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Qi, Y.

Publications and source records attributed to Qi, Y..

At least 55 records · Page 3Linked to original sources

Whole genome sequencing reveals the phylogenetic relationship and reticulate evolution of Phrynocephalus lizards in Eurasia

Toad-headed agama (genus Phrynocephalus) is a widely distributed group of lizards across Central Eurasia, inhabiting diverse arid and semi-arid environments from the Caspian Basin to the Qinghai-Tibetan Plateau (QTP). Despite considerable research efforts over the past decades, a robust phylogenetic framework for Phrynocephalus has remained elusive. In this study, we collected 26 samples representing a substantial portion of the distribution of this genus and established a well-supported phylogeny based on whole-genome sequencing and phylogenomic approaches. We found that the Phrynocephalus lizards comprised of three major clades, including the Western Asia, Central Asia and viviparous clades. Furthermore, we provided compelling evidence for an ancient hybridization event that led to the speciation of P. mystaceus, which likely contributed to the observed phylogenetic discordance across the genome. Divergence time estimation and ancestral area reconstruction indicated that Phrynocephalus lizards originated approximately 31.57 million years ago in the Central Asia and Iranian Plateau region, followed by Miocene dispersals into the Arabian Peninsula, the Gobi Desert, and the QTP. Our results illuminate how hybridization and historical range dynamics have jointly driven the origin and diversification of Phrynocephalus, providing new insights into the formation of biodiversity in Eurasia.

bioinformatics↗

Purity and stability of modified nucleosides in the context of accurate quantification by LC-MS

Accurate LC-MS (liquid chromatography coupled mass spectrometry) analysis of RNA modifications relies on synthetic nucleoside standards whose chemical integrity determines both qualitative identification and quantitative measurements. While the purity of these standards is typically verified prior to use, their long-term chemical stability during storage has not been systematically investigated. Here, we evaluated the stability of 44 canonical and modified ribonucleosides in aqueous solution during storage at -80 {degrees}C and -20 {degrees}C. Initial quality control confirmed the identity of all tested standards and revealed purity issues in selected compounds, including contamination of 1-methyladenosine (m1A) with 6-methyladenosine (m6A) and the presence of S- and R-isomers of 5-(carboxyhydroxymethyl)-2'-O-methyluridine (mchm5Um). Long-term LC-UV-MS monitoring over 12 months showed that 30 nucleosides remained stable, two were stable for at least six months, and 12 exhibited substantial quantitative changes. Seven nucleosides formed detectable degradation products, most of which could be structurally assigned. Quantum-chemical calculations of reaction free energies for deglycosylation, deamination, deacetylation and desulfurization correlated with the experimentally observed stability trends. Based on these results, we propose a practical guideline for the preparation, storage and analytical quality control of nucleoside standards, including recommendations for purity verification by UV spectroscopy and quantitative NMR. These guidelines provide an experimental framework to improve the robustness and inter-laboratory comparability of LC-MS-based RNA modification analysis.

molecular biology↗

BrainBeacon: A Cross-Species Foundation Model for Single-cell Resolved Brain Spatial Transcriptomics

The brains functional complexity emerges from spatiotemporal heterogeneity in molecular, cellular, and circuit organization, shaped by evolution, aging, and disease. Single-cell spatial transcriptomics provides a transformative framework to decode this complexity, resolving cell-type-specific expression patterns, region-specific regulation, evolutionary divergence, and disease-associated disruptions. Despite recent advances in spatial transcriptomics, a unified foundation model capturing cross-species, whole-brain cellular architecture remains lacking. Here, we introduce BrainBeacon, the first cross-species foundation model for whole-brain spatial transcriptomics. Trained on 133 million spatially resolved cells covering a total area of 210194 mm2 from human, macaque, marmoset and mouse brains profiled across five major platforms, BrainBeacon integrates gene expression rankings, spatial cellular organization, and evolutionarily conserved genetic relationships into a unified transformer-based architecture. A two-stage training strategy captures both intra-cellular transcriptional dependencies and inter-cellular spatial interactions, yielding biologically grounded and interpretable representations of brain structure. Subsequently, BrainBeacon enables cross-species alignment of brain cell types and anatomical regions, facilitating integrative analyses of conserved and divergent cellular architectures. Moreover, it uncovers spatial regulatory mechanisms of aging by predicting bidirectional perturbation responses between cells and their local niche. Together, BrainBeacon serves as a foundational cross-species model for whole-brain spatial transcriptomics, enabling virtual brain atlas construction, systematic in silico perturbation studies, and mechanistic insights into brain disease pathogenesis.

bioinformatics↗

TDP-43 pathology induces CD8+ T cell activation through cryptic epitope recognition

Aggregation and nuclear depletion of the RNA binding protein TDP-43 are the crucial pathological features of amyotrophic lateral sclerosis (ALS) and inclusion body myositis (IBM), two degenerative diseases of the CNS and muscle. The loss of TDP-43 nuclear function results in the aberrant inclusion of cryptic exons in mRNA transcripts, leading to the expression of de novo proteins. Clonally expanded and highly differentiated CD8+ T cells have been observed in individuals with TDP-43 proteinopathies and therapeutics modulating the T cell response have recently been found to extend survival. However, the target antigens mediating T cell activation have remained elusive. Here, we investigate whether the de novo proteins induced by aberrant cryptic splicing due to TDP-43 nuclear loss can act as neo-antigens. We detect the HDGFL2 cryptic peptide and multiple other TDP-43 cryptic exons in IBM skeletal muscle, where their presence correlates with enrichment of T cells and class I antigen presentation pathways. Furthermore, we identify epitopes deriving from HDGFL2 and IGLON5 cryptic peptides which are recognized by clonally expanded and functionally differentiated populations of CD8+ T cells in ALS and IBM Patients. Finally, we demonstrate that T cells engineered to express the identified TCRs can bind and activate in response to the cryptic peptide derived epitopes (cryptic epitopes) and are able to kill TDP-43 deficient astrocytes. This work identifies for the first time specific T cell antigens in ALS and IBM, directly linking adaptive immune response to TDP-43 pathology.

immunology↗

Scavenger Receptor class F member 2 is an intracellular receptor for Hepatitis B virus

Hepatitis B virus (HBV) infects hepatocytes by specific binding to the cell-surface receptor --sodium taurocholate cotransporting polypeptide (NTCP)--through the preS1 region of its large envelop protein, followed by a less well understood transport process across the cytoplasm to the nucleus. Here, we report that scavenger receptor class F member 2 (SCARF2), a single-pass transmembrane protein, functions as an intracellular receptor for HBV. SCARF2 binds to a preS1 region downstream of the NTCP binding site through its N-terminal EGF-like domains 4-6, and its proline-rich C-terminal domain also plays an indispensable role in the infection. The internalized HBV virions are transported to the cytoplasmic side of nuclear pore complexes (NPCs) within the SCARF2-containing endosomes. HBV capsid release from the endosomal vesicles is significantly impaired by knockdown of SCARF2. These results suggest a model that SCARF2 conveys HBV to the periphery of NPCs and ultimately leads to viral capsid release for nuclear entry.

microbiology↗

A Single-cell and Spatially Resolved Cell Atlas of Human Esophageal Squamous Cell Carcinoma

Tumor heterogeneity and the suppressive microenvironment are key challenges that limit the effectiveness of cancer treatment. In this study, we systematically elucidated the molecular characteristics and mechanisms underlying the suppressive immune microenvironment via a combination of single-cell RNA sequencing, spatial transcriptomics, and metabolomics for a series of human esophageal squamous cell carcinoma (ESCC) and matched nontumor tissues. We found that COL17A1+ epithelial cells presented greater malignancy, characterized by triglyceride (TG) and phosphocholine (PC) accumulation. We also identified a tumor-specific POSTN+ fibroblast subgroup. We found a unique epithelial-fibroblast niche with low infiltration of effector immune cells and substantial enrichment of lipids, composed of POSTN+ fibroblasts and COL17A1+ epithelial cells, where their crosstalk contributed to tumor progression. We confirmed that the INHBA/TP63 axis plays a key role in mediating the regulation of COL17A1+ tumor cells by POSTN+ fibroblasts. Our findings provided new insights into the characteristics of the tumor microenvironment and the crosstalk between tumor and fibroblasts, offering valuable multiomics data resources for elucidating tumor progression mechanisms.

genomics↗

Spatial geometry-aware deep learning for deciphering tissue structure from spatially resolved transcriptomics

Recent advances in spatially resolved transcriptomics have enabled high-throughput gene expression profiling while preserving spatial context, thereby facilitating the investigation of spatial heterogeneity within tissues. Here, we present SpatialGEO, a spatial geometry-aware deep learning framework designed to decipher tissue organizational structures through dual-encoder feature extraction and geometric graph learning. Experimental results demonstrate the superior accuracy of SpatialGEO in identifying spatial regions across datasets encompassing diverse biological contexts and spatial resolutions. Moreover, SpatialGEO uncovers key mechanisms of immune evasion and regulation within the tumor microenvironment and provides novel biological insights into mouse embryonic development.

bioinformatics↗

A Multimodal Graph Learning Framework for Versatile Spatial Transcriptomics Analysis with SpatialModal

The development of spatial transcriptomics(ST) technologies enables the exploration of tissue structure and cellular function within a spatial context. However, mainstream analytical methods primarily focus on the gene expression modality itself and struggle to fully leverage auxiliary information from histological images, which limits precise dissection of complex biological structures. To address this, we propose SpatialModal, a multimodal graph learning framework that effectively integrates gene expression data and histological images from spatial transcriptomics to construct unified spatial representations. SpatialModal effectively captures synergistic interactions between modalities by jointly modeling intra- and inter-modal complementary features while incorporating spatial adjacency information. Furthermore, it employs a dual contrastive learning strategy to enhance the discriminative power of representations, thereby enabling efficient and robust analysis of tissue structures. We validate the effectiveness of this approach on multiple public datasets covering diverse tissue types, species, and resolutions. Experiments demonstrate that SpatialModal exhibits significant advantages in downstream tasks, including spatial domain identification, gene expression reconstruction, and pseudotime inference, and accurately elucidates the hierarchical structure of the mouse cortex as well as the metabolic-immune dynamic boundaries in the breast cancer microenvironment. Additionally, SpatialModal shows exceptional robustness in single-cell resolution and multi-slice integration tasks, providing an efficient and broadly applicable analytical tool for spatial transcriptomics research.

bioinformatics↗

Neural organoids protect engineered heart tissues from glucolipotoxicity by transferring versican in a co-culture system

Metabolic disorders could cause dysregulated glucose and lipid at the systemic level, but how inter-tissue/organ communications contribute to glucolipotoxicity is difficult to dissect in animal models. To solve this problem, myocardium and nerve tissues were modeled by 3D engineered heart tissues (EHTs) and neural organoids (NOs), which were co-cultured in a generalized medium with normal or elevated glucose/fatty acid contents. Morphology, gene expression, cell death and functional assessments detected no apparent alterations of EHTs and NOs in co-culture under normal conditions. By contrast, NOs significantly ameliorated glucolipotoxicity in EHTs. Transcriptomic and protein secretion assays identified the extracellular matrix protein versican as a key molecule that was transferred from NOs into EHTs in the high-glucose/fatty acid condition. Recombinant versican protein treatment was sufficient to reduce glucolipotoxicity in EHTs. Adeno-associated virus-delivered versican overexpression was sufficient to ameliorate cardiac dysfunction in a murine model of diabetic cardiomyopathy. These data provide the proof-of-concept evidence that inter-tissue/organ communications exist in the co-culture of engineered tissues and organoids, which could be systemically studied to explore potential pathological mechanisms and therapeutic strategies for multi-organ diseases in vitro.

cell biology↗

A Highly Protective Clade 1 and 2 Cross-Reactive Pandemic Influenza Virus Vaccine Based on a 4th Generation Fully Deleted Adenoviral Vector of a Rare Serotype

The GreVac vaccine technology was created as a fast and flexible plug-and-play vaccine platform based on a 4th generation architecture of fully deleted (fd) helper virus-independent (hi) adenoviral (Ad) vectors. For the initial proof-of-principle studies, we at Greffex had engineered an avian influenza vaccine, which delivered a transgene expression cassette for an avian influenza virus H5 hemagglutinin and N1 neuraminidase genes in a capsid of the common human Ad serotype 5 (Ad5). This vaccine proved highly immunogenic and protective in mice. These studies revealed that intramuscular (i.m.) delivery proved more efficient than subcutaneous (s.c.) or intranasal (i.n.) routes. In the human population, pre-exposure to the Ad5 virus is common. To minimize interference by pre-existing anti-Ad5 immunities, we created a new GreVac-based avian influenza vaccine, in which the fd Ad genome was packaged into a capsid of the rare human Ad serotype 6 (Ad6). We now report that at very low doses, the resulting GreFluVie6 vaccine given i.m. fully protected mice and ferrets against lethal challenges with the clade 1 A/Vietnam/1203/2004 avian influenza virus associated with induction of potent immune cellular and humoral immune responses. The recipients serum antibodies strongly cross-reacted with clade 2.1.3.2 (A/Indonesia/05/2005) and clade 2.3.4.4b H5 hemagglutinins.

immunology↗

SCRIPT: predicting single-cell long-range cis-regulation based on pretrained graph attention networks

Single-cell cis-regulatory relationships (CRRs) are essential for deciphering transcriptional regulation and understanding the pathogenic mechanisms of disease-associated non-coding variants. Existing computational methods struggle to accurately predict single-cell CRRs due to inadequately integrating causal biological principles and large-scale single-cell data. Here, we present SCRIPT (Single-cell Cis-regulatory Relationship Identifier based on Pre-Trained graph attention networks) that infers single-cell CRRs from transcriptomic and chromatin accessibility data. SCRIPT incorporates two key innovations: graph causal attention networks supported by empirical CRR evidence, and representation learning enhanced through pretraining on atlas-scale single-cell chromatin accessibility data. Validation using cell-type-specific chromatin contact data demonstrates that SCRIPT achieves a mean AUC of 0.9, significantly outperforming state-of-the-art methods (AUC: 0.68). Notably, SCRIPT obtains a threefold improvement in predicting long-range CRRs (>100 Kb) compared to existing methods. Applying SCRIPT to Alzheimers disease and schizophrenia, we establish a framework for prioritizing disease-causing variants and elucidating their functional effects in a cell-type-specific manner. By uncovering molecular genetic mechanisms undetected by existing computational methods, SCRIPT provides a roadmap for advancing genetic diagnosis and target discovery.

bioinformatics↗

C9orf50 is a Targetable Spliceosome Regulator for Cancer Immunotherapy

Cancer cells harbor cell-intrinsic programs capable of sculpting immunogenic landscapes, yet molecular brakes that enforce immune evasion remain poorly defined. Here, we identify C9ORF50, a previously uncharacterized intrinsically disordered protein, as a liquid-liquid phase separation-driven regulator of RNA processing and actionable immunotherapy target. Genetic ablation of C9ORF50 induces selective intron retention in spliceosome component transcripts, leading to cytoplasmic accumulation of immunogenic double-stranded RNA (dsRNA). This dsRNA activates type I interferon pathway that in turn orchestrates a chemokine secretory program critical for T cell recruitment. The resultant enhancement of tumor immunogenicity and reprogramming of tumor immune microenvironment drives robust antitumor immunity, effectively converting immunologically "cold" tumors to "hot" phenotypes. Therapeutic targeting of C9ORF50 via RNA interference achieved robust tumor suppression in syngeneic models, suggesting its translational relevance. Notably, C9ORF50 exhibits tumor-predominant expression, with minimal baseline levels detected in healthy tissues or immune cell populations, underscoring its potential safety as a therapeutic target. Our study not only identifies C9ORF50 as a novel LLPS-dependent regulator of RNA splicing but also establishes it as a promising and potentially safe therapeutic target for cancer immunotherapy.

cancer biology↗

Luminos: open-source software for bidirectional microscopy

Bidirectional microscopy (BDM) combines simultaneous targeted optical perturbation and imaging of biophysical or biochemical signals (e.g. membrane voltage, Ca2+, or signaling molecules). A core challenge in BDM is precise spatial and temporal alignment of stimulation, imaging, and other experimental parameters. Here we present Luminos, an open-source MATLAB library for modular and precisely synchronized control of BDM experiments. The system supports hardware-triggered synchronization across stimulation, recording, and imaging channels with microsecond accuracy. Source code and documentation for Luminos are available online at https://www.luminosmicroscopy.com and https://github.com/adamcohenlab/luminos-microscopy. This library will facilitate development of bidirectional microscopy methods across the biological sciences.

bioengineering↗

Cryptic variation fuels plant phenotypic change through hierarchical epistasis

Cryptic genetic variants exert minimal or no phenotypic effects alone but have long been hypothesized to form a vast, hidden reservoir of genetic diversity that drives trait evolvability through epistatic interactions. This classical theory has been reinvigorated by pan-genome sequencing, which has revealed pervasive variation within gene families and regulatory networks, including extensive cis-regulatory changes, gene duplication, and divergence between paralogs. Nevertheless, empirical testing of cryptic variations capacity to fuel phenotypic diversification has been hindered by intractable genetics, limited allelic diversity, and inadequate phenotypic resolution. Here, guided by natural and engineered cis-regulatory cryptic variants in a recently evolved paralogous gene pair, we identified an additional pair of redundant trans regulators, establishing a regulatory network that controls tomato inflorescence architecture. By combining coding mutations with a cis-regulatory allelic series in populations segregating for all four network genes, we systematically constructed a collection of 216 genotypes spanning the full spectrum of inflorescence complexity and quantified branching in over 27,000 inflorescences. Analysis of the resulting high-resolution genotype-phenotype map revealed a layer of dose-dependent interactions within paralog pairs that enhances branching, culminating in strong, synergistic effects. However, we also uncovered an unexpected layer of antagonism between paralog pairs, where accumulating mutations in one pair progressively diminished the effects of mutations in the other. Our results demonstrate how gene regulatory network architecture and complex dosage effects from paralog diversification converge to shape phenotypic space under a hierarchical model of epistatic interactions. Given the prevalence of paralog evolution in genomes, we propose that paralogous cryptic variation within regulatory networks elicits hierarchies of epistatic interactions, catalyzing bursts of phenotypic change. Keyword: cryptic mutations, paralogs, redundancy, cis-regulatory, tomato, inflorescence, gene regulatory network, modeling, epistasis

plant biology↗

Mosquito Cell Atlas: A single-nucleus transcriptomic atlas of the adult Aedes aegypti mosquito

The female Aedes aegypti mosquitos remarkable ability to hunt humans and transmit pathogens relies on her unique biology. Here, we present the Aedes aegypti Mosquito Cell Atlas, a comprehensive single-nucleus RNA sequencing dataset of more than 367,000 nuclei from 19 dissected tissues of adult female and male Aedes aegypti, providing cellular-level resolution of mosquito biology. We identify novel cell types and expand our understanding of sensory neuron organization of chemoreceptors to all sensory tissues. Our analysis uncovers male-specific cells and sexually dimorphic gene expression in the antenna and brain. In female mosquitoes, we find that glial cells in the brain, rather than neurons, undergo the most extensive transcriptional changes following blood feeding. Our findings provide insights into the cellular basis of mosquito behavior and sexual dimorphism. The Aedes aegypti Mosquito Cell Atlas resource enables systematic investigation of cell type-specific expression across all mosquito tissues.

genomics↗

Unraveling the Neurocognitive Mechanisms of Delayed Punishment in Second- and Third-Party Contexts

Second-party punishment (SPP) and third-party punishment (TPP) are essential in regulating social behavior and maintaining social norms, yet the effectiveness may wane when punishment is delayed. Currently, the decision-making and neural mechanisms underlying SPP and TPP under temporal delays remain largely unexplored. This study investigated both SPP and TPP punishment decisions with time-delay (immediate vs. delayed) using a hypothetical criminal scenario assessment task with fMRI. Results showed increased activity in the bilateral precuneus and left temporoparietal junction (TPJ) and stronger left TPJ-dorsolateral prefrontal cortex (dlPFC) connectivity in SPP compared to TPP. Interestingly, third-parties imposed more severe punishment in delayed conditions than in immediate ones, accompanied by enhanced neural activity in dorsomedial prefrontal cortex (dmPFC), left TPJ, ventrolateral prefrontal cortex (vlPFC), ventromedial prefrontal cortex (vmPFC), and caudate nucleus. This delay effect was evident only in misdemeanor and felony cases, with no differences in capital offenses, suggesting a moderating effect of criminal severity. In contrast, SPP showed no significant changes in punishment or neural response across immediate and delayed conditions. Multivariate pattern analysis further indicated that dmPFC, TPJ, vlPFC, vmPFC and caudate function together to encode punishment severity in TPP contexts, a pattern not observed in SPP. These findings underscore distinct decision-making mechanisms between SPP and TPP under temporal delays, with implications for understanding justice-related processing in the human brain under time constraints. Significance statementWithin the justice system, punishing norm violators is often hindered when they flee, resulting in delayed punishments. However, little is known about how second-party (SPP) and third-party (TPP) implement punishment with time delays. The current study investigated this using real criminal scenarios with time delays under fMRI scanning. We found that third parties imposed more severe punishment on defendants in delayed conditions than in immediate ones, reflected by enhanced neural activity in the dorsomedial prefrontal cortex, left temporoparietal junction, ventrolateral prefrontal cortex, ventromedial prefrontal cortex, and caudate nucleus. In contrast, no significant differences were observed in second-party punishment. We also found a moderating effect of criminal severity: the difference between immediate and delayed sanctions by third-parties was present in misdemeanor and felony cases but not in capital offenses. These results shed light on the decision-making mechanisms of SPP and TPP in contexts involving temporal delay, which may have deep impact in different disciplines, e.g., social science, cognitive neuroscience and legal system.

neuroscience↗

Neuromodulation of the endbulb of Held synapse in the cochlear nucleus

Synapses vary greatly in synaptic strength and plasticity, even within the same circuitry or set of pre- and postsynaptic neurons. Neuromodulation is a candidate mechanism to explain some of this variability. Neuromodulators such as monoamines can differentially regulate presynaptic function as well as neuronal excitability. Variability is found also for the large calyceal synapses of the auditory pathway that are endowed with high synaptic vesicle (SV) release probability (Pvr) and large postsynaptic currents enabling reliable and temporally precise transmission of auditory information. Here we investigated whether the calyceal endbulb of Held synapse formed by auditory nerve fibers onto bushy cells (BCs) in the anteroventral cochlear nucleus (AVCN) is modulated by norepinephrine (NE) and serotonin (5-HT). Using electron microscopy (EM) of the cochlear nucleus we found evidence for putative monoaminergic varicosities in both ventral and dorsal divisions. Immunostaining for vesicular 5-HT and NE transporters revealed NE-containing and 5-HT-containing varicosities in the AVCN, juxtaposed to both endbulbs and BCs. Furthermore, we detected immunofluorescence for 5-HT1B, 5-HT4, 5-H7 receptors (R) and 2C-adrenergic receptors (AR) in BCs. We used voltage-clamp recordings from mouse BCs in order to uncover potential presynaptic effects of neuromodulation, which revealed an increase in frequency of miniature excitatory postsynaptic currents (mEPSCs) upon application of NE but not 5-HT. Evoked synaptic transmission was unaffected by the application of either NE or 5-HT. Likewise, while studying the biophysical properties of the BCs, we did not observe effects of NE or 5-HT on low-voltage-activated K+ (K+LVA) and hyperpolarization-activated mixed cation (HCN) channels during application. In summary, we report evidence for the presence of monoaminergic innervation in the cochlear nucleus and for subtle functional NE-neuromodulation at the endbulb of Held synapse.

neuroscience↗

TaWUS2D regulates the number of grains per spikelet by enhancing the number of fertile ovaries in Multi-Ovary Wheat

Innovative genetic improvements in the staple crop Triticum aestivum (bread wheat) are urgently needed to address the growing global food security crisis. Here, we report the map-based cloning of TaWUS2D, the gene responsible for the dominant multi-ovary phenotype in wheat. Multi-ovary lines are characterized by the development of three fertile ovaries per floret that results in three grains, as opposed to wildtype single ovary wheat. We used HiFi long-reads to assemble a 14.48 Gbp genome scaffold assembly in the background of mutli-ovary wheat line MOV. Using high-resolution genetic mapping, combined with additional genomic resources, we defined the Mov-1 locus to a 135 Kbp region containing two genes. Using five independent deletion mutants and eight TILLING mutants, we demonstrate that a functional WUSCHEL-like protein, TaWUS2D, is required for the multi-ovary phenotype. TaWUS2D is upregulated in the MOV genetic background. This research lays the groundwork for developing new approaches to improve wheat production potential and sustainability in the face of current and future global food challenges.

plant biology↗