Biology subjects

Ma, Z.

Publications and source records attributed to Ma, Z..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Differentiation of Xanthomonas oryzae pv. oryzae in vitro and during rice leaf infection

Highlights- Xoo produces filamentous morphology, which is transient and yields pleomorphic progenies in vitro - In planta, initial attachment of rod-shaped Xoo is detected at xylem pits - The Xoo infection front migrates basipetally in the vascular bundle and progresses laterally from major to minor veins via transverse veins - Xoo breaks out of the xylem vessels and enter the neighboring xylem parenchyma - Xoo assumes filamentous morphology that can traverse from the xylem across the bundle sheath into mesophyll tissue - Mobility in xylem vessels depends predominantly on rod-shaped Xoo, while infection of mesophyll tissue at later stages appears to be linked to filamentous morphology SummaryXanthomonas oryzae pv. oryzae (Xoo) is classified as a xylem pathogen responsible for bacterial blight of rice causing substantial yield losses in Asia and Africa. Xoo virulence depends on the ability to trigger SWEET sucrose efflux transporters in the xylem parenchyma (XP) by injection of transcription activation like effectors (TALe) into host cells, likely to access host-derived sucrose. To establish infection, Xoo must overcome physical barriers, immune responses and the hydraulic xylem flow. To gain insights into the colonization process, we used translational SWEET11a-GUS reporter lines, scanning electron microscopy, and confocal laser scanning microscopy of Xoo tagged with a fluorescent protein. We found that Xoo can differentiate in vitro into filamentous forms. We mapped the infection route of Xoo along the vasculature, identified distinct spatiotemporal phases of Xoo colonization marked by rod-shaped and, notably, filamentous Xoo cells. Rod-shaped Xoo were found to attach to xylem pits during basipetal progression of the infection. Notably, we found that at later infection stages, Xoo could enter the XP. Strikingly, Xoo adopted a filamentous phenotype that traversed bundle sheath cells and entered mesophyll cells. Chlorosis and necrosis of leaves is thus likely not just due to blockage of xylem flow, but to direct tissue damage. Filamentation had been reported as important for virulence of human pathogens e.g. Yersinia pestis, uropathogenic E. coli and Shigella and had been associated to sugar utilization in Bacillus subtilis. We thus hypothesize that Xoo differentiation during host colonization is critical for virulence. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/680524v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@f66d8borg.highwire.dtl.DTLVardef@91ca66org.highwire.dtl.DTLVardef@17f2846org.highwire.dtl.DTLVardef@12d46e7_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Synthetic signaling platform uncovers and rewires cellular responses to PD-1 perturbation

Tyrosine phosphorylation motifs are central regulators of cell signaling, yet methods to selectively detect and reprogram these events have been lacking. Here we introduce Sphyder (Selective PHosphotYrosine DEtection and Rewiring), which enables precise detection of signaling at the resolution of individual phosphorylation motifs. Using Sphyder biosensors, we resolved phosphorylation dynamics and uncovered regulatory mechanisms of the checkpoint receptor PD-1 in living cells. Sphyder also provided a framework for reconstructing phosphosignaling pathways. With this approach, we redirected PD-1 signaling from immunosuppressive to immunoactivating outputs and engineered synthetic receptors that linked extracellular sensing to customized transcriptional programs. In addition, Sphyder biosensors revealed previously unrecognized mechanisms of the PD-1/VEGF bispecific antibody Ivonescimab, showing that it induces VEGF-dependent clustering, phosphorylation, and degradation of PD-1. These findings may underlie its promising clinical activity relative to conventional PD-1 blockade. Together, our study establishes a broadly applicable strategy for sensing and reprogramming cell signaling, while also providing mechanistic insights into a new class of immune checkpoint inhibitors of major clinical interest.

immunology↗

bioRxiv2025

ALDH2 Deficiency Drives Proliferative Mammary Morphogenesis and Epithelial Cell Stemness via Oxidative Stress and Estrogen Receptor Activation

Alcohol consumption has been linked to breast cancer, partly due to the accumulation of toxic aldehydes like acetaldehyde, a carcinogenic byproduct of ethanol metabolism. ALDH2, a key mitochondrial enzyme, detoxifies acetaldehyde and other harmful aldehydes that drive oxidative stress, DNA damage, and hormonal dysregulation, key factors in carcinogenesis. Despite the possible link between alcohol consumption and breast cancer risk, little is known about how ALDH2 deficiency itself, independent of alcohol exposure, affects mammary gland biology and cancer susceptibility. Genetic variants leading to ALDH2 deficiency are highly prevalent in East Asian populations, where individuals carrying inactive ALDH2 alleles experience impaired aldehyde detoxification. While these individuals are at increased risk for alcohol-related cancers, the impact of ALDH2 deficiency on mammary gland development and homeostasis in the absence of alcohol exposure remains unexplored. To address this, we utilized a C57BL/6-based ALDH2 knockout (Aldh2-/-) mouse model to investigate its effects on mammary proliferation and development. Our findings revealed that Aldh2-/- mice exhibited hyperproliferative mammary glands, characterized by increased epithelial cell density, ductal expansion, and elevated Ki67+ cells. Flow cytometry analysis demonstrated a rise in luminal and basal epithelial subpopulations, alongside enhanced mammary epithelial stemness, as evidenced by increased mammosphere formation and colony-forming efficiency. At the molecular level, ALDH2 deficiency activated oxidative stress pathways, marked by elevated 8-OHdG, p38 MAPK, NF-{kappa}B, and Nrf2 signaling, alongside DNA damage responses involving p53 and H2A.X. Importantly, we also identified a previously unrecognized upregulation of RANKL in Aldh2-/- mammary glands, implicating the RANK/RANKL axis as a critical mediator linking aldehyde stress to NF-{kappa}B/p38 MAPK activation and enhanced mammary stemness. Furthermore, hormonal dysregulation was observed, with a significant increase in ER and PR expression and phosphorylation. Dysregulated ER signaling was further linked to enhanced erbB3 activation and downstream signaling, including the cyclin D1-pRb-E2F1 axis. Our results suggest that the accumulation of endogenous aldehydes, independent of alcohol exposure, profoundly alters mammary morphogenesis, epithelial repopulation, and stemness. Mechanistically, this occurs through oxidative stress activation and DNA damage pathways, leading to metabolic changes and upregulation of estrogen receptor and receptor tyrosine kinase signaling. This study highlights for the first time the potential role of ALDH2 deficiency in increasing mammary tissue susceptibility to oncogenic factors and breast cancer risk.

cancer biology↗

bioRxiv2025

RemoteFoldSet: Benchmarking Structural Awareness of Protein Language Models

Protein language models (pLMs) have the capacity to infer structural information from amino acid sequences. Evaluating the extent to which structural information they truly encode is crucial for assessing their generalizability and the interpretability of their latent representations, yet current approaches lack a model-free, quantitative framework to evaluate these encodings. We introduce RemoteFoldSet, a curated collection of protein sequence sets stratified by high structural similarity but minimal sequence identity. We also define the Structural Awareness (SA) score, a novel metric that enables model-agnostic, unsupervised, and training-free quantification of structure-related patterns in pLM embeddings. Using RemoteFoldSet together with the SA score, we benchmark a range of existing pLMs, elucidating how models with different training objectives, architectures, and sizes discriminate and distribute proteins within their embedding spaces, both quantitatively and qualitatively. We expect that this methodology will serve as a reliable benchmark for evaluating the performance of pLMs for structural and functional applications.

biochemistry↗

bioRxiv2025

Convergent utilization of APN receptor by hedgehog merbecoviruses

Dipeptidyl peptidase-4 (DPP4) and angiotensin-converting enzyme 2 (ACE2) are well-established receptors for merbecoviruses, yet the receptor usage of merbecoviruses of European and Asian hedgehogs (EriCoVs) remains unknown. Here, by testing hedgehog orthologs of known coronavirus receptors, we identify hedgehog aminopeptidase N (APN) as a functional receptor for EriCoVs. Analysis of 94 APN orthologs indicates that EriCoVs have a limited host range, primarily utilizing hedgehog APN and, to a lesser extent, APN from certain felids, shaped by specific determinants at the virus-receptor interface. Cryo-EM reveals an APN-binding mode distinct from those used by alpha- and deltacoronaviruses. Functional assays indicate that hedgehog transmembrane serine protease 2 (TMPRSS2) enhances spike activation and promotes pseudovirus entry. Neutralizing antibodies targeting RBD and APN were developed and could effectively block EriCoV pseudovirus entry and propagation. These findings reveal an unexpected convergent evolution of APN utilization among merbecovirus, establishing a foundation for risk assessment and countermeasure development. Graphic abstractConvergent utilization of hedgehog APN by EriCoVs O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/676546v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1ea334aorg.highwire.dtl.DTLVardef@cd53bforg.highwire.dtl.DTLVardef@352102org.highwire.dtl.DTLVardef@a1eed_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids

The human heart, originating from the splanchnic mesoderm, is the first functional organ to develop, co-evolving with the foregut endoderm through reciprocal signaling. Previously, cardioid models offered new insights on cardiovascular cell lineages and tissue morphogenesis during heart development, while mesoderm-endoderm crosstalk remain incompletely understood. Here, we integrated micropatterned cardioids, CRISPR-engineered reporter hiPSCs, deep-tissue imaging, and single-cell RNA sequencing (scRNA-seq) to explore synergistic mesoderm-endoderm co-development. scRNA-seq with PHATE trajectory mapping reconstructed lineage bifurcations of mesoderm-heart and endoderm-foregut lineages, identifying key cell types in cardiac and hepatic development. Ligand-receptor interaction analysis highlighted mesodermal cells enriched in non-canonical WNT, NRG, and TGF-{beta} signaling, while endodermal cells exhibited VEGF and Hedgehog activity. We found that micropattern sizes influenced cellular composition, cardioid cavitation, contractile functions, and mesoderm-endoderm signaling crosstalk. The cardioids generated from 600 {micro}m diameter circle patterns showed larger cavity formation resembling early heart chamber formation. Our findings establish micropatterned cardioids as a model for mesoderm-endoderm co-development, enhancing our understanding of heart-foregut synergy during early embryogenesis.

bioengineering↗

bioRxiv2025

Polyclonal origins of human premalignant colorectal lesions

Cancer is generally thought to be caused by expansion of a single mutant cell1. However, analyses of early colorectal cancer lesions suggest that tumors may instead originate from multiple, genetically distinct cell populations2,3. Detecting polyclonal tumor initiation is challenging in patients, as it requires profiling early-stage lesions before clonal sweeps obscure diversity. To investigate this, we analyzed normal colorectal mucosa, benign and dysplastic premalignant polyps, and malignant adenocarcinomas (123 samples) from six individuals with familial adenomatous polyposis (FAP). Individuals with FAP have a germline heterozygous APC mutation, predisposing them to colorectal cancer and numerous premalignant polyps by early adulthood4. Whole-genome and/or whole-exome sequencing revealed that many premalignant polyps--40% with benign histology and 28% with dysplasia--were composed of multiple genetic lineages that diverged early, consistent with polyclonal origins. This conclusion was reinforced by whole-genome sequencing of single crypts from multiple polyps in additional patients which showed limited sharing of mutations among crypts within the same lesion. In some cases, multiple distinct APC mutations co-existed in different lineages of a single polyp, consistent with polyclonality. These findings reshape our understanding of early neoplastic events, demonstrating that tumor initiation can arise from the convergence of diverse mutant clones. They also suggest that cell-intrinsic growth advantages alone may not fully explain tumor initiation, highlighting the importance of microenvironmental and tissue-level factors in early cancer evolution.

cancer biology↗

bioRxiv2025

Mechanistic insights and in vivo HIV suppression by the BRD4-targeting small molecule ZL0580

Epigenetic suppression and durable silencing of HIV represent a promising strategy to achieve ART-free remission, consistent with the "block and lock" HIV cure paradigm. BRD4 is a host epigenetic reader and plays a critical role in HIV transcriptional regulation. We previously identified ZL0580, a first-in-class BRD4-selective small molecule distinct from the pan-BET inhibitor JQ1, which induces HIV epigenetic suppression. However, detailed molecular mechanisms, pharmacokinetics (PK), and in vivo HIV-suppressive efficacy of ZL0580 remain undefined. Here, we show that ZL0580 selectively targets BRD4 bromodomain 1 (BD1) through interaction with a key glutamic acid residue (E151), as determined by structural modeling and mutagenesis. Transcriptomic profiling by RNA-seq reveals that ZL0580 and JQ1 induce opposing gene expression programs, consistent with their distinct effects on HIV proviral transcription and latency. In a humanized mouse model of HIV infection, ZL0580 monotherapy, or in combination with ART, potently suppressed active HIV replication, reducing the plasma viremia to nearly undetectable levels, and delayed viral rebound following treatment interruption. Collectively, these findings establish ZL0580 as an epigenetic suppressor of HIV in vivo and provide proof-of-concept for its potential as a "block and lock" HIV cure candidate, warranting further optimization and development.

microbiology↗

bioRxiv2025

The X-ray crystal structure of BorF, the flavin reductase subunit of a two-component flavin-dependent tryptophan halogenase

BorF is a short-chain flavin reductase from a desert soil bacterium that uses NADH to reduce FAD to FADH2, which is used by the tryptophan-6-halogenase BorH to chlorinate tryptophan in the biosynthetic pathway of borregomycin A. The X-ray crystal structure of BorF bound to FAD was solved to 2.37 [A] by molecular replacement and consists of a homodimer of single-domain protomers with a Greek key split {beta}-barrel topology containing a domain-swapped N-terminal -helix, as seen in other members of this family. Insertions and deletions in the region between 3 and {beta}5 lead to a variety of different conformations of the adenosine portion of FAD bound to BorF and structurally related reductases. Comparison of the FAD-bound structures of BorF and BorH suggests that FAD must completely dissociate from BorH in order to be reduced by BorF.

biochemistry↗

bioRxiv2025

RIG-I-dependent tumor-intrinsic type I interferon signaling restricts growth in breast cancer 3D culture

Discovery of key growth drivers that can be targeted for therapy is a central goal in cancer research. While high-throughput CRISPR screens have revolutionized our ability to identify gene dependencies in cancer, most large-scale screens are conducted in two-dimensional (2D) culture systems that fail to recapitulate tumor organization and behavior. To uncover architecture-dependent vulnerabilities in breast cancer, we performed parallel CRISPR interference (CRISPRi) screens in 2D and three-dimensional (3D) cultures of MCF7 cells, an estrogen receptor-positive (ER+) breast cancer model representative of a high risk of relapse, luminal subtype. Knockdown of IFNAR2 and TYK2 conferred a growth advantage in 3D cultures, implicating type I interferon signaling as a tumor-intrinsic suppressor of proliferation in 3D spheroids. Transcriptomic and functional analyses demonstrated that type I IFN signaling is endogenously activated in 3D spheroids via RIG-I-mediated sensing of cytosolic double-stranded RNA, leading to TBK1 activation and induction of interferon-stimulated genes (ISGs). This tumor-intrinsic IFN response slowed proliferation in 3D culture, independent of exogenous stimuli or the presence of immune cells. Analysis of bulk, single-cell, and spatial transcriptomic datasets from breast cancer patients revealed that a subset of tumors exhibit elevated IFN signaling in cancer cells, including in immune-depleted tumor cores, consistent with a tumor-intrinsic IFN signature. Our findings uncover an IFN-mediated growth-suppressive program shaped by 3D tumor architecture, and contribute towards a better understanding of the role of tumor-intrinsic IFN activity.

cancer biology↗

bioRxiv2025

Self-Reactive B Cells in Artery Tertiary Lymphoid Organs Encode Pathogenic High Affinity Autoantibody in Atherosclerosis

Artery tertiary lymphoid organs (ATLOs) emerge in atherosclerosis which is a chronic inflammatory artery disease with an autoimmune component. However, whether disease-relevant autoimmune B cells emerge in ATLOs and their impacts remains unknown. To map atherosclerosis-specific humoral autoimmunity and define its roles, we isolated germinal-center (GC) B cells from ATLOs and lymph-nodes, expression-cloned 60 autoantibodies and screened them for arterial wall reactivity. ATLO-derived autoantibodies markedly skewed to atherosclerosis-relevant autoantigens versus those of lymph-nodes. One ATLO GC-derived autoantibody bound to histone 2B (H2B) with high-affinity ([~]25 nM). Moreover, vaccination with H2B or adoptive transfer of its cognate autoantibody markedly accelerated atherosclerosis suggesting that ATLOs fail to delete pathogenic high-affinity self-reactive B cells. In a human cohort, total circulating anti H2B antibody titers positively correlated with aortic and coronary artery calcification. We conclude that ATLOs harbor a dysregulated immune tolerance environment permissive for autoreactive B cells that express pathogenic autoantibodies driving atherosclerosis.

immunology↗

bioRxiv2025

Tryptophan and IFN-γ Differentially Modulate Cellular Uptake, Intracellular Trafficking, and Gene Expression of Messenger RNA-Loaded Lipid Nanoparticles in Dendritic Cells

Lipid nanoparticle (LNP)-mediated mRNA delivery has emerged as a powerful platform for both immunostimulatory and immunomodulatory applications. However, the influence of local immunometabolic cues on the intracellular fate and translational efficiency of mRNA-LNPs remains poorly understood. In this study, we investigated how interferon-gamma (IFN-{gamma}), a potent inducer of indoleamine 2,3-dioxygenase 1 (IDO1), and tryptophan (Trp) deprivation independently and combinatorially affect mRNA-LNP function in DC2.4 dendritic cells. These two cues are canonical drivers of immunoregulatory microenvironments, particularly those that favor tolerogenic dendritic cell programming and the induction of regulatory T cells. Using dual-reporter mRNA constructs and high-resolution confocal imaging, we show that IFN-{gamma} stimulation reduces total cellular mRNA uptake and lysosomal accumulation without affecting translation efficiency and endosomal escape efficiency. Whereas Trp deprivation also reduces the overall cellular uptake of mRNA-LNPs, it also significantly impairs protein synthesis from mRNA-LNPs and modestly reduces endosomal escape, despite having minimal impact on lysosomal mRNA levels. Spatial compartmentalization analysis revealed that IFN-{gamma} and Trp limitation disrupt distinct steps in the delivery-translation cascade, acting independently but additively to suppress the ultimate protein translation from mRNA-LNPs in DC2.4 dendritic cells. These findings highlight the importance of considering local metabolic and cytokine contexts when deploying mRNA-LNPs for immunological applications. Our work provides mechanistic insights into how immunoregulatory environments impair the delivery and translation of mRNA-LNPs, suggesting strategies to tune delivery outcomes for tolerogenic purposes.

biochemistry↗

bioRxiv2025

Metabolic basis of the astrocyte-synapse interaction governs dopaminergic-motor connection

Perisynaptic astrocyte processes are constitutive attachments of synapses in the central nervous system. However, the molecular mechanisms that control perisynaptic astrocyte ensheathment and their implications in the wiring of neural circuits remain unclear. Here, we report that glycolysis controls astrocyte-synapse contact. In the Drosophila larval dopaminergic (DAergic) circuit, blocking astrocyte glycolysis stimulated perisynaptic ensheathment by attenuating astrocyte-to-DAergic neuron neuroligin 2-neurexin 1 signaling. As a result, the larvae executed more reorientation actions during locomotion. At the circuit level, behavioral alterations were found to arise from increased DAergic neuronal synaptogenesis and DAergic-motor connection. Our research uncovers an ancient metabolic basis that determines perisynaptic astrocyte ensheathment abundance through a conserved neuroligin-neurexin signaling pathway and demonstrates the role of astrocyte glycolysis in controlling DAergic-motor circuit assembly and function.

neuroscience↗

bioRxiv2025

Computational Assessment of Circularization Impact on Saxitoxin G-quadruplex Aptamer Performance

Although high-affinity and high-specificity aptamers can be obtained by SELEX (Systematic Evolution of Ligands by Exponential Enrichment), and have good activity in vitro, their performance in vivo is poor. This is mainly because of the degradation of linear nucleic acids by nucleases in body fluids and the difficulty of maintaining stable 3D structures in complex body fluid environments, which seriously hinders the clinical application of aptamers. This makes circular aptamers, which can resist degradation and are more stable in complex body fluid environments, an attractive option. However, the cyclization process may have a considerable impact on the structure of the original linear aptamer, and blind cyclization may lead to a decrease in its affinity. Here, we developed a new method to guide the cyclization of saxitoxin (STX) aptamers based on molecular computation, and verified the activity of circular aptamers through bioactivity experiments to further verify the authenticity and reliability of our methods. Consistent with the computational analysis, although circularization disrupts the G4 structure, circular aptamer not only has a higher affinity than the linear one but also provides certain protection to mice and greatly prolongs their survival, which proves the accuracy and reliability of the circular structure designed by our computational method. Our findings provide important ideas for better guidance in the design of circular aptamers and demonstrate their great potential in therapeutic applications.

biochemistry↗

bioRxiv2025

Role of Thioredoxin Reductase (TrxB) in Oxidative Stress Response of Francisella tularensis Live Vaccine Strain

Francisella tularensis is an important human pathogen responsible for causing tularemia in the Northern Hemisphere. Francisella has been developed as a biological weapon in the past due to its extremely high virulence. F. tularensis is a Gram-negative, intracellular pathogen that primarily infects macrophages. To counteract the reactive oxygen and nitrogen species (ROS/RNS) produced by macrophages in response to infection, F. tularensis encodes a repertoire of antioxidant enzymes. Among these, the thioredoxin system is critical for maintaining cellular redox homeostasis by regulating the balance between oxidation and reduction within bacterial cells. This system includes thioredoxins, thioredoxin reductase, and NADPH. Despite its potential importance, the thioredoxin system of F. tularensis remains understudied. F. tularensis possesses two thioredoxin genes, trxA1 (FTL_0611) and trxA2 (FTL_1224), and a single thioredoxin reductase gene, trxB (FTL_1571). In this study, we characterized the role of trxB in oxidative stress resistance. Our findings demonstrate that trxB is essential for oxidative stress resistance in F. tularensis and that its loss increases susceptibility to several antibiotics. However, unlike in other bacterial species, TrxB in F. tularensis is not a functional target of the gold-containing antimicrobial agent auranofin. We also show that OxyR, the master regulator of oxidative stress responses, directly controls trxB expression under oxidative stress conditions. Furthermore, TrxB contributes to intramacrophage survival by enabling the bacterium to withstand ROS-induced oxidative stress. Collectively, this study highlights a critical, previously uncharacterized antioxidant defense mechanism in F. tularensis, highlighting its importance in oxidative stress resistance and intramacrophage survival.

microbiology↗

bioRxiv2025

BABA: Naturalistic fMRI and MEG recordings during viewing of a reality TV show

Prior neuroimaging datasets using naturalistic listening paradigms have predominantly focused on single-talker scenarios. While these studies have been invaluable for advancing our understanding of speech and language processing in the brain, they do not capture the complexities of real-world multi-talker environments. Here, we introduce the "Le Petit Prince (LPP) Multi-talker Dataset", a high-quality, naturalistic neuroimaging dataset featuring 40 minutes of electroencephalogram (EEG) and 7T functional magnetic resonance imaging (fMRI) recordings from 26 native Mandarin Chinese speakers as they listened to both single-talker and multi-talker speech streams. Validation analyses conducted on both EEG and fMRI data demonstrate the datasets high quality and robustness. Additionally, the dataset includes detailed transcriptions and prosodic and linguistic annotations of the speech stimuli, enabling fine-grained analyses of neural responses to specific linguistic and acoustic features. The LPP Multi-talker Dataset is well-suited for addressing a wide range of research questions in cognitive neuroscience, including selective attention, auditory stream segregation, and working memory processes in naturalistic listening contexts.

neuroscience↗

bioRxiv2025

The Stmn1-lineage contributes to acinar regeneration but not to neoplasia upon oncogenic Kras expression

BACKGROUND & AIMSThe exocrine pancreas has a limited regenerative capacity, but to what extent all acinar cells are involved in this process is unclear. Nevertheless, the heterogenous nature of acinar cells suggests that cells exhibiting higher plasticity might play a more prominent role in acinar regeneration. In that regard, Stmn1-expressing acinar cells have been identified as potential facultative progenitor-like cells in the adult pancreas. Here, we studied Stmn1-progeny under physiological conditions, during regeneration, and in the context of KrasG12D expression. METHODSWe followed the fate of Stmn1-progenies both under baseline conditions, following caerulein-induced acute or chronic pancreatitis, pancreatic duct ligation, and in the context of KrasG12D expression. RESULTSThe Stmn1-lineage contributes to baseline acinar cell turnover under physiological conditions. Furthermore, these cells rapidly proliferate and repopulate the acinar compartment in response to acute injury in an ADM-independent manner. Moreover, acinar regeneration during chronic pancreatitis progression is in conjunction with a decline in the proliferative capacity of the Stmn1-lineage. Interestingly, newly generated acinar cells display increased susceptibility to additional injury during recurrent acute pancreatitis (RAP). Finally, given their inability to form ADMs, the Stmn1-lineage fails to form PanINs upon oncogenic Kras expression. CONCLUSIONSOur findings establish the Stmn1-lineage as a pivotal subpopulation for acinar regeneration. The ability of these cells to restore acinar tissue in an ADM-independent manner distinguishes them as a critical regenerative population. This study presents a new paradigm for acinar regeneration and repair in the context of pancreatitis and neoplasia.

cell biology↗

bioRxiv2025

CHIEF: An Attention-based Ensemble Learning Framework for Functional Protein Design

Protein de novo design is a longstanding challenge in biological field due to the multifaceted physicochemical properties and complexities of proteins. Several deep learning models have emerged for protein de novo design. However, each model exhibits distinct strengths and limitations because of the differences in training strategies or neural network architectures. Therefore, improving the effectiveness of protein design, particularly for functional protein, requires further improvement. To tackle this challenge, we developed CHIEF (Chimera Ensemble Inverse Folding), an attention-based ensemble framework that integrates five pretrained base models (ProteinMPNN-vanilla, ProteinMPNN-soluble, ESM-IF, Frame2seq and PiFold) to leverage their complementary strengths and mitigate limitations. Compared with the base models, CHIEF significantly improved the sequence recovery rate by 16.6-28.0%, while reducing the prediction perplexity by 22.7-34.6%. CHIEF also exhibited superior protein-designing capacity in variable sequence- and structure-based metrics and in large and complex proteins. CHIEF dynamically captured the semantic information from base models in a context-dependent manner and was minimally affected by the ablation of each base model. More importantly, CHIEF demonstrates real-world applicability to design functional malate dehydrogenase (MDH), achieving a 100% success rate. In summary, our study develops an ensemble deep learning model that improves the efficacy of protein sequence design, and will be a valuable platform for protein engineering and drug development.

bioengineering↗