Biology subjects

Li, K.

Publications and source records attributed to Li, K..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Global shifts in vegetation compositional resilience over the past 8,000 years

Vegetation resilience is critical for sustaining biodiversity and ecosystem services, yet its long-term dynamics and underlying drivers remain poorly resolved. Here, we assess changes in continental-scale vegetation compositional resilience over the past 8,000 years by applying established leading indicators (including autocorrelation, standard deviation, skewness, and kurtosis) to 482 fossil pollen records from all major landmasses except Antarctica. Using a machine learning approach, we evaluate the relative contributions of anthropogenic land cover change (ALCC) and climatic parameters (annual mean temperature, temperature seasonality, annual precipitation, and precipitation seasonality) in driving resilience shifts across continents. We further employ structural equation modeling (SEM) to disentangle how abiotic factors (ALCC and climatic variables) and biotic factors (species richness, evenness, synchrony, and temporal {beta} diversity) jointly shape long-term trends in vegetation resilience at the continental scale. Our results reveal a persistent, millennia-scale decline in resilience during the past 1.6 to 4.4 thousand years before present, with intensified anthropogenic land-use change identified as the dominant global driver. This finding suggests that the global decline in vegetation resilience observed over recent decades likely represents a continuation of the long-term trend established during the preceding Holocene. Notably, North America exhibited a resurgence in resilience over the past 1,200 years, primarily attributed to enhanced resilience in tundra and savanna ecosystems. SEM analyses uncover complex pathways through which abiotic and biotic predictors interact to shape millennial-scale resilience changes across continents. Despite the complexity of these underlying mechanisms, the analyses demonstrate that biotic factors collectively exert substantial, and often predominant, influences on long-term resilience dynamics. This underscores the indispensable role of biotic attributes in modulating long-term vegetation resilience, highlighting their potential as critical targets for ecosystem conservation and restoration.

ecology↗

bioRxiv2025

Pan-cancer analysis reveals that tumor microbiomes generate specific epitopes through transcriptional reprogramming

The therapeutic promise of tumor microbial peptides faces a critical safety paradox: tumors and peritumor tissues harbor compositionally similar microbiomes, yet safe immunotherapy demands tumor-specific targeting. We performed comprehensive transcriptomic analysis of microbial communities from 1,868 tumor and peritumor samples across 11 cancer types. Although 88.5% of microbial species are present in both tissue types, tumor and peritumor tissues exhibit profound transcriptional divergence: only 34.1% of microbial genes are expressed in both tissue types, and merely 18.2% of predicted HLA-binding peptides overlap. This transcriptional divergence represents microbial transcriptional reprogramming (MTR) in tumor tissues, through which microbes activate distinct genomic regions while adapting to tumor microenvironmental pressures, thereby generating tumor-specific peptide repertoires. Using Microbial Transcriptional Reprogramming Index (MiTRI) to quantify MTR, we found that higher MiTRI values correlate with expanded immunogenic peptide repertoires. Mass spectrometry-based immunopeptidomics confirmed that 25% of naturally presented microbial peptides originate from MTR regions. Crucially, in microsatellite-stable colorectal cancer, neo-adjuvant therapy responders exhibited significantly higher MiTRI values. T cell receptors (TCRs) recognized MTR-derived epitopes at 2.10-fold higher rates than genome-wide epitopes, accounting for 79.1% of clonally expanded TCRs. These findings establish MTR as the principle that ensures the tumor-specificity and safety of micorbiome-directed immunotherapy.

cancer biology↗

bioRxiv2025

Modeling σE biochemical network reveals context-dependent feedback control and kinetic constraints in the envelope stress response

The bacterial cell envelope is essential for mechanical stability, barrier function, defining cell size and shape, and supporting cellular processes. Because external or internal stressors can challenge its integrity, bacteria have evolved stress response systems to maintain envelope homeostasis. For example, under stress, E. coli activates {sigma}E to induce a regulon that restores envelope homeostasis. The molecular mechanisms underlying the transcriptional and post-translational regulation of {sigma}E and its anti-sigma factor RseA have been well-mapped. However, how these regulatory layers function at the systems level to regulate {sigma}E activity remains unclear. Here, we combine mathematical modeling with quantitative gene expression measurements to determine how the interplay of transcription and post-translational regulation affects the dynamics of the {sigma}E response. The results suggest that the {sigma}E activity is determined by the balance between the release from RseA, resulting from its degradation, and slow binding of free {sigma}E to the intact RseA. Notably, the combined action of transcriptional and post-translational regulation reveals that autoregulation, traditionally assumed to be a positive feedback, transitions from negative to positive feedback under extreme stress, enabling a finely tuned response that prevents premature activation while ensuring a robust response under severe envelope stress. In summary, our findings elucidate the mechanisms of {sigma}E regulation, thereby advancing our understanding of how alternative sigma factor bacterial networks control stress-response pathways.

systems biology↗

bioRxiv2025

Parallelized Brightfield and Fluorescence Imaging of Organoids Using a Scalable Multi-Camera Platform

Organoid viability, maturation, and growth is commonly assayed through brightfield and fluorescence microscopy using a single objective lens. However, standard microscopic imaging systems pose significant limitations for high-throughput applications, particularly in large-scale experiments where simultaneous imaging of multiple organoids requires increased throughput. There is a strong need for systems that can capture organoid growth rapidly and consistently while minimizing disturbances to culture conditions. Here, we present a novel multi-camera array scanner (MCAS) that parallelizes imaging through the simultaneous use of 48 objective lenses and sensors, resulting in a 95% reduction in acquisition times compared to commercial high-content imagers. We demonstrate and validate this system in multiple well plate formats, in both 2D and 3D neural cell cultures, and in brightfield and fluorescence. The MCAS improves efficiency for measuring organoid growth rates, assessing responses to morphogens and drugs, and measuring viral transduction efficiency. Together, these findings establish the MCAS as a scalable and versatile imaging platform for rapid phenotyping in organoid research.

neuroscience↗

bioRxiv2025

JMJD1B-mediated FEN1 demethylation allows timely switching of Okazaki fragment maturation core enzymes to avoid mutagenic flap ligation by PARP1-LIG3

Efficient and faithful Okazaki fragment maturation (OFM) depends on the PCNA-coordinated actions of core enzymes Pol{delta}, FEN1, and LIG1. We demonstrate that Pol{delta}, FEN1, and LIG1 sequentially but not simultaneously bind to PCNA in mammalian cells. The association of FEN1 with PCNA, which lies at the center of this orderly program, is mediated by FEN1 R192 methylation, which is also crucial for preventing premature loading of LIG1. Conversely, FEN1 demethylation by the recently identified arginine demethylase JMJD1B promotes FEN1 dissociation from PCNA and LIG1 recruitment. Disruption of the sequential PCNA binding program in R192Q or Jmjd1b-/- cells results in unprocessed 5 flaps that prevent OFM and induction of PARP1-dependent recruitment of LIG3, which has flap ligation activity to join incompletely processed OFs. This alternative OFM process supports cell survival but causes duplications and other DNA mutations. Our findings define fundamental and alternative DNA replication processes underlying mutagenesis and cell survival. HighlightsO_LIThe core enzymes involved in Okazaki fragment maturation (OFM), DNA polymerase {delta} (Pol{delta}), flap endonuclease 1 (FEN1), and ligase 1 (LIG1), sequentially bind to the scaffold protein PCNA for their concerted actions C_LIO_LIFEN1 R192 methylation enables FEN1 binding to PCNA; JMJD1B-mediated FEN1 arginine demethylation provokes FEN1 exit from PCNA and LIG1 recruitment C_LIO_LIFEN1 R192Q mutation and JMJD1B deficiency oppositely alter dynamic PCNA interactions with FEN1 and LIG1 and result in distinct OFM DNA intermediate structures C_LIO_LIActivation of PARP1 at replication forks due to disruption of the sequential PCNA binding program induces LIG3-mediated alternative mutagenic 5 flap ligation for survival. C_LI

cell biology↗

bioRxiv2025

Integrated analysis reveals neuro-immune pathway in the central nervous system that supports SGLT2i`s protective effects in treatment of cardiac remodeling

BackgroundDespite growing evidence of sodium-dependent glucose transporters 2 inhibitors (SGLT2i) improving heart failure, their mechanisms remain unclear. This study explored the effects of empagliflozin (EM) on sympathetic nerve activity and potential neuroimmune pathways. MethodsSingle-nucleus RNA sequencing (snRNA-seq) was performed in hypothalamic tissue of a DOCA-salt mouse model to screen for cellular changes. Validation of relevant mechanisms in DOCA-salt and high-salt diet (HSD) mouse models. Additionally, clinical data from 1,189 hospitalized heart failure patients were analyzed to evaluate the translational relevance of the experimental findings. ResultsEM treatment was associated with protective effects against cardiac remodeling in both DOCA-salt and HSD mice. Both models exhibited sympatho-excitation and neuronal hyperactivity in pre-autonomic brain regions, which appeared to be blunted by EM co-treatment. snRNA-seq analysis suggested that cellular interplay among vascular cells, microglia, and inhibitory neurons might be involved in these processes. Specifically, high-salt intake was linked to peripheral immune activation, including lymphocytosis and elevated plasma interferon-{gamma}, which potentially mediated microglial state transitions. EM might counteract the disease-associated upregulation of protein ubiquitination. Clinically, SGLT2i use was significantly associated with reduced lymphocyte counts in specific patient subgroups. ConclusionsEmpagliflozin may attenuate cardiac remodeling caused by high sodium intake through neuroimmune effects by restoring microglial homeostasis and inhibiting sympathetic nerve activity.

molecular biology↗

bioRxiv2025

PI-FC: Pre-training Individual-specific Functional Connectome through State-invariant Contrastive Learning

Functional MRI enables non-invasive mapping of brain connectivity, yet its clinical translation remains hindered by uncontrolled state-dependent variability that obscures individual-specific signatures during routine scanning. Here we introduce PI-FC -- a deep learning framework leveraging state-invariant contrastive learning to extract stable individual brain signatures across diverse arousal levels, cognitive states, and temporal scales spanning tens of seconds to hours. PI-FC achieves equivalent phenotypic prediction accuracy using substantially reduced scanning time, and eliminates state-dependent effects varying task demands and brain states. Trained on 36,119 subjects across 8 independent datasets, our model demonstrates superior cross-site generalization and outperforms traditional functional connectome (FC) in predicting neuropsychiatric conditions including schizophrenia, autism, depression, and anxiety. Furthermore, PI-FC enables zero-shot inference of brain age, biological sex, and cognitive ability without site-specific retraining. Overall, PI-FC represents a robust, clinically scalable framework that overcomes fundamental barriers to real-world deployment of precision functional neuroimaging.

neuroscience↗

bioRxiv2025

In Vitro Wound Simulation: A High-Throughput Device for ScratchAssays

Traumatic injury to the healthy central nervous system (CNS) causes mechanical tissue damage that results in localized cell death and blood-brain-barrier (BBB) disruption. CNS tissue damage stimulates a multicellular wound response to limit the extent of damage but fails to reestablish the normal function of injured tissue. There is strong interest in developing new strategies to augment regeneration after CNS injury. To enable therapy development, reliable assays to screen and identify molecular approaches to augment glial-based wound responses over fibrotic scarring are needed. Scratch assays, which involve mechanically removing cells from an in vitro culture, allow for the simulation of wounds with high throughput and tight control over applied treatments to mechanistically study cell migration and proliferation functions that are critical to effective repair. Current methods require researchers to individually scratch each well with a pipette tip, resulting in low throughput as well as inconsistent scratch widths, straightness, and efficacy within and between wells. Here, we describe the design of a quickly assembled (<30min), inexpensive (<$110) scratch assay rig that readily creates uniform scratches that are straight (average tortuosity < 1.1), have tunable widths (730-1100{micro}m), and fully remove damaged cells from the simulated wound region. Designed for a 24-well plate, the rig allows for high-throughput screening of varied experimental conditions or for testing many replicates. Application of the scratch assay device on an in vitro culture of neural progenitor cells (NPC) demonstrates the ability to detect differences in wound closure rate for three unique media conditions. These results support the implementation of this high-throughput scratch assay rig as a method to standardize and improve the efficiency of in vitro wound healing studies.

bioengineering↗

bioRxiv2025

Heterogeneity in inhibition of genetically diverse dengue virus strains by Wolbachia

The release of Aedes aegypti mosquitoes transinfected with the virus-inhibiting Wolbachia bacterium has the potential to reduce the burden caused by dengue virus (DENV). However, the robustness of this control strategy across the wide genetic diversity of DENV remains unknown. Here, we systematically tested two commonly used Wolbachia strains (wAlbB and wMelM) for their ability to inhibit 60 genetically diverse DENV isolates spanning all four serotypes. We found stronger inhibition by wMelM (median relative dissemination: 0.04) than wAlbB (median relative dissemination: 0.19). Furthermore, while we found substantial heterogeneity in inhibition across DENV isolates, we found that more DENV-3 isolates were weakly inhibited (median relative dissemination: 0.47 for wAlbB and 0.39 for wMelM) compared to the other serotypes (median relative disseminations: 0.10-0.18 for wAlbB and 0-0.11 for wMelM). Using transmission dynamic models, we further showed that differential Wolbachia inhibition results in increased probability of reemergence, particularly in high transmission intensity settings, with strong selection for DENV strains that have higher relative dissemination in mosquitoes. Our work highlights the importance of considering DENV genetic diversity, including the long-term risk of selection, in Wolbachia-based control interventions.

microbiology↗

bioRxiv2025

Multiscale Analysis of Candida albicans Biofilms

Candida albicans is an opportunistic fungal pathogen of significant biomedical concern. Its ability to colonize abiotic surfaces of clinical devices -- such as catheters and airway management systems -- can result in life-threatening sepsis, especially in immunocompromised patients. A deeper understanding of C. albicans biofilm development under different environmental conditions is essential for improving antifungal treatments. In this study, we examine C. albicans biofilm formation using live fluorescence microscopy across multiple scales and modalities, and introduce new quantification approaches. High-magnification tracking of hyphal tips reveals that hyphal elongation occurs intermittently rather than continuously. Using a new automated tracking approach, we show that hyphal emergence is initially rapid and slows down after approximately two hours. At lower magnifications, area coverage across large fields of view proves to be a robust and scalable metric. It is strongly influenced by seed density and extends analysis to later stages of growth. Elevated carbon dioxide levels significantly accelerate area coverage, promoting rapid biofilm expansion. Blue light illumination reduces C. albicans growth in a dose-dependent manner. Light-sheet imaging enables the long-term capture of vertical biofilm growth, complementing widefield-based approaches. We introduce logistic model parameters to effectively quantify the dynamics of surface area growth. The methodologies presented here are well-suited for high-content screening applications aimed at identifying compounds that inhibit or suppress fungal biofilm formation under clinically relevant conditions.

microbiology↗

bioRxiv2025

Agent-based modelling and time series inference of filamentous yeast colonies

The bakers yeast Saccharomyces cerevisiae can form invasive filamentous colonies with non-uniform spatiotemporal patterns. We aimed to better understand how individual cellular actions give rise to colony-scale patterns. We used an off-lattice agent-based model to simulate colony growth, and used a neural likelihood estimator (NLE) to infer parameters for experimental photographs. Li et al. [1] used approximate Bayesian computation (ABC) to infer parameters using coarse summary statistics obtained from a single time point averaged across experimental replicates. The NLE overcomes the computational expense of ABC, allowing us to infer the parameters of individual colonies from a full time series of experimental photographs. To demonstrate the capabilities of our model and inference technique, we tested extensively on synthetic data and then predicted yeast growth under three different experimental conditions. As before, the proportion of total colony growth above which pseudohyphal growth is permitted was a key parameter that contributed to colony morphology. Since our NLE-based approach incorporates time series data, it yielded better parameter estimates and more accurate predictions compared to our ABC-based method. This updated approach improved understanding of how the probability that a stated cell produces a pseudohyphal cell influences colony morphology. In this way, the model also has the potential to generate hypotheses, which can be tested through biological experiments to increase the understanding of the basis for different growth patterns in yeast.

cell biology↗

bioRxiv2025

PhyloAug: An Evolutionary and Structure-Aware Data Augmentation Tool

Genomic Language Models (GLMs) suffer from the inherent problem of data scarcity, due to the cost, time and complexity of wet-lab experiments. Data augmentation offers a solution; however traditional methods may unintentionally affect the underlying structure or function. By combining evolutionary signals with the RNA secondary structure, augmentations can retain original function, and remain structurally coherent. To implement this, we developed PhyloAug, a structure-aware, evolution-inspired augmentation method grounded in neutral theory. We employ Genomic Foundation Models (GFMs) to accurately perturb RNA sequences, and utilise phylogenetic analysis via PAML to provide site-wise restrictions based on evolutionary principles. These principles are obtained through the identification of evolutionarily neutral sites (sequence positions where mutations are unlikely to alter function), which are concatenated with the predicted (or known) secondary structure. We thereby ensure adherence to the underlying structure whilst enabling biologically plausible variation. To validate the biological validity of our augmentations, we compare our predicted neutral sites with Rfam-annotated conserved regions and assess sequence similarity to the underlying multiple sequence alignments. We next fine-tune GLMs on augmented data, yielding significant performance improvements up to 12.9% MCC, and 17.2% F1-Score.

bioinformatics↗

bioRxiv2025

Human-scATAC-Corpus: a comprehensive database of scATAC-seq data

Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) profiles chromatin accessibility at cellular resolution, making it possible to reveal epigenomic landscapes that govern gene regulation in a variety of cells. Nevertheless, heterogeneous feature spaces and complex processing pipelines have impeded the construction of an ensemble resource capable of supporting diverse downstream analytical scenarios. To address this gap, we present Human-scATAC-Corpus (https://health.tsinghua.edu.cn/human-scatac-corpus/), a comprehensive database of human scATAC-seq comprising 5,407,621 cells from 35 datasets across 37 tissues or cell lines. To support complementary use cases, each dataset is distributed in three aligned formats: cell-by-candidate cis-regulatory element matrices for cross-dataset integration, raw fragment files for flexible processing, and cell-by-peak matrices for within-dataset analyses. This resource spans diverse biological contexts and includes rich metadata, enabling method benchmarking and development, as well as pretraining of foundation models. The website offers searchable browsing, detailed dataset pages, on-demand downloads, and tutorials. EpiAgent, a foundation model pretrained on Human-scATAC-Corpus, is further integrated to provide online analyses, including reference mapping, embedding extraction, and cell type annotation. Human-scATAC-Corpus establishes a unified and scalable substrate for single-cell epigenomics and is intended to accelerate discovery while standardizing evaluation across tasks. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/674505v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@e2c4c3org.highwire.dtl.DTLVardef@1e3eaf8org.highwire.dtl.DTLVardef@5768c1org.highwire.dtl.DTLVardef@9e96ad_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Dysregulation of innate immunity and cellular metabolism through virus-induced deISGylation

Interferon-stimulated gene 15 (ISG15) regulates diverse cellular responses including antiviral immunity through its conjugation to proteins, a process known as ISGylation. Several pathogens, including SARS-CoV-2, subvert ISGylation by encoding deISGylating enzymes. However, the direct targets and physiological consequences of coronaviral deISGylation remain poorly defined. Here, we ablated the deISGylating activity of the SARS-CoV-2 papain-like protease (PLpro) and found that loss of deISGylation boosted innate immune activation, attenuated virus replication, and promoted viral clearance in human cells and in mice. Through untargeted metabolomics and ISGylome proteomics analyses, combined with functional studies, we discovered in molecular detail how the activities of key metabolic enzymes in glycolysis, the pentose phosphate pathway, and oxidative stress are controlled by PLpro deISGylation. These findings provide fundamental new insight into how reversible ISGylation regulates immunity and metabolic processes at the molecular level and highlight viral deISGylation as a major viral tactic for rewiring immunometabolism.

microbiology↗

bioRxiv2025

Modelling the emergence of spiral colony morphology in the yeast Magnusiomyces magnusii

Yeast species have several adaptations that enable them to survive in harsh environments. These adaptations include biofilm formation, where the secretion of extracellular polymeric substances can protect the cells from a hostile environment, or, under nutrient-limited conditions, pseudohyphal or hyphal growth, where the colony can send out long tendrils to explore the environment and seek nutrients. Recently, we observed a spiral colony morphology emerge in an isolate of the hyphae-forming yeast Magnusiomyces magnusii grown under laboratory conditions. We use an off-lattice agent-based model (ABM) that simulates colony development to investigate the hypothesis that bias in the angle between successive hyphal segments causes the spiral morphology. The model involves biologically-motivated rules of hyphal extension, with key model parameters including the colony size at the onset of hyphal filaments, and the angle between the penultimate and the apical segments. Using one example of an experimentally-grown colony, we use a sequential neural likelihood method to perform likelihood-free Bayesian inference to infer the model parameters. Our results indicate a mean angle between hyphal segments of 2.3{whitebullet} [1.1{whitebullet}, 3.6{whitebullet}] (95% credible interval). To confirm the models applicability to colony growth, we use biologically-feasible parameter values to yield morphologies observed in M. magnusii experiments.

microbiology↗

bioRxiv2025

Tumor-initiating genetics and therapy drive divergent molecular evolution in IDH-mutant gliomas

Astrocytomas and oligodendrogliomas are slow-growing and treatment-sensitive IDH-mutant gliomas diagnosed at ages 30-50. Local tumor regrowth and treatment resistance is inevitable resulting in 3-10 year astrocytoma and up to >20 years oligodendroglioma survival. We sought to identify genetic changes associated with tumor evolution in response to therapy through multi-timepoint whole-genome/whole-exome sequencing of 206 IDH-mutant glioma patient samples collected through the Glioma Longitudinal Analysis (GLASS) Consortium. We validated known genomic markers of tumor progression, including hypermutation and CDKN2A homozygous deletion, and discovered novel genetic alterations that distinguish the response to treatment in astrocytomas compared to oligodendrogliomas. Point mutations in PIK3CA, PIK3R1, and NOTCH1 were newly acquired in recurrent oligodendrogliomas and associated with increased mutation rates. Focal oncogene amplifications, together with CDKN2A homozygous deletions, were associated with an increase in recurrence-specific chromosomal imbalances in astrocytomas. Mutational signature analysis revealed additional differences and detected enrichment for the SBS11, and SBS119 mutational signatures after temozolomide treatment in both IDH-glioma subtypes, whereas astrocytomas showed increased ID8 signatures after radiotherapy. These signatures suggest that the genomes of oligodendroglioma and astrocytoma adapt to the selective pressures of tumor progression and treatment in different ways. However, in both IDH-mutant glioma subtypes we observed a convergence of acquired driver gene alterations with genome-wide changes and worse patient outcomes, signaling selection of treatment-refractory clones. By identifying new prognostic markers and delineating the genomic divergence of oligodendrogliomas and astrocytomas after diagnosis, our results suggest that different DNA damage response mechanisms are engaged following chemo- and radiation therapy.

cancer biology↗

bioRxiv2025

Granulin+ macrophages promote lineage plasticity in prostate cancer through paracrine signaling loops

The role of tumor-infiltrating immune cells in driving phenotype switching remains unclear, despite the well-established association between lineage transition and drug resistance in prostate cancer. This study employed an integrated analysis of single-cell multiomics to investigate the dynamics of immune infiltration, transcriptional programs, and cell-cell communication in prostate cancer. Our results demonstrated that granulin (GRN) positive macrophages facilitated the transition from adenocarcinoma to a multilineage state with mesenchymal and stem-like traits by activating intra-tumoral NF-{kappa}B signaling. Subsequently, the multilineage clones induced macrophages to highly express granulin through the secretion of CSF1, forming a positive feedback cell communication loop. Next, we validated the biological function of granulin in mediating epithelial-mesenchymal transition in vitro. Additionally, organoids drug resistance assay demonstrated that granulin drove resistance to androgen receptor (AR)-targeted drug (enzalutamide). Moreover, pharmacologic blockade of the CSF-1/CSF-1R axis in TRAMP mouse models reduced the expression of GRN in macrophages and suppressed the formation of multilineage subclones in prostate malignant cells. Furthermore, multiplex immunofluorescence staining of tumor samples from TRAMP mouse models revealed the VIM lineages were spatially in close contact with macrophages. Meanwhile, Cytometry by Time-Of-Flight (CyTOF) analysis validated our findings at single-cell protein level in patients with castration-resistant prostate cancer. Besides, three distinct tumor-infiltrating subsets associated with disease relapse were identified, including DCN+ endothelial cells, CCL7+ fibroblasts, and IFIT1+ neutrophils. These results offer potential therapeutic targets to address lineage plasticity-driven resistance to AR-targeted therapy.

cancer biology↗

bioRxiv2025

Scar-associated endothelial-stellate cellular crosstalk drives fibrosis resolution in MASH

Fibrosis, or scarring, can affect many organs including liver, lung, heart, kidney, intestines etc. and is responsible for [~]40% of mortality in the industrialized world. Compared to other organs, fibrosis in the liver typically resolves when the source of injury is extinguished. Elucidating the molecular mechanisms that underlie spontaneous fibrosis resolution in the liver may lead to novel antifibrotic strategies for all organs. In this study we established a robust mouse model of fibrosis regression in MASH (Metabolic dysfunction-Associated Steatohepatitis), a highly prevalent chronic liver diseases worldwide, and performed single cell and in situ molecular profiling of the liver to define novel drivers of fibrosis regression. As fibrosis regressed, we detected a reduction of inflammatory cells and an expansion of endothelial cells. Prediction of cell-cell communication using the Calligraphy pipeline identified a Wnt9b-Sfrp2 crosstalk that emerges as fibrosis resolved in our model. To establish the Wnt9b-Sfrp2 crosstalk as a driver of fibrosis resolution we treated mice with recombinant Sfrp2, which slowed spontaneous fibrosis regression compared to vehicle treated mice. From our single cell datasets we identified a subset of endothelial cells, termed "Endo4", as the source of Wnt9b. Immunostaining of the Endo4 marker VWF using tissue clearing and 3D imaging revealed VWF+ vasculature enveloped by activated hepatic stellate cells (HSCs) that penetrated deep into the fibrotic septa, establishing Endo4 as de facto scar-associated endothelial cells and providing a structural basis of their cellular crosstalk with HSCs. Finally, using a recently developed in situ protease activity screen, prominent serine protease activity co-localized with both scar-associated Endo4 cells and HSCs. In summary, we uncovered an WNT-dependent endo-stellate crosstalk within the fibrotic niche as a novel regulatory node underlying murine MASH fibrosis regression, and a promising therapeutic target.

molecular biology↗