PLoS Negl Trop Dis. 2025 Jul 7;19(7):e0013241. doi: 10.1371/journal.pntd.0013241. Online ahead of print.

ABSTRACT

BACKGROUND: To achieve sustainable and integrated control of schistosomiasis, it necessitates the implementation of comprehensive strategies, where effective vaccines could play a pivotal role. The limited identification and validation of schistosome antigens hinders the progress of vaccine development for the disease. Schistosome cysteine proteinases are considered as important targets for novel anti-schistosomiasis immunoprophylaxis due to their primary role in nutrient absorption. Previous research on the Schistosoma japonicum degradome has identified a group of cathepsin L-like proteases (SjCLs) that are up-regulated in hepatic schistosomula and adult worms.

METHODS/FINDINGS: In this study, five recombinant proteins representing the mature form of these SjCLs, designated as rSjCL1-5, were successfully produced. Mice immunized with the rSjCLs were subsequently challenged with cercariae to evaluate the immunoprotective efficacy of these proteins. The expression and localization of SjCL1 were analyzed by qRT-PCR, western blotting and immunofluorescence assays. Among these five rSjCLs, only the immunization with rSjCL1 conferred partial protection to the mice against S. japonicum infection, resulting in a reduction in worm burden by 34.9% ~ 38.0% and a decrease of egg burden by 46.2% ~ 48.3%. This immunization also effectively mitigated body weight loss and hepatomegaly in the challenged mice. SjCL1 was primarily localized along the intestinal intima of hepatic schistosomulum, as well as male and female adults, and on the tegument of male adults. The mature form of SjCL1 was detected in the excretory/secretory products of the parasites. Hepatic schistosomulum treated with SjCL1 antibodies in vitro showed significant growth retardation, although remained viable and developed intestinal heme pigmentation, indicative of hemoglobin digestion.

CONCLUSIONS/SIGNIFICANCE: Our study revealed that SjCL1 is essential for normal parasite growth and shed new light for the development of schistosomiasis vaccines targeting cathepsins, which play a key role in the early intra-mammalian stages of schistosomes.

PMID:40623040 | DOI:10.1371/journal.pntd.0013241

J Vis Exp. 2025 Jun 20;(220). doi: 10.3791/67174.

ABSTRACT

The drug discovery process is a rigorous, time-consuming, and expensive operation. The computational approach in drug discovery allows researchers to prioritize the most promising compounds for further testing, which would greatly reduce the required resources, leading to an increment of the overall efficiency in the drug discovery pipelines. Structure-based drug discovery is a common approach that requires the structural information of the target protein in a three-dimensional format. However, the current limitation of most computer-aided drug discovery strategies is their inability to introduce the flexibility and dynamics of the target protein structure during the ligand-protein docking simulation. While both induced fit docking and ensemble-based docking aim to address protein flexibility in the docking procedure, the latter can provide a more comprehensive view of dynamic protein behavior by incorporating multiple conformations throughout the simulation. In this report, we demonstrate and discuss the application of a technique called ensemble-based docking analysis that indirectly introduces the target protein structure's flexibility and dynamics in the molecular docking process. The protein and ligand selected for ensemble-based docking studies were lysozyme and Flovokawain B (FB), respectively. FB has been previously reported to have binding activity with lysozyme. A molecular dynamics (MD) simulation was performed on lysozyme in the presence of water, and the total energy, root-mean-square deviation (RMSD), and root-mean-square fluctuation (RMSF) were examined. Conformation clustering was generated based on several clustering cutoff values and was chosen for additional docking analysis with FB. Cluster no 2 gives the lowest binding energy at -29.37 kJ/mol. Molecular docking images were generated to anticipate the presence of binding forces. By incorporating the structural dynamics of the protein, the ensemble-based docking approach can better capture the range of possible binding scenarios, leading to more reliable predictions of binding outcomes.

PMID:40622888 | DOI:10.3791/67174

Hepatology. 2025 Jul 4. doi: 10.1097/HEP.0000000000001451. Online ahead of print.

ABSTRACT

BACKGROUND AND AIMS: Aging-induced degenerative changes in the liver are not inherently pathologic but pose an increased risk for liver diseases. However, the molecular mechanisms underlying aging-induced hepatic dyshomeostasis remain incompletely characterized. Here, we investigate how aging alters liver architecture, cellular communication, and hepatocyte zonation.

APPROACH AND RESULTS: Histological analyses of aged (>24-month-old) wild-type mouse livers showed no fibrosis, but a uniform cellular enlargement compared to young (2-month-old) mouse livers. For an unbiased characterization of aging-driven changes, we used single-nucleus RNA sequencing and found that aged livers had altered cell-cell interactions and hepatocyte zonation with zone-specific transcriptomic changes. Immunostaining confirmed aging-induced expansion of ASS1+, CYP2E1+ and GS+ hepatic zones, and an aberrant expression of ASS1+-GS+ "bi-zonal" hepatocytes, causing loss of distinct zonation. Mechanistically, this breakdown was associated with downregulation of key zonation regulators (Ctnnb1, Foxo1, Tcf7l2) and compensatory alterations in Wnt and Rspo3 signaling from NPCs. To assess translational relevance, liver biopsies from young (≤25YO) and aged (>60YO) human donors were analyzed, revealing comparable zonal alterations and supporting the conservation of these aging-associated phenotypes across species.

CONCLUSION: These findings reveal that aging causes loss of distinct hepatic zonation and alters intercellular communication through widespread transcriptional and architectural remodeling of liver cell types. The emergence of bi-zonal hepatocytes and expansion of hepatic zones in aged livers represent key hallmarks of hepatic aging. Our study provides new insights into mechanisms of liver aging and may inform therapeutic strategies targeting age-associated liver dysfunction.

PMID:40622856 | DOI:10.1097/HEP.0000000000001451

J Exp Med. 2025 Sep 1;222(9):e20240677. doi: 10.1084/jem.20240677. Epub 2025 Jul 7.

ABSTRACT

Obesity worsens inflammatory arthritis severity, even in non-load-bearing joints, but the mechanism is unknown. Here, we show that there is an immunological mechanism mediated by T cells in adipose tissue. Using an antigen-induced arthritis model with trackable, arthritis-inducing CD8+ OT-I T cells, we found that OT-I T cells home to visceral adipose tissue (VAT) and expand there in the obese high-fat diet (HFD) context. Transplant of VAT from arthritic mice increased arthritis severity in naïve recipient mice and was ameliorated by CD8 T cell depletion. Bulk RNA sequencing identified pro-inflammatory changes to OT-I T cells in VAT characterized by increased IFN α and γ signaling after HFD. Intraperitoneal injection of IFNα, but not IFNγ, expanded CD8 T cell numbers in VAT. HFD-induced expansion of VAT CD8 T cells was ameliorated with global Ifnar1 deletion, and importantly, genetic deletion of Ifnar1 in T cells decreased arthritis severity in obese mice. These results provide a mechanistic explanation of how obesity worsens autoimmunity.

PMID:40622306 | DOI:10.1084/jem.20240677

Chem Commun (Camb). 2025 Jul 7. doi: 10.1039/d5cc02404h. Online ahead of print.

ABSTRACT

Late-stage protein modification strategies have emerged as transformative approaches for enhancing protein functionality and expanding the applications of proteins in biological research and drug development. In recent years, several different modification methods have been developed based on the reaction characteristics of different groups. In this highlight article, we review the recent advancements in late-stage protein modification methodologies that have enabled the creation of a wide array of modified proteins. These methods have significantly advanced the field of protein engineering by addressing key challenges and enhancing the versatility of protein modification techniques.

PMID:40622108 | DOI:10.1039/d5cc02404h

mBio. 2025 Jul 7:e0050025. doi: 10.1128/mbio.00500-25. Online ahead of print.

ABSTRACT

In many bacteria, polyphosphate kinase (PPK) enzymes use ATP to synthesize polyphosphate (polyP) in response to cellular stress. These chains of inorganic phosphates are joined by high-energy bonds and can reach hundreds of residues in length. PolyP plays diverse functions in helping bacteria adjust to changing environmental conditions. However, the molecular mechanisms underlying these functions are poorly understood. In eukaryotic cells, polyacidic serine- and lysine-rich (PASK) motifs of proteins can mediate binding to polyP chains. Whereas PASK motifs are relatively common in yeast and human cells, we report that these sequences are rare in bacteria commonly used for polyP research. Thus, to identify novel polyP-binding proteins in Escherichia coli, we carried out a screen and identified seven novel targets with links to translation control and ribosome biogenesis. For two targets, the GTPase activating protein YihI and the ribonuclease Rnr, we mapped the regions of polyP interaction to non-PASK sequences and identified lysine residues critical for binding. We found that deletion of rnr suppressed the slow-growth phenotype of Δppk mutants grown on minimal media. Conversely, ppk deletion resulted in decreased Rnr protein expression. These phenotypes were dependent on the polyP-binding region of Rnr but independent of polyP binding itself, suggesting a complex interplay between PPK and Rnr function in E. coli. Overall, our work provides new insights into the scope of polyP-binding proteins and extends the connections between polyP and the regulation of protein translation in E. coli.

IMPORTANCE: In bacteria, polyphosphate (polyP) molecules are important regulators of cellular stress responses. Accordingly, cells that cannot make polyP display defects in processes that are important for bacterial survival, infection, and antibiotic resistance. The molecular mechanisms by which polyP exerts its functions are poorly understood. In eukaryotic cells, there has been much interest in the identification and characterization of polyP-binding proteins that act as effectors of polyP in vivo. By comparison, much less is known about polyP-binding proteins in bacteria. In this study, we take advantage of large-scale collections of Escherichia coli strains expressing epitope-tagged proteins to carry out the first systematic search for bacterial polyP-binding proteins. We describe seven novel polyP-binding proteins with links to ribosome biogenesis or translation. We further identify a complex genetic and molecular interplay between polyphosphate kinase, the enzyme that makes polyP, and the polyP-binding protein RNase R. Given the importance of translational control for bacteria survival, investigation of these pathways is expected to reveal new targets that can be leveraged for therapeutic exploration.

PMID:40621900 | DOI:10.1128/mbio.00500-25

Genome Biol Evol. 2025 Jul 7:evaf134. doi: 10.1093/gbe/evaf134. Online ahead of print.

ABSTRACT

Viral host-switching from host H1 to host H2 is often associated with changes in viral evolutionary rate r. The pre-switching rate r1 in H1 may stay the same or increase/decrease to a new rate r2 in H2 during the host-switching and host-adapting process, depending on the difference between H1 and H2. The changing rate has previously been modeled by a linear function when the time interval is short but is better modeled by a sigmoidal function. I present the mathematical model, illustrate its application, and implement the rooting and dating methods in a new version of the user-friendly TRAD program, which is freely available at https://dambe.bio.uottawa.ca/TRAD/TRAD.aspx. Application of the method to a phylogeny of early SARS-CoV-2 genomes revealed 1) an increase in r in late February 2020 contributed mainly by the D614G lineage, 2) a significantly better fit of the sigmoidal-rate model to the SARS-CoV-2 evolution than the constant-rate model, and 3) the common ancestor of the included SARS-CoV-2 genomes dated to 2019/11/20.

PMID:40621860 | DOI:10.1093/gbe/evaf134

Bioinform Adv. 2025 Jun 12;5(1):vbaf141. doi: 10.1093/bioadv/vbaf141. eCollection 2025.

ABSTRACT

MOTIVATION: Structured representations of clinical data can support computational analysis of individuals and cohorts, and ontologies representing disease entities and phenotypic abnormalities are now commonly used for translational research. The Medical Action Ontology (MAxO) provides a computational representation of treatments and other actions taken for clinical management. Currently, manual biocuration is used to annotate MAxO terms to rare diseases. However, it is challenging to scale manual curation to comprehensively capture information about medical actions for the more than 10 000 rare diseases.

RESULTS: We present AutoMAxO, a semi-automated workflow that leverages Large Language Models (LLMs) to streamline MAxO biocuration. AutoMAxO first uses LLMs to retrieve candidate curations from abstracts of relevant publications. Next, the candidate curations are matched to ontology terms from MAxO, Human Phenotype Ontology (HPO), and MONDO disease ontology via a combination of LLMs and post-processing techniques. Finally, the matched terms are presented in a structured form to a human curator for approval. We used this approach to process abstracts related to 37 rare genetic diseases and identified 958 novel treatment annotations that were transferred to the MAxO annotation dataset.

AVAILABILITY AND IMPLEMENTATION: AutoMAxO is a Python package freely available at https://github.com/monarch-initiative/automaxo.

PMID:40621601 | PMC:PMC12228962 | DOI:10.1093/bioadv/vbaf141

Front Vet Sci. 2025 Jun 20;12:1489905. doi: 10.3389/fvets.2025.1489905. eCollection 2025.

ABSTRACT

INTRODUCTION: The domestication of dogs is regarded as an evolutionary adaptation influenced by artificial selective pressures, leading to the fruition of diverse canine breeds across regions. Indigenous breeds, developed in tandem with local environments, display unique conformations and disease resistance, yet many remain understudied at the molecular level. The Gaddi dog, originating in the northern parts of India and used by local tribes for livestock guarding, exemplifies such a breed with potential for transcriptomic research. Despite its vital role, it remains unrecognized by the National Bureau of Animal Genetic Resources (NBAGR). This study addresses the gaps in understanding the genetics and immune responses of Indigenous breeds, emphasizing their importance as holders of unique genetic heritage. This study explores the molecular profiles of Indigenous Gaddi dogs and exotic Labrador retrievers, focusing on their immune responses to TLR ligand-induced infections.

METHODS: The mRNA and miRNA sequencing were performed separately using the Illumina NovaSeq 6,000 platform (150 bp). The study involved comparing the Control group (i.e., without treatment of any TLR-ligand) with each of the Poly I: C, LPS, and CpG ODN-treated groups for Labrador and Gaddi dogs. Functional enrichment analysis of differentially expressed genes (DEGs) (fold change >3 and <-3, p < 0.05) was conducted to identify enriched pathways in each breed.

RESULTS: The analysis revealed that Labrador dogs had more DEGs across all treatment groups than Gaddi dogs. The enriched pathways in Labradors included Th1, Th2, Th17 cell differentiation, and T-cell receptor signaling. In contrast, Gaddi dogs significantly enriched 'Wnt' signaling, T cell activation, and immune regulation pathways. The differential expression (DE) analysis of miRNA-Seq results indicated that Labradors had more DE miRNAs (with expression levels of the original level >1.5 and <-1.5), such as miR-204, miR-206, miR-106a, miR-132, miR-335, and miR-676, which help regulate inflammation, autophagy, and immune responses. Gaddi dogs had unique miRNAs (miR-551 and miR-1249) associated with tumor suppression and inflammation.

DISCUSSION: The study highlights distinct immunological profiles between Labrador and Gaddi dogs, with no shared genes responding to TLR-ligand stimulation. The functional enrichment of miRNA targets demonstrated consistent regulatory patterns at both the mRNA and miRNA levels. These findings emphasize the importance of preserving the genetic diversity of indigenous Gaddi dogs and utilizing advanced sequencing techniques to explore immunological diversity for disease resistance and the selection of breeding individuals.

PMID:40621499 | PMC:PMC12226298 | DOI:10.3389/fvets.2025.1489905

Plant Soil. 2025;511(1-2):855-866. doi: 10.1007/s11104-024-07025-7. Epub 2024 Oct 31.

ABSTRACT

BACKGROUND & AIMS: Ginsenosides are triterpene saponins produced by ginseng (Panax spp.). Ginsenosides are secreted into the soil during ginseng growth and are mildly anti-fungal and autotoxic. While an ecological role for ginsenosides in maintenance of the sparse density growth habit of wild ginseng populations can be inferred, the consequence of ginsenoside accumulation in densely populated commercial ginseng gardens remains unknown. The potential for residual ginsenosides in former ginseng gardens to contribute to ginseng replant disease (GRD), a condition in which a new ginseng crop cannot be successfully cultivated in a garden used for ginseng cultivation in the past, has been suggested. However, the extent to which ginsenosides accumulate in ginseng garden soil and persist beyond harvest is poorly documented.

METHODS: We developed an extraction protocol to extract ginsenosides from ginseng garden soil, and established the behaviour of ginsenosides in soil in controlled experiments using ginseng garden soil packed into columns.

RESULTS: Ginsenosides accumulate throughout the first three and a half years of ginseng cultivation and decline during the fourth year. Residual ginsenosides present in garden soil at the time of harvest are largely gone by the following spring. Soil column data revealed that sandy-loam soil has capacity to bind and retain ginsenosides, and that protopanaxatriol-type ginsenosides are more mobile than the protopanaxadiol-type.

CONCLUSION: Ginsenosides accumulate in ginseng garden soil during cultivation, but do not persist. Our data suggest that the impact of ginsenosides on the establishment of GRD occurs during crop growth rather than during the time between plantings.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-024-07025-7.

PMID:40621106 | PMC:PMC12227356 | DOI:10.1007/s11104-024-07025-7

Brain Behav Immun Health. 2025 Jun 18;47:101039. doi: 10.1016/j.bbih.2025.101039. eCollection 2025 Aug.

ABSTRACT

Monoamine oxidase A (MAO A) is a key enzyme for serotonin metabolism. Knockout MAO A in mice results in elevated serotonin, altered serum autoantibodies, and autistic-like behavior. There is a subset of patients with autism spectrum disorder (ASD) who exhibit hyperserotonemia. The link between the MAO A, hyperserotonemia, immunity, and ASD is still unknown. To address this question, we harness the high-density human proteome microarray to profile the serum autoantibodies in ASD patients with or without MAO A deficiency. We recruited 25 subjects, including 20 ASD patients, from National Yang Ming Chiao Tung University Hospital and determined their plasma serotonin levels, screened for MAO A gene mutations and identified one patient with a C374 G mutation, which abolished MAO A activity and showed the highest serotonin level (hsASD; 518.42 ng/ml) and severe ASD symptoms. In another family with twin brothers, one was diagnosed with mild ASD and exhibited an increased serotonin level (isASD; 31.48 ng/ml), while the other twin was a healthy control. These three subjects were used for serum autoantibody profiling using high-density human proteome microarrays. Comparing serum antibodies from hsASD with healthy control, we identified 354 up-regulated and 398 down-regulated autoantibodies in hsASD. By comparing isASD with healthy controls, we reported 235 up-regulated and 279 down-regulated autoantibodies in isASD. Interestingly, the up-regulated autoantibodies for hsASD were enriched in the brain region and exhibited distinct features from that of isASD. This study indicates that MAO A deficiency and serotonin levels significantly impact the immunological changes in ASD patients, which may shed some light on pathological mechanisms and provide potential biomarkers for translational research in ASD.

PMID:40620708 | PMC:PMC12226381 | DOI:10.1016/j.bbih.2025.101039

Curr Zool. 2024 Oct 26;71(3):273-283. doi: 10.1093/cz/zoae068. eCollection 2025 Jun.

ABSTRACT

The study of temperament and behavioral syndromes in insects is still in its early stage, and research conducted to date has mainly focused on locomotor activity and thanatosis. Dung beetles have been the subject of extensive behavioral studies; however, very few studies have addressed the expression of temperament. Those doing so only looked at subsocial and sexual horn dimorphic species, suggesting subsociality and/or sexual horn-dimorphism as possible facilitators of temperament expression. To test this assumption, we conducted a temperament study in a hornless, non-subsocial species, namely Geotrupes mutator (Marsham, 1802). We set up laboratory tests to evaluate 3 behaviors (activity, thanatosis, and distress calls) through the measurement of 7 distinct behavioral traits (3 activity-, 1 thanatosis-, and 3 call-related traits). We found high levels of individual repeatability in all activity- and thanatosis-related traits. We also identified behavioral differences between individuals, which may reflect differences in temperament. Statistical analyses revealed a negative correlation between activity and thanatosis. These results show that the temperament and behavioral syndromes related to activity and thanatosis may also be expressed in dung beetle species that are neither subsocial nor sexual horn dimorphic. By contrast, we only found one of 3 sound-related traits tested (frequency) to be clearly repeatable. Males and females presented a different structure of the stridulatory apparatus, suggesting that morphology may affect the frequency of sounds emitted. These results indicate that certain sound traits might not be good descriptors of individual temperament revealing the need for future research addressing the role of bioacoustics.

PMID:40620587 | PMC:PMC12227424 | DOI:10.1093/cz/zoae068

Adv Sci (Weinh). 2025 Jul 7:e05411. doi: 10.1002/advs.202505411. Online ahead of print.

ABSTRACT

Vertebrates have undergone two rounds of whole-genome duplication (WGD), termed 1R and 2R, with a third, teleost-specific duplication (TSGD or 3R) occurring in ray-finned fishes. In the order Cypriniformes, additional lineage-specific WGDs have further contributed to species diversification. While polyploidy is well characterized in species like common carp and goldfish, other polyploid taxa-particularly loaches-remain understudied. Here, high-quality, chromosome-level genome assemblies are presented for two loach species: Sinibotia superciliaris (Golden Chinese Loach) and Parabotia fasciatus (Yichang Sand Loach). By integrating these genomes into a comparative framework with 20 other cypriniform species, key phylogenetic relationships are reconstructed, and introduce a novel subgenome partitioning method (M3). Unlike previous approaches, M3 uses differential sequence divergence to accurately and rapidly assign subgenomes, completing partitioning within minutes and outperforming existing tools. Applying M3, a markedly reduced subgenome is uncovered in the Golden Chinese Loach, with lineage-specific molecular changes in several candidate genes, suggesting potential adaptive significance. This study offers a comprehensive view of polyploidy and subgenome evolution in loaches, highlighting the genomic complexity shaped by repeated WGDs in Cypriniformes and providing valuable resources for future research on vertebrate genome evolution and adaptation.

PMID:40620001 | DOI:10.1002/advs.202505411

Brief Bioinform. 2025 Jul 2;26(4):bbaf323. doi: 10.1093/bib/bbaf323.

ABSTRACT

Microbiomes are crucial for human health and well-being, with microbial dysbiosis being linked to various complex diseases. Therefore, understanding the structural and functional changes in the microbiome, along with the underlying mechanisms in disease conditions, is essential. In this review, we outline the structure and function of different human microbiomes and examine how changes in their composition may contribute to diseases. We highlight critical information associated with microbial dysbiosis and explore various therapeutic strategies for restoring a healthy microbiome, including microbiota transplantation, phage therapy, probiotics, prebiotics, dietary interventions, and drug-based approaches. Further, to better understand microbiome dysbiosis, we discuss multi-omics approaches including metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics, alongside computational modeling approaches such as ecological and metabolic network analysis. We outline key challenges associated with multi-omics techniques and emphasize the importance of integrative systems biology approaches that combine multi-omics data with computational modeling. These approaches are crucial for effectively analyzing microbiome data, providing deeper insights into species interactions and microbiome dynamics. Finally, we offer insights into future research directions in the field of microbiome research. This review makes a unique contribution to microbiome research by presenting a holistic framework that integrates multi-omics data with multi-scale modeling to elucidate microbial interactions, microbiome dysbiosis, and their modulation in disease-associated contexts.

PMID:40619813 | DOI:10.1093/bib/bbaf323

Adv Sci (Weinh). 2025 Jul 6:e16687. doi: 10.1002/advs.202416687. Online ahead of print.

ABSTRACT

Uncontrolled cell proliferation drives tumorigenesis and malignant progression, making cell cycle regulation a promising strategy for cancer therapy. Phosphorylation plays pivotal roles in cancer initiation and metastasis by regulating the cancer-related proteins. Identifying key phosphorylation sites is essential for inhibiting tumor cell proliferation and optimizing therapy strategy. Here, this study reveals the strong association of oncogene Collaborator of ARF (CARF), a cell-division regulator interacting with p53, with prognosis and survival of lymphoma patients through pan-cancer analysis. In addition, this study finds that mammalian CARF shares homology with Kip-Related Protein6 (KRP6), a cell cycle inhibitor from higher plant Arabidopsis. KRP6 is regulated by casein kinase1 via phosphorylation at serines 75 and 109, which are conservative in CARF at serines 316 and 356. Systemic assays conducted with various B-cell lymphoma cell lines and a mouse xenograft model demonstrate that the non-phosphorylation variant of CARF inhibited cell proliferation and lymphoma formation more effectively than wild-type CARF, highlighting the crucial regulatory role of phosphorylation at these conserved sites in controlling B-cell lymphoma cell proliferation. A similar suppressive effect is observed with plant KRP6, suggesting a cross-species bioengineering application. These findings enlighten the application of phosphorylation-modified proteins as therapeutic targets in precise lymphoma treatments.

PMID:40619590 | DOI:10.1002/advs.202416687

Mol Cell Proteomics. 2025 Jul 4:101028. doi: 10.1016/j.mcpro.2025.101028. Online ahead of print.

ABSTRACT

Epithelial-mesenchymal transition (EMT) is a key biological process in physiological and pathological conditions, spanning development, wound healing, and cancer. Vimentin, a key cytoskeletal intermediate filament (IF) protein, is an established intracellular determinant of EMT. Recently, extracellular vimentin has also emerged with important functions, and we demonstrated that vimentin from fibroblast-derived extracellular vesicles (EVs) promotes wound healing. Building on these findings, we explored whether extracellular vimentin regulates EMT. We employed fibroblast-derived EVs to assess their EMT-driving capacity. Using co-culture models and EV treatments from wild-type and vimentin-knockout fibroblasts, we observed that fibroblasts induce an EMT phenotype in epithelial cells, marked by elevated mesenchymal markers and reduced epithelial markers. EVs from vimentin-deficient fibroblasts showed a decreased EMT-inducing capacity and failed to stimulate cell cover closure, underscoring vimentin's critical role in orchestrating these processes. Co-culturing epithelial cells with wild-type fibroblasts mirrored these outcomes, while vimentin-deficient fibroblasts produced similarly poor EMT induction. Proteomic profiling revealed that wild-type EVs contained an enriched set of EMT-associated proteins, including those involved in cytoskeletal organization, cell adhesion, and EMT-regulating signaling pathways. Notably, these proteins, such as fibronectin and N-cadherin, were significantly diminished in vimentin-deficient EVs. Moreover, we identified over 600 additional proteins uniquely present in WT-derived EVs, with enrichment in key biological processes like wound healing and cell migration. These findings demonstrate that vimentin-positive EVs drive EMT by transmitting a specific protein cargo that supports EMT-related cellular changes. The vimentin-positive EV proteome will help understand EMT mechanisms and develop targeted therapies for pathological conditions related to abnormal EMT.

PMID:40618999 | DOI:10.1016/j.mcpro.2025.101028

Eur J Pharmacol. 2025 Jul 4:177916. doi: 10.1016/j.ejphar.2025.177916. Online ahead of print.

NO ABSTRACT

PMID:40618977 | DOI:10.1016/j.ejphar.2025.177916

Oncogene. 2025 Jul 6. doi: 10.1038/s41388-025-03486-x. Online ahead of print.

ABSTRACT

The MYC oncogene is a frequently activated oncogene in human cancers, and its high expression is strongly correlated with a poor prognosis. The lack of conventional enzyme-binding sites in MYC poses significant challenges for the development of small-molecule-based therapies to treat MYC-deregulated cancer. In particular, only one transmembrane peptide that targets c-MYC has advanced to early clinical trials, thus highlighting the need of effective and direct approaches for targeting c-MYC in cancer treatment. In this study, we developed a conjugated nanobody (NB) that specifically targets MYC, termed a cell-permeable MYC-targeting nanobody (CPMycNB), via sortase-mediated protein ligation. CPMycNB effectively entered the nucleus and bound to c-MYC, thereby disrupting the c-MYC-MAX interaction. This disruption resulted in the downregulation of c-MYC-targeted genes, activation of apoptotic pathways, and inhibition of cell growth and proliferation in c-MYC-driven tumor cells. Using hydrogen-deuterium exchange mass spectrometry, we found that CPMycNB interacted with the leucine zipper domain of c-MYC. Furthermore, xenograft studies confirmed the therapeutic efficacy of CPMycNB, which significantly reduced tumor size and weight. Our findings highlight the potential of CPMycNB for the treatment of c-MYC-associated malignancies.

PMID:40617995 | DOI:10.1038/s41388-025-03486-x

J Lipid Res. 2025 Jul 3:100857. doi: 10.1016/j.jlr.2025.100857. Online ahead of print.

NO ABSTRACT

PMID:40617356 | DOI:10.1016/j.jlr.2025.100857

Neurosci Lett. 2025 Jul 3:138309. doi: 10.1016/j.neulet.2025.138309. Online ahead of print.

ABSTRACT

In the brain of hypoxia-intolerant vertebrates, hypoxia induces neuronal depolarization, chronic activation of voltage-gated excitatory glutamatergic receptors, and rapid accumulation of Ca2+ in the cytosol, which induces downstream activation of cell death pathways. Conversely, deleterious Ca2+ accumulation and cell death is avoided in the brain of hypoxia-tolerant vertebrates. One neuroprotective adaptation that is present in some of the most hypoxia-tolerant vertebrates is channel arrest, whereby Ca2+ ion influx through glutamate receptors is reduced in hypoxia, and cytotoxic accumulation of Ca2+ is avoided. Naked mole-rats are a hypoxia-tolerant mammal and avoid neurotoxic Ca2+ accumulation during hypoxia; however, the underlying mechanisms are poorly understood. In the present study, we tested the hypothesis that channel arrest of glutamatergic receptors occurs in hypoxic naked mole-rat neurons, which would help to limit Ca2+ influx during hypoxia. Using the Ca2+-sensitive fluorophore Fura-2, we measured Ca2+ flux through glutamatergic receptors in live brain slices exposed to a normoxic or hypoxic (1 % O2) perfusate and following application of either glutamate or NMDA to stimulate glutamatergic receptors. We found no differences in the magnitude of the evoked Ca2+ transients or the total amount of Ca2+ movement following ligand stimulus. Our results indicate that channel arrest is not an important strategy to limit deleterious Ca2+ influx into naked mole-rat neurons during hypoxia. Other mechanisms, such as enhanced mitochondrial buffering of cytosolic Ca2+, may play a more important role in hypoxic Ca2+ homeostasis in this species.

PMID:40617310 | DOI:10.1016/j.neulet.2025.138309