Biology subjects

Zhou, C.

Publications and source records attributed to Zhou, C..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Hepatitis E ORF2 blocks trophoblast autophagy to induce miscarriage via LC3B binding rather than PI3K/Akt/mTOR pathway suppression

Hepatitis E virus (HEV) is a zoonotic pathogen that can infect pregnant women and cause adverse pregnancy outcomes, including miscarriage and preterm delivery. The previous study demonstrated that HEV genotype 3 (HEV-3) inhibits complete autophagic flux in both mouse placental tissue and human trophoblast cells (JEG-3), evidenced by reduced expression of ATG proteins (including LC3, Beclin1, ATG4B, ATG5, and ATG9A) and accumulation of p62. However, the specific regulatory pathway involved remains unclear. Thus, eukaryotic expression vectors for HEV open reading frames (ORFs) were constructed, and ORF2 and ORF3 proteins were transiently overexpressed in JEG-3 cells via liposome transfection.. While both ORF2 and ORF3 significantly reduced LC3B protein levels (p < 0.01), only ORF2 induced p62 accumulation (p < 0.01), indicative of autophagic inhibition, which indicates that ORF2 was the key viral protein mediating autophagy suppression in JEG-3. The results of WB and RT-qPCR show that ORF2 suppressed the PI3K/Akt/mTOR pathway while enhancing nuclear translocation of TFEB (p < 0.01) and AMPK phosphorylation (p < 0.01), suggesting paradoxical activation of upstream autophagy regulators. Through co-transfection of mCherry-LC3 with ORF2, co-localization studies, and AlphaFold 3-based intermolecular interaction predictions, we proposed that ORF2 directly binds LC3B to block autophagosome formation. Finally, co-immunoprecipitation confirmed physical interaction between HEV ORF2 and LC3B, elucidating the molecular mechanism of HEV-induced autophagy suppression in trophoblasts. These findings reveal the molecular mechanism by which HEV inhibits autophagy leading to miscarriage in mice, providing new insights into HEV-induced reproductive damage.

pathology↗

bioRxiv2025

Fork Reversal Safeguards Epigenetic Inheritance during DNA Replication Under Stress

During DNA replication, epigenetic information carried by histone modifications is faithfully propagated and re-established on sister chromatids, ensuring cell identity. Chromatin reassembly is tightly coupled to DNA replication, therefore whether and how perturbations to DNA replication affects the fidelity of epigenetic inheritance remain poorly understood. In this study, we reveal a critical role for replication fork reversal in maintaining the transmission of epigenetic information under replication stress. We identify that cells defective in fork reversal exhibit reduced nucleosome density at replication forks, accompanied by the loss of parental histones during their transfer onto nascent DNA. Mechanistically, we demonstrate that PrimPol activation leads to single-stranded DNA gaps in fork reversal deficient cells, and that subsequent PARylation (poly ADP-ribosylation) and DNA-protein crosslinking on these gaps evicts nucleosomes. Our findings demonstrate that replication fork reversal, a widespread physiological process, is not only essential for preserving genome integrity but also for safeguarding epigenetic stability.

biochemistry↗

bioRxiv2025

Zebrafish Xenografts Reveal a Context-dependent Roleof PFKFB4 in Melanoma Cell.

Cutaneous melanoma is a highly metastatic cancer in which tumor cell plasticity drives transitions between proliferative and invasive states. The glycolytic regulator PFKFB4 has been implicated in cancer cell motility, but its role in melanoma progression in vivo remains unclear. Using zebrafish larval xenografts, we found that PFKFB4 depletion reduced invasion in MeWo cells without affecting tumor growth, whereas in A375P cells it decreased tumor growth but had no effect on invasion or metastasis. In MeWo, PFKFB4 loss was associated with reduced SNAIL2 expression, while no effect on EMT transcription factors was observed in A375P cells. Rescue experiments indicated that PFKFB4 and SNAIL2 acted independently in regulating Mewo migration in vitro. These findings identify PFKFB4 as a context-dependent regulator of melanoma progression.

cancer biology↗

bioRxiv2025

STX4 is indispensable for mitochondrial homeostasis in skeletal muscle

BackgroundMitochondrial homeostasis is vital for optimal skeletal muscle integrity. Mitochondrial quality control (MQC) mechanisms that are essential for maintaining proper functions of mitochondria include mitochondrial biogenesis, dynamics and mitophagy. Previously, Syntaxin 4 (STX4) traditionally considered a cell surface protein known for glucose uptake in skeletal muscle, was also identified at the outer mitochondrial membrane. STX4 enrichment was sufficient to reverse Type 2 diabetes-associated mitochondrial damage in skeletal muscle by inactivation of mitochondrial fission. However, whether STX4 could modulate skeletal muscle mitochondrial homeostasis through MQC mechanisms involving mitochondrial biogenesis or mitophagy remains to be determined. MethodsTo determine the requirements of STX4 in mitochondrial structure, function and MQC processes of biogenesis and mitophagy, we implemented our in-house generated inducible skeletal muscle-specific STX4-knockout (skmSTX4-iKO) mice (Stx4fl/fl; Tg(HSA-rtTA/TRE-Cre)/B6) and STX4-depleted immortalized L6.GLUT4myc myotubes via siRNA knockdown (siSTX4). ResultsWe found that non-obese skmSTX4-iKO male mice (>50% reduced STX4 abundance, Soleus and Gastrocnemius ***p<0.001, Tibialis anterior (TA) ****p<0.0001) developed insulin resistance (**p<0.01), together with reduced energy expenditure (AUC *p<0.05), respiratory exchange ratio (AUC **p<0.01), and grip strength (*p<0.05). STX4 ablation in muscle also impaired mitochondrial oxygen consumption rate (****p<0.0001). Mitochondrial morphological damage was heterogenous in STX4 depleted muscle, presenting with small fragmented mitochondria (****p<0.0001) and deceased electron transport chain (ETC) abundance (CI ***p<0.001, CII *p<0.05, CIV **p<0.01) in oxidative soleus muscle, while glycolytic TA fibers display enlarged swollen mitochondria (****p<0.0001) with no change in ETC abundance. Notably, >60% reduction of STX4 in siSTX4 L6.GLUT4myc myotubes (****p<0.0001) also decreased ETC abundance (CI ****p<0.0001, CII ****p<0.0001, CIV *p<0.05) without changes in mitochondrial glucose metabolism, as shown by [U-13C] glucose isotope tracing. For MQC, both skmSTX4-iKO male mice (*p<0.05) and siSTX4 L6.GLUT4myc myotubes (*p<0.05) showed decreased mitochondrial DNA levels alongside reduced mRNA expression of mitochondrial biogenesis genes Ppargc1a (PGC1-, *p<0.05) and Tfam (*p<0.05) in skmSTX4-iKO soleus muscle and PGC1- (mRNA *p<0.05, protein ***p<0.001), NRF1 (mRNA and protein *p<0.05) and Tfam (mRNA *p<0.05) in siSTX4 L6.GLUT4myc myotubes. Furthermore, live cell imaging using mt-Keima mitophagy biosensor in siSTX4 L6.GLUT4myc cells revealed significantly impaired mitochondrial turnover by mitophagy (*p<0.05) and mitochondria-lysosome colocalization (*p<0.05). STX4 depletion also reduced canonical mitophagy markers, PINK1 and PARKIN in both skmSTX4-iKO muscle (PARKIN *p<0.05, PINK1 **p<0.01) and siSTX4 L6.GLUT4myc myotubes (PARKIN ****p<0.0001, PINK1 *p<0.05). ConclusionsOur study demonstrated STX4 as a key mitochondrial regulator required for mitochondrial homeostasis in skeletal muscle.

cell biology↗

bioRxiv2025

CRISPR screen identifies BAP1 as a deubiquitinase regulating SPIN4 stability

Protein homeostasis is tightly controlled by the coordinated actions of E3 ubiquitin ligases and deubiquitinases (DUBs). We identify Spindlin-4 (SPIN4), a histone H3K4me3 reader, as a substrate regulated by opposing pathways: degradation mediated by the Cullin-RING E3 ligase DCAF16 and stabilization by the DUB BAP1. Through CRISPR-Cas9 knockout screens and biochemical analyses, we demonstrate that DCAF16 promotes SPIN4 degradation, while BAP1 interacts with and stabilizes SPIN4 through its catalytic activity. Inhibition or loss of BAP1 reduces SPIN4 levels, highlighting its critical role in maintaining SPIN4 homeostasis. Proteomics and interactome analyses further support this regulatory axis. These findings reveal a dynamic balance controlling SPIN4 stability, with potential implications for epigenetic regulation and disease processes.

biochemistry↗

bioRxiv2025

Glycemia Shift Pancreatic Islets Rhythmicity via δ-α Cell in vivo, Impairment in Diabetes

Blood glucose homeostasis relies on the well-coordinated rhythmic activity of millions of islets throughout the pancreas. Islet rhythmicity is triggered by glucose elevation and mediated by paracrine interactions. However, the dynamics of islet population rhythmicity in healthy and diabetic pancreases in vivo remain poorly understood. Using simultaneous multi-islet Ca2+ imaging (20-100 islets per experiment) in both live mice and pancreatic tissue slices, we systematically studied how glycemia fluctuations and intra-islet paracrine signaling collectively shape the islet rhythmicity. In this study, we report that a transition from Hyperglycemia to Euglycemia induces a coordinated shift from slow to fast islet Ca2+ oscillations (HESF) in vivo. HESF is conserved in pancreatic tissue slices and isolated islets, however, not dispersed single cells in vitro, suggesting a mechanistic link with paracrine interactions. We found HESF arises from -cell activation, which is inhibited by {delta} cells upon glucose elevation. The autonomous islets mostly differ in phase and period at high glucose level. Diabetic mice with disrupted glycemic stability lost HESF both in vivo and in vitro. Interestingly, HESF is preserved in {beta}-cell knockout Gcgr transgenetic mice, both in vivo and in vitro, suggesting HESFs dependence on Glp1r. Indeed, HESF was restored in semaglutide-treated diabetic mice with stabilized glycemic stability. These findings offer a comprehensive understanding of how {delta} and cells influence islet rhythmicity and precisely maintain the stability of blood glucose.

physiology↗

bioRxiv2025

Pangenome-guided sequence assembly via binary optimisation

De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex regions without bias towards a single reference genome. Our method frames assembly as a graph traversal optimisation problem, which can be implemented on quantum computers. The pipeline first annotates pangenome graphs with estimated copy numbers for each node, then finds a path on the graph that best explains those copy numbers. On simulated data, our approach significantly reduces the number of contigs compared to de novo assemblers. While it introduces a small increase in inaccuracies, such as false joins, our optimisation-based methods are competitive with current exhaustive search techniques. They are also designed to scale more efficiently as the problem size grows and will run effectively on future quantum computers.

genomics↗

bioRxiv2025

Synaptic sign switching mediates online dopamine updates

In the mammalian brain, excitatory and inhibitory synapses are generally distinct and have fixed synaptic signs. Therefore, unlike in artificial neural networks, learning in biological networks is thought to be manifested by plasticity mechanisms that modify synaptic weights but not signs. Here, we demonstrate experience-dependent sign switching at synapses between glutamate and GABA co-releasing neurons of the entopedunculus (EP) and their targets in the lateral habenula (LHb). Pairing of reward or punishment with activation of EP co-releasing neurons makes EP-LHb synapses relatively more inhibitory or excitatory, respectively. Synaptic sign switching modulates downstream dopaminergic signaling, correlates with recent dopamine updates, and contributes to reinforcement learning. These data unveil a plasticity mechanism that alters both synaptic signs and weights to rapidly update dopamine release and drive learning.

neuroscience↗

bioRxiv2025

Human cortex organizes dynamic co-fluctuations along sensation-association axis

The human brain dynamically organizes its activity through coordinated fluctuations, whose spatiotemporal interactions form the foundation of functional networks. While large-scale co-fluctuations are well-studied, the principles governing their amplitude-dependent transitions--particularly across high, intermediate, and low-amplitude regimes--remain unknown. We introduce a co-fluctuation score to quantify how instantaneous functional interactions reorganize with global amplitude dynamics. Using resting-state fMRI data, we identified amplitude-dependent co-fluctuation transitions between functional systems hierarchically aligned with the sensorimotor-association (SA) axis: sensorimotor networks dominated high-amplitude co-fluctuations, associative systems prevailed during intermediate amplitudes, and limbic system preferentially engaged in low-amplitude states. This hierarchy underwent developmental refinement from childhood to adulthood and adaptively reconfigured under external stimuli. Replicated across four independent samples including 7T fMRI, these findings establish the SA axis as infrastructure for amplitude-dependent transitions of co-fluctuation states. Our framework bridges transient coordination and stable functional architecture, demonstrating how brain networks balance external processing (high-amplitude states) with internal cognition/emotion (mid-to-low amplitude states) through amplitude-stratified interactions.

neuroscience↗

bioRxiv2025

Expanding the repertoire of chemically induced covalent neoantigens

The ubiquitin-proteasome system generates peptide fragments that are displayed on MHC-I molecules. Recent studies revealed that covalent small molecules can hijack this process, leading to the presentation of hapten-modified peptide fragments, or covalent neoantigens. Here, we report a chemical proteomics platform to systematically investigate this process and harness covalent neoantigens for immune cell recruitment and activation. Using a bioorthogonal cysteine-reactive probe (IA-mTz), we demonstrate that diverse intracellular proteins can be modified, processed, and presented as covalent neoantigens across multiple cell lines. Mass spectrometry confirmed the presence of IA-mTz-modified peptides within the MHC-I immunopeptidome, and structural modeling revealed stable peptide-MHC-I interactions. We further integrated a bioorthogonal strategy that enables immune engagement: IA-mTz-modified cells conjugated with trans-cyclooctene (TCO)-IgG elicited Fc receptor activation in a reporter assay, supporting immune recruitment via antibody-dependent cellular phagocytosis. This approach was extended to additional cysteine-reactive probes and to 2,4-dinitrochlorobenzene (DNCB), a common skin sensitizer, which we show induces covalent neoantigen formation in a cell- and HLA-dependent manner. These findings reveal a previously underappreciated breadth of covalent neoantigen formation and provide a generalizable strategy for immune targeting of covalent neoantigens.

biochemistry↗

bioRxiv2025

Clade V MLO proteins are bona fide host susceptibility factors required for powdery mildew pathogenesis in Arabidopsis

Obligate biotrophic powdery mildew (PM) fungi strictly require living host to survive. To search for host factors or processes essential for PM pathogenesis, a tailored genetic screen was conducted with the immuno-compromised eds1-2/pad4-1/sid2-2 (eps) triple Arabidopsis mutant. This led to the identification of five allelic disruptive mutations in Mildew Locus O 2 (MLO2) to be responsible for the compromised-immunity-yet-poor infection (cipi) mutant phenotype upon challenge from an adapted PM isolate. Moreover, the eds1/pad4/sid2/mlo2/mlo6/mlo12 (eps3m) sextuple mutant display near complete immunity to the adapted PM fungus without sign of defense activation, demonstrating that these three clade V MLOs in Arabidopsis are bona fide host susceptibility factors of PM fungi. Confocal imaging revealed focal accumulation of MLO2-GFP in the peri-penetration peg membranous space, implicating MLO2 in repairing and stabilizing the damaged host plasma membrane, which may be co-opted by PM fungi for haustorium differentiation. Results from domain-swapping analysis between MLO1 and MLO2 suggest a bipartite functional configuration for MLO2: its C-terminus determines where and when MLO2 functions, while its N-terminal seven transmembrane domain region executes the cellular function that is critical for PM pathogenesis. Genetic studies further demonstrate that, unlike MLO7 in synergids, focal accumulation of MLO2 does not depend on FERONIA (FER) and its five other family members, nor does it require phosphatidylinositol 4,5-bisphosphate produced from phosphatidylinositol 4-phosphate 5-kinase 1 (PIP5K1) and PIP5K2. Together, these findings define clade V MLOs as host factors co-opted by obligate biotrophic PM fungi for successful host colonization.

plant biology↗

bioRxiv2025

FastGA: Fast Genome Alignment

FastGA finds alignments between two genome sequences more than an order of magnitude faster than previous methods that have comparable sensitivity. Its speed is due to (a) a carefully engineered architecture involving only cache-coherent MSD radix sorts and merges, (b) a novel algorithm for finding adaptive seed hits in a linear merge of sorted k-mer tables, and (c) a variant of the Myers adaptive wave algorithm [1] to find alignments around a chain of seed hits that detects alignments with up to 25-30% variation. It further does not require pre-masking of repetitive sequence, and stores millions of alignments in a fraction of the space of a conventional CIGAR-string [2] using a trace-point encoding that is further compressed by the ONEcode data system [3] introduced here. As an example, two bat genomes of size 2.2Gbp and 2.5Gbp can be compared in a little over 2 minutes using 8 threads on an Apple M4 Max laptop using 5.7GB of memory and producing 1.05 million alignments totaling 1.63Gbp of aligned sequence that cover about 60% of each genome. The output "ALN"-formatted file occupies 66MB. This file can be converted to a PAF file with CIGAR strings in 6 seconds, where the PAF representation is a significantly larger 1.03GB file. FastGA is freely available at github: http://www.github.com/thegenemyers/FASTGA along with utilities for viewing inputs, intermediate files, and outputs and transforming outputs into other common formats. Specifically, FastGA can, in addition to its highly efficient ONEcode representation, output PSL-formatted alignments, or PAF-formatted alignments with or without CIGAR strings explicitly encoding the alignments. There is also a utility to chain FastGAs alignments and display them in a dot-plot like view in Postscript files, and an interactive viewer is in development.

bioinformatics↗

bioRxiv2025

Personalized whole-brain Ising models with heterogeneous nodes capture differences among brain regions

Multiple lines of research have studied how complex brain dynamics emerge from underlying connectivity by using Ising models as simplified neural mass models. However, limitations on parameter estimation have prevented their use with individual, high-resolution human neuroimaging data. Furthermore, most studies focus only on connectivity, ignoring node heterogeneity, even though real brain regions have different structural and dynamical properties. Here we present an improved approach to fitting Ising models to 360-region functional MRI data: derivation of an initial guess model from group data, optimization of simulation temperature, and two stages of Boltzmann learning, first with group data, then with individual data. Our implementation uses GPU acceleration to mitigate the high computational cost of this approach. We then analyze how data binarization threshold affects goodness-of-fit, the role of the external field in model behavior, consistency among models fitted to different scans of the same individual, and correlations between model parameters and features from structural MRI, including measures of myelination and cortical folding. We find that binarizing fMRI data at higher thresholds decreases correlation between model and data functional connectivity but increases the heterogeneity of node external fields and their correlations with structural features. A choice of threshold that achieves both goodness-of-fit and intrinsic heterogeneity of regions results in a model that better reflects the reality of the brain as a network of intrinsically heterogeneous nodes. By enabling personalized, biophysically interpretable modeling of structure-function mapping across the whole brain, this approach can aid understanding of individual differences in brain network organization and bridge the gap between the network-focused methodology of connectomics and the region-focused paradigm typical of translational research.

neuroscience↗

bioRxiv2025

CD14 plays a critical role in pain and inflammation across multiple models of post-traumatic osteoarthritis

Inflammation is a primary driver of osteoarthritis (OA), and no therapies exist to halt or delay disease progression or substantially ameliorate the chronic pain, inflammation and disability that are characteristic of disease. Soluble CD14 (sCD14), a co-factor that enhances inflammatory toll-like receptor signaling, is present in synovial fluid in patients with OA and positively associates with joint space narrowing, synovial macrophage content, and pain. In this study, we show that increased sCD14 within human synovial fluid correlates with joint effusion volume and increased knee hyperalgesia. Next, we evaluated CD14 as a potential therapeutic target in three pre-clinical models of post traumatic OA (PTOA), using both genetic deficiency and pharmacologic blockade to modulate its activity. We demonstrate that deficiency or blockade of CD14 results in significant protection from increased evoked pain behaviors and from OA driven mobility impairments (i.e. decreased cage activity) across models that differ in severity, and across male and female cohorts. Using flow cytometry, single cell transcriptomics, and spatial proteomics, we further show that CD14-deficiency drastically influences the local synovial inflammatory landscape post-injury, reducing monocyte and macrophage populations and modulating local fibroblast populations. Targeting CD14 via genetic deficiency or therapeutic blockade revealed no substantial protection, but no worsening, of cartilage degeneration. Ultimately, our results provide strong support that targeting synovial inflammation through blockade of CD14 can safely ameliorate OA pain and disability after a pre-disposing injury. One Sentence SummaryThe study demonstrates the key role of CD14 in pain, mobility loss, and inflammation in PTOA, and demonstrates the therapeutic potential of CD14 blockade for OA pain relief.

immunology↗

bioRxiv2025

Application of Spectral Domain Optical Coherence Tomography To Guide Cochlear Implant Electrode Array

HypothesisA custom spectral domain optical coherence tomography (SD-OCT) platform can be used for real-time guidance of a cochlear implant electrode array (EA). BackgroundWith current cochlear implant surgical techniques, placement of the EA is a blind maneuver in which the surgeon relies on tactile feedback as the EA advances through the cochlear lumen. Cochlear implant trauma is a leading factor for poor speech performance outcomes and loss of residual hearing following surgery. Optical coherence tomography (OCT) is a non-invasive imaging modality that provides real-time visualization of tissue microstructure at higher spatial resolutions compared to clinical CT and MRI. Already adopted as standard of care in ophthalmology, OCT has the potential to assist the surgeon in real-time visualization of the EA trajectory. Unlike commercial systems, our custom OCT system allows tailored wavelength, scanning geometry, and real-time processing, which are critical factors for navigating the compact anatomy of the facial recess to image the cochlea. MethodsA custom-built SD-OCT system was used to image cochlear microanatomy in mice and human cadaveric temporal bones. The OCT system was then used to guide a mock EA in human cadaveric temporal bones in real-time using individual B scans that were reviewed sequentially as the EA was being advanced through the round window. ResultsUsing our OCT system, high-resolution (< 5.0 m) images of cochlear microanatomy were obtained in both mice and cadaveric human temporal bones with an image sensitivity of [~]104 dB. Following cochleostomy in cadaveric temporal bones, real-time sequential OCT B-scans were used to reliably guide placement of the EA through the scala tympani. ConclusionOur custom-built SD-OCT platform can generate high-resolution real-time visualization and orientation of mammalian cochlear microanatomy that can be used to assist with real time guidance of a CI EA. This technology has the potential to serve as a real-time surgical image guidance tool to minimize EA trauma and further our understanding of human cochlear pathophysiology.

bioengineering↗

bioRxiv2025

Forty New Genomes Shed Light on Sexual Reproduction and the Origin of Tetraploidy in Microsporidia

Microsporidia are single-celled, obligately intracellular parasites with growing public health, agricultural, and economic importance. Despite this, Microsporidia remain relatively enigmatic, with many aspects of their biology and evolution unexplored. Key questions include whether Microsporidia undergo sexual reproduction, and the nature of the relationship between tetraploid and diploid lineages. While few high-quality microsporidian genomes currently exist to help answer such questions, large-scale biodiversity genomics initiatives, such as the Darwin Tree of Life project, can generate high-quality genome assemblies for microsporidian parasites when sequencing infected host species. Here, we present 40 new microsporidian genome assemblies from infected arthropod hosts that were sequenced to create reference genomes. Out of the 40, 32 are complete genomes, eight of which are chromosome-level, and eight are partial microsporidian genomes. We characterised 14 of these as polyploid and five as diploid. We found that tetraploid genome haplotypes are consistent with autopolyploidy, in that they coalesce more recently than species, and that they likely recombine. Within some genomes, we found large-scale rearrangements between the homeologous genomes. We also observed a high rate of rearrangement between genomes from different microsporidian groups, and a striking tolerance for segmental duplications. Analysis of chromatin conformation capture (Hi-C) data indicated that tetraploid genomes are likely organised into two diploid compartments, similar to dikaryotic cells in fungi, with evidence of recombination within and between compartments. Together, our results provide evidence for the existence of a sexual cycle in Microsporidia, and suggest a model for the microsporidian lifecycle that mirrors fungal reproduction.

genomics↗

bioRxiv2025

Lignature: A Comprehensive Database of Ligand Signatures to Predict Cell-Cell Communication

Ligand-receptor interactions mediate intercellular communication, inducing transcriptional changes that regulate physiological and pathological processes. Ligand-induced transcriptomic signatures can be used to predict active ligands; however, the absence of a comprehensive set of ligand-response signatures has limited their practical application in predicting ligand-receptor interactions. To bridge this gap, we developed Lignature, a curated database encompassing intracellular transcriptomic signatures for 362 human ligands, significantly expanding the repertoire of ligands with available intracellular response signatures. Lignature compiles signatures from published transcriptomic datasets and established resources such as CytoSig and ImmuneDictionary, generating both gene- and pathway-based signatures for each ligand. We applied Lignature to predict active ligands driving transcriptomic changes in controlled in vitro experiments and real-world single-cell sequencing datasets. Lignature outperformed existing methods such as NicheNet, achieving higher accuracy in identifying active ligands at both the gene and pathway levels. These results establish Lignature as a robust platform for ligand signaling inference, providing a powerful tool to explore ligand-receptor interactions across diverse experimental and physiological contexts.

bioinformatics↗

bioRxiv2025

Epigenetic Reprogramming Alters Intestinal Stem Cell Fate in Pouchitis

Intestinal stem cells (ISCs) mediate the continuous renewal of the epithelium during homeostasis and recovery from injury. To investigate the molecular impact of inflammation on human ISCs and the role of janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling, we established an organoid model derived from individuals with pouchitis, a form of inflammatory bowel disease that develops in an organ generated from ileal pouch-anal anastomosis (IPAA) surgery. Compared with non-inflamed specimens, pouchitis organoids exhibited increased apoptosis and secretory lineage differentiation that were stable after multiple passages, mirroring findings in primary pouch tissue. Chromatin accessibility and histone modification profiling of ISCs revealed inflammation-driven epigenetic remodeling, particularly involving activator protein 1 (AP-1) transcription factors such as c-Jun and excessive STAT1 activity. Loss of c-Jun disrupted ISC viability and enhanced secretory cell differentiation in non-inflamed organoids, whereas therapies targeting JAK/STAT reversed these ISC defects and chromatin changes in pouchitis organoids. Together, these results associated inflammation with epigenetic changes in human ISCs, suggesting that immune-mediated injury has lasting effects on the pouch epithelium that can potentially be reversed through JAK/STAT therapies.

cell biology↗