Biology subjects

Zhu, Y.

Publications and source records attributed to Zhu, Y..

At least 289 records · Page 16Linked to original sources

bioRxiv2024

Effects of combined application of organic fertilizer and inorganic fertilizer on soil and yield of Gaodan grass

Using Sorghum bicolor x sudanense as test material, the effects of inorganic fertilizer and different proportions of organic fertilizer application on soil properties, yield and quality of sorghum were studied under conventional nitrogen application levels, aiming to provide data support for efficient production of green cycle forage. Five treatments were set up in the experiment, namely blank treatment (CK), conventional fertilization (HF), equivalent cow manure organic fertilizer (NF2), equivalent sheep manure organic fertilizer (YF2), 150% equivalent cow manure organic fertilizer (NF5) and 150% equivalent sheep manure organic fertilizer (YF5). In general, NF5 treatment was excellent in improving soil organic matter, enzyme activity and nutrient content, and the yield of Gaodan grass was significantly increased.

plant biology↗

bioRxiv2024

Protein kinase G inhibition preserves photoreceptor viability and function in a new mouse model for autosomal dominant retinitis pigmentosa

Retinitis Pigmentosa (RP) is the most common inherited retinal degeneration, characterized by an initial loss of rod photoreceptor cells. Photoreceptor cell death has been associated with high levels of cyclic guanosine-3', 5'-monophosphate (cGMP) in animal models of autosomal recessive RP (ARRP) and autosomal dominant RP (ADRP). cGMP analogues inhibiting protein kinase G (PKG) have been found to prevent rod degeneration in ARRP disease models, but their effects on ADRP are unknown. Here, we used the recently generated rhodopsin-mutant RhoI255d/+ ADRP mouse model to investigate cGMP-signaling and the effects of cGMP analogues targeting PKG. cGMP accumulation was investigated by retinal immunostaining in wild-type (WT), RhoI255d/+, and RhoI255d/I255d mice. The therapeutic efficacy of the cGMP analogues CN03 and CN238 was evaluated on organotypic retinal explant cultures derived from WT and RhoI255d/+ mice. Readouts included the TUNEL assay and immunostaining for cone arrestin-3. Downstream effectors of cell death were visualized using calpain, poly-ADP-ribose polymerase (PARP), and histone deacetylase (HDAC) in situ assays, as well as caspase-3 immunostaining. Photoreceptor function was assessed using micro-electroretinogram ({micro}ERG) recordings. When compared with WT, RhoI255d photoreceptors displayed cGMP accumulation in outer segments. In the RhoI255d/+ ADRP model, CN03 and CN238 significantly reduced the number of dying photoreceptors. However, the relatively small number of photoreceptors exhibiting caspase-3 activity was not changed by the treatment. Remarkably, CN238 effectively provided long-lasting neuroprotection of cone photoreceptors and preserved retinal light responsiveness of RhoI255d/+ retina. Overall, this study suggests caspase-independent but cGMP-dependent cell death as a dominant degenerative mechanism in the RhoI255d/+ ADRP mouse model. PKG inhibition demonstrated robust neuroprotection of both rod and cone photoreceptors, while the marked preservation of retinal function, especially with the compound CN238, highlighted cGMP analogues for the treatment of ADRP.

neuroscience↗

bioRxiv2024

Radiation damage behavior of soft matter in ultrafast cryo-electron microscopy (cryo-UEM)

Whether time-modulated pulsed-electron imaging in ultrafast electron microscopy (UEM) can mitigate the electron radiation damage that occurs to samples, is still controversial. The effectiveness of such mitigation effect and relevant potential application in cryo-EM remain to be explored. Herein, we built an ultrafast cryo-EM (cryo-UEM) device based on an ultrafast laser system. Using such equipment and the saturated aliphatic hydrocarbon compounds (C44H90), the fading curves of diffraction intensity and corresponding critical electron doses (Ne) of the samples were carefully measured under different imaging modes, temperatures, imaging dose rates and pulsed repetition rates. Our experimental results show that, the fading curves and Ne values of the C44H90 crystals are uncorrelated with the imaging electron dose rates and do not show dependence on the dose-rate effect. As the temperature decreased, the Ne values of the sample increased, indicating the cryoprotective effect on radiation damage to the samples. Surprisingly, at a constant temperature, the fading curves and Ne values of the sample in multi-electrons-packet and near-single-electron-packet pulsed modes are all approximately the same as those in conventional continuous electron-beam mode, even when the results are obtained at different pulsed repetition rates. These results show that the time-modulated pulsed electron beam does not seem to mitigate the electron radiation damage that occurs on samples. Our findings offer new insights and experimental basis for the radiation damage behavior of samples under electron beams, and provide guidance and inspiration for elucidating the fundamental principles of radiation damage.

biophysics↗

bioRxiv2024

Immune mechanisms of type 1 diabetes revealed by single-cell transcriptomics, bulk transcriptomics, and experimental validation

BackgroundType 1 diabetes (T1D) is an autoimmune disorder characterized by the destruction of insulin-producing pancreatic {beta} cells. Understanding the immune mechanisms underlying T1D is crucial for developing effective diagnostic and therapeutic strategies. This study aimed to elucidate the immune mechanisms of T1D by integrating single-cell RNA sequencing (scRNA-seq), bulk RNA-seq, and experimental validation. MethodsscRNA-seq data (GSE200695) and bulk RNA-seq data (GSE9006) were obtained from the Gene Expression Omnibus (GEO) database. After data preprocessing, principal component analysis (PCA), and clustering, cell subtypes were annotated using ImmGenData as a reference. Receptor-ligand interactions were analyzed to identify key cell subtypes. Least absolute shrinkage and selection operator (LASSO) regression was performed to identify characteristic genes and construct a diagnostic model. Key genes were further validated using the training and validation sets. Functional enrichment and immune infiltration analyses were conducted for the key genes. In vitro experiments were performed to validate the findings using a high-glucose model in the monocytic cell line THP-1. siRNA-mediated knockdown of TRIB1 was performed to investigate its role in regulating monocyte activation and immune-related pathways under high-glucose conditions. Monocyte activation markers, inflammatory cytokines, apoptosis, and the expression of key genes and immune-related genes were assessed using immunofluorescence staining, ELISA, flow cytometry, qPCR, and Western blot. ResultsMonocytes were identified as the key cell subtype with the most interactions with other cell subtypes. Eleven characteristic genes were selected to construct a diagnostic model, which demonstrated high validation efficiency (AUC > 0.8). Three key genes (ACTG1, REL, and TRIB1) showed consistent expression trends in the training and validation sets. Functional analyses revealed that these genes were involved in immune regulation and PI3K/AKT/mTOR signaling. In vitro experiments confirmed that high glucose induced monocyte activation, as evidenced by increased expression of activation markers (CD86) and pro-inflammatory cytokines (IL-8 and TNF-). High glucose also increased monocyte apoptosis and altered the expression of key genes (ACTG1, REL, and TRIB1) and immune-related genes (CXCL16, TGFBR1, CTLA4, CD48, TMIGD2, and HLA-DPB1). Knockdown of TRIB1 attenuated high glucose-induced monocyte activation, as demonstrated by decreased expression of activation markers and pro-inflammatory cytokines. TRIB1 knockdown also modulated the expression of immune-related genes and PI3K/AKT/mTOR signaling under high-glucose conditions. ConclusionsThis study integrates scRNA-seq, bulk RNA-seq, and experimental validation to unravel the immune mechanisms of T1D. Key genes (ACTG1, REL, and TRIB1) and monocytes were identified as crucial players in T1D pathogenesis. The constructed diagnostic model showed high validation efficiency. In vitro experiments confirmed the role of TRIB1 in regulating monocyte activation and immune-related pathways in a high-glucose model. These findings provide novel insights into the immune mechanisms of T1D and potential diagnostic and therapeutic targets.

bioinformatics↗

bioRxiv2024

ANKRD5: a key component of the axoneme required for spermmotility and male fertility

Sperm motility is essential for male fertility and depends on the structural integrity of the sperm axoneme, which features a canonical "9+2" microtubule arrangement. This structure comprises nine outer doublet microtubules (DMTs) that are associated with various macromolecular complexes. Among them, the nexin-dynein regulatory complex (N-DRC) forms crossbridges between adjacent DMTs, contributing to their stabilization and enabling flagellar bending. In this study, we investigated Ankyrin repeat domain 5 (ANKRD5, also known as ANK5 or ANKEF1), a protein highly expressed in the sperm axoneme. We found that ANKRD5 interacts with DRC5/TCTE1 and DRC4/GAS8, two key components of the N-DRC, and these interactions occur independently of calcium regulation. Male Ankrd5-/- mice exhibited impaired sperm motility and infertility. Cryo-electron tomography revealed a typical "9+2" axoneme structure with intact DMTs in Ankrd5 null sperm; however, the DMTs showed pronounced morphological variability and increased structural heterogeneity. Notably, ANKRD5 deficiency did not alter ATP levels, reactive oxygen species (ROS) levels, or mitochondrial membrane potential. These findings suggest that ANKRD5 may attenuate the N-DRCs mechanical buffering-akin to a "car bumper"-between adjacent DMTs, thereby compromising axonemal stability under high mechanical stress during vigorous flagellar beating. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=184 HEIGHT=200 SRC="FIGDIR/small/626701v3_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1ca36eforg.highwire.dtl.DTLVardef@dcafe3org.highwire.dtl.DTLVardef@9f6086org.highwire.dtl.DTLVardef@17a0a0b_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementMale infertility affects approximately 8%-12% of men globally, with defects in sperm motility accounting for over 80% of these cases. The axoneme, which functions as the motor apparatus of the sperm, adopts a canonical "9+2" microtubule arrangement, where the nexin-dynein regulatory complex (N-DRC) plays a critical role in providing structural support between adjacent outer microtubule doublets. Elucidating the interplay between the structural organization and protein composition of the N-DRC is essential for advancing the understanding of male reproductive biology. In this study, we identify ANKRD5 as a new component of N-DRC that is essential for maintaining normal sperm motility. These findings contribute to the molecular understanding of sperm motility and highlight ANKRD5 as a potential target for the development of novel male contraceptives.

developmental biology↗

bioRxiv2024

The mechanisms by which miRNAs critically contribute to differential roles of Nrf1 and Nrf2 in modulating the epithelial-mesenchymal transformation of hepatocellular carcinoma

Accumulation of various genetics and epigenetics alterations are accepted to result in the initiation and progression of hepatocellular carcinoma (HCC), and its high metastasis is viewed as a critical bottleneck leading to its treatment failure. Amongst them, the abnormal expression of several microRNAs arising from lack of antioxidant transcription factor Nrf2 (encoded by Nfe2l2) leads to cancer metastasis. However, much less known is about regulation of microRNAs by Nrf1 (encoded by Nfe2l1), even though it acts as an essential determinon of cell homeostasis by governing the transcriptional expression of those driver genes contributing to the epithelial-mesenchymal transition (EMT) involved in its metastasis. In this study, distinctive EMT phenotypes were unveiled to result from specific knockout of Nrf1 and Nrf2 in HepG2 cells, as accompanied by differential migratory and invasive capabilities. The Nrf1-/--leading EMT results from a significantly decrease in the epithelial CDH1 expression, plus another increased expression of the mesenchymal CDH2. Such distinct phenotypes of Nrf1-/- from Nrf2-/- cell lines were also attributable to differential regulation of two key microRNAs, i.e., miR3187-3P and miR1247-5p. Further experiments unraveled that Nrf1 activates the expression of miR-3187-3p, directly targeting for the inhibition of SNAI1, leading to CDH1 activation but CDH2 inhibition insomuch as to prevent the process of EMT. By contrast, Nrf2 inhibits the expression of miR1247-5p, relieving its inhibitory effect on MMP15 and MMP17 to promote the EMT. Collectively, these demonstrate that the EMT of liver cancer cells is likely prevented by Nrf1 via the miR3187-3P signaling to the SNAI1-CDH1/2 axis, but conversely promoted by Nrf2 through the miR1247-5p-MMP15/17 signaling axis.

molecular biology↗

bioRxiv2024

BPMs regulate Arabidopsis seedling development by promoting auxin-independent degradation of the Aux/IAA protein IAA10

After germination, seedlings undergo etiolated development (skotomorphogenesis), enabling them to grow towards the soil surface. In Arabidopsis, etiolated seedlings exhibit rapid hypocotyl elongation, apical hook formation and closed cotyledons to protect the meristem. In this study, we found that high-order mutants in the BPM gene family displayed defects in seedling development, characterized by a shorter hypocotyl, early apical hook opening, and opened cotyledons in the dark. BPM1, BPM2, BPM4, and BPM5 exhibit distinct expression patterns and subcellular localization in etiolated seedlings. In a hypocotyl segment assay the bpm mutants showed defects in auxin response indicating impaired auxin signaling in the hypocotyl. Expression of the auxin reporter DR5:GFP was also altered in the bpm1,4,5 mutant in various tissues compared to the wild type. Furthermore, we showed that BPM1 and IAA10 interact in yeast two-hybrid, BiFC, and Co-IP assays. Experiments in protoplasts indicated that BPM1 promotes ubiquitylation and degradation of IAA10, and the level of IAA10 protein is greater in the bpm1,4,5 mutant. In addition, IAA10 over-expression resulted in phenotypes similar to the bpm mutants. These results indicate that the BPMs target the Aux/IAA proteins for ubiquitylation and degradation. Overall, our findings shed light on the key roles of the BPMs in auxin signaling during seedling development.

plant biology↗

bioRxiv2024

A library of lineage-specific driver lines connects developing neuronal circuits to behavior in the Drosophila Ventral Nerve Cord.

Understanding developmental changes in neuronal lineages is crucial to elucidate how they assemble into functional neural networks. Studies investigating nervous system development in model systems have only focused on select regions of the central nervous system due to the limited availability of genetic drivers that target specific neuronal lineages throughout development and adult life. This has hindered our understanding of how distinct neuronal lineages interconnect to form neuronal circuits during development. Here, we present a split-GAL4 library composed of genetic driver lines, which we generated via editing the genomic locus of lineage-specific transcription factors and demonstrate that we can use this library to specifically target most individual neuronal hemilineages in the Drosophila ventral nerve cord (VNC) throughout development and into adulthood. Using these genetic driver lines, we found striking morphological changes in neuronal processes within a lineage during metamorphosis. We also demonstrated how neurochemical features of neuronal classes can be quickly assessed. Lastly, we documented behaviors elicited in response to optogenetic activation of individual neuronal lineages and generated a comprehensive lineage-behavior map of the entire fly VNC. Looking forward, this lineage-specific split-GAL4 driver library will provide the genetic tools needed to address the questions emerging from the analysis of the recent VNC connectome and transcriptome datasets.

developmental biology↗

bioRxiv2024

NEMF inhibits proliferation and migration of ovarian cancer cells by blocking the PI3K/mTOR pathway

Nuclear export mediator factor (NEMF) is considered to be a tumor suppressor in Drosophila. Based on the analysis of data from an online database, NEMF is downregulated in ovarian cancer. However, the mechanism underlying its expression has not been reported thus far.In this study, the immunohistochemistry results showed that the expression of NEMF may be related to patient age and tissue differentiation. In vitro experiments indicated that overexpression of NEMF may inhibit cell proliferation and migration by inhibiting the PI3K/mTOR signaling pathway, thereby blocking cell cycle progression and promoting apoptosis (P < 0.05).Therefore, we speculate that NEMF is a potential tumor suppressor gene. Targeting NEMF may be an innovative therapeutic approach for ovarian cancer. Summary blurbNEMF is downregulated in ovarian cancer and the mechanism underlying its expression has not been reported thus far.In vitro experiments indicated that overexpression of NEMF inhibit cell proliferation and migration by inhibiting the PI3K/mTOR signaling pathway,thereby blocking cell cycle progression.

cancer biology↗

bioRxiv2024

In depth sequencing of a serially sampled household cohort reveals the within-host dynamics of Omicron SARS-CoV-2 and rare selection of novel spike variants

SARS-CoV-2 has undergone repeated and rapid evolution to circumvent host immunity. However, outside of prolonged infections in immunocompromised hosts, within-host positive selection has rarely been detected. The low diversity within-hosts and strong genetic linkage among genomic sites make accurately detecting positive selection difficult. Longitudinal sampling is a powerful method for detecting selection that has seldom been used for SARS-CoV-2. Here we combine longitudinal sampling with replicate sequencing to increase the accuracy of and lower the threshold for variant calling. We sequenced 577 specimens from 105 individuals from a household cohort primarily during the BA.1/BA.2 variant period. There was extremely low diversity and a low rate of divergence. Specimens had 0-12 intrahost single nucleotide variants (iSNV) at >0.5% frequency, and the majority of the iSNV were at frequencies <2%. Within-host dynamics were dominated by genetic drift and purifying selection. Positive selection was rare but highly concentrated in spike. Two individuals with BA.1 infections had S:371F, a lineage defining substitution for BA.2. A Wright Fisher Approximate Bayesian Computational model identified positive selection at 14 loci with 7 in spike, including S:448 and S:339. We also detected significant genetic hitchhiking between synonymous changes and nonsynonymous iSNV under selection. The detectable immune-mediated selection may be caused by the relatively narrow antibody repertoire in individuals during the early Omicron phase of the SARS-CoV-2 pandemic. As both the virus and population immunity evolve, understanding the corresponding shifts in SARS-CoV-2 within-host dynamics will be important.

microbiology↗

bioRxiv2024

Chaperonin TRiC bridges radial spokes for folding proteins locally translated in mammalian sperm flagella

As animals evolved from external to internal fertilization, sperm flagella, which once transiently propelled sperm in water to reach nearby eggs, developed to beat for days or even longer within the female reproductive tract. How flagella were remodeled accordingly remains unclear. Unlike externally fertilizing zebrafish and sea urchin, mammalian sperm flagella feature a unique barrel-shaped bridge between axonemal radial spokes RS1 and RS2, though its components and function remain unknown. Here, using cryo-EM and cryo-ET combined with mass spectrometry and immunofluorescence staining, we reveal that this RS1-RS2 barrel (RRB) in mammalian sperm flagella is a group II chaperonin TRiC/CCT. We purified and resolved the unforeseen cryo-EM structure of TRiC from bovine sperm flagella, discovering that flagella TRiC contains the testis-specific CCT6B subunit. Additionally, we resolved the cryo-ET map of mouse sperm flagella RSs, containing the RRB, achieving unprecedented local resolution of 10-14 [A]. The in-situ RRB map displays two extra densities within its chambers in a polarized manner, suggesting the presence of folding substrates and a co-chaperone (likely phosducin-like 2). Notably, mammalian flagella also contain components of translation machineries and actively synthesize proteins. Our results suggest that the RRB TRiC folds locally translated proteins to sustain mammalian flagella, providing new insights into flagellar remodeling in internally fertilizing species. Our findings also shed lights on male fertility and potential treatments for infertility.

biophysics↗

bioRxiv2024

CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation during cellular differentiation

Enhancers and promoters interact in 3D chromatin structures to regulate gene expression. Here, we characterize the mechanisms that drive the formation of these structures and their function in gene regulation in a lymphoid-to-myeloid transdifferentiation system. Based on analyses at base-pair resolution, we demonstrate a close correlation between binding of regulatory proteins, formation of chromatin interactions, and gene expression. Integration of multi-way interaction analyses and computational modeling shows that tissue-specific gene loci are organized into chromatin hubs, characterized by cooperative interactions between multiple enhancers, promoters, and CTCF-binding sites. Depletion of CTCF strongly impairs the formation of these structures. However, the effects of CTCF depletion on gene expression are modest and can be explained by rewired enhancer-promoter interactions. This demonstrates an instructive role for enhancer-promoter interactions in gene regulation that is independent of cooperative interactions in chromatin hubs. Together, these results contribute to a mechanistic understanding of the structure-function relationship of the genome during cellular differentiation.

genomics↗

bioRxiv2024

De novo identification of protein domains in cryo-electron tomography maps from AlphaFold2 models

In situ cryo-electron tomography (cryo-ET) enables visualization of protein complexes within their native cellular environments. However, sub-tomogram averaging (STA) often fails to achieve resolutions sufficient for atomic model building based on side-chain information, hindering accurate protein identification and assignment. To address this challenge, we developed DomainSeeker, a computational workflow that integrates AlphaFold2-predicted structures with experimental data to identify protein domains in cryo-ET density maps. DomainSeeker partitions AlphaFold2-predicted structures into domains using clique analysis based on predicted aligned errors and then fits these domains into target densities segmented from input cryo-ET maps. Each domain-density fit is evaluated globally and locally to derive prior probabilities, which are subsequently integrated with complementary data, such as cross-linking mass spectrometry (XL-MS), through Bayesian inference to compute posterior probabilities. Applying DomainSeekers prior probability analysis to densities from mouse sperm microtubule doublets revealed substantially higher recognition accuracy and resolution robustness compared with existing approaches. Incorporating XL-MS data for yeast nuclear pore complex densities further enhanced both recognition performance and confidence. Finally, we implemented an interactive ChimeraX plugin to facilitate user access. Together, DomainSeeker overcomes a key bottleneck in in situ structural biology, providing a robust and accessible tool for visual proteomics to uncover the structural and functional organization of native cellular assemblies.

biophysics↗

bioRxiv2024

Squidiff: Predicting cellular development and responses to perturbations using a diffusion model

Single-cell sequencing has revolutionized our understanding of cellular heterogeneity and responses to environmental stimuli. However, mapping transcriptomic changes across diverse cell types in response to various stimuli and elucidating underlying disease mechanisms remains challenging. Studies involving physical stimuli, such as radiotherapy, or chemical stimuli, like drug testing, demand labor-intensive experimentation, hindering mechanistic insight and drug discovery. Here we present Squidiff, a diffusion model-based generative framework that predicts transcriptomic changes across diverse cell types in response to environmental changes. We demonstrate Squidiffs robustness across cell differentiation, gene perturbation, and drug response prediction. Through continuous denoising and semantic feature integration, Squidiff learns transient cell states and predicts high-resolution transcriptomic landscapes over time and conditions. Furthermore, we applied Squidiff to model blood vessel organoid development and cellular responses to neutron irradiation and growth factors. Our results demonstrate that Squidiff enables in silico screening of molecular landscapes, facilitating rapid hypothesis generation and providing valuable insights for precision medicine.

bioinformatics↗

bioRxiv2024

Offset mass carrier proteome improves quantification of multiplexed single cell proteomics

Multiplexed single cell proteomics by mass spectrometry (scpMS) approaches currently offer the highest throughput as measured by cells analyzed per day. These methods employ isobaric labels and typically a carrier proteome - a sample added at 20-500x the single cell level that improves peptide sampling and identification. Peptides from the carrier and single cell proteomes exist within the same precursor isotopic cluster and are co-isolated for identification and quantification. This represents a challenge as high levels of carrier proteome limit the sampling of peptide ions from single cell samples and can potentially lead to decreased accuracy of quantitative measurements. Here, we address this limitation by introducing a triggered by offset mass acquisition method for scpMS (toma-scpMS) that utilizes a carrier proteome labeled with non-isobaric tags that have the same chemical composition but different mass as the labels used for quantitative multiplexing. Within toma-scpMS the carrier proteome and single cell proteome are separated at the precursor level, enabling separate isolation, fragmentation, and quantitation of the single cell samples. To enable this workflow we implemented a custom data acquisition scheme within inSeqAPI, an instrument application programming interface program, that performed real-time identification of carrier proteome peptides and subsequent triggering of offset single cell quantification scans. We demonstrate that toma-scpMS is more robust to high-levels of carrier proteome and offers superior quantitative accuracy as compared to traditional multiplexed scpMS approaches when similar carrier proteome levels are employed.

systems biology↗

bioRxiv2024

Tardigrade Dsup: Interactions with DNA and protection of cells from oxidative stress

The remarkable capability of Tardigrade to survive under extreme conditions has been partially attributed to Dsup, an intrinsically disordered, highly positively charged protein. Dsup has been shown to bind to DNA in vitro, a property that has been associated with the capability of Dsup to exhibit stress-protective effects when expressed in mammalian cells. However, DNA binding of Dsup has not been visualized in living cells and expression of Dsup in different cell types was associated with either protective or detrimental effects. In addition, the effect of Dsup expression has not been clearly demonstrated at the organism level. Here we combined molecular dynamics (MD) simulations and fluorescence lifetime imaging microscopy (FLIM)-Forster resonance energy transfer (FRET) to interrogate Dsup-DNA interactions and demonstrated Dsup binding to DNA in living mammalian cells. Furthermore, Dsup expression in both HEK293T cells and yeast enhanced cell survival in the presence of hydrogen peroxide, suggesting that the presence of Dsup allows both mammalian and yeast cells to better cope with oxidative stress conditions. This study provides a better understanding of the property and functional role of Dsup and lays a foundation to explore new approaches to enhance stress resistance.

biophysics↗

bioRxiv2024

Spatiotemporally restricted Hippo signalings instruct the fate and maturation of hepatobiliary cells

The Hippo pathway is an evolutionary conserved signaling cascade involved in organ size control and tumorigenesis, but its cellular functions and regulatory mechanisms are not fully understood. Recently, we have defined two independent modules (HPO1 and HPO2) in the Hippo signaling network. Here, by using spatially resolved transcriptomic and imaging analysis of mouse livers with defective Hippo signaling, we show that HPO1 and HPO2 operate in distinct cells at different developmental stages to regulate the fate and maturation of liver parenchymal cells. HPO1 controls the maturation of hepatocytes postnatally, and its perturbation leads to the expansion of immature hepatocytes (imHep). HPO2, on the other hand, regulates the maturation of cholangiocytes perinatally, and its ablation results in the accumulation of immature cholangiocytes (imCho2) identical to developing ductal plate cells. Moreover, the inactivation of HPO1 or HPO2 causes the conversion of hepatocytes into immature cholangiocytes (imCho1). These immature cells are also observed in regenerating livers following different damages. In contrast, deletion of Yap/Taz encoding downstream effectors of the Hippo pathway accelerates liver maturation and promotes cell death. These findings suggest that the spatiotemporally restricted Hippo signaling modules act as checkpoints in liver development and may coordinate cell proliferation and maturation to ensure proper liver size and function.

cell biology↗

bioRxiv2024

Embryonic Mast Cells Arise from Cpa3-expressing Precursors Independent of Granulocyte-Monocyte Progenitors

Most of the mast cells (MCs) in connective tissues, such as skin, are long-lived embryonic-derived immune cells that play important roles in host defense and various immunological diseases, including allergies. Their embryonic origin and ontogeny remain to be fully studied since several overlapping waves of embryonic hematopoiesis have been shown to give rise to these cells. Here, combining single-cell RNA sequencing and new genetic fate mapping models, we identified a Cpa3-expressing population sequentially appearing in the yolk sac, fetal liver, and peripheral tissues which gives rise to dermal MCs during embryonic days 11.5 to 14.5. Using in vitro differentiation and in vivo transplant methods, we identified a Ter119-F4/80- CD45+CD117+CD16/32+CD135-CD115-Ly6C-CD34lo population as potential fetal liver MC precursors. Fate mapping with Cpa3CreERT2and Zbtb16CreERT2 models, as well as the granulocyte-monocyte progenitor (GMP) models Ms4a3Cre and ElaneCre, demonstrated that MCs arise from Cpa3+ progenitors rather than Ms4a3+ or Elane+ GMPs. A corresponding population with a similar developmental trajectory was also identified in human early yolk sac and fetal liver, suggesting a conserved MC developmental program across species. These findings delineate the detailed developmental path of MCs in embryos, permitting future functional studies in immunity and development. HighlightsO_LICpa3-expressing cells in the yolk sac and fetal liver contain mast cell precursors C_LIO_LICpa3CreERT2 labels embryonic mast cells and their precursors C_LIO_LIEmbryonic mast cells arise through Cpa3+ mast cell precursors, but not Elane+/Ms4a3+ GMPs C_LIO_LIThe seeding of MCPs to embryonic skin slows down after E14.5 C_LI

immunology↗