Biology subjects

Yu, L.

Publications and source records attributed to Yu, L..

At least 127 records · Page 7Linked to original sources

bioRxiv2024

Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain

A multitude of functional mutations continue to emerge on the N-terminal domain (NTD) of the spike protein in SARS-CoV-2 Omicron subvariants. Understanding the immunogenicity of Omicron NTD and the properties of antibodies elicited by it is crucial for comprehending the impact of NTD mutations on viral fitness and guiding vaccine design. In this study, we find that most of NTD-targeting antibodies isolated from individuals with BA.5/BF.7 breakthrough infection (BTI) are ancestral (wildtype or WT)-reactive and non-neutralizing. Surprisingly, we identified five ultra-potent neutralizing antibodies (NAbs) that can only bind to Omicron but not WT NTD. Structural analysis revealed that they bind to a unique epitope on the N1/N2 loop of NTD and interact with the receptor-binding domain (RBD) via the light chain. These Omicron-specific NAbs achieve neutralization through ACE2 competition and blockage of ACE2-mediated S1 shedding. However, BA.2.86 and BA.2.87.1, which carry insertions or deletions on the N1/N2 loop, can evade these antibodies. Together, we provided a detailed map of the NTD-targeting antibody repertoire in the post-Omicron era, demonstrating their vulnerability to NTD mutations enabled by its evolutionary flexibility, despite their potent neutralization. These results highlighted the importance of considering the immunogenicity of NTD in vaccine design. Author SummaryCOVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be a major global public health concern four years after its emergence. The N-terminal domain (NTD) is a critical component of the spike glycoprotein, which is pivotal for SARS-CoV-2 cellular entry and serves as a primary target for antibody therapeutics and vaccine development. Characterizing the properties of antibodies elicited by NTD of Omicron sublineages is crucial for understanding viral evolution and guiding vaccine design. Here, we show that Omicron infection after vaccination induces majorly non-neutralizing NTD antibodies. Still, we identified a class of ultra-potent neutralizing antibodies (NAbs) which specifically bind to the NTD of Omicron sublineages. These NAbs neutralize the virus by competing with ACE2 and blocking ACE2-mediated S1 shedding. Structural analyses reveal that these antibodies target a unique epitope on the N1/N2 loop of NTD, and intriguingly interact with the receptor-binding domain (RBD) of spike glycoprotein. This class of NAbs with the special binding pattern, are escaped by BA.2.86 and BA.2.87.1 sublineages, shedding light on the role of recently emerged mutations in the N1/N2 loop of NTD. Our findings provide fresh insights into the immunogenicity of Omicron NTD, highlighting its capacity for antibody evasion due to its evolutionary flexibility. This underscores the importance of carefully considering the NTD component in vaccine design.

immunology↗

bioRxiv2024

Polymerization of Tspan7 into Helical Transmembrane Skeletons for Membrane Tether Stabilization

Tubular cell membrane protrusions, such as filopodia1, dendrites2, tunneling nanotubes (TNTs)3 and retraction fibers4, are prevalent on the cell surface. They play crucial roles in various physiological processes and disease states, including angiogenesis, wound healing, and cancer metastasis5-7. The shaping and stabilization of these protrusions are crucial for their function, and the molecular machineries involved have long been an active area of investigation. Here we employed an integrative approach combining live-cell imaging, in vitro reconstitution, and in situ cryo-EM analysis to reveal that the transmembrane protein tetraspanin 7 (TSPAN7) senses membrane curvature and polymerizes into a helical configuration on highly curved tubular membranes. These spirals act as a "transmembrane skeleton", effectively maintaining the structural integrity of membrane protrusions under mechanical stress. Our findings reveal a previously unreported assembly strategy for transmembrane proteins and a mechanism for maintaining tubular membrane protrusions.

cell biology↗

bioRxiv2024

Activity and function of the endothelial sodium channel is regulated by the effector domain of MARCKS like protein 1 in mouse aortic endothelial cells

The endothelial sodium channel (EnNaC) plays an important role in regulating vessel stiffness. Here, we investigated the regulation of EnNaC in mouse aortic endothelial cells (mAoEC) by the actin cytoskeleton and lipid raft association protein myristoylated alanine-rich C-kinase substrate like protein 1 (MLP1). We hypothesized that mutation of specific amino acid residues within the effector domain of MLP1 or loss of association between MLP1 and the anionic phospholipid phosphate PIP2 would significantly alter membrane association and EnNaC activity in mAoEC. mAoEC transiently transfected with a mutant MLP1 construct (three serine residues in the effector domain replaced with aspartate residues) showed a significant decrease in EnNaC activity compared to cells transfected with wildtype MLP1. Compared to vehicle treatment, mAoEC treated with the PIP2 synthesis blocker wortmannin showed less colocalization of EnNaC and MLP1. In other experiments, Western blot and densitometric analysis showed a significant decrease in MLP1 and caveloin-1 protein expression in mAoEC treated with wortmannin compared to vehicle. Finally, wortmannin treatment decreased sphingomyelin content and increased membrane fluidity in mAoEC. Taken together, our results suggest constitutive phosphorylation of MLP1 attenuates the function of EnNaC in aortic endothelial cells by a mechanism involving a decrease in association with MLP1 and EnNaC at the membrane, while deletion of PIP2 decreases MARCKS expression and overall membrane fluidity.

physiology↗

bioRxiv2024

Dissecting the genetic regulation of lateral root development in tomato under salt stress

Roots are the primary site for sensing salt, making them critical to understanding how plants adapt to salinity. Unraveling the genetic and molecular mechanisms that maintain root growth under salt stress is essential for developing resilient crops. Tomatoes are vulnerable to salinity, as over 50% of arable land is projected to become saline by 2050. While salt stress effects on tomato seed germination, shoot growth, and fruit yield are well-documented, the genetic basis of root development under salinity remains underexplored. Previous studies focused on physiological responses of roots in a narrow range of cultivated-tomatoes, overlooking the genetic diversity for salt resilience in wild-relatives like Solanum pimpinellifolium. Here, we investigated salt-induced changes in root system architecture (RSA) across a natural diversity panel of 220 wild- and 25 cultivated-tomato varieties. We identified tolerant accessions with different RSA strategies; prioritizing lateral root elongation versus emergence. To identify genes involved in specific aspects of lateral root development, an F1 hybrid was generated that exhibited both parents combined characteristics. An F2-segregating population was then used to identify four distinct subpopulations for Bulk Segregant Analysis (BSA). Simultaneously, we conducted Genome-Wide-Association Studies (GWAS) on root architecture of wild-tomato accessions under salt stress. By integrating the results of BSA and GWAS, we identified 22 candidates involved in the maintenance of root architecture. We utilized RNA-Seq to examine transcriptome reprogramming of the 22 genes in tomato accessions with contrasting lateral root responses. This approach resulted in the identification of 2 genes, AP2-like-ethylene-responsive transcription factor TOE3 and L-ascorbate peroxidase. Using exogenous ethylene, we demonstrated that root architecture exhibits plasticity, which benefits the plant by reducing Na+ accumulation. We profiled H2O2 waves across root systems of tomatoes, emphasizing the role of ROS in maintaining root system architecture under salt stress. These findings provide novel genetic targets for enhancing salt resilience in tomatoes, opening avenues for future research and breeding programs.

plant biology↗

bioRxiv2024

High resolution profiling of cell cycle-dependent protein and phosphorylation abundance changes in non-transformed cells

The cell cycle governs a precise series of molecular events, regulated by coordinated changes in protein and phosphorylation abundance, that culminates in the generation of two daughter cells. Here, we present a proteomic and phosphoproteomic analysis of the human cell cycle in hTERT-RPE-1 cells using deep quantitative mass spectrometry by isobaric labelling. Through analysing non-transformed cells, and improving the temporal resolution and coverage of key cell cycle regulators, we present a dataset of cell cycle-dependent protein and phosphorylation site oscillation that offers a foundational reference for investigating cell cycle regulation. These data reveal uncharacterised regulatory intricacies including proteins and phosphorylation sites exhibiting previously unreported cell cycle-dependent oscillation, and novel proteins targeted for degradation during mitotic exit. Integrated with complementary resources, our data link cycle-dependent abundance dynamics to functional changes and are accessible through the Cell Cycle database (CCdb), an interactive web-based resource for the cell cycle community. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/599917v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@bb2a69org.highwire.dtl.DTLVardef@1dd55ecorg.highwire.dtl.DTLVardef@34073eorg.highwire.dtl.DTLVardef@1c7a8c9_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

Convergent Acquisition of Glucomannan β-galactosyltransferases in Asterids and Rosids

{beta}-Galactoglucomannan ({beta}-GGM) is a primary cell wall polysaccharide in rosids and asterids. The {beta}-GGM polymer has a backbone of repeating glucose and mannose, usually with mono- or di-galactosyl sidechains on the mannosyl residues. CELLULOSE SYNTHASE-LIKE 2 (CSLA2), MANNAN -GALACTOSYLTRANSFERASE (MAGT), and MANNAN {beta}-GALACTOSYLTRANSFERASE (MBGT) are required for {beta}-GGM synthesis in Arabidopsis thaliana. The single MBGT identified so far, AtMBGT1, lies in glycosyltransferase family 47A subclade VII, and was identified in Arabidopsis. However, despite the presence of {beta}-GGM, an orthologous gene is absent in tomato (Solanum lycopersicum), a model asterid. In this study, we screened candidate MBGT genes from the tomato genome, functionally tested the activities of encoded proteins, and identified the tomato MBGT (SlMBGT1) in GT47A-III. Interestingly therefore, AtMBGT1 and SlMBGT1 are located in different GT47A subclades. Further, phylogenetic and glucomannan structural analysis from different species raised the possibility that various asterids possess conserved MBGTs in GT47A-III, indicating that MBGT activity has been acquired convergently among asterids and rosids. Although functional convergence was observed, the acquired amino acid substitutions among the two MBGT groups were not shared, suggesting different evolutionary pathways to achieve the same biochemical outcome. The present study highlights the promiscuous emergence of donor and acceptor preference in GT47A enzymes, and suggests an adaptive advantage for eudicots to acquire {beta}-GGM {beta}-galactosylation.

plant biology↗

bioRxiv2024

Potent and broadly neutralizing antibodies against sarbecoviruses elicited by single ancestral SARS-CoV-2 infection

Monoclonal antibody (mAb) therapeutics hold promise for both preventing and treating infectious diseases, especially among vulnerable populations. However, the emergence of various variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents challenges for current mAb treatments, emphasizing the need for more potent and broadly neutralizing antibodies. In this study, we employed an unbiased screening approach to discover broadly neutralizing antibodies and successfully isolated two mAbs from individuals with only exposure to ancestral SARS-CoV-2. One of these antibodies, CYFN1006-1, exhibited robust cross-neutralization against a spectrum of SARS-CoV-2 variants, including the latest JN.1 and KP.2 variants, with consistent IC50 values ranging from [~]1 to 5 ng/mL. Notably, it also displayed broad neutralization activity against SARS-CoV and related sarbecoviruses, such as WIV1, SHC014, RaTG13, and GD-Pangolin. Structural analysis revealed that these mAbs target shared hotspot but mutation-resistant epitopes, with their Fabs locking the RBD in the "down" conformation through interactions with adjacent Fabs and RBDs, and cross-linking Spike trimers into di-trimers to block viral infection. In vivo studies conducted in a JN.1-infected hamster model validated the protective efficacy of CYFN1006-1, emphasizing its therapeutic potential. These findings suggest that, through meticulous approaches, rare antibodies with cross-neutralization activities against SARS-CoV-2 and related sarbecoviruses can be identified from individuals with exclusively ancestral virus exposure.

microbiology↗

bioRxiv2024

A Regularized Bayesian Dirichlet-multinomial Regression Model for Integrating Single-cell-level Omics and Patient-level Clinical Study Data

SummaryThe abundance of various cell types can vary significantly among patients with varying phenotypes and even those with the same phenotype. Recent scientific advancements provide mounting evidence that other clinical variables, such as age, gender, and lifestyle habits, can also influence the abundance of certain cell types. However, current methods for integrating single-cell-level omics data with clinical variables are inadequate. In this study, we propose a regularized Bayesian Dirichlet-multinomial regression framework to investigate the relationship between single-cell RNA sequencing data and patient-level clinical data. Additionally, the model employs a novel hierarchical tree structure to identify such relationships at different cell-type levels. Our model successfully uncovers significant associations between specific cell types and clinical variables across three distinct diseases: pulmonary fibrosis, COVID-19, and non-small cell lung cancer. This integrative analysis provides biological insights and could potentially inform clinical interventions for various diseases.

bioinformatics↗

bioRxiv2024

Genome-wide mapping of native co-localized G4s and R-loops in living cells

The non-B DNA structures can act as dynamic functional genomic elements regulating gene expression. Among them, G4s and R-loops are two of the best studied. The interplay between R-loops and G4s are emerging in regulating DNA repair, replication and transcription. A comprehensive picture of native co-localized G4s and R-loops in living cells is currently lacking. Here, we describe the development of HepG4-seq and an optimized HBD-seq methods, which robustly capture native G4s and R-loops, respectively, in living cells. We successfully employed these methods to establish comprehensive maps of native co-localized G4s and R-loops in human HEK293 cells and mouse embryonic stem cells (mESCs). We discovered that co-localized G4s and R-loops are dynamically altered in a cell type-dependent manner and are largely localized at active promoters and enhancers of transcriptional active genes. We further demonstrated the helicase Dhx9 as a direct and major regulator that modulates the formation and resolution of co-localized G4s and R-loops. Depletion of Dhx9 impaired the self-renewal and differentiation capacities of mESCs by altering the transcription of co-localized G4s and R-loops - associated genes. Taken together, our work established that the endogenous co-localized G4s and R-loops are prevalently persisted in the regulatory regions of active genes and are involved in the transcriptional regulation of their linked genes, opening the door for exploring broader roles of co-localized G4s and R-loops in development and disease.

genomics↗

bioRxiv2024

Muscone-specific olfactory protein reveals the putative scent-marking pheromone in the Sunda pangolin (Manis javanica)

The Sunda pangolin (Manis javanica) is a burrowing and nocturnal animal, and they have poor vision, thus, intraspecies communication relies on olfaction, such as mating, warning, and scent-marking. However, the intraspecies pheromone in pangolins remains unknown. In this study, all the odorant-binding proteins in Sunda pangolins were functionally expressed, and they were screened against a panel of 32 volatiles that were derived from the pangolins urine, feces, and anal gland secretions. Reverse chemical ecology identified that M. javanica odorant-binding protein 3 (MjavOBP3) possesses the highest binding affinity to muscone. A subsequent behavior-tracking assay showed that only males can sense muscone; thus, we hypothesize that muscone is a male-specific scent-marking pheromone. Meanwhile, the structural study showed that Tyr117 contributes the most to muscones binding, which was further validated by site-directed mutagenesis. The findings clarify the scent-marking mechanism in pangolins, and muscone could potentially be used to support the monitoring and conservation of this endangered animal. Author SummaryThe Sunda pangolin is an endangered mammal that is native to Southeast Asia and is threatened due to its economic value. They are cave-living and nocturnal, poor vision; thus, their intraspecies communication is highly reliant on olfaction. Although they are generally solitary, they have been observed to have some social aspects in the wild, such as breeding and territorial behaviors, which are mediated by scents. However, no previous study has investigated the type of pheromones and how they are detected. Using the reverse chemical ecology approach, MjavOBP3 was found to bind to muscone with high affinity, and behavior-tracking assay was performed under well-controlled artificial rearing conditions, which showed only male pangolins can recognize muscone, suggesting its potential male-specific pheromone role.

zoology↗

bioRxiv2024

Stabilizing mammalian RNA thermometer confers neuroprotection in subarachnoid hemorrhage

Mammals tightly regulate their core body temperature, yet how cells sense and respond to small temperature changes at the molecular level remains incompletely understood. Here, we discover a significant enrichment of RNA G-quadruplex (rG4) motifs around splice sites of cold-repressed exons. These thermosensing RNA structures, when stabilized, mask splice sites, reducing exon inclusion. Focusing on cold-induced neuroprotective RBM3, we demonstrate that rG4s near splice sites of a cold-repressed poison exon are stabilized at low temperatures, leading to exon exclusion. This enables evasion of nonsense-mediated decay, increasing RBM3 expression at cold. Additionally, increasing intracellular potassium concentration stabilizes rG4s and enhances RBM3 expression, leading to RBM3-dependent neuroprotection in a mouse model of subarachnoid hemorrhage. Our findings unveil a mechanism how mammalian RNAs directly sense temperature and potassium perturbations, integrating them into gene expression programs. This opens new avenues for treating diseases arising from splicing defects and disorders benefiting from therapeutic hypothermia. HighlightsO_LIrG4s are enriched near splice sites of cassette exons repressed upon cold shock C_LIO_LIrG4s act as RNA thermometers in mammals by controlling accessibility of splice sites C_LIO_LIrG4 stability mediates temperature-dependent RBM3 expression ex vivo and in vivo C_LIO_LIStabilizing rG4s in RBM3 exon 3a reduces brain damage in subarachnoid hemorrhage C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/594628v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@e1d625org.highwire.dtl.DTLVardef@b22d21org.highwire.dtl.DTLVardef@1b0faeaorg.highwire.dtl.DTLVardef@294ac1_HPS_FORMAT_FIGEXP M_FIG C_FIG Here is a refined model of RNA G-quadruplexes acting as evolutionarily conserved thermo- and potassium sensors, modulating alternative splicing in mammals. RNA G-quadruplexes (rG4s) function as reversible temperature sensors, impacting alternative splicing dynamics. In low temperatures or high potassium conditions, rG4s can mask surrounding splice sites, rendering these sites inaccessible, thereby promoting exon skipping. Conversely, at high temperatures or under low potassium conditions, rG4s become destabilized, allowing splice sites to be exposed, and facilitating efficient exon inclusion. RBM3, a well-known cold-induced protein with neuroprotective functions, harbors a poison exon with rG4s around splice sites, that, upon inclusion, triggers NMD (non-sense mediated decay) of the RBM3 mRNA. Under low temperatures or high potassium conditions, rG4s shield the splice sites, leading to poison exon skipping and increased RBM3 expression. Stabilization of these rG4s through increased K+ promotes poison exon skipping, enabling escape from NMD, and ultimately elevating RBM3 expression. Notably, 4-AP, a clinically used pan voltage-gated potassium channel blocker, protects against neuronal damage in a subarachnoid hemorrhage mouse model in an RBM-dependent manner. (ISS: intronic splicing silencer, ESE: exon splicing enhancer, ACA: anterior cerebral artery, MCA: middle cerebral artery, PPA: pterygopalatine artery, ICA: internal carotid artery, ECA: external carotid artery, CCA: common carotid artery)

molecular biology↗

bioRxiv2024

A left-lateralized dorsolateral prefrontal network for naming

The ability to connect the form and meaning of a concept, known as word retrieval, is fundamental to human communication. While various input modalities could lead to identical word retrieval, the exact neural dynamics supporting this process relevant to daily auditory discourse remain poorly understood. Here, we recorded neurosurgical electrocorticographic (ECoG) data from 48 patients and dissociated two key language networks that highly overlap in time and space critical for word retrieval. Using unsupervised temporal clustering techniques, we found a semantic processing network located in the middle and inferior frontal gyri. This network was distinct from an articulatory planning network in the inferior frontal and precentral gyri, which was invariant to input modalities. Functionally, we confirmed that the semantic processing network encodes word surprisal during sentence perception. These findings elucidate neurophysiological mechanisms underlying the processing of semantic auditory inputs ranging from passive language comprehension to conversational speech.

neuroscience↗

bioRxiv2024

Ferroptosis mediates the progression of hyperuricemic nephropathy by activating RAGE signaling

Hyperuricemic nephropathy (HN) represents a prevalent complication arising from hyperuricemia, typified by tubular dysfunction, inflammation, and progressive renal fibrosis, whose pathogenic mechanisms remain enigmatic. Ferroptosis, a newly elucidated iron-dependent form of regulated cell death, plays a role in various disease states. However, its involvement in HN has seldom been explored. In this study, we observed indications of ferroptosis in the renal tissues of urate oxidase knockout (UOX-/-) mice, a model of hyperuricemia, as evidenced by increased iron deposition and reduced expression of glutathione peroxidase 4 (GPX4). These findings suggest a substantial role of ferroptosis in the pathogenesis of HN. To further explore this hypothesis, UOX-/- mice were administered Ferrostatin-1, a known inhibitor ferroptosis. This treatment markedly ameliorated tubular injury, necrosis, and inflammatory cell infiltration, mitigated renal fibrosis, reinstated the expression of proteins associated with ferroptosis in renal tissues, and reduced iron overload, lipid peroxidation, and mitochondrial damage in UOX-/- mice. Additionally, we found that receptor for advanced glycation end products (RAGE) propagates ferroptosis-induced renal injury, inflammation and fibrosis, albeit without directly facilitating ferroptosis. Finally, ferroptosis and RAGE upregulation were validated in renal tissues of patients with hyperuricemia-related kidney disease. Collectively, our research elucidates the critical contribution of ferroptosis to HN pathogenesis, indicating that therapeutic strategies targeting ferroptosis and the related RAGE signaling may offer novel therapeutic approaches for managing this condition.

ecology↗

bioRxiv2024

Omicron-specific naive B cell maturation alleviates immune imprinting induced by SARS-CoV-2 inactivated vaccine

SARS-CoV-2 ancestral strain-induced immune imprinting poses great challenges to vaccine updates. Studies showed that repeated Omicron exposures could override immune imprinting induced by inactivated vaccines but not mRNA vaccines, a disparity yet to be understood. Here, we analyzed the underlying mechanism of immune imprinting alleviation in inactivated vaccine (CoronaVac) cohorts. We observed in CoronaVac-vaccinated individuals who experienced BA.5/BF.7 breakthrough infection (BTI), the proportion of Omicron-specific memory B cells (MBCs) substantially increased after an extended period post-Omicron BTI, with their antibodies displaying enhanced somatic hypermutation and neutralizing potency. Consequently, the neutralizing antibody epitope distribution encoded by MBCs post-BA.5/BF.7 BTI after prolonged maturation closely mirrors that in BA.5/BF.7-infected unvaccinated individuals. Together, these results indicate the activation and expansion of Omicron-specific naive B cells generated by first-time Omicron exposure helped to alleviate CoronaVac-induced immune imprinting, and the absence of this process should have caused the persistent immune imprinting seen in mRNA vaccine recipients. HighlightsO_LILongitudinal MBC profiling of CoronaVac-vaccinated individuals following BA.5 BTI C_LIO_LIOmicron-specific MBC proportion rises greatly after extended period post-BA.5 BTI C_LIO_LIOmicron-specific naive B cell maturation reduces ancestral strain immune imprinting C_LI

immunology↗

bioRxiv2024

Unbiased metastatic niche-labeling identifies estrogen receptor-positive macrophages as a barrier of T cell infiltration during bone colonization

Microenvironment niches determine cellular fates of metastatic cancer cells. However, robust and unbiased approaches to identify niche components and their molecular profiles are lacking. We established Sortase A-Based Microenvironment Niche Tagging (SAMENT), which selectively labels cells encountered by cancer cells during metastatic colonization. SAMENT was applied to multiple cancer models colonizing the same organ and the same cancer to different organs. Common metastatic niche features include macrophage enrichment and T cell depletion. Macrophage niches are phenotypically diverse between different organs. In bone, macrophages express the estrogen receptor alpha (ER) and exhibit active ER signaling in male and female hosts. Conditional knockout of Esr1 in macrophages significantly retarded bone colonization by allowing T cell infiltration. ER expression was also discovered in human bone metastases of both genders. Collectively, we identified a unique population of ER+ macrophages in the metastatic niche and functionally tied ER signaling in macrophages to T cell exclusion during metastatic colonization. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/593016v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@1cd65b6org.highwire.dtl.DTLVardef@1d099e2org.highwire.dtl.DTLVardef@26cd91org.highwire.dtl.DTLVardef@181f5f3_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LISAMENT is a robust metastatic niche-labeling approach amenable to single-cell omics. C_LIO_LIMetastatic niches are typically enriched with macrophages and depleted of T cells. C_LIO_LIDirect interaction with cancer cells induces ER expression in niche macrophages. C_LIO_LIKnockout of Esr1 in macrophages allows T cell infiltration and retards bone colonization. C_LI

cancer biology↗

bioRxiv2024

Single cell profiling of bone metastasis ecosystems from multiple cancer types reveals convergent and divergent mechanisms of bone colonization.

Bone represents congenial soil for metastatic seeds and is frequently affected by metastasis of multiple cancer types. The histological and molecular characteristics of bone metastases (BMs) are diverse but poorly understood. Herein, we performed single-cell RNA-seq on 34 BMs from 6 cancer types and identified 3 ecosystem archetypes characterized by enrichment of macrophages/osteoclasts (M{varphi}-OC), regulatory/exhausted T cells (Treg-Tex), and monocytes (Mono), respectively. Breast cancer BMs are mostly the M{varphi}-OC archetype driven by the osteolytic vicious cycle, whereas kidney cancers BMs mainly belong to the Treg-Tex archetype that lacks osteoclasts. Lung cancers BMs evenly distributed across all archetypes. Further analyses revealed parallel mechanisms of immunosuppression and bone remodeling. Elevated estrogen signaling distinguishes macrophages in the M{varphi}-OC subtype, which was investigated in a companion study. Together, we elucidated that divergent mechanisms toward bone colonization and that BMs of different origins can adopt the same mechanism through convergent evolution or adaptation. HIGHLIGHTSO_LIAnalyses of bone metastases from 6 cancer types revealed three immune archetypes. C_LIO_LIArchetypes diverge on immune trajectories, and features of tumor and stromal cells. C_LIO_LIDominant cell type in each archetype undergoes convergent evolution. C_LIO_LIRegulatory networks converge on osteoclasts and Tregs to drive archetype formation. C_LI Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/593027v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@82cef6org.highwire.dtl.DTLVardef@1e1b021org.highwire.dtl.DTLVardef@1f2881eorg.highwire.dtl.DTLVardef@1c6874a_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Protein S-glutathionylation confers cell resistance to ferroptosis

Ferroptosis is a type of cell death that is strongly associated with the cellular redox state. Glutathione is the key to buffering lipid peroxidation in ferroptosis and can also modify proteins by S-glutathionylation under oxidative stress. Here, we showed that the strong associations among glutathione pools, protein S-glutathionylation, and susceptibility to ferroptosis existed broadly in ferroptosis induced by erastin or acetaminophen. Deficiency of CHAC1, a glutathione-degrading enzyme, led to decreased glutathione pools and reduced protein S-glutathionylation, improved liver function and attenuated hepatocyte ferroptosis upon acetaminophen challenge, which could be retarded by CHAC1 overexpression. We conducted quantitative redox proteomics in primary mouse hepatocytes to identify glutathione pool-sensitive S-glutathionylated proteins and found that S-glutathionylation is required to maintain the function of ADP-ribosylation factor 6 (ARF6). Our data suggest that aberrant ARF6 S-glutathionylation increases the labile iron pool by delaying the recycling of transferrin receptors, thereby promoting ferroptosis. Our study reveals the importance of protein S-glutathionylation in conferring cell resistance to ferroptosis. O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/592374v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@82dbaeorg.highwire.dtl.DTLVardef@1247cc5org.highwire.dtl.DTLVardef@7b7147org.highwire.dtl.DTLVardef@49ff07_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIHighly upregulated CHAC1 decreases glutathione pools and protein S-glutathionylation. C_LIO_LIReduced protein S-glutathionylation associated with decreased glutathione pools promotes ferroptosis. C_LIO_LIS-glutathionylation of ARF6 at Cys90 promotes ARF6 activation. C_LIO_LIReduced S-glutathionylation of ARF6 provides a labile iron pool to drive ferroptosis. C_LI

cell biology↗

bioRxiv2024

Skeletal Muscle Mitochondrial Dysfunction Mediated by Pseudomonas aeruginosa Quorum Sensing Transcription Factor MvfR: Reversing Effects with Anti-MvfR and Mitochondrial-Targeted Compounds

Sepsis and chronic infections with Pseudomonas aeruginosa, a leading "ESKAPE" bacterial pathogen, are associated with increased morbidity and mortality and skeletal muscle atrophy. The actions of this pathogen on skeletal muscle remain poorly understood. In skeletal muscle, mitochondria serve as a crucial energy source, which may be perturbed by infection. Here, using the well-established backburn and infection model of murine P. aeruginosa infection, we deciphered the systemic impact of the quorum sensing (QS) transcription factor MvfR by interrogating five days post-infection its effect on mitochondrial-related functions in the gastrocnemius skeletal muscle and the outcome of the pharmacological inhibition of MvfR function and that of the mitochondrial-targeted peptide, Szeto-Schiller 31 (SS-31). Our findings show that the MvfR perturbs ATP generation, oxidative phosphorylation (OXPHOS), and antioxidant response, elevates the production of reactive oxygen species, and promotes oxidative damage of mitochondrial DNA in the gastrocnemius muscle of infected mice. These impairments in mitochondrial-related functions were corroborated by the alteration of key mitochondrial proteins involved in electron transport, mitochondrial biogenesis, dynamics and quality control, and mitochondrial uncoupling. Pharmacological inhibition of MvfR using the potent anti-MvfR lead, D88, we developed, or the mitochondrial-targeted peptide SS-31 rescued the MvfR- mediated alterations observed in mice infected with the wild-type strain PA14. Our study provides insights into the actions of MvfR in orchestrating mitochondrial dysfunction in the skeletal murine muscle, and it presents novel therapeutic approaches for optimizing clinical outcomes in affected patients.

microbiology↗