Biology subjects

Huang, F.

Publications and source records attributed to Huang, F..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Human transmembrane protein 68 links triacylglycerol synthesis to membrane lipid homeostasis

Transmembrane protein 68 (TMEM68) is a recently identified mammalian triacylglycerol (TAG) synthase with high expression in the brain. How TMEM68 regulates cellular lipid metabolism in concert with other enzymatic pathways remains poorly understood. In this study, we assessed TMEM68 function in neuro- and gliablastoma cells by combining genetic gain- and loss-of-function approaches with lipidomics. We found that TMEM68 promotes TAG synthesis and lipid droplet formation independently of canonical acyl-CoA:diacylglycerol acyltransferase (DGAT) 1 and 2 enzymes and contributes a discrete fraction of basal cellular TAG storage. Notably, TMEM68 overexpression increased storage lipids at the expense of membrane lipids leading to a profound reduction of ether-linked glycerophospholipids (GPLs). Moreover, altered TMEM68 expression levels were associated with diminished prevalence of polyunsaturated GPLs. We conclude that TMEM68, besides its TAG synthesis function, acts as a multifaceted regulator of membrane lipid composition and polyunsaturated fatty acid homeostasis.

biochemistry↗

bioRxiv2024

Hepatitis E virus infection upregulates ING5 expression in vitro and vivo

Hepatitis E virus (HEV) is the major pathogen of viral hepatitis. Immunocompromised individual infected by HEV is prone to chronic hepatitis and increases the risk of hepato-cellular carcinoma (HCC). Inhibitor of growth family member 5 (ING5) is a tumor suppressor gene, is low expressed in cancer tumor or cells. However, the underlying relationship between ING5 and HEV infection is unclear. In the present study acute and chronic HEV animal models were employed to explore the interaction between ING5 and HEV. Notably, the expression of ING5 was significantly increased both in the liver of acute HEV infected BALB/c mice and chronic HEV infected rhesus macaques. In addition, the relationship between HEV infection and ING5 expression was further identified in human hepatoma (HepG-2) cells. In conclusion, HEV infection strongly upregulated ING5 expression in vivo and in vitro, bearing significant implications in further understanding the pathogenic mechanism of HEV infection.

microbiology↗

bioRxiv2024

Alterations in Lysosomal, Glial and Neurodegenerative Biomarkers in Patients with Sporadic and Genetic Forms of Frontotemporal Dementia

BackgroundFrontotemporal dementia (FTD) is the most common cause of early-onset dementia with 10-20% of cases caused by mutations in one of three genes: GRN, C9orf72, or MAPT. To effectively develop therapeutics for FTD, the identification and characterization of biomarkers to understand disease pathogenesis and evaluate the impact of specific therapeutic strategies on the target biology as well as the underlying disease pathology are essential. Moreover, tracking the longitudinal changes of these biomarkers throughout disease progression is crucial to discern their correlation with clinical manifestations for potential prognostic usage. MethodsWe conducted a comprehensive investigation of biomarkers indicative of lysosomal biology, glial cell activation, synaptic and neuronal health in cerebrospinal fluid (CSF) and plasma from non-carrier controls, sporadic FTD (symptomatic non-carriers) and symptomatic carriers of mutations in GRN, C9orf72, or MAPT, as well as asymptomatic GRN mutation carriers. We also assessed the longitudinal changes of biomarkers in GRN mutation carriers. Furthermore, we examined biomarker levels in disease impacted brain regions including middle temporal gyrus (MTG) and superior frontal gyrus (SFG) and disease-unaffected inferior occipital gyrus (IOG) from sporadic FTD and symptomatic GRN carriers. ResultsWe confirmed glucosylsphingosine (GlcSph), a lysosomal biomarker regulated by progranulin, was elevated in the plasma from GRN mutation carriers, both symptomatic and asymptomatic. GlcSph and other lysosomal biomarkers such as ganglioside GM2 and globoside GB3 were increased in the disease affected SFG and MTG regions from sporadic FTD and symptomatic GRN mutation carriers, but not in the IOG, compared to the same brain regions from controls. The glial biomarkers GFAP in plasma and YKL40 in CSF were elevated in asymptomatic GRN carriers, and all symptomatic groups, except the symptomatic C9orf72 mutation group. YKL40 was also increased in SFG and MTG regions from sporadic FTD and symptomatic GRN mutation carriers. Neuronal injury and degeneration biomarkers NfL in CSF and plasma, and UCHL1 in CSF were elevated in patients with all forms of FTD. Synaptic biomarkers NPTXR, NPTX1/2, and VGF were reduced in CSF from patients with all forms of FTD, with the most pronounced reductions observed in symptomatic MAPT mutation carriers. Furthermore, we demonstrated plasma NfL was significantly positively correlated with disease severity as measured by CDR+NACC FTLD{square}SB in genetic forms of FTD and CSF NPTXR was significantly negatively correlated with CDR+NACC FTLD{square}SB in symptomatic GRN and MAPT mutation carriers. ConclusionsIn conclusion, our comprehensive investigation replicated alterations in biofluid biomarkers indicative of lysosomal function, glial activation, synaptic and neuronal health across sporadic and genetic forms of FTD and unveiled novel insights into the dysregulation of these biomarkers within brain tissues from patients with GRN mutations. The observed correlations between biomarkers and disease severity open promising avenues for prognostic applications and for indicators of drug efficacy in clinical trials. Our data also implicated a complicated relationship between biofluid and tissue biomarker changes and future investigations should delve into the mechanistic underpinnings of these biomarkers, which will serve as a foundation for the development of targeted therapeutics for FTD.

neuroscience↗

bioRxiv2024

RBM7 deficiency promotes breast cancer metastasis by coordinating MFGE8 splicing switch and NF-kB pathway

Aberrant alternative splicing is well-known to be closely associated with tumorigenesis of various cancers. However, the intricate mechanisms underlying breast cancer metastasis driven by deregulated splicing events remain largely unexplored. Here, we unveiled that RBM7 is decreased in lymph node and distant organ metastases of breast cancer as compared to primary lesions and low expression of RBM7 is correlated with the reduced disease-free survival of breast cancer patients. Breast cancer cells with RBM7 depletion exhibited an increased potential for lung metastasis compared to scramble control cells. The absence of RBM7 stimulated breast cancer cell migration, invasion, and angiogenesis. Mechanistically, RBM7 controlled the splicing switch of MFGE8, favoring the production of the predominant isoform of MFGE8, MFGE8-L. This resulted in the attenuation of STAT1 phosphorylation and alterations in cell adhesion molecules. MFGE8-L exerted an inhibitory effect on the migratory and invasive capability of breast cancer cells, while the truncated isoform MFGE8-S, which lack the second F5/8 type C domain had the opposite effect. In addition, RBM7 negatively regulates the NF-{kappa}B cascade and an NF-{kappa}B inhibitor could obstruct the increase in HUVEC tube formation caused by RBM7 silencing. Clinically, we noticed a positive correlation between RBM7 expression and MFGE8 exon7 inclusion in breast cancer tissues, providing new mechanistic insights for molecular-targeted therapy in combating breast cancer.

cancer biology↗

bioRxiv2023

Activating SRC/MAPK signaling via 5-HT1A receptor contributes to the effect of vilazodone on improving thrombocytopenia

Thrombocytopenia caused by long-term radiotherapy and chemotherapy exists in cancer treatment. Previous research demonstrates that 5-Hydroxtrayptamine (5-HT) and its receptors induces the formation of megakaryocytes (MKs) and platelets. However, the relationships between 5-HT1A receptor (5-HTR1A) and MKs is unclear so far. We screened and investigated the mechanism of vilazodone as a 5-HTR1A partial agonist in promoting MK differentiation and evaluated its therapeutic effect in thrombocytopenia. We employed a drug screening model based on machine learning (ML) to screen the megakaryocytopoiesis activity of VLZ. The effects of Vilazodone (VLZ) on megakaryocytopoiesis were verified in HEL and Meg-01 cells. Tg (itga2b: eGFP) zebrafish was performed to analyze the alterations in thrombopoiesis. Moreover, we established a thrombocytopenia mice model to investigate VLZ administration accelerates platelet recovery and function. We carried out network pharmacology, Western blot and immunofluorescence to demonstrate the potential targets and pathway of VLZ. VLZ has been predicted to have a potential biological action. Meanwhile, VLZ administration promotes MK differentiation and thrombopoiesis in cells and zebrafish models. Progressive experiments showed that VLZ has a potential therapeutic effect on radiation-induced thrombocytopenia in vivo. The network pharmacology and associated mechanism study indicated that SRC and MAPK signaling are both involved in the processes of megakaryopoiesis facilitated by VLZ. Furthermore, the expression of 5-HTR1A during megakaryocyte differentiation is closely related to the activation of SRC and MAPK. Our findings demonstrated that the expression of 5-HTR1A on MK, VLZ could bind to the 5-HTR1A receptor and further regulate the SRC/MAPK signaling pathway to facilitate megakaryocyte differentiation and platelet production, which provides new insights into the alternative therapeutic options for thrombocytopenia.

pharmacology and toxicology↗

bioRxiv2023

Measurement precision bounds on aberrated single molecule emission patterns

Single-Molecule Localization Microscopy (SMLM) has revolutionized the study of biological phenomena by providing exquisite nanoscale spatial resolution. However, optical aberrations induced by sample and system imperfections distort the single molecule emission patterns (i.e. PSFs), leading to reduced precision and resolution of SMLM, particularly in three-dimensional (3D) applications. While various methods, both analytical and instrumental, have been employed to mitigate these aberrations, a comprehensive analysis of how different types of commonly encountered aberrations affect single molecule experiments and their image formation remains missing. In this study, we addressed this gap by conducting a quantitative study of the theoretical precision limit for position and wavefront distortion measurements in the presence of aberrations. Leveraging Fisher information and Cramer-Rao lower bound (CRLB), we quantitively analyzed and compared the effects of different aberration types, including index mismatch aberrations, on localization precision in both biplane and astigmatism 3D modalities as well as 2D SMLM imaging. Furthermore, we studied the achievable wavefront estimation precision from aberrated single molecule emission patterns, a pivot step for successful adaptive optics in SMLM through thick specimens. This analysis lays a quantitative foundation for the development and application of SMLM in whole-cells, tissues and with large field of view, providing in-depth insights into the behavior of different aberration types in single molecule imaging and thus generating theoretical guidelines for developing highly efficient aberration correction strategies and enhancing the precision and reliability of 3D SMLM.

biophysics↗

bioRxiv2023

Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output

Estrogen Receptor alpha (ER) is the main driver and prime drug target in luminal breast. ER chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ER chromatin action, along with its biological implications. Here, we use a large set of ER ChIP-seq data from 70 ER+ breast cancers to explore inter-patient heterogeneity in ER DNA binding, to reveal a striking inter-tumor heterogeneity of ER action. Interestingly, commonly-shared ER sites showed the highest estrogen-driven enhancer activity and were most-engaged in long-range chromatin interactions. In addition, the most-commonly shared ER-occupied enhancers were enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ER and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we could confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ER-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ER landscape, with the most-common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.

genomics↗

bioRxiv2023

Suppression of the Integrated Stress Response in Islet β Cells Decreases Risk of Autoimmune Diabetes

Preventing the onset of autoimmune type 1 diabetes (T1D) is feasible through pharmacological interventions that target molecular stress-responsive mechanisms. Cellular stresses, such as nutrient deficiency, viral infection, or unfolded proteins, trigger the integrated stress response (ISR), which curtails protein synthesis by phosphorylating eIF2. In T1D, maladaptive unfolded protein response (UPR) in insulin-producing {beta} cells renders these cells susceptible to autoimmunity. We show that inhibition of the eIF2 kinase PERK, a common component of the UPR and ISR, reverses the mRNA translation block in stressed human islets and delays the onset of diabetes, reduces islet inflammation, and preserves {beta} cell mass in T1D-susceptible mice. Single-cell RNA sequencing of islets from PERK-inhibited mice shows reductions in the UPR and PERK signaling pathways and alterations in antigen processing and presentation pathways in {beta} cells. Spatial proteomics of islets from these mice shows an increase in the immune checkpoint protein PD-L1 in {beta} cells. Golgi membrane protein 1, whose levels increase following PERK inhibition in human islets and EndoC-{beta}H1 human {beta} cells, interacts with and stabilizes PD-L1. Collectively, our studies show that PERK activity enhances {beta} cell immunogenicity, and inhibition of PERK may offer a strategy to prevent or delay the development of T1D.

cell biology↗

bioRxiv2023

Tunable PhenoCycler Imaging of the Murine Pre-Clinical Tumour Microenvironments

The tumour microenvironment (TME) consists of tumour-supportive immune cells, endothelial cells, and fibroblasts. PhenoCycler, a high-plex single cell imaging platform, is used to characterize the complexity of the TME. Here, we used PhenoCycler to spatially resolve the TME of 8 routinely employed pre-clinical models of lymphoma, breast cancer, and melanoma. Our data reveal distinct TMEs in the different cancer models that were imaged, and show that cell-cell contacts differ depending on the tumour type examined. For instance, we found that the immune infiltration in a murine model of melanoma is altered in cellular organization in melanomas that become resistant to PD-1 therapy, with depletions in a number of cell-cell interactions. Furthermore, we provide detailed pipelines for the conjugation of antibodies that are optimized for PhenoCycler staining of murine FFPE tissues specifically, alongside open-source data analysis procedures. Overall, this is a valuable resource study seamlessly adaptable to any field of research involving murine models.

cancer biology↗

bioRxiv2023

Multi-omics map revealed PPARalpha activation protecting against myocardial ischemia-reperfusion injury by maintaining cardiac metabolic homeostasis

Timely percutaneous coronary intervention is the most effective initial therapy for the acute myocardial infarction (MI). However, the mechanism in energy metabolism underlying time-dependent coronary reperfusion remains largely unknown. Here, we generated an integrative map of cardiac cells using bulk and single-nucleus RNA-seq combined with metabolomics profiling of hearts with reperfusion at distinct time points post MI in rat. We found early time reperfusion (ETR), but not late time reperfusion (LTR) reduced myocardial injury by maintaining cardiac energy homeostasis. PPAR was identified as a key regulator for maintaining fatty acid metabolism after MI/R injury. Importantly, pretreatment with FDA-approved PPAR agonist, fenofibrate, improved the transcriptional signatures, and ameliorated the function of the MI/R injured hearts, particularly in the ETR. Together, our data not only deciphered the protective effect of ETR by maintaining cardiac energy homeostasis, but also provided insights into the translational potential of PPAR activation in alleviating MI/R injury.

cell biology↗

bioRxiv2023

Comprehensive catalogs for microbial genes and metagenome-assembled genomes of the swine lower respiratory tract microbiome identify the relationship of microbial species with lung lesions

Understanding the community structure and functional capacity of the lower respiratory tract microbiome is crucial for elucidating its roles in respiratory tract diseases. However, there are few studies about it owing to the difficulty in obtaining microbial samples from the lower respiratory tract. Here we collected 745 microbial samples from the porcine lower respiratory tract by harvesting 675 pigs, and constructed a gene catalog containing 10,337,194 nonredundant genes, of which only 30% could be annotated taxonomically. We obtained 397 metagenome-assembled genomes (MAGs) including 111 MAGs with high-quality. These 397 MAGs were further clustered into 292 species-level genome bins (SGBs), among which 56% SGBs are unknown with current databases. Combining with the lung lesion phenotype, we found that Mycoplasma hyopneumoniae strains and the adhesion-related virulence factors harboring in their genomes were significantly associated with porcine lung lesions, implying the role of adhesion and overgrowth of pathogenic M. hyopneumoniae in host lung diseases. This study provided important resources for the study of porcine lower respiratory tract microbiome and lung health.

microbiology↗

bioRxiv2023

Molecular recognition of an aversive odorant by the murine trace amine-associated receptor TAAR7f

There are two main families of G protein-coupled receptors that detect odours in humans, the odorant receptors (ORs) and the trace amine-associated receptors (TAARs). Their amino acid sequences are distinct, with the TAARs being most similar to the aminergic receptors such as those activated by adrenaline, serotonin and histamine. To elucidate the structural determinants of ligand recognition by TAARs, we have determined the cryo-EM structure of a murine receptor, mTAAR7f, coupled to the heterotrimeric G protein Gs and bound to the odorant N,N-dimethylcyclohexylamine (DMCH) to an overall resolution of 2.9 [A]. DMCH is bound in a hydrophobic orthosteric binding site primarily through van der Waals interactions and a strong charge-charge interaction between the tertiary amine of the ligand and an aspartic acid residue. This site is distinct and non-overlapping with the binding site for the odorant propionate in the odorant receptor OR51E2. The structure, in combination with mutagenesis data and molecular dynamics simulations suggests that the activation of the receptor follows a similar pathway to that of the {beta}-adrenoceptors, with the significant difference that DMCH interacts directly with one of the main activation microswitch residues.

molecular biology↗

bioRxiv2023

Intrinsically disordered CsoS2 acts as a general molecular thread for α-carboxysome shell assembly

Carboxysomes are a paradigm of self-assembling proteinaceous organelles found in nature, offering compartmentalisation of enzymes and pathways to enhance carbon fixation. In -carboxysomes, the disordered linker protein CsoS2 plays an essential role in carboxysome assembly and Rubisco encapsulation. Its mechanism of action, however, is not fully understood. Here we synthetically engineered -carboxysome shells using minimal shell components and determined cryoEM structures of these to decipher the principle of shell assembly and encapsulation. The structures reveal that the intrinsically disordered CsoS2 C-terminus is well-structured and acts as a universal "molecular thread" stitching through multiple shell protein interfaces. We further uncovered in CsoS2 a remarkable highly conserved repetitive key interaction motif, [IV]TG, which is critical to the shell assembly and architecture. Our study provides a general mechanism for the CsoS2-govern carboxysome shell assembly and cargo encapsulation and further advances synthetic engineering of carboxysomes for diverse biotechnological applications.

microbiology↗

bioRxiv2023

Gut microbiota-derived gamma-aminobutyric acid from metformin treatment reduces hepatic ischemia/reperfusion injury through inhibiting ferroptosis.

Hepatic ischemia/reperfusion injury (HIRI) is a common and inevitable factor leading to poor prognosis in various liver diseases, making the outcomes of current treatments in clinic unsatisfactory. Metformin has been demonstrated to be beneficial to alleviate HIRI in recent studies, however, the underpinning mechanism remains unclear. In this study, we found metformin mitigates HIRI-induced ferroptosis through reshaped gut microbiota in mice, which was confirmed by the results of fecal microbiota transplantation (FMT) treatment but showed the elimination of the beneficial effects when gut bacteria were depleted using antibiotics. Detailedly, through 16S rRNA and metagenomic sequencing, we identified that the metformin-reshaped microbiota was characterized by the increase of gamma-aminobutyric acid (GABA) producing bacteria. This increase was further confirmed by the elevation of GABA synthesis key enzymes, glutamic acid decarboxylase (GAD) and putrescine aminotransferase (PAT), in gut microbes of metformin-treated mice and healthy volunteers. Furthermore, the benefit of GABA against HIRI-induced ferroptosis was demonstrated in GABA-treated mice. Collectively, our data indicate that metformin can mitigate HIRI-induced ferroptosis by reshaped gut microbiota, with GABA identified as a key metabolite.

microbiology↗

bioRxiv2023

Mechanisms underlying the therapeutic effects of Semen Cuscutae in treating Recurrent Spontaneous Abortion based on Network Pharmacology and Molecular Docking

BackgroundThis paper aims to analyze the active components of SC by network pharmacology and screen the most stable compounds with TNF-a by molecular docking, to explore the mechanism of SC treatment of RSA and provide theoretical basis for drug development. MethodsActive compounds of SC and the potential inflammatory targets of RSA were obtained from the Traditional Chinese Medicine Systematic Pharmacology Database and GeneCard, respectively. The interaction network of RSA-SC-target gene was accomplished and Visualizing by STRING database and Cytoscape software.GO and KEGG pathway enrichment analyses were obtained from DAVID to further explore the RSA mechanism and therapeutic effects of SC. Interactions between TNF- and active compounds were analyzed by molecular docking. Results10 active ingredients and 128 target genes were screened from SC, and 79 of them intersected with RSA target inflammatory genes,which were considered to be potential therapeutic targets. Network pharmacological analysis showed that Sesamin, matrine, matrol and other SC active components had good correlation with the inflammatory target genes of RSA.Related genes include PGR, PTGS1, PTGS2, TGFB1 and CHRNA7. Multiple signaling pathways are involved in RSA pathogenesis,sunh as TNF- signaling pathway, HIF-1 signaling pathway, estrogen signaling pathway, proteoglycans in cancer, FoxO signaling pathway, etc. Molecular docking results suggested that sesamin was the most appropriate natural TNFis. ConclusionOur findings provide an important role and basis for further research on the molecular mechanism of SC treatment of RSA and drug development of TNFis.

bioinformatics↗

bioRxiv2023

Prokaryotic Gabija complex senses and executes nucleotide depletion and DNA cleavage for antiviral defense

The Gabija antiviral system consists of the GajA and GajB proteins. We previously revealed that GajA is a DNA nicking endonuclease. In this work, we found that the DNA binding of GajA is strictly inhibited by NTP. Furthermore, the antiviral defense of GajA requires the assistance from GajB, which senses DNA termini produced from the DNA nicking by GajA to hydrolyze (d)A/(d)GTP. The synergy between the DNA cleavage by GajA and the nucleotide hydrolysis by GajB results in an efficient abortive infection defense against virulent bacteriophages. GajA binds to GajB to form stable complexes in vivo and in vitro. However, a functional Gabija complex requires the molecular ratio between GajB and GajA below 1:1. Through (i) sequential sensing and executing the nucleotide depletion and DNA cleavage to cause a cascade suicide effect and (ii) stoichiometry regulation of the DNA/nucleotide processing complex, the Gabija system exhibits a unique mechanism distinct from other known prokaryotic antiviral systems.

microbiology↗

bioRxiv2023

The establishment of HP1-independent heterochromatin reveals an essential role for HP1 proteins in maintaining epigenetic memory

H3K9 methylation (H3K9me) marks transcriptionally silent genomic regions called heterochromatin. HP1 proteins are required to establish and maintain heterochromatin. HP1 proteins bind to H3K9me, recruit factors that promote heterochromatin formation, and oligomerize to form phase-separated condensates. We do not understand how HP1 protein binding to heterochromatin establishes and maintains transcriptional silencing. Here, we demonstrate that the S.pombe HP1 homolog, Swi6, can be completely bypassed to establish silencing at ectopic and endogenous loci when an H3K4 methyltransferase, Set1 and an H3K14 acetyltransferase, Mst2 are deleted. Deleting Set1 and Mst2 enhances Clr4 enzymatic activity, leading to higher H3K9me levels and spreading. In contrast, Swi6 and its capacity to oligomerize were indispensable during epigenetic maintenance. Our results demonstrate the role of HP1 proteins in regulating histone modification crosstalk during establishment and identifies a genetically separable function in maintaining epigenetic memory.

genetics↗

bioRxiv2023

scART: recognizing cell clusters and constructing trajectory from single-cell epigenomic data

The development of single-cell assay for transposase-accessible chromatin using sequencing data (scATAC-seq) has allowed the characterization of epigenetic heterogeneity at single-cell resolution. However, the sparse and noisy nature of scATAC-seq data poses unique computational challenges. To address this, we introduce scART, a novel bioinformatics tool specifically designed for scATAC-seq data analysis. scART utilizes analytical methods highly stable for processing sparse and noisy data, such as k-nearest neighbor (KNN) imputation, Term Frequency-Inverse Document Frequency (TF-IDF) weighting scheme, and the cosine similarity metric to identify underlying cellular heterogeneity in scATAC-seq data. It accurately and robustly identifies cell identities, particularly in data with low sequencing depth, and constructs the trajectory of cellular states. As a demonstration of its utility, scART successfully reconstructed the development trajectory of the embryonic mouse forebrain and uncovered the dynamics of layer-specific neurogenesis. scART is available at GitHub.

bioinformatics↗