Biology subjects

Xia, T.

Publications and source records attributed to Xia, T..

At least 55 records · Page 3Linked to original sources

bioRxiv2023

Stereopy: modeling comparative and spatiotemporal cellular heterogeneity via multi-sample spatial transcriptomics

Tracing cellular dynamic changes across conditions, time, and space is crucial for understanding the molecular mechanisms underlying complex biological systems. However, integrating multi-sample data in a unified and flexible way to explore cellular heterogeneity remains a major challenge. Here, we present Stereopy, a flexible and versatile framework for modeling and dissecting comparative and spatiotemporal patterns in multi-sample spatial transcriptomics with interactive data visualization. To optimize this flexible framework, we have developed three key components: a multi-sample tailored data container, a scope controller, and an analysis transformer. Furthermore, Stereopy showcases three transformative applications supported by pivotal algorithms. Firstly, the multi-sample cell community detection (CCD) algorithm introduces an innovative capability to detect specific cell communities and identify genes responsible for pathological changes in comparable datasets. Secondly, the spatially resolved temporal gene pattern inference (TGPI) algorithm represents a notable advancement in detecting important spatiotemporal gene patterns while concurrently considering spatial and temporal features, which enhances the identification of important genes, domains and regulatory factors closely associated with temporal datasets. Finally, the 3D niche-based regulation inference tool, named NicheReg3D, reconstructs the 3D cell niches to enable the inference of cell-gene interaction network within the spatial texture, thus bridging intercellular communications and intracellular regulations to unravel the intricate regulatory mechanisms that govern cellular behavior. Overall, Stereopy serves as both a bioinformatics toolbox and an extensible framework that provides researchers with enhanced data interpretation abilities and new perspectives for mining multi-sample spatial transcriptomics data.

bioinformatics↗

bioRxiv2023

Sustained store-operated calcium entry utilizes activated chromatin state leads to instability in iTregs

Thymus-originated tTregs and in vitro induced iTregs are subsets of regulatory T cells. While they share the capacity of immune suppression, their stabilities are different, with iTregs losing their phenotype upon stimulation or under inflammatory milieu. Epigenetic differences, particularly methylation state of Foxp3 CNS2 region, provide an explanation for this shift. Whether additional regulations, including cellular signaling, could directly lead phenotypical instability requires further analysis. Here we show that upon TCR triggering, store-operated calcium entry (SOCE) and NFAT nuclear translocation are blunted in tTregs, yet fully operational in iTregs, similar to Tconvs. On the other hand, tTregs show minimal changes in their chromatin accessibility upon activation, in contrast to iTregs that demonstrate an activated chromatin state with highly accessible T cell activation and inflammation related genes. Assisted by several cofactors, NFAT driven by strong SOCE signaling in iTregs preferentially binds to primed opened T helper (TH) genes, resulting in their activation normally observed only in Tconv activation, ultimately leads to instability. Conversely, suppression of SOCE in iTregs can partially rescue their phenotype. Thus our study adds two new layer, cellular signaling and chromatin accessibility, of understanding in Treg stability, and may provide a path for better clinical applications of Treg cell therapy.

immunology↗

bioRxiv2023

Item-specific memory reactivation supports overnight memory consolidation

Memory consolidation stabilizes newly acquired information. Understanding how individual memories are reactivated during sleep is essential in theorizing memory consolidation. Via unobtrusively re-playing auditory memory cues to sleeping human participants, we identified the reactivation of individual memories during slow-wave sleep (SWS). Using representational similarity analysis (RSA) on cue-elicited electroencephalogram (EEG), we found functionally segregated item-specific representations: the early post-cue EEG activity (0-2 seconds) contained comparable representations for memory cues and for non-memory control cues, thus reflecting sensory processing. Critically, the later EEG activity (2.5-3 s) showed greater item-specific representations for post-sleep remembered items than for forgotten and control cues, demonstrating the reactivation and consolidation of individual memories. Moreover, spindles preferentially supported item-specific memory reactivation for items that were not tested before sleep. These findings delineated how cue-triggered item-specific memory reactivation, subserved by spindles during SWS, contributed to memory consolidation. These results will benefit future research aiming to perturb specific memory episodes during sleep.

neuroscience↗

bioRxiv2022

Spateo: multidimensional spatiotemporal modeling of single-cell spatial transcriptomics

Cells do not live in a vacuum, but in a milieu defined by cell-cell communication that can be measured via emerging high-resolution spatial transcriptomics approaches. However, analytical tools that fully leverage such data for kinetic modeling remain lacking. Here we present Spateo (aristoteleo/spateo-release), a general framework for quantitative spatiotemporal modeling of single-cell resolution spatial transcriptomics. Spateo delivers novel methods for digitizing spatial layers/columns to identify spatially-polar genes, and develops a comprehensive framework of cell-cell interaction to reveal spatial effects of niche factors and cell type-specific ligand-receptor interactions. Furthermore, Spateo reconstructs 3D models of whole embryos, and performs 3D morphometric analyses. Lastly, Spateo introduces the concept of "morphometric vector field" of cell migrations, and integrates spatial differential geometry to unveil regulatory programs underlying various organogenesis patterns of Drosophila. Thus, Spateo enables the study of the ecology of organs at a molecular level in 3D space, beyond isolated single cells.

systems biology↗

bioRxiv2022

Reactivating Positive Personality Traits During Sleep Impacts Self-Evaluative Memories

Positive self-view is evident by a bias in favor of positive self-referential processing, as individuals tend to endorse positive characteristics over negative ones when making self-judgments. While research suggests that a positivity bias can contribute to psychological well-being, it remains unclear how to enhance positive self-referential processing. Here, we reported an integrated training procedure that aimed at enhancing individuals positive self-referential processing. Specifically, participants engaged in a cue-approach training task (CAT) during wakefulness where they gave speeded motor responses to positive personality traits. In a subsequent nap, we unobtrusively re-played half of the trained positive traits during participants slow-wave sleep to reactivate memories associated with these positive traits (targeted memory reactivation, TMR). Upon awakening, we found that CAT+TMR enhanced participants positive self-referential processing, as evidenced by faster endorsement of positive traits. Further analysis revealed that this enhancement was associated with specific brainwave patterns during sleep: delta (1-4 Hz) traveling waves moving from posterior to anterior brain regions. These findings demonstrate the potential benefits of integrated wakeful cue-approach training and sleep-based memory reactivation in strengthening positive self-referential processing.

neuroscience↗

bioRxiv2022

Detection of adaptation to light environment in myopia-associated loci: Diversity of the myopia genetic background

The time spent outdoors and exposure to bright sunlight have been reported to play important roles in preventing myopia progression. Myopia prevalence is generally low in Europe, and we hypothesized that local adaptation of ancestors in insufficient sunlight regions might underlie this low prevalence in Europeans. To verify this conjecture and understand how ancestry adaptation influenced on the diversity of myopia genetic background, polygenic risk scores (PRS) was calculated and revealed that the genetic risk of myopia increased as latitude decreased in the 1000 genome projects (1KGP) EUR, and we further determined selection signatures near the rhodopsin (RHO) coding region in 1KGP Finnish. The derived allele frequencies of identified loci correlated with sunshine duration worldwide, and the allele age was estimated to be [~]20,000 years, coincidently after the divergence of Europeans and East Asians. TSPAN10 (rs9747347) is significantly associated with both myopia and pigmentation in Europeans, and we found selection favored the myopia risk allele in EUR. Haplotype comparison highlighted the divergence between EAS and EUR in RHO and pigmentation-associated loci, and the frequency diversity in Admixed American (AMR) of these loci was found to originate from recent admixture and local adaptation. We concluded that local adaptation played a role in myopia prevalence deviation, and selective pressure in the myopia-associated loci may originate from adaptation to sunlight environments rather than myopia itself. These findings reveal traces of evolution history of myopias genetic background, providing a new aspect of understanding the patterns and diversity of myopia prevalence. Author SummaryThe explanation for the distinct bias of myopia prevalence among ethnicities remains controversial, we took an evolutionary approach to understanding the history and diversity of the genetic background of myopia. We detected selection signatures of myopia-associated loci near the rhodopsin gene (RHO) in the 1000 Genome Project Europeans. Ambient light exposure is crucial for myopia; RHO is mainly expressed in rod cells and is extremely sensitive to light, indicating that local adaptation might contribute to myopia prevalence bias. Parallel geographical disposition of allele frequencies of myopia-associated loci in RHO and pigmentation-associated markers was observed, implying that selective pressure in myopia-associated loci may originate from adaptation events involved in sunlight exposure rather than myopia itself.

genetics↗

bioRxiv2022

Updating memories of unwanted emotions during human sleep

Post-learning sleep contributes to memory consolidation. Yet, it remains contentious whether sleep affords opportunities to modify or update emotional memories, such as those people would prefer to forget. Here we attempted to update memories during sleep using spoken positive emotional words paired with cues to recent memories for aversive events. Affect updating using positive words during human non-rapid-eye-movement (NREM) sleep, compared with using neutral words instead, reduced negative affect judgments in post-sleep tests, suggesting that the recalled events were perceived as less aversive. EEG analyses showed that emotional words modulated theta and spindle/sigma activity. Specifically, to the extent that theta power was larger for the positive word than for the following memory cue, participants judged the memory cues less negatively. Moreover, to the extent that sigma power was larger for the emotional word than for the following memory cue, participants showed higher forgetting of unwanted memories. Notably, when the onset of individual positive word coincided with the upstate of slow oscillations, a state characterized by increased cortical excitability during NREM sleep, affective updating was more successful. In sum, the affect content of memories was altered via strategic spoken words presentations during sleep, in association with theta power increases and slow-oscillation upstates. These findings offer novel possibilities for modifying unwanted memories during sleep, without requiring conscious confrontations with aversive memories that people would prefer to avoid.

neuroscience↗

bioRxiv2022

Molecular atlas reveals the tri-sectional spinning mechanism of spider dragline silk

We performed the first molecular atlas of natural spider dragline silk production using genome assembly for the golden orb-web spider Trichonephila clavata and multiomics defining for the segmented major ampullate (Ma) gland: Tail, Sac, and Duct. We uncovered a hierarchical biosynthesis of spidroins, organic acids, lipids, and chitin in the sectionalized Ma gland dedicated to fine silk constitution. The ordered secretion of spidroins was achieved by the synergetic regulation of epigenetic and ceRNA signatures for genomic group-distributed spidroin genes. Single-cellular and spatial RNA profiling identified ten cell types with partitioned functional division determining the tri-sectional organization of the Ma gland. Convergent evolution and genetic manipulation analyses further validated that this tri-sectional architecture of the silk gland was analogous in silk-spinning animals and inextricably linked with silk formation. Our study provided multiple levels of data that significantly expand the knowledge of spider dragline silk generation and may eventually benefit spider-inspired fiber innovations.

genomics↗

bioRxiv2022

The immunogenomic landscape of cattle

Here, we report the de novo assembly of a cattle genome using ultra-long-read nanopore sequencing in conjunction with other advanced technologies. The assembled genome contains only 145 contigs (N50 [~] 74.0 Mb). Compare to the current reference cattle genome ARS-UCD1.2, 154 gaps are closed, and 467 scaffolds are further placed in our assembly. Importantly, except two remained gaps in the T-cell receptor /{delta} (TRA/TRD) region, the gene loci of other TRs and immunoglobulins (IGs) are seamlessly assembled and exquisitely annotated. With the characterization of 258 IG genes and 626 TR genes that distributed in seven genomic loci, we illustrate the highest immune gene diversity in mammals to our knowledge. Moreover, the gene structures of major histocompatibility complex (MHC) are integrally depicted with properly phased haplotypes. Thus, our work not only reports a cattle genome with the most continuity and completeness, but also provide a comprehensive view of the complex immune- genome.

genomics↗

bioRxiv2022

FoxP3-mediated blockage of ryanodine receptor 2 is the molecular basis for the contact-based suppression by regulatory T cells

The suppression mechanism of regulatory T cells is an intensely investigated topic. As our focus has shifted towards a model centered on indirect inhibition of dendritic cells, a universally applicable effector mechanism controlled by FoxP3 expression has not been found. Here, we report that FoxP3 blocks the transcription of ER Ca2+-release channel ryanodine receptor 2. Reduced RyR2 shuts down basal Ca2+ oscillation in Tregs, which reduces m-Calpain activities that is needed for T cells to disengage from DCs, suggesting a persistent blockage of DC antigen presentation. RyR2 deficiency renders the CD4+ T cell pool to become immune suppressive, and behave in the same manner as FoxP3+ Tregs in viral infection, asthma, hypersensitivity, colitis and tumor development. In the absence of FoxP3, RyR2-deficient CD4+ T cells rescue the systemic autoimmunity associated with Scurfy mice. Therefore, FoxP3-mediated Ca2+ signaling inhibition may be a central effector mechanism of Treg immune suppression. One Sentence SummaryCalcium channel RyR2 dictates Treg adhesion-based suppression

immunology↗

bioRxiv2022

Identification and calibration of ultrabright localizations to eliminate quantification error in SMLM

Single molecule localization microscopy (SMLM) is irreplaceable among super-resolution microscopies in revealing biological ultra-structures, given its unmatched high resolution. However, its sub-optimal quantitative capability, which is critical for characterizing true biomolecular organization of ultra-structures in cells, has hindered its widest application in biomedical research. Here, in SMLM imaging of cellular structures such as lipid rafts and microtubules with saturation labelling, we identified ultra-bright localizations, each of which is contributed by simultaneous emission of multiple molecules within a diffraction-limit region and has been regarded before as a regular localization from single molecule. Consistently, ultra-bright localizations are also observed in simulated SMLM imaging of endoplasmic reticulum or microtubules from public resource. Furthermore, after calibrating each ultrabright localization into multiple single-molecule localizations using the photon-number-based models, the density of total localizations shows linear correlation with the true molecule density, presenting SMLM with new reconstruction method as a quantitative analysis approach. Therefore, identification and dissection of ultra-bright localizations in SMLM enable the close and quantitative estimate of the true biomolecular organization.

biophysics↗

bioRxiv2022

The genomics and physiology of abiotic stressors associated with global elevation gradients in Arabidopsis thaliana

Phenotypic and genetic diversity in Arabidopsis thaliana may be associated with adaptation along its wide elevational range. We took a multi-regional view of elevational adaptation and in a diverse panel of ecotypes measured plant responses to high elevation stressors: low partial CO2 pressure, high light, and night freezing. We conducted genome-wide association studies (GWAS) and found evidence of contrasting locally adaptive clines between regions. Western Mediterranean ecotypes showed low {delta}13C/early flowering at low elevations to high {delta}13C/late flowering at high elevations, while Asian ecotypes showed the opposite pattern. We mapped different candidate genes for each region, and trait-associated SNPs often showed elevational clines likely maintained by selection. Antioxidants and pigmentation showed regional differentiation but rarely elevational clines. GWAS for antioxidants identified an ascorbate transporter PHT4;4 (AT4G00370), which we show alters non-photochemical quenching kinetics under high light and may be involved in local adaptation to Moroccan mountains. The low-antioxidant PHT4;4 GWAS allele was associated with lower PHT4;4 expression and this haplotype was characterized by binding sites of a transcription factor family, DOF, involved in light response. Our results highlight how physiological and genomic elevational clines in different regions can be unique, underlining the complexity of local adaptation in widely distributed species.

evolutionary biology↗

bioRxiv2022

Genomic signatures of host-specific selection in a parasitic plant

PremiseParasitic plants and their hosts are model systems for studying genetic variation in species interactions across environments. The parasitic plant Striga hermonthica (witchweed) attacks a range of cereal crop hosts in Africa and exhibits substantial variation in performance on different host species. Some of this variation is due to local adaptation, but the genetic basis of specialization on certain hosts is unknown. MethodsTo identify genomic regions that are strongly differentiated between parasites attacking different host species, we present an alignment-free analysis of S. hermonthica population diversity using whole genome sequencing (WGS) data for 68 individuals from western Kenya. We validate our findings with germination experiments and analyses based on a de novo assembled draft genome. ResultsReference-free and reference-based analyses suggest that only a small portion of the S. hermonthica genome is strongly differentiated by host species in populations from western Kenya. Analysis of host-associated k-mers implicated genes involved in development of the parasite haustorium (a specialized structure used to establish vascular connections with host roots) and a potential role of chemocyanins in molecular host-parasitic plant interactions. Conversely, no phenotypic or genomic evidence was observed suggesting host-specific selection on parasite response to strigolactones, hormones exuded by host roots and required for parasite germination. ConclusionsThis study demonstrates the utility of WGS for plant species with large, complex genomes and no available reference. Contrasting with theory emphasizing the role of early recognition loci for host specificity, our findings support host-specific selection on later interaction stages, recurring each generation after homogenizing gene flow.

evolutionary biology↗

bioRxiv2022

Structural basis of peptidomimetic agonism revealed by small molecule GLP-1R agonists Boc5 and WB4-24

Glucagon-like peptide-1 receptor (GLP-1R) agonists are effective in treating type 2 diabetes and obesity with proven cardiovascular benefits. However, most of them are peptides and require subcutaneous injection except for orally available semaglutide. Boc5 was identified as the first orthosteric non-peptidic agonist of GLP-1R that mimics a broad spectrum of bioactivities of GLP-1 in vitro and in vivo. Here, we report the cryo-electron microscopy structures of Boc5 and its analog WB4-24 in complex with the human GLP-1R and Gs protein. Bound to the extracellular domain, extracellular loop 2, and transmembrane (TM) helices 1, 2, 3 and 7, one arm of both compounds inserted deeply into the bottom of the orthosteric binding pocket that is usually accessible by peptidic agonists, thereby partially overlapping with the residues A8-D15 in GLP-1. The other three arms, meanwhile, extended to the TM1-TM7, TM1-TM2, and TM2-TM3 clefts showing an interaction feature substantially similar to a previously known small molecule agonist LY3502970. Such a unique binding mode creates a distinct conformation that confers both peptidomimetic agonism and biased signaling induced by non-peptidic modulators at GLP-1R. Further, the conformational difference between Boc5 and WB4-24, two closed related compounds, provides a structural framework for fine tuning of pharmacological efficacy in the development of future small molecule therapeutics targeting GLP-1R. SignificanceGLP-1R agonists are efficacious in the treatment of type 2 diabetes and obesity. While most clinically used agents require subcutaneous injection, Boc5, as the first orthosteric non-peptidic agonist of GLP-1R, suffers from poor oral bioavailability that hinders its therapeutic development. The cryo-electron microscopy structures of Boc5 and its closely related analog WB4-24 presented here reveal a previously unknown binding pocket located deeper in the transmembrane domain for non-peptidic GLP-1R agonists. Molecular interaction with this site may facilitate a broad spectrum of in vivo agonistic activities, in addition to that with the upper helical bundles presumably responsible for biased signaling. These findings deepen our understanding of peptidomimetic agonism at GLP-1R and may help design better drug leads against this important target.

molecular biology↗

bioRxiv2021

Cold protection allows local cryotherapy in a clinical-relevant model of traumatic optic neuropathy

Therapeutic hypothermia (TH) is potentially an important therapy for central nervous system (CNS) trauma. However, its clinical application remains controversial, hampered by two major factors: 1) Many of the CNS injury sites, such as the optic nerve (ON), are deeply buried, preventing access for local TH. The alternative is to apply TH systemically, which significantly limits the applicable temperature range. 2) Even with possible access for "local refrigeration", cold-induced cellular damage offsets the benefit of TH. Here we present a clinically translatable model of traumatic optic neuropathy (TON) by applying clinical trans-nasal endoscopic surgery to goats and non-human primates. This model faithfully recapitulates clinical features of TON such as the injury site (pre-chiasmatic ON), the spatiotemporal pattern of neural degeneration, and the accessibility of local treatments with large operating space. We also developed a computer program to simplify the endoscopic procedure and expand this model to other large animal species. Moreover, applying a cold-protective treatment, inspired by our previous hibernation research, enables us to deliver deep hypothermia (4{degrees}C) locally to mitigate inflammation and metabolic stress (indicated by the transcriptomic changes after injury) without cold-induced cellular damage, and confers prominent neuroprotection both structurally and functionally. Intriguingly, neither treatment alone was effective, demonstrating that in situ deep hypothermia combined with hibernation-mimicking cold protection constitutes a breakthrough for TH as a therapy for TON and other CNS traumas.

neuroscience↗

bioRxiv2021

CsMYB4a from Camellia sinensis Regulates the Auxin Signaling Pathway by Interacting with CsIAA4

Members of the R2R3-MYB4 subgroup are well-known negative regulatory transcription factors of phenylpropane and lignin pathways. In this study, we found that transgenic tobacco plants overexpressing a R2R3-MYB4 subgroup gene from Camellia sinensis (CsMYB4a) showed inhibited growth that was not regulated by phenylpropane and lignin pathways, and these plants exhibited altered sensitivity to synthetic auxin 1-naphthaleneacetic acid (-NAA) treatment. An auxin/indole-3-acetic acid 4 (AUX/IAA4) gene from Camellia sinensis (CsIAA4) participating in the regulation of the auxin signal transduction pathway was screened from the yeast two-hybrid library with CsMYB4a as the bait protein, and tobacco plants overexpressing this gene showed a series of auxin-deficiency phenotypes, such as dwarfism, small leaves, reduced lateral roots, and a shorter primary root. CsIAA4 transgenic tobacco plants were less sensitive to exogenous -NAA than control plants, which was consistent with the findings for CsMYB4a transgenic tobacco plants. The knockout of the endogenous NtIAA4 gene (a CsIAA4 homologous gene) in tobacco plants alleviated growth inhibition in CsMYB4a transgenic tobacco plants. Furthermore, protein-protein interaction experiments proved that domain II of CsIAA4 is the key motif for the interaction between CsIAA4 and CsMYB4a and that the degradation of CsIAA4 is prevented when CsMYB4a interacts with CsIAA4. In summary, our results suggest that CsMYB4a is a multifunctional transcription factor that regulates the auxin signaling pathway, phenylpropane and lignin pathways. This study provides new insights into the multiple functions of R2R3-MYB4 subgroup members as a group of well-known negative regulatory transcription factors. One-sentence summaryCsMYB4a act as multifunctional transcription factor that regulates the auxin signaling pathway, phenylpropane and lignin pathways.

physiology↗

bioRxiv2021

Midkine noncanonically suppresses AMPK activation through disrupting the LKB1-STRAD-Mo25 complex

Midkine (MDK), an extracellular growth factor, regulates signal transduction and cancer progression by interacting with receptors, and it can be internalized into the cytoplasm by endocytosis. However, its intracellular function and signaling regulation remain unclear. Here, we show that intracellular MDK interacts with LKB1 and STRAD to disrupt the LKB1-STRAD-Mo25 complex. Consequently, MDK decreases the activity of LKB1 to dampen both the basal and stress-induced activation of AMPK by glucose starvation or treatment of 2-DG. We also found that MDK accelerates cancer cell proliferation by inhibiting the activation of the LKB1-AMPK axis. In human cancers, compared to other well-known growth factors, MDK expression is most significantly upregulated in cancers, especially in liver, kidney and breast cancers, correlating with clinical outcomes and inversely correlating with PRKAA1 (encoding AMPK1) expression and phosphorylated AMPK levels. Our study elucidates an inhibitory mechanism for AMPK activation, which is mediated by the intracellular MDK through disrupting the LKB1-STRAD-Mo25 complex.

cancer biology↗

bioRxiv2021

A distinctive ligand recognition mechanism by the human vasoactive intestinal polypeptide receptor 2

Activated by physiologically important peptide hormones, class B1 G protein-coupled receptors (GPCRs) modulate key physiological functions and serve as valuable drug targets for many diseases. Among them, vasoactive intestinal polypeptide receptor 2 (VIP2R) is the last member whose full-length 3-dimensional structure has yet to be determined. VIP2R, expressed in the central and peripheral nervous systems and involved in a number of pathophysiological conditions, is implicated in pulmonary arterial hypertension, autoimmune and psychiatric disorders. Here, we report the cryo-electron microscopy structure of the human VIP2R bound to its endogenous ligand PACAP27 and the stimulatory G protein. Different from all reported peptide-bound class B1 GPCR structures, the N-terminal -helix of VIP2R adopts a unique conformation that deeply inserts into a cleft between PACAP27 and the extracellular loop 1, thereby stabilizing the peptide-receptor interface. Its truncation or extension significantly decreased VIP2R-mediated cAMP accumulation. Our results provide additional information on peptide recognition and receptor activation among class B1 GPCRs and may facilitate the design of better therapeutics.

molecular biology↗