Biology subjects

Yang, J.

Publications and source records attributed to Yang, J..

At least 343 records · Page 19Linked to original sources

bioRxiv2024

Mouse Forebrain Region-specific Molecular Characteristics and Cholinergic Neurons Subtyping: An Integrated Analysis Based on Spatial Multi-omics

The forebrain regions displays distinct yet under-characterized gene expression patterns. This study analyzed region-specific feature genes in forebrain regions and Isocortex sub-regions at both transcriptomic and proteomic levels. The key finding is the observation of low correlation but high functional similarity between mRNA and protein expression, which offers insights into the connection between gene expression forms in neuronal pathways and the neuronal activity state. Cholinergic neurons (CNs), play a vital role for the forebrains sensory and motor regulation. With Spatial-transcriptome and immunofluorescence joint analysis (STIF), which overcomes the limited resolution of the 10X Visium system, CNs- and CN-subtypes specific feature genes in the striatum and basal forebrain were identified, which providing crucial insights into the heterogeneity and functional diversity of these neuronal populations. The spatial distribution and expression pattern of the feature genes in this study were validated with either external datasets or rolling circle amplification-FISH, coincident results were revealed.

bioinformatics↗

bioRxiv2024

Nitrogen response and growth trajectory of sorghum CRISPR-Cas9 mutants using high-throughput phenotyping

Inorganic nitrogen (N) fertilizer has emerged as one of the key factors driving increased crop yields in the past several decades; however, the overuse of chemical N fertilizer has led to severe ecological and environmental burdens. Understanding how crops respond to N fertilizer has become a central topic in plant science and plant genetics, with the ultimate goal of enhancing N use efficiency (NUE) in crop production. As one of the most essential macronutrients, N significantly influences crop performance across different developmental stages of plant, phenotypic traits result from the accumulative effects of genetic factors, prevailing environmental conditions (specifically N availability), and their complex interactions. To characterize the targeting N-responsiveness and growth trajectory, we employed CRISPR-Cas9 technique to generate sorghum mutants using CRISPR technology. Using a LemnaTec plant imaging system, we obtained time series imagery data from 29 to 130 days after sowing (DAS) for these CRISPR-edited mutants under high N and low N greenhouse conditions. After imagery data analysis, we extracted a number of morphological and greenness index traits as a proxy of plant growth and N responses. Subsequently, we employed two different methods to model the temporal N-responsive traits, allowing us to estimate seven key parameters from the growth curve. Our findings revealed that the wildtype and the edited sorghum lines exhibited differences in N responses for several of the key growth-related parameters. The high-throughput N phenotyping pipeline paves the way for a better understanding of the N responses of edited lines in a dynamic manner and sheds light on further improvements in crop NUE.

plant biology↗

bioRxiv2024

Small Extracellular Vesicles Isolated from Cardiac Tissue Matrix or Plasma Display Distinct Aging-Related Changes in Cargo Contributing to Chronic Cardiovascular Disease

Aging is a major risk factor for cardiovascular disease, the leading cause of death worldwide, and numerous other diseases, but the mechanisms of these aging-related effects remain elusive. Recent evidence suggests that chronic changes in the microenvironment and local paracrine signaling are major drivers of these effects, but the precise effect of aging on these factors remains understudied. Here, for the first time, we directly compare extracellular vesicles obtained from young and aged patients to identify therapeutic or disease-associated agents, and directly compare vesicles isolated from heart tissue matrix (TEVs) or plasma (PEVs). While young TEVs and PEVs showed notable overlap of miRNA cargo, aged EVs differed substantially, indicating differential aging-related changes between TEVs and PEVs. TEVs overall were uniquely enriched in miRNAs which directly or indirectly demonstrate cardioprotective effects, with 45 potential therapeutic agents identified in our analysis. Both populations also showed increased predisposition to disease with aging, though through different mechanisms. Changes in PEV cargo were largely correlated with chronic systemic inflammation, while those in TEVs were more related to cardiac homeostasis and local inflammation. From this, 17 protein targets were identified which were unique to TEVs and highly correlated with aging and the onset of cardiovascular disease. Further analysis via machine learning techniques implicated several new miRNA and protein targets, independently suggesting several of the targets identified by non-machine learning analysis, which correlated with aging-related changes in TEVs. With further study, this biomarker set may serve as a powerful, potential indicator of cardiac health and age which can be measured from PEVs. Additionally, several proposed "young-enriched" therapeutic agents were validated and, when tested, could successfully prevent cell death and cardiac fibrosis in disease-like conditions.

bioinformatics↗

bioRxiv2024

Multimodal single-cell analyses reveal molecular markers of neuronal senescence in human drug-resistant epilepsy

The histopathological neurons in the brain tissue of drug-resistant epilepsy exhibit aberrant cytoarchitecture and imbalanced synaptic circuit function. However, the gene expression changes of these neurons remain unknown, making it difficult for the diagnosis or to dissect the mechanism of drug-resistant epilepsy. By integrating whole-cell patch clamp recording and single-cell RNA sequencing approaches, we identified a transcriptionally distinct subset of cortical pyramidal neurons. These neurons highly expressed genes CDKN1A (P21), CCL2 and NFKBIA that associated with mTOR pathway, inflammatory response and cellular senescence. We confirmed the expression of senescent marker genes in a subpopulation of cortical pyramidal neurons with enlarged soma size in the brain tissue of drug-resistant epilepsy. We further revealed the expression of senescent cell markers P21, P53, COX2, {gamma}-H2AX, {beta}-Gal and reduction of nuclear integrity marker Lamin B1 in histopathological neurons in the brain tissue of drug-resistant epilepsy patients with different pathologies, but not in control brain tissue with no history of epilepsy. Additionally, chronic, but not acute, epileptic seizures induced senescent markers expression in cortical neurons in mouse models of drug-resistant epilepsy. These results provide important molecular markers for histopathological neurons and new insights into the pathophysiological mechanisms of drug-resistant epilepsy.

neuroscience↗

bioRxiv2024

Assessing target genes for homing suppression gene drive

Gene drives are engineered alleles that bias their own inheritance in offspring, enabling the spread of specific traits throughout a population. Targeting female fertility genes in a gene drive can be an efficient strategy for population suppression. In this study, we investigated nine female fertility genes in Drosophila melanogaster using CRISPR-based homing gene drives. Employing a multiplexed gRNA approach to prevent the formation of functional resistance alleles, we aimed to maintain high drive conversion efficiency with low fitness costs in female drive carriers. Drive efficiency was assessed in individual crosses and had varied performance across different target genes. Notably, drives targeting the octopamine {beta}2 receptor (oct) and stall (stl) genes exhibited the highest drive conversion rates and were further tested in cages. A drive targeting stl successfully suppressed a cage population with a high release frequency, though suppression failed in another replicate cage with a lower initial release frequency. Fitness costs in female drive carriers were observed in test cages, impacting the overall efficiency of population suppression. Further tests on the fertility of these lines using individual crosses indicated that some fitness costs were due to maternal deposition of Cas9 combined with new gRNA expression, which would only occur in progeny of drive males when testing split drives with separate Cas9 (when mimicking cages with complete drives) but not for complete drive systems. This could enable success in complete drives with higher maternal Cas9 deposition, even if cage experiments in split drives fail. Our findings underscore the potential and challenges of assessing gene drives for population control, providing valuable insights for optimizing and testing suppression gene drive designs.

genetics↗

bioRxiv2024

Investigating the impact of fibroblast proximity to a tumor on fibroblast extracellular vesicle production utilizing 3D bioprinted stromal models

Extracellular vesicles (EVs) are an important carrier of cellular communication that are secreted from the cell. Different cells will produce EVs with different cargo such as cytokines, RNAs, or microRNAs (miRNA). EVs have been proven to play an important role in breast cancer tumorigenesis, progression, and metastasis. Although the role of cancer associated fibroblasts (CAFs), and EVs originated from them have been studied extensively, there is a lack in knowledge on the contribution of normal fibroblasts surrounding the tumor and their roles with respect to their proximity to the tumor. Here we investigate how the proximity of the tumor affects the EV production of the normal fibroblasts. We created stromal models by 3D bioprinting two different fibroblasts, normal human mammary fibroblasts (hMFs) and normal tumor adjacent fibroblasts (NTAF), within a collagen gel. After one week of culture, we isolated EVs from both the effluent media and the 3D stromal model, which were then characterized using nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), ELISA, zeta potential, and cytokine array analysis of the cargo. The EVs from each group were of consistent exosome size and displayed traditional exosome markers, however the EVs from different groups also displayed different cytokine profiles of their cargo, with the NTAF media group showing an upregulation of cytokines associated with breast cancer progression. After this, we used the EVs to treat breast cancer cells to investigate the effects the EVs from different tumor proximities have on the breast cancer cell behavior. The breast cancer cells treated with the NTAF groups had increased migration. Finally, we utilized a 3D breast tumor model to investigate the effects of the EVs on a tumor spheroid. Tumor spheroids treated with either NTAF EV groups showed increased proliferation, tumor radius, and local invasion. This study is the first to investigate the effect of proximity to a breast tumor on EV production and the first to utilize 3D bioprinting of stromal models specifically to obtain EVs. Overall, our results show that EVs from normal fibroblasts closer to a tumor produce EVs that promote breast cancer progression, regardless of the secretion location of the EVs. These cells have a distinct EV secretome different from normal human mammary fibroblasts, showing that the proximity to a tumor influences the normal fibroblasts surrounding the tumor.

bioengineering↗

bioRxiv2024

Ubiquitin Ligase ITCH Regulates Life Cycle of SARS-CoV-2 Virus

SARS-CoV-2 infection poses a major threat to public health, and understanding the mechanism of viral replication and virion release would help identify therapeutic targets and effective drugs for combating the virus. Herein, we identified E3 ubiquitin-protein ligase Itchy homolog (ITCH) as a central regulator of SARS-CoV-2 at multiple steps and processes. ITCH enhances the ubiquitination of viral envelope and membrane proteins and mutual interactions of structural proteins, thereby aiding in virion assembly. ITCH-mediated ubiquitination also enhances the interaction of viral proteins to the autophagosome receptor p62, promoting their autophagosome-dependent secretion. Additionally, ITCH disrupts the trafficking of the protease furin and the maturation of cathepsin L, thereby suppressing their activities in cleaving and destabilizing the viral spike protein. Furthermore, ITCH exhibits robust activation during the SARS-CoV-2 replication stage, and SARS-CoV-2 replication is significantly decreased by genetic or pharmacological inhibition of ITCH. These findings provide new insights into the mechanisms of the SARS-CoV-2 life cycle and identify a potential target for developing treatments for the virus-related diseases.

molecular biology↗

bioRxiv2024

NaDyNet: A Toolbox for Dynamic Network Analysis of Naturalistic Stimuli

Experiments with naturalistic stimuli (e.g., listening to stories or watching movies) are emerging paradigms in brain function research. The content of naturalistic stimuli is rich and continuous. The fMRI signals of naturalistic stimuli are complex and include different components. A major challenge is isolate the stimuli-induced signals while simultaneously tracking the brains responses to these stimuli in real-time. To this end, we have developed a user-friendly graphical interface toolbox called NaDyNet (Naturalistic Dynamic Network Toolbox), which integrates existing dynamic brain network analysis methods and their enhanced versions. The main features of NaDyNet are: 1) extracting signals of interest from naturalistic fMRI signals; 2) incorporating six commonly used dynamic analysis methods and three static analysis methods; 3) enhanced versions of these dynamic methods by adopting inter-subject analysis to eliminate the effects of non-interest signals; 4) performing K-means clustering analysis to identify temporally reoccurring states along with their temporal and spatial attributes. We then introduced the rationale for incorporating inter-subject analysis to improve existing dynamic brain network analysis methods, and presented numerous examples. We also summarized research progress in comparing methodological efficacy, offered our recommendations for method selection in dynamic network analysis, and discussed the limitations of current approaches and directions for future research. We hope that this open source toolbox will promote the development of naturalistic neuroscience. The toolbox is available at https://github.com/yuanbinke/Naturalistic-Dynamic-Network-Toolbox.

neuroscience↗

bioRxiv2024

VIACOT: a web server for interactive visualization and comparison of cell lineage trees

The cell lineage tree (CLT) records some or all cell division events during the development of multicellular organisms, as well as the functional characteristics of terminal cells, and is therefore commonly considered one of the most fundamental types of biological data. The combining of single-cell RNA sequencing with DNA barcoding has recently led to the rapid accumulation of CLT datasets. Unlike biological sequence data, web-based analysis and visualization tools for CLT data are currently lacking. In order to facilitate studies surrounding CLT, we built a webserver named VIACOT (Visualize Interactively And COmpare Trees). VIACOT is not only a comprehensive repository of published CLT datasets, but also a web tool that enables three preliminary analyses of preprocessed CLT datasets, including. (i) interactive visualization of CLT allowing fine-grain or coarse-grain exploration. (ii) calculations of correlations among single-cell metrics, such as gene expression levels, either using the original metrics or their phylogenetic independent contrasts. (iii) comparison among different CLTs to identify differences in cell fate. We anticipate that VIACOT will be a useful tool for exploration and biological interpretation of CLTs.

bioinformatics↗

bioRxiv2024

An immunomechanical checkpoint PYK2 governs monocyte-to-macrophage differentiation in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is characterized by a fibrotic, stiff tumor microenvironment (TME), where tumor-associated macrophages (TAMs) drive ECM remodeling, progression, and immune evasion. The contribution of mechanical cues to monocyte differentiation into TAMs remains largely unexplored. Here we show that mechanical force is required for monocyte-to-macrophage differentiation. PYK2, as an innovative immunomechanical checkpoint, de facto governs this differentiation process. We demonstrated that PYK2 senses mechanical signals via Piezo1 and integrins, triggering F-actin polymerization and translocating to the nucleus to regulate mechanotransduction and differentiation genes (e.g., ACTR3, RELA). Targeted deletion of PYK2 impairs the differentiation and polarization of monocyte-derived macrophages, reshapes the PDAC microenvironment, and enhances the efficacy of anti-PD-1 immunotherapy. These findings underscore the critical role of mechanical cues in monocyte differentiation and suggest that targeting PYK2 is a promising strategy to modulate TAM function and improve immunotherapy outcomes in patients with PDAC. Statement of significanceThis study identifies PYK2 as an immunomechanical checkpoint that drives monocyte-to-macrophage differentiation in PDAC via Piezo1/integrin-mediated mechanical cues. Targeted deletion of PYK2 reshapes the PDAC microenvironment, and enhances the efficacy of anti-PD-1 immunotherapy, suggesting PYK2 as a promising therapeutic target to overcome immunotherapy resistance.

immunology↗

bioRxiv2024

Nanoparticles loaded with a CSF1R antagonist selectively depletes microglial cells and modulates inflammation in spinal cord injury

Neuroinflammation is a principal event occurring after spinal cord injury (SCI). M1-like microglia are key players in the inflammatory response after injury. We hypothesize that the depletion of this microglia subtype would result in a more pro-resolutive environment, favorable to SCI repair. The colony-stimulating factor 1 receptor (CSF1R) antagonist PLX5622 has been used to deplete microglia in the central nervous system. Although PLX5622 can freely cross the blood-brain barrier after systemic administration, the low drug concentration within the SCI site hampers its effectiveness. Additionally, systemic administration of PLX5622 in the scope of SCI treatment can induce side effects due to off-target accumulation. In this study, we specifically depleted M1- like microglia by designing polymeric nanoparticles loaded with PLX5622 (PLX NPs) to locally treat spinal cord contusion. PLX NP was prepared using a microfluidic-assisted approach showing high encapsulation efficiency (approx. 84%), nanosized dimensions (100 nm), and batch-to-batch reproducibility. PLX NP displayed selective activity in depleting M1-like microglial cells in both resting and lipopolysaccharide (LPS)-activated mixed microglial cell models compared with the free drug counterparts while preserving non-targeted glial cells. Furthermore, locally administered PLX NP downregulated proinflammatory cytokines (e.g., TNF-, IL-6, and IL-1{beta}), increasing the M2/M1-like microglia ratio, thus reducing inflammation in a SCI contusion model. Our data support the hypothesis that local treatment with PLX NPs, a formulation with a high translational value, reduces neuroinflammation, with potential applications in SCI and central nervous system inflammatory diseases. Graphical abstract. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/624647v1_ufig1.gif" ALT="Figure 1000"> View larger version (55K): org.highwire.dtl.DTLVardef@1bfd912org.highwire.dtl.DTLVardef@446923org.highwire.dtl.DTLVardef@1527c0borg.highwire.dtl.DTLVardef@4df259_HPS_FORMAT_FIGEXP M_FIG The colony-stimulating factor 1 receptor (CSF1R) antagonist PLX5622 loaded in polymeric nanoparticles (PLX NP) is delivered for the treatment of neuroinflammation in spinal cord injury. C_FIG

neuroscience↗

bioRxiv2024

Limited involvement of Ca2+/calmodulin-dependent kinase II alpha and beta in mammalian sleep

While sleep is important, our understanding of its molecular mechanisms is limited. Over the last two decades, protein kinases have been implicated in sleep regulation, with a prominent role for Ca++/calmodulin-dependent kinase II (CaMKII) {beta}. Of all the known mouse genetic mutants, the biggest changes in sleep was reported to be observed in Camk2b gene knockout mice: sleep was reduced by approximately 120 minutes (mins) over 24 hours (hrs). We have reexamined the sleep phenotype in Camk2a and Camk2b knockout mice, and while we have observed sleep reduction in Camk2a knockout mice, we did not find sleep reduction in Camk2b mutants.We did find both Camk2a and Camk2b participated in homeostatic sleep rebound, though. Because CamKII and {beta} are widely known to be crucial kinases with interesting properties, it is worthwhile to keep our results in record for a general service to the field.

animal behavior and cognition↗

bioRxiv2024

CellPatch: a Highly Efficient Foundation Model for Single-Cell Transcriptomics with Heuristic Patching

The rapid advancement of foundation models has significantly enhanced the analysis of single-cell omics data, enabling researchers to gain deeper insights into the complex interactions between cells and genes across diverse tissues. However, existing foundation models often exhibit excessive complexity, hindering their practical utility for downstream tasks. Here, we present CellPatch, a lightweight foundation model that leverages the strengths of the cross-attention mechanism and patch tokenization to reduce model complexity while extracting efficient biological representations. Comprehensive evaluations conducted on single-cell RNA-sequencing datasets across multiple organs and tissue states demonstrate that CellPatch achieves state-of-the-art performance in downstream analytical tasks while maintaining ultra-low computational costs during both pretraining and finetuning phases. Moreover, the flexibility and scalability of CellPatch allow it to serve as a general framework that can be incorporated with other well established single-cell analysis software, thereby enhancing their performance through transfer learning on diverse downstream tasks.

bioinformatics↗

bioRxiv2024

Improved automated model building for cryo-EM maps using CryFold

Constructing atomic models from cryogenic electron microscopy (cryo-EM) density maps is essential for interpreting molecular mechanisms. In this study, we present CryFold, an approach for de novo model building for cryo-EM maps, leveraging recent advancements in AlphaFold2 (1) to improve the state-of-the-art method ModelAngelo (2). To accommodate the cryo-EM map information, CryFold replaces the global attention mechanism in AlphaFold2 with local attention, which is further enhanced by a novel 3D rotary position embedding. CryFold produces more complete models, reduces the resolution requirement, and accelerates the modeling. The application of CryFold to three new maps with unknown structure demonstrates its ability to accurately distinguish between paralog sequences in noisy regions, detect previously uncharacterized proteins with unknown functions, precisely compartmentalize the map to isolate non-protein components, and improve the modeling of conformational changes. A particular case includes a 104-protein complex that has been modeled within a few hours, and a minor conformational change of a single protein domain has been detected at the periphery when models from two different maps were compared. CryFold stands as an accurate method currently available for model building of proteins in cryo-EM structure determination. The source code and model parameters are available at https://github.com/SBQ-1999/CryFold.

bioinformatics↗

bioRxiv2024

Reduction of DNA Topoisomerase Top2 reprograms the epigenetic landscape and extends health and life span across species

DNA topoisomerases are essential molecular machines that manage DNA topology in the cell and play important roles in DNA replication and transcription. We find that knocking down the enzyme Topoisomerase Top2 or its mammalian homolog Top2b increases the life span of S. cerevisiae, C. elegans, and mice. Top2b reduction also extends the health span of mice and alleviates the pathologies of aging in multiple tissues. At the cellular/molecular level, Top2b reduction attenuates the major hallmarks of aging, such as cellular senescence, de-regulated nutrient sensing, epigenetic alteration, and lysosomal biogenesis. We observed that Top2b reduction significantly changes the epigenetic landscape in various mouse tissues toward those of the young animals, and differentially down-regulates genes with active promoter and high expression. Our observations suggest that Top2 reduction confers longevity effect across species via a conserved mechanism, and may be used as a novel therapeutic strategy for countering aging.

biochemistry↗

bioRxiv2024

Cryo-EM structures of human ClpXP reveal mechanisms of assembly and proteolytic activation

The human ClpXP complex (hClpXP) plays a central role in mitochondrial protein quality control by degrading misfolded or unneeded proteins. While bacterial ClpXP complexes have been extensively characterized, the molecular determinants underlying hClpXP assembly and regulation are not as well understood. We determined cryo-electron microscopy (cryo-EM) structures of hClpP in isolation and in complex with hClpX, revealing how hClpX binding promotes rearrangement of an asymmetric hClpP heptamer to assemble as a symmetric tetradecamer. Our hClpXP structure also highlights the stabilizing role of a previously uncharacterized eukaryotic ClpX sequence, referred to as the E-loop, and its importance in ATPase activity and hexamer assembly. We further show that peptide interaction with the hClpP proteolytic active site promotes the complex to adopt a proteolytically competent conformation. Together, these findings advance our understanding of the molecular mechanisms defining hClpXP activation and function.

molecular biology↗

bioRxiv2024

Spotiphy enables single-cell spatial whole transcriptomics across the entire section

Spatial transcriptomics (ST) has advanced our understanding of tissue regionalization by enabling the visualization of gene expression within whole tissue sections1, but the approach remains dogged by the challenge of achieving single-cell resolution without sacrificing whole genome coverage2,3. Here we present Spotiphy (Spot imager with pseudo single-cell resolution histology), a novel computational toolkit that transforms sequencing-based ST data into single-cell-resolved whole-transcriptome images. In evaluations with Alzheimers disease (AD) and normal mouse brains, Spotiphy delivers the most precise cellular compositions. For the first time, Spotiphy reveals novel astrocyte regional specification in mouse brains. It distinguishes sub-populations of DAM (Disease-Associated Microglia) located in different AD mouse brain regions. Spotiphy also identifies multiple spatial domains as well as changes in the patterns of tumor-tumor microenvironment interactions using human breast ST data. Spotiphy enables visualization of cell localization and gene expression in tissue sections, offering key insights into the function of complex biological systems.

systems biology↗

bioRxiv2024

TLL1 knockdown attenuates prostate cancer progression by enhancing antitumor immunity

Due to the inevitable progression to castration-resistant prostate cancer (CRPC) following treatment with androgen deprivation therapy (ADT), it is essential to develop novel treatment approaches for managing CRPC. Here we showed that metalloproteinase TLL1 was positively associated with prostate cancer aggressiveness. Mechanistically, TLL1 promoted prostate cancer cells migration and metastasis through cleaving latent TGF-{beta}1 to activate TGF-{beta} signaling pathway. Moreover, LINC01179 interacted with Miz1 to attenuate TLL1 expression and LINC01179 impaired prostate cancer cell proliferation and migration ability by suppressing TLL1 expression to deactivate TGF-{beta} signaling activity. Meanwhile, we observed that TLL1 increased the expression of PD-L1 by activating TGF-{beta} signaling pathway and TLL1 depletion enhanced the antitumor efficacy by anti-PD-1 antibody via augmenting the infiltration proportions of CD8+ T cells in tumors. In addition, T cell-specific overexpression of TLL1 disrupted T cell development in the thymus. TLL1 overexpression in T cells accelerated RM-1 prostate tumor growth in mice by decreasing the infiltration of CD8+ T cells into tumors. Collectively, our results revealed that TLL1 may be a potential therapeutic target to alter prostate cancer progression.

cancer biology↗