Biology subjects

Chen, X.

Publications and source records attributed to Chen, X..

At least 721 records · Page 40Linked to original sources

bioRxiv2023

Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes

Long-read sequencing holds great potential for characterizing complex microbial communities, yet taxonomic profiling tools designed specifically for long reads remain lacking. Here we introduce Melon, a novel marker-based taxonomic profiler that capitalizes on the unique attributes of long reads. Melon employs a two-stage classification scheme to reduce computational time and is equipped with an expectation-maximization-based post-correction module to handle ambiguous reads. Melon achieves superior performance compared to other existing tools in both mock and simulated samples. Using wastewater metagenomic samples, we demonstrate the applicability of Melon by showing it is capable in providing reliable estimates of overall genome copies, and species-level taxonomic profiles.

bioinformatics↗

bioRxiv2023

Function-associated scRNA-seq on single lung cancer organoids unravels the immune landscape of tumor parenchyma

In vitro models coupled with multimodal approaches are urgently needed to decipher the local tumor immune microenvironment (TIME) owing to the heterogeneous nature of immune cells and their diverse spatial distributions. Here we generate primary lung cancer organoids (pLCOs) by isolating the tumor cell clusters, including the infiltrated immune cells, from dissected lung cancer samples. A FascRNA-seq platform allowing both phenotypic evaluation and the scRNA-seq of all the single cells in an organoid was developed to dissect the TIME in individual pLCOs. Our analysis on 171 individual pLCOs derived from 7 patients revealed that pLCOs retained the fundamental features as well as intra-tumor heterogeneity of local TIME in the parenchyma of parental tumor tissues, providing a series of models with consistent genetic background but various TIME. Linking the single cell transcriptome data of individual pLCOs with their responses to ICB allowed us to confirm the pivotal role of CD8+ Ts in ICB induced anti-tumor immunity, to identify the potential tumor-reactive T cells with a set of 10 genes, and to unravel the factors regulating T cell activity.

cancer biology↗

bioRxiv2023

DSMBind: SE(3) denoising score matching for unsupervised binding energy prediction and nanobody design

Modeling the binding between proteins and other molecules is pivotal to drug discovery. Geometric deep learning is a promising paradigm for protein-ligand/protein-protein binding energy prediction, but its accuracy is limited by the size of training data as high-throughput binding assays are expensive. Herein, we propose an unsupervised binding energy prediction framework, named DSMBind, which does not need experimental binding data for training. DSMBind is an energy-based model that estimates the likelihood of a protein complex via SE(3) denoising score matching (DSM). This objective, applied at both backbone and side-chain levels, builds on a novel equivariant rotation prediction network derived from Eulers Rotation Equations. We find that the learned log-likelihood of protein complexes is highly correlated with experimental binding energy across multiple benchmarks, even matching the performance of supervised models trained on experimental data. We further demonstrate DSMBinds zero-shot binder design capability through a PD-L1 nanobody design task, where we randomize all three complementarity-determining regions (CDRs) and select the best CDR sequences based on DSMBind score. We experimentally tested the designed nanobodies with ELISA binding assay and successfully discovered a novel PD-L1 binder. In summary, DSMBind offers a versatile framework for binding energy prediction and binder design. Our code is publicly available at github.com/wengong-jin/DSMBind.

bioinformatics↗

bioRxiv2023

Cryptic endogenous retrovirus subfamilies in the primate lineage

Many endogenous retroviruses (ERVs) in the human genome are primate-specific and have contributed novel cis-regulatory elements and transcripts. However, current approaches for classifying and annotating ERVs and their long terminal repeats (LTRs) have limited resolution and are inaccurate. Here, we developed a new annotation based on phylogenetic analysis and cross-species conservation. Focusing on the evolutionary young MER11A/B/C subfamilies, we revealed the presence of 4 new subfamilies, that better explained the epigenetic heterogeneity observed within the MER11 instances, suggesting a new annotation for 412 (19.8%) of these repeat elements. Furthermore, we functionally validated the regulatory potential of these four new subfamilies using a massively parallel reporter assay (MPRA), which also identified motifs associated with their differential activities. Combining MPRA with new annotations across primates revealed an apes-specific gain of SOX related motifs through a single-nucleotide deletion. Lastly, by applying our approach across 53 simian-enriched LTR subfamilies, we defined a total of 75 new subfamilies and found that 3,807 (30.0%) instances from 26 LTR subfamilies could be categorized into a novel annotation, many of which with a distinct epigenetic profile. Thus, with our refined annotation of simian-enriched LTRs, it will be possible to better understand the evolution in primate genomes and potentially identify new roles for ERVs and their LTRs in the hosts.

genomics↗

bioRxiv2023

Golgi-associated retrograde protein (GARP) complex recruits retromer to trans-Golgi network for FgKex2 and FgSnc1 recycling, necessary for development and pathogenicity of Fusarium graminearum

In eukaryotic cells, the retromer complex plays a crucial role in orchestrating the sorting and retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN). Despite its significance, the molecular details of this intracellular trafficking process remain unclear. Here, we identified a Golgi-associated retrograde protein (GARP) complex as a mediator of vesicular transport, facilitating the recruitment of the retromer complex to TGN to exert its functions. The GARP complex is mainly localized to the TGN, where it interacts with the retromer complex. This interaction is evolutionarily conserved across different species. Furthermore, we identified FgKex2 and Fgsnc1 as cargo proteins in the GARP/retromer-mediated recycling pathway. Loss of GARP or retromer results in a complete mis-sorting of FgKex2 and FgSnc1 to the vacuolar degradation pathway, which affects the growth, development, toxisome biogenesis, and pathogenicity of F. graminearum. In summary, we assert that GARP facilitates the recruitment of retromer from endosomes to the TGN, orchestrating the recycling of FgKex2 and FgSnc1. This is integral to sustaining continuous growth, development and contributes significantly to the pathogenicity of F. graminearum.

microbiology↗

bioRxiv2023

Effects of greening-induced warming and cooling on tree phenology in temperate and boreal forests

Tree phenology, periodic biological events in trees, is highly sensitive to climate change. It has been reported that forest greening can influence the local climate by altering the seasonal surface energy budget. However, tree phenological responses to forest greening remains poorly understood at large spatial scales. Combining remote-sensing derived phenological and leaf area indices since 2001, herein we show that forest greening led to earlier spring (-1.05 {+/-} 0.17 d) and autumn phenology (-1.95 {+/-} 0.14 d) in temperate and boreal forests. Our results show that forest greening in winter and spring decreased surface albedo and thus resulted in biophysical warming that caused earlier spring leaf phenology. In contrast, forest greening in summer and autumn triggered biophysical cooling by enhancing evapotranspiration, which led to earlier autumn leaf phenology. These findings suggest that forest greening could significantly alter tree phenology through seasonal biophysical impacts. Therefore, it is essential to incorporate these complicated biophysical impacts of greening into tree phenology models to accurately predict future shifts in tree phenology under future climate change.

ecology↗

bioRxiv2023

Germ granule compartments coordinate specialized small RNA production

Germ granules are biomolecular condensates present in most animal germ cells. One function of germ granules is to help maintain germ cell totipotency by organizing mRNA regulatory machinery, including small RNA-based gene regulatory pathways. The C. elegans germ granule is compartmentalized into multiple subcompartments whose biological functions are largely unknown. Here, we identify a new subcompartment of the C. elegans germ granule, which we term the E compartment. The E compartment is nonrandomly positioned within the germ granule. We identified five proteins that localize to the E compartment, including the RNA-dependent RNA polymerase (RdRP) EGO-1, the Dicer-related helicase DRH-3, the Tudor domain-containing protein EKL-1, and two intrinsically disordered proteins, EGC-1 and ELLI-1. Localization of EGO-1 to the E granule enables synthesis of a specialized class of 22G RNAs, which derive exclusively from 5 regions of a subset of germline-expressed mRNAs. Defects in E compartment assembly elicit disordered production of endogenous siRNAs, which disturbs fertility and the RNAi response. Our results define a new subcompartment of the C. elegans germ granule and suggest that one function of germ granule compartmentalization is to facilitate the localized production of specialized classes of small regulatory RNAs.

cell biology↗

bioRxiv2023

Artificial intelligence-assisted stimulated Raman molecular cytology enables accurate and rapid intraoperative assessment of the surgical margin in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is a highly mortal cancer whose only potentially curative treatment is surgical resection. Intraoperative assessment of its surgical margins is vital for patient survival. Frozen-section biopsy is routinely performed for this purpose. However, its high dependence on pathologists experience frequently poses diagnostic discrepancies. The essential invasiveness of PDAC also causes sampling errors. This study developed an intelligent molecular cytology approach with improved diagnostic objectivity and broader sampling coverage. Our method, Multi-Instance Cytology with Learned Raman Embedding (MICLEAR), is characterized by compositional information provided by label-free Raman imaging. First, 4085 cells were brushed off from the pancreases of 41 patients and imaged using stimulated Raman scattering microscopy. Then, a contrastive learning-based cell embedding model was developed to compress each cells morphological and compositional information into a compact cell vector. Finally, a multi-instance learning-based diagnosis model using cell vectors was employed to predict the likelihood of a patients margin being positive. MICLEAR achieved 80% sensitivity, 94.1% specificity, and an AUC of 0.86 on 27 patients for validation, comprising 10 with positive margins and 17 with negative ones, within approximately 8 minutes per patient. It may hold promises for more efficient and accurate intraoperative assessment of PDAC surgical margins.

biophysics↗

bioRxiv2023

Shared architectural patterns across the human cortical mantle predict visual representations and capture behavior across the lifespan

The microstructure of cells within human cerebral cortex varies across the cortical ribbon, where changes in cytoarchitecture and myeloarchitecture are thought to endow each region of cortex with its unique function. While fine-scale relative to a cell, these changes at population level impact architectural properties of cortex measurable in vivo by noninvasive MRI, such as the thickness and myelin content of cortex. This raises the question of whether or not we can use these in vivo architectural measures to understand cortical organization, function, and development more broadly. Using human visual cortex as a test bed, we demonstrated two architectural gradients, one in which cytoarchitecture and myeloarchitecture converge and another in which they diverge. These two gradients underlie the structural and functional topography of visual cortex, even predicting the presence of new visual representations. Moreover, the two gradients show distinct visual behavior relevance and lifespan trajectory. These findings provide a more general framework for understanding human cortex, showing that architectural gradients are a measurable fingerprint of functional organization and ontogenetic routines in the human brain.

neuroscience↗

bioRxiv2023

Upper bound on the mutational burden imposed by a CRISPR-Cas9 gene-drive element

CRISPR-Cas9 gene drives (CCGDs) are powerful tools for genetic control of wild populations, with applications from disease eradication to species conservation. However, Cas9 alone and in a complex with gRNA can cause double-stranded DNA breaks at off-target sites, which could increase the mutational load and lead to unintended loss-of-heterozygosity (LOH) events. These undesired effects raise potential concerns about the long-term evolutionary safety of CCGDs, but the magnitude of these effects is unknown. To measure how the presence of a CCGD or a Cas9 alone in the genome affects the rates of LOH events and de novo mutations, we carried out a mutation accumulation experiment in yeast Saccharomyces cerevisiae. We found no detectable effects on the genome-wide rates of mutations or LOH events. Our power calculations suggest that CCGD or Cas9 affect these rates by less than 30%, which is much less than natural variation for these traits in yeast. A more detailed examination shows that CCGD or Cas9 may alter the lengths and genomic distributions of LOH events, but the statistical support for these effects is weak. Thus, our results demonstrate that CCGDs impose at most a weak additional mutational burden in the yeast model. Although mutagenic effects of gene drives need to be further evaluated in other systems, our results add credence to the proposition that the evolutionary risks posed by well designed gene drives are likely acceptable.

evolutionary biology↗

bioRxiv2023

A multistage, dual voxel study of glutamate in the anterior cingulate cortex in schizophrenia supports a primary pyramidal dysfunction model of disorganization

BackgroundSchizophrenia is an illness where glutamatergic dysfunction in the anterior cingulate cortex (ACC) has been long suspected; Recent in vivo evidence (Adams et al. 2022) has implicated pyramidal dysfunction (reduced glutamate tone) as the primary pathophysiology contributing to subtle features, with a secondary disinhibition effect (higher glutamate tone) resulting in the later emergence of prominent clinical symptoms. We investigate if genetic high risk (GHR) for schizophrenia reduces glutamatergic tone in ACC when compared to the states of clinical high risk (CHR) and first episode schizophrenia (FES) where symptoms are already prominent. MethodsWe recruited 302 individuals across multiple stages of psychosis (CHR, n=63; GHR, n=76; FES, n=96) and healthy controls (n=67) and obtained proton magnetic resonance spectroscopy of glutamate from perigenual ACC (pACC) and dorsal ACC (dACC) using 3-Tesla scanner. ResultsGHR had lower Glu compared to CHR while CHR had higher Glu compared to FES and HC. Higher disorganization burden, but not any other symptom domain, was predicted by lower levels of Glu in the GHR group (dACC and pACC) and in the CHR group (pACC only). ConclusionsThe reduction in glutamatergic tone in GHR supports the case for a pyramidal dysfunction contributing to higher disorganization, indicating disorganization to be the core domain in the pathophysiology of schizophrenia. Higher glutamate (likely due to disinhibition) is apparent when psychotic symptoms are raising to be prominent (CHR), though at the full-blown stage of psychosis, the relationship between glutamate and symptoms ceases to be a simple linear one.

neuroscience↗

bioRxiv2023

H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs

Polycomb Repressive Complex 2 (PRC2)-mediated histone H3K27 tri-methylation (H3K27me3) recruits canonical PRC1 (cPRC1) to maintain heterochromatin. In early development, polycomb-regulated genes are connected through long-range 3D interactions which resolve upon differentiation. Here, we report that polycomb looping is controlled by H3K27me3 spreading and regulates target gene silencing and cell fate specification. Using glioma-derived H3 Lys-27-Met (H3K27M) mutations as tools to restrict H3K27me3 deposition, we show that H3K27me3 confinement concentrates the chromatin pool of cPRC1, resulting in heightened 3D interactions mirroring chromatin architecture of pluripotency, and stringent gene repression that maintains cells in progenitor states to facilitate tumor development. Conversely, H3K27me3 spread in pluripotent stem cells, following neural differentiation or loss of the H3K36 methyltransferase NSD1, dilutes cPRC1 concentration and dissolves polycomb loops. These results identify the regulatory principles and disease implications of polycomb looping and nominate histone modification-guided distribution of reader complexes as an important mechanism for nuclear compartment organization. Highlights{square} The confinement of H3K27me3 at PRC2 nucleation sites without its spreading correlates with increased 3D chromatin interactions. {square}The H3K27M oncohistone concentrates canonical PRC1 that anchors chromatin loop interactions in gliomas, silencing developmental programs. {square}Stem and progenitor cells require factors promoting H3K27me3 confinement, including H3K36me2, to maintain cPRC1 loop architecture. {square}The cPRC1-H3K27me3 interaction is a targetable driver of aberrant self-renewal in tumor cells.

molecular biology↗

bioRxiv2023

Tropism of AAV.CPP.16 in the respiratory tract and its application for a CRISPR-based gene therapy against SARS-CoV-2

Efficient gene delivery vectors are essential for developing gene therapies for respiratory diseases. Here, we report that AAV.CPP.16, a novel AAV9-derived adeno-associated virus vector, can efficiently transduce airway epithelium systems and lung parenchyma cells in both mice and non-human primates after intranasal administration. AAV.CPP.16 outperforms AAV6 and AAV9, two wild-type AAVs with demonstrated tropism to respiratory tract tissues, and can target major cell types in the respiratory tract and the lung. We also report an "all-in-one", CRISPR-Cas13d-based AAV gene therapy vector that targets the highly conserved RNA-dependent RNA polymerase (Rdrp) gene in SARS-CoV-2, and show the potential of such gene therapy against a broad range of circulating and emergent SARS-CoV-2 variants. Thus, AAV.CPP.16 could be a useful gene delivery vector for treating genetic respiratory diseases and airborne infections including for developing a potential prophilaxis to SARS-CoV-2.

bioengineering↗

bioRxiv2023

Photosymbiosis reduces the environmental stress response under a heat challenge in a facultatively symbiotic coral

The symbiosis between corals of the order Scleractinia and dinoflagellates of the family Symbiodiniaceae is sensitive to environmental stress. The oxidative bleaching hypothesis posits that extreme temperatures lead to accumulation of photobiont-derived reactive oxygen species ROS, which exacerbates the coral environmental stress response (ESR). To understand how photosymbiosis modulates coral ESRs, these responses must be explored in hosts in and out of symbiosis. We leveraged the facultatively symbiotic coral Astrangia poculata, which offers an opportunity to uncouple the ESR across its two symbiotic states (symbiotic, aposymbiotic). Colonies of both symbiotic states were exposed to three temperature treatments for 15 days: i) control (static 18{degrees}C), ii) heat challenge (increasing from 18 to 32{degrees}C), and iii) cold challenge (decreasing from 18 to 6{degrees}C) after which host gene expression was profiled. Cold challenged corals elicited widespread differential expression, however, there were no differences between symbiotic states. In contrast, symbiotic colonies exhibited greater gene expression plasticity under heat challenge, including enrichment of cell cycle pathways involved in controlling photobiont growth. Counter to the oxidative bleaching hypothesis, this plasticity did not include signatures of stress, and rather a dampened ESR under heat challenge was observed, suggesting that photobionts reduce the hosts ESR under elevated temperatures in A. poculata.

ecology↗

bioRxiv2023

Noise reduction as a unified mechanism of perceptual learning in humans, macaques, and convolutional neural networks

Visual perceptual learning (VPL), defined as long-term improvement in a visual task, is considered a crucial tool for elucidating underlying visual and brain plasticity. However, the identification of a unified theory of VPL has long been controversial. Multiple existing models have proposed diverse mechanisms, including improved signal-to-noise ratio, changes in tuning curves, and reduction of noise correlations, as major contributors to improved neural representations associated with VPL. However, each model only accounts for specific aspects of the empirical findings, and there exists no theory that can comprehensively explain all empirical results. Here, we argue that all neural changes at single units can be conceptualized as geometric transformations of population response manifolds in a high-dimensional neural space. This approach enables conflicting major models of VPL to be quantitatively tested and compared within a unified computational theory. Following this approach, we found that changes in tuning curves and noise correlations, as emphasized by previous models, make no significant contributions to improved population representations by visual training. Instead, we identified neural manifold shrinkage due to reduced trial-by-trial neural response variability, a previously unexplored factor, as the primary mechanism underlying improved population representations. Furthermore, we showed that manifold shrinkage successfully accounts for learning effects across various domains, including artificial neural responses in deep neural networks trained on typical VPL tasks, multivariate BOLD signals in humans, and multi-unit activities in monkeys. These converging results suggest that our neural geometry theory offers a quantitative and comprehensive approach to explain a wide range of empirical results and to reconcile previously conflicting models of VPL.

neuroscience↗

bioRxiv2023

Xanthomonas citri subsp. citri type III effector PthA4 directs the dynamical expression of a putative citrus carbohydrate-binding gene for canker formation

Xanthomonas citri subsp. citri (Xcc), the causal agent of citrus canker, elicits canker symptoms in citrus plants because of the transcriptional activator-like (TAL) effector PthA4, which activates the expression of the citrus susceptibility gene CsLOB1. This study reports the regulation of the putative carbohydrate-binding protein gene Cs9g12620 by PthA4-mediated induction of CsLOB1 during Xcc infection. We found that the transcription of Cs9g12620 was induced by infection with Xcc in a PthA4-dependent manner. Even though it specifically bound to a putative TAL effector-binding element in the Cs9g12620 promoter, PthA4 exerted a suppressive effect on the promoter activity. In contrast, CsLOB1 bound to the Cs9g12620 promoter to activate its expression. The silencing of CsLOB1 significantly reduced the level of expression of Cs9g12620, which demonstrated that Cs9g12620 was directly regulated by CsLOB1. Intriguingly, PhtA4 interacted with CsLOB1 and exerted feedback control that suppressed the induction of expression of Cs9g12620 by CsLOB1. Transient overexpression and gene silencing revealed that Cs9g12620 was required for the optimal development of canker symptoms. These results support the hypothesis that the expression of Cs9g12620 is dynamically directed by PthA4 for canker formation through the PthA4-mediated induction of CsLOB1.

plant biology↗

bioRxiv2023

PCDH15 Dual-AAV Gene Therapy for Deafness and Blindness in Usher Syndrome Type 1F

Usher syndrome type 1F (USH1F), resulting from mutations in the protocadherin-15 (PCDH15) gene, is characterized by congenital lack of hearing and balance, and progressive blindness in the form of retinitis pigmentosa. In this study, we explore a novel approach for USH1F gene therapy, exceeding the single AAV packaging limit by employing a dual adeno-associated virus (AAV) strategy to deliver the full-length PCDH15 coding sequence. We demonstrate the efficacy of this strategy in mouse USH1F models, effectively restoring hearing and balance in these mice. Importantly, our approach also proves successful in expressing PCDH15 in clinically relevant retinal models, including human retinal organoids and non-human primate retina, showing efficient targeting of photoreceptors and proper protein expression in the calyceal processes. This research represents a major step toward advancing gene therapy for USH1F and the multiple challenges of hearing, balance, and vision impairment.

neuroscience↗

bioRxiv2023

Bni5 tethers myosin-II to septins to enhance retrograde actin flow and the robustness of cytokinesis

The collaboration between septins and myosin-II in driving processes outside of cytokinesis remains largely uncharted. Here, we demonstrate that Bni5 in the budding yeast S. cerevisiae interacts with myosin-II, septin filaments, and the septin-associated kinase Elm1 via distinct domains at its N- and C-termini, thereby tethering the mobile myosin-II to the stable septin hourglass at the division site from bud emergence to the onset of cytokinesis. The septin and Elm1-binding domains, together with a central disordered region, of Bni5 control timely remodeling of the septin hourglass into a double ring, enabling the actomyosin ring constriction. The Bni5-tethered myosin-II enhances retrograde actin cable flow, which contributes to the asymmetric inheritance of mitochondria-associated protein aggregates during cell division, and also strengthens cytokinesis against various perturbations. Thus, we have established a biochemical pathway involving septin-Bni5-myosin-II interactions at the division site, which can inform mechanistic understanding of the role of myosin-II in other retrograde flow systems. SummaryOkada et al. have determined the molecular mechanism underlying the Bni5 interactions with septins and myosin-II at the cell division site and uncovered its roles in promoting retrograde actin flow and the robustness of cytokinesis in budding yeast.

cell biology↗