J Integr Neurosci. 2025 Feb 19;24(2):36279. doi: 10.31083/JIN36279.

NO ABSTRACT

PMID:40018783 | DOI:10.31083/JIN36279

Chem Biomed Imaging. 2024 Dec 19;3(2):111-122. doi: 10.1021/cbmi.4c00077. eCollection 2025 Feb 24.

ABSTRACT

The COVID-19 pandemic has underscored the importance of in-depth research into the proteins encoded by coronaviruses (CoV), particularly the highly conserved nonstructural CoV proteins (nsp). Among these, the nsp13 helicase of severe pathogenic MERS-CoV, SARS-CoV-2, and SARS-CoV is one of the most preserved CoV nsp. Utilizing single-molecule FRET, we discovered that MERS-CoV nsp13 unwinds DNA in distinct steps of about 9 bp when ATP is employed. If a different nucleotide is introduced, these steps diminish to 3-4 bp. Dwell-time analysis revealed 3-4 concealed steps within each unwinding process, which suggests the hydrolysis of 3-4 dTTP. Combining our observations with previous studies, we propose an unwinding model of CoV nsp13 helicase. This model suggests that the elongated and adaptable 1B-stalk of nsp13 may enable the 1B remnants to engage with the unwound single-stranded DNA, even as the helicase core domain has advanced over 3-4 bp, thereby inducing accumulated strain on the nsp13-DNA complex. Our findings provide a foundational framework for determining the unwinding mechanism of this unique helicase family.

PMID:40018651 | PMC:PMC11863148 | DOI:10.1021/cbmi.4c00077

Front Mol Neurosci. 2025 Feb 13;18:1544971. doi: 10.3389/fnmol.2025.1544971. eCollection 2025.

ABSTRACT

INTRODUCTION: Growing recognition of microglia's role in neurodegenerative disorders has accentuated the need to characterize microglia profiles and their influence on pathogenesis. To understand changes observed in the microglial profile during the progression of synucleinopathies, microglial gene expression and DNA methylation were examined in the mThy1-α-synuclein mouse model.

METHODS: Disease progression was determined using behavioral tests evaluating locomotor deficits before DNA and RNA extraction at 7 and 10 months from isolated microglia for enzymatic methyl-sequencing and RNA-sequencing.

RESULTS: Pathway analysis of these changes at 7 months indicates a pro-inflammatory profile and changes in terms related to synaptic maintenance. Expression and methylation at both 7 and 10 months included terms regarding mitochondrial and metabolic stress. While behavior symptoms progressed at 10 months, we see many previously activated pathways being inhibited in microglia at a later stage, with only 8 of 53 shared pathways predicted to be directionally concordant. Despite the difference in pathway directionality, 21 of the 22 genes that were differentially expressed and annotated to differentially methylated regions at both 7 and 10 months had conserved directionality changes.

DISCUSSION: These results highlight a critical period in disease progression, during which the microglia respond to α-synuclein, suggesting a transition in the role of microglia from the early to late stages of the disease.

PMID:40018011 | PMC:PMC11865073 | DOI:10.3389/fnmol.2025.1544971

Front Oral Health. 2025 Feb 13;6:1543667. doi: 10.3389/froh.2025.1543667. eCollection 2025.

ABSTRACT

INTRODUCTION: Derivatives from Saccharomyces cerevisiae yeast including yeast extracts and yeast cell walls are sustainable sources of valuable nutrients, including dietary fibers and proteins. Previous studies have shown that certain components from these yeast derivatives can inhibit the growth of harmful intestinal bacteria and promote the growth of beneficial bacteria. However, the effects of yeast derivatives on oral health have not yet been investigated.

METHODS: An in vitro oral biofilm model was employed to examine the impacts of yeast derivatives on the oral microbiota and their potential benefits for maintaining oral homeostasis. The model incorporated dental plaque donor material from both healthy and periodontitis diagnosed individuals. Biofilm formation, density, and microbial composition were quantified. Additionally, the production of short-chain fatty acids in the biofilm supernatants was measured.

RESULTS: Yeast extracts had only minor effects on oral biofilm formation. In contrast, yeast cell wall derivatives, which are rich in polysaccharides such as beta-glucans and mannans, significantly reduced the density of the oral biofilms in vitro. This reduction in biofilm density was associated with an overall shift in the bacterial community composition, including an increase in beneficial bacteria and a decrease in the abundance of Tannerella forsythia, an important species involved in bacterial coaggregation and the development and maturation of the oral biofilm. Furthermore, the yeast cell wall derivatives decreased the production of short-chain fatty acids, including acetic and butyric acid. These findings were consistent across both healthy and periodontitis microbiomes.

CONCLUSION: This study has demonstrated the potential of yeast cell wall derivatives to positively impact oral health by significantly reducing biofilm density, modulating the oral microbial composition, and decreasing the production of short-chain fatty acids. The observed effects highlight the promising applications of these yeast-based compounds as an approach to managing oral diseases. Further research is needed to fully elucidate the mechanisms of action and explore the clinical potential of yeast cell wall derivatives in promoting and maintaining oral health.

PMID:40017617 | PMC:PMC11865069 | DOI:10.3389/froh.2025.1543667

Alzheimers Res Ther. 2025 Feb 27;17(1):52. doi: 10.1186/s13195-025-01697-8.

ABSTRACT

BACKGROUND: Recent studies have focused on improving our understanding of gut microbiome dysbiosis and its impact on cognitive function. However, the relationship between gut microbiome composition, accelerated brain atrophy, and cognitive function has not yet been fully explored.

METHODS: We recruited 292 participants from South Korean memory clinics to undergo brain magnetic resonance imaging, clinical assessments, and collected stool samples. We employed a pretrained brain age model- a measure associated with neurodegeneration. Using cluster analysis, we categorized individuals based on their microbiome profiles and examined the correlations with brain age, Mental State Examination (MMSE) scores, and the Clinical Dementia Rating Sum of Box (CDR-SB).

RESULTS: Two clusters were identified in the microbiota at the phylum level that showed significant differences on a few microbiotas phylum. Greater gut microbiome dysbiosis was associated with worse cognitive function including MMSE and CDR-SB; this effect was partially mediated by greater brain age even when accounting for chronological age, sex, and education.

CONCLUSIONS: Our findings indicate that brain age mediates the link between gut microbiome dysbiosis and cognitive performance. These insights suggest potential interventions targeting the gut microbiome to alleviate age-related cognitive decline.

PMID:40016766 | DOI:10.1186/s13195-025-01697-8

BMC Biol. 2025 Feb 27;23(1):62. doi: 10.1186/s12915-025-02168-0.

ABSTRACT

BACKGROUND: Melanin pigmentation in oocytes is a critical feature for both the esthetic and developmental aspects of oocytes, influencing their polarity and overall development. Despite substantial knowledge of melanogenesis in melanocytes and retinal pigment epithelium cells, the molecular mechanisms underlying oocyte melanogenesis remain largely unknown.

RESULTS: Here, we compare the oocytes of wild-type, tyr-/- and mitf-/- Xenopus tropicalis and found that mitf-/- oocytes exhibit normal melanin deposition at the animal pole, whereas tyr-/- oocytes show no melanin deposition at this site. Transmission electron microscopy confirmed that melanogenesis in mitf-/- oocytes proceeds normally, similar to wild-type oocytes. Transcriptomic analysis revealed that mitf-/- oocytes still express melanogenesis-related genes, enabling them to complete melanogenesis. Additionally, in Xenopus tropicalis oocytes, the expression of the MiT subfamily factor tfe3 is relatively high, while tfeb, mitf, and tfec levels are extremely low. The expression pattern of tfe3 is similar to that of tyr and other melanogenesis-related genes. Thus, melanogenesis in Xenopus tropicalis oocytes is independent of Mitf and may be regulated by other MiT subfamily factors such as Tfe3, which control the expression of genes like tyr, dct, and tyrp1. Furthermore, transcriptomic data revealed that changes in the expression of genes related to mitochondrial cloud formation represent the most significant molecular changes during oocyte development.

CONCLUSIONS: Overall, these findings suggest that further elucidation of Tyr-dependent and Mitf-independent mechanisms of melanin deposition at the animal pole will enhance our understanding of melanogenesis and Oogenesis.

PMID:40016733 | DOI:10.1186/s12915-025-02168-0

Cell Res. 2025 Feb 28. doi: 10.1038/s41422-025-01084-w. Online ahead of print.

ABSTRACT

The spliceosome, a highly dynamic macromolecular assembly, catalyzes the precise removal of introns from pre-mRNAs. Recent studies have provided comprehensive structural insights into the step-wise assembly, catalytic splicing and final disassembly of the spliceosome. However, the molecular details of how the spliceosome recognizes and rejects suboptimal splicing substrates remained unclear. Here, we show cryo-electron microscopy structures of spliceosomal quality control complexes from a thermophilic eukaryote, Chaetomium thermophilum. The spliceosomes, henceforth termed B*Q, are stalled at a catalytically activated state but prior to the first splicing reaction due to an aberrant 5' splice site conformation. This state is recognized by G-patch protein GPATCH1, which is docked onto PRP8-EN and -RH domains and has recruited the cognate DHX35 helicase to its U2 snRNA substrate. In B*Q, DHX35 has dissociated the U2/branch site helix, while the disassembly helicase DHX15 is docked close to its U6 RNA 3'-end substrate. Our work thus provides mechanistic insights into the concerted action of two spliceosomal helicases in maintaining splicing fidelity by priming spliceosomes that are bound to aberrant splice substrates for disassembly.

PMID:40016598 | DOI:10.1038/s41422-025-01084-w

Commun Med (Lond). 2025 Feb 27;5(1):49. doi: 10.1038/s43856-025-00764-3.

ABSTRACT

BACKGROUND: Accurately recognizing that a person may be dying is central to improving their experience of care at the end-of-life. However, predicting dying is frequently inaccurate and often occurs only hours or a few days before death.

METHODS: We performed urinary metabolomics analysis on patients with lung cancer to create a metabolite model to predict dying over the last 30 days of life.

RESULTS: Here we show a model, using only 7 metabolites, has excellent accuracy in the Training cohort n = 112 (AUC = 0·85, 0·85, 0·88 and 0·86 on days 5, 10, 20 and 30) and Validation cohort n = 49 (AUC = 0·86, 0·83, 0·90, 0·86 on days 5, 10, 20 and 30). These results are more accurate than existing validated prognostic tools, and uniquely give accurate predictions over a range of time points in the last 30 days of life. Additionally, we present changes in 125 metabolites during the final four weeks of life, with the majority exhibiting statistically significant changes within the last week before death.

CONCLUSIONS: These metabolites identified offer insights into previously undocumented pathways involved in or affected by the dying process. They not only imply cancer's influence on the body but also illustrate the dying process. Given the similar dying trajectory observed in individuals with cancer, our findings likely apply to other cancer types. Prognostic tests, based on the metabolites we identified, could aid clinicians in the early recognition of people who may be dying and thereby influence clinical practice and improve the care of dying patients.

PMID:40016594 | DOI:10.1038/s43856-025-00764-3

Lab Anim (NY). 2025 Feb 27. doi: 10.1038/s41684-025-01506-7. Online ahead of print.

ABSTRACT

HSALR mice are the most broadly used animal model for studying myotonic dystrophy type I (DM1). However, so far, HSALR preclinical studies have often excluded female mice or failed to document the biological sex of the animals. This leaves an unwanted knowledge gap concerning the differential development of DM1 in males and females, particularly considering that the disease has a different clinical presentation in men and women. Here we compared typical functional measurements, histological features, molecular phenotypes and biochemical plasma profiles in the muscles of male and female HSALR mice in search of any significant between-sex differences that could justify this exclusion of female mice in HSALR studies and, critically, in candidate therapy assays performed with this model. We found no fundamental differences between HSALR males and females during disease development. Both sexes presented comparable functional and tissue phenotypes, with similar molecular muscle profiles. The only sex differences and significant interactions observed were in plasma biochemical parameters, which are also intrinsically variable in patients with DM1. In addition, we tested the influence of age on these measurements. We therefore suggest including female HSALR mice in regular DM1 studies, and recommend documenting the sex of animals, especially in studies focusing on metabolic alterations. This will allow researchers to detect and report any potential differences between male and female HSALR mice, especially regarding the efficacy of experimental treatments that could be relevant to patients with DM1.

PMID:40016516 | DOI:10.1038/s41684-025-01506-7

Nat Med. 2025 Feb 27. doi: 10.1038/s41591-025-03530-z. Online ahead of print.

ABSTRACT

Brain metastases frequently develop in patients with non-small cell lung cancer (NSCLC) and are a common cause of cancer-related deaths, yet our understanding of the underlying human biology is limited. Here we performed multimodal single-nucleus RNA and T cell receptor, single-cell spatial and whole-genome sequencing of brain metastases and primary tumors of patients with treatment-naive NSCLC. Chromosomal instability (CIN) is a distinguishing genomic feature of brain metastases compared with primary tumors, which we validated through integrated analysis of molecular profiling and clinical data in 4,869 independent patients, and a new cohort of 12,275 patients with NSCLC. Unbiased analyses revealed transcriptional neural-like programs that strongly enriched in cancer cells from brain metastases, including a recurring, CINhigh cell subpopulation that preexists in primary tumors but strongly enriched in brain metastases, which was also recovered in matched single-cell spatial transcriptomics. Using multiplexed immunofluorescence in an independent cohort of treatment-naive pairs of primary tumors and brain metastases from the same patients with NSCLC, we validated genomic and tumor-microenvironmental findings and identified a cancer cell population characterized by neural features strongly enriched in brain metastases. This comprehensive analysis provides insights into human NSCLC brain metastasis biology and serves as an important resource for additional discovery.

PMID:40016452 | DOI:10.1038/s41591-025-03530-z

EMBO Rep. 2025 Feb 27. doi: 10.1038/s44319-025-00389-6. Online ahead of print.

NO ABSTRACT

PMID:40016427 | DOI:10.1038/s44319-025-00389-6

NPJ Syst Biol Appl. 2025 Feb 27;11(1):21. doi: 10.1038/s41540-025-00498-x.

ABSTRACT

More than 20% of the population across the world is affected by non-communicable inflammatory skin diseases including psoriasis, atopic dermatitis, hidradenitis suppurativa, rosacea, etc. Many of these chronic diseases are painful and debilitating with limited effective therapeutic interventions. This study aims to identify common regulatory pathways and master regulators that regulate the molecular pathogenesis of inflammatory skin diseases. We designed an integrative systems biology framework to identify the significant regulators across several diseases. Network analytics unraveled 55 high-value proteins as significant regulators in molecular pathogenesis which can serve as putative drug targets for more effective treatments. We identified IKZF1 as a shared master regulator in hidradenitis suppurativa, atopic dermatitis, and rosacea with known disease-derived molecules for developing efficacious combinatorial treatments for these diseases. The proposed framework is very modular and indicates a significant path of molecular mechanism-based drug development from complex transcriptomics data and other multi-omics data.

PMID:40016271 | DOI:10.1038/s41540-025-00498-x

Nat Commun. 2025 Feb 27;16(1):2020. doi: 10.1038/s41467-025-57034-y.

ABSTRACT

G protein-coupled receptors (GPCRs) constitute a functionally diverse protein family and are targets for a broad spectrum of pharmaceuticals. Technological progress in X-ray crystallography and cryogenic electron microscopy has enabled extensive, high-resolution structural characterisation of GPCRs in different conformational states. However, as highly dynamic events underlie GPCR signalling, a complete understanding of GPCR functionality requires insights into their conformational dynamics. Here, we present a large dataset of molecular dynamics simulations covering 60% of currently available GPCR structures. Our analysis reveals extensive local "breathing" motions of the receptor on a nano- to microsecond timescale and provides access to numerous previously unexplored receptor conformational states. Furthermore, we reveal that receptor flexibility impacts the shape of allosteric drug binding sites, which frequently adopt partially or completely closed states in the absence of a molecular modulator. We demonstrate that exploring membrane lipid dynamics and their interaction with GPCRs is an efficient approach to expose such hidden allosteric sites and even lateral ligand entrance gateways. The obtained insights and generated dataset on conformations, allosteric sites and lateral entrance gates in GPCRs allows us to better understand the functionality of these receptors and opens new therapeutic avenues for drug-targeting strategies.

PMID:40016203 | DOI:10.1038/s41467-025-57034-y

Gut. 2025 Feb 27:gutjnl-2024-333944. doi: 10.1136/gutjnl-2024-333944. Online ahead of print.

ABSTRACT

BACKGROUND: Despite the success of immune checkpoint blockade, a lack of understanding of the hepatocellular carcinoma (HCC) immune microenvironment impedes its development.

OBJECTIVE: We aim to elucidate the essential function of E-twenty-six-specific sequence variant 5 (ETV5) in regulating the immune microenvironment in HCC.

DESIGN: Humanised mouse models, murine orthotopic models and diethylnitrosamine/carbon tetrachloride (DEN/CCl4)-induced HCC models were used to examine the function of ETV5. The downstream targets of ETV5 were screened using chromatin immunoprecipitation sequencing, CUT&Tag and RNA sequencing. Immune cells were examined using flow cytometry and immunofluorescence. S100 calcium-binding protein A9 (S100A9) was targeted by neutralising antibodies.

RESULTS: Overexpression of ETV5 in HCC cells facilitated HCC metastasis and immune escape by recruiting and enhancing the immunosuppressive capabilities of polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs). Mechanistically, ETV5 transactivated programmed death ligand 1 (PD-L1) and S100A9 expression. Inhibition of S100A9 or myeloid-specific knockout of toll-like receptor 4 (TLR4)/receptor for advanced glycation endproducts (RAGE), the receptors of S100A9, impeded ETV5-induced PMN-MDSC recruitment. Meanwhile, S100A9 within the tumour microenvironment elevated ETV5 expression via the extracellular signal-regulated kinase (ERK)/nuclear factor-kappa B pathway. Additionally, ETV5 transcriptionally upregulated PD-L1 in MDSCs as well, thereby augmenting their immunosuppressive functions. Myeloid-specific Etv5 knockout attenuated HCC progression. We developed monoclonal neutralising-S100A9 antibodies that effectively inhibited ETV5-mediated PMN-MDSC infiltration. Synergistic application of anti-S100A9 or TLR4/RAGE inhibitors with anti-PD-L1 therapy significantly suppressed ETV5-mediated HCC progression.

CONCLUSION: ETV5 facilitates HCC progression and metastasis by promoting the recruitment, infiltration and activation of PMN-MDSCs. Synergistic application of anti-S100A9 or TLR4/RAGE inhibitors with anti-PD-L1 therapy holds great promise as an effective combinational treatment strategy for ETV5-positive HCC.

PMID:40015948 | DOI:10.1136/gutjnl-2024-333944

J Proteomics. 2025 Feb 25:105414. doi: 10.1016/j.jprot.2025.105414. Online ahead of print.

ABSTRACT

Acute pancreatitis (AP) is a common acute abdominal condition in clinical practice, associated with high morbidity and mortality rates. Forsythia constitutes a component of traditional Chinese medicinal decoctions used for clinical AP treatment; however, the efficacy of its active monomer in treating AP has yet to be completely substantiated. Here, we engineered an AP cell and mouse model by administering a combination of caerulein and LPS. In vitro experiments utilizing AR42J cells demonstrated that forsythoside B (FST·B) was the most effective monomer in mitigating cellular inflammation. Subsequently, a comprehensive evaluation of FST·B concentrations and efficacy was performed in animal models. Next Mass spectrometry analysis of pancreatic from AP mice treated with 50 mg/kg FST·B was conducted to elucidate its primary regulatory molecular signaling and key targets. FST·B effectively mitigated pathological damage in mice with acute pancreatitis, leading to a reduction in the expression of inflammatory cytokines in both pancreatic tissue and serum. Proteomics and phosphoproteomic profiles revealed that FST·B significantly enhanced the level of oxidative phosphorylation and spliceosome pathway in the AP mice. This research provides initial evidence of the regulatory molecular signals and targets of FST·B in AP, laying a potential foundation for its clinical use in treating AP. SIGNIFICANCE: Acute pancreatitis (AP) is a common acute abdominal condition in clinical practice, associated with high morbidity and mortality rates, and the global incidence of AP has increased by approximately 25 % over the past 15 years. Despite the complexity of AP's causes and the high susceptibility of proteins to degradation during lesions, systems biology studies, such as proteomics, have been limited in investigating the molecular mechanisms involved in its pharmacological treatment. Forsythoside B, a phenylethanol glycoside isolated from the air-dried fruit of forsythia, is a traditional oriental anti-inflammatory drug commonly used in clinical practice. We demonstrated in the AP mouse model that forsythoside B can alleviate pancreatic inflammatory damage in vivo. To elucidate the molecular mechanisms underlying the anti-inflammatory effect of forsythoside B, a comprehensive proteomic and phosphoproteomic analysis was conducted on AP mice models prior to and subsequent to forsythoside B intervention. Finally, 1640 significantly differentially expressed proteins, 1448 significantly differentially expressed phosphoproteins corresponding to 2496 significantly differentially expressed phosphosites were identified. Functional analysis revealed that forsythoside B significantly enhanced the level of oxidative phosphorylation in the AP mice in proteomic profiles, and the spliceosome pathway at the phosphorylation level was significantly affected by forsythoside B. This research provides initial evidence of the regulatory molecular signals and targets of forsythoside B in AP, laying a potential foundation for its clinical use in treating AP.

PMID:40015372 | DOI:10.1016/j.jprot.2025.105414

Microbiol Res. 2025 Feb 25;295:128112. doi: 10.1016/j.micres.2025.128112. Online ahead of print.

ABSTRACT

Heavy metals (HMs) toxicity finds substantial plant health risk, affecting germination, growth, productivity, and survival. HMs exposure can interrupt cellular function, increase oxidative stress and affect physiological processes. Plants have developed array of adaptive responses, with proteins playing key role in detecting, signalling, and mitigating metal-induced stress. Under stress, posttranslational modifications, including phosphorylation, ubiquitination, glycosylation and acetylation, are essential regulators of protein stability, localization, and function. This review examines the comprehensive profiling of PTMs in HMs stress responses, including how PTMs regulate the signalling pathways, degradation pathways, and TFs modulation. Specifically, discuss the role of phosphorylation, ubiquitination, and sumoylation, neddylation, lipidation, and S-nitrosylation in specifically under HMs stress with PTMs regulation of antioxidant enzymes, stress proteins, metal transporters and chelators of detoxification. This review illustrates the crosstalk of PTMs to show how synergistic interactions regulate protein stability, activity, and localization upon HMs stress. In cross talk, ubiquitination often starts from phosphorylation to subsequent degradation of proteins in a timely and reversible way to trigger stress responses. However, sumoylation stabilizes key transcription factors that are rapidly dephosphorylated and integral in metal detoxification, form a synergistic combination with phosphorylation to maintain their activity. It explains the future research directions, focusing on PTM engineering to generate stress tolerant plant varieties. By studying the response of plants to HMs stress through PTMs, emphasizes the relevance of PTMs towards plant resilience and advocates for systems biology integrative approach to advancing plant stress biology.

PMID:40015082 | DOI:10.1016/j.micres.2025.128112

ACS Appl Bio Mater. 2025 Feb 27. doi: 10.1021/acsabm.4c01621. Online ahead of print.

ABSTRACT

Bacterial microcompartments (BMCs) are self-assembling protein shell structures that are widely investigated across a broad range of biological and abiotic chemistry applications. A central challenge in BMC research is the targeted capture of enzymes during shell assembly. While crystallography and cryo-EM techniques have been successful in determining BMC shell structures, there has been only limited success in visualizing the location of BMC-captured enzyme cargo. Here, we demonstrate the opportunity to use small-angle X-ray scattering (SAXS) and pair distance distribution function (PDDF) measurements combined with quantitative comparison to coordinate structure models as an approach to characterize BMC shell structures in solution conditions directly relevant to biochemical function. Using this approach, we analyzed BMC shells from Haliangium ochraceum (HO) that were isolated following expression in E. coli. The analysis allowed the BMC shell structures and the extent of encapsulated enzyme cargo to be identified. Notably, the results demonstrate that HO-BMC shells adventitiously capture significant amounts of cytoplasmic cargo during assembly in E. coli. Our findings highlight the utility of SAXS/PDDF analysis for evaluating BMC architectures and enzyme encapsulation, offering valuable insights for designing BMC shells as platforms for biological and abiotic catalyst capture within confined environments.

PMID:40014870 | DOI:10.1021/acsabm.4c01621

ACS Nano. 2025 Feb 27. doi: 10.1021/acsnano.4c16988. Online ahead of print.

ABSTRACT

Exosomes present in the circulatory system demonstrate considerable promise for the diagnosis and treatment of diseases. Nevertheless, the complex nature of blood samples and the prevalence of highly abundant proteins pose a significant obstacle to prompt and effective isolation and functional evaluation of exosomes from blood. Here, we present a fully integrated lab-on-a-disc equipped with two nanofilters, also termed iExoDisc, which facilitates automated isolation of exosomes from 400 μL blood samples within 45 min. By integrating the plasma separation module, highly abundant protein removal module, and nanopore membrane-based total isolation module, the resulting exosomes exhibited significantly increased purity (∼3-6-fold) compared to conventional ultracentrifugation and polymer precipitation. Additionally, we then successfully performed nontargeted and targeted glycan profiling on exosomes derived from clinical triple-negative breast cancer (TNBC) patients using MALDI-TOF-MS and lectin microarray containing 56 kinds of lectins. The findings from both methodologies indicated that galactosylation and sialylation exhibit potential as diagnostic indicators for TNBC. Finally, by utilizing the exosome-specific glycosylated protein CD63 as a proof-of-concept, we successfully realized the integration of point-of-care on-chip exosome separation and in situ detection with 2 h. Thus, the iExoDisc provides a potential approach to early cancer detection, liquid biopsy, and point-of-care diagnosis.

PMID:40014808 | DOI:10.1021/acsnano.4c16988

Science. 2025 Feb 27:eadv9789. doi: 10.1126/science.adv9789. Online ahead of print.

ABSTRACT

RNA-guided systems provide remarkable versatility, enabling diverse biological functions. Through iterative structural and sequence homology-based mining starting with a guide RNA-interaction domain of Cas9, we identified a family of RNA-guided DNA-targeting proteins in phage and parasitic bacteria. Each system consists of a Tandem Interspaced Guide RNA (TIGR) array and a TIGR-associated (Tas) protein containing a Nop domain, sometimes fused to HNH (TasH) or RuvC (TasR) nuclease domains. We show that TIGR arrays are processed into 36-nt RNAs (tigRNAs) that direct sequence-specific DNA binding through a tandem-spacer targeting mechanism. TasR can be reprogrammed for precise DNA cleavage, including in human cells. The structure of TasR reveals striking similarities to box C/D snoRNPs and IS110 RNA-guided transposases, providing insights into the evolution of diverse RNA-guided systems.

PMID:40014690 | DOI:10.1126/science.adv9789

Science. 2025 Feb 27:eadk3248. doi: 10.1126/science.adk3248. Online ahead of print.

ABSTRACT

During infections, CD4+ Foxp3+ regulatory T (Treg) cells must control autoreactive CD4+ conventional T (Tconv) cell responses against self-peptide antigens while permitting those against pathogen-derived "nonself" peptides. We defined the basis of this selectivity using mice in which Treg cells reactive to a single prostate-specific self-peptide were selectively depleted. We found that self-peptide-specific Treg cells were dispensable for the control of Tconv cells of matched specificity at homeostasis. However, they were required to control such Tconv cells and prevent autoimmunity toward the prostate following exposure to elevated self-peptide during infection. Importantly, the Treg cell response to self-peptide did not impact protective Tconv cell responses to a pathogen-derived peptide. Thus, self-peptide-specific Treg cells promoted self-nonself discrimination during infection by selectively controlling Tconv cells of shared self-specificity.

PMID:40014689 | DOI:10.1126/science.adk3248