Biology subjects

Ye, X.

Publications and source records attributed to Ye, X..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Exploratory study of pulsed electric field ablation on atherosclerotic plaque in a rabbit model

New understanding of the pathogenesis of atherosclerotic diseases has led to the emergence of new therapeutic approaches. We explored the potential therapeutic effects of pulsed field potential ablation (PFA), a non-thermal ablation technique with high tissue selectivity, on atherosclerotic plaques. Carotid arteries of 30 high-fat rabbits were dilated with a balloon to obtain atherosclerotic plaques. PFA was administered on the carotid atherosclerotic plaques with 1000V/cm, 2000V/cm, and 1000V/cm ablation followed by rapamycin infusion. There were no visible changes in blood vessels after acute ablation, but apoptosis and polarity of cells were observed in atherosclerotic plaques. At 7 and 30 days after ablation, the density of lipid deposition in the plaque was significantly reduced, and multiple layers of new arranged anterograde smooth muscle cells appeared, replacing the original atherosclerotic plaque. The residual atherosclerotic structure is sandwiched between the new smooth muscle layer and the original smooth muscle layer, which makes vascular wall thicker and makes vascular wall elasticity increased. Rapamycin delays the vascular remodeling process. Conclusion: PFA ablation can reduce lipid deposition in atherosclerotic plaques, cause vascular remodeling, and enhance vascular elasticity. We believe that it may be a potential method for the treatment of atherosclerotic plaques.

biophysics↗

bioRxiv2023

The heparin-binding domain of VEGF165 directly binds to integrin αvβ3 and plays a critical role in signaling.

VEGF-A is a key cytokine in tumor angiogenesis and a major therapeutic target for cancer. VEGF165 is the predominant isoform and is the most potent angiogenesis stimulant. VEGFR2/KDR domains 2 and 3 (D2D3) bind to the N-terminal domain (NTD, residues 1-110) of VEGF165. Since removal of the heparin-binding domain (HBD, residues 111-165) markedly reduced the mitogenic activity of VEGF165, it has been proposed that the HBD plays a critical role in the mitogenicity of VEGF165. Integrin v{beta}3 has been shown to bind to VEGF165, but the role of integrin v{beta}3 in VEGF165 signaling are unclear. Here we describe that v{beta}3 specifically bound to the isolated HBD, but not to the NTD. We identified several critical amino acid residues in HBD for integrin binding (Arg-123, Arg-124, Lys-125, Lys-140, Arg-145, and Arg-149) by docking simulation and mutagenesis, and generated full-length VEGF165 that is defective in integrin binding by including mutations in the HBD. The full-length VEGF165 mutant defective in integrin binding (R123A/R124A/K125A/K140A/R145A/R149A) was defective in ERK1/2 phosphorylation, integrin {beta}3 phosphorylation, and KDR phosphorylation, although the mutation did not affect KDR binding to VEGF165. We propose a model in which VEGF165 induces KDR (through NTD)-VEGF165 (through HBD)-integrin v{beta}3 ternary complex formation on the cell surface and this process is critically involved in potent mitogenicity of VEGF165.

biochemistry↗

bioRxiv2023

Multimodal single cell-resolved spatial proteomics reveals pancreatic tumor heterogeneity

Despite the advances in antibody-guided cell typing and mass spectrometry-based proteomics, their integration is hindered by challenges for processing rare cells in the heterogeneous tissue context. Here, we introduce Spatial and Cell-type Proteomics (SCPro), which combines multiplexed imaging and flow cytometry with ion exchange-based protein aggregation capture technology to characterize spatial proteome heterogeneity with single cell resolution. The SCPro was employed to explore the pancreatic tumor microenvironment and revealed the spatial alternations of over 5,000 proteins by automatically dissecting up to 100 single cells guided by multi-color imaging of centimeter-scale formalin-fixed, paraffin-embedded tissue slide. To enhance cell-type resolution, we characterized the proteome of 14 different cell types by sorting up to 1,000 cells from the same tumor, which allows us to deconvolute the spatial distribution of immune cell subtypes and leads to the discovery of a novel subtype of regulatory T cells. Together, the SCPro provides a multimodal spatial proteomics approach for profiling tissue proteome heterogeneity.

systems biology↗

bioRxiv2023

Murine uterine gland branching is necessary for gland function in implantation

Uterine glands are branched, tubular structures whose secretions are essential for pregnancy success. It is known that pre-implantation glandular expression of leukemia inhibitory factor (LIF) is crucial for embryo implantation, however contribution of uterine gland structure to gland secretions such as LIF is not known. Here we use mice deficient in estrogen receptor 1 (ESR1) signaling to uncover the role of ESR1 signaling in gland branching and the role of a branched structure in LIF secretion and embryo implantation. We observed that deletion of ESR1 in neonatal uterine epithelium, stroma and muscle using the progesterone receptor PgrCre causes a block in uterine gland development at the gland bud stage. Embryonic epithelial deletion of ESR1 using a mullerian duct Cre line - Pax2Cre, displays gland bud elongation but a failure in gland branching. Surprisingly, adult uterine epithelial deletion of ESR1 using the lactoferrin-Cre (LtfCre) displays normally branched uterine glands. Intriguingly, unbranched glands from Pax2Cre Esr1flox/flox uteri fail to express glandular pre-implantation Lif, preventing implantation chamber formation and embryo alignment along the uterine mesometrial-antimesometrial axis. In contrast, branched glands from LtfCre Esr1flox/flox uteri display reduced expression of glandular Lif resulting in delayed implantation chamber formation and embryo-uterine axes alignment but deliver a normal number of pups. Finally, pre-pubertal unbranched glands in control mice express Lif in the luminal epithelium but fail to express Lif in the glandular epithelium even in the presence of estrogen. These data strongly suggest that branched glands are necessary for pre-implantation glandular Lif expression for implantation success. Our study is the first to identify a relationship between the branched structure and secretory function of uterine glands and provides a framework for understanding how uterine gland structure-function contributes to pregnancy success.

developmental biology↗

bioRxiv2023

LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins

Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies implicate LARP1 in 40S- or 80S-ribosome complexes that repress and stabilize TOPs. However, a mechanistic understanding of how LARP1 and TOPs interact with these complexes to coordinate TOP outcomes is lacking. Here, we show that LARP1 senses the cellular supply of ribosomes by directly binding non-translating ribosomal subunits. Cryo-EM structures reveal a previously uncharacterized domain of LARP1 bound to and occluding the 40S mRNA channel. Free cytosolic ribosomes induce sequestration of TOPs in repressed 80S-LARP1-TOP complexes independent of alterations in mTOR signaling. Together, this work demonstrates a general ribosome-sensing function of LARP1 that allows it to tune ribosome protein synthesis to cellular demand. One-Sentence SummaryLARP1 directly binds free ribosomal subunits to repress TOP mRNAs

molecular biology↗

bioRxiv2023

One-pot virus detection based on isothermal amplificationcoupled with temperature-activated argonaute

Advances in programmable nucleases like CRISPR-associated protein (Cas) and Argonaute (Ago), combined with isothermal amplification, have made point-of-care testing (POCT) more accessible. However, the specific binding of the nuclease resulted in compatibility issues between the amplification and nuclease systems, substantially limiting the feasibility of a one-step workflow. Here, a temperature control solution based on immobilized thermotolerant Pyrococcus furiosus Ago (PfAgo) has been proposed. The use of immobilized PfAgo can effectively prevent interference with loop-mediated isothermal amplification (LAMP) at 65{degrees}C and accurately identifies amplicons when activated at 95{degrees}C. Following optimization, a sensitivity of 0.6 copies/L was achieved within 45 minutes, and high specificity was verified with no cross-reactivity among 22 other viruses. Additionally, the multiplex detection was designed for herpes virus sensing, with agreements of 86.4% for positive and 100% for negative samples. Our research presents an effective method for combining amplification and cleavage through the use of controllable nucleases, significantly improving the clinical applicability of diagnostic techniques dependent on programmable nucleases.

biochemistry↗

bioRxiv2023

Targeting the Hippo pathway in cancers via ubiquitination dependent TEAD degradation

The Hippo pathway is among the most frequently altered key signaling pathways in cancer. TEAD1-4 are essential transcription factors and key downstream effectors in the Hippo pathway in human cells. Here, we identified RNF146 as a ubiquitin ligase (E3) of TEADs, which negatively regulates their stability in cells through proteasome-mediated degradation. We show that RNF146-mediated TEAD ubiquitination is dependent on the TEAD PARylation state. We further validated the genetic interaction between RNF146 and the Hippo pathway in cancer cell lines and the model organism Drosophila melanogaster. Despite the RNF146 and proteasome-mediated degradation mechanisms, TEADs are stable proteins with a long half-life in cells. We demonstrate that degradation of TEADs can be greatly enhanced pharmacologically with heterobifunctional chemical inducers of protein degradation (CIDEs). These TEAD-CIDEs can effectively suppress activation of YAP/TAZ target genes in a dose-dependent manner and exhibit significant anti-proliferative effects in YAP/TAZ-dependent tumor cells, thus phenocopying the effect of genetic ablation of TEAD protein. Collectively, this study demonstrates that the ubiquitin-proteasome system plays an important role in regulating TEAD functions and provides a proof-of-concept demonstration that pharmacologically induced TEAD ubiquitination could be leveraged to target YAP/TAZ-driven cancers.

cancer biology↗

bioRxiv2023

Tissue-Specific Dependence of Th1 Cells on the Amino Acid Transporter SLC38A1 in Inflammation

Amino acid (AA) uptake is essential for T cell metabolism and function, but how tissue sites and inflammation affect CD4+ T cell subset requirements for specific AA remains uncertain. Here we tested CD4+ T cell AA demands with in vitro and multiple in vivo CRISPR screens and identify subset- and tissue-specific dependencies on the AA transporter SLC38A1 (SNAT1). While dispensable for T cell persistence and expansion over time in vitro and in vivo lung inflammation, SLC38A1 was critical for Th1 but not Th17 cell-driven Experimental Autoimmune Encephalomyelitis (EAE) and contributed to Th1 cell-driven inflammatory bowel disease. SLC38A1 deficiency reduced mTORC1 signaling and glycolytic activity in Th1 cells, in part by reducing intracellular glutamine and disrupting hexosamine biosynthesis and redox regulation. Similarly, pharmacological inhibition of SLC38 transporters delayed EAE but did not affect lung inflammation. Subset- and tissue-specific dependencies of CD4+ T cells on AA transporters may guide selective immunotherapies. HIGHLIGHTSO_LIT cells dynamically regulate glutamine amino acid transporters when activated C_LIO_LISLC38A1 supports Th1 cell mTORC1 and proliferation by redox and hexosamine pathways C_LIO_LITargeting SLC38A1 does not affect lung inflammation but delays IBD and EAE C_LIO_LINutrient transporter needs of T cell subsets vary based on disease and tissue site C_LI

immunology↗

bioRxiv2023

Unravelling cancer subtype-specific driver genes in single-cell transcriptomics data with CSDGI

Cancer is known as a heterogeneous disease. Cancer driver genes (CDGs) need to be inferred for understanding tumor heterogeneity in cancer. However, the existing computational methods have identified many common CDGs. A key challenge exploring cancer progression is to infer cancer subtype-specific driver genes (CSDGs), which provides guidane for the diagnosis, treatment and prognosis of cancer. The significant advancements in single-cell RNA-sequencing (scRNA-seq) technologies have opened up new possibilities for studying human cancers at the individual cell level. In this study, we develop a novel unsupervised method, CSDGI (Cancer Subtype-specific Driver Gene Inference), which applies Encoder-Decoder-Framework consisting of low-rank residual neural networks to inferring driver genes corresponding to potential cancer subtypes at single-cell level. To infer CSDGs, we apply CSDGI to the tumor single-cell transcriptomics data. To filter the redundant genes before driver gene inference, we perform the differential expression genes (DEGs). The experimental results demonstrate CSDGI is effective to infer driver genes that are cancer subtype-specific. Functional and disease enrichment analysis shows these inferred CSDGs indicate the key biological processes and disease pathways. CSDGI is the first method to explore cancer driver genes at the cancer subtype level. We believe that it can be a useful method to understand the mechanisms of cell transformation driving tumours. Author summaryCancer is recognized as a complex disease with diverse characteristics. In order to comprehend the diversity within tumors, it is essential to infer cancer subtype-specific driver genes (CSDGs), which offer valuable insights for investigating cancer progression and treatment. The remarkable progress made in single-cell RNA-sequencing (scRNA-seq) technologies has ushered in new prospects for studying human cancers at the cellular level. Cancer Subtype-specific Driver Gene Inference (CSDGI) is a novel unsupervised method proposed. In our study, we use Encoder-Decoder-Framework to infer driver genes specific to cancer subtypes in the CSDGI. We apply CSDGI to three tumor single-cell transcriptomics data. The experimental results have shown the effectiveness of CSDGI. Furthermore, functional and disease enrichment analyses illustrate that these inferred CSDGs shed light on crucial biological processes and disease pathways. Our collection of driver genes will serve as a valuable resource in unraveling the mechanisms driving cell transformation in tumors.

bioinformatics↗

bioRxiv2023

Discovery of reactive peptide inhibitors of human papillomavirus oncoprotein E6

Human papillomavirus (HPV) infections account for nearly all cervical cancer cases, which is the fourth most common cancer in women worldwide. High-risk variants, including HPV16, drive tumorigenesis in part by promoting the degradation of the tumor suppressor p53. This degradation is mediated by the HPV early protein 6 (E6), which recruits the E3 ubiquitin ligase E6AP and redirects its activity towards ubiquitinating p53. Targeting the protein interaction interface between HPV E6 and E6AP is a promising modality to mitigate HPV-mediated degradation of p53. In this study, we designed a covalent peptide inhibitor, termed reactide, that mimics the E6AP LXXLL binding motif by selectively targeting cysteine 58 in HPV16 E6 with quantitative conversion. This reactide provides a starting point in the development of covalent peptidomimetic inhibitors for intervention against HPV-driven cancers.

molecular biology↗

bioRxiv2023

Archaeal self-activating GPN-loop GTPases involve a lock-switch-rock mechanism for GTP hydrolysis

Three GPN-loop GTPases, GPN1-GPN3, are central to the maturation and trafficking of eukaryotic RNA polymerase II. This GTPase family is widely represented in archaea but typically occurs as single paralogs. Structural analysis of the GTP- and GDP-bound states of the Sulfolobus acidocaldarius GPN enzyme (SaGPN) showed that this central GPN-loop GTPase adopts two distinct quaternary structures. In the GTP-bound form the {gamma}-phosphate induces a tensed dimeric arrangement by interacting with the GPN region that is relaxed upon hydrolysis to GDP. Consequently, a rocking-like motion of the two protomers causes a major allosteric structural change towards the roof-like helices. Using a lock-switch-rock (LSR) mechanism, homo- and heterodimeric GPN-like GTPases are locked in the GTP-bound state and undergo large conformational changes upon GTP hydrolysis. A{Delta} saGPN strain of S. acidocaldarius was characterized by impaired motility and major changes in the proteome underscoring its functional relevance for S. acidocaldarius in vivo. Significance StatementGPN-loop GTPases have been found to be crucial for eukaryotic RNA polymerase II assembly and nuclear trafficking. Despite their ubiquitous occurrence in eukaryotes and archaea the mechanism by which these self-activating GTPases mediate their function is unknown. Our study on an archaeal representative from Sulfolobus acidocaldarius showed that these dimeric GTPases undergo large-scale conformational changes upon GTP hydrolysis, which can be summarized as a lock-switch-rock mechanism. The observed requirement of SaGPN for motility appears to be due to its large footprint on the archaeal proteome.

biochemistry↗

bioRxiv2023

Olfactory and neuropeptide inputs to appetite neurons in the arcuate nucleus

The sense of smell has potent effects on appetite, but the underlying neural pathways remain undefined. Here we investigated how olfactory signals reach two subsets of appetite-linked neurons in the hypothalamic arcuate nucleus: AgRP (agouti-related peptide) neurons, which stimulate appetite, and POMC (pro-opiomelanocortin) neurons, which suppress it. Using polysynaptic viral tracing, we show that AgRP and POMC neurons receive indirect input from partially overlapping but distinct areas of the olfactory cortex, indicating that they process different sets of olfactory information. We also identify different complements of neurons directly upstream of AgRP and POMC neurons that can relay olfactory cortical signals to the appetite neurons. Single cell transcriptomics shows heterogeneous expression of neuromodulator receptors among AgRP neurons, suggesting variations in the signals they receive. Integrated viral tracing and RNA localization further reveals selected brain areas where upstream neurons express cognate receptor ligands. Together, these findings outline multiple pathways by which distinct olfactory and modulatory signals are differentially routed to neurons that promote versus inhibit appetite.

neuroscience↗

bioRxiv2023

Androgen Signaling Restricts Glutaminolysis to Drive Sex-Specific Th17 Metabolism

Females have increased prevalence of many Th17-mediated diseases. While androgen signaling decreases Th17-mediated inflammation, the mechanisms are not fully understood. Th17 cells rely on glutaminolysis; however, it remains unclear whether androgen receptor (AR) signaling in males modifies glutamine metabolism to suppress Th17-mediated inflammation. We show that Th17 cells from male humans and mice had decreased glutaminolysis compared to females, and AR signaling attenuated Th17 cell mitochondrial respiration and glutaminolysis. Using allergen-induced airway inflammation models, we determined females, but not males, had a critical reliance upon glutaminolysis for Th17-mediated airway inflammation, and AR signaling attenuated glutamine uptake by reducing expression of glutamine transporters. These findings were confirmed in circulating human Th17 cells with minimal reliance on glutamine uptake in male compared to female Th17 cells. We found that AR signaling attenuates glutaminolysis, demonstrating sex-specific metabolic regulation of Th17 cells with implications for design and implementation of Th17 or glutaminolysis targeted therapeutics. HighlightsO_LIHuman male CD4+ T cells have decreased expression of metabolic enzymes and decreased reliance on glutaminolysis compared to female CD4+ T cells. C_LIO_LIAndrogen signaling decreased mitochondrial metabolism in Th17 cells and decreased airway inflammation. C_LIO_LIAndrogen signaling decreased glutamine uptake and utilization in Th17 cells. C_LI

immunology↗

bioRxiv2023

Taxonomical and ontological analysis of verified natural and laboratory human coronavirus hosts

To fully understand COVID-19, it is critical to identify and analyze all the possible hosts of SARS-CoV-2 (the pathogen of COVID-19) and compare them with the hosts of other human coronaviruses. In this study, we collected, annotated, and performed taxonomical and ontological analysis of all the reported and verified hosts for all human coronaviruses including SARS-CoV, MERS-CoV, SARS-CoV-2, and four others that cause the common cold. A total of 37 natural hosts and 19 laboratory animal hosts of host human coronaviruses were identified based on experimental or clinical evidence. Our taxonomical ontology-based analysis found that all the verified susceptible natural and laboratory animals belong to therian mammals. Specifically, these 37 natural therian hosts include one wildlife marsupial mammal (i.e., Didelphis virginiana) and 36 Eutheria mammals (a.k.a. placental mammals). The 19 laboratory animal hosts are also classified as placental mammals. While several non-therian animals (including snake, housefly, zebrafish) were reported to be likely SARS-CoV-2 hosts, our analysis excluded them due to the lack of convincing evidence. Genetically modified mouse models with human Angiotensin-converting enzyme 2 (ACE2) or dipeptidyl peptidase-4 (DPP4) protein were more susceptible to virulent human coronaviruses with clear symptoms. Coronaviruses often became more virulent and adaptive in the mouse hosts after a series of viral passages in the mice. To support knowledge standardization and analysis, we have also represented the annotated host knowledge in the Coronavirus Infectious Disease Ontology (CIDO) and provided ways to automatically query the knowledge.

bioinformatics↗

bioRxiv2023

Constitutive protein degradation induces acute cell death via proteolysis products

Modulation of proteolysis is an emerging therapeutic mainstay. The clinical success of thalidomide and analogs has inspired development of rationally-designed therapeutics that repurpose endogenous degradation machinery to target pathogenic proteins. However, it is unknown whether target removal is the critical effect that drives degrader-induced efficacy. Here we report that proteasome-generated peptides actively initiate degrader-induced cell death. Utilizing BET family degraders as exemplars, we find that induced proteasomal degradation of the BRD4-long isoform (BRD4-L) generates neo-amino-terminal peptides that neutralize Inhibitor of Apoptosis (IAP) proteins to precipitate cell death. Depletion of BRD4-L paradoxically suppresses caspase activation induced by numerous BET degraders. An unbiased screen revealed that other degrader compounds, including clinical CELMoDs, rely on the same mechanism to potentiate caspase activation and apoptosis. Finally, in the context of constitutive immunoglobulin proteostasis within multiple myeloma cells, we report that therapeutic proteasomal protease inhibition alters the peptide repertoire to neutralize IAPs, thus contributing to the clinical efficacy of bortezomib. Together, these findings clarify the counterintuitive clinical benefit achieved by combining thalidomide analogs with proteasome inhibitors. Our study reveals a previously unrealized pro-apoptotic function of the peptides generated by a variety of proteolysis-modulating compounds, that provide design considerations to maximize therapeutic benefit.

cell biology↗

bioRxiv2023

Branched multimeric peptides as affinity reagents for detection of α-Klotho protein

-Klotho is a protein associated with aging that is expressed in the kidney, parathyroid gland, and choroid plexus. As a transmembrane protein, it acts as an essential co-receptor with the fibroblast growth factor 23 receptor complex to regulate serum phosphate and vitamin D levels. -Klotho has an extracellular domain that can be cleaved, released and circulated in the blood stream as a soluble form. Decreased levels of -Klotho are an indication of chronic kidney disease and other age-associated diseases. Detecting or labeling transmembrane and soluble -Klotho is a longstanding challenge that has impeded the in-depth understanding of its role. Here we describe branched multimeric peptides that recognize -Klotho with high affinity and selectivity in the biological milieu. The branched peptides are prepared in a single-shot synthesis by parallel automated fast-flow synthesis in under one hour. The branched -Klotho-binding peptides show improvement in affinity relative to the monomeric versions and can be used to label Klotho for live imaging in kidney cells. Our results demonstrate the potential of automated flow technology to deliver peptide-based reagents with complex architecture and improved affinity for the selective binding of target proteins in physiological settings.

molecular biology↗

bioRxiv2022

Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which harnesses software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes a browser-accessible virtual desktop environment and a command line interface, mediating access to containerized neuroimaging software libraries on various computing platforms, including personal and high-performance computers, cloud computing and Jupyter Notebooks. This community-oriented, open-source platform enables a paradigm shift for neuroimaging data analysis, allowing for accessible, flexible, fully reproducible, and portable data analysis pipelines.

neuroscience↗

bioRxiv2022

Rapid generation of CD19 CAR-T Cells by minicircle DNA enables anti-tumor activity and prevents fatal CAR-B leukemia

Manufacturing CAR (chimeric antigen receptor)-T cell with viral vector is expensive and time-consuming. Besides, during viral transduction, the genes encoding CARs are randomly integrated into the genome, which could cause oncogenesis or produce devastating CAR-tumor cells. Here, using virus-free and non-transgenic minicircle DNA (mcDNA) vector, we enable rapid generation of CD19 CAR-T cells within two days. Further, we demonstrate in vitro and in xenograft models that the anti-tumor effects of CD19 CAR-T cells produced by mcDNA are as effective as those produced by viral vectors. Finally, we show that our manufacturing process can avoid the production of fatal CAR-tumor cells. Taken together, we provide a fast, effective, and therapeutically safe method to generate CD19 CAR-T cells for treating leukemia.

cancer biology↗