Int J Biol Macromol. 2025 Jun 23:145497. doi: 10.1016/j.ijbiomac.2025.145497. Online ahead of print.

ABSTRACT

This work reports on the engineering of the linker between P450 SPα (CYP152B1) and sarcosine oxidase (SOX), with the aim of enhancing the structural rigidity of the fusion protein (SPα-SOX) and study the effect on its stability and catalytic performance. Differential scanning calorimetry shows that the construct bearing the rigid linker (SPα-rigid-SOX) results in a higher energy barrier to unfolding (764.8 kcal/mol) compared to the previous fusion system (SPα-flexible-SOX) (561 kcal/mol), as well as a Tonset above 50 °C. Furthermore, residual CO-binding after heat treatment was investigated for both the fusion systems, and a 5.7 °C increase of the T50 of SPα-rigid-SOX is shown. Interestingly, a stabilized P420 semi-folded state of the SPα is also observed after SPα-rigid-SOX incubation at high temperature (40°). The two fusion systems were studied at high temperature for the turnover of lauric acid: SPα-rigid-SOX shows a 98 % conversion yield using 5 mM substrate compared to the 24 % conversion of SPα-flexible-SOX when the catalysis is carried out at 40 °C. Finally, the activity of the two constructs was tested using styrene as a substrate, and three products of catalysis were observed: styrene oxide (85 %), phenylacetaldehyde (0-3 %) and 2-phenylpropenal (12-15 %). Interestingly, 2-phenylpropenal is observed for the first time and only for the fusion enzymes. Also in this case, SPα-rigid-SOX outperformed SPα-flexible-SOX with a 3-fold higher conversion yield. Overall, we demonstrate that the rigid linker improves the fusion enzyme thermal stability and catalytic performances, both at high temperature and in mild conditions, resulting also in the production of new molecules of biotechnological interest.

PMID:40562140 | DOI:10.1016/j.ijbiomac.2025.145497

Phys Med Biol. 2025 Jun 25. doi: 10.1088/1361-6560/ade841. Online ahead of print.

ABSTRACT

This study presents FREDopt, a newly developed GPU-accelerated open-source optimization software for simultaneous proton dose and dose-averaged LET (LETd) optimization in IMPT treatment planning. FREDopt was implemented entirely in Python, leveraging CuPy for GPU acceleration and incorporating fast Monte Carlo (MC) simulations from the FRED code.
The treatment plan optimization workflow includes pre-optimization and optimization, the latter equipped with a novel superiorization of feasibility-seeking algorithms. Feasibility-seeking requires finding a point that satisfies prescribed constraints. Superiorization interlaces computational perturbations into iterative feasibility-seeking steps to steer them toward a superior feasible point, replacing the need for costly full-fledged constrained optimization.
The method was validated on two treatment plans of patients treated in a clinical proton therapy center, with dose and LETd distributions compared before and after reoptimization. Simultaneous dose and LETd optimization using FREDopt led to a substantial reduction of LETd and (dose)×(LETd) in organs at risk (OARs) while preserving target dose conformity. Computational performance evaluation showed execution times of 14-50 minutes, depending on the algorithm and target volume size-satisfactory for clinical and research applications while enabling further development of the well-tested, documented open-source software.

PMID:40562074 | DOI:10.1088/1361-6560/ade841

Colloids Surf B Biointerfaces. 2025 Jun 21;255:114902. doi: 10.1016/j.colsurfb.2025.114902. Online ahead of print.

ABSTRACT

The development of nanozyme to intervene in the tumor microenvironment (TME) is significant for tumor treatment. Comprehensive interventions of the TME based on different components and combined with advanced therapies are expected to improve tumor therapeutic effects, which could provide patients with new choices for therapeutic. Here, we developed a novel biomineralized nanosystem (CaCO3@Pd@C) as multifunctional nanozyme for intervening in the microenvironment to effectively treat cancer. The CaCO3@Pd@C was synthesized using the Stöber-like method and calcination treatment. The CaCO3@Pd@C possesses excellent peroxidase-like activity, good acid consumption capability, and efficient photothermal conversion effect in the TME. Mechanistic studies have shown that the inner CaCO3 core consume H+ to change the acidity, the middle layer of Pd nanoparticles catalyze the intracellular hydrogen peroxide conversion into hydroxyl radicals, and the outer layer of carbon nanosphere can convert near-infrared light into thermal energy in the TME. The cell and animal experiment results showed that the biocompatible biomineralized nanosystem can rapidly induce tumor cell apoptosis under synergistic effects. This work not only provides new perspectives for constructing microenvironmentally responsive nanosystems but also puts forward new prospects for developing fully active nanozymes and their biomedical applications.

PMID:40561689 | DOI:10.1016/j.colsurfb.2025.114902

OMICS. 2025 Jun 25. doi: 10.1089/omi.2025.0058. Online ahead of print.

ABSTRACT

Circadian rhythm and the sleep/wake cycle can influence metabolic regulation, eating habits, hormone release, and common chronic health conditions such as obesity, depression, diabetes, and sleep disorders. Drosophila melanogaster, the fruit fly, with its conserved molecular clocks and accessible assays, has been used as an ideal model system to study biological processes, for example, circadian rhythms, sleep, neurodevelopment, genetics, and behavior. Using an integrated approach combining high-throughput locomotor activity monitoring and untargeted metabolomics, we analyzed the behavioral and metabolic effects of a chronobiotic melatonin. The behavioral activity of fruit flies was recorded using an infrared-based monitoring device, followed by data analysis with open-source data packages ShinyR-DAM and VANESSA. We found that 1 mM and 4 mM melatonin doses significantly increased Drosophila locomotor activity. Melatonin at a high concentration (4 mM) exhibited a protective effect to reduce mortality in Drosophila. Despite these changes, melatonin preserved the flies' endogenous bimodal activity pattern, maintaining circadian alignment. Metabolomics analysis using high-performance liquid chromatography-mass spectrometry identified differentially abundant metabolites after melatonin administration compared with the vehicle treatment. We discovered 20 biologically relevant metabolites altered by melatonin, including key perturbations in arginine biosynthesis, alanine/aspartate/glutamate metabolism, and pyrimidine pathways. Notably, melatonin upregulated glutamine, a potential indicator of enhanced neurotransmitter synthesis and broadly modulated amino acid and nucleotide metabolism, suggesting dual roles in neuroprotection and energy homeostasis. This high-throughput omics study uncovers melatonin-induced behavioral and metabolic perturbations in Drosophila as a model organism, revealing how melatonin modulates locomotor activity and circadian integrity through specific alterations in metabolism.

PMID:40560839 | DOI:10.1089/omi.2025.0058

J Extracell Vesicles. 2025 Jun;14(6):e70102. doi: 10.1002/jev2.70102.

ABSTRACT

Xylella fastidiosa (Xf) is a Gram-negative bacterial plant pathogen responsible for severe diseases in a variety of economically important crops. A critical aspect of its virulence is the production of extracellular vesicles (EVs). In this study, we discovered that DNA-binding proteins and nonribosomal RNA-binding proteins are abundant in the corona of Xf-EVs. DNA-seq revealed enrichment of three genomic islands (GIs) in EVs, which carry molecular signatures indicative of horizontal gene transfer (HGT). The most abundant GI encodes five homologous small RNAs designated sXFs. RNA sequencing revealed a distinct pattern of noncoding RNAs enriched in EVs, including four island-encoded sXFs. One of the sXF's stem-loops contains motifs for binding the RNA chaperone Hfq, which is also abundant in EVs. Predicted target analysis suggests that sXFs play a role in regulation of natural competence in bacteria. Additionally, sXF plant target prediction identifies a coiled-coil nucleotide-binding domain leucine-rich repeat receptor (CNL) immune gene that is downregulated following Xf infection and Xf-EV treatment. We propose a model where Xf releases nucleic acid carrying EVs with two functions: one to deliver RNA-related cargo that regulates gene expression in both bacterial and plant cells, and another to deliver DNA-related cargo for the genetic transfer of genomic islands. We highlight island-encoded sXFs as potential virulence factors and vesiduction as a mechanism of HGT of sXFs in Xf. Taken together, our data on Xf-EV cargoes provide a molecular framework for understanding the virulence of Xf.

PMID:40560800 | DOI:10.1002/jev2.70102

Cell Rep. 2025 Jun 24;44(7):115898. doi: 10.1016/j.celrep.2025.115898. Online ahead of print.

ABSTRACT

Cell-type-specific alternative splicing (AS) enables differential gene isoform expression between diverse neuron types with distinct identities and functions. Current studies linking individual RNA-binding proteins (RBPs) to AS in a limited number of neuron types underscore the need for holistic modeling. Here, we use network reverse engineering to derive a map of the neuron-type-specific AS-regulatory landscape of 133 mouse neocortical cell types using pseudobulk transcriptomes derived from single-cell data. We infer the regulons of 350 RBPs and their cell-type-specific activities, among which we validate Elavl2 as a key RBP for medial ganglionic eminence (MGE)-specific splicing in GABAergic interneurons using an in vitro embryonic stem cell (ESC) differentiation system. We also identify a module of exons and candidate regulators specific to long- and short-projection neurons across multiple neuronal classes. This study provides a resource for elucidating splicing-regulatory programs that drive neuronal molecular diversity, including those that do not align with gene-expression-based classifications.

PMID:40560724 | DOI:10.1016/j.celrep.2025.115898

Elife. 2025 Jun 25;14:RP104278. doi: 10.7554/eLife.104278.

ABSTRACT

Tissue-resident memory T cells (TRM) protect from repeat infections within organs and barrier sites. The breadth and duration of such protection are defined at minimum by three quantities: the rate at which new TRM are generated from precursors, their rate of self-renewal, and their rate of loss through death, egress, or differentiation. Quantifying these processes individually is challenging. Here we combine genetic fate mapping tools and mathematical models to untangle these basic homeostatic properties of CD4+ TRM in the skin and gut lamina propria (LP) of healthy adult mice. We show that CD69+CD4+ TRM in skin reside for ∼24 days and self-renew more slowly, such that clones halve in size approximately every 5 weeks, and approximately 2% of cells are replaced daily from precursors. CD69+CD4+ TRM in LP have shorter residencies (∼14 days) and are maintained largely by immigration (4-6% per day). We also find evidence that the continuous replacement of CD69+CD4+ TRM at both sites derives from circulating effector-memory CD4+ T cells, in skin possibly via a local CD9- intermediate. Our approach maps the ontogeny of CD4+ TRM in skin and LP and exposes their dynamic and distinct behaviours, with continuous seeding and erosion potentially impacting the duration of immunity at these sites.

PMID:40560630 | DOI:10.7554/eLife.104278

Proc Natl Acad Sci U S A. 2025 Jul;122(26):e2422267122. doi: 10.1073/pnas.2422267122. Epub 2025 Jun 25.

ABSTRACT

Prostate cancer is a global health challenge, particularly for patients resistant to the second-generation anti-androgen receptor pathway inhibitors. The steroidogenic enzyme 3β-hydroxysteroid dehydrogenase type 1 (3βHSD1) has emerged as a promising therapeutic target and the corresponding inhibitors, biochanin-A (BCA) and its derivatives, suppress tumor growth in preclinical models and patients. However, the poor oral bioavailability of BCA hinders its clinical application. Here, we employed a sophisticated computational approach to refine the structural design of 3βHSD1 inhibitors. AlphaFold2 was utilized to construct detailed models of 3βHSD1 binding to various substrates. These models, in conjunction with the elucidated enzymatic mechanism of 3βHSD1, guided the optimization of a series of BCA-related compounds. Our structure-activity relationship studies identified HEAL-116 as a potent 3βHSD1 inhibitor. HEAL-116 exhibited enhanced binding specificity to the substrate-binding pocket of 3βHSD1 and effectively neutralized the local charge environment. The incorporation of hydrophilic groups in its structure also markedly enhanced its oral bioavailability. HEAL-116 robustly inhibited 3βHSD1 activity and exerted pronounced antitumor effect in biochemical, cellular, and mouse models. Our findings lay the foundation for the clinical translation of 3βHSD1 inhibitors, offering a promising therapeutic strategy for the management of prostate cancer and potentially other diseases.

PMID:40560608 | DOI:10.1073/pnas.2422267122

Proteomes. 2025 Jun 3;13(2):21. doi: 10.3390/proteomes13020021.

ABSTRACT

Myelodysplastic syndromes (MDS) belong to a category of malignant stem-cell and myeloid disorders that deteriorate the function of the hematopoietic system exacerbated by the omnipresent anemia that characterizes myelodysplasia. The pathogenesis of MDS is driven by cytogenetic abnormalities along with the excessive production of pro-inflammatory cytokines and disruptions in inflammatory signaling pathway, particularly through the influence of carbonylated proteins, which are linked to MDS progression. An additional and major contributor to the pathogenesis of MDS is oxidative stress marked by uncontrolled levels of reactive oxygen species (ROS), which have been suggested as potential biomarkers for assessing disease severity and stratifying MDS cases throughout a variety of methods. Excessive and non-accumulative levels of free iron can also lead to iron overload (IOL)-related promotion of a high oxidative state, whether we refer to treatment-related IOL or natural IOL mechanisms. Proteomic analysis has emerged as a powerful tool for profiling protein samples, and, consequently, understanding the molecular changes underlying MDS. In this review, we evaluated studies and their methodologies aiming in investigating distinctive proteomics signatures associated with MDS pathogenesis, focusing on the role of oxidative stress at the protein level.

PMID:40559994 | DOI:10.3390/proteomes13020021

Metabolites. 2025 Jun 13;15(6):399. doi: 10.3390/metabo15060399.

ABSTRACT

Background: Autism spectrum disorder (ASD) is increasingly linked to systemic metabolic dysfunction, potentially influenced by gut-brain axis dysregulation, but the underlying mechanisms remain unclear. Methods: We developed Personalized Metabolic Margin Mapping (PM3), a computational systems biology framework, to analyze RNA-seq data from 12 ASD and 12 control postmortem brain samples. The model focused on 158 curated metabolic genes selected for their roles in redox balance, mitochondrial function, neurodevelopment, and gut-brain interactions. Results: Using unsupervised machine learning (Isolation Forest) to detect outlier expression patterns, Euclidean distance, and percent expression difference metrics, PM3 revealed a consistent downregulation of glycolysis (e.g., -5.4% in PFKM) and mitochondrial enzymes (e.g., -12% in SUCLA2). By incorporating cofactor dependency and subcellular localization, PM3 identified a coordinated suppression of multivitamin transporters (e.g., -4.5% in SLC5A6, -3.5% in SLC19A2), potentially limiting cofactor availability and compounding energy deficits in ASD brains. Conclusions: These findings suggest a convergent metabolic dysregulation signature in ASD; wherein the subtle suppression of cofactor-dependent pathways may impair energy metabolism and neurodevelopment. We propose that chronic microbial lipopolysaccharide (LPS) exposure in ASD suppresses vitamin transporter function, initiating mitochondrial dysfunction and transcriptomic reprogramming. Validation in LPS-exposed systems using integrated transcriptomic-metabolomic analysis is warranted.

PMID:40559423 | DOI:10.3390/metabo15060399

NeuroSci. 2025 May 26;6(2):47. doi: 10.3390/neurosci6020047.

ABSTRACT

SH-SY5Y neuroblastoma cells can be effectively differentiated into a neuronal phenotype using retinoic acid (RA) and brain-derived neurotrophic factor (BDNF), making them a valuable in vitro model for studying neuronal differentiation. This study aimed to investigate the electrophysiological properties of SH-SY5Y cells following prolonged differentiation, with a focus on membrane characteristics, evoked action potentials, and the functionality of cellular components such as N-methyl-D-aspartate (NMDA) receptor. Whole-cell patch-clamp recordings were employed to evaluate ionic currents and action potentials in embryonic mouse cortical neurons (mCNs) and in both differentiated and undifferentiated SH-SY5Y neuroblastoma cells. Differentiated SH-SY5Y cells exhibited neurite outgrowth, evoked action potential firing, and functional NMDA receptor-mediated currents. Notably, atorvastatin significantly modulated the duration and firing of action potentials as well as NMDA receptor-mediated currents in differentiated SH-SY5Y cells. These findings highlight that neuronally differentiated SH-SY5Y cells expressing functional NMDA receptor-mediated currents serve as a robust and convenient model for investigating the molecular mechanisms of NMDA receptor function and for screening pharmacological agents targeting these receptors.

PMID:40559208 | DOI:10.3390/neurosci6020047

Cells. 2025 Jun 8;14(12):864. doi: 10.3390/cells14120864.

ABSTRACT

The role of periodontal ligament stem cells (PDLSCs) and dental pulp stem cells (DPSCs) in stimulating angiogenesis has been reported, but their angiogenetic potential has not been directly compared. In this work, paired PDLSCs and DPSCs, i.e., derived from the same donor, were tested for their immunophenotype and multi-differentiation capabilities, with particular emphasis on their pro-angiogenic activity. Flow cytometry was utilized to study the expression of mesenchymal stem cell, pericyte, and endothelial markers, while gene expression was evaluated through real-time PCR. The angiogenic potential was assessed recurring to tubulogenesis assay, co-cultures with Human Microvascular Endothelial Cell (HMEC-1), and VEGF-A quantification. The immunophenotype of DPSCs and PDLSCs was different in CD146+ and CD31+ cell subsets, but both cell types promoted HMEC-1 tubulogenesis in vitro. Consistently, VEGF-A gene expression level and its quantification in cell-conditioned media of PDLSCs and DPSCs was comparable between them, and both promoted the formation of vessel-like structures, when co-cultured with HMEC-1 cells. All together, these results showed the heterogeneity of PDLSCs and DPSCs, which are constituted of different cellular subsets, likely modulated by the microenvironmental cues. PDLSCs and DPSCs showed comparable pro-angiogenic activity, enhanced by the contemporary expression of angiogenic and chemotactic factors.

PMID:40558491 | DOI:10.3390/cells14120864

Adv Respir Med. 2025 Jun 16;93(3):19. doi: 10.3390/arm93030019.

ABSTRACT

Dormancy occurs when Mycobacterium tuberculosis (Mtb) enters a non-replicating and metabolically inactive state in response to hostile environment. During this state, it is highly resistant to conventional antibiotics, which increase the urgency to develop new potential drugs against dormant bacilli. In view of this, the dormancy survival regulator (DosR) protein is thought to be an essential component that plays a key role in bacterial adaptation to dormancy during hypoxic conditions. Herein, the NP-lib database containing natural product compounds was screened virtually against the binding site of the DosR protein using the MTiopen screen web server. A series of computational analyses were performed, including redocking, intermolecular interaction analysis, and MDS, followed by binding free energy analysis. Through screening, 1000 natural product compounds were obtained with docking energy ranging from -8.5 to -4.1 kcal/mol. The top four lead compounds were then selected for further investigation. On comparative analysis of intermolecular interaction, dynamics simulation and MM/GBSA calculation revealed that M3 docked with the DosR protein (docking score = -8.1 kcal/mol, RMSD = ~7 Å and ΔG Bind = -53.51 kcal/mol) exhibited stronger stability than reference compound Ursolic acid (docking score = -6.2 kcal/mol, RMSD = ~13.5 Å and ΔG Bind = -44.51 kcal/mol). Hence, M3 is recommended for further validation through in vitro and in vivo studies against latent tuberculosis infection.

PMID:40558118 | DOI:10.3390/arm93030019

mSystems. 2025 Jun 25:e0031225. doi: 10.1128/msystems.00312-25. Online ahead of print.

ABSTRACT

Growing research evidence indicates a substantial influence of the intra-tumor microbiome on tumor outcome. However, there is currently no consistent criterion for identifying the association of microbes with tumor progression and response to treatment across various types of cancer. In this study, we concentrate on the intra-tumor microbiome and develop the Tumor Microbiome Survival Index (TMSI), a measure indicative of cancer patient survival risk. Our indices revealed notable distinctions between two stratified risk groups for each of the 10 cancer types and could precisely predict patients' overall survival. For each type of cancer, our findings unveiled two distinct gene expression profiles and shed light on the varying patterns of immune and stromal cell enrichment between the two risk groups. Additionally, we noted that the high-TMSI group exhibited substantially elevated IC50 values for a number of drugs, indicating that individuals in the low-TMSI group might experience superior therapeutic effects from chemotherapy. These findings illuminate the complex dynamics between the tumor microbiome, the patient's immune reaction, and medical outcomes, thus shedding light on microbiome-based personalized therapeutic interventions.

IMPORTANCE: This work presents the Tumor Microbiome Survival Index (TMSI), a crucial innovation. It stratifies cancer patients into risk groups across 10 cancer types, accurately predicting survival. By uncovering distinct gene expression and immune/stromal cell patterns, it deepens understanding of tumor complexity. The finding of altered drug sensitivity in different TMSI groups offers insights for personalized chemotherapy. Overall, it paves the way for microbiome-targeted cancer therapies and enhanced patient prognostication.

PMID:40558028 | DOI:10.1128/msystems.00312-25

Front Microbiol. 2025 Jun 10;16:1570127. doi: 10.3389/fmicb.2025.1570127. eCollection 2025.

ABSTRACT

Tannins are plant secondary metabolites that bind organic carbon (C) and nitrogen (N), potentially altering substrate bioavailability for enteric fermentation in ruminants. This interaction may reduce greenhouse gas (GHG) emissions and influence nitrogen partitioning. Given tannins' resistance to ruminal degradation and persistence through the gastrointestinal tract, this study investigated the effects of a tannin-based feed additive on fecal microbial diversity, fecal chemical composition, and GHG emissions. Twenty-four early- to mid-lactation dairy cows were randomized to receive either a tannin-based feed additive (TRT; containing condensed and hydrolyzable tannins from Schinopsis quebracho-colorado [Schltdl.]) or a control diet (CON) for 64 days. Cows were blocked by parity, dry matter intake, milk yield, body weight, and days in milk. Fecal samples were collected on days 0, 16, 32, and 64 and analyzed using 16S rRNA gene amplicon sequencing. Fecal C, N, and indole-3-lactate were measured, and GHG emissions (N2O, CH4, CO2) were assessed via 14-day laboratory incubation. A total of 1,538 amplicon sequence variants were identified, with Firmicutes as the dominant phylum. Fecal phylogenetic diversity showed a significant treatment × day interaction (p < 0.01), with TRT cows exhibiting reduced microbial diversity from day 16 to 64. Fecal C and N concentrations were significantly lower (p < 0.01) in TRT cows on day 16, while indole-3-lactate levels were higher on day 64 (p = 0.02). GHG emissions did not differ significantly between treatments. The tannin-based feed additive influenced fecal microbial community structure and select chemical parameters but did not significantly affect GHG emissions from feces. These findings suggest that dietary tannins may modulate gut microbial ecology with minimal impact on downstream manure-related emissions.

PMID:40556886 | PMC:PMC12186457 | DOI:10.3389/fmicb.2025.1570127

Anal Methods. 2025 Jun 25. doi: 10.1039/d5ay00550g. Online ahead of print.

ABSTRACT

In the ToF-SIMS in situ analysis of mouse liver tissue, freeze-drying is superior to room-temperature drying and chemical fixation, minimizing lipid spillage while maintaining structural integrity. Freeze-drying preserves tissue structure with minimal lipid loss, whereas room-temperature drying leads to lipid spreading and chemical fixation results in background noise. Freeze-drying balances structural integrity, molecular preservation, and spectral clarity, making it the optimal ToF-SIMS prep method. Although the method was tested on lipid-rich liver tissue, it provides a framework for tissue specific preparation of ToF-SIMS.

PMID:40556438 | DOI:10.1039/d5ay00550g

Nat Comput Sci. 2025 Jun 24. doi: 10.1038/s43588-025-00820-x. Online ahead of print.

ABSTRACT

Despite recent advances in RNA-targeting drug discovery, the development of data-driven deep learning models remains challenging owing to limited validated RNA-small molecule interaction data and scarce known RNA structures. In this context, we introduce RNAsmol, a sequence-based deep learning framework that incorporates data perturbation with augmentation, graph-based molecular feature representation and attention-based feature fusion modules to predict RNA-small molecule interactions. RNAsmol employs perturbation strategies to balance the bias between the true negative and unknown interaction space, thereby elucidating the intrinsic binding patterns between RNA and small molecules. The resulting model demonstrates accurate predictions of the binding between RNA and small molecules, outperforming other methods in ten-fold cross-validation, unseen evaluation and decoy evaluation. Moreover, we use case studies to visualize molecular binding profiles and the distribution of learned weights, providing interpretable insights into RNAsmol's predictions. In particular, without requiring structural input, RNAsmol can generate reliable predictions and be adapted to various drug design scenarios.

PMID:40555786 | DOI:10.1038/s43588-025-00820-x

Nat Commun. 2025 Jun 24;16(1):5370. doi: 10.1038/s41467-025-58897-x.

ABSTRACT

The development of non-human primate models is essential for the fields of developmental and regenerative biology because those models will more closely approximate human biology than do murine models. Based on single cell RNAseq and fluorescence-activated cell sorting, we report the identification and functional characterization of two quiescent stem cell populations (skeletal muscle stem cells (MuSCs) and mesenchymal stem cells termed fibro-adipogenic progenitors (FAPs)) in the non-human primate Microcebus murinus (the gray mouse lemur). We demonstrate in vivo proliferation, differentiation, and self-renewal of both MuSCs and FAPs. By combining cell phenotyping with cross-species molecular profiling and pharmacological interventions, we show that mouse lemur MuSCs and FAPs are more similar to human than to mouse counterparts. We identify unexpected gene targets involved in regulating primate MuSC proliferation and primate FAP adipogenic differentiation. Moreover, we find that the cellular composition of mouse lemur muscle better models human muscle than does macaque (Macaca fascicularis) muscle. Finally, we note that our approach presents as a generalizable pipeline for the identification, isolation, and characterization of stem cell populations in new animal models.

PMID:40555729 | DOI:10.1038/s41467-025-58897-x

J Immunother Cancer. 2025 Jun 24;13(6):e011355. doi: 10.1136/jitc-2024-011355.

ABSTRACT

Abrogating the immunoevasive role of the tumor immune microenvironment (TIME) represents a critical yet still elusive challenge in cancer treatment. Progress in this area has been hampered by both technological limitations and incomplete understanding of TIME-dependent immunoevasion mechanisms. We hypothesize that the immune-evasive role of TIME subpopulations-including regulatory T cells, cancer-associated fibroblasts, and tumor-associated macrophages-is critically mediated by hyperconnected Master Regulator Checkpoint (MRC) modules whose aberrant activity, as induced by paracrine signals, can be abrogated or modulated either genetically or pharmacologically. MRCs are primarily composed of transcription and co-transcription factors, acting downstream of surface receptors and signal transduction cascades to control the transcriptional identity and, ultimately, the phenotype of individual TIME subpopulations. Pharmacological inhibition of subpopulation-specific MRC proteins can thus help reprogram the TIME and potentially abrogate or modulate its immunosuppressive state. This paradigm shift, away from single ligand/receptor targeting, is supported by recent algorithmic, experimental, and clinical advances allowing systematic identification of MRCs and their pharmacological modulators using systems immunology-based approaches. Refocusing the deployment of existing tools and experimental methods that have proven successful in tumor cell contexts to identify and validate MRC-targeting agents capable of remodeling the immunosuppressive cell states of the tumor microenvironment can potentially pave the road to novel combination therapy synergizing with immune checkpoint inhibitors.

PMID:40555564 | DOI:10.1136/jitc-2024-011355

J Immunother Cancer. 2025 Jun 24;13(6):e011458. doi: 10.1136/jitc-2025-011458.

ABSTRACT

Tumor-initiated emergency granulopoiesis results in expansion of the circulating neutrophil compartment and neutrophil recruitment into the tumor microenvironment (TME), which may in turn promote tumor progression. Although an elevated circulating neutrophil-to-lymphocyte ratio (cNLR) has repeatedly been demonstrated to be an adverse prognostic factor in patients with non-small cell lung cancer (NSCLC), whether this neutrophil expansion in circulation reflects a similar relative neutrophil abundance in the TME remains unclear. We sought to characterize the relationships between cNLR and the intratumoral neutrophil-to-lymphocyte ratio (tNLR), between tNLR and proteogenomic and immune features of NSCLC tumors, and between tNLR and prognosis.We analyzed tNLR (transcriptomic signatures) and cNLR in a prospectively-enrolled cohort of patients with NSCLC (stage IA-III) that was subjected to multifaceted immunoprofiling (ImmunogenomiC prOfiling of early-stage Non-small cell lung cancer (ICON), N=150). We examined the relationship between tNLR and genomic, transcriptomic, and proteomic features of NSCLC tumors in The Cancer Genome Atlas (TCGA) and ICON. Finally, tNLR was analyzed for associations with postoperative recurrence-free survival (ICON) and overall survival (TCGA).In the ICON cohort, tNLR was significantly positively correlated with cNLR, but there was no association between intratumoral and circulating neutrophils or lymphocytes alone. High tNLR was associated with poor postoperative recurrence-free survival, and multivariate analysis indicated tNLR was a stronger driver of outcomes than cNLR. Mutations in KEAP1, STK11, PTEN, PI3K, and TSC2 were associated with an increased tNLR. Tumors with elevated tNLR were marked by proteomic and transcriptomic features indicative of increased cell cycle, receptor tyrosine kinase, and YAP signaling, as well as immunosuppression (reduced IFNG and GZMB expression). Flow cytometry and multiplex immunofluorescence confirmed reduced CD8+granzyme B+ T cells in the TME of tumors with high tNLR. Finally, TCGA confirmed associations between tNLR with prognosis, mutational status, and proteomic/transcriptomic features, and further showed that tNLR is prognostically relevant in multiple solid cancers.tNLR is mirrored by NLR in circulation (cNLR) in NSCLCs. High tNLR is associated with an immunosuppressed TME phenotype and poor prognosis across multiple cancers. These findings support ongoing investigations of the utility of cNLR and tNLR as clinical biomarkers in the context of patients with NSCLC treated with immune checkpoint inhibitor therapies.

PMID:40555561 | DOI:10.1136/jitc-2025-011458