Biology subjects

Fang, N.

Publications and source records attributed to Fang, N..

10 recordsLinked to original sources

bioRxiv2025

Gasdermin E couples mitochondrial damage to pyroptotic neurodegeneration in Parkinson disease

Parkinsons disease (PD) features progressive loss of nigrostriatal dopamine neurons, but how mitochondrial damage engages programmed cell death pathways remains unresolved. Here, we identify gasdermin E (GSDME), the caspase-3-activated executor of pyroptosis, as a critical mediator of neurodegeneration in toxin-based PD models. In primary neurons and SH-SY5Y cells, the mitochondrial complex I inhibitor MPTP/MPP triggered caspase-3 activation, GSDME cleavage, and lytic membrane rupture. Genetic silencing of Gsdme or its transcriptional regulator SP1 reduced neuronal death. In vivo, Gsdme deficiency preserved substantia nigra pars compacta dopaminergic neurons, improved motor performance, and mitigated anxiety- and depression-like behaviors after MPTP administration. Loss of Gsdme also dampened microglial and astrocytic activation and lowered proinflammatory cytokines in striatum and substantia nigra. Mechanistically, cleaved GSDME localized to mitochondria, disrupted membrane potential, increased reactive oxygen species, and precipitated organelle injury, thereby coupling mitochondrial dysfunction to pyroptotic cell death. These findings identify GSDME-mediated pyroptosis as a mechanistic link between mitochondrial toxicity and neuroinflammation in PD and nominate GSDME as a therapeutic entry point to slow disease progression. SignificanceHow mitochondrial injury kills dopamine neurons in Parkinsons disease is a central unresolved question. We show that the pyroptosis executor GSDME is required for neurodegeneration and neuroinflammation in MPTP models, mechanistically linking caspase-3 activation and mitochondrial damage to lytic cell death. Targeting GSDME may provide a strategy to protect vulnerable neurons in PD. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/694264v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@15364e7org.highwire.dtl.DTLVardef@57b65org.highwire.dtl.DTLVardef@1e85108org.highwire.dtl.DTLVardef@1200d34_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsGSDME drives PD-linked neuronal loss. Silencing GSDME (or its transcriptional factor Sp1) ameliorates MPTP-triggered neuronal cell death. Genetic ablation of Gsdme is protective in the MPTP-induced PD mouse model. Gsdme-/-mice retain nigrostriatal DA neurons, show improved motor and affective behaviors, and exhibit reduced microglial and astrocytic activation and cytokines release upon MPTP treatment. Cleaved GSDME accumulates on mitochondria, collapses {Delta}{Psi}m, raises ROS, and links mitochondrial toxicity to pyroptosis, thus positioning GSDME as a tractable target to slow PD progression.

neuroscience↗

bioRxiv2025

The relationship between pain and depression among middle-aged and older adults in China: Functional limitation as a mediating factor

AimThe association between pain and depression has become a matter of considerable concern in public health. Nevertheless, the fundamental reasons connecting these two phenomena remain unclear. This study sought to explore whether functional limitation serves as an intermediary factor in the link between pain and depression. Materials and MethodsThis analysis enrolled 6046 adults aged 45 and older using data from the 2015 wave of the China Longitudinal Study of Health and Retirement (CHARLS)dataset. Statistical approaches included conducting linear regression models alongside bootstrap analyses to evaluate whether functional limitation mediated the association between pain and depression. ResultsIn models adjusted for confounders, pain intensity showed a positive association with depressive symptoms ({beta} = 0.271, P < 0.001) and also exhibited a positive link with functional limitation ({beta} = 0.223, P < 0.001). The pathway between pain and depression exhibited a functional limitation that constituted 14.2% of the total effect, with the mediating pathway magnitude estimated at a*b = 0.615(95% CI: 0.521- 0.720). ConclusionsOur findings indicated that pain directly influences depression and also affects them indirectly through functional limitation. Interventions focused on pain management and addressing functional limitation may effectively prevent and alleviate depressive symptoms.

animal behavior and cognition↗

bioRxiv2025

Lysosome-like structures in the nucleolus mediate H2Aub degradation under glucose starvation

Glucose starvation leads to the degradation of intracellular proteins to generate amino acids for energy production. However, it remains unclear which proteins undergo rapid degradation to supply amino acids as energy sources during glucose starvation. To investigate the molecular mechanism underlying the transition of carbon source from glucose to proteins under glucose starvation, we first employed quantitative proteomics to examine the impact of glucose deprivation on protein levels. We discovered that histone degradation produces the highest amount of glutamine during glucose starvation. Further investigation revealed that histone H2A undergo degradation in the nucleolus in the form of mono-ubiquitination (H2Aub). The nucleolus contains lysosome-like structures that degrade monoubiquitinated histones, potentially participating in the carbon source shift from glucose to amino acids for energy production. Through preliminary screening, we identified Midnolin as the receptor for H2Aub, mediating its degradation in nucleolar lysosome-like structures. Dysregulation of carbon source transition from glucose to proteins, through knockdown of Midnolin results in cell cycle arrest, affecting cellular growth and proliferation. In conclusion, our findings demonstrate that nucleolar lysosome-like structures degrading monoubiquitinated histones exist during glucose starvation, which may play crucial roles in the carbon source transition from glucose to proteins, providing new potential therapeutic targets for metabolic disorders.

cell biology↗

bioRxiv2025

Interpretable adenylation domain specificity prediction using protein language models

Natural products have long been a rich source of diverse and clinically effective drug candidates. Non-ribosomal peptides (NRPs), polyketides (PKs), and NRP-PK hybrids are three classes of natural products that display a broad range of bioactivities, including antibiotic, antifungal, anticancer, and immunosuppressant activities. However, discovering these compounds through traditional bioactivity-guided techniques is costly and time-consuming, often resulting in the rediscovery of known molecules. Consequently, genome mining has emerged as a high-throughput strategy to screen hundreds of thousands of microbial genomes to identify their potential to produce novel natural products. Adenylation domains play a key role in the biosynthesis of NRPs and NRP-PKs by recruiting substrates to incrementally build the final structure. We propose MASPR, a machine learning method that leverages protein language models for accurate and interpretable predictions of A-domain substrate specificities. MASPR demonstrates superior accuracy and generalization over existing methods and is capable of predicting substrates not present in its training data, or zero-shot classification. We use MASPR to develop Seq2Hybrid, an efficient algorithm to predict the structure of hybrid NRP-PK natural products from microbial genomes. Using Seq2Hybrid, we propose putative biosynthetic gene clusters for the orphan natural products Octaminomycin A, Dityromycin, SW-163B, and JBIR-39.

bioinformatics↗

bioRxiv2024

CellFM: a large-scale foundation model pre-trained on transcriptomics of 100 million human cells

The rapid evolution of single-cell sequencing technologies has facilitated precise transcriptomics profiling at the single-cell level, shedding light on the intricate heterogeneity within cellular populations. Despite these advances, the inherent diversity of cells and data challenges such as noise, batch effects, and sparsity, underscores the pressing need for a unified model to learn and represent cellular states effectively. Single-cell Large Language Models (LLMs) have been crafted to bridge this gap yet exhibit limited performance on human cells. This short-fall may stem from the confounding effects of training data from diverse species, partly because of limited cells for the single species. Here, we have compiled a dataset of approximately 100 million human cells sequenced by multiple technolo-gies from human single-cell datasets with various file types deposited in public databases and websites. Leveraging these extensive data cohorts, we developed CellFM, a robust single-cell foundation model with an impressive 800 million parameters, marking an eight-fold increase over the current largest single-species model. To ensure the training of CellFM on the MindSpore AI framework from Huawei, we have integrated RetNet, a Transformer architecture variant with lin-ear complexity for a balance between efficiency and performance, serving as the backbone of our model. Our comprehensive experiments have shown that CellFM outperforms existing models across diverse applications, such as cell annotation, perturbation prediction, and gene function prediction.

bioinformatics↗

bioRxiv2023

SynEcoSys: a multifunctional platform of large-scale single-cell omics data analysis

Next generation sequencing technologies enable the analysis of the transcriptomes of individual cells, providing a higher resolution of gene expression and function at the single cell level. Various single-cell data are continuously generated every year, covering fields from scientific research to clinical development. The fast-growing public datasets are collected by distinctive platforms, which are designed to facilitate biological discoveries, disease diagnosis, and new treatments. However, these platforms are hard to meet the urgency of having a unified data integration pipeline to improve comparability between datasets. Here we present SynEcoSys, an online multifunctional platform for single-cell transcriptomic data analysis, visualization, and exploration. SynEcoSys by Singleron Biotechnologies currently provides a massive collection of publicly available single-cell sequencing dataset, involving 46,326,175 cells from 731 datasets across multiple platforms and species. All datasets are generated with a strict and uniform data analysis pipeline and cell marker-based manual annotation, thus facilitating more comprehensive and reliable data mining. SynEcoSys is available at: https://www.synecosys.com.

bioinformatics↗

bioRxiv2022

Arc ubiquitination regulates endoplasmic reticulum-mediated Ca2+ release and CaMKII signaling

Synaptic plasticity relies on rapid, yet spatially precise signaling to alter synaptic strength. Arc is a brain enriched protein that is rapidly expressed during learning-related behaviors and is essential for regulating metabotropic glutamate receptor-mediated long-term depression (mGluR-LTD). We previously showed that disrupting the ubiquitination capacity of Arc enhances mGluR-LTD; however, the mechanism by which this occurs and its consequences on other mGluR-mediated signaling events is unknown. Here we show that disrupting Arc ubiquitination on key amino acid residues leads to derangements in Ca2+ release from the endoplasmic reticulum (ER) during pharmacological activation of Group I mGluRs. These alterations were observed in all neuronal subregions except secondary branchpoints. Deficits in Arc ubiquitination increased Arc self-association and enhanced its interaction with calcium/calmodulin-dependent protein kinase IIb (CaMKIIb) and constitutively active forms of CaMKII. Notably, these interactions were also excluded at secondary branchpoints. Finally, disruptions in Arc ubiquitination were found to increase Arc interaction with the integral ER protein Calnexin. These results suggest a previously unknown role for Arc ubiquitination in the fine tuning of ER-mediated Ca2+ signaling that is needed for mGluR-LTD, which in turn, may regulate CaMKII and its interactions with Arc.

neuroscience↗

bioRxiv2021

The E3 ubiquitin ligase RNF216/TRIAD3 is a central regulator of the hypothalamic-pituitary-gonadal axis

RNF216/TRIAD3 is an E3 ligase that ubiquitinates substrates in the nervous system. Recessive mutations in RNF216/TRIAD3 cause Gordon Holmes syndrome (GHS), where hypogonadotropic hypogonadism is a core phenotype. However, the functions of RNF216/TRIAD3 within the neuroendocrine system are not well-understood. Here, we used the CRISPR-Cas9 system to knock out Rnf216/Triad3 in GT1-7 cells, a GnRH immortalized cell line derived from mouse hypothalamus. Rnf216/Triad3 knockout cells had decreased steady state Gnrh and reduced calcium transient frequency. To address functions of RNF216/TRIAD3 in vivo, we generated a Rnf216/Triad3 constitutive knockout (KO) mouse. KO mice of both sexes showed reductions in GnRH and soma size. Furthermore, KO mice exhibited sex-specific phenotypes with males showing gonadal impairment and derangements in gonadotropin release compared to KO females, which only had irregular estrous cyclicity. Our work shows that dysfunction of RNF216/TRIAD3 affects the HPG axis in a sex-dependent manner, implicating sex-specific therapeutic interventions for GHS. HighlightsO_LIRnf216/Triad3 controls Gnrh and intrinsic hypothalamic cell activity C_LIO_LIRnf216/Triad3 knockout male mice have greater reproductive impairments than females C_LIO_LIRnf216/Triad3 controls the HPG axis at multiple levels C_LI

neuroscience↗

bioRxiv2020

Resolving Cargo-motor-track Interactions in Living Cells with Bifocal Parallax Single Particle Tracking

Resolving coordinated biomolecular interactions in living cellular environments is vital for understanding the mechanisms of molecular nanomachines. The conventional approach relies on localizing and tracking target biomolecules and/or subcellular organelles labeled with imaging probes. However, it is challenging to gain information on rotational dynamics, which can be more indicative of the work done by molecular motors and their dynamic binding status. Herein, a bifocal parallax single particle tracking method using half-plane point spread functions has been developed to resolve the full-range azimuth angle (0-360°), polar angle, and 3D displacement in real time under complex living cell conditions. Using this method, quantitative rotational and translational motion of the cargo in a 3D cell cytoskeleton was obtained. Not only well-known active intracellular transport and free diffusion were observed but new interactions, tight attachment and tethered rotation, were discovered for better interpretation of the dynamics of cargo-motor-track interactions at various types of microtubule intersections.Significance Statement Translation and rotational motion of cargo during pauses at the microtubule intersections in living cells were revealed by high-accuracy three-dimensional single particle rotational tracking. The current study demonstrates the potential of studying coordinated interactions in living cellular environments by resolving characteristic rotational motions.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biophysics↗

bioRxiv2020

Specific ACE2 Expression in Cholangiocytes May Cause Liver Damage After 2019-nCoV Infection

A newly identified coronavirus, 2019-nCoV, has been posing significant threats to public health since December 2019. ACE2, the host cell receptor for severe acute respiratory syndrome coronavirus (SARS), has recently been demonstrated in mediating 2019-nCoV infection. Interestingly, besides the respiratory system, substantial proportion of SARS and 2019-nCoV patients showed signs of various degrees of liver damage, the mechanism and implication of which have not yet been determined. Here, we performed an unbiased evaluation of cell type specific expression of ACE2 in healthy liver tissues using single cell RNA-seq data of two independent cohorts, and identified specific expression in cholangiocytes. The results indicated that virus might directly bind to ACE2 positive cholangiocytes but not necessarily hepatocytes. This finding suggested the liver abnormalities of SARS and 2019-nCoV patients may not be due to hepatocyte damage, but cholangiocyte dysfunction and other causes such as drug induced and systemic inflammatory response induced liver injury. Our findings indicate that special care of liver dysfunction should be installed in treating 2019-nCoV patients during the hospitalization and shortly after cure.

genomics↗