Biology subjects

Liang, W.

Publications and source records attributed to Liang, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Reverberation exacerbates effects of interruption on auditory spatial selective attention

Everyday listening requires focusing on one talker while ignoring competing sounds, a process challenged by reverberation and unexpected distractions. Here, we asked whether reverberation decreases effects of distractions by reducing the salience of new onsets, or compounds disruption by increasing task difficulty. Across five online experiments, participants recalled spatialized syllable streams presented with or without interrupters under pseudo-anechoic and reverberant conditions. Interrupters consistently impaired recall, especially the syllables following the interrupter. For the syllable immediately after the interruption, this effect was larger in reverberation than in anechoic conditions. These results demonstrate that distractions are especially disruptive in reverberant settings.

neuroscience↗

bioRxiv2025

Ferrapoptosis: Discovery of a Hybrid Programmed Cell Death

Traditional taxonomies classify ferroptosis and apoptosis as distinct forms of regulated cell death. Here, we challenge this view by defining and validating a previously unrecognized neuronal death entity in traumatic brain injury (TBI), which we term "Ferrapoptosis". This hybrid mode of death is characterized by the coexistence of ferroptotic and apoptotic molecular and ultrastructural features within the same neuron-- ultrastructural alterations that cannot be fully characterized by any known cell death modalities. By integrating single-cell transcriptomics with multi-layered functional assays, we show that Ferrapoptosis dominates in severe injury and the acute phase, and is critically driven by mitochondrial oxidative stress. Over time, its predominance is gradually replaced by death modes in which either ferroptosis or apoptosis alone becomes the major pathway. Genome-wide CRISPR screening further identifies Smg7 as a key regulator that synchronously activates both death programs to drive the hybrid phenotype, whereas genetic or viral inhibition of Smg7 reduces Ferrapoptosis and promotes neurological recovery after TBI in mice. Our work systematically delineates a previously unrecognized form of cell death and its pathogenetic mechanisms, providing experimental evidence to refine cell death classification, and suggesting a conceptual strategy for treating complex diseases such as TBI by targeting shared regulatory nodes. HIGHLIGHTSO_LIDefined and validated a previously unrecognized cell death modality, termed "Ferrapoptosis". C_LIO_LIElucidated the ordered pattern of Ferrapoptosis across key stages of TBI pathogenesis. C_LIO_LIRevealed mitochondrial oxidative stress as the pivotal hub integrating ferroptosis and apoptosis. C_LIO_LIIdentify Smg7 as a core driver of Ferrapoptosis and a promising neuroprotective target. C_LI

cell biology↗

bioRxiv2025

Transcriptional regulation of disease-relevant microglial activation programs

Microglia, the brains innate immune cells, can adopt a wide variety of activation states relevant to health and disease. Dysregulation of microglial activation occurs in numerous brain disorders, and driving or inhibiting specific states could be therapeutic. To discover regulators of microglia activation states, we conducted CRISPR interference screens in iPSC-derived microglia for inhibitors and activators of six microglial states. We characterized 31 regulators at the single-cell transcriptomic and cell-surface proteome level in two distinct iPSC-derived microglia models, uncovering new protein markers of relevant states. We functionally characterized several multi- state regulators. ZNF532 and PRDM1 knockdown drive disease-associated, lipid-rich signatures and enhance phagocytosis while showing opposing effects on antigen-presentation signatures. DNMT1 knockdown results in widespread loss of methylation, activating negative regulators of interferon signaling. These findings provide a framework to direct microglial activation to selectively enrich microglial activation states, define their functional outputs, and inform future therapies. HighlightsO_LICRISPRi screening reveals novel regulators of six microglia activation states C_LIO_LIMulti-modal single-cell screens highlight new markers of microglial states C_LIO_LIDifferent iPSC-microglia models show different landscapes of activation states at baseline C_LIO_LILoss of DNMT1 leads to widespread DNA demethylation, promoting some states but limiting the interferon-response state C_LIO_LILoss of PRDM1 or ZNF532 drives the microglial disease-associated state C_LI

neuroscience↗

bioRxiv2025

TaPGS1 Driven Flavonol Accumulation Delays Endosperm Cellularization and Enlarges Wheat Grains

Flavonols play a crucial role in seed development by regulating multiple physiological processes, including seed coat pigmentation, dormancy, fertilization, and endosperm formation. Notably, flavonols influence the polar transport of auxin, thereby affecting seed growth dynamics. In our previous work, we found that overexpression of the wheat bHLH transcription factor TaPGS1 results in increased grain size; however, the underlying mechanism remained unclear. In this study, metabolomic and transcriptomic analyses of TaPGS1 overexpressing wheat lines revealed enhanced flavonol accumulation and upregulation of key flavonol biosynthetic genes. Further investigations suggested that flavonol accumulation in the seed coat may disrupt auxin transport, leading to localized auxin buildup, delayed endosperm cellularization, and an increase in endosperm cell number. These changes collectively contribute to grain enlargement. Our findings uncover a TaPGS1 flavonol regulatory module that links auxin distribution to endosperm development and seed size control in wheat.

plant biology↗

bioRxiv2025

Regulators of Interferon-Responsive Microglia Uncovered by Genome-wide CRISPRi Screening

Microglia dynamically support brain homeostasis through the induction of specialized activation programs or states. One such program is the Interferon-Responsive Microglia state (IRM), which has been identified in developmental windows, aging, and disease. While the functional importance of this state is becoming increasingly clear, our understanding of the regulatory networks that govern IRM induction remain incomplete. To systematically identify genetic regulators of the IRM state, we conducted a genome-wide CRISPR interference (CRISPRi) screen in human iPSC-derived microglia (iPS-Microglia) using IFIT1 as a representative IRM marker. We identified 772 genes that modulate IRM, including canonical type I interferon signaling genes (IFNAR2, TYK2, STAT1/2, USP18) and novel regulators. We uncovered a non-canonical role for the CCR4-NOT complex subunit CNOT10 in IRM activation, independent of its traditional function. This work provides a comprehensive resource for dissecting IRM biology and highlights both established and novel targets for modulating microglial interferon signaling in health and disease.

neuroscience↗

bioRxiv2025

Mesoscopic SCAPE Microscope with a Rescanned, Super-oblique Illumination Plane

Investigating structural and functional dynamics across large spatial scales in living organisms calls for volumetric microscopy that combines a wide field of view (FOV), high spatial resolution, and sufficient temporal resolution. Swept confocally-aligned planar excitation (SCAPE) microscopy offers a compelling balance of optical sectioning, cellular resolution, and high-speed volumetric imaging. However, extending SCAPE to mesoscopic scales has been hindered by the limited tilting angle of the oblique illumination light sheet achievable with commercial low-magnification objectives. Here, we present a mesoscopic SCAPE microscope that overcomes this constraint by implementing a super-oblique light sheet--tilted up to ~60{degrees} relative to the optical axis of a 0.5-NA primary objective--enabled by an air-to-water bridging reflector. In addition, we introduce a single-galvanometer, self-conjugating rescanning strategy that allows arbitrary customization of the optical-to-mechanical angle ratio. This innovation accommodates the reversed and modulated scan displacement of the reflected light sheet and preserves descanned epi-fluorescence detection. Together, these advancements enable our mesoscopic SCAPE microscope to achieve a lateral FOV of 5.0 mm x 2.9 mm, cellular-level spatial resolution (~9.4 m x ~5.9 m lateral, and ~6.0 m axial), and a volumetric imaging rate of 9 volumes per second.

bioengineering↗

bioRxiv2025

Ethylene modulates cell wall mechanics for root responses to compaction

Soil stresses impact crop yields, presenting global agricultural challenges. Soil compaction triggers root length reduction and radial expansion driven by the plant hormone ethylene. We report how ethylene controls cell wall properties to promote root radial expansion. We demonstrate how soil compaction stress, via ethylene, upregulates Auxin Response Factor1 in the root cortex, which represses Cellulose Synthase (CESA) genes. CESA repression drives radial expansion of root cortical cells by modifying the thickness and mechanics of their cell walls, which result in a "stiff epidermis-soft cortex" contrast. Our research thus connects ethylene signaling with root mechanics via cell wall strength, and reveals how dynamic regulation of cellulose synthesis crucially controls root growth in compacted soil.

plant biology↗

bioRxiv2025

Single-nuclear transcriptomics of lymphedema-associated adipose reveals a pro-lymphangiogenic stromal cell population

Chronic lymphedema is a progressive, disfiguring disease that results from dysfunction of the lymphatic vasculature, causing distal accumulation of interstitial fluid, localized development of tissue edema, and expansion of subcutaneous adipose tissue (SAT). As the molecular mechanisms governing SAT remodeling in this disease are unclear, we performed single-nucleus RNA sequencing on paired control and affected SAT biopsies from patients with unilateral lymphedema. Lymphedema samples were characterized by expansion of SAA+ adipocytes, pro-adipogenic stem cells, and proliferation of lymphatic capillaries. A GRIA1+ lymphedema-enriched stromal cell population expressing VEGFC, ADAMTS3, and CCBE1 was identified, suggesting an enhanced axis of communication between adipose stem and progenitor cells (ASPCs) and lymphatic endothelial cells. Furthermore, lymphedema ASPC-conditioned media promoted lymphatic endothelial tube elongation and proliferation in vitro. These findings indicate a critical role for ASPCs in regulating adipocyte differentiation and lymphatic vascular remodeling in lymphedema, and provide a valuable resource for better understanding this disease.

cell biology↗

bioRxiv2024

Morphological brain alterations and morphological brain network disorganizations in heroin and methamphetamine abstinent patients

Heroin and methamphetamine are the two common types of drugs abused, which poses significant health risks. However, the neural mechanisms underlying the effects of drug addiction on human brain are unclear. In this study, we collected T1-weighted magnetic resonance imaging data from 26 heroin abstinent (HA) patients, 24 methamphetamine abstinent (MA) patients and 32 healthy controls. Four surface-based morphological features including cortical thickness (CT), fractal dimension (FD), gyrification index (GI), and sulcal depth (SD) were calculated, and further used to construct the morphological brain networks. We observed the common CT reductions of the right TE 1.0 and TE 1.2 and SD reductions of the right intermediate lateral area 20 for HA and MA patients, HA-specific CT reductions in the left area 2, and the MA-specific GI reductions in the left medial area 6 and right dorsomedial parietooccipital sulcus. For the morphological brain networks, HA patients exhibited the global disorganizations (higher shortest path length) in CT-based networks, whereas MA patients showed the disrupted nodal efficiency of the left medial area 38 in CT-based networks, the right caudal area 7 in GI-based networks, and the right inferior occipital gyrus in SD-based networks. Furthermore, the altered SD of HA patients and disrupted nodal efficiency of MA patients were associated with drug abuse-related clinical variables. Our findings suggest the morphological index-dependent effects of drug addiction on human brain morphology, and indicate the differential neural mechanism underlying heroin and methamphetamine abuses which attack the global and local information transfer of morphological brain networks, respectively.

neuroscience↗

bioRxiv2024

A necroptotic-to-apoptotic signaling axis underlies inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic condition caused by altered cytokine signaling, maladaptive immunity, dysbiosis, and intestinal barrier dysfunction. Patients with IBD receive therapy to correct these imbalances and achieve remission. However, most patients relapse, suggesting that pathological mechanisms persist during remission. Here, we show that excess epithelial cell death is an underlying feature of IBD that arises in patients in remission and on advanced therapy. Mechanistically, nascent inflammation reprograms epithelial cells into a macrophage-like state that promotes RIPK1-independent necroptotic signaling, then triggers iNOS-mediated mitochondrial apoptosis of absorptive epithelial cells and PUMA-mediated intestinal stem cell death. These findings reveal aberrant epithelial cell death signaling as a hallmark of IBD that occurs early in mucosal lesion development and persists despite current therapeutic approaches. One-Sentence SummaryEpithelial cell death is dysregulated in patients with inflammatory bowel disease.

cell biology↗

bioRxiv2024

Conjugation of dn-OPDA with amino acids inhibits its hormonal bioactivity in Marchantia polymorpha

Jasmonates are important phytohormones activating plant tolerance to biotic and abiotic stress, as well as different development processes. A conserved signalling pathway activated by distinct hormones in different plant species mediates these responses: dinor-12-oxo-phytodienoic acid (dn-OPDA) isomers in bryophytes and lycophytes, and JA-Ile in most vascular plants. The final responses depend, in many cases, on the accumulation of specialized metabolites. To identify novel compounds regulated by the dn-OPDA pathway in Marchantia, untargeted metabolomic analyses were carried out in response to dn-OPDA-regulated stress. A novel group of molecules were identified as dn-OPDA-amino acid conjugates (dn-OPDA-aas), and their accumulation after wounding and herbivory confirmed by targeted metabolic profiling in Marchantia and all species in which we previously found dn-iso-OPDA. Mutants in GRETCHEN-HAGEN 3A (MpGH3A) failed to accumulate dn-OPDA-aa conjugates, and showed a constitutive activation of the OPDA pathway and increased resistance to herbivory. Our results show that dn-iso-OPDA bioactivity is reduced by conjugation with amino acids. Therefore, a dichotomous role of jasmonate conjugation in land plants is highlighted: jasmonic acid (JA) conjugation with isoleucine (Ile) produce the bioactive JA-Ile in tracheophytes, whereas conjugation of dn-iso-OPDA with different amino acids disactivate the hormone in bryophytes and lycophytes.

plant biology↗

bioRxiv2024

Differential antigenic imprinting effects between influenza H1N1 hemagglutinin and neuraminidase in a mouse model

Understanding how immune history influences influenza immunity is essential for developing effective vaccines and therapeutic strategies. This study investigates the antigenic imprinting of influenza hemagglutinin (HA) and neuraminidase (NA) using a mouse model with sequential infection by four seasonal H1N1 strains. Our findings reveal that, among pre-2009 H1N1 strains, the extent of infection history correlates with the restriction of antibody responses to antigenically drifted HA, but not NA. This suggests the mouse model failed to recapitulate NA imprinting in humans, likely due to the difference in NA immunodominance hierarchy between humans and mice. Nevertheless, pre-existing antibodies induced by infection with pre-2009 influenza virus impeded both functional HA and NA antibody responses against a 2009 pandemic H1N1 strain. Overall, this study provides insights into antigenic imprinting for influenza virus, as well as the limitations of using mouse models for studying antigenic imprinting. ImportanceInfluenza viruses continue to pose a significant threat to human health, with vaccine effectiveness being a persistent concern. One important factor is the individual immune history can influence subsequent antibody responses. While many studies have focused on how pre-existing antibodies influence the induction of anti-HA antibodies after influenza virus infections or vaccinations, the impact on anti-NA antibodies has been less extensively investigated. In this study, using a mouse model, we highlighted within the pre-2009 H1N1 strains, a greater extent of immune history negatively affected anti-HA antibodies but positively influenced anti-NA antibody responses. However, for the 2009 pandemic H1N1 strain, which underwent with antigenic shift, both anti-HA and anti-NA antibody responses have been impeded by the antibodies induced by pre-2009 H1N1 virus infection. These findings have important implications for enhancing our understanding of antigenic imprinting on anti-HA and anti-NA antibody response and for developing more effective vaccination strategies.

immunology↗

bioRxiv2024

Cervical collagen network porosity assessed by SHG endomicroscopy distinguishes preterm and normal pregnancy - a pilot study

Structured AbstractO_ST_ABSBackgroundC_ST_ABSPreterm birth (PTB) is a global public health issue affecting millions of newborns every year. Orchestrated remodeling of the cervix is essential for normal pregnancy and birth, while PTB is closely related with premature cervical ripening and loss of cervical mechanical strength. The structure and organization of fibrillar collagen in the extracellular matrix are of vital importance to the biomechanical properties of the cervix. Second harmonic generation (SHG) microscopy has proved capable of revealing the progressive changes in cervical collagen morphology over the course of pregnancy. To translate this promising imaging technology to clinical practice, a flexible SHG endomicroscope has long been envisaged for label-free, non-invasive visualization of cervical collagen architecture and for assessment of PTB risk. ObjectiveTo evaluate the potential of our newly-developed SHG endomicroscope for imaging-based differentiation of cervical collagen architecture between normal pregnant mice and RU486/mifepristone-induced PTB mouse models. Study DesignWe undertook endomicroscopy SHG imaging of cervical collagen on two types of ex vivo samples: 1) frozen cervical tissue sections ([~]50 {micro}m thick) and 2) resected intact cervices, and performed SHG-image-based quantitative collagen morphology analysis to distinguish RU486 mouse models from normal pregnant mice. ResultsEndomicroscopic SHG images of cervical tissue sections from mifepristone-treated mouse models exhibit statistically larger collagen fiber diameter, increased pore size, and reduced pore numbers than those of normal pregnant mice. Similar changes are also observed on SHG images of subepithelial collagen fibers acquired from intact cervices by the endomicroscope. ConclusionThe experiment results demonstrated that SHG endomicroscopy along with quantitative image analysis holds promising potential for clinical assessment of cervical collagen remodeling and preterm birth risk.

bioengineering↗

bioRxiv2024

Deep learning-based Spatial Feature Extraction for Prognostic Prediction of Hepatocellular Carcinoma from Pathological Images

The spatial structures of various cell types in tumor tissues have been demonstrated to be able to provide useful information for the evaluation of the disease progression as well as the responsiveness to targeted therapies. Therefore, powered by machine-learning, several image segmentation methods have been developed to identify tumor-cells, stromal, lymphocytes, etc., in hematoxylin and eosin (H&E) stained pathological images. However, the quantitative and systematic characterization of the spatial structures of various cell types is still challenging. In this work, we first developed a robust procedure based on deep learning to precisely recognize cancer cells, stromal and lymphocytes in H&E-stained pathological images of hepatocellular carcinoma (HCC). In order to quantitatively characterize the composition and spatial arrangement of the tumor microenvironment, we then systematically constructed 109 spatial features based on locations of the 3 major types of cells in the H&E images. Interestingly, we discovered that the absolute values of several spatial features are significantly associated with patient overall survival in two independent patient cohorts, such as the cellular diversity around stromal cells (StrDiv), the average distance between stromal cells (StrDis), the coefficient of variation of the tumor-cell polygon area in the Voronoi diagram (TumCV), etc., based on univariate analysis. In addition, multivariate Cox regress analyses further demonstrated that StrDiv and StrDis are independent survival prognostic factors for HCC patient from The Cancer Genome Atlas Program (TCGA). Furthermore, we demonstrated that a combination analysis with cell spatial features, i.e. StrDiv or TumCV, and another important clinical feature, i.e. microvascular invasion (MVI), can further improve the efficacy of prognostic stratification for patients from the Beijing Hospital cohorts. In summary, the spatial features of tumor microenvironment enabled by the digital image analysis pipeline developed in this work can be effective in patient stratification, which holds the promise for its usage in predicting the therapeutic response of patients in the future.

bioinformatics↗

bioRxiv2024

A single-cell 3D spatiotemporal multi-omics atlas from Drosophila embryogenesis to metamorphosis

The development of a multicellular organism is a highly intricate process tightly regulated by numerous genes and pathways in both spatial and temporal manners. Here, we present Flysta3D, a comprehensive multi-omics atlas of the model organism Drosophila, spanning its developmental lifespan from embryo to pupa. Our datasets encompass 3D single-cell spatial transcriptomic, single-cell transcriptomic, and single-cell chromatin accessibility information. By integrating these multi-dimensional data, we constructed cell state trajectories that uncover the detailed profiles of tissue development. With a focus on the central nervous system (CNS) and midgut, we dissected the spatiotemporal dynamics of gene regulatory networks, cell type diversity, and morphological changes from a multi-omics perspective. This extensive atlas provides an unprecedentedly rich resource and serves as a systematic platform for studying Drosophila development with integrated single-cell data at an ultra-high spatiotemporal resolution.

developmental biology↗

bioRxiv2024

The J-Like Protein ARC6 Regulates Chloroplast FtsZ-Ring Assembly through Fine-tuning ARC3 Activity in Arabidopsis

Chloroplast division is initiated by the establishment of the stromal FtsZ ring (Z ring). Assembly and positioning of the Z ring are governed by the chloroplast Min system, which inhibits Z-ring formation everywhere but the middle of the chloroplast. ACCUMULATION AND REPLICATION OF CHLOROPLASTS3 (ARC3), the core component of this system, is a direct inhibitor of Z-ring assembly. Regulation of ARC3 activity is vital thus for chloroplast division. Here, we report that ARC6, which localizes on the chloroplast inner envelope membrane, interacts with ARC3 and acts upstream of ARC3 during chloroplast division. We show that the C-terminal MORN domain of ARC3, demonstrated previously to prevent ARC3-FtsZ interaction, binds to the J-like domain (JLD) of ARC6, enabling full-length ARC3 to interact with FtsZ proteins and activating the inhibitory activity of ARC3 on the assembly of FtsZ filaments. Overexpression of a JLD-deleted version of ARC6 causes disruption of Z-ring formation in an ARC3-dependent manner. Finally, we reveal that ARC6 recruits ARC3 to the middle of the chloroplast. Our findings suggest a model whereby ARC6 regulates the assembly and positioning of the Z ring through fine-tuning the inhibitory activity of ARC3 at the chloroplast division site. One Sentence SummaryThe chloroplast membrane protein ARC6 recruits ARC3 to the chloroplast division site and regulates the assembly of the FtsZ ring by fine-tuning ARC3 activity through its J-like domain. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (https://academic.oup.com/plcell/pages/General-Instructions) is: Cheng Chen (cgchen@sjtu.edu.cn).

plant biology↗

bioRxiv2023

Long noncoding RNA Hottip maintained skeletal homeostasis via suppressing the enhancer of zeste homolog 2 (Ezh2)/histone methylation regulatory axis

Recent evidence suggests that long noncoding RNAs (lncRNAs) play a crucial role in regulating bone remodeling and skeletal homeostasis by coordinating the development of osteoblasts and osteoclasts. Several lncRNAs have been identified to participate in bone formation and resorption processes. Among them, the well-known oncogenic lncRNA, Hottip, has been reported to be involved in osteogenesis regulation. However, the specific function and underlying mechanisms remain poorly understood. In this study, we investigated the role of lncRNA Hottip in bone remodeling and skeletal homeostasis. Hottip knockout mice exhibited disrupted bone metabolism, abnormal bone tissue, and compromised bone quality, resulting in delayed fracture healing. In vitro experiments demonstrated that Hottip knockdown inhibited osteoblast differentiation while promoting osteoclast differentiation, with the opposite effect observed upon Hottip overexpression. Mechanistically, Hottip physically interacted with EZH2, leading to its degradation and facilitating the transcription of osteogenic genes by suppressing H3K9me3 and H3K27me3. In vivo experiments further validated the potential of Hottip overexpression to promote bone regeneration and accelerate fracture healing. In conclusion, our study reveals Hottip as a critical regulator in the differentiation of osteoblasts and osteoclasts, crucial for maintaining skeletal homeostasis. This lncRNA shows potential as a promising therapeutic target for bone regeneration.

cell biology↗

bioRxiv2023

An axonemal intron splicing program sustains Plasmodium male development

Differentiation of male gametocyte into flagellated fertile male gamete relies on the axoneme assembly, a major component of male development for mosquito transmission of malaria parasite. RNA-binding protein (RBP)-mediated post-transcription regulation plays important roles in eukaryotic sexual development, including the Plasmodium female development. However, the role of RBP in defining the Plasmodium male transcriptome and its function in the male gametogenesis remain elusive. Here, we screened the gender expression of the genome-wide RBPs and identified an undescribed male-specific RBP gene Rbpm1 in the Plasmodium. RBPm1 is localized in the nucleus of male gametocytes. RBPm1-deficient parasites fail to assemble the axoneme for male gametogenesis and thus mosquito transmission. RBPm1 interacts with spliceosome E complex and regulates splicing initiation of certain introns in a group of 26 axonemal genes. RBPm1 deficiency results in intron retention and protein loss of these axonemal genes. Intron deletion restores axonemal proteins expression and partially rectifies axonemal defects in RBPm1-null gametocytes. Further splicing assays in both reporter and endogenous genes exhibit stringent recognition of the axonemal introns by RBPm1. Therefore, the splicing activator RBPm1 and its target introns constitute an axonemal intron splicing program in the post-transcription regulation essential for Plasmodium male development.

microbiology↗