Biology subjects

Liu, Y.

Publications and source records attributed to Liu, Y..

At least 541 records · Page 30Linked to original sources

bioRxiv2025

Leonardo: a toolset to correct sample-induced artifacts in light sheet microscopy images

Selective plane illumination microscopy (SPIM, also known as light sheet fluorescence microscopy) is the method of choice for studying morphogenesis and function in biological specimens over extended periods, as it permits gentle and rapid volumetric imaging. In inhomogeneous samples, however, sample-induced artifacts, including light absorption, scattering, and refraction, can impact the image quality, particularly as the focal plane gets deeper into the sample. Here, we present Leonardo, the first toolbox designed to address the major sample-induced artifacts by using two modules: (1) DeStripe removes stripe artifacts in SPIM caused by light absorption while preserving fine sample structures; (2) Fuse reconstructs a single high-quality image from dualsided illumination and/or dual-sided detection, while eliminating blur and optical distortions caused by light scattering and refraction. The efficacy of Leonardo is validated on a wide range of biological samples, from minimally invasive experiments on sensitive specimens (translucent embryonic and optically opaque larval zebrafish) to cleared mouse samples up to two centimeters in size. We provide model code and a Napari-based graphical user interface, enabling the SPIM community to easily apply Leonardo to advance light sheet imaging of inhomogeneous and complex specimens.

bioinformatics↗

bioRxiv2025

A novel molecular interaction in bronchiolitis obliterans syndrome in lung transplantation patients: the role of SERPINA3 and osteoprotegerin

Background and objectiveChronic lung allograft dysfunction, significantly limits survival after lung transplantation. The obstructive phenotype bronchiolitis obliterans syndrome (BOS) is characterized by the abnormal activation of epithelium in airways accompanied by fibrotic changes with excessive deposition of extracellular matrix, resulting in narrowing and ultimately obliteration of airways. Mast cells, characterized by mediators such as tryptase and chymase, play a role in lung fibrosis. The proteins, osteoprotegerin (OPG) and SERPIN family member A 3 (SERPINA3) have previously been associated with progression of lung fibrosis. Tryptase-mast cells can produce OPG, while chymase released from mast cells interacts with SERPINA3. This study aimed to investigate if and how SERPINA3, OPG and tryptase/chymase-positive mast cells are related to fibrotic airway obliteration, and potentially show an association with BOS severity. MethodsSERPINA3 levels in serum from patients with or without BOS were examined using ELISA. In lung tissue from patients with BOS, we identified non-cartilaginous airways and classified them into normal, partially and completely obstructed airways. Immunohistochemistry was used for detection of SERPINA3, OPG, chymase and tryptase. Colocalization of, and interactions between, SERPINA3, OPG and tryptase were assessed by immunofluorescence, proximity ligation assay, and AlphaFold modeling. ResultsSERPINA3 levels in serum from BOS patients were higher compared to non-BOS patients. A low percentage of SERPINA3 and OPG was detected in partially and completely obstructed airways. Cells positive for OPG and SERPINA3 colocalized with tryptase-mast cells in airways from BOS lung tissue. OPG colocalized with SERPINA3 and their staining positively correlated in partially obstructed airways. In completely obstructed airways, OPG, SERPINA3 and tryptase staining areas all positively correlated with each other. ConclusionSERPINA3 and OPG are expressed by mast cells and these proteins may form a complex in lung tissue with potential for contributing to airway remodeling in BOS.

pathology↗

bioRxiv2025

CRISPR-engineered deletion of POGZ alters transcription factor binding at promoters of genes involved in synaptic signaling

One of the seminal discoveries from genetic studies of autism spectrum disorder and related neurodevelopmental disorders (NDD) has been that loss-of-function (LoF) mutations in many genes that impact chromatin and transcriptional regulation confer substantial liability to NDD. Haploinsufficiency of the epigenetic regulator POGZ represents one of the strongest such associations; however, little is known about the direct or indirect regulatory targets of POGZ, or the mechanisms by which loss of this chromatin modifier alters early neuronal development and synaptic functions. Here, we created an allelic series of CRISPR-engineered human induced pluripotent stem cell (hiPSC) clones harboring mono- and biallelic POGZ deletions. In hiPSC-derived neural stem cells (NSC) and Neurogenin 2-induced neurons (iN), POGZ LoF altered the expression of genes associated with critical cellular processes and neuronal functions, including synaptic and intracellular signaling and extracellular matrix organization. Our multiomics profiling also showed altered footprinting of critical transcription factors (e.g., activator protein 1 complexes) that were enriched at promoters of differentially expressed genes associated with synaptic function. To further interrogate the shared molecular changes in neuronal development associated with NDD and POGZ regulation, we compared our results to deletions of the transcription factor MEF2C and the sodium channel gene SCN2A that we generated in these same isogenic iN. These analyses revealed strong enrichment of extracellular matrix and intracellular signaling disruption associated with POGZ and MEF2C deletion, whereas POGZ and SCN2A haploinsufficiency exhibited shared transcriptional effects on gene modules enriched for NDD-associated genes with opposing regulatory effects. Notably, we also observed alterations to synaptic firing rate and neurite extension with biallelic deletions, but not heterozygous lines, suggesting subtle effects in neuronal development associated with haploinsufficiency. Overall, these shared molecular consequences suggest key points of convergence that connect epigenetic regulation to neuronal function in the etiology of neurodevelopmental pathologies.

genomics↗

bioRxiv2025

Integrated multi-omic and functional evidence uncover substantial strain-specific divergence in zebrafish

The zebrafish (Danio rerio) is a foundational vertebrate model in biomedical and developmental research, yet genetic divergence among laboratory strains remains an underappreciated source of biological and experimental variation. Among these, the AB and Tubingen (TU) strains are used globally, forming the basis for most zebrafish-based discoveries. Here, we integrated long- and short-read sequencing, ATAC-seq, Hi-C, transcriptomics, and functional assays to generate a comprehensive multi-omic comparison of these two strains. Our analyses revealed substantial genomic and regulatory divergence, including a 62-bp insertion in the asmt promoter that elevates transcription and alters melatonin biosynthesis, driving strain-specific circadian phenotypes. We also identify a non-synonymous variant (mybbp1aG2612C) associated with heightened immune responsiveness. Together, these findings construct the first genome-wide atlas of functional variation between zebrafish strains, illuminating how hidden genetic differences can shape phenotype, regulatory architecture, and experimental reproducibility in this essential vertebrate model.

genomics↗

bioRxiv2025

Failure of DNA repair leads to the tumorigenic transformation of a regenerating blastema in Drosophila imaginal discs

We present a Drosophila model demonstrating that repeated cycles of tissue regeneration following localized apoptosis can induce tumorigenesis in the absence of oncogene activation or tumor suppressor loss. Chronic regenerative stress leads to epithelial disorganization, loss of cell polarity, immune cell infiltration, DNA damage, centrosomal defects, and aneuploidy-- classical hallmarks of cancer. A subset of "walking dead" cells resists apoptosis and contributes to tissue overgrowth and heterogeneity. Single-cell transcriptomics identifies a distinct cell population, absent from normal tissue, emerging under both regenerative and tumorigenic conditions and characterized by enrichment in JNK pathway components. The tumorigenic signature specifically features distinctive JNK regulatory elements while excluding chaperone proteins. Notably, inhibition of JNK signaling or modulation of DNA repair suppresses neoplastic transformation. This model reveals how chronic injury and defective regeneration drive cancer initiation, establishing a mechanistic link between wound healing and tumorigenesis, and providing a powerful system to explore early tumor development and therapeutic intervention.

developmental biology↗

bioRxiv2025

Mechanistic Insights into Cyclic Penta-Adenylate-Mediated Activation of Type III CRISPR Ribonuclease Csm6

Type III CRISPR systems generate cyclic oligoadenylate (cOA, 3 to 6 AMPs) messengers upon detecting viral RNA, activating downstream effectors to defend against viral infection. Although cOA-activated effectors have been extensively characterized, the cA5-specific effectors remained unexplored despite cA5 being among the most abundant cOA species produced during phage infection. Here, we report that Actinomyces procaprae Csm6 (ApCsm6) selectively employs cA5 as its activator. Unlike other characterized Csm6 proteins, ApCsm6 self-limits its ribonuclease activity by degrading cOAs via its HEPN domain, rather than relaying on the CARF domain. Cryo-EM structures of ApCsm6 and its complexes with cA5 and cA6 reveal a homotetrameric assembly, where each monomer binds a single cOA within a composite pocket formed by two tandem CARF-HEPN domains. Binding of cA5, but not cA6, enhances tetramerization and induces large conformational shifts in CARF, which in turn allosterically activates ssRNA cleavage in HEPN. These findings advance our understanding of ligand discrimination and signaling regulation in type III CRISPR immunity. HighlightsO_LIApCsm6 preferentially recognizes cA5 as its activator. C_LIO_LICryo-EM structures of ApCsm6 and its complexes with cA5 or cA6 reveal the structural basis for cA5-selective recognition and allosteric activation. C_LIO_LIApCsm6 acts as a self-limiting ribonuclease by degrading cOAs via its HEPN domain rather than relaying on the CARF domain. C_LI

biochemistry↗

bioRxiv2025

Multiple Allosteric Sites Allow for Synergistic Enhancement of GPCR Signaling

Allosteric modulation of G protein-coupled receptors (GPCRs) is an emerging therapeutic paradigm that has proven effective, yet the cooperative action of multiple modulators remains unexplored. Here, we reveal how positive allosteric modulators (PAMs) synergistically enable extraordinary signal amplification through the D1 dopamine receptor (D1R). We developed UNC9815 and UNC10062 as enhanced D1R PAMs from the parent compound MLS6585, and then employed cryo-electron microscopy to reveal concurrent occupancy of three distinct allosteric sites by PAMs of different scaffolds, including LY3154207, BMS-A1, and our UNC compounds. Remarkably, we discovered two adjacent allosteric pockets at the transmembrane helix (TM) 1-7 interface: BMS-A1 occupies an intracellular site promoting activation through TM7 conformational shifts, while the UNC compounds complementarily stabilize the extracellular side of the interface. When combined with LY3154207, this cooperative architecture enhances dopamine potency by more than 1,000-fold. These findings elucidate the first structural blueprint for multi-site GPCR cooperativity, unlocking transformative therapeutic strategies inaccessible to orthosteric and single- site allosteric drugs.

molecular biology↗

bioRxiv2025

An oncogenotype-immunophenotype paradigm governing the myeloid landscape in genetically engineered mouse models of prostate cancer

Distinct oncogenotypes sculpt divergent myeloid landscapes in prostate cancer. Using prostate-specific Ptenpc-/-, Ptenpc-/- Trp53pc-/-, Ptenpc-/- Smad4pc-/-, and Ptenpc-/- Trp53pc-/- Smad4pc-/- models, we identify a Smad4-loss-driven neutrophil-enriched subtype (NES) characterized by CXCL5, CXCL2, and CCL20 upregulation, polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) infiltration, and immune checkpoint resistance. In contrast, Smad4-intact tumors form macrophage-enriched subtypes (MES) responsive to immunotherapy. Mechanistically, Smad4 ablation activates YAP signaling and elevates histone epigenetic regulatory enzymes that enhance histone modification, chromatin accessibility, and transcription of neutrophil-recruiting cytokines. Genetic or pharmacologic inhibition of these enzymes suppresses chemokine expression, reduces neutrophil accumulation, restores CD8 T-cell activity, and limits tumor growth in immunocompetent hosts. Analyses of human prostate cancers support the findings from the murine NES prostate tumors. These findings establish a Smad4-YAP-epigenetic axis linking oncogenotype to immunophenotype and uncover a therapeutic vulnerability within the myeloid-dominant prostate tumor microenvironment.

cancer biology↗

bioRxiv2025

M1 Macrophage-Derived Small Extracellular Vesicles as Synergistic Nanotherapeutics: Harnessing Intrinsic Anticancer Activity and Drug Delivery Capacity

Small extracellular vesicles (sEVs) have emerged as next-generation multifunctional nanotherapeutics due to their parental-cell traits and role in intercellular communication. Among them, immune cell-derived sEVs are uniquely positioned to couple innate immunomodulatory activities with therapeutic payload delivery, making them highly attractive for cancer therapy. In particular, M1 macrophage-derived sEVs (M1-sEVs) preserve the tumor-suppressive functions of their parent cells, including tumor microenvironment (TME) reprogramming, immune activation, and inhibition of cancer progression. However, the mechanisms by which these activities are coordinated within the TME, and whether they act independently or synergistically, remain poorly understood. Clarifying these mechanisms is crucial for harnessing their intrinsic bioactivity in combination with their natural capacity as drug delivery nanocarriers to optimize therapeutic efficacy. Here, we demonstrate that M1-sEVs exhibit intrinsic stability and circulation longevity via do not eat me ligands, as well as tumor-homing ability revealed by proteomic profiling, enabling efficient uptake and deep infiltration in breast cancer models. Functionally, M1-sEVs deliver antiproliferative microRNAs that suppress tumor metabolism, growth, and progression by inhibiting self-renewal, adhesion, migration, motility, and invasion. Importantly, by integrating this endogenous bioactivity with exogenous doxorubicin loading, we achieved synergistic efficacy: a 3-fold reduction in IC50 in vitro (0.46 M vs. 1.45 M for free drug) and 70.18% tumor growth inhibition in vivo. These findings highlight M1-sEVs as dual-action nanotherapeutics that combine innate immune-regulatory and tumor-inhibitory functions with efficient drug delivery, advancing their development as powerful platforms for cancer therapy.

bioengineering↗

bioRxiv2025

Automatic Classification of Circulating Blood Cell Clusters based on Multi-channel Flow Cytometry Imaging

Circulating blood cell clusters (CCCs) containing red blood cells (RBCs), white blood cells (WBCs), and platelets are significant biomarkers linked to conditions like thrombosis, infection, and inflammation. Flow cytometry, paired with fluorescence staining, is commonly used to analyze these cell clusters, revealing cell morphology and protein profiles. While computational approaches based on machine learning have advanced the automatic analysis of single-cell flow cytometry images, there is a lack of effort to build tools to automatically analyze images containing CCCs. Unlike single cells, cell clusters often exhibit irregular shapes and sizes. In addition, these cell clusters often consist of heterogeneous cell types, which require multi-channel staining to identify the specific cell types within the clusters. This study introduces a new computational framework for analyzing CCC images and identifying cell types within clusters. Our framework uses a two-step analysis strategy. First, it categorizes images into cell cluster and non-cluster groups by fine-tuning the You Only Look Once(YOLOv11) model, which outperforms traditional convolutional neural networks (CNNs), Vision Transformers (ViT). Then, it identifies cell types by overlaying cluster contours with regions from multi-channel fluorescence stains, enhancing accuracy despite cell debris and staining artifacts. This approach achieved over 95% accuracy in both cluster classification and phenotype identification. In summary, our automated framework effectively analyzes CCC images from flow cytometry, leveraging both bright-field and fluorescence data. Initially tested on blood cells, it holds potential for broader applications, such as analyzing immune and tumor cell clusters, supporting cellular research across various diseases.

bioinformatics↗

bioRxiv2025

Lymphatics unload VEGFR3 in response to the endothelial stress upon VEGFR2 insufficiency

Vascular endothelial growth factor receptor 2 (VEGFR2) is a key target for regulating the endothelial cell lineage and angiogenesis. It is also expressed by lymphatic endothelial cells (LEC) while its participation in the process of lymphangiogenesis remains inadequately characterized. We show in this study that VEGFR2 is highly expressed in dermal initial lymphatic vessels and valves. The induced deletion of pan-endothelial Vegfr2 at the neonatal stage produced a potent suppression of dermal lymphatic growth, including the thinner lymphatic diameter, the decrease of LEC number and lymphatic valves. Mechanistically, the VEGFR2 insufficiency led to a dramatic decrease of lymphatic VEGFR3, a key regulator mediating signals for lymphatic growth and remodeling. The RNA sequencing analysis revealed that GO terms enriched for the downregulated genes included biological processes related to the EC development while pathways related to the hematopoiesis and immune responses were upregulated in the skin of Vegfr2 mutants compared with the littermate controls. This was further confirmed by the RNA-seq analysis of dermal tissues 48 hours after the endothelial Vegfr2 deletion. Consistently, an inhibitory effect on the dermal lymphatic growth was also observed by targeting Vegfr2 in PROX1+ cells, manifesting a similarly altered transcriptome signature. The alteration of lymphatic gene expression was further validated by the siRNA mediated knockdown of Vegfr2 in primary lymphatic endothelial cells, showing a transcriptional trend of LEC to hematopoietic transition. Findings from this study imply that VEGFR2 is required for the maintenance of endothelial identity and its insufficiency may trigger the alteration of lymphatic transcriptional programs to diminish the VEGFR3-mediated lymphangiogenesis.

developmental biology↗

bioRxiv2025

Molecular Mechanisms Underlying Human Vγ9Vδ2 T Cell Activation by Butyrophilin-3 (BTN3) Targeted Antibodies

{gamma}{delta} T cells express T cell receptors (TCRs) composed of paired {gamma} and {delta} chains. The V{gamma}9V{delta}2 T cells are the main subpopulation of {gamma}{delta} T cells in human peripheral blood, which responds to phosphoantigens (pAgs) through butyrophilins (BTN) molecules, such as BTN3A1/2/3 and BTN2A1. Antibodies targeting BTN3As, such as ICT01, can activate V{gamma}9V{delta}2 T cells independently of pAgs, although the underlying mechanism remains poorly characterized. In this study, we reveal the molecular basis of ICT01-mediated V{gamma}9V{delta}2 T cell activation using structural, biochemical, and cellular analyses. ICT01 binds to a unique region in the extracellular domain of BTN3As, destabilizing the BTN2A1-BTN3As interface and facilitating V{gamma}9V{delta}2 TCR engagement, ultimately resulting in activation of V{gamma}9V{delta}2 T cells. Our findings provide insights into the mechanism by which agonist antibodies induce {gamma}{delta} T cell activation and provide guide strategies for developing BTN-targeted immunotherapies.

immunology↗

bioRxiv2025

RNA viruses in water shape the viromes of shrimp and fish in aquaculture systems

Aquatic environments host immense RNA viral diversity, yet the extent to which waterborne viruses influence the virome of aquatic animals remains unclear. Here, we conducted a comprehensive longitudinal metatranscriptomic analysis of water, shrimp, and fish across multiple culture stages in aquaculture systems. We identified 3,211 RNA viruses spanning 21 viral supergroups, with 97.4% representing novel species. Water exhibited the greatest viral diversity (3,093 species), followed by shrimp (1,280) and fish (398), with most viruses detected in shrimp and fish also detected in water. Diversity analyses revealed increasing richness and significant compositional shifts in 92 high-abundance viruses (>1,000 RPM) across culture stages. Viral abundance in aquatic animals was strongly correlated with that in water, and the temporal trajectories of the 16 most abundant viruses were closely synchronized between water and shrimp. Furthermore, 337 virus species were shared among shrimp and two fish species, of which 309 were present in water. These findings demonstrated that RNA viruses in water shape the composition and dynamics of aquatic animal viromes, underscoring the importance of water virome surveillance and management for disease prevention in shrimp aquaculture.

microbiology↗

bioRxiv2025

Phylogenetic and functional characterization of Asgard primases

Eukarya resemble Archaea in DNA replication. Analysis of the DNA replication machinery of Asgard archaea may provide a valuable test of the hypothesis of this phylum being the origin of Eukarya. Among the replication proteins, primase, which comprises the catalytic subunit PriS and the noncatalytic subunit PriL, synthesizes primers for extension by DNA polymerase. Here we show that Asgard primases fall into two major groups, denoted the Heimdall group and the Loki group, which are phylogenetically and structurally more closely related to eukaryotic primases and primases from non-Asgard archaea, respectively. Notably, like human PriL, PriL of the Heimdall group possesses an extra C-terminal domain, which, absent in archaeal PriL of the non-Heimdall group, presumably serves to enhance the stability of the conserved iron-sulfur cluster in PriL. We overproduced in Escherichia coli and purified the PriS and PriL subunits of the Heimdall group from the Candidatus Gerdarchaeota archaeon B18_G1. Biochemical characterization reveals that the B18_G1 primase is capable of primer synthesis and extension, using preferentially dNTPs as the substrates, as shown for primases from non-Asgard archaea, but, unlike the non-Asgard archaeal primases, it produces short primers, a feature typical of eukaryotic primases. These results shed significant light on the evolutionary pathway of primase, and are consistent with the hypothesis of the Asgard origin of Eukarya.

microbiology↗

bioRxiv2025

Origin and rapid evolution of minicircular and highly heteroplasmic mitogenome in the holoparasitic plant genus Rhopalocnemis

The holoparasitic plant Rhopalocnemis phalloides displays unique features in mitogenome organization, sequence heteroplasmy, DNA replication and gene transcription. To understand the origin and evolution of these unique features, we compared the mitogenomes of three R. phalloides individuals and one individual of a newly discovered congeneric species. These mitogenomes comprise dozens of minicircular chromosomes ([~]2-8 kb), with fairly small mitogenome sizes between 121.1 and 147.5 kb. Each R. phalloides individual contains extremely conserved regions (CRs) on all chromosomes, yet these CRs vary significantly among individuals, suggesting rapid divergence in a concerted manner. In contrast, the congeneric species lacks such CRs. Although nearly identical gene and intron content, there is significant sequence divergence between the two species. Extremely high mitogenome heteroplasmy was observed in all three individuals of R. phalloides and all the variants of protein coding genes are transcribed, but few heteroplasmic variants are shared among the three individuals. No sequence heteroplasmy was detected in the congeneric species. PacBio sequencing revealed concatenated mitochondrial chromosomes in the two species, suggesting rolling circle replication of mitochondrial DNA. We infer that the origins of the CR and sequence heteroplasmy are later than the origin of all-minicircular chromosomes in Rhopalocnemis, and propose a plasmid incorporation model to explain the origin of the CR. The rapid intraspecific variation in mitogenome structure, sequence and heteroplasmy in R. phalloides may result from relaxed selective constraint. The striking heteroplasmy in the R. phalloides mitogenome can not be explained by mitochondrion-targeted DNA-RRR gene loss characterized in this study.

evolutionary biology↗

bioRxiv2025

Gain and loss of plasmid-borne antibiotic resistance genes are associated with their chromosomal counterparts and the broader plasmid gene repertoire in Enterobacteriaceae

Plasmids are central vehicles for the dissemination of antibiotic resistance genes (ARGs). They are among the most mobile and evolvable genetic elements, with broad host ranges and high rates of gene turnover, making them especially effective in spreading antibiotic resistance across bacterial lineages. Using the phylogeny-aware gene gain and loss model applied to 6,895 Enterobacteriaceae genomes, we quantified four evolutionary processes--gene gain, loss, expansion, and reduction--for plasmid-borne genes. We found that, overall, plasmid-borne ARGs (pARGs) exhibit similar gain rates compared with other plasmid genes, but significantly higher expansion and reduction rates. All four processes were strongly species dependent, with only a minor influence of antibiotic class. Further, bacterial clades harboring chromosomal ARGs (cARGs) showed significantly higher acquisition and lower loss of plasmid-borne resistance than did their sister clades lacking corresponding cARGs. Moreover, we found that the IncQ2 backbone was associated with qnrS2 and exclusively identified in Leclercia adecarboxylata, while Col(VCM04) plasmids carrying mprF were predominantly (71.4%) distributed within the Citrobacter genus. In summary, plasmid-mediated resistance is primarily species-dependent, and cARGs effectively mark lineages with a high capacity for plasmid-borne resistance acquisition. ImportancePlasmids play a central role in the spread of antibiotic resistance genes (ARGs), and the long-term evolutionary behavior of plasmid-borne ARGs (pARGs) could provide insights into the emergence of novel multidrug resistance. We studied nearly 7,000 Enterobacteriaceae genomes and show that pARGs evolve through the same gain processes as other plasmid genes but exhibit markedly higher and species-dependent copy number changes. Crucially, the strong association between chromosomal and plasmid ARGs reflect a lineage-level pattern of resistance retention, likely shaped by historical selective pressures or specific genomic backgrounds. Identifying such evolutionarily lineages may provide a basis for predicting and monitoring the emergence of multidrug resistance.

microbiology↗

bioRxiv2025

Atlas of Breast Cancer in Chinese Young Women Revealed by Single-cell RNA and ATAC Sequencing

Young women with breast cancer (YBC, age[<=]40) are particularly prevalent in Asian. YBCs usually show more aggressive pathology and poorer outcomes than non-young patients. However, YBCs are underrepresented in current BC risk models, with their tumor intrinsic subtypes and microenvironments lacking a systematic elucidation at the single-cell level, thereby limiting the young-specific therapies. We established a single-cell Chinese YBC landscape baseline, including 246,659 cells, by applying scRNA-seq and scATAC-seq on untreated patients. We developed a cross-modal feature selection algorithm to construct a young-intrinsic subtype classifier BCYtype, outperforming existing classifiers in pseudobulk, cellular, and external cohorts. Comparative analyses with non-young samples revealed a direct differentiation trajectory from mammary stem cells to mature luminal cells. Pseudotemporal analysis also demonstrated that tumor cells in younger patients undergo earlier carcinogenesis. Mechanistically, we found that CDH1 interacts with pTex and NKT cells, serving as a young-specific marker and a potential therapeutic target for HR+ young patients. The interaction between exhausted T cells and antigen-presenting cells revealed NKG2A as a candidate therapeutic target for triple-negative breast cancer in young patients.

cancer biology↗

bioRxiv2025

Ptf1a robustly drives the gliogenic switch in the rodent embryonic cortex in a dosage-dependent manner by activating pro-glial gene expression programs

It is widely believed that the gliogenic switch during rodent embryonic development is governed by the orchestrated crosstalk between a cohort of genes and extracellular cues. Here we report that ectopic expression of the single bHLH factor, pancreas transcription factor 1 (PTF1A), is sufficient to drive radial glial progenitors (RGPs)-regardless of progenitor heterogeneity and developmental stage-to differentiate into glial cells. Ptf1a- expressing RGPs exhibit progenitor behaviors indicative of a neurogenic-to-gliogenic fate transition, resembling endogenous progenitors at the late stages of embryonic development, and preferentially produce OLIG2+ oligodendrocytes in vivo, some of which are positive for PDGFR or CC1. This robust gliogenic competency depends on the dosage of stable Ptf1a expression in RGPs. RNAseq reveals the glial transcriptome, including upregulated expression of several notch signaling components and the endothelin receptors in Ptf1a RGPs. We further identify Ednrb as one of the downstream targets of Ptf1a that directs RGPs toward gliogenesis via the ERK1/2 signaling pathway. In summary, our study uncovers a novel and robust role for Ptf1a in glial fate specification, offering a potential strategy for generating human oligodendrocytes in vitro.

neuroscience↗