Biology subjects

Dou, X.

Publications and source records attributed to Dou, X..

14 recordsLinked to original sources

bioRxiv2026

Adipose GPD2 Couples Glycolytic Signals to Epigenetic Control of Metabolic Homeostasis

The glycerol-3-phosphate shuttle (G3PS) is a classic reducing equivalent transferring system, yet its role in adipose metabolism remains poorly understood. Here, we identify mitochondrial glycerol-3-phosphate dehydrogenase (GPD2), the core enzyme of G3PS, as a critical orchestrator of adipose thermogenesis and systemic metabolic homeostasis. Adipocyte-specific GPD2 knockout mice exhibited impaired thermogenic capacity and energy expenditure, rendering them susceptible to obesity and metabolic dysfunction. Mechanistically, GPD2 deficiency elevated cytosolic NADH, which suppressed glycolysis and decreased the levels of key metabolites, such as acetyl-CoA, thereby diminishing H3K27ac at thermogenic gene loci and silencing these genes. NADH depletion with an NADH oxidase rescued both glycolysis and thermogenic gene expression. In support of this mechanism, we defined a previously undescribed enhancer of Ucp1 whose H3K27ac was tightly controlled by GPD2. Remarkably, replenishing the acetyl-CoA pool or directly restoring H3K27ac at the Ucp1 enhancer reversed UCP1 expression in GPD2-deficient adipocytes. Importantly, we find that human adipose GPD2 expression is inversely correlated with BMI, WHR, and HOMA-IR, underscoring its clinical relevance. Collectively, our findings establish GPD2 as an essential node in the metabolic-epigenetic axis that governs thermogenic activation and energy balance.

biochemistry↗

bioRxiv2026

Structural basis for GluA1 AMPA receptor regulation by PRRT1/SynDIG4 in LTP

AMPA receptor (AMPAR) signalling underlies long-term potentiation (LTP), a cellular mechanism for learning that selectively involves GluA1-type AMPARs through incompletely understood mechanisms. Here, we report a key role for the auxiliary subunit PRRT1/SynDIG4 in LTP. Cryo-EM structures of hippocampal AMPARs reveal preferential association of PRRT1 with GluA1 via its membrane-embedded CD225 domain, which sequesters the GluA1 C-terminus through a previously unexplored lipid modification on Cys825. Consequently, GluA1 regulatory motifs implicated in LTP, including the CaMKII binding site, are inaccessible. PRRT1 overexpression impairs LTP, which is rescued by the Cys825Ser mutation, presumably by restoring access of the GluA1 tail to Ser831 phosphorylation by CaMKII. Our data uncover a mechanism wherein PRRT1/SynDIG4 controls the availability of the GluA1 pool that is released upon the induction of LTP.

neuroscience↗

bioRxiv2026

Application of Engineered NK-92 Cell Extracellular Vesicles in the Treatment of Systemic Lupus Erythematosus

IntroductionSystemic Lupus Erythematosus (SLE) is a chronic autoimmune disease characterized by loss of immune tolerance, autoantibody production, and multi-organ damage. Current therapies, including glucocorticoids and CAR-T/CAR-NK cell therapies, are limited by adverse effects, high cost, and safety concerns. ObjectivesTo develop engineered NK-92 cell-derived extracellular vesicles displaying CD19 single-chain variable fragment (V-CD19-Exo) and evaluate their therapeutic efficacy in an MRL/lpr mouse model of SLE. MethodsThe CD19scFv-LAMP-2B fusion construct was stably expressed in NK-92 cells via lentiviral transduction. Extracellular vesicles were isolated by differential centrifugation and characterized by NTA, TEM, and Western Blot. In vivo efficacy was assessed in MRL/lpr mice through B cell depletion analysis, renal function monitoring, cytokine profiling, autoantibody detection, and survival observation. ResultsV-CD19-Exo significantly reduced splenic CD19{square}CD20{square} B cells from 10.53% to 1.51% (p < 0.0001). Treatment attenuated proteinuria, ameliorated lupus nephritis pathology, reversed splenomegaly, and downregulated serum IgE, IL-17A, IFN-{gamma}, anti-dsDNA, and ANA levels. Notably, V-CD19-Exo improved survival to approximately 80% compared to 25% in untreated controls. ConclusionEngineered NK-92 cell-derived extracellular vesicles represent a novel, safe, and effective cell-free therapeutic strategy for SLE, offering advantages over conventional cell therapies including lower immunogenicity, scalable production, and no requirement for lymphodepletion.

synthetic biology↗

bioRxiv2026

m6A-dependent microRNA binding to chromatin-associated RNA for transcriptional activation

For decades, microRNAs (miRNAs) have been canonically viewed as post-transcriptional repressors. We discovered extensive binding of microRNAs to chromatin-associated RNAs (caRNAs) and uncovered an N6-methyladenosine (m6A)-dependent transcriptional activation mechanism of microRNAs. We show that m6A-binding proteins FXR1/2 anchor AGO1/2 at m6A-marked caRNAs, where AAGUGC-seed microRNAs function as guide RNAs to direct AGO positioning. This dual anchoring stabilizes the AGO-microRNA/FXR-m6A complex at specific loci, which in turn recruits the ATP-dependent chromatin remodeler SMARCA4 (BRG1) to promote local chromatin opening and TET1 for DNA demethylation, respectively. Together, these coordinated activities establish a transcriptionally permissive chromatin environment, enhancing accessibility and transcription across hundreds of genes in diverse cell types. Beyond the AAGUGC-seed family, additional microRNAs and siRNAs also enhance transcription, suggesting that caRNA binding and transcriptional activation may represent a broader property of small RNAs.

molecular biology↗

bioRxiv2025

LINE1 RNA dysregulation impairs chromatin accessibility in C9ORF72- and TDP-43-linked ALS/FTD

The long interspersed element-1 (LINE1) retrotransposon RNAs are abnormally elevated in various neurodegenerative disorders, but their pathogenic roles remain unclear. Here we investigated the mechanism of LINE1 RNA accumulation and its function in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) associated with C9ORF72 repeat expansion and TDP-43 loss-of-function, the leading causes of familial and sporadic forms of these neurodegenerative diseases. We show that LINE1 RNA is dysregulated due to an impaired nuclear exosome targeting (NEXT) degradation pathway. Its elevation epigenetically increases chromatin accessibility, enhancing global transcription via a retrotransposon-independent mechanism. Reducing LINE1 RNA mitigates chromosomal abnormalities and improves the survival of disease-relevant neurons. These findings uncover an essential noncoding RNA function and regulatory mechanism of LINE1 in neurons, providing insights into disease pathogenesis and highlighting potential therapeutic targets for neurodegenerative diseases.

neuroscience↗

bioRxiv2025

5-azacytosine induces cytotoxicity via 5-methylcytosine depletion on chromatin-associated RNA in leukemia

5-azacytidine (5-azaC) is a DNA hypomethylating agent clinically used to improve outcomes in myeloid malignancies. However, 5-azaC treatment causes gene dysregulation inconsistent with DNA hypomethylation changes, suggesting alternative mechanisms of action by 5-azaC. As a ribonucleoside analogue, 5-azaC is more readily incorporated into nascent RNA. Here, we demonstrate that RNA 5-methylcytosine (m5C) depletion by 5-azaC treatment, particularly at early time points, is sufficient to induce leukemia cell death. In contrast to its DNA demethylation function, the RNA-dependent effect of 5-azaC causes transcriptional repression, disrupting genes involved in cell cycle regulation and DNA repair. Mechanistically, 5-azaC impairs two specific m5C-mediated transcriptional regulatory pathways. First, depletion of m5C in chromatin-associated RNA (caRNA) disrupts the MBD6-mediated H2AK119ub deubiquitination. In parallel, this also impairs SRSF2 recruitment and the downstream H3K27ac deposition by p300. Indeed, loss of the caRNA methyltransferase NSUN2 caused prolonged cell cycle, defective DNA repair, and shifted hematopoietic lineage commitment toward erythropoiesis, mirroring the effects of 5-azaC treatment. Furthermore, we performed a leukemia cell line screen and identified that TET2 and IKZF1 depletion can sensitize 5-azaC treatment, consistent with the observed RNA-dependent cytotoxicity of 5-azaC in leukemic cells. In summary, our findings highlight the transcription repression by 5-azaC through depleting caRNA m5C, providing additional insights into the mechanism of action for 5-azaC, the prediction of its efficacy, and future directions for therapy developments based on 5-azaC. HIGHLIGHTO_LIRNA-dependent effects of 5-azaC are sufficient to drive leukemia cell cytotoxicity through transcriptional repression. C_LIO_LI5-azaC-induced caRNA m5C depletion impairs MBD6 binding and H2AK119ub deubiquitination. C_LIO_LI5-azaC-induced caRNA m5C depletion disrupts SRSF2 chromatin-binding, impeding p300 recruitment and H3K27ac deposition. C_LIO_LITET2 or IKZF1 depletion synergizes leukemia sensitivity to 5-azaC C_LI

molecular biology↗

bioRxiv2024

Mechanistic basis of lineage restriction

Lineage restriction is the biological phenomenon where cells lose developmental potency during differentiation for all except their adopted lineages. Lineage restriction is foundational to multicellularity as it secures the functional identities of the myriad cell types in the body. As yet, the mechanisms of lineage restriction remain enigmatic. By developing Potency-Seq to systematically map transcriptional potency of genes across the genome, we uncovered a link between the restriction of developmental potency of cells and the occlusion of transcriptional potency of their genomes. We further showed that, strikingly, genes can undergo irreversible occlusion of their transcriptional potency simply by chromatinization into the nucleosomal form with unmodified histones. These findings led to a comprehensive mechanistic account of lineage restriction as driven by gene occlusion. Specifically, naive pluripotent stem cells at the onset of development possess the unique capacity to erase occlusion globally to reset full transcriptional potency of the genome, which in turn establishes full developmental potency of the cells. Such deocclusion capacity is abolished when cells progress from naive to primed pluripotency. From this stage onward, lineage-inappropriate genes can undergo nucleosome-mediated occlusion in an irreversible manner when their cognate transcription factors (TFs) and/or placeholder factors (PFs) no longer exist in cells to protect them. Consequently, the transcriptionally potent portion of the genome shrinks progressively and irreversibly during differentiation, thus permanently restricting the developmental potency of differentiating cells. ONE-SENTENCE SUMMARYDevelopmental potency of cells is linked to transcriptional potency of their genomes

developmental biology↗

bioRxiv2023

S2' cleavage site plays a decisive role in expansion of Vero cell tropism by infectious bronchitis virus HV80, with Q855H promoting cell-to-cell fusion

Infectious bronchitis virus (IBV) has restricted cell tropism. Apart from the Beaudette strain, other IBVs cannot infect mammalian cell lines. The limited cell tropism of other IBVs has hindered the development of IBV vaccines and research on mechanisms of IBV infection. In a previous study, a new Vero-cell-adapted strain HV80 was obtained via serial chicken embryo and cell passaging of strain H120 and 17 mutations leading to amino acid substitutions occurred in replication gene 1a, S gene and E gene. This study, we constructed recombinants that expressed chimeric S glycoprotein, S1 or S2 subunit of strain H120, and demonstrated that mutations in S2 subunit were related to the Vero cell adaption of strain HV80. With a genome backbone of strain HV80 or H120, and expression of chimeric S2' cleavage site of H120 or HV80, two recombinants demonstrated that the RRRR690/S motif at the S2' cleavage site played a key role in Vero cell adaption of strain HV80. Another six amino acid substitutions in the S2 subunit of the recombinants showed that F692V enhanced the capability of invasion of HV80 strain, and Q855H induced the formation of syncytia. A transient transfection assay demonstrated different mechanisms for virus-to-cell fusion and cell-to-cell fusion induced by S glycoprotein. The PRRR690/S motif at the S2' cleavage site could be activated by proteases in the process of cell-to-cell fusion, while H855Q substitution did not affect the cell invasion of HV80, but hindered the cell-to-cell fusion by blocking activation of the S2' cleavage site. IMPORTANCEInfectious bronchitis is an acute respiratory disease that has caused large economic losses to the poultry industry. As a member of the gamma-coronaviruses, the restricted cell tropism of infectious bronchitis virus (IBV) limits the development of cellular vaccines and research on infection mechanisms. As a strain that can replicate effectively in mammalian cell lines, studies of HV80s adaptive mechanisms point a way for engineering other IBVs for adaptation in mammalian cell lines. In our study, different recombinants were constructed by reverse genetic techniques, and demonstrated the different mechanism between virus-to-cell and cell-to-cell fusion induced by HV80 S glycoprotein. The acquisition of a highly efficient S2' cleavage site enabled the virus to invade Vero cells. The Q855H substitution played a key role in cell-to-cell fusion, and provided a more efficient model of infection in Vero cells. Our study provides new theoretical insights into mechanisms of IBV adaptation in mammalian cell lines.

microbiology↗

bioRxiv2022

Senescent cells develop PDK4-dependent hypercatabolism and form an acidic microenvironment to drive cancer resistance

Cellular senescence is a state of stable growth arrest, usually accompanied by development of the senescence-associated secretory phenotype (SASP). Although senescent cells remain metabolically active, little is known about their metabolic landscape and in vivo pathophysiological implications. Here we show that expression of the pyruvate dehydrogenase (PDH) inhibitory enzyme, pyruvate dehydrogenase kinase 4 (PDK4), is significantly upregulated in human senescent stromal cells. Preferentially expressed upon genotoxicity-induced senescence (GIS), PDK4 is negatively correlated with posttreatment survival of cancer patients. Upon cellular senescence, PDK4 shifts glucose metabolic flux from oxidative phosphorylation to aerobic glycolysis, causing enhanced lactate production and forming an acidic microenvironment. However, distinct from the cancer cell-featured Warburg effect, senescent cells maintain an intensive use of pyruvate through the tricarboxylic acid cycle (TCA), displaying increased respiration and redox activity, indicative of a special form of metabolic reprogramming. Conditioned media from PDK4+ stromal cells change global expression and promote malignancy of recipient cancer cells in vitro and accelerate tumor progression in vivo. Pharmacologically targeting PDK4 restrains the adverse effects of PDK4 in cell-based assays, while promoting tumor regression and extending posttreatment survival in preclinical trials. Together, our study substantiates the hypercatabolic nature of senescent cells, and reveals a metabolic link between senescence-associated acidic microenvironment and age-related pathologies including but not limited to cancer.

cell biology↗

bioRxiv2022

MoIsw2 activity could be the missing link between adaptation and mutation instrumental for natural adaptation-directed fast evolution (NADFE) of Magnaporthe oryzae

Isw2 proteins are conserved in eukaryotes and are known to bind to DNA and dynamically influence local chromosome condensation close to their DNA binding site in an ATP-dependent manner making genes close to the binding sites more accessible for transcription and repression. A putative MoISW2 gene was deleted with large effects on plant pathogenicity as a result. The gene was complemented and a ChIP-sec was performed to identify binding sites. RNAsec showed effects on the overall regulation of genes along the chromosomes for mutant and background strains and this was compared with RNAseq from 55 downloaded RNA-seq datasets from the same strain and found similar. MoIsw2 binding and activities create genomic regions affected by MoIsw2 with high gene expression variability close to the MoIsw2 binding sites while surrounding regions have lower gene expression variability. The genes affected by the MoIsw2 activity are niche-determinant genes (secreted proteins, secondary metabolites and stress-coping genes) and avirulence genes. We further show that MoIsw2 binding sites with the DNA binding motifs coincide with known transposable elements (TE) making it likely that TE-transposition at the binding sites can affect the transcription profile of M. oryze in a strain-specific manner. We conclude that MoIsw2 is a likely candidate for a master regulator, regulating the dynamic balance between biomass growth genes (like housekeeping genes) and nich-determinant genes important for ecological fitness. Stress-induced TE transposition is together with MoIsw2 activity a likely mechanism creating more mutations and faster evolution of the niche-determinant genes than for housekeeping genes.

evolutionary biology↗

bioRxiv2021

Nuclear m6A reader Ythdc1 regulates the scaffold function of LINE1 in mouse ESCs

N6-methyladenosine (m6A) on chromosome-associated regulatory RNAs (carRNAs), including repeat RNAs, play important roles in tuning the chromatin state and transcription1. Among diverse RNA-chromatin interacting modes, the nuclear RNA scaffold is considered important for trans-interactions2,3 but has not yet been connected with m6A yet. Here, we found that Ythdc1 played indispensable roles in the embryonic stem cell (ESC) self-renewal and differentiation potency, and these roles highly depended on its m6A-binding ability. Ythdc1 deficiency in ESCs resulted in decreased rRNA synthesis and the activation of 2-cell (2C) embryo-specific transcriptional program, and these observations recapitulated the transcriptome defects induced by dysfunction of the long interspersed nuclear element-1 (LINE1)-scaffold, which were unrelated to the direct targeting of Ythdc1. A detailed analysis revealed that Ythdc1 recognized m6A on LINE1 and was physically involved in the formation of the LINE1-Nucleolin partnership and the chromatin recruitment of Kap1. In summary, our study reveals a new link between m6A and the RNA scaffold and thus provides a new regulatory model for the crosstalk between RNA and the chromatin epigenome.

cell biology↗

bioRxiv2020

Senescent stromal cells promote cancer resistance through SIRT1 loss-potentiated overproduction of small extracellular vesicles

Cellular senescence is a potent tumor-suppressive program that prevents neoplastic events. Paradoxically, senescent cells develop an inflammatory secretome, termed the senescence-associated secretory phenotype (SASP) and implicated in age-related pathologies including cancer. Here we report that senescent cells actively synthesize and release small extracellular vesicles (sEVs) with a distinctive size distribution. Mechanistically, SIRT1 loss supports accelerated sEV production despite enhanced proteome-wide ubiquitination, a process correlated with ATP6V1A downregulation and defective lysosomal acidification. Once released, senescent stromal sEVs significantly alter the expression profile of recipient cancer cells and enhance their aggressiveness, specifically drug resistance mediated by expression of ATP binding cassette subfamily B member 4 (ABCB4). Targeting SIRT1 with an agonist SRT2104 prevents development of cancer resistance through restraining sEV production by senescent stromal cells. In clinical oncology, sEVs in peripheral blood of posttreatment cancer patients are readily detectable by routine biotechniques, presenting a novel biomarker to monitor therapeutic efficacy and to predict long term outcome. Together, our study identifies a distinct mechanism supporting pathological activities of senescent cells, and provides a novel avenue to circumvent advanced human malignancies by co-targeting cancer cells and their surrounding microenvironment, which contributes to drug resistance via secretion of sEVs from senescent stromal cells.

cell biology↗

bioRxiv2019

Predicting functional long non-coding RNAs validated by low throughput experiments

High-throughput techniques have uncovered hundreds and thousands of long non-coding RNAs (lncRNAs). Among them, only a small fraction has experimentally validated functions (EVlncRNAs) by low-throughput methods. What fraction of lncRNAs from high-throughput experiments (HTlncRNAs) is truly functional is an active subject of debate. Here, we developed the first method to distinguish EVlncRNAs from HTlncRNAs and mRNAs by using Support Vector Machines and found that EVlncRNAs can be well separated from HTlncRNAs and mRNAs with 0.6 for Matthews correlation coefficient, 64% for sensitivity, and 81% for precision for the independent human test set. The most discriminative features are related to sequence conservations at RNA (for separating from HTlncRNAs) and protein (for separating from mRNA) levels. The method is found to be robust as the human-RNA-trained model is applicable to independent mouse RNAs with similar accuracy and to a lesser extent to plant RNAs. The method can recover newly discovered EVlncRNAs with high sensitivity. Its application to randomly selected 2000 human HTlncRNAs indicates that a large number of functional lncRNAs are waiting to be validated. The method is expected to speed up and reduce the cost of the discovery by prioritizing potentially functional lncRNAs prior to experimental validation. EVlncRNA-pred is available as a web server at http://biophy.dzu.edu.cn/lncrnapred/index.html. All datasets used in this study can be obtained from the same website.

bioinformatics↗

bioRxiv2017

Comprehensive Analysis of Constraint on the Spatial Distribution of Missense Variants in Human Protein Structures

The spatial distribution of genetic variation within proteins is shaped by evolutionary constraint and thus can provide insights into the functional importance of protein regions and the potential pathogenicity of protein alterations. Here, we comprehensively evaluate the 3D spatial patterns of constraint on human germline and somatic variation in 4,568 solved protein structures. Different classes of coding variants have significantly different spatial distributions. Neutral missense variants exhibit a range of 3D constraint patterns, with a general trend of spatial dispersion driven by constraint on core residues. In contrast, germline and somatic disease-causing variants are significantly more likely to be clustered in protein structure space. We demonstrate that this difference in the spatial distributions of disease-associated and benign germline variants provides a signature for accurately classifying variants of unknown significance (VUS) that is complementary to current approaches for VUS classification. We further illustrate the clinical utility of our approach by classifying new mutations identified from patients with familial idiopathic pneumonia (FIP) that segregate with disease.

genetics↗