Biology subjects

Sheng, C.

Publications and source records attributed to Sheng, C..

10 recordsLinked to original sources

bioRxiv2025

Protracted fate acquisition and epigenetic de-aging during induced neural stem cell conversion of human blood cells

Transcription factor-based direct conversion of somatic cells represents an interesting avenue for generating induced neural stem cells (iNSCs) from peripheral blood without transit through a pluripotent stage. While this paradigm has been shown to be associated with epigenetic de-aging, the dynamics of this process have remained unclear. Here, we used overexpression of the two reprogramming factors SOX2 and cMYC to generate iNSC from erythroid progenitors of donors ranging from neonatal to 101 years of age. Using an epigenetic clock algorithm, we corroborated our previous finding that iNSCs generated from aged donors show pronounced epigenetic de-aging, preserving around 13 % and 5 % of the original donor age at low and high passages, respectively. Studying the dynamic of epigenetic de-aging during iNSC conversion across time, we found that this process is largely protracted, continuing for several weeks and even beyond forced neuronal differentiation of iNSCs. Transcriptomic differences between young and old donor-derived iNSCs dissipate with extended time in conversion, too. Concordant with this observation, established iNSC lines lack age-associated cellular hallmarks, similar to induced pluripotent stem cells and their derivatives. Interestingly, time course analysis of DNA methylation and RNA sequencing data revealed that acquisition of a bona fide NSC signature extends greatly beyond the time point when proliferative PAX6-positive iNSCs emerge. The unexpected slow dynamics of these processes makes iNSC conversion an attractive model for dissecting the mechanisms underlying somatic transdifferentiation and de-aging. Statement of Ethical ApprovalsThe collection of human somatic material (i.e., blood) from healthy donors for iPSC reprogramming and iNSC conversion was conducted in accordance with German law and approved by the Ethics Committee of the University of Bonn Medical Center (approval number: 275/08). All subjects gave written informed consent.

neuroscience↗

bioRxiv2025

BIN1 deficiency leads to DNA damage and neuronal insulin resistance through ATM dysregulation

The major neuronal isoform of the AD risk gene BIN1 is specifically reduced in patients. In the present work, we demonstrate that BIN1 is necessary for intact insulin signaling and its loss leads to cellular-level insulin resistance. Persistently activated mTORC1 feedback inhibits the insulin signaling; meanwhile, ATM-dependent DNA Damage Response decreases the expression of multiple insulin signaling pathway members. Unexpectedly, nuclear ATM activation is accompanied by autophagic degradation of the cytoplasmic ATM, rendering neurons susceptible to oxidative stress, which predisposes oxidative DNA damage, DNA strand breaks, and ATM-dependent DNA Damage Response. Treating BIN1-deficient mice with rapamycin or liraglutide to improve the insulin response, or with the natural antioxidant alpha-lipoic acid to attenuate oxidative stress, both effectively preserved the spatial cognitive ability. Lastly, we reanalyzed a single-cell transcriptomic dataset from human neurons and identified positive correlations between levels of BIN1 and the insulin signaling, as well as neuronal activity. Together, this work revealed an ATM-centered mechanism that globally damages neuronal health in BIN1-deficient pyramidal neurons, which could be a driving force in the AD disease course.

cell biology↗

bioRxiv2022

Probabilistic modeling of ambient noise in single-cell omics data

Droplet-based single-cell omics, including single-cell RNA sequencing (scRNAseq), single-cell CRISPR perturbations (e.g., CROP-seq), and single-cell protein and transcriptomic profiling (CITE-seq) hold great promise for comprehensive cell profiling and genetic screening at the single-cell resolution. However, these technologies suffer from substantial noise, among which ambient signals present in the cell suspension may be the predominant source. Current models to address this issue are highly technology-specific and relatively scRNAseq-centric. while a universal model to describe the noise across these technologies may reveal this common source, improving the denoising accuracy. To this end, we explicitly examined these unexpected signals in multiple datasets across droplet-based technologies, summarised a predictable pattern, and developed single-cell Ambient Remover (scAR) - a hypothesis-driven machine learning model to predict and remove ambient signals (including mRNA counts, protein counts, and sgRNA counts) at the molecular level. We benchmarked scAR on three technologies - single-cell CRISPR screens, CITE-seq, and scRNAseq along with the state-of-the-art single-technology-specific approaches. scAR showed high denoising accuracy for each type of dataset.

bioinformatics↗

bioRxiv2021

A water-reward task assay for evaluating mouse mutualistic cooperative behavior

Social cooperation is fundamentally important for group animals but rarely studied with mice because of their natural aggressiveness. In the present work, we induced pairs of mice to develop a mutualistic cooperative behavior in a non-divided chamber. Each mouse was first trained to learn to use a water dispenser by occupying a particular zone served as a switch to the dispenser. Two trained mice were then put into a chamber containing two separate zones jointly controlling two dispensers. We recorded the latency before each co-drinking, the number and cumulated time of co-drinking each day during the test. These parameters served as quantitative measurements of cooperative behavior in mice. The whole procedure includes preparation, training and testing phases, which take 15 days in total. This assay provides detailed procedures and analytical methods for investigators to characterize and quantify the mutualistic cooperative behavior. The use of mice as subjects allows convenient coupling to other behavior assays and is amiable to genetic manipulations for mechanistic study.

animal behavior and cognition↗

bioRxiv2020

Pulmonary B cells ameliorate Alzheimer's disease-like neuropathology

Increasing evidence shows that the peripheral immune system is involved in the pathogenesis of Alzheimers disease (AD). Here, we report that pulmonary B cells mitigate beta-Amyloid (A{beta}) pathology in 5xFAD mice. The proportion of B cells rather than T cells increases in brain, meningeal and lung tissues in 3-month-old 5xFAD mice. Deletion of B cells aggravates A{beta} load and memory deficits of 5xFAD mice. Mechanimsly, pulmonary B cells can migrate to the brain parenchyma and produce interleukin-35 that inhibits neuronal {beta}-site APP-cleaving enzyme 1 expression, subsequently reducing the production of A{beta}. In turn, proliferation of pulmonary B cells is associated with activation of toll-like receptor/nuclear factor kappa-B pathway by elevated A{beta} that is drained from the brain parenchyma to the lungs via meningeal lymphatics. Furthermore, promoting pulmonary B cell proliferation via overexpression of B-cell-activating factor ameliorates brain A{beta} load and improves cognitive functions of 10-month-old 5xFAD mice. Together, these results highlight the lungs as both immune targets and effector organs in A{beta} pathogenesis. Pulmonary B cells might be a potential target against AD.

neuroscience↗

bioRxiv2020

Virus-free and live-cell visualizing SARS-CoV-2 cell entry for studies of neutralizing antibodies and compound inhibitors

The ongoing COVID-19 pandemic, caused by SARS-CoV-2 infection, has resulted in hundreds of thousands of deaths. Cellular entry of SARS-CoV-2, which is mediated by the viral spike protein and host ACE2 receptor, is an essential target for the development of vaccines, therapeutic antibodies, and drugs. Using a mammalian cell expression system, we generated a recombinant fluorescent protein (Gamillus)-fused SARS-CoV-2 spike trimer (STG) to probe the viral entry process. In ACE2-expressing cells, we found that the STG probe has excellent performance in the live-cell visualization of receptor binding, cellular uptake, and intracellular trafficking of SARS-CoV-2 under virus-free conditions. The new system allows quantitative analyses of the inhibition potentials and detailed influence of COVID-19-convalescent human plasmas, neutralizing antibodies and compounds, providing a versatile tool for high-throughput screening and phenotypic characterization of SARS-CoV-2 entry inhibitors. This approach may also be adapted to develop a viral entry visualization system for other viruses.

microbiology↗

bioRxiv2020

Population Pharmacokinetics of an Anti-PD-1 Antibody Camrelizumab in Patients with Multiple tumor types and model informed dosing strategy

Objective Camrelizumab, a programmed cell death 1 (PD-1) inhibitor, has been approved for the treatment of relapsed or refractory classical Hodgkin lymphoma. The aim of this study was to perform a population pharmacokinetics (PK) analysis of camrelizumab to quantify the impact of patient characteristics on PK and to investigate the appropriateness of flat dose in the dosing regimen.Methods A total of 3298 camrelizumab concentrations from 133 patients from four studies were analyzed using nonlinear mixed effects modeling. Covariate model building was conducted using stepwise forward addition and backward elimination. Monte Carlo simulation was conducted to compare exposures of 200 mg and 3 mg/kg every 2-week regimens.Results The PK of camrelizumab were adequately described by a two-compartment model with parallel linear and nonlinear clearances. Baseline albumin had significant effects on linear clearance, and weight had effects on inter-compartmental clearance. Moreover, 200 mg and 3 mg/kg regimens provide similar exposure distributions with no advantage to either dosing approach.Conclusion Population PK analysis provided an integrated evaluation of the impact of albumin and weight on the PK of camrelizumab. It also provided evidence that neither the flat-dose nor the weight-based dose regimen was advantageous over the other for most patients with tumors.Competing Interest StatementThis study was sponsored by Jiangsu Hengrui Medicine Co. Ltd. Guang-li Ma, Da Xu and Yu-ya Wang are employees of Jiangsu Hengrui Medicine Co. Ltd.AbbreviationsAICAkaike’s information criterion;AUCarea under the concentration-time curve;AUCsssteady-state area under the concentration-time curve;BSVBetween-subject variability;Ccamrelizumab concentration;C1concentration of central compartment;Caverage,sssteady-state average concentration;CLclearance;CLlinearclearance of linear elimination;Cmax,sssteady-state peak concentration;CLnonlinearclearance of nonlinear elimination;Cmin,sssteady-state trough concentration;CWRESconditional weighted residuals;DVobserved concentration;IPREDindividual predicted concentrations;k0infusion rate;k23elimination rate from central compartment to peripheral compartment;k32elimination rate from peripheral compartment to central compartment;klinearlinear elimination rate;knonlinearnonlinear elimination rate;KmMichaelis–Menten constant;mAbmonoclonal antibody;NONMEMnonlinear mixed effect modeling;PD-1programmed cell death 1 receptor;PKpharmacokinetics;PREDpopulation predicted concentration;Qinter-compartmental clearance;Q2Wevery 2 weeks;Vmmaximum elimination rate;VPCvisual predictive check;V1distribution volume of central compartment;V2distribution volume of peripheral compartment;WBCwhite blood cell.View Full Text

cancer biology↗

bioRxiv2019

Establishment of the trans-resveratrol-induced mouse pulmonary fibrosis model and its comparison with the bleomycin-induced model

Pulmonary fibrosis (PF) is a progressive, fatal disease, and its pathogenic mechanism has not yet been identified. The bleomycin (BLM)-induced animal model has several shortcomings that cannot be overcome. We accidentally found that the continuous oral administration of trans-resveratrol (TR) at levels above the prescribed dose can induce PF within a certain period of time, and this model can be successfully replicated in mice, as indicated by the hydroxyproline (HYP) test and pathological analysis. The TR model requires no anesthesia or surgery and thus causes less damage to mice than the BLM model. The progress of fibrosis in the TR model was slow but progressed steadily compared with the BLM model, and the TR model was more comparable to human PF. Although the pathogenesis is not understood, the TR-induced PF model indicated that there may be a close relationship between PF and tumors and antitumor drugs, which requires further exploration.

pharmacology and toxicology↗

bioRxiv2019

Temporal regulation of nicotinic acetylcholine receptor subunits supports central cholinergic synapse development

Construction and maturation of the postsynaptic apparatus are crucial for synapse and dendrite development. The fundamental mechanisms underlying these processes are most often studied in glutamatergic central synapses in vertebrates. Whether the same principles apply to excitatory cholinergic synapses in the insect central nervous system (CNS) is not known. To address this question, we investigated Drosophila ventral lateral neurons (LNvs) and identified nAchR1 (D1) and nAchR6 (D6) as the main functional nicotinic acetylcholine receptor (nAchR) subunits in these cells. With morphological and calcium imaging studies, we demonstrated their distinct roles in supporting dendrite morphogenesis and synaptic transmission. Furthermore, our analyses revealed a transcriptional upregulation of D1 and downregulation of D6 during larval development, indicating a close association between the temporal regulation of nAchR subunits and synapse maturation. Together, our findings show transcriptional regulation of nAchR composition is a core element of developmental and activity-dependent regulation of central cholinergic synapses.

neuroscience↗

bioRxiv2017

CRootBox: A Structural-Functional Modelling Framework For Root Systems

Background and AimsRoot architecture development determines the sites in soil where roots provide input of carbon and take up water and solutes. However, root architecture is difficult to determine experimentally when grown in opaque soil. Thus, root architectural models have been widely used and been further developed into functional-structural models that simulate the fate of water and solutes in the soil-root system. We present a root architectural model, CRootBox, as a flexible framework to model architecture and its interactions with static and dynamic soil environments.\n\nMethodsCRootBox is a C++ -based root architecture model with Python binding, so that CRootBox can be included via a shared library into any Python code. Output formats include VTP, DGF, RSML and CSV. We further created a database of published root architectural parameters. The capabilities of CRootBox for the unconfined growth of single root systems, as well as the different parameter sets, are highlighted into a freely available web application.\n\nKey resultsWe demonstrate the use of CRootBox for 5 different cases (1) free growth of individual root systems (2) growth of root systems in containers as a way to mimic experimental setups, (3), field scale simulation, (4) root growth as affected by heterogeneous, static soil conditions, and (5) coupling CRootBox with Soil Physics with Python code to dynamically compute water flow in soil, root water uptake, and water flow inside roots.\n\nConclusionsIn conclusion, we present a fast and flexible functional-structural root model which is based on state-of-the-art computational science methods. Its aim is to facilitate modelling of root responses to environmental conditions as well as the impact of root on soil. In the future, we plan to extend this approach to the aboveground part of the plant.

plant biology↗