Biology subjects

Song, X.

Publications and source records attributed to Song, X..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Host EV derived lipids promote malaria parasite development via mosquito fatty acid oxidation

Malaria parasites must transition between mammals and mosquitoes, but how they adapt to such distinct environments is unclear. We show that blood from infected mammals buffers this environmental shift by packaging parasite-induced signals into extracellular vesicles (EVs). EVs internalized by mosquito midgut increases expression of VLCAD and raises levels of a 22-carbon fatty acid, driving fatty acid breakdown and acetyl-CoA production. The parasite exploits this metabolic shift to synthesize its own lipids during oocyst growth. Stable isotope tracing confirmed that13C4-labelled behenic acid is degraded and incorporated into parasite fatty acids. Lipidomic profiling further revealed that ceramides enriched in the EVs are key mediators. These findings identify a mechanism by which host bood-derived EVs reprogram mosquito lipid metabolism to promote parasite transmission.

microbiology↗

bioRxiv2025

A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex

The genetic and spatial determinants of cell type diversity in human cerebral cortices remain poorly defined. Here, we present a population-level single-cell spatial transcriptomic atlas of human cortices from 71 donors across the lifespan. We identified 906 layer-specific genes showing conserved and divergent laminar expression patterns between humans and other species. Spatial analysis revealed neuronal vulnerability and glial activation during aging, together with a decline in the proportion of superficial SST neurons and their interactions with other cells. Disease-associated genes exhibited high cell-type and layer-specific expression, implicating the pathogenic role of spatially specific gene expression. Spatial cis-eQTL analysis identified regulatory variants linked to genes related to diseases like Tourette syndrome. Cross-species comparison demonstrated glial expansion in the human cortex, accompanied by enhanced neuron-glia communication via the neuregulin signaling. Together, we provide a comprehensive single-cell atlas of the human cortex that is essential for understanding aging, evolution, and disease pathogenesis.

neuroscience↗

bioRxiv2025

Dynamic Meta-Networking Identifies Distinct Network Correlates of Positive and Negative Formal Thought Disorder in Schizophrenia

Formal thought disorder (FTD) is a core symptom of schizophrenia, yet the neural network mechanisms underlying this phenotype remain poorly understood. In this study, we applied a dynamic meta-networking framework, which captures temporally recurring functional network states, to investigate alterations in the language and executive control networks and their associations with positive and negative FTD. Resting-state fMRI data were collected from three independent cohorts: a discovery cohort comprising 150 first-episode, drug-naive patients with schizophrenia and 175 healthy controls (HCs); a replication cohort including 183 first-episode, drug-naive patients and 109 HCs; and a third cohort consisting of 71 patients who had received two weeks of antipsychotic treatment and 71 HCs. Meta-networking analysis identified four distinct resting-state meta-states within both the language and executive control networks. Connectivity-behavior correlation analyses and machine-learning regression models revealed that positive FTD was associated with aberrant connectivity across specific meta-states in both networks. In contrast, negative FTD was linked exclusively to dysfunction within two meta-states of the executive control network. Notably, these polarity-specific, multi-state connectivity disruptions normalized following short-term antipsychotic treatment, highlighting their potential as clinically relevant neuroimaging biomarkers.

neuroscience↗

bioRxiv2025

Distilling Direct Effects via Conditional Differential Gene Expression Analysis

Differential gene expression (DGE) analysis is foundational for interpreting RNA sequencing data, but it conflates direct biological effects with correlations propagated through gene co-expression. Across three RNA sequencing datasets (including a genome-scale perturb-seq experiment), we find that only a small fraction of differentially expressed genes have direct effects on the trait of interest, while the majority are undirected or passengers whose associations are mediated through other genes. To distinguish direct effect genes, we introduce conditional differential gene expression (CDGE) analysis, a framework that tests for conditional rather than marginal association between each gene and the trait of interest. Implemented via the GhostKnockoff procedure with lasso regression, CDGE delivers false discovery rate control, operates on summary statistics from existing DGE pipelines, and accommodates batch effects. The genes identified by CDGE mediate the effects of most other differentially expressed genes and show stronger enrichment for known protein-protein interactions and biological pathways than DGE-identified genes. These results suggest that the field has been systematically over-interpreting DGE outputs, and that distinguishing direct from mediated effects is essential for prioritizing genes for functional follow-up and therapeutic development.

bioinformatics↗

bioRxiv2025

Programmable multiplexed phosphosignaling networks in bacteria

Natural bacterial two-component systems use crosstalk between histidine kinases to integrate multiple environmental cues, enabling complex multi-signal decisions. In comparison, most synthetic bacterial phosphosignaling circuits remain confined to single-input designs. Here, we establish a bottom-up framework for phosphosignaling circuits using two histidine kinases (2HKs) that converge on a shared response regulator (RR). As a proof of concept, we built a synthetic 2HK-1RR circuit in Escherichia coli that consists of a blue-light sensor (YF1) and an indole-3-aldehyde sensor, integrating opto- and chemo-signals through their shared RR. By using distinct dimerization tags on each HK, tuning HK activities, and reversing HK response modes, we program a spectrum of logic behaviors. These include ternary gates (an inverse count gate, a count gate, and two context gates), as well as a binary NAND gate. This work establishes fundamental phosphosignaling circuit design rules based on two-component systems that expand the scope of synthetic gene circuit design and pave the way towards complex, multi-input environmental biosensors and programmable therapeutics.

synthetic biology↗

bioRxiv2025

Epigenetic signature of heterogeneity in aging: Findings from the Canadian Longitudinal Study on Aging

Background: Human aging does not follow a single trajectory. Epigenetic changes offer insight into the heterogeneity in aging by reflecting the combined influence of genetic, environmental, and lifestyle factors on the timing and progression of age-related changes beyond what chronological age alone can explain. Recent studies in cancer and aging underscore the importance of methylation variability as a marker of biological dysregulation. Methods: We investigated the role of DNA methylation in aging heterogeneity by performing epigenome-wide differential methylation and variance association analyses in blood samples from 1,445 Canadians aged 45 to 85 from the Canadian Longitudinal Study on Aging. Results: We identified 448 differentially methylated regions and 488 differentially variable regions associated with health decline as measured by the health deficit accumulation Frailty Index, cognitive function, and physical function. These two classes of regions showed minimal overlap, with distinct gene coverage, suggesting that variability contributes a complementary signal to aging heterogeneity. Genes overlapped by differentially methylated regions were enriched for immune and inflammation-related pathways, whereas differentially variable regions highlighted additional localized, CpG-island-enriched signals shared across health domains, consistent with regionally structured rather than diffuse dysregulation. By integrating significant CpGs from both analyses, we constructed an epigenetic biomarker. The biomarker was associated with all-cause mortality and showed higher discrimination than biomarkers constructed from differential methylation or variability alone, with a similar pattern reproduced in the Baltimore Longitudinal Study of Aging. Conclusions: These findings suggest that DNA methylation variability may provide a complementary dimension of epigenetic aging and support further evaluation in larger cohorts with more mortality events.

genomics↗

bioRxiv2025

Exogenous Photoreceptor-Specific N-Glycosylated PROM1 Rescues Retinal Degeneration in Patient and Mouse Models

PROM1 is widely expressed across various tissues. However, its pathogenic mutations are exclusively associated with inherited retinal dystrophy (IRD). The mechanisms underlying this retina-specific vulnerability remain poorly understood, and no effective treatment currently exists for PROM1-IRD. Here, we utilized urine cells, hiPSCs, hiPSC-RPE cells, retinal organoids (ROs) and Prom1-/- mice to address these challenges. During photoreceptor development in ROs, PROM1 co-localized with ciliary marker ARL13B and outer segment (OS) marker PRPH2. It exhibited photoreceptor-specific mRNA splicing isoforms and unique N-glycosylation. In IRD patient-specific models with the PROM1 c.619G>T (p.E207X) homozygous mutation, we observed nonsense-mediated mRNA decay and altered splicing, leading to complete loss of PROM1 protein and OS-like structure disruption, faithfully recapitulating PROM1-IRD pathology. To rescue these defects, we engineered a photoreceptor-specific AAV7m8-CRXp-hPROM1, which successfully restored PROM1 expression and OS-like structures in patient-derived ROs. Therapeutic efficacy was further validated in Prom1-/- mice, where subretinal delivery of AAV8-CRXp-hPROM1 led to photoreceptor-specific expression of human PROM1, significantly preserving OS morphology and improving visual function. These findings not only provide the first solid preclinical evidence supporting gene therapy for PROM1-IRD, but also reveal photoreceptor-specific vulnerability to PROM1 mutations, offering a novel conceptual framework for investigating and treating related IRDs.

neuroscience↗

bioRxiv2025

TRPM7 Annexin A1 Mechanosensitive Pathway Drives Capillary Infiltration by Circulating Tumor Cells

Successful metastatic dissemination requires tumor cells to overcome significant physical barriers. When circulating tumor cells (CTCs) become lodged in capillary beds, studies reveal that only a small subset can adapt to fluid shear stress (FSS) within the constricted vasculature. These rare, mechanically resilient cells may subsequently extravasate and form metastatic lesions, but details on this adaptation of the physical environment and its molecular basis are not well understood. Utilizing a microfluidics platform that mimics microcirculatory dynamics, we discover that only breast cancer cells with high metastatic potential maintain directional migration under physiologically relevant FSS conditions. This highlights the mechanical selection process of metastatic precursors during hematogenous dissemination. We identify the TRPM7-Annexin A1-actin signaling pathway as essential for overcoming physical barriers and regulating cell motility under capillary FSS. FSS prompts cytoskeletal reorganization and actin disassembly, restricting cell movement. Cancer cells respond to this by increasing mechanical loading, activating TRPM7 and triggering calcium influx, which then activates Annexin A1. This calcium-dependent protein, Annexin A1, interacts with the actin cortex to prevent FSS-induced actin disassembly, thus aiding migration. Experiments conducted in mouse liver capillaries validate the critical role of this pathway in cancer cell motility. Additionally, we propose a mechano-pharmacological strategy using FTY720 to target the TRPM7 pathway, highlighting its therapeutic potential to modify CTC receptor specificity and inhibit distant metastasis.

cancer biology↗

bioRxiv2025

MiroSCOPE: An AI-driven digital pathology platform for annotating functional tissue units

Cancer tissue analysis in digital pathology is typically conducted across different spatial scales, ranging from high-resolution cell-level modeling to lower-resolution tile-based assessments. However, these perspectives often overlook the structural organization of functional tissue units (FTUs), the small, repeating structures which are crucial to tissue function and key factors during pathological assessment. The incorporation of FTU information is hindered by the need for detailed manual annotations, which are costly and time-consuming to obtain. While artificial intelligence (AI)-based solutions hold great promise to accelerate this process, there is currently no comprehensive workflow for building the large, annotated cohorts required. To remove these roadblocks and advance the development of more interpretable approaches, we developed MiroSCOPE, an end-to-end AI-assisted platform for annotating FTUs at scale, built on QuPath. MiroSCOPE integrates a fine-tunable multiclass segmentation model and curation-specific usability features to enable a human-in-the-loop system that accelerates AI annotation by a pathologist. The system is used to efficiently annotate over 71,900 FTUs on 184 prostate cancer hematoxylin and eosin (H&E)-stained tissue samples and demonstrates ready translation to breast cancer. Furthermore, we publicly release a dataset named Miro-120, consisting of 120 prostate cancer H&E with 30,568 annotations, which can be used by the community as a high-quality resource for FTU-level machine learning aims. In summary, MiroSCOPE provides an adaptable AI-driven platform for annotating functional tissue units, facilitating the use of structural information in digital pathology analyses.

bioinformatics↗

bioRxiv2025

Human Decidual RUNX1 Promotes Angiogenesis and Trophoblast Differentiation by Regulating Extracellular Vesicle Signaling

During early pregnancy, human endometrial stromal cells differentiate into secretory decidual cells via a process regulated by ovarian steroid hormones. Decidual cells play a crucial role by secreting various factors that support essential events in forming a functional placenta, including uterine angiogenesis and the differentiation and development of trophoblasts. We previously reported that the conditional ablation of the transcription factor RUNX1 in the mouse uterus leads to subfertility due to insufficient maternal angiogenesis and impaired trophoblast differentiation. In this study, we examined the role of RUNX1 in facilitating communication mechanisms among human decidual cells and other cell types present in the pregnant uterus. We demonstrated that RUNX1 regulates the conserved HIF2-RAB27B pathway in primary human endometrial stromal cells (HESC) during decidualization, which promotes the secretion of extracellular vesicles (EVs) by these cells. Consequently, the depletion of RUNX1 in HESC led to reduced EV secretion. Mass spectrometry identified several cargo proteins in decidual EVs, including ANGPTL2 and IGF2, which could regulate angiogenesis or trophoblast differentiation. We found that RUNX1 directly regulates their expression, resulting in partial changes to these cargoes when it is absent. We observed that delivering EVs lacking ANGPTL2 or IGF2 to human endothelial cells significantly decreased the formation of vascular networks compared to introducing control EVs carrying these factors. Furthermore, adding IGF2-depleted EVs to human trophoblast cells inhibited their differentiation into the extravillous trophoblast lineage. These findings collectively highlight the crucial role of decidual RUNX1 in promoting essential cell-cell interactions for angiogenesis and trophoblast differentiation during placenta formation.

physiology↗

bioRxiv2025

Hybrid Scaffolds Decouple Biochemical & Biophysical Regulation of Cell Phenotype

The extracellular matrix changes dramatically during the progression of diseases like cancer. These complex, tissue-specific changes are not adequately replicated by most current biomaterial disease models. Here we demonstrate, for the first time, a biomaterial system allowing combined, independent control over stiffness, composition and 3D collagen architecture. We demonstrate successful perfusion of defined hydrogel formulations into ice-templated collagen scaffolds, controlling the composition of these hybrid scaffolds at constant stiffness. The Youngs moduli of these hybrid scaffolds can also be tuned independently of composition via chemical crosslinking. Encapsulation of human dermal fibroblasts reveals that fibroblast morphology depends on hybrid scaffold composition and on viscoelasticity, highlighting the importance of a system that decouples biophysical from biochemical properties. Finally, we demonstrate application of this system to exert combined control over biochemical and biophysical drivers of cell growth and invasion, focussing on breast cancer as proof-of-concept. We show that collagen fibre patterning enhances breast cancer cell proliferation, also directing the invasion of patient-derived breast cancer cells. These hybrid scaffolds are therefore promising new tools for dissecting the diverse but complementary roles played by the extracellular matrix in regulating cell phenotype, in a range of healthcare applications.

bioengineering↗

bioRxiv2025

Aggregating multimodal cancer data across unaligned embedding spaces maintains tumor of origin signal

AI based embeddings offer the possibilities of encoding complex biological data into low dimensional spaces, called embedding spaces, that maintain the relationships between entities. There is an open question about the compatibility of embedding spaces that are created without any coordination. It has been assumed that signals in these unaligned embedding spaces would be destroyed if vectors were aggregated into summed values. We trained embedding models across different data modalities and tested aggregating the values together to test this assumption. Our research shows that signal from unaligned embedded values is conserved and able to still be used for learning tasks, such as data modality and tumor of origin recognition.

bioinformatics↗

bioRxiv2025

Cross-species analysis of experimental PH at single cell resolution reveals prominent contributions Ednrb+ EC and Dhcr24+ macrophage populations

BackgroundAnimal models are used widely to study pulmonary hypertension (PH). The cell populations that respond to disease-inducing stimuli in these models and their relationship to human disease remain incompletely defined. Materials and methodThis study analyzed the relationship between several rodent models of PH and human disease at single-cell resolution. scRNA-seq was performed on lungs from mice exposed to hypoxia or Sugen/hypoxia, rats exposed to monocrotaline, and controls. A cross-species single-cell dataset was integrated with human lung cell atlas (HLCA) and single-cell dataset from idiopathic pulmonary arterial hypertension (IPAH) to identify overlapping cell subsets between experimental and human disease and species. ResultsHigh levels of overlap were found between species and models of PH, HLCA, and IPAH datasets. Cell subsets perturbed in rat and mouse PH were similar to those found in human disease, with macrophages and endothelial cells being most affected. A novel Dhcr24high macrophage subset harboring both tissue-remodeling and pro- inflammatory features was consistently increased across models. Several functionally diverse endothelial subtypes were found, including novel Ednrb+ and Nox2+ subpopulations, reflecting enhanced apoptosis, dysregulated angiogenesis and proliferation, and reactive oxygen species-mediated stress. These macrophage and endothelial subtypes expressed numerous PH drug target genes, and exhibited potential disease-specific intercellular interactions involving Angptl4, Cxcl12, and Sema3 signaling. Disease-associated changes in these populations were confirmed by immunofluorescence in lung tissues from animals and patients. ConclusionsWe established a comprehensive cross-species single-cell atlas of mainstream rodent PH models, highlighting several novel macrophage and endothelial subtypes and signaling motifs potentially contributing to human disease.

bioinformatics↗

bioRxiv2025

Decisional reference point pathology: a mechanism and marker for major depressive disorder in humans

The decisional reference point, the central mechanism of behavioral economics, conditions our evaluations of reinforcers. It determines whether a given event is experienced as positive or negative. Here we show, for the first time, a significant and pathological elevation of the reference point in patients with depression that correlates with disease severity. We also show that the mechanism for reference point setting is profoundly impaired in patients with depression. These findings link the previously demonstrated treatment of depression by deep brain stimulation to modulation of the reference point in the anterior cingulate cortex and identify pathology in the dynamics of reference point setting as a novel mechanism in the disorder. Finally, these results lay the foundation for a three-minute virtual diagnostic test for depression.

neuroscience↗

bioRxiv2025

A Single-Cell Atlas of RNA Alternative Splicing in the Glioma-Immune Ecosystem

Single-cell analysis has refined our understanding of cellular heterogeneity in glioma, yet RNA alternative splicing (AS)--a critical layer of transcriptome regulation--remains underexplored at single-cell resolution. Here, we present a pan-glioma single-cell AS analysis in both tumor and immune cells through integrating seven SMART-seq2 datasets of human gliomas. Our analysis reveals lineage-specific AS across glioma cellular states, with the most divergent AS landscapes between mesenchymal- and neuronal-like glioma cells, exemplified by AS in TCF12 and PTBP2. Comparison between core and peripheral glioma cells highlights AS-redox co-regulation of cytoskeleton organization. Further analysis of glioma-infiltrating immune cells reveals potential isoform-level regulation of protein glycosylation in regulatory T cells and a link between MS4A7 AS in macrophages and clinical response to anti-PD-1 therapy. This study emphasizes the role of AS in glioma cellular heterogeneity, highlighting the importance of an isoform-centric approach to better understand the complex biological processes driving tumorigenesis.

genomics↗

bioRxiv2025

Longitudinal analysis of retinal cell state transitions in RB1-deficient retinal organoids reveals the nascent cone precursors are the earliest cell-origin of human retinoblastoma

All cancers develop from malignant transformation of normal cells, while it is challenging to identify these "cells-of-origin" since it is impossible to witness the dynamic changes in human cancers. Retinoblastoma (Rb), an intraocular malignant cancer, is a typical model for study the molecular and cellular mechanisms of cancers. Although the maturing cone precursors (CPs) are proposed as the cellular origin of human Rb, it is unknow whether other retinal cells are also sensitive to RB1 inactivation. Here we developed RB1-deficient human retinal organoids (ROs) models from RB1-/- or RB1+/- human induced pluripotent stem cells (hiPSCs). RB1-/- hiPSCs developed into Rb tumors which recapitulated the features of human native Rb and had the ability to form consecutive orthotopic xenografts in mice. Importantly, RB1 loss induced the overproliferation of ATOH7+ neurogenic retinal progenitor cells (nRPCs), which disrupted the retinal development by generating proliferative, nascent retinal cells including retinal ganglion cells and CPs. scRNA-seq analysis verified the ATOH7+/RXR{gamma}+ nascent CPs survived and finally drove Rb development. In contrast, monoallelic RB1 inactivation with low pRB expression did not induce nascent CPs proliferation, but only induced nRPCs overproliferation which caused retinocytoma-like phenotype. Finally, a potential therapeutic agent for Rb was identified from multi-omics data. Our findings firstly indicate that nRPCs are the most sensitive cells to RB1 loss inducing nascent retinal cells abnormal proliferation, and ATOH7+ nascent CPs are the earliest cellular origin of human Rb, facilitating drug development for Rb.

cell biology↗

bioRxiv2025

circASbase：A Comprehensive Database of Alternative Splicing Events in circRNAs

Despite extensive studies highlight the critical roles of alternative splicing in generating mature circRNA isoforms and enhancing their function diversity, a significant gap remains in the availability of dedicated databases for circRNA alternative splicing events. To bridge this gap, we developed circASbase, a pioneering and comprehensive database that catalogues 452,129 alternative splicing events in 884,047 full-length circRNAs from 581 samples across 13 species, and provides rich annotations to facilitate understanding the splicing regulation of circRNAs. Our findings reveal substantial differences between circRNAs and linear transcripts regarding the distribution and occurrence of alternative splicing events, highlighting the unique regulatory landscape of circRNAs. These unique splicing events result in functional differences of circRNAs by affecting IRES sites, m6A sites, ORFs, protein features, miRNA targets, and more. In summary, circASbase not only covers the urgent need of the research community for data repositories, but also represents a significant advancement in our understanding of circRNA biology. With its user-friendly interfaces and web-based visualization tools, circASbase is poised to become an indispensable resource for researchers exploring the regulatory mechanisms and functional roles of alternative splicing events in circRNAs. This database will continuously drive new insights and discoveries in the field, setting the stage for further advancements in circRNA research. circASbase is available at http://reprod.njmu.edu.cn/cgi-bin/circASbase/

bioinformatics↗

bioRxiv2025

Targeting CHEK2-YBX1&YBX3 regulatory hub to potentiate immune checkpoint blockade response in gliomas

Although GBMs immunosuppressive environment is well known, the tumors resistance to CD8+ T cell killing is not fully understood. Our previous study identified Checkpoint Kinase 2 (Chek2) as the key driver of CD8+ T cell resistance in mouse glioma through an in vivo CRISPR screen and demonstrated that Chk2 inhibition, combined with PD-1/PD-L1 blockade, significantly enhanced CD8+ T cell-mediated tumor killing and improved survival in preclinical model. Here, we aimed to elucidate the immunosuppressive function of Chek2. Immunoprecipitation (IP) followed by mass spectrometry (MS) and phosphoproteomics identified an association between Chek2 with the DNA/RNA-binding proteins YBX1 and YBX3 that are implicated in transcriptional repression of pro-inflammatory genes. Single-gene knock-out and overexpression studies of CHEK2, YBX1, and YBX3 in multiple glioma cell lines revealed that these proteins positively regulate each others expression. RNA sequencing coupled with chromatin immunoprecipitation-sequencing (ChIP-seq) analysis demonstrated common inflammatory genes repressed by CHK2-YBX1&YBX3 hub. Targeting one of the hub proteins, YBX1, with the YBX1 inhibitor SU056 led to degradation of CHK2-YBX1&YBX3 hub. Targeting of this hub by SU056 led to enhanced antigen presentation and antigen specific CD8+ T cell proliferation. Further, combination of SU056 with ICB significantly improved survival in multiple glioma models. Collectively, these findings reveal an immunosuppressive mechanism mediated by the CHK2-YBX1&YBX3 hub proteins. Therefore, CHK2-YBX1&YBX3 hub targeting in combination with immune checkpoint blockade therapies in gliomas is warranted.

cancer biology↗