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Biology subjects

zhang, j.

Publications and source records attributed to zhang, j..

13 recordsLinked to original sources

NMDA receptor-dependent presynaptic homeostatic plasticity?

Excitatory glutamatergic synapses in the brain are remarkably plastic. Two forms of plasticity have received the most attention: long-term potentiation (LTP) and synaptic homeostasis. While LTP requires the activation of NMDA receptors, synaptic homeostasis does not. However, both phenomena are mediated by the recruitment of postsynaptic AMPA receptors to the synapses. Recently a new form of plasticity has been described referred to as presynaptic homeostatic plasticity (PHP) (Chipman et al., 2022; Chipman et al., 2025). Pharmacological inhibition of AMPA synaptic responses in CA1 hippocampal pyramidal cells initiates a rapid homeostatic response that results in the recovery of the AMPA responses to normal values in the continued presence of the inhibitor. Accompanying this recovery is a doubling of the NMDA response which is interpreted as an increase in the release of glutamate. This is provocative since it is the first report claiming that a reduction in AMPA responses triggers an enhancement in NMDA responses. Using three different protocols to monitor synaptic responses we fail to observe any recovery of synaptic responses in the presence of an AMPA inhibitor. Furthermore, there was no enhancement in NMDA responses. Thus, we find no evidence for the presence of PHP at CA1 hippocampal synapses.

neuroscience↗

The Notch/snRNA negative feedback regulation and its implications in Alzheimer's disease

Alzheimers disease (AD) is a multifactorial disorder whose hallmark lesions have been recognized for more than a century, yet its molecular pathobiology remains fragmentary. During our AD research, we discovered a direct mechanistic axis that links the Notch signalling pathway -- a crucial regulator of cell differentiation and proliferation--with the small nuclear RNAs (snRNAs) that drive pre-mRNA splicing. For the first time, our discovery unifies two previously siloed paradigms -- cell signal transduction and RNA splicing, expanding the fundamental knowledge of gene expression and its regulation. The first contribution of the present study is the discovery and validation of the Notch/snRNA negative feedback regulation. More implications include: (1) it reframes splicing-related diseases as dynamic consequences of pathway dysregulation rather than static snRNA-gene mutations; (2) it explains why global splicing abnormalities appear in AD, aging, and cancer even when snRNA genes themselves are not mutated; and (3) it provides an immediate, druggable "splicing rheostat" for any Notch-hyperactive disorder, such as AD.

cell biology↗

Linker histone regulates the myeloid versus lymphoid bifurcation of multipotent hematopoietic stem and progenitors

Myeloid-biased differentiation of multipotent hematopoietic stem and progenitor cells (HSPCs) occurs with aging or exhaustion. The molecular mechanism(s) responsible for this fate bias remain unclear. Here we report that linker histone regulates HSPC fate choice at the lymphoid versus myeloid bifurcation. HSPCs expressing H1.0 from a doxycycline (dox) inducible transgene favor the lymphoid fate, display strengthened nucleosome organization and reduced chromatin accessibility at genomic regions hosting key myeloid fate drivers. The transcription factor Hlf is located in one of such regions, where chromatin accessibility and gene expression is reduced in H1.0high HSPCs. Furthermore, H1.0 protein in HSPCs decreases in an aspartyl protease dependent manner, a process enhanced in response to interferon alpha (IFN) signaling. Aspartyl protease inhibitors preserve endogenous H1.0 levels and promote the lymphoid fate of wild type HSPCs. Thus, our work uncovers a point of intervention to mitigate myeloid skewed hematopoiesis.

developmental biology↗

A multi-gene predictive model for the radiation sensitivity of nasopharyngeal carcinoma based on machine learning

BackgroundRadiotherapy resistance is a major obstacle to the long-term survival of nasopharyngeal cancer patients, as it is a primary cause of recurrence and metastasis. Identifying radiotherapy-associated biomarkers can help improve the survival prognosis of nasopharyngeal cancer patients. Consequently, discovering biomarkers associated with radiosensitization is crucial. MethodsWe evaluated 113 combinations of machine learning algorithms and ultimately selected 48 to construct a radiotherapy sensitivity score (NPC-RSS) that can predict radiosensitivity in nasopharyngeal cancer patients. Furthermore, we analyzed the relationship between NPC-RSS and the expression of genes associated with immune and radiotherapy sensitivity profiles. We employed GSEA and ssGSEA to investigate the connection between NPC-RSS and signaling pathways. ResultsWe selected the combined model glmBoost+NaiveBayes, which had the best AUC among 48 models, for our subsequent study. The NPC-RSS, built based on the 18 genes included in this model, can predict the results of the public dataset and the in-house dataset of Zhujiang Hospital, Southern Medical University, with considerable efficiency. The key genes of NPC-RSS are closely associated with immune characteristics, including chemokine and chemokine receptor families, and histocompatibility complex (MHC), and show more active immune processes. Meanwhile, these key genes were significantly associated with the expression of radiosensitization-related genes. Furthermore, GSVA and GSEA analyses demonstrated that different expression levels of key NPC-RSS genes influenced signaling pathways, such as the Wnt/{beta}-catenin signaling pathway, JAK-STAT signaling pathway,NF-kappa B signaling pathway and T cell receptor signaling pathway, which are associated with immunity and disease progression. The consistency of the expression of key genes SMARCA2 and CD9 with NPC-RSS was validated in in-house cell lines. The radiosensitive group, classified according to NPC-RSS, exhibited a more enriched and activated state of immune infiltration compared to the radioresistant group. Moreover, in single-cell samples, NPC-RSS was higher in the radiotherapy-sensitive group, with immune cells playing a predominant role. ConclusionsIn this study, we used machine learning to construct a predictive score, called NPC-RSS, associated with radiosensitivity in nasopharyngeal carcinoma patients; moreover, NPC-RSS is strongly associated with immune characteristics, expression of radiosensitivity-related genes, and signaling pathways related to disease progression. We hope that the NPC-RCC will enable more precise selection of the NPC population of potential beneficiaries of radiation therapy.

bioinformatics↗

Modelling cell type-specific lncRNA regulatory network in autism with Cycle

Autism spectrum disorder (ASD) is a class of complex neurodevelopment disorders with high genetic heterogeneity. Long non-coding RNAs (lncRNAs) are vital regulators that perform specific functions within diverse cell types and play pivotal roles in neurological diseases including ASD. Therefore, studying the specific regulation of lncRNAs in various cell types is crucial for deciphering ASD molecular mechanisms. Existing computational methods utilize bulk transcriptomics data across all of cells or samples, which could reveal the commonalities of lncRNA regulation in the pathogenesis of ASD, but ignore the specificity of lncRNA regulation across various cell types. Here, we present Cycle (Cell type-specific lncRNA regulatory network) to construct the landscape of cell type-specific lncRNA regulation in ASD. We have found that each ASD cell type is unique in lncRNA regulation, and more than one-third and all of cell type-specific lncRNA regulatory networks are characterized as scale-free and small-world, respectively. Across 17 ASD cell types, we have discovered 19 rewired and 11 conserved modules, and eight rewired and three conserved hubs underlying within the discovered cell type-specific lncRNA regulatory networks. Moreover, the discovered rewired and conserved modules and hubs are significantly enriched in ASD-related terms. Furthermore, more similar ASD cell types tend to be connected with higher strength in the constructed cell similarity network. Finally, the comparison results demonstrate that Cycle is a potential method for uncovering cell type-specific lncRNA regulation.

bioinformatics↗

COCOA: A Framework for Fine-scale Mapping Cell-type-specific Chromatin Compartmentalization Using Epigenomic Information

Chromatin compartmentalization and epigenomic modification are crucial factors in cell differentiation and diseases development. However, mapping precise chromatin compartmental patterns across multiple cell types requires Hi-C or Micro-C data at high sequencing depth. Exploring the systematic relationship between epigenomic modifications and compartmental patterns remains a challenge. To address these issues, we present COCOA, a deep neural network framework that uses convolution and attention mechanisms to infer reliable fine-scale chromatin compartment patterns from six representative histone modification signals. COCOA achieves this by extracting 1-D track features through bi-directional feature reconstruction after resolution-specific binning epigenomic signals. These track features are then cross-fused with contact features using an attention mechanism. Subsequently, the contact features are transformed into chromatin compartment patterns through residual feature reduction. COCOA demonstrates accurate inference of chromatin compartmentalization at a fine-scale resolution and exhibits stable performance on test sets. In addition, we explored the impact of histone modifications on the chromatin compartmentalization through in silico epigenomic perturbation experiments. When using 1kb resolution high-depth experimental data, obscure compartments are observed, whereas COCOA can generate clear and detailed compartmental patterns. Finally, we demonstrated that COCOA enables cell-type-specific prediction of unrevealed chromatin compartment patterns in various biological processes. Thus, COCOA is an effective tool for gaining chromatin compartmentalization insights from epigenomics in a wide range of biological scenarios.

bioinformatics↗

Designing a Minimal Artificial Glycolytic Pathway

The canonical glycolysis generates two molecules of acetyl-coenzyme A (acetyl-CoA) from one glucose through eleven cascade biochemical reactions. Here, we designed and constructed a Minimal Artificial Glycolytic (MAG) pathway consisting of only three types of biochemical reactions, with phosphoketolase as the core, combined with phosphatase and isomerase as auxiliary enzymes. It could theoretically achieve a 100% carbon yield to acetyl-CoA from any monosaccharide by integrating one-carbon condensation reaction. We tested the MAG pathway in vitro and in vivo, demonstrating the catabolism of typical C1-C6 carbohydrates to acetyl-CoA with yields from 82% to 95%. This novel glycolytic pathway provides a promising route for biomanufacturing with stoichiometric productivity from multiple carbon sources in the future.

synthetic biology↗

IDOL deficiency inhibits cholesterol-rich diet-induced atherosclerosis in rabbits

BACKGROUNDThe E3 ubiquitin ligase IDOL (Inducible Degrader of the LDL-Receptor) contributes to regulation of cholesterol metabolism through degradation of LDLR, VLDLR and ApoER2. Human genetic studies support the hypothesis that IDOL could serve as a target for the treatment of dyslipidemia. However, species-specific differences in overall lipid metabolism and IDOL regulation require new preclinical models to realize its therapeutic potential. We leveraged the advantages afforded by the rabbit model to address those limitations and generated a novel rabbit IDOL knockout, which we characterized in the context of atherosclerosis. METHODSIDOL-/- rabbits were generated by CRISPR/Cas9 technology. IDOL-/- and wildtype littermates, on standard (SD) and atherogenic high-cholesterol diets (HCDs) were compared through assessment of lipid and lipoprotein profiles, triglyceride clearance, lipoprotein lipase (LPL) activity, liver pathology, atherosclerosis development, and fecal cholesterol, with bile acid contents assessed by mass spectrometry. ResultsHepatic IDOL expression was increased in response to hypercholesterolemia and hypertriglyceridemia induced by HCD. On SD, loss of IDOL increased LDLR stability with reduced total cholesterol in plasma. On HCD, IDOL-/- rabbits showed simultaneous and remarkable reduction in hypercholesterolemia and hypertriglyceridemia associated with enhanced lipid clearance and LPL activity as well as increased bile acid excretion in feces. IDOL-/- rabbits presented markedly reduced HCD-induced atherosclerosis in the aorta and left coronary artery, without enhanced liver steatosis. CONCLUSIONSLoss of IDOL in rabbits recapitulates human genetic findings, thus setting the stage to accelerate preclinical studies towards development of strategies targeting IDOL for the treatment of atherosclerotic cardiovascular disease.

physiology↗

Biochemical analysis challenging Western blot analysis as validation step for antibodies intended for ELISA and immunohistochemistry

The relative contributions of the conformation and primary structure of an epitope to overall antigen-antibody interaction (AAI) at denatured, native or formalin fixed (FF) state were compared using six randomly chosen commercial antibodies using Quantitative Dot Blot (QDB) method. AAIs at native and FF states were found ranged 1.3 [~] 10.2 and 0.5 [~] 45.4 folds, respectively, over those at denatured state in cellular and tissue lysates. Using two antibodies against different epitopes of PYGL protein, we showed that PYGL levels in several types of tissues and cell lines were highly correlated (r=0.99 from Pearson, p<0.0001, n=25) when measured with these two antibodies at native state. Yet, one antibody was found to be nonspecific with one type of these tissues using Western blot analysis. These observations suggested that the conformation of an epitope may serve as dominant contributor of overall AAI at native state in general, regardless of linear or conformational epitopes. In many cases, it would override nonspecific interactions formed at denatured state to challenge Western blot analysis as a validation tool for antibodies intended for immunohistochemistry (IHC) and ELISA.

biochemistry↗

Evidence for the Presence of Hyphae and Fruiting Body Calcium Oxalate Crystallites in Schizophyllum commune

Biomineralization is a phenomenon in which organisms form crystals. Studies have shown that many fungi have the ability to biomineralize, it can exhibit calcium oxalate crystals on their hyphae and fruiting body. Schizophyllum commune is a common saprophytic fungus distributed all over the world, but there is little research on its biomineralization. In this paper, S. commune fruiting body from three different provinces of China were collected, and isolation for hyphal cultured to obtain several samples. Utilizing light microscope, FE-SEM, and EDAX, the existence of crystals on the fruiting body and mycelium of each strain was found, and their morphological characteristics and ion content were analyzed. It was ultimately established that biomineralization occurs on S. commune.

biochemistry↗

Differential effect of ethanol intoxication on peripheral markers of cerebral injury in murine blunt TBI

Blood-based biomarkers have proven to be a reliable measure of traumatic brain injury (TBI) severity and outcome, in both murine models and patients. In particular, neuron-specific enolase (NSE) and neurofilament light (NFL) have been investigated in the clinical setting post injury. Ethanol intoxication (EI) remains a significant comorbidity in TBI, with 30-40% of patients having a positive blood alcohol level (BAC) post TBI. The effect of ethanol on blood-based biomarkers on the prognosis and diagnosis of TBI remain unclear. In this study, we investigated the effect of EI on NSE and NFL and their correlation with blood-brain barrier (BBB) integrity in a murine model of TBI. We have used ultra-sensitive single molecule array technology (SIMOA) and ELISA methods to measure NFL, NSE and Claudin-5 concentrations in plasma 3h post TBI. We showed that both NFL and NSE were increased 3h post TBI. However, ethanol blood concentrations only showed an inverse correlation with NSE, but not NFL. Claudin-5 levels were increased post injury, but no difference was detected in EI. The Claudin-5 increase post TBI was correlated with NFL, but not with NSE. Thus, the data indicate that ethanol has a confined effect on biomarker release in the bloodstream and neuronal biomarkers reflect a different pathophysiology upon TBI.

neuroscience↗

3D Bioprinting of Graphene Oxide-Incorporated Cell-laden Bone Mimicking Scaffolds for Promoting Scaffold Fidelity, Osteogenic Differentiation and Mineralization

Bioprinting is a promising technique for facilitating the fabrication of engineered bone tissues for patient-specific defect repair and for developing in vitro tissue/organ models for ex vivo tests. However, polymer-based ink materials often result in insufficient mechanical strength, low scaffold fidelity and loss of osteogenesis induction because of the intrinsic swelling/shrinking and bioinert properties of most polymeric hydrogels. In this work, we developed a novel human mesenchymal stem cell (hMSC)-laden graphene oxide (GO)/alginate/gelatin composite bioink to form 3D bone mimicking scaffolds. Our results showed that the GO composite bioinks with higher GO concentrations improved the bioprintability, scaffold fidelity, compressive modulus and cell viability. The higher GO concentration increased the cell body size and DNA content. The 1GO group had the highest osteogenic differentiation of hMSC with the upregulation of osteogenic-related gene expression at day 42. To mimic critical-sized calvarial bone defects in mice, 3D cell-laden GO defect scaffolds with complex geometries were successfully bioprinted. 1GO maintained the best scaffold fidelity and had the highest mineral volume after culturing in the bioreactor for 42 days. Finally, the 1GO bioink has been demonstrated great potential for 3D bioprinting in applications of bone model and bone tissue engineering.

bioengineering↗

NDRG2 Regulates Adherens Junction Integrity to Restrict Colitis and Tumorigenesis

Paracellular barriers play an important role in the pathogenesis of IBDs and maintain gut homeostasis. N-myc downstream-regulated gene 2 (NDRG2) has been reported to be a tumor suppressor gene and inhibits colorectal cancer metastasis. However, whether NDRG2 affects colitis initiation and colitis-associated colorectal cancer is unclear. Here, We found that intestine-specific Ndrg2 deficiency caused mild spontaneous colitis with ageing, aggravated DSS and TNBS induced colitis, increased AOM-DSS induced colitis-associated tumor. Ndrg2 loss led to adherens junction (AJ) structure destruction via E-cadherin expression attenuation, resulting in diminished epithelial barrier function and increased intestinal epithelial permeability. Mechanistically, NDRG2 enhancing the interaction of E3 ligase FBXO11 with Snail, the repressor of E-cadherin, to promote Snail degradation by ubiquitination, and maintained E-cadherin expression. In human ulcerative colitis patients, reduced NDRG2 expression is positively correlated with severe inflammation. These findings demonstrate that NDRG2 is an essential colonic epithelial barrier regulator and plays important role in gut homeostasis maintenance and colitis-associated tumor development. SUMMARYAdherens junctoin (AJ) as the key part of intestinal epithelial barrier plays important role in the pathogenesis of IBDs. Intestinal specific Ndrg2 loss attenuates E-cadherin expression and disrupts the integrity of AJ structure which is feasible for colitis and tumor development.

cancer biology↗