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Biology subjects

He, R.

Publications and source records attributed to He, R..

At least 37 records · Page 2Linked to original sources

Myeloid CD209 impairs T-cell activation by inducing ICAM-2-ERM-dependent cortical stiffening

Resistance to PD-1-based immunotherapy remains a major challenge in cancer treatment, especially in immunologically "cold" tumors characterized by T-cell exclusion and impaired effector function. Tumor-associated myeloid cells are important mediators of this resistance, but whether they directly suppress T-cell immunity through mechanical regulation remains unclear. Here, we identify DC-SIGN (CD209), a myeloid-expressed C-type lectin receptor, as a mechanosuppressive regulator of antitumor T-cell immunity. DC-SIGN is selectively enriched in tumor-infiltrating M2-like macrophages and monocytes, and its expression is associated with poor clinical response to PD-1 blockade and elevated TIDE scores across multiple cancer types. Mechanistically, DC-SIGN directly engages ICAM-2 on T cells and activates ROCK1-ERM signaling. This interaction increases T-cell cortical stiffness, destabilizes T cell-antigen-presenting cell interactions, and attenuates T-cell receptor signaling. Blocking the DC-SIGN-ICAM-2-ERM pathway restores T-cell activation and promotes CD8+ T-cell infiltration and effector function in mouse, humanized, and ex vivo human tumor systems. Importantly, DC-SIGN blockade overcomes resistance to PD-1-based immunotherapy in refractory and immunologically "cold" tumor models, and further enhances the response to PD-1 inhibition. Together, our findings define a myeloid-derived mechanical immune checkpoint and reveal T-cell mechanosuppression as a targetable mechanism of tumor immune evasion and immunotherapy resistance.

immunology↗

Gn1a rice promotes symbiotic fish growth via reprogramming soil microbiome

Rice-fish symbiotic ecosystems significantly contribute to world food supply. Mutation in rice (Oryza sativa) quantitative trait locus Gn1a, encoding a cytokinin oxidase/dehydrogenase (OsCKX2), leads to cytokinin accumulation in plant, which promotes tillering and panicle branching to achieved higher yield and also shows a selective effect on soil microbial composition. Given that the growth of aquatic animals can be shaped by their surrounding microbial communities, we asked whether adjusting rice cytokinin levels might synergistically boosts both rice yield and fish growth. Herein, we co-cultured common carp (Cyprinus carpio) with ckx2 rice plants to determine the effect of cytokinins on fish. Surprisingly, compared to wild-type plants, the ckx2 plants enhanced nearly 10% fish growth and improved fish antibacterial capacity against Aeromonas hydrophila and Edwardsiella tarda. In fact, the growth-promoting effect on fish requires mediation by the soil microbiota. Mechanistically, ckx2 plants secreted more cytokinins into soil to reprogram the microbial composition, which subsequently translocated to fish gut and modulated the keystone microbes in gut to facilitate short-chain fatty acid production and carbohydrate degradation. These findings provide the first evidence that rice-derived cytokinins exert a cross-kingdom growth-promoting effect on fish, providing a boosting dual-production strategy for advancing rice-fish symbiotic ecosystem.

plant biology↗

Discovery of potent oligopeptides for various metabolic diseases using deep learning

Artificial intelligence (AI)-based methods are increasingly critical in peptide drug discovery, but their applications are limited in a narrow scope such as antimicrobial peptides. For indications where peptide therapy inherently excels, such as metabolism, endocrinology, and tissue regeneration, AI-based pipeline for therapeutic peptide discovery is long awaited but still unmet. Here, we propose a deep learning-based pipeline, Deepeptide, capable of identifying therapeutic oligopeptides for various metabolism-related indications. Leveraging the intrinsical relationship of disease indication -- biological processes -- molecular functions, Deepeptide discovers oligopeptides with indication-ameliorating-related molecular functions as lead candidates for indication of interest. Deepeptide was applied in five representative indications of metabolism, endocrinology, and tissue regeneration: angiogenesis, lipid metabolism, osteogenesis, glucose metabolism, and anti-angiogenesis. Overall, 62% of the identified oligopeptide candidates demonstrated significant bioactivity in vitro, with most of them showing comparable potency to the first-line drugs. Notably, the heptapeptide AP7 exhibited angiogenic potency comparable to VEGF in excisional wound splinting mouse model by promoting cell migration rather than proliferation, and hexapeptide TP6 showed significant dual-efficacy against hyperlipidemia and obesity in high-fat diet mice by inhibiting lipid synthesis and regulating gut microbiota. These findings highlight the potential and generalizability of Deepeptide in therapeutic oligopeptide discovery for metabolic diseases.

bioinformatics↗

Ergothioneine: Evaluation of a Novel Antioxidant for Targeting Ocular Oxidative Stress

PurposeTo evaluate L-Ergothioneine (EGT), a naturally occurring amino acid and endogenous antioxidant, as a novel therapeutic agent for oxidative stress-related ocular diseases. This evaluation specifically aimed to address the challenge of targeted ocular delivery by assessing EGT s antioxidant potency, stability, ocular tolerance, and crucially, its ability to reach the posterior segment (fundus) via topical administration. MethodsThis study evaluated EGT as a novel ocular antioxidant by examining its radical scavenging capacity (DPPH assay compared to glutathione, astaxanthin, and coenzyme Q10), stability (at 40{degrees}C/75% relative humidity for six months using HPLC), ocular tolerance (using a New Zealand rabbit model), and fundus delivery efficiency (topical D9-EGT eye drops quantified by LC-MS/MS). ResultsEGT demonstrated significantly superior radical scavenging activity, exhibiting 6.4-fold and 46-fold higher rates than glutathione and coenzyme Q10, respectively, at 50 ppm. It also showed excellent stability, retaining over 97% of its initial concentration after six months, and caused no ocular irritation at any tested concentration (score 0). Importantly, topical administration of EGT resulted in effective fundus delivery, with peak concentrations reached at 0.5 hours post-application (1181 {+/-} 56 ng/g), confirming successful penetration through corneal and scleral barriers. These findings establish EGT as a potent, multi-mechanistic antioxidant characterized by high stability, ocular safety, and exceptional posterior segment penetrance via non-invasive eye drops. ConclusionThese findings establish EGT as a potent, multi-mechanistic antioxidant characterized by high stability, ocular safety, and exceptional posterior segment penetrance via non-invasive eye drops. By overcoming key delivery limitations, EGT presents a promising therapeutic strategy for oxidative stress-related ocular diseases such as age-related macular degeneration and diabetic retinopathy. Further studies are warranted to evaluate its long-term efficacy and clinical translation potential.

pharmacology and toxicology↗

Oxa1L-Mediated Co-translational Protein Insertion Maintains Mitochondrial Function in Parkinson's Disease Models

Mitochondrial respiratory chain integrity relies on the coordinated synthesis and membrane insertion of mitochondrially encoded proteins. How limitations in this process contribute to mitochondrial dysfunction under stress remains poorly understood. Here, we identify the mitochondrial insertase Oxa1L as a key buffering factor that modulates mitochondrial vulnerability under Parkinsonian stress conditions. Transcriptomic analyses and cellular stress models reveal pronounced disruption of oxidative phosphorylation pathways accompanied by reduced Oxa1L abundance. Functional gain- and loss-of-function analyses demonstrate that Oxa1L actively influences mitochondrial membrane potential, reactive oxygen species levels, and ATP production during stress. Notably, Oxa1L selectively governs the abundance of mitochondrially encoded respiratory chain subunits, indicating that co-translational membrane insertion represents a rate-limiting step in mitochondrial protein biogenesis. Structural analyses position Oxa1L at the mitoribosomal exit site, providing a spatial framework for coupling translation to inner membrane insertion. Together, our findings uncover a critical layer of mitochondrial quality control at the level of co-translational insertion and establish Oxa1L as a determinant of mitochondrial resilience under stress.

cell biology↗

Molecular Arms Race: Tannin Biosynthesis and Laccase-Based Detoxification in the Aphid-Gall System

O_LIPlant-insect coevolution is exemplified by Schlechtendalia chinensis inducing gallnuts with record-breaking hydrolyzable tannin (HT) concentrations of 74.49%--32-fold higher than normal leaves. How do plants achieve this extreme defensive chemistry, and how do aphids survive it? C_LIO_LIWe integrated transcriptomics, heterologous gene validation in Arabidopsis, and enzyme assays to investigate both plant HT biosynthesis and aphid detoxification mechanisms throughout gall development. C_LIO_LIThree key genes--Phosphoglucomutase (PGM), UDP-glucosyltransferase BX9 (BX9), and gallate 1-beta-D-glucosyltransferase (GDG) -- govern HT biosynthesis, with expression patterns closely tracking tannin accumulation dynamics, and GDG as the rate-limiting enzyme. Arabidopsis transformants showed threefold HT increases. Critically, S. chinensis employs specialized laccases rather than tannase for detoxification, with laccase activity exceeding tannase by 20,000-fold. The aphid genome encodes three laccase genes, with Sc-Lac1 expressed in digestive tissues, achieving 39-54% HT degradation. C_LIO_LIThese findings reveal how plants weaponize secondary metabolism while herbivores evolve enzymatic countermeasures. The identified genes enable engineering enhanced defenses or pharmaceutical tannin production, while laccase-based detoxification offers new insights into insect adaptation to chemical defenses. C_LI

evolutionary biology↗

mRNA vaccination overcomes hemozoin-mediated impairment of whole parasite vaccine efficacy for malaria

Malaria is a persistent global public health threat. Immunization with Radiation Attenuated Sporozoites (RAS) drives efficient CD8+ T cell dependent sterilizing immunity to malaria in humans. However, this protection is compromised in individuals living in malaria endemic regions and the mechanism(s) of the vaccine failure remain incompletely understood. In this study, we develop a murine model of Plasmodium infection where prior blood-stage exposure compromises RAS-induced CD8+ T cell responses and subsequent protection. We further identify the persisting malarial pigment hemozoin as a mediator of impaired CD8+ T cell responses. Mechanistically, we link this defect to impaired antigen uptake by dendritic cells, leading to reduced T cell activation. Importantly, we designed a lipid nanoparticle-encapsulated mRNA vaccine that encodes a string of Plasmodium CD8+ T cell epitopes and found that this vaccine overcomes the T cell defect and restores protection in Plasmodium exposed mice. Moreover, a combined RAS+mRNA vaccine regimen enhances liver resident memory T cells and protection even in malaria experienced hosts. These findings support the identification of hemozoin as a long-lived obstacle to vaccine efficacy in malaria endemic areas and provide a rational framework for designing malaria vaccines that are effective in endemic settings.

microbiology↗

A Genome-Based Pipeline for Digital Siderophore Typing in Pseudomonas Iron-Interaction Network

Siderophores are key mediators of microbial interactions, especially in iron-limited environments. While traditional experimental methods for siderophore typing are time-consuming and low-throughput, we present a genome-based pipeline for high-throughput digital siderophore typing in Pseudomonas. Our approach integrates profile Hidden Markov Models (pHMMs), substrate-specific motif identification, and co-evolutionary analysis to predict both the structure of pyoverdines and their corresponding uptake receptors from any given Pseudomonas genome. By this approach, we developed pHMM from 94 previously defined receptor groups and validated their accuracy and robustness across 14,230 Pseudomonas genomes. Application of our method to this large dataset demonstrated the potential of our algorithm for identifying both novel "lock-key" receptor groups and previously uncharacterized pyoverdine structures. Notably, our pipeline corrected long-term misclassifications in classical strains and proposed a new reference for the canonical Group III pyoverdine. Furthermore, interaction network analysis supports the observation of distinct siderophore utilization patterns between pathogenic and non-pathogenic strains. This standardized, user-friendly platform offers a robust tool for annotating siderophore behaviors in Pseudomonas and demonstrates the potential of digital siderophore typing in exploring iron-mediated ecology across microbes. Impact statementIron is vital for microbes. In most environments, they secrete diverse siderophores to scavenge iron. The types of siderophores a strain produces and uptakes shape its interactions, from cooperation to cheating and competition; characterizing this is called "siderophore typing." While traditional methods are limited by experimental capacities, our genome-based digital pipeline revolutionizes the process by predicting siderophore structures and receptor types directly from genomes, enabling large-scale analysis of 14,230 Pseudomonas strains. The results reveal novel groups, correct historical misclassifications, and link patterns to pathogenicity, providing a standardized software for ecological studies, antibiotic design, and bioremediation.

microbiology↗

Tracing Siderophore Precursors to Primary Metabolism for Ecological Applications

Microbial fitness depends on balancing between primary metabolism supporting basic survival, and secondary metabolism producing metabolites for environmental adaptation. These two systems are interconnected, with most secondary metabolites deriving from primary metabolic precursors. However, systematic frameworks for studying their relationships across diverse microbes remain limited. Using siderophores--iron-chelating secondary metabolites crucial for microbial competition--as a model, we developed a stepwise "siderophore-monomer-precursor-pathway analysis" framework to trace the biosynthetic connections from siderophore structures to primary metabolism. We applied this framework to an expanded SIDERITE database containing 1018 siderophore structures. To demonstrate practical applications, we identified specific precursors utilized by the beneficial rhizobacterium Bacillus amyloliquefaciens but not by the plant pathogen Ralstonia solanacearum. Supplementing these precursors under iron-limited conditions enhanced both siderophore production in B. amyloliquefaciens and its inhibitory activity against R. solanacearum. This work establishes a direct link between primary metabolism and siderophore-mediated microbial interactions, offering new strategies for pathogen suppression through targeted metabolic interventions.

biochemistry↗

The Role of N-acetylcysteine Amide in Acute Graft-versus-host Disease Mouse Model

Graft-versus-host disease (GvHD) remains one of the major complications following allogeneic hematopoietic cell transplantation (allo-HCT), resulting in reduced quality of life, morbidity, and mortality in transplanted patients. Clinical strategies to prevent GvHD are frequently associated with off-target effects and dose-related toxicity. Given that oxidative stress is elevated in allo-HCT recipients and contributes to the pathogenesis of GvHD, the current study aims to characterize the role of N-acetylcysteine amide (NACA), a novel antioxidant, as the prophylactic treatment for acute GvHD. Using a murine GvHD model, we found that oral administration of NACA significantly reduced GvHD severity, prolonged survival, and improved the clinical manifestations and integrity of target organs compared to saline or N-acetylcysteine (NAC) treatment. NACA modulated splenic T cells differentiation with an increase in the regulatory (Treg) subset and a decrease in the cytotoxic (CD8+) subset. Moreover, inflammatory mediators, such as ROS and pro-inflammatory cytokines were downregulated by NACA treatment. In addition, NACA hindered donor T-cell proliferation in the recipients, and restrained Th1 and Th17, but not Th2 polarization. Importantly, NACA did not influence full donor engraftment in bone marrow and spleen. Taken together, our findings provide a new candidate for GvHD prophylactic treatment by targeting oxidative stress that can be easily translated to clinical use. Key PointsO_LINACA provides superior prophylactic effect against aGvHD compared to NAC in an allogeneic transplantation mouse model. C_LIO_LINACA treatment neither showed systemic toxicity nor altered the engraftment of the donor cells. C_LI

pharmacology and toxicology↗

A novel antioxidant N-acetylcysteine Amide Alleviates Cyclophosphamide-induced Endothelial Damage

The alkylating agent cyclophosphamide (Cy) is one of the important corner stones in cancer treatment. Cy is used also as a part of conditioning regimens prior to hematopoietic cell transplantation and as a prophylactic treatment post transplantation in graft-versus-host disease. Existing evidence showed that high doses of Cy are associated with a number of side effects, including damage on arterial endothelium, which might contribute to late cardiovascular disorders. Oxidative stress has been characterized in such pathogenesis and is an exploitable target for treatment. Herein, the study aimed to investigate the protective role of the novel antioxidant N-acetylcysteine amide (NACA) in Cy-induced endothelial injury and explore the underlying mechanism. Our in vivo results showed that NACA partially reduced the endothelial injury and recovered the integrity of arterial endothelium in the mice treated with Cy. In addition, we found that NACA decreased the cytotoxicity of Cy on endothelial cells through alleviating caspase-dependent apoptosis, DNA damage and oxidative stress. Meanwhile, NACA pre-treatment rebalanced endothelial nitric oxide synthase (eNOS) and arginase I and preserved the angiogenic capability of endothelial cells which was compromised by Cy through blockage of Notch signaling pathway. Interestingly, in comparison to N-acetylcysteine (NAC), its amide derivative NACA showed superior ability to alleviate Cy-induced endothelial damage. In conclusion, the current study proved the robust endothelial protective potential of NACA, facilitating clinical use of the novel antioxidant.

pharmacology and toxicology↗

SPAC: a scalable, integrated enterprise platform for end-to-end single cell spatial analysis of multiplexed tissue imaging

BackgroundMultiplexed tissue imaging enables the simultaneous detection of dozens of proteins at single-cell resolution, providing unprecedented insights into tissue organization and disease microenvironments. However, the resulting high-dimensional, gigabyte-scale datasets pose significant computational and methodological challenges. Existing analytical workflows, often fragmented between bespoke scripts and static visualizations, lack the scalability and user-friendly interfaces required for efficient, reproducible analysis. To overcome these limitations, we developed SPAC (analysis of SPAtial single-Cell datasets), a scalable, web-based ecosystem that integrates modular pipelines, high-performance computing (HPC) connectivity, and interactive visualization to democratize end-to-end single-cell spatial analysis applied to cellular positional data and protein expression levels. ResultsSPAC is built on a modular, layered architecture that leverages community-based and newly developed tools for single-cell and spatial proteomics analysis. A specialized Python package extends these functionalities with custom analysis routines and established software engineering practices. An Interactive Analysis Layer provides web-hosted pipelines for configuring and executing complex workflows, and scalability enhancements that support distributed or parallel execution on GPU-enabled clusters. A Real-Time Visualization Layer delivers dynamic dashboards for immediate data exploration and sharing. As a showcase of its capabilities, SPAC was applied to a 4T1 breast cancer model, analyzing a multiplex imaging dataset comprising 2.6 million cells. GPU acceleration reduced unsupervised clustering runtimes from several hours to under ten minutes, and real-time visualization enabled detailed spatial characterization of tumor subregions. ConclusionsSPAC effectively overcomes key challenges in spatial single-cell analysis by streamlining high-throughput data processing and spatial profiling within an accessible and scalable framework. Its robust architecture, interactive interface and ease of access have the potential to accelerate biomedical research and clinical applications by converting complex imaging data into actionable biological and clinical insights.

bioinformatics↗

Effects of amendments on remediation of heavy metal contaminated soil and accumulation of Cd and Pb in potato

With the development of agriculture and industry, a large amount of heavy metals are loaded into the soil, posing a high ecological and public health risk. Many methods have been proposed to repair heavy metal contaminated soil, such as electroremediation, chemical washing, phytoremediation and in situ fixation. In the above methods, the application of passivators to in-situ immobilization of heavy metals is an environmentally friendly and cost-effective choice. The effects of different amendments on the improvement of heavy metal contaminated soil and the accumulation of Cd and Pb in potato plants were investigated by using attapulgite, diatomite and humic acid as materials.The results showed that soil pH, organic matter content and cation exchange capacity increased after the application of amendments. Under the treatment of attapulgite+humic acid, the soil pH, organic matter content and cation exchange capacity were increased by 0.57units, 10.0 mg/kg and 7.28cmol/kg, respectively, compared with the control. The content of soil hydrolyzable nitrogen increased, and the content of available phosphorus decreased. The application of amendments increased soil enzyme activity; effectively reduce the bioavailability of Cd and Pb in soil ; under the treatment of attapulgite+humic acid, the contents of Cd and Pb in potato plants decreased by 85.50%and 55.54%respectively, and the contents of Cd and Pb in potato tubers decreased to 0.08 mg/kg and 1.41 mg/kg respectively. The application of amendments affected the accumulation and transport of heavy metals Cd and Pb in potato plants to a certain extent and promoted the transformation of Cd and Pb from acid-soluble and reduced states to oxidized and residual states.

ecology↗

Sidero-Mining: Systematic Extraction of Siderophore Biosynthetic Information Using Large Language Models

Siderophores are central mediators of microbial iron acquisition, competition, and ecological adaptation, yet their biosynthetic diversity remains difficult to resolve across species because existing sequence-based BGC comparison is strongly constrained by phylogenetic background. Here we combine large-language-model-assisted literature mining, functional-space comparison, and genome-scale analysis to resolve the global organization of siderophore biosynthesis across bacteria. We first built SideroBank, a manually curated cross-species benchmark of siderophore biosynthetic gene clusters (BGCs), and used it to show that many identical products recur across distant taxa whereas the corresponding BGCs often fail to cluster in sequence space. We then developed BGC Block Aligner, which compares BGCs as ordered systems of functionally meaningful blocks and thereby converts comparison from sequence space to functional space. Applied to 97,432 bacterial genomes, this framework produced the Siderophore Atlas, revealing that siderophore synthesis is a remarkably pervasive trait encoded by over 60% of the analyzed genomes, with certain clusters being the most widely disseminated secondary metabolites across the bacterial domain. This global landscape suggests that the adoption of specific biosynthetic strategies is predominantly driven by ecological lifestyle rather than strict phylogenetic relatedness. Furthermore, a stark macro-evolutionary dichotomy was observed between the continuous structural diversification of NRPS pathways and the standardized, HGT-driven dissemination of NIS systems, linking functional-space genomics to the global ecology and evolution of siderophore biosynthesis..

bioinformatics↗

Niche-driven phenotypic plasticity and cis-regulatory dynamics of a revised model for intestinal secretory differentiation

HIGHLIGHTSO_LIDelineation of chromatin and mRNA dynamics of intestinal secretory differentiation C_LIO_LIPaneth cells have few unique enhancers and share mRNAs and TFs with goblet cells C_LIO_LIUnlike other secretory derivatives, goblet and Paneth cells are not specified per se C_LIO_LINiche factors, especially BMP signaling, define goblet and Paneth phenotypes C_LI Enterocytes and four secretory cell types derive from stem cells located in intestinal crypts. Whereas secretory goblet and Paneth cells have long been considered distinct, we find high overlap in their transcripts and sites of accessible chromatin, in marked contrast to those of sibling enteroendocrine or tuft cells. Mouse and human goblet and Paneth cells express extraordinary fractions of selective antimicrobial genes, reflecting specific and variable gene responses to local niche signals. Wnt signaling retains few ATOH1+ secretory daughters in crypt bottoms, where an absence of BMP signaling potently induces Paneth features; those that move away from crypt bottoms acquire classic goblet properties. These post-mitotic cellular phenotypes and their underlying accessible cis-elements interconvert readily. Thus, goblet and Paneth properties represent alternative manifestations of a single versatile signal-responsive secretory cell. These findings reveal exquisite niche-dependent cell plasticity and the cis-regulatory dynamics of an updated unitarian model of the intestinal epithelial lineage.

cell biology↗

scTFBridge: A Disentangled Deep Generative Model Informed by TF-Motif Binding for Gene Regulation Inference in Single-Cell Multi-Omics

The interplay between transcription factors (TFs) and regulatory elements (REs) drives gene transcription, forming gene regulatory networks (GRNs). Advances in single-cell technologies now enable simultaneous measurement of RNA expression and chromatin accessibility, offering unprecedented opportunities for GRN inference at single-cell resolution. However, heterogeneity across omics layers complicates regulatory feature extraction. We present scTFBridge, a multi-omics deep generative model for GRN inference. scTFBridge disentangles latent spaces into shared and specific components across omics layers. By integrating TF-motif binding knowledge, scTFBridge aligns shared embeddings with specific TF regulatory activities, enhancing biological interpretability. Using explainability methods, scTFBridge computes regulatory scores for REs and TFs, enabling robust GRN inference. It consistently outperformed baseline methods in both cis- and trans-regulation inference tasks. Our results demonstrate that scTFBridge can uncover cell-type-specific susceptibility genes and distinct regulatory programs, offering new insights into gene regulation mechanisms at single-cell resolution.

bioinformatics↗

Mapping spatially-resolved transcriptomes in systemic sclerosis

Systemic sclerosis (SSc) is a prototypical fibrotic disease with high mortality and limited treatment options. Despite advances in single-cell RNA sequencing (scRNA-seq), the comprehensive understanding of cellular heterogeneity and cell-cell interaction within the fibrogenesis microenvironment remains limited. We generated spatially resolved transcriptome maps from healthy and SSc skin and built a scRNA-seq atlas to map the single-cell data to spatial space. This enabled us to identify a fibrotic niche, enriched with fibroblasts and macrophages, which is significantly expanded in SSc and correlated with clinical outcome. We revealed disease-specific cell states of fibroblasts and macrophages, and evaluated their spatial dependency on other cell types. We identified selective expression of ACKR3 in fibroblast progenitors that diminishes with SSc progression, which may serve to regulate CXCL12/CXCR4-mediated macrophage recruitment and fibrotic remodeling. Together, we provided an in-depth description at cellular and spatial levels of fine-tuned regulatory events occurring in SSc, offering spatiotemporal insights. One Sentence SummaryIntegrated spatial omics provide insight into the cellular and transcriptional landscape in spatially distinct microenvironments, which may drive fibrosis progression in SSc.

immunology↗

The membrane topology problem inherent in ciliogenesis is solved by ciliary recruitment of a phospholipid flippase

The cilium is a slender cellular projection whose membrane transduces signals essential in development and homeostasis. Although assembly of the axonemal core of the organelle is well-studied, the mechanisms that underlie formation of the [~]250 nm diameter ciliary membrane from oppositely curved 50-100 nm diameter pre-ciliary vesicles remain poorly understood. Here we report that during ciliogenesis in the bi-ciliated alga, Chlamydomonas reinhardtii, aminophospholipid flippase 2 (ALA2) is recruited laterally from a reservoir on the plasma membrane onto the nascent ciliary membrane where it transfers conically shaped phosphatidyl ethanolamine (PE) from the outer to the inner leaflet. In cells lacking ALA2, initiation of cilia regeneration after experimentally induced de-ciliation is delayed, PE flipping is impaired, the ciliary membrane becomes distorted, and cilia that do form are shorter than wild type. Our results uncover a membrane topology problem inherent in ciliogenesis and demonstrate that it is resolved by a phospholipid flippase. HighlightsO_LIMembranes of pre-ciliary vesicles reverse curvature to become the ciliary membrane C_LIO_LIUpon initiation of ciliogenesis, plasma membrane ALA2 transits laterally to cilia C_LIO_LIThe ciliary membranes of ala2 mutants fail to conform to axonemal shape C_LIO_LIALA2 flips PE to establish ciliary membrane curvature C_LI

cell biology↗