BioFactors最新文献

Colorectal cancer (CRC) exhibits a complex tumor microenvironment with significant cellular heterogeneity, particularly involving cancer-associated fibroblasts that influence tumor behavior and metastasis. This study integrated single-cell RNA sequencing and spatial transcriptomics to dissect fibroblast heterogeneity in CRC. Data processing employed Seurat for quality control, principal component analysis for dimensionality reduction, and t-Distributed Stochastic Neighbor Embedding for visualization. Differentially expressed genes were identified using DESeq2. Immune infiltration was assessed via Single-Sample Gene Set Enrichment Analysis, CIBERSORT, and xCell algorithms. Prognostic genes were identified through univariate Cox regression, followed by consensus clustering and survival analysis. Metabolic pathways were explored using scMetabolism. Experimental validation involved CCK8, scratch, and Transwell assays to evaluate the roles of key genes BGN and CERCAM in CRC cell proliferation and metastasis. Machine learning-driven analysis identified four fibroblast-associated genes (TRIP6, TIMP1, BGN, and CERCAM) demonstrating significant prognostic relevance in CRC. Consensus clustering based on these biomarkers stratified CRC patients into three distinct molecular subtypes (Clusters A–C). Notably, Cluster C exhibited the most unfavorable clinical outcomes coupled with marked upregulation of all four fibroblast-related genes. Comprehensive immune profiling revealed paradoxical features in Cluster C: heightened global immune activation (characterized by substantial leukocyte infiltration) coexisted with specific immunosuppressive elements, including significant enrichment of pro-tumorigenic M0 macrophages, depletion of anti-tumor plasma cells, and resting memory CD4+ T cells, along with coordinated upregulation of multiple immune checkpoint molecules. Computational prediction using the TIDE platform suggested enhanced immunotherapy responsiveness in Cluster C patients. Functional validation demonstrated that knockdown of BGN or CERCAM significantly impaired malignant phenotypes, reducing proliferative capacity, migration potential, and invasive ability. Fibroblasts demonstrate significant heterogeneity within the CRC immune microenvironment, impacting prognosis and therapeutic responses. Key genes BGN and CERCAM emerge as potential immunotherapeutic targets, offering new strategies for precision treatment of CRC.

Chronic exposure to arsenic can lead to various health issues, including cancer. Concerns have been mounting about the enhancement of arsenic toxicity through co-exposure to various prevalent lifestyle habits. Smokeless tobacco (SLT) products are commonly consumed in South Asian countries, where their use frequently co-occurs with exposure to arsenic from contaminated groundwater. To decipher the in vitro molecular and cellular responses to arsenic and/or smokeless tobacco, we performed temporal multi-omics analysis of the transcriptome and DNA methylome remodeling in exposed hTERT-immortalized human normal oral keratinocytes (NOK), as well as arsenic and/or smokeless tobacco genotoxicity and mutagenicity investigations in NOK cells and in human p53 knock-in murine embryonic fibroblasts (Hupki MEF). RNAseq results from acute exposures of NOK cell to arsenic alone and in combination with smokeless tobacco extract revealed upregulation of genes with roles in cell cycle changes, apoptosis and inflammatory responses. This was in keeping with global DNA hypomethylation affecting genes involved in the same processes after chronic treatment. At the phenotypic level, we observed a dose-dependent decrease in NOK cell viability, induction of DNA damage, cell cycle changes and increased apoptosis, with the most pronounced effects observed under arsenic and SLT co-exposure conditions. Live-cell imaging experiments indicated that the DNA damage likely resulted from induction of apoptosis, an observation validated by a lack of exome-wide mutagenesis in response to chronic exposure to arsenic and/or smokeless tobacco. In sum, our integrative omics study provides novel insights into the acute and chronic responses to arsenic and smokeless tobacco (co-)exposure, with both types of responses converging on several key mechanisms associated with cancer hallmark processes. The resulting rich catalogue of molecular programs in oral cells regulated by arsenic and smokeless tobacco (co-)exposure may provide bases for future development of biomarkers for use in molecular cancer epidemiology studies of exposed populations at risk.

Calciprotein particles (CPPs) are blood-borne circulating nanoparticles composed of calcium phosphate and proteins that are known to exacerbate pathological processes such as chronic kidney disease-mineral bone disorder (CKD-MBD). Despite the significant interest in CKD-MBD pathogenesis, research directly addressing CPP-induced fibrosis in renal proximal tubules is rare, largely owing to the lack of suitable in vitro tissue models. Our study confirmed that 3D-cultured renal proximal tubule epithelial cells (PTECs) exhibited enhanced pathological characteristics compared to 2D-cultured PTECs when treated with CPPs, a key factor in CKD-MBD, and the uremic toxin. 3D-cultured PTECs under CKD-inducing conditions by CPPs were associated with epithelial–mesenchymal transition (EMT), mediated by transforming growth factor-β1 (TGF-β1), with notable changes in early EMT marker expression. Furthermore, this was attributed to increased expression of the calcium-sensing receptor (CASR), a receptor for CPPs, and activation of the downstream cell division control protein 42 (CDC42), leading to EMT progression. This study underscores the potential of PTEC-on-a-chip systems to serve as drug testing models, given the heightened sensitivity of these cells to external environments. This approach provides a better understanding of the pathological features of CKD and could contribute to the development of more effective in vitro models and therapeutics.

Compared to the well-defined immune-modulating effect of butyrate, the understanding of the effect of other protein fermentation metabolites is limited. This study aimed to investigate the impact of protein-derived metabolites (valerate, branched-chain fatty acids, ammonium, phenol, p-Cresol, indole, and hydrogen sulfide) on cytokine production in murine bone marrow-derived dendritic cells (BMDCs) stimulated with lipopolysaccharides (LPS), Lactobacillus acidophilus NCFM, or Staphylococcus aureus USA300. Some of the metabolites, but not the short-chain fatty acids (SCFAs), strongly affected cell viability. After short-term treatment and depending on the microbial stimulus, SCFAs affected the cytokine profile similarly but weaker than butyrate, as reflected by inhibition of IL-12p70 and IL-10 but enhanced IL-23 (LPS and S. aureus USA300) and IL-1β production. Compared to butyrate, valerate exhibited a weaker and slower effect on cytokine expression. Two-day treatment with valerate and butyrate resulted in similar effects, that is, LPS-induced IL-12 abrogation and IL-10 enhancement, increased aryl hydrocarbon receptor (Ahr) expression, and after LPS stimulation, increased expression of dual specificity phosphatase 1 (Dusp1). In conclusion, SCFAs exhibited low toxicity and modulated microbially stimulated BMDCs. Valerate and butyrate showed the strongest effect, which was dependent on the specific microbial stimulation and the course of the SCFA treatment. Our work adds knowledge regarding the role of protein-derived metabolites from gut bacterial fermentation on the immune system.

The Ras-related protein RAB7A has been implicated in the development and prognosis of various cancers. This study aims to investigate the prognostic significance of RAB7A in colon adenocarcinoma (COAD). We conducted a retrospective cohort study of COAD cases to assess RAB7A expression and its clinical relevance. The chi-square test was employed to establish associations between clinical features and RAB7A expression. Survival analyses, including Kaplan–Meier and Cox regression, were employed to evaluate the impact of RAB7A expression and clinical characteristics on COAD patient outcomes. Furthermore, we validated our clinical findings using The Cancer Genome Atlas (TCGA) dataset. To elucidate the tumor-related role of RAB7A in COAD, we conducted cellular assays and mouse models. Elevated RAB7A expression in COAD tissues exhibited significant associations with tumor size, invasion depth, and lymph node metastasis (all p < 0.05). Univariate and multivariate analyses revealed that high RAB7A expression was significantly correlated with poorer overall survival. In vitro cellular assays, coupled with knockdown strategies, demonstrated that RAB7A promotes COAD tumor proliferation and invasion, a finding further substantiated by in vivo xenograft experiments. RAB7A may serve as a valuable biomarker and potential therapeutic target in the management of COAD.

Ectoine, a natural bacterial osmolyte, suppressed UVA irradiated-α-melanocyte stimulating hormone (MSH) stimulated melanogenesis through antioxidant Nrf2 pathways in human keratinocytes; however, the underlying skin whitening mechanisms were not elucidated. The depigmenting efficiency of Ectoine (0–400 μM) through antimelanogenesis and melanin degradation by autophagy promotion was investigated in melanoma (B16F10) and melanin-feeding keratinocyte (HaCaT) cells and in vivo zebrafish model. MTT assay, Western blotting, GFP-LC3 puncta, AVO formation, melanin assay, immunofluorescence staining, TEM techniques, siLC3 transfection, and zebrafish model were utilized. Ectoine-induced autophagy in B16F10 and HaCaT cells was shown by enhanced LC3-II accumulation, autophagosome GFP-LC3 puncta, autolysosome AVOs formation, ATG4B downregulation, and Beclin-1/Bcl-2 dysregulation. The immunoprecipitation data revealed that Ectoine increased the association between LC3-II and p62 proteins in B16F10 and HaCaT cells. Importantly, antioxidant NAC pretreatment antagonized the Ectoine-induced ATG4B diminution in B16F10 and HaCaT cells. Ectoine inhibited melanogenesis by suppressing melanosome gp100, tyrosinase, TRP-1/-2, and/or melanin formation via autophagy in α-MSH-stimulated B16F10 and melanin-feeding HaCaT cells. TEM findings displayed that Ectoine increased melanosome-engulfing autophagosomes and autolysosomes in α-MSH-stimulated B16F10 and melanin-feeding HaCaT cells. Ectoine-inhibited melanogenesis in α-MSH-stimulated B16F10 cells and melanin-feeding HaCaT cells was reversed by pretreatment with the autophagy inhibitor 3-MA or LC3 silencing. In vivo study demonstrated that Ectoine (5 mM) suppressed endogenous body pigmentation by antimelanogenesis and melanin degradation through autophagy induction in a zebrafish model. The in vitro and in vivo study demonstrated that Ectoine inhibits melanogenesis and enhances melanin degradation by triggering autophagy. Ectoine could be utilized as a whitening ingredient in cosmetic formulations.

Supramolecular systems, intricate assemblies of molecular subunits organized through various intermolecular interactions, offer versatile platforms for diverse applications, including gene therapy, antimicrobial therapy, and cellular engineering. These systems are cost-effective and environmentally friendly, contributing to their attractiveness in biomaterial design. Furthermore, supramolecular biomaterials based on acyclic, macrocyclic compounds and lipid-based assembly offer potential applications in distinct types of biomedical approaches. In this context, they can transport several therapeutic agents very effectively to the target site. Supramolecular hydrogels exhibit potent antimicrobial activity by disrupting microbial membranes, offering promising solutions to combat drug-resistant pathogens. Additionally, supramolecular luminescent nanoparticles enable targeted cell imaging, facilitating disease diagnosis and treatment with high specificity and sensitivity. In cellular engineering, supramolecular assemblies of small molecules demonstrate biological activities, overcoming challenges in cancer treatment by inhibiting signaling pathways and inducing apoptosis in cancer cells. This review emphasizes the applications of supramolecular systems from gene therapy to cellular imaging, tissue engineering, and antimicrobial therapy, showcasing their potential to drive innovation and address pressing healthcare challenges.

With the increase in the elderly population worldwide, the number of subjects suffering from tuberculosis (TB) has shown an increased prevalence in this group. Immunosenescence is essential in this phenomenon because it may reactivate the lesions and render their adaptive immunity dysfunctional. In addition, inflammation in the lungs of the elderly subjects is also dysfunctional. Although effective drugs are available, they are often tolerated inadequately, reducing adherence to the therapy and leading to therapeutic failure. Comorbidities, poor general health status, and other medications may lead to increased drug adverse reactions and reduced adherence to treatment in the elderly. Hence, older adults require an individualized approach for better outcomes. Trained immunity, which involves epigenetic reprogramming, may contribute to balancing the dysfunction of innate and adaptive immunity in older people. This review analyzes the relationship between inflammation, age, and Mycobacterium tuberculosis. Moreover, we hypothesize that immunomodulation using trained immunity activators will help reduce inflammation while enhancing antimicrobial responses in the elderly. Understanding immunomodulation's molecular and physiological effects will lead to informed decisions about TB prevention and treatment strategies uniquely designed for the elderly.

Modulating metabolic pathways in activated microglia can alter their phenotype, which is relevant in uncontrolled neuroinflammation as a component of various neurodegenerative diseases. Here, we investigated how pretreatment with agmatine, an endogenous polyamine, affects metabolic changes in an in vitro model of neuroinflammation, a murine microglial BV-2 cell line exposed to lipopolysaccharide (LPS). Hence, we analyzed gene expression using qPCR and protein levels using Western blot and ELISA. Microglial metabolic status was assessed by measuring lactate release and cellular ATP by enzymatic and luminescence spectrophotometry. Mitochondrial functionality was analyzed by fluorescent probes detecting mitochondrial membrane potential (mtMP) and superoxide production. Our findings suggest that kinase pathways associated with hypoxia-inducible factor-1α (HIF-1α) regulate energy metabolism in pro-inflammatory activated microglia. We have shown that LPS induces HIF-1α and genes for glucose transporter and glycolytic rate, increases lactate production and causes mitochondrial dysfunction, suggesting a metabolic shift towards glycolysis. Agmatine inhibits the PI3K/Akt pathway and negatively regulates mammalian target of rapamycin (mTOR) phosphorylation and HIF-1α levels, reducing lactate and tumor necrosis factor (TNF) production, which is supported by pharmacological blockade of PI3K. Pretreatment with agmatine also rescues mitochondrial function by counteracting the LPS-induced decline in mtMP and increase in mitochondrial superoxide, resulting in an anti-apoptotic effect. Agmatine alone increases intracellular ATP levels and maintains this effect even under pro-inflammatory conditions. Our study emphasizes the ability of agmatine to engage in metabolic reprogramming of pro-inflammatory microglia through increased ATP production and modulation of signaling pathway involved in promoting glycolysis and cytokine release.

Atherosclerosis is a major cause of morbidity and mortality worldwide; in Israel, ischemic heart disease is the second leading cause of death for both genders aged 45 and above. Atherosclerosis involves stiffening of the arteries due to the accumulation of lipids and oxidized lipids on the blood vessel walls, triggering the development of artery plaque. Coronary artery disease (CAD) is the most common manifestation of atherosclerosis. The prevalence of CAD in the general population remains high, despite efforts to improve the identification of risk factors and preventive treatments. The discovery of new biomarkers is vital to improving the diagnosis of CAD and its risk factors. We aimed to identify novel biomarkers that could provide an early diagnosis of coronary artery atherosclerotic plaques, their type, and the percentage of stenosis. We used an untargeted metabolomics approach to identify potential biomarkers that could enable highly sensitive and specific CAD detection. The study consisted of 109 patients who underwent cardiac computed tomography angiography at the Cardiology Department of Ziv Medical Center. Fifty-four patients were diagnosed with coronary atherosclerotic plaques (CAD group), and 55 without plaques used control. Untargeted metabolomics using LC–MS/MS revealed 2560 metabolites in the patients' serum: 106 showed statistically significant upregulation in the serum of the CAD group compared with the healthy control group (p < 0.05). These metabolites belonged to the following chemical families: acyl-carnitines, cyclodipeptides, lysophosphatidylcholine, and primary bile acids. In contrast, 98 metabolites displayed statistically significant downregulation in the serum of the CAD group compared with the control group, belonging to the following chemical families: GABA amino acids and derivatives (inhibitory neurotransmitters), lipids, and secondary bile acids. Our comprehensive untargeted serum metabolomic analysis revealed biomarkers that can be used for the diagnosis of patients with CAD. Further cohort studies with a larger number of participants are needed to validate the detected biomarkers.