Biology subjects

Zeng, H.

Publications and source records attributed to Zeng, H..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Imaging high-frequency voltage dynamics in multiple neuron classes of behaving mammals

Fluorescent genetically encoded voltage indicators report transmembrane potentials of targeted cell-types. However, voltage-imaging instrumentation has lacked the sensitivity to track spontaneous or evoked high-frequency voltage oscillations in neural populations. Here we describe two complementary TEMPO voltage-sensing technologies that capture neural oscillations up to [~]100 Hz. Fiber-optic TEMPO achieves [~]10-fold greater sensitivity than prior photometry systems, allows hour-long recordings, and monitors two neuron-classes per fiber-optic probe in freely moving mice. With it, we uncovered cross-frequency-coupled theta- and gamma-range oscillations and characterized excitatory-inhibitory neural dynamics during hippocampal ripples and visual cortical processing. The TEMPO mesoscope images voltage activity in two cell-classes across a [~]8-mm-wide field-of-view in head-fixed animals. In awake mice, it revealed sensory-evoked excitatory-inhibitory neural interactions and traveling gamma and 3-7 Hz waves in the visual cortex, and previously unreported propagation directions for hippocampal theta and beta waves. These technologies have widespread applications probing diverse oscillations and neuron-type interactions in healthy and diseased brains.

neuroscience↗

bioRxiv2024

Targeting mechanistic target of rapamycin complex 2 attenuates immunopathology in Systemic Lupus Erythematosus

ObjectiveWe aim to explore the role of mechanistic target of rapamycin complex (mTORC) 2 in systemic lupus erythematosus (SLE) development, the in vivo regulation of mTORC2 by type I interferon (IFN) signaling in autoimmunity, and to use mTORC2 targeting therapy to ameliorate lupus-like symptoms in an in vivo lupus mouse model and an in vitro coculture model using human PBMCs. MethodWe first induced lupus-like disease in T cell specific Rictor, a key component of mTORC2, deficient mice by topical application of imiquimod (IMQ) and monitored disease development. Next, we investigated the changes of mTORC2 signaling and immunological phenotypes in type I IFNAR deficient Lpr mice. We then tested the beneficial effects of anti-Rictor antisense oligonucleotide (Rictor-ASO) in a mouse model of lupus: MRL/lpr mice. Finally, we examined the beneficial effects of RICTOR-ASO on SLE patients PBMCs using an in vitro T-B cell coculture assay. ResultsT cell specific Rictor deficient mice have reduced age-associated B cells, plasma cells and germinal center B cells, and less autoantibody production than WT mice following IMQ treatment. IFNAR1 deficient Lpr mice have reduced mTORC2 activity in CD4+ T cells accompanied by restored CD4+ T cell glucose metabolism, partially recovered T cell trafficking, and reduced systemic inflammation. In vivo Rictor-ASO treatment improves renal function and pathology in MRL/lpr mice, along with improved immunopathology. In human SLE (N = 5) PBMCs derived T-B coculture assay, RICTOR-ASO significantly reduce immunoglobulin and autoantibodies production (P < 0.05). ConclusionTargeting mTORC2 could be a promising therapeutic for SLE.

immunology↗

bioRxiv2024

Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque

Experimental access to cell types within the mammalian spinal cord is severely limited by the availability of genetic tools. To enable access to lower motor neurons (LMNs) and LMN subtypes, we generated single cell multiome datasets from mouse and macaque spinal cords and discovered putative enhancers for each neuronal population. We cloned these enhancers into adeno-associated viral vectors (AAVs) driving a reporter fluorophore and functionally screened them in mouse. We extensively characterized the most promising candidate enhancers in rat and macaque and developed an optimized pan LMN enhancer virus. Additionally, we generated derivative viruses expressing iCre297T recombinase or ChR2-EYFP for labeling and functional studies, and we created a single vector with combined enhancer elements to achieve simultaneous labeling of layer 5 extratelencephalic projecting (ET) neurons and LMNs. This unprecedented LMN toolkit will enable future investigations of cell type function across species and potential therapeutic interventions for human neurodegenerative diseases.

neuroscience↗

bioRxiv2024

Efficient generation of CAR NK cells from human umbilical cord blood CD34+ stem and progenitors for democratizing affordable immunotherapy

Chimeric antigen receptor (CAR) natural killer cells (CAR NK) cells, leveraging safety and not requiring HLA match in adoptive infusion, have emerged as promising alternative cells to CAR-T cells for immunotherapies. High and multiple doses of CAR NK cell infusions are essential to maintain therapeutic efficacy in clinical trials. This requires efficient methods for generating large-scale CAR NK cells and significantly reducing CAR engineering costs. In this study, we develop a three-step strategy to generate highly high yields of induced NK (iNK) and CAR iNK cells from human umbilical cord blood CD34+ hematopoietic stem and progenitor cells (CD34+ HSPCs). Starting from a single umbilical cord blood CD34+ HSPC, our reliable method efficiently produces 14-83 million mature iNK cells or 7-32 million CAR iNK cells with high expression levels of CD16 and zero T cell contaminations. Introducing CAR expression elements at the HSPC level reduces the quantities of CAR pseudoviruses to 1 / 140.000 - 1 / 600,000 compared to engineering CARs in mature NK cells. The iNK and CAR iNK cells, including fresh cells and thawed cells from cryopreserved conditions, demonstrate remarkable tumoricidal activities against various human cancer cells and significantly prolong the survival of human tumor-bearing animals. The high yields of CAR NK cells and negligible costs of CAR engineering of our method support the broad applications of CAR NK cells for treating cancer patients.

cell biology↗

bioRxiv2024

NSP4 mutation T492I drives rapid evolution of SARS-CoV-2 toward Omicron

T492I, a mutation encountered in SARS-CoV-2 nonstructural protein 4 (NSP4), enhances viral replication and alters nonstructural protein cleavage, causing potential evolutionary impacts. Through comprehensive comparative analyses based on evolve-and-resequence experiments of SARS-CoV-2 wild-type and Delta strains with or without T492I, we demonstrate that NSP4 T492I not only increases the mutation rate, but also accelerates the emergence of many mutations characteristic for Omicron variants. Accordingly, viral populations that evolved from ancestors with T492I, show Omicron-biased selective forces and increases in viral replication, infectivity, immune evasion capacity, potentials for cross-species transmission and receptor-binding affinity. Aside from enhanced replication, we observed stronger epistasis regarding viral replication and infectivity in T492I than in S N501Y and NSP6 {Delta}SGF; this facilitates the regulation of mutation types, which can drive fast evolution of Omicron specific mutations. Our results highlight the role of an important replication-enhancing mutation in regulating the evolutionary rates and mutational trends of SARS-CoV-2.

evolutionary biology↗

bioRxiv2024

Neocortical long-range inhibition promotes cortical synchrony and sleep

Sleep and wakefulness are associated with distinct cortical patterns of rhythmic activity. During low-arousal states such as slow wave sleep, synchronous low-frequency rhythms dominate activity across widespread cortical regions. Although inhibitory neurons are increasingly recognized as key players of cortical state, the in vivo circuit mechanisms coordinating synchronized activity across local and distant neocortical networks remain poorly understood. Here, we show that somatostatin and chondrolectin co-expressing cells (Sst-Chodl), a sparse and genetically distinct class of neocortical GABAergic inhibitory neurons, are selectively active during low-arousal states and largely silent during periods of high arousal. In contrast to most neocortical inhibitory neurons, Sst-Chodl cells, despite being extremely sparse, exert widespread influence across the neocortex via long-range axons that simultaneously target multiple regions. Selective activation of Sst-Chodl cells is sufficient to promote multi-region cortical synchronization characteristic of low-arousal states and to induce sleep. Together, these findings show that long-range Sst-Chodl inhibitory neurons not only track behavioral state but can actively promote sleep-like cortical activity and sleep behavior, highlighting an important contribution of cortical circuits to sleep regulation alongside established subcortical mechanisms.

neuroscience↗

bioRxiv2024

The transcriptomic and spatial organization of telencephalic GABAergic neuronal types

The telencephalon of the mammalian brain comprises multiple regions and circuit pathways that play adaptive and integrative roles in a variety of brain functions. There is a wide array of GABAergic neurons in the telencephalon; they play a multitude of circuit functions, and dysfunction of these neurons has been implicated in diverse brain disorders. In this study, we conducted a systematic and in-depth analysis of the transcriptomic and spatial organization of GABAergic neuronal types in all regions of the mouse telencephalon and their developmental origins. This was accomplished by utilizing 611,423 single-cell transcriptomes from the comprehensive and high-resolution transcriptomic and spatial cell type atlas for the adult whole mouse brain we have generated, supplemented with an additional single-cell RNA-sequencing dataset containing 99,438 high-quality single-cell transcriptomes collected from the pre- and postnatal developing mouse brain. We present a hierarchically organized adult telencephalic GABAergic neuronal cell type taxonomy of 7 classes, 52 subclasses, 284 supertypes, and 1,051 clusters, as well as a corresponding developmental taxonomy of 450 clusters across different ages. Detailed charting efforts reveal extraordinary complexity where relationships among cell types reflect both spatial locations and developmental origins. Transcriptomically and developmentally related cell types can often be found in distant and diverse brain regions indicating that long-distance migration and dispersion is a common characteristic of nearly all classes of telencephalic GABAergic neurons. Additionally, we find various spatial dimensions of both discrete and continuous variations among related cell types that are correlated with gene expression gradients. Lastly, we find that cortical, striatal and some pallidal GABAergic neurons undergo extensive postnatal diversification, whereas septal and most pallidal GABAergic neuronal types emerge simultaneously during the embryonic stage with limited postnatal diversification. Overall, the telencephalic GABAergic cell type taxonomy can serve as a foundational reference for molecular, structural and functional studies of cell types and circuits by the entire community.

neuroscience↗

bioRxiv2024

Receptor tyrosine kinase inhibition leads to regression of acral melanoma by targeting the tumor microenvironment

Acral melanoma (AM) is an aggressive melanoma variant that arises from palmar, plantar, and nail unit melanocytes. Compared to non-acral cutaneous melanoma (CM), AM is biologically distinct, has an equal incidence across genetic ancestries, typically presents in advanced stage disease, is less responsive to therapy, and has an overall worse prognosis. Independent analysis of published genomic and transcriptomic sequencing identified that receptor tyrosine kinase (RTK) ligands and adapter proteins are frequently amplified, translocated, and/or overexpressed in AM. To target these unique genetic changes, a zebrafish acral melanoma model was exposed to a panel of narrow and broad spectrum multi-RTK inhibitors, revealing that dual FGFR/VEGFR inhibitors decrease acral-analogous melanocyte proliferation and migration. The potent pan-FGFR/VEGFR inhibitor, Lenvatinib, uniformly induces tumor regression in AM patient-derived xenograft (PDX) tumors but only slows tumor growth in CM models. Unlike other multi-RTK inhibitors, Lenvatinib is not directly cytotoxic to dissociated AM PDX tumor cells and instead disrupts tumor architecture and vascular networks. Considering the great difficulty in establishing AM cell culture lines, these findings suggest that AM may be more sensitive to microenvironment perturbations than CM. In conclusion, dual FGFR/VEGFR inhibition may be a viable therapeutic strategy that targets the unique biology of AM.

cancer biology↗

bioRxiv2024

Neurogliaform Cells Exhibit Laminar-specific Responses in the Visual Cortex and Modulate Behavioral State-dependent Cortical Activity

Neurogliaform cells are a distinct type of GABAergic cortical interneurons known for their "volume transmission" output property. However, their activity and function within cortical circuits remain unclear. Here, we developed two genetic tools to target these neurons and examine their function in the primary visual cortex. We found that the spontaneous activity of neurogliaform cells positively correlated with locomotion. Silencing these neurons increased spontaneous activity during locomotion and impaired visual responses in L2/3 pyramidal neurons. Furthermore, the contrast-dependent visual response of neurogliaform cells varies with their laminar location and is constrained by their morphology and input connectivity. These findings demonstrate the importance of neurogliaform cells in regulating cortical behavioral state-dependent spontaneous activity and indicate that their functional engagement during visual stimuli is influenced by their laminar positioning and connectivity.

neuroscience↗

bioRxiv2024

Trajectory-centric Framework TrajAtlas reveals multi-scale differentiation heterogeneity among cells, genes, and gene module in osteogenesis

Osteoblast differentiation is crucial for bone formation and maintaining skeletal integrity. Although it is now understood that this process exhibits significant heterogeneity across developmental stages and tissue microenvironments, the underlying mechanisms remain largely unexplored. In the present study, we introduce TrajAtlas, a comprehensive framework that addresses this gap in knowledge. TrajAtlas comprises four modules: a reference atlas (Differentiation Atlas), a differentiation model (Differentiation Model), a tool for differential pseudotime analysis (TrajDiff), and a method for pseudotemporal gene module detection (TRAVMap). By leveraging single-cell technologies, TrajAtlas offers a systematic approach to exploring the multi-scale heterogeneity among cells, genes, and gene modules within population-level trajectories across diverse tissues and age groups. We systematically investigate the impact of age and injury on osteogenesis, providing new insights into osteoporosis and bone regeneration. In conclusion, our comprehensive framework offers novel insights into osteogenesis and provides a valuable resource for understanding the complexities of bone formation. Author SummaryOsteoblasts, the cells responsible for bone formation, can originate from various cellular sources. However, its unclear how different progenitor cells differentiate into osteoblasts, and how this process is influenced by factors such as age and tissue location. This knowledge gap stems from the lack of comprehensive databases and tools to decipher the differentiation process. In this study, we introduce TrajAtlas, a comprehensive framework designed to bridge this gap. To explore the cellular origins of osteoblasts, we constructed an atlas centered on osteogenesis. To answer how progenitor cells differentiate to osteoblasts, we developed a model that reveals the dynamic regulatory landscape during this process. To elucidate the influence of age and tissue location on differentiation, we built a tool for differential analysis. Furthermore, to identify conserved patterns of differentiation, we developed an approach to detect pseudotemporal gene modules. We validated the effectiveness of this framework by applying it to more datasets, unveiling novel cell states associated with injury. Notably, this framework focuses on dynamic processes, with the potential for broader applications in studying cell differentiation and complementing cell-centric analyses.

bioinformatics↗

bioRxiv2024

CPT2 mediated fatty acid oxidation is dispensable for humoral immunity

B cell activation is accompanied by dynamic metabolic reprogramming, supported by a multitude of nutrients that include glucose, amino acids and fatty acids. While several studies have indicated that fatty acid mitochondrial oxidation is critical for immune cell functions, contradictory findings have been reported. Carnitine palmitoyltransferase II (CPT2) is a critical enzyme for long-chain fatty acid oxidation in mitochondria. Here, we test the requirement of CPT2 for humoral immunity using a mouse model with a lymphocyte specific deletion of CPT2. Stable 13C isotope tracing reveals highly reduced fatty acid-derived citrate production in CPT2 deficient B cells. Yet, CPT2 deficiency has no significant impact on B cell development, B cell activation, germinal center formation, and antibody production upon either thymus-dependent or -independent antigen challenges. Together, our findings indicate that CPT2 mediated fatty acid oxidation is dispensable for humoral immunity, highlighting the metabolic flexibility of lymphocytes.

immunology↗

bioRxiv2024

Immunopipe: A comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline

Single-cell sequencing technologies provide us with information at the level of individual cells. The combination of single-cell RNA-seq and single-cell TCR-seq profiling enables the exploration of cell heterogeneity and T-cell receptor repertoires simultaneously. The integration of both types of data can play a crucial role in enhancing our understanding of T-cell-mediated immunity and, in turn, facilitate the advancement of immunotherapy. Here, we present immunopipe, a comprehensive and flexible pipeline to perform integrated analysis of scRNA-seq and scTCR-seq data. In addition to the command line tool, we provide a user-friendly web interface for pipeline configuration and execution monitoring, benefiting researchers without extensive programming experience. With its comprehensive functionality and ease of use, immunopipe empowers researchers to uncover valuable insights from scRNA-seq and scTCR-seq data, ultimately advancing the understanding of immune responses and immunotherapy development.

bioinformatics↗

bioRxiv2024

Data-driven fine-grained region discovery in the mouse brain with transformers

Spatial transcriptomics offers unique opportunities to define the spatial organization of tissues and organs, such as the mouse brain. We address a key bottleneck in the analysis of organ-scale spatial transcriptomic data by establishing a workflow for self-supervised spatial domain detection that is scalable to multimillion cell datasets. This workflow uses a self-supervised framework for learning latent representations of tissue spatial domains or niches. We use a novel encoder-decoder architecture, which we named CellTransformer, to hierarchically learn higher-order tissue features from lower-level cellular and molecular statistical patterns. Coupling our representation learning workflow with minibatched GPU-accelerated clustering algorithms allows us to scale to multi-million cell MERFISH datasets where other methods cannot. CellTransformer is effective at integrating cells across tissue sections, identifying domains highly similar to ones in existing ontologies such as Allen Mouse Brain Common Coordinate Framework (CCF) while allowing discovery of hundreds of uncataloged areas with minimal loss of domain spatial coherence. CellTransformer domains recapitulate previous neuroanatomical studies of areas in the subiculum and superior colliculus, and characterize putatively uncataloged subregions in subcortical areas which currently lack subregion annotation. CellTransformer is also capable of domain discovery in whole-brain Slide-seqV2 datasets. Our workflows enable complex multi-animal analyses, achieving nearly perfect consistency of up to 100 spatial domains in a dataset of four individual mice with nine million cells across more than 200 tissue sections. CellTransformer advances the state of the art for spatial transcriptomics, by providing a performant solution for detection of fine-grained tissue domains from spatial transcriptomics data.

bioinformatics↗

bioRxiv2024

Proteome trade-off between primary and secondary metabolism shapes acid stress induced bacterial exopolysaccharide production

The exopolysaccharide (EPS) produced by Lactiplantibacillus plantarum is a high-value bioproduct in food and health industries, and its biosynthesis has been found as a secondary metabolic pathway to mediate acid stress. To quantitatively investigate acid stress response in L. plantarum and model EPS production, this study measured metabolomics, proteomics and growth data for L. plantarum HMX2 cultured at 4 different pH values. The growth and metabolomics data showed that under acid stress, the EPS production flux was evidently enhanced while the glycolysis and cellular growth were inhibited. The following proteomic analysis found that EPS biosynthetic proteins were significantly up-regulated under acid stress and pinpointed Fur as the most probable transcriptional factor controlling EPS biosynthesis in L. plantarum. Furthermore, we identified a proteome trade-off between primary metabolism and EPS biosynthesis, which were then mechanistically depicted by a regulatory proteome constrained flux balance analysis (RPCFBA) model. As the first metabolic model that can simulate secondary metabolism, the RPCFBA model demonstrated good accuracy in predicting growth rates and EPS production fluxes of L. plantarum HMX2, validated by experimental data. The in-silico perturbation on carbon sources further showed the potential of applying the presented modeling framework to the design and control of microbial secondary metabolism.

systems biology↗

bioRxiv2024

The subcommissural organ regulates brain development via secreted peptides

The subcommissural organ (SCO) is a gland located at the entrance of the aqueduct of Sylvius in the brain. It exists in species as distantly related as amphioxus and humans, but its function is largely unknown. To explore its function, we compared transcriptomes of SCO and non-SCO brain regions and found three genes, Sspo, Car3, and Spdef, that are highly expressed in the SCO. Mouse strains expressing Cre recombinase from endogenous promoter/enhancer elements of these genes were used to genetically ablate SCO cells during embryonic development, resulting in severe hydrocephalus and defects in neuronal migration and development of neuronal axons and dendrites. Unbiased peptidomic analysis revealed enrichment of three SCO-derived peptides, namely thymosin beta 4, thymosin beta 10, and NP24, and their reintroduction into SCO-ablated brain ventricles substantially rescued developmental defects. Together, these data identify a critical role for the SCO in brain development.

neuroscience↗

bioRxiv2024

PI3K-dependant reprogramming of hexokinase isoforms controls glucose metabolism and functional responses of B lymphocytes

B lymphocyte metabolic reprogramming is essential for B cell differentiation and mounting a healthy immune response. The PI3K signaling pathway regulates B cell metabolism, but the mechanisms involved are not well understood. Here we report that signaling via PI3K8 can impact B cell glucose metabolism and immune functions via selective upregulation of hexokinase 2 (HK2). Three HK enzymes can catalyze the critical first step for glucose utilization and may selectively direct glucose into specific catabolic and anabolic pathways. While HK1 is constitutively expressed in B cells, HK2 is strikingly upregulated during B cell activation in a PI3K8-dependent manner. HK2 shows a unique distribution between mitochondrial and cytoplasmic pools that is also regulated by PI3K. Genetic deletion of HK2 significantly impairs extracellular acidification rate and glycolytic ATP production despite strong expression of HK1. B cell-specific deletion of HK2 in mice caused mild perturbations in B cell development but did not prevent generation of mature B cell subsets. HK2-deficient B cells show altered functional responses in vitro and evidence of metabolic adaptation to become less dependent on glucose and more dependent on glutamine. HK2-deficient B cells exhibit impaired glycolysis, altered metabolite profiles and altered flux of labeled glucose carbons into the pentose phosphate pathway. Upon immunization, HK2-deficient mice exhibit impaired generation of germinal centre B cells, plasmablasts and antibody responses. We further found that HK2 expression in primary human chronic lymphocytic leukemia (CLL) cells was associated with recent proliferation and could be reduced by PI3K inhibition. Our study identifies hexokinase 2 upregulation as a functionally important component of B cell metabolic reprogramming dependent on the PI3K pathway.

immunology↗

bioRxiv2024

A resource to enable chemical biology and drug discovery of WDR Proteins

Protein class-focused drug discovery has a long and successful history in pharmaceutical research, yet most members of druggable protein families remain unliganded, often for practical reasons. Here we combined experiment and computation to enable discovery of ligands for WD40 repeat (WDR) proteins, one of the largest human protein families. This resource includes expression clones, purification protocols, and a comprehensive assessment of the druggability for hundreds of WDR proteins. We solved 21 high resolution crystal structures, and have made available a suite of biophysical, biochemical, and cellular assays to facilitate the discovery and characterization of small molecule ligands. To this end, we use the resource in a hit-finding pilot involving DNA-encoded library (DEL) selection followed by machine learning (ML). This led to the discovery of first-in-class, drug-like ligands for 9 of 20 targets. This result demonstrates the broad ligandability of WDRs. This extensive resource of reagents and knowledge will enable further discovery of chemical tools and potential therapeutics for this important class of proteins.

biochemistry↗

bioRxiv2024

The nutrient-sensing Rag-GTPase complex in B cells controls humoral immunity via TFEB/TFE3-dependent mitochondrial fitness

During the humoral immune response, B cells undergo rapid metabolic reprogramming with a high demand for nutrients, which are vital to sustain the formation of the germinal centers (GCs). Rag-GTPases sense amino acid availability to modulate the mechanistic target of rapamycin complex 1 (mTORC1) pathway and suppress transcription factor EB (TFEB) and transcription factor enhancer 3 (TFE3), members of the microphthalmia (MiT/TFE) family of HLH-leucine zipper transcription factors. However, how Rag-GTPases coordinate amino acid sensing, mTORC1 activation, and TFEB/TFE3 activity in humoral immunity remains undefined. Here, we show that B cell-intrinsic Rag-GTPases are critical for the development and activation of B cells. RagA/RagB deficient B cells fail to form GCs, produce antibodies, and generate plasmablasts in both T-dependent (TD) and T-independent (TI) humoral immune responses. Deletion of RagA/RagB in GC B cells leads to abnormal dark zone (DZ) to light zone (LZ) ratio and reduced affinity maturation. Mechanistically, the Rag-GTPase complex constrains TFEB/TFE3 activity to prevent mitophagy dysregulation and maintain mitochondrial fitness in B cells, which are independent of canonical mTORC1 activation. TFEB/TFE3 deletion restores B cell development, GC formation in Peyers patches and TI humoral immunity, but not TD humoral immunity in the absence of Rag-GTPases. Collectively, our data establish Rag-GTPase-TFEB/TFE3 pathway as an mTORC1 independent mechanism to coordinating nutrient sensing and mitochondrial metabolism in B cells. One sentence summaryRag-GTPases restrain TFEB/TFE3 to prevent abnormal mitophagy, maintain mitochondrial fitness, and support B cell development, Peyers patch germinal center formation, and T-independent humoral immunity.

immunology↗