Biology subjects

Xie, R.

Publications and source records attributed to Xie, R..

At least 55 records · Page 3Linked to original sources

bioRxiv2022

Overcoming the Blood-Brain Barrier for Gene Therapy via Systemic Administration of GSH-Responsive Silica Nanocapsules

CRISPR genome editing has demonstrated great potential to treat the root causes of many genetic diseases, including central nervous system (CNS) disorders. However, the promise of brain-targeted therapeutic genome editing relies on the efficient delivery of biologics bypassing the blood-brain barrier (BBB), which represents a substantial challenge in the development of CRISPR therapeutics. In this study, we created a library of GSH-responsive silica nanocapsules (SNCs) and screened them for brain targeting via systemic delivery of nucleic acids and CRISPR genome editors. In vivo studies demonstrated that systemically delivered SNCs conjugated with glucose and RVG peptide under glycemic control can efficiently bypass the intact BBB, enabling brain-wide delivery of various biologics (mRNA, Cas9 mRNA/sgRNA, and Cas9/sgRNA ribonucleoprotein) targeting both exogenous genes (i.e., Ai14 stop cassette) and disease-relevant endogenous genes (i.e., App and Th genes) in Ai14 reporter mice and wild-type mice, respectively. In particular, we observed up to 28% neuron editing via systemic delivery of Cre mRNA in Ai14 mice, up to 6.1% amyloid precursor protein (App) gene editing (resulting in 19.1% reduction in the expression level of intact APP), and up to 3.9% tyrosine hydroxylase (Th) gene editing (resulting in 30.3% reduction in the expression level of TH) in wild-type mice. This versatile SNC nanoplatform may offer a novel strategy for the treatment of CNS disorders including Alzheimers, Parkinsons, and Huntingtons disease.

neuroscience↗

bioRxiv2022

Droplet microfluidics forward for tracing target cells at single-cell transcriptome resolution

The rapid promotion of single-cell omics in various fields has begun to help solve many problems encountered in research including precision medicine, prenatal diagnosis, and embryo development. Meanwhile, single-cell techniques are also constantly updated with increasing demand. For some specific target cells, the workflow from droplet screening to single-cell sequencing is a preferred option, which also should reduce the impact of operation steps such as demulsification and cell recovery. We developed an all-in-droplet method integrating cell encapsulation, target sorting, droplet picoinjection, and single-cell transcriptome profiling on chips to achieve a labor-saving monitor of TCR-T cells. As a proof of concept, in this research, TCR-T cells were encapsulated, sorted, and performed single-cell transcriptome sequencing (scRNA-seq) by injecting reagents into droplet. It avoided the tedious operation of droplet breakage and re-encapsulation between droplet sorting and scRNA-seq. Moreover, convenient device operation will accelerate the progress of chip marketization. The strategy achieved an excellent recovery performance of single cell transcriptome with a median gene number over 4000 and a cross-contamination rate of 8.2 {+/-} 2%. Furthermore, this strategy allows us to develop a device with high integrability to monitor infused TCR-T cells, which will promote the development of adoptive T cell immunotherapy and their clinical application.

cell biology↗

bioRxiv2022

Combinatorial perturbation sequencing on single cells using microwell-based droplet random pairing

Combinatorial drug therapy reduces drug resistance and disease relapse, but informed drug combinations are lacking due to the high scale of possible combinations and the relatively simple phenotyping strategies. Here we report combinatorial perturbation sequencing (CP-seq) on single cells using microwell-base droplet random pairing. CP-seq uses oligonucleotides to barcode drugs, encapsulates drugs and cells in separate droplets, and pairs cell droplets with two drug droplets randomly on a microwell array chip to complete combinatorial drug treatment and barcode-tagging on cells. The subsequent single-cell RNA sequencing simultaneously detects the single-cell transcriptomes and drug barcodes to demultiplex the corresponding drug treatment. The microfluidic droplet operations had robust performance, with overall success rate among the microwells being up to 83%. We then progressively validated the CP-seq by performing single drug treatment and then combinatorial drug treatment. Leveraging the advantage of droplet microfluidics in massive multiplexing, the CP-seq can test thousands of drug combinations in a single experiment and represents a great technology for combinatorial perturbation screening with high throughput and comprehensive profiling.

bioengineering↗

bioRxiv2022

Efficient in vivo neuronal genome editing in the mouse brain using nanocapsules containing CRISPR-Cas9 ribonucleoproteins

Genome editing of somatic cells via clustered regularly interspaced short palindromic repeats (CRISPR) offers promise for new therapeutics to treat a variety of genetic disorders, including neurological diseases. However, the dense and complex parenchyma of the brain and the post-mitotic state of neurons make efficient genome editing challenging. In vivo delivery systems for CRISPR-Cas proteins and single guide RNA (sgRNA) include both viral vectors and non-viral strategies, each presenting different advantages and disadvantages for clinical application. We developed non-viral and biodegradable PEGylated nanocapsules (NCs) that deliver preassembled Cas9-sgRNA ribonucleoproteins (RNPs). Here, we show that the RNP NCs led to robust genome editing in neurons following intracerebral injection into the mouse striatum. Genome editing was predominantly observed in medium spiny neurons (>80%), with occasional editing in cholinergic, calretinin, and parvalbumin interneurons. Glial activation was minimal and was localized along the needle tract. Our results demonstrate that the RNP NCs are capable of safe and efficient neuronal genome editing in vivo. SIGNIFICANCE STATEMENTModifying the DNA of cells in the brain could present opportunities for new treatments of neurological diseases. In this report, we describe a nanocapsule system designed to deliver the elements needed to modify the DNA of brain cells, also known as genome editing. These nanocapsules are created by chemically encapsulating the genome editing components, such that the nanocapsules are stable when prepared and biodegradable to release their payload upon entering cells. When injected into the mouse brain, our research shows that the nanocapsules lead to safe and efficient editing of DNA in neurons.

neuroscience↗

bioRxiv2022

Specific Deletion of Axin1 Leads to Activation of β-Catenin/BMP Signaling Resulting in Fibular Hemimelia Phenotype in Mice

Axin1 and Axin2 are key regulators of canonical Wnt signaling pathway. The roles of Axin1 and Axin2 in skeletal development and in disease development have not been fully defined. Here, we reported that Axin1 and Axin2 are essential for lower limb development. Specific deletion of Axin1 in limb mesenchymal cells leads to fibular hemimelia (FH)-like phenotype, associated with tarsal coalition. Further studies demonstrated that FH disease is associated with additional defects resembling to the proximal femoral focal deficiency (PFFD) in Axin1/Axin2 double knockout (KO) mice. We then provided in vivo evidence showing that Axin1 controls limb development through both canonical {beta}-catenin and BMP signaling pathways. We demonstrated that inhibition of {beta}-catenin or BMP signaling could significantly reverse the FH phenotype in mice. Together, our findings revealed that integration of Wnt and BMP signaling by Axin1 is required for lower limb development. Defects in Axin1 and Axin2 signaling could lead to the development of FH disease.

developmental biology↗

bioRxiv2022

A super robust and efficient DNA storage architecture based on modulation encoding and decoding

Thanks to its high density and long durability, synthetic DNA has been widely considered as a promising solution to the data explosion problem. However, due to the large amount of random base insertion-deletion-substitution (IDSs) errors from sequencing, reliable data recovery remains a critical challenge, which hinders its large-scale application. Here, we propose a modulation-based DNA storage architecture. Experiments on simulation and real datasets demonstrate that it has two distinct advantages. First, modulation encoding provides a simple way to ensure the encoded DNA sequences comply with biological sequence constraints (i.e., GC balanced and no homopolymers); Second, modulation decoding is highly efficient and extremely robust for the detection of insertions and deletions, which can correct up to ~40% errors. These two advantages pave the way for future high-throughput and low-cost techniques, and will kickstart the actualization of a viable, large-scale system for DNA data storage.

synthetic biology↗

bioRxiv2022

Real-time feeding behavior monitoring by electrical penetration graph rapidly reveals host plant susceptibility to crapemyrtle bark scale (Hemiptera: Eriococcidae)

Host range confirmation of invasive hemipterans relies on the evaluation of plant susceptibility though greenhouse or field trials, which are inefficient and time-consuming. When the green industry faces the fast-spreading threat of invasive pests such as crapemyrtle bark scale (Acanthococcus lagerstroemiae), it is imperative to timely identify potential host plants and evaluate plant resistance/susceptibility to pest infestation. In this study, we developed an alternative technology to complement the conventional host confirmation methods. We used electrical penetration graph (EPG) based technology to monitor the A. lagerstroemiae stylet-tip position when it was feeding on different plant tissues in real-time. The frequency and relative amplitude of insect feeding waveforms (recorded by EPG) were extracted by an R programming-based software written to generate eleven feeding parameters for comparative analysis between plant species. The results demonstrated that the occurrences of phloem phase and xylem phase offered conclusive evidence for host plant evaluation. Furthermore, parameters including the percentage of insects capable of accessing phloem tissue, time duration spent on initiating phloem phase and ingesting phloem sap, provided insight into why host plant susceptibility differs among similar plant species. In summary, this study developed a novel real-time diagnostic tool for quick A. lagerstroemiae host confirmation, which laid the essential foundation for effective pest management. Simple SummaryCrapemyrtle bark scale (CMBS; Acanthococcus lagerstroemiae), an invasive polyphagous sap feeder in the United States, has spread across 16 U.S. states in less than two decades, posing potential risks to the Green Industry. Confirming the host range is crucial for effective pest management of invasive insects. However, host range confirmation relying on greenhouse or field trials is often inefficient and time-consuming. In this study, we used the electrical penetration graph (EPG) to monitor the stylet penetration of CMBS in plant tissue in real-time. An R programming-based application was developed to better characterize the insect feeding waveforms recorded by EPG. By analyzing EPG-based feeding parameters, we demonstrated that CMBS have difficulty accessing the phloem tissue (salivation and ingestion) of a resistant plant compared to a susceptible plant. Importantly, we hereby present CMBS typical feeding behaviors on susceptible and non-susceptible plants comparatively, which provides direct evidence for revealing unknown hosts rapidly.

plant biology↗

bioRxiv2022

Green Lacewing Chrysoperla rufilabris (Neuroptera: Chrysopidae) is a potential biological agent for controlling crapemyrtle bark scale (Hemiptera: Eriococcidae)

Crapemyrtle bark scale (CMBS; Acanthococcus lagerstroemiae), an invasive sap-sucking hemipteran, has spread across 16 U.S. states. Infestation of CMBS negatively impacts the flowering of crapemyrtles and reduces the aesthetic quality of ornamental plants. The widespread use of soil-applied neonicotinoid insecticides to repress the CMBS infestation could threaten important beneficial insects; therefore, using natural enemies to control CMBS is greatly needed. This study evaluated larval green lacewing (Chrysoperla rufilabris) as a biocontrol agent of CMBS. Predatory behavior of the larval C. rufilabris upon CMBS was documented under a stereomicroscope using infested crapemyrtle samples collected from different locations in College Station. Predation potential of C. rufilabris upon CMBS eggs and foraging performance using Y-maze assay were both investigated in laboratory conditions. Results confirmed that larval C. rufilabris preyed on CMBS nymphs, eggs, and adult females. The evaluation of predation potential results showed that the number of CMBS eggs consumed in 24 hours by 3rd instar C. rufilabris (176.4 {+/-}6.9) was significantly higher than by 2nd instar (151.5{+/-}6.6) and by 1st instar (11.8{+/-}1.3). The foraging performance results showed that larval C. rufilabris could target CMBS under dark, indicating that some cues associated with olfactory response were likely involved when preying on CMBS. This study is the first report that validated C. rufilabris as a natural predator of CMBS and its potential as a biological agent to control CMBS. Future investigation about the olfactory response of larval C. rufilabris to CMBS would benefit the development of environmental-friendly strategies to control CMBS spread.

ecology↗

bioRxiv2021

A connectivity signature for glioblastoma

Tumor cell extensions called tumor microtubes (TMs) in glioma resemble neurites during neurodevelopment and connect glioma cells to a network that has considerable relevance for tumor progression and therapy resistance. The determination of interconnectivity in individual tumors has been challenging and the impact of tumor cell connectivity on patient survival remained unresolved so far. Here, a connectivity signature from single-cell RNA-sequenced (scRNA-Seq) xenografted primary glioblastoma (GB) cells was established and clinically validated. Thirty-four of 40 connectivity genes were related to neurogenesis, neural tube development or glioma progression, including the TM-network-relevant GAP43 gene. Astrocytic-like and mesenchymal-like GB cells had the highest connectivity signature scores in scRNA-Seq data of patient-derived xenografts and patient samples. In 230 human GBs, high connectivity correlated with the mesenchymal expression subtype, TP53 wildtype, and with dismal patient survival. CHI3L1 was identified as a robust molecular marker of connectivity. Thus, the connectivity signature allows novel insights into brain tumor biology, provides a proof-of-principle that tumor cell connectivity is relevant for patients prognosis, and serves as a robust biomarker that can be used for future clinical trials. Statement of significanceIntegration of GB cells into functional networks drives tumor progression and resistance. Here, we established and validated a novel connectivity gene expression signature of single GB cells and whole tumors that can be easily applied to clinical and preclinical samples. It is shown that connectivity is determining prognosis combining molecular, functional and clinical insights into the disease.

cancer biology↗

bioRxiv2021

Constructing the hierarchy of predictive auditory sequences in the marmoset brain

Our brains constantly generate predictions of sensory input that are compared with actual inputs, propagate the prediction-errors through a hierarchy of brain regions, and subsequently update the internal predictions of the world. However, the essential feature of predictive coding, the notion of hierarchical depth and its neural mechanisms, remains largely unexplored. Here, we investigated the hierarchical depth of predictive auditory processing by combining functional magnetic resonance imaging (fMRI) and high-density whole-brain electrocorticography (ECoG) in marmoset monkeys during an auditory local-global paradigm in which the temporal regularities of the stimuli were designed at two hierarchical levels. The prediction-errors and prediction updates were examined as neural responses to auditory mismatches and omissions. Using fMRI, we identified a hierarchical gradient along the auditory pathway: midbrain and sensory regions represented local, short-time-scale predictive processing followed by associative auditory regions, whereas anterior temporal and prefrontal areas represented global, long-time-scale sequence processing. The complementary ECoG recordings confirmed the activations at cortical surface areas and further differentiated the signals of prediction-error and update, which were transmitted via putatively bottom-up {gamma} and top-down {beta} oscillations, respectively. Furthermore, omission responses caused by absence of input, reflecting solely the two levels of prediction signals that are unique to the hierarchical predictive coding framework, demonstrated the hierarchical predictions in the auditory, temporal, and prefrontal areas. Thus, our findings support the hierarchical predictive coding framework, and outline how neural circuits and spatiotemporal dynamics are used to represent and arrange a hierarchical structure of auditory sequences in the marmoset brain.

neuroscience↗

bioRxiv2021

Expanding Asgard members in the domain of Archaea shed new light on the origin of eukaryotes

The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. At present, only six phyla are described in the Asgard superphylum, which limits our understanding of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of the Asgard archaea. Here, we describe five previously unknown phylum-level Asgard archaeal lineages, tentatively named Tyr-, Sigyn-, Freyr-, Njord- and Balderarchaeota. Comprehensive phylogenomic analyses further supported the origin of eukaryotes within Archaea and a new Asgard lineage Njordarchaeota was supposed as the known closest branch with the eukaryotic nuclear host lineage. Metabolic reconstruction suggests that the Asgard archaea described here have potential to fix inorganic carbon via the Wood-Ljungdahl pathway and degrade organic matters except Njordarchaeota, which may possess a heterotrophic lifestyle with capability of peptides and amino acids utilization. Additionally, the Ack/Pta pathway for homoacetogenesis and de novo anaerobic cobalamin biosynthesis pathway were found in Balderarchaeota and Tyrarchaeota, respectively. This study largely expands the Asgard superphylum, provides additional evidences to support the 2-domain life tree and sheds new light on the evolution of eukaryotes.

evolutionary biology↗

bioRxiv2021

Expanded Asgard archaea shed new light on the origin of eukaryotes and support a 2-domain tree of life

The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. At present, only seven phyla are described in the Asgard superphylum, which limits our understanding of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of Asgard archaea. Here, we describe five novel phylum-level Asgard archaeal lineages, tentatively named Tyr-, Sigyn-, Freyr-, Hoder- and Balderarchaeota. Comprehensive phylogenomic analyses supported a new Asgard lineage Tyrarchaeota was identified as a deeper branching lineage cluster with the eukaryotic nuclear host lineage than Heimdallarchaeota that were previously considered as the closest archaeal relatives of eukaryotes. Metabolic reconstruction of Tyrarchaeota suggests a mixotrophic lifestyle of this archaea, capable of peptides and amino acids utilization while having the potential using the Wood-Ljungdahl pathway for carbon fixation and acetogenesis. This study largely expands the Asgard superphylum, provides additional evidences to support the 2-domain life tree thus sheds new light on the evolution and geochemical functions of the Asgard archaea.

evolutionary biology↗

bioRxiv2021

Plant pathogens convergently evolved to counteract redundant nodes of an NLR immune receptor network

In plants, NLR (nucleotide-binding domain and leucine-rich repeat-containing) proteins can form receptor networks to confer hypersensitive cell death and innate immunity. One class of NLRs, known as NRCs (NLR required for cell death), are central nodes in a complex network that protects against multiple pathogens and comprises up to half of the NLRome of solanaceous plants. Given the prevalence of this NLR network, we hypothesized that pathogens convergently evolved to secrete effectors that target NRC activities. To test this, we screened a library of 167 bacterial, oomycete, nematode and aphid effectors for their capacity to suppress the cell death response triggered by the NRC-dependent disease resistance proteins Prf and Rpi-blb2. Among five of the identified suppressors, one cyst nematode protein and one oomycete protein suppress the activity of autoimmune mutants of NRC2 and NRC3, but not NRC4, indicating that they specifically counteract a subset of NRC proteins independently of their sensor NLR partners. Whereas the cyst nematode effector SPRYSEC15 binds the nucleotide-binding domain of NRC2 and NRC3, the oomycete effector AVRcap1b suppresses the response of these NRCs via the membrane trafficking-associated protein NbTOL9a (Target of Myb 1-like protein 9a). We conclude that plant pathogens have evolved to counteract central nodes of the NRC immune receptor network through different mechanisms. Coevolution with pathogen effectors may have driven NRC diversification into functionally redundant nodes in a massively expanded NLR network.

plant biology↗

bioRxiv2020

DUBStepR: correlation-based feature selection for clustering single-cell RNA sequencing data

Feature selection (marker gene selection) is widely believed to improve clustering accuracy, and is thus a key component of single cell clustering pipelines. However, we found that the performance of existing feature selection methods was inconsistent across benchmark datasets, and occasionally even worse than without feature selection. Moreover, existing methods ignored information contained in gene-gene correlations. We therefore developed DUBStepR (Determining the Underlying Basis using Stepwise Regression), a feature selection algorithm that leverages gene-gene correlations with a novel measure of inhomogeneity in feature space, termed the Density Index (DI). Despite selecting a relatively small number of genes, DUBStepR substantially outperformed existing single-cell feature selection methods across diverse clustering benchmarks. In a published scRNA-seq dataset from sorted monocytes, DUBStepR sensitively detected a rare and previously invisible population of contaminating basophils. DUBStepR is scalable to over a million cells, and can be straightforwardly applied to other data types such as single-cell ATAC-seq. We propose DUBStepR as a general-purpose feature selection solution for accurately clustering single-cell data.

bioinformatics↗

bioRxiv2020

Imaging transmembrane dynamics of biomolecules at live cell plasma membranes using quenchers in extracellular environment

It is a big challenge to measure position changes of biomolecules in the direction normal to the plasma membranes of living cells. We developed a one donor-multiple quenchers F[o]rster resonance energy transfer method by using non-fluorescent quenchers in the extracellular environment. It senses subnanometer position changes of a fluorophore-labeled biomolecule in the plasma membrane. The method was validated by monitoring flip-flops of individual lipid molecules incorporated in plasma membranes. We studies membrane perforation by a host defense peptide from the extracellular side and found that the pore-forming peptide is dynamic, switching among different insertion depths. The method is especially useful in studying interactions of membrane proteins with the inner surfaces of plasma membranes. Our method will find wide applications in systematic analysis of fundamental cellular processes at plasma membranes.

biophysics↗

bioRxiv2020

Drug Screening with Zebrafish Visual Behavior Identifies Carvedilol as a Potential Treatment for Retinitis Pigmentosa

Retinitis Pigmentosa (RP) is an incurable inherited retinal degeneration affecting approximately 1 in 4,000 individuals globally. The goal of this work was to identify drugs that can help patients suffering from the disease. To accomplish this, we screened drugs on a zebrafish RP model. This model expresses a truncated human rhodopsin transgene (Tg(rho:Hsa.RH1_Q344X)) causing significant rod degeneration by 7 days post-fertilization (dpf). Consequently, the larvae displayed a deficit in visual motor response (VMR) under scotopic condition. The diminished VMR was leveraged to screen an ENZO SCREEN-WELL(R) REDOX library since oxidative stress is postulated to play a role in RP progression. Our screening identified a beta-blocker, carvedilol, that ameliorated the deficient VMR of the RP larvae and increased their rod number. Carvedilol can act directly on rods as it affected the adrenergic pathway in a rod-like human Y79 cell line. Since carvedilol is an FDA-approved drug, our findings suggest that carvedilol can potentially be repurposed to treat RP patients. Summary StatementThis paper presents the utilization of zebrafish visual behavior, a novel paradigm to screen and identify drugs to treat retinitis pigmentosa, an incurable retinal-degenerative disease.

neuroscience↗

bioRxiv2020

Biased Auditory Nerve Central Synaptopathy Exacerbates Age-related Hearing Loss

Sound information is transmitted from the cochlea to the brain by different subtypes of spiral ganglion neurons (SGN), which show varying degrees of vulnerbility under pathological conditions. It remains unclear how information from these SGNs reassemble among target neurons in the cochlear nucleus (CN) at the auditory nerve (AN) central synapses, and how different synapses change during hearing loss. Combining immunohistochemistry with electrophysiology, we investigated the giant endbulb of Held synapses and their postsynaptic bushy neurons in mice under normal hearing and age-related hearing loss (ARHL). We found that calretinin-expressing and non-calretinin-expressing endbulbs converge at continuously different ratios onto bushy neurons with varying physiological properties. Endbulbs degenerate during ARHL, and the degeneration is more severe in non-calretinin-expressing synapses, which correlates with a gradual decrease in neuronal subpopulation predominantly innervated by these inputs. Our findings suggest that biased AN central synaptopathy and shifted CN neuronal composition underlie reduced auditory input and altered central auditory processing during ARHL.

neuroscience↗

bioRxiv2020

TET1 dioxygenase is required for FOXA2-associated chromatin remodeling in pancreatic beta-cell differentiation

Existing knowledge of the role of epigenetic modifiers in pancreas development has exponentially increased. However, the function of TET dioxygenases in pancreatic endocrine specification remains obscure. We set out to tackle this issue using a human embryonic stem cell (hESC) differentiation system, in which TET1/TET2/TET3 triple knock-out cells display severe defects in pancreatic {beta}-cell specification. Integrative whole-genome analysis identifies unique cell-type-specific hypermethylated regions (hyper-DMRs) displaying reduced chromatin activity and remarkable enrichment of FOXA2, a pioneer transcription factor essential for pancreatic endoderm specification. Intriguingly, TET depletion leads to significant changes in FOXA2 binding at pancreatic progenitor stage, in which gene loci with decreased FOXA2 binding features low levels of active chromatin modifications and enriches for bHLH motifs. Transduction of full-length TET1 but not the TET1-catalytic-domain in TET-deficient cells effectively rescues {beta}-cell differentiation accompanied by restoring PAX4 hypomethylation. Taking these findings together with the defective generation of functional {beta}-cells upon TET1-inactivation, our study unveils an essential role of TET1-dependent demethylation in establishing {beta}-cell identity. Moreover, we discover a physical interaction between TET1 and FOXA2 in endodermal lineage intermediates, which provides a new mechanistic clue regarding the complex crosstalk between TET dioxygenases and pioneer transcription factors in epigenetic regulation during pancreas specification.

developmental biology↗