Systems Biology
A laboratory-friendly protocol for freeze-drying sample preparation in ToF-SIMS single-cell imaging
Front Chem. 2025 Mar 7;13:1523712. doi: 10.3389/fchem.2025.1523712. eCollection 2025.
ABSTRACT
ToF-SIMS is a high spatial resolution imaging technique for cellular or subcellular analysis of biological samples. Accurate molecular data in single-cell studies depend on proper cell morphology and chemical integrity, highlighting the importance of sample preparation. In this work, we standardized a more efficient freeze-drying method using standard lab materials and improved the sample preparation process. Our comprehensive freeze-drying protocol for cellular samples, encompassing washing, fixation, and drying steps, facilitates the acquisition of enhanced cellular information and ensures high reproducibility. These improvements are poised to significantly advance single-cell mass spectrometry imaging research.
PMID:40124708 | PMC:PMC11925917 | DOI:10.3389/fchem.2025.1523712
Evolving concepts of the protein universe
iScience. 2025 Feb 13;28(3):112012. doi: 10.1016/j.isci.2025.112012. eCollection 2025 Mar 21.
ABSTRACT
The protein universe is the collection of all proteins on earth from all organisms both extant and extinct. Classical studies on protein folding suggested that proteins exist as a unique three-dimensional conformation that is dictated by the genetic code and is critical for function. In this perspective, we discuss ideas and developments that emerged over the past three decades regarding the protein structure-function paradigm. It is now clear that ordered (active/functional) and disordered/denatured (and hence inactive/non-functional) represent a continuum of states rather than binary states. Some proteins can switch folds without sequence change. Others exist as conformational ensembles lacking defined structure yet play critical roles in many biological processes, including forming membrane-less organelles driven by liquid-liquid phase separation. Numerous diverse proteins harbor segments with the potential to form amyloid fibrils, many of which are functional, and some possess prion-like properties enabling conformation-based transfer of heritable information. Taken together, these developments reveal the remarkable complexity of the protein universe.
PMID:40124498 | PMC:PMC11926713 | DOI:10.1016/j.isci.2025.112012
Obesity may extend the time required to reach a steady-state 25(OH)D level after initiating vitamin D supplementation
JBMR Plus. 2025 Feb 8;9(4):ziaf030. doi: 10.1093/jbmrpl/ziaf030. eCollection 2025 Apr.
ABSTRACT
Obesity is known to influence the circulating 25(OH)D level but less is known about whether it influences the time required to reach a stable 25(OH)D level after initiating vitamin D supplementation. This observational study was done to investigate whether BMI modified the time required to reach a steady-state 25(OH)D level in response to vitamin D supplementation. Participants in the Boston STOP IT study who were treated for 12 mo with 700 IU of vitamin D3 and 500 mg of calcium daily and had 25(OH)D measures at 0, 6, and 12 mo, were included. We assessed the trajectory of 25(OH)D levels by baseline BMI category (normal weight, BMI 18.5-24.9 kg/m2, n = 62; overweight and obese, BMI ≥ 25 kg/m2, n = 105). Baseline 25(OH)D levels were 78 ± 31.3 nmol/L (normal weight) and 74.7 ± 36.5 nmol/L (overweight and obese). In a linear mixed model examining the influence of time and baseline BMI category on change in the mean 25(OH)D level, there was a significant time x BMI group interaction (p = .024. The normal weight participants had reached steady-state 25(OH)D levels by 6 mo whereas 25(OH)D levels continued to rise between 6 and 12 mo in the overweight and obese participants. This analysis suggests that the time required to reach a steady-state 25(OH)D level after initiating vitamin D supplementation in overweight and obese adults is greater than the usual 3-mo time point commonly used in clinical practice. A more refined definition of the time course of circulating 25(OH)D response to supplementation is needed in overweight and obese individuals in order to optimize clinical monitoring of vitamin D status.
PMID:40124405 | PMC:PMC11929376 | DOI:10.1093/jbmrpl/ziaf030
Entinostat, a histone deacetylase inhibitor, enhances CAR-NK cell anti-tumor activity by sustaining CAR expression
Front Immunol. 2025 Mar 7;16:1533044. doi: 10.3389/fimmu.2025.1533044. eCollection 2025.
ABSTRACT
Allogeneic natural killer (NK) cell therapy has demonstrated significant potential in cancer immunotherapy by harnessing NK cells to target malignancies. CD138-targeting chimeric antigen receptor (CAR)-engineered NK cells offer a promising therapeutic option for multiple myeloma (MM). However, sustaining CAR expression on CAR-NK cells during ex vivo expansion poses a challenge to developing effective immunotherapies. In this study, primary NK cells were isolated, cryopreserved, and modified to express anti-CD138 CARs through retroviral transduction. Histone deacetylase inhibitors (HDACi), particularly entinostat (ENT), were applied to enhance CAR expression stability in CAR-NK cells. Our findings indicate that ENT treatment significantly improves and maintains CAR expression, thereby enhancing the cytotoxic activity of CAR-NK cells against CD138-positive multiple myeloma cells. ENT-treated CAR-NK cells exhibited prolonged persistence and more significant tumor reduction in an MM tumor-bearing mouse model, highlighting the therapeutic potential of HDACi-treated CAR-NK cells. This study provides the first evidence that HDAC inhibitors can sustain CAR expression in CAR-NK cells in a promoter-dependent manner, potentially enhancing anti-tumor efficacy in multiple myeloma and underscoring the possible need for further clinical evaluation.
PMID:40124378 | PMC:PMC11925867 | DOI:10.3389/fimmu.2025.1533044
Corrigendum: Differential co-expression network analysis reveals key hub-high traffic genes as potential therapeutic targets for COVID-19 pandemic
Front Immunol. 2025 Mar 7;16:1572273. doi: 10.3389/fimmu.2025.1572273. eCollection 2025.
ABSTRACT
[This corrects the article DOI: 10.3389/fimmu.2021.789317.].
PMID:40124368 | PMC:PMC11926803 | DOI:10.3389/fimmu.2025.1572273
TF-chRDP: a method for simultaneously capturing transcription factor binding chromatin-associated RNA, DNA and protein
Front Cell Dev Biol. 2025 Mar 7;13:1561540. doi: 10.3389/fcell.2025.1561540. eCollection 2025.
ABSTRACT
Transcription factors (TFs) play a crucial role in the regulation of gene expression and the structural organization of chromatin. They interact with proteins, RNA, and chromatin DNA to exert their functions. Therefore, an efficient and straightforward experimental approach that simultaneously captures the interactions of transcription factors with DNA, RNA, and proteins is essential for studying these regulatory proteins. In this study, we developed a novel method, TF-chRDP (Transcription Factor binding Chromatin-associated RNA, DNA, and Protein), which allows for the concurrent capture of these biomolecules in a single experiment. We enriched chromatin complexes using specific antibodies and divided the chromatin into three fractions: one for DNA library preparation to analyze the genomic binding sites of transcription factors, another for RNA library preparation to investigate the RNA associated with transcription factor binding, and the third for proteomic analysis to identify protein cofactors interacting with transcription factors. We applied this method to study the transcription factor p53 and its associated chromatin complexes. The results demonstrated high specificity in the enrichment of DNA, RNA and proteins. This method provides an efficient tool for simultaneously capturing chromatin-associated RNA, DNA and protein bound to specific TF, making it particularly useful for analyzing the role of protein-DNA-RNA complexes in transcriptional regulation.
PMID:40123855 | PMC:PMC11925928 | DOI:10.3389/fcell.2025.1561540
<em>Pseudobaeosporoideae</em>, a new subfamily within the <em>Tricholomataceae</em> for the genus <em>Pseudobaeospora</em> (<em>Agaricales</em>, <em>Tricholomatineae</em>) based on morphological and molecular inference
IMA Fungus. 2025 Mar 13;16:e144994. doi: 10.3897/imafungus.16.144994. eCollection 2025.
ABSTRACT
Based on molecular and morphological evidence the new subfamily Pseudobaeosporoideae of the Tricholomataceae is established within the Tricholomatineae for accommodating the unique features of Pseudobaeospora such as gymnocarpic mycenoid/collybioid habit, small-sized spores with thick and dextrinoid wall, and presence of crassobasidia. Twenty-six Pseudobaeospora collections corresponding to eleven species (five types) were newly sequenced. Collections morphologically attributable to P.oligophylla (type of the genus) or to P.pillodii are here sequenced for the first time: accordingly, P.oligophylla is considered as a posterior synonym of P.pillodii. Quélet's original plate is selected as a lectotype for Collybiapillodii and a French collection as its epitype collection. Pseudobaeosporadeceptiva is described as a new species from Italy very close to P.pillodii from which it differs mainly by bigger spores and SSU and LSU rDNA sequences. The presence of P.pyrifera in Italy is documented for the first time and P.mutabilis is reduced to its later synonym. A neotype is established for P.jamonii which is here proved to be an independent species. Finally, a critical review of the characters used for interspecific distinctions in Pseudobaeospora was provided.
PMID:40123765 | PMC:PMC11926610 | DOI:10.3897/imafungus.16.144994
Conserved Biological Processes in Partial Cellular Reprogramming: Relevance to Aging and Rejuvenation
Ageing Res Rev. 2025 Mar 21:102737. doi: 10.1016/j.arr.2025.102737. Online ahead of print.
ABSTRACT
Partial or transient cellular reprogramming is defined by the limited induction of pluripotency factors without full dedifferentiation of cells to a pluripotent state. Comparing in vitro and in vivo mouse studies, and in vitro studies in humans, supported by visualizations of data interconnections, we show consistent patterns in how such reprogramming modulates key biological processes. Generally, partial reprogramming drives dynamic chromatin remodelling, involving histone modifications that regulate accessibility and facilitate pluripotency gene activation while silencing somatic identity. These changes are accompanied by modifications in stress response programs, such as inflammation, autophagy, and cellular senescence, as well as improved mitochondrial activity and dysregulation of extracellular matrix pathways. We also underscore the challenges in evaluating complex processes like aging and cellular senescence, given the variability in biomarkers used across studies. Overall, we highlight biological processes consistently influenced by reprogramming while noting that some effects are context-dependent, varying according to cell type, species, sex, recovery time, and the reprogramming method employed. These insights inform future research and potential therapeutic applications in aging and regenerative medicine.
PMID:40122394 | DOI:10.1016/j.arr.2025.102737
Lifestyle interventions in older adults with type 2 diabetes mellitus: The key for healthy ageing
J Nutr Health Aging. 2025 Mar 22;29(4):100546. doi: 10.1016/j.jnha.2025.100546. Online ahead of print.
NO ABSTRACT
PMID:40121957 | DOI:10.1016/j.jnha.2025.100546
Immune prognostic model for glioblastoma based on the ssGSEA enrichment score
Cancer Genet. 2025 Mar 22;294-295:32-41. doi: 10.1016/j.cancergen.2025.03.005. Online ahead of print.
ABSTRACT
PURPOSE: Few effective immune prognostic models based on the tumor immune microenvironment (TIME) for glioblastoma have been reported. Therefore, this study aimed to construct an immune prognostic model for glioblastoma by analyzing enriched biological processes and pathways in tumors.
METHODS: A comprehensive single-sample gene set enrichment analysis (ssGSEA) of gene sets from the Molecular Signatures Database was performed using TCGA RNA sequencing data (141 glioblastoma cases). After evaluating gene sets associated with prognosis using univariable Cox regression, gene sets related to biological processes and tumor immunity in gliomas were extracted. Finally, the least absolute shrinkage and selection operator Cox regression refined the gene sets and a nomogram was constructed. The model was validated using CGGA (183 cases) and Aichi Cancer Center (42 cases) datasets.
RESULTS: The immune prognostic model consisted of three gene sets related to biological processes (sphingolipids, steroid hormones, and intermediate filaments) and one related to tumor immunity (immunosuppressive chemokine pathways involving tumor-associated microglia and macrophages). Kaplan-Meier curves for the training (TCGA) and validation (CGGA) cohorts showed significantly worse overall survival in the high-risk group compared to the low-risk group (p < 0.001 and p = 0.04, respectively). Furthermore, in silico cytometry revealed a significant increase in macrophages with immunosuppressive properties and T cells with effector functions in the high-risk group (p < 0.01) across all cohorts.
CONCLUSION: Construction of an immune prognostic model based on the TIME assessment using ssGSEA could potentially provide valuable insights into the prognosis and immune profiles of patients with glioblastoma and guide treatment strategies.
PMID:40121844 | DOI:10.1016/j.cancergen.2025.03.005
Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework
BMC Bioinformatics. 2025 Mar 22;26(1):87. doi: 10.1186/s12859-025-06105-4.
ABSTRACT
BACKGROUND: Computational approaches to support rare disease diagnosis are challenging to build, requiring the integration of complex data types such as ontologies, gene-to-phenotype associations, and cross-species data into variant and gene prioritisation algorithms (VGPAs). However, the performance of VGPAs has been difficult to measure and is impacted by many factors, for example, ontology structure, annotation completeness or changes to the underlying algorithm. Assertions of the capabilities of VGPAs are often not reproducible, in part because there is no standardised, empirical framework and openly available patient data to assess the efficacy of VGPAs-ultimately hindering the development of effective prioritisation tools.
RESULTS: In this paper, we present our benchmarking tool, PhEval, which aims to provide a standardised and empirical framework to evaluate phenotype-driven VGPAs. The inclusion of standardised test corpora and test corpus generation tools in the PhEval suite of tools allows open benchmarking and comparison of methods on standardised data sets.
CONCLUSIONS: PhEval and the standardised test corpora solve the issues of patient data availability and experimental tooling configuration when benchmarking and comparing rare disease VGPAs. By providing standardised data on patient cohorts from real-world case-reports and controlling the configuration of evaluated VGPAs, PhEval enables transparent, portable, comparable and reproducible benchmarking of VGPAs. As these tools are often a key component of many rare disease diagnostic pipelines, a thorough and standardised method of assessment is essential for improving patient diagnosis and care.
PMID:40121479 | DOI:10.1186/s12859-025-06105-4
Tryptic oncopeptide secreted from the gut bacterium Cronobacter malonaticus PO3 promotes colorectal cancer
Sci Rep. 2025 Mar 22;15(1):9958. doi: 10.1038/s41598-025-94666-y.
ABSTRACT
The involvement of Cronobacter, which is frequently associated with meningitis and necrotizing enterocolitis, in human colorectal cancer remains unexplored. In this study, we isolate and characterize a novel strain of C. malonaticus designated PO3 from a fecal sample of a colon cancer patient and demonstrate its proliferative effects on colorectal cancer both in vitro and in vivo. The secretome of PO3 significantly promoted cell proliferation, as evidenced by increased cell viability, fluorescence intensity, and Ki-67 expression, without inducing cell death. Furthermore, using high-resolution mass spectrometry (HRMS), we identified a novel tryptic oncopeptide designated P506, in the PO3 secretome that promotes colorectal cancer. Synthetic P506 further stimulated human colorectal adenocarcinoma cell line HT-29 cell proliferation in a dose-dependent manner. Experiments with the BALB/c mouse model in vivo revealed that both the PO3 secretome and P506 contributed to the development of colorectal polyps and associated histological changes, including dysplasia and altered colonic architecture. These findings suggest that P506, a potent peptide from the PO3 secretome, may have oncogenic potential, promoting colorectal cancer progression.
PMID:40121280 | DOI:10.1038/s41598-025-94666-y
Hydrolytic endonucleolytic ribozyme (HYER): Systematic identification, characterization and potential application in nucleic acid manipulation
Methods Enzymol. 2025;712:197-223. doi: 10.1016/bs.mie.2025.01.033. Epub 2025 Mar 6.
ABSTRACT
Group II introns are transposable elements that can propagate in host genomes through the "copy and paste" mechanism. They usually comprise RNA and protein components for effective propagation. Recently, we found that some bacterial GII-C introns without protein components had multiple copies in their resident genomes, implicating their potential transposition activity. We demonstrated that some of these systems are active for hydrolytic DNA cleavage and proved their DNA manipulation capability in bacterial or mammalian cells. These introns are therefore named HYdrolytic Endonucleolytic Ribozymes (HYERs). Here, we provide a detailed protocol for the systematic identification and characterization of HYERs and present our perspectives on its potential application in nucleic acid manipulation.
PMID:40121073 | DOI:10.1016/bs.mie.2025.01.033
Lack of pre-movement facilitation as neurophysiological hallmark of fatigue in patients with Parkinson's disease: A single pulse TMS study
Neurobiol Dis. 2025 Mar 20:106878. doi: 10.1016/j.nbd.2025.106878. Online ahead of print.
ABSTRACT
BACKGROUND: Fatigue is a debilitating symptom in Parkinson's disease (PD), significantly affecting quality of life. Despite its prevalence, the underlying neurophysiological mechanisms remain poorly understood. Recent evidence suggests that deficits in cortical motor preparation processes may contribute to PD-related fatigue.
METHODS: This study investigated premovement facilitation (PMF), a marker of corticospinal excitability during motor preparation, in 20 healthy subjects (HS) and 28 PD patients, subdivided into those with fatigue (PDwF, n = 14) and without fatigue (PDwoF, n = 14). Participants performed a reaction time (RT) task involving thumb abduction following a visual go signal, while transcranial magnetic stimulation (TMS) was applied over the primary motor cortex (M1) at intervals of 50, 100, and 150 ms before movement onset. Motor-evoked potentials (MEPs) were recorded from the abductor pollicis brevis (APB) and the task-irrelevant abductor digiti minimi (ADM).
RESULTS: In HS and PDwoF, MEP APB amplitude increased progressively when TMS was applied at 150, 100, and 50 ms before movement onset, reflecting intact PMF, with the greater MEP APB amplitude at the shorter interval (50 ms). However, in PDwF patients, PMF was absent on the most affected side, while it remained preserved on the less affected side. Furthermore, the absence of PMF correlated with fatigue severity (FSS scores) and rigidity subscores, highlighting a link between impaired motor preparation and clinical symptoms.
CONCLUSION: These findings suggest that cortical dysfunction in motor preparation contributes to PD-related fatigue, particularly in the most affected hemisphere. The observed PMF deficits provide a potential neurophysiological marker for fatigue in PD, supporting future investigations into targeted therapeutic interventions to restore motor excitability and alleviate fatigue symptoms.
PMID:40120830 | DOI:10.1016/j.nbd.2025.106878
Cytosolic Peroxiredoxin <em>TSA1</em> Influences Acetic Acid Metabolism and pH Homeostasis in Wine Yeasts
J Agric Food Chem. 2025 Mar 22. doi: 10.1021/acs.jafc.4c13199. Online ahead of print.
ABSTRACT
Acetic acid is a key metabolite in yeast fermentation, influencing wine quality through its role in volatile acidity. In Saccharomyces cerevisiae, acetic acid production involves aldehyde dehydrogenases, primarily Ald6p during fermentation and Ald4p under respiratory conditions. However, the regulatory mechanisms of these enzymes throughout fermentation and how they differ in commonly used strains remain partially unclear. This study explores cytosolic peroxiredoxin Tsa1p as a novel regulator of acetic acid metabolism. TSA1 gene deletion revealed strain-dependent effects on acetic acid metabolism and tolerance, showing reduced production and enhanced consumption in the laboratory media. Under respiration, Ald4p-driven acetic acid production, which raises extracellular pH, was mitigated by the absence of Tsa1p. During wine fermentation, TSA1 deletion decreased the initial acetic acid surge by downregulating the ALD6 transcription and enzymatic activity. These findings establish Tsa1p as a metabolic regulator and a potential target for modulating acetic acid levels to manage volatile acidity and improve wine quality.
PMID:40120136 | DOI:10.1021/acs.jafc.4c13199
Refining Boolean models with the partial most permissive scheme
Bioinformatics. 2025 Mar 22:btaf123. doi: 10.1093/bioinformatics/btaf123. Online ahead of print.
ABSTRACT
MOTIVATION: In systems biology, modelling strategies aim to decode how molecular components interact to generate dynamical behaviour. Boolean modelling is more and more used, but the description of the dynamics generated by discrete variables with only two values may be too limited to capture certain dynamical properties. Multivalued logical models can overcome this limitation by allowing more than two levels for each component. However, multivaluing a Boolean model is challenging.
RESULTS: We present MRBM, a method for efficiently identifying the components of a Boolean model to be multivalued in order to capture specific fixed-point reachabilities in the asynchronous dynamics. To this goal, we defined a new updating scheme locating reachability properties in the most permissive dynamics. MRBM is supported by mathematical demonstrations and illustrated on a toy model and on two models of stem cell differentiation.
AVAILABILITY AND IMPLEMENTATION: The MRBM method and the BMs used in this manuscript are available on GitHub at: https://github.com/NdnBnBn/MRBM, and archived in Zenodo (doi: 10.5281/ZENODO.14979798).
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
PMID:40119940 | DOI:10.1093/bioinformatics/btaf123
New insights in metabolism modelling to decipher plant-microbe interactions
New Phytol. 2025 Mar 21. doi: 10.1111/nph.70063. Online ahead of print.
ABSTRACT
Plant disease outbreaks, exacerbated by climate change, threaten food security and environmental sustainability world-wide. Plants interact with a wide range of microorganisms. The quest for resilient agriculture requires a deep insight into the molecular and ecological interplays between plants and their associated microbial communities. Omics methods, by profiling entire molecular sets, have shed light on these complex interactions. Nonetheless, deciphering the relationships among thousands of molecular components remains a formidable challenge, and studies that integrate these components into cohesive biological networks involving plants and associated microbes are still limited. Systems biology has the potential to predict the effects of biotic and abiotic perturbations on these networks. It is therefore a promising framework for addressing the full complexity of plant-microbiome interactions.
PMID:40119556 | DOI:10.1111/nph.70063
The OsZHD1 and OsZHD2, Two Zinc Finger Homeobox Transcription Factor, Redundantly Control Grain Size by Influencing Cell Proliferation in Rice
Rice (N Y). 2025 Mar 22;18(1):20. doi: 10.1186/s12284-025-00774-8.
ABSTRACT
Grain size is vital determinant for grain yield and quality, which specified by its three-dimensional structure of seeds (length, width and thickness). The ZINC FINGER-HOMEODOMAIN (ZHD) proteins play critical roles in plant growth and development. However, the information regarding the function in reproductive development of ZHD proteins is scarce. Here, we deeply characterized the phenotype of oszhd1, oszhd2, and oszhd1oszhd2. The single mutants of OsZHD1/2 were similar with wild type. Nevertheless, the double mutant displayed dwarfism and smaller reproductive organs, and shorter, narrower, and thinner grain size. oszhd1oszhd2 revealed a significant decrease in total cell length and number, and single cell width in outer parenchyma; reducing the average width of longitudinal epidermal cells, but the length were increased in outer and inner glumes of oszhd1oszhd2 compared with wild-type, oszhd1-1, oszhd2-1, respectively. OsZHD1 and OsZHD2 encoded the nucleus protein and were distributed predominately in stem and the developing spikelets, asserting their roles in grain size. Meanwhile, yeast two-hybrid, bimolecular fluorescence complementation, and Co-immunoprecipitation assay clarified that OsZHD1 could directly interacted with OsZHD2. The differential expression analysis showed that 839 DEGs, which were down-regulated in oszhd1oszhd2 than wild type and single mutants, were mainly enriched in secondary metabolite biosynthetic, integral component of membrane, and transporter activity pathway. Moreover, it is reliable that the altered expression of cell cycle and expansion-related and grain size-related genes were observed in RNA-seq data, highly consistent with the qRT-PCR results. Altogether, our results suggest that OsZHD1/2 are functional redundancy and involved in regulating grain size by influencing cell proliferation in rice.
PMID:40119214 | DOI:10.1186/s12284-025-00774-8
Molecular mechanism of the arrestin-biased agonism of neurotensin receptor 1 by an intracellular allosteric modulator
Cell Res. 2025 Mar 21. doi: 10.1038/s41422-025-01095-7. Online ahead of print.
ABSTRACT
Biased allosteric modulators (BAMs) of G protein-coupled receptors (GPCRs) have been at the forefront of drug discovery owing to their potential to selectively stimulate therapeutically relevant signaling and avoid on-target side effects. Although structures of GPCRs in complex with G protein or GRK in a BAM-bound state have recently been resolved, revealing that BAM can induce biased signaling by directly modulating interactions between GPCRs and these two transducers, no BAM-bound GPCR-arrestin complex structure has yet been determined, limiting our understanding of the full pharmacological profile of BAMs. Herein, we developed a chemical protein synthesis strategy to generate neurotensin receptor 1 (NTSR1) with defined hexa-phosphorylation at its C-terminus and resolved high-resolution cryo-EM structures (2.65-2.88 Å) of NTSR1 in complex with both β-arrestin1 and the BAM SBI-553. These structures revealed a unique "loop engagement" configuration of β-arrestin1 coupling to NTSR1 in the presence of SBI-553, markedly different from the typical "core engagement" configuration observed in the absence of BAMs. This configuration is characterized by the engagement of the intracellular loop 3 of NTSR1 with a cavity in the central crest of β-arrestin1, representing a previously unobserved, arrestin-selective conformation of GPCR. Our findings fill the critical knowledge gap regarding the regulation of GPCR-arrestin interactions and biased signaling by BAMs, which would advance the development of safer and more efficacious GPCR-targeted therapeutics.
PMID:40118988 | DOI:10.1038/s41422-025-01095-7
Intratracheal Candida administration induced lung dysbiosis, activated neutrophils, and worsened lung hemorrhage in pristane-induced lupus mice
Sci Rep. 2025 Mar 21;15(1):9768. doi: 10.1038/s41598-025-94632-8.
ABSTRACT
Because the innate immunity might and fungi in the lungs might enhance the severity of lupus-induced diffuse alveolar hemorrhage (DAH), intraperitoneal pristane injection was performed in C57BL6 mice with intratracheal administration by Candida albicans or phosphate buffer solution (PBS). Despite the similar pristane-induced lupus (proteinuria, serum creatinine, and serum anti-dsDNA) at 5 weeks of the model, Candida administration worsened several characteristics, including mortality, body weight, serum cytokines (TNF-α and IL-6), and lung hemorrhage score, and cytokines in the lung tissue (TNF-α, IL-6, and IL-10), but not gut permeability (FITC-dextran assay), serum IL-10, immune cells in the spleens (flow cytometry analysis), and activities of peritoneal macrophages (polymerase-chain reaction). Although Candida administration reduced proteobacterial abundance and altered alpha and beta diversity compared with PBS control, lung microbiota was not different between Candida administration in pristane- and non-pristane-administered mice. Because of the prominent Gram-negative bacteria in lung microbiota and the role of neutrophils in DAH, lipopolysaccharide (LPS) with and without heat-killed Candida preparation was tested. Indeed, Candida preparation with LPS induced more severe pro-inflammatory neutrophils than LPS stimulation alone as indicated by the expression of several genes (TNF-α, IL-6, IL-1β, IL-10, Dectin-1, and NF-κB). In conclusion, the intratracheal Candida worsened pristane-induced lung hemorrhage partly through the enhanced neutrophil responses against bacteria and fungi. More studies on Candida colonization in sputum from patients with lupus-induced DAH are interesting.
PMID:40118938 | DOI:10.1038/s41598-025-94632-8