Biology subjects

Xiong, Y.

Publications and source records attributed to Xiong, Y..

At least 145 records · Page 8Linked to original sources

bioRxiv2022

NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations

As one of the state-of-the-art automated function prediction (AFP) methods, NetGO 2.0 integrates multi-source information to improve the performance. However, it mainly utilizes the proteins with experimentally supported functional annotations without leveraging valuable information from a vast number of unannotated proteins. Recently, protein language models have been proposed to learn informative representations (e.g., Evolutionary Scale Modelling (ESM)-1b embedding) from protein sequences based on self-supervision. We represent each protein by ESM-1b and use logistic regression (LR) to train a new model, LR-ESM, for AFP. The experimental results show that LR-ESM achieves comparable performance with the best-performing component of NetGO 2.0. Therefore, by incorporating LR-ESM into NetGO 2.0, we develop NetGO 3.0 to improve the performance of AFP extensively. NetGO 3.0 is freely accessible at https://dmiip.sjtu.edu.cn/ng3.0.

bioinformatics↗

bioRxiv2022

Photonic-Plasmonic Coupling Enhanced Fluorescence Enabling Digital-Resolution Ultrasensitive Protein Detection

Assays utilizing molecular fluorophores are common throughout life science research and diagnostic testing, although detection limits are generally limited by weak emission intensity, thus requiring many labeled target molecules to combine their output to achieve signal-to-noise greater than the background. Here, we describe how the synergistic coupling of plasmonic and photonic resonance modes can significantly boost the emission from fluorescent dye molecules without increasing the illumination intensity while utilizing a microscopy approach with a broad field of view. By optimally matching the resonant modes of a plasmonic fluor (PF) nanoparticle and a photonic crystal (PC) surface with the absorption and emission spectrum of the PFs fluorescent dye, we observe a 52-fold improvement in signal intensity, enabling individual PFs to be observed and digitally counted, using an approach in which one PF tag represents detection of one target molecule. The photonic amplification from the PF can be attributed to the strong near-field enhancement due to the cavity-induced activation of the PF, PC band structure-mediated improvement in collection efficiency of emitted photons, and increased rate of spontaneous emission. We demonstrate the applicability of the method by dose-response characterization of a sandwich immunoassay for human interleukin-6, a biomarker commonly used to assist diagnosis of cancer, inflammation, sepsis, and autoimmune disease. We achieve a limit of detection of 10 fg/ml, representing a capability three orders of magnitude lower than standard immunoassays.

bioengineering↗

bioRxiv2022

scCobra: Contrastive cell embedding learning with domain adaptation for single-cell data integration

The rapid development of single-cell technologies has underscored the need for more effective methods in the integration and harmonization of single-cell sequencing data. The prevalent challenge of batch effects, resulting from technical and biological variations across studies, demands accurate and reliable solutions for data integration. Traditional tools often have limitations, both due to reliance on gene expression distribution assumptions and the common issue of over-correction, particularly in methods based on anchor alignments. Here we introduce scCobra, a deep neural network tool designed specifically to address these challenges. By leveraging a deep generative model that combines a contrastive neural network with domain adaptation, scCobra effectively mitigates batch effects and minimizes over-correction without depending on gene expression distribution assumptions. Additionally, scCobra enables online label transfer across datasets with batch effects, facilitating the continuous integration of new data without retraining, and offers features for batch effect simulation and advanced multi-omic batch integration. These capabilities make scCobra a versatile data integration and harmonization tool for achieving accurate and insightful biological interpretations from complex datasets.

bioinformatics↗

bioRxiv2022

A ubiquitous spectrolaminar motif of local field potential power across the primate cortex

The mammalian cerebral cortex is anatomically organized into a six-layer motif. It is currently unknown whether a corresponding laminar motif of neuronal activity exists across the cortex. Here, we report such a motif in the power of local field potentials (LFP). We implanted multicontact laminar probes in five macaque monkeys and recorded activity across layers in 14 cortical areas at various hierarchical processing stages in all cortical lobes. The anatomical laminar locations of recordings were histologically identified via electrolytic lesions. In all areas, we found a common spectrolaminar pattern characterized by an increasing deep-to-superficial layer gradient of gamma frequency LFP power peaking in layers 2/3, and an increasing superficial-to-deep gradient of alpha-beta power peaking in layers 5/6. Our results show an electrophysiological dissociation between superficial and deep layers that is preserved across the cortex, suggesting a ubiquitous layer and frequency-based mechanism for cortical computation.

neuroscience↗

bioRxiv2022

Identify the origin and end cells and infer the trajectory of cellular fate automatically

Cellular state identification and trajectory inference enable reconstructions of cell fate dynamics from single-cell RNA sequencing. However, the identification of cell fate trajectories requires a large number of computational resources or known biological process, and lack a method to alleviate both of these deficiencies at the same time. Here, we present scLTNN, a method that automatically infers origin and end cell state from scRNA-seq data and calculates the developmental trajectory and differentiation direction of cells with only a few computational resources and time consummation. We apply scLTNN to disentangling subpopulation kinetics in CD8+ T cell, pancreatic endocrinogenesis, and the development of zebrafish embryos. scLTNN displays a strong trajectory inference ability cross-species. scLTNN features a modular design that can be flexibly extended to any scRNA-seq analysis task. The complete package is available online at https://github.com/Starlitnightly/scltnn.

bioinformatics↗

bioRxiv2022

Single-cell Atlas of Human Fetal Cerebellum Decoding Medulloblastoma Origin and Oncogenesis

Medulloblastoma (MB) is the most common malignant childhood brain tumor1,2, yet the origin of the most aggressive subgroup-3 form remains elusive, impeding development of effective targeted treatments. Previous analyses of mouse cerebella3,4 or human counterparts from frozen tissue nuclei5 have not fully defined the compositional heterogeneity of MBs. Here, we undertook an unprecedented single-cell profiling of freshly-isolated human fetal cerebella to establish a reference map delineating hierarchical cellular states in MBs. We identified a unique transitional cerebellar progenitor connecting neural stem cells to neuronal lineages in developing fetal cerebella. Intersectional analysis revealed that the transitional progenitors were enriched in aggressive MB subgroups, including group-3 and metastatic tumors. Single-cell multi-omics revealed underlying regulatory networks in the transitional progenitor populations, including transcriptional determinants HNRNPH1 and SOX11, which are correlated with clinical prognosis in group-3 MBs. Genomic and Hi-C profiling identified de novo long-range chromatin-loops juxtaposing HNRNPH1/SOX11-targeted super-enhancers to cis-regulatory elements of MYC, an oncogenic driver for group-3 MBs. Targeting the transitional progenitor regulators inhibited MYC expression and MYC-driven group-3 MB growth. Our integrated single-cell atlases of human fetal cerebella and MBs reveal potential cell populations predisposed to transformation and regulatory circuitries underlying tumor cell states and oncogenesis, highlighting hitherto unrecognized transitional progenitor intermediates predictive of disease prognosis and potential therapeutic vulnerabilities.

cancer biology↗

bioRxiv2022

Function and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages

The SARS-CoV-2 variant, Omicron (B.1.1.529), rapidly swept the world since its emergence. Compared with previous variants, Omicron has a high number of mutations, especially those in its spike glycoprotein that drastically dampen or abolish the efficacy of currently available vaccines and therapeutic antibodies. Several major sublineages of Omicron evolved, including BA.1, BA.1.1, BA.2, BA.2.12.1, BA.3, BA.4/5, and BA.2.75, which rapidly changing the global and regional landscape of the pandemic. Although vaccines are available, therapeutic antibodies remain critical for infected and especially hospitalized patients. To address this, we have designed and generated a panel of human/humanized therapeutic bispecific antibodies against Omicron and its sub-lineage variants, with activity spectrum against other lineages. Among these, the top clone CoV2-0213 has broadly potent activities against multiple SARS-CoV-2 ancestral and Omicron lineages, including BA.1, BA.1.1, BA.2, BA.2.12.1, BA.3, BA.4/5, and BA.2.75. We have solved the cryo-EM structure of the lead bi-specific antibody CoV-0213 and its major Fab arm MB.02. Three-dimensional structural analysis shows distinct epitope of antibody - spike receptor binding domain (RBD) interactions and reveals that both Fab fragments of CoV2-0213 can simultaneously target one single spike RBD or two adjacent ones in the same spike trimer, further corroborating its mechanism of action. CoV2-0213 represents a unique and potent broad-spectrum SARS-CoV-2 neutralizing bispecific antibody (nbsAb) against the currently circulating major Omicron variants (BA.1, BA.1.1, BA.2, BA.2.12.1, BA.2.75, BA.3, and BA.4/5). CoV2-0213 is primarily human and ready for translational testing as a countermeasure against the ever-evolving pathogen.

immunology↗

bioRxiv2022

Revisiting the effects of Cas9 on p53-inactivating mutations reveals sex-biased genome editing by CRISPR-Cas9

CRISPR-Cas9 system has emerged as the dominant technology for gene editing and has great potential for large-scale clinical applications. One major concern is its off-target issue and other potential side effects after the introduction of exogenous CRISPR-Cas9 into cells. Several previous studies investigated CRISPR-Cas9 interactions with p53 mainly in non-transformed cells, such as RPE1 (retinal pigmented epithelium cells) and H9 (embryonic stem cells [ESC]). Recently, it has been reported that Cas9 alone can activate the p53 pathway and select for p53-inactivating mutations after studying hundreds of cancer cell lines. We reanalyzed the reported data of Cas9-associated p53-inactivating mutations and observed large significant sex difference when comparing Cas9 activities in p53-wildtype and p53-mutant cell lines. To expand the impact of this finding, we further examined all protein-coding genes screening by the CRISPR-Cas9 system in a large-scale dataset from the DepMap project. We highlight the p53 status-dependent sex bias of CRISPR-Cas9 effect across cancer cell types (genes including MYC, PIK3CA, KAT2B, KDM4E, SUV39H1, FANCB, TLR7, and APC2) and potential mechanisms (mediated by transcriptional factors including SOX9, FOXO4, LEF1, and RYBP) underlying this phenomenon, which suggest that the p53-dependent sex bias effect may need to be considered in future clinical applications, especially in cancer, when using this genome editing system.

genetics↗

bioRxiv2022

Novel leaf-root coordination driven by leaf water storage tissues in mangroves

Interactions among root and leaf traits (in particular, leaf hydraulic and leaf economics traits) are fundamental in generating diverse strategies in land plants, yet it remains a knowledge gap in mangrove plants that experiences saline stress distinct from most other vascular plants. Here, we tested the trait relationships in mangrove plants and compared them with typical land plants (non-mangrove). Consistent with non-mangrove plants, leaf hydraulic and economics traits were decoupled in mangrove plants. However, mangrove leaf economics traits correlated strongly with root hydraulic traits, which are normally decoupled in non-mangrove plants. Moreover, we observed a unique scaling relationship between leaf dry mass per area and root hydraulic traits in mangroves. The novel coordination between leaves and roots arises from the wide-presence of leaf water storage tissues in mangroves, and this potentially represents a new paradigm with which we look into the ecology, physiology and evolution of this important vegetation.

ecology↗

bioRxiv2022

Identifying new regulators of evolutionarily conserved differential chromosome X dosage compensation

The active X chromosome in mammals is upregulated to balance its dosage to autosomes during evolution. However, it is elusive why the currently known dosage compensation machinery showed uneven and small influence on X genes, necessitating systemic investigation of X dosage in different angles and identification of new dosage regulators. Here, based on >20,000 transcriptomes, we identified two X gene groups (genome ploidy-sensitive [PSX] and ploidy-insensitive [PIX] genes), showing distinct but evolutionarily-conserved (in both primates and mouse) dosage compensations (termed X-over-Autosome dosage Ratio, or XAR). We then explored XAR in diseases and in stem cells, where XAR is potentially important. We demonstrated that XAR-PIX was downregulated while XAR-PSX upregulated across cancer types at both RNA and protein levels. In contrast, XAR-PIX was upregulated while XAR-PSX downregulated during stem cell differentiation. Interestingly, XAR-PIX, but not XAR-PSX, was significantly lower and associated with autoantibodies and inflammation in lupus patients, suggesting that insufficient dosage of PIX genes may contribute to lupus pathogenesis. We further identified and experimentally validated two new XAR regulators, TP53 and ATRX. Collectively, we provided insights to further unravel the mystery of X dosage compensation in mammals and its pathophysiological roles in human diseases.

cancer biology↗

bioRxiv2022

In vivo functional genomics identifies essentiality of potassium homeostasis in medulloblastoma

The identification of cancer maintenance genes--driver genes essential to tumor survival--is fundamental for developing effective cancer therapy. Transposon-based insertional mutagenesis screens can identify cancer driver genes broadly but not discriminate maintenance from progression or initiation drivers, which contribute to cancer phenotypes and tumorigenesis, respectively. We engineered a nested, double-jumping transposon system to first dysregulate gene expression during tumorigenesis and then restore gene expression following tumor induction, allowing for genome-wide screening of maintenance essentiality in vivo. In a mouse model of medulloblastoma, the most common pediatric malignancy, insertion and remobilization of this nested transposon uncovers potassium channel genes as recurrent maintenance drivers. In human medulloblastoma, KCNB2 is the most overexpressed potassium channel across Group 3, Group 4, and SHH subgroups, and Kcnb2 knockout in mice diminishes the replicative potential of medulloblastoma-propagating cells to mitigate tumor growth. Kcnb2 governs potassium homeostasis to regulate plasma membrane tension-gated EGFR signaling, which drives proliferative expansion of medulloblastoma-propagating cells. Thus, our novel transposon system reveals potassium homeostasis as essential to tumor maintenance through biomechanical modulation of membrane signaling.

cancer biology↗

bioRxiv2022

α-synucleinopathy associated calcium overload and autophagy failure is regulated by gain-of-function of Tousled-like kinase

As a pathological hallmark in Parkinsons disease (PD), -synucleinopathy causes multiple cellular damages, including calcium overload, mitochondrial and autophagic dysfunction, and eventually dopamine neuron death. However, the hierarchy of these detrimental events is unclear. In Drosophila, we confirmed that overexpression of -synuclein could induce all these cytotoxic events. To determine the specific cytotoxic events induced by calcium overload, we established a calcium overload model in Drosophila and performed genetic screens. We found that calcium overload caused mitochondrial damage and autophagy failure and cell death, and these cytotoxic processes could be strongly rescued by loss of Tousled-like kinase (TLK). Interestingly, loss of TLK also rescued defects induced by -synuclein overexpression in Drosophila. This suggests that calcium overload acts as the crucial event upstream of mitochondrial and autophagy dysfunction. For TLK regulation of autophagy, our data indicated that a transcriptional factor REPTOR, which regulated the expression of several lysosomal genes, functioned downstream of TLK. In mammalian cells and mice, TLK2 (the homolog of Drosophila TLK) was phosphorylated under calcium overload. Upon phosphorylation, TLK2 increased its kinase activity. In addition, TLK2 could phosphorylate CREBRF (the human homolog of REPTOR) to cause its loss of transcription on the lysosomal genes. Moreover, TLK2 knockout mice rescued multi-aspect cytotoxicity induced by calcium overload and -synuclein overexpression. Our research demonstrates that TLK2 acts as a key regulator to mediate cell death and dysfunctions of mitochondria and autophagy downstream of calcium overload.

neuroscience↗

bioRxiv2022

Grk7 but not Grk1 undergoes cAMP-dependent phosphorylation in zebrafish cone photoreceptors in the dark and mediates recovery of the cone photoresponse in response to forskolin

In the vertebrate retina, phosphorylation of photoactivated visual pigments in rods and cones by G protein-coupled receptor kinases is essential for sustained visual function. In vitro analysis demonstrates that GRK1 and GRK7 are phosphorylated by PKA and that phosphorylation is associated with a decreased capacity to phosphorylate rhodopsin, while in vivo observations show that GRK phosphorylation is cAMP-dependent. In many vertebrates, including humans, GRK1 is expressed in both rods and cones while GRK7 is expressed only in cones. However, mice express only GRK1 in both rods and cones and lack GRK7. We recently reported that a mutation deleting the phosphorylation site, Ser21, in GRK1 is associated with a delay in dark adaptation in mouse rods but not in cones, suggesting that GRK1 may serve a different role depending upon the photoreceptor cell type in which it is expressed. Here, we present immunochemical and electrophysiological studies using zebrafish as a model. Since zebrafish display a retinal GRK expression profile similar to humans, these studies will allow us to further evaluate the role of cAMP-dependent GRK phosphorylation in cone photoreceptor recovery that may be relevant to human physiology. ERG analyses of wildtype and Grk-knockout zebrafish larvae treated with forskolin show that elevated intracellular cAMP significantly decreases recovery of the cone photoresponse, which is mediated by Grk7a rather than Grk1b. Using a cone-specific dominant negative PKA transgenic zebrafish, we show for the first time that PKA is required for Grk7a phosphorylation in vivo. Lastly, immunoblot analyses in rod grk1a and cone grk1b knockout zebrafish, as well as the all cone Nrl-/- mouse, show that cone-expressed Grk1 does not undergo cAMP-dependent phosphorylation in vivo. These results provide a better understanding of the function of Grk phosphorylation in the context of cone adaptation and recovery.

cell biology↗

bioRxiv2022

Abl2 mediates microtubule nucleation and repair via tubulin co-condensation.

Abl family kinases are evolutionarily conserved regulators of cell migration and morphogenesis. Genetic experiments in Drosophila suggest that Abl family kinases interact functionally with microtubules to regulate axon guidance and neuronal morphogenesis. Vertebrate Abl2 binds to microtubules and promotes their plus-end elongation both in vitro and in cells, but the molecular mechanisms by which Abl2 regulates microtubule (MT) dynamics were unclear. We report here that Abl2 regulates MT assembly via condensation and direct interactions with both the MT lattice and tubulin dimers. We find that Abl2 promotes MT nucleation, which is further facilitated by the ability of the Abl2 C-terminal half to undergo phase separation and form co-condensates with tubulin. A naturally occurring tubulin binding-deficient Abl2 splice isoform fails to promote nucleation. Abl2 binds to regions adjacent to MT damage and facilitates their repair via fresh tubulin recruitment and increases MT rescue frequency and lifetime. MT recovery after nocodazole treatment is greatly slowed in Abl2 knockout COS-7 cells compared to wild type cells. We propose a model in which Abl2 locally concentrates tubulin and recruits it to MT tips or to defects in the MT lattice to promote MT repair, rescue, and nucleation.

biochemistry↗

bioRxiv2022

Plant-based Production and Characterization of a Promising Fc-fusion Protein against Bone Mass Density Loss

Microgravity-induced bone loss is a main obstacle for long term space missions as it is difficult to maintain bone mass when loading stimuli is reduced. With a typical bone mineral density loss of 1.5% per month of microgravity exposure, the chances for osteoporosis and fractures may endanger astronauts health. Parathyroid Hormone or PTH (1-34) is an FDA approved treatment for osteoporosis, and may reverse microgravity-induced bone loss. However, PTH proteins requires refrigeration, daily subcutaneous injection, and have a short shelf-life, limiting its use in a resource-limited environment, like space. In this study, PTH was produced in an Fc-fusion form via transient expression in plants, to improve the circulatory half-life which reduces dosing frequency and to simplify purification if needed. Plant-based expression is well-suited for space medicine application given its low resource consumption and short expression timeline. The PTH-Fc accumulation profile in plant was established with a peak expression on day 5 post infiltration of 373 {+/-} 59 mg/kg leaf fresh weight. Once the PTH-Fc was purified, the amino acid sequence and the binding affinity to its target, PTH 1 receptor (PTH1R), was determined utilizing biolayer interferometry (BLI). The binding affinity between PTH-Fc and PTH1R was 2.30 x 10-6 M, similar to the affinity between PTH (1-34) and PTH1R (2.31 x 10-6 M). Its function was also confirmed in a cell-based receptor stimulation assay, where PTH-Fc was able to stimulate the PTH1R producing cyclic adenosine monophosphate (cAMP) with an EC50 of (8.54 {+/-} 0.12) x 10-9 M, comparable to the EC50 from the PTH (1-34) of 1.49 x 10-8 M. These results suggest that plant recombinant PTH-Fc exhibits a similar potency compared to PTH. Furthermore, it can be produced rapidly at high levels with minimal resources and reagents, making it ideal for production in low resource environments such as space.

synthetic biology↗

bioRxiv2022

An Engineered Amber-Emitting Nano Luciferase and Its Use for Immunobioluminescence Imaging in Vivo

The NanoLuc luciferase (NLuc) and its furimazine (FRZ) substrate have revolutionized bioluminescence (BL) assays and imaging. However, the use of the NLuc-FRZ luciferase-luciferin pair for mammalian tissue imaging is hindered by the low tissue penetration of the emitting blue photons. Here, we present the development of an NLuc mutant, QLuc, which catalyzes the oxidation of a synthetic QTZ luciferin for bright and red-shifted emission peaking at [~] 585 nm. This amber-light-emitting luciferase-luciferin pair exhibited improved performance for imaging deep-tissue targets in live mice. Leveraging this novel bioluminescent reporter, we further pursued in vivo immunobioluminescence imaging (immunoBLI), which used a fusion protein of a single-chain variable antibody fragment (scFv) and QLuc for molecular imaging of tumor-associated antigens in a xenograft mouse model. As one of the most red-shifted NLuc variants, we expect QLuc to find broad applications in noninvasive imaging in mammals. Moreover, the immunoBLI method complements immunofluorescence imaging and immuno-positron emission tomography (immunoPET), serving as a convenient and nonradioactive molecular imaging tool for animal models in basic and preclinical research.

biochemistry↗

bioRxiv2022

Net-shaped DNA nanostructure designed for rapid/sensitive detection and potential inhibition of SARS-CoV-2 virus

We present a net-shaped DNA nanostructure (called "DNA Net" herein) design strategy for selective recognition and high-affinity capture of the intact SARS-CoV-2 virions through spatial pattern-matching and multivalent interactions between the aptamers (targeting wild type spike-RBD) positioned on the DNA Net and the trimeric spike glycoproteins displayed on the viral outer surface. Carrying a designer nanoswitch, the DNA Net-aptamers releases fluorescent signal upon virus binding that is easily read by a hand-held fluorimeter for a rapid (in 10 mins), simple (mix- and-read), sensitive (PCR equivalent), room temperature compatible, and inexpensive ([~] $1.26/test) COVID-19 test assay. The DNA Net-aptamers also impede authentic wild-type SARS-CoV-2 infection in cell culture with a near 1x103-fold enhancement of the monomeric aptamer. Furthermore, our DNA Net design principle and strategy can be customized to tackle other life-threatening and economically influential viruses like influenza and HIV, whose surfaces carry class-I viral envelope glycoproteins like the SARS-CoV-2 spikes in trimeric forms.

bioengineering↗

bioRxiv2022

A Self-attention Graph Convolutional Network for Precision Multi-tumour Early Diagnostics with DNA Methylation Data

DNA methylation data-based precision tumor early diagnostics is emerging as state of the art technology, which could capture the signals of cancer occurrence 3[~]5 years in advance and clinically more homogenous groups. At present, the sensitivity of early detection for many tumors is about 30%, which needs to be significantly improved. Nevertheless, based on the genome wide DNA methylation information, one could comprehensively characterize the entire molecular genetic landscape of the tumors and subtle differences among various tumors. With the accumulation of DNA methylation data, we need to develop high-performance methods that can model and consider more unbiased information. According to the above analysis, we have designed a self-attention graph convolutional network to automatically learn key methylation sites in a data-driven way for precision multi-tumor early diagnostics. Based on the selected methylation sites, we further trained a multi-class classification support vector machine. Large amount experiments have been conducted to investigate the performance of the computational pipeline. Experimental results demonstrated the effectiveness of the selected key methylation sites which are highly relevant for blood diagnosis.

bioinformatics↗