Biology subjects

Meng, H.

Publications and source records attributed to Meng, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Targeted tumor desialylation by engineered probiotic reprograms the tumor microenvironment to potentiate immunotherapy

Tumor hypersialylation drives immunosuppression and limits immunotherapy efficacy by shielding tumor cells and engaging inhibitory immune receptors. Here, we engineered Escherichia coli Nissle 1917 (EcN{Delta}pgi-SAS) as a metabolically confined "desialylation catalyst" to remodel the tumor microenvironment. This strain combines HER2-directed adhesion, hypoxia-inducible surface sialidase display for targeted glycan cleavage, and sialic acid catabolism to prevent glycolytic recycling. Critically, disrupting glucose metabolism ({Delta}pgi) restricts bacterial proliferation to sialic acid-rich tumor microenvironment, significantly enhancing biosafety. In mice, EcN{Delta}pgi-SAS colonized tumors and effectively desialylated tumor cells, synergizing with anti-PD-L1 to suppress growth of immunologically "cold" tumors. Mechanistically, desialylation reversed immunosuppression by broadly enhancing antitumor immunity. Orally administered EcN{Delta}pgi-SAS substantially inhibited colorectal carcinogenesis, repaired epithelial barrier integrity by restoring tight junctions, and prevented adenoma formation. This integrated strategy establishes a clinically translatable platform for reversing immunosuppression in solid tumors.

synthetic biology↗

bioRxiv2026

Restoring the Chondron: Pericellular Matrix Reconstitution Enhances Mechano-Inflammatory Resilience and Modulates Chondrocyte-Neuron Crosstalk

Abstract Chondrocytes in native articular cartilage are enclosed within a collagen VI (COL VI)-rich pericellular matrix (PCM), forming functional units known as chondrons. However, enzymatic isolation disrupts the PCM, and the functional consequences of its loss and restoration remain poorly understood. In this study, primary human chondrocytes were cultured in alginate beads to promote PCM reconstitution and subsequently recovered as reconstituted chondrons. Chondrocytes and reconstituted chondrons were encapsulated in gelatin methacryloyl hydrogels and compared under inflammatory and mechanical stimulation. Alginate preconditioning generated chondron-like units with a distinct COL VI-positive PCM that was retained after transfer to three-dimensional culture. Under inflammatory conditions, reconstituted chondrons exhibited reduced inflammatory, catabolic, neuroinflammatory, and angiogenic responses compared with isolated chondrocytes at both gene and protein levels. Under interleukin-1{beta} stimulation, mechanical loading further increased inflammatory gene expression in chondrocytes in a donor-dependent manner, whereas responses remained comparatively limited in reconstituted chondrons. Conditioned medium from reconstituted chondrons was also associated with lower capsaicin- and potassium chloride-evoked calcium responses in human induced pluripotent stem cell-derived sensory neurons than corresponding chondrocyte-conditioned medium. These findings demonstrate that reconstitution of a COL VI-rich PCM restores a chondron-like pericellular microenvironment that attenuates inflammatory activation and buffers load-associated inflammatory amplification, while exploratory sensory neuron experiments suggest downstream modulation of neuronal responsiveness. PCM restoration may therefore provide a promising strategy for cartilage tissue engineering and regenerative applications.

molecular biology↗

bioRxiv2026

The kinetochore proteins Ndc80 and Dsn1 are required for survival of postmitotic neurons

Dsn1 and Ndc80 are essential proteins of the kinetochore complex and required for chromosome segregation in dividing cells and for regulating development and microtubule dynamics in postmitotic neurons. With conditional deletion of floxed alleles, we here show that Dsn1 and Ndc80 are also required for the viability of postmitotic neurons, both in cultures of hippocampal and cortical neurons and in vivo in the retina. Loss of these proteins triggers apoptosis, as indicated by caspase cleavage and an increase in nuclear DNA breakage. The pro-survival function of the kinetochore components is distinct from that which was previously demonstrated for regulation of neuronal synaptogenesis. The microtubule-binding domain of Ndc80 is required for the synaptogenic functions but Ndc80 lacking this domain can nonetheless rescue the viability of neurons from which Ndc80 has been deleted. Similarly, whereas the synaptogenic function involves regulation of microtubules in axons and dendrites, a nucleus-localized Dsn1 is sufficient to rescue the viability of neurons from which Dsn1 has been deleted. Thus, postmitotic neurons retain a nuclear requirement for components of the kinetochore in order to prevent apoptosis.

neuroscience↗

bioRxiv2026

Engineering Pseudomonas putida KT2440 for open-loop upcycling of mixed plastics

Current mechanical and chemical recycling strategies address less than 10% of global plastic waste, necessitating alternative valorization routes. Biological upcycling via enzymatic depolymerization combined with microbial conversion of the resulting monomers offers a promising pathway to transform mixed plastic waste into valuable alternatives. Here, we employed a single engineered Pseudomonas putida KT2440 for simultaneous co-utilization of five plastic monomers including ethylene glycol, terephthalic acid, adipic acid, 1,4-butanediol, and L-lactic acid, which can be derived from enzymatic hydrolysis of polyethylene terephthalate (PET), polybutylene adipate-co-terephthalate (PBAT), polyester-polyurethanes (PUs), and polylactic acid (PLA). Continuous fermentation over 21 days with alternating mixed-monomer feeds achieved steady state growth and complete substrate depletion, yielding adaptive mutations that informed iterative strain improvement. Further engineering enabled the biosynthesis of (R)-3-hydroxybutyrate (R-3HB), and 0.70 g L-1 R-3HB was produced directly from enzymatic hydrolysates of blended PET, PBAT, and TPU. These results establish a viable bio-based approach for upcycling realistic mixed plastics into value-added bioproducts.

microbiology↗

bioRxiv2026

Stage-adaptive integration of polydopamine promotes hPSC-derived alveolar organoids differentiation and maturation

Human pluripotent stem cell (hPSC)-derived alveolar organoids (ALOs) have emerged as a powerful tool for modeling human lung development and disease, and accelerating respiratory drug discovery. However, achieving the functional maturation of ALOs remains challenging. Polydopamine (PDA) is a mussel-inspired polyphenolic biomaterial with antioxidant and adhesive properties that can be deployed as surface coatings and nanoparticles (NPs) in cell culture systems. Here, we integrate PDA coatings and NPs sequentially in a stage-adaptive manner throughout the hPSC-derived ALOs differentiation system and study their contributions to ALOs maturation. Our results demonstrated PDA coating yielded more anterior foregut endoderm (AFE) spheroids by strengthening the interaction between Matrigel and substrate. Bulk RNA-seq revealed enrichment of cell-cell and cell-extracellular matrix interactions by PDA. The subsequent incorporation of PDA NPs in Matrigel at lung progenitor cells (LPCs) stage significantly mitigated reactive oxygen species (ROS) accumulation and enhanced LPCs generation. Functionally, AT2 cells in ALOs exhibit characteristic lysosome-to-lamellar body (LB) maturation due to the traffic of internalized PDA NPs to endolysosome. Transcriptomics further indicated enrichment of endocytic-phagosome and epithelium development pathways by PDA treatment. Together, our study establishes a stage-adaptive-integrated PDA strategy throughout hPSC-to-ALOs differentiation and demonstrates that PDA robustly enhances ALOs maturation and secretory function. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC="FIGDIR/small/708928v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@88208dorg.highwire.dtl.DTLVardef@1111590org.highwire.dtl.DTLVardef@9ea9b0org.highwire.dtl.DTLVardef@969fad_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Spatial and Single-Cell Transcriptomics Decipher the Crosstalk Environment of DEFB1+ Cancer Cells and IFI30+ Macrophages in Intrahepatic Cholangiocarcinoma

Intrahepatic cholangiocarcinoma (ICC) is a rare but highly aggressive primary liver malignancy distinguished by a profoundly heterogeneous tumor microenvironment, which underlies its limited response to targeted and immune-based therapies. Deciphering the cellular composition and intercellular signaling within this complex ecosystem is critical to understanding ICC progression and to identifying actionable therapeutic targets. Here, we integrated single-cell RNA sequencing and spatial transcriptomics to construct a comprehensive cellular and transcriptional atlas of human ICC. Our analyses revealed a continuous trajectory of T-cell state transition from activation to exhaustion, with CD8+ proliferating T cells exhibiting two distinct exhaustion programs, namely terminal and progenitor-like exhaustion. Notably, DEFB1+ cholangiocytes and IFI30+ macrophages displayed a strong positive correlation across independent ICC cohorts and were found in close spatial proximity within the tumor microenvironment. Mechanistically, their interaction appears to be mediated by the TGFB1 - TGFBR1 signaling pathway, contributing to tumor progression and immunotherapy resistance. Together, these findings delineate the cellular architecture and spatial organization of the ICC microenvironment, uncovering a key cholangiocyte-macrophage axis that shapes immune dysfunction and offers a potential therapeutic entry point to enhance immunotherapy efficacy in ICC.

bioinformatics↗

bioRxiv2025

Study on Dianthus superbus L. against Acute Liver Injury via the Gut-Liver Axis -- Regulation of Gut Microbiota and Tryptophan Metabolism to Activate AhR Signaling

BackgroundDianthus superbus L. (DS) treats liver diseases, but its ALI mechanism via gut microbiota/metabolites is unclear. PurposeInvestigate DS effects on CCl-induced ALI and mechanisms. MethodsDS components (HPLC-MS/MS) were identified. ALI rats received DS. Liver/colon injury, fibrosis (biochemistry, histology, IHC, IF, WB for -SMA, Collagen I, Occludin, ZO-1), serum metabolomics, fecal 16S rRNA, and tryptophan-targeted metabolomics were assessed. Antibiotics and FMT from DS-treated donors explored microbiota roles. Results37 components, including Kaempferol and Aurantiamide, were identified. DS attenuated ALI, reducing hepatic -SMA/Collagen I while increasing AhR/Cyp1a1, and upregulating colonic Occludin/ZO-1. FMT replicated DS benefits. Untargeted metabolomics linked effects to Linoleic/Tryptophan metabolism. 16S rRNA showed increased beneficial microbiota (HT002, Lactobacillus, Romboutsia); FMT confirmed Lactobacillus enrichment. DS normalized tryptophan metabolites (4-Hydroxybenzoic acid, L-Kynurenine, Indole-3-carboxaldehyde). ConclusionDS ameliorates ALI gut-microbiota-dependently by modulating tryptophan metabolism, enhancing intestinal barrier function, activating AHR signaling, and suppressing fibrosis biomarkers, indicating its potential as a microbiota modulator for ALI. ImportanceAcute liver injury is a serious health threat with limited treatment options. This study explores how a traditional medicinal herb, Dianthus superbus L. (DS), protects the liver through an unexpected route: the gut. We discovered that DS works by rebalancing the community of gut bacteria, which in turn improves the intestinal barrier and fine-tunes the bodys tryptophan metabolism. This cascade of effects ultimately activates a key cellular pathway (AhR) that reduces liver inflammation and fibrosis. Our findings not only clarify how this traditional remedy works but also highlight the critical role of the gut-liver axis, positioning DS as a promising, microbiota-targeting therapeutic candidate for preventing and treating liver disease.

microbiology↗

bioRxiv2025

Engineering of Pseudomonas putida KT2440 for Broad-Chain-Length 3-Hydroxy Fatty Acid Biosynthesis

3-Hydroxy fatty acids (3-HFAs) are versatile intermediates for bio-based polymers, fuels, and surfactants, and are advancing circular economy manufacturing. We built an acyl- CoA ligase-deficient chassis of Pseudomonas putida KT2440, thereby blocking 3-HFA activation and preventing its use as carbon source. This strategy decoupled synthesis from catabolism and enabled 3-HFA accumulation. We then compared two different routes for modifying the free 3-HFA composition. 1. In a direct route, overexpressing native PhaG produced C8, C10, C12, and C14 3-HFAs, achieving a total titer of 0.73 g/L in shake flasks. Functional analyses under our tested conditions support a re-assignment of PhaG: rather than acting primarily as a 3-hydroxyacyl-ACP:CoA transacylase, it functions mainly as a thioesterase, liberating free 3-HFAs from hydroxyacyl-ACP. 2. In an indirect route, overexpressing RhlA variants generated hydroxyalkanoyl-alkanoates (HAAs) that were converted to free 3-HFAs by endogenous esterase(s): RhlA from Pseudomonas aeruginosa PAO1 favored C8-C12 and yielded 0.47 g/L 3-HFAs, whereas RhlA from Burkholderia plantarii PG1 favored C10-C14 with 0.14 g/L, of which 80% was C14. Finally, we demonstrated process feasibility by up-scaling the PhaG pathway in a stirred-tank reactor. These results establish modular, stable, chassis-compatible routes for tailoring 3-HFA chain-length distributions, thereby providing a foundation for scalable, bio-based monomer supply in a circular economy.

synthetic biology↗

bioRxiv2025

Therapeutic Potential of a Tectorigenin Derivative (TED) in Herpetic Stromal Keratitis: Antiviral and lmmunomodulatory Mechanisms

ObjectivesIn this study, the anti-HSV-1 effects of TED were investigated in vitro and in vivo, its therapeutic efficacy against herpetic stromal keratitis (HSK) was evaluated, and its mechanism of action was examined. MethodsWe assessed the cytotoxicity and anti-HSV-1 activity of TED in Vero cells using CCK-8 and plaque assays. The HSK model mice received TED (2.5, 5, or 15 mg/kg), and symptom progression was monitored. The therapeutic effects were evaluated through HE staining, corneal immunofluorescence, and HSV-1 gB quantification. Mechanistic studies were performed to examine the expression of TLR pathway genes, CD4+/CD8+ T-cell infiltration in the cornea and draining lymph nodes, and dendritic cell activation. ResultsTED showed potent anti-HSV-1 activity in vitro and ameliorated HSK in mice, improving body weight and reducing corneal pathology and the incidence of encephalitis. It decreased HSV-1 loads in the cornea, trigeminal ganglion, and brain while modulating cytokines (downregulating IFN-/{gamma}, TNF-, and IL-1{beta} and upregulating IL-10). TED suppressed the TLR pathway (TLR2/3/9, TRAF6, IRF3, and NF-{kappa}B) in the corneal epithelium and reduced CD4+/CD8+ T-cell and dendritic cell infiltration while increasing the number of CD4+ T cells in the lymph nodes. ConclusionsTED has significant anti-HSV-1 activity and effectively treats HSK by reducing viral loads, improving symptoms, and modulating immune responses through TLR pathway inhibition and immune cell regulation, suggesting its potential as an HSK therapeutic.

pharmacology and toxicology↗

bioRxiv2025

O-GlcNAcylation-Ubiquitin Crosstalk of METTL1 Drives m7G Epitranscriptomic Collapse and Lipid Metabolic Reprogramming in Diabetic Cardiomyopathy

BackgroundMetabolic remodelling and memory in cardiomyocytes is a pivotal mechanism underlying cardiomyopathy pathogenesis. Clinical observations demonstrate persistent progression of hyperglycaemia-induced multiorgan damage following blood glucose stabilization, which is predominantly mediated through epigenetic regulation. While prior studies have identified epigenetic contributions to hyperglycaemic myocardial injury, the involvement of RNA methylation-particularly N7-methylguanosine (m7G) modification-in this regulatory network remains undefined. MethodsClinical specimens were collected from diabetic patients, and cardiomyocyte-specific METTL1 and ob/ob knockout murine models were established in parallel. Multiomic profiling (proteomics, glycoproteomics, ubiquitinomics, m7G-MeRIP sequencing, and metabolomics) was systematically conducted. The molecular mechanisms governing METTL1 regulation via O-GlcNAcylation and ubiquitination were elucidated through integrated in vitro and in vivo assays. A DUB siRNA library and computational strategies combining molecular docking with molecular dynamics simulations were employed for screening drugs targeting METTL1 O-GlcNAcylation, followed by in vivo therapeutic validation. ResultsComparative analysis of diabetic murine and human samples revealed strong METTL1 downregulation in cardiomyopathy contexts. Tamoxifen-inducible METTL1 knockout mice presented exacerbated diabetic cardiomyopathy phenotypes, confirming its cardioprotective function. Multiomic integration demonstrated that METTL1-mediated m7G modification critically regulates cardiomyocyte fatty acid metabolism. Mechanistically, hyperglycaemia was found to induce O-GlcNAcylation at the METTL1-T268 residue, suppressing m7G methyltransferase activity by 38% (p < 0.01). Subsequent investigations revealed that USP5 deubiquitinase activity is impaired under hyperglycaemic conditions, leading to accelerated METTL1 degradation. Notably, administration of the first-in-class small drug HIT106265621 significantly attenuated cardiomyopathy-associated pathological alterations in ob/ob mice in vivo. ConclusionHyperglycaemia promotes METTL1 O-GlcNAcylation, which impedes USP5-mediated deubiquitination, consequently reducing cardiomyocyte METTL1 protein levels and m7G modification. METTL1 deficiency drives diabetic cardiomyopathy progression through fatty acid metabolic dysregulation, inflammatory activation, and myocardial hypertrophy. Pharmacological inhibition of the OGT-METTL1 interaction using HIT106265621 has therapeutic potential for metabolic cardiomyopathy intervention.

pathology↗

bioRxiv2025

Single cell immunophenotyping identifies CD8+ GZMK+ IFNG+ T cells as a key immune population in cutaneous Lyme disease

The skin lesion erythema migrans (EM) is the first clinical sign of Lyme disease, an infection due to the tick-transmitted bacterium Borrelia burgdorferi (Bb). Previously, we used scRNA-Seq to characterize the cutaneous immune response in the EM lesion, focusing on B cells. Here, with an expanded sample size, we profiled T cell responses in EM lesions compared to autologous uninvolved skin. In addition to CD4+ T cell subsets known to be abundant in the EM, we identified clonal expansion of CD8+ GZMK+ IFNG+ T cells that exhibited significant differential expression of interferon-regulated genes. This subset included IFNG+ cells with low cytotoxic gene expression, which may promote inflammation. While FOXP3+ regulatory T cells were also increased in EM, they exhibited little IL10 expression. In contrast, a CD4+ FOXP3- tissue-resident T cell subset contained the largest population of cells with IL10 expression. Fibroblasts, endothelial cells, and pericytes were the principal cells that significantly differentially expressed key T cell-recruiting chemokines. These studies represent the first comprehensive interrogation of the cutaneous T cell response to Bb infection using single cell transcriptomics with adaptive immune receptor sequencing, providing insight into the skin barrier defense and orchestration of the immune response to this vector-borne pathogen.

immunology↗

bioRxiv2025

The Regulation of COX-2, ABCA1 and ABCG1 by the lncRNA PACERR links the inflammatory response and cholesterol homeostasis

Cyclooxygenase-2 (COX-2) has an established role in inflammation and its inhibition by non-steroidal anti-inflammatory drugs (NSAIDs) is clinically efficacious1,2. However, placebo-controlled trials of COX-2 inhibitors have revealed a cardiovascular hazard. This has been attributed to suppression of COX-2 dependent cardioprotective prostaglandins (PGs), especially prostacyclin, produced by endothelial (EC) and vascular smooth muscle cells (vSMC) 1-3. Upstream of these effects, we have found that the COX-2 antisense long non-coding RNA (lncRNA) PACERR interacts with discrete RNA binding proteins to mediate the cell specific COX-2 response to both anti-[high-density lipoprotein (HDL)] and pro-inflammatory [lipopolysaccharide (LPS)] stimuli. PACERR exerts its action both in cis and in trans, controlling the expression of COX-2 and the cholesterol transport genes, ABCA1 and ABCG1. When cells are exposed to HDL, PACERR is transcribed, leading to the release of bound histone acetyltransferase p300 and its relocation to the promoter of COX-2 which is then transcribed leading to PG formation. In concert, PACERR also releases heterogeneous nuclear ribonucleoprotein L (hnRNPL) which relocates to the ABCA1 and ABCG1 gene loci, controlling mRNA alternative splicing and subsequent cholesterol efflux to HDL. Silencing PACERR, with an antisense oligonucleotide (ASO), augments the COX-2 and cholesterol efflux in response to HDL. In response to HDL, PACERR associates with its neighboring gene, cytosolic phospholipase A2 (cPLA2/PLA2G4A) both interacting with an enhancer element affecting cPLA2 transcriptional activation and escorting the cPLA2 protein to the nuclear membrane. There, it releases arachidonic acid, further activating COX-2 but limiting ABCA1 and ABCG1 by suppressing the formation of the LXR/RXR heterodimers required for their transcription when cholesterol efflux is no longer required4. In response to LPS, PACERR controls the action of the NF{kappa}B repressive protein, I{kappa}B{zeta}. When PACERR is silenced in a humanized mouse model with the ASO, I{kappa}B{zeta} is free to bind to the NF{kappa}B site in the COX-2 promoter, suppressing transcription, PG formation and systemic inflammation. In summary, these studies reveal dual and complementary mechanisms by which PACERR modulates PG production by COX-2. In response to HDL, it enhances production of prostacyclin whereas it dampens production of the PG response to LPS.

cell biology↗

bioRxiv2025

Self-contrastive learning enables interference-resilient and generalizable fluorescence microscopy signal detection without interference modeling

Every weak signal in fluorescence microscopy may contain critical biological information. However, the inter-ference resilience required to detect such signals has traditionally relied on task-specific interference modeling, which limits generalizability. Here, we present a self-contrastive learning-based signal detection solution that achieves interference resilience without the need for interference modeling, thereby offering high generalizability. The method, DEep PAttern Fitting (DEPAF), is a module that contrasts asynchronously generated data views from asymmetric model paths to extract signals from interference, while incorporating highly parallel signal recognition and localization in the process. Benchmarking shows that DEPAF substantially improves signal detection performance across diverse imaging modalities and dimensions, especially under challenging conditions such as low SNRs and ultra-high signal densities. It is also compatible with, and consistently enhances the performance of various imaging techniques, such as super-resolution imaging, spatial transcriptomic imaging, and two-photon calcium imaging. Notably, DEPAF relies only on image patches with signal patterns and one tunable hyperparameter to adapt to new tasks, making it accessible to users without domain-specific expertise and lowering the barrier to broader adoption. DEPAF is expected to advance the signal-centric fluorescence microscopy techniques and inspire further advancements, especially in the era of image-based multi-omics.

bioinformatics↗

bioRxiv2025

Extracellular Nanobody Screening using Conformationally Stable GPCR

G protein-coupled receptors (GPCRs) are prominent drug targets that have attracted intensive efforts in drug screening. Binding-based screening methods for GPCR ligands often require conformationally stable, purified receptors. However, obtaining large quantities of GPCRs in stable states, particularly with unoccupied extracellular ligand-binding pockets and especially in their active conformations, remains challenging due to the inherent dynamic nature of these receptors. To address this challenge, we propose a universal approach for stabilizing GPCRs in specific conformations. Using the M1 muscarinic acetylcholine receptor (M1R) as a model, we successfully stabilized M1R in its active conformation through de novo design of a fusion protein. We screened a synthetic yeast display library of nanobodies against both the stabilized active-state and previously reported inactive-state M1R, identifying several nanobodies that specifically recognize each conformation. This method not only facilitates the stabilization of GPCRs in desired states but also provides valuable tools for developing more selective therapeutic agents, enhancing drug discovery efficiency and specificity.

biochemistry↗

bioRxiv2025

StrPhaser constructs tandem repeat alleles from VCF data

Variant calling is a ubiquitous genomic technique that underpins many scientific disciplines. From a computational perspective, variant calling is a form of logical compression; neglecting large variation, a persons genome can be losslessly described as a set of differences (SNP and small InDel alleles) relative to the reference sequence. Another common genomic technique is haplotype phasing, wherein alleles are partitioned into their paternal and maternal components (as haplotypes). Some classes of alleles are more difficult to describe than others, e.g., short tandem repeats (STRs). STRs serve as a critical marker for many genetic assays. However, STRs tend not to be explicitly reported in most genomic workflows. Here, we present StrPhaser, a novel algorithm that leverages phased variant calling datasets in the VCF file format to construct STR alleles. We evaluated StrPhaser on [~]10,000 STR alleles from 284 human genomes, achieving an average allele accuracy of 91%. In addition, StrPhaser better recovers longer STR alleles than competing approaches; in principle, STR alleles that are longer than the maximum read length can be characterized. This capability, combined with its user-friendly interface, speed, and generation of both STR genotypes and visualizations, makes StrPhaser a valuable tool for a wide range of genomic studies. AvailabilityThe StrPhaser is publicly available at https://github.com/XuewenWangUGA/StrPhaser.

bioinformatics↗

bioRxiv2025

Extracellular stiffness regulates site-specific lung development

Extracellular matrix (ECM) stiffness plays a crucial role in regulating cell fate and maturation, but its influence on lung development is limited known. Here we utilized stiffness-tunable gelatin methacryloyl (GelMA) hydrogels to investigate how ECM stiffness influences site-specific lung development in a stem cell-derived lung organoid model. We found increased stiffness promoted NKX2-1+ lung progenitor cells (LPCs) generation. In airway organoids (hAWOs), stiff hydrogels directed proximal airway differentiation enriched with goblet, ciliated, and basal cells; whereas the decreased stiffness favored emergence of secretory cells in the proximal-distal transition zone and distal airway. In alveolar organoids (hALOs), increased stiffness enhanced AT2 and AT1 cells transition. Moreover, infection assays with Omicron BA.1.1 and Delta variants recapitulated the proximal-to-distal tropism of SARS-CoV-2 in the lung. Transcriptomic sequencing revealed ECM stiffness regulates lung development via Hippo, TGF-{beta}, HIF and Wnt pathways. These findings advance mechanism understanding of ECM stiffness on lung development and provide a novel mechanical regulation for generating site-specific lung organoids.

cell biology↗

bioRxiv2024

Aluminium induces suberin biosynthesis in barley roots via ABA

Aluminum (Al) toxicity is a major factor limiting plant growth in acidic soils. The beneficial element silicon (Si) can mitigate some effects of Al. However, the impact of Al on suberized apoplastic barriers in roots are largely unknown while the effects of Si on suberin remains controversial. This study employed physiological, histochemical, and analytical methods, along with Laser Capture Microdissection (LCM) RNA-sequencing, to explore the effects of Al and Si on suberin development in barley (Hordeum vulgare L.), a species sensitive to Al stress. Exposure of barley seedlings to Al resulted in increased suberin deposition, which could be restored with the addition of Si, particularly in the root endodermis. Gene expression analyses using LCM RNA-seq across different root tissues demonstrated that Al-induced suberin biosynthesis is mainly regulated by the abscisic acid (ABA) pathway. In addition, the application of fluridone, an inhibitor of ABA synthesis and a suberin mutant, further supported the pivotal role of ABA in the Al response and the role of suberin in influencing Al uptake. Our findings underscore the complex interplay between Al stress and suberin biosynthesis in barley, providing insights into potential strategies for enhancing crop resilience to Al toxicity.

plant biology↗

bioRxiv2024

Genomic insights into the successful invasion of the avian vampire fly (Philornis downsi) in the Galapagos Islands

Invasive species disrupt island ecosystems, posing significant threats to native species. The avian vampire fly (Philornis downsi), introduced into the Galapagos Islands, has become a major threat to endemic birds including Darwins finches, yet the genetic mechanisms of its invasion remain unclear. This study used whole-genome sequencing of P. downsi populations from Galapagos and its native range in mainland Ecuador, revealing reduced genetic diversity in Galapagos, indicative of a recent bottleneck. We found evidence of ongoing gene flow among island populations and identified regions under positive selection near genes related to neural signaling, muscle development, and metabolic processes, which may have contributed to the flys invasion success in Galapagos. These findings highlight the importance of genomic research for mitigating the impact of P. downsi on Galapagos biodiversity.

evolutionary biology↗