Microbiol Spectr. 2025 Jun 23:e0335424. doi: 10.1128/spectrum.03354-24. Online ahead of print.

ABSTRACT

The effectiveness of the seasonal influenza vaccine varies between individuals. Specific risk groups with comorbidities, such as the obese, have an increased risk of infection even when vaccinated. It has been proposed that a heightened baseline inflammatory state and alterations in adaptive immune cell populations in obese individuals may adversely impact immune responses to pathogens and vaccines. Therefore, understanding differences in vaccine responses in obese individuals is critical for the development of improved influenza vaccine design and strategies. Previously, we identified a transcriptomic signature prior to seasonal influenza vaccination that is predictive of an individual's response to the influenza vaccine. To understand the dynamics of host responses following vaccination, we studied systemic gene expression from whole blood collected from 163 vaccinated individuals on days 3, 7, and 28 post-vaccination. Gene expression profiles were compared between high and low vaccine responders in both obese and non-obese groups. We detected characteristic changes in gene expression over time, with a peak at day 7 post-vaccination. A large subset of genes associated with the adaptive immune response exhibited significantly different expressions in high responders and non-responders to the vaccine. Distinct gene sets presented differing temporal patterns in different weight and response groups, indicative of molecular processes impacting the immune response to vaccination.

IMPORTANCE: This study yields insights into how co-morbidities, such as obesity, impact the immune response to the seasonal influenza vaccine. By analyzing blood samples collected days and weeks after the vaccination of a cohort of subjects, we can examine changes in gene expression over time and how those changes are similar or different depending on risk factors. This provides clues into potential molecular mechanisms behind an effective immune response to vaccination.

PMID:40548708 | DOI:10.1128/spectrum.03354-24

Brief Bioinform. 2025 May 1;26(3):bbaf292. doi: 10.1093/bib/bbaf292.

ABSTRACT

RNA-protein interactions (RPIs) are essential for many biological functions and are associated with various diseases. Traditional methods for detecting RPIs are labor-intensive and costly, necessitating efficient computational methods. In this study, we proposed a novel sequence-based RPI prediction framework based on graph neural networks (GNNs) that addressed key limitations of existing methods, such as inadequate feature integration and negative sample construction. Our method represented RNAs and proteins as nodes in a unified interaction graph, enhancing the representation of RPI pairs through multi-feature fusion and employing self-supervised learning strategies for model training. The model's performance was validated through five-fold cross-validation, achieving accuracy of 0.880, 0.811, 0.950, 0.979, 0.910, and 0.924 on the RPI488, RPI369, RPI2241, RPI1807, RPI1446, and RPImerged datasets, respectively. Additionally, in cross-species generalization tests, our method outperformed existing methods, achieving an overall accuracy of 0.989 across 10 093 RPI pairs. Compared with other state-of-the-art RPI prediction methods, our approach demonstrates greater robustness and stability in RPI prediction, highlighting its potential for broad biological applications and large-scale RPI analysis.

PMID:40548542 | DOI:10.1093/bib/bbaf292

Curr Opin Pulm Med. 2025 Jun 24. doi: 10.1097/MCP.0000000000001190. Online ahead of print.

ABSTRACT

PURPOSE OF REVIEW: Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) leads to poor survival, on average only 3-5 years from time of diagnosis. Despite its clinical impact, evidence-based treatment approaches remain limited, creating urgent clinical uncertainty about optimal management strategies. This review examines emerging precision medicine approaches that may guide more effective, individualized treatment decisions.

RECENT FINDINGS: Current treatment paradigms based on radiologic patterns lack empirical validation, with recent evidence suggesting radiologic features poorly predict immunomodulatory response. Advances in RA joint precision medicine using synovial biopsy and RNA sequencing have identified molecular endotypes predicting differential treatment response, establishing a framework that could be applied to RA-ILD. Emerging biomarkers including leukocyte telomere length, circulating proteomics, and lung-based systems biology show promise for identifying RA-ILD molecular heterogeneity and guiding treatment selection.

SUMMARY: Progress in RA-ILD precision medicine requires multimodal approaches integrating molecular phenotyping with targeted therapeutic trials. Lessons from RA joint precision medicine suggest accessing the disease compartment directly through bronchoscopy may provide crucial information beyond peripheral biomarkers. Prospective biomarker-stratified trials are urgently needed to overcome clinical equipoise and improve outcomes for this challenging condition.

PMID:40548519 | DOI:10.1097/MCP.0000000000001190

Emerg Microbes Infect. 2025 Jun 23:2521840. doi: 10.1080/22221751.2025.2521840. Online ahead of print.

ABSTRACT

The study aimed to analyze epidemiological, clinical, and genome characteristics of acute gastroenteritis (AGE) outbreaks caused by sapovirus in Beijing. Epidemiological and clinical characteristics of sapovirus detected by RT-qPCR were collected from AGE surveillance. Descriptive statistics were used for epidemiological analysis, and both genotype identification and sequence analysis were conducted on the VP1 regions, RNA-dependent RNA polymerase regions, and whole genomes. From 2014 to 2021, sapovirus was the second most common pathogen in AGE outbreaks, causing 216 outbreaks (6.85%) with peaks in 2017, 2019, and 2021. The predominant outbreaks occurred in kindergartens (76.39%, 165) and primary schools (18.98%, 41) within urban (62.96%, 136) and suburban (35.19%, 76) by person-to-person transmission (97.73%, 172). Outbreaks in outer suburbs lasted longer duration[median 7 days, IQR: 6-8)]. Comprehensive schools (21.62%, IQR: 10.00-35.00%) and kindergartens (18.18%, IQR: 13.51-22.72%) showed higher attack rates. Clinical symptoms included vomiting (97.27%, 1,462), diarrhea (18.44%, 277), fever (8.32%, 125), nausea (28.72%, 432), and abdominal pain (33.94%, 510). Vomiting prevalence was higher in children aged ≤5 years (96.94%, 983/1,014), while diarrhea prevalence was higher in those >5 years (31.29%, 153/489). Eight genotypes (GI.1-3, 5, 6; GII.1, 3, 5) were identified, and the predominant genotype changed from GII.3 (2016-2019) to GI.2 (2020-2021). Phylogenetic analysis revealed emerging clades in GII.3 and GI.2, with nucleotides and amino acids mutations confirmed by whole-genome sequencing. Therefore, sapovirus is a significant AGE pathogen in Beijing, China, warranting its inclusion in surveillance among sporadic outbreaks of AGE in China necessitating genotyping and whole-genome sequencing.

PMID:40548408 | DOI:10.1080/22221751.2025.2521840

JCI Insight. 2025 Jun 23;10(12):e182123. doi: 10.1172/jci.insight.182123. eCollection 2025 Jun 23.

ABSTRACT

Spinal and bulbar muscular atrophy (SBMA) is a neuromuscular disease caused by an expanded CAG repeat in the androgen receptor (AR) gene. To elucidate the cell type-specific temporal gene expression in SBMA, we performed single-nucleus RNA sequencing on the spinal cords of an SBMA mouse model (AR-97Q). Among all cell types, oligodendrocytes had the highest number of differentially expressed genes before disease onset. Analysis of oligodendrocyte clusters suggested that pathways associated with cation channels and synaptic function were activated before disease onset, with increased output from oligodendrocytes to neurons in AR-97Q mice compared with wild-type mice. These changes in the early stages were abrogated at the advanced stages. An oligodendrocyte model of SBMA showed phenotypes similar to those of AR-97Q mice at early stages, such as increased transcriptional changes in synapse organization, and Ca2+ imaging of oligodendrocytes in AR-97Q mice revealed the increased Ca2+ responses. A coculture system of primary rat oligodendrocytes and neurons revealed that the mutant AR in oligodendrocytes affected the activity and synchronization of neurons. These findings suggest that dysregulated cell-to-cell communication plays a critical role in early SBMA pathology and that synaptic or ion channel-related proteins, such as contactin associated protein 2 (Cntnap2) and NALCN channel auxiliary factor 1 (Fam155a), are potential therapeutic targets for SBMA.

PMID:40548375 | DOI:10.1172/jci.insight.182123

Curr Res Food Sci. 2025 May 26;11:101095. doi: 10.1016/j.crfs.2025.101095. eCollection 2025.

ABSTRACT

The wheat flour proteome is a complex mixture of non-gluten and gluten proteins. The large number of repetitive sequences, special amino acid composition and similarity of gluten protein isoforms pose a major challenge in bottom-up proteomics. The standard peptidase used in shotgun proteomics is trypsin, which may not be suitable for all wheat proteins. In this study, flour extracts of nine common wheat genotypes were digested with the peptidases trypsin, chymotrypsin, thermolysin, pepsin and the combination of trypsin and chymotrypsin. The results showed large differences for the number of identified peptides. With 4115 peptides, trypsin resulted in by far the most peptide identifications, followed by thermolysin with 1421 peptides. However, this no longer applied at protein level. Most metabolic protein groups (673) were identified with trypsin. Among the gluten protein groups, however, around 130 were identified with each peptidase. The ω-gliadins were detected with all peptidases except trypsin. A comparison with quantitative RP-UHPLC-UV results showed that there was the greatest overlap after thermolysin digestion. Otherwise, there was no great similarity between the different peptidases, which is why their results cannot be compared with one another. The sequence coverage of gluten proteins was 51 % after thermolysin digestion, 27 % after trypsin digestion and 61 % when all peptidases were evaluated together. The results showed that digestion with various peptidases provides a more detailed picture of the wheat proteome. Some wheat protein groups could only be identified with certain peptidases, which is important if these protein groups are to be studied in more detail.

PMID:40548313 | PMC:PMC12182313 | DOI:10.1016/j.crfs.2025.101095

Alzheimers Dement (N Y). 2025 Jun 19;11(2):e70119. doi: 10.1002/trc2.70119. eCollection 2025 Apr-Jun.

ABSTRACT

INTRODUCTION: CT1812 (zervimesine) is an orally dosed modulator of the sigma-2 receptor (S2R) currently in clinical development for the treatment of Alzheimer's disease (AD). CT1812 has been shown in preclinical and early clinical trials to selectively prevent and displace binding of amyloid beta oligomers from their synaptic receptors and has improved cognitive function in animal models of AD.

METHODS: SEQUEL (NCT04735536) is a completed Phase 2, randomized, placebo-controlled 4-week crossover trial in adults with mild-to-moderate AD that investigated the effect of CT1812 on safety, synaptic function using quantitative electroencephalography (qEEG), and biomarkers. CT1812 improved established qEEG markers of spontaneous brain activity, suggesting improved neuronal and synaptic function. In the present study, cerebrospinal fluid (CSF)-based tandem mass tag mass spectrometry (TMT-MS) was performed on participant samples to investigate proteomic effects and identify potential biomarkers of CT1812.

RESULTS: Biomarkers found through proteomics analyses to be significantly differentially abundant in CT1812- versus placebo-treated participants supported pathway engagement and proof of mechanism for CT1812. Impacted proteins support a role for CT1812 at synapses, in vesicle trafficking, and in lipoprotein biology. Biomarkers correlated with the previously reported improvements in qEEG-based functional connectivity (inferred through alpha band Amplitude Envelope Correlations) with CT1812 treatment were also identified and may be potential early surrogate biomarkers of efficacy for CT1812. The processes and functions supported by biomarkers were congruent with those previously revealed in CSF proteomics analyses from phase 1 and 2 AD clinical trials with CT1812.

DISCUSSION: After 1 month of treatment, the identification of biomarkers supporting pathway engagement, the replication of biomarker findings from prior trials, and the discovery of molecular correlates of improved functional connectivity with CT1812 treatment bolster support for and expound upon the mechanism of action for CT1812 in displacing Aβ oligomers at neuronal synapses, as well as underscores the CT1812 relevance to AD.

HIGHLIGHTS: Exploratory proteomics identified candidate CSF biomarkers of CT1812 in SEQUEL.Molecular correlates of functional brain connectivity (qEEG) were identified.Proteins impacted by 1 month CT1812 treatment support target engagement.Pharmacodynamic changes found in synapse, immune, vesicle, and lipoprotein biologies.SEQUEL proteomics findings replicated previous trial findings with CT1812.

PMID:40547328 | PMC:PMC12178945 | DOI:10.1002/trc2.70119

Bioinform Adv. 2025 May 19;5(1):vbaf113. doi: 10.1093/bioadv/vbaf113. eCollection 2025.

ABSTRACT

SUMMARY: The increasing availability of high-throughput technologies in systems biology has advanced predictive tools like genome-scale metabolic models. Despite this progress, integrating omics data to create accurate, context-specific metabolic models for different tissues or cells remains challenging. A significant issue is that many existing tools rely on proprietary software, which limits accessibility. We introduce TROPPO, an open-source Python library designed to overcome these challenges. TROPPO supports a wide range of context-specific reconstruction algorithms, provides validation methods for assessing generated models, and includes gap-filling algorithms to ensure model consistency, integrating well with other constraint-based tools.

AVAILABILITY AND IMPLEMENTATION: TROPPO is implemented in Python and is freely available at https://github.com/BioSystemsUM/TROPPO and https://pypi.org/project/TROPPO/.

PMID:40546819 | PMC:PMC12179386 | DOI:10.1093/bioadv/vbaf113

IMA Fungus. 2025 Jun 12;16:e144731. doi: 10.3897/imafungus.16.144731. eCollection 2025.

ABSTRACT

Hortiboletus (the former Xerocomusrubellus species complex) is one of the most taxonomically critical and difficult genera for species identification in the family Boletaceae. Here, we provide a detailed morphological and molecular re-assessment of European and Levantine species of Hortiboletus. A new species, H.hershenzoniae, is described from Israel. It is sister to H.engelii and associated with the evergreen oak Quercuscalliprinos and potentially also with Q.ithaburensis. Based on the sequence retrieved from INSDC, this species is also found in Lebanon. Accurate morphological descriptions, comprehensive sampling, type studies, biogeography, macro- and microphotographs and a historical overview on the nomenclatural issues surrounding H.rubellus, H.bubalinus, H.engelii, and H.hershenzoniae are given. An epitype collection is designated for H.rubellus. A key is provided for identification of the European and Levantine taxa. In addition, we propose a novel taxonomic combination Hortiboletusflavorubellus, which is conspecific with Boletusrubellusvar.flammeus, based on the DNA barcoding and phylogenetic analysis of type material. Boletusharrisonii is also shown to be conspecific with H.campestris. A multilocus phylogenetic analysis of four markers (ITS, LSU, tef1-α, and rpb2) reveals that Hortiboletus is a sister genus to Xerocomellus. Using the Genealogical Concordance Phylogenetic Species Recognition method, at least 19 phylogenetic species and eight putative phylogenetic species of the genus Hortiboletus can be delimited. Based on multilocus analysis, it contains from 24 to 25 species-level clades worldwide, 17 out of which represent known species, one newly described and potentially six to seven undescribed species. Tandem repeat insertions within the ITS region (both in ITS1 and ITS2) are reported for the first time, not only in the genus Hortiboletus, but in the entire subfamily Boletoideae. Their identification and characterisation were based on Tandem Repeat Finder analysis and visual assessment of the ITS alignment.

PMID:40546449 | PMC:PMC12179652 | DOI:10.3897/imafungus.16.144731

Proteins. 2025 Jun 23. doi: 10.1002/prot.70008. Online ahead of print.

ABSTRACT

The grand challenge of protein engineering is the development of computational models to characterize and generate protein sequences for arbitrary functions. Progress is limited by lack of (1) benchmarking opportunities, (2) large protein function datasets, and (3) access to experimental protein characterization. We introduce the Protein Engineering Tournament-a fully-remote competition designed to foster the development and evaluation of computational approaches in protein engineering. The tournament consists of a predictive round, predicting biophysical properties from protein sequences, followed by a generative round where novel protein sequences are designed, expressed, and characterized using automated methods. Upon completion, all datasets, experimental protocols, and methods are made publicly available. We detail the structure and outcomes of a pilot Tournament involving seven protein design teams, powered by six multi-objective datasets, with experimental characterization by our partner, International Flavors and Fragrances. Forthcoming Protein Engineering Tournaments aim to mobilize the scientific community towards transparent evaluation of progress in the field.

PMID:40546234 | DOI:10.1002/prot.70008

Proteomics. 2025 Jun 23:e13983. doi: 10.1002/pmic.13983. Online ahead of print.

ABSTRACT

Advances in methodologies and technologies over the past decade have led to an unprecedented depth of analysis of a cell's biomolecules, with entire genomes able to be sequenced in hours and up to 10,000 transcripts or ORF products (proteins) able to be quantified from a single cell. Methods for analysing individual omes are now optimised, reliable and robust but are often performed in isolation with other biomolecules considered contaminants. However, there is a growing body of systems biology studies that aim to study multiple omes from the same sample. This review details the current state of the "multi-omics" field, trying to define what the field is, the methodologies employed and the challenges facing researchers in this field. It also critically evaluates whether these approaches are "fit-for-purpose" and how the field needs to evolve to enhance our understanding of how biomolecules from distinct omes interact with one another to alter cellular phenotype in response to change.

PMID:40545987 | DOI:10.1002/pmic.13983

Plant Commun. 2025 Jun 21:101425. doi: 10.1016/j.xplc.2025.101425. Online ahead of print.

ABSTRACT

Plants are continuously threatened by numerous stresses that cause detrimental damage to plant health and constrain crop productivity worldwide. Metabolic regulation, hence an important tool to regulate the stress tolerance of plants. Tryptophan, as a precursor of various plant natural products, including auxin, melatonin and glucosinolates, plays crucial roles in supporting plant health. To date, remarkable progress has been made in exploring the metabolism of tryptophan, particularly its involvement in enhancing plant stress tolerance. However, there is still a lack of systematic discussion on the crosstalk manipulation of tryptophan metabolites for protecting plants from stresses. Here, we attempt to dive into the tryptophan metabolism and its related crosstalk regulation under stresses. We provide an overview of the biosynthesis and biofunctions of tryptophan metabolites with a main focus on the crosstalk manipulation of tryptophan metabolites in plant stress resistance. The perspective applications of using tryptophan metabolism under stresses are also analyzed. This work endeavors to construct a fundamental framework regarding the regulatory role of tryptophan metabolites on plant health and related mechanisms in sustainable agriculture.

PMID:40545720 | DOI:10.1016/j.xplc.2025.101425

J Med Virol. 2025 Jun;97(6):e70463. doi: 10.1002/jmv.70463.

ABSTRACT

We evaluated homologous neutralizing antibody (NtAb) and T-cell responses after receipt of a JN.1-adapted mRNA vaccine in a mixed population comprising healthy controls (HC) (n = 15), end-stage chronic kidney disease (CKD) patients (n = 17), and allogeneic hematopoietic stem cell transplant recipients (allo-HCT) (n = 13). Most participants (42/45) were SARS-CoV-2-experienced at the time of immunological testing. JN.1-spike-binding NtAbs were measured with a vesicular stomatitis virus pseudotype-based neutralization assay, whereas interferon (IFN)-γ-producing spike-directed CD4+ or CD8+ T-cell frequencies were enumerated using flow cytometry for intracellular staining. All participants had detectable JN.1 NtAbs at baseline; overall, JN.1-NtAb levels increased in HC (median, ∼1 log10; p < 0.001) and CKD patients (median, 0.8 log10; p = 0.06) but not in allo-HCT (p = 0.10). JN.1-NtAb titers measured after vaccination were significantly higher in HC than in CKD and allo-HCT (p = 0.01). The number of participants exhibiting detectable JN.1 T-cell responses did not significantly increase following booster vaccination in any of the study groups. Likewise, receipt of the Omicron JN.1 vaccine failed to significantly boost SARS-CoV-2 JN.1 CD8+ and CD4+ T-cell frequencies in any study groups. Nevertheless, trends in JN.1 T-cell frequencies following the JN-1 booster varied widely on an individual basis. JN.1 T-cell frequencies following JN.1 vaccination were comparable across study groups. Our results could have implications for the development of vaccines for future SARS-CoV-2 variants and the optimization of booster vaccination policies in allogeneic hematopoietic transplant recipients and patients with end-stage chronic kidney diseases.

PMID:40545672 | DOI:10.1002/jmv.70463

Virol Sin. 2025 Jun 21:S1995-820X(25)00072-0. doi: 10.1016/j.virs.2025.06.001. Online ahead of print.

NO ABSTRACT

PMID:40545389 | DOI:10.1016/j.virs.2025.06.001

J Allergy Clin Immunol. 2025 Jun 20:S0091-6749(25)00651-7. doi: 10.1016/j.jaci.2025.06.009. Online ahead of print.

ABSTRACT

BACKGROUND: Deficiency of adenosine deaminase 2 (DADA2) is an inborn error of immunity causing vasculitis and bone marrow failure. Bone marrow failure is mostly unresponsive to tumor necrosis factor-alpha inhibitors. The limited understanding of the pathomechanisms driving the disease impedes the development of new treatment options. Unlike cellular model systems expressing pathogenic ADA2 variants, primary monocytes from DADA2 patients lack ADA2 protein expression.

OBJECTIVES: This study aimed to analyze the role of protein degradation in the pathogenesis of DADA2 and the therapeutic potential of the lysosomotropic drug hydroxychloroquine in the treatment of DADA2 patients.

METHODS: ADA2 protein expression in CD14+ monocytes from healthy controls (n=8) and DADA2 patients (n=11) was determined by western blot after inhibition of lysosomal and proteasomal degradation as well as after hydroxychloroquine treatment in vivo in one DADA2 patient. Lipidation of microtubule associated protein 1 light chain 3 beta (LC3B) was analyzed as a measure of autophagic activity. Clinical and laboratory data were recorded in two cytopenic DADA2 patients treated with 200 mg/day hydroxychloroquine.

RESULTS: We demonstrated that inhibition of lysosomal degradation restores ADA2 protein expression in DADA2 monocytes in vitro. DADA2 monocytes exhibited increased autophagic activity. We observed clinical improvement in two cytopenic DADA2 patients treated with hydroxychloroquine and showed a concomitant increase in ADA2 protein levels in monocytes from one of these patients in vivo.

CONCLUSION: We identify lysosomal protein degradation of ADA2 as a pathomechanism of DADA2 and introduce hydroxychloroquine as a potential treatment option in DADA2 patients with refractory cytopenia.

PMID:40545182 | DOI:10.1016/j.jaci.2025.06.009

Bioresour Technol. 2025 Jun 20:132833. doi: 10.1016/j.biortech.2025.132833. Online ahead of print.

ABSTRACT

Polyhydroxyalkanoates (PHAs) constitute a diverse family of biodegradable and biocompatible polymers with potential as sustainable alternatives to petroleum-based plastics. Microbial poly(3-hydroxybutyrate-co-lactate), abbreviated as P(3HB-co-LA), as member of the PHA family exhibiting a wide range of lactate (LA) molar ratios, was biosynthesized by engineered Halomonas bluephagenesis (H. bluephagenesis). With genome integration of four copies of mutated PHA synthase PhaC1Ps (E130D, S325T, S477G and Q481K) and propionyl-CoA transferase (Pct540), the resulting H. bluephagenesis produced 6.1 g L-1 cell dry weight (CDW), with 48.4 wt% P(3HB-co-27.6 mol% LA). H. bluephagenesis CJN29 with deletion in ppc, pta and dld genes, encoding phosphoenolpyruvate carboxylase, phosphate acetyltransferase, and lactate dehydrogenase, respectively, reached 6.8 g L-1 CDW containing 54.8 wt% P(3HB-co-35.9 mol% LA). After medium optimization, H. bluephagenesis CJN29 produced 10.8 g L-1 CDW containing 54.1 wt% P(3HB-co-36.2 mol% LA). Deletion of mreB encoding a cytoskeletal protein significantly enlarged the cells for convenient downstream purification. Using glucose as the sole carbon source in a 7-L fermenter, H. bluephagenesis CJN29 achieved 93.8 g L-1 CDW, with 57.3 wt% P(3HB-co-31.6 mol% LA). The record-high P(3HB-co-LA) production achieved in this study, coupled with its adjustable material properties, establishes engineered H. bluephagenesis as a customized P(3HB-co-LA) producer under non-sterile conditions, enabling cost-effective bioproduction.

PMID:40545052 | DOI:10.1016/j.biortech.2025.132833

Eur J Pharmacol. 2025 Jun 20:177864. doi: 10.1016/j.ejphar.2025.177864. Online ahead of print.

ABSTRACT

Glioblastoma multiforme (GBM), a multifactorial deadliest cancer with constrained clinical efficacy due to heterogeneity, drug resistance, side effects of the chemotherapeutic drug, necessitating the development of novel cancer therapeutics. The adenosine A2A receptor targeted binding of antagonist leads to regulation of downstream effectors, mediating the phosphorylation of Casein kinase 1δ kinase domain (CK1δ) in cancers. Here, we performed a comparative investigation of Food and Drug Administration (FDA) approved drugs, istradefylline and riluzole inhibiting adenosine A2A receptor and CK1δ isoform in GBM cell growth. Molecular interaction of riluzole with CK1δ isoform and istradefylline with adenosine A2A receptor was identified through molecular docking and dynamic simulations. The potential of these two FDA approved drugs in inhibiting GBM cell growth was investigated through various in-vitro analysis including dose-dependent dynamic assay, cell cycle assay, apoptosis assay by flow cytometry. Further the effect of these drugs on spheroid cell growth and cell size was measured. In silico analyses demonstrated that riluzole binds strongly to CK1δ isoform with a binding energy of -9.02 kcal/mol, whereas istradefylline binds to adenosine A2A receptor with -9.88 kcal/mol. In vitro evaluation revealed that riluzole increased cell growth inhibition by 24% in LN229 cells and 36% in SNB19 cells than istradefylline. Riluzole arrested the cell cycle at S phase in both cell lines, whereas istradefylline arrest was cell line specific. Three-dimensional (3D) spheroid model of 1321N1 GBM cells further demonstrated that riluzole inhibits ∼50 % higher cell growth inhibition than istradefylline with effective reduction in spheroid volume and size. Overall, our analysis revealed that blocking of adenosine A2A receptor downstream signaling pathway protein CK1δ with its inhibitor, riluzole, showed higher anti-GBM effect than its upstream signaling blocker, istradefylline. Thus, blocking adenosine A2A receptor downstream effector signaling protein through its antagonist and blocking its effector protein CK1δ could provide an opportunity to develop targeted therapy for GBM.

PMID:40544936 | DOI:10.1016/j.ejphar.2025.177864

Biochim Biophys Acta Mol Basis Dis. 2025 Jun 20:167957. doi: 10.1016/j.bbadis.2025.167957. Online ahead of print.

ABSTRACT

Accelerated cholesterol and lipid metabolism are hallmarks of non-small cell lung cancer (NSCLC). Recently, epidermal growth factor receptor (EGFR) signaling has been shown to regulate de novo cholesterol synthesis and low-density lipoprotein receptor (LDLR) expression through SREBP-1-dependent pathways. This suggests that targeting EGFR signaling in cholesterol metabolism might provide a new therapeutic strategy for NSCLC. In this study, we demonstrated that AX-0085, a small-molecule drug, significantly inhibits EGFR kinase activity and subsequently suppresses cholesterol and lipid metabolism in NSCLC. Transcriptomic analysis showed that cholesterol and lipid metabolism-related transcripts were significantly downregulated in AX-0085-treated NSCLC cells compared to the mock control. In addition, AX-0085 downregulates EGF signaling-dependent SREBP1-mediated cholesterol biosynthesis-related enzymes and LDLR in NSCLC. Moreover, AX-0085 dramatically reduced proliferation, colony-forming ability, and migration in NSCLC cells by blocking EGFR signaling. Furthermore, treatment with AX-0085 decreased both tumor size and volume in the LLC-xenograft model. These results demonstrate that AX-0085 effectively suppresses cholesterol metabolism in NSCLC cells by inhibiting EGF-mediated SREBP1 signaling, suggesting a potential therapeutic strategy targeting cholesterol metabolism in NSCLC.

PMID:40544893 | DOI:10.1016/j.bbadis.2025.167957

Phytomedicine. 2025 Jun 15;145:156985. doi: 10.1016/j.phymed.2025.156985. Online ahead of print.

ABSTRACT

BACKGROUND: Tiebangchui (TBC), is a well-known traditional Tibetan medicine that coexists with toxicity and effects. Highland barley wine is an effective and unique processing method to reduce TBC's toxic side effects. However, the toxicity reduction mechanism is ambiguous and needs to be explored urgently. Meanwhile, the limitations of traditional animal models and two-dimensional (2D) cell culture models urgently require the development of more reliable analytical platforms for drug detection.

STUDY DESIGN: The integrated metabolomics and biomimetic 3D anisotropic heart-on-a-chip were utilized to reveal the toxicity-attenuating effect of highland barley wine-processed TBC from the dual perspectives of in vitro compositional changes and in vivo toxicity mechanisms. The combination of organ-on-a-chip and metabolomics provides a powerful tool for achieving spatiotemporal control of cell growth and biochemistry, as well as rapid detection of small molecule metabolites.

METHODS: Ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) coupled with global natural products social molecular networking (GNPS) was utilized for the expeditious identification of chemical constituents in both raw and processed TBC products. Multivariate statistical analysis was applied to screen for differential constituents before and after processing, followed by quantification of these constituents using ultra-performance liquid chromatography-triple quadrupole tandem mass spectrometry (UPLC-QqQ-MS/MS). After constructing a 3D heart-on-a-chip model, the structure and function of the chip model were validated via COMSOL finite element analysis, immunofluorescence, and qPCR. Leveraging this chip model, integrating molecular biology and metabolomics was employed to further elucidate the detoxification mechanism by highland barley wine-processed TBC.

RESULTS: The comprehensive analytical strategies demonstrated that the loss of the toxic constituents of TBC through leaching during steeping and the esterification of diterpene alkaloids with long-chain fatty acids in highland barley wine to produce less toxic lipid alkaloids were the main mechanisms of toxicity reduction. Furthermore, a biomimetic 3D anisotropic heart-on-a-chip was fabricated to evaluate differences in cardiotoxicity before and after processing. The results illustrated that the raw TBC and aconitine caused a significant increase in the extracellular LDH level, resulting in intracellular Ca2+ overload, substantial ROS production, and metabolite disorders primarily associated with the tricarboxylic acid cycle. This cascade of reactions ultimately led to apoptosis; however, highland barley wine processing of TBC mitigated these cardiotoxic effects.

CONCLUSION: This work not only revealed the toxicity-reducing mechanism of highland barley wine-processed TBC but also provided a novel paradigm for drug toxicity evaluation integrating metabolomics and organ-on-a-chip technologies.

PMID:40544734 | DOI:10.1016/j.phymed.2025.156985

STAR Protoc. 2025 Jun 21;6(3):103917. doi: 10.1016/j.xpro.2025.103917. Online ahead of print.

ABSTRACT

Bacteriophages and lipids in human milk may benefit preterm infant health by modulating gut microbiomes. Here, we present a protocol for analyzing the phageome and lipidome in preterm milk using shotgun metagenomics and untargeted lipidomics approaches, respectively. We describe steps for extracting phages and lipids in low-volume milk, characterizing phageome using an in-house bioinformatic pipeline, and statistical analysis to correlate the phageome and lipidome. Finally, we detail an in vitro assay to examine the associations between fatty acid chain length and phage morphotype. For complete details on the use and execution of this protocol, please refer to Yew et al.1.

PMID:40544449 | DOI:10.1016/j.xpro.2025.103917