Biology subjects

Yu, Y.

Publications and source records attributed to Yu, Y..

At least 163 records · Page 9Linked to original sources

bioRxiv2025

Role of DEPDC1 in Glioblastoma Malignant Phenotype and Radiosensitivity

Radiotherapy has significantly improved survival outcomes in glioblastoma (GBM) patients, particularly when combined with tumor resection and temozolomide chemotherapy. However, radioresistance remains a major obstacle, limiting further advances in prognosis and potential cure. DEPDC1, a gene implicated in various malignant phenotypes, has not yet been investigated for its role in GBM radioresistance, despite suggestive evidence from previous studies. In this study, analysis of the cancer database and GBM tissue microarrays revealed that DEPDC1 expression is significantly elevated in GBM tissues compared to normal brain tissues. Using GBM cell lines with DEPDC1 knockdown, we observed markedly reduced proliferation and motility. Notably, DEPDC1 downregulation significantly enhanced radiosensitivity, as demonstrated by increased radiation-induced apoptosis, G2/M phase arrest, DNA damage, and impaired DNA repair post-radiation, resulting in lower survival rates in clonogenic assays. Mechanistically, these effects may be mediated through DEPDC1-driven upregulation of NF-{kappa}B, supported by tumor sample analysis from our xenograft mouse model. Collectively, our findings suggest that DEPDC1 is not only involved in GBM malignancy but also represents a promising therapeutic target for overcoming radioresistance and developing effective radiosensitizers.

cancer biology↗

bioRxiv2025

Denoising Single-Cell RNA-Seq Data with a Deep Learning-Embedded Statistical Framework

Single-cell RNA sequencing (scRNA-seq) provides extensive opportunities to explore cellular heterogeneity, but is often limited by substantial technical noise and variability. To overcome these issues, we present ZILLNB, a novel computational framework that integrates zero-inflated negative binomial regression with deep generative modeling to simultaneously denoise and impute scRNA-seq data. By integrating a deep generative model, ZILLNB effectively captures latent group structures at both the cellular and gene levels, thereby enhancing the accuracy of recovered gene expression profiles while retaining cell-type-specific expression patterns. Comparative evaluations demonstrate that ZILLNB outperforms existing methods in accurately identifying differentially expressed genes and delineating biologically meaningful cell subpopulations. Moreover, ZILLNB exhibits versatile applicability, including effective correction of batch effects, making it a broadly useful tool for enhancing scRNA-seq data analyses.

bioinformatics↗

bioRxiv2025

Beyond the Axoneme: Whole-Cell Proteomics Identifies Novel Regulators of Ciliogenesis in Xenopus Epidermal Multiciliated Cells

Motile cilia generate directional fluid flow critical for development and tissue homeostasis, and their dysfunction underlies a range of human diseases. Prior proteomic studies have focused on isolated axonemes, leaving the regulatory components of ciliogenesis located in other cellular compartments of multiciliated cells (MCCs) largely unidentified. To bridge this gap, we performed whole-cell proteomic profiling of MCCs in Xenopus using an inducible system that enables selective MCC-enrichment. Leveraging a single-vessel in-cell proteomics approach with ultra-high sample preservation, we identified over 9,000 proteins, including 832 upregulated in MCCs. These encompassed both established ciliary components and novel candidates localized to distinct ciliary structures. Functional validation confirmed the involvement of previously uncharacterized proteins in ciliogenesis. This study presents a high-resolution, whole-cell proteome of vertebrate MCCs, providing critical insights into the molecular networks that govern ciliogenesis and offering a valuable resource for understanding the mechanisms of cilia-related disorders.

developmental biology↗

bioRxiv2025

Locus-specific Convergent Evolution and Interchromosomal Rearrangements Contribute Type I Interferon Diversification in Amniotes

Type I interferons (IFN-Is) play essential roles in antiviral immune responses. The extensive diversification of IFN-Is into multiple subtypes and redundant gene copies has posed significant challenges for evolutionary reconstruction. To address this, we developed an integrated analytical pipeline combining the IFN-SCOPE classification model and GENE-GRADE algorithm. Through comprehensive synteny-guided phylogenetic analysis, we identified three evolutionarily conserved IFN-I loci (HACD4, MOB3B, and UBAP2) that maintain chromosomal colocalization across all major amniote lineages - mammals, squamates, and Archelosauria (turtles, crocodilians, and birds). While MOB3B-locus maintains a single IFN-{kappa} ortholog, the HACD4 (IFN-H) and UBAP2 (IFN-U) loci show lineage-specific expansion patterns: IFN-H proliferated in mammals/reptiles but remained single-copy in birds, whereas IFN-U expanded in birds but not in other lineages. Phylogenetic analysis reveals these independently evolved multicopy genes nevertheless cluster into two conserved subgroups (IFN-H2/H1 and IFN-U2/U1), suggesting convergent functional specialization. Within IFN-H and IFN-U clusters, the single-copy IFN-H2 and IFN-U2 genes - positioned at the ancestral ends of their respective genomic arrays - likely represent the progenitor sequences of each locus. Notably, among mammalian IFN-H2 genes, we identified the poorly characterized IFN-{upsilon} (rather than IFN-{beta}) as the ancestral form of mammalian IFN-H subtypes. Furthermore, we identified IFN-I genes at non-canonical loci resulting from interchromosomal duplication events in tortoises and diving ducks and provide clear evidence that interchromosomal duplications contributed to IFN-I gene diversity. These discoveries advance our understanding of the evolutionary mechanisms shaping intronless IFN-I genes in amniotes, and potentially beneficial for developing novel IFN-I based antiviral treatments through comparative immunological approaches.

bioinformatics↗

bioRxiv2025

MAPT Splicing Modulators as a Therapeutic Strategy for Tauopathies

Tauopathies are neurodegenerative diseases characterized by the abnormal accumulation of microtubule-associated protein tau (MAPT) in the brain. These disorders, like frontotemporal dementia (FTD-Tau), currently lack effective therapies and can occur sporadically or be inherited when associated with MAPT gene mutations. The MAPT gene region encompassing exon 10 and adjacent introns is a hotspot for pathogenic variants, including splicing mutations that enhance exon 10 inclusion and increase 4R tau expression, and gain-of-function mutations that generate aggregation-prone mutant 4R tau protein. For these 4R-specific tauopathies, a targeted mRNA splicing approach that promotes exon 10 exclusion may offer therapeutic benefit. In this study, we discovered novel splicing modulator compounds (SMCs) that promote MAPT exon 10 exclusion, and demonstrated their efficacy in FTD patient-derived neuronal models carrying the tau-P301L gain-of-function mutation or the tau-S305N splicing mutation. Treatment with SMC reduced 4R tau expression and decreased the accumulation of hyperphosphorylated tau (pTau), oligomeric and insoluble tau, thereby rescuing tau-associated neuronal toxicity. Importantly, our lead SMC corrected the 3R/4R splice ratio in vivo and significantly reduced pTau in the brain of a gene- replacement (GR) mouse model expressing the human tau-N279K splicing mutation. These findings support the therapeutic potential of this class of small molecules and establish MAPT pre- mRNA splicing modulation as a promising strategy for the treatment of 4R tauopathies. One Sentence SummaryDiscovery of SMCs that correct MAPT splicing, reduce 4R tau, and rescue pathology in patient- derived neuronal and in vivo models of 4R tauopathies.

neuroscience↗

bioRxiv2025

Antigenic and Virological Characteristics of SARS-CoV-2 Variant BA.3.2, XFG, and NB.1.8.1

The emergence of the SARS-CoV-2 saltation variant BA.3.2, which harbors over 50 mutations relative to its ancestral BA.3 lineage, has raised concerns about its potential to drive outbreaks similar to BA.2.86/JN.1. Concurrently, variants such as NB.1.8.1, LF.7.9, XEC.25.1, XFH, and XFG exhibit enhanced growth advantages over LP.8.1.1, necessitating a comparative analysis of their antigenic and virological characteristics. Here, we evaluated the infectivity, ACE2-binding efficiency, and immune evasion of these variants. Pseudovirus assays revealed BA.3.2s robust antibody evasion, including resistance to Class 1/4 monoclonal antibodies; however, its ACE2 engagement efficiency was markedly reduced due to a closed spike conformation, leading to low infectivity. While XFG and LF.7.9 demonstrated strong immune escape associated with A475V and N487D mutations, their reduced receptor-binding efficiency suggested a need for compensatory adaptations. In contrast, NB.1.8.1 retained high ACE2 affinity and humoral immune evasion, supporting its potential for future dominance. Collectively, BA.3.2s current profile limits its ability to compete with emerging variants like NB.1.8.1. Sustained monitoring of BA.3.2s evolution-- particularly for mutations stabilizing an open RBD conformation or enhancing escape from Class 1 antibodies--is essential to assess its outbreak potential.

immunology↗

bioRxiv2025

PepSeek: Universal Functional Peptide Discovery with Cooperation Between Specialized Deep Learning Models and Large Language Model

Recent computational foundation models have revitalized the scientific discovery pipeline. However, developing foundational models for functional peptide discovery is costly due to the scarcity of wet-lab validated data. Meanwhile, conventional deep learning models are hard to generalize to unseen tasks or data distribution. Here, we introduce PepSeek, a universal approach for peptide discovery that synergistically integrates the most advanced large language model (LLM) with specialized small models. PepSeek harnesses the robust reasoning and generalization capabilities of LLM while leveraging the high predictive accuracy of specialized models trained for tasks such as antimicrobial activity regression and functional peptide generation. We have devised multiple collaborative strategies and task-specific modules demonstrating leading performance in peptide identification and generation. Notably, PepSeek achieves remarkable zero-shot prediction accuracy for peptides with diverse functionalities. We used PepSeek to identify a group of broad-spectrum antimicrobial peptide that exhibits low toxicity and high activity against drug-resistant bacteria, with the best surpassing all peptides currently undergoing clinical trials. Our framework establishes a new pipeline for scientific discovery with the help of LLM and specialized models.

bioinformatics↗

bioRxiv2025

Robotic performance is comparable to human operators for cell therapy manufacturing tasks

Although numerous cell and gene therapies have received regulatory approval, their adoption has been hampered by high cost and challenges in scaling out manufacturing. Many autologous cell therapies are individually manufactured for each patient using traditional manual methods in high-cost environments. Therefore, robotics and automation offer a potential solution to meet the growing demand for such therapies. To ensure identical biological outcomes, automation must replicate validated manual workflows, a requirement that poses significant engineering challenges, especially for aseptic manipulation and compatibility with manual-centric instruments and consumables. Here we describe the design and performance of a modular robotic cluster consisting of specialized modules containing widely adopted equipment. The robotic arm uses custom end-effectors to handle standard consumables and instruments such as syringes, vials, bags, cell counters, bioreactors, incubators, and closed centrifuges. We compared the performance of skilled human operators against the robotic cluster across multiple tasks: transferring cells between sterile bags, cell counting, drawing volume from a vial to a syringe, and resuspension and sampling from both a bag and G-Rex 100M-CS bioreactor. The robotic system also executed high-complexity operations with industry-standard instruments: cell selection using a CytoSinct 1000 and wash/buffer exchange with a CTS Rotea Counterflow centrifugation system. Experimental results for each unit operation show that the robotic clusters performance is equivalent to manual operations on the selected key metrics. These data demonstrate that the robotic system can efficiently and robustly perform specific unit operations, which can be combined in any order for end-to-end cell therapy manufacturing processes. One Sentence summaryA modular robotic system can perform key unit operations in cell therapy manufacturing with accuracy comparable to human operators while ensuring throughput and flexibility.

bioengineering↗

bioRxiv2025

Sleep firing rate homeostasis is disrupted in mild parkinsonism

Sleep-associated downscaling of neuronal firing, i.e., firing rate homeostasis (FRH), is essential for restorative sleep. Sleep dysfunction is common in Parkinsons disease (PD), but FRH has not been investigated. Here, using a within-subject design in the nonhuman primate model of PD, we report that thalamocortical FRH is disrupted in parkinsonism. These findings can inform therapeutic approaches tailored towards normalizing FRH to reestablish restorative sleep in PD.

neuroscience↗

bioRxiv2025

Harnessing the Power of Single-Cell Large Language Models with Parameter Efficient Fine-Tuning using scPEFT

Single-cell large language models (scLLMs) capture essential biological insights from vast single-cell atlases but struggle in out-of-context applications, where zero-shot predictions can be unreliable. To address this, we introduce a single-cell parameter-efficient fine-tuning (scPEFT) framework that integrates learnable, low-dimensional adapters into scLLMs. By freezing the backbone model and updating only the adapter parameters, scPEFT efficiently adapts to specific tasks using limited custom data. This approach mitigates catastrophic forgetting, reduces parameter tuning by over 96%, and decreases GPU memory usage by more than half, significantly enhancing scLLMss accessibility for resource-constrained researchers. Validated across diverse datasets, scPEFT outperformed zero-shot models and traditional fine-tuning in disease-specific, cross-species, and under-characterized cell population tasks. Its attention-mechanism analysis identified COVID-related genes associated with specific cell states and uncovered unique blood cell subpopulations, demonstrating scPEFTs capacity for condition-specific interpretations. These findings position scPEFT as an efficient solution for improving scLLMs utilities in general single-cell analyses.

cell biology↗

bioRxiv2025

DICAR-JP Regulates Ribosome Migration, a New Theory of Mitochondrial Protein Production

BackgroundDICAR plays a cardioprotection of diabetic models. DICAR-JP, a short sequence of DICAR, may represent DICARs active functional domain. NAC is necessary for the heart tissue development. Addtionally, OGDHL is a metabolism regulator. In this study, we examine a new mechanism of DICAR via NAC/OGDHL on regulating cardiomyocyte metabolism in DCM. We also sought to elucidate the function of DICAR/DICAR-JP in modulating NAC-dependent production of OGDHL nascent peptides and their mitochondrial translocation, and we also aimed to optimize the DICAR-JP sequence to be better therapy on DCM. MethodsSPR was to investigate the binding interaction between DICAR-JP and NAC. The function of DICAR-JP and DICAR-JP45 on OGDHL nascent peptide transfection was detected by in vitro translation approach. Biotin-DICAR-JP was transfected to study the function of DICAR-JP, NAC and OGDHL. Untargeted metabolomics was utilized to characterize the metabolic reprogramming of cardiomyocytes. AAV9-DICAR-JP and DICAR-JP45 were constructed and administered to db/db mice for 1-2 months to assess their cardioprotective effects detected by Echocardiography confirmed mouse cardiac function. ResultsOur findings demonstrated that DICAR-JP be the functional domain that interacts with NAC to regulate OGDHL nascent peptide expression. Disruption of OGDHL expression reversed the metabolic reprogramming observed in diabetic cardiomyocytes, highlighting its crucial role in maintaining cardiac metabolic homeostasis. DICAR-JP facilitated the translocation of OGDHL nascent peptides from the cytoplasm to the mitochondria, leading us to hypothesize that DICAR-JP plays a key role in regulating ribosomal migration from the endoplasmic reticulum to the mitochondria. We refer to this process as the Ribosome Migration. In our studies using AAV9-mediated DICAR-JP and DICAR-JP45 overexpression in heart tissue. DICAR-JP and DICAR-JP45 both exhibited significant cardioprotective effects against diabetic cardiomyopathy (DCM), comparable to those observed with Empagliflozin. ConclusionsIn a conclusion, we propose a new endogenous nucleic acid candidate drug library, and a new molecular framework, the Ribosome Migration, which implicates the DICAR-JP/NAC/OGDHL nascent peptide axis in metabolic reprogramming related to DCM. This theory constructs a new mitochondrion protein from nuclear original protein. Moreover, DICAR-JP45 shows strong potential as a nucleic acid-based therapeutic candidate for treating DCM. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSDICAR is a new protective circular noncoding RNA for diabetic cardiomyopathy. NAC is located in ribosome and regulates new peptide production, which is also a key factor in heart tissue development. OGDHL can regulate different energy metabolism in mitochondria. What New Information Does This Article Contribute?DICAR-JP is the functional domain that interacts with NAC to regulate OGDHL nascent peptide expression. There is an interaction between DICAR-JP and NAC. DICAR-JP sequence is protected by NAC and NAC function is mediated by DICAR-JP. We called this RNA functional domain. OGDHL expression reversed the metabolic reprogramming observed in diabetic cardiomyocytes, highlighting its crucial role in maintaining cardiac metabolic homeostasis. DICAR-JP takes part in tanscription and translocation of OGDHL nascent peptides from the cytoplasm to the mitochondria via plasma ribosome. We call this process the Ribosome Migration Theory. DICAR-JP and DICAR-JP45 both exhibited significant cardioprotective effects against diabetic cardiomyopathy (DCM), comparable to those observed with Dapagliflozin (DAPA). Our study revealed a novel molecular framework, the Ribosome Migration Theory, which implicates the DICAR-JP/NAC/OGDHL nascent peptide axis in metabolic reprogramming related to DCM. Moreover, DICAR-JP45 shows strong potential as a nucleic acid-based therapeutic candidate for treating DCM.

pharmacology and toxicology↗

bioRxiv2025

Intestinal Tissue Mechanics Regulate Angiogenesis and Stem Cell Proliferation via Vascular Piezo

The vasculature is a prominent component of developmental and adult tissue microenvironments. How tissue specific characteristics and environmental states influence vascular biology and function, remains largely understudied. Using the fruit fly Drosophila melanogaster midgut and its associated vascular-like tracheal system, we discover reciprocal, mechanochemical interorgan communication between the adult intestine and its vascular microenvironment, which influences vascular and stem cell adaptations during intestinal regeneration. Mechanistically, apoptotic epithelial cells contribute to biomechanical remodelling of the regenerating midgut, which is associated with activation of Piezo in a subset of gut tracheal cells. Piezo drives activation of the mechanosensitive transcription factor Yorkie/YAP, leading to tracheal remodelling and intestinal stem cell proliferation. Furthermore, we identify a conserved role of mammalian vascular Piezo1 influencing remodelling of the intestinal crypt vasculature, and intestinal regeneration upon DNA damage and inflammation in mice. Our cross-species in vivo study reveals the presence of biomechanically distinct compartments in the regenerative intestine and identifies mechanosensory interorgan signalling, which contributes to intestinal regeneration through the vascular-stem cell niche. Furthermore, our work highlights the importance of studying tissue- and context-specific vascular biology to better understand intestinal compartmentalization, plasticity, and the complexity of tissue/vasculature interactions within a living organ.

developmental biology↗

bioRxiv2025

A biGWAS strategy reveals the genetic architecture of the interaction between wheat and Blumeria graminis f. sp. tritici

BackgroundWheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt) is one of the most significant diseases affecting global wheat production. Breeding for disease resistance (R) genes against Bgt often follows a boom-bust cycles, where cultivars with effective resistance are widely deployed on an expanding area until virulence emerges in the avirulence (Avr) pathogen population. While extensive effort has been devoted to identifying and cloning R genes, Avr genes remain relatively understudied, limiting our understanding of R-Avr interactions. That said, understanding R-Avr interactions is crucial for developing durable resistance strategies. ResultsWe conducted whole genome sequencing on 245 Bgt isolates collected from major wheat-growing regions in China, identifying 120 genetically unique isolates. Each of these unique isolates was inoculated and phenotyped on a diverse panel of wheat germplasm. Through Genome-Wide Association Analysis (GWAS) in both Bgt and wheat, we identified 65 Avr loci and 251 R loci overlapping with nine and eight cloned Avr or R genes, respectively. On average, each isolate carries eight Avr alleles, ranging from one to 17. Little geographical preference for Avr alleles or their combinations was observed, suggesting that disease resistance breeding against this pathogen should be coordinated at the national level. The level of resistance level is positively correlated with the number of R alleles carried by a wheat line, and the average frequency of an R allele is 2% among the wheat panel, indicating the potential for accumulating R alleles in breeding programs. We mapped 212 R-Avr interactions based on joint GWAS using both plant and pathogen genomes and cross-species epistasis, where a network of interactions was formed between wheat and Bgt. These interactions indicate that pyramiding five major R loci has the potential to confer resistance to half of the Avr loci. As a proof of concept, we successfully verified two previously described R-Avr pairs using tobacco experiments. Furthermore, we provided molecular validation evidence for three new Avr genes, including Bgt-50651, BgtE-5826 and BgtE-20009, and two new R-Avr interactions. Among them, Bgt-50651 interacts with Pm1a, Pm2a, and another unidentified R gene located near the Pm6/Pm52 interval. ConclusionOur study provides a framework for understanding the genetic interaction between plants and pathogens. The discovery of novel R/Avr loci and their complex interaction network underscores the need to integrate crop and pathogen genetic background, particularly the R/Avr allele composition, into breeding program design. These findings have significant implications for developing durable resistance strategies in wheat alongside offering valuable insights into the broader dynamics of plant-pathogen interactions.

genomics↗

bioRxiv2025

SpatioCell: A Deep Learning Algorithm for High-resolution Single-cell Mapping through Deep Integration of Histology Image and Sequencing Data

Spatial transcriptomics (ST) is a powerful assay to capture gene expression in tissue context. However, due to the limitation of resolution, most existing ST datasets remain at multicellular resolution which hinders comprehensive understanding of the spatial organization. We propose SpatioCell, a computational algorithm to automatically extract both cell type and expression information at single-cell resolution from ST data, through a morpho-transcriptomic spatial reconstruction framework solved via dynamic programming, integrating morphological and transcriptomic information. This framework enables deterministic single-cell spatial reconstruction, assigning cell identities to precise locations rather than inferring spot-level cell-type composition and expression, and further uncovers overlooked microenvironment features while correcting deconvolution errors. Using the ST data from triple negative breast cancer as an example, SpatioCell reveals the significance of the distance between cancer-associated fibroblast (CAF) and tumor or immune cells for disease progression. The establishment of SpatioCell will broaden the biomedical applications of ST and facilitate investigations of single-cell spatial organization.

bioinformatics↗

bioRxiv2025

Developing a zebrafish xenograft model of diffuse midline glioma

Diffuse midline glioma (DMG) is a highly aggressive brain tumor that predominantly affects children. Conventional treatments such as radiation therapy can control progression for a time, but DMG kills nearly 100 percent of patients. Although murine models have provided critical insights into the biology of DMG and in assessing new therapeutic strategies, they are not suitable for high-throughput screening to identify and profile novel therapies due to technical challenges, ethical considerations and high cost. Zebrafish (Danio rerio) is an established vertebrate model for large-scale drug screening, and zebrafish have demonstrated the ability to replicate the key biological and pathlogical aspects of human malignancies. Here, we developed a novel method for transplanting human DMG cells into large numbers of zebrafish embyros to speed the assessment of anti-tumor drug efficacy in vivo and thereby facilitate the development of novel therapeutics for clinical translation. We transplanted red fluorescent protein (RFP)-labeled, patient-derived DMG cell lines into zebrafish blastulas. Remarkably, many DMG cells migrate into the developing brain and are present in the midline of the brain 24 hours after blastula injection. Tumor cell burden was monitored by measuring RFP fluorescence intensity changes over time. Time-course images of transplanted tumor cell volumes were acquired, and the interactions between transplanted DMG cells and microglial cells were further analyzed using Imaris software. We have developed a simple and rapid transplantation protocol to establish a zebrafish xenograft model of DMG. Our method involves transplanting DMG cells into the blastula stage (1000 cell stage) of zebrafish embryos, which does not require complex surgical techniques. This approach allows for the transplantation of hundreds of embryos per hour, significantly increasing the efficiency of creating DMG zebrafish xenografts that are suitable for high-throughput drug and gene discovery screens.

cancer biology↗

bioRxiv2025

Emergence of a New ST617 Hypervirulent Klebsiella pneumoniaewith ESBL+ and Strong Biofilm Forming Ability in China

The increasing infections caused by hypervirulent Klebsiella pneumoniae (hvKP) resistant to carbapenem, broad-spectrum {beta}-lactam and colistin has posed great challenges to global public health. However, the typing and detailed molecular features of the multi-drug resistant hvKP remain to be improved. Here, we characterized a broad-spectrum {beta}-lactam-resistant K. pneumoniae ST617 isolate that has not been previously reported to cause severe disease in China. We obtained the whole-genome sequence of one K. pneumoniae ST617 isolate--HZ7--from a patient with bile duct infection. Phylogenetic reconstruction was performed to investigate the possible host evolutionary origin of HZ7, and the virulence property was studied in comparison with the nearest ST617 neighbours--YZ strains isolated from patient blood infections. Our studies indicated that the HZ7 is an ESBL+ Kp that is likely evolved from environmental or animal-derived sources. Importantly, the virulence assay showed that HZ7 was highly virulent and compared with the well known hvKP strain--NTUH-K2044 and the highly virulent clinical strain ST11-K64--HZ54--isolated from a patient with severe pneumonia. In addition, HZ7 showed strong biofilm formation ability. Whole-genome sequencing analysis identified seven potential virulence genes in HZ7: kp7_000748, kp7_002156, kp7_002157, kp7_002158, kp7_002159, kp7_003103, kp7_003104, which are absent in K. pneumoniae patient isolates from Yangzhou and the environmental samples. Finally, transcriptomic analysis of HZ7 identified six genes--wcaJ, fimA, mrkH, pgaA, ugd, and gndA that are associated with biofilm formation. Given its high virulence likely associated with the seven unique genes acquired via horizontal transfer and strong biofilm forming ability, this strain should be closely monitored to prevent wider spread in the clinic.

microbiology↗

bioRxiv2025

Deep Spatial Sequencing Revealing Differential Immune Responses in Human Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is one of the most lethal cancers for humans. HCC is highly heterogeneous. In this study, we performed ultra-depth ([~]1 million reads per spot) spatial sequencing on a case of HCC. Sixteen distinct spatial expression clusters were identified. Each of these clusters was spatially contiguous and had distinct gene expression patterns. In contrast, benign liver tissues showed minimal heterogeneity in terms of gene expression. Numerous immune cell-enriched spots were identified in both HCC and benign liver regions. Cells adjacent to these immune cell-enriched spots showed significant alterations in their gene expression patterns. Interestingly, the responses of HCC cells to the nearby immune cells were significantly more intense and broader, while the responses of benign liver cells to immune cells were somewhat narrow and muted, suggesting an innate difference in immune cell activities towards HCC cells in comparison with benign liver cells. When standard-depth sequencing was performed, significant numbers of genes and pathways that were associated with these changes disappeared. Qualitative differences in some pathways were also found. These results suggest that deep spatial sequencing may help to uncover previously unidentified mechanisms of liver cancer development.

cancer biology↗

bioRxiv2025

A large-scale method to measure the absolute stoichiometries of protein Poly-ADP-Ribosylation

Poly-ADP-ribosylation (PARylation) is a reversible posttranslational modification that occurs in higher eukaryotes. While thousands of PARylated substrates have been identified, the specific biological functions of most PARylated proteins remain elusive. PARylation stoichiometry is a critical parameter to assess the potential functions of a PARylated protein. Here, we developed a large-scale strategy to measure the absolute stoichiometries of protein PARylation. By integrating mild cell lysis, boronate enrichment and carefully designed titration experiments, we were able to determine the PARylation stoichiometries for a total of 235 proteins. This approach enables the capture of all PARylation events on various amino acid acceptors. We revealed that PARylation occupancy spans over three orders of magnitude. However, most PARylation events occur at low stoichiometric values (median 0.578%). Notably, we observed that high stoichiometry PARylation (>1%) predominantly targets proteins involved in transcription regulation and chromatin remodeling. Thus, our study provides a systems-scale, quantitative view of PARylation stoichiometries under genotoxic conditions, which serves as invaluable resources for future functional studies of this important protein posttranslational modification.

biochemistry↗