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Yu, S.

Publications and source records attributed to Yu, S..

At least 55 records · Page 3Linked to original sources

Combined antagonism of Oncostatin M (OSM) and Interleukin 6 (IL-6) provides both anti-fibrotic and anti-inflammatory benefit in pulmonary fibrosis

Interstitial lung diseases (ILDs), including idiopathic pulmonary fibrosis (IPF) and systemic sclerosis-associated ILD (SSc-ILD), are irreversible fibrosing diseases with a mean survival time of less than 5 years for IPF. Poorly understood etiology and complex pathogenesis of these diseases have hampered the identification and development of effective therapeutics. Existing treatments can slow progressive fibrosis and lung function decline but do not stop it entirely, resulting in a minimal impact on patient survival. Thus, novel therapeutic interventions are needed. Tocilizumab, an anti-IL-6 receptor antibody, was recently approved by FDA for the treatment of SSc-ILD based on evidence demonstrating a reduction in the rate of lung function decline. In this study, we have characterized an IL-6-driven feed-forward myeloid axis contributing to lung inflammation providing a mechanistic hypothesis for tocilizumab. Concomitantly we have identified an oncostatin M (OSM) orchestrated lung injury response contributing to epithelial and endothelial cell disruption, myofibroblast activation and fibrosis. Despite dysregulated expression of IL11 in IPF, SSc-ILD, and murine models of fibrosis, we found no evidence for a pro-fibrotic role for IL-11 in vitro or in vivo. Instead, in pre-clinical models of IPF we demonstrate that antagonism of OSM alone, or to a greater degree in combination with IL-6, reduced lung fibrosis and inflammation. Translating these observations, we validated gp130:OSMR, rather than gp130:LIFR, as the dominant human receptor complex used by OSM, identifying OSMR as a potential therapeutic target to stall fibrosis.

immunology↗

Multicolored, Sonosensitizer-optimized Organic Mechanoluminescent Nanoparticles for Functional Sono-optogenetics

Light enables precise visualization and control of cellular processes, but its utility in deep tissues is fundamentally limited by poor optical penetration, particularly in the deep brain. Ultrasound-triggered mechanoluminescence offers a non-invasive strategy for remote light delivery, yet existing organic systems remain monochromatic and low-intensity, largely due to an incomplete understanding of ultrasound-induced emission. Here, we report a multicolor mechanoluminescence platform that couples reactive oxygen species-responsive chemiluminescent donors with fluorescent acceptors via Forster resonance energy transfer, generating tunable emission from blue (459 nm) to red (592 nm). Systematic screening potentially reveals that electronic energy gap-dependent reactive oxygen species generation serves as a predictive design principle for high-performance mechanoluminescent materials. The emitted spectrum and intensity are sufficient to activate ChR2 and ChRmine and inhibit eOPN3, enabling bidirectional, fiber-free neuromodulation under focused ultrasound. By integrating spatially precise ultrasound with programmable photon output, this platform establishes a non-invasive strategy for deep-tissue neural monitoring and provides a foundation for applications in bioimaging, gene editing, and precision therapeutics.

bioengineering↗

Unlocking karst biodiversity with eDNA: a validated qPCR toolkit for discovery and monitoring the worlds largest cavefish radiation (Cyprinidae: Sinocyclocheilus)

Environmental DNA (eDNA) enables non-invasive detection of aquatic species through trace genetic material, but uncertainties regarding DNA persistence, detection accuracy, and the limited taxonomic resolution of stygian fauna have constrained its use in subterranean aquatic environments. The species-rich cavefish genus Sinocyclocheilus, endemic to the karst landscapes of southwestern China, offers an excellent model for understanding these issues. With over eighty species, many of which are endemics, and many still being described, this lineage is taxonomically rich, poorly understood, and highly threatened. However, access to these deep habitats remains challenging, making eDNA detection one of the most practical methods for documenting and monitoring them. We developed and validated a qPCR assay targeting a hypervariable region of the mitochondrial 16S rRNA gene, allowing for genus-specific detection and species-level identification. Laboratory and field evaluations involving 47 representative species confirmed high specificity and a detection limit of around 20 DNA copies per reaction (R{superscript 2} = 0.995). Controlled degradation studies indicated that temperature and pH strongly affect DNA persistence. Field surveys across 47 karst sites (37 caves and 10 surface sites) detected Sinocyclocheilus eDNA in only 33 caves. Dideoxy sequencing of qPCR amplicons provided species-level identification and phylogenetic validation, including detection of a new species. At three cave sites yielding multiple qPCR detections, 16S metabarcoding enabled species discrimination. By integrating qPCR assay validation, eDNA degradation modelling, hierarchical genetic identification via dideoxy sequencing, and selective NGS metabarcoding, this study presents a strategic framework for applying eDNA methods in subterranean environments.

evolutionary biology↗

The protein phosphatase 2C domain contributes to the pathobiological function of adenylyl cyclase in Cryptococcus neoformans

Adenylyl cyclase produces cyclic adenosine monophosphate, a signalling molecule that controls fungal development and virulence. Fungal adenylyl cyclases are distinguished by the presence of a conserved protein phosphatase 2C domain, whose function remains unknown. Here we show that the protein phosphatase 2C domain of Cac1, the adenylyl cyclase of the human pathogen Cryptococcus neoformans, has an unusual structure but functions as a metal-dependent serine/threonine phosphatase. Deletion of this domain or the adenylyl cyclase catalytic domain demonstrated that the protein phosphatase 2C domain is required for full Cac1 activity, influencing melanin and capsule synthesis, sexual differentiation, titan cell formation, and cell wall integrity. Notably, loss of the protein phosphatase 2C domain induces type 2 helper T-cell-biased immunity and extensive pulmonary damage yet does not cause mortality in mice. Integrated transcriptomic and phosphoproteomic analyses further revealed shared and domain-specific signalling outputs. Together, these findings define a pivotal role for the adenylyl cyclase-linked protein phosphatase 2C domain in C. neoformans pathobiology.

microbiology↗

A genetic screen in enteroendocrine cells reveals mechanisms that control protein sensing and GLP-1 release

Enteroendocrine cells (EECs) are the principal nutrient sensors in the gastrointestinal (GI) tract and release hormones such as glucagon-like-peptide 1 (GLP-1) that modulate GI function and appetite. While some of the molecules involved in nutrient sensing within EECs have been described, there have been no systematic studies to map the relevant genes and pathways. Here, we developed a strategy to perform a high-throughput screen for genes that are required for nutrient-induced activation of EECs, and we applied this to probe mechanisms for sensing dietary protein. We found that all of the genes previously proposed to function as protein sensors in EECs are, collectively, dispensable for protein sensing in an EEC cell line. Instead, a screen of >20,000 sgRNAs identified numerous genes associated with mitochondrial respiration as being necessary for this process. We showed through secondary assays that impairing oxidative phosphorylation (OXPHOS) reduced EEC activation and GLP-1 release in response to nutrients but not in response to a non-nutritive stimulus. On the other hand, boosting OXPHOS increased EEC activation and GLP-1 release. These data reveal that intracellular metabolism within EECs controls the detection of dietary protein, possibly by monitoring the entry of ingested amino acids into the TCA cycle. More broadly, these findings suggest a general strategy to screen for genes and pathways that might be used to boost the nutrient-regulated release of gut peptides such as GLP-1.

physiology↗

Spatially-resolved Photoproximity Profiling of MYC Identifies a MYC-BAF Liability in Cancer Cells

The c-MYC transcription factor is aberrantly expressed in most human cancers to enhance expression of proliferative gene programs. Owing to its pseudo-ordered structure and reliance on extensive and dynamic protein-protein interactions in distinct transcriptional regulatory complexes, defining context-specific MYC interactors has remained challenging. Therefore, mapping MYC-centered complex topologies in disease relevant models could identify components critical for its function which may serve as therapeutic targets in MYC-driven cancers. Here, we present a matched pair of photoproximity probes coupled with quantitative proteomics which enable context-dependent mapping of protein complex topology inside cells. We applied this spatially resolved, intracellular photoproximity (siPROX) profiling workflow to map MYC interactomes across temporal, spatial and disease-relevant contexts. Basal and inhibitor-treated profiles confirmed interactions with a wide range of known chromatin-associated transcriptional regulatory factors that define the extended MYC transcriptional bubble in live cells. Time-resolved mapping of inhibitor treated cells identified dynamic remodeling of numerous transcriptional regulatory factors and identified several BAF complex members (e.g., PBRM1 and SMARCC1)1 that persist in the presence of bromodomain inhibition. Furthermore, spatial MYC topology maps in small cell lung cancer cells confirmed the presence of BAF complex members under conditions where MYC induced target gene expression, altered cell morphology and enhanced proliferation. Lastly, loss of BAF function via inhibition of SMARCA2/4 ATPase activity resulted in rapid loss of chromatin-bound and nuclear MYC levels, downregulation of MYC-dependent transcripts and MYC-specific cell growth in several cancer cell models. Together, these data highlight the potential for siPROX to identify spatially resolved, dynamic TF interactors and highlight MYC-proximal BAF interactions as a targetable liability to regulate MYC-dependent transcription and proliferation.

cancer biology↗

Molecular Dynamics-Guided Design and Chemoproteomic Profiling of Covalent Kinase Activity Probes

Covalent small molecule activity probes can be powerful tools to interrogate protein function in native cellular environments. The design of family-wide activity probes requires an understanding of the molecular sources of general targeting potential and specificity to enable broad targeting of protein family members. Here, we developed and applied a multifaceted docking and molecular dynamics (MD) simulation pipeline to design and test cell-permeable covalent kinase activity probes from a set of hinge-binding pharmacophores. This computationally-guided approach yielded a new cell-active probe, K60P, which targets around 114 kinases across distinct kinase classes in live cells. Chemoproteomic profiling of this probe and a clinical candidate sharing the same indazole core, KW-2449, identified kinase and non-kinase target profiles that differ from recombinant protein assay profiles, underscoring the utility of native kinase profiling in situ. Biochemical studies with a model target kinase, ABL1, confirmed covalent labeling of the active site lysine across several kinase probes with distinct kinetics, as well as covalent labeling of key tyrosines in trans between ABL1 monomers. Finally, focused proteomics, kinetic modeling, and molecular dynamics simulations revealed that K60P, as well as the comparator probe XO44, preferentially engage with target kinases in their active, DFG-in conformations, which is driven by increasing population of reaction-ready small molecule conformation. These results together establish a computational and kinetic modeling framework for designing covalent activity probes and highlight the balance of target selectivity and kinetic efficiency as a key factor in determining their proteome-wide reactivity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/683178v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1ea3e5forg.highwire.dtl.DTLVardef@1a4e999org.highwire.dtl.DTLVardef@1e468c3org.highwire.dtl.DTLVardef@99e04e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Phosphatidylcholine Metabolism Controls Alveolar Progenitor Renewal and Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease marked by alveolar type 2 (AT2) stem cell dysfunction and excessive matrix deposition, with no effective treatments. Recent advances have recognized that AT2 cells act as stem cells, in addition to their role in the production of pulmonary surfactants in the distal alveolar space. We and others have reported a failure of AT2 regeneration and a loss of AT2 cells in IPF. We recently further reported that there is a defect in lipid metabolism in IPF AT2 cells and we discovered a selective loss of lysophosphatidylcholine acyltransferase 1 (LPCAT1) in AT2 cells from IPF, as well as in AT2 cells from bleomycin-injured mice. Pharmacological and genetic experiments confirm that LPCAT1 is required for AT2 cell renewal in 3D organoid assays. AT2 cell-specific Lpcat1 deletion resulted in reduced AT2 renewal, spontaneous lung fibrosis, and heightened susceptibility to bleomycin-induced fibrosis in mice in vivo. Expression-based high-content drug screening with an LPCAT1 knock-in cell line identified several drug families that upregulated LPCAT1 expression. We further confirmed that anti-malarial artesunate and PLA2 inhibitor ONO-RS-082 increased LPCAT1 mRNA expression, promoted AT2 renewal, and attenuated bleomycin-induced lung fibrosis in mice in vivo. Our findings establish LPCAT1 as a critical regulator of AT2 renewal and lipid metabolism in IPF, suggesting that reactivation of LPCAT1 could offer a novel therapeutic strategy for restoring alveolar progenitor function and mitigating lung fibrosis.

cell biology↗

A machine-learning-guided hydrogen-bonded organic framework for long-term, ultrasound-triggered pain therapy

Effective treatment of chronic pain remains hindered by the lack of drug delivery systems that simultaneously achieve long-term stability, high spatial precision, and non-invasiveness1,2,3. Here, we utilize a programmable, ultrasound-responsive drug delivery platform based on hydrogen-bonded organic framework (HOF) nanoparticles, enabling on-demand anesthetic release with long-term and durable analgesic efficacy. A machine learning (ML)-guided screening pipeline was developed to evaluate about 250 FDA-approved drugs, spanning both hydrophilic and lipophilic agents, and identified bupivacaine (lipophilic) and lidocaine hydrochloride (hydrophilic) as optimal candidates. These agents were efficiently encapsulated into HOF nanoparticles via diffusion and double-solvent methods. Ultrasound-triggered drug release in vitro transiently suppressed calcium signaling in adeno-associated virus (AAV)-transfected neurons. In vivo, ultrasound-activated release of bupivacaine or lidocaine HCl at the sciatic nerve site significantly elevated mechanical nociceptive thresholds for up to seven days, reduced autotomy (self-mutilaion) behavior, and improved motor function in a rat model of chronic pain. Notably, the machine learning-identified top candidates not only exhibited high loading efficiency, but also demonstrated superior therapeutic outcomes in vivo, establishing a direct link between computational prediction and biological efficacy. This non-invasive, programmable HOF-based system provides a clinically translatable platform for on-demand, spatiotemporally precise pain management.

bioengineering↗

Scaling Molecular Representation Learning with Hierarchical Mixture-of-Experts

Recent advancements in large-scale self-supervised pretraining have significantly improved molecular representation learning, yet challenges persist, particularly when addressing distributional shifts (e.g., under scaffold-split). Drawing inspiration from the success of Mixture-of-Experts (MoE) networks in NLP, we introduce H-MoE, a hierarchical MoE model tailored for molecular representation learning. Since conventional routing strategies struggle to capture global molecular information--such as scaffold structures, which are crucial for enhancing generalization--we propose a hierarchical routing mechanism. This mechanism first utilizes scaffold-level structural guidance before refining molecular characteristics at the atomic level. To optimize expert assignment, we incorporate scaffold routing contrastive loss, ensuring scaffold-consistent routing while preserving discriminability across molecular categories. Furthermore, a curriculum learning approach and dynamic expert allocation strategy are employed to enhance adaptability. Extensive experiments on molecular property prediction tasks demonstrate the effectiveness of our method in capturing molecular diversity and improving generalization across different tasks.

bioinformatics↗

Angiogenic CD8 T cells from PWH induce Granzymes-dependent PAR1 activation promoting endothelial inflammation

In people with HIV (PWH), T cell immune activation and endothelial inflammation are contributors of the increased cardiovascular risk, however the mechanisms remain poorly understood. PAR1 connects the coagulation cascade, endothelial cells and CD8 T cells at the site of endothelial inflammation and we hypothesized that HIV driven CD8 T cell immune activation alters endothelial repair mechanisms. Endothelial repair is partially mediated by angiogenic T (Tang) cells that facilitate proliferation of endothelial cells, and differentiation of endothelial progenitor cells at site of vascular injury. During LCMV infection, we identified a subset of CD31highCD8 T cells that exhibited a long-lived memory precursor phenotype (CD127+KLRG1-) and secreted the proangiogenic cytokine vascular endothelial growth factor (VEGF) after viral control. Furthermore, in PWH, the frequencies of CD8 Tang cells were reduced and showed an activated phenotype and expression of granzymes. GZMA+GZMB+CD8 Tang cells correlated with atherosclerotic cardiovascular disease (ASCVD) risk. In vitro, granzyme dependent PAR1 activation led to calcium mobilization and secretion of proinflammatory cytokines IL-6, IL-8 and angiopoietin-2 by primary human endothelial cells. Altogether, these findings suggest that CD8 T cells are involved in immunity against viruses and endothelial homeostasis and HIV driven immune activation alters these functions.

immunology↗

Keystone Bacterial Taxa Drive Denitrification and N2O Emission via Adaptive Genomic and Metabolic Strategies in Contrasting Agricultural Soils

Soil denitrification mediated by microbial communities is a major driver of nitrous oxide (N2O) emissions, yet the regulatory roles of keystone taxa remain largely unexplored, particularly under distinct edaphic conditions. Black soil (BS) and fluvo-aquic soil (FS), two representative agricultural soils in China, exhibit contrasting N2O emission potentials, providing a unique model system for disentangling microbial mechanisms underlying soil-specific denitrification dynamics. Here, we integrated microbial co-occurrence networks, metagenomics, and functional phenotyping to identify and characterize keystone bacterial taxa involved in denitrification across the above mentioned two contrasting agricultural soils, BS and FS. Structural equation modeling (SEM) and correlation analyses revealed that keystone taxa are significantly associated with soil denitrification rates and N2O emission patterns. Among these, Ramlibacter ASV104 was identified as a conserved keystone in both soils, exhibiting genomic potential for key denitrification genes (nirK/nirS/norB/nosZ) to mediate N2O turnover. In contrast, Ensifer ASV205 was a FS-specific keystone taxon, exhibiting strain-level niche specialization. Comparative genomics revealed that variations in denitrification gene composition and carbon-nitrogen metabolism enable different Ensifer strains to function either as N2O sources or sinks. This functional divergence was linked to their genomic plasticity and growth strategies under nutrient-rich conditions. Our findings demonstrate that soil-specific denitrification processes and N2O emissions are governed by keystone taxa through adaptive genomic and metabolic strategies shaped by environmental filtering. This study improves our understanding of the microbial mechanisms driving N2O emissions and provides a foundation for future strategies targeting microbial taxa to mitigate N2O emissions in agricultural soils. IMPORTANCEThis study provides new insights into the ecological complexity underlying soil N2O emissions by integrating strain-level diversity, genomic attributes, and microbial interaction networks. Key microbial taxa involved in denitrification and N2O emissions were identified in black soil and fluvo-aquic soil. By combining network-based ecological modeling and functional assays, it is revealed that taxa such as Ramlibacter ASV104 and Ensifer ASV205 play significant roles in regulating N2O emissions. Strain-level functional diversity within the keystone taxa of Ensifer ASV205 highlights their varying contributions to nitrogen cycling. Our findings provide a deeper understanding of the microbial mechanisms governing N2O emissions, offering valuable insights for developing microbial-based strategies to mitigate N2O emissions in agricultural soils in the future.

ecology↗

ndufs2-/- zebrafish have impaired survival, neuromuscular activity, morphology, and one-carbon metabolism treatable with folic acid

Mitochondrial complex I (CI) deficiency represents a common biochemical pathophysiology underlying Leigh syndrome spectrum (LSS), manifesting with progressive multi-system dysfunction, lactic acidemia, and early mortality. To facilitate mechanistic studies and rigorous screening of therapeutic candidates for CI deficient LSS, we used CRISPR/Cas9 to generate an ndufs2-/- 16 bp deletion zebrafish strain. ndufs2-/- larvae exhibit markedly reduced survival, severe neuromuscular dysfunction including impaired swimming capacity, multiple morphologic malformations, reduced growth, hepatomegaly, uninflated swim bladder, yolk retention, small intestines, and small eyes and pupils with abnormal retinal ganglion cell layer. Transcriptome profiling of ndufs2-/- larvae revealed dysregulation of the electron transport chain, TCA cycle, fatty acid beta-oxidation, and one-carbon metabolism. Similar transcriptomic profiles were observed in ndufs2-/- missense mutant C. elegans (gas-1(fc21)) and two human CI-disease fibroblast cell lines stressed in galactose media. ndufs2-/- zebrafish had 80% reduced CI enzyme activity. Unbiased metabolomic profiling showed increased lactate, TCA cycle intermediates, and acyl-carnitine species. One-carbon metabolism associated pathway alterations appear to contribute to CI disease pathophysiology, as folic acid treatment rescued the growth defect and hepatomegaly in ndufs2-/-larvae. Overall, ndufs2-/- zebrafish recapitulate severe CI deficiency, complex metabolic pathophysiology, and relevant LSS neuromuscular and survival phenotypes, enabling future translational studies of therapeutic candidates.

pharmacology and toxicology↗

Copper-Containing ROS-Scavenging Nanozyme Paradoxically Drives Alpha-Synucleinopathy by Amplifying Nitrosative Stress

Reactive oxygen and nitrogen species (RONS) are implicated in neurodegeneration, but their specific pathogenic roles remain unclear. Here, we developed a pair of iridium-based nanozymes with opposing functionalities to dissect these pathways. We show that a copper-tuned iridium nanozyme (Ir{square}Cu), despite being a superior ROS scavenger, paradoxically and dramatically exacerbated -synuclein (Syn) pathology in vivo. This pathology was causally linked to its ability to amplify RNS, as pharmacological inhibition of nitric oxide synthase (NOS) with L-NAME completely abrogated the pathology and reversed a human Parkinsons disease (PD)-like transcriptomic signature. In contrast, a copper-free, broad-spectrum RONS-scavenging iridium (Ir) nanozyme demonstrated substantial therapeutic efficacy across diverse brain-first, body-first, and Alzheimers disease with Lewy body co-pathology models. Our findings uncover the importance of the RNS pathway in driving -synucleinopathies and establish a critical design principle for nanomedicine, mandating caution in the use of redox-active copper for neuroprotective applications.

pathology↗

The gut microbiome shapes pharmacology and treatment outcomes for a key anti-inflammatory therapy

The human gut microbiome encodes a formidable metabolic repertoire that harvests nutrients from the diet, but these same pathways may also metabolize medications. Indeed, large screens have revealed extensive microbial metabolism of drugs in vitro, but the pharmacologic and clinical repercussions of microbiota-mediated metabolism in vivo remain to be discerned. As a proof-of-concept, we investigate how human gut microbes contribute to in vivo pharmacology and efficacy of a key anti-inflammatory drug, methotrexate (MTX). Specifically, we demonstrate that the gut microbiome shapes drug pharmacology in vivo in mice, both by directly metabolizing the drug and by inducing host pathways that promote drug metabolism. Moreover, interindividual variation in the human gut microbiome contributes to variation in pharmacokinetic (PK) profiles. When we quantified metabolites produced by microbes, we unexpectedly identified novel MTX metabolites, one of which, p-methylaminobenzoyl-L-glutamic acid (pMABG), was a major byproduct of microbial metabolism both in vitro and in vivo. Further, we find that a large proportion of patient-associated microbes are capable of metabolizing MTX. Finally, we show that microbial metabolism of MTX is linked to PK profiles and disease outcomes in a mouse model of inflammatory arthritis. Taken together, these findings provide evidence that the human gut microbiome causally contributes to drug pharmacology in vivo for a key anti-inflammatory drug through known and novel mechanisms. Our studies provide a framework for elucidating the clinical relevance of drug microbial metabolism in the context of treatment response. These results are a first step towards understanding and manipulating the human gut microbiome in the treatment of autoimmunity and the advancement of precision medicine for millions of patients taking MTX for immune or inflammatory conditions. HighlightsO_LIThe gut microbiome impacts methotrexate (MTX) pharmacology in mice C_LIO_LIThe human gut microbiome contributes to interindividual variation in MTX pharmacology C_LIO_LIHuman gut microbes produce novel MTX metabolites, pMABG and 6-MPDA C_LIO_LIMicrobial metabolism of MTX is linked to treatment outcomes C_LI

pharmacology and toxicology↗

Paclitaxel-induced mitotic arrest results in a convergence of apoptotic dependencies that can be safely exploited by BCL-XL degradation to overcome cancer chemoresistance

Paclitaxel and other microtubule-targeting agents are cornerstone therapies for diverse cancers, including lung, breast, cervical, pancreatic, and ovarian malignancies. Paclitaxel induces tumor cell apoptosis during mitosis by disrupting microtubule dynamics required for chromosome segregation. However, despite initial responsiveness, many tumors develop resistance, limiting therapeutic durability. Here, we used high-grade serous ovarian carcinoma (HGSOC), the most common and lethal subtype of ovarian cancer, as a model to dissect the mechanisms underlying this resistance. We find that paclitaxel-induced mitotic arrest triggers degradation of the pro-survival protein MCL-1 and upregulation of BCL-XL, followed by inactivating phosphorylation of BCL-XL at Ser62 to promote apoptosis. In resistant cells, this MCL-1 downregulation is insufficient to commit cells to apoptosis but instead results in a transient convergence of apoptotic dependencies by forcing BCL-XL to sequester the pro-apoptotic proteins BIM, BAX, and BAK. During this state, BCL-XL inhibition induces synergistic apoptosis, even in chemoresistant cells. Surprisingly, we also discover that loss of substrate attachment recapitulates this apoptotic convergence both in vitro and in vivo, with HGSOC cells growing in metastasis-promoting malignant ascites displaying heightened apoptotic priming and dependence on BCL-XL relative to solid tumors. In HGSOC xenografts, targeted degradation of BCL-XL using the platelet-sparing proteolysis-targeting chimera (PROTAC) DT2216 matches the efficacy of paclitaxel monotherapy while avoiding the chronic thrombocytopenia induced by BCL-XL inhibitors such as navitoclax (ABT-263). Strikingly, combination therapy leveraging the synergy between paclitaxel and DT2216 leads to complete eradication of HGSOC cell line and patient-derived xenografts. Moreover, DT2216 treatment blunts the rapid apoptotic adaptation caused by other BCL-XL inhibitors, indicating that targeted degradation of pro-survival proteins may yield more durable responses than inhibition alone. These findings uncover a mechanistic framework for safely exploiting the apoptotic dependency convergence caused by mitotic arrest and substrate detachment and support the clinical development of BCL-XL-targeting PROTACs to overcome chemoresistance in ovarian cancer and other solid tumors.

cancer biology↗

CPT1B-Mediated Fatty Acid Oxidation Induces Pigmentation in Solar Lentigo

IntroductionCellular senescence is associated with altered lipid metabolism, including increased cellular lipid uptake, upregulated lipid biosynthesis, and deregulated lipid breakdown. Previous studies have reported that carnitine palmitoyltransferase (CPT), the rate-limiting enzyme in fatty acid oxidation that catalyzes the conversion of acyl-CoA to acylcarnitine, is involved in various senescence-related diseases. Although solar lentigo (SL) is an age-related pigmentary disorder characterized by the accumulation of senescent cells, its role in metabolic dysregulation has rarely been investigated. Methods and ResultsIntegrated transcriptomic profiling of SL skin samples, combining mRNA sequencing, differential gene expression, pathway enrichment analyses, metabolic flux simulations, and protein-protein interaction analysis, was conducted to demonstrate the molecular alterations in SL compared to perilesional normal skin. We found transcriptomic alterations in mitochondrial energy metabolism-associated genes. Metabolic flux simulations revealed that carnitine-associated reactions involved in fatty acid oxidation were upregulated. Using a multi-omics approach, CPT1B was selected as a potential marker for SL, which was confirmed via its overexpression in immunohistochemical studies. Using a zebrafish model, CPT1B was implicated in melanogenesis. DiscussionCPT1B-mediated metabolic alteration is a key driver of SL pathogenesis. Targeting CPT1B and the associated lipid metabolism pathways is a novel therapeutic approach for managing SL and age-related pigmentation disorders. Research HighlightsSolar lentigo (SL) exhibits altered mitochondrial metabolism and fatty acid oxidation. CPT1B activation regulates pigmentation, suggesting that targeting CPT1B may offer a novel therapy for SL and other age-related pigmentary disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=176 HEIGHT=200 SRC="FIGDIR/small/659823v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@81fce3org.highwire.dtl.DTLVardef@1bf3forg.highwire.dtl.DTLVardef@b2c119org.highwire.dtl.DTLVardef@1a38b23_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

Determinants of fleshiness or dryness for fruits at maturity: fruit shapes and pericarp permeability

[A hypothesis was proposed that fleshiness or dryness of fruits at maturity were determined just by fruit shapes and pericarp permeability influenced by heterogeneous habitats] The ecological origins of diverse fruit types still remain unresolved due to the lack of knowledge about fruit water content variation patterns during fruit development and after fruit maturity. In this study, we explore factors influencing fleshiness or dryness of fruits at maturity through examining the water content variation patterns before and after fruit maturity, and identify biological and environmental mechanisms about fleshiness or not for fruits at maturity, using data from a survey on fruit shapes of 29760 species and one experiment involving water content measure of fruits. Results show that water content in majority of the fleshy (except for drupes and rosehips) and dry fruits increases or decreases, respectively, during fruit development i.e. prior to maturity, and the water variation patterns are determined by fruit shapes and pericarp permeability. After maturation, water loss occurs slowly at room temperature for fleshy fruits, but it is fast for most dry fruits. In general, declining fruit water content due to pericarp lignification occurring and rising pericarp permeability with the development of dry fruits in later stage of fruit development as well as water imbalance between supply and loss induced by open habitats may lead to the formation of dryness for elongated or flaky dry fruits owing to allometric growth between pedicel diameter (or fruit mass) and fruit surface area. Resulted from water balance, the emergence of fleshiness in mature fleshy fruits is attributed to slow water loss through the pericarp influenced by globular shapes (i.e. greater fruit thickness) and pericarp waxification induced by shaded habitats, or by sporoderm lignification occurring (inside the pericarp) induced by open habitats for a subset of fleshy fruits such as drupes and rosehips.

plant biology↗