Biology subjects

Pei, W.

Publications and source records attributed to Pei, W..

12 recordsLinked to original sources

bioRxiv2026

Steller: a high-resolution platform for spatial clonal tracing of mammalian brain development

Resolving both lineage history and spatial position at single-cell resolution is essential for understanding how tissue assemble, yet simultaneously interrogation of both dimensions remains technically challenging. Here, we present Steller (Spatio-temporal cell lineage tracker), an integrated experimental and computational framework that overcomes the sensitivity bottleneck limiting lineage barcode detection in high-resolution spatial transcriptomics (ST). By co-depositing capture probes alongside conventional poly(T) oligonucleotides on high-density spatial arrays, Steller achieves targeted enrichment of lineage barcodes at spatial single cell resolution. Applied to clonally labeled embryonic day 12.5 (E12.5) mouse forebrain development harvested at postnatal day 4 (P4), Steller increased the proportion of barcode-detectable cells and recovered higher clonal diversity compared with poly(T) chip. Leveraging this enhanced sensitivity, we resolved distinct spatial clonal architectures across three forebrain regions: horizontal or radial-to-horizontal transitions in hippocampal pyramidal neurons, dorsoventrally restricted yet multi-nuclei spread in thalamus, and fate-restricted spiny projection neuron lineages. Steller establishes a generalizable strategy for lineage-enhanced spatial profiling compatible with existing high-resolution spatial transcriptomics platforms and adaptable to diverse biologic process, providing a framewrok for investigating lineage-dependent tissue organization. HighlightsO_LISteller integrates targeted lineage-barcode enrichment with high-resolution spatial transcriptomics C_LIO_LISteller substantially improves clonal detection sensitivity at single-cell resolution C_LIO_LISteller reveals region-specific spatial clonal architectures across the developing mouse forebrain C_LI

Developmental Biology↗

bioRxiv2026

Detection of Somatic Point Mutations Directly from Spatial Transcriptomics Enables in vivo Spatiotemporal Lineage Tracing

Spatial transcriptomics reveals tissue organization but lacks in vivo lineage-tracing methods applicable to humans. We introduce SpaceTracer, a computational framework that accurately detects somatic single-nucleotide variants (SNVs) directly from spatial transcriptomics data. By leveraging naturally occurring somatic SNVs, SpaceTracer reconstructs cellular phylogenies within native tissue architecture, enabling the mapping of lineage spread, migration, lineage-coupled expression changes and lineage-aware local interactions. Applied to human cutaneous squamous cell carcinoma, it traced tumor initiation and progressions, uncovered widespread pre-invasive migration of dedifferentiated epithelial cells and characterized mutant B cells migrating from tertiary lymphoid structures (TLS) into the tumor boundary. The framework also reconstructed developmental lineages across multiple tissues and identified tissue-resident mutant immune cells. SpaceTracer thus provides a perturbation-free platform for high-resolution spatiotemporal lineage tracing, offering a transformative tool for elucidating complex biological systems--especially tumor-immune ecosystems--with direct implications for advancing cancer immunotherapy.

bioinformatics↗

bioRxiv2025

Tnfrsf10 Signaling is Required to Maintain the Stem Cell Niche in the Zebrafish Lateral Line

Regenerative capacity varies significantly among species and across different organs. In mammals, the inner ear exhibits a limited ability to regenerate hair cells, whereas the lateral line sensory organ of zebrafish demonstrates apparently limitless capability to spontaneously regenerate hair cells following injury. However, the specific cell populations representing the stem cells in the neuromast and the mechanism of stem cell self-renewal remain unclear. In this study, we show that a mutation in tnfrsfa led to the depletion of neuromast sensory organs and impairment of hair cell regeneration in zebrafish. The decrease of cells peripheral to the neuromasts in tnfrsfa mutants indicates that these peripheral cells, particularly cells called "mantle cells", serve as the stem cells within the neuromast. Furthermore, our findings indicate that the ligands Tnfsf10 and Tnfsf10l3 (TRAIL) act through Tnfrsfa activating the NF-{kappa}B signaling pathway in the mantle cells in a non-cell-autonomous manner. NF-{kappa}B signaling is crucial for maintaining the stem cell identity of the mantle cells through activation or maintenance of sox2 expression. These findings demonstrate a critical role for TNF superfamily signaling in stem cell maintenance. HighlightsO_LIZebrafish tnfrsfa maintains the stem cell niche in neuromasts and is necessary for hair cell regeneration of the lateral line C_LIO_LITnfrsfa is essential for mantle cell proliferation during lateral line development and hair cell regeneration C_LIO_LITnfsf10 and Tnfsf10l3 signal through Tnfrsfa, activating NF-{kappa}B signaling and Sox2 expression in the mantle cells in a non-cell-autonomous manner C_LIO_LITnfrsfa regulates the development of neuromast independently of the Notch signaling pathway C_LI

developmental biology↗

bioRxiv2024

Stiffness-tunable neurotentacles for minimally invasive implantation and long-term neural activity recordings

Flexible implantable microelectrodes have been demonstrated to exhibit excellent biocompatibility for chronic neural activity recordings. However, the low bending strength of the commonly employed flexible materials presents a significant challenge for probe insertion into the brain. Traditional implantation methods for flexible electrodes generally require additional auxiliary materials or tools, which tend to have a much larger footprint than the probes themselves, greatly increasing the damage to neurons during insertion. Here we have proposed a stiffness-tunable polyimide probe for deep brain implantation, referred to as Neurotentacle, enabled by embedded microchannels in which the liquid pressure is controllable (from 0.1MPa to more than 2.0MPa). During the insertion phase into the brain, the neurotentacle can pose a high stiffness under elevated internal pressure to penetrate the brain tissues without the use of any additional materials or tools. Once the device has been successfully inserted, it can regain its flexibility by reducing the internal pressure. Importantly, the novel multilayer microfabrication process keeps the structural dimensions of the neurotentacle similar to those of a regular flexible probe. Therefore, the neurotentacle can produce an extremely low level of damage to brain tissue during its insertion phase, while extending its long-term biocompatibility and stability, which has been experimentally verified in histological evaluations conducted on both acute and chronic animal specimens. In addition, the chronically implanted neurotentacles enabled stable neural activity recordings in mice with an average spike yield of 96% and an average signal-to-noise ratio of 15.2. The proposed neurotentacle does not necessitate the use of complex devices and its insertion process is straightforward and highly controllable, thus rendering it an appealing technique for minimally invasive implantation and long-term neural recording of flexible electrodes.

neuroscience↗

bioRxiv2024

Spatiotemporally resolved transcriptome atlas of developing mouse placenta reveals mechanisms of embryonic lethality.

Proper placentation is fundamental to the growth and viability of the maturing embryo. However, a thorough grasp of the spatial organization of cell types, their interactions, and gene expression patterns along the maternal-fetal function during placental development remains incomplete. Here, we utilized Stereo-seq to construct the spatiotemporal transcriptomic atlas of the mouse placenta (STAMP) spanning embryonic (E) days 9.5 to 18.5 at single cell resolution (https://db.cngb.org/stomics/stamp/). This resource delineates spatially resolved cellular dynamics and gene expression patterns across placental and maternal compartments. We identified distinct glycogen trophoblast cell (GC) subclusters, mapped their developmental trajectories, and uncovered transcriptional transitions accompanying their migration from the junctional zone to the maternal decidua from E12.5 onward. In a defective placentation model with perinatal lethality, GCs abnormally persisted at E18.5 with excessive glycogen and reduced degradation metabolites in placenta and fetal liver, indicating impaired glycogen breakdown. Maternal glucose supplementation restored glucose levels and rescued fetal survival, underscoring GC-mediated metabolic support as critical for viability. Together, this study provides a comprehensive spatiotemporal placental atlas and demonstrates that GC-mediated glycogen metabolism is essential for sustaining fetal viability.

developmental biology↗

bioRxiv2024

Megabarcoding reveals a tale of two very different dark taxa along the same elevational gradient

AbstractOur planet is entering the sixth mass extinction without detailed spatio-temporal distribution and abundance information for most insect species. Particularly lacking is this information for dark taxa although they contain most animal species. This problem can be addressed with high-throughput single specimen barcoding (megabarcoding), but it remain unknown to what extent one dark taxon can be used as a proxy for another because of similar biodiversity patterns. This is here tested and we show that two Diptera taxa (Phoridae, Mycetophilidae) have very different spatio-temporal distributions across the same elevational gradient. We applied COI megabarcoding to samples collected every 14 days over three seasons at six elevations (800 to 1,800 m) in a temperate forest ecosystem in Northern China (Baihua Mountain Reserve). Elevation, precipitation, and temperature were used as environmental variables to understand the data obtained for 17,179 specimens representing 492 mOTUs of Phoridae and 2,281 specimens of 148 mOTUs of Mycetophilidae. Congruent is that the alpha diversity for both taxa increased in the summer and there is evidence for a mid-domain effect and phylogenetic clustering in high elevations. However, the extent and pattern of seasonal variation differed considerably. Phorid communities exhibited shifts between spring, summer and autumn seasons, but surprisingly little difference between elevations. In contrast, mycetophilid communities were structured along the elevational gradient and dependent on precipitation. Our study highlights the urgent need for obtaining detailed spatio-temporal information for the most diverse dark taxa, but also illustrates that these data can be readily obtained with megabarcoding.

ecology↗

bioRxiv2022

A Scalable and Adaptive Ultra-high-density Fan-out Strategy for High-throughput Flexible Microelectrodes

Flexible neural microelectrodes demonstrate higher compliance and better biocompatibility than rigid electrodes. They have multiple microfilaments can be freely distributed across different brain regions. However, high-density fan-out of high-throughput flexible microelectrodes remains a challenge since monolithic integration between electrodes and circuits is not currently available as it is for silicon electrodes. Here, we proposed a high-density fan-out strategy for high-throughput flexible electrodes. The flexible electrodes are partially overlapped on the printed circuit board (PCB). A modified wire bonding method is used to reduce the pads area on the PCB. Both the traces and pads on the PCB are optimized to minimize the back-end package. It is significantly reducing the connection area. In addition, the vertical rather than horizontal connection between the connector and the PCB further decrease the volume of the package. 1024 channel flexible electrodes are bonded to the high-density PCB within an area of 11.8x10mm2, and the success connection rate can reach 100%. The high-density fan-out strategy proposed in this paper can effectively reduce the volume of high-throughput flexible electrodes after packaging, which facilitates the miniaturization of in vivo multichannel recording devices and contributes to long-term recording.

bioengineering↗

bioRxiv2021

Olanzapine leads to nonalcoholic fatty liver disease through the apolipoprotein A5 pathway

The antipsychotic drug olanzapine was reported to induce nonalcoholic fatty liver disease (NAFLD), whereas the underlying mechanism remains incompletely understood. This study investigated whether apolipoprotein A5 (apoA5) and sortilin, two interactive factors involved in NAFLD pathogenesis, are implicated in olanzapine-induced NAFLD. In the present study, at week 8, olanzapine treatment successfully induced hepatic steatosis in male C57 BL/6J mice, even when fed a normal chow diet, which was independent of animal body weight gain. Likewise, olanzapine effectively mediated hepatocyte steatosis in human HepG2 cells in vitro, characterized by substantially elevated intracellular lipid droplets. Increased plasma triglyceride concentration and decreased plasma apoA5 levels were observed in mice treated for 8 weeks with olanzapine. Surprisingly, olanzapine markedly enhanced hepatic apoA5 protein levels in mice, without a significant effect on rodent hepatic ApoA5 mRNA expression. Our in vitro study showed that olanzapine reduced apoA5 protein levels in the medium and enhanced apoA5 protein expression in hepatocytes, whereas this drug exerted no effect on hepatocyte APOA5 mRNA expression. By transfecting APOA5 siRNA into HepG2 cells, it was demonstrated that APOA5 knockdown effectively reversed olanzapine-induced hepatocyte steatosis. In addition, olanzapine drastically increased sortilin mRNA and protein levels in vivo and in vitro. Interestingly, SORT1 knockdown reduced intracellular apoA5 protein expression and increased medium apoA5 protein levels in vitro, without affecting intracellular APOA5 mRNA expression. Furthermore, SORT1 knockdown greatly ameliorated hepatocyte steatosis in vitro. This study provides the first evidence that sortilin inhibits the hepatic apoA5 secretion that is attributable to olanzapine-induced NAFLD, which provides new insight into effective strategies against NAFLD for patients with schizophrenia administered olanzapine.

pathology↗

bioRxiv2020

Suppressing STAT3 activity protects the endothelial barrier from VEGF-mediated vascular permeability

Vascular permeability triggered by inflammation or ischemia promotes edema, exacerbates disease progression, and impairs tissue recovery. Vascular endothelial growth factor (VEGF) is a potent inducer of vascular permeability. VEGF plays an integral role in regulating vascular barrier function physiologically and in pathologies, such as cancer, ischemic stroke, cardiovascular disease, retinal conditions, and COVID-19-associated pulmonary edema and sepsis, which often leads to acute lung injury, including acute respiratory distress syndrome. However, after initially stimulating permeability, VEGF subsequently mediates angiogenesis to repair damaged tissue. Consequently, understanding temporal molecular regulation of VEGF-induced vascular permeability will facilitate developing therapeutics that achieve the delicate balance of inhibiting vascular permeability while preserving tissue repair. Here, we demonstrate that VEGF signals through signal transducer and activator of transcription 3 (STAT3) to promote vascular permeability. Specifically, we show that genetic STAT3 ablation reduces vascular permeability in STAT3-deficient endothelium of mice and VEGF-inducible zebrafish crossed with CRISPR/Cas9 generated genomic STAT3 knockout zebrafish. Importantly, STAT3 deficiency does not impair vascular development and function in vivo. We identify intercellular adhesion molecule 1 (ICAM-1) as a STAT3-dependent transcriptional regulator and show VEGF-dependent STAT3 activation is regulated by JAK2. Pyrimethamine, an FDA-approved anti-microbial agent that inhibits STAT3-dependent transcription, substantially reduces VEGF-induced vascular permeability in zebrafish, mouse, and human endothelium. Indeed, pharmacologically targeting STAT3 increases vascular barrier integrity using two additional compounds, atovaquone and C188-9. Collectively, our findings suggest that the VEGF, VEGFR-2, JAK2, and STAT3 signaling cascade regulates vascular barrier integrity, and inhibition of STAT3-dependent activity reduces VEGF-induced vascular permeability in vertebrate models. Key PointsO_LIGenetic STAT3 deficiency in VEGF-inducible zebrafish and mice reveals that VEGF signals through STAT3 to promote vascular permeability C_LIO_LIPyrimethamine, a clinically available agent that inhibits STAT3 activity, reduces VEGF-induced vascular permeability in preclinical models C_LI

molecular biology↗

bioRxiv2020

Resolving fate and transcriptome of hematopoietic stem cell clones

Adult bone marrow harbors a mosaic of hematopoietic stem cell (HSC) clones of embryonic origin, and recent work suggests that such clones may have coherent lineage fates. To probe under physiological conditions whether HSC clones with different fates are transcriptionally distinct, we developed PolyloxExpress - a Cre recombinase-dependent DNA substrate for in situ barcoding that allows parallel readout of barcodes and transcriptomes in single cells. We describe differentiation-inactive, multilineage and lineage-restricted HSC clones, find that they reside in distinct regions of the transcriptional landscape of hematopoiesis, and identify corresponding gene signatures. All clone types contain proliferating HSCs, indicating that differentiation-inactive HSCs can undergo symmetric self-renewal. Our work establishes an approach for studying determinants of stem cell fate in vivo and provides molecular evidence for fate coherence of HSC clones.

immunology↗

bioRxiv2019

A subset of SMN complex members have a specific role in tissue regeneration via ERBB pathway-mediated proliferation

Spinal Muscular Atrophy (SMA) is the most common genetic disease in childhood. SMA is generally caused by mutations in SMN1. The Survival of Motor Neurons (SMN) complex consists of SMN1, Gemins (2-8) and Strap/Unrip. We previously demonstrated smn1 and gemin5 inhibited tissue regeneration in zebrafish. Here we investigated each individual SMN complex member and identified gemin3 as another regeneration-essential gene. These three genes are likely pan-regenerative since they affect the regeneration of hair cells, liver and caudal fin. RNA-Seq and miRNA-Seq analyses reveal that smn1, gemin3, and gemin5 are linked to a common set of genetic pathways, including the tp53 and ErbB pathways. Additional studies indicated all three genes facilitate regeneration by inhibiting the ErbB pathway, thereby allowing cell proliferation in the injured neuromasts. This study provides a new understanding of the SMN complex and a potential etiology for SMA and potentially other rare unidentified genetic diseases with similar symptoms.

genetics↗

bioRxiv2019

LncRNA Dnmt3aos regulates Dnmt3a expression leading to aberrant DNA methylation in macrophage polarization

Long non-coding RNAs (lncRNAs) play key roles in various biological processes. However, the roles of lncRNAs in macrophage polarization remain largely unexplored. In this study, thousands of lncRNAs were identified that are differentially expressed in distinct polarized bone marrow-derived macrophages (BMDMs). Among them, Dnmt3aos (DNA methyltransferase 3A, opposite strand), as a known lncRNA, locates on the antisense strand of Dnmt3a. Functional experiments further confirmed that Dnmt3aos were highly expressed in M(IL-4) macrophages and participated in the regulation of Dnmt3a expression, and played a key role in macrophage polarization. The DNA methylation profiles between the Dnmt3aos knockdown group and the control group in M(IL-4) macrophages were determined by MeDIP-seq technique for the first time, and the Dnmt3aos-Dnmt3a axis-mediated DNA methylation modification-regulated macrophage polarization related gene IFN-{gamma} was identified. Our study will help to enrich our knowledge of the mechanism of macrophage polarization and will provide new insights for immunotherapy in macrophage-associated diseases.

cell biology↗