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Biology subjects

He, S.

Publications and source records attributed to He, S..

At least 181 records · Page 10Linked to original sources

Default But Not Rest: Topological Discrimination Defines the Default Mode Network

The default mode network (DMN), a set of transmodal cortical regions, has historically been argued to serve the internal functions of brain. The discovery of this network highlighted the brains intrinsic operations. The DMN generally decreases its activity during tasks and increases its activity during relaxed non-task states. It is important to investigate the nature of the DMN in order to understand the human brain in health and disease. In the current study, we discovered a task-related cortical network we called the Topological Discrimination Network (TDN), which was consistently revealed by contrasting activations from topological discrimination tasks with local geometric discrimination tasks. The TDN and the DMN consist of essentially the same group of brain regions and the fMRI response of topological discrimination in those regions exhibited consistent temporal dynamics with resting state. The robustness of the TDN is supported by multiple experiments performed at different field strengths (3T and 7T MRI scanner) as well as different types of signals measured (BOLD and CBF). The collective results suggest that the process of topological discrimination could almost be considered as a functional "default mode" of our brain. The TDN, like the DMN, could define the functional baseline of brain, with the advantage of functional consistency across participants and experimental sessions.

neuroscience↗

The rVSV-EBOV vaccine provides limited cross-protection against Sudan virus in guinea pigs

Recombinant vesicular stomatitis viruses (rVSVs) engineered to express heterologous viral glycoproteins have proven to be remarkably effective vaccines. Indeed, rVSV-EBOV, which expresses the Ebola virus (EBOV) glycoprotein, recently received clinical approval in the United States and Europe for its ability to prevent EBOV disease. Analogous rVSV vaccines expressing the glycoproteins of different human-pathogenic filoviruses have also been developed and shown to be effective in pre-clinical evaluations, yet these vaccine candidates have not progressed far beyond research laboratories. As the current outbreak of Sudan virus (SUDV) intensifies in Uganda, the need for proven countermeasures is rendered even more acute. Here we demonstrate that an rVSV-based vaccine expressing the SUDV glycoprotein (rVSV-SUDV) generates a potent humoral immune response that completely protects guinea pigs from SUDV disease and death. Although the cross-protection generated by rVSV vaccines for different filoviruses is thought to be limited, we wondered whether rVSV-EBOV might also provide protection against SUDV, which is closely related to EBOV. Surprisingly, nearly 60% of guinea pigs that were vaccinated with rVSV-EBOV and challenged with SUDV survived, suggesting that rVSV-EBOV offers limited protection against SUDV, at least in the guinea pig model. These results were confirmed by a back-challenge experiment in which animals that had been vaccinated with rVSV-EBOV and survived EBOV challenge were inoculated with SUDV and survived. Whether these data are applicable to the efficacy of rVSV-EBOV in humans is unknown, and they should therefore be interpreted cautiously. Nevertheless, this study confirms the potency of the rVSV-SUDV vaccine, and it highlights the potential for rVSV-EBOV to elicit a cross-protective immune response.

microbiology↗

A non-human primate model with Alzheimer's disease-like pathology induced by hippocampal overexpression of human tau

Alzheimers disease (AD) is one of the most burdening diseases of the century with no disease-modifying treatment yet. Non-human primates (NHPs) share genetic, anatomical and physiological similarities with humans, making them an ideal model for investigating the pathogenesis and therapeutics of AD. However, the applications of NHPs in AD research have been hindered by the paucity of spontaneous or induced monkey models for AD due to their long generation time, ethical considerations and technical challenges in making genetically modified monkeys. Here we developed an AD-like NHP model by overexpressing human tau in bilateral hippocampi of adult rhesus macaque monkeys. We evaluated the pathological features of these monkeys with immunostaining, cerebrospinal fluid (CSF) analysis, magnetic resonance imaging (MRI), positron emission tomography (PET) scan, and behavioral tests. We demonstrated that after hippocampal overexpression of human tau, the rhesus macaque monkeys displayed multiple pathological features of AD, including neurofibrillary tangle formation, neuronal loss, hippocampal atrophy, neuroinflammation, A{beta} clearance deficit, blood vessel damage and cognitive decline. This work establishes a human tau-induced AD-like NHP model that may facilitate mechanistic studies and therapeutic treatments for AD.

neuroscience↗

Transcriptomics reveals amygdala neuron regulation by fasting and ghrelin thereby promoting feeding

The central amygdala (CeA) consists of numerous genetically-defined inhibitory neurons that control defensive and appetitive behaviors including feeding. Transcriptomic signatures of cell types and their links to function remain poorly understood. Using single-nucleus RNA-sequencing, we describe nine CeA cell clusters, of which four are mostly associated with appetitive and two with aversive behaviors. To analyze the activation mechanism of appetitive CeA neurons, we characterized Serotonin receptor 2a (Htr2a)-expressing neurons (CeAHtr2a) that comprise three appetitive clusters and were previously shown to promote feeding. In vivo calcium imaging revealed that CeAHtr2a neurons are activated by fasting, the hormone ghrelin, and the presence of food. Moreover, these neurons are required for the orexigenic effects of ghrelin. Appetitive CeA neurons responsive to fasting and ghrelin project to the parabrachial nucleus (PBN) causing inhibition of target PBN neurons. These results illustrate how the transcriptomic diversification of CeA neurons relates to fasting and hormone-regulated feeding behavior. HighlightsTranscriptomics reveals four appetitive, two aversive and three unknown CeA clusters Ghrelin and fasting activate CeAHtr2a neurons comprising three appetitive clusters Ghrelins orexigenic effects require the activity of appetitive CeA neurons CeA[->]PBN inhibition is necessary for ghrelin/fasting induced feeding

neuroscience↗

Insitutype: likelihood-based cell typing for single cell spatial transcriptomics

Accurate cell typing is fundamental to analysis of spatial single-cell transcriptomics, but legacy scRNA-seq algorithms can underperform in this new type of data. We have developed a cell typing algorithm, Insitutype, designed for statistical and computational efficiency in spatial transcriptomics data. Insitutype is based on a likelihood model that weighs the evidence from every expression value, extracting all the information available in each cells expression profile. This likelihood model underlies a Bayes classifier for supervised cell typing, and an Expectation-Maximization algorithm for unsupervised and semi-supervised clustering. Insitutype also leverages alternative data types collected in spatial studies, such as cell images and spatial context, by using them to inform prior probabilities of cell type calls. We demonstrate rapid clustering of millions of cells and accurate fine-grained cell typing of kidney and non-small cell lung cancer samples.

bioinformatics↗

Synthetic lethal targeting of TET2-mutant hematopoietic stem and progenitor cells by XPO1 inhibitors

TET2 inactivating mutations serve as initiating genetic lesions in the transformation of hematopoietic stem and progenitor cells (HSPCs). In this study, we analyzed known drugs in zebrafish embryos for their abilities to selectively kill tet2-mutant HSPCs in vivo, and we found that the exportin 1 (XPO1) inhibitors, selinexor and eltanexor, selectively kill tet2-mutant HSPCs. In serial replating colony assays, these small molecules were selectively active in killing murine Tet2-deficient Lineage-, Sca1+, Kit+ (LSK) cells, and also TET2-inactivated human acute myeloid leukemia (AML) cells. Selective killing of TET2-mutant HSPCs and human AML cells by these inhibitors was due to increased levels of apoptosis, without evidence of DNA damage based on increased {gamma}H2AX expression. The finding that TET2 loss renders HSPCs and AML cells selectively susceptible to cell death induced by XPO1 inhibitors provides preclinical evidence of selective activity of these drugs, justifying further clinical studies of these small molecules for the treatment of TET2-mutant hematopoietic malignancies and to suppress clonal expansion in age-related TET2-mutant clonal hematopoiesis.

cancer biology↗

Signatures of Microbial Diversity at Multiple Scales of Resolution within Engineered Enrichment Communities

Microbial community dynamics are dictated by both abiotic environmental conditions and biotic interactions. These communities consist of individual microorganisms across the continuum of phylogenetic diversity, ranging from coexisting members of different domains of life and phyla to multiple strains with only a handful of single nucleotide variants. Ecological forces act on a shifting template of population-level diversity that is shaped by evolutionary processes. However, understanding the ecological and evolutionary forces contributing to microbial community interactions and overall ecosystem function is difficult to interrogate for complex, naturally occurring microbial communities. Here, we use two time series of lab-scale engineered enrichment microbial communities simulating phosphorus removal to explore signatures of microbial diversity at multiple phylogenetic scales. We characterized microbial community dynamics and diversity over the course of reactor start-up and long-term dynamics including periods of eubiosis and dysbiosis as informed by the intended ecosystem function of phosphorus removal. We then compared these signatures to lineages from full-scale WWTPs performing phosphorus removal. We found that enriched lineages in lab-scale bioreactors harbor less intra-population diversity than lineages from the full-scale WWTP overall. Our work establishes a foundation for using engineered enrichment microbial communities as a semi-complex model system for addressing the fundamental ecological and evolutionary processes necessary for developing stable microbiome based biotechnologies.

microbiology↗

Engineering a plant polyketide synthase for the biosynthesis of methylated flavonoids

Homoeriodictyol and hesperetin are naturally occurring O-methylated flavonoids with many health-promoting properties. They are produced in plants in low abundance and as complex mixtures of similar compounds that are difficult to separate. Synthetic biology offers the opportunity to produce various flavonoids in a targeted, bottom-up approach in engineered microbes with high product titers. However, the production of O-methylated flavonoids is currently still highly inefficient. In this study, we investigated and engineered a combination of enzymes that had previously been shown to support homoeriodictyol and hesperetin production in Escherichia coli from fed O-methylated cinnamic acids. We determined the crystal structures of the enzyme catalyzing the first committed step of the pathway, chalcone synthase from Hordeum vulgare, in three ligand-bound states. Based on these structures and a multiple sequence alignment with other chalcone synthases, we constructed mutant variants and assessed their performance in E. coli towards producing methylated flavonoids. With our best mutant variant, HvCHS (Q232P, D234V), we were able to produce homoeriodictyol and hesperetin at 2 times and 10 times higher titers than previously reported. Our findings will facilitate the further engineering of this enzyme towards higher production of methylated flavonoids.

biochemistry↗

An Immune Cell Recirculation-Enabled Microfluidic Array to Study Dynamic Immunotherapeutic Activity in Recapitulated Tumor Microenvironment

The efficacy of immunotherapeutic treatment protocols to enable immune cell mediated treatment of cancer is significantly modulated in the presence of tumor microenvironment (TME) which is a key factor in providing both a physical barrier and immunosuppressive stimuli. Herein, we developed a recirculating, high-throughput microfluidic cell array to capture these crucial players - cytotoxic T cells in circulation, endothelium, and tumor stroma. The system consisted of a three-layered cell array spatially emulating TME, with T cell circulation sustained via fluidic recirculating circuits. This allowed us to study the dynamic TME/circulation system and cancer cell response thereof. The system further revealed that tumor endothelium exhibited a hindrance to T cell infiltration into the breast cancer tumor compartment, which was alleviated when treated with anti-human PD-L1 antibody. The other key stromal component, cancer associated fibroblasts, further attenuated T cell infiltration, and led to reduced apoptosis activity in cancer cells. These results confirm the capability of our tumor-on-a-chip system to recapitulate some key immune cell interactions with the reconstructed TME, along with demon-strating as the feasibility of using this system for high-throughput cancer immunotherapeutic screening.

bioengineering↗

lncRNA-WAL Promotes Aggressiveness of Triple-Negative Breast Cancer via inducing β-Catenin nuclear translocation.

Because of its insensitive to existing radiotherapy, chemotherapy and targeted treatments, Triple-negative breast cancer (TNBC) remains a great challenge to overcome. More and more evidence has indicated abnormal wnt/{beta}-catenin pathway activation in TNBC but not luminal or her2+ breast cancer, and lncRNAs play a key role in a variety of cancers. Through lncRNA microarray profiling between Activated and inactivated Wnt/{beta}-catenin pathway of TNBC tissues, lnc-WAL (Wnt/{beta}-catenin associated lncRNA; WAL) was selected as the top up-regulated lncRNA in Wnt/{beta}-catenin pathway activation compared with the inactivation group. RIP-seq was analyzed between {beta}-catenin and IgG groups of, where lnc-WAL could interact with {beta}-catenin. Clinically, increased lnc-WAL in the TNBC tumor tissue was associated with shorter survival. lnc-WAL promoted the EMT, the ability of breast cancer stem cells (BCSC), proliferation, migration and invasion of TNBC cells. Mechanistically, lnc-WAL inhibited {beta}-catenin protein degradation via Axin-mediated phosphorylation at serine 45. Subsequently, {beta}-catenin was accumulated in nuclear and activated the target genes. Importantly, Wnt/{beta}-catenin pathway activation stimulated the transcription of lnc-WAL. These results pointed to a master regulatory role of lnc-WAL/Axin/{beta}-catenin in the malignant progression of TNBC. Our findings provide important clinical translational evidence that lnc-WAL maybe as potential therapeutic target against TNBC.

genetics↗

STAT3 cooperates with the core transcriptional regulatory circuitry to drive MYC expression and oncogenesis in anaplastic large cell lymphoma

Anaplastic large cell lymphoma (ALCL) is an aggressive, CD30+ T-cell lymphoma of children and adults. ALK fusion transcripts or mutations in the JAK-STAT pathway are observed in most ALCL tumors, but the mechanisms underlying tumorigenesis are not fully understood. Here we show that dysregulated STAT3, together with a core transcriptional regulatory circuit consisting of BATF3-IRF4- IKZF1, co-occupies gene enhancers to establish an oncogenic transcription program and maintain the malignant state of ALCL. Critical downstream targets of this network in ALCL cells include the proto-oncogene MYC, which requires active STAT3 to facilitate high levels of MYC transcription. The activity of this auto-regulatory transcription loop is reinforced by MYC binding to the enhancer regions associated with STAT3 and each of the core regulatory transcription factors. These findings provide new insights for understanding how dysregulated signaling pathways hijack cell-type-specific transcriptional machinery to drive tumorigenesis and create therapeutic vulnerabilities in genetically defined tumors.

cancer biology↗

Model Choice Metrics to Optimize Profile-QSAR Performance

BackgroundPredicting molecular activity against protein targets is difficult because of the paucity of experimental data. Approaches like multitask modeling and collaborative filtering seek to improve model accuracy by leveraging results from multiple targets, but are limited because different compounds are measured with different assays, leading to sparse data matrices. Profile-QSAR (pQSAR) 2.0 addresses this problem by fitting a series of partial least squares models for each target, using as features the predictions from single-task models on the remaining targets. This method has been shown to produce better results than single task and multitask models. However, the factors determining the success of pQSAR 2.0 have as yet not been characterized. In this paper we examine the experimental conditions that lead to better pQSAR models. We limit the amount of data available to the method by retraining with decreasing amounts of data and explore the models ability to generalize to compounds that have never been assayed. Finally, we look at the properties of training data needed to demonstrate pQSAR improvement. ResultsWe apply pQSAR 2.0 on a collection of GPCR and safety targets collected from Drug Target Commons, ExcapeDB, and ChEMBL. We found that pQSAR improved models on 34 of the 149 assays selected. In the other 115 assays, single task random forests offered better performance. There are many factors that contribute to an increase in performance, but the main factor is compound assay coverage. The pQSAR model improves when more compounds are measured in multiple assays. ConclusionIt is necessary to consider the available data before applying pQSAR. Successful pQSAR models require a profile made of correlated targets that share compounds with other assays. This technique is best used when experimental data is available as random forest regressors often do not generalize well enough for virtual drug search applications.

bioinformatics↗

A reductase in the lipid metabolism at cross roads between cuticular wax production and jasmonic acid-mediated defenses in maize

Cuticular wax is the first physical layer to protect plants from herbivore infestations. Although wax and jasmonic acid (JA) biosynthesis are the two most studied branches of lipid metabolism, the mechanism how cuticular wax production modulates plant chemical defenses is unclear. Here, we show that the maize (Zea mays) GL8 gene, encoding 3-ketoacyl reductase during fatty acid elongation in the biosynthesis of very long chain fatty acids (VLCFA), functions as a turning point between wax production and JA-mediated defenses. The fall armyworm (Spodoptera frugiperda) larvae consumed more tissue but gained a lower performance on gl8/Ye478 mutant plants. gl8/Ye478 mutant displayed higher JA-mediated defenses constitutively, and also more inducible by herbivore stimulation. The comprehensive transcriptomic and lipidomic analyses further demonstrated that ZmGL8 mutation up-regulates the JA biosynthesis pathway by promoting the accumulation of lysophospholipids and modulation of galactolipid synthase genes ZmDGD and ZmMGD. The phenotypic and transcription comparisons of the maize and Arabidopsis wax-deficient mutants suggest a conserved wide-spread trade-off between wax production and chemical defense in both 18:3 and 16:3 plants. These results illustrate a critical role of VLCFA metabolism as a switch to control the balance between cuticular wax physical barrier and JA-mediated chemical defenses during plant-herbivore coevolution history.

plant biology↗

Diversity, distribution, and expression of opsin genes in freshwater lakes

Microbial rhodopsins are widely distributed in aquatic environments and may significantly contribute to phototrophy and energy budgets in global oceans. However, the study of freshwater rhodopsins has been largely limited. Here, we explored the diversity, ecological distribution, and expression of opsin genes that encode the apoproteins of Type I rhodopsins in humic and clearwater lakes with contrasting physicochemical and optical characteristics. Using metagenomes and metagenome-assembled genomes, we recovered opsin genes from a wide range of taxa, mostly predicted to encode green light-absorbing proton pumps. Viral opsin and novel bacterial opsin clades were recovered. Opsin genes occurred more frequently in taxa from clearwater than from humic water, and opsins in some taxa have non-typical ion-pumping motifs that might be associated with physicochemical conditions of these two freshwater types. Analyses of the surface layer of 33 freshwater systems revealed an inverse correlation between opsin gene abundance and lake dissolved organic carbon (DOC). In humic water with high terrestrial DOC and light-absorbing humic substances, opsin gene abundance was low and dramatically declined within the first few meters, whereas the abundance remained relatively high along the bulk water column in clearwater lakes with low DOC, suggesting opsin gene distribution is influenced by lake optical properties and DOC. Gene expression analysis confirmed the significance of rhodopsin-based phototrophy in clearwater lakes and revealed different diel expressional patterns among major phyla. Overall, our analyses revealed freshwater opsin diversity, distribution and expression patterns, and suggested the significance of rhodopsin-based phototrophy in freshwater energy budgets, especially in clearwater lakes.

microbiology↗

Generation of functional posterior spinal motor neurons from hPSCs-derived human spinal cord neural progenitor cells

Spinal motor neurons deficiency results in a series of devastating disorders such as amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA) and spinal cord injury (SCI). These disorders are currently incurable, while human pluripotent stem cells (hPSCs)-derived spinal motor neurons are promising but suffered from low-efficiency, functional immaturity and lacks of posterior cellular identity. In this study, we have established human spinal cord neural progenitor cells (hSCNPCs) via hPSCs differentiated neuromesodermal progenitors (NMPs) and demonstrated the hSCNPCs can be continuously expanded up to 40 passages. hSCNPCs can be rapidly differentiated into posterior spinal motor neurons with high efficiency. The functional maturity has been examined in detail. Moreover, a co-culture scheme which is compatible for both neural and muscular differentiation is developed to mimic the neuromuscular junction (NMJ) formation in vitro. Together, these studies highlight the potential avenues for generating clinically relevant spinal motor neurons and modeling neuromuscular diseases through our defined hSCNPCs.

cell biology↗

Enhancing NeuroD1 Expression to Convert Lineage-Traced Astrocytes into Neurons

Regenerating functional new neurons in adult mammalian brains has been proven a difficult task for decades. Recent advancement in direct glia-to-neuron conversion in vivo opens a new field for neural regeneration and repair. However, this emerging new field is facing serious challenges from misuse of viral vectors to misinterpretation of conversion data. Here, we employ a variety of AAV vectors with different promoters and enhancers to demonstrate that astrocytes can be converted into neurons in a NeuroD1 dose-dependent manner in both wildtype (WT) and transgenic mice. Notably, astrocytes in WT mice were relatively easy to convert with higher conversion efficiency, whereas lineage-traced astrocytes in Aldh1l1-CreERT2 mice showed high resistance to reprogramming but were still converted into neurons after enhancing NeuroD1 expression with CMV enhancer. Furthermore, under two-photon microscope, we observed direct astrocyte-to-neuron conversion within 3 weeks of serial live imaging in the mouse cortex. We also demonstrated that high titre AAV reaching 1013 GC/ml caused severe neuronal leakage using a variety of AAV GFAP::GFP vectors, highlighting the necessity to inject low titre AAV into healthy brains to avoid artifactual results. Together, our studies suggest that lineage-traced astrocytes can be converted into neurons but require stronger conversion force such as enhanced NeuroD1 expression. Failure to recognize the difference between WT astrocytes and lineage-traced astrocytes in terms of conversion barrier will lead to misinterpretation of data.

neuroscience↗

Role of Paravertebral muscle myostatin upregulation in the development of idiopathic scoliosis

Paravertebral muscle (PVM) abnormalities play important roles in the pathogenesis of idiopathic scoliosis (IS), and elevated oxidative stress could result in PVM injury in IS patients, but the underlying mechanism of oxidative stress generation is still unclear. Increased apoptosis, impaired myogenesis and elevated oxidative stress were found in primary skeletal muscle mesenchymal progenitor cells (hSM-MPCs), which are essential for the myogenesis process of vertebrate skeletal muscles, of IS patients. Through RNA-sequencing and further analysis, we identified significantly upregulated myostatin (MSTN) in IS hSM-MPCs. Overexpression of MSTN in hSM-MPCs from control patients increased the expression of NADPH oxidase 4, promoted reactive oxygen species production and apoptosis, and suppressed myogenesis. However, MSTN knockdown decreased the expression of NADPH oxidase 4, inhibited reactive oxygen species production and apoptosis, and enhanced myogenesis in IS hSM-MPCs. In addition, overexpression of MSTN in the PVMs of mice induced elevated oxidative stress and scoliosis without abnormal vertebral structure. Altogether, our study suggested that abnormal PVM changes and accumulated oxidative stress in IS patients may result from upregulation of MSTN, which could contribute to the development of IS.

pathology↗

Structure of nucleosome-bound human PBAF complex

BAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create nucleosome-depleted/free regions for transcription activation. Despite structural studies of nucleosome-bound human BAF and yeast SWI/SNF family complexes, it remains elusive how PBAF-nucleosome complex is organized. Here we determined structure of 13-subunit human PBAF in complex with acetylated nucleosome in ADP-BeF3-bound state. Four PBAF-specific subunits work together with nine BAF/PBAF-shared subunits to generate PBAF-specific modular organization, distinct from that of BAF at various regions. PBAF-nucleosome structure reveals six histone-binding domains and four DNA-binding domains/modules, the majority of which directly bind histone/DNA. This multivalent nucleosome-binding pattern, not observed in previous studies, suggests that PBAF may integrate comprehensive chromatin information to target genomic loci for function. Our study reveals molecular organization of subunits and histone/DNA-binding domains/modules in PBAF-nucleosome complex and provides a framework to understand chromatin targeting of SWI/SNF family complexes.

molecular biology↗