Biology subjects

Zhu, Y.

Publications and source records attributed to Zhu, Y..

At least 325 records · Page 18Linked to original sources

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

Phosphorylation of Zearalenone retains its toxicity

Microbial biotransformation of Zearalenone (ZEN) is a promising deactivation approach. The residual toxicity and stability of Zearalenone-14-phosphate (ZEN-14-P) and Zearalenone-16-phosphate (ZEN-16-P), two novel microbial phosphorylation products of ZEN, remain unknown. We investigated the cytotoxicity, oxidative stress, pro-inflammatory, and estrogenic activity of phosphorylated ZENs using porcine intestinal cells and uterine explants, and human endometrial cells, and traced their metabolic fate by LC-MS/MS analysis. The phosphorylated ZENs significantly decreased the viability of IPEC-J2 and Ishikawa cells. Similar to ZEN, phosphorylation products induced significant oxidative stress, activated the expression of pro-inflammatory cytokines, and demonstrated estrogenic activity through upregulation of estrogen-responsive genes, activation of alkaline phosphatase and proliferation of endometrial glands. LC-MS/MS analysis pointed that although phosphorylated ZENs are partially hydrolyzed to ZEN, their respective metabolic pathways differ. We conclude that phosphorylation might not be sufficient to detoxify ZEN, leaving its cytotoxic, pro-inflammatory and estrogenic properties intact. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=60 SRC="FIGDIR/small/605906v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@94e741org.highwire.dtl.DTLVardef@1da9d53org.highwire.dtl.DTLVardef@18ee655org.highwire.dtl.DTLVardef@b4035b_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2024

Non-genetic messenger RNA silencing reveals essential genes in phage-host interplay

Bacteriophages are the most abundant entities on earth and exhibit vast genetic and phenotypic diversity. Exploitation of this largely unexplored molecular space requires identification and functional characterisation of genes that act at the phage-host interface. To date, this is restricted to few model phage-host systems that are amenable to genetic manipulation. To overcome this limitation, we introduce a non-genetic mRNA targeting approach using exogenous delivery of programmable antisense oligomers (ASOs) to silence genes of both DNA and RNA phages. A systematic knockdown screen of core and accessory genes of the nucleus-forming jumbo phage {Phi}KZ, coupled to RNA-sequencing and microscopy analyses, reveals previously unrecognised proteins that are essential for phage replication and that, upon silencing, elicit distinct phenotypes at the level of the phage and host response. One of these factors is a {Phi}KZ-encoded nuclease that acts at a major decision point during infection, linking the formation of the protective phage nucleus to phage genome amplification. The non-genetic ASO-based gene silencing used here promises to be a versatile tool for molecular discovery in phage biology, will help elucidate defence and anti-defence mechanisms in non-model phage-host pairs, and offers potential for optimising phage therapy and biotechnological procedures.

molecular biology↗

bioRxiv2024

Intraperitoneal programming of tailored CAR macrophages via mRNA-LNP to boost cancer immunotherapy

Therapeutic strategies for peritoneal metastasis in solid tumors are urgently needed in the clinic. Programming chimeric antigen receptor macrophages (CAR-Ms) in situ offers opportunities for an unmet demand. However, potential intracellular domains (ICDs) for CAR design and their antitumor mechanisms for macrophage empowerment remain to be explored systematically. By developing a targeted mRNA-LNP delivery system for macrophages, we have investigated 36 CAR combinations to determine the impact of CAR-Ms on immune regulation in vitro and in vivo. In two solid tumor mouse models, intraperitoneal programming of CAR-Ms was shown to elicit robust adaptive immune activation and significantly synergize with PD-1/L1 therapy. Single-cell RNA sequencing (scRNA-seq) analysis revealed that CAR-Ms could reshape the immunosuppressive tumor microenvironment (TME) and boost the TCF1+PD-1+ progenitor- exhausted CD8+ T cells (Tpex) population. Meanwhile, we found that tailored CAR-M with CD3{zeta}/TLR4 ICDs could favorably maintain proinflammatory phenotype and simultaneously upregulate MHC I and PD-L1 expression by perturbing NF-{kappa}B pathways. Moreover, the synergism between macrophage PD-L1 knockdown and CAR-M therapy highlighted the need to block the PD-1/L1 axis in antigen cross-presentation. In short, we developed an mRNA-LNP delivery system for intraperitoneal programming of tailored CAR-Ms in vivo and broadened understanding of both regulatory and feedback mechanisms for CAR-M therapies against solid tumors.

bioengineering↗

bioRxiv2024

Proteomics Landscape of Triple-Negative Apocrine Breast Carcinoma Reveals Molecular Mechanisms of Tumorigenesis and Characteristics of Chemo-insensitivity

Triple-negative apocrine carcinoma (TNAC) is an exceptionally rare, chemotherapy-insensitive subtype of triple-negative breast cancer (TNBC) characterized by androgen receptor (AR) positivity and low proliferative activity. Despite poor chemotherapy response, TNAC exhibits favorable long-term survival, suggesting distinct resistance mechanisms. Here, we integrate mass spectrometry-based proteomics and whole-exome sequencing (WES) to characterize TNACs molecular features. We identify progressive overexpression of PI3K/AKT and AR signaling proteins, along with ECM remodeling and upregulation of GTPase-related proteins, highlighting TNACs invasive potential. WES reveals somatic mutations in ECM-related genes (COL18A1) and immune-associated genes (C3, NRDC), implicating the tumor microenvironment. Unlike TNBC, post-chemotherapy TNAC proteomics shows mixed ribosomal regulation and heightened inflammation, rather than reliance on proliferation, suggesting a need for targeted metabolic and immune therapies. Our findings support PI3K/AKT inhibitors and AR antagonists, potentially alongside GTPase inhibitors, metabolic disruptors, and immune therapy, as alternative strategies to standard chemotherapy in TNAC.

cancer biology↗

bioRxiv2024

Multi-Modal CLIP-Informed Protein Editing

AO_SCPLOWBSTRACTC_SCPLOWProteins govern most biological functions essential for life, but achieving controllable protein discovery and optimization remains challenging. Recently, machine learning-assisted protein editing (MLPE) has shown promise in accelerating optimization cycles and reducing experimental workloads. However, current methods struggle with the vast combinatorial space of potential protein edits and cannot explicitly conduct protein editing using biotext instructions, limiting their interactivity with human feedback. To fill these gaps, we propose a novel method called ProtET for efficient CLIP-informed protein editing through multi-modality learning. Our approach comprises two stages: in the pretraining stage, contrastive learning aligns protein-biotext representations encoded by two large language models (LLMs), respectively. Subsequently, during the protein editing stage, the fused features from editing instruction texts and original protein sequences serve as the final editing condition for generating target protein sequences. Comprehensive experiments demonstrated the superiority of ProtET in editing proteins to enhance human-expected functionality across multiple attribute domains, including enzyme catalytic activity, protein stability and antibody specific binding ability. And ProtET improves the state-of-the-art results by a large margin, leading to significant stability improvements of 16.67% and 16.90%. This capability positions ProtET to advance real-world artificial protein editing, potentially addressing unmet academic, industrial, and clinical needs.

bioinformatics↗

bioRxiv2024

Unveiling Assembly Errors in Immunoglobulin Loci: A Comprehensive Evaluation of Long-read Genome Assemblies Across Vertebrates

Long-read sequencing technologies have revolutionized genome assembly producing near-complete chromosome assemblies for numerous organisms, which are invaluable to research in many fields. However, regions with complex repetitive structure continue to represent a challenge for genome assembly algorithms, particularly in areas with high heterozygosity. Robust and comprehensive solutions for the assessment of assembly accuracy and completeness in these regions do not exist. In this study we focus on the assembly of biomedically important antibody-encoding immunoglobulin (IG) loci, which are characterized by complex duplications and repeat structures. High-quality full-length assemblies for these loci are critical for resolving haplotype-level annotations of IG genes, without which, functional and evolutionary studies of antibody immunity across vertebrates are not tractable. To address these challenges, we developed a pipeline, "CloseRead", that generates multiple assembly verification metrics for analysis and visualization. These metrics expand upon those of existing quality assessment tools and specifically target complex and highly heterozygous regions. Using CloseRead, we systematically assessed the accuracy and completeness of IG loci in publicly available assemblies of 74 vertebrate species, identifying problematic regions. We also demonstrated that inspecting assembly graphs for problematic regions can both identify the root cause of assembly errors and illuminate solutions for improving erroneous assemblies. For a subset of species, we were able to correct assembly errors through targeted reassembly. Together, our analysis demonstrated the utility of assembly assessment in improving the completeness and accuracy of IG loci across species.

genomics↗

bioRxiv2024

FLASH radiotherapy using high-energy X-rays: validation of the FLASH effect triggered by a compact single high-energy X-ray source device

PurposeThis preclinical study aimed to verify the FLASH effect of compact single high-energy X-ray source (CHEXs) and to explore whether three irradiations with single-gantry rotation two 30 s pauses can generate FLASH effect in mice. Materials and methodsThe absolute dose and pulsed beam of the CHEXs were measured using an EBTXD radiochromic film and fast current transformer. Healthy C57BL/6J female mice and a subcutaneous tumor model were irradiated under different conditions: sham (control), FLASH-RT (FLASH1: delivering the total dose in 1 fraction; FLASH3: delivering the total dose with two 30 second pauses to simulate a three-field delivery where the gantry rotation is occurring within 30 seconds), and conventional dose rate radiotherapy (CONV-RT). Various total doses were administered to the corresponding normal tissues (whole thorax, 30 Gy; whole abdomen, 12 Gy; and skin, 36 Gy) and tumors (CT26, 16.5 Gy; and LLC, 18 Gy). Survival status, normal tissue damage, and tumor growth suppression were recorded in each group. ResultsThe average dose rate of the CHEXs exceeded 40 Gy/s. For whole-thorax and skin irradiation, both FLASH1 and FLASH3 demonstrated protective effects. For whole-abdomen irradiation, FLASH1 exhibited a superior protective effect. No significant differences in tumor growth responses were observed between the FLASH1, FLASH3, and CONV-RT groups (P>0.05). ConclusionThis study confirmed that the FLASH effect could be triggered using CHEXs FLASH radiotherapy, and demonstrated that three irradiations with single gantry rotation two 30 s pauses can trigger the FLASH effect, indicating the potential benefit of CHEXs 3D conformal radiotherapy. Our findings indicate that further clinical trials on CHEXs are warranted.

cancer biology↗

bioRxiv2024

The noncoding circular RNA circHomer1 regulates developmental experience-dependent plasticity in mouse visual cortex

Circular RNAs (circRNAs) are a class of closed-loop, single stranded RNAs whose expression is particularly enriched in the brain. Despite this enrichment and evidence that the expression of circRNAs are altered by synaptic development and in response to synaptic plasticity in vitro, the regulation by and function of the majority of circRNAs in experience-dependent plasticity in vivo remain unexplored. Here, we employed transcriptome-wide analysis comparing differential expression of both mRNAs and circRNAs in juvenile mouse primary visual cortex (V1) following monocular deprivation (MD), a model of experience-dependent developmental plasticity. Among the differentially expressed mRNAs and circRNAs following 3-day MD, the circular and the activity-dependent mRNA forms of the Homer1 gene, circHomer1 and Homer1a respectively, were of interest as their expression changed in opposite directions: circHomer1 expression increased while the expression of Homer1a decreased following 3-day MD. Knockdown of circHomer1 delayed the depression of closed-eye responses normally observed after 3-day MD. circHomer1-knockdown also led to a reduction in average dendritic spine size prior to MD but critically there was no further reduction after 3-day MD, consistent with impaired structural plasticity. circHomer1-knockdown also prevented the reduction of surface AMPA receptors after 3-day MD. Synapse-localized puncta of the AMPA receptor endocytic protein Arc increased in volume after MD but were smaller in circHomer1-knockdown neurons, suggesting that circHomer1 knockdown impairs experience-dependent AMPA receptor endocytosis. Thus, the expression of multiple circRNAs are regulated by experience-dependent developmental plasticity, and our findings highlight the essential role of circHomer1 in V1 synaptic development and experience-dependent plasticity. Significance StatementCircular RNAs (circRNAs) are a class of closed-loop RNAs formed through back-splicing of exon and/or intron junctions. Initially considered as byproducts of aberrant RNA splicing with limited function, recent studies have implicated circRNAs in various neurological disorders. Despite their abundant expression in the brain, the role of circRNAs in experience-dependent plasticity remains poorly understood. We conducted an in vivo transcriptome analysis of circRNAs whose expression was regulated by experience-dependent plasticity in the mouse visual cortex and highlight circHomer1, a circRNA derived from the Homer1 gene, as a circRNA critical for synaptic development and experience-dependent plasticity in vivo.

neuroscience↗

bioRxiv2024

A new alignment-free method: Subsequence Correlation Coefficient Vector(SCCFV) for influenza A comparison using virus genomes

Withdrawal StatementThe authors have withdrawn their manuscript because I discovered some important missing data that is crucial for supporting my viewpoint and research findings. Although I tried to supplement this data through other means, I was unable to complete it before the deadline. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

bioinformatics↗

bioRxiv2024

Senescent cells cluster CTCF on nuclear speckles to sustain their splicing program

Senescence --the endpoint of replicative lifespan for normal cells-- is established via a complex sequence of molecular events. One such event is the dramatic reorganization of CTCF into senescence-induced clusters (SICCs). However, the molecular determinants, genomic consequences, and functional purpose of SICCs remained unknown. Here, we combine functional assays, super-resolution imaging, and 3D genomics with computational modelling to dissect SICC emergence. We establish that the competition between CTCF-bound and non-bound loci dictates clustering propensity. Upon senescence entry, cells repurpose SRRM2 --a key component of nuclear speckles-- and BANF1 --a molecular glue for chromosomes-- to cluster CTCF and rewire genome architecture. This CTCF-centric reorganization in reference to nuclear speckles functionally sustains the senescence splicing program, as SICC disruption fully reverts alternative splicing patterns. We therefore uncover a new paradigm, whereby cells translate changes in nuclear biochemistry into architectural changes directing splicing choices so as to commit to the fate of senescence. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/603680v1_ufig1.gif" ALT="Figure 1"> View larger version (85K): org.highwire.dtl.DTLVardef@cfb561org.highwire.dtl.DTLVardef@8cfdf3org.highwire.dtl.DTLVardef@7485d5org.highwire.dtl.DTLVardef@1fe9051_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIHMGB2-bound loci compete with CTCF-bound ones for nuclear speckle association C_LIO_LISenescent cells repurpose SRRM2 and BANF1 to cluster CTCF on speckles C_LIO_LIBANF1 is essential, but not sufficient for CTCF clustering C_LIO_LIThe SRRM2 RNA-binding domain directs CTCF clustering C_LIO_LISICCs rewire chromatin positioning to sustain the senescence splicing program C_LI

cell biology↗

bioRxiv2024

The Open Pediatric Cancer Project

BackgroundIn 2019, the Open Pediatric Brain Tumor Atlas (OpenPBTA) was created as a global, collaborative open-science initiative to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Here, we present an extension of the OpenPBTA called the Open Pediatric Cancer (OpenPedCan) Project, a harmonized open-source multi-omic dataset from 6,112 pediatric cancer patients with 7,096 tumor events across more than 100 histologies. Combined with RNA-Seq from the Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA), OpenPedCan contains nearly 48,000 total biospecimens (24,002 tumor and 23,893 normal specimens). FindingsWe utilized Gabriella Miller Kids First (GMKF) workflows to harmonize WGS, WXS, RNA-seq, and Targeted Sequencing datasets to include somatic SNVs, InDels, CNVs, SVs, RNA expression, fusions, and splice variants. We integrated summarized CPTAC whole cell proteomics and phospho-proteomics data, miRNA-Seq data, and have developed a methylation array harmonization workflow to include m-values, beta-vales, and copy number calls. OpenPedCan contains reproducible, dockerized workflows in GitHub, CAVATICA, and Amazon Web Services (AWS) to deliver harmonized and processed data from over 60 scalable modules which can be leveraged both locally and on AWS. The processed data are released in a versioned manner and accessible through CAVATICA or AWS S3 download (from GitHub), and queryable through PedcBioPortal and the NCIs pediatric Molecular Targets Platform. Notably, we have expanded PBTA molecular subtyping to include methylation information to align with the WHO 2021 Central Nervous System Tumor classifications, allowing us to create research-grade integrated diagnoses for these tumors. ConclusionsOpenPedCan data and its reproducible analysis module framework are openly available and can be utilized and/or adapted by researchers to accelerate discovery, validation, and clinical translation.

genomics↗

bioRxiv2024

Coordination of transcription-coupled repair and repair-independent release of stalled RNA polymerase II in response to transcription-blocking lesions

Transcription-blocking lesions (TBLs) stall elongating RNA polymerase II (PolII), which then initiates transcription-coupled repair (TCR) to remove TBLs and allow transcription recovery. In the absence of TCR, eviction of lesion-stalled PolII is required for alternative pathways to address the damage, but the mechanism is unclear. This study, utilizing Protein-Associated DNA Damage Sequencing (PADD-seq), reveals that the p97-proteasome pathway can evict lesion-stalled PolII independently of repair. Both TCR and repair-independent eviction require CSA and ubiquitination. However, p97 is dispensable for TCR and PolII eviction in TCR-proficient cells, highlighting repairs prioritization over repair-independent eviction. Moreover, ubiquitination of RPB1-K1268 is important for both pathways, with USP7s deubiquitinase activity promoting TCR without abolishing repair-independent PolII release. In summary, this study elucidates the fate of lesion-stalled PolII, and may shed light on the molecular basis of genetic diseases caused by the defects of TCR genes.

molecular biology↗

bioRxiv2024

Regulation of proteostasis by sleep through autophagy in Drosophila models of Alzheimer's Disease

Sleep and circadian rhythm dysfunctions are common clinical features of Alzheimers Disease (AD). Increasing evidence suggests that in addition to being a symptom, sleep disturbances can also drive the progression of neurodegeneration. Protein aggregation is a pathological hallmark of AD, however the molecular pathways behind how sleep affects protein homeostasis remain elusive. Here we demonstrate that sleep modulation influences proteostasis and the progression of neurodegeneration in Drosophila models of Tauopathy. We show that sleep deprivation enhanced Tau aggregational toxicity resulting in exacerbated synaptic degeneration. In contrast, sleep induction using gaboxadol led to reduced hyperphosphorylated Tau accumulation in neurons as a result of modulated autophagic flux and enhanced clearance of ubiquitinated Tau, suggesting altered protein processing and clearance that resulted in improved synaptic integrity and function. These findings highlight the complex relationship between sleep and autophagy, in regulating protein homeostasis, and the neuroprotective potential of sleep-enhancing therapeutics to slow the progression or delay the onset of neurodegeneration.

neuroscience↗

bioRxiv2024

Single-cell proteomics of Arabidopsis leaf mesophyll identifies drought stress-related proteins

The application of single-cell omics tools to biological systems can provide unique insights into diverse cellular populations and their heterogeneous responses to internal and external perturbations. Thus far, most single-cell studies in plant systems have been limited to RNA-sequencing approaches, which only provide indirect readouts of cellular functions. Here, we present a single-cell proteomics workflow for plant cells that integrates tape-sandwich protoplasting, piezoelectric cell sorting, nanoPOTS sample preparation, and FAIMS-based MS data acquisition method for label-free single-cell proteomics analysis of Arabidopsis leaf mesophyll cells. From a single leaf protoplast, over 3,000 proteins were quantified with high precision. The workflow is demonstrated to identify stress associated changes in protein abundance by analyzing >80 protoplasts from well-watered and water-deficit stressed plants. Additionally, we describe a new approach for constructing covarying protein networks at the single-cell level and demonstrate how single-cell protein covariation analysis can reveal previously unrecognized protein functions while also capturing stress-induced changes in protein-protein dynamics. HighlightsO_LIThis study describes the first application of scProteomics to study abiotic stress-induced proteome regulation in leaf mesophyll cells C_LIO_LIFrom a single Arabidopsis mesophyll protoplast, [~]2800 proteins on average were quantified with high precision using label free scProteomics C_LIO_LIscProteomics of water-deficit Arabidopsis leaves revealed known and novel proteins involved in drought response C_LIO_LISingle-protoplast proteomics revealed water deficit-induced changes in protein covariation networks independent of changes in abundance C_LI

plant biology↗

bioRxiv2024

PRISM: Multiplexed Profiling of RNA In-Situ through Single-round of Imaging in Three-Dimensional Tissue

Spatial RNA imaging has not been widely adopted because conventional fluorescence microscopy is limited to only a few channels, and the cyclic reactions needed to increase multiplexing in techniques such as sequential fluorescence in-situ hybridization (FISH) require sophisticated instrumentation. Here, we introduce Profiling of RNA In-situ through Single-round iMaging (PRISM), a method that expands coding capacity through color intensity grading. Using a radius vector filtering strategy to ensure the distinguishability of codewords in color space, PRISM achieves up to 64-plex color-barcoded RNA imaging in a single imaging round with conventional microscopes. We validate PRISMs versatility across various tissues by generating a 3D atlas of mouse embryonic development from E12.5 to E14.5, a quasi-3D tumor-normal transition landscape of human hepatocellular carcinoma (HCC), and a 3D cell atlas and subcellular RNA localization landscapes of mouse brain. Additionally, we show the critical role of cancer-associated fibroblasts (CAFs) in mediating immune infiltration and immune response heterogeneity within and between tumor microenvironments.

bioengineering↗

bioRxiv2024

Intraperitoneal activation of myeloid cells clears ascites and reveals IL27-dependent regression of metastatic ovarian cancer

Patients with metastatic ovarian cancer (OvCa) have a 5-year survival rate of less than 30% due to persisting dissemination of chemoresistant cells in the peritoneal fluid and the immunosuppressive microenvironment in the peritoneal cavity. Here, we report that intraperitoneal administration of {beta}-glucan and IFN{gamma} (BI) induced robust tumor regression in clinically relevant models of metastatic OvCa. BI induced tumor regression by controlling fluid tumor burden and activating localized antitumor immunity. {beta}-glucan alone cleared ascites and eliminated fluid tumor cells by inducing intraperitoneal clotting in the fluid and Dectin-1-Syk-dependent NETosis in the omentum. In omentum tumors, BI expanded a novel subset of immunostimulatory IL27+ macrophages and neutralizing IL27 impaired BI efficacy in vivo. Moreover, BI directly induced IL27 secretion in macrophages where single agent treatment did not. Finally, BI extended mouse survival in a chemoresistant model and significantly improved chemotherapy response in a chemo-sensitive model. In summary, we propose a new therapeutic strategy for the treatment of metastatic OvCa.

immunology↗

bioRxiv2024

Unraveling Lineage Roadmaps and Cell Fate Determinants to Postnatal Neural Stem Cells and Ependymal cells in the Developing Ventricular Zone

The ventricular zone (VZ) is made up of adult neural stem cells (NSCs) and multi-ciliated ependymal cells (EPCs). Both NSCs and EPCs are derived from radial glial cells (RGCs). To date, the transcriptomic dynamics and the molecular mechanisms guiding the cell fate commitment during the differentiation remain poorly understood. In this study, we analysed the developing VZ at the single-cell resolution and identified three distinct cellular states of RGCs: bipotent glial progenitor cells (bGPCs), neonatal NSC-neuroblasts (nNSC-NBs) and neonatal EPCs (nEPCs). The differentiation from bGPCs to nNSC-NBs and nEPCs forms a continuous bifurcating trajectory. Further molecular analysis along the NSC branch unveiled a novel intermediate state of cells expressing oligodendrocyte precursor cell (OPC) and neuroblast (NB) marker genes. Several transcription factors (TFs) were proved to be essential for the EPC-lineage differentiation, with TFEB emerging as a key regulator dictating the bGPC fate. The activation of TFEB promoted differentiation towards NSC-NBs while restrained the trajectory towards EPCs. Our findings offer detailed insights into further understanding VZ development and lay the groundwork for investigating potential therapeutic strategies against VZ-related disorders, such as hydrocephalus and neurodegenerative diseases (NDDs).

genomics↗