Biology subjects

Chen, Y.-R.

Publications and source records attributed to Chen, Y.-R..

9 recordsLinked to original sources

bioRxiv2026

HSC70 prevents TDP-43 nuclear puncta formation and toxicity in a novel nuclear puncta cell model for ALS

Amyotrophic lateral sclerosis (ALS) is categorized by TDP-43 proteinopathy, however, the nuclear pathological events remain poorly defined. While cytoplasmic TDP-43 inclusions dominate the late disease stages, accumulating evidence indicates that nuclear TDP-43 assemblies arise earlier and impair RNA splicing. Here, we characterized a single RRM-proximal TDP-43 variant, G148V, designed to disrupt nucleic-acid engagement without altering canonical RNA-binding residues. Structural and biophysical analyses revealed conformational changes and loss of DNA/RNA binding. In mammalian cells, TDP-43 G148V robustly formed nuclear puncta with high penetrance, exhibiting solid-like properties, pathological phosphorylation, splicing dysfunction, and toxicity. Furthermore, we identified molecular chaperone HSC70 as an important regulator of the nuclear puncta assembly. HSC70 redistributed into G148V nuclear puncta to modulate their material state, whereas HSC70 depletion significantly promoted puncta solidification, increased insoluble TDP-43 accumulation, and enhanced cytotoxicity. Disease-associated K181E and K263E mutants also formed nuclear puncta and induced HSC70 nuclear redistribution. These findings establish G148V as a model of early nuclear TDP-43 pathology and highlight HSC70-mediated regulation as a key factor of TDP-43 nuclear assembly. HighlightsO_LIA single TDP-43 mutation, G148V, in RRM1 domain robustly induces nuclear puncta without exogenous stress. C_LIO_LIG148V disrupts nucleic-acid binding, driving solid-like nuclear assemblies with hyperphosphorylation. C_LIO_LINuclear G148V puncta impair splicing regulation and reduce cell viability, recapitulating early ALS pathology. C_LIO_LIThe molecular chaperone HSC70 modulates puncta material states and mitigates G148V-associated cytotoxicity. C_LI Graphical abstrac O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/739729v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@d019c8org.highwire.dtl.DTLVardef@4ca632org.highwire.dtl.DTLVardef@331fd9org.highwire.dtl.DTLVardef@6fe8e4_HPS_FORMAT_FIGEXP M_FIG C_FIG eTOC blurbA structure-guided TDP-43 G148V mutation reveals how loss of nucleic-acid engagement promotes early nuclear condensation, splicing dysfunction, and toxicity, while uncovering a protective role for HSC70 in regulating condensate properties during ALS pathogenesis.

cell biology↗

bioRxiv2026

O-GlcNAcylation effect on Tau in modulating its seeding and cellular transmission in Alzheimer's Disease

Post-translational modifications critically regulate neurodegenerative disease progression. In Alzheimers disease (AD) and tauopathies, Tau hyperphosphorylation promotes aggregation and pathological spreading, whereas O-GlcNAcylation has emerged as a protective modification alongside its interplay with phosphorylation. However, the role of in vitro site-specific and global O-GlcNAcylation in Tau proteinopathy remains elusive. Here, using full-length Tau-441 (2N4R), we showed that O-GlcNAcylated Tau aggregated slowly, formed distinct aggregate morphology and exhibited reduced seeding capacity compared to wild-type (WT) Tau. Under phase-separated conditions, O-GlcNAcylated Tau formed oligomer like condensates. Mutation of the key O-GlcNAc sites reduced O-GlcNAc-transferase (OGT) mediated O-GlcNAcylation, cellular transmission and affected cross-talk with phosphorylation relative to WT. OGT overexpression alleviated WT-Tau toxicity in cells, and O-Tau fibrils were less toxic to primary cortical neurons compared to WT Tau fibrils. Finally, an in-house novel site-specific S422 O-GlcNAc-Tau antibody revealed reduced S422 O-GlcNAcylation in AD brain tissues, highlighting its protective role in AD pathogenesis.

neuroscience↗

bioRxiv2024

Challenging the Conventional Treatment Initiation Paradigm: Early Detection of Irreversible Cellular Damage in Cardiac Biopsies of Fabry Disease Before the Formation of Gb3 Inclusion Bodies

BackgroundFabry disease (FD) is a lysosomal storage disorder impacting multiple organs, including the heart. We investigated whether early-stage globotriaosylceramide (Gb3) accumulation, before occurrence of inclusion bodies, could cause significant stress and irreversible damages of the cardiomyocytes in FD patients. To assess the cellular stress and irreversible damage of cardiomyocytes in FD during early-stage Gb3 accumulation before the occurrence of typical pathology. MethodsImmunofluorescent (IF) staining or Western blotting were performed on fibroblasts from FD patients and myocardial biopsies from G3Stg/GLAko mice and FD patients. Notably, all biopsies exhibited detectable Gb3 accumulation under IF but lacked typical FD (Gb3 inclusion body) pathology. Staining targeted nuclear factor-{kappa}B (NF-{kappa}B), interleukin-18 (IL-18), phospho-p42/44 mitogen-activated protein kinase (MAPK), and inducible nitric oxide synthase (iNOS) as inflammatory and oxidative stress markers. Alpha-smooth muscle actin (-SMA) IF staining was conducted to detect myofibroblasts. ResultsFibroblasts from FD patients, in conjunction with cardiomyocytes from both G3Stg/GLAko mice and FD patients, exhibited significant accumulation of inflammatory markers such as NF-{kappa}B IL-18 and phospho-p42/44 MAPK, as well as the oxidative stress marker iNOS. Despite the absence of typical FD pathology, the presence of fibrosis was confirmed in myocardial biopsies from these patients through strong positive staining of -SMA. ConclusionsSignificant cellular stress and even irreversible damage may occur before the onset of typical pathological changes in cardiomyocytes of FD. Based on our findings, treatment should be initiated much earlier than we currently thought to prevent irreversible damage and improve the prognosis of FD patients.

pathology↗

bioRxiv2023

The non-mitotic role of HMMR in regulating the localization of TPX2 and the dynamics of microtubules in neurons

A functional nervous system is built upon the proper morphogenesis of neurons to establish the intricate connection between them. The microtubule cytoskeleton is known to play various essential roles in this morphogenetic process. While many microtubule-associated proteins (MAPs) have been demonstrated to participate in neuronal morphogenesis, the function of many more remains to be determined. This study focuses on a MAP called HMMR, which was originally identified as a hyaluronan binding protein and later found to possess microtubule and centrosome binding capacity. HMMR exhibits high abundance on neuronal microtubules and altering the level of HMMR significantly affects the morphology of neurons. Instead of confining to the centrosome(s) like cells in mitosis, HMMR localizes to microtubules along axons and dendrites. Furthermore, transiently expressing HMMR enhances the stability of neuronal microtubules and increases the formation frequency of growing microtubules along the neurites. HMMR regulates the microtubule localization of a non-centrosomal microtubule nucleator TPX2 along the neurite, offering an explanation for how HMMR contributes to the promotion of growing microtubules. This study sheds light on how progenitor cells utilize proteins involved in mitosis for non-mitotic functions.

cell biology↗

bioRxiv2023

Admixture as a source for HLA variation in Neolithic European farming communities

The northern European Neolithic is characterized by two major demographic events: immigration of early farmers (EF) from Anatolia (5500 BCE) and their admixture (from [~]4200 BCE) with western hunter-gatherers (WHG) forming late farmers (LF). The influence of this admixture event on variation in the immune-relevant human leukocyte antigen (HLA) region is understudied. Here, we conducted population and immunogenetic analyses on 83 individuals from six EF and LF sites located in present-day Germany. We observed significant shifts in HLA allele frequencies from EF to LF. The HLA diversity increased from EF to LF, likely due to admixture with WHG. However, it was considerably lower than in modern populations. Both EF and LF exhibited a relatively narrow HLA allele spectrum compared to today. This coincides with sparse traces of pathogen DNA, potentially indicating a lower pathogen pressure at the time. We additionally noted that LF resulted from sex-biased admixture from male WHG. TEASERMore restricted HLA allele spectrum and lower diversity in Neolithic farmers than in modern populations

genetics↗

bioRxiv2022

Nucleic Acid Adductomics - the Next Generation of Adductomics for Assessing Environmental Health Risk

The exposome describes the totality of internal and external environmental exposures, across the life course. Components of the exposome have been linked to an increased risk of various, major diseases. To identify the precise nature, and size, of risk, in this complex mixture of exposures, powerful tools are needed to link exposure, cellular consequences, and health/disease. The most biologically informative biomarkers of the exposome should, to varying extents, reflect the dose of the exposure on the body or target organ(s), a subsequent effect on the biological system and, ideally, possess a role in disease. Modification of nucleic acids (NA) is a key consequence of environmental exposures, and while cellular DNA adductomics aims to evaluate the totality to DNA modifications in the genome, an approach which encompasses modifications of all nucleic acids, would be far more comprehensive, and therefore informative. To address this, we propose a cellular and urinary NA adductomics approach for the assessment of both DNA and RNA modifications, including modified (2-deoxy)ribonucleosides (2dN/rN), modified nucleobases (nB), plus: DNA-DNA, RNA-RNA, DNA-RNA, DNA-protein, and RNA-protein crosslinks (DDCL, RRCL, DRCL, DPCL, and RPCL, respectively). Supporting the feasibility of this approach, we presented preliminary, proof-of-principle results, which revealed the presence of over 1,000 modified NA moieties, and at least six types of NA modifications, in a representative, pooled urine from healthy subjects, including modified 2-dN, modified rN, modified nB, DRCL, RRCL and RPCL, many of which were novel/unexpected. We suggest that NA adductomics will provide a more comprehensive approach to the study of nucleic acid modifications, which will facilitate a range of advances, including the identification of novel, unexpected modifications e.g., RNA-RNA, and DNA-RNA crosslinks; key modifications associated with mutagenesis; agent-specific mechanisms; and adductome signatures of key environmental agents, leading to the dissection of the exposome, and its role in human health/disease, across the life course.

pharmacology and toxicology↗

bioRxiv2021

Mechanism of the Switch from NO to H2O2 in Endothelium-Dependent Vasodilation in Diabetes

Coronary microvascular dysfunction is prevalent among diabetics and is correlated with cardiac mortality. Compromised endothelial-dependent dilation (EDD) is an early event in the progression of diabetes, but the mechanisms remain incompletely understood. Nitric oxide (NO) is the major endothelium-dependent vasodilatory metabolite in the healthy coronary circulation, but switches to hydrogen peroxide (H2O2) in coronary artery disease (CAD) patients. Because diabetes is a major risk factor for CAD we hypothesized that a similar switch from NO-to-H2O2 occurs in diabetes. Methods: Vasodilation was measured ex vivo in isolated coronary arteries from wild type (WT) and microRNA-21 (miR-21) null mice fed chow or high fat and sugar diet, and LepR null (db/db) mice using myography. Myocardial blood flow (MBF), blood pressure, and heart rate were measured in vivo using contrast echocardiography and a solid-state pressure sensor catheter. RNA from coronary arteries, endothelial cells and hearts were analyzed via qPCR for gene expression and protein expression was assessed via Western-Blot analyses. Superoxide was detected via electron paramagnetic resonance (EPR). Results: 1) Ex vivo coronary EDD and in vivo MBF was impaired in diabetes. 2) L-NAME (NO-synthase inhibitor) inhibited ex vivo coronary EDD and in vivo MBF in WT, while PEG-catalase (H2O2 scavenger) inhibited diabetic EDD ex vivo and MBF in vivo. 5) miR-21 deficiency blocked the NO-to-H2O2 switch and prevented diabetic vasodilation impairments. 6) Diabetic mice displayed increased serum NO and H2O2, upregulated mRNA expression of Sod1, Sod2, iNos, and Cav-1, and downregulated Pgc-1. Deficiency of miR-21 reversed these changes. 7) miR-21 deficiency increased PGC1, PPAR and eNOS protein and reduced detection of endothelial superoxide. Conclusions: Diabetics exhibit an NO-to-H2O2 switch in the mediator of EDD coronary dilation, which contributed to microvascular dysfunction and is mediated by miR-21. This study represents the first mouse model recapitulating the NO-to-H2O2 switch seen in CAD patients.

physiology↗

bioRxiv2020

Structure-based functional study of a peptide of an ecdysozoan superfamily: reveling a common molecular architecture and receptor-interacting residues

A neuropeptide (Sco-CHH-L), belonging to the crustacean hyperglycemic hormone (CHH) superfamily and preferentially expressed in the pericardial organs (POs) of the mud crab Scylla olivacea, was functionally and structurally studied. Its expression levels were significantly higher than the alternative splice form (Sco-CHH) in the POs and increased significantly after animals were subjected to a hypo-osmotic stress. Sco-CHH-L, but not Sco-CHH, significantly stimulated in vitro the Na+, K+-ATPase activity in the posterior (6th) gills. Furthermore, solution structure of Sco-CHH-L was resolved using nuclear magnetic resonance spectroscopy revealing that it has an N-terminal tail, three -helices (2, Gly9-Asn28; 3, His34-Gly38; 5, Glu62-Arg72), and a {pi}-helix ({pi}4, Cys43-Tyr53) and is structurally constrained by a pattern of disulfide bonds (Cys7-Cys43, Cys23-Cys39, Cys26-Cys52), which is characteristic of the CHH superfamily-peptides. Sco-CHH-L is topologically most similar to the molt-inhibiting hormone from the Kuruma prawn Marsupenaeus japonicus with a backbone root-mean-square-deviation of 3.12 [A]. Ten residues of Sco-CHH-L were chosen for alanine-substituted and the resulting mutants were functionally tested using the gill Na+, K+-ATPase activity assay, showing that the functionally important residues (I2, F3, E45, D69, I71, G73) are located at either end of the sequence, which are sterically close to each other and presumably constitutes the receptor binding sites. Sco-CHH-L was compared with other members of the superfamily revealing a molecular architecture, which is suggested to be common for the crustacean members of the superfamily, with the properties of the residues constituting the presumed receptor binding sites being the major factors dictating the ligand-receptor binding specificity.

biochemistry↗

bioRxiv2017

The fruitENCODE project sheds light on the genetic and epigenetic basis of convergent evolution of climacteric fruit ripening

Fleshy fruit evolved independently multiple times during angiosperm history. Many climacteric fruits utilize the hormone ethylene to regulate ripening. The fruitENCODE project shows there are multiple evolutionary origins of the regulatory circuits that govern climacteric fruit ripening. Eudicot climacteric fruits with recent whole-genome duplications (WGDs) evolved their ripening regulatory systems using the duplicated floral identity genes, while others without WGD utilised carpel senescence genes. The monocot banana uses both leaf senescence and duplicated floral-identity genes, forming two interconnected regulatory circuits. H3K27me3 plays a conserved role in restricting the expression of key ripening regulators and their direct orthologs in both the ancestral dry fruit and non-climacteric fleshy fruit species. Our findings suggest that evolution of climacteric ripening was constrained by limited availability of signalling molecules and genetic and epigenetic materials, and WGD provided new resources for plants to circumvent this limit. Understanding these different ripening mechanisms makes it possible to design tailor-made ripening traits to improve quality, yield and minimize postharvest losses.\n\nOne Sentence SummaryThe fruitENCODE project discovered three evolutionary origins of the regulatory circuits that govern climacteric fruit ripening.

genomics↗