Biology subjects

Zhou, T.

Publications and source records attributed to Zhou, T..

At least 109 records · Page 6Linked to original sources

bioRxiv2024

Targeting NOTCH2-JAG1 juxtacrine signaling reverses macrophage-mediated tumor resistance to taxol

Taxanes are widely used in chemotherapy, but primary and acquired resistance limit the clinical efficacy. Studies have shown tumor interaction with macrophages in the tumor microenvironment (TME) plays a significant role in taxane resistance, yet therapeutic strategies that directly deplete or repolarize macrophages are challenging and with considerable risk of side effects. Here we uncovered that tumor-macrophage interaction can be selectively targeted by inhibiting post-mitotic NOTCH2-JAG1 juxtacrine signaling in the TME, which strongly sensitizes paclitaxel response. Using translatome profiling, we found significant NOTCH2 upregulation during paclitaxel-induced prolonged mitosis. NOTCH2 was subsequently activated in the post-mitotic G1 phase by JAG1 expressed on the neighboring macrophages and tumor cells, which promoted tumor cell survival and upregulated cytokines that recruited JAG1-expressing macrophages, thus generating a positive feedback loop that further enhanced the pro-tumor NOTCH2 activity. By targeting this NOTCH2-JAG1 axis using NOTCH2 shRNA or a pan-NOTCH inhibitor, macrophage recruitment and paclitaxel resistance were significantly attenuated in multiple mouse tumor models of ovarian cancer. Clinical samples from paired primary and recurrent ovarian cancer patients also showed significant correlation of higher NOTCH2 expression with worse prognosis. Our results thus point to combining NOTCH2 inhibitor with taxane as an effective therapeutic strategy to selectively disrupt tumor-macrophage interaction in the TME and overcome macrophage-mediated taxane resistance in NOTCH2-positive tumors.

cancer biology↗

bioRxiv2024

Brain virtual histology of a lizard species (Podarcis bocagei) using X-ray micro-tomography and deep-learning segmentation

Lately, there has been an emphasis on the importance of studying inter-individual variation in animal behaviour and cognition and understanding its underlying mechanisms. What was once considered mere noise around population mean can be explained by individual characteristics such as brain morphology and functionality. However, logistical limitations can be faced when studying the brain, especially for research involving wild animals, such as dealing with small sample sizes and time-consuming methods. Here, we combined an efficient and accurate method using X-ray micro-tomography and deep-learning (DL) segmentation to estimate the volume of six main brain areas of wild lizards, Podarcis bocagei: olfactory bulbs, telencephalon, diencephalon, midbrain, cerebellum and brain stem. Through quantitative comparison, we show that a sufficient deep-learning neural network can be trained with as few as five data sets. From this, we applied the trained deep-learning algorithm to obtain volume data of the six brain regions from 29 brains of Podarcis bocagei. We provide a detailed protocol for our methods, including sample preparation, X-ray tomography, and 3D volumetric segmentation. Our work is open-access and freely available, with the potential to benefit researchers in various fields, such as animal physiology, biomedical studies, and computer sciences.

zoology↗

bioRxiv2024

GeneLLM: A Large cfRNA Language Model for Cancer Screening from Raw Reads

We present GeneLLM, a novel large language model that offers a transformative approach to non-invasive cancer detection and biomarker discovery by directly interpreting plasma cell-free RNA (cfRNA) sequences. Unlike traditional annotation-dependent methods, GeneLLM operates without prior knowledge, achieving significantly improved multi-cancer detection accuracy. Critically, GeneLLM identifies novel cfRNAs ( pseudo-biomarkers) originating from previously unannotated genomic regions-overlooked by existing methods-offering new therapeutic targets and insights into intercellular communication. This innovative, cost-effective approach bypasses traditional bioinformatics tools, generating novel pseudo-biomarkers that outperform existing methods even with low-depth sequencing data. Consequently, GeneLLM opens new avenues for biomarker discovery and expands our understanding of the extracellular transcriptomes role in cancer development.

bioinformatics↗

bioRxiv2024

Genome-wide association study for age-related hearing loss in CFW mice

Age-related hearing impairment is the most common cause of hearing loss and is one of the most prevalent conditions affecting the elderly globally. It is influenced by a combination of environmental and genetic factors. The mouse and human inner ears are functionally and genetically homologous. Investigating the genetic basis of age-related hearing loss (ARHL) in an outbred mouse model may lead to a better understanding of the molecular mechanisms of this condition. We used Carworth Farms White (CFW) outbred mice, because they are genetically diverse and exhibit variation in the onset and severity of ARHL. The goal of this study was to identify genetic loci involved in regulating ARHL. Hearing at a range of frequencies was measured using Auditory Brainstem Response (ABR) thresholds in 946 male and female CFW mice at the age of 1, 6, and 10 months. We obtained genotypes at 4.18 million single nucleotide polymorphisms (SNP) using low-coverage (mean coverage 0.27x) whole-genome sequencing followed by imputation using STITCH. To determine the accuracy of the genotypes we sequenced 8 samples at >30x coverage and used calls from those samples to estimate the discordance rate, which was 0.45%. We performed genetic analysis for the ABR thresholds for each frequency at each age, and for the time of onset of deafness for each frequency. The SNP heritability ranged from 0 to 42% for different traits. Genome-wide association analysis identified several regions associated with ARHL that contained potential candidate genes, including Dnah11, Rapgef5, Cpne4, Prkag2, and Nek11. We confirmed, using functional study, that Prkag2 deficiency causes age-related hearing loss at high frequency in mice; this makes Prkag2 a candidate gene for further studies. This work helps to identify genetic risk factors for ARHL and to define novel therapeutic targets for the treatment and prevention of ARHL.

genetics↗

bioRxiv2024

Determinants of de novo mutations in extended pedigrees of 43 dog breeds

Intensive breeding of dogs has had dramatic effects on genetic variants underlying phenotypes. To investigate whether this also affected mutation rates, we deep-sequenced pedigrees from 43 different dog breeds representing 404 trios. We find that the mutation rate is remarkably stable across breeds and is predominantly influenced by variation in parental ages. The effect of paternal age per year on mutation rates is approximately 1.5 times greater in dogs than humans, suggesting that the elevated yearly mutation rate in dogs is only partially attributed to earlier reproduction. While there is no significant effect of breeds on the overall mutation rate, larger breeds accumulate proportionally more mutations earlier in development than small breeds. Interestingly, we find a 2.6 times greater mutation rate in CG Islands (CGIs) compared to the remaining genome in dogs, unlike humans, where there is no difference. Our estimated rate of mutation by recombination in dogs is more than 10 times larger than estimates in humans. We ascribe these to the fact that canids have lost PRDM9-directed recombination and draw away recombination from CGIs. In conclusion, our study sheds light on stability of mutation processes and disparities in mutation accumulation rates reflecting the influence of differences in growth patterns among breeds, and the impact of PRDM9 gene loss on the de novo mutations of canids.

evolutionary biology↗

bioRxiv2024

The novel role of Kallistatin in linking metabolic syndromes and cognitive memory deterioration by inducing amyloid-β plaques accumulation and tau protein hyperphosphorylation

Accumulation of amyloid {beta} (A{beta}) peptides and hyperphosphorylated tau proteins in the hippocampus triggers cognitive memory decline in Alzheimers disease (AD). The incidence and mortality of sporadic AD were tightly associated with diabetes and hyperlipidemia, while the exact linked molecular is uncertain. Here, we reported that serum Kallistatin concentrations were meaningfully higher in AD patients, with a higher concentration of fasting blood glucose and triglyceride. In addition, the constructed Kallistatin-transgenic (KAL-TG) mice defined its cognitive memory impairment phenotype and lower LTP in hippocampal CA1 neurons accompanied by increased A{beta} deposition and tau phosphorylation. Mechanistically, Kallistatin could directly bind to the Notch1 receptor and thereby upregulate BACE1 expression by inhibiting PPAR{gamma} signaling, resulting in A{beta} cleavage and production. Besides, Kallistatin could promote the phosphorylation of tau by activating GSK-3{beta}. Fenofibrate, a hypolipidemic drug, could alleviate cognitive memory impairment by down-regulating A{beta} and tau phosphorylation of KAL-TG mice. Collectively, our data clarified a novel mechanism for A{beta} accumulation and tau protein hyperphosphorylation regulation by Kallistatin, which might play a crucial role in linking metabolic syndromes and cognitive memory deterioration, and suggested that fenofibrate might have the potential for treating metabolism-related AD. HighlightsO_LIKallistatin-transgenic (KAL-TG) mice defined its cognitive memory impairment phenotype accompanied by increased A{beta} deposition and tau phosphorylation. C_LIO_LIKallistatin could directly bind to the Notch1 receptor and thereby upregulate BACE1 expression by inhibiting PPAR{gamma} signaling. C_LIO_LIFenofibrate could alleviate cognitive memory impairment and down-regulate the serum Kallistatin level. C_LI

neuroscience↗

bioRxiv2024

Spatiotemporal transcriptomic profiling reveals the dynamic immunological landscape of alveolar echinococcosis

Alveolar echinococcosis (AE) is caused by the invasive growth of the metacestodes of Echinococcus multilocularis (E. multilocularis). The early diagnosis, management, and treatment of AE remains challenging. Herein, we integrated bulk RNA-seq, scRNA-seq, and ST technologies to reveal the immune characteristics both spatially and chronologically in E. multilocularis infected mouse liver. An unprecedented high-resolution spatial atlas of the E. multilocularis infection foci was obtained, revealing the pivotal role of neutrophils, Spp1+ monocyte-derived macrophages (MoMFs), and fibroblasts in AE progression. We observed continuous recruitment of neutrophils and macrophages into the infected tissues, indicating prolonged immune stimulation by the growing metacestodes. However, their spatial distribution patterns and functions changed during the infection cause. At the early infection stage, Il1bhi neutrophils aggregated in the lesion displayed the highest pattern-recognition receptor activity and may kill the metacestodes through NETosis, but their death in the infection foci might also trigger immune suppression. Meanwhile, Spp1+ MoMFs attached to the protoscoleces to clear the infection. At the late infection stage, the neutrophils failed to infiltrate into the lesion although their continuous recruitment into the infected liver. Even though the Spp1+ MoMFs enclosing the microcysts of E. multilocularis may retain their pathogen-killing ability, they may also promote fibrosis and angiogenesis through interaction with fibroblasts. The pro- and anti-inflammatory phenotype balance of these immune cells may be associated with the transition of parasite control strategy from "active killing" to "negative segregation" by the host. Our findings identify key molecular traits involved in AE development, which may benefit the treatment of echinococcosis.

immunology↗

bioRxiv2024

Rapid High-Throughput Isolation and purification of Chicken Myoblasts Based on Deterministic Lateral Displacement Microfluidic Chips

Myoblasts are defined as stem cells containing skeletal muscle cell precursors. However, there are some challenges associated with the purification of myoblast samples, including long culture times and ease of bacterial contamination. In this study, we propose a microfluidic myoblast cell enrichment and purification platform based on the principle of deterministic lateral displacement (DLD). To achieve this, we designed a DLD chip with three outlets and tested it on 11-day-old Wenchang chicken pectoral muscle tissue. A cell suspension was prepared using the collagenase method, pretreated, and then passed into the designed DLD chip for myoblast enrichment and purification. In this study, the number of myoblasts and the diameter of myoblasts increased slowly before E9, and the diameter of myofibers decreased and the number of myofibers increased rapidly after E9. The period when the number of muscle fibers is highest is E12, and the period when the diameter of muscle fibers increases again after the lowest point is also E12. After E12, the diameter of the muscle fibers increased and the number of muscle fibers decreased. At E12, myoblasts clustered and fused, and the proliferation of myoblasts was greatly reduced. E12 is both intact myoblasts and the most vigorous proliferation period, so the best time to determine isolation is E12. We attained a myoblast cell recovery rate of 80%, a target outlet collection purity of 99%, and a chip throughput of 50 m/min. This study provides a novel and effective method for the isolation and purification of skeletal muscle myoblasts.

cell biology↗

bioRxiv2024

Human iPSC-derived Committed Cardiac Progenitors Generate Cardiac Tissue Grafts in a Swine Ischemic Cardiomyopathy Model without Triggering Ventricular Arrhythmias

BackgroundIntramyocardial injection of human pluripotent stem cell-derived cardiomyocytes following a myocardial infarction (MI) improves cardiac function in large animal models, but associated ventricular arrhythmias are major safety concern. We hypothesized that transendocardial injection of human induced pluripotent stem cell (hiPSC)-derived committed cardiac progenitor cells (CCPs), combined with cardiac fibroblast-derived extracellular matrix (cECM) to enhance cell retention, will generate cardiac tissue grafts improving contractility without triggering ventricular arrhythmias. MethodshiPSCs were differentiated using bioreactors and small molecules to produce committed cardiac progenitor cells (CCPs). MI was created using a coronary artery balloon occlusion and reperfusion model in Yucatan mini pigs. Four weeks later, epicardial needle injections of CCPs+cECM were performed in a small initial feasibility cohort (n=6), and then transendocardial injections of CCPs+cECM (n=14), CCPs alone (n=14), cECM alone (n=4) or vehicle control (n=13) into the peri-infarct region in a randomized cohort. Arrhythmias were evaluated using implanted event recorders. Magnetic resonance imaging (MRI) and invasive pressure-volume assessment were used to evaluate left ventricular anatomic and functional performance. Detailed histology was performed to detect and characterize human grafts. ResultsA scalable biomanufacturing protocol was developed generating CCPs which can efficiently differentiate into cardiomyocytes or endothelial cells in vitro. Intramyocardial delivery of CCPs to post-MI porcine hearts resulted in engraftment and differentiation of CCPs to form ventricular cardiomyocyte rich grafts. There was no significant difference in cardiac MRI-based measured cardiac volumes or function between control, CCP and CCP+cECM groups; however, pressure-volume analysis showed an improvement in dobutamine-stimulated functional reserve in CCP and CCP+cECM groups. Delivery of CCPs did not result in tumors or ventricular arrhythmias. ConclusionsTransendocardial delivery of CCPs with or without cECM into post-MI porcine hearts resulted in comparable human cardiomyocyte grafts which did not improve resting LV function but did improve stress-induced contractile reserve without triggering ventricular arrhythmias.

pathology↗

bioRxiv2024

A microglia clonal inflammatory disorder in Alzheimer's Disease

Somatic genetic heterogeneity resulting from post-zygotic DNA mutations is widespread in human tissues and can cause diseases, however few studies have investigated its role in neurodegenerative processes such as Alzheimers Disease (AD). Here we report the selective enrichment of microglia clones carrying pathogenic variants, that are not present in neuronal, glia/stromal cells, or blood, from patients with AD in comparison to age-matched controls. Notably, microglia-specific AD-associated variants preferentially target the MAPK pathway, including recurrent CBL ring-domain mutations. These variants activate ERK and drive a microglia transcriptional program characterized by a strong neuro-inflammatory response, both in vitro and in patients. Although the natural history of AD-associated microglial clones is difficult to establish in human, microglial expression of a MAPK pathway activating variant was previously shown to cause neurodegeneration in mice, suggesting that AD-associated neuroinflammatory microglial clones may contribute to the neurodegenerative process in patients. One-Sentence SummaryA subset of Alzheimer Disease patients carry mutant microglia somatic clones which promote neuro-inflammation.

neuroscience↗

bioRxiv2024

A robust and inducible precise genome editing via an all-in-one prime editor in human pluripotent stem cells

Prime editing (PE) allows for precise genome editing in human pluripotent stem cells (hPSCs), such as introducing single nucleotide modifications, small deletions, or insertions at a specific genomic locus, a strategy that shows great promise for creating "Disease in a dish" models. To improve the effectiveness of prime editing in hPSCs, we systematically compared and combined the "inhibition of mismatch repair pathway and p53" on top of the "PEmax" to generate an all-in-one "PE-Plus" prime editor. We show that PE-Plus conducts the most efficient editing among the current PE tools in hPSCs. We further established an inducible prime editing platform in hPSCs by incorporating the all-in-one PE vector into a safe-harbor locus and demonstrated temporal control of precise editing in both hPSCs and differentiated cells. By evaluating disease-associated mutations, we show that this platform allows efficient creation of both monoallelic and biallelic disease-relevant mutations in hPSCs. In addition, this platform enables the efficient introduction of single or multiple edits in one step, demonstrating potential for multiplex editing. Therefore, our method presents an efficient and controllable multiplex prime editing tool in hPSCs and their differentiated progeny.

cell biology↗

bioRxiv2024

The asymmetric transfers of visual perceptual learning determined by the stability of geometrical invariants

We quickly and accurately recognize the dynamic world by extracting invariances from highly variable scenes, a process can be continuously optimized through visual perceptual learning (VPL). While it is widely accepted that the visual system prioritizes the perception of more stable invariants, the influence of the structural stability of invariants on VPL remains largely unknown. In this study, we designed three geometrical invariants with varying levels of stability for VPL: projective (e.g., collinearity), affine (e.g., parallelism), and Euclidean (e.g., orientation) invariants, following the Kleins Erlangen program. We found that learning to discriminate low-stability invariant transferred asymmetrically to those with higher stability, and that training on high-stability invariants enabled location transfer. To explore learning-associated plasticity in the visual hierarchy, we trained deep neural networks (DNNs) to model this learning procedure. We reproduced the asymmetric transfer between different invariants in DNN simulations and found that the distribution and time course of plasticity in DNNs suggested a neural mechanism similar to the reverse hierarchical theory (RHT), yet distinct in that invariant stability--not task difficulty or precision--emerged as the key determinant of learning and generalization. We propose that VPL for different invariants follows the Klein hierarchy of geometries, beginning with the extraction of high-stability invariants in higher-level visual areas, then recruiting lower-level areas for the further optimization needed to discriminate less stable invariants.

neuroscience↗

bioRxiv2024

Histone acetyltransferase HAF2 associates with PDC to control H3K14ac and H3K23ac in ethylene response

Ethylene plays its essential roles in plant development, growth, and defense responses by controlling the transcriptional reprogramming, in which EIN2-C-directed regulation of histone acetylation is the first key-step for chromatin to perceive ethylene signaling. However, the histone acetyltransferase in this process remains unknown. Here, we identified histone acetyltransferase HAF2, and mutations in HAF2 confer plants with ethylene insensitivity. Furthermore, we found that HAF2 interacts with EIN2-C in response to ethylene. Biochemical assays demonstrated that the bromodomain of HAF2 binds to H3K14ac and H3K23ac peptides with a distinct affinity for H3K14ac; the HAT domain possesses acetyltransferase catalytic activity for H3K14 and H3K23 acetylation, with a preference for H3K14. ChIP-seq results provide additional evidence supporting the role of HAF2 in regulating H3K14ac and H3K23ac levels in response to ethylene. Finally, our findings revealed that HAF2 co-functions with pyruvate dehydrogenase complex (PDC) to regulate H3K14ac and H3K23ac in response to ethylene in an EIN2 dependent manner. Overall, this research reveals that HAF2 as a histone acetyltransferase that forms a complex with EIN2-C and PDC, collectively governing histone acetylation of H3H14ac and H3K23ac, preferentially for H3K14 in response to ethylene.

plant biology↗

bioRxiv2023

Analytical distribution of nascent RNA in a queuing model with applications

Transcription is a stochastic process that involves several downstream operations, which make it difficult to model and infer transcription kinetics from mature RNA numbers in individual cell. However, recent advances in single-cell technologies have enabled a more precise measurement of the fluctuations of nascent RNA that closely reflect transcription kinetics. In this paper, we introduce a general stochastic model to mimic nascent RNA kinetics with complex promoter architecture. We derive the exact distribution and moments of nascent RNA using queuing theory techniques, which provide valuable insights into the effect of the molecular memory created by the multistep activation and deactivation on the stochastic kinetics of nascent RNA. Moreover, based on the analytical results, we develop a statistical method to infer the promoter memory from stationary nascent RNA distributions. Data analysis of synthetic data and a realistic example, the HIV-1 gene, verifies the validity of this inference method.

biophysics↗

bioRxiv2023

COL: a pipeline for identifying putatively functional back-splicing

Circular RNAs (circRNAs) are a class of generally non-coding RNAs produced by back- splicing. Although the vast majority of circRNAs are likely to be products of splicing error and thereby confer no benefits to organisms, a small number of circRNAs have been found to be functional. Identifying other functional circRNAs from the sea of mostly non-functional circRNAs is an important but difficult task. Because available experimental methods for this purpose are of low throughput or versality and existing computational methods have limited reliability or applicability, new methods are needed. We hypothesize that functional back- splicing events that generate functional circRNAs (i) exhibit substantially higher back-splicing rates than expected from the total splicing amounts, (ii) have conserved splicing motifs, and (iii) show unusually high back-splicing levels. We confirm these features in back-splicing shared among human, macaque, and mouse, which should enrich functional back-splicing. Integrating the three features, we design a computational pipeline named COL for identifying putatively functional back-splicing. Different from the methods that require multiple samples, COL can predict functional back-splicing using a single sample. Under the same data requirement, COL has a lower false positive rate than that of the commonly used method that is based on the back- splicing level alone. We conclude that COL is an efficient and versatile method for rapid identification of putatively functional back-splicing and circRNAs that can be experimentally validated. COL is available at https://github.com/XuLabSJTU/COL.

genomics↗

bioRxiv2023

Plasma membrane abundance dictates phagocytic capacity and functional crosstalk in myeloid cells

Professional phagocytes like neutrophils and macrophages tightly control what they eat, how much they eat, and when they move after eating. We show that plasma membrane abundance is a key arbiter of these cellular behaviors. Neutrophils and macrophages lacking the G-protein subunit G{beta}4 exhibit profound plasma membrane expansion due to enhanced production of sphingolipids. This increased membrane allocation dramatically enhances phagocytosis of bacteria, fungus, apoptotic corpses, and cancer cells. G{beta}4 deficient neutrophils are also defective in the normal inhibition of migration following cargo uptake. In G{beta}4 knockout mice, myeloid cells exhibit enhanced phagocytosis of inhaled fungal conidia in the lung but also increased trafficking of engulfed pathogens to other organs. These results reveal an unexpected, biophysical control mechanism lying at the heart of myeloid functional decision-making.

cell biology↗

bioRxiv2023

A key role of pectin demethylation-mediated cell wall Na+ retention in regulating differential salt stress resistance in allotetraploid rapeseed genotypes

Allotetraploid rapeseed (Brassica napus L.) is highly susceptible to salt stress, a worldwide limiting factor that causes severe losses in seed yield. Genetic variations in the resistance against salt stress found in rapeseed genotypes emphasizes the complex response architecture. Westar is ubiquitously used as a major transgenic receptor, and ZS11 is widely grown as a high production and good quality cultivar. In this study, Westar was identified to outperform than ZS11 under salt stress. Through cell component isolation, non-invasive micro-test, X-ray energy spectrum analysis, and ionomic profiling characterization, pectin demethylation was found to be a major regulator for differential salt resistance between Westar and ZS11. Integrated analyses of genome-wide DNA variations, differentially expression profiling, and gene co-expression network identified BnaC9.PME47, encoding pectin methyl esterase, as a positive regulator mainly responsible for salt stress resistance. BnaC9.PME47, located in two reported QTLs regions for salt resistance, was strongly induced by salt stress and localized on the cell wall. Natural variation of the promoter regions conferred higher expression of BnaC9.PME47 in Westar than in other salt-sensitive rapeseed genotypes. Loss-of-function of AtPME47 resulted in the hypersensitivity of Arabidopsis plants to salt stress. This study facilitates a more comprehensive understanding of the differential morpho-physiological and molecular responses to salt stress and abundant genetic diversity in rapeseed genotypes, and the integrated multiomics analyses provide novel insights regarding the rapid dissection of quantitative trait genes responsible for nutrient stresses in plant species with complex genomes.

plant biology↗

bioRxiv2023

High-throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF

The extracellular matrix (ECM) is a complex assembly of proteins that provide interstitial scaffolding and elastic recoil to human lungs. The pulmonary extracellular matrix (ECM) is increasingly recognized as an independent bioactive entity by creating biochemical and mechanical signals that influence disease pathogenesis, making it an attractive therapeutic target. However, the pulmonary ECM proteome ("matrisome") remains challenging to analyze by mass spectrometry due to its inherent biophysical properties and relatively low abundance. Here, we introduce a strategy designed for rapid and efficient characterization of the human pulmonary ECM using the photocleavable surfactant Azo. We coupled this approach with trapped ion mobility MS with diaPASEF to maximize depth of matrisome coverage. Using this strategy, we identify nearly 400 unique matrisome proteins with excellent reproducibility that are known to be important in lung biology, including key insoluble ECM proteins.

systems biology↗