Biology subjects

Ren, X.

Publications and source records attributed to Ren, X..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Three-step docking by WIPI2, ATG16L1 and ATG3 delivers LC3 to the phagophore

The covalent attachment of ubiquitin-like LC3 proteins prepares the autophagic membrane for cargo recruitment. We resolve key steps in LC3 lipidation by combining molecular dynamics simulations and experiments in vitro and in cellulo. We show how the E3-like ligase ATG12- ATG5-ATG16L1 in complex with the E2-like conjugase ATG3 docks LC3 onto the membrane in three steps by (1) the PI(3)P effector protein WIPI2, (2) helix 2 of ATG16L1, and (3) a membrane-interacting surface of ATG3. Phosphatidylethanolamine (PE) lipids concentrate in a region around the thioester bond between ATG3 and LC3, highlighting residues with a possible role in the catalytic transfer of LC3 to PE, including two conserved histidines. In a near-complete pathway from the initial membrane recruitment to the LC3 lipidation reaction, the three-step targeting of the ATG12-ATG5-ATG16L1 machinery establishes a high level of regulatory control.

cell biology↗

bioRxiv2023

High throughput PRIME editing screens identify functional DNA variants in the human genome

Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and base-pair resolution manner remains challenging. Here, we develop a novel pooled prime editing screen method, PRIME, which can be applied to characterize thousands of coding and non-coding variants in a single experiment with high reproducibility. To showcase its applications, we first identified essential nucleotides for a 716 bp MYC enhancer via PRIME-mediated saturation mutagenesis. Next, we applied PRIME to functionally characterize 1,304 non-coding variants associated with breast cancer and 3,699 variants from ClinVar. We discovered that 103 non-coding variants and 156 variants of uncertain significance are functional via affecting cell fitness. Collectively, we demonstrate PRIME capable of characterizing genetic variants at base-pair resolution and scale, advancing accurate genome annotation for disease risk prediction, diagnosis, and therapeutic target identification.

genomics↗

bioRxiv2023

Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex

The unc-51-like kinase protein kinase complex (ULK1C) is the most upstream and central player in the initiation of macroautophagy in mammals. Here, the cryo-EM structure of the human ULK1C core was determined at amino acid residue-level resolution. A moderate resolution structure of the ULK1C core in complex with another autophagy core complex, the class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1) was also determined. The two complexes co-assemble through extensive contacts between the FIP200 scaffold subunit of ULK1C and the VPS15, ATG14, and BECN1 subunits of PI3KC3-C1. The FIP200:ATG13:ULK1 core of ULK1C undergoes a rearrangement from 2:1:1 to 2:2:2 stoichiometry in the presence of PI3KC3-C1. This suggests a structural mechanism for the initiation of autophagy through formation of a ULK1C:PI3KC3-C1 supercomplex and dimerization of ULK1 on the FIP200 scaffold.

biochemistry↗

bioRxiv2023

Co-engagement of TIGIT+ immune cells to PD-L1+ tumours by a bispecific antibody potentiates T-cell response and tumour control

Co-targeting PD-1/PD-L1 and TIGIT/CD226 is being pursued to broaden the efficacy of current immunotherapy. Here we demonstrate that a bispecific antibody (BsAb) targeting PD-L1 and TIGIT, HB0036, shows major advantages over the combination of the two parental monoclonal Abs (mAbs). We demonstrated that HB0036 co-engages PD-L1+ tumour cells and TIGIT+ T cells, and thereby upregulates CD226 on T cells and induces a greater T-cell proliferative response compared to the combination of the parental antibodies in vitro. In vivo, HB0036 recruits greater amounts of TIGIT antibody in PD-L1+ tumours but not in PD-L1- tumours, compared with therapy using the two parental antibodies. We also observed improved tumour control and favourable immunological signatures with HB0036 in syngeneic and xenograft tumour models. Collectively, these findings demonstrate that bispecific antibodies targeting PD-L1 and TIGIT offer superior benefits in cancer immunotherapy compared with therapy using the two parental antibodies. Based on these studies, a phase I clinical trial with HB0036 has been initiated in patients with solid tumours (NCT05417321).

immunology↗

bioRxiv2023

Membrane and glycocalyx tethering of DNA nanostructures for enhanced uptake

DNA nanostructures (DNs) have been increasingly utilized in biosensing, drug delivery, diagnostics and therapeutics, because of their programmable assembly, control over size and shape, and ease of functionalization. However, the low cellular uptake of DNs has limited their effectiveness in these biomedical applications. Here we demonstrate the potential of membrane and glycocalyx binding as general strategies to enhance the cellular uptake of DNs. By targeting the plasma membrane and cell-surface glycocalyx, the uptake of all three distinct DNs is significantly enhanced as compared to uptake of bare DNs. We also demonstrate the viability of single-step membrane labeling by cholesterol-DNs as competitive with previous multistep approaches. Further, we show that the endocytic pathway of membrane-bound DNs is an interdependent process that involves scavenger receptors, clathrin-, and caveolinmediated endocytosis. Our findings may potentially expand the toolbox for effective cellular delivery of DNA nanostructured systems.

bioengineering↗

bioRxiv2023

Synthetic cell armor made of DNA origami

Therapeutic and bioengineering applications of cells, such as cell printing and cell delivery, are directly limited by cell damage and death due to harsh mechanical conditions. Improved cellular robustness thus motivates investigations into cell encapsulation that provides essential protection. Here we target the cell-surface glycocalyx and crosslink two layers of DNA origami nanorods on the cellular plasma membrane to form a nanoscale protective shell. This modular and programmable approach enables fine control over the layering and composition of membrane-deposited nanorods. We show that the DNA origami nanoshell modulates the biophysical properties of cell membranes by enhancing membrane stiffness and lowering lipid fluidity. Moreover, the nanoshell serves as armor, protecting cells, limiting swelling and ultimately improving their viability against mechanical stress from osmotic imbalance and centrifugal forces. Our results demonstrate the potential of the nanoshell, not only as a cellular protection strategy, but also as a platform for manipulating and studying plasma membrane mechanics.

bioengineering↗

bioRxiv2022

Principles of assembly and regulation of condensates of Polycomb repressive complex 1 through phase separation

PRC1 (Polycomb repressive complex 1) plays a significant role in cellular differentiation and development by repressing lineage-inappropriate genes. PRC1 proteins phase separate to form Polycomb condensates (bodies) that are multi-component hubs for silencing Polycomb target genes; however, the molecular principles that underpin the condensate assembly and biophysical properties remain unknown. Here, by using biochemical reconstitution, cellular imaging, and multiscale molecular simulations, we show that PRC1 condensates are assembled via a scaffold-client liquid-liquid phase separation (LLPS) model by which Chromobox 2 (CBX2) is the scaffold and other subunits of the CBX2-PRC1 complex act as clients. The clients induce a reentrant phase transition of CBX2 condensates in a concentration-dependent manner. The composition of the multi-component, heterotypic LLPS systems directs the assembly and biophysical properties of CBX2-PRC1 condensates and selectively promotes the formation of CBX4-PRC1 condensates, but specifically dissolves condensates of CBX6-, CBX7-, and CBX8-PRC1. Additionally, the composition of CBX2-PRC1 condensates controls the enrichment of CBX4-, CBX7-, and CBX8-PRC1 into condensates but the exclusion of CBX6-PRC1 from condensates. Our results show the composition- and stoichiometry-dependent scaffold-client assembly of multi-component PRC1 condensates and supply a conceptual framework underlying the molecular basis and dynamics of Polycomb condensate assembly.

biochemistry↗

bioRxiv2022

Multi-center integrated analysis of non-coding CRISPR screens

The ENCODE Consortiums efforts to annotate non-coding, cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes which play a major role in health and disease. Pooled, non-coding CRISPR screens are a promising approach for systematically investigating gene regulatory mechanisms. Here, the ENCODE Functional Characterization Centers report 109 screens comprising 346,970 individual perturbations across 13.3Mb of the genome, using a variety of methods, readouts, and statistical analyses. Across 332 functionally confirmed CRE-gene links, we identify principles for screening endogenous, non-coding elements for causal regulatory mechanisms. Nearly all CREs show strong evidence of open chromatin, and targeting accessibility peak summits is a critical component of our proposed sgRNA design rules. We provide experimental guidelines to accurately detect CREs with variable, often low, transcriptional effects. We discover a previously undescribed DNA strand-bias for CRISPRi in transcribed regions with implications for screen design and analysis. Benchmarking five screen analysis tools, we find CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity sgRNAs. Together, we provide an accessible data resource, predesigned sgRNAs targeting 3,275,697 ENCODE SCREEN candidate CREs, and screening guidelines to accelerate functional characterization of the non-coding genome.

genomics↗

bioRxiv2022

Spatial transcriptomics deconvolution at single-cell resolution by Redeconve

Computational deconvolution with single-cell RNA sequencing data as reference is pivotal to interpreting spatial transcriptomics data, but the current methods are limited to cell type resolution. Here we present Redeconve, an algorithm to deconvolute spatial transcriptomics data at single-cell resolution, enabling interpretation of spatial transcriptomics data with thousands of nuanced cell states. We benchmarked Redeconve with the state-of-the-art algorithms on diverse spatial transcriptomics datasets and platforms and demonstrated the superiority of Redeconve in terms of accuracy, resolution, robustness, and speed. Applications to a human pancreatic cancer dataset revealed cancer clone-specific T cell infiltration, and application to lymph node samples identified subtle cellular surroundings between IgA+ and IgG+ spots, providing novel insights into tumor immunology and the regulatory mechanisms underlying antibody class switch.

bioinformatics↗

bioRxiv2022

A novel method revealing animal evolutionary relationships based on milk Mid-infrared

Mid-infrared spectra (MIRS) can effectively reflect the chemical bonds in milk, which has been widely used in dairy herd improvement. However, the relationship between MIRS and animal evolution remains largely unclear. This study firstly found great differences in MIRS and the components of milk by analyzing MIRS information of 12 different mammal species. A five-level discriminant model of evolutionary level based on MIRS was established with a test set kappa coefficient >0.97. In addition, a regression model of genetic distance was also established to estimate the genetic distance of different animal species with a correlation coefficient of R >0.94. These results showed that this method could be used for accurate mammalian evolutionary relationship assessment. We further clarified the potential relationship between MIRS and genes, such as PPP3CA and SCD that could change MIRS by regulating specific milk components. In conclusion, we expand the application of MIRS in animal species identification and evolution research and provide new perspectives for the research on the formation mechanism of different animal milk special components.

evolutionary biology↗

bioRxiv2022

Rapid and Signal Crowdedness-Robust In-Situ Sequencing through Hybrid Block Coding

Spatial transcriptomics technology has revolutionized our understanding of cell types and tissue organization, opening new possibilities for researchers to explore transcript distributions at subcellular levels. However, existing methods have limitations in resolution, sensitivity, or speed. To overcome these challenges, we introduce SPRINTseq (Spatially Resolved and signal-diluted Next-generation Targeted sequencing), an innovative in situ sequencing strategy that combines hybrid block coding and molecular dilution strategies. Our method enables fast and sensitive high-resolution data acquisition, as demonstrated by recovering over 142 million transcripts using a 108 gene panel from 453,843 cells from four mouse brain coronal slices in less than two days. Using this advanced technology, we uncover the cellular and subcellular molecular architecture of Alzheimers disease, providing additional information into abnormal cellular behaviors and their subcellular mRNA distribution. This improved spatial transcriptomics technology holds great promise for exploring complex biological processes and disease mechanisms.

genomics↗

bioRxiv2022

Three-dimensional molecular architecture of mouse organogenesis

Mammalian embryos have sophisticated cell organizations that are orchestrated by molecular regulation at cellular and tissue level. It has recently been appreciated that the cells that make up the animal body themselves harbor significant heterogeneity in the context of both cellular and particularly spatial dimension. However, current spatial transcriptomics profiling of embryonic tissues either lack three-dimensional representation or are restricted to limited depth and organs. Here, we reported a holistic spatial transcriptome atlas of all major organs at embryonic day 13.5 of mouse embryo and delineated a 3D rendering of the molecular regulation of embryonic patterning. By integrating with corresponding single-cell transcriptome data, the spatial organogenesis atlas provides rich molecular annotation of the dynamic organ nature, spatial cellular interaction, embryonic axes and divergence of cell fates underlying mammalian development, which would pave the way for precise organ-engineering and stem-cell based regenerative medicine.

developmental biology↗

bioRxiv2022

Inference of Presynaptic Connectivity from Temporally Blurry Spike Trains by Supervised Learning

Reconstruction of neural network connectivity is a central focus of neuroscience. The ability to use neuronal connection information to predict activity at single unit resolution and decipher its effect on whole systems can provide critical information about behavior and cognitive processing. Neuronal sensing modalities come in varying forms, but there is yet to exist a modality that can deliver readouts that sufficiently address the spatiotemporal constraints of biological nervous systems. This necessitates supplementary approaches that rely on mathematical models to mitigate physical limitations and decode network features. Here, we introduce a simple proof-of-concept model that addresses temporal constraints by reconstructing presynaptic connections from temporally blurry data. We use a variation of the perceptron algorithm to process firing rate information at multiple time constraints for a heterogenous feed-forward network of excitatory, inhibitory, and unconnected presynaptic units. We evaluate the performance of the algorithm under these conditions and determine the optimal learning rate, firing rate, and the ability to reconstruct single unit spikes for a given degree of temporal blur. We then test our method on a physiologically relevant configuration by sampling network subpopulations of leaky integrate-and-fire neuronal models displaying bursting firing patterns and find comparable learning rates for optimized reconstruction of network connectivity. Our method provides a recipe for reverse engineering neural networks based on limited data quality that can be extended to more complicated readouts and connectivity distributions relevant to multiple brain circuits.

neuroscience↗

bioRxiv2022

Chaperones Hsc70 and Hsp70 Play Distinct Roles in Bocaparvovirus Minute Virus of Canines Infection

Minute virus of canines (MVC) belongs to the genus Bocaparvovirus and reproduces rapidly in its permissive cells Walter Reed/3873D (WRD). The crosstalk between MVC and WRD is poorly characterized in terms of molecular requirements and mechanisms. Here, we identified two novel cellular proteins Hsc70 and Hsp70 that interact with both NS1 and VP2 via mass spectrometry (MS), co-immunoprecipitation (Co-IP) and confocal immunofluorescence assays (IFA). Hsp70 was upregulated upon MVC infection. Respective silencing of Hsc70 and Hsp70 led to contrasting results at nearly every stage of MVC life cycle, including virus entry, transcription, translation, replication and production. Strikingly, transfection with low and high dose of pFlag-Hsp70 contributed to opposing impacts on viral protein levels and virus production possibly through a ubiquitin-dependent manner, indicating that MVC is quite sensitive to the levels of Hsp70. Treatment with quercetin and VER155008, two Hsp70 family inhibitors, both significantly decreased viral replication and particle levels. Together, these results illustrated that both Hsc70 and Hsp70 are involved in MVC life cycle, and targeting to Hsp70 family may represent a novel anti-MVC mechanism.

molecular biology↗

bioRxiv2022

Senescent cells develop PDK4-dependent hypercatabolism and form an acidic microenvironment to drive cancer resistance

Cellular senescence is a state of stable growth arrest, usually accompanied by development of the senescence-associated secretory phenotype (SASP). Although senescent cells remain metabolically active, little is known about their metabolic landscape and in vivo pathophysiological implications. Here we show that expression of the pyruvate dehydrogenase (PDH) inhibitory enzyme, pyruvate dehydrogenase kinase 4 (PDK4), is significantly upregulated in human senescent stromal cells. Preferentially expressed upon genotoxicity-induced senescence (GIS), PDK4 is negatively correlated with posttreatment survival of cancer patients. Upon cellular senescence, PDK4 shifts glucose metabolic flux from oxidative phosphorylation to aerobic glycolysis, causing enhanced lactate production and forming an acidic microenvironment. However, distinct from the cancer cell-featured Warburg effect, senescent cells maintain an intensive use of pyruvate through the tricarboxylic acid cycle (TCA), displaying increased respiration and redox activity, indicative of a special form of metabolic reprogramming. Conditioned media from PDK4+ stromal cells change global expression and promote malignancy of recipient cancer cells in vitro and accelerate tumor progression in vivo. Pharmacologically targeting PDK4 restrains the adverse effects of PDK4 in cell-based assays, while promoting tumor regression and extending posttreatment survival in preclinical trials. Together, our study substantiates the hypercatabolic nature of senescent cells, and reveals a metabolic link between senescence-associated acidic microenvironment and age-related pathologies including but not limited to cancer.

cell biology↗

bioRxiv2022

Structural basis for ATG9A recruitment to the ULK1 complex in mitophagy initiation

The assembly of the autophagy initiation machinery nucleates autophagosome biogenesis, including in the PINK1- and Parkin-dependent mitophagy pathway implicated in Parkinsons disease. The structural interaction between the sole transmembrane autophagy protein, ATG9A, and components of the ULK1 complex is one of the major missing links needed to complete a structural map of autophagy initiation. We determined the 2.4 [A] x-ray crystallographic structure of the ternary structure of ATG9A C-terminal tail bound to the ATG13:ATG101 HORMA dimer, which is part of the ULK1 complex. We term the interacting portion of the extreme C-terminal part of the ATG9A tail the "HORMA dimer interacting region" (HDIR). This structure shows that the HDIR binds to the HORMA domain of ATG101 by {beta}-sheet complementation such that the ATG9A tail resides in a deep cleft at the ATG13:ATG101 interface. Disruption of this complex in cells impairs damage induced PINK1/Parkin mitophagy mediated by the cargo receptor NDP52.

cell biology↗

bioRxiv2022

Mcm2 promotes stem cell differentiation via its ability to bind H3-H4

Mcm2, a subunit of the Mcm2-7 helicase best known for its role in DNA replication, contains a histone binding motif that facilitates the transfer of parental histones following DNA replication. Here we show that Mcm2 is important for the differentiation of mouse embryonic stem (ES) cells. The Mcm2-2A mutation defective in histone binding impairs differentiation and disrupts the programmatic changes in gene expression and histone modifications during differentiation. Mcm2 localizes at transcription starting sites and the binding of Mcm2 at gene promoters is disrupted in both Mcm2-2A ES cells and neuro-precursor cells (NPCs). Reduced Mcm2 binding at bivalent chromatin domains containing repressive H3K27me3 and active H3K4me3 modifications in Mcm2-2A ES cells correlates with decreased chromatin accessibility at corresponding sites in NPCs. Together, our studies reveal a novel function of Mcm2 in ES cell differentiation, likely through manipulating chromatin landscapes at bivalent chromatin domains.

developmental biology↗

bioRxiv2022

Metabolomics and transcriptomics reveal the response mechanisms of Mikania micrantha to Puccinia spegazzinii infection

Mikania micrantha is one of the 100 worst invasive species globally and can cause significant negative impacts to agricultural and forestry economics, particularly in Asia and the Pacific region. The rust Puccinia spegazzinii has been used successfully as a biological control agent in several countries to help manage M. micrantha. However, the response mechanisms of M. micrantha to P. spegazzinii infection have never been studied. To investigate the response of M. micrantha to infection by P. spegazzinii, an integrated analysis of metabolomics and transcriptomics was performed. The levels of 101 metabolites, including organic acids, amino acids and secondary metabolites in M. micrantha infected with P. spegazzinii, were significantly different compared to those in plants that were not infected. The relative amounts of L-leucine, L-ioleucine, L-tryptophan, histidine, L-phenylalanine and L-citrulline were increased under P. spegazzinii infection. These may convert to intermediates within the TCA cycle, participating in energy biosynthesis. In addition, phytoalexins, such as maackiain, nobiletin, vasicin, arachidonic acid and JA-Ile, were synthesized and accumulated in M. micrantha in response to P. spegazzinii infection. A total of 4,978 differentially expressed genes were identified in M. micrantha infected by P. spegazzinii. Many key genes of the Mitogen-activated protein kinase (MAPK) signalling pathway, showed significantly higher expression under P. spegazzinii infection. These results not only help us to understand the response of metabolites and gene expression in M. micrantha following infection by P. spegazzinii, but also help us understand the potential for the continuous biological control of M. micrantha using P. spegazzinii.

pathology↗