Search bioRxiv⌕ Search

Biology subjects

Chen, C.

Publications and source records attributed to Chen, C..

At least 379 records · Page 21Linked to original sources
bioRxiv2023

Cell and tissue-specific glycosylation pathways and transcriptional regulation informed by single-cell transcriptomics

While single cell studies have made significant impacts in various subfields of biology, they lag in the Glycosciences. To address this gap, we analyzed single-cell glycogene expressions in the Tabula Sapiens dataset of human tissues and cell types using a recent glycosylation-specific gene ontology (GlycoEnzOnto). At the median sequencing (count) depth, [~]40-50 out of 400 glycogenes were detected in individual cells. Upon increasing the sequencing depth, the number of detectable glycogenes saturates at [~]200 glycogenes, suggesting that the average human cell expresses about half of the glycogene repertoire. Hierarchies in glycogene and glycopathway expressions emerged from our analysis: nucleotide-sugar synthesis and transport exhibited the highest gene expressions, followed by genes for core enzymes, glycan modification and extensions, and finally terminal modifications. Interestingly, the same cell types showed variable glycopathway expressions based on their organ or tissue origin, suggesting nuanced cell- and tissue-specific glycosylation patterns. Probing deeper into the transcription factors (TFs) of glycogenes, we identified distinct groupings of TFs controlling different aspects of glycosylation: core biosynthesis, terminal modifications, etc. We present webtools to explore the interconnections across glycogenes, glycopathways, and TFs regulating glycosylation in human cell/tissue types. Overall, the study presents an overview of glycosylation across multiple human organ systems.

bioinformatics↗
bioRxiv2023

A suite of engineered mice for interrogating psychedelic drug actions

Psychedelic drugs like lysergic acid diethylamide (LSD) and psilocybin have emerged as potentially transformative therapeutics for many neuropsychiatric diseases, including depression, anxiety, post-traumatic stress disorder, migraine, and cluster headaches. LSD and psilocybin exert their psychedelic effects via activation of the 5-hydroxytryptamine 2A receptor (HTR2A). Here we provide a suite of engineered mice useful for clarifying the role of HTR2A and HTR2A-expressing neurons in psychedelic drug actions. We first generated Htr2a-EGFP-CT-IRES-CreERT2 mice (CT:C-terminus) to independently identify both HTR2A-EGFP-CT receptors and HTR2A-containing cells thereby providing a detailed anatomical map of HTR2A and identifying cell types that express HTR2A. We also generated a humanized Htr2a mouse line and an additional constitutive Htr2A-Cre mouse line. Psychedelics induced a variety of known behavioral changes in our mice validating their utility for behavioral studies. Finally, electrophysiology studies revealed that extracellular 5-HT elicited a HTR2A-mediated robust increase in firing of genetically-identified pyramidal neurons--consistent with a plasma membrane localization and mode of action. These mouse lines represent invaluable tools for elucidating the molecular, cellular, pharmacological, physiological, behavioral, and other actions of psychedelic drugs in vivo.

neuroscience↗
bioRxiv2023

A role for JAK2 in mediating cell surface GHR-PRLR interaction

Growth hormone (GH) receptor (GHR) and (full-length) prolactin (PRL) receptor (PRLR) are transmembrane class I cytokine receptors that co-exist in various normal and cancerous cells. Both receptors respond to their associated ligands predominantly by activating the Janus Kinase 2 (JAK2)-signal transducer and activator of transcription (STAT) signaling pathways, and both are also known to initiate receptor-specific JAK2-independent signaling. Together with their cognate ligands, these receptors have been associated with pro-tumorigenic effects in various cancers, including breast cancer (BC). Human GH is known to bind GHR and PRLR, while PRL can only bind PRLR. A growing body of work suggests that GHR and PRLR can form heteromers in BC cells, modulating GH signal transduction. However, the dynamics of PRLR and GHR on the plasma membrane and how these could affect their respective signaling still need to be understood. To this end, we set out to unravel the spatiotemporal dynamics of GHR and PRLR on the surface of human T47D breast cancer cells and {gamma}2A-JAK2 cells. We applied direct stochastic optical reconstruction microscopy (dSTORM) and quantified the colocalization and availability of both receptors on the plasma membrane at the nanometer scale at different time points following treatment with GH and PRL. In cells co-expressing GHR and PRLR, we surprisingly observed that not only GH but also PRL treatment induces a significant loss of surface GHR. In cells lacking PRLR or expressing a mutant PRLR deficient in JAK2 binding, we observed that GH induces downregulation of cell surface membrane-bound GHR, but PRL no longer induces loss of surface GHR. Colocalizations of GHR and PRLR were confirmed by proximity ligation (PL) assay. Our results suggest that PRLR-GHR interaction, direct or indirect, is indispensable for PRL- but not GH- induced loss of surface GHR and for both GH-induced and PRL-induced increase of surface PRLR, with potential consequences for downstream signaling. Furthermore, our results suggest that JAK2 binding via the receptor intracellular domains Box1 element is crucial for the observed regulation of one class I cytokine receptors cell surface availability via ligand-induced activation of another class I cytokine receptor. Our findings shed new light on the reciprocal and collective role that PRLR and GHR play in regulating cell signaling.

biophysics↗
bioRxiv2023

A mathematical model for velocity-selective arterial spin labeling

PurposeTo present a theoretical framework that rigorously defines and analyzes key concepts and quantities for velocity selective arterial spin labeling (VSASL). Theory and MethodsAn expression for the VSASL arterial delivery function is derived based on (1) labeling and saturation profiles as a function of velocity and (2) physiologically plausible approximations of changes in acceleration and velocity across the vascular system. The dependence of labeling efficiency on the amplitude and effective bolus width of the arterial delivery function is defined. Factors that affect the effective bolus width are examined, and timing requirements to minimize quantitation errors are derived. ResultsThe model predicts that a flow-dependent negative bias in the effective bolus width can occur when velocity selective inversion (VSI) is used for the labeling module and velocity selective saturation (VSS) is used for the vascular crushing module. The bias can be minimized by choosing a nominal labeling cutoff velocity that is lower than the nominal cutoff velocity of the vascular crushing module. ConclusionThe elements of the model are specified in a general fashion such that future advances can be readily integrated. The model can facilitate further efforts to understand and characterize the performance of VSASL and provide critical theoretical insights that can be used to design future experiments and develop novel VSASL approaches.

bioengineering↗
bioRxiv2023

ZC3H11A mutations cause high myopia by triggering PI3K-AKT and NF-κB mediated inflammatory reactions in humans and mice

High myopia (HM) is a severe form of refractive error that results in irreversible visual impairment and even blindness. However, the genetic and pathological mechanisms underlying this condition are not yet fully understood. From a cohort of 1015 patients with high myopia in adolescents, likely pathogenic missense mutations were identified in the ZC3H11A gene in four patients by whole exome sequencing. This gene is a zinc finger and stress-induced protein that plays a significant role in regulating nuclear mRNA export. To better understand the function and molecular pathogenesis of myopia in relation to gene mutations, a Zc3h11a knock-out (KO) mouse model was created. The heterozygous KO (Het-KO) mice exhibited significant shifts in refraction towards myopia. Myopia-related factors, including TGF-{beta}1, MMP-2 and IL-6 were found to be upregulated in the retina or sclera, and electroretinography and immunofluorescence staining results showed dysfunction and reduced number of bipolar cells in the retina. Transmission electron microscopy findings suggesting ultrastructural abnormalities of the retina and sclera. Retinal transcriptome sequencing showed that 769 genes were differentially expressed, and Zc3h11a was found to have a negative impact on the PI3K-AKT and NF-{kappa}B signaling pathways by quantitative PCR and western blotting. In summary, this study characterized a new candidate pathogenic gene associated with high myopia, and indicated that the ZC3H11A protein may serve as a stress-induced nuclear response trigger, and its abnormality causes disturbances in a series of inflammatory and myopic factors. These findings offer potential therapeutic intervention targets for controlling the development of HM.

genetics↗
bioRxiv2023

Identification and functional analysis of extrachromosomal circular DNA in plasma extracellular vesicles of liver failure patients

Withdrawal statementThe authors have withdrawn their manuscript owing to having identified certain issues with the current representation of the data in the manuscript after performing further analyses of the bioinformatics data from their eccDNA sequencing results. Therefore, the authors do not wish this work to be cited as reference for the project. A revised and corrected version will be submitted in the future. If you have any questions, please contact the corresponding authors.

genomics↗
bioRxiv2023

Multi-omics analysis reveals critical cis-regulatory roles of transposable elements in livestock genomes

As a major source of genetic and regulatory variation in their host genome, transposable elements (TEs) have gained a growing interest in research on humans and model organisms. In this species, integrative analysis of multi-omics data has shed light on the regulatory functions of TEs. However, there remains a notable gap in our understanding of TEs in domesticated animals. we annotated TEs in the genomes of pigs, cattle, and chickens, respectively, and systematically compared the genome distributions and amplification patterns of TEs across these three species. Furthermore, by integrating multi-tissue RNA-seq, ATAC-seq, and histone modification ChIP-seq data, we explored the expression atlas of TEs and their contribution to cis-regulatory elements (CREs) in different tissues of the three species. Most importantly, we developed a novel computational framework that revealed TE-mediated gene regulatory networks (TE-GRNs) underlying tissue-related biological processes. To demonstrate the power of this approach, we applied our framework to analyze liver tissues across the three different species. Overall, our research provides novel insights into the regulatory functions of TEs in livestock animals and highlights a computational framework to uncover TE-GRNs in various biological contexts.

genomics↗
bioRxiv2023

Ubiquitin phosphorylation accelerates protein aggregation and promotes neurodegeneration in the aging brain

Ser65-phosphorylated ubiquitin (pUb) was found elevated in neurons of aged and neurodegenerative brains. Yet little is known whether a causative link exists between pUb level and brain aging. Here we show that the knockout of pink1, a Ub kinase, abolished pUb elevation and decelerated protein aggregation in aged mouse brains and cells with proteasomal inhibition. Conversely, over-expression of PINK1 but not the kinase-dead version increased the pUb level and accelerated protein aggregation by suppressing of proteasomal degradation. Furthermore, PINK1 over-expression in mouse hippocampus neurons increased pUb level and protein aggregation, slowly leading to mitochondrial injury, neurodegeneration, and cognitive impairment. Notably, the neuronal damages induced by PINK1 were rescued by the dominant negative Ub/S65A mutant, while Ub/S65E phosphomimetic mutant caused neuronal death. Together, an incidental increase of Ub phosphorylation can progressively and cumulatively cause the decline of Ub-dependent proteasomal activity, consequenting promotes neurodegeneration in the aging brain.

cell biology↗
bioRxiv2023

NUCLEOPORIN1 mediates proteasome-based degradation of ABI5 to regulate Arabidopsis seed germination

NUCLEOPORIN1 (NUP1), a member of the Nuclear Pore Complex (NPC), is located on the inner side of the nuclear membrane. It is highly expressed in seeds; however, its role in seeds including germination has not been explored yet. Here, we identified an abscisic acid (ABA) hypersensitive phenotype of nup1 during germination. ABA treatment drastically changes the expression pattern of thousands of genes in nup1, including the major transcription factors (TFs) involved in germination, ABI3, ABI4, and ABI5. Double mutant analysis of NUP1 and these ABA-related genes showed that mutations in ABI5 can rescue the phenotype of nup1, suggesting that NUP1 acts upstream of ABI5 to regulate seed germination. ABI5, a key negative regulator of germination, is abundant in dry seeds and rapidly degrades during germination. However, its spatiotemporal regulation and interaction with other molecular players during degradation remained to be fully elucidated. We found that NUP1 is physically associated with ABI5 and the 26S proteasome. Mutation in NUP1 delayed ABI5 degradation through its post-translational retention in nucleolus under abiotic stress. Taken together, our findings suggest that NUP1 anchors the proteasome to NPC and modulates seed germination through proteasome-mediated degradation of ABI5 in the vicinity of NPC in the nucleoplasm.

plant biology↗
bioRxiv2023

ccTCM: a quantitative component and compound platform for promoting the research of traditional Chinese medicine

Traditional Chinese medicine (TCM) databases play a vital role in bridging the gap between TCM and modern medicine, as well as in promoting the popularity of TCM. Elucidating the bioactive ingredients of Chinese medicinal materials is key to TCM modernization and new drug discovery. However, one drawback of current TCM databases is the lack of quantitative data on the constituents of Chinese medicinal materials. Herein, we present ccTCM, a web-based platform designed to provide a component and compound-content-based resource on TCM and analysis services for medical experts. In terms of design features, ccTCM combines resource distribution, similarity analysis, and molecular-mechanism analysis to accelerate the discovery of bioactive ingredients in TCM. ccTCM contains 273 Chinese medicinal materials commonly used in clinical settings, covering 29 functional classifications. By searching and comparing, we finally adopted 2043 studies, from which we collected the compounds contained in each TCM with content greater than 0.001%, and a total of 1 449 were extracted. Subsequently, we collected 40767 compound-target pairs by integrating multiple databases. Taken together, ccTCM is a versatile platform for that can be used by TCM scientists to perform scientific and clinical TCM studies based on quantified ingredients of Chinese medicinal materials. ccTCM is freely accessible at http://www.cctcm.org.cn.

bioinformatics↗
bioRxiv2023

Exploring NCATS In-House Biomedical Data for Evidence-based Drug Repurposing

AbstractDrug repurposing is a strategy for identifying new uses of approved or investigational drugs that are outside the scope of the original medical indication. Even though many repurposed drugs have been found serendipitously in the past, the increasing availability of large volumes of biomedical data has enabled more systemic, data-driven approaches for drug candidate identification. At National Center of Advancing Translational Sciences (NCATS), we invent new methods to generate new data and information publicly available to spur innovation and scientific discovery. In this study, we aimed to explore and demonstrate biomedical data generated and collected via two NCATS research programs, the Toxicology in the 21st Century program (Tox21) and the Biomedical Data Translator (Translator) for the application of drug repurposing. These two programs provide complementary types of biomedical data from uncovering underlying biological mechanisms with bioassay screening data from Tox21 for chemical clustering, to enrich clustered chemicals with scientific evidence mined from the Translator towards drug repurposing. 129 chemical clusters have been generated and three of them have been further investigated for drug repurposing candidate identification, which is detailed as case studies.

bioinformatics↗
bioRxiv2023

Comprehensive catalogs for microbial genes and metagenome-assembled genomes of the swine lower respiratory tract microbiome identify the relationship of microbial species with lung lesions

Understanding the community structure and functional capacity of the lower respiratory tract microbiome is crucial for elucidating its roles in respiratory tract diseases. However, there are few studies about it owing to the difficulty in obtaining microbial samples from the lower respiratory tract. Here we collected 745 microbial samples from the porcine lower respiratory tract by harvesting 675 pigs, and constructed a gene catalog containing 10,337,194 nonredundant genes, of which only 30% could be annotated taxonomically. We obtained 397 metagenome-assembled genomes (MAGs) including 111 MAGs with high-quality. These 397 MAGs were further clustered into 292 species-level genome bins (SGBs), among which 56% SGBs are unknown with current databases. Combining with the lung lesion phenotype, we found that Mycoplasma hyopneumoniae strains and the adhesion-related virulence factors harboring in their genomes were significantly associated with porcine lung lesions, implying the role of adhesion and overgrowth of pathogenic M. hyopneumoniae in host lung diseases. This study provided important resources for the study of porcine lower respiratory tract microbiome and lung health.

microbiology↗
bioRxiv2023

The balance between shear flow and extracellular matrix in ovarian cancer-on-chip

Ovarian cancer is the most lethal gynecologic cancer in developed countries. Silent onset of the metastatic activity of ovarian tumor cells is factor for poor outcomes. In the tumor microenvironment, the extracellular matrix (ECM) and flow shear stress are known to play key roles in directing cell invasion. Hence, acute and tunable tools are critical to mimic scaffold and fluid for building clinically relevant in vitro models. We have built an ovarian tumor-on-chip where tunable ECM models are easily seeded with tumor spheroids and integrated within a microfluidic chip. This allows the investigation of the crosstalk between the characteristics of the ECM models and shear stress on the migratory behavior and cellular heterogeneity of ovarian tumor cells. We vary the composition of the ECM playing with type I and IV collagens and laminin, and control the shear stress in the chip. This work shows that in the shear stress regime of the peritoneal cavity, the ECM plays a major role in driving individual or collective modes of migration. In the presence of basement membrane proteins, migration is more collective that on type I collagen regardless of shear stress level. In addition, with increasing shear stress, individual cell migration was enhanced, while no significant impact on collective migration could be measured. This highlights our ability to discriminate relevant parameters for onset and shifts of cell behavior using our in vitro models. Furthermore, we described the ability to shift cells from an epithelial phenotype to a more mesenchymal phenotype, which could allow us to describe the role of these parameters during epithelial-to-mesenchymal (EMT) transition as a continuous process. Finally, we conclude that the ECM should hold a central position in in vitro cancer models, to understand cell response and develop platforms for therapeutic development.

bioengineering↗
bioRxiv2023

Identifying novel radioprotective drugs via salivary gland tissue chip screening

During head and neck cancer treatment, off-target ionizing radiation damage to the salivary glands commonly causes a permanent loss of secretory function. Due to the resulting decrease in saliva production, patients have trouble eating, speaking and are predisposed to oral infections and tooth decay. While the radioprotective antioxidant drug Amifostine is approved to prevent radiation-induced hyposalivation, it has intolerable side effects that limit its use, motivating the discovery of alternative therapeutics. To address this issue, we previously developed a salivary gland mimetic (SGm) tissue chip platform. Here, we leverage this SGm tissue chip for high-content drug discovery. First, we developed in-chip assays to quantify glutathione and cellular senescence ({beta}-galactosidase), which are biomarkers of radiation damage, and we validated radioprotection using WR-1065, the active form of Amifostine. Following validation, we tested other reported radioprotective drugs, including, Edaravone, Tempol, N-acetylcysteine (NAC), Rapamycin, Ex-Rad, and Palifermin, confirming that all drugs but NAC and Ex-Rad exhibited robust radioprotection. Next, a Selleck Chemicals library of 438 FDA-approved drugs was screened for radioprotection. We discovered 25 hits, with most of the drugs identified with mechanisms of action other than antioxidant activity. Hits were down-selected using EC50 values and pharmacokinetics and pharmacodynamics data from the PubChem database leading to testing of Phenylbutazone (anti-inflammatory), Enoxacin (antibiotic), and Doripenem (antibiotic) for in vivo radioprotection in mice using retroductal injections. Results confirm that Phenylbutazone and Enoxacin exhibited equivalent radioprotection to Amifostine. This body of work demonstrates the development and validation of assays using a SGm tissue chip platform for high-content drug screening and the successful in vitro discovery and in vivo validation of novel radioprotective drugs with nonantioxidant primary indications pointing to possible, yet unknown novel mechanisms of radioprotection.

bioengineering↗
bioRxiv2023

Accurate prediction of RNA translation with a deep learning architecture

Accurate annotation of coding regions in RNAs is essential for understanding gene translation. We developed a deep neural network to directly predict and analyze translation initiation and termination sites from RNA sequences. Trained with human transcripts, our model learned hidden rules of translation control and achieved a near perfect prediction of canonical translation sites across entire human transcriptome. Surprisingly, this model revealed a new role of codon usage in regulating translation termination, which was experimentally validated. We also identified thousands of new open reading frames in mRNAs or lncRNAs, some of which were confirmed experimentally. The model trained with human mRNAs achieved high prediction accuracy of canonical translation sites in all eukaryotes and good prediction in polycistronic transcripts from prokaryotes or RNA viruses, suggesting a high degree of conservation in translation control. Collectively, we present a general and efficient deep learning model for RNA translation, generating new insights into the complexity of translation regulation.

molecular biology↗
bioRxiv2023

Functional variations in gamma-secretase activity are critical determinants of the clinical, biomarker, and cognitive progression of autosomal dominant Alzheimer's disease

BackgroundThe balance between production, clearance, and toxicity of A{beta} peptides is central to Alzheimers disease (AD) pathobiology. Though highly variable in terms of age at symptom onset (AAO), hundreds of variants in PSEN1 cause autosomal dominant forms of AD (ADAD) with nearly complete penetrance. PSEN1 forms the catalytic core of the {gamma}-secretase complex and thereby directly mediates the production of longer, aggregation-prone A{beta} peptides relative to shorter, non-aggregating peptides. We hypothesized that the broad AAO and biomarker heterogeneity seen across ADAD would be predictable based on mutation-specific differences in the production of A{beta} species. MethodsA{beta}-37, 38, 40, 42, and 43 production was quantified from 161 unique PSEN1 variants expressed in HEK293 cells. Prediction of AAO was carried out in 106 variants with available AAO and then replicated in 55 variants represented across 190 PSEN1 mutation carriers who have detailed cognitive and biomarker data from the Dominantly Inherited Alzheimers Network (DIAN). ResultsVariations in A{beta} production across the 161 mutations examined in cell-based models were highly predictive of AAO. In those with corresponding in vivo data from the DIAN study, our cell-based {gamma}-secretase composite was strongly associated with biomarker and cognitive trajectories. ConclusionsThese findings elucidate the critical link between {gamma}-secretase function, A{beta} production, and AD progression and offer mechanistic support for the amyloid hypothesis. The approach used here represents a powerful tool to account for heterogeneity in disease progression in ADAD clinical trials and to assess the pathogenicity of variants of unknown significance or with limited family history.

neuroscience↗
bioRxiv2023

Degradation of amyloid beta species by multi-copper oxidases

Reduction of the production of amyloid beta (A{beta}) species has been intensively investigated as potential therapeutic approaches for Alzheimers disease (AD). However, the degradation of A{beta} species, another potential beneficial approach, has been far less explored. In this study, we discovered that ceruloplasmin (CP), an important multi-copper oxidase (MCO) in human blood, could degrade A{beta} peptides. We also found that the presence of Vitamin C could enhance the degrading effect in a concentration-dependent manner. We then validated the CP-A{beta} interaction using total internal reflection fluorescence (TIRF) microscopy, fluorescence photometer, and fluorescence polarization measurement. Based on the above discovery, we hypothesized that other MCOs had similar A{beta}-degrading functions. Indeed, we found that other MCOs could induce A{beta} degradation as well. Remarkably, we revealed that ascorbate oxidase (AO) had the strongest degrading effect among the tested MCOs. Using induced pluripotent stem (iPS) neuron cells, we observed that AO could rescue neuron toxicity which induced by A{beta} oligomers. In addition, our electrophysiological analysis with brain slices suggested that AO could prevent an A{beta}-induced deficit in synaptic transmission in the hippocampus. To the best of our knowledge, our report is the first to demonstrate that MCOs have a degrading function for peptides/proteins. Further investigations are warranted to explore the possible benefits of MCOs for future AD treatment.

neuroscience↗