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Objective: Probiotics are living microorganisms that can provide health benefits when consumed. Here, we investigated the effects of probiotics on gene expression in the spleen of mice using RNA-sequencing analysis between negative control and probiotic groups (including 4 Lactobacillus strains: Lactobacillus fermentum, L. casei, L. plantarum, and L. brevis). Methods: Mice exposed with probiotic in 4 weeks by intragastric administration. Then, spleen tissues of the control and probiotics groups were collected on days 14 and 28 for RNA sequencing. Results: In total, 665, 186, and 81 differentially expressed genes (DEGs) were significantly expressed on day 14 vs control, day 28 vs control groups, and probiotics day 28 vs day 14 groups, respectively. On the other hand, 12 toll-like receptor genes underwent additional validation through quantitative real-time polymerase chain reaction (qRT-PCR), affirming the increased alignment between qRT-PCR and RNA-Seq findings. In addition, the Kyoto encyclopedia of genes and genomes and gene ontology analyses revealed that the DEGs were predominantly enriched in defense responses to pathogens, including inflammatory bowel diseases, malaria, leukaemia virus 1, and herpes virus, as well as immune processes related to immune response and signal transduction. This study represents the first investigation into mice's gene expression in the spleen exposed to probiotics using Lactobacillus spp. isolated from a field strain in Vietnam. Conclusion: Our results provide valuable insights into the impacts and functions of probiotics on mammalian development, offering crucial information for the potential therapeutic use of probiotics in defending against pathogens in Vietnam. The findings from this study highlight the potential of probiotics in modulating gene expression in the spleen, which may have implications for immune function and overall health in mice. [ABSTRACT FROM AUTHOR]

While durable antibody responses from long-lived plasma cell (LLPC) populations are important for protection against pathogens, LLPC may be harmful if they produce antibodies against self-proteins or self-nuclear antigens as occurs in autoimmune diseases such as systemic lupus erythematosus (SLE). Thus, the elimination of autoreactive LLPC may improve the treatment of antibody-driven autoimmune diseases. However, LLPC remain a challenging therapeutic target. Here, we compare the matched bone marrow (BM) and peripheral blood (PBL) plasma cell (PC) compartments of SLE and healthy donors (HD). We show a similar distribution of CD138- and CD138+ PC, including putative LLPC (CD19- CD138+ CD38+), between SLE and HD BM. For both SLE and HD, CD138+ PC are at a higher frequency in BM than PBL. Expression of Ki-67 associates with the PBL compartment where it is found on all PC subsets regardless of CD19 or CD138 expression. Transcriptomic analysis identifies an interferon (IFN) gene signature in transitional B cells in the SLE BM, but surprisingly also in the BM PC derived from SLE. BM PC and B cells phosphorylate STAT1 in response to type I IFN stimulation in vitro , but with decreased fold change compared to those from the PBL. While BM PC bind type I IFN receptor-blocking antibody anifrolumab, it is to a lesser degree than circulating B cells. Anti-nuclear autoantibodies (ANA) are found in the BM supernatant and PBL serum of SLE patients. Both SLE and HD BM-derived PC have increased survival compared to their PBL counterparts when treated with verdinexor. In summary, these findings show evidence of IFN activation in BM PC from SLE. [ABSTRACT FROM AUTHOR]

Background and Objective: Mitochondria are crucial to the function of renal tubular cells, and their dynamic perturbation in many aspects is an important mechanism of diabetic kidney disease (DKD). Single-nucleus RNA sequencing (snRNA-seq) technology is a high-throughput sequencing analysis technique for RNA at the level of a single cell nucleus. Here, our DKD mouse kidney single-cell RNA sequencing conveys a more comprehensive mitochondrial profile, which helps us further understand the therapeutic response of this unique organelle family to drugs. Methods: After high fat diet (HFD), mice were intraperitoneally injected with streptozotocin (STZ) to induce DKD, and then divided into three subsets: CON (healthy) subset, DKD (vehicle) subset, and LST (losartan; 25 mg/kg/day) subset. Divide HK-2 cell into LG (low glucose; 5 mM) and HG (high glucose; 30 mM) and HG + LST (losartan; 1 µ M) subsets. snRNA-seq was performed on the renal tissues of LST and DKD subset mice. To reveal the effects of losartan on gene function and pathway changes in renal tubular mitochondria, Gene Ontology (GO) enrichment analysis and GSEA/GSVA scoring were performed to analyze the specific response of proximal tubular (PT) cell mitochondria to losartan treatment, including key events in mitochondrial homeostasis such as mitochondrial morphology, dynamics, mitophagy, autophagic flux, mitochondrial respiratory chain, apoptosis, and ROS generation. Preliminary validation through in vitro and in vivo experiments, including observation of changes in mitochondrial morphology and dynamics using probes such as Mitotracker Red, and evaluation of the effect of losartan on key events of mitochondrial homeostasis perturbation using electron microscopy, laser confocal microscopy, immunofluorescence, and Western blotting. Detection of autophagic flux in cells by transfecting Ad-mCherry-GFP-LC3B dual fluorescence labeled adenovirus. Various fluorescent probes and energy detector are used to detect mitochondrial apoptosis, ROS, and respiration of mitochondrion. Results: Through the single-cell atlas of DKD mouse kidneys, it was found that losartan treatment significantly increased the percentage of PT cells. Gene Ontology (GO) enrichment analysis of differentially expressed genes showed enrichment of autophagy of mitochondrion pathway. Further GSEA analysis and GSVA scoring revealed that mitophagy and other key mitochondrial perturbation events, such as ROS production, apoptosis, membrane potential, adenosine triphosphate (ATP) synthesis, and mitochondrial dynamics, were involved in the protective mechanism of losartan on PT cells, thereby improving mitochondrial homeostasis. Consistent results were also obtained in mice and cellular experiments. In addition, we highlighted a specific renal tubular subpopulation with mitophagy phenotype found in single-cell data, and preliminarily validated it with co-localization and increased expression of Pink1 and Gclc in kidney specimens of DKD patients treated with losartan. Conclusions: Our research suggests that scRNA-seq can reflect the multifaceted mitochondrial landscape of DKD renal tubular cells after drug treatment, and these findings may provide new targets for DKD therapy at the organelle level. [ABSTRACT FROM AUTHOR]

Reconstructing large, inflammatory maxillofacial defects using stem cell-based therapy faces challenges from adverse microenvironments, including high levels of reactive oxygen species (ROS), inadequate oxygen, and intensive inflammation. Here, inspired by the reaction mechanisms of intracellular antioxidant defense systems, we propose the de novo design of an artificial antioxidase using Ru-doped layered double hydroxide (Ru-hydroxide) for efficient redox homeostasis and maxillofacial bone regeneration. Our studies demonstrate that Ru-hydroxide consists hydroxyls-synergistic monoatomic Ru centers, which efficiently react with oxygen species and collaborate with hydroxyls for rapid proton and electron transfer, thus exhibiting efficient, broad-spectrum, and robust ROS scavenging performance. Moreover, Ru-hydroxide can effectively sustain stem cell viability and osteogenic differentiation in elevated ROS environments, modulating the inflammatory microenvironment during bone tissue regeneration in male mice. We believe this Ru-hydroxide development offers a promising avenue for designing antioxidase-like materials to treat various inflammation-associated disorders, including arthritis, diabetic wounds, enteritis, and bone fractures. Reconstructing inflammatory maxillofacial defects is a global health challenge. This study presents an artificial antioxidase with rapid proton/electron transfer for efficient redox homeostasis and maxillofacial bone regeneration. [ABSTRACT FROM AUTHOR]

Methamphetamine is a highly addictive stimulant known to cause neurotoxicity, cognitive deficits, and immune dysregulation in the brain. Despite significant research, the molecular mechanisms driving methamphetamine-induced neurotoxicity and glial cell dysfunction remain poorly understood. This study investigates how methamphetamine disrupts glial cell function and contributes to neurodevelopmental and neurodegenerative processes. Using single-cell RNA sequencing (scRNA-seq), we analyzed the transcriptomes of 4000 glial cell-associated genes from the cortical regions of mice chronically administered methamphetamine. Methamphetamine exposure altered the key pathways in astrocytes, including the circadian rhythm and cAMP signaling; in microglia, affecting autophagy, ubiquitin-mediated proteolysis, and mitophagy; and in oligodendrocytes, disrupting lysosomal function, cytoskeletal regulation, and protein processing. Notably, several transcription factors, such as Zbtb16, Hif3a, Foxo1, and Klf9, were significantly dysregulated in the glial cells. These findings reveal profound methamphetamine-induced changes in the glial transcriptomes, particularly in the cortical regions, highlighting potential molecular pathways and transcription factors as targets for therapeutic intervention. This study provides novel insights into the glial-mediated mechanisms of methamphetamine toxicity, contributing to our understanding of its effects on the central nervous system and laying the groundwork for future strategies to mitigate its neurotoxic consequences. [ABSTRACT FROM AUTHOR]

Hypoxic tumors present a significant challenge in cancer therapy due to their ability to adaptation in low-oxygen environments, which supports tumor survival and resistance to treatment. Enhanced mitophagy, the selective degradation of mitochondria by autophagy, is a crucial mechanism that helps sustain cellular homeostasis in hypoxic tumors. In this study, we develop an azocalix[4]arene-modified supramolecular albumin nanoparticle, that co-delivers hydroxychloroquine and a mitochondria-targeting photosensitizer, designed to induce cascaded oxidative stress by regulating mitophagy for the treatment of hypoxic tumors. These nanoparticles are hypoxia-responsive and release loaded guest molecules in hypoxic tumor cells. The released hydroxychloroquine disrupts the mitophagy process, thereby increasing oxidative stress and further weakening the tumor cells. Additionally, upon laser irradiation, the photosensitizer generates reactive oxygen species independent of oxygen, inducing mitochondria damage and mitophagy activation. The dual action of simultaneous spatiotemporal mitophagy activation and mitophagy flux blockade results in enhanced autophagic and oxidative stress, ultimately driving tumor cell death. Our work highlights the effectiveness of hydroxychloroquine-mediated mitophagy blockade combined with mitochondria-targeted photosensitizer for cascade-amplified oxidative stress against hypoxic tumors. Enhanced mitophagy has been recognized as crucial mechanism to sustain cellular homeostasis in hypoxic tumors. Here, this group fabricates an azocalix[4]arene-modified supramolecular albumin nanoparticle codelivering hydroxychloroquine (HCQ) and sulfur-substituted methylated nile blue analog, capable of inducing cascaded oxidative stress via regulating mitophagy for hypoxic tumors treatment. [ABSTRACT FROM AUTHOR]

As a form of skin cancer, melanoma's incidence rate is continuing to rise globally. Therefore, there is an urgent need to find new agents to improve survival in melanoma patients. Isoflavones, a class of phytoestrogens, are primarily found in soy and other legumes. Cumulating evidence demonstrates that isoflavones exhibits significant anti-tumor properties and is beneficial for the prevention and treatment of melanoma. In the present study, we aim to investigate the anti-melanoma role of tricholoma isoflavone derivative CA028. By using in vitro melanoma cell line models, A375 and A2058 and in vivo xenograft mouse model, our results indicate that melanoma proliferation, migration, and invasion are attenuated following CA028 treatment. In addition, the treatment of CA028 induced cell apoptosis of melanoma. Finally, we addressed the mechanism of CA028 against melanoma by comparative transcriptomic analysis. The results of gene ontology highlighted the involvement of CA028's targets in the cell proliferation, cell apoptosis, and migration ability of melanoma cells. Furthermore, Ingenuity Pathway Analysis constructed the network involved in the apoptotic roles of CA028 through targeting p53 signaling and death receptor signaling. For the first time, our data suggested the possible use of modified isoflavone for therapeutic applications against melanoma. [ABSTRACT FROM AUTHOR]

Symbioses are major drivers of organismal diversification and phenotypic innovation. However, how long-term symbioses shape whole genome evolution in metazoans is still underexplored. Here, we use a giant clam (Tridacna maxima) genome to demonstrate how symbiosis has left complex signatures in an animal's genome. Giant clams thrive in oligotrophic waters by forming a remarkable association with photosymbiotic dinoflagellate algae. Genome-based demographic inferences uncover a tight correlation between T. maxima global population change and major paleoclimate and habitat shifts, revealing how abiotic and biotic factors may dictate T. maxima microevolution. Comparative analyses reveal genomic features that may be symbiosis-driven, including expansion and contraction of immunity-related gene families and a large proportion of lineage-specific genes. Strikingly, about 70% of the genome is composed of repetitive elements, especially transposable elements, most likely resulting from a symbiosis-adapted immune system. This work greatly enhances our understanding of genomic drivers of symbiosis that underlie metazoan evolution and diversification. The Tridacna maxima genome reveals how long-term symbiosis drives evolution, highlighting climate-driven population shifts, immune gene adaptations, and transposable element expansions shaping its genetic landscape. [ABSTRACT FROM AUTHOR]

SGLT2 inhibitors (SGLT2i) and GLP1 receptor (GLP1R) agonists have kidney protective effects. To better understand their molecular effects, RNA sequencing was performed in SGLT2-positive proximal tubule segments isolated by immunostaining-guided laser capture microdissection. Male adult DBA wild-type (WT) and littermate diabetic Akita mice ± Sglt1 knockout (Sglt1-KO) were given vehicle or SGLT2i dapagliflozin (dapa; 10 mg/kg diet) for 2 wk, and other Akita mice received GLP1R agonist semaglutide [sema; 3 nmol/(kg body wt·day), sc]. Dapa (254 ± 11 mg/dL) and Sglt1-KO (367 ± 11 mg/dL) but not sema (407 ± 44 mg/dL) significantly reduced hyperglycemia in Akita mice (480 ± 33 mg/dL). The 20,748 detected annotated protein-coding genes included robust enrichment of S1-segment marker genes. Akita showed 198 (∼1%) differentially expressed genes versus WT (DEGs; adjusted P ≤ 0.1), including downregulation of anionic transport, unsaturated fatty acid, and carboxylic acid metabolism. Dapa changed only two genes in WT but restored 43% of DEGs in Akita, including upregulation of the lipid metabolic pathway, carboxylic acid metabolism, and organic anion transport. In Akita, sema restored ∼10% of DEGs, and Sglt1-KO and dapa were synergistic (restored ∼61%), possibly involving additive blood glucose effects (193 ± 15 mg/dL). Targeted analysis of transporters and channels (t test, P < 0.05) revealed that ∼10% of 526 detectable transporters and channels were downregulated by Akita, with ∼60% restored by dapa. Dapa, dapa + Sglt1-KO, and sema also altered Akita-insensitive genes. Among DEGs in Akita, ∼30% were unresponsive to any treatment, indicating potential new targets. In conclusion, SGLT2i restored transcription for multiple metabolic pathways and transporters in SGLT2-positive proximal tubule segments in diabetic mice, with a smaller effect also observed for GLP1R agonism. NEW & NOTEWORTHY: SGLT2 inhibitors and GLP1 receptor agonists have kidney protective effects. By combining immunostaining-guided laser capture microdissection and RNA sequencing, the study established how the gene expression profile changes in SGLT2-positive proximal tubule cells in response to type 1 Akita diabetes and to pharmacological intervention by SGLT2 inhibition or GLP1R agonism and genetic deletion of SGLT1. The data also indicate genes unresponsive to those treatments that may include new therapeutical candidates. [ABSTRACT FROM AUTHOR]

Melatonin is a hormone released by the pineal gland that regulates the sleep–wake cycle. It has been widely studied for its therapeutic effects on Alzheimer's disease (AD), particularly through the amyloidosis, oxidative stress, and neuroinflammation pathways. Nevertheless, the mechanisms through which it exerts its neuroprotective effects in AD are still largely unknown. Data mining was used to identify potential gene targets that link melatonin's effects to AD pathways, yielding a comprehensive view of the underlying molecular mechanisms. We identified 3397 genes related to AD from DisGeNet and 329 melatonin gene targets from ChEMBL, which revealed 223 overlapping genes and the potential shared pathways. These genes were used to construct a protein–protein interaction (PPI) network comprising 143 nodes and 823 edges, which demonstrated significant PPI enrichment. A cluster analysis highlighted two key clusters centered on MMP2 and NR3C1, with both genes playing crucial roles in steroid hormone signaling, apoptosis, and monoamine neurotransmission. Gene Ontology (GO) enrichment and KEGG pathway analyses further elucidated their involvement in critical pathways, for instance, steroid hormone signaling and apoptosis regulation, significantly influencing AD pathology through mechanisms such as extracellular matrix remodeling, epigenetic modifications, and neuroinflammation. Our findings emphasize MMP2 and NR3C1 as important gene targets for future research on melatonin treatment in AD, paving the way for further investigations into their roles in AD pathophysiology. [ABSTRACT FROM AUTHOR]

Hepatocellular carcinoma (HCC) is a highly heterogeneous cancer with a poor prognosis. During the development of cancer cells, mitochondria influence various cell death patterns by regulating metabolic pathways such as oxidative phosphorylation. However, the relationship between mitochondrial function and cell death patterns in HCC remains unclear. In this study, we used a comprehensive machine learning framework to construct a mitochondrial functional activity-associated programmed cell death index (MPCDI) based on scRNA-seq and RNA-seq data from TCGA, GEO, and ICGC datasets. The index signature was used to classify HCC patients, and studied the multi-omics features, immune microenvironment, and drug sensitivity of the subtypes. Finally, we constructed the MPCDI signature consisting of four genes (S100A9, FYN, LGALS3, and HMOX1), which was one of the independent risk factors for the prognosis of HCC patients. The HCC patients were divided into high- and low-MPCDI groups, and the immune status was different between the two groups. Patients with a high MPCDI had higher TIDE scores and poorer responses to immunotherapy, suggesting that high-MPCDI patients might not be suitable for immunotherapy. By analyzing the drug sensitivity data of CTRP, GDSC, and PRISM databases, it was found that staurosporine has potential therapeutic significance for patients with a high MPCDI. In summary, based on the characteristics of mitochondria function and PCD patterns, we used single-cell and transcriptome data to identify four genes and construct the MPCDI signature, which provided new perspectives and directions for the clinical diagnosis and personalized treatment of HCC patients. [ABSTRACT FROM AUTHOR]

Dissecting the genetic mechanisms underlying urinary metabolite concentrations can provide molecular insights into kidney function and open possibilities for causal assessment of urinary metabolites with risk factors and disease outcomes. Proton nuclear magnetic resonance metabolomics provides a high-throughput means for urinary metabolite profiling, as widely applied for blood biomarker studies. Here we report a genome-wide association study meta-analysed for 3 European cohorts comprising 8,011 individuals, covering both people with type 1 diabetes and general population settings. We identify 54 associations (p < 9.3 × 10−10) for 19 of 54 studied metabolite concentrations. Out of these, 33 were not reported previously for relevant urinary or blood metabolite traits. Subsequent two-sample Mendelian randomization analysis suggests that estimated glomerular filtration rate causally affects 13 urinary metabolite concentrations whereas urinary ethanolamine, an initial precursor for phosphatidylcholine and phosphatidylethanolamine, was associated with higher eGFR lending support for a potential protective role. Our study provides a catalogue of genetic associations for 53 metabolites, enabling further investigation on how urinary metabolites are linked to human health. Here, the authors identified genetic variants associated with urinary metabolites in 8,011 individuals. Further causal analysis suggested estimated kidney filtration rate (eGFR) affected 13 metabolites while ethanolamine was associated with higher eGFR. [ABSTRACT FROM AUTHOR]

Acute myeloid leukemia (AML) is a hematological cancer prevalent worldwide. Anoikis-related genes (ARGs) are crucial in the progression of cancer and metastasis of tumors. However, their role in AML needs to be clarified. In the present study, differential analysis was performed on data from The Cancer Genome Atlas database to identify differentially expressed ARGs (DE-ARGs). Subsequently, a prognostic model for patients with AML was constructed using univariate Cox, Least Absolute Shrinkage and Selection Operator and multivariate Cox regression analyses. This model was based on four key DE-ARGs [lectin galactoside-binding soluble 1 (LGALS1), integrin subunit α 4 (ITGA4), hepatocyte growth factor (HGF) and Ras homolog gene family member C (RHOC)]. Independent prognostic factors for AML included prior treatment, age, risk scores and diagnosis. A nomogram was constructed based on these factors to aid clinical decision-making. Furthermore, bone marrow samples were collected from individuals diagnosed with AML and healthy donors to validate the expression of the identified ARGs using reverse transcription-quantitative PCR. The mRNA levels of LGALS1 and RHOC were significantly higher, while those of ITGA4 and HGF were significantly lower in patients with AML than in healthy donors (all P<0.05). The results of the present study expands the understanding of the function of ARGs in AML, providing a new theoretical basis for the treatment of AML. [ABSTRACT FROM AUTHOR]