bioRxiv Science⌕ Search

Biology subjects

Zhu, X.

Publications and source records attributed to Zhu, X..

At least 217 records · Page 12Linked to original sources

Co-engagement of TIGIT+ immune cells to PD-L1+ tumours by a bispecific antibody potentiates T-cell response and tumour control

Co-targeting PD-1/PD-L1 and TIGIT/CD226 is being pursued to broaden the efficacy of current immunotherapy. Here we demonstrate that a bispecific antibody (BsAb) targeting PD-L1 and TIGIT, HB0036, shows major advantages over the combination of the two parental monoclonal Abs (mAbs). We demonstrated that HB0036 co-engages PD-L1+ tumour cells and TIGIT+ T cells, and thereby upregulates CD226 on T cells and induces a greater T-cell proliferative response compared to the combination of the parental antibodies in vitro. In vivo, HB0036 recruits greater amounts of TIGIT antibody in PD-L1+ tumours but not in PD-L1- tumours, compared with therapy using the two parental antibodies. We also observed improved tumour control and favourable immunological signatures with HB0036 in syngeneic and xenograft tumour models. Collectively, these findings demonstrate that bispecific antibodies targeting PD-L1 and TIGIT offer superior benefits in cancer immunotherapy compared with therapy using the two parental antibodies. Based on these studies, a phase I clinical trial with HB0036 has been initiated in patients with solid tumours (NCT05417321).

immunology↗

Wnt/β-catenin signaling controls mouse eyelid growth by mediating epithelial-mesenchymal interactions

Eyelid closure is required for the development of multiple ocular tissues. Interactions between the epithelium and underlying mesenchyme play a pivotal role in regulating eyelid development. However, the molecular mechanisms underlying these interactions remain unclear. Wnt signaling pathways regulate the development of ocular tissues, but their functions in eyelid development are not fully defined. In this study, we find that deletion of {beta}-catenin in supraorbital mesenchyme abolishes eyelid growth by causing decreased proliferation in supraorbital epithelium and underlying mesenchyme. Inhibition of Wnt secretion by deleting Wls in supraorbital epithelium results in failure of eyelid developing, similar to the effects of deleting mesenchymal {beta}-catenin, suggesting that mesenchymal Wnt/{beta}- catenin signaling is controlled by epithelial Wnt ligands during eyelid development. We also found that deletion of p63 results in formation of hypoplastic eyelids and reduced expression of several Wnt ligands in eyelid epithelium, indicating that expression of Wnt ligands in eyelid development is at least partially regulated by p63. Taken together, our data indicate that Wnt/{beta}-catenin signaling controls eyelid growth by orchestrating epithelial- mesenchymal interactions.

developmental biology↗

Overexpression of the violaxanthin de-epoxidase confers faster NPQ and photosynthesis induction in rice

Plants in the field experience fluctuations in light conditions. Plants with swift responses to dynamic light conditions usually gain competitive advantage in the field. The dynamic photosynthesis can be reflected in dynamic changes in almost all processes in photosynthesis, with dominant factors being dynamic changes in non-photochemical quenching, Rubisco activation and stomatal dynamics. Each of these dynamic responses is controlled by defined mechanisms. In this study, we showed that overexpression of VDE, an enzyme involved in the xanthophyll cycle and non-photochemical quenching, in rice resulted in faster NPQ induction, less photoinhibition, and faster photosynthesis induction, which together caused increased biomass production by about 11[~]16%. This study, demonstrating a previously unnoticed role of VDE in altering the dynamics of photosynthesis induction besides decreasing photoinhibition, offers a potential strategy to improve canopy photosynthesis through capitalizing the ability of plants to use dynamic light. HighlightThe overexpression of VDE in rice resulted in faster NPQ induction, less photoinhibition, and faster photosynthesis induction, which together caused increased biomass in field.

plant biology↗

Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift

Developing broad coronavirus vaccines requires identifying and understanding the molecular basis of broadly neutralizing antibody (bnAb) spike sites. In our previous work, we identified sarbecovirus spike RBD group 1 and 2 bnAbs. We have now shown that many of these bnAbs can still neutralize highly mutated SARS-CoV-2 variants, including the XBB.1.5. Structural studies revealed that group 1 bnAbs use recurrent germline encoded CDRH3 features to interact with a conserved RBD region that overlaps with class 4 bnAb site. Group 2 bnAbs recognize a less well-characterized "site V" on the RBD and destabilize spike trimer. The site V has remained largely unchanged in SARS-CoV- 2 variants and is highly conserved across diverse sarbecoviruses, making it a promising target for broad coronavirus vaccine development. Our findings suggest that targeted vaccine strategies may be needed to induce effective B cell responses to escape resistant subdominant spike RBD bnAb sites.

immunology↗

RNA landscapes of brain tissue and brain tissue-derived extracellular vesicles in simian immunodeficiency virus (SIV) infection and SIV-related central nervous system pathology

IntroductionAntiretroviral treatment regimens can effectively control HIV replication and some aspects of disease progression. However, molecular events in end-organ diseases such as central nervous system (CNS) disease are not yet fully understood, and routine eradication of latent reservoirs is not yet in reach. Brain tissue-derived extracellular vesicles (bdEVs) act locally in the source tissue and may indicate molecular mechanisms in HIV CNS pathology. Regulatory RNAs from EVs have emerged as important participants in HIV disease pathogenesis. Using brain tissue and bdEVs from the simian immunodeficiency virus (SIV) model of HIV disease, we profiled messenger RNAs (mRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), seeking to identify possible networks of RNA interaction in SIV infection and neuroinflammation. MethodsPostmortem occipital cortex tissue were collected from pigtailed macaques: uninfected controls and SIV-infected subjects (acute phase and chronic phase with or without CNS pathology). bdEVs were separated and characterized in accordance with international consensus standards. RNAs from bdEVs and source tissue were used for sequencing and qPCR to detect mRNA, miRNA, and circRNA levels ResultsMultiple dysregulated bdEV RNAs, including mRNAs, miRNAs, and circRNAs, were identified in acute infection and chronic infection with pathology. Most dysregulated mRNAs in bdEVs reflected dysregulation in their source tissues. These mRNAs are disproportionately involved in inflammation and immune responses, especially interferon pathways. For miRNAs, qPCR assays confirmed differential abundance of miR-19a-3p, let-7a-5p, and miR-29a-3p (acute SIV infection), and miR- 146a-5p and miR-449a-5p (chronic with pathology) in bdEVs. In addition, target prediction suggested that several circRNAs that were differentially abundant in source tissue might be responsible for specific differences in small RNA levels in bdEVs during SIV infection. ConclusionsRNA profiling of bdEVs and source tissues reveals potential regulatory networks in SIV infection and SIV-related CNS pathology.

neuroscience↗

Two haplotype-resolved genomes of highly heterozygous AAB allotriploid bananas provide insights into subgenome asymmetric evolution and banana wilt control

Bananas (Musa spp.) are one of the most important tropical fruits and staple food, which are of great significance to human societies. Plantain and Silk are two important banana subgroups, which are both triploid hybrids (AAB) between the wild diploid Musa acuminata and M. balbisiana. In this study, we reported the first haplotype-resolved genome assembly of Plantain and Silk bananas with genome size of approximately 1.4 Gb. We discovered widespread asymmetric evolution in the subgenomes of Plantain and Silk, which could be linked to frequent homologous exchanges (HEs) events. This is the first study to uncover the genetic makeup of triploid banana and verify that subgenome B harbors a rich source of resistance genes. Of the 88,078 and 94,988 annotated genes in Plantain and Silk, only 58.5% and 59.4% were present in all three subgenomes, with >50% genes containing differently expressed alleles in different haplotypes. We also found that Plantain is more resistant to banana Fusarium wilt, exhibiting a much faster defense response after pathogenic fungi infection. Many differentially expressed genes in abscisic acid, ethylene, jasmonic acid and salicylic acid pathways were identified in Plantain. Our analysis revealed that MpMYB36 promotes the biosynthesis of secondary cell wall and deposition of lignin by directly binding to the promoter of MpPAL and MpHCT, which allows Plantain to inhibit the penetration of early infection. Moreover, the insertion of the key carotenoid synthesis gene (CRTISO) may be the potential genetic basis for the richness of carotenoids in Plantain. Our study provides an unprecedented genomic basis for basic research and the development of elite germplasm in cultivated bananas.

plant biology↗

Electrophysiological signatures of temporal context in the bisection task

Despite relatively accurate time judgment, subjective time is susceptible to various contexts, such as sample spacing and frequency. Several electroencephalographic (EEG) components have been linked to timing, including the contingent negative variation (CNV), offset P2, and late positive component of timing (LPCt). However, the specific role of these components in the contextual modulation of perceived time remains unclear. In this study, we conducted two temporal bisection experiments, where participants had to judge if a test duration was close to a short or long standard. Unbeknownst to participants, the sample spacing (Experiment 1) and frequency (Experiment 2) were altered to create short and long contexts while keeping the test range and standards the same in different sessions. The results showed that the bisection threshold shifted toward the ensemble mean and that CNV and LPCt were sensitive to context modulation. Compared to the long context, the CNV climbing rate increased in the short context, and the amplitude and latency of the LPCt were reduced. These findings suggest the CNV represents an expectancy wave for upcoming decision-making, while LPCt reflects the decision-making process, both influenced by the temporal context.

neuroscience↗

Development of membrane-like pre-stem cells after released from tube-shaped niches

We previously identified three distinct pre-stem cell lineages that further develop into blood CD34-positive stem cells, and mesenchymal stem cells. The pre-CD34-positive stem cells are spore-like, while the pre-mesenchymal stem cells are fusiform-shaped. All of them originate or released from tube-shaped tissue structures, or niches. In the current study, we present two membrane-like pre-stem progenitors. One of them had red thin membrane structures that were from disconnection of bamboo-like tissues and developed into thin membrane-like multi-nucleated cells. The other membrane-like structure had geometric-shape and was the place of developing numerous c-kit-positive stem cell progenitors. One geometric-shaped membrane could produce dozens to hundreds of progenitors in a synchronized pattern. Our findings provide more evidence that postnatal stem cells are unipotent and self-renewed in sealed tube-shaped structures. The tube-shaped structures released their inclusions that have distinct morphological differences among the cellular lineages. Thus, the self-renewal of each lineage-distinct stem cell has its unique pattern. Further, our data suggests that postnatal stem cells are renewed via a recurrent pattern. Our findings again challenged the old concepts of stem cell niche components, the origins of stem cell lineages and the self-renewal of stem cells.

cell biology↗

A proximity-dependent biotinylation map of cytosol-facing organelle outer membrane proteome in living Arabidopsis cells

The cytosol-facing outer membrane (OM) of organelles communicates with other cellular compartments to exchange proteins, metabolites and signaling molecules. Cellular surveillance systems also target OM-resident proteins to control organellar homeostasis and ensure cell survival under stress. Using traditional approaches to discover OM proteins and identify their dynamically interacting partners remains challenging. In this study, we developed an OM proximity labeling (OMPL) system using biotin ligase-mediated proximity biotinylation to map the proximity proteome of the OMs of mitochondria, chloroplasts, and peroxisomes in living Arabidopsis (Arabidopsis thaliana) cells. We demonstrate the power of this system with the discovery of cytosolic factors and OM receptor candidates involved in local protein translation and translocation, membrane contact sites, and organelle quality control. This system also performed admirably for the rapid isolation of intact mitochondria and peroxisomes. Our data support the notion that TOM20-3 is a candidate for both a mitochondrial and a chloroplast receptor, and that PEX11D is a candidate for a peroxisome receptor for the coupling of protein translation and import. OMPL-generated OM proximity proteomes are valuable sources of candidates for functional validation and suggest directions for further investigation of important questions in cell biology.

cell biology↗

RIPK3-dependent necroptosis is the primary cause of RIPK1-deficient-induced immunodeficiency.

RIPK1 (receptor-interacting serine/threonine kinase 1) plays a pivotal role in developing the immune system--patients with homozygous loss-of-function mutations of RIPK1 present with immunodeficiency and intestinal inflammation. Here, we reported that RIPK1-deficient rats represented defects of human patients and were certified as a suitable disease model. Knocking out Ripk3 rather than Caspase-8 nearly completely corrected immunodeficiency disorders, developmental defects, and necroptosis in the thymus of RIPK1-deficient rats. However, inflammatory enteritis was still detected in either Ripk1/Ripk3-or Ripk1/Casp-8-double deficient rats and only rescued in Ripk1/Ripk3/Caspase-8-triple deficient rats, suggesting RIPK3 mediated necroptosis and Caspase-8 dependent apoptosis contribute in different part in RIPK1-deficient caused the syndrome. Moreover, RIPK1-deficient rat dermal fibroblasts (RDFs) showed sensitive necroptosis and impaired NF-{kappa}B activation, also reported in RIPK1-deficient human patients. And pharmacological inhibition of NF-{kappa}B activation could sensitize necroptosis of rat cells. Since mutations that damage NF-{kappa}B activation could cause immunodeficiency in human patients, it suggested that aberrantly activated necroptosis play a vital role in certain kinds of primary immunodeficiency syndromes and pharmacological inhibition of necroptosis could be a novel therapeutic strategy for those diseases.

immunology↗

Ferroptosis is determined by chloride ions

Ferroptosis has emerged as a deliberate type of programmed cell death that manifests marked importance ubiquitously in health and diseases. However, after a decade of research, the mechanisms of ferroptosis execution remain unclear. Here we identify chloride ions (Cl-) as essential determinants of ferroptosis. Water homeostasis manipulated by extracellular solute concentration disrupts ferroptotic cell death. Hyperosmotic stress attenuates ferroptosis and endues cells with high lipid peroxidation. Analyses of a fluorescent chloride probe show that Cl- fluxes into the cytoplasm during ferroptosis, substantiating a role for Cl- to drive water flow. Depletion of extracellular chloride ions ([Cl-]o) from culture media congruously confers resistance to ferroptosis. The [Cl-]o-depleted ferroptotic cells fall into two populations: cells with low lipid peroxidation; cells with high lipid peroxidation but not cell swelling or cell rupture. Contrarily, solitary [Cl-]o overload is sufficient to elicit ferroptosis without canonical ferroptosis inducers. Further experiments show that ferroptotic cells depolarize and [Cl-]o is positively correlated with this process. Membrane depolarization upregulates the level of lipid peroxidation, suggesting that membrane potential may be a universal mechanism governing ferroptosis. Together, our findings reveal that ferroptosis is determined by chloride ions.

cell biology↗

The self-renewal procedures of mesenchymal stem cells in the blood

BackgroundAlthough mesenchymal stem cells (MSCs) are most commonly used in cell therapy and stem cell research, the mechanism and the locations of their self-renewal are still unknown. MethodMouse blood was collected, and examined under microscopy. The results were compared with the data of human umbilical cord blood (hUCB) collected 10 years ago. ResultsWe found that the procedure of self-renewal for the mesenchymal stem cells in mouse blood and hUCB needs at least 5 steps. First, tube-shaped stem cell niches release long segmented materials composed of sand-like particles and semitransparent granules. Second, the sand-like particles and semitransparent granules separate from the segmented materials. Third, each of the individual semitransparent granules releases groups of fusiform-shaped structures that do not stain to H&E. The sizes of the fusiform-shaped structures range from 1 to 100 m in length in mouse blood, but can be 200 m in hUCB. Fourth, the large-sized fusiform structures can directly transform into lineage-restricted cellular structures; the medium-sized fusiform structures fuse or engulf each other to form cellular structures. The cellular structures further acquire membranes from the adjacent nucleated cells. Fifth, the nucleolus appears in the new cellular structures before the nucleus. During all the procedures, the adjacent nucleated mesenchymal cells are must needed. Thus, these newly formed cellular structures will further differentiate into nucleated mesenchymal stem cells. ConclusionOur findings again provide new evidence that, in physiological conditions, mesenchymal stem cell self-renewal needs several steps to complete, which, however, does not occur by mitotic division. The tube-shaped structures are the niches of the stem cells.

cell biology↗

IMPACT: a web server for exploring immunotherapeutic predictive and cancer prognostic biomarkers

Immune checkpoint inhibitors (ICIs) are a breakthrough in oncology treatment, and studies of screening predictive biomarkers of ICIs are emerging. We developed a web server named IMPACT (http://impact.brbiotech.com/) to thoroughly explore immunotherapeutic predictive or prognostic biomarkers. IMPACT contains a large dataset of 6,276 patients treated with ICIs and integrates 11 well-designed function modules, enabling an in-depth solution for biomarkers exploration. Compared with the existing tools, IMPACT was implemented with one exclusive module for interaction analysis and several optimized conventional functions for discovering novel biomarkers. Specifically, the interaction analysis of biomarker-treatment effect is essential to determine whether a biomarker is predictive and/or prognostic for ICIs. Moreover, several optimized functions allow complicated biomarker exploration, including customized selections of variant types in more detail, automatically screening meaningful co-mutations among multiple genes, and selecting cut-off values for gene expression biomarkers. In summary, IMPACT is a comprehensive analysis resource to facilitate biomarker research of ICIs.

bioinformatics↗

Marmoset Brain Mapping V5: an Anatomical and Connectivity Atlas of the Cerebellum

The cerebellum is a key region of the brain for motor control and cognitive functioning, and it is involved bidirectional communication with the cerebral cortex. As one of the smallest non-human primates, the common marmoset provides many advantages in the study of the anatomy and the functions of cerebello-cerebral circuits. However, the cerebellum of the marmoset is far from being well described in published resources. In this study, we present a comprehensive atlas of the marmoset cerebellum in three parts: 1) fine-detailed anatomical atlases and surface-analyzing tools of the cerebellar cortex, based on ultra-high resolution ex-vivo MRI; 2) functional-connectivity gradients of the cerebellar cortex, based on awake resting-state fMRI; and 3) structural-connectivity based mapping of the cerebellar nuclei, based on high-resolution diffusion tractography. The atlas shows the anatomical details of the marmoset cerebellum; reveals distinct gradient patterns of the intra-cerebellar and the cerebello-cerebral functional connectivity; and maps the topological relationship of the cerebellar nuclei in cerebello-cerebral circuits. As version 5 of the Marmoset Brain Mapping project, the atlas describes the anatomical and connectivity details of the marmoset cerebellum and is publicly available via marmosetbrainmapping.org.

neuroscience↗

MRBEE: A novel bias-corrected multivariable Mendelian Randomization method

Mendelian randomization (MR) is an instrumental variable approach used to infer causal relationships between exposures and outcomes and can apply to summary data from genome-wide association studies (GWAS). Since GWAS summary statistics are subject to estimation errors, most existing MR approaches suffer from measurement error bias, whose scale and direction are influenced by weak instrumental variables and GWAS sample overlap, respectively. We introduce MRBEE (MR using Bias-corrected Estimating Equation), a novel multivariable MR method capable of simultaneously removing measurement error bias and identifying horizontal pleiotropy. In simulations, we showed that MRBEE is capable of effectively removing measurement error bias in the presence of weak instrumental variables and sample overlap. In two independent real data analyses, we discovered that the causal effect of BMI on coronary artery disease risk is entirely mediated by blood pressure, and that existing MR methods may underestimate the causal effect of cannabis use disorder on schizophrenia risk compared to MRBEE. MRBEE possesses significant potential for advancing genetic research by providing a valuable tool to study causality between multiple risk factors and disease outcomes, particularly as a large number of GWAS summary statistics become publicly available.

genomics↗

An electrostatic cluster guides Aβ40 fibril formation in cerebral amyloid angiopathy

Cerebral amyloid angiopathy (CAA) is associated with the accumulation of fibrillar A{beta} peptides upon and within the cerebral vasculature, which leads to loss of vascular integrity and contributes to disease progression in Alzheimers disease (AD). We investigate the structure of human-derived A{beta}40 fibrils obtained from patients diagnosed with sporadic or familial Dutch-type (E22Q) CAA. Using cryo-EM, two primary structures are identified containing elements that have not been observed in in vitro A{beta}40 fibril structures. One population has an ordered N-terminal fold comprised of two {beta}-strands stabilized by electrostatic interactions involving D1, E22, D23 and K28. This charged cluster is disrupted in the second population, which exhibits a disordered N-terminus and is favored in fibrils derived from the familial Dutch-type CAA patient. These results illustrate differences between human-derived CAA and AD fibrils, and how familial CAA mutations guide fibril formation.

neuroscience↗

Salmonella succinate utilisation is inhibited by multiple regulatory systems

Succinate is a potent immune signalling molecule that is present in the mammalian gut and within macrophages. Both of these niches are colonised by the pathogenic bacterium Salmonella enterica serovar Typhimurium during infection. Succinate is a C4-dicarboyxlate that can serve as a source of carbon for bacteria. When succinate is provided as the sole carbon source for in vitro cultivation, Salmonella and other enteric bacteria exhibit a slow growth rate and a long lag phase. This growth inhibition phenomenon was known to involve the sigma factor RpoS, but the genetic basis of the repression of bacterial succinate utilisation was poorly understood. Here, we used an experimental evolution approach to isolate fast-growing mutants during growth of S. Typhimurium on succinate containing minimal medium. Our approach reveals novel RpoS-independent systems that inhibit succinate utilisation. The CspC RNA binding protein restricts succinate utilisation, an inhibition that is antagonised by high levels of the small regulatory RNA (sRNA) OxyS. We discovered that the Fe-S cluster regulatory protein IscR inhibits succinate utilisation by repressing the C4-dicarboyxlate transporter DctA. The RNA chaperone Hfq, the exoribonuclease PNPase and their cognate sRNAs function together to repress succinate utilisation via RpoS induction. Furthermore, the ribose operon repressor RbsR is required for the complete RpoS-driven repression of succinate utilisation, suggesting a novel mechanism of RpoS regulation. Our discoveries shed light on redundant regulatory systems that tightly regulate the utilisation of succinate. We propose that the control of central carbon metabolism by multiple regulatory systems in Salmonella governs the infection niche-specific utilisation of succinate.

microbiology↗

Multimodal Imaging-Based Classification of PTSD Using Data-Driven Computational Approaches: A Multisite Big Data Study from the ENIGMA-PGC PTSD Consortium

BackgroundCurrent clinical assessments of Posttraumatic stress disorder (PTSD) rely solely on subjective symptoms and experiences reported by the patient, rather than objective biomarkers of the illness. Recent advances in data-driven computational approaches have been helpful in devising tools to objectively diagnose psychiatric disorders. Here we aimed to classify individuals with PTSD versus controls using heterogeneous brain datasets from the ENIGMA-PGC PTSD Working group. MethodsWe analyzed brain MRI data from 3,527 structural-MRI; 2,502 resting state-fMRI; and 1,953 diffusion-MRI. First, we identified the brain features that best distinguish individuals with PTSD from controls (TEHC and HC) using traditional machine learning methods. Second, we assessed the utility of the denoising variational autoencoder (DVAE) and evaluated its classification performance. Third, we assessed the generalizability and reproducibility of both models using leave-one-site-out cross-validation procedure for each modality. ResultsWe found lower performance in classifying PTSD vs. controls with data from over 20 sites (60% test AUC for s-MRI, 59% for rs-fMRI and 56% for d-MRI), as compared to other studies run on single-site data. The performance increased when classifying PTSD from HC without trauma history across all three modalities (75% AUC). The classification performance remained intact when applying the DVAE framework, which reduced the number of features. Finally, we found that the DVAE framework achieved better generalization to unseen datasets compared with the traditional machine learning frameworks, albeit performance was slightly above chance. ConclusionOur findings highlight the promise offered by machine learning methods for the diagnosis of patients with PTSD. The utility of brain biomarkers across three MRI modalities and the contribution of DVAE models for improving generalizability offers new insights into neural mechanisms involved in PTSD. Significance Classifying PTSD from trauma-unexposed healthy controls (HC) using three imaging modalities performed well ([~]75% AUC), but performance suffered markedly when classifying PTSD from trauma-exposed healthy controls (TEHC) using three imaging modalities ([~]60% AUC). Using deep learning for feature reduction (denoising variational auto-encoder; DVAE) dramatically reduced the number of features with no concomitant performance degradation. Utilizing denoising variational autoencoder (DVAE) models improves generalizability across heterogeneous multi-site data compared with the traditional machine learning frameworks

neuroscience↗