Biology subjects

Huang, Z.

Publications and source records attributed to Huang, Z..

At least 235 records · Page 13Linked to original sources

bioRxiv2023

Engineering Regionally-Activated Drugs for Neuroscience

The brain is comprised of multiple regions performing distinct functions. Within each of these regions, there are multiple cell types that can affect brain physiology. Finally, within each cell there are multiple signaling pathways, that, when activated or inhibited, control the cells activity, and consequently the brain function. For these reasons, methods that can control the brain with regional, cell-type, and molecular precision have been widely used in neuroscience. However, so far, achieving sustained control over a brain region with that level of specificity relied either on gene delivery or placement of invasive devices. While gene therapy holds great promise, the risks of genomic integration, vector toxicity, vector-directed immune response, high cost, and gene delivery to the brain pose significant challenges. On the other hand, invasive devices enable site-specific delivery of drugs but can also surgically damage the modulated brain region, carrying risks of infection and hemorrhage. Here, we present a new approach that can provide multi-day, noninvasive, site-specific control over specific cell types in the brain without the need to use invasive devices or gene delivery. To achieve this, we introduce a new paradigm called Regionally Activated Interstitial Drugs, or RAID, which delivers a protein-based catalytic centers, or RAID enzymes, to the brain using focused ultrasound blood-brain barrier opening. This catalytic center is designed to attach to the interstitial space in the brain where it remains for days after initial delivery. While the catalytic center is present in the brain, it can locally process an inert BBB permeable prodrug into an active drug, resulting in localized therapy. Our proof-of concept studies demonstrated that the engineered RAID enzymes can retain activity in the brain parenchyma for several days, allowing for noninvasive site-specific induction of neuronal activity that was sufficiently potent to elicit behavioral effects. Overall, the RAID paradigm enabled noninvasive, tunable, temporally-re-solved, site-specific, non-genetic, neuromodulation over multiple days. The RAID paradigm is versatile and can be applied to any enzyme and prodrug pair to control various aspects of central nervous system physiology.

bioengineering↗

bioRxiv2023

Transcriptional signatures associated with waterlogging stress responses and aerenchyma formation in barley root tissue

The negative impact of soil waterlogging on crop production is expected to increase due higher frequencies of extreme rainfall events arising from climate change. Consequently, understanding the molecular mechanisms that enable plants to mitigate waterlogging stress is critical for breeding programmes, particularly in the case of waterlogging-susceptible crop species, such as barley (Hordeum vulgare). Aerenchyma formation is a key morphological adaptation allowing plants to cope with waterlogging stress and hypoxic conditions, however, the genetic regulation of its development in barley remains largely unresolved. In this study, two barley cultivars with contrasting waterlogging tolerance (Franklin and Yerong) were subjected to waterlogging stress, followed by analysis of phenotypic traits including root aerenchyma formation, and transcriptomic profiling of root tissue samples. Differential expression analyses identified genes transcriptionally responsive to 24 and 72 h of waterlogging in both cultivars, and highlighted metabolic adaptations, regulation of ROS signalling and management of stress responses as key elements of the waterlogging response. The results revealed large intra-individual variations in root aerenchyma formation, and these variations were exploited to isolate 81 candidate aerenchyma-associated genes from the generated RNA-seq datasets. Network analyses suggest the involvement of the DNA damage response gene, DRT100 and cell wall modifying genes, XHT16 and XHT15 as regulatory hub genes in aerenchyma formation. Collectively, the generated data provide insights into transcriptional signatures associated with the barley root responses to waterlogging and aerenchyma formation, informing our understanding of strategies that plants employ to cope with the negative impacts of heavy rainfall.

plant biology↗

bioRxiv2023

Harnessing Landrace Diversity Empowers Wheat Breeding for Climate Resilience

Breeding crops resilient to climate change is urgently needed to help ensure food security. A key challenge is to harness genetic diversity to optimise adaptation, yield, stress resilience and nutrition. We examined the genetic and phenotypic diversity of the A.E. Watkins landrace collection of bread wheat (Triticum aestivum), a major global cereal, through whole-genome re-sequencing (827 Watkins landraces and 208 modern cultivars) and in-depth field evaluation spanning a decade. We discovered that modern cultivars are derived from just two of the seven ancestral groups of wheat, leaving five groups as previously untapped sources for breeding. This provides access to landrace-specific functional variations using structured germplasm, genotyping and informatics resources. Employing complementary genetic populations and approaches, we identified thousands of high-resolution quantitative trait loci (QTL) and significant marker-trait associations for major traits, revealing many Watkins-unique loci that can confer superior traits in modern wheat. Furthermore, we identified and functionally verified causative genes for climate-change adaptation, nutritional enhancement and resistance to wheat blast. Finally, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritised QTL in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilising genetic diversity in crop improvement to achieve sustainable food security.

plant biology↗

bioRxiv2023

A resource for probing influences of perinatal factors on neurodevelopment in 3-10-years-old Chinese children

Adverse perinatal factors can disrupt the normal development of the brain, with potential long-term impacts on childrens overall development. Currently, the neuropathological mechanisms by which these factors lead to various neurodevelopmental disorders (NDDs) remain largely unknown. An open resource that integrate perinatal factors with brain and mental health development is essential for investigating NDD-related aetiology. In this Data Descriptor, we introduce a multicentre database containing information on perinatal factors that influence childrens brain-mind development, namely, periCBD, that combines neuroimaging and behavioural phenotypes with perinatal factors associated with a high incidence of NDDs at county/region/central district hospitals. PeriCBD was designed to establish a platform for the investigation of individual differences in brain-mind development among children aged 3-10 years are associated with perinatal factors. Ultimately, our goal was to develop an early prediction and screening model for NDDs that leverages normative data to facilitate NDD aetiology research. Herein, we provide a systematic overview of the data acquisition/cleaning/quality control/sharing, processes of periCBD and present preliminary brain-mind associations.

neuroscience↗

bioRxiv2023

MicroRNAs are necessary for the emergence of Purkinje cell identity

Brain computations are dictated by the unique morphology and connectivity of neuronal subtypes, features established by closely timed developmental events. MicroRNAs (miRNAs) are critical for brain development, but current technologies lack the spatiotemporal resolution to determine how miRNAs instruct the steps leading to subtype identity. Here, we developed new tools to tackle this major gap. Fast and reversible miRNA loss-of-function revealed that miRNAs are necessary for cerebellar Purkinje cell (PC) differentiation, which previously appeared miRNA-independent, and resolved distinct miRNA critical windows in PC dendritogenesis and climbing fiber synaptogenesis, key determinants of PC identity. To identify underlying mechanisms, we generated a mouse model, which enables precise mapping of miRNAs and their targets in rare cell types. With PC-specific maps, we found that the PC-enriched miR-206 drives exuberant dendritogenesis and modulates synaptogenesis. Our results showcase vastly improved approaches for dissecting miRNA function and reveal that many critical miRNA mechanisms remain largely unexplored. HighlightsO_LIFast miRNA loss-of-function with T6B impairs postnatal Purkinje cell development C_LIO_LIReversible T6B reveals critical miRNA windows for dendritogenesis and synaptogenesis C_LIO_LIConditional Spy3-Ago2 mouse line enables miRNA-target network mapping in rare cells C_LIO_LIPurkinje cell-enriched miR-206 regulates its unique dendritic and synaptic morphology C_LI

neuroscience↗

bioRxiv2023

Progressive community, biogeochemical and evolutionary remodeling of the soil microbiome underpins long-term desert ecosystem restoration

Ecological restoration of degraded lands is essential to human sustainability. Yet, an in-depth community, functional, and evolutionary microbial perspective of long-term restoration of damaged ecosystems is lacking. Herein, we comprehensively assessed the impact of long-term (up to 17 years) restoration of Tengger Desert, China, by multi-omic profiling of 1,910 topsoil samples. The soil biophysiochemical properties, especially soil hydraulics, microbiome stability, and functional diversity, significantly improved during restoration. The soil microbiome transitioned from an extreme oligotrophic and autotrophic community to a diverse copiotrophic ecosystem. The soil microbiota, including fungi, could mediate the soil physicochemical changes through metabolites. Importantly, the systematic rewiring of nutrient cycles featured the multi-domain preference of an efficient carbon fixation strategy in the extreme desert environment. Finally, the microbiome was evolving via positive selections of genes of biogeochemical cycles, resistance, and motility. In summary, we present a comprehensive community, functional, biogeochemical, and evolutionary landscape of the soil microbiome during the long-term restoration of desert environments. We highlight the crucial microbial role in restoration from soil hydraulic and biogeochemical perspectives, offering promising field applications. HighlightsO_LIThe desert soil microbiome transformed from simple oligotrophic to a diverse, stable, and nutrient-rich ecosystem with expanded functional diversity. C_LIO_LIRestoration led to systematically rewired biogeochemical cycles, which are highly efficient in carbon fixation in the desert environment. C_LIO_LIThe microbiome was evolving via positive selections of genes involved in biogeochemical cycles and environmental adaptations. C_LIO_LIMicrobes and metabolites could facilitate desert restoration from hydraulic and biogeochemical aspects, offering promising field applications. C_LI

microbiology↗

bioRxiv2023

A simple statistical framework for small sample studies

Most studies in psychology, neuroscience, and life science research make inferences about how strong an effect is on average in the population. Yet, many research questions could instead be answered by testing for the universality of the phenomenon under investigation. By using reliable experimental designs that maximise both sensitivity and specificity of individual experiments, each participant or subject can be treated as an independent replication. This approach is common in certain subfields. To date, there is however no formal approach for calculating the evidential value of such small sample studies and to define a priori evidence thresholds that must be met to draw meaningful conclusions. Here we present such a framework, based on the ratio of binomial probabilities between a model assuming the universality of the phenomenon versus the null hypothesis that any incidence of the effect is sporadic. We demonstrate the benefits of this approach, which permits strong conclusions from samples as small as 2-5 participants and the flexibility of sequential testing. This approach will enable researchers to preregister experimental designs based on small samples and thus enhance the utility and credibility of such studies.

neuroscience↗

bioRxiv2023

Rapid optogenetic clustering of a cytoplasmic BcLOV4 variant

Protein clustering is a powerful form of optogenetic control, yet there is currently only one protein --Cry2--whose light-induced clustering has been harnessed for these purposes. Recently, the photoreceptor BcLOV4 was found to form protein clusters in mammalian cells in response to blue light, although clustering coincided with its translocation to the plasma membrane, potentially constraining its application as an optogenetic clustering module. Herein we identify key amino acids that couple clustering to membrane binding, allowing us to engineer a variant of BcLOV4 that clusters in the cytoplasm and does not associate with the membrane in response to blue light. This variant, BcLOVclust, clustered over many cycles with dramatically faster clustering and de-clustering kinetics compared to Cry2. The magnitude of BcLOVclust clustering could be strengthened by appending an intrinsically disordered region from the fused in sarcoma (FUS) protein, or by optimizing the fluorescent protein to which it was fused. BcLOVclust retained the temperature sensitivity of BcLOV4 such that light induced clustering was transient, and the rate of spontaneous declustering increased with temperature. At low temperatures, BcLOVclust and Cry2 could be multiplexed in the same cells, allowing light control of independent protein condensates. BcLOVclust could also be applied to control signaling proteins and stress granules in mammalian cells. Thus BcLOVclust provides an alternative to Cry2 for optogenetic clustering and a method for multiplexed clustering. While its usage is currently suited for organisms that can be cultured below [~]30 {degrees}C, a deeper understanding of BcLOVclust thermal response will further enable its use at physiological mammalian temperatures. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/557726v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@15e80f3org.highwire.dtl.DTLVardef@163d54corg.highwire.dtl.DTLVardef@1489845org.highwire.dtl.DTLVardef@10505c1_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LILight-responsive clustering of BcLOV4 can be decoupled from its membrane association C_LIO_LIBcLOVclust clusters in the cytoplasm with faster ON and OFF kinetics than Cry2 C_LIO_LIBcLOVclust and Cry2 can be multiplexed in the same cell C_LIO_LIBcLOVclust can control RhoA activity and stress granule formation C_LI

bioengineering↗

bioRxiv2023

CLOCK Mediates Delay in Cardiac Myofibroblast Formation and Attenuates Progression of Myocardial Fibrosis through Inhibition of Smad 3 Transcriptional Activity

IntroductionMyocardial fibrosis, characterized by excessive extracellular matrix deposition, leading to adverse cardiac remodeling and impaired function. The differentiation of cardiac fibroblasts into myofibroblasts plays a pivotal role in this process. The involvement of the core clock protein CLOCK in the formation of cardiac myofibroblasts and the advancement of myocardial fibrosis is not well understood. This study aims to investigate how CLOCK modulates cardiac myofibroblast differentiation and attenuates myocardial fibrosis by inhibiting Smad3 transcriptional activity. MethodsIn vivo, adeno-associated virus 9 was utilized for overexpression or silencing of the CLOCK gene via mice intravenous injection. In vitro experiments were conducted using primary cultures of cardiac fibroblasts isolated from mouse hearts to examine the expression levels of molecular markers associated with myofibroblast differentiation, such as -smooth muscle actin (-SMA) and collagen I. Additionally, a Smad3 luciferase reporter gene experiment was employed to assess the transcriptional activity of Smad3 under CLOCK regulation. ResultsThe results demonstrate that CLOCK overexpression significantly reduces the expression of -SMA and collagen I in cardiac fibroblasts, indicating a suppression of myofibroblast formation. Conversely, CLOCK knockdown enhances the expression of these fibrotic markers. Interestingly, CLOCK was found to negatively regulate the transcriptional activity of Smad3, suggesting a potential mechanism by which CLOCK exerts its inhibitory effect on cardiac fibrosis. Specifically, CLOCK interacts with Smad3, inhibiting its nuclear translocation and subsequent activation of fibro genic gene expression. ConclusionThese findings highlight the crucial role of CLOCK in the regulation of cardiac myofibroblast formation and the progression of myocardial fibrosis. CLOCK appears to exert an inhibitory effect on fibrotic signaling pathways, partially through the inhibition of Smad3 transcriptional activity. This study provides novel insights into the molecular mechanisms underlying cardiac fibrosis and emphasizes the therapeutic potential of targeting CLOCK-mediated pathways for treating myocardial fibrosis.

molecular biology↗

bioRxiv2023

Network state changes in sensory thalamus represent learned outcomes.

Thalamic brain areas play an important role in adaptive behaviors. Nevertheless, the population dynamics of thalamic relays during learning across sensory modalities remain mostly unknown. Using a cross-modal sensory reversal learning paradigm combined with deep brain two-photon calcium imaging of large populations of auditory thalamus (MGB) neurons, we identified that MGB neurons are biased towards reward predictors independent of modality. Additionally, functional classes of MGB neurons aligned with distinct task periods and behavioral outcomes, both dependent and independent of sensory modality. During non-sensory delay periods, MGB ensembles developed coherent neuronal representation as well as distinct co-activity network states reflecting predicted task outcome. These results demonstrate flexible cross-modal ensemble coding in auditory thalamus during adaptive learning and highlight its importance in brain-wide cross-modal computations during complex behavior. SummaryDeep brain imaging reveals flexible network states of sensory thalamus predicting task outcome in mice.

neuroscience↗

bioRxiv2023

GetPrimers: a generalized PCR-based genetic targeting primer designer enabling easy and standardized targeted gene modification across multiple systems

Genetic targeting (e.g., gene knockout and tagging) based on polymerase chain reaction (PCR) is a simple yet powerful approach for studying gene functions. Although originally developed in classic budding and fission yeast models, the same principle applies to other eukaryotic systems with efficient homologous recombination. One-step-PCR-based genetic targeting is conventionally used but the sizes of the homologous arms that it generates for recombination-mediated genetic targeting are usually limited. Alternatively, gene targeting can also be performed via fusion PCR, which can create homologous arms that are orders of magnitude larger, therefore substantially increases the efficiency of recombination-mediated genetic targeting. Here we present GetPrimers (https://www.evomicslab.org/app/getprimers/), a generalized computational framework and web tool to assist automatic targeting and verification primer design for both one-step-PCR-based and fusion-PCR-based genetic targeting experiments. Moreover, GetPrimers by design runs for any given genetic background of any species with full genome scalability. Therefore, GetPrimers is capable of empowering high-throughput functional genomics assays at multi-population and multi-species levels. Comprehensive experimental validations have been performed for targeting and verification primers designed by GetPrimers across multiple organism systems and experimental setups. We anticipate GetPrimers to become a highly useful and popular tool to facilitate easy and standardized gene modification across multiple systems. Take AwaysDeveloped GetPrimers for generalized primer design of PCR-based genetic targeting. GetPrimers shines with its high versatility and genome-wide scalability. GetPrimers was validated across multiple organisms and experimental setups.

genetics↗

bioRxiv2023

Monomeric amyloid-β inhibits microglial inflammatory activity in the brain via an APP/heterotrimeric G protein-mediated pathway

Microglia, the resident immune cell of the brain, play critical roles in brain development, function, and disease. However, how microglial activity is regulated in this process remains to be elucidated. Here we report an amyloid precursor protein (APP) and heterotrimeric G protein-mediated pathway that negatively regulates microglial inflammatory activation during cerebral cortex development. Disruption of this pathway results in dysregulated microglial activity, excessive extracellular matrix proteinase production, cortical basement membrane breach, and laminar assembly disruption. We further show that this pathway is activated by amyloid {beta} (A{beta}), the cleavage product of APP that accumulates in large quantities as plaques in the Alzheimers disease brain. Specifically, we find A{beta} monomers potently suppress inflammatory cytokine transcription and secretion by brain microglia, in an APP and heterotrimeric G protein-dependent manner. These results discover a previously unknown activity of A{beta} as a negative regulator of brain microglia as well as a new pathway that mediates the signal transduction. They shed new light on the cell-cell communication mechanisms that regulate brain immune homeostasis and may facilitate further insight into Alzheimers disease pathogenesis.

neuroscience↗

bioRxiv2023

Three-dimensional single-cell transcriptome imaging of thick tissues

Multiplexed error-robust fluorescence in-situ hybridization (MERFISH) allows genome-scale imaging of RNAs in individual cells in intact tissues. To date, MERFISH has been applied to image thin tissue samples of [~]10-{micro}m thickness. Here, we present a thick-tissue three-dimensional (3D) MERFISH imaging method, which uses confocal microscopy for optical sectioning, deep learning for increasing imaging speed and quality, as well as sample preparation and imaging protocol optimized for image registration of thick samples. We demonstrated 3D MERFISH on mouse brain tissue sections of up to 200 {micro}m thickness with high detection efficiency and accuracy. We anticipate that 3D thick-tissue MERFISH imaging will broaden the scope of questions that can be addressed by spatial genomics.

neuroscience↗

bioRxiv2023

Highly accurate estimation of cell type abundance in bulk tissues based on single-cell reference and domain adaptive matching

Accurately identifying the cellular composition of complex tissues is critical for understanding disease pathogenesis, early diagnosis, and prevention. However, current methods for deconvoluting bulk RNA sequencing (RNA-seq) typically rely on matched single-cell RNA sequencing (scRNA-seq) as a reference, which can be limiting due to differences in sequencing distribution and the potential for invalid information from single-cell references. To overcome these limitations, we introduced SCROAM, a novel computational method that overcomes these challenges. SCROAM transforms scRNA-seq and bulk RNA-seq into a shared feature space, effectively eliminating distributional differences in the latent space. We then generate cell-type-specific expression matrices from scRNA-seq, enabling accurate identification of cell types in bulk tissues. We evaluated the performance of SCROAM by benchmarking it against simulated datasets and human breast cancer and peripheral blood datasets, demonstrating its accuracy and robustness. To further validate SCROAMs performance, we conducted single-cell and bulk RNA-seq experiments on mouse spinal cord tissue and applied SCROAM to identify bulk tissue cell types. Our results indicate that SCROAM is a highly effective tool for identifying similar cell types, surpassing the performance of existing methods. We then performed an integrated analysis of liver cancer and primary glioblastoma to investigate the relationship between cell type composition and clinical outcomes in various tumor types, highlighting the significance of SCROAM for understanding cellular heterogeneity in complex diseases. Overall, our work presents a novel perspective to accurately infer cellular composition and expression in bulk RNA-seq, offering valuable insights into disease pathogenesis and potential therapeutic strategies.

bioinformatics↗

bioRxiv2023

Eugenol mimics exercise to promote skeletal muscle fiber remodeling and myokine IL-15 expression by activating TRPV1 channel

Metabolic disorders are highly prevalent in modern society. Exercise mimetics are defined as pharmacologic compounds that can produce the beneficial effects of fitness. Recently, there has been increased interest in the role of eugenol and transient receptor potential vanilloid 1 (TRPV1) in improving metabolic health. The aim of this study was to investigate whether eugenol acts as an exercise mimetic by activating TRPV1. Here, we showed that eugenol improved endurance capacity, caused the conversion of fast to slow muscle fibers, and promoted white fat browning and lipolysis in mice. Mechanistically, eugenol promoted muscle fiber type transformation by activating TRPV1-mediated CaN signaling pathway. Subsequently, we identified IL-15 as a myokine that is regulated by the CaN/Nuclear factor of activated T cells cytoplasmic 1 (NFATc1) signaling pathway. Moreover, we found that TRPV1-mediated CaN/NFATc1 signaling, activated by eugenol, controlled IL-15 levels in C2C12 myotubes. Our results suggest that eugenol may act as an exercise mimetic to improve metabolic health via activating the TRPV1-mediated CaN signaling pathway.

molecular biology↗

bioRxiv2023

CircRNAs and their regulatory networks associated with the antioxidant enzymes and immune responses of Asian honey bee larvae to fungal infection

Non-coding RNA (ncRNA) plays an important role in the regulation of immune responses, growth, and development in plants and animals. Here, the identification, characteristic investigation, and molecular verification of circRNAs in Apis cerana cerana larval guts were conducted, and the expression pattern of larval circRNAs during Ascosphaera apis infection was analyzed. This was followed by exploration of the potential regulatory part of differentially expressed circRNAs (DEcircRNAs) in host immune responses. A total of 3178 circRNAs in the larval guts of A. c. cerana were identified, with a length distribution ranging from 15 nt to 96007 nt. Additionally, 45, 33, and 48 up-regulated circRNAs, as well as 110, 62, and 38 down-regulated circRNAs were identified in the A.-apis-inoculated 4-, 5-, and 6-day-old larval guts in comparison with the corresponding uninoculated larval guts. These DEcircRNAs were predicted to target 29, 25, and 18 parental genes, which were relative to 12, 20, and 17 GO terms as well as 144, 114, and 61 KEGG pathways, including five cellular and four humoral immune pathways containing melanization, phagosomes, lysosomes, endocytosis, apoptosis, MAPK, Ras, and Jak-STAT signaling pathways. Furthermore, complex competing endogenous RNA (ceRNA) regulatory networks were detected as being formed among DEcircRNAs, DEmiRNAs, and DEmRNAs. The target DEmRNAs were engaged in 36, 47, and 47 GO terms as well as 331, 332, and 331 pathways, including six cellular and six humoral immune-related pathways. In total, nineteen DEcircRNAs, five DEmiRNAs, and three mRNAs were included in the sub-networks relative to three antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), and glutathione S-transferase (GST). Finally, back-splicing sites within 15 circRNAs and the difference in the 15 DEcircRNAs expression between uninoculated and A.-apis-inoculated larval guts were confirmed utilizing molecular methods. These findings not only enrich our understanding of bee host-fungal pathogen interactions, but also lay a foundation for illuminating the mechanism underlying the DEcircRNA-mediated immune defense of A. c. cerana larvae against A. apis invasion.

molecular biology↗

bioRxiv2023

Joint analysis of single-cell and bulk tissue sequencing data to reveals the adaptation and remodeling of the tumor microenvironment by breast cancer cells at different stages of brain metastasis process

ObjectiveTo integrate macro-transcriptomics and single-cell sequencing to analyze the differential gene expression between primary and brain metastatic breast cancer cells, as well as between active and dormant cancer cells within brain metastases, exploring their adaptation and remodeling abilities at different stages of brain metastasis. MethodsFour public datasets were used: three mRNA microarray datasets from breast cancer and brain metastasis tissues, and one single-cell RNA sequencing (scRNA-seq) dataset from active and dormant brain metastatic cells. Gene differential expression, pathway enrichment, and cell clustering analyses were performed to compare primary and metastatic breast cancer cells, as well as active and dormant cells in brain metastases, focusing on gene expression, metabolic pathways, and functional pathways. ResultsMetastatic breast cancer cells showed weakened pathways related to the extracellular matrix and protein digestion. Active cells exhibited enhanced cell cycle regulation, tumor proliferation, and hypoxia resistance pathways compared to dormant cells. Clustering analysis revealed that cluster 6, unique to dormant cells, had enhanced functions in epithelial-mesenchymal transition (EMT), extracellular matrix (ECM), collagen formation, tumor inflammation siganure (TIS), and IL-10 signaling. Cluster 3 and 4 in active cells had enhanced DNA replication and tumor proliferation pathways, respectively. ConclusionThis study highlights the role of cancer cell characteristics and heterogeneity in the invasiveness of brain metastasis. Understanding these mechanisms can guide the development of more effective treatment strategies for breast cancer brain metastasis (BCBM) patients.

cancer biology↗

bioRxiv2023

Leucine alleviates cytokine storm syndrome by regulating macrophage polarization via the mTORC1/LXRα signaling pathway

Cytokine storms are associated with severe pathological damage and death in some diseases. Excessive activation of M1 macrophages and the subsequent secretion of pro-inflammatory cytokines are a major cause of cytokine storms. Therefore, promoting the polarization of M2 macrophages to restore immune balance is a promising therapeutic strategy for treating cytokine storm syndrome (CSS). This study was aimed at investigating the potential protective effects of leucine on lipopolysaccharide (LPS)-induced CSS in mice and exploring the underlying mechanisms. CSS was induced by LPS administration in mice, which were concurrently administered leucine orally. In vitro, BMDMs were polarized to M1 and M2 phenotypes with LPS and IL-4, respectively, and treated with leucine. Leucine decreased mortality in mice treated with lethal doses of LPS. Specifically, leucine decreased M1 polarization and promoted M2 polarization, thus diminishing pro-inflammatory cytokine levels and ameliorating CSS in mice. Further studies revealed that leucine induced macrophage polarization through the mechanistic target of rapamycin complex 1 (mTORC1)/liver X receptor (LXR) pathway, which synergistically enhanced the expression of the IL-4-induced M2 marker Arg1 and subsequent M2 polarization. In summary, this study revealed that leucine ameliorates CSS in LPS mice by promoting M2 polarization through the mTORC1/LXR/Arg1 signaling pathway. Our findings indicate that a fundamental link between metabolism and immunity contributes to the resolution of inflammation and the repair of damaged tissues.

immunology↗