Biology subjects

Du, Y.

Publications and source records attributed to Du, Y..

At least 199 records · Page 11Linked to original sources

bioRxiv2022

CXCL4 signaling and gene induction in human monocytes involve a TLR4 response divergent from LPS

The chemokine CXCL4 activates myeloid cells and contributes to the pathogenesis of inflammatory and fibrotic diseases. One mechanism of CXCL4 action is binding of nucleic acids to promote their internalization and activation of endosomal TLRs. However, the signaling pathways and receptors that mediate myeloid cell responses to CXCL4 alone are not well characterized. Here, we report that in primary human monocytes, CXCL4 activated NF-{kappa}B and a TBK1-JNK signaling axis that drive the expression of inflammatory, fibrotic and neutrophil chemokine genes, and also RIPK3-dependent necroptosis. Surprisingly, six distinct lines of evidence targeting TLR4 expression and function suggested a role for TLR4 in CXCL4 responses. However, we were not able to completely dissect the contributions of CXCL4 alone to the observed results versus a contribution from endotoxin contamination. Our findings suggest that the interactions between CXCL4 and TLR4 merit further study.

immunology↗

bioRxiv2022

Microsecond pulse electrical stimulation modulates cell migration

Wound healing is a complicated process for maintaining skin integrity after injury, for which electrical stimulations (ES) are ascribed to promote wound healing by facilitating cell migration. Time-shortening of the stimulation treatment from current hours to minutes for efficient wound healing but free of cell damage in return, is however rather a challenge. Here, a novel mechanism of ultrashort pulse electric field (PEF), microsecond PEF at higher voltage, is proposed and realized to promote wound healing under a much short time (seconds) for the total treatment. We revealed that microsecond PEF regulated actin cytoskeleton reorganization and focal adhesion turnover, promoting fibroblasts migration in 2D cell cultures under the pulse stimulation. This accelerated fibroblast migration was accompanied by the mutual promotion with extracellular matrix (ECM) alignment in 3D microenvironments, which cooperatively benefit the eventual wound healing, and these findings were further confirmed by the enhanced skin wound healing in a classic mouse model. Additionally, we coined an actin- and collagen-dependent mechanism of microsecond PEF-mediated wound healing. The quantitative mechanism proposed here for our novel microsecond pulse electric filed (sPEF) methodology orients the new practical electric treatment in a wide range of biomedical applications, such as wound healing, regenerative medicine, and tissue engineering.

bioengineering↗

bioRxiv2022

Screening and Development of Constitutively Synergistic Combination Drug Formulations for T Cell Acute Lymphoblastic Leukemia

Advances in multiagent chemotherapy have led to recent improvements in overall survival for patients with acute lymphoblastic leukemia (ALL); however, a significant fraction do not respond to frontline chemotherapy or later relapse with recurrent disease, after which long-term survival rates remain low. To address the challenge of developing new, effective treatment options for these patients, we conducted a series of high-throughput combination drug screens to identify chemotherapies that synergize in a lineage-specific manner with MRX-2843, a small molecule dual MERTK and FLT3 kinase inhibitor currently in clinical testing for treatment of relapsed/refractory leukemias and solid tumors. Using experimental and computational approaches, we found that MRX-2843 synergized strongly - and in a ratio-dependent manner - with vincristine chemotherapy to inhibit T-ALL cell expansion and, based on these findings, we developed multiagent lipid nanoparticle formulations of these drugs that not only constitutively maintained ratiometric drug synergy following T-ALL cell delivery, but also improved anti-leukemic activity following drug encapsulation. To determine the clinical relevance of these combination drug formulations and the therapeutic impact of ratiometric drug synergy, we compared the efficacy of lipid nanoparticles comprising synergistic, additive, and antagonistic ratios of MRX-2843 and vincristine, and observed that trends in in vitro synergy were directly recapitulated in primary T-ALL patient samples. Together, these findings present a systematic approach to high-throughput combination drug screening and multiagent drug delivery that maximizes the therapeutic potential of combined MRX-2843 and vincristine in T-ALL. This broadly generalizable approach could lead to the development of constitutively synergistic combination products for the treatment of cancer and other diseases.

bioengineering↗

bioRxiv2022

Control of alveolar macrophage differentiation by Siah1a/2 ubiquitin ligases limits carcinogen-induced lung adenocarcinoma

Tumor microenvironment components, including T and myeloid cells, play important roles in lung adenocarcinoma (LADC) progression and response to therapy. Here, we identify a role for Siah1a/2 ubiquitin ligases in controlling alveolar macrophage (AM) differentiation and urethane-induced LADC. Genetic ablation of Siah1a/2 in AMs enriched their immature state, coinciding with increased pro-tumorigenic and inflammatory gene signatures and abundance of Siah1a/2 substrates NRF2 and {beta}-catenin. Urethane administration to mice enriched the population of monocytic and immature-like AMs, which were more prevalent in the lungs of mice carrying Siah1a/2-ablated macrophages. While resembling transitional profibrotic macrophages often seen in lung fibrosis, enrichment of immature AMs coincided with the development of more frequent and larger lung tumors in urethane-treated mice harboring Siah1a/2 ablated macrophages compared with controls. Gene expression signature of Siah1a/2 ablated immature-like AMs is associated with increased infiltration of CD14+ immune cells and worse survival of LADC patients. Our findings identify Siah1a/2 as gatekeepers of cancer development by controlling AM differentiation and profibrotic phenotypes contributing to carcinogen-induced lung cancer.

cancer biology↗

bioRxiv2022

ATFS-1 regulates peroxisome assembly genes and protects both mitochondria and peroxisomes during peroxin perturbations

Peroxisome biogenesis disorders lead to a myriad of clinical manifestations, among which is the dysfunction of the mitochondria. Mitochondria dysfunction is typically sensed by the UPRmt, a broad protective transcriptional response governed by the transcription factor ATFS-1. Here, we investigated the role of the UPRmt during peroxisomal stress. We show that mutations or knockdown of peroxins, the genes required for peroxisome assembly, lead to mitochondria dysfunction and the induction of the UPRmt in C.elegans. The UPRmt induced the transcription of the mitochondrial outer membrane translocase mspn-1 (ATAD-1), that in turn alleviated mitochondrial stress most likely by extracting mislocalized proteins. Importantly, ATFS-1 regulated the transcription of peroxins and the peroxisomal transporter pmp-4. A prx-5 loss of function strain induced a retrograde response that resulted in the transcriptional induction of peroxins, peroxisomal transporters, chaperons and proteases. And was dependent on ATFS-1 and on the peroxisome proliferator activator receptor alpha, NHR-49. Knockout of atfs-1 during peroxisomal stress resulted in severe developmental delays, import defects to peroxisomes and the appearance of large peroxisomal structures. We propose that ATFS-1 regulates the biogenesis of peroxisomes and protects the organism by alleviating the stress of both peroxisomes and mitochondria during peroxisomal stress.

developmental biology↗

bioRxiv2022

Canonical and Replicable Multi-Scale Intrinsic Connectivity Networks in 100k+ Resting-State fMRI Datasets

Resting-state functional magnetic resonance imaging (rsfMRI) has shown considerable promise for improving our understanding of brain function and characterizing various mental and cognitive states in the healthy and disordered brain. However, the lack of accurate and precise estimations of comparable functional patterns across datasets, individuals, and ever-changing brain states in a way that captures both individual variation and inter-subject correspondence limits the clinical utility of rsfMRI and its application to single-subject analyses. We posit that using reliable network templates and advanced group-informed network estimation approaches to accurately and precisely obtain individualized (dynamic) networks that retain cross-subject correspondence while maintaining subject-specific information is one potential solution to overcome the aforementioned barrier when considering cross-study comparability, independence of subject-level estimates, the limited data available in single studies, and the low signal-to-noise ratio (SNR) of rsfMRI. Toward this goal, we first obtained a reliable and replicable network template. We combined rsfMRI data of over 100k individuals across private and public datasets and selected around 58k that meet quality control (QC) criteria. We then applied multi-model-order independent component analysis (ICA) and subsampling to obtain reliable canonical intrinsic connectivity networks (ICNs) across multiple spatial scales. The selected ICNs (i.e., network templates) were also successfully replicated by independently analyzing the data that did not pass the QC criteria, highlighting the robustness of our adaptive template to data quality. We next studied the feasibility of estimating the corresponding subject-specific ICNs using a multivariate-spatially constrained ICA as an example of group-informed network estimation approaches. The results highlight that several factors, including ICNs themselves, data length, and spatial resolution, play key roles in successfully estimating the ICNs at the subject level. Large-scale ICNs, in general, require less data to achieve a specific level of spatial similarity with their templates (as well as within- and between-subject spatial similarity). Moreover, increasing data length can reduce an ICNs subject-level specificity, suggesting longer scans might not always be desirable. We also show spatial smoothing can alter results, and the positive linear relationship we observed between data length and spatial smoothness (we posit that it is at least partially due to averaging over intrinsic dynamics or individual variation) indicates the importance of considering this factor in studies such as those focused on optimizing data length. Finally, the consistency in the spatial similarity between ICNs estimated using the full-length of data and subset of it across different data lengths may suggest that the lower within-subject spatial similarity in shorter data lengths is not necessarily only defined by lower reliability in ICN estimates; rather, it can also be an indication of brain dynamics (i.e., different subsets of data may reflect different ICN dynamics), and as we increase the data length, the result approaches the average (also known as static) ICN pattern, and therefore loses its distinctiveness.

neuroscience↗

bioRxiv2022

High-Resolution 3D Ultra-Short Echo Time MRI with Rosette k-Space Pattern for Brain Iron Content Mapping

BackgroundThe iron concentration increases during normal brain development and is identified as a risk factor for many neurodegenerative diseases, it is vital to monitor iron content in the brain non-invasively. PurposeThis study aimed to quantify in vivo brain iron concentration with a 3D rosette-based ultra-short echo time (UTE) magnetic resonance imaging (MRI) sequence. MethodsA cylindrical phantom containing nine vials of different iron concentrations (iron (II) chloride) from 0.5 millimoles to 50 millimoles and six healthy subjects were scanned using 3D high-resolution (0.94x0.94x0.94 mm3) rosette UTE sequence at an echo time (TE) of 20 s. ResultsIron-related hyperintense signals (i.e., positive contrast) were detected based on the phantom scan, and were used to establish an association between iron concentration and signal intensity. The signal intensities from in vivo scans were then converted to iron concentrations based on the association. The deep brain structures, such as the substantia nigra, putamen, and globus pallidus, were highlighted after the conversion, which indicated potential iron accumulations. ConclusionThis study suggested that T1-weighted signal intensity could be used for brain iron mapping.

neuroscience↗

bioRxiv2022

Tex2 is required for lysosomal functions at TMEM55-dependent ER membrane contact sites

ER tubules form and maintain membrane contact sites (MCSs) with late endosomes/lysosomes (LE/lys). The molecular composition and cellular functions of these MCSs are poorly understood. Here we find that Tex2, an SMP domain-containing lipid transfer protein conserved in metazoen and yeast, is a tubular ER protein, and enriches at ER-LE/lys MCSs dependent on TMEM55, phosphatases that convert PI(4,5)P2 to PI5P on LE/lys. We show that the Tex2-TMEM55 interaction occurs between a N-terminal region of Tex2 and a catalytic motif in PTase domain of TMEM55. The Tex2-TMEM55 interaction can be regulated by endosome-resident type 2 PI4K activities. Functionally, Tex2 knockout results in severe defects in lysosomal digestive capacity and blocked autophagic flow, as well as an aberrant accumulation of PI3P on the LE/lys membranes. These defects can be substantially rescued by wild type Tex2 other than a lipid transfer-defective Tex2 mutant, indicating an important role of lipid transfer in these processes. Together our data identify Tex2 as a tubular ER protein that resides at TMEM55-depedent ER-LE/lys MCSs required for lysosomal functions.

cell biology↗

bioRxiv2022

Action inhibition revisited: Stopping is not faster than going

Much work has examined the process of canceling or inhibiting an impending action. However, the converse process of initiating a movement has, comparatively, been much less studied. Action initiation and action inhibition are generally considered to be independent and qualitatively distinct processes, while the exact relationship between these processes remains unclear. One respect in which action initiation and action inhibition are often thought to differ is in their speed; action inhibition is typically considered to be faster than action initiation, which allows for impending actions to be inhibited before they are initiated. This apparent contrast is, however, largely observed in tasks in which there is much greater urgency to inhibit an action that there is to initiate an action. This asymmetry in the urgency between action initiation and action inhibition, as well as other asymmetries in how action initiation and inhibition are cued, make it impossible to compare their relative time courses. Here, we demonstrate that, when action initiation and action inhibition are measured under conditions that are matched as closely as possible, their speed is the same. In light of this, we suggest that action initiation and action inhibition may not necessarily be qualitatively distinct processes, but may instead reflect two opposing states of a single process supporting a decision about whether to act or not. This perspective carries significant implications for computational models and presumed neural mechanisms of action control.

neuroscience↗

bioRxiv2022

Cardiac performance and heat shock response variation related to shell colour morphs in the mudflat snail Batillaria attramentaria

Physiological and transcriptomic response to thermal stress were investigated in the mudflat snail Batillaria attramentaria of different shell colour morphs. Despite no difference in upper lethal temperatures among shell colour morphs, their Arrhenius breakpoint temperatures (ABT) for cardiac thermal performance differed significantly, and the ABT of snails with D type morph was higher than snails with UL type morph. The transcriptomic analysis showed that D type snails exhibit higher levels of four HSPs than UL type snails at control temperature. Unfolded protein response was activated in UL type snails but not in D type snails under moderate thermal stress. And there were 11 HSPs increased in UL type snails in contrast to 1 HSP in D type snails, suggesting a "preparative defense" strategy of heat shock response in D type snails under moderate thermal stress. When exposed to sublethal temperature, eight molecular chaperones were uniquely upregulated in D type snails, suggesting these genes may allow for D type snails improved their cardiac thermal tolerance. The "preparative defense" strategies and higher ABT of cardiac thermal performance may adapt the dark shell snails to the rapid and stronger thermal stress in the field. Our results suggested that physiological selection imposed by moderate and sublethal thermal stress, instead of upper lethal limits, may be a driving force shaping shell colour frequency in the mudflat snail B. attramentaria.

physiology↗

bioRxiv2022

Underlying beneficial effects of Rhubarb on constipation-induced inflammation, disorder of gut microbiome and metabolism

BackgroundAlthough constipation is a common syndrome and a worldwide health problem. Constipation patients are becoming younger with a 29.6% overall prevalence in the children, which has captured great attention because of its epigenetic rejuvenation and recurrent episodes. Despite the usage of rhubarb to relieve constipation, novel targets and genes involved in target-relevant pathways with remarkable functionalities should still be sought after. Materials and methodsWe established a reliable constipation model in C57B/6N male mice using intragastric administration diphenoxylate and the eligible subjects received 600mg/25g rhubarb extraction to ameliorate constipation. Resultant constipation was morphological and genetically compared with the specimen from different groups. ResultsThe constipation mice exhibited thicker muscle layers, improved content of cytokines, including IL-17 and IL-23, and lower content of IL-22. The bacterial abundance and diversity varied tremendously. Notably, the alterations were reversed after rhubarb treatment. Additionally, SCFA and MLCFA were significantly influenced by constipation accompanied by enhanced expressions of SCFA receptors, GPR41 and GPR43. ConclusionThis thesis has provided an insight that rhubarb promoted the flexibility of collagen fiber, reduced pro-inflammatory cytokines and enhanced anti-inflammatory cytokines, and maintained intestinal microflora balance with potential effects on affecting the metabolism of fatty acids and polyamines.

pharmacology and toxicology↗

bioRxiv2022

Mechanical Deformation Behaviors and Structural Properties of Ligated DNA Crystals

DNA self-assembly has emerged as a powerful strategy for constructing complex nanostructures. While the mechanics of individual DNA strands have been studied extensively, the deformation behaviors and structural properties of self-assembled architectures are not well understood. This is partly due to the small dimensions and limited experimental methods available. DNA crystals are macroscopic crystalline structures assembled from nanoscale motifs via sticky-end association. The large DNA constructs may thus be an ideal platform to study structural mechanics. Here we have investigated the fundamental mechanical properties and behaviors of ligated DNA crystals made of tensegrity triangular motifs. We performed coarse-grained molecular dynamics simulations and confirmed the results with nanoindentation experiments using atomic force microscopy. We observed various deformation modes including un-tension, linear elasticity, duplex dissociation, and single-stranded component stretch. We found that the mechanical properties of a DNA architecture are correlated with those of its components, however the structure shows complex behaviors which may not be predicted by components alone.

biophysics↗

bioRxiv2022

Guided construction of single cell reference for human and mouse lung

Accurate cell type identification is a key and rate-limiting step in single cell data analysis. Single cell references with comprehensive cell types, reproducible and functional validated cell identities, and common nomenclatures are much needed by the research community to optimize automated cell type annotation and facilitate data integration, sharing, and collaboration. In the present study, we developed a novel computational pipeline to utilize the LungMAP CellCards as a dictionary to consolidate single-cell transcriptomic datasets of 104 human lungs and 17 mouse lung samples and constructed "LungMAP CellRef" and "LungMAP CellRef Seed" for both normal human and mouse lungs. "CellRef Seed" has an equivalent prediction power and produces consistent cell annotation as does "CellRef" but improves computational efficiency and simplifies its utilization for fast automated cell type annotation and online visualization. This atlas set incorporates 48 human and 40 mouse well-defined lung cell types catalogued from diverse anatomic locations and developmental time points. Using independent datasets, we demonstrated the utility of our CellRefs for automated cell type annotation analysis of both normal and disease lungs. User-friendly web interfaces were developed to support easy access and maximal utilization of the LungMAP CellRefs. LungMAP CellRefs are freely available to the pulmonary research community through fast interactive web interfaces to facilitate hypothesis generation, research discovery, and identification of cell type alterations in disease conditions.

bioinformatics↗

bioRxiv2022

Mitochondrial genome recovery by ATFS-1 is essential for development following starvation

Nutrient availability regulates the C. elegans life cycle as well as mitochondrial physiology. Food deprivation significantly reduces mitochondrial genome (mtDNA) number and leads to aging-related phenotypes. Here, we demonstrate that the bZIP protein ATFS-1, a mediator of the mitochondrial unfolded protein response (UPRmt), is required to promote growth and establish a functional germline following prolonged starvation. Surprisingly, we found that the recovery of mtDNA copy number and development following starvation required mitochondrial-localized ATFS-1 but not its nuclear transcription activity. Lastly, we found that the insulin-like receptor DAF-2, functions upstream of ATFS-1 to modulate mtDNA content. We demonstrate that reducing DAF-2 activity represses ATFS-1 nuclear function while causing an increase in mtDNA content partly mediated by mitochondrial-localized ATFS-1. Combined, our data indicate the importance of the UPRmt in recovering mitochondrial mass and suggests that atfs-1-dependent mtDNA replication precedes mitochondrial network expansion following starvation.

cell biology↗

bioRxiv2022

Evidence for a common mechanism supporting invigoration of action selection and action execution

The speed, or vigor, of our movements can vary depending on circumstances. For instance, the promise of a reward leads to faster movements. Reward also leads us to move with a lower reaction time, suggesting that the process of action selection can also be invigorated by reward. It has been proposed that invigoration of action selection and of action execution might occur through a common mechanism, and thus these aspects of behavior might be coupled. To test this hypothesis, we asked participants to make reaching movements to "shoot" through a target at varying speeds to assess whether moving more quickly was also associated with more rapid action selection. We found that, when participants were required to move with a lower velocity, the speed of their action selection was also significantly slowed. This finding was recapitulated in a further dataset in which participants determined their own movement speed, but had to move slowly in order to stop their movement inside the target. By re-analyzing a previous dataset, we also found evidence for the converse relationship between action execution and action selection: when pressured to select actions more rapidly, people also executed movements with higher velocity. Our results establish that invigoration of action selection and action execution vary in tandem with one another, supporting the hypothesis of a common underlying mechanism. Significance statementWe show that voluntary increases in the vigor of action execution lead action selection to also occur more rapidly. Conversely, hastening action selection by imposing a deadline to act also leads to increases in movement speed. These findings provide evidence that these two distinct aspects of behavior are modulated by a common underlying mechanism.

neuroscience↗

bioRxiv2022

Stem Cell Secretome Promotes Scarless Corneal Wound Healing and Rescues Corneal Sensory Nerves

Corneal scarring is a leading cause of blindness in the world. In this study, we explored the therapeutic potential of corneal stromal stem cell (CSSC)-derived secretome in a mechanical debridement mouse model of corneal scarring. CSSC secretome was able to promote scarless corneal wound healing. The mechanisms include 1) dampening inflammation with reduced CD45+, CD11b+/GR1+, and CD11b+/F4/80+ inflammatory cells in the wounded corneas; 2) reducing fibrotic extracellular matrix deposition such as collagen IV, collagen 3A1, SPARC, and -SMA; 3) rescuing sensory nerves. The proteomic analysis shows upregulated proteins related to wound healing and cell adhesion which boost scarless wound healing. It also shows upregulated neuroprotective proteins in CSSC secretome related to axon guidance, neurogenesis, neuron projection development, and neuron differentiation. Four unique complement inhibitory proteins CD59, vitronectin, SERPING1, and C1QBP found in CSSC secretome contribute to reducing a complement cascade mediating cell death and membrane attacking complex autoantibodies after corneal injury. This study provides novel insights into mechanisms of stem cell secretome induced scarless corneal wound healing and neuroprotection and identifies regenerative proteins in the CSSC secretome. Significance StatementIn this study, we report the therapeutic role of corneal stromal stem cell (CSSC) secretome for scarless corneal wound healing and corneal sensory nerve rescuing. We uncovered that CSSC secretome dampens inflammation, reduces fibrosis, induces sensory nerve regeneration, and rescues corneal cells by inhibiting the complement system in the wounded mouse corneas. This study provides pre-clinical evidence for the use of CSSC secretome as a biologic treatment for corneal scarring to prevent corneal blindness. We delineated a plethora of proteins in the CSSC secretome, which individually or in combination have the potential as future therapies for scarless corneal wound healing.

cell biology↗

bioRxiv2022

Circular mRNA encoded PROTAC (RiboPROTAC) as a new platform for the degradation of intracellular therapeutic targets

Although proteolysis targeting chimera (PROTAC) technology that hijacking the ubiquitin-proteasome system (UPS) to artificially degrade protein is an emerging promising technology for many undruggable targets, it still faces several challenges, such as the difficulty to select high specificity molecule to protein of interest (POI), and only few of the E3-ligase are suitable for PROTAC mediated protein degradation. Protein-based PROTAC, termed BioPROTAC, owns the advantage of specificity but lacks membrane permeability. Here, we develop a new targeted protein degrading platform, which we termed RiboPROTAC, by encoding BioPROTAC protein degraders with circular mRNA (cmRNA) and delivering intracellularly. In this way, intracellular protein GFP and nuclear protein PCNA were successfully degraded. For PCNA targeting, not only the level of target protein is strongly decreased, but also the cell function related is strongly interfered, such as cell proliferation, apoptosis, as well as the cell cycle. What is more, for the first time, we observed that degrading PCNA with RiboPROTAC causes immunogenic cell death (ICD), although not strong, but was verified in vivo. Importantly, our in vivo results demonstrated that cmRNA encoded PCNA degrader exhibited significant tumor suppression effect, thus we provide the first proof of concept for the application of RiboPROTAC as potential mRNA therapeutic. We consider that RiboPROTAC is a new and superior PROTAC technology for targeting the undruggable targets.

molecular biology↗

bioRxiv2022

Self-avoidance alone does not explain the function of Dscam1 in mushroom body axonal wiring

Alternative splicing of Drosophila Dscam1 into 38,016 isoforms provides neurons with a unique molecular code for self-recognition and self-avoidance. A canonical model suggests that homophilic binding of identical Dscam1 isoforms on sister branches of mushroom body (MB) axons supports segregation with high fidelity, even when only a single isoform is expressed. Here we generated a series of mutant flies with a single exon 4, 6, or 9 variant, encoding 1,584, 396, or 576 potential isoforms, respectively. Surprisingly, most of the mutants in the latter two groups exhibited obvious defects in the growth, branching, and segregation of MB axonal sister branches. This demonstrates that repertoires of 396 and 576 Dscam1 isoforms were not sufficient for normal patterning of axonal branches. Moreover, reducing Dscam1 levels largely reversed the defects caused by reduced isoform diversity, suggesting a functional link between Dscam1 expression levels and isoform diversity. Taken together, these results indicate that canonical self-avoidance alone does not explain the function of Dscam1 in MB axonal wiring.

neuroscience↗