Biology subjects

Zhu, L.

Publications and source records attributed to Zhu, L..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

STEAP4+ neutrophils: a promising circulating biomarker for lung metastasis

As the leading contributor to cancer-related mortality, metastasis often evades detection until advanced stages, underscoring the critical need for early predictive biomarkers. Neutrophils are naturally circulating sentinels that have been implicated in pioneering pre-metastatic niche formation in distant organs. Nevertheless, their heterogeneity within evolving metastatic microenvironments remains poorly characterized. Here, through dynamically delineating neutrophil subsets via single-cell transcriptomics, we identified a conserved feature of lung metastasis in breast cancer and other cancer models. Among the core genes, a cell surface marker, STEAP4, was selected and validated to indicate lung metastases at both RNA and protein levels. In both humans and mice, these STEAP4+ neutrophils were detectable not only in lung metastatases but also in the circulation. Clinically, the abundance of circulating STEAP4+ neutrophils robustly discriminates patients with lung metastasis from those with localized primary tumor. Our findings uncover STEAP4+ neutrophils as a promising biomarker and lay the groundwork for a non-invasive, blood-based diagnostic strategy for metastatic disease.

cancer biology↗

bioRxiv2025

A scaffold attachment factor PHM-2 regulates synaptic transmission through SLO-2 potassium channel in C. elegans

Scaffold attachment factor B (SAFB) proteins are evolutionarily conserved DNA/RNA binding proteins that are involved in multiple processes of gene expression. These proteins are broadly expressed with particular high expression observed in the nervous system. However, their physiological roles in neurons are largely unclear. Here we show that PHM-2, the sole SAFB ortholog in C. elegans, regulates synaptic transmission at the neuromuscular junctions through an effect on SLO-2 potassium channel. We found that phm-2 knockout suppresses a sluggish phenotype of worms expressing a hyperactive SLO-2 channel, greatly reduces SLO-2-mediated neuronal whole-cell currents, and enhances neuromuscular synaptic transmission. In addition, we found that PHM-2 genetically interacts with another DNA/RNA binding protein, HRPU-2/hnRNP U, to control SLO-2 expression through a posttranscriptional mechanism. These results reveal a novel function of a SAFB protein in regulating neuronal activity, and may help understand the physiological roles of SAFB proteins in the nervous system of other species. Author SummaryProteins in the SAFB family are found in many species, and they help control how genes are expressed in cells. These proteins are commonly present in the nervous system, but their exact roles in nerve cells are not well understood. In this study, we examined the single SAFB-like protein called PHM-2 in the nematode C. elegans to learn how it affects the nervous system. We discovered that PHM-2 plays an important role in communication between nerve cells and muscles. Worms lacking PHM-2 were able to counteract the sluggish movement caused by a hyperactive potassium channel called SLO-2. Without PHM-2, nerve cells had much smaller electrical currents mediated by SLO-2 and a stronger signaling from nerves to muscles. We also found that PHM-2 works together with another genetic regulator, HRPU-2, to control the amount of SLO-2 protein made in nerve cells. These findings reveal a new role for SAFB proteins in shaping neuronal activity by regulating potassium channels. Understanding this process in worms may provide clues about how these proteins contribute to brain function in humans.

neuroscience↗

bioRxiv2025

MAGNET: an all-in-one foundation model for cross-modal and cross-dimensional microscopic image restoration

The application of emerging Foundation models in current microscopy has remained limited due to task-specific model designs, strong modality dependence and insufficient robustness under complex degradations. Here, we introduce MAGNET (Microscopic All-in-one General fouNdation model for imagE resToration), the first end-to-end All-in-One foundation model designed for universal microscopic image restoration. MAGNET integrates multi-task, cross-modal and cross-dimensional (2D + 3D) image restoration capabilities within a single unified architecture, and it is specifically designed to handle composite degradations in practical imaging systems. The framework comprises three components: (i) a task-aware, prompt-guided feature enhancement module for adaptive learning across diverse degradations; (ii) an LIIF-based reconstruction module enabling continuous, resolution-adaptive restoration; and (iii) a dimension-compatible triple-plane projection module supporting both 2D and 3D data. Trained on large-scale datasets spanning 5 major microscopy modalities (structured illumination, confocal, light-sheet, wide-field and two-photon) and 8 representative restoration tasks, MAGNET achieves state-of-the-art performance across super-resolution, denoising, deblurring, background suppression, isotropic reconstruction, aberration correction, de-scattering and virtual staining. Beyond supervised training, MAGNET supports direct inference on unseen systems, efficient few-shot fine-tuning and self-supervised test-time optimization, enabling robust performance across diverse data and imaging conditions. MAGNET serves as a unified, generalizable, and scalable computational framework for microscopy, enabling more efficient and reliable downstream analyses in cell biology, neuroscience, and pathology.

cell biology↗

bioRxiv2025

The conserved NUS-1/DHDDS complex links N-glycosylation to lipid and lysosomal homeostasis in C. elegans

N-glycosylation, driven by the cis-prenyltransferase (cis-PT) complex, a NUS1 and DHDDS heterotetramer, is vital for proteome integrity. Despite being linked to severe congenital disorders of glycosylation (CDGs), the systemic role of NUS1/DHDDS remains elusive. Here, we characterize the conserved C. elegans cis-PT complex and uncover a critical crosstalk with global lipid metabolism. cis-PT deficiency induces catastrophic ER stress, global glycoprotein defects, and developmental failure. Mechanistically, NUS-1 physically interacts with the core oligosaccharyltransferase (OST) complex, directly coupling substrate synthesis to N-glycan transfer. Loss of NUS-1 or DHDDS causes systemic lipopenia, lysosomal dysfunction, and cholesterol sequestration, resulting from impaired N-glycosylation of key regulatory glycoproteins like SCAP. Utilizing CDG-associated CRISPR models, we resolve the molecular basis for cis-PT dysfunction, identifying interface disruption and catalytic impairment as distinct disease etiologies. These findings collectively reveal a critical and previously unappreciated crosstalk between protein glycosylation and global lipid metabolism, establishing a robust system to explore CDG pathology and therapeutic strategies.

cell biology↗

bioRxiv2025

A high-throughput methods SNIPR-Nm reveals small RNA methylation ratio

Small RNAs regulate gene expression and genome stability, and their functions are shaped by 3'-terminal 2'-O-methylation (Nm). Although Nm is universal in plants and mainly marks animal piRNAs, recent evidence reveals Nm on mammalian miRNAs, highlighting broader regulatory roles. However, current sequencing underestimates Nm-modified RNAs due to ligation bias, and existing qPCR-based methods cannot simultaneously quantify abundance and modification, leaving Nm dynamics largely unexplored. We developed a unified enzymatic strategy that integrates poly(A) polymerase and a thermostable ligase to measure both small RNA abundance and 3'-end Nm status. Applied to mouse testis, it enables robust quantification of Nm ratios for piRNAs and miRNAs. Our method offers a versatile tool for dissecting small RNA methylation in development and disease.

genetics↗

bioRxiv2025

Epitope and functional classification of human neutralizing antibodies against SFTSV Gn

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a lethal bunyavirus lacking approved countermeasures. From SFTS survivors, we isolate 84 human monoclonal antibodies (mAbs) against the viral glycoproteins Gn and Gc. Gn-specific mAbs demonstrate superior neutralization breadth and potency compared to the restricted neutralizing activity observed with Gc. Using a high-throughput yeast display deep mutational scanning (DMS) platform, we classify Gn-head mAbs into eight epitope groups, among which four groups (IA, ID, IIIA, IIIB) conferring neutralization. Notably, mAbs BD70-4003 (group IA) and BD70-4017 (group IIIA) exhibit broad neutralization and provide 100% protection in a lethal mouse model. Cryo-EM structural analysis of these mAbs in complex with the Gn-head reveal their binding interfaces, directly validating the epitope residues identified by DMS. Our study delineates the antigenic landscape of SFTSV Gn, identifies potent therapeutic candidates, and establishes DMS coupled with structural validation as a powerful framework for antibody discovery against bunyavirus.

immunology↗

bioRxiv2025

A Precisely Controlled Long-Acting Immunosuppression Platform Enables Prolonged Survival of Vascularized Composite Allografts

Vascularized composite allotransplantation (VCA) restores complex tissue defects but demands lifelong systemic immunosuppression. Oral tacrolimus (TAC) is limited by a narrow therapeutic window, pharmacokinetic variability, adherence challenges, and toxicity. Local delivery could mitigate these issues, yet clinical translation has been hindered by burst release, short duration, and the inability to co-deliver agents. We developed PRECISE (Programmable, REtrievable, Controlled ImmunoSuppression Encapsulator), an injectable, in-situ-forming PLGA depot that achieves long-acting, tightly controlled TAC release via structure-guided co-formulation with drug-binding agents (DBAs). GRAS small molecules (e.g., EGCG, maltotriose) identified by in silico docking and in vitro screening suppressed burst and modulated solvent efflux. Notably, rapamycin (RAPA) served dually as an mTOR inhibitor and a TAC-binding excipient, enabling synchronized dual-agent delivery. PRECISE eliminated burst in vitro and produced coordinated TAC+RAPA release with clinically compatible injectability. In rats, monthly intragraft dosing maintained systemic TAC/RAPA within the therapeutic window ([~]5-10 ng/mL) for >300 days, prolonged hindlimb allograft survival, expanded Tregs, and induced donor-specific hyporesponsiveness. Surgical retrieval of the depot triggered rapid TAC decline, demonstrating reversibility. In a stringent, fully MHC-mismatched porcine VCA model, PRECISE maintained on-target drug levels and extended graft survival beyond 90 days with minimal rejection and preserved vascular integrity. PRECISE is, to our knowledge, the first retrievable, injectable platform to deliver long-acting, dual-agent immunosuppression with controlled kinetics, rapid attainment of therapeutic steady state, and sustained graft protection. Its modular, structure-guided design enables clinical translation across VCA and solid-organ transplantation, delivering precise, durable, and safer immunosuppression.

bioengineering↗

bioRxiv2025

High-Concordance Validation of Droplet Digital PCR and Next-Generation Sequencing for EGFR Mutation Detection Across Diverse Biospecimens in a Large-scale NSCLC Cohort Study

BackgroundsNext-generation sequencing (NGS) and droplet digital PCR (ddPCR) are both established methods for detecting EGFR mutations in non-small cell lung cancer (NSCLC). However, comprehensive validation of their concordance in mutation detection and variant allele frequency (VAF) quantification across heterogeneous sample types remains limited. Inconsistent results from different sample types (e.g., cfDNA, FFPE) pose a significant challenge to clinical decisions. This is particularly critical for advanced NSCLC patients, who often rely on liquid biopsy, yet the concordance between liquid and tissue-based testing lacks validation in large-scale studies. Another issue in clinical practice is that many tumor samples are limited in quantity, making it difficult to meet testing requirements. Therefore, it is worth exploring whether pre-capture NGS libraries can serve as substitutes for original DNA. MethodsIn this study, we first developed three assays to detect EGFR L858R, exon 19 deletions (Ex19del) and T790M, respectively using ddPCR platform. Their Limit of Detection (LOD) could reach 0.01% at 100 ng of input DNA. Subsequently, we conducted a large retrospective clinical study to systematically compare the detection performance of ddPCR and NGS across three mutation types using approximately 1,000 EGFR-positive samples, including cell-free DNA (cfDNA), pre-capture NGS libraries of cfDNA (cfDNA-prePCR), FFPE-derived DNA (ffpeDNA), pre-capture NGS libraries of FFPE-derived DNA (ffpeDNA-prePCR), fresh tumor tissue DNA (ttDNA), pre-capture NGS libraries of ttDNA (ttDNA-prePCR), pleural effusion supernatants DNA (peDNA), and pre-capture NGS libraries of peDNA (peDNA-prePCR). They were analyzed for detection concordance and VAF correlation. Especially, we made comparisons of the tumor DNA, including ctDNA and tumor tissue DNA, with their paired pre-capture NGS library. ResultsKey findings demonstrated excellent overall agreement between NGS and ddPCR. The mutation detection concordance rates were 98.72% (overall), with subtype-specific rates of 98.93% (L858R), 99.23% (Ex19del), and 97.14% (T790M). VAF measurements between ddPCR and NGS showed exceptional correlation (Pearsons r = 0.975, P<0.001). Notably, pre-capture NGS libraries showed remarkable VAF concordance with their source materials (0.993 for cfDNA libraries vs cfDNA; 0.998 for tumor tissue libraries vs tumor DNA with EGFR L858R; 0.991 for tumor tissue libraries vs tumor DNA with EGFR Ex19del). ConclusionsNGS and ddPCR demonstrate high concordance in EGFR mutation detection and VAF quantification, supporting their complementary roles in clinical testing. Using pre-capture libraries as an alternative to source samples can avoid repeat biopsies and enables subsequent testing for patients with inadequate FFPE sample quantity. These findings establish an evidence base for integrated diagnostic paradigms leveraging NGSs multiplexing power and ddPCRs sensitivity.

cancer biology↗

bioRxiv2025

Co-opting the bacterial lipoprotein pathway in the biosynthesis of a lipidated macrocyclic peptide

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are structurally diverse natural products that possess a range of bioactivities, often acting as antibiotics, antifungals, or metallophores. In RiPP biosynthesis, different modifying enzymes install an array of chemical motifs onto a precursor peptide. A recently described RiPP-modifying enzyme, ChrH, catalyzes a remarkably complex reaction on its precursor peptide that results in a macrocycle, heterocycle, and S-methyl group. By leveraging comparative genomics, we demonstrate that the products from a subfamily of enzymes related to ChrH display unexpected structural diversity, including the production of unmethylated macrocyclic congeners and C-terminally modified proteins over 30 kDa in size. Several of these precursors contain a signal peptide, sending them for downstream maturation by the bacterial lipoprotein biosynthetic pathway. Like bacterial lipoproteins, such peptides are modified by addition of a diacylglycerol (DAG) group to the N-terminal cysteine residue along with acylation of the N-terminal amine. Genome mining reveals that these RiPP-lipoprotein hybrids, which we term DAG-RiPPs, are widespread across bacterial phyla and are likely involved in different biological roles. Together, these results highlight a novel maturation paradigm for membrane-bound RiPPs and lay the foundation for the discovery and bioengineering of other RiPP-lipoprotein hybrids. SignificanceRibosomally synthesized and post-translationally modified peptides (RiPPs) are a superfamily of natural products that display antibiotic, antifungal, anticancer, and metal-binding activities. Their biosynthesis typically follows a common logic in which modifying enzymes install chemical motifs onto a precursor peptide, followed by proteolytic processing and export from the cell. Herein, we describe the discovery and biochemical characterization of a new class of lipid-RiPP hybrid products. These RiPPs contain a signal peptide that exploits the endogenous bacterial lipoprotein biosynthesis pathway for lipidation, membrane localization, and potential secretion. Genome mining shows that these lipid-peptide hybrids are widespread across bacterial phyla.

biochemistry↗

bioRxiv2025

Oxidative Peptide Backbone Cleavage by a HEXXH Enzyme During RiPP Biosynthesis

Ribosomally synthesized and post-translationally modified peptides (RiPPs) rely on a diverse array of enzymes to tailor peptide backbones and side chains. In this study, we characterized enzymes from two different biosynthetic gene clusters (BGCs) from Pseudomonas strains (pfl and pos) that catalyze new transformations in RiPP biosynthesis. Two -ketoglutarate-dependent HEXXH enzymes, PflC and PosC, perform hydroxylation of multiple consecutive glutamine residues and selectively recognize a C-terminal ARMD tetrapeptide to trigger oxidative backbone cleavage that generates an amide terminus. Mutational analysis pinpoints the first position of this motif as a critical determinant. Notably, PflC displays proteolytic activity in the absence of the leader peptide, indicating that leader peptide-enzyme interactions modulate the observed reaction selectivity. The biosynthetic gene clusters also encode a unique MNIO-nitroreductase fusion enzyme that installs a rare Z-dehydrophenylalanine and hydroxylates an Asp residue. Collectively, this work expands both the catalytic repertoire and structural diversity accessible through bacterial RiPP biosynthesis.

biochemistry↗

bioRxiv2025

An unusual ring pattern in the Rosβ lanthipeptide of the two-component lantibiotic roseocin

Two-component lantibiotics comprise two post-translationally modified peptides that synergistically exert antimicrobial activity. Most known two-component lantibiotics are made up of a structurally conserved -lanthipeptide that binds to the peptidoglycan precursor lipid II and a {beta}-lanthipeptide that is believed to interact with the -peptide-lipid II complex to form pores in the membranes of susceptible bacteria. A few two-component lantibiotics including roseocin do not follow this general scheme and act by different, currently unresolved mechanisms. An important first step in studying this group of lanthipeptides is determination of their chemical structure. Roseocins {beta}-peptide (Ros{beta}) is formed by the RosM lanthipeptide synthetase from the RosA1 precursor peptide. RosM carries out nine dehydrations of Ser and Thr residues to the corresponding dehydroamino acids followed by six Michael-type additions of the thiols of Cys residues to a subset of the dehydroamino acids forming six thioether crosslinks. Sequence alignment with structurally characterized lanthipeptides does not allow prediction of its ring pattern. In this study, Ros{beta} was produced in Escherichia coli and its ring pattern was established by multi-dimensional NMR spectroscopy. The stereochemistry of the lanthionine and methyllanthionine residues was determined by Marfeys analysis with authentic standards. Ros{beta} is shown to have a unique ring pattern amongst previously characterized lanthipeptides. TOC graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/684949v2_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@125226borg.highwire.dtl.DTLVardef@f6a170org.highwire.dtl.DTLVardef@1e0e57corg.highwire.dtl.DTLVardef@1fa4c8d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

A neuroendocrine principle: Pancreatic islets actively shape sympathetic innervation

Survival critically depends on maintaining blood glucose levels to provide essential energy, especially during emergencies such as the fight-or-flight response, when timely glucose control via neural integration is vital. However, pancreatic islets constitute only a small fraction of the pancreas and are dispersed throughout the organ, raising the fundamental question of how the nervous system coordinates synchronized control of multiple islets. Using whole-organ clearing and 3D imaging, we mapped pancreatic sympathetic innervation, revealing specialized anatomical integration between sympathetic nerves and islets. Transplanted islets intrinsically attracted sympathetic nerves independent of their native environment. Chronic islet injury disrupted sympathetic innervation and markedly impaired nerve regeneration after denervation. Sympathetic denervation markedly elevated islet-derived Reg2 and Reg3{beta}; administration of these proteins accelerated sympathetic regeneration and improved islet graft function. Our findings identify an islet-sympathetic architecture actively maintained by islets, uncovering an endocrine-driven mechanism for neural regulation, highlighting Reg2 and Reg3{beta} as therapeutic candidates for diabetes management.

neuroscience↗

bioRxiv2025

The Biosynthetic Pathway to the Pyrroloiminoquinone Marine Natural Product Ammosamide C

Ammosamide C is a marine natural product containing a highly decorated pyrroloiminoquinone core. Studies on the biosynthetic gene cluster (BGC) that produces ammosamides previously revealed that they are made by a series of posttranslational modifications (PTMs). The BGC includes genes encoding a precursor peptide AmmA and four enzymes known as PEptide Aminoacyl-tRNA Ligases (PEARLs). Initial studies into the ammosamide biosynthetic pathway demonstrated Trp addition to a precursor peptide by the PEARL AmmB2. Thereafter, sequential modifications by several enzymes including two other PEARLs lead to the formation of a peptide intermediate bearing a C-terminal diaminoquinone. In the present work, we present the biosynthetic steps that convert this intermediate to ammosamide C. The PEARL AmmB4 unexpectedly appends an arginine to the C-terminus of the aforementioned intermediate. Then, C-terminal proteolysis by the heterodimeric TldD/E-like protease Amm12/13 releases a dipeptide, which is subsequently cleaved by the dipeptidase Amm19 to produce a Trp-derived diaminoquinone. Amm3 next catalyzes the conversion of this Trp derivative to the corresponding chlorinated ammosamaic acid. Finally, Amm23 methylates this intermediate and a putative aminotransferase Amm20 performs an amidation to arrive at ammosamide C; the order of these last two steps could not be determined. This study reveals an unexpectedly lengthy route to ammosamide that illustrates the opportunistic nature of natural product biosynthesis, demonstrates a role for a PEARL that is unlike previous roles, identifies steps that are not PTMs, and adds Arg-tRNA to the growing repertoire of amino acyl tRNAs that are used by PEARLs.

biochemistry↗

bioRxiv2025

A Multi-Disciplinary Framework for Decoding S1PR1-Selective Agonism

Sphingosine-1-phosphate (S1P), a key metabolite of sphingolipids, plays crucial roles in a wide range of physiological and pathological processes. S1P primarily exerts its functions by binding to G protein-coupled sphingosine-1-phosphate receptors (S1PRs), which include five subtypes (S1PR1-5), thereby activating these receptors and their downstream signaling pathways. Understanding the molecular determinants that govern agonist selectivity among different S1PR subtypes is vital for the rational and precise development of targeted therapeutic agents. Here, four cryo-electron microscopy structures of agonist-bound S1PR1-Gi complexes are reported. Through an integrated approach combining structural analysis, molecular dynamics simulations, and pharmacological assays, the molecular basis for the selectivity of CYM5442, HY-X-1011, Ponesimod, and SAR247799 toward S1PR1 over S1PR3 and S1PR5 is uncovered. Specifically, the selectivity arises from a combination of non-conserved residues within the ligand-binding pocket and at the Gi-protein interface, distinct curved agonist-binding modes oriented toward transmembrane helices 5-7 that cause steric clashes with S1PR3, and the presence of branched moieties at the lower part of three agonists. These features collectively enhance agonist potency and efficacy for S1PR1 while reducing activity at S1PR3 and S1PR5. These findings establish a structural framework for the rational design of next-generation S1PR1 highly selective agonists with improved therapeutic potential.

biochemistry↗

bioRxiv2025

Mechano-activated chondroprogenitors (MACs) drive intrinsic cartilage repair; a process that is arrested in osteoarthritis

Articular cartilage, an avascular, matrix-rich tissue, is thought to have limited repair, thereby contributing to osteoarthritis (OA), the common degenerative disease of joints. Cartilage regeneration does occur, however, in OA joints that are mechanically off-loaded. Here we show that mechanical stress, through release of matrix-bound growth factors, reprogrammes chondrocytes, the primary cells of cartilage, into mechano-activated chondroprogenitors (MACs). Studying OA joint fluid before and after mechanical off-loading, reveals evidence of chronic MAC activity, which switches back to a chondrogenic one when mechanical stress is removed. Taken together, we conclude that OA is a disease of arrested repair in which mechanical stress signals need to be switched off before full repair can occur. This novel paradigm uncovers exciting new treatment opportunities.

cell biology↗

bioRxiv2025

Paclitaxel Alleviates Pulmonary Arterial Hypertension by Modulating Macrophage M2a Polarization via the NF-κB Pathway

BackgroundPulmonary arterial hypertension (PAH) is primarily associated with vascular remodeling, in which macrophage polarization is considered to play a major role. Paclitaxel(PTX) has been shown to modulate macrophage polarization in tumors. We investigated whether PTX could alleviate PAH by altering macrophage polarization, particularly M2a macrophages. MethodsTo establish PAH, rats underwent left pneumonectomy followed by monocrotaline (MCT) injection. In vitro, THP-1 cells were differentiated into macrophages using PMA and polarized with LPS+IFN-{gamma} (M1), IL-4 (M2a), or IL-10 (M2c), followed by PTX intervention. Hemodynamic parameters (mPAP) and right ventricular hypertrophy index (RVHI) were measured. Pathological changes were assessed via HE staining. Single-cell RNA sequencing analyzed macrophage subsets in lung tissues. Macrophage polarization and NF-{kappa}B pathway activity were evaluated using immunohistochemistry, qPCR, cytokine profiling and Western blot. ResultsIn a severe PAH model induced by left pneumonectomy plus monocrotaline, pulmonary interstitial macrophages initially exhibited a predominant M1-polarized phenotype in the early stage, which transitioned to an M2a-polarized phenotype in the later stage and eventually stabilized. Low-dose PTX alleviated severe PAH by reducing perivascular macrophage infiltration. Cytological studies confirmed that PTX inhibited M2a polarization via suppression of NF-{kappa}B, thereby attenuating its proliferative effects on pulmonary arterial smooth muscle cells (PASMCs). ConclusionM2a macrophages play a crucial role in PAH progression. PTX may alleviate PAH by suppressing M2a polarization via the NF-{kappa}B pathway.

immunology↗

bioRxiv2025

HDAC inhibition unlocks tumor plasticity and enhances immunotherapy response in Myc- Driven Small Cell Lung Cancer

Small Cell Lung Cancer (SCLC) is a highly aggressive malignancy, accounting for approximately 15% of all lung cancer cases. Characterized by low immunogenicity, SCLC may utilize epigenetic mechanisms to evade immune detection. Here, we demonstrate that entinostat, a class I histone deacetylase inhibitor (HDACi) upregulates immune-related genes in human SCLC cells. In vivo, we confirmed entinostat treatment increased expression of immunecheckpoint ligands and antigen presentation machinery in Myc-driven tumors in a Rb1/Trp53/MycT58A (RPM) SCLC mouse model, while shifting tumors from a neuroendocrine(NE)-high to a NE-low phenotype. Notably, combining entinostat with anti-PD-1 immunotherapy significantly enhances T-cell infiltration, suppresses tumor growth, and prolongs survival in RPM allograft models. These findings underscore the potential of entinostat to reprogram the immunological landscape and NE status of SCLC, enhance immune checkpoint blockade efficacy, and improve therapeutic outcomes.

cancer biology↗

bioRxiv2025

Efficient spatial gene expression profiling using split-probe ligation and rolling circle amplification

Spatial transcriptomics has transformed our understanding of gene regulation by enabling high-resolution mapping of RNA molecules within their native cellular and tissue environments. This is typically accomplished by capturing or imaging RNA in situ, thereby preserving spatial context. Here, we introduce an in situ RNA imaging method based on split-probe ligation and rolling circle amplification (RCA) for profiling spatial gene expression. In this approach, split-probes hybridize to adjacent regions of a target RNA fragment and are then enzymatically ligated to form circular DNA templates, which are subsequently amplified via RCA to boost signal. We demonstrate that this method enables robust in situ RNA detection and genotyping in both tissue sections and whole-mount tissue samples. By coupling this technique with in situ sequencing, we mapped the spatial expression patterns of 82 genes in the kidneys of healthy and diabetic male and female mice. This analysis revealed distinct localization of Aqp4 in proximal tubules and principal cells of the collecting ducts, and uncovered sex-specific transcriptomic alterations in diabetic kidneys with spatial resolution. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/668044v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@c8efaborg.highwire.dtl.DTLVardef@1eef010org.highwire.dtl.DTLVardef@1d2bbd7org.highwire.dtl.DTLVardef@2a482b_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗