Biology subjects

Pan, X.

Publications and source records attributed to Pan, X..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

The oncogene SLC35F2 is a high-specificity transporter for the micronutrients queuine and queuosine

The nucleobase queuine (q) and its nucleoside queuosine (Q) are micronutrients derived from bacteria that are acquired from the gut microbiome and/or diet in humans. Following cellular uptake, Q is incorporated at the wobble base (position 34) of tRNAs with a GUN anticodon, which is important for efficient translation. Early studies suggested that cytosolic uptake of queuine is mediated by a selective transporter that is regulated by mitogenic signals, but the identity of this transporter has remained elusive. Here, through a cross-species bioinformatic search and genetic validation, we have identified the solute carrier family member SLC35F2 as a unique transporter for both queuine and queuosine in Schizosaccharomyces pombe and Trypanosoma brucei. Furthermore, gene disruption in HeLa cells revealed that SLC35F2 is the sole transporter for queuosine in HeLa cells (Km 174 nM) and a high-affinity transporter for the queuine nucleobase (Km 67 nM), with the presence of another low-affinity transporter (Km 259 nM) in these cells. Competition uptake studies show that SLC35F2 is not a general transporter for other canonical ribonucleobases or ribonucleosides, but selectively imports q and Q. The identification of SLC35F2, an oncogene, as the transporter of both q and Q advances our understanding of how intracellular levels of queuine and queuosine are regulated and how their deficiency contributes to a variety of pathophysiological conditions, including neurological disorders and cancer. Significance StatementThe discovery of SLC35F2 as the eukaryotic transporter of queuine and queuosine is key to understanding how these micronutrients are salvaged from the human gut and distributed to different body tissues. Queuosine modification of tRNAs enhances the accuracy and efficiency of codon-anticodon pairing and regulates a range of biological and pathophysiological states, including oxidative stress responses, cancer, learning, memory, and gut homeostasis.

biochemistry↗

bioRxiv2024

Employing Microsoft Sway as a Repository for Data Generated in Pharmaceutics Experimental Courses: A Case study on Topical Formulation Characterization

Microsoft Sway is an easy-to-use online creative software developed by Microsoft. It has many advantages as follows: easy to operate and does not require long-term practice and learning; network links can be created and accessed by devices such as Personal Computer (PC) and mobile terminals; Educators and Learners are allowed to browse this repository at anytime to facilitate the application prospects of mining relevant data. Therefore, the author proposes that Microsoft Sway may be a very promising data repository for pharmaceutical experimental teaching courses, and is expected to be extended to undergraduate experimental teaching in other natural science fields.

scientific communication and education↗

bioRxiv2024

A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function

Organ function requires coordinated activities of thousands of genes in distinct, spatially organized cell types. Understanding the basis of emergent tissue function requires approaches to dissect the genetic control of diverse cellular and tissue phenotypes in vivo. Here, we develop paired imaging and sequencing methods to construct large-scale, multi-modal genotype-phenotypes maps in tissue with pooled genetic perturbations. Using imaging, we identify genetic perturbations in individual cells while simultaneously measuring their gene expression and subcellular morphology. Using single-cell sequencing, we measure transcriptomic responses to the same genetic perturbations. We apply this approach to study hundreds of genetic perturbations in the mouse liver. Our study reveals regulators of hepatocyte zonation and liver unfolded protein response, as well as distinct pathways that cause hepatocyte steatosis. Our approach enables new ways of interrogating the genetic basis of complex cellular and organismal physiology and provides crucial training data for emerging machine-learning models of cellular function.

genomics↗

bioRxiv2024

Mapping lineage-resolved scRNA-seq data with spatialtranscriptomics using TemSOMap

Spatial transcriptomics (ST) has revolutionized the study of cell spatial organization and cell-cell interactions. However, current ST technologies face limitations such as lower gene coverage and spatial resolution compared to single-cell RNA sequencing (scRNA-seq). Integrating scRNA-seq with ST can address these issues by mapping single cells onto spatial data, thereby inferring their spatial coordinates. During tissue formation, cells derived from the same ancestor often remain spatially proximate, making lineage data valuable for cell location inference. Certain single-cell multi-omics technologies including lineage tracing provide paired gene expression and induced or sometic mutation information in single cells, which can be used to reconstruct the cell lineage tree, representing the clonal relationships of cells. To incorporate this information, we developed TemSOMap (Temporal dynamics guided Spatial Omics Mapping), which infers the spatial coordinates of cells by mapping a paired gene expression and mutation barcode dataset onto a spatial transcriptomics dataset. TemSOMap infers a cell-to-spot mapping matrix by minimizing a loss function incorporating gene expression, cell lineage and cell location information. We show that TemSOMap more accurately infers the spatial location of single cells compared to state-of-the-art baseline methods under various scenarios, using both simulated and real datasets. The resulting lineage-resolved ST data can help us better understand the spatio-temporal dynamics of cells in a tissue. TemSOMap is publicly available at https://github.com/ZhangLabGT/TemSOMap.

bioinformatics↗

bioRxiv2024

DGRNA: a long-context RNA foundation model with bidirectional attention Mamba2

Ribonucleic acid (RNA) is an important biomolecule with diverse functions i.e. genetic information transfer, regulation of gene expression and cellular functions. In recent years, the rapid development of sequencing technology has significantly enhanced our understanding of RNA biology and advanced RNA-based therapies, resulting in a huge volume of RNA data. Data-driven methods, particularly unsupervised large language models, have been used to automatically hidden semantic information from these RNA data. Current RNA large language models are primarily based on Transformer architecture, which cannot efficiently process long RNA sequences, while the Mamba architecture can effectively alleviate the quadratic complexity associated with Transformers. In this study, we propose a large foundational model DGRNA based on the bidirectional Mamba trained on 100 million RNA sequences, which has demonstrated exceptional performance across six RNA downstream tasks compared to existing RNA language models.

bioinformatics↗

bioRxiv2024

Sodium Benzoate Promotes Fat Accumulation and Aging via the SKN-1/Nrf2 Signaling Pathway: Evidence from the Caenorhabditis elegans Model

Sodium benzoate (SB) is widely used in food products, cosmetics, and medical solutions due to its antimicrobial properties. While it is generally considered safe and has potential neuroprotective benefits, SB has also been linked to adverse effects, including hepatic oxidative stress and inflammation. However, the potential effects of SB on obesity and aging remain poorly understood. In this study, we investigated the effects of SB on fat accumulation and aging using the nematode Caenorhabditis elegans (C. elegans) as a model system. Wild-type worms were exposed to various SB concentrations (0%, 0.0004%, 0.0008%, 0.004%, and 0.1%) and 0.016% glucose as a positive control for 72 hours in liquid or on NGM agar plates. Fat accumulation was assessed through the Oil Red O staining, which revealed that SB induced more fat accumulation compared to vehicle control, even at low concentrations, including the dosage of 0.0004%. Lifespan analysis also demonstrated that SB significantly accelerated aging in wild-type worms in a dose-dependent manner. Further investigations found that SKN-1 (an Nrf2 homolog) is necessary for SB-induced fat accumulation and aging. Moreover, SB inhibited the nuclear localization of SKN-1 under oxidative stress conditions. These findings suggest that SB may induce fat accumulation and aging by inhibiting the oxidative stress-mediated SKN-1 signaling pathway.

pharmacology and toxicology↗

bioRxiv2024

LAPTM4B Alleviates Pulmonary Fibrosis by Enhancing NEDD4L-Mediated TGF-beta Signaling Suppression

Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease with fatal outcome and a poorly understood pathogenesis. The lysosomal protein transmembrane 4 beta (LAPTM4B), a multi-transmembrane endo-lysosomal membrane protein, has been implicated in the pathogenesis of several diseases. However, its involvement in IPF remains unexplored. This study aimed to investigate the role of LAPTM4B in lung fibrosis and elucidate its underlying mechanisms. The results showed that LAPTM4B was significantly reduced in IPF and mouse fibrotic lungs. In vivo studies showed that the deficiency of LAPTM4B exacerbated bleomycin-induced lung fibrosis, while the restoration of LAPTM4B alleviated fibrosis. Mechanistically, LAPTM4B recruits the NEDD4 like E3 ubiquitin protein ligase (NEDD4L) to endosomes, leading to increased ubiquitin-mediated proteasomal degradation of TGFRB2 and active SMAD2/3, thereby blocking the TGF-{beta}/SMAD signaling pathway. Overall, our data provided a novel insight for a deeper understanding of the pathogenesis of IPF, supporting the therapeutic potential of restoration of LAPTM4B as a promising therapeutic approach for the treatment of pulmonary fibrosis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/610429v1_ufig1.gif" ALT="Figure 1"> View larger version (98K): org.highwire.dtl.DTLVardef@1272d12org.highwire.dtl.DTLVardef@10030baorg.highwire.dtl.DTLVardef@17f1756org.highwire.dtl.DTLVardef@d54f78_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

Proteolysis targeting chimera extracellular vesicles for therapeutic development treating triple negative breast cancer

Proteolysis targeting chimeras (PROTACs) are an emerging targeted cancer therapy approach, but wide-spread clinical use of PROTAC is limited due to poor cell targeting and penetration, and instability in vivo. To overcome such issues and enhance the in vivo efficacy of PROTAC drugs, microfluidic droplet-based electroporation ({micro}DES) was developed as a novel extracellular vesicle (EVs) transfection system, which enables the high-efficient PROTAC loading and effective delivery in vivo. Our previously developed YX968 PROTAC drug had shown the selectively degradation of HDAC3 and 8, which effectively suppresses the growth of breast tumor cell lines, including MDA-MB-231 triple negative breast cancer (TNBC) line, via dual degradation without provoking a global histone hyperacetylation. In this study, we demonstrated that {micro}DES-based PROTAC loading in EVs significantly enhanced therapeutic function of PROTAC drug in vivo in the TNBC breast tumor mouse model. NSG mice with pre-established MDA-MB-231 tumors and treated with intraperitoneal injection of EVs for tumor inhibition study, which showed significantly higher HDAC 3 and 8 degradation efficiency and tumor inhibition than PROTAC only group. The liver, spleen, kidney, lung, heart, and brain were collected for safety testing, which exhibited improved toxicity. The EV delivery of PROTAC drug enhances drug stability and bioavailability in vivo, transportability, and drug targeting ability, which fills an important gap in current development of PROTAC therapeutic functionality in vivo and clinical translation. This novel EV-based drug transfection and delivery strategy could be applicable to various therapeutics for enhancing in vivo delivery, efficacy, and safety.

bioengineering↗

bioRxiv2024

Spatiotemporally-resolved mapping of extracellular proteomes via in vivo-compatible TyroID

Extracellular proteins play pivotal roles in both intracellular signaling and intercellular communications in health and disease. While recent advancements in proximity labeling (PL) methods, such as peroxidase- and photocatalyst-based approaches, have facilitated the resolution of extracellular proteomes, their in vivo compatibility remains limited. Here, we report TyroID, an in vivo-compatible PL method for unbiased mapping of extracellular proteins with high spatiotemporal resolution. TyroID employs plant- and bacteria-derived tyrosinases to produce reactive o-quinone intermediates, enabling the labeling of multiple residues on endogenous proteins with bioorthogonal handles, thereby allowing for their identification via chemical proteomics. We validate TyroIDs specificity by mapping extracellular proteomes and HER2-neighboring proteins using nanobody-directed recombinant tyrosinases. Demonstrating its superiority over other PL methods, TyroID enables in vivo mapping of extracellular proteomes, including mapping HER2-proximal proteins in tumor xenografts, quantifying the turnover of plasma proteins and labeling hippocampal-specific proteomes in live mouse brains. TyroID emerges as a potent tool for investigating protein localization and molecular interactions within living organisms.

biochemistry↗

bioRxiv2024

Berberine is a novel mitochondrial calcium uniporter (MCU) inhibitor that disrupts MCU-EMRE assembly

The mitochondrial calcium uniporter (MCU) complex mediates Ca2+ entry into mitochondrial, which plays a crucial role in regulating cellular energy metabolism and apoptosis. Dysregulation of MCU is implicated in various diseases, such as neurodegenerative disorders, cardiac diseases and cancer. Despite its importance, developing specific and clinically viable MCU inhibitors has been challenging. Here, we identify Berberine, a well-established drug with a documented safety profile, as a potent MCU inhibitor through a virtual screening of an FDA-approved drug library. Berberine localizes within mitochondria and directly binds to the juxtamembrane loop domain of MCU. This binding disrupts the interaction of MCU with its essential regulator, EMRE, thereby inhibiting rapid Ca2+ entry into the mitochondria. Notably, Berberine pretreatment reduces mitochondrial Ca2+ overload and mitigate ischemia/reperfusion-induced myocardial injury in mice. Our findings establish Berberine as a potent MCU inhibitor, offering a safe therapeutic strategy for diseases associated with dysregulated mitochondrial calcium homeostasis.

cell biology↗

bioRxiv2024

Discovering nuclear localization signal universe through a novel deep learning model with interpretable attention units

Nuclear localization signals (NLSs) are essential peptide fragments within proteins that play a decisive role in guiding proteins into the cell nucleus. Determining the existence and precise locations of NLSs experimentally is time-consuming and complicated, resulting in a scarcity of experimentally validated NLS fragments. Consequently, annotated NLS datasets are relatively limited, presenting challenges for data-driven approaches. In this study, we propose an innovative interpretable approach, NLSExplorer, which leverages large-scale protein language models to capture crucial biological information with a novel attention-based deep network for NLS identification. By enhancing the knowledge retrieved from protein language models with a novel attention to key area module, NLSExplorer achieves superior predictive performance compared to existing methods on two NLS benchmark datasets. Additionally, NLSExplorer is able to detect various kinds of segments highly correlated with nuclear transport, such as nuclear export signals. We employ NLSExplorer to investigate potential NLSs and other domains that are important for nuclear transport in nucleus-localized proteins in the Swiss-Prot database. Furthermore, the comprehensive pattern analysis for all these segments uncovers a potential NLS space and internal relationship of important nuclear transport segments for 416 species. This study not only introduces a powerful tool for predicting and exploring NLS space, but also offers a versatile network that is powerful for detecting characteristic domains and motifs of NLSs.

bioinformatics↗

bioRxiv2024

A Tough Biointerface in Human Knee Empowered by Dynamic Phase-transforming Minerals in Collagenous Matrix

Joining heterogeneous materials in engineered structures remains a daunting challenge because of stress concentration, often resulting in unexpected failures1,2. Studying the structures in organisms that evolved for centuries provides valuable insights that can be instrumental in addressing this mechanical challenge3-5. The human meniscus root-bone interface is a remarkable example known for its exceptional fatigue resistance, toughness and interfacial adhesion properties throughout its lifespan6-8. We studied the multiscale graded mineralization structure designs within the 30-micron soft-hard interface at the root-bone junction and examined its toughening mechanisms. This graded interface with interdigitated structures and exponential modulus increase exhibits a phase transition from amorphous calcium phosphate (ACP) to gradually matured hydroxyapatite (HAP) crystals, mediated by location-specific distributed biomolecules. In coordination with collagen fibril deformation and reorientation, ACP particles debond with collagen and slide to new positions which enable frictional energy dissipation, and HAP particles arrest cracks. The mineral in transforming phases work synergistically to provide interfacial toughening. The presented biointerface model exemplifies human musculoskeletal systems adaptations to mechanical requirements, offering a blueprint for developing tough interfaces in broad applications.

bioengineering↗

bioRxiv2024

Harnessing in vivo Synthesis of Bioactive Multiarylmethanes in Escherichia coli via Oxygen-Mediated Free Radical Reaction Induced by Simple Phenols

BackgroundXanthenes and multi-aryl carbon core containing compounds represent different types of complex and condensed architectures that have impressive wide range of pharmacological, industrial and synthetic applications. Moreover, indoles as building blocks were only found in naturally occurring metabolites with di-aryl carbon cores and in chemically synthesized tri-aryl carbon core containing compounds. Up to date, rare xanthenes with indole bearing multicaryl carbon core have been reported in natural or synthetic products. The underlying mechanism of fluores-cein-like arthrocolins with tetra-arylmethyl core were synthesized in an engineered Escherichia coli fed with toluquinol remained unclear. ResultsIn this study, the Keio collection of single gene knockout strains of 3901 mutants of E. coli BW25113, together with 14 distinct E. coli strains, was applied to explore the origins of endoge-nous building blocks and the biogenesis for arthrocolin assemblage. Deficiency in bacterial res-piratory and aromatic compound degradation genes ubiX, cydB, sucA and ssuE inhibited the mu-tant growth fed with toluquinol. Metabolomics of the cultures of 3897 mutants revealed that only disruption of tnaA involving in transforming tryptophan to indole, resulted in absence of arthro-colins. Further media optimization, thermal cell killing and cell free analysis indicated that a non-enzyme reaction was involved in the arthrocolin biosynthesis in E. coli. Evaluation of redox potentials and free radicals suggested that an oxygen-mediated free radical reaction was respon-sible for arthrocolins formation in E. coli. Regulation of oxygen combined with distinct phenol derivatives as inducer, 31 arylmethyl core containing metabolites including 13 new and 8 biolog-ical active, were isolated and characterized. Among them, novel arthrocolins with p-hydroxylbenzene ring from tyrosine were achieved through large scale of aerobic fermentation and elucidated x-ray diffraction analysis. Moreover, most of the known compounds in this study were for the first time synthesized in a microbe instead of chemical synthesis. Through feeding the rat with toluquinol after colonizing the intestines of rat with E. coli, arthrocolins also ap-peared in the rat blood. ConclusionOur findings provide a mechanistic insight into in vivo synthesis of complex and condensed ar-throcolins induced by simple phenols and exploits a quinol based method to generate endoge-nous aromatic building blocks, as well as a methylidene unit, for the bacteria-facilitated synthesis of multiarylmethanes.

biochemistry↗

bioRxiv2024

PIN2-mediated self-organizing transient auxin flow contributes to auxin maxima at the tip of Arabidopsis cotyledons

Directional auxin transport and formation of auxin maxima are critical for embryogenesis, organogenesis, pattern formation, and growth coordination in plants, but the mechanisms underpinning the initiation and establishment of these auxin dynamics are not fully understood. Here we show that a self-initiating and - terminating transient auxin flow along the marginal cells (MCs) contributes to the formation of an auxin maximum at the tip of Arabidopsis cotyledon that globally coordinates the interdigitation of puzzle-shaped pavement cells in the cotyledon epidermis. Prior to the interdigitation, indole butyric acid (IBA) is converted to indole acetic acid (IAA) to induce PIN2 accumulation and polarization in the marginal cells, leading to auxin flow toward and accumulation at the cotyledon tip. When IAA levels at the cotyledon tip reaches a maximum, it activates pavement cell interdigitation as well as the accumulation of the IBA transporter TOB1 in MCs, which sequesters IBA to the vacuole and reduces IBA availability and IAA levels. The reduction of IAA levels results in PIN2 down-regulation and cessation of the auxin flow. Hence, our results elucidate a self-activating and self-terminating transient polar auxin transport system in cotyledons, contributing to the formation of localized auxin maxima that spatiotemporally coordinate pavement cell interdigitation.

plant biology↗

bioRxiv2024

Development, validation and application of an LC-MS/MS method quantifying free forms of the micronutrients queuine and queuosine in human plasma using a surrogate matrix approach

Queuosine (Q) is a hypermodified 7-deaza-guanosine nucleoside exclusively synthesized by bacteria. This micronutrient and its respective nucleobase form queuine (q) are salvaged by humans either from gut microflora, or digested food. Depletion of Q-tRNA in human or mouse cells causes protein misfolding that triggers endoplasmic reticular stress and activation of the unfolded protein responses. In vivo, this reduces neuronal architecture of the mouse brain affecting learning and memory. Herein, a sensitive method for quantifying free q and Q in human blood was developed, optimised and validated. After evaluating q/Q extraction efficiency in several different solid-phase sorbents, Bond Elut PBA (phenylboronic acid) cartridges were found to have the highest extraction recovery for q (82%) and Q (71%) from pooled human plasma. PBS with 4% BSA was used as surrogate matrix for method development and validation. An LC-MS/MS method was validated across the concentration range of 0.0003 - 1 {micro}M for both q and Q, showing excellent: linearity (r2 = 0.997 (q) and r2 = 0.998 (Q)), limit of quantification (0.0003 {micro}M), accuracy (100.39% - 125.71%) and precision (CV% < 15.68%). In a sampling of healthy volunteers (n = 44) there was no significant difference in q levels between male (n = 14; mean = 0.0068 {micro}M) and female (n = 30; mean = 0.0080 {micro}M) participants (p = 0.50). Q was not detected in human plasma. This validated method can now be used to further our understanding of the role of q/Q in nutrition, physiology and pathology.

biochemistry↗

bioRxiv2024

Hierarchical global and local auxin signals coordinate cellular interdigitation in Arabidopsis

The development of multicellular tissues requires both local and global coordination of cell polarization, however, the mechanisms underlying their interplay are poorly understood. In Arabidopsis, leaf epidermal pavement cells (PC) develop a puzzle-piece shape locally coordinated through apoplastic auxin signaling. Here we show auxin also globally coordinates interdigitation by activating the TIR1/AFB-dependent nuclear signaling pathway. This pathway promotes a transient maximum of auxin at the cotyledon tip, which then moves across the leaf activating local PC polarization, as demonstrated by locally uncaged auxin globally rescuing defects in tir1;afb1;afb2;afb4;afb5 mutant but not in tmk1;tmk2;tmk3;tmk4 mutants. Our findings show that hierarchically integrated global and local auxin signaling systems, which respectively depend on TIR1/AFB-dependent gene transcription in the nucleus and TMK-mediated rapid activation of ROP GTPases at the cell surface, control PC interdigitation patterns in Arabidopsis cotyledons, revealing a mechanism for coordinating a local cellular process with the development of whole tissues.

plant biology↗

bioRxiv2024

Urine Proteomics in Methamphetamine Addicted Patients

Drug addiction is a serious chronic relapsing brain disease, and methamphetamine dependence has a complex course and is difficult to treat, causing a serious public health burden. In this study, we compared and analyzed the urine proteome of methamphetamine-using patients, methamphetamine-withdrawing patients, healthy individuals. The urine proteome of methamphetamine-using patients and methamphetamine-withdrawing patients was significantly different from that of healthy individuals, and some differential proteins and their enriched biological functions showed that they were associated with addiction or neurotoxicity of methamphetamine. The fact, that the urine proteome of patients who withdrew methamphetamine for more than 3 months were significantly different from that of healthy patients, may reveal the reasons for the high rate of methamphetamine relapse and potential intervention targets. This study proved that urine proteome can reflect the effects of addiction on the body comprehensively, and has the potential to provide clues for addiction.

biochemistry↗

bioRxiv2024

The 11β-hydroxysteroid dehydrogenase type 1 inhibitor SPI-62 prevents morbidity in a mouse model of Cushing's syndrome

11{beta}-hydroxysteroid dehydrogenase type 1 (HSD-1) inhibitors represent a potential therapeutic approach for patients with Cushings syndrome, autonomous cortisol secretion (ACS), or iatrogenic glucocorticoid (GC) excess. We assessed whether the HSD-1 inhibitor SPI-62 prevents GC-associated morbidity in a mouse Cushings syndrome model. Corticosterone (CORT) was administered to mice for 5 weeks. Animals who received CORT were randomized between vehicle and 3 SPI-62 regimens. A control group received neither CORT nor SPI-62. Body weight was measured daily to enable weight-based SPI-62 administration. Food consumption by pair-housed animals was reported weekly. Insulin sensitivity was evaluated by fasting homeostatic model assessment of insulin resistance. Adiposity and skeletal myopathy were measured using magnetic resonance imaging and post-mortem weights of fat depots and skeletal muscles. Grip strength was measured with a digital meter. Ambulation behavior in an open field maze was assessed. Post-mortem dermal thickness was quantified. Skin structure was evaluated by histology. CORT was associated with decreased insulin sensitivity, increased adiposity, skeletal myoatrophy, reduced grip strength, decreased dermal thickness, and skin structural changes. A trend of increased food consumption and an unexpected biphasic weight change were observed with CORT. SPI-62 attenuated all observed adverse effects in a dose-dependent manner. In general, results for the high SPI-62 regimen were similar as those in animals who received no CORT, suggesting that full HSD-1 inhibition should be maintained throughout a dose interval to mitigate the effects of glucocorticoid excess.

pharmacology and toxicology↗