriptional signatures of ADHD exhibited enriched expression of oligodendrocyte precursors and endothelial cells, and were mainly involved as variants of chromosome 18, 19 and X. In conclusion, our findings bridged in-vivo neuroimging assessed functional brain organization patterns to a multi-level molecular pathway in ADHD, possibly shedding light on the interrelation of biological systems that may coalesce to the emergence of this disorder.

neuroscience↗

bioRxiv2021

Super-Resolution Label-free Volumetric Vibrational Imaging

Innovations in high-resolution optical imaging have allowed visualization of nanoscale biological structures and connections. However, super-resolution fluorescence techniques, including both optics-oriented and sample-expansion based, are limited in quantification and throughput especially in tissues from photobleaching or quenching of the fluorophores, and low-efficiency or non-uniform delivery of the probes. Here, we report a general sample-expansion vibrational imaging strategy, termed VISTA, for scalable label-free high-resolution interrogations of protein-rich biological structures with resolution down to 82 nm. VISTA achieves decent three-dimensional image quality through optimal retention of endogenous proteins, isotropic sample expansion, and deprivation of scattering lipids. Free from probe-labeling associated issues, VISTA offers unbiased and high-throughput tissue investigations. With correlative VISTA and immunofluorescence, we further validated the imaging specificity of VISTA and trained an image-segmentation model for label-free multi-component and volumetric prediction of nucleus, blood vessels, neuronal cells and dendrites in complex mouse brain tissues. VISTA could hence open new avenues for versatile biomedical studies.

neuroscience↗

bioRxiv2019

Olfactory receptors tuned to volatile mustard oils in drosophilid flies

The diversity of herbivorous insects is attributed to their propensity to specialize on toxic plants. In an evolutionary twist, toxins betray the identity of their bearers when herbivores co-opt them as cues for host-plant finding, but the mechanisms underlying this process are poorly understood. We focused on Scaptomyza flava, an herbivorous drosophilid specialized on isothiocyanate (ITC)-producing (Brassicaceae) plants, and identified Or67b paralogs that were triplicated as mustard-specific herbivory evolved. Using heterologous systems for the expression of olfactory receptors, we found that S. flava Or67bs, but not homologs from microbe-feeding relatives, responded selectively to ITCs, each paralog detecting different ITC subsets. Consistent with this, S. flava was attracted to ITCs, as was Drosophila melanogaster expressing S. flava Or67b3 in the homologous Or67b olfactory circuit. Thus, our results show that plant toxins were likely co-opted as olfactory attractants through gene duplication and functional specialization (neofunctionalization and subfunctionalization) in drosophilid flies.

evolutionary biology↗

bioRxiv2019

Live-Cell Imaging and Quantification of PolyQ Aggregates by Stimulated Raman Scattering of Selective Deuterium Labeling

Huntingtons disease, a major neurodegenerative disorder, involves deposition of aggregation-prone proteins with long polyglutamine (polyQ) expansions. The ability to non-perturbatively visualize the formation of aggregates could offer new molecular insight for their pathologic roles. Here, we propose stimulated Raman scattering imaging of deuterium-labeled glutamine to investigate native polyQ aggregates in live cells with subcellular resolution. Through the enrichment of deuterated glutamine in the polyQ sequence of mutant Huntingtin (mHtt) proteins, we first achieved sensitive and specific SRS imaging of carbon-deuterium bonds (C-D) from aggregates without GFP labeling. These aggregates become 1.8-fold denser compared to those with GFP. Second, we performed ratiometric quantification, which revealed a dependence of protein compositions on aggregation sizes. Moreover, we calculated the absolute concentrations for sequestered mHtt and non-mHtt proteins within the same aggregates. Our method may readily reveal new features of polyQ aggregates and could be suited for in vivo investigations on multicellular organisms.

biophysics↗