Biology subjects

Zhao, X.

Publications and source records attributed to Zhao, X..

At least 235 records · Page 13Linked to original sources

bioRxiv2024

Causal role of frontocentral beta oscillation in comprehending linguistic communicative functions

Linguistic communication is often considered as an action serving the function of conveying the speakers goal to the addressee. Although neuroimaging studies have suggested a role of the motor system in comprehending communicative functions, the underlying mechanism is yet to be specified. Here, by 2 EEG experiments and a tACS experiment, we demonstrate that the frontocentral beta oscillation, which represents action states, plays a crucial part in linguistic communication understanding. Participants read scripts involving 2 interlocutors and rated the interlocutors attitudes. Each script included a critical sentence said by the speaker expressing a context-dependent function of either promise, request, or reply to the addressees query. These functions were behaviorally discriminated, with higher addressees will rating for the promise than for the reply and higher speakers will rating for the request than for the reply. EEG multivariate analyses showed that different communicative functions were represented by different patterns of frontocentral beta activity but not by patterns of alpha activity. Further tACS results showed that, relative to alpha tACS and sham stimulation, beta tACS improved the predictability of communicative functions of request or reply, as measured by the speakers will rating. These results convergently suggest a causal role of the frontocentral beta activities in comprehending linguistic communications. HighlightsO_LIThe frontocentral beta activity patterns discriminate communicative functions. C_LIO_LIThe frontocentral beta activity plays a causal role in comprehending the functions. C_LIO_LIThe comprehension could be subserved by the mental simulation of the communication. C_LIO_LIOur findings connect the idea of embedded semantics with the speech act theory. C_LI

neuroscience↗

bioRxiv2024

Biologically informed machine learning modeling of immune cells to reveal physiological and pathological aging process

The immune system undergoes progressive functional remodeling from neonatal stages to old age. Therefore, understanding how aging shapes immune cell function is vital for precise treatment of patients at different life stages. Here, we constructed the first transcriptomic atlas of immune cells encompassing human lifespan, ranging from newborns to supercentenarians, and comprehensively examined gene expression signatures involving cell signaling, metabolism, differentiation, and functions in all cell types to investigate immune aging changes. By comparing immune cell composition among different age groups, HLA highly expressing NK cells and CD83 positive B cells were identified with high percentages exclusively in the teenager (Tg) group, whereas CD4_CTL precursors were exclusively enriched in the supercentenarian (Sc) group. Notably, we found that the biological age (BA) of pediatric COVID-19 patients with multisystem inflammatory syndrome accelerated aging according to their chronological age (CA). Besides, we proved that inflammatory shift-myeloid abundance and signature correlate with the progression of complications in Kawasaki disease (KD). Finally, based on those age-related immune cell compositions, we developed a novel BA prediction model, PHARE (https://xiazlab.org/phare/), which applies to both scRNA-seq and bulk RNA-seq data. Overall, our study revealed changes in immune cell proportions and function associated with aging, both in health and disease, and provided a novel tool for successfully capturing features that accelerate or delay aging.

immunology↗

bioRxiv2024

Cryo-electron tomographic investigation of native hippocampal glutamatergic synapses

Chemical synapses are the major sites of communication between neurons in the nervous system and mediate either excitatory or inhibitory signaling [1]. At excitatory synapses, glutamate is the primary neurotransmitter and upon release from presynaptic vesicles, is detected by postsynaptic glutamate receptors, which include ionotropic AMPA and NMDA receptors [2, 3]. Here we have developed methods to identify glutamatergic synapses in brain tissue slices, label AMPA receptors with small gold nanoparticles (AuNPs), and prepare lamella for cryo-electron tomography studies. The targeted imaging of glutamatergic synapses in the lamella is facilitated by fluorescent pre- and postsynaptic signatures, and the subsequent tomograms allow for identification of key features of chemical synapses, including synaptic vesicles, the synaptic cleft and AuNP-labeled AMPA receptors. These methods pave the way for imaging brain regions at high resolution, using unstained, unfixed samples preserved under near-native conditions.

biochemistry↗

bioRxiv2024

GABAAR-PPT1 palmitoylation homeostasis controls synaptic transmission and circuitry oscillation in CLN1 disease

CLN1 disease, also called infantile neuronal ceroid lipofuscinosis, is a fatal neurodegenerative disease caused by mutations in the CLN1 gene encoding palmitoyl protein thioesterase 1 (PPT1). To identify depalmitoylation substrate of PPT1 is crucial to understand CLN1 disease. In this study, we found that PPT1 depalmitoylates GABAAR 1 subunit at Cystein-260, while binding to Cystein-165 and -179. Mutations of PPT1 or its GABAAR 1 subunit binding site result in enhanced inhibitory synaptic transmission, strengthened and oscillation but disrupted phase coupling in CA1 region and impaired learning and memory in 1- to 2-months-old PPT1-deficient and Gabra1em1 mice. Our study highlights the critical role of PPT1 in maintaining GABAAR palmitoylation homeostasis and reveals a previously unknown molecular pathway in PPT1 induced diseases.

neuroscience↗

bioRxiv2024

Srs2 binding to PCNA and its sumoylation contribute to RPA antagonism during the DNA damage response

Activation of the DNA damage checkpoint upon genotoxin treatment induces a multitude of cellular changes to cope with genome stress. After prolonged genotoxin treatment, the checkpoint can be downregulated to allow cell cycle and growth resumption. In yeast, downregulation of the DNA damage checkpoint requires the Srs2 DNA helicase, which removes the ssDNA binding complex RPA and the associated Mec1 checkpoint kinase from DNA, thus dampening Mec1-mediated checkpoint. However, it is unclear whether the anti-checkpoint role of Srs2 is temporally and spatially regulated to allow timely checkpoint termination while preventing superfluous RPA removal. Here we address this question by examining regulatory elements of Srs2, such as its phosphorylation, sumoylation, and protein-interaction sites. Our genetic analyses and checkpoint level assessment suggest that the RPA countering role of Srs2 is promoted by Srs2 binding to PCNA, which recruits Srs2 to a subset of ssDNA containing regions. RPA antagonism is further fostered by Srs2 sumoylation, which we found depending on the Srs2-PCNA interaction and Mec1, and peaking after Mec1 activity reaches maximal levels. These data suggest that Srs2 recruitment to PCNA proximal ssDNA-RPA filaments followed by its sumoylation can promote checkpoint recovery, whereas Srs2 action is minimized at regions with no proximal PCNA to permit RPA-mediated ssDNA protection.

molecular biology↗

bioRxiv2024

Granzyme B-based CAR T cells block metastasis by eliminating circulating tumor cells

Chimeric antigen receptor (CAR) T cells have limited efficacy against solid tumors due to the hostile microenvironment. Circulating tumor cells (CTCs) are essential to metastasis, which is the cause of most of cancer-related death. Here, we generated GrB-CAR T cells targeting membrane-bound HSP70 (mHSP70), a highly tumor-specific antigen detected in numerous cancers. GrB-CAR T cells exhibited potent cytotoxicity against a broad spectrum of cancer cell lines and stem-like cancer cells in vitro and effectively inhibited xenograft tumor growth in vivo. Importantly, GrB-CAR T cells markedly decreased the number of CTCs and, therefore, hindered cancer metastasis in spontaneous metastasis models with uncontrollable primary tumor growth, a scenario commonly encountered in clinical trials of CAR T therapies for solid tumors. Furthermore, despite the 100% homology between human and macaque HSP70 protein, the autotransplantation of macaque T cells expressing human GrB-CAR did not cause any obvious toxic effects. These results not only demonstrate GrB-CAR T cells as a safe and effective tactic with broad-spectrum anticancer activity, but also offer strong experimental evidence and proof-of-concept validation for CAR T cell-mediated metastasis inhibition by targeting CTCs.

immunology↗

bioRxiv2024

BinDash 2.0: New MinHash Scheme Allows Ultra-fast and Accurate Genome Search and Comparisons

MotivationComparing large number of genomes in term of their genomic distance is becoming more and more challenging because there is an increasing number of microbial genomes deposited in public databases. Nowadays, we may need to estimate pairwise distances between millions or even billions of genomes. Few softwares can perform such comparisons efficiently. ResultsHere we update the multi-threaded software BinDash by implementing several new MinHash algorithms and computational optimization (e.g. Simple Instruction Multiple Data, SIMD) for ultra-fast and accurate genome search and comparisons at trillion scale. That is, we implemented b-bit one-permutation rolling MinHash with optimal/faster densification with SIMD. Now with BinDash 2, we can perform 0.1 trillion (or [~]10^11) pairs of genome comparisons in about 1.8 hours on a descent computer cluster or several hours on personal laptops, a [~]50% or more improvement over original version. The ANI (average nucleotide identity) estimated by BinDash is well correlated with other accurate but much slower ANI estimators such as FastANI or alignment-based ANI. In line with the findings from comparing 90K genomes ([~]10^9 comparisons) via FastANI, the 85% [~] 95% ANI gap is consistent in our study of [~]10^11 prokaryotic genome comparisons via BinDash2, which indicates fundamental ecological and evolutionary forces keeping species-like unit (e.g., > 95% ANI) together. Availability and implementationBinDash is released under the Apache 2.0 license at: https://github.com/zhaoxiaofei/bindash Contactkostas.konstantinidis@gatech.edu Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2024

The Compensatory Mechanism of the Prefrontal Cortex in Preserving Speech-in-Noise Comprehension Among Older Adults

The capacity of comprehending others amidst noise is essential for human communication. However, it presents significant challenges for the elderly who often face progressive declines in the peripheral auditory system and the whole brain. While previous studies have suggested the existence of neural reserve and neural compensation as potential mechanisms for preserving cognitive abilities in aging, the specific mechanisms supporting speech-in-noise comprehension among the elderly remain unclear. To address this question, the present study employs an inter-brain neuroscience approach by analyzing the neural coupling between brain activities of older adults and those of speakers under noisy conditions. Results showed that the neural coupling encompassed more extensive brain regions of older listeners compared to young listeners, with a notable engagement of the prefrontal cortex. Moreover, the neural coupling from prefrontal cortex was coordinated with that from classical language-related regions. More importantly, as background noise increases, the older listeners speech comprehension performance was more closely associated with the neural coupling from prefrontal cortex. Taken together, this study reveals the compensatory recruitment of neurocognitive resources, particularly within the prefrontal cortex, to facilitate speech processing in the aging brain, and further highlights the critical role of prefrontal cortex in maintaining the elderlys ability to comprehend others in noisy environments. It supports the neural compensation hypothesis, extending the knowledge about the neural basis that underlies cognitive preservation in the aging population.

neuroscience↗

bioRxiv2024

Insights into Cellular Evolution: Temporal Deep Learning Models and Analysis for Cell Image Classification

I.AO_SCPLOWBSTRACTC_SCPLOWUnderstanding the temporal evolution of cells poses a significant challenge in developmental biology. This study embarks on a comparative analysis of various machine-learning techniques to classify sequences of cell colony images, thereby aiming to capture dynamic transitions of cellular states. Utilizing transfer learning with advanced classification networks, we achieved high accuracy in single-timestamp image categorization. We introduce temporal models--LSTM, R-Transformer, and ViViT--to explore the effectiveness of integrating temporal features in classification, comparing their performance against non-temporal models. This research benchmarks various machine learning approaches in understanding cellular dynamics, setting a foundation for future studies to enhance our understanding of cellular developments with computational methods, contributing significantly to biological research advancements.

cell biology↗

bioRxiv2024

Impaired central pattern generators due to abnormal EPHA4 signaling leads to idiopathic scoliosis

Idiopathic scoliosis (IS) is the most common form of spinal deformity with unclear pathogenesis. In this study, we firstly reanalyzed the loci associated with IS, drawing upon previous studies. Subsequently, we mapped these loci to candidate genes using either location-based or function-based strategies. To further substantiate our findings, we verified the enrichment of variants within these candidate genes across several large IS cohorts encompassing Chinese, East Asian, and European populations. Consequently, we identified variants in the EPHA4 gene as compelling candidates for IS. To confirm their pathogenicity, we generated zebrafish mutants of epha4a. Remarkably, the zebrafish epha4a mutants exhibited pronounced scoliosis during later stages of development, effectively recapitulating the IS phenotype. We observed that the epha4a mutants displayed defects in left-right coordination during locomotion, which arose from disorganized neural activation in these mutants. Our subsequent experiments indicated that the disruption of the central pattern generator (CPG) network, characterized by abnormal axon guidance of spinal cord interneurons, contributed to the disorganization observed in the mutants. Moreover, when knocked down efnb3b, the ligand for Epha4a, we observed similar CPG defects and disrupted left-right locomotion. These findings strongly suggested that ephrin B3-Epha4 signaling is vital for the proper functioning of CPGs, and defects in this pathway could lead to scoliosis in zebrafish. Furthermore, we identified two cases of IS in NGEF, a downstream molecule in the EPHA4 pathway. Collectively, our data provide compelling evidence that neural patterning impairments and disruptions in CPGs may underlie the pathogenesis of IS.

genetics↗

bioRxiv2024

Role of Hepatocyte RIPK1 in Maintaining Liver Homeostasis during Metabolic Challenges

As a central hub for metabolism, the liver exhibits strong adaptability to maintain homeostasis in response to food fluctuations throughout evolution. However, the mechanisms governing this resilience remain incompletely understood. In this study, we identified Receptor interacting protein kinase 1 (RIPK1) in hepatocytes as a critical regulator in preserving hepatic homeostasis during metabolic challenges, such as short-term fasting or high-fat dieting. Our results demonstrated that hepatocyte-specific deficiency of RIPK1 sensitized the liver to short-term fasting-induced liver injury and hepatocyte apoptosis in both male and female mice. Despite being a common physiological stressor that typically does not induce liver inflammation, short-term fasting triggered hepatic inflammation and compensatory proliferation in hepatocyte-specific RIPK1-deficient (Ripk1{Delta}hep) mice. Transcriptomic analysis revealed that short-term fasting oriented the hepatic microenvironment into an inflammatory state in Ripk1{Delta}hep mice, with upregulated expression of inflammation and immune cell recruitment-associated genes. Single-cell RNA sequencing further confirmed the altered cellular composition in the liver of Ripk1{Delta}hep mice during fasting, highlighting the increased recruitment of macrophages to the liver. Mechanically, our results indicated that ER stress was involved in fasting-induced liver injury in Ripk1{Delta}hep mice. Overall, our findings revealed the role of RIPK1 in maintaining liver homeostasis during metabolic fluctuations and shed light on the intricate interplay between cell death, inflammation, and metabolism.

immunology↗

bioRxiv2024

HER2 Prognostic Significance and Therapeutic Implications in Gastric Cardia Adenocarcinoma: Insights from Multi-Omics Profiling

Therapeutic targets for Gastric Cardia Adenocarcinoma (GCA), particularly for HER2- negative patients, are lacking. Here, we conducted multi-omics profiling on 128 GCA patients using mass spectrometry, whole-exome sequencing, RNA-Seq, and metabolomics. We found HER2 to be a favorable prognostic marker for GCA. Employing molecular counting, we categorized patients into HER2-high, -low, and -negative groups. We uncovered an enrichment of DNA repair features in the HER2-high group, while HER2-low and -negative groups exhibited strong inflammation. We found that tumor mutation burden may not be the distinguishing factor among these three groups. We revealed that the HER2-negative and -low groups have a tumor-suppressive immune microenvironment, and HER2 expression is associated with fatty acid metabolic profiles and inflammation in the blood of patients. Our study revealed anti-inflammatory and immune checkpoint inhibition, targeting PD-L2 and the CD47/SIRPA pair, as therapeutic strategies for HER2-negative GCA patients. These findings highlight promising avenues for personalized treatment for GCA.

cancer biology↗

bioRxiv2024

Architecture and flexibility of native kinetochores revealed by structural studies utilizing a thermophilic yeast

Eukaryotic chromosome segregation requires kinetochores, multi-megadalton protein machines that assemble on the centromeres of chromosomes and mediate attachments to dynamic spindle microtubules. Kinetochores are built from numerous complexes, and understanding how they are arranged is key to understanding how kinetochores perform their multiple functions. However, an integrated understanding of kinetochore architecture has not yet been established. To address this, we purified functional, native kinetochores from Kluyveromyces marxianus and examined them by electron microscopy, cryo-electron tomography and atomic force microscopy. The kinetochores are extremely large, flexible assemblies that exhibit features consistent with prior models. We assigned kinetochore polarity by visualizing their interactions with microtubules and locating the microtubule binder Ndc80c. This work shows that isolated kinetochores are more dynamic and complex than what might be anticipated based on the known structures of recombinant subassemblies, and provides the foundation to study the global architecture and functions of kinetochores at a structural level.

biophysics↗

bioRxiv2024

High-accuracy crRNA array assembly strategy for multiplex CRISPR

Simultaneous targeting of multiple loci with CRISPR system, a tool known as multiplex CRISPR, offers us more feasibility to manipulate and elucidate the intricate and redundant endogenous networks underlying complex cellular functions. Owing to the versatility of the continuously emerging Cas nucleases and the utilization of CRISPR arrays, multiplex CRISPR has been implemented by numerous in vitro and in vivo studies. However, a streamlined practical strategy for CRISPR array assembly with both convenience and accuracy is still lacking. Here, we present a novel high-accuracy, cost- and time-saving strategy for CRISPR array assembly. Using this strategy, we efficiently accomplished the assembly of up to twelve crRNAs (for AsCas12a) or fifteen crRNAs (for RfxCas13d) in a single reaction. Moreover, we reveal that CRISPR arrays driven by Pol II promoters exhibit a distinct targeting pattern compared to Pol III promoters, which could be exploited for specific distributions of CRISPR intensity. For long CRISPR arrays, we designed a better approach than simply selecting one from U6 or EF1a. Collectively, our study provides a flexible and powerful tool for the convenient implementation of multiplex CRISPR across DNA to RNA, facilitating the dissection of sophisticated cellular networks and the future realization of multi-target gene therapy.

synthetic biology↗

bioRxiv2024

SUMO Promotes DNA Repair Protein Collaboration to Support Alterative Telomere Lengthening in the Absence of PML

Alternative lengthening of telomeres (ALT) pathway maintains telomeres in a significant fraction of cancers associated with poor clinical outcomes. A better understanding of ALT mechanisms can provide a basis for developing new treatment strategies for ALT cancers. SUMO modification of telomere proteins plays a critical role in the formation of ALT telomere-associated PML bodies (APBs), where telomeres are clustered and DNA repair proteins are enriched to promote homology-directed telomere DNA synthesis in ALT. However, whether and how SUMO contributes to ALT beyond APB formation remains elusive. Here, we report that SUMO promotes collaboration among DNA repair proteins to achieve APB-independent telomere maintenance. By using ALT cancer cells with PML protein knocked out and thus devoid of APBs, we show that sumoylation is required for manifesting ALT features, including telomere clustering and telomeric DNA synthesis, independent of PML and APBs. Further, small molecule-induced telomere targeting of SUMO produces signatures of phase separation and ALT features in PML null cells in a manner depending on both sumoylation and SUMO interaction with SUMO interaction motifs (SIMs). Mechanistically, SUMO-induced effects are linked to the enrichment of DNA repair proteins, including Rad52, Rad51AP1, and BLM, to the SUMO-containing telomere foci. Finally, we find that Rad52 can undergo phase separation, enrich SUMO on telomeres, and promote telomere DNA synthesis in collaboration with the BLM helicase in a SUMO-dependent manner. Collectively, our findings suggest that, in addition to forming APBs, SUMO also promotes collaboration among DNA repair proteins to support telomere maintenance in ALT cells. Given the promising effects of sumoylation inhibitors in cancer treatment, our findings suggest their potential use in perturbing telomere maintenance in ALT cancer cells.

cell biology↗

bioRxiv2024

Schlafen-11 and -9 are innate immune sensors for intracellular single-stranded DNA

Nucleic acids are major structures detected by the innate immune system. Although intracellular single-stranded DNA (ssDNA) is accumulated during pathogen infection or pathogenesis, it remains unclear whether and how intracellular ssDNA stimulates the immune system. We report that intracellular ssDNA triggers cytokine expression and cell death in a CGT motif-dependent manner. Through a genome-wide CRISPRLCas9 screen, we identified Schlafen-11 (SLFN11), which is essential for the response to endogenous and pathogen ssDNA. SLFN11 directly binds ssDNA containing CGT motifs and translocates to the cytoplasm upon ssDNA recognition. The mice deficient in SLFN9, the homologue of SLFN11, were resistant to CGT ssDNA-induced inflammation, acute hepatitis and septic shock. This study establishes CGT ssDNA and SLFN11/9 as a novel type of immunostimulatory nucleic acids and pattern recognition receptors, respectively. One-sentence summariessingle-stranded DNA inside cells can awaken Schlafens with a CGT motif to trigger cytokine expression and lytic cell death.

immunology↗

bioRxiv2024

Genetic evolution analysis of hemagglutinin and neuraminidase genes of H9N2 avian influenza virus in external environment of some areas of Yunnan Province, China from 2020 to 2023

ObjectiveTo understand the molecular characteristics and genetic variation of hemagglutinin (HA) and neuraminidase (NA) genes of H9N2 subtype avian influenza virus (AIV) in the external environment of Yunnan Province, and to provide evidence for the prevention and control of H9N2 subtype AIV in this area. ResultsThe HA and NA genes of 20 isolates belonged to Y280-like sub-branch. The nucleotide and amino acid homology of HA gene were 88.46%-99.81% and 89.08% -99.61%, respectively. The nucleotide and amino acid homology of NA gene were 88.85%-100% and 90.09%-100%, respectively. The HA protein cleavage site of 20 isolates was PSRSSRGLF, which was consistent with the molecular characteristics of low pathogenic avian influenza virus. The 226 th and 228 th positions of the receptor binding site are all L and G, which have the ability to bind to the mammalian sialic acid -2,6 sialic acid receptor; HA protein had 7-8 glycosylation sites, and the main variation was the deletion of one site at 218 and the addition of one glycosylation site at 313 and 491. The main antigenic sites were G90E, S/T145D, D/N153G, A/S/F168N/E, T200R, N/D201G/T mutations. The NA protein neck of 20 isolates lacked 3 amino acids (TEI), which had the molecular characteristics of highly pathogenic avian influenza. NA protein had 6-8 glycosylation sites. The main variation was that two isolates increased a new glycosylation site NPTQ at the 2nd position, and one isolate increased a new glycosylation site NTTI at the 67th position. All isolates lost one site at the 402nd position, and some isolates lost at the 83rd and 365th positions. The amino acids at the active site and key site of NA protease were not mutated, and the isolates did not produce resistance to neuraminidase inhibitors. ConclusionThe HA and NA genes of H9N2 subtype avian influenza virus in Yunnan Province have evolved continuously, but they still belong to the Y280 branch of the Eurasian lineage. Mutations in key sites may cause increased infectivity and transmission. The monitoring of H9N2 subtype avian influenza virus should be strengthened to prevent it from breaking the interspecies barrier and spreading to humans and lower mammals, so as to prevent the outbreak of H9N2 subtype avian influenza.

molecular biology↗

bioRxiv2024

Biallelic pathogenic variants in DNAH3 cause male infertility in humans and mice

Axonemal protein complexes, including the outer and inner dynein arms (ODA/IDA), are highly ordered structures of the sperm flagella that drive sperm motility. Deficiencies in several axonemal proteins have been associated with male infertility, which is characterized by asthenozoospermia or asthenoteratozoospermia. Dynein axonemal heavy chain 3 (DNAH3) resides in the IDA and is highly expressed in the testis. However, the relationship between DNAH3 and male infertility is still unclear. Herein, we identified biallelic variants of DNAH3 in four unrelated Han Chinese infertile men with asthenoteratozoospermia through whole-exome sequencing (WES). These variants contributed to deficient DNAH3 expression in the patients sperm flagella. Importantly, the patients represented the anomalous sperm flagellar morphology, and the flagellar ultrastructure was severely disrupted. Intriguingly, Dnah3 knockout (KO) male mice were also infertile, especially showing the severe reduction in sperm movement with the abnormal IDA and mitochondrion structure. Mechanically, nonfunctional DNAH3 expression resulted in decreased expression of IDA-associated proteins in the spermatozoa flagella of patients and KO mice, including DNAH1, DNAH6, and DNALI1, the deletion of which has been involved in disruption of sperm motility. Moreover, the infertility of patients with DNAH3 variants and Dnah3 KO mice could be rescued by intracytoplasmic sperm injection (ICSI) treatment. Our findings indicated that DNAH3 is a novel pathogenic gene for asthenoteratozoospermia and may further contribute to the diagnosis, genetic counseling, and prognosis of male infertility.

genetics↗