Biology subjects

Yang, Y.

Publications and source records attributed to Yang, Y..

At least 901 records · Page 50Linked to original sources

bioRxiv2022

A tissue injury repair pathway distinct but parallel to host pathogen defense

Pathogen infection and tissue injury are universal insults that disrupt homeostasis. Innate immunity senses microbial infections and induces interferons (IFNs) to activate resistance mechanisms. Applying unbiased phylogenetic analysis, we show that interleukin-24 (IL24) is among the closest evolutionary homologs to the IFN family and shares a common ancestral origin. However, in contrast to IFNs, IL24 induction occurs specifically in barrier epithelial progenitors after injury and is independent of microbiome or adaptive immunity. Surprisingly, Il24 ablation impedes not only epidermal proliferation and re-epithelialization, but also capillary and fibroblast regeneration within the dermal wound bed. Conversely, ectopic Il24 induction in homeostatic epidermis triggers global epithelial-mesenchymal tissue repair responses. Mechanistically, sustained Il24 expression depends upon both IL24 receptor/STAT3 signaling and also hypoxia-stabilized HIF1, which converge following injury. Thus, parallel to the IFN-mediated innate immune sensing of pathogens to resolve infections, epithelial stem cells sense injury signals to orchestrate IL24-mediated tissue repair.

immunology↗

bioRxiv2022

Abundant Aβ fibrils in ultracentrifugal supernatants of aqueous extracts from Alzheimer's disease brains

Soluble aggregates of amyloid-{beta} (A{beta}), often called oligomers, are believed to be principal drivers of neurotoxicity, spreading of pathology, and symptoms in Alzheimers disease (AD), but little is known about their structures in human brain. A{beta} oligomers have been defined as aggregates found in supernatants following ultracentrifugation of aqueous extracts. We now report the unexpected presence of abundant A{beta} fibrils in high-speed supernatants from AD brains that were extracted by soaking in aqueous buffer. The fibrils did not appear to form during extract preparation, and their numbers by EM correlated with ELISA quantification of aggregated A{beta}42. Cryo-EM structures of A{beta} fibrils from aqueous extracts were identical to those from sarkosyl-insoluble AD brain homogenates. The fibrils in aqueous extracts were immunolabeled by lecanemab, an A{beta} aggregate-directed antibody reported to improve cognitive outcomes in AD. We conclude that A{beta} fibrils are abundant in aqueous extracts from AD brains and have the same structures as those from amyloid plaques. These findings have implications for understanding the nature of A{beta} oligomers and for designing oligomer-preferring therapeutic antibodies.

neuroscience↗

bioRxiv2022

MAP4Ks inhibition promotes retinal neuron regeneration from Muumlller glia in adult mice

Mammalian Muller glia (MG) possess limited regenerative capacities. However, the intrinsic capacity of mammalian MG to transdifferentiate to generate mature neurons without transgenic manipulations remains speculative. Here we show that MAP4K4, MAP4K6 and MAP4K7, which are conserved Misshapen subfamily of ste20 kinases homologs, repress YAP activity in mammalian MG and therefore restrict their ability to be reprogrammed. However, by treating with a small molecule inhibitor of MAP4K4/6/7, mouse MG regain their ability to proliferate and enter into a retinal progenitor cell (RPC)-like state after NMDA-induced retinal damage; such plasticity was lost in YAP knockout MG. Moreover, spontaneous trans-differentiation of MG into retinal neurons expressing both amacrine and retinal ganglion cell (RGC) markers occurs after inhibitor withdrawal. Taken together, these findings suggest that MAP4Ks block the reprogramming capacity of MG in a YAP-dependent manner in adult mammals, which provides a novel avenue for the pharmaceutical induction of retinal regeneration in vivo.

neuroscience↗

bioRxiv2022

Damage dynamics in single E. coli and the role of chance in the timing of cell death

Genetically identical cells in the same stressful condition die at different times. The origin of this stochasticity is unclear; it may arise from different initial conditions that affect the time of demise, or from a stochastic damage accumulation mechanism that erases the initial conditions and instead amplifies noise to generate different lifespans. To address this requires measuring damage dynamics in individual cells over the lifespan, but this has rarely been achieved. Here, we used a microfluidic device to measure membrane damage in 648 carbon-starved E. coli cells at high temporal resolution. We find that initial conditions of damage, size or cell-cycle phase do not explain most of the lifespan variation. Instead, the data points to a stochastic mechanism in which noise is amplified by a rising production of damage that saturates its own removal. Surprisingly, the relative variation in damage drops with age: cells become more similar to each other in terms of relative damage, indicating increasing determinism with age. Thus, chance erases initial conditions and then gives way to increasingly deterministic dynamics that dominate the lifespan distribution.

systems biology↗

bioRxiv2022

Innate immune sensing of self-derived double-stranded RNA by RIG-I-MAVS-TNF-α regulates the survival and senescence fate of SARS-2-S syncytia

Patients with pre-existing heart failure are at a particularly high risk of morbidity and mortality resulting from SARS-CoV-2 infection. Direct acute cardiac injury or cytokine storms have been proposed to contribute to depressed cardiac function. However, the pathogenic mechanisms underlying the increased vulnerability to heart failure in SARS-CoV-2 infected patients are still largely unknown. Here, we found that the senescent outcome of SARS-CoV-2 spike protein (SARS-2-S)-induced syncytia exacerbated heart failure progression. We first demonstrated that syncytium formation in cells expressing SARS-2-S delivered by DNA plasmid or LNP-mRNA exhibits a senescence-like phenotype. Extracellular vesicles containing SARS-2-S (S-EVs) also confer a potent ability to form senescent syncytia without denovosynthesis of SARS-2-S. Mechanistically, SARS-2-S syncytia provoke the formation of functional MAVS aggregates, which regulate the senescence fate of SARS-2-S syncytia by TNF . We further demonstrate that senescent SARS-2-S syncytia exhibit shrinked morphology, leading to the activation of WNK1 and impaired cardiac metabolism. In pre-existing heart failure mice, the WNK1 inhibitor WNK463, anti-syncytial drug niclosamide, and senolytic dasatinib protect the heart from exacerbated heart failure triggered by pseudovirus expressing SARS-2-S (SARS-2-Spp). Signs of senescent multinucleated cells are identified in ascending aorta from SARS-CoV-2 omicron variant-infected patient. Our findings thus suggest a potential mechanism for COVID-19-mediated cardiac pathology and recommend the application of WNK1 inhibitor for therapy. Significance StatementIn this paper, we directly linked SARS-2-S-triggered syncytium formation with the ensuing induction of cellular senescence and its pathophysiological contribution to heart failure. We propose that both SARS-2-S expression and SARS-2-S protein internalization were sufficient to induce senescence in nonsenescent ACE2-expressing cells. This is important because of the persistent existence of SARS-2-S or extracellular vesicles containing SARS-2-S during the acute and post-acute stages of SARS-CoV-2 infection in human subjects. In searching for the underlying molecular mechanisms determining syncytial fate, the formation of functional MAVS aggregates dependent on RIG-I was observed at an early stage during fusion and regulated the anti-death to senescence fate of SARS-2-S syncytia through the TNF-TNFR2 axis. We also found impaired cardiac metabolism in SARS-2-S syncytia induced by condensed WNK1. Importantly, SARS-2-Spp-exacerbated heart failure could be largely rescued by WNK1 inhibitor, anti-syncytial drug or senolytic agent. Together, we suggest that rescuing metabolism dysfunction in senescent SARS-2-S syncytia should be taken into consideration in individuals during the acute or post-acute stage of SARS-CoV-2 infection.

cell biology↗

bioRxiv2022

Convergent evolution of plant pattern recognition receptors sensing cysteine-rich patterns from three microbial kingdoms

The Arabidopsis thaliana receptor-like protein RLP30 contributes to immunity against the fungal pathogen Sclerotinia sclerotiorum. Here we identified the RLP30-ligand as a small cysteine-rich protein (SCP) that occurs in many fungi and oomycetes and is also recognized by the Nicotiana benthamiana RLP RE02. However, RLP30 and RE02 share little sequence similarity and respond to different parts of the native/folded protein. Interestingly, some Brassicaceae other than Arabidopsis also respond to a linear SCP peptide, suggesting that SCP is an eminent immune target that led to the convergent evolution of distinct immune receptors in plants. Surprisingly, RLP30 shows a second ligand specificity for a SCP-nonhomologous protein secreted by bacterial Pseudomonads. RLP30 expression in N. tabacum resulted in lower susceptibility to bacterial, fungal and oomycete pathogens, thus demonstrating that detection of immunogenic patterns by Arabidopsis RLP30 is involved in defense against pathogens from three microbial kingdoms.

plant biology↗

bioRxiv2022

Deciphering Spatial Domains by Integrating Histopathological Image and Transcriptomics via Contrastive Learning

Recent advances in spatial transcriptomics have enabled measurements of gene expression at cell/spot resolution meanwhile retaining both the spatial information and the histopathological images of the tissues. Deciphering the spatial domains of spots in the tissues is a vital step for various downstream tasks in spatial transcriptomics analysis. Existing methods have been developed for this purpose by combining gene expression and histopathological images to conquer noises in gene expression. However, current methods only use the histopathological images to construct spot relations without updating in the training stage, or simply concatenate the information from gene expression and images into one feature vector. Here, we propose a novel method ConGI to accurately decipher spatial domains by integrating gene expression and histopathological images, where the gene expression is adapted to image information through contrastive learning. We introduce three contrastive loss functions within and between modalities to learn the common semantic representations across all modalities while avoiding their meaningless modality-private noise information. The learned representations are then used for deciphering spatial domains through a clustering method. By comprehensive tests on tumor and normal spatial transcriptomics datasets, ConGI was shown to outperform existing methods in terms of spatial domain identification. More importantly, the learned representations from our model have also been used efficiently for various downstream tasks, including trajectory inference, clustering, and visualization.

bioinformatics↗

bioRxiv2022

A minimally-invasive method for serial cerebrospinal fluid collection and injection in rodents with high survival rates

Cerebrospinal fluid (CSF) is a clear fluid surrounding and nourishing the brain and spinal cord. Molecular profiling of the CSF is a common diagnostic approach for central nervous system (CNS) diseases, including infectious diseases, autoimmune disorders, brain hemorrhage and traumatic brain injury, CNS tumors, and Alzheimers disease1-10. Rodent models are critical for investigating CNS disease mechanisms and therapeutics, however, both collecting CSF and injecting materials into CSF in small animals are technically challenging and often result in high rates of postoperative mortality. Here, we present an easy-to-practice and cost-effective protocol with minimum instrument requirements to access the CSF in live rodents for collection and infusion purposes. By introducing a metal needle tool bent at a unique angle and length, we could steadily reach the CSF via the foramen magnum. Compared with prior methods, this protocol requires neither the operator to discern the changes in resistance from solid tissues while puncturing the needle, nor surgical opening of the skin and muscle covering the rodent neck. Using this method, we frequently obtain 5-15 L of CSF from mice and 70-120 L from rats to enable diverse downstream analyses including mass spectrometry. Due to the minimal invasiveness, this procedure allows iterative CSF collection from the same animal every few days - a major improvement over prior protocols that require extensive surgical operations. Moreover, we demonstrate that this method could be used for injecting desired solutions including dyes into mouse CSF with high success rates. Our method shortens the time required for CSF collection or injection to 3-5 minutes. Notably, we could reach near 100% postoperative recovery rates in both mice and rats even with repetitive collections. Together, we establish an efficient and minimally-invasive protocol for collecting CSF and inoculating reagents into the CSF in live rodents to enable various longitudinal studies at the forefronts of CNS investigation.

neuroscience↗

bioRxiv2022

Wildflower phenological escape differs by continent and spring temperature

Temperate understory plant species are at risk from climate change and anthropogenic threats that include increased deer herbivory, habitat loss, pollinator declines and mismatch, and nutrient pollution. Recent work suggests that spring ephemeral wildflowers may be at additional risk due to phenological mismatch with deciduous canopy trees. The study of this dynamic, commonly referred to as "phenological escape", and its sensitivity to spring temperature is limited to eastern North America. Here, we use herbarium specimens to show that phenological sensitivity to spring temperature is remarkably conserved for understory wildflowers across North America, Europe, and Asia, but that canopy trees in North America are significantly more sensitive to spring temperature compared to in Asia and Europe. We predict that advancing tree phenology will lead to decreasing spring light windows in North America while spring light windows will be maintained or even increase in Asia and Europe in response to projected climate warming.

ecology↗

bioRxiv2022

Microglia are involved in regulating histamine dependent and non-dependent itch transmissions with distinguished signal pathways

Although itch and pain have many similarities, they are completely different in perceptual experience and behavioral response. In recent years, we have a deep understanding of the neural pathways of itch sensation transmission. However, there are few reports on the role of non-neuronal cells in itch. Microglia are known to play a key role in chronic neuropathic pain and acute inflammatory pain. It is still unknown whether microglia are also involved in regulating the transmission of itch sensation. In the present study, we used several kinds of transgenic mice to specifically deplete CX3CR1+ central microglia and peripheral macrophages together (whole depletion), or selectively deplete central microglia alone (central depletion). We observed that the acute itch responses to histamine, compound 48/80 and chloroquine were all significantly reduced in mice with either whole or central depletion. Spinal c-fos mRNA assay and further studies revealed that histamine and compound 48/80, but not chloroquine elicited primary itch signal transmission from DRG to spinal Npr1- and somatostatin-positive neurons relied on microglial CX3CL1-CX3CR1 pathway. Our results suggested that central microglia were involved in multiple types of acute chemical itch transmission, while the underlying mechanisms for histamine dependent and non-dependent itch transmission were different that the former required the CX3CL1-CX3CR1 signal pathway.

neuroscience↗

bioRxiv2022

Genetic risk for Multiple Sclerosis originated in Pastoralist Steppe populations

Multiple sclerosis (MS) is a modern neuro-inflammatory and -degenerative disease, which is most prevalent in Northern Europe. Whilst it is known that inherited risk to MS is located within or within close proximity to immune genes, it is unknown when, where and how this genetic risk originated 1. By using the largest ancient genome dataset from the Stone Age 2, along with new Medieval and post-Medieval genomes, we show that many of the genetic risk variants for MS rose to higher frequency among pastoralists located on the Pontic Steppe, and were brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the Steppe population, and later in Europe, likely driven by pathogenic challenges coinciding with dietary, lifestyle, and population density changes. This study highlights the critical importance of this period as a determinant of modern immune responses and its subsequent impact on the risk of developing MS in a changing environment.

evolutionary biology↗

bioRxiv2022

OpenPBTA: An Open Pediatric Brain Tumor Atlas

SummaryPediatric brain and spinal cancer are the leading disease-related cause of death in children, thus we urgently need curative therapeutic strategies for these tumors. To accelerate such discoveries, the Childrens Brain Tumor Network and Pacific Pediatric Neuro-Oncology Consortium created a systematic process for tumor biobanking, model generation, and sequencing with immediate access to harmonized data. We leverage these data to create OpenPBTA, an open collaborative project which establishes over 40 scalable analysis modules to genomically characterize 1,074 pediatric brain tumors. Transcriptomic classification reveals that TP53 loss is a significant marker for poor overall survival in ependymomas and H3 K28-altered diffuse midline gliomas and further identifies universal TP53 dysregulation in mismatch repair-deficient hypermutant high-grade gliomas. OpenPBTA is a foundational analysis platform actively being applied to other pediatric cancers and inform molecular tumor board decision-making, making it an invaluable resource to the pediatric oncology community. In BriefThe OpenPBTA is a global, collaborative open-science initiative which brought together researchers and clinicians to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Shapiro, et. al create over 40 open-source, scalable modules to perform cancer genomics analyses and provide a richly-annotated somatic dataset across 58 brain tumor histologies. The OpenPBTA framework can be used as a model for large-scale data integration to inform basic research, therapeutic target identification, and clinical translation. HighlightsOpenPBTA collaborative analyses establish resource for 1,074 pediatric brain tumors NGS-based WHO-aligned integrated diagnoses generated for 641 of 1,074 tumors RNA-Seq analysis infers medulloblastoma subtypes, TP53 status, and telomerase activity OpenPBTA will accelerate therapeutic translation of genomic insights

genomics↗

bioRxiv2022

Co-targeting BCL-XL and MCL-1 with DT2216 and AZD8055 synergistically inhibits small-cell lung cancer growth without causing on-target toxicities in mice

Small-cell lung cancer (SCLC) is an aggressive malignancy with limited therapeutic options. The dismal prognosis in SCLC is in part associated with an upregulation of BCL-2 family anti-apoptotic proteins, including BCL-XL and MCL-1. Unfortunately, the currently available inhibitors of BCL-2 family anti-apoptotic proteins, except BCL-2 inhibitors, are not clinically relevant because of various on-target toxicities. We, therefore, aimed to develop an effective and safe strategy targeting these anti-apoptotic proteins with DT2216 (our platelet-sparing BCL-XL degrader) and AZD8055 (an mTOR inhibitor) to avoid associated on-target toxicities while synergistically optimizing tumor response. Through BH3 mimetic screening, we identified a subset of SCLC cell lines that is co-dependent on BCL-XL and MCL-1. After screening inhibitors of selected tumorigenic pathways, we found that AZD8055 selectively downregulates MCL-1 in SCLC cells and its combination with DT2216 synergistically killed BCL-XL/MCL-1 co-dependent SCLC cells, but not normal cells. Mechanistically, the combination caused BCL-XL degradation and suppression of MCL1 expression, and thus disrupted MCL-1 interaction with BIM leading to an enhanced apoptotic induction. In vivo, DT2216+AZD8055 combination significantly inhibited the growth of cell line-derived and patient-derived xenografts and reduced tumor burden accompanied with extended survival in a genetically-engineered mouse (GEM) model of SCLC without causing significant thrombocytopenia or other normal tissue injury. Thus, these preclinical findings lay a strong foundation for future clinical studies to test DT2216+mTOR inhibitor combination in a subset of SCLC patients whose tumors are co-driven by BCL-XL and MCL-1.

cancer biology↗

bioRxiv2022

A Meta-learning based Graph-Hierarchical Clustering Method for Single Cell RNA-Seq Data

Single cell sequencing techniques enable researchers view complex bio-tissues from a more precise perspective to identify cell types. However, more and more recent works have been done to find more detailed subtypes within already known cell types. Here, we present MeHi-SCC, a method which utilized meta-learning protocol and brought in multi scRNA-seq datasets information in order to assist graph-based hierarchical sub-clustering process. In result, MeHi-SCC outperformed current-prevailing scRNA clustering methods and successfully identified cell subtypes in two large scale cell atlas. Our codes and datasets are available online at https://github.com/biomed-AI/MeHi-SCC

bioinformatics↗

bioRxiv2022

Self-generated brain-wide spiking cascades govern replay dynamics in the hippocampus

During states of behavioral quiescence, neurons in the hippocampus replay sequences of spiking activity experienced in earlier behavioral episodes. While such replay sequences are hypothesized to serve learning and memory by facilitating synaptic consolidation, their generative mechanisms remain poorly understood. Increasing evidence suggests that they might be generated internally, or at least strongly constrained by internal circuit dynamics. Recent work demonstrated that, across the forebrain, approximately 70% of neurons participate in a pattern of sequential spiking cascades during rest. Like hippocampal replay sequences, these brain-wide spiking cascades occur together with high-frequency hippocampal ripples and therefore may share a common generative mechanism. Here we systematically investigated the relationship between replay activity and sequential spiking cascades by analyzing a database of intracortical electrocortical recordings in mice. For neuronal subpopulations in the hippocampus and visual cortex, we assessed spiking sequences elicited during video viewing as well as potential replay events during subsequent periods of rest. We found that replay events were unique to hippocampal time-sensitive neurons and occurred together with spiking cascades throughout the forebrain. Furthermore, forward and time-reversed replay sequences were associated with different types of spiking cascades. Overall, these findings indicate that hippocampal replay events are generated and structured according to resting state circuit dynamics manifest across a large portion of the brain.

neuroscience↗

bioRxiv2022

SE(3) Equivalent Graph Attention Network as an Energy-Based Model for Protein Side Chain Conformation

Protein design energy functions have been developed over decades by leveraging physical forces approximation and knowledge-derived features. However, manual feature engineering and parameter tuning might suffer from knowledge bias. Learning potential energy functions fully from crystal structure data is promising to automatically discover unknown or high-order features that contribute to the proteins energy. Here we proposed a graph attention network as an energy-based model for protein conformation, namely GraphEBM. GraphEBM is equivariant to the SE(3) group transformation, which is the important principle of modern machine learning for molecules-related tasks. GraphEBM was benchmarked on the rotamer recovery task and outperformed both Rosetta and the state-of-the-art deep learning based methods. Furthermore, GraphEBM also yielded promising results on combinatorial side chain optimization, improving 22.2%{chi} 1 rotamer recovery to the PULCHRA method on average.

bioinformatics↗

bioRxiv2022

Reducing the Complexity of Fc Glycan Enables the Construction of Antibody Conjugates with Unexpected High Efficiency and Payload Capacity via Glycoengineering

Glycoengineering has been demonstrated to be a powerful tool to construct site-specific antibody conjugates. However, with most glycoengineering strategies, several hours to days are needed to complete the reaction, and the payloads are limited to small molecules. Herein, we show that reducing the complexity of Fc glycan could dramatically boost the enzymatic glycoengineering of IgG molecules to achieve unexpectedly high efficiency and payload capacity. Notably, antibodies with the modified Fc glycan were successfully conjugated with biomacromolecules, e.g., oligonucleotides and nanobodies, in one step by an engineered fucosyltransferase. Moreover, the conversion of this chemoenzymatic engineering could be finished in minutes, or up to hours, affording homogeneous products. The trisaccharide linker of these antibody conjugates exhibits excellent hydrophilicity and stability and reduced ADCC activity. Using this platform, we successfully synthesized an antibody-conjugate-based HER2/CD3 bispecific antibody and applied it to selectively destroy patient-derived cancer organoids by reactivating endogenous T cells inside the organoid. These results suggest that this bispecific antibody format has a high translational value.

biochemistry↗

bioRxiv2022

Efficient repair of human homozygous genetic mutation by CRISPR/Cas9 mediated interlocus gene conversion

DNA double-strand breaks (DSBs) induced by gene editing tools are primarily resolved either by non-homologous end joining (NHEJ) or homology-directed repair (HDR) using exogenous synthetic DNA templates. Repaired by error-prone NHEJ may lead to unexpected indels at the targeted site. In the case of most genetic disorders, HDR-mediated precise correction using an exogenous homologous sequence is ideal. However, the therapeutic application of HDR might be especially challenging given the requirement for the codelivery of exogenous DNA templates with toxicity into cells, and the low efficiency of HDR could also limit its clinical application. Here, we used hematopoietic stem cells (HSCs) with genetic mutations to cause {beta}-thalassemia in HBB coding regions and discovered that many cells are actually repaired by CRISPR/Cas9-mediated gene conversion (GC) independent of exogenous synthetic DNA templates. We show that pathogenic mutations in the HBB coding regions of HSCs can be repaired efficiently through CRISPR/GC using the paralog gene HBD as the internal template. Electroporations of Cas9 for ribonucleoprotein with sgRNA into haematopoietic stem and progenitor cells (HSPCs) with a variety of pathogenic gene mutations also resulted in effective conversion of mutations to normal wild-type sequences without exogenous DNA template. Moreover, the edited HSCs can repopulate the haematopoietic system and generate erythroid cells with a greatly reduced propensity for thalassemia after transplantations. Thus, CRISPR/GC, independent of exogenous DNA templates, holds great promise for gene therapy of genetic diseases.

genetics↗