Biology subjects

Liu, H.

Publications and source records attributed to Liu, H..

At least 181 records · Page 10Linked to original sources

bioRxiv2025

Human spastin functions as an ATPase-independent microtubule nucleator via ring-stack formation

Microtubule severing enzyme spastin plays pivotal roles in cytokinesis and neuronal outgrowth, and its mutations cause hereditary spastic paraplegia (HSP). Here we show that, at physiological tubulin concentrations, human spastin behaves predominantly as an ATPase- independent microtubule nucleator rather than a severase. Biochemical and structural analyses revealed that spastin assembles tubulin into stacked-ring intermediates via strategically positioned microtubule-binding domains, thereby generating nucleation-competent sites for polymerization. Tubulin subunits within these spastin-induced rings adopt a straight, microtubule-like interface, in marked contrast to the twisted tubulin spirals characteristic of depolymerizing microtubule ends. Our results redefine the mechanistic landscape of multifaceted spastin functions and provide insights that may inform the pathological basis of HSP and guide future therapeutic strategies.

biophysics↗

bioRxiv2025

SIRP: A Self-Supervised Fluorescence Denoising method with Implicit Representation Priors

Fluorescence microscopy plays a critical role in live-cell imaging, yet the captured images often suffer from significant noise due to limited excitation intensity and constrained exposure times. Deep learning has emerged as a powerful solution for image denoising, especially the self-supervised methods can achieve good restoration performance without requiring clean target data. However, their performance in preserving fine image details remains challenging under low signal-to-noise ratio (SNR) conditions. In this work, we propose a novel self-supervised denoising framework named Self-Supervised Implicit Representation Prior Image Restoration Network (SIRP). It is based on the neighbor-sampling strategy and leverages image representation priors to guide the network training procedure. The neighbor-sampling strategy takes advantage of the inherent statistical consistency within local image regions to denoise. The image representation priors are learned through the Implicit Neural Representations (INR) that map spatial coordinates directly to their corresponding pixel intensities to suppress noise and effectively preserve details. Results of SIRP on simulated data and experimental-acquired data showed superior denoising performance and detail-preserving ability compared to filter-based approaches and self-supervised approaches, highlighting the potential of INR-guided architectures for fluorescence microscopy image restoration.

cell biology↗

bioRxiv2025

An ancient transcription factor functions as the master regulator of primary cilia formation

How ancient transcription factors are repurposed during evolution to drive the functional diversification of conserved organelles remains a fundamental question in biology. Although highly conserved in basic morphology, eukaryotic cilia vary extensively in their sizes and functions. Previously, we showed that an evolutionarily ancient transcription factor, X chromosome-associated protein 5 (Xap5), controls motile ciliogenic transcriptional programs during mouse spermatogenesis (Wang et al., 2025). Here we show that Xap5 functions as the master regulator of primary ciliogenesis. Xap5 associates with the nuclear protein Non-POU domain-containing octamer-binding protein (Nono) to form a regulatory module that directly binds and activates the transcription factors Sox5 and Sox9. Genetic ablation of Xap5 or Nono impairs primary ciliogenesis, and loss of Sox5 disrupts the downstream ciliogenic program, consistent with the established role of Sox9. Collectively, our results provide new insight into how complex ciliary transcription factor networks determine ciliary diversity during evolution, and suggest that defects in this regulatory axis may contribute to the etiology of human ciliopathies.

cell biology↗

bioRxiv2025

An inherent T cell-activating mRNA delivery platform for in vivo CAR T generation

The clinical success of CAR T cell therapy has underscored the need for scalable, non-invasive strategies for in vivo T cell engineering. Although mRNA delivery offers a promising alternative, current lipid-based vectors lack intrinsic T cell tropism and often rely on antibody conjugation, complicating manufacturing and raising safety concerns. Here we present an inherent T cell-activating polymer-lipid nanoparticle (ERTLNPs) that enable ligand-free, efficient mRNA transfection and activation of T cells in vivo. ERTLNPs, composed of p-toluenesulfonyl arginine (RT)-functionalized polyethylenimine (denoted as PEI-RT) and helper lipids, preferentially accumulate in the spleen following systemic administration. Without exogenous stimulation, ERTLNPs intrinsically activate T cells, triggering robust mRNA expression and proliferation. Mechanistically, ERTLNPs engage the PI3K/AKT/mTOR signaling axis to reprogram T cell metabolism, promoting expansion while restraining exhaustion. Systemic delivery of mRNA encoding fibroblast activation protein chimeric antigen receptor (mFAP CAR) via ERTLNPs leads to in situ generation of functional CAR T cells, which efficiently eliminate pathological fibroblasts in models of cancer and fibrosis, with minimal off-target effects. This ligand-free, metabolically reprogramming mRNA delivery platform provides a clinically translatable approach for in vivo CAR T cell generation and broadens the landscape of non-viral immunotherapeutic engineering.

bioengineering↗

bioRxiv2025

The HosA histone deacetylase regulates stress resistance, host cell interactions, and virulence in Aspergillus fumigatus

The capacity of Aspergillus fumigatus to cause invasive pulmonary aspergillosis depends on its ability to adapt to dynamic and stressful microenvironments within the host. Epigenetic regulation, including histone deacetylation, plays a critical role in fungal adaptation to stress. Here, we investigated the role of the class I histone deacetylase (HDAC) HosA in A. fumigatus stress resistance, host cell interactions, and virulence. A {Delta}hosA mutant had increased susceptibility to intracellular oxidant stress induced by menadione. It also had impaired capacity to invade and damage two pulmonary epithelial cell lines in vitro. In a corticosteroid-immunosuppressed mouse model of invasive aspergillosis, mice infected with the {Delta}hosA mutant survived significantly longer than those infected with the wild-type strain, despite having similar pulmonary fungal burden. The {Delta}hosA mutant also induced a weaker inflammatory response than the wild-type strain. Transcriptomic analysis revealed that HosA regulates genes involved in secondary metabolite biosynthesis and energy metabolism, functioning as both an activator and repressor of distinct gene sets. Collectively, these results indicate that HosA is a key epigenetic regulator that governs A. fumigatus interactions with host cells and virulence during invasive pulmonary aspergillosis. ImportanceEpigenetic modifications in A. fumigatus can be induced by environmental changes and stresses such as those induced by interaction with host cells. HosA, a class I histone deacetylase, has been shown to play a key role in regulating secondary metabolism in several Aspergillus species, but its function in A. fumigatus was previously unknown. We found that deletion of hosA increased susceptibility to intracellular, but not extracellular, oxidative stress. The {Delta}hosA mutant also exhibited significantly reduced pulmonary epithelial cell invasion and host cell damage, as well as attenuated virulence in immunosuppressed mice. Together, these findings indicate that HosA functions as a key epigenetic regulator that governs stress resistance, secondary metabolism, and fungal-host interactions. Defining the functions of HosA could provide critical insight into the epigenetic mechanisms that control fungal pathogenicity and may reveal a potential therapeutic target for invasive aspergillosis.

microbiology↗

bioRxiv2025

A Syngeneic Immunocompetent Mouse Model of Gallbladder Cancer Reveals Tumorigenesis and Therapeutic Response

PurposeGallbladder cancer (GBC) is a rare but highly lethal malignancy with one of the poorest prognoses among cancers of the digestive system cancers. However, current experimental models of GBC face critical limitations, particularly their dependence on immunodeficient hosts, which precludes the investigation of the tumor microenvironment. We aimed to establish a novel syngeneic immunocompetent mouse model that recapitulates human GBC and enables the investigation of tumor-immune interactions. Experimental DesignWe engineered a murine cell line (mGBC1-ZH) from normal mouse gallbladder organoids expressing Kras and Trp53 (encoding mouse p53) mutations. Tumorigenic potential of mGBC1-ZH was evaluated by subcutaneous and orthotopic implantation. RNA-Seq and WES was used to demonstrate its characterization and similarity with human GBC. Immunohistochemistry, CCK8, and transwell assays wereused to investigate the role of CXCL5 in GBC. Therapeutic responses to standard first-line chemotherapeutic agents was evaluated in the syngeneic GBC model. ResultsThis model supports both subcutaneous and orthotopic tumor growth in immunocompetent C57BL/6J hosts while preserving hallmark features of human GBC, including biliary epithelial differentiation (CK7+/CK19+), aggressive histopathology, and an immunosuppressive "cold" tumor microenvironment. Genomic characterization revealed recurrent chromosomal instability and copy number alterations mirroring human GBC. Comprehensive transcriptomic profiling revealed profound gene expression changes during the model development, and resembled transcriptional features between mGBC1-ZH and human GBC cell lines and samples. CXCL5 was found to be upregulated in human GBC, and promote proliferation, metastasis, and neutrophils infiltration of GBC in the syngeneic mouse model. Functional validation of the syngeneic GBC model demonstrated therapeutic responsiveness to frontline chemotherapeutics gemcitabine and cisplatin with significant in vivo tumor regression. ConclusionsIn summary, we establised a novel syngeneic GBC mouse model, overcoming the limitations of traditional models by enabling studies in immunocompetent hosts. This model provides valuable insights into the molecular evolution from normal gallbladder cells to transformed cancer cells and establishes a robust platform for both mechanistic studies and therapeutic development.

cancer biology↗

bioRxiv2025

Deep learning reveals a microprotein atlas in maize and uncovers novel regulators of seed amino acid metabolism

Microproteins represent a vast and functionally important class of genes that remain largely unexplored in plant genomes. Here, we developed DeepMp, a deep learning framework that integrated multi-omics evidence and built the most comprehensive plant microprotein atlas to date, identifying 18,338 high-confidence candidates in maize. The majority of these appear to have originated de novo from regions previously annotated as noncoding, and they show hallmarks of rapid, lineage-specific evolution and pronounced tissue specificity. These novel microproteins were found integrated into core regulatory networks, particularly in organ development and nutrient storage. Focusing on the maize kernel, population-scale analyses linked microprotein expression to natural variation in amino acid content. We functionally validated three grain-filling-specific candidates originating from noncoding regions by CRISPR-Cas9 knockouts, which confirmed their roles as precise modulators of arginine, aspartate, and methionine levels, without pleiotropic effects on kernel morphology. Our study provides a foundational resource and analytical framework, establishes microproteins as a new and functionally important coding layer in maize, and uncovers a previously untapped source of targets for crop improvement.

genomics↗

bioRxiv2025

Random barcode transposon-site sequencing in Mycobacterium tuberculosis reveals the functions of uncharacterized genes

Mycobacterium tuberculosis (Mtb) is a human bacterial pathogen that establishes chronic infection in the lung. Although the genome of Mtb was sequenced nearly 25 years ago, the genetic basis of Mtbs success as a human pathogen remains to be fully elucidated. Large-scale genetic approaches to understanding gene function are hindered by the limited throughput of traditional transposon sequencing strategies used in mycobacteria. To create a resource for determining the function of genes, we generated a pooled random barcode transposon-site sequencing (RB-TnSeq) library in Mycobacterium tuberculosis (Mtb). A unique twenty-nucleotide barcode in the transposon allows for rapid, high-throughput genetic screening without the laborious protocol of standard bacterial TnSeq screens. We performed 95 RB-TnSeq screens on an array of carbon sources, nitrogen sources, stressors, and antibiotics. Using the resulting dataset, we examined phenotypes of PE/PPE genes, a mycobacterial gene family whose function has long been elusive, uncovering 187 novel phenotypes across 37 genes in this family. We propose a pathway for lactate utilization in which the ESX-5 type VII secretion system exports PPE3, facilitating the import of D- and L-lactate into the bacterial cell. Notably, we identify a candidate D-lactate dehydrogenase that may mediate this metabolic capability. Additionally, we find that the proton-pumping NADH dehydrogenase Nuo is required for utilization of propionate, highlighting the metabolic flexibility of Mtb. Lastly, we characterize a novel mutant that confers resistance to the new tuberculosis antibiotic pretomanid. Results from these genetic screens will facilitate the development of additional new hypotheses about the function of uncharacterized genes and will expand our knowledge of Mtb metabolism and resistance to stress.

microbiology↗

bioRxiv2025

A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing

Antimicrobial resistance (AMR) poses a significant threat to public health. Rapid and accurate antimicrobial sensitivity testing is essential to guide effective treatment. Here, we present "simplified 5PSeq" (s5PSeq), a streamlined protocol for profiling 5 monophosphorylated (5P) mRNA degradation intermediates that reflect ribosome dynamics in vivo. By capturing antibiotic-induced, context-specific ribosome stalling events, s5PSeq provides a molecular proxy for bacterial growth inhibition--offering a molecular phenotypic readout without the need for culturing. s5PSeq reduces library preparation time to under four hours and incorporates a novel rRNA blocking strategy. We demonstrated its clinical utility by identifying erythromycin-resistant and sensitive Clostridioides difficile clinical isolates. Combining s5PSeq with real-time nanopore sequencing enables fast AMR diagnosis with as few as 3000 reads. In addition to simplifying the study of 5P co-translational mRNA decay, our work suggests that utilizing information-rich phenotypic molecular readouts can significantly improve AMR diagnostics. HighlightsO_LIs5PSeq is a streamlined protocol for profiling 5P mRNA degradation intermediates. C_LIO_LIContext-specific ribosome stalls can be used to assess phenotypic antimicrobial sensitivity at the molecular level. C_LIO_LIBlocking rRNA sequencing at the ligation step streamlines library preparation and lowers costs and hands-on time. C_LIO_LIIntegration with nanopore sequencing allows same-day antimicrobial sensitivity testing in species with 5-3 exonuclease. C_LI

microbiology↗

bioRxiv2025

Oxidative stress triggers RNAPII arrest through PARylation and DNA damage

UV or gamma irradiation, as well as certain chemicals, generate DNA damage that disrupts transcription through a variety of well-characterised mechanisms. In contrast, the transcriptional response to oxidative stress remains poorly understood. Here, we describe a rapid and widespread shutdown of transcription following oxidative DNA base damage. By monitoring RNAPII occupancy and elongation dynamics, we demonstrate that oxidative stress temporarily halts RNAPII pause release and arrests the progression of elongation complexes within the gene body. We present evidence that this occurs in a unique and transient manner, characterised by abrupt arrest of elongating RNAPII dead in its tracks, followed by rapid transcriptional recovery as DNA lesions are repaired. We find that the restriction of initiation and early elongation complexes is regulated by PARylation, whereas recovery of RNAPII arrested within the gene body requires DNA repair mediated by the base excision repair (BER) and single-strand break repair (SSBR) pathways.

molecular biology↗

bioRxiv2025

The dominance of gene expression controlled by trans-eQTL hotspots contributes to phenotypic heterosis in maize

Heterosis, or hybrid vigor, is a key phenomenon in genetics research and agricultural production, and has been primarily attributed to non-additive genetic effects such as dominance -- a prevailing consensus shaped by decades of empirical research and theoretical debate. Although dominance may arguably arise from distal modifiers, their selective advantage is debated due to presumably small individual effects. To address this long-standing question, particularly how genetic dominance manifests at the transcriptomic level and contributes to phenotypic heterosis, we integrated transcriptomic and phenotypic data from a large population of maize hybrids and their inbred parents. We found that [~] 30% of the expressed seedling genes in a significant proportion of hybrids exhibited expression patterns deviating from the average of the two parents, indicative of non-additivity. Further analysis suggests that while hybrid gene expression per se is primarily regulated by cis-eQTLs, expression dominance (or non-additivity) is disproportionately controlled by trans-eQTLs. These trans-eQTLs cluster into hotspots that regulate the non-additivity of hundreds of target genes, mostly within co-expression networks, and are notably enriched for transcription factors (TFs). Focusing on one such hotspot, we functionally validated a classical maize gene ZmR1, a basic helix-loop-helix (bHLH) TF associated with multiple seedling trait heterosis, as a candidate regulator of expression dominance across hundreds of genes. Overexpression of ZmR1 enhances expression dominance of downstream genes and increases phenotypic heterosis in both seedling and adult traits. Further experiments confirmed its direct regulatory role in modulating genes involved in anthocyanin biosynthesis and lignin metabolism, driving transcriptome-level dominance. These results provide empirical support for the modifier hypothesis under an omnigenic model, suggesting that heterosis arises not from the modification of a single genes inheritance but through the coordinated regulation of hundreds of phenotype-associated genes, thereby helping to reconcile the long-standing debate over the genetic basis of dominance in heterosis.

genetics↗

bioRxiv2025

TSProm: Deciphering the Genomic Context of Tissue Specificity

Characterizing tissue-specific (TSp) gene expression is crucial for understanding development and disease; however, traditional expression-based methods often overlook the latent "regulatory grammar" embedded in the non-coding DNA, particularly in distal promoter regions. Here, we introduce TSProm, a framework that specializes a DNA foundation model (DNABERT2) to decipher the long-range regulatory logic of TSp promoters at the gene isoform level. The contributions of our work are two-fold. First, we propose a novel comparative design that trains two distinct models, A: for general promoter biology and B: for TSp regulation. These models enable the precise isolation of sequence motifs around the transcription start site that uniquely define tissue identity. Second, we introduce a comprehensive explainable AI (xAI) module that integrates attention-based discovery with model-agnostic SHAP analysis to provide robust, cross-validated interpretations of learned features. Applying this framework to human brain, liver, and testis promoters, we identified and validated clinically relevant transcription factors (TFs) in the brain, including SP1, MYC, and HES6, and confirmed their known roles in diseases such as gliomas and neuroblastomas. Our analysis further revealed that C2H2 Zinc Finger proteins are a dominant feature of the global landscape of TSp gene regulation. TSProm provides a novel and interpretable framework for identifying TSp gene regulatory elements, offering powerful computational tools for the study of tissue-specific gene regulation in normal and disease conditions.

bioinformatics↗

bioRxiv2025

An intron-based timer for circadian rhythms

Abstract: Circadian clocks regulate daily rhythms in all eukaryotes through [~]24-hour transcriptional-translational feedback loops driven by clock proteins. However, the molecular mechanisms that set the 24-hour period remain poorly defined. Here, using single-molecule imaging and nascent RNA sequencing, we uncover an unexpected RNA-based molecular timer: a single intron in the Drosophila timeless (tim) gene that regulates circadian period length by controlling mRNA localization. Strikingly, we find that [~]50% of tim mRNAs are localized to the nucleus due to inefficient post-transcriptional splicing of a single intron (which we named intron P), in contrast to other core clock transcripts that localize predominantly to the cytoplasm. CRISPR-mediated removal of intron P abolishes nuclear retention of tim transcripts, leading to accelerated TIM protein accumulation and a shortened [~]22-hour period with reduced rhythmic robustness. Remarkably, insertion of intron P alone into heterologous reporters is sufficient to promote nuclear retention in both Drosophila and human cells, acting as a conserved checkpoint that withholds transcripts in the nucleus until splicing is complete. Finally, we identify three RNA-binding proteins, two repressors (Hrb27C and Squid) and one activator (Qkr58E-2, a Sam68 homolog), that modulate intron P splicing in a rheostat-like manner. Together, these findings establish tim intron P as the first intron-based molecular timer in circadian clocks and reveal splicing kinetics as a critical regulatory layer in temporal gene expression programs, with broad implications for other processes such as development and immunity.

molecular biology↗

bioRxiv2025

CellBin:a generalist framework to process spatial omics data to cell level

Spatial omics has rapidly expanded with increasingly diverse imaging modalities, molecular targets, and chip sizes. However, no general framework currently exists to construct cell level matrices that are robust across platforms and omics types. Here we present CellBin, a universal and scalable frame-work that unifies image stitching, cell segmentation, and spot-to-cell mapping for multiple spatial omics technologies. CellBin integrates a multi-field weighted stitching algorithm for large-area images, a family of U-Net-based models trained across diverse staining modalities, and an optimized computational architecture for high-throughput processing. Across five technological platforms and three omics data types, CellBin achieves robust segmentation and accurate single-cell matrix construction, consistently outperforming seven state-of-the-art methods in F1-score, cell size precision, and annotation accuracy. By providing a generalizable, cross-platform solution, CellBin bridges multiple spatial omics, enabling unified, high-resolution cell level analyses across technologies.

bioinformatics↗

bioRxiv2025

Selectivity Filter Dynamics Define Ion Conductance and Selectivity Differences in CNG and HCN Channels

Cyclic nucleotide-gated (CNG) channels and hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are key members of the cyclic nucleotide-activated ion channel family that translate intracellular cyclic nucleotide binding into electrical signals. Functionally, CNG channels drive large inward currents in photoreceptors and olfactory sensory neurons, whereas HCN channels are best known for their roles in pacemaker activity in the heart and the regulation of neuronal excitability. Despite their considerable sequence similarity and conserved overall architecture, these channels exhibit striking differences in ion conductance, K+ selectivity, and voltage dependence. Here, we performed microsecond-timescale atomistic molecular dynamics (MD) simulations to directly compare the ion conduction mechanisms of HCN and CNG channels, using the prototypical K+-selective channel MthK as a reference. Our simulations reproduced key features observed in single-channel patch-clamp electrophysiology and revealed that distinct selectivity filter architectures and dynamic behaviors are the primary determinants underlying the divergence in ion conductance and K+ selectivity between HCN and CNG channels. Together, these results provide a mechanistic framework for understanding the physiological roles of these channels and pave the way for the rational design of cation channels with tailored functional properties.

biophysics↗

bioRxiv2025

Targeted α-Synuclein mRNA Degradation by PMO-Based RNA-Degrading Chimeras

-Synucleinopathies are devastating neurodegenerative diseases characterized by pathological accumulation of a neuronal protein, -synuclein (Syn). Lowering soluble Syn levels is a promising therapeutic strategy to limit aggregation and neurotoxicity, but directly targeting this protein is hindered by its intrinsically disordered structure and other factors, such as its conformational heterogeneity and intracellular drug delivery barriers. Consequently, increasing attention has been directed toward targeting the SNCA transcript, which encodes Syn. Here, we developed phosphorodiamidate morpholino oligonucleotide (PMO)-based RNA-degrading chimeras (RDCs) that selectively bind the 5' untranslated region of SNCA mRNA and recruit RNase L for targeted RNA degradation. Through the systematic evaluation of 10 RDCs, we identified and optimized 4-D1, which effectively reduced SNCA mRNA and Syn protein expression in HEK293T cells in an RNase L-dependent manner. 4-D1 lowered SNCA transcript and Syn protein levels in both primary cortical neurons from humanized SNCA mice and in human induced pluripotent stem cell-derived cortical neurons. This reduction prevented prion-like seeding induced by patient-derived Syn fibrils and protected neurons from fibril-induced cytotoxicity. Finally, in vivo studies confirmed the efficacy of 4-D1 in reducing Syn mRNA expression in humanized SNCA mice. These findings indicate that PMO-based RDCs may represent a promising therapeutic modality for -synucleinopathies. Significance StatementAbnormal aggregation of the neuronal protein -synuclein is central to Parkinsons disease and related disorders, yet therapeutic candidates that directly target this protein have yet to demonstrate efficacy. in clinical trials. We developed a new strategy that lowers -synuclein production at the RNA level using phosphorodiamidate morpholino oligonucleotide (PMO)-based RNA-degrading chimeras (RDCs). These molecules recruit a natural RNA-degrading enzyme to selectively destroy the RNA transcript encoding -synuclein. Our lead RDC reduced -synuclein levels in cultured cells, humanized mouse and human neurons, blocked -synuclein pathological aggregation, and protected neurons from toxicity. This study establishes RDCs as a promising therapeutic platform for Parkinsons disease and other neurodegenerative diseases driven by -synuclein.

biochemistry↗

bioRxiv2025

Human Organoids Reveal PTEN-driven Mesendoderm Specification via Retinoic Acid Signaling Suppression

During early embryogenesis, epiblast cells ingress through the primitive streak (PS) and commit to a mesendoderm (MES) fate, giving rise to both mesodermal and endodermal lineages. Despite advancements in human organoid technology for modeling pre-implantation blastocyst stage, robust systems that accurately recapitulate MES specification and PS formation during the post-implantation stage remain limited. Here, we show that human induced pluripotent stem cells can be used to generate three-dimensional MES organoids that faithfully mimic in vivo human MES specification, particularly from the anterior PS. We demonstrate that MES organoid formation is dependent on PTEN expression and that loss of PTEN severely impairs the formation of mesoderm and definitive endoderm derivatives arising from MES organoids. To elucidate the molecular mechanisms underlying these defects, we conducted an integrative multi-omics analysis, including transcriptome, chromatin accessibility profiling, metabolism, and phosphoproteomics, on wild-type and PTEN-/-MES cells. These analyses revealed that PTEN suppresses retinoic acid (RA) signaling during MES lineage commitment. Furthermore, we identified the RA-degrading enzyme CYP26A1 as a downstream effector of PTEN. Notably, while excessive RA induced by PTEN ablation is detrimental to MES cell generation, physiological levels of RA are necessary. Collectively, our human MES organoids offer a valuable model for dissecting early human development, and our findings identify PTEN as a key regulator of MES fate commitment through inhibition of RA signaling.

developmental biology↗

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↗