Biology subjects

Zhou, J.

Publications and source records attributed to Zhou, J..

At least 379 records · Page 21Linked to original sources

bioRxiv2023

cGAS-activating lupus autoantibody for cancer immunotherapy

Cytoplasmic DNA triggers a cGAS-mediated signaling cascade that promotes an innate immune response and is potentially actionable in cancer immunotherapy. Here we show that a cytoplasmic-localizing lupus anti-DNA autoantibody activates cGAS and facilitates an immune-mediated prolongation of survival in orthotopic models of glioblastoma (GBM). Mechanistically, cellular penetration and blood-brain barrier crossing by the anti-DNA autoantibody is linked to nucleoside transport. Pulldown, knockdown, signaling, and cytotoxicity assays demonstrate autoantibody association with and activation of cGAS. In orthotopic GBM models, the autoantibody localizes to brain tumor, increases tumor CD8+ T cell content, and prolongs survival in immunocompetent but not immunodeficient mice. This work introduces the new concept of a cGAS-activating anti-DNA autoantibody, which impacts theories on mechanisms of autoimmunity and has translational applications in cancer immunotherapy.

immunology↗

bioRxiv2023

In vivo photopharmacology with light-activated opioid drugs

Traditional methods for site-specific drug delivery in the brain are slow, invasive, and difficult to interface with recordings of neural activity. Here, we demonstrate the feasibility and experimental advantages of in vivo photopharmacology using "caged" opioid drugs that are activated in the brain with light after systemic administration in an inactive form. To enable bidirectional manipulations of endogenous opioid receptors in vivo, we developed PhOX and PhNX, photoactivatable variants of the mu opioid receptor agonist oxymorphone and the antagonist naloxone. Photoactivation of PhOX in multiple brain areas produced local changes in receptor occupancy, brain metabolic activity, neuronal calcium activity, neurochemical signaling, and multiple pain- and reward-related behaviors. Combining PhOX photoactivation with optical recording of extracellular dopamine revealed adaptations in the opioid sensitivity of mesolimbic dopamine circuitry during chronic morphine administration. This work establishes a general experimental framework for using in vivo photopharmacology to study the neural basis of drug action. HighlightsA photoactivatable opioid agonist (PhOX) and antagonist (PhNX) for in vivo photopharmacology. Systemic pro-drug delivery followed by local photoactivation in the brain. In vivo photopharmacology produces behavioral changes within seconds of photostimulation. In vivo photopharmacology enables all-optical pharmacology and physiology.

neuroscience↗

bioRxiv2023

Delayed normalization model captures disparate nonlinear neural dynamics measured with different techniques in macaque and human V1

Neuronal representations throughout the primate visual system display a wide range of nonlinear dynamics in response to static visual stimuli. To understand the neural basis of visual perception, it is important to quantify these nonlinearities and to develop general models that allow one to predict response dynamics to visual stimuli with arbitrary temporal waveform. Voltage-sensitive dye imaging (VSDI) is a powerful method for measuring neural population responses from the cortex of awake, behaving, subjects. Here we used VSDI to measure the dynamics of neural population responses in macaque V1 to visual stimuli with a wide range of time courses. We found that beyond clear nonlinearities for briefly presented visual stimuli, stimulus-evoked VSDI responses are surprisingly near additive in time. These results are qualitatively different from neural dynamics to similar stimuli previously measured in human visual cortex using fMRI and electrocorticography (ECoG), which show strong sub-additivity in time. To test whether this discrepancy is specific to VSDI, a signal dominated by subthreshold neural activity, we repeated our measurements using a genetically encoded calcium indicator (GCaMP), a signal dominated by spiking activity. We found that GCaMP signals in macaque V1 are also near-additive. Therefore, the discrepancies in the degree of additivity between these different measurements are not attributed to the difference between sub- and supra-threshold neural response. Finally, we show that a simple yet flexible delayed normalization model can capture the dynamics of all of these measurements, suggesting that dynamic gain-control is an important mechanism contributing to neural processing in the brain.

neuroscience↗

bioRxiv2023

Genome expansion by a CRISPR trimmer-integrase

CRISPR-Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity. CRISPR systems maintain genome integrity and avoid autoimmunity by distinguishing between self and non-self, a process for which the CRISPR-Cas1:Cas2 integrase is necessary but not sufficient. In some microbes, the Cas4 endonuclease assists CRISPR adaptation, but many CRISPR-Cas systems lack Cas4. We show here that an elegant alternative pathway employs an internal exonuclease to select and process DNA for integration using the protospacer adjacent motif (PAM). A natural Cas1:Cas2-exonuclease fusion (trimmer-integrase) catalyzes coordinated DNA capture, trimming and integration. Five cryo-EM structures of the CRISPR trimmer-integrase, visualized both before and during DNA integration, show how asymmetric processing generates size-defined, PAM-containing substrates. Before genome integration, the PAM sequence is released by Cas1 and cleaved by the exonuclease, marking inserted DNA as self and preventing aberrant CRISPR targeting of the host. Together, these data support a model in which CRISPR systems lacking Cas4 use fused or recruited exonucleases for faithful acquisition of new CRISPR immune sequences.

biochemistry↗

bioRxiv2023

Bromodomain-containing Protein 4 Regulates Innate Inflammation in Airway Epithelial Cells via Modulation of Alternative Splicing

Bromodomain-containing Protein 4 (BRD4) is a transcriptional regulator which coordinates gene expression programs controlling cancer biology, inflammation, and fibrosis. In airway viral infection, non-toxic BRD4-specific inhibitors (BRD4i) block the release of pro-inflammatory cytokines and prevent downstream remodeling. Although the chromatin modifying functions of BRD4 in inducible gene expression have been extensively investigated, its roles in post-transcriptional regulation are not as well understood. Based on its interaction with the transcriptional elongation complex and spliceosome, we hypothesize that BRD4 is a functional regulator of mRNA processing. To address this question, we combine data-independent analysis - parallel accumulation-serial fragmentation (diaPASEF) with RNA-sequencing to achieve deep and integrated coverage of the proteomic and transcriptomic landscapes of human small airway epithelial cells exposed to viral challenge and treated with BRD4i. The transcript-level data was further interrogated for alternative splicing analysis, and the resulting data sets were correlated to identify pathways subject to post-transcriptional regulation. We discover that BRD4 regulates alternative splicing of key genes, including Interferon-related Developmental Regulator 1 (IFRD1) and X-Box Binding Protein 1 (XBP1), related to the innate immune response and the unfolded protein response, respectively. These findings extend the transcriptional elongation-facilitating actions of BRD4 in control of post-transcriptional RNA processing in innate signaling.

systems biology↗

bioRxiv2023

The emergence of goblet inflammatory or ITGB6hi nasal progenitor cells determines age-associated SARS-CoV-2 pathogenesis

Children infected with SARS-CoV-2 rarely progress to respiratory failure, but the risk of mortality in infected people over 85 years of age remains high, despite vaccination and improving treatment options. Here, we take a comprehensive, multidisciplinary approach to investigate differences in the cellular landscape and function of paediatric (<11y), adult (30- 50y) and elderly (>70y) nasal epithelial cells experimentally infected with SARS-CoV-2. Our data reveal that nasal epithelial cell subtypes show different tropism to SARS-CoV-2, correlating with age, ACE2 and TMPRSS2 expression. Ciliated cells are a viral replication centre across all age groups, but a distinct goblet inflammatory subtype emerges in infected paediatric cultures, identifiable by high expression of interferon stimulated genes and truncated viral genomes. In contrast, infected elderly cultures show a proportional increase in ITGB6hi progenitors, which facilitate viral spread and are associated with dysfunctional epithelial repair pathways. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/524211v2_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@dab12aorg.highwire.dtl.DTLVardef@1a57334org.highwire.dtl.DTLVardef@12e7983org.highwire.dtl.DTLVardef@2bbe6e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

Defective transfer of parental histone decreases frequency of homologous recombination in budding yeast

Recycling of parental histones is an important step in epigenetic inheritance. During DNA replication, DNA polymerase epsilon subunit DPB3/DPB4 and DNA replication helicase subunit MCM2 are involved in the transfer of parental histones to the leading and lagging DNA strands, respectively. Single Dpb3 deletion (dpb3{Delta}) or Mcm2 mutation (mcm2-3A), which each disrupt one parental histone transfer pathway, leads to the others predominance. However, the impact of the two histone transfer pathways on chromatin structure and DNA repair remains elusive. In this study, we used budding yeast Saccharomyces cerevisiae to determine the genetic and epigenetic outcomes from disruption of parental histone H3-H4 tetramer transfer. We found that a dpb3{Delta}/mcm2-3A double mutant did not exhibit the single dpb3{Delta} and mcm2-3A mutants asymmetric parental histone patterns, suggesting that the processes by which parental histones are transferred to the leading and lagging strands are independent. Surprisingly, the frequency of homologous recombination was significantly lower in dpb3{Delta}, mcm2-3A, and dpb3{Delta}/mcm2-3A mutants relative to the wild-type strain, likely due to the elevated levels of free histones detected in the mutant cells. Together, these findings indicate that proper transfer of parental histones to the leading and lagging strands during DNA replication is essential for maintaining chromatin structure and that high levels of free histones due to parental histone transfer defects are detrimental to cells.

molecular biology↗

bioRxiv2023

Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14

Arabidopsis telomeric repeat binding factors (TRBs) can bind telomeric DNA sequences to protect telomeres from degradation. TRBs can also recruit Polycomb Repressive Complex 2 (PRC2) to deposit tri-methylation of H3 lysine 27 (H3K27me3) over certain target loci. Here, we demonstrate that TRBs also associate and colocalize with JUMONJI14 (JMJ14) and trigger H3K4me3 demethylation at some loci. The trb1/2/3 triple mutant and the jmj14-1 mutant show an increased level of H3K4me3 over TRB and JMJ14 binding sites, resulting in up-regulation of their target genes. Furthermore, tethering TRBs to the promoter region of genes with an artificial zinc finger (TRB-ZF) successfully triggers target gene silencing, as well as H3K27me3 deposition, and H3K4me3 removal. Interestingly, JMJ14 is predominantly recruited to ZF off-target sites with low levels of H3K4me3, which is accompanied with TRB-ZFs triggered H3K4me3 removal at these loci. These results suggest that TRB proteins coordinate PRC2 and JMJ14 activities to repress target genes via H3K27me3 deposition and H3K4me3 removal.

plant biology↗

bioRxiv2023

Decoding CRISPR-Cas9 PAM recognition with UniDesign

The critical first step in CRISPR-Cas mediated gene editing is recognizing a preferred protospacer adjacent motif (PAM) on target DNAs by the proteins PAM-interacting amino acids (PIAAs). Thus, accurate computational modeling of PAM recognition is useful in assisting CRISPR-Cas engineering to relax or tighten PAM requirement for subsequence applications. Here we describe a universal computational protein design framework (UniDesign) for designing protein-nucleic acid interactions. As a proof of concept, we applied UniDesign to decode the PAM-PIAA interactions for eight Cas9 proteins. We show that, given native PIAAs, the UniDesign-predicted PAMs are largely identical to the natural PAMs of all Cas9s. In turn, given natural PAMs, the computationally redesigned PIAA residues largely recapitulated the native PIAAs (>70% and >80% in terms of identity and similarity, respectively). These results demonstrate that UniDesign faithfully captures the mutual preference between natural PAMs and native PIAAs, suggesting it as a useful tool for engineering CRISPR-Cas and other nucleic acid-interacting proteins. UniDesign is open-sourced at https://github.com/tommyhuangthu/UniDesign.

bioinformatics↗

bioRxiv2022

Drivers of plant intraspecific variation are trait-specific

O_LIThe importance of intraspecific trait variation (ITV) in community dynamics is increasingly being recognised, but the drivers of ITV have not yet been well-studied. Here, we analysed whether environmental conditions, biotic interactions and species features are related to ITV on a global scale. C_LIO_LIWe compiled a global species ITV database including 2064 species which occurred in 1068 communities (plots) across 19 countries with 11 functional traits. The magnitudes of species ITV in this database were calculated according to the trait-gradient analysis which is independent of the length of the environmental gradient. C_LIO_LIWe found that different traits had different main drivers, so we consider the drivers of ITV to be trait-specific. However, our findings still brought some order among these idiosyncratic patterns: leaf economics spectrum traits were more related to environmental conditions and leaf morphology traits were more related to biotic interactions. Size-related traits were related to both abiotic and biotic conditions. C_LIO_LIOur research suggests that the drivers of ITV deviated from the drivers of the mean trait values and that some trait coordination may fall apart upon climate change. Thus, our analysis enhances our understanding of trait variation and has important implications for models predicting vegetation responses to environmental change. C_LI

ecology↗

bioRxiv2022

Genetic adaptation rates differ by trait and plant type-a comprehensive meta-analysis

O_LIPlants can respond to changing climatic conditions through genetic adaptation of their functional traits. Despite the relevance of adaptation to climate change, much remains unknown about plant genetic adaptation rates, including whether these rates differ among plant characteristics and trait types. C_LIO_LIWe performed a meta-analysis to investigate patterns of genetic adaptation rates and assess how these rates differ among plant species groups, growth forms and trait types, using a newly compiled database from 74 studies, comprising 35 functional traits across 72 angiosperm species. This database specifically focuses on genetic adaptation of plant functional traits, as separating from phenotypic plasticity. C_LIO_LIBoth annual and generational adaptation rates of plant traits decrease non-linearly with increasing elapsed time since divergence. Plants adapt fastest when first introduced to a changing environment, but these rates go slow subsequently. Overall, shrubs have higher adaptation rates than trees, which confers shrubs an adaptive advantage over trees. Different adaptation rates among growth forms, life histories and trait types suggest an important additional mechanism through which climate change may affect community composition. C_LIO_LIOur study has important implications regarding plant adaptation to new environments and will improve the prediction of vegetation responses and ecosystem functioning upon climate change. C_LI

ecology↗

bioRxiv2022

How does perceptual discriminability relate to neuronal receptive fields?

AO_SCPLOWBSTRACTC_SCPLOWPerception is an outcome of neuronal computations. Our perception changes only when the underlying neuronal responses change. Because visual neurons preferentially respond to adjustments in some pixel values of an image more than others, our perception has greater sensitivity in detecting change to some pixel combinations more than others. Here, we examined how perceptual discriminability varies to arbitrary image perturbations assuming different models of neuronal responses. In particular, we investigated that under the assumption of different neuronal computations, how perceptual discriminability relates to neuronal receptive fields - the change in pixel combinations that invokes the largest increase in neuronal responses. We assumed that perceptual discriminability reflects the magnitude of change (the L2 norm) in neuronal responses, and the L2 norm assumption gained empirical support. We examined how perceptual discriminability relates to deterministic and stochastic neuronal computations. In the case of deterministic neuronal computations, perceptual discriminability is completely determined by neuronal receptive fields. For multiple layers of canonical linear-nonlinear (LN) computations in particular (which is a feed-forward neural network), neuronal receptive fields are linear transforms of the first-layer neurons image filters. When one image is presented to the neural network, the first-layer neurons filters and the linear transform completely determine neuronal receptive fields across all layers, and perceptual discriminability to arbitrary distortions to the image. We expanded our analysis to examine stochastic neuronal computations, in which case perceptual discriminability can be summarized as the magnitude of change in stochastic neuronal responses, with the L2 norm being replaced by a Fisher-information computation. Using a practical lower bound on Fisher information, we showed that for stochastic neuronal computations, perceptual discriminability is completely determined by neuronal receptive fields, together with how responses co-variate across neurons.

neuroscience↗

bioRxiv2022

Deep learning-based predictive identification of functional subpopulations of hematopoietic stem cells and multipotent progenitors

Hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) are crucial for maintaining lifelong hematopoiesis. Developing methods to distinguish stem cells from other progenitors and evaluate stem cell functions has been a central task in stem cell research. Deep learning has been demonstrated as a powerful tool in cell image analysis and classification. In this study, we explored the possibility of using deep learning to differentiate HSCs and MPPs based on their light microscopy (DIC) images. After extensive training and validation with large image data sets, we successfully develop a three-class classifier (we named it the LSM model) that reliably differentiate long-term HSCs (LT-HSCs), short-term HSCs (ST-HSCs), and MPPs. Importantly, we demonstrated that our LSM model achieved its differentiating capability by learning the intrinsic morphological features from cell images. Furthermore, we showed that the performance of our LSM model was not affected by how these cells were identified and isolated, i.e., sorted by surface markers or intracellular GFP markers. Prospective identification of HSCs and MPPs in Evi1GFP transgenic mice by LSM model suggested that the cells with the highest GFP expression were LT-HSCs, and this prediction was substantiated later by a long-term competitive reconstitution assay. Moreover, based on DIC image data sets, we also successfully built another two-class classifier that can effectively distinguish aged HSCs from young HSCs, which both express the same surface markers but are functionally different. This finding is of particular interest since it may provide a novel quick and efficient approach, obviating the need for a time-consuming transplantation experiment, to evaluate the functional states of HSCs. Together, our study provides evidence for the first time that HSCs and MPPs can be differentiated by deep learning based on cell morphology. This novel and robust deep learning-based platform will provide a basis for the future development of a new generation stem cell identification and separation system. It may also provide new insight into molecular mechanisms underlying the self-renewal feature of stem cells.

bioengineering↗

bioRxiv2022

New insight into the Germline Genes and CDR3 Repertoire of the TCRβ chain in Chiroptera

Bats are known to be natural reservoirs of many viruses, yet their unique immune system enables them to coexist with viruses without frequently exhibiting disease symptoms. The current understanding of the bat adaptive immune system is limited, as there is no database or tool capable of processing T-cell receptor (TCR) sequences for bats, and the diverse nature of the Chiroptera. We established a reference library of TCR-{beta} germline genes by annotating three Chiroptera: The Greater Horseshoe Bat (Rhinolophus ferrumequinum, R. ferrumequinum), The Pale spear-nosed Bat (Phyllostomus discolor, P. discolor), and the Common Pipistrelle (Pipistrellus pipistrellus, P. pipistrellus). The distinct variations in the distribution of TRBV genes among the three types of bats could have a direct impact on the diversity of the TCR repertoire, as evidenced by the presence of conserved amino acids that indicate the T-cell recognition of antigens in bats is MHC-restricted. Furthermore, we conducted an analysis of the TCR-{beta} repertoire in the Intermediate Horseshoe Bat (Rhinolophus affinis, R. affinis) using high-throughput sequencing (HTS). The bats TCR-{beta} repertoire is formed through rearrangement of the V-D-J-C genes, with D-J/V-D deletions and insertion resulting a high diversity.

immunology↗

bioRxiv2022

Epigenomic complexity of the human brain revealed by single-cell DNA methylomes and 3D genome structures

Delineating the gene regulatory programs underlying complex cell types is fundamental for understanding brain functions in health and disease. Here, we comprehensively examine human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in over 500,000 cells from 46 brain regions. We identified 188 cell types and characterized their molecular signatures. Integrative analyses revealed concordant changes in DNA methylation, chromatin accessibility, chromatin organization, and gene expression across cell types, cortical areas, and basal ganglia structures. With these resources, we developed scMCodes that reliably predict brain cell types using their methylation status at select genomic sites. This multimodal epigenomic brain cell atlas provides new insights into the complexity of cell type-specific gene regulation in the adult human brain.

neuroscience↗

bioRxiv2022

The endogenous modulation of visual plasticity in human adults

The adult human visual system can exhibit a degree of neuroplastic change under the right conditions which has implications for future treatments to recover vision loss that have occurred in infancy. The exogenous factors that promote neuroplastic change have been the focus of human psychophysical, electrophysiological and neuroimaging research over the last decade. What has not been considered is the importance of endogenous factors. In this study we modulate the neural oscillations that determines the internal neural state to demonstrate that endogenous factors play a critical role in not only baseline contrast sensitivity but also the extent to which the adult visual system can undergo neuroplastic change in binocular balance.

neuroscience↗

bioRxiv2022

A general approach to discover conformational epitope-directed binders for selective inhibition of protein proteolytic activation

Directing antibodies to a particular epitope among many possible on a target protein is a significant challenge. Here we present a simple and general method for epitope-directed selection (EDS) using a differential phage selection strategy. This involves engineering the protein of interest (POI) with the epitope of interest (EOI) mutated using a systematic bioinformatics algorithm to guide the local design of an EOI decoy variant. Using several alternating rounds of negative selection with the EOI decoy variant followed by positive selection on the wild-type (WT) POI, we were able to identify highly specific and potent antibodies to five different EOI antigens that bind and functionally block known sites of proteolysis. Among these we developed highly specific antibodies that target the proteolytic site on the CUB domain containing protein 1 (CDCP1) to prevent its proteolysis allowing us to study the cellular maturation of this event that triggers malignancy. We generated antibodies that recognize the junction between the pro and catalytic domains for four different matrix metalloproteases (MMPs), such as MMP1, MMP3, and MMP9, that selectively block activation of each of these enzymes and impairs cell migration. We targeted a proteolytic epitope on the cell surface receptor, EPH Receptor A2, that is known to transform it from a tumor suppressor to an oncoprotein. We believe the EDS method greatly facilitates the generation antibodies to specific EOIs on a wide range of proteins and enzymes for broad therapeutic and diagnostic applications. SignificanceWe have developed a highly efficient platform to facilitate the directed selection in vitro of antibodies to a wide range of functional epitopes on proteins. This method uses a bioinformatic program to guide mutations in the local site of interest to create a decoy antigen that can effectively remove antibodies not binding the site of interest by negative selection, followed by positive selection with the WT antigen to identify antibodies to the epitope of interest. We demonstrate the generality and versatility of this method by successfully producing functional antibodies to block specific proteolytically sensitive epitopes on five different proteins including enzymes important in cancer. The epitope-directed selection (EDS) approach greatly facilitates the identification of binders to specific sites of interest on proteins to probe function and as potential immunotherapeutics.

animal behavior and cognition↗

bioRxiv2022

Manipulating Oxalate Decarboxylase Provides the Basis of Antilithic Therapy by Acting on the Gut Microbiota

A high concentration of oxalate is associated with an increased risk of kidney calcium oxalate (CaOx) stones, and the degradation of exogenous oxalate mainly depends on oxalate-degrading enzymes from the intestinal microbiome. We found that Zinc Gluconate supplement to patients with CaOx kidney stones could significantly improve the abundance of oxalate metabolizing bacteria in human body through clinical experiments on the premise of simultaneous antibiotic treatment and the imbalance of Lactobacillus and OxDC was involved in CaOx kidney stones through clinical sample analysis. Then, we identified that Zn2+ could be used as an external factor to improve the activity of OxDC and protect Lactobacillus, achieved the preventive effect on rats with stones aggravated by antibiotics. Finally, by analyzing the three-dimensional structure of OxDC and some in vitro experiments, we propose a hypothesis Zn2+ increases the metabolism of oxalate in humans through its positive effects on Lactobacillus and OxDC to reduce CaOx kidney stone symptoms in rats. IMPORTANCEUrinary stone disease is one of the most common urological disorders, and 70%-80% of urinary stones are calcium oxalate (CaOx) stones. We found the structural basis and metabolic mechanism by which oxalate decarboxylase metabolizes oxalate were elucidated, and Zn2+ was illustrated to have therapeutic effects on CaOx stones by improving the tolerance of Lactobacillus to antibiotics. According to that, proper Zn2+ levels in the diet, the consumption of more probiotic food and avoidance of the antibiotic overuse might be desirable measures for the prevention and treatment of kidney stones. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/512337v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@d3df85org.highwire.dtl.DTLVardef@1f7b3f5org.highwire.dtl.DTLVardef@147d861org.highwire.dtl.DTLVardef@1cf046e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗