Biology subjects

Xie, L.

Publications and source records attributed to Xie, L..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Optic nerve regeneration requires the intracellular domain of LIFRa/CD118

Identifying cell-autonomous and non-autonomous factors that govern retinal ganglion cells (RGCs) ability to extend axons is an important step in developing therapies to achieve recovery after optic nerve injury. Here we report that the intracellular domain of the leukemia inhibitory factor receptor (LIFR/CD118) is essential for mature RGCs ability to regenerate injured axons independent of the cognate ligand (LIF) and other therapies. Overexpression of LIFR in adult RGCs induces neurite outgrowth in cultured RGCs and axon regeneration in vivo while strongly amplifying RGCs response to LIF itself and to unrelated growth factors. Conversely, in loss-of-function studies, down-regulation of LIFR eliminates the pro-regenerative effects of Pten deletion and other potent stimuli. LIFR bidirectionally regulates the constitutive activity of the MAP kinase pathway, in contrast to LIF itself, which primarily activates pSTAT3. Expression of a truncated LIFR lacking the extracellular domain is sufficient to promote axon regeneration and selectively increases the survival of particular RGC subtypes, placing the LIFR intracellular domain as an essential, cell-autonomous regulator of optic nerve regeneration.

neuroscience↗

bioRxiv2025

Chromatin is a long-range force generator that regulates plasma membrane tension and cell integrity independently of gene expression

Primarily studied for its role in gene expression, chromatin organization is emerging as an important regulator of nuclear mechanics. Although the nucleus is in mechanical equilibrium with the cell, we do not know whether and how chromatin reorganization actively regulates the mechanical properties and downstream behaviors of cells. Here, we tested the hypothesis that as a dynamic crosslinked polymer, chromatin directly impacts cell mechanics independently of transcription by studying NETosis: a transcription-independent process where chromatin decompacts and the plasma membrane (PM) ruptures. Using high resolution microscopy and ATAC-see, we found that chromatin accessibility progressively increases during NETosis suggesting that chromatin binding proteins (CBPs) dissociate from chromatin during NETosis. To determine the identity and dynamics of these dissociated CBPs, we used fluorescent recovery after photobleaching to measure the mobility and localization of the linker histone H1, the nucleosomal histone H3 and the heterochromatin binding protein HP1. We found that the mobile fraction of nuclear H1 increases during NETosis while fractions of HP1 and H3 diffuse outside of the nucleus suggesting that they become cytosolic osmolytes and potentially alter the mechanical state of cells. Consistently, we found that plasma membrane tension and cell volume increase as chromatin decompacts during NETosis. In non-NETing U2OS cells, we found that inducing chromatin decompaction increases plasma membrane tension, independently of the cytoskeleton, indicating a causal relationship between chromatin organization, cell volume and plasma membrane tension. Our findings reveal a novel non- genetic role of chromatin in cellular biophysics: regulating cell volume, PM tension, and thus, overall cell mechanics. Considering the critical role of cell mechanics in biological processes such as cell migration, proliferation and pathogen killing, our work broadens our understanding of how chromatin regulates cell physiology and pathology. Significance StatementChromatin organizes our DNA inside the nucleus and is important for gene expression. However, chromatin is also a polymer which can passively regulate the rigidity of the nucleus, but whether and how chromatin can actively regulate the mechanical properties of the whole cell remains unknown. Here, we leverage the immune process of NETosis to show that the organization of chromatin inside the nucleus actively regulates the volume and tension of cells. Our work establishes chromatin as a long-range force generator in cells, broadening our understanding of the roles of this crucial polymer network in cells and opening the door to new strategies for controlling the mechanical properties of cells as needed by their physiology.

cell biology↗

bioRxiv2025

A time-resolved atlas of histone modifications during mitotic entry

Mitotic chromosome formation is essential for faithful chromosome segregation in metazoans. While condensin complexes are critical for the formation of rod-shaped mitotic chromosomes, additional mechanisms--particularly those involving phosphorylation and deacetylation of specific histone residues--have been proposed to contribute a further 2- to 4-fold reduction in mitotic chromatin volume. In this study, we employ high-resolution mass spectrometry to determine the kinetics of histone modifications in cell cultures undergoing a highly synchronous mitotic entry at 2.5-minute resolution. Our analysis reveals three different programmes of histone H3 phosphorylation on T3, S10 and S28. These modifications are consistent with methyl-phos switches regulating the association of readers with chromatin other than at promoters. Mass spectrometry and quantitative ChIP-Seq reveal that H3 T3 phosphorylation is a general marker of heterochromatin and not specifically centromeres as previously suggested. Finally, we show that histone acetylation undergoes only modest changes as rod-shaped chromosomes form during unperturbed mitotic entry. Thus, previously reported reductions in acetylation associated with chromosome formation were apparently attributable to delays in mitotic exit used as part of mitotic synchronisation protocols. The mechanism of condensin-independent chromatin compaction in mitosis remains unexplained.

cell biology↗

bioRxiv2025

Long-lived IgE plasma cells that reside in the spleen contribute to the persistence of the IgE response

IgE plasma cells (PC) producing high affinity antibodies are critical players in allergic diseases. Allergies may persist or resolve over time, but the factors involved in their evolution are not well known. Sustained production of IgE antibodies, even in the absence of allergen exposure in persistent allergy, suggests the existence of long-lived IgE PC. However, the ability of IgE PC to undergo terminal differentiation and become long-lived has been questioned. Here we demonstrate that IgE PC undergo swift maturation into non-dividing MHCIIlowCD93+CD98high PC in immunized mice. Mature IgE PC have a distinct transcriptional profile for adaptation to high protein synthesis, glycosylation, and survival. Using PC timestamping, long-lived IgE PC could be found several months after immunization in mice. Remarkably, the spleen rather than the bone marrow, was a main tissue of residence of mature long-lived IgE PC. Our findings provide key insights to understand IgE production in persistent allergy. HighlightsO_LIIgE PC form in a narrow window after immunization and undergo swift maturation. C_LIO_LITimestamping reveals the existence of CD93+CD98highMHCIIlow long-lived IgE PC. C_LIO_LIThe spleen and lymph nodes are the main tissues of mature IgE PC residence. C_LIO_LIIgE PC use distinct adaptations to high antibody secretion and survival. C_LI

immunology↗

bioRxiv2025

DNA Sequence Trace Reconstruction Using Deep Learning

Deciphering DNA sequences is fundamental to unlocking the mysteries of life, but the high dimensionality and complexity of biological sequence data significantly hinder knowledge discovery. In particular, the challenges of sequence length, repetitive regions, and structural complexity make it difficult to directly reconstruct complete DNA sequences from raw data. Therefore, this paper proposes a DNA sequence trace reconstruction model, DNARetrace, which performs preprocessing and dataset construction, and then employs a Bidirectional Fourier-Kolmogorov-Arnold Network (Bi-FKGAT), using an extremely unbalanced loss function for link prediction, so as to reconstruct the original DNA sequence. In multi-angle experiments using both simulated and real data, DNARetrace successfully reconstructs DNA sequence traces across large-scale datasets derived from various DNA sequencing methods, overcoming the bias of current approaches toward specific sequencing platforms, and achieves competitive outcomes in DNA storage and genomics downstream tasks. We further validated the expandability of the proposed methods in DNA sequence classification and metagenomic binning tasks. In summary, DNARetrace is compatible with various sequencing scenarios; it reduces the difficulty of discovering novelty knowledge directly from high-complexity raw data, and it provides a reusable tool to accelerate DNA sequence processing and applications.

genomics↗

bioRxiv2025

HPInet: Interpretable prediction of Host-Pathogen protein-protein Interactions using a transformer-based neural network

Gram-negative bacteria utilize a series of secretion systems (T1SS-T10SS) to deliver secreted effector proteins (T1SE-T10SE) into host cells, leading to infections and diseases. Understanding the interactions between these effector proteins and host proteins is crucial for unraveling the pathogenic mechanisms of bacterial pathogens. Despite advancements in sequencing technologies that have significantly enhanced our knowledge of effector protein diversity and structure, the molecular mechanisms underlying their interactions with human host proteins remain unclear. Experimental approaches to validate these interactions are labor-intensive, time-consuming, and insufficient to comprehensively map the extensive effector-host protein interaction (PPI) network. Additionally, specialized computational tools for predicting these interactions remain scarce. To address this gap, we developed HPInet, a transformer-based deep learning model for predicting interactions between bacterial effector proteins and human host proteins. HPInet introduces convolutional layers and global response normalization (GRN) into the feed-forward network (FFN) of the transformer architecture, enhancing the extraction of local sequence features. Compared to existing state-of-the-art methods, HPInet significantly improves prediction performance, increasing accuracy from 0.502 to 0.891 and boosting sensitivity by 35.3%. Furthermore, by leveraging the models attention mechanism, HPInet identifies critical residues at interaction sites, demonstrating its capability to capture local structural features of PPI sites solely from sequence information. To facilitate its application in research, HPInet has been implemented as a freely accessible web server available at https://bis.zju.edu.cn/hpinet. This platform provides a powerful and interpretable tool for studying effector-host protein interactions, offering valuable insights into bacterial pathogenesis and potential therapeutic targets.

bioinformatics↗

bioRxiv2025

Uranium mining fuels evolution in deep groundwater microbiomes

Deep-biosphere microbes have been underpinning global biogeochemical cycles throughout Earth history, yet their evolutionary responses to long-term anthropogenic disturbance remain poorly understood. Neutral-pH in-situ leaching (ISL), the dominant uranium-mining strategy, imposes persistent radiochemical and redox stress offering rare natural experiments across decades for observing subsurface microbial evolution. Here, by exploiting metagenomics and metatranscriptomics in examining microbial responses through various mining stages, we show that neutral U ISL causes substantial changes in microbial communities spanning 2,294 strains accompanied by diversification and selection of active microbial species. These changes occurred during elevated dissolved uranium and radiological activity which correlated with a substantial transcriptional change in energy metabolism, and with an overexpression of specific genes for oxidative-stress defence and DNA-repair pathways. Increased nucleotide diversity in 101 out of 392 species clusters and nonsynonymous/synonymous polymorphism ratios greater than one in 139 species clusters were predominantly observed in metatranscriptomes with elevated radiation, highlighting positive selection of transcriptionally active populations. These findings demonstrate that neutral U ISL drives functional and genetic diversification of subsurface microbiomes, revealing a dynamic and evolutionarily responsive deep biosphere.

genomics↗

bioRxiv2025

MViewEMA: Efficient Global Accuracy Estimation for Protein Complex Structural Models Using Multi-View Representation Learning

Estimation of model accuracy (EMA) is crucial for the reliable application of protein structure models in biological research. With the rapid advancement of protein structure prediction techniques and the explosive growth of predicted structural data, existing EMA methods struggle to balance computational efficiency with estimation performance. Here, we present MViewEMA, a single-model EMA method that leverages a multi-view representation learning framework to integrate residue-residue interaction features from micro-environment, meso-environment, and macro-environment levels for global accuracy assessment of protein complex models. Benchmark results demonstrate that MViewEMA outperforms state-of-the-art EMA methods in global accuracy assessment, achieving more than a 10-fold improvement in computational efficiency compared to our previous method, DeepUMQA3. This method enables efficient selection of high-quality protein complex models from large-scale structural datasets and achieved top performance in model selection tracks during the CASP16 blind test, demonstrating its potential to enhance the accuracy of complex structure prediction when integrated into modern frameworks such as AlphaFold-Multimer, AlphaFold3, and DiffDock-PP.

bioinformatics↗

bioRxiv2025

Comprehensive profiling of antibiotic resistance, virulence genes, and mobile genetic elements in the gut microbiome of Tibetan antelopes

Tibetan antelopes, native to high-altitude plateau regions, play a vital role in the local ecosystem. However, their gut microbiota harbors diverse antibiotic resistance genes (ARGs) and virulence genes (VFGs), raising concerns about the potential spread of antibiotic resistance in wildlife. In this study, in addition to collecting 26,608 metagenome-assembled genomes (MAGs) from public databases, we performed gut metagenomic sequencing on 68 Tibetan antelopes and obtained 7,318 MAGs through binning. A total of 2,968 ARGs were identified, conferring resistance to 23 antibiotic classes, with elfamycin resistance being the most prevalent. Comparative analysis revealed 7 ARGs unique to Tibetan antelopes, suggesting species-specific adaptations. Additionally, during the analysis of shared antibiotic resistance profiles between Tibetan antelopes and humans, two bacterial strains were identified within the Tibetan antelope gut microbiota: Enterococcus gallinarum exhibiting resistance to extended-spectrum class A beta-lactamases and Klebsiella grimontii demonstrating vancomycin resistance. Mobile genetic elements played a key role in ARG dissemination. ARGs were significantly correlated with VFGs, particularly those linked to adherence and effector delivery systems. These findings underscore for the first time the potential ecological and health implications of ARG dissemination in Tibetan antelopes, highlighting the need for further surveillance to assess its impact on wildlife and environmental resistomes.

microbiology↗

bioRxiv2025

Calyculin A Induces Premature Chromosome Condensation and Chromatin Compaction in G1-Phase HeLa Cells without Histone H1 Phosphorylation

We show here that treatment of HeLa cells with calyculin A, an inhibitor of Protein Phosphatases 1 and 2A, induces premature chromosome condensation (PCC) at any point in interphase of the cell cycle. Chromosomes in G1-phase PCC closely resemble metaphase chromatids in the light microscope, and measurements using FLIM-FRET show that they have the same level of chromatin compaction as metaphase chromosomes. However, histone H1 is not phosphorylated in G1- or early S-phase PCC. These results suggest that H1 phosphorylation is not required for mitotic chromosome condensation and chromatin compaction. They also confirm that Cdk1/cyclin B, which directly phosphorylates histone H1, is not active in G1 and thus is not essential for G1- PCC. We suggest that induction of G1-PCC involves protein kinases or other factors that are either held in an inactive state by protein phosphatases, or constitutively active but countered by phosphatases. The same factors may be involved in the onset of normal mitosis, becoming active when protein phosphatases are downregulated. Induction of PCC with calyculin A should provide a useful system for identifying and studying the biochemical pathways that are required for mitotic chromosome compaction, nuclear envelope breakdown, and other events of mitosis.

cell biology↗

bioRxiv2025

Rediscovery of the Enigmatic Paroxygraphis in Xizang, China: Phylogenetic Evidence for its Reclassification Within Oxygraphis (Ranunculaceae)

The enigmatic monotypic genus Paroxygraphis (Ranunculaceae, trib. Ranunculeae), represented solely by P. sikkimensis, has long posed taxonomic uncertainties due to its rarity. Through field rediscovery in southern Xizang province, China, and comprehensive molecular phylogenetic analyses combining nrITS and four plastid regions, we resolve its phylogenetic position within the Oxygraphis clade, with an estimated divergence time of about 3.73 Ma (95% HPD: 1.98-5.77 Ma) from its sister clade. Morphological and ecological characteristics, including small herb with a rosette of basal simple leaves, longitudinally ribbed achenes, and its alpine adaptations, further support this relationship. Furthermore, the results showed that persistent sepals and unisexual flowers in trib. Ranunculeae reflects multiple independent evolutionary origins. We propose the new combination Oxygraphis sikkimensis and highlight its critically endangered status due to habitat vulnerability. Lectotypification of P. sikkimensis is also made. This study provides new data for the floristic research of China and resolves the long-standing taxonomic controversy of this problematic genus within trib. Ranunculeae.

evolutionary biology↗

bioRxiv2025

Complement C3aR deletion does not attenuate neurodegeneration in a tauopathy model or alter acute inflammation-induced gene expression changes in the brain

Aberrant activation of the classical complement pathway in the brain is implicated in contributing to synapse loss and neurodegeneration in various neurodegenerative conditions. Given that C3aR is a druggable target in the complement pathway, we evaluated the potential of C3aR KO to rescue neurodegeneration in a tauopathy model and neuroinflammatory responses in an acute endotoxemia model. We found that C3aR KO did not rescue tau pathology, microglia activation markers, neurodegeneration, or behavioral abnormalities in tauopathy model mice. While we found that endotoxemia resulted in numerous transcriptional changes including distinct alterations in subpopulations of microglia, astrocytes and oligodendrocytes, C3aR KO did not impact these alterations. Together, our results suggest that the beneficial effects of blocking the complement classical pathway in neurodegeneration models is likely independent of C3aR activation and raise questions about the rationale for therapeutically targeting C3aR for neurodegenerative disease.

neuroscience↗

bioRxiv2025

Towards Unmanned Proteomics Data Generation: A Fully Automated Sample-to-Data System for Proteomic Experiments

The {pi}-HuB project requires proteomic measurements of millions of low-input samples that are challenging with current technology. Here, we introduce a pilot {pi}-HuB data factory that features a fully automated sample-to-data system to enable high-throughput digitization of human samples. Our platform, as a proof-of-concept towards unmanned proteomics, was demonstrated to show longitudinal robustness and applied for spatial proteomics and the profiling of plasma and cell lines, thereby serving as the workhorse to drive {pi}-HuB.

biochemistry↗

bioRxiv2025

The intratumoral microbiome is negatively associated with malignancy in dermatofibrosarcoma protuberans

In recent years, growing evidence demonstrated the critical roles of intratumoral microbes in tumors. However, the characteristics of intratumoral microbiome in dermatofibrosarcoma protuberans (DFSP) and their associations with tumor malignancy remains unexplored. Here, 106 whole-genome sequencing (WGS) data of the paired biopsy and blood samples from 53 DFSP patients were utilized, in which we extracted high-quality non-human reads to assign microbial taxonomic annotation by Kraken2 and PlusPF database. Meanwhile, significantly elevated non-human reads, microbial abundance, and bacterial load were detected in tumor compared to blood samples. To minimize the impact of contaminants and noise, we conducted a series of filtering procedures and treated blood samples as negative controls. Notably, we found that over 98% of intratumor microbes belonged to bacteria, and that the dominant taxa and alpha-diversity of intratumoral bacteria all exhibited significantly negative correlations with Ki67 expression in tumors. Specifically, the 84 key intratumoral species were identified to be associated with the reduced tumor malignancy, as evidenced by the diminished Ki67 expression, decreased tumor volume, and fewer COL1A1-PDGFB fusion events. These findings highlighted the tumor-suppressive potential of intratumoral microbiome, thereby providing a novel insight into DFSP pathogenesis and clinical management. IMPORTANCETo our knowledge, this is the first study to explore the intratumoral microbiome in DFSP. Microbial DNA signatures could be detected by whole-genome sequencing (WGS) and enabled a comprehensive view of the microbial landscape, thus we analyzed 106 WGS data of the paired biopsy and blood samples from 53 DFSP patients. Our analysis revealed that the dominant taxa and alpha-diversity of intratumoral microbiome all showed significantly negative correlations with Ki67 expression of tumor samples. This study indicated the tumor-suppressive role of intratumoral microbiome in DFSP and highlighted the potential clinical significance in understanding DFSP pathogenesis and guiding therapeutic management strategies.

microbiology↗

bioRxiv2025

A novel tool for labeling intermediary proteins between two non-interacting proteins

Decoding the complexities of signaling pathways is fundamental for deciphering the mechanisms underlying tissue development, homeostasis, and disease pathogenesis. Proximity labeling tools have been instrumental in identifying upstream or downstream effectors of specific proteins within signaling pathways. However, currently, there are no tools available to directly label and capture intermediary proteins that bridge two non-interacting proteins. Here, we developed STUPPIT (Split-TurboID and PUP-IT based Protein Identification Tool), a novel method combining split-TurboID and PUP-IT to biotinylate intermediary proteins of two non-interacting proteins through a two-step enzymatic reaction. Two approaches of STUPPIT were validated using three well-characterized protein triad, including YAP1/AMOT/{beta}-actin, YAP1/LATS1/MOB1A, and {beta}-catenin/-catenin/{beta}-actin. Combining STUPPIT and proteomics, we identified novel intermediary proteins including RNF20, ERC1, USP7 and TRIM33, which interact both with {beta}-catenin and SMAD4, key components of the Wnt and BMP signaling pathways. In conclusion, STUPPIT represents a powerful tool for labeling and capturing intermediary proteins between non-interacting partners, offering new insights into protein-protein interactions and advancing signal transduction research.

cell biology↗

bioRxiv2025

Alternating 2D and 3D Culture Reduces Cell Size and Extends the Lifespan of Placenta-Derived MSCs

Mesenchymal stem cells (MSCs) offer significant therapeutic potential, but traditional 2D culture on rigid substrates results in progressive cell enlargement and senescence, reducing proliferative capacity and therapeutic potency. This poses a major challenge for widespread clinical application. We explored a novel strategy for placenta-derived MSCs combining 2D expansion with 3D spheroid culture to address these limitations. Our research shows that culturing MSCs as 3D spheroids significantly reduces individual cell size and size distribution compared to 2D culture. Spheroid formation is feasible in chemically defined media with minimal cell death, and is enhanced by extracellular matrix protein supplementation. Although MSCs do not proliferate in 3D suspension, an alternating 2D/3D culture protocol, transitioning cells between 2D flasks and 3D spheroids after each passage, effectively slows MSC enlargement and senescence over long periods. This alternating method also preserves MSC immunomodulatory function, unlike continuous 2D culture which leads to its loss. For scalability, we developed an RGD-functionalized alginate hydrogel tube (AlgTube) system that mimics this alternating environment, supporting both adherent growth and chemically triggered spheroid formation. This alternating 2D/3D culture strategy and the scalable AlgTube platform provide a foundation for developing next-generation MSC manufacturing technologies to meet future clinical demands.

bioengineering↗

bioRxiv2025

Low-Strength Type I Interferon Signaling Promotes CAR T-Cell Treatment Efficacy

CD19-directed chimeric antigen receptor (CAR) T-cell therapy has significantly advanced the treatment landscape for relapsed/refractory diffuse large B-cell lymphoma (r/r DLBCL). However, up to 60% of patients do not achieve a complete response. To uncover determinants of therapeutic efficacy, we analyzed the infusion products of eight r/r DLBCL patients with distinct clinical responses to axicabtagene ciloleucel using single-cell transcriptomics. Compared to patients who exhibited progressive disease, infusion products of complete responders demonstrated enriched signatures of type I interferon (IFN-I) signaling. Based on these findings, we developed a novel strategy to improve CD19-directed CAR T-cell treatment efficacy by incorporating IFN-I as an enhancer during the ex vivo manufacturing process, with IFN-I removal before CAR T-cell infusion to avoid in vivo toxicities. For both CD28- and 4-1BB-costimulated second-generation CARs, we found that low-strength IFN-I signaling enhanced CAR T-cell cytotoxicity and treatment efficacy against B-cell lymphoma and leukemia. Our low-strength IFN-I-enhanced CAR T-cell ex vivo manufacturing approach leverages an existing FDA-approved pharmacologic agent, circumvents in vivo interferon-associated toxicities, and remains fully compatible with current CAR constructs and manufacturing workflows. Together, our results establish IFN-I as a potent and costimulation-independent enhancer of CAR T-cell efficacy and provide a translationally feasible approach to enhance CAR T-cell therapies.

immunology↗

bioRxiv2025

Serpine1 plays a critical role in Th17 cell differentiation and psoriasis pathogenesis

A large body of evidence indicates that Th17 cells play essential roles in mucosal immune responses and trigger autoimmune diseases, including multiple sclerosis, inflammatory bowel disease, and psoriasis. Targeting Th17 cells holds promise for therapeutic innovation. However, the molecular mechanisms underlying Th17 cell differentiation remain poorly understood. Here, we found that Serpine1 was preferentially induced in Th17 cells. Genetic ablation of Serpine1 inhibited Th17 cell polarization in vitro, reproducing the phenotype caused by pharmaceutical inhibition against Serpine1 product PAI-1. Moreover, we confirmed that, despite normal T-cell initiation in vivo, deletion or inhibition of Serpine1 significantly attenuated disease severity and notably reduced skin inflammation in an IMQ-induced psoriasis model. Notably, this protective effect was also recapitulated in the CD4 conditional knockout mouse pathogenic model, ruling out the non-T cell autologous effect of Serpine1. Collectively, our results revealed a critical role of Serpine1 in regulating Th17 cell differentiation and autoimmune diseases, suggesting that Serpine1 is a promising therapeutic target for autoimmune disease treatment. SignificanceUsing multiple genetic and pharmaceutical ablation model systems, we have demonstrated that Serpine1 plays a critical role in regulating Th17 differentiation and psoriasis pathogenesis. Serpine1 intervention attenuates disease symptoms in a psoriatic mouse model in a Th17 cell-dependent manner. This finding extends our understanding of Serpine1s role in inflammatory diseases, highlighting its therapeutic potential.

immunology↗