Biology subjects

Yang, M.

Publications and source records attributed to Yang, M..

At least 235 records · Page 13Linked to original sources

bioRxiv2023

Competitive Microarray Screening Reveals Functional Ligands for the DHX15 RNA G-quadruplex

RNAs are increasingly considered valuable therapeutic targets, and in turn the development of methods to identify and validate both RNA targets and RNA-binding compounds is more important than ever. In this study, we utilized a bioinformatic approach to identify a hairpin-containing RNA G-quadruplex (rG4) in the 5' UTR of DHX15 mRNA. By using a competitive small molecule microarray (SMM) approach, we identified a compound that specifically binds to the DHX15 rG4 with a KD of 12.6 {+/-} 1 {micro}M. This rG4 directly impacts translation of a DHX15 reporter mRNA in vitro, and binding of our compound (F1) to the structure inhibits translation up to 57% with an IC50 of 22.9 {+/-} 3.8 {micro}M. The DHX15 protein is an "undruggable" helicase associated with several types of cancer progression, and our data represent the first published effort to target the rG4 in DHX15 mRNA to inhibit its translation. Overall, our work is informative for the development of novel small molecule cancer therapeutics for RNA targets starting from target identification. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=66 SRC="FIGDIR/small/550542v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@19eb40borg.highwire.dtl.DTLVardef@3e6a17org.highwire.dtl.DTLVardef@1a71f9eorg.highwire.dtl.DTLVardef@10ce4df_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2023

PolyGR and polyPR knock-in mice reveal a conserved neuroprotective extracellular matrix signature in C9orf72 ALS/FTD neurons

A GGGGCC repeat expansion in C9orf72 is the most common genetic cause of ALS and FTD (C9ALS/FTD). The presence of dipeptide repeat (DPR) proteins, generated by translation of the expanded repeat, is a major pathogenic feature of C9ALS/FTD pathology, but their most relevant effects in a physiological context are not known. Here, we generated C9orf72 DPR knock-in mouse models characterised by physiological expression of 400 codon-optimised polyGR or polyPR repeats, and heterozygous C9orf72 reduction. (GR)400 and (PR)400 knock-in mice exhibit cortical neuronal hyperexcitability, age-dependent spinal motor neuron loss and progressive motor dysfunction, showing that they recapitulate key features of C9FTD/ALS. Quantitative proteomics revealed an increase in extracellular matrix (ECM) proteins in (GR)400 and (PR)400 spinal cord, with the collagen COL6A1 the most increased protein. This signature of increased ECM proteins was also present in C9ALS patient iPSC-motor neurons indicating it is a conserved feature of C9ALS/FTD. TGF-{beta}1 was one of the top predicted regulators of this ECM signature and polyGR expression in human iPSC-neurons was sufficient to induce TGF-{beta}1 followed by COL6A1, indicating TGF-{beta}1 is one driver of the ECM signature. Knockdown of the TGF-{beta}1 or COL6A1 orthologue in Drosophila dramatically and specifically exacerbated neurodegeneration in polyGR flies, showing that TGF-{beta}1 and COL6A1 protect against polyGR toxicity. Altogether, our physiological C9orf72 DPR knock-in mice have revealed a neuroprotective and conserved ECM signature in C9FTD/ALS.

neuroscience↗

bioRxiv2023

Hypervirulent pneumococci display high levels of nasopharyngeal shedding and rapid onward transmission

Streptococcus pneumoniae serotype 1 is a major cause of invasive pneumococcal disease. Despite its high attack rate, serotype 1 exhibits a low carriage prevalence within the population, which raises important questions about the relationship between carriage and transmission of hypervirulent pneumococcal strains between individuals. We compared the transmission dynamics of serotype 1 sequence type ST217 to serotype 2 strain D39 using a novel model of transmission in young adult mice. Donor index mice were intranasally infected with ST217, D39 or isogenic pneumolysin-deficient mutants and co-housed with recipient naive contact mice. Three days later, all mice were infected with influenza A virus (IAV). Pneumococcal transmission was analysed during colonisation alone and co-infection with IAV by quantification of shedding and nasal colonisation in index and contact mice. The role of the toxin pneumolysin in shedding, transmission and colonisation, and the host nasopharyngeal immune response were investigated. We show that ST217 was shed in index mice at significantly greater levels compared to D39. Upon viral co-infection, ST217 was shed and transmitted at a faster rate to contact mice and displayed higher transmission levels compared to D39. Interestingly, the toxin pneumolysin did not play a role in shedding. However, upon acquisition by contact mice, pneumolysin-dependent macrophage recruitment was observed in the nasopharynx. Our results show that the rapid and high transmission rate of serotype 1 is a key factor in its ability to disseminate quickly within the population and cause disease outbreaks.

microbiology↗

bioRxiv2023

Inhibition of Retinoic Acid Signaling in Proximal Tubular Epithelial cells Protects against Acute Kidney Injury by Enhancing Kim-1-dependent Efferocytosis

Retinoic acid receptor (RAR) signaling is essential for mammalian kidney development, but in the adult kidney is restricted to occasional collecting duct epithelial cells. We now show there is widespread reactivation of RAR signaling in proximal tubular epithelial cells (PTECs) in human sepsis-associated acute kidney injury (AKI), and in mouse models of AKI. Genetic inhibition of RAR signaling in PTECs protects against experimental AKI but is associated with increased expression of the PTEC injury marker, Kim-1. However, Kim-1 is also expressed by de-differentiated, proliferating PTECs, and protects against injury by increasing apoptotic cell clearance, or efferocytosis. We show that the protective effect of inhibiting PTEC RAR signaling is mediated by increased Kim-1 dependent efferocytosis, and that this is associated with de-differentiation, proliferation, and metabolic reprogramming of PTECs. These data demonstrate a novel functional role that reactivation of RAR signaling plays in regulating PTEC differentiation and function in human and experimental AKI. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/545113v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@140ba6borg.highwire.dtl.DTLVardef@8f02f0org.highwire.dtl.DTLVardef@10a123eorg.highwire.dtl.DTLVardef@33b564_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2023

Cell age drives asynchronous transcriptome aging

Organs age at different rates within a single individual. Such asynchrony in aging has been widely observed at multiple levels, from functional hallmarks, such as anatomical structures and physiological processes, to molecular endophenotypes, such as the transcriptome and metabolome. However, we lack a conceptual framework to understand why some components age faster than others. Just as demographic models explain why aging evolves, here we test the hypothesis that demographic differences among cell types, determined by cell-specific differences in turnover rate, can explain why the transcriptome shows signs of aging in some cell types but not others. Through analysis of mouse single-cell transcriptome data across diverse organs and ages, we find that cellular age explains a large proportion of the variation in the age-related increase in transcriptome variance. We further show that long-lived cells are characterized by relatively high expression of genes associated with proteostasis, and that the transcriptome of long-lived cells shows greater evolutionary constraint than short-lived cells. In contrast, in short-lived cell types the transcriptome is enriched for genes associated with DNA repair. Based on these observations, we develop a novel heuristic model that explains how and why aging rates differ among cell types.

systems biology↗

bioRxiv2023

Urinary protein changes during the short-term growth and development of rats

Can the urine proteome reflect short-term changes in the growth and development of animals? Do short-term developmental effects on urinary protein need to be considered when performing urine marker studies using model animals with faster growing periods? In this study, urine samples were collected from 10 Wistar rats aged 6-8 weeks 3 and 6 days apart. The results showed that the urine proteome could sensitively reflect short-term growth and development in rats. For example, comparing the urine proteome of Day 0 and Day 6, 195 differential proteins were identified after screening (FC [≥] 1.5 or [≤] 0.67, P < 0.05), and verified by randomization, the average number of randomly generated differential proteins was 17.99. At least 90.77% of the differential proteins were not randomly generated. This finding demonstrates that the differential proteins identified in the samples collected at different time points were not randomly generated. A large number of biological processes and pathways related to growth and development were enriched, which shows that the urine proteome reflects the short-term growth and development of rats, and provides a means for in-depth and meticulous study of growth and development. Moreover, an interfering factor in animal experiments using 6-to 8-week-old rats to construct models was identified. The results of this study demonstrated that there were differences in the urinary proteome in rats aged 6-8 weeks only 3-6 days apart, which suggests that the sensitivity of urinary proteomics is high and shows the sensitive and precise response of the urinary proteome to body changes.

biochemistry↗

bioRxiv2023

The emergence of human gastrulation upon in vitro attachment

While studied extensively in model systems, human gastrulation remains obscure. This process starts upon blastocyst implantation into the uterine wall, which is assumed to occur after 14 days post-fertilization. The scarcity and limited access to fetal biological material as well as ethical considerations limit our understanding of the cellular and molecular portrait of human gastrulation. In vitro culture of natural human blastocysts shed light on the second week of human development, unveiling an unexpected level of self-organization embedded in the pre-gastrulating embryo, yet whether they can undergo gastrulation upon in vitro attachment remains elusive. Blastocyst models called blastoids, which are derived from human pluripotent stem cells, provide the opportunity to reconstitute post-implantation human development in vitro with unlimited biological material. Here we show that human blastoids break symmetry and undergo gastrulation upon in vitro attachment. scRNA-seq of these models replicate the transcriptomic signature of the natural human gastrula, recapitulating aspects of the second to the third week of human development. Surprisingly, analysis of developmental timing reveals that in both blastoid models and natural in vitro attached human embryos, the onset of gastrulation as defined by molecular makers, can be traced to time scales equivalent to 12 days post-fertilization, which appeals for a reconsideration of the onset of human gastrulation upon extended in vitro culture.

developmental biology↗

bioRxiv2023

Identification of cytokine predominant immunosuppressive class and prognostic risk signatures in glioma

PurposeThe advent of immune checkpoint blockade (ICB) therapies this year has changed the way glioblastoma (GBM) is treated. Meanwhile, some patients with strong PD-L1 expression remain immune checkpoint resistant. To better understand the molecular processes that influence the immune environment, there is an urgent need to characterize the immunosuppressive tumor microenvironment and identify biomarkers to predict patient survival outcomes. Patients and methodsOur study analyzed RNA-sequencing data from 178 GBM samples. Their unique gene expression patterns in the tumor microenvironment were analyzed by an unsupervised clustering algorithm. Through these expression patterns, a panel of T-cell exhaustion signatures, immunosuppressive cells, and clinical features correlates with immunotherapy response. The presence or absence of immune status and prognostic signatures was then validated with the test dataset. Results38.2% of GBM patients showed increased expression of anti-inflammatory cytokines, significant enrichment of T cell exhaustion signals, higher proportion of immunosuppressive cells (macrophages and CD4 regulatory T cells) and nine inhibitory checkpoints (CTLA4, PDCD1, LAG3, BTLA, TIGIT, HAVCR2, IDO1, SIGLEC7, and VISTA). The immunodepleted class (IDC) was used to classify these immunocompromised individuals. Despite the high density of tumor-infiltrating lymphocytes shown by IDC, such patients have a poor prognosis. Although PD-L1 was highly expressed in IDC, it suggested that there might be ICB resistance. There are many IDC predictive signatures to discover. ConclusionPD-1 is strongly expressed in a novel immunosuppressive class of GBM, but this cluster may be resistant to ICB therapy. A comprehensive description of this drug-resistant tumor microenvironment could provide new insights into drug resistance mechanisms and improved immunotherapy techniques.

immunology↗

bioRxiv2023

Asymmetric control of food intake by left and right vagal sensory neurons

We investigated the lateralization of gut-innervating vagal sensory neurons and their roles in feeding behavior. Using genetic, anatomical, and behavioral analyses, we discovered a subset of highly lateralized vagal sensory neurons with distinct sensory responses to intestinal stimuli. Our results demonstrated that left vagal sensory neurons (LNG) are crucial for distension-induced satiety, while right vagal sensory neurons (RNG) mediate preference for nutritive foods. Furthermore, these lateralized neurons engage different central circuits, with LNG neurons recruiting brain regions associated with energy balance and RNG neurons activating areas related to salience, memory, and reward. Altogether, our findings unveil the diverse roles of asymmetrical gut-vagal-brain circuits in feeding behavior, offering new insights for potential therapeutic interventions targeting vagal nerve stimulation in metabolic and neuropsychiatric diseases. One Sentence SummaryLateralized gut-brain circuits respond to different sensory modalities and control distinct feeding behaviors.

neuroscience↗

bioRxiv2023

SEQUENCE VS. STRUCTURE: DELVING DEEP INTO DATA DRIVEN PROTEIN FUNCTION PREDICTION

AO_SCPLOWBSTRACTC_SCPLOWPredicting protein function is a longstanding challenge that has significant scientific implications. The success of amino acid sequence-based learning methods depends on the relationship between sequence, structure, and function. However, recent advances in AlphaFold have led to highly accurate protein structure data becoming more readily available, prompting a fundamental question: given sufficient experimental and predicted structures, should we use structure-based learning methods instead of sequence-based learning methods for predicting protein function, given the intuition that a proteins structure has a closer relationship to its function than its amino acid sequence? To answer this question, we explore several key factors that affect function prediction accuracy. Firstly, we learn protein representations using state-of-the-art graph neural networks (GNNs) and compare graph construction(GC) methods at the residue and atomic levels. Secondly, we investigate whether protein structures generated by AlphaFold are as effective as experimental structures for function prediction when protein graphs are used as input. Finally, we compare the accuracy of sequence-only, structure-only, and sequence-structure fusion-based learning methods for predicting protein function. Additionally, we make several observations, provide useful tips, and share code and datasets to encourage further research and enhance reproducibility.

bioinformatics↗

bioRxiv2023

Reversing myeloid-derived suppressor cells mediated immunosuppression via p38α inhibition enhances immunotherapy efficacy in triple negative breast cancer

Infiltration of myeloid-derived suppressor cells (MDSCs) leads to Immunosuppressive tumor microenvironment (TME), which is one of the major causes for low objective response rates of immune checkpoint blockade (ICB) therapy. Here, we report that chemical inhibition of p38 reverses this MDSC-induced immunosuppressive TME and improves the immunotherapy efficacy in triple negative breast cancer (TNBC). Firstly, by combining the tumor immunological phenotype (TIP) gene signature and high throughput sequencing based high throughput screening (HTS2), we identified that ponatinib significantly inhibits the expression of "cold" tumor associated chemokines CXCL1 and CXCL2 in cancer cells. This inhibition decreases the infiltration of MDSCs and consequently increased the accumulation of "hot" tumor associated T cells and NK cells and thus reverses the immunosuppressive TME. Then, by multiple preclinical models, we found that ponatinib significantly inhibits tumor growth in a TME-dependent manner and enhances the efficacy of anti-PD-L1 immunotherapy on TNBC in vivo. Notably, ponatinib exhibits no significant inhibition on immune cells in mouse spleens. Mechanistically, ponatinib directly inhibits the kinase activity of p38, which results in the reduction of the phosphorylation of STAT1 at Ser727, and thus the decreased expression of CXCL1 and CXCL2 in cancer cells. Our study provided the therapeutic potential of combining p38 inhibition with ICB for the treatment of TNBC.

cancer biology↗

bioRxiv2023

Identification of RNA-Binding Protein Targets with HyperTRIBE in Saccharomyces cerevisiae

As a mater regulator in cells, RNA-binding protein (RBP) plays critical roles in organismal development, metabolism and various diseases. It controls gene expression at multiple levels mostly by specific recognition of target RNA. The traditional CLIP-seq method to detect transcriptome-wide RNA targets of RBP is less efficient in yeasts due to their cell walls. Here, we established an efficient HyperTRIBE (Targets of RNA-binding proteins Identified By Editing) in yeast, by fusing a RBP to the hyper active catalytic domain of human RNA editing enzyme ADAR2 and expressing the fusion protein in yeast cells. The target transcripts of RBP were marked with new RNA editing events and identified by high-throughput sequencing. We successfully applied TRIBE to identifying the RNA targets of two yeast RBPs, KHD1 and BFR1. The antibody-free HyperTRIBE has competitive advantages including low background, high sensitivity and reproducibility, and a simple library preparation procedure, which provides a reliable strategy for RBP target identification in Saccharomyces cerevisiae.

molecular biology↗

bioRxiv2023

Assessing the performance of the Cell Painting assay across different imaging systems

Quantitative microscopy is a powerful method for performing phenotypic screens from which image-based profiling can extract a wealth of information, termed profiles. These profiles can be used to elucidate the changes in cellular phenotypes across cell populations from different patient samples or following genetic or chemical perturbations. One such image-based profiling method is the Cell Painting assay, which provides morphological insight through the imaging of eight cellular compartments. Here, we examine the performance of the Cell Painting assay across multiple high-throughput microscope systems and find that all are compatible with this assay. Furthermore, we determine independently for each microscope system the best performing settings, providing those who wish to adopt this assay an ideal starting point for their own assays. We also explore the impact of microscopy setting changes in the Cell Painting assay and find that few dramatically reduce the quality of a Cell Painting profile, regardless of the microscope used.

cell biology↗

bioRxiv2023

5-HT4 receptor agonists treatment reduces tau pathology and behavioral deficit in the PS19 mouse model of tauopathy

Accumulation of tau in synapses in Alzheimers disease (AD) has been shown to cause synaptic damage, synaptic loss, and the spread of pathology through synaptically connected neurons. Synaptic loss correlates with a decline in cognition, providing an opportunity to investigate strategies to target synaptic tau to rescue or prevent cognitive decline. One of the promising synaptic targets is the 5-HT4 receptor present post-synaptically in the brain areas involved in the memory processes. 5-HT4R activation exerts synaptogenic and pro-cognitive effects involving synapse-to-nucleus signaling essential for synaptic plasticity. However, it is not known whether 5-HT4R activation has a therapeutic effect on tauopathy. The goal of this study was to investigate the impact of stimulation of 5-HT4R in tauopathy mice. Our results show that 5-HT4R agonism led to reduced tauopathy and synaptic tau and correlated with increased proteasome activity and improved cognitive functioning in PS19 mice. Thus, stimulation of 5-HT4R offers a promising therapy to rescue synapses from toxic synaptic tau.

neuroscience↗

bioRxiv2023

Protein aggregation in plant mitochondria inhibits translation and induces an NAC017-dependent ethylene-associated unfolded protein response

Loss of Lon1 in plant mitochondria led to stunted plant growth and accumulation of nuclear-encoded mitochondrial proteins, including Lon1 substrates, while mitochondrial-encoded proteins typically decreased in abundance. Lon1 mutants contained protein aggregates in the mitochondria matrix which were enriched in PPR-containing proteins and ribosomal subunits of the translation apparatus and were slowed in mitochondrial RNA splicing, editing and general translation rate. Transcriptome analysis showed multiple organellar unfolded protein responses involving ethylene biosynthesis were induced by either Lon1 loss, mitochondrial ribosomal protein loss, translation or respiratory inhibition and most were regulated by the mitochondrial retrograde signaling pathway dependent on the transcription factor NAC017. The short hypocotyl in lon1 mutants during skotomorphogenesis was partially rescued by ethylene inhibitors and mutants showed higher ethylene production rates than wildtype. Together this provides multiple steps in the link between loss of Lon1 and its whole plant phenotype. Single Sentence SummaryLon1 knockout inhibits mitochondrial-encoded gene translation and induces retrograde signaling involving unfolded protein responses.

plant biology↗

bioRxiv2023

A converged ubiquitin-proteasome pathway for the degradation of TOC and TOM tail-anchored receptors

In plants, thousands of nucleus-encoded proteins translated in the cytosol are sorted to chloroplasts and mitochondria by binding to specific receptors of the TOC (translocon at the outer membranes of chloroplasts) and the TOM (translocon at the outer membranes of mitochondria) complexes for import into those organelles. The degradation pathways for these receptors are unclear. Here, we discovered a converged ubiquitin-proteasome pathway for the degradation of Arabidopsis thaliana TOC and TOM tail-anchored receptors. The receptors are ubiquitinated by E3 ligase(s) and pulled from the outer membranes by the AAA+ ATPase CDC48, after which a previously characterized cytosolic protein, TTOP, binds to the exposed transmembrane domains (TMDs) at the C termini of the receptors and CDC48, and delivers these complexes to the 26S proteasome.

plant biology↗

bioRxiv2022

Oxygen is a critical regulator of cellular metabolism and function in cell culture

Cell culture is generally considered to be hyperoxic. However, the importance of cellular oxygen consumption is often underappreciated, with rates of oxygen consumption often sufficient to cause hypoxia at cell monolayers. We initially focused on cultured adipocytes as a terminally differentiated cell-type with substantial oxygen consumption rates to support diverse cellular functions. Under standard conditions, cultured adipocytes are hypoxic and highly glycolytic. Increasing oxygen diverted glucose flux toward mitochondria and resulted in thousands of gene expression changes that pointed toward alleviated physiological transcriptional responses to hypoxia. Phenotypically, providing more oxygen increased adipokine secretion and rendered adipocytes more sensitive to insulin and lipolytic stimuli. The functional benefits of increasing pericellular oxygen were transferable to other cellular systems including hPSC-derived hepatocytes and cardiac organoids. Our findings suggest that oxygen is limiting in many terminally-differentiated cell culture systems, and that controlling oxygen availability can improve the quality and translatability of cell models.

cell biology↗

bioRxiv2022

Multi-'Omic Integration via Similarity Network Fusion to Detect Molecular Subtypes of Aging

BackgroundMolecular subtyping of brain tissue provides insights into the heterogeneity of common neurodegenerative conditions, such as Alzheimers disease (AD). However, existing subtyping studies have mostly focused on single data modalities and only those individuals with severe cognitive impairment. To address these gaps, we applied Similarity Network Fusion (SNF), a method capable of integrating multiple high-dimensional multi-omic data modalities simultaneously, to an elderly sample spanning the full spectrum of cognitive aging trajectories. MethodsWe analyzed human frontal cortex brain samples characterized by five omic modalities: bulk RNA sequencing (18,629 genes), DNA methylation (53,932 cpg sites), histone H3K9 acetylation (26,384 peaks), proteomics (7,737 proteins), and metabolomics (654 metabolites). SNF followed by spectral clustering was used for subtype detection, and subtype numbers were determined by eigen-gap and rotation cost statistics. Normalized Mutual Information (NMI) determined the relative contribution of each modality to the fused network. Subtypes were characterized by associations with 13 age-related neuropathologies and cognitive decline. ResultsFusion of all five data modalities (n=111) yielded two subtypes (nS1=53, nS2=58) which were nominally associated with diffuse amyloid plaques; however, this effect was not significant after correction for multiple testing. Histone acetylation (NMI=0.38), DNA methylation (NMI=0.18) and RNA abundance (NMI=0.15) contributed most strongly to this network. Secondary analysis integrating only these three modalities in a larger subsample (n=513) indicated support for both 3- and 5-subtype solutions, which had significant overlap, but showed varying degrees of internal stability and external validity. One subtype showed marked cognitive decline, which remained significant even after correcting for tests across both 3- and 5-subtype solutions (pBonf=5.9x10-3). Comparison to single-modality subtypes demonstrated that the three-modal subtypes were able to uniquely capture cognitive variability. Comprehensive sensitivity analyses explored influences of sample size and cluster number parameters. ConclusionWe identified highly integrative molecular subtypes of aging derived from multiple high dimensional, multi-omic data modalities simultaneously. Fusing RNA abundance, DNA methylation, and H3K9 acetylation measures generated subtypes that were associated with cognitive decline. This work highlights the potential value and challenges of multi-omic integration in unsupervised subtyping of postmortem brain.

genomics↗