Biology subjects

Yang, Y.

Publications and source records attributed to Yang, Y..

At least 613 records · Page 34Linked to original sources

bioRxiv2024

5-HT Neurons Integrate GABA and Dopamine Inputs to Regulate Meal Initiation

Obesity is a growing global health epidemic with limited effective therapeutics. Serotonin (5-HT) is one major neurotransmitter which remains an excellent target for new weight-loss therapies, but there remains a gap in knowledge on the mechanisms involved in 5-HT produced in the dorsal Raphe nucleus (DRN) and its involvement in meal initiation. Using a closed-loop optogenetic feeding paradigm, we showed that the 5-HTDRN{lozenge}arcuate nucleus (ARH) circuit plays an important role in regulating meal initiation. Incorporating electrophysiology and ChannelRhodopsin-2-Assisted Circuit Mapping, we demonstrated that 5-HTDRN neurons receive inhibitory input partially from GABAergic neurons in the DRN, and the 5-HT response to GABAergic inputs can be enhanced by hunger. Additionally, deletion of the GABAA receptor subunit in 5-HT neurons inhibits meal initiation with no effect on the satiation process. Finally, we identified the instrumental role of dopaminergic inputs via dopamine receptor D2 in 5-HTDRN neurons in enhancing the response to GABA-induced feeding. Thus, our results indicate that 5-HTDRN neurons are inhibited by synergistic inhibitory actions of GABA and dopamine, which allows for the initiation of a meal.

neuroscience↗

bioRxiv2024

Riluzole reverses blood-testis barrier loss to rescue chemotherapy induced male infertility by binding to TRPC

Cancer treatments, including cytotoxic therapy, often result in male infertility, necessitating the development of safe and effective strategies to preserve male reproductive potential during chemotherapy. Notably, our study uncovers the potential of repurposing riluzole, an FDA-approved drug for amyotrophic lateral sclerosis (ALS), in enhancing spermatogenesis. Hence, this research aims to explore the feasibility of utilizing riluzole to alleviate male infertility induced by busulfan (BSF), a commonly used chemotherapy drug. We established a BSF-induced oligospermia model in 4-week-old male mice and found that riluzole could effectively countered the detrimental effects of BSF on sperm production in mice with oligospermia. By restoring blood-testis barrier (BTB) functionality, riluzole improves sperm quality and reduces testicular atrophy. Through transcriptomic and molecular docking analyses, we identify transient receptor potential canonical subfamily member 5 (TRPC5) as a potential target for riluzole-mediated regulation of blood-testis barrier function. These findings propose riluzole as a promising therapeutic option for chemotherapy-induced male infertility, thereby addressing the fertility challenges associated with cancer treatments. Moreover, repurposing riluzole could streamline the drug development process, providing a cost-effective approach with reduced risk compared to developing entirely new drugs.

pharmacology and toxicology↗

bioRxiv2024

Genetic tuning of intrinsically photosensitive retinal ganglion cell subtype identity to drive visual behavior

The melanopsin-expressing, intrinsically photosensitive retinal ganglion cells (ipRGCs) comprise a subset of the [~]40 retinal ganglion cell types in the mouse retina and drive a diverse array of light-evoked behaviors from circadian photoentrainment to pupil constriction to contrast sensitivity for visual perception. Central to the ability of ipRGCs to control this diverse array of behaviors is the distinct complement of morphophysiological features and gene expression patterns found in the M1-M6 ipRGC subtypes. However, the genetic regulatory programs that give rise to subtypes of ipRGCs are unknown. Here, we identify the transcription factor Brn3b (Pou4f2) as a key genetic regulator that shapes the unique functions of ipRGC subtypes and their diverse downstream visual behaviors.

neuroscience↗

bioRxiv2024

Upregulated expression of ubiquitin ligase TRIM21 promotes PKM2 nuclear translocation and astrocyte activation in experimental autoimmune encephalomyelitis

Reactive astrocytes play critical roles in the occurrence of various neurological diseases such as multiple sclerosis. Activation of astrocytes is often accompanied by a glycolysis-dominant metabolic switch. However, the role and molecular mechanism of metabolic reprogramming in activation of astrocytes have not been clarified. Here, we found that PKM2, a notoriously known rate-limiting enzyme of glycolysis, displayed nuclear translocation in astrocytes of EAE (experimental autoimmune encephalomyelitis) mice, an animal model of multiple sclerosis. Prevention of PKM2 nuclear import by DASA-58 significantly reduced the activation of primary astrocytes, which was observed by decreased proliferation, glycolysis and secretion of inflammatory cytokines. Most importantly, we identified the ubiquitination-mediated regulation of PKM2 nuclear import by ubiquitin ligase TRIM21. TRIM21 interacted with PKM2, promoted its nuclear translocation and stimulated its nuclear activity to phosphorylate STAT3, NF-{kappa}B and interact with c-myc. Further single-cell RNA sequencing and immunofluorescence staining demonstrated that TRIM21 expression was upregulated in astrocytes of EAE. TRIM21 overexpressing in primary astrocytes enhanced PKM2-dependent glycolysis and proliferation, which could be reversed by DASA-58. Moreover, intracerebroventricular injection of a lentiviral vector to knockdown TRIM21 in astrocytes or intraperitoneal injection of TEPP-46, which inhibit the nuclear translocation of PKM2, effectively decreased disease severity, CNS inflammation and demyelination in EAE. Collectively, our study provides novel insights into the pathological function of nuclear glycolytic enzyme PKM2 and ubiquitination-mediated regulatory mechanism that are involved in astrocyte activation. Targeting this axis may be a potential therapeutic strategy for the treatment of astrocyte-involved neurological disease.

neuroscience↗

bioRxiv2024

CRISPR-Cas9 knockout screen informs efficient reduction of the Komagataella phaffii secretome

The yeast Komagataella phaffii is widely used for manufacturing recombinant proteins, but secreted titers of recombinant proteins could be improved by genetic engineering. In this study, we hypothesized that cellular resources could be redirected from production of endogenous proteins to production of recombinant proteins be deletion of unneeded endogenous proteins. We identified a set of endogenous secreted proteins in K. phaffii and attempted to disrupt these genes, but our efforts were hindered by limited annotation of genes, especially essential ones--this is a common problem for genetic engineering of non-model organisms. To predict essential genes, therefore, we designed, transformed, and sequenced a pooled library of guide RNAs for CRISPR-Cas9-mediated knockout of all endogenous secreted proteins. We then used predicted gene essentiality to guide iterative disruptions of up to 11 non-essential genes. Engineered strains exhibited a [~]20x increase in the production of human serum albumin and a twofold increase in the production of a monoclonal antibody. The pooled library of secretome-targeted guides for CRISPR-Cas9 and knowledge of gene essentiality reported here will facilitate future efforts to engineer K. phaffii for production of other recombinant proteins and enzymes.

bioengineering↗

bioRxiv2024

Cold induces brain region-selective neuronal activity-dependent lipid metabolism

It has been well documented that cold is an enhancer of lipid metabolism in peripheral tissues, yet its effect on central nervous system lipid dynamics is underexplored. It is well recognized that cold acclimations enhance adipocyte functions, including white adipose tissue (WAT) lipid lipolysis and beiging, and brown adipose tissue (BAT) thermogenesis in mammals. However, it remains unclear whether and how lipid metabolism in the brain is also under the control of cold acclimations. Here, we show that cold exposure predominantly increases the expressions of the lipid lipolysis genes and proteins within the paraventricular nucleus of the hypothalamus (PVH). Mechanistically, we find that cold activates cells within the PVH and pharmacological inactivation of cells blunts cold-induced effects on lipid peroxidation, accumulation of lipid droplets (LDs), and lipolysis in the PVH. Together, these findings suggest that PVH lipid metabolism is cold sensitive and integral to cold-induced broader regulatory responses.

neuroscience↗

bioRxiv2024

Controlled Noise: Evidence of Epigenetic Regulation of Single-Cell Expression Variability

MotivationUnderstanding single-cell expression variability (scEV) or gene expression noise among cells of the same type and state is crucial for delineating population-level cellular function. While epigenetic mechanisms are widely implicated in gene expression regulation, a definitive link between chromatin accessibility and scEV remains elusive. Advances in single-cell techniques now enable simultaneous measurement of scATAC-seq and scRNA-seq within individual cells, presenting an unprecedented opportunity to address this gap. ResultsThis paper introduces an innovative testing pipeline to investigate the association between chromatin accessibility and scEV. The pipeline hinges on comparing the prediction performance of scATAC-seq data on gene expression levels between highly variable genes (HVGs) and non-highly variable genes (non-HVGs). Applying this pipeline to paired scATAC-seq and scRNA-seq data from human hematopoietic stem and progenitor cells, we observed a significantly superior prediction performance of scATAC-seq data for HVGs compared to non-HVGs. Notably, there was substantial overlap between well-predicted genes and HVGs. The gene pathways enriched from well-predicted genes are highly pertinent to cell type-specific functions. Our findings support the notion that scEV largely stems from cell-to-cell variability in chromatin accessibility, providing compelling evidence for the epigenetic regulation of scEV and offering promising avenues for investigating gene regulation mechanisms at the single-cell level. Availability and implementationThe source code and data used in this paper can be found at https://github.com/SiweiCui/EpigeneticControlOfSingle-CellExpressionVariability.

bioinformatics↗

bioRxiv2024

CCDC113 stabilizes sperm axoneme and head-tail coupling apparatus to ensure male fertility

The structural integrity of the sperm is crucial for male fertility, defects in sperm head-tail linkage and flagellar axoneme are associated with acephalic spermatozoa syndrome (ASS) and the multiple morphological abnormalities of the sperm flagella (MMAF). Notably, impaired head-tail coupling apparatus (HTCA) often accompanies defects in the flagellum structure, however, the molecular mechanisms underlying this phenomenon remain elusive. Here, we identified an evolutionarily conserved coiled-coil domain-containing (CCDC) protein, CCDC113, and found the disruption of CCDC113 produced spermatozoa with disorganized sperm flagella and HTCA, which caused male infertility. Further analysis revealed that CCDC113 could bind to CFAP57 and CFAP91, and function as an adaptor protein for the connection of radial spokes, nexin-dynein regulatory complex (N-DRC) and doublet microtubules (DMTs) in the sperm axoneme. Moreover, CCDC113 was identified as a structural component of HTCA, collaborating with SUN5 and CENTLEIN to connect sperm head to tail during spermiogenesis. Together, our studies reveal that CCDC113 serve as a critical hub for sperm axoneme and HTCA stabilization, providing insights into the potential pathogenesis of infertility associated with human CCDC113 mutations.

developmental biology↗

bioRxiv2024

Originator: Computational Framework Separating Single-Cell RNA-Seq by Genetic and Contextual Information

Single-cell RNA sequencing (scRNA-Seq) data from complex human tissues have prevalent blood cell contamination during the sample preparation process. They may also comprise cells of different genetic makeups. These issues demand rigorous preprocessing and filtering prior to the downstream functional analysis, to avoid biased conclusions due to cell types not of interest. Towards this, we propose a new computational framework, Originator, which deciphers single cells by the genetic origin and separates immune cells of blood contamination from those of expected tissue-resident cells. We demonstrate the accuracy of Originator at separating immune cells from the blood and tissue as well as cells of different genetic origins, using a variety of artificially mixed and real datasets. We show the prevalence of blood contamination in scRNA-Seq data of many tissue types. We alert the significant consequences if failing to adjust for these confounders, using scRNA-Seq data of pancreatic cancer and placentas as examples.

bioinformatics↗

bioRxiv2024

SwinCell: a transformer-based framework for dense 3D cellular segmentation

Segmentation of three-dimensional (3D) cellular images is fundamental for studying and understanding cell structure and function. However, 3D cellular segmentation is challenging, particularly for dense cells and tissues. This challenge arises mainly from the complex contextual information within 3D images, anisotropic properties, and the sensitivity to internal cellular structures, which often lead to miss-segmentation. In this work, we introduce SwinCell, a 3D transformer-based framework that leverages Swin-transformer for flow prediction and effectively distinguishes individual cell instances in 3D. We demonstrate the broad utility of the SwinCell in the segmentation of nuclei, colon tissue cells, and dense cultured cells. SwinCell strikes a balance between maintaining detailed local feature recognition and understanding broader contextual information. Tested extensively with both public and in-house 3D cell imaging datasets, SwinCell shows superior performance in segmenting dense cells in 3D, making it a powerful 3D segmentation tool for cellular analysis that could expedite research in cell biology and tissue engineering.

cell biology↗

bioRxiv2024

Macro-environment strongly interacts with warming in a global analysis of decomposition

Empirical studies worldwide show substantial variability in plant litter decomposition responses to warming, leaving the overall impact of climate change on this process uncertain. We conducted a meta-analysis of 109 experimental warming studies across seven continents, utilizing natural and standardized plant material, to assess the overarching effect of warming on decomposition and identify potential moderating factors. Warming influences decomposition differently across macro-environmental gradients of moisture and temperature. Negative warming effects on decomposition in warmer, low-moisture areas were counterbalanced by the positive, though not significant, warming effects in colder areas, resulting in an overall non-significant effect. We determine that at least 5.2 degrees of warming is required for a significant increase in decomposition. This is particularly relevant given the past decades global warmth in higher latitudes, holding a significant proportion of terrestrial carbon. Low-quality plant litter was more sensitive to warming. Therefore, future vegetation changes toward low-quality, temperature-sensitive plants could increase carbon release and reduce the net supply of stored organic matter in the soil by increasing the decomposition of low-quality litter with warming. Our findings emphasize the connection between warming responses, macro-environment, and litter characteristics, refining predictions of climate changes consequences on key ecosystem processes and its contextual dependencies.

ecology↗

bioRxiv2024

Quinoline-based compounds can inhibit diverse enzymes that act on DNA

DNA methylation, as exemplified by cytosine-C5 methylation in mammals and adenine-N6 methylation in bacteria, is a crucial epigenetic mechanism driving numerous vital biological processes. Developing non-nucleoside inhibitors to cause DNA hypomethylation is a high priority, in order to treat a variety of significant medical conditions without the toxicities associated with existing cytidine-based hypomethylating agents. In this study, we have characterized fifteen quinoline-based analogs. Notably, compounds with additions like a methylamine (9) or methylpiperazine (11) demonstrate similar low micromolar inhibitory potency against both human DNMT1 (which generates C5-methylcytosine) and Clostridioides difficile CamA (which generates N6-methyladenine). Structurally, compounds 9 and 11 specifically intercalate into CamA-bound DNA via the minor groove, adjacent to the target adenine, leading to a substantial conformational shift that moves the catalytic domain away from the DNA. This study adds to the limited examples of DNA methyltransferases being inhibited by non-nucleotide compounds through DNA intercalation, following the discovery of dicyanopyridine-based inhibitors for DNMT1. Furthermore, our study shows that some of these quinoline-based analogs inhibit other enzymes that act on DNA, such as polymerases and base excision repair glycosylases. Finally, in cancer cells compound 11 elicits DNA damage response via p53 activation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/587980v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@da2e94org.highwire.dtl.DTLVardef@27f909org.highwire.dtl.DTLVardef@4ec628org.highwire.dtl.DTLVardef@1b384df_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISix of fifteen quinoline-based derivatives demonstrated comparable low micromolar inhibitory effects on human cytosine methyltransferase DNMT1, and the bacterial adenine methyltransferases Clostridioides difficile CamA and Caulobacter crescentus CcrM. C_LIO_LICompounds 9 and 11 were found to intercalate into a DNA substrate bound by CamA. C_LIO_LIThese quinoline-based derivatives also showed inhibitory activity against various base excision repair DNA glycosylases, and DNA and RNA polymerases. C_LIO_LICompound 11 provokes DNA damage response via p53 activation in cancer cells. C_LI

molecular biology↗

bioRxiv2024

SLIRP mediates nuclear-mitochondrial communication during antiviral signaling to promote robust interferon response

The abnormal innate immune response is a prominent feature underlying autoimmune diseases. One emerging factor that can trigger dysregulated immune activation is cytosolic mitochondrial double-stranded RNAs (mt-dsRNAs). However, the mechanism by which mt-dsRNAs stimulate immune responses remains poorly understood. Here, we discover SRA stem-loop interacting RNA binding protein (SLIRP) as a key amplifier of mt-dsRNA-triggered antiviral signals. In autoimmune diseases, SLIRP is commonly upregulated, and targeted knockdown of SLIRP dampens the interferon response. We find that the activation of melanoma differentiation-associated gene 5 (MDA5) by exogenous dsRNAs upregulates SLIRP, which then stabilizes mt-dsRNAs and promotes their cytosolic release to activate MDA5 further, augmenting the interferon response. Furthermore, the downregulation of SLIRP partially rescues the abnormal interferon-stimulated gene expression in autoimmune patients primary cells and makes cells vulnerable to certain viral infections. Our study unveils SLIRP as a pivotal mediator of interferon response through positive feedback amplification of antiviral signaling.

molecular biology↗

bioRxiv2024

Inferring gene regulatory networks by hypergraph variational autoencoder

In constructing Gene Regulatory Networks (GRNs), it is crucial to consider cellular heterogeneity and differential gene regulatory modules. However, traditional methods have predominantly focused on cellular heterogeneity, approaching the subject from a relatively narrow scope. We present HyperG-VAE, a Bayesian deep generative model that utilizes a hypergraph to model single-cell RNA sequencing (scRNA-seq) data. HyperG-VAE employs a cell encoder with a Structural Equation Model to address cellular heterogeneity and build GRNs, alongside a gene encoder using hypergraph self-attention to identify gene modules. Encoders are synergistically optimized by a decoder, enabling HyperG-VAE to excel in GRN inference, single-cell clustering, and data visualization, evidenced by benchmarks. Additionally, HyperG-VAE effectively reveals gene regulation patterns and shows robustness in varied downstream analyses, demonstrated using B cell development data in bone marrow. The interplay of encoders by the overlapping genes between predicted GRNs and gene modules is further validated by gene set enrichment analysis, underscoring that the gene encoder boosts the GRN inference. HyperG-VAE proves efficient in scRNA-seq data analysis and GRN inference.

bioinformatics↗

bioRxiv2024

Tuning Collective Behaviour in Zebrafish with Genetic Modification

Zebrafish collective behaviour is widely used to assess their physical and mental state, serving as a valuable tool to assess the impact of ageing, disease genetics, and the effect of drugs. The essence of these macroscopic phenomena can be represented by active matter models, where the individuals are abstracted as interactive self-propelling agents. The behaviour of these agents depends on a set of parameters in a manner reminiscent of those between the constituents of physical systems. In a few cases, the system may be controlled at the level of the individual constituents such as the interactions between colloidal particles, or the enzymatic behaviour of de novo proteins. Usually, however, while the collective behaviour may be influenced by environmental factors, it typically cannot be changed at will. Here, we challenge this scenario in a biological context by genetically modifying zebrafish. We thus demonstrate the potential of genetic modification in the context of controlling the collective behaviour of biological active matter systems at the level of the constituents, rather than externally. In particular, we probe the effect of the lack of col11a2 gene in zebrafish, which causes the early onset of osteoarthritis. The resulting col11a2 -/- zebrafish exhibited compromised vertebral column properties, bent their body less while swimming, and took longer to change their orientations. Surprisingly, a group of 25 mutant fish exhibited more orderly collective motion than the wildtype. We show that the collective behaviour of wildtype and col11a2 -/- zebrafish are captured with a simple active matter model, in which the mutant fish are modelled by self-propelling agents with a higher orientational noise on average. In this way, we demonstrate the possibility of tuning a biological system, changing the state space it occupies when interpreted with a simple active matter model.

animal behavior and cognition↗

bioRxiv2024

Motion vision is tuned to maximize sensorimotor energy transfer in blowfly flight

Insects achieve agile flight using a sensor-rich control architecture whose embodiment eliminates the need for complex computation. For example, their visual systems are tuned to detect the optic flow associated with specific self-motions, but what functional principle does this tuning embed and how does it facilitate motor control? Here we test the hypothesis that evolution co-tunes physics and physiology by aligning an insects sensors to its dynamically-significant modes of self-motion. Specifically, we show that the tuning of the blowfly motion vision system maximizes the flow of signal energy from gust disturbances and control inputs to sensor outputs, jointly optimizing observability and controllability. This evolutionary principle differs from the conventional engineering-design paradigm of optimizing state estimation, with implications for novel robotic systems combining high performance with low power-consumption.

neuroscience↗

bioRxiv2024

Regenerative human liver organoids (HLOs) in a pillar/perfusion plate for hepatotoxicity assays

Human liver organoids (HLOs) differentiated from embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and adult stem cells (ASCs) can recapitulate the structure and function of human fetal liver tissues, thus being considered as a promising tissue model for liver diseases and predictive compound screening. However, the adoption of HLOs in drug discovery faces several technical challenges, which include the lengthy differentiation process with multiple culture media leading to batch-to-batch variation, short-term maintenance of hepatic functions post-maturation, low assay throughput due to Matrigel dissociation and HLO transfer to a microtiter well plate, and insufficient maturity levels compared to primary hepatocytes. To address these issues, expandable HLOs (Exp-HLOs) derived from human iPSCs were generated by optimizing differentiation protocols, which were rapidly printed on a 144-pillar plate with sidewalls and slits (144PillarPlate) and dynamically cultured for up to 20 days into differentiated HLOs (Diff-HLOs) in a 144-perfusion plate with perfusion wells and reservoirs (144PerfusionPlate) for in situ organoid culture and analysis. The dynamically cultured Diff-HLOs exhibited greater maturity and reproducibility than those cultured statically, especially after a 10-day differentiation period. In addition, Diff-HLOs in the pillar/perfusion plate were tested with acetaminophen and troglitazone for 3 days to assess drug-induced liver injury (DILI) and then incubated in an expansion medium for 10 days to evaluate liver recovery from DILI. The assessment of liver regeneration post-injury is critical to understanding the mechanism of recovery and determining the threshold drug concentration beyond which there will be a sharp decrease in the livers regenerative capacity. We envision that bioprinted Diff-HLOs in the pillar/perfusion plate could be used for high-throughput screening (HTS) of hepatotoxic compounds due to the short-term differentiation of passage-able Exp-HLOs, stable hepatic function post-maturation, high reproducibility, and high throughput with capability of in situ organoid culture, testing, staining, imaging, and analysis. Graphical abstractThe overall process of dynamic liver organoid culture and in situ analysis in the 144PillarPlate/144PerfusionPlate for high-throughput hepatotoxicity assays. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=56 SRC="FIGDIR/small/586638v3_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@1f2902aorg.highwire.dtl.DTLVardef@1d6e074org.highwire.dtl.DTLVardef@2a0dc0org.highwire.dtl.DTLVardef@eccde0_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

How short peptides can disassemble ultra-stable tau fibrils extracted from Alzheimers disease brain by a strain-relief mechanism

Reducing fibrous aggregates of protein tau is a possible strategy for halting progression of Alzheimers disease (AD). Previously we found that in vitro the D-peptide D-TLKIVWC disassembles tau fibrils from AD brains (AD-tau) into benign segments with no energy source present beyond ambient thermal agitation. This disassembly by a short peptide was unexpected, given that AD-tau is sufficiently stable to withstand disassembly in boiling SDS detergent. To consider D peptide-mediated disassembly as a potential therapeutic for AD, it is essential to understand the mechanism and energy source of the disassembly action. We find assembly of D-peptides into amyloid-like fibrils is essential for tau fibril disassembly. Cryo-EM and atomic force microscopy reveal that these D-peptide fibrils have a right-handed twist and embrace tau fibrils which have a left-handed twist. In binding to the AD-tau fibril, the oppositely twisted D-peptide fibril produces a strain, which is relieved by disassembly of both fibrils. This strain-relief mechanism appears to operate in other examples of amyloid fibril disassembly and provides a new direction for the development of first-in-class therapeutics for amyloid diseases.

neuroscience↗