Biology subjects

Zhang, Z.

Publications and source records attributed to Zhang, Z..

At least 631 records · Page 35Linked to original sources

bioRxiv2024

Reciprocal regulation of m6A modification and miRNA production machineries via phase separation-dependent and -independent mechanisms

Methyltransferase complex (MTC) deposits N6-adenosine (m6A) onto RNA, whereas microprocessor produces miRNA. Whether and how these two distinct complexes cross-regulate each other has been poorly studied. Here we report that the MTC subunit B (MTB) tends to form insoluble condensates with poor activity, with its level monitored by 20S proteasome. Conversely, the microprocessor component SERRATE (SE) forms liquid-like condensates, which in turn promotes solubility and stability of MTB, leading to increased MTC activity. Consistently, the hypomorphic lines expressing SE variants, defective in MTC interaction or liquid-like phase behavior, exhibit reduced m6A level. Reciprocally, MTC can recruit microprocessor to MIRNA loci, prompting co-transcriptional cleavage of primary miRNA (pri-miRNAs) substrates. Additionally, pri-miRNAs carrying m6A modifications at their single-stranded basal regions are enriched by m6A readers, which retain microprocessor in the nucleoplasm for continuing processing. This reveals an unappreciated mechanism of phase separation in RNA modification and processing through MTC and microprocessor coordination.

plant biology↗

bioRxiv2024

Diversity and ecological roles of RNA viral communities in the cryosphere of the Tibetan Plateau

RNA viruses play crucial roles in modulating host communities, but their diversity and ecological roles in the cryosphere are poorly understood. We investigated the RNA virome from the cryosphere of the Tibetan Plateau (TPC), the largest area of the cryosphere in the mid-low latitude regions, which includes 79 metatranscriptomes from ecosystems including glaciers, proglacial lake sediments, permafrost wetland and upland soils. We obtained 8,799 RNA-dependent RNA polymerase encoding contigs, which clustered into 5,333 viral species, adding more than 4,900 new RNA viral species to the global RNA virome database. The recovered RNA viruses primarily infect prokaryotes, distinctively different from the dominance of eukaryotic RNA viruses in oceanic ecosystems. In addition to the known taxa such as Leviviricetes, we identified novel clades of putative prokaryotic RNA viruses, which greatly extended our understanding of their diversity. We further expanded the host of RNA virus by 20 additional prokaryotic phylum- or class-level taxonomic groups. Moreover, the TPC RNA viruses encoded dozens of auxiliary metabolic genes that could reprogram the metabolisms of diverse hosts, including photosynthesis in glacier eukaryotic algae and cyanobacteria, which may exert great impacts on glacier dynamics through modulating host adaptation. Furthermore, we identified potential pathogenic RNA viruses in various cryosphere environments, though their overall risks are low. This study provides the first comprehensive view of cryosphere RNA virome, highlighting their high diversity, vital ecological functions, and potential health impacts.

ecology↗

bioRxiv2024

Imaging the interactions of chimeric antigen receptor-expressing T-cells with colorectal cancer cells

Chimeric antigen receptor (CAR) T-cell therapy has shown unprecedented success in haematological cancers but faces challenges in solid tumours. Although carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) is differentially expressed in many solid tumours, anti-CEACAM5 CAR T-cells are ineffective. Here, we have studied the interaction of CEACAM5 targeting primary CAR T-cells with colorectal cancer (CRC) cells using fluorescence microscopy. We found that CRC cells glycocalyx is much deeper than that of the CAR T cell causing delayed activation. Oscillating calcium fluxes, indicative of non-sustained CAR T cell activation and reduced cytotoxicity, were observed when CAR T cells interacted with CRC cells, which increased with increasing cell-seeding time. Imaging revealed that this effect correlated with a progressive loss of accessible CEACAM5 antigen on the CRC cell surface, possibly due to their sequestration in the intercellular junction, rendering CAR T cell engagement less effective. Local proteolytic treatment with trypsin to disrupt the CRC cell monolayer, using a micropipette, increased CEACAM5 availability, decreased glycocalyx thickness, and restored sustained CAR T cell calcium fluxes, increasing the killing of CRC cells. Similar enhanced interaction was observed after treatment of CRC cell monolayer with hyaluronidase, approved for use in humans. We observed limited availability of CEACAM5 on human colorectal cancer tissues, whereas treatment with trypsin or hyaluronidase increased accessibility. Our results reveal why CAR T cells targeting CEACAM5 are ineffective and suggest possible routes to improved therapy for CRC.

immunology↗

bioRxiv2024

Identification of a new ORF3a-E fusion subgenomic RNA of SARS-CoV-2 and its biological features in the infection process

Subgenomic RNAs (sgRNAs) are discontinuous transcription products of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that are involved in viral gene expression and replication, but their exact functions are still being studied. Here, we report the identification of a new type of sgRNA, the fusion ORF3a-E-sgRNA, involved in the infection process of SARS-CoV-2. This sgRNA codes both ORF3a and E and can be detected throughout the viral life cycle in SARS-CoV-2-infected cells with high copy numbers. ORF3a-E-sgRNA guides more ORF3a translation and promotes the expression of cellular ribosomal protein S3 (RPS3) and the binding of eukaryotic translation initiation factor 4E (eIF4E). Single-cell sequencing of a SARS-CoV-2-infected human bronchial epithelial cell line (16HBE) revealed that maintenance of this stable translational environment by ORF3a-E-sgRNA is important for the SARS-CoV-2 assembly and release capabilities and is also beneficial for viral evasion of host innate immunity. More importantly, the transcription level of ORF3a-E-sgRNA contributes to differences in infection processes between the Wuhan strain and XBB strain of SARS-CoV-2.

microbiology↗

bioRxiv2024

MED26-enriched condensates drive erythropoiesis through modulating transcription pausing

The Mediator complex regulates various aspects of hematopoietic development, but whether composition of the Mediator complex undergoes dynamic changes for diversifying transcription and functional outputs is unknown. Here, we found that MED26, a subunit in the core Mediator complex, played a distinctive role in facilitating transcription pausing essential for erythroid development. While most Mediator subunits drastically decreased during this process, MED26 remained relatively abundant. Intriguingly, in the early stages, more than half of MED26 occupancy sites did not co-localize with MED1, a representative Mediator subunit, suggesting these subunits exert context-dependent gene regulation. We revealed that MED26-enriched loci were associated with RNA polymerase pausing. MED26 manifested a markedly preferential recruitment of pausing-related factors, leading to an increase in Pol pausing critical for genome-wide transcription repression during erythropoiesis. Moreover, MED26 exhibited pronounced condensate-forming capability, which was necessary for its function in promoting erythropoiesis and recruiting pausing-related factors. Collectively, this study provides mechanistic insights into the functional coordination of distinct Mediator subunits during development and highlights the switch of transcription condensates towards a MED26 enriched form, which modulates transcription pausing to facilitate transcription repression and erythroid development.

cell biology↗

bioRxiv2024

Spatiotemporally-resolved mapping of extracellular proteomes via in vivo-compatible TyroID

Extracellular proteins play pivotal roles in both intracellular signaling and intercellular communications in health and disease. While recent advancements in proximity labeling (PL) methods, such as peroxidase- and photocatalyst-based approaches, have facilitated the resolution of extracellular proteomes, their in vivo compatibility remains limited. Here, we report TyroID, an in vivo-compatible PL method for unbiased mapping of extracellular proteins with high spatiotemporal resolution. TyroID employs plant- and bacteria-derived tyrosinases to produce reactive o-quinone intermediates, enabling the labeling of multiple residues on endogenous proteins with bioorthogonal handles, thereby allowing for their identification via chemical proteomics. We validate TyroIDs specificity by mapping extracellular proteomes and HER2-neighboring proteins using nanobody-directed recombinant tyrosinases. Demonstrating its superiority over other PL methods, TyroID enables in vivo mapping of extracellular proteomes, including mapping HER2-proximal proteins in tumor xenografts, quantifying the turnover of plasma proteins and labeling hippocampal-specific proteomes in live mouse brains. TyroID emerges as a potent tool for investigating protein localization and molecular interactions within living organisms.

biochemistry↗

bioRxiv2024

Endothelial MICU1 protects against vascular inflammation and atherosclerosis by inhibiting mitochondrial calcium uptake

Atherosclerosis is triggered by endothelial activation and vascular inflammation, which is closely related to mitochondrial dysfunction. Mitochondrial calcium uptake 1 (MICU1), as the gatekeeper of mitochondrial Ca2+ homeostasis, is a critical player in mitochondrial function and implicated in a plethora of pathophysiological conditions. However, the role of MICU1 in the pathogenesis of vascular inflammation and atherosclerosis is unknown. We ask whether endothelial MICU1 can prevent vascular inflammation and atherosclerosis by maintaining mitochondrial homeostasis. We observed that vascular inflammation in response to LPS was aggravated in EC-specific Micu1 knockout mice (Micu1ECKO) and reduced in EC-specific Micu1 transgenic mice (Micu1ECTg). Furthermore, hypercholesterolemic Micu1ECKO mice also showed accelerated formation of atherosclerotic plaques, while Micu1ECTg mice protected against atherosclerosis. Mechanistically, MICU1 regulated mitochondrial Ca2+ influx, thereby reducing the expression of the mitochondrial deacetylase SIRT3 and the ensuing deacetylation of SOD2, leading to the burst of mitochondrial reactive oxygen species (mROS). Of clinical relevance, we identified decreased MICU1 level in endothelial layer of human atherosclerotic plaques, as well as in primary human aortic endothelial cells (HAECs) exposed to serum from patients with coronary artery diseases. Two-sample Wald ratio Mendelian randomization further revealed that increased expression of MICU1 was associated with decreased risk of coronary artery bypass grafting (CABG). Our findings unravel a critical and unrecognized role of MICU1 in preventing vascular inflammation and atherosclerosis by maintaining mitochondrial Ca2+ homeostasis.

molecular biology↗

bioRxiv2024

Three-dimension transcriptomics maps of whole mouse embryo during organogenesis

Understanding mammalian development heavily relies on classical animal models like the house mouse (Mus musculus). Advanced spatial transcriptomics has enabled biologists to break new ground in studies of molecular dynamics and cellular patterning during embryonic development with spatiotemporal resolution. To construct a comprehensive developmental trajectory, current three-dimensional (3D) spatial transcriptomic profiling leverages mouse embryos from gastrulation (E5.5) to organogenesis (E13.5) in continuity. However, a crucial phase for early organogenesis between E9.5 and E11.5 was deficient. To unveil the mystery of this stage, we present the 3D transcriptomics of mouse embryos at E9.5 and E11.5, with a widely applicable reconstruction workflow that bypasses sophisticated bioinformatic calculations. As our 3D atlas is generated at single-cell resolution, we demonstrate how organogenetic processes can be interpreted at different levels of granularity, from local cellular interactions to whole embryonic regionalization. We release the open-access database MOSTA3D (Mouse Organogenesis Spatiotemporal Transcriptomic Atlas in Three-dimensional) and hope a broader community will contribute to extending this framework from conception to senility in the near future.

developmental biology↗

bioRxiv2024

The clinical antiprotozoal drug halofuginone promotes weight loss by elevating GDF15 and FGF21

Obesity is a debilitating disease with increasing worldwide prevalence. Despite its high prevalence, specific pharmacologic intervention for obesity is challenging. Here, we report that halofuginone, an FDA-approved anti-scleroderma and anti-protozoal drug, is a promising anti-obesity agent in rodent models. Halofuginone suppressed food intake, increased energy expenditure, and resulted in weight loss in preclinical diet-induced obese mouse models, while also decreasing insulin resistance and hepatic steatosis. By combining genetic and pharmacological tools with transcriptomics, we identified that halofuginone increases FGF21 and GDF15 levels via ATF4. Using knockout mice, we show these hormones are both necessary for its anti-obesity effects. Thus, our study first reports the beneficial metabolic effects of halofuginone and underscores its utility to treat obesity and its associated metabolic complications.

pharmacology and toxicology↗

bioRxiv2024

Bioinspired Bimetallic Ions Functionalized MOF SAzyme Nanocomposites for Synergistic Ferroptosis/Cuproptosis-Enhanced Immune Checkpoint Therapy

Immune checkpoint blockade (ICB) generates sustained responses in immunogenic cancers, but its effectiveness is limited in tumors lacking immune activity. Here, we construct a bioinspired bimetallic ions functionalized nanoscale metal-organic framework (NMOF) single-atom nanozyme (SAzyme) loaded with doxorubicin (Dox) (NMOF-Fe/Cu-Dox nanocomposite) to effectively trigger anti-tumor immune responses while addressing the immunosuppressive tumor microenvironment (TME). The NMOF-Fe/Cu-Dox nanocomposite has been demonstrated to efficiently reverse the TME by generating reactive oxygen species and oxidizing glutathione. Camouflaging NMOF-Fe/Cu-Dox nanocomposites with bioinspired cancer cell membrane (NMOF-Fe/Cu-Dox@M) enables its navigation to the tumor region through homologous targeting. The highly efficient uptaken by cancer cells selectively induced synergistic ferroptosis and cuproptosis in these cells. Furthermore, in vitro and in vivo experiments demonstrate that the ferroptosis in cancer cells can polarize tumor-associated macrophages (TAMs) towards anti-tumoral M1 phenotype and significantly diminish pro-tumoral M2 phenotype. We find that NMOF-Fe/Cu-Dox@M could induce the ferroptosis of M2 macrophages, while no effect to M1 macrophages. In addition, a significant increase of anti-tumor infiltrating CD8+ T cells, while a remarkable decrease of CD4+ regulatory T cells were observed. These findings suggested that NMOF-Fe/Cu-Dox@M could efficiently modulate TME, enhance tumoricidal immunity and elevate the therapeutic efficiency of ICB. Moreover, the combination of NMOF-Fe/Cu-Dox@M with PD-1 effectively eradicated hepatocellular carcinoma cells in vivo, outperforming the use of either NMOF-Fe/Cu-Dox@M or PD-1 alone. In summary, our study presents a therapeutic strategy that leverages coordinated ferroptosis and cuproptosis with therapeutic efficiency of ICB, underscoring the promise of combined chemoimmunotherapy.

bioengineering↗

bioRxiv2024

A biofilm-tropic Pseudomonas aeruginosa bacteriophage uses the exopolysaccharide Psl as receptor

Bacteria in nature can exist in multicellular communities called biofilms. Biofilms also form in the course of many infections. Pseudomonas aeruginosa infections frequently involve biofilms, which contribute materially to the difficulty to treat these infections with antibiotic therapy. Many biofilm-related characteristics are controlled by the second messenger, cyclic-di-GMP, which is upregulated on surface contact. Among these factors is the exopolysaccharide Psl, which is a critically important component of the biofilm matrix. Here we describe the discovery of a P. aeruginosa bacteriophage, which we have called Clew-1, that directly binds to and uses Psl as a receptor. While this phage does not efficiently infect planktonically growing bacteria, it can disrupt P. aeruginosa biofilms and replicate in biofilm bacteria. We further demonstrate that the Clew-1 can reduce the bacterial burden in a mouse model of P. aeruginosa keratitis, which is characterized by the formation of a biofilm on the cornea. Due to its reliance on Psl for infection, Clew-1 does not actually form plaques on wild-type bacteria under standard in vitro conditions. This argues that our standard isolation procedures likely exclude bacteriophage that are adapted to using biofilm markers for infection. Importantly, the manner in which we isolated Clew-1 can be easily extended to other strains of P. aeruginosa and indeed other bacterial species, which will fuel the discovery of other biofilm-tropic bacteriophage and expand their therapeutic use.

microbiology↗

bioRxiv2024

Optics-free Spatial Genomics for Mapping Mouse Brain Aging

Spatial transcriptomics has revolutionized our understanding of cellular network dynamics in aging and disease by enabling the mapping of molecular and cellular organization across various anatomical locations. Despite these advances, current methods face significant challenges in throughput and cost, limiting their utility for comprehensive studies. To address these limitations, we introduce IRISeq (Imaging Reconstruction using Indexed Sequencing), a optics-free spatial transcriptomics platform that eliminates the need for predefined capture arrays or extensive imaging, allowing for the rapid and cost-effective processing of multiple tissue sections simultaneously. Its capacity to reconstruct images based solely on sequencing local DNA interactions allows for profiling of tissues without size constraints and across varied resolutions. Applying IRISeq, we examined gene expression and cellular dynamics in thirty brain regions of both adult and aged mice, uncovering region-specific changes in gene expression associated with aging. Further cell type-centric analysis further identified age-related cell subtypes and intricate changes in cell interactions that are distinct to certain spatial niches, emphasizing the unique aspects of aging in different brain regions. The affordability and simplicity of IRISeq position it as a versatile tool for mapping region-specific gene expression and cellular interactions across various biological systems. One Sentence Summary: IRISeq, an innovative optics-free spatial transcriptomics method, uncovers aging-related changes in spatial gene expression and focal cell interactions in brain aging.

genomics↗

bioRxiv2024

PTEN neddylation aggravates CDK4/6 inhibitor resistance in breast cancer

The gradual emergence of a novel therapeutic approach lies in the restoration of tumor suppressive machinery. PTEN is a crucial negative regulator of the PI3K/Akt signaling pathway. Protein neddylation modification contributes to PTEN inactivation and fuels breast cancer progression. Here, we highlight that an elevated level of PTEN neddylation is markedly associated with resistance to palbociclib, a CDK4/6 inhibitor used in luminal subtype breast cancer patients. Mechanistically, PTEN neddylation activates the PI3K/Akt signaling pathway, and more notably, upregulates the activity of the AP-1 transcription factor. Our data showed that PTEN neddylation stabilizes JUND, a transcription factor involved in the AP-1 complex, by disrupting its interaction with the E3 ubiquitin ligase ITCH. Consequently, activated JUND leads to the release of cytokines and chemokines, which in turn may drive an inflammatory tumor microenvironment, potentially contributing to drug resistance. Then, we identified Echinacoside as a potent inhibitor of PTEN neddylation both in vivo and in vitro by disrupting its interaction with XIAP, the E3 ligase responsible for PTEN neddylation. Combination of Echinacoside effectively overcome resistance to palbociclib in breast cancer treatment. These findings highlight targeting PTEN neddylation as a promising strategy for restoring tumor suppressor activity and overcoming resistance.

cell biology↗

bioRxiv2024

In-cell structural insight into the asymmetric assembly of central apparatus in mammalian sperm axoneme

In motile cilia or flagella, the axoneme typically exhibits a "9+2" configuration, with the central apparatus (CA) consisting of extensively modified microtubules C1 and C2 to regulate ciliary motility. How C1 and C2 are interconnected asymmetrically remains unknown due to the lack of complete structural model of CA. Here, we utilized the in situ cryo-electron tomography approach to solve the in-cell structure of intact mouse sperm CA at sub-nanometer resolution and built its near-complete atomic model with the aid of AlphaFold2. We identified 39 different CA-associated proteins with 8 never reported from isolated specimen. We assigned the long chain-like ASH-containing proteins CFAP47 and HYDIN responsible for connecting C1 and C2. Sperm from Cfap47-knockout mice displayed a hollowing bridge in the CA structure, correlating with its reduced progressive motility. Our findings elucidate the molecular mechanisms of CA components in ciliary motility, and the implications of their mutations in human ciliopathies.

molecular biology↗

bioRxiv2024

RIPK4 driven by TP53 mutations promotes resistance to redox stress of CRC by phosphorylating MTHFD1

This study investigates advanced colorectal cancer (CRC), focusing on its tendency for distant metastasis and chemotherapy resistance. It highlights the importance of PANoptosis, a cell death pathway, and the role of the Receptor-interacting serine/threonine-protein kinase (RIPK) family in tumor progression. RIPK4s tissue-specific functions in cancer cell behavior are emphasized, including its influence on invasion, migration, and oxidative stress resistance. The study reveals the critical balance of reactive oxygen species (ROS) in cancer cells, linked to antioxidant defenses and NADPH production for survival. A key finding is the connection between TP53 mutations in CRC and increased RIPK4 expression, which enhances MTHFD1 phosphorylation, boosts NADPH production, reduces ROS, and promotes resistance to PANoptosis, leading to metastasis. The research identifies the molecular basis of CRC metastasis, showing how RIPK4 regulates MTHFD1 to resist PANoptosis, offering new therapeutic targets for metastatic CRC and potential improvements in patient outcomes.

molecular biology↗

bioRxiv2024

Genomic and transcriptomic profiles influence on brain morphology and their interactions with pain sensitivity

Pain sensitivity varies widely among individuals and is influenced by a complex interplay of multi-omics factors, including genetic variations, gene expression, and brain morphology. While previous studies have identified associations between pain sensitivity and brain morphology, the exact mechanisms by which genetic profiles interact with brain structure to influence individual pain sensitivity remain unclear. In this study, we used aggregated datasets, including magnetic resonance imaging (MRI) and single nucleotide polymorphism (SNP) genotypes from 432 healthy participants, along with gene expression data from the Allen Human Brain Atlas (AHBA), to explore this multi-omics interplay. We first measured individual pain thresholds using laser stimuli and discovered structural brain differences between high and low pain sensitivity groups. We then identified two key gene sets with polarized expression patterns linked to brain morphology variations, enriched in functions related to ion channels and transmembrane transporter activities. Further statistical and mediation analyses revealed specific SNPs from ECM1, SLC24A2, and SCN9A genes that influence pain sensitivity, mediated through brain morphological changes in multiple basal ganglia regions. Our findings suggested that these SNPs not only affect brain structure but also modulate how individuals pain perception. Finally, we proposed an interpretation model integrating genomic, transcriptomic, and neuroimaging data, providing a detailed framework that illustrates the multi-omics contributions to individual difference in pain sensitivity. This study advances our understanding of how genetic and brain structural factors combine to shape pain perception, offering potential targets for personalized pain management strategies.

bioinformatics↗

bioRxiv2024

Cross-view graph neural networks for spatial domain identification by integrating gene expression, spatial locations with histological images

The latest developments in spatial transcriptomics technology provide an unprecedented opportunity for in situ elucidation of tissue structure and function. Spatial transcriptomics can provide simultaneous, multi-modal, and complementary information, including gene expression profiles, spatial positions, and histological images. Despite these capabilities, current methodologies often fall short in fully integrating these multi-modal datasets, thereby limiting their ability to fully understand tissue heterogeneity. In this study, we propose XVGAE (cross-view graph autoencoders), a novel approach that integrates gene expression data, spatial coordinates, and histological images to identify spatial domains. XVGAE constructs two distinct graphs: a spatial graph from spatial coordinates and a histological graph from histological images, and these graphs enable XVGAE to learn specific representations for each view and propagate information between them using cross-view graph convolutional networks. The experiments on benchmark datasets of the human dorsolateral prefrontal cortex show demonstrate that the XVGAE could achieve better clustering accuracy than state-of-the-art methods, and further experiments on four real spatial transcriptomics datasets on different sequencing platforms show that the XVGAE could identify biologically meaningful spatial domains with smoother boundary than other methods.

bioinformatics↗

bioRxiv2024

2'-O-Methyl-guanosine 3-base RNA fragments mediate essential natural TLR7/8 antagonism

Recognition of RNA fragments by Toll-like receptors (TLR) 7 and 8 is a key contributor to the initiation of a protective innate immune response against pathogens. A long-standing enigma is how degradation products of host RNAs, generated by the daily phagocytic clearance of billions of apoptotic cells, fail to activate TLR7 and TLR8 signalling1. Here, we report that select 2-O-methyl (2-Ome) guanosine RNA fragments as short as 3 bases, including those derived from host-RNAs, are potent TLR7 and TLR8 antagonists that reduce TLR7 sensing in vivo. Mechanistically, antagonistic fragments are directed towards a distinct binding site on these proteins by 5-end 2-Ome guanosine. Our results indicate that host-RNAs evade detection by TLR7/8 due to a pool of abundant host ribosomal 2-Ome-modified RNA fragments that naturally antagonize TLR7 and TLR8 sensing to avoid auto-immunity. Crucially, rare TLR7 and TLR8 mutations located at this antagonistic site decrease the inhibitory activity of 2-Ome guanosine RNA fragments and lead to auto-immunity in patients. Our findings also establish that select chemically synthesised 3-base oligonucleotides can harness the protective anti-inflammatory activity of this natural immune checkpoint for therapeutic targeting of TLR7-driven diseases. One Sentence SummaryShort 2-O-Methyl RNA fragments are natural TLR7/8 antagonists

immunology↗