Retinol Research Articles

Full-length transcriptome reveals alternative splicing regulation pattern of skin color variant in red tilapia (Oreochromis spp.)

The hybrid species red tilapia (Oreochromis spp.) is favored in aquaculture for its bright color, rapid growth, and high market value. However, color variation hinders market development, which is influenced by both genetic and environmental factors. We aim to identify candidate genes and pathways related to pigmentation, uncovering the molecular basis of these color variations in red tilapia by employing third-generation full-length transcriptome sequencing combined with second-generation transcriptome analysis. Our analysis focused on three distinct phenotypic classes: whole pink, pink with black blotch, and whole black. Pigment cell and pigment composition analysis highlighted that the pigment pattern in red tilapia is primarily determined by the distribution and interaction of various pigment cells, including melanophores, xanthophores, erythrophores, and iridophores. The whole pink individuals were characterized by an absence of melanophores and a high concentration of carotenoids, while the whole black individuals exhibited active melanogenesis. Transcriptomic data indicated that genes associated with melanin synthesis (wnt, fzd7, lef, tcf7, tyrp1, oca2, pmel, bmp2, cbs) were up-regulated in whole black individuals, while genes related to carotenoid uptake and deposition (scarb1, ldlr, ttc39b, stard5, stard10, plin2, fitm2, bscl2), as well as pteridine synthesis (gch1, ptps), were more actively expressed in whole pink individuals. Retinol metabolism was identified as a mediator of the interaction between melanin synthesis and carotenoid deposition. Further, alternative splicing (AS) act as a crucial post-transcriptional mechanism regulating body coloration, beyond transcriptional differences. Analysis of AS events identifies multiple splice variants of pigment-related genes (scarb1, pax7, ctnnb1, rxrb, bscl2, gjb10, bmp4, frzb) that exhibit differential expression and splicing patterns across different color phenotypes. Notably, AS events of the scarb1 gene, related to carotenoid deposition, and the polr2d gene, associated with the transcription machinery, may significantly influence pigment deposition patterns in red tilapia. Our work not only deepens the genetic understanding of pigmentation in red tilapia but also establishes a solid foundation for improving color stability through selective breeding and genetic improvement programs across various hybrid species in aquaculture, which is crucial for marketability and consumer attraction.

Study on the protective mechanism of Xuemaitong Capsule against acute myocardial ischemia rat based on network pharmacology and metabolomics

BackgroundXuemaitong Capsule (XMT) is a widely recognized traditional Miao medicine extensively utilized in Chinese clinical settings. Previous studies have demonstrated XMT protective effects against acute myocardial ischemia (AMI). However, the mechanism by which XMT provides protection to AMI rats is yet to be fully understood. Aim of the studyThe purpose of this study was to investigate the protective mechanism of XMT on AMI rats through network pharmacology, traditional pharmacodynamics and metabolomics. Material and methodsThe components and potential targets of XMT were identified through the application of traditional Chinese medicine system pharmacology and traditional Chinese medicine molecular mechanism bioinformatics analysis tools. We constructed herb-composition-target networks and analyzed protein–protein interaction (PPI) networks. The potential mechanism was explored by pathway enrichment analysis. Subsequently, the AMI model was constructed by ligation of the anterior descending branch of the left coronary artery, and XMT protective effects on AMI rats were evaluated by analyzing the myocardial enzyme profiles, electrocardiograms(ECG), Triphenyltetrazolium chloride(TTC) staining, and Hematoxylin-Eosin (HE) staining in AMI rats. Metabolomics based on UHPLC-Q-Exactive Orbitrap MS was used to observe the protective effect of XMT on the serum metabolic profile of AMI, and multivariate statistical analysis further revealed the differential patterns of metabolites after XMT treatment. Finally, integrated pathway analysis was carried out to reveal the biological metabolic mechanism. ResultsA total of 392 active components of XMT acted with 624 targets for treating AMI. Pathway enrichment analysis revealed that XMT could treat AMI through TNF, MAPK and PI3K-Akt signaling pathways. Further, XMT could effectively prevent ST-segment elevation in the ECG, reduce the size of myocardial infarction, decrease cardiac weight index and cardiac enzyme levels, and mitigate histological damage in the hearts of AMI rats. In addition, XMT callback 117 metabolites and four metabolic pathways, including taurine and hypotaurine metabolism, phenylalanine metabolism, pyrimidine metabolism and retinol metabolism. Through integrating network pharmacology and metabolomics, we explored the biological mechanism by which XMT treats AMI. It was speculated that the mechanism of XMT is to regulate TNF signaling, PI3K-Akt pathway and MAPK signaling pathway, and participate in cell apoptosis, oxidative stress, immune and inflammatory reaction and other biological processes. ConclusionXMT plays a protective role in AMI rats by regulating multiple metabolic biomarkers, multiple targets and pathways. Therefore, XMT may provide a potential strategy for the treatment of AMI.

Effects of aflatoxin B1 on subacute exposure of hybrid groupers (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂): Growth, liver histology, and integrated liver transcriptome and metabolome analysis

With the increasing incorporation of plant-based ingredients into the grouper diet, the issue of aflatoxin B1 (AFB1) contamination in the diet has become a significant concern. In this study, the negative effects of AFB1 on the growth and liver health of hybrid grouper (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂) were investigated in the context of growth, liver histology, serum biochemical indices, and integrated transcriptomic and metabolomic data. A total of 540 healthy hybrid groupers, initially weighing 11.59 ± 0.03 g, were randomly divided into six groups (three replicates of 30 fish each): the Control group was fed a basal diet, and the experimental groups were supplemented with 7 (AF7), 30 (AF30), 111 (AF111), 445 (AF445) and 2230 μg/kg AFB1 (AF2230) in the basal diet respectively, for 56 days. Groups Control, AF445, and AF2230 were selected for subsequent histological, muscle fatty acid, and transcriptomic and metabolomic analyses based on the results of hybrid grouper growth and serum biochemical indices. Compared to the Control group, both whole-body crude lipid and muscle crude lipid contents showed significant decreases in the AF2230 group (P < 0.05), while only muscle crude lipid content showed a significant decrease in the AF445 group (P = 0.001). Liver damage was seen in the histology of the liver of AF445 and AF2230 groups. Muscle fatty acid results showed that the addition of 445 and 2230 μg/kg AFB1 to the ration increased saturated fatty acids and monounsaturated fatty acids and decreased polyunsaturated fatty acids and highly unsaturated fatty acids in muscle (P < 0.05). Transcriptome analyses revealed multiple metabolic pathways associated with AFB1 metabolism, and metabolomics analyses further confirmed changes in the activity of these pathways. The results of the combined transcriptomic and metabolomic analyses indicated that AFB1 causes liver injury mainly by affecting liver retinol metabolism, metabolism of xenobiotics by cytochromes P450, drug metabolism-cytochromes P450 and biosynthesis of unsaturated fatty acids. In conclusion, dietary AFB1 levels above 445 μg/kg resulted in growth inhibition, liver injury, liver AFB1 accumulation, and reduced muscle polyunsaturated fatty acid content in grouper, thereby affecting muscle quality. This study provides novel insights into the detrimental effects of AFB1 on aquatic species and contributes to the scientific basis for the health and sustainability of aquaculture practices.

534 A multi-omics analysis identifies retinol metabolism as a key pathway in wound healing

534 A multi-omics analysis identifies retinol metabolism as a key pathway in wound healing

Validity of a Web-Based 24-Hour Dietary Recall of Energy and Nutrient Intakes in Japanese Adults

Recently, web-based dietary assessment tools for the targeted population have been developed and used to estimate the dietary intake level in several epidemiological studies. This study aimed to examine the validity of estimating energy and nutrient intake by the web-based 24 h dietary recall (Web24HR), which we developed for the Japanese population. Overall, 228 adults aged ≥20 years who agreed to participate were included. Web24HR was administered three times per person: twice within 3 weeks and once 3 months later. The data on 3-day weighed food records (WFR) at 3-month intervals in the four seasons were collected using the reference method. The intake of energy and nutrients between Web24HR and WFR were compared using Pearson’s correlation coefficients and the Bland–Altman analysis. As results, the correlations were moderate for both men (median r = 0.51) and women (median r = 0.38) except for iodine, retinol, retinol equivalents, and β-tocopherol. The Bland–Altman method revealed that the bias in intake was within ±10% for most nutrients, except for cholesterol, iodine, vitamin C, and the water content, in both sexes. Additionally, monounsaturated fatty acids in men and β-cryptoxanthin in women exhibited an underestimation of more than 10%. In conclusion, the Web24HR intake assessment showed moderate correlations for most nutrients in both sexes. The bias in intake was within ±10% for most nutrients, but there were discrepancies for some nutrients. This tool’s performance is comparable to Japan’s standard dietary exposure assessment methods and will be helpful for future applications in epidemiological studies, though caution is needed for certain nutrient assessments.

Spatio-Temporal Dynamics of Lettuce Metabolome: A Framework for Targeted Nutritional Quality Improvement

Lettuce (Lactuca sativa L.) is a popular leafy vegetable valued for its dietary fiber, antioxidants, and beneficial vitamins. This study presents a comprehensive spatio-temporal analysis of the lettuce metabolome, revealing complex dynamics in metabolite accumulation influenced by plant age, leaf position, proximodistal distribution within a leaf, and head closure. Samples were collected from plants at five maturity stages (ranging from baby leaf to full commercial maturity and eventually to bolting) and from five leaf positions (from the apex to the base of each plant). A widely targeted metabolomics approach identified 1905 compounds, with flavonoids, phenolic acids, and lipids as the largest classes. Younger plants exhibited higher levels of flavonoids, while older plants accumulated more saccharides and amino acids. Metabolites showed distinct proximodistal distributions, with flavonoids and vitamins concentrated at leaf tips and terpenoids declining from base to tip. Head closure significantly reduced levels of flavonoids, retinol (vitamin A1), and riboflavin (vitamin B2), while it was associated with increased content of other beneficial vitamins, such as thiamine (B1), pantothenate (B5), and pyridoxine (B6). Broad-sense heritability (H2) estimates for metabolites yielded mean H2 values of 0.648 and 0.743 for plants at baby-leaf and commercial maturity stages, respectively. The overall highest heritability was observed in tannins (H2 = 0.909) in younger plants and chalcones (H2 = 0.894) in older plants, suggesting strong genetic control over specific metabolite classes and subclasses. These findings offer a robust framework for optimizing lettuce’s nutritional profile by linking metabolite distributions to developmental processes, plant architecture, and genetic regulation. By leveraging these insights, breeders and producers can develop targeted strategies to enhance metabolite content through optimized breeding and harvesting strategies.

Interpretable Machine Learning Algorithms Identify Inetetamab-Mediated Metabolic Signatures and Biomarkers in Treating Breast Cancer.

HER2-positive breast cancer (BC), a highly aggressive malignancy, has been treated with the targeted therapy inetetamab for metastatic cases. Inetetamab (Cipterbin) is a recently approved targeted therapy for HER2-positive metastatic BC, significantly prolonging patients' survival. Currently, there is no established biomarker to reliably predict or assess the therapeutic efficacy of inetetamab in BC patients. This study harnesses the power of metabolomics and machine learning to uncover biomarkers for inetetamab in BC therapy. A total of 23 plasma samples from inetetamab-treated BC patients were collected and stratified into responders and nonresponders. Ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry was utilized to analyze the metabolites in blood samples. A combination of univariate and multivariate statistical analyses was employed to identify these metabolites, and their biological functions were then ascertained by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Finally, machine learning algorithms were employed to screen responsive biomarkers from all differentially expressed metabolites. Our finding revealed 6889 unique metabolites that were detected. Pathways like retinol metabolism, fatty acid biosynthesis, and steroid hormone biosynthesis were enriched for differentially expressed metabolites. Notably, two key metabolites associated with inetetamab response in BC were identified: FAPy-adenine and 2-Pyrocatechuic acid. There was some negative correlation between progress-free survival (PFS) and their kurtosis content. In summary, the identification of these two significant differential metabolites holds promise as potential biomarkers for evaluating and predicting inetetamab treatment outcomes in BC, ultimately contributing to the diagnosis of the disease and the discovery of prognostic markers.

Transcriptional profiling of the M. complexus in naked neck chickens suggest a direct pleiotropic effect of GDF7 on feathering and reduced hatchability

BackgroundThe locus for naked neck (Na) in chickens reduces feather coverage and leads to increased heat dissipation from the body surface resulting in better adaptability to hot conditions. However, the Na gene is linked to significantly lower hatchability due to an increased late embryonic mortality. It has been argued that the causative gene GDF7 may have a direct pleiotropic effect on hatchability via its effect on muscle development. Thus, the study presented here analyses the transcriptome of the hatching muscle (M. complexus) and shows how GDF7 impacts development leading to reduced hatching rates in Na chickens.ResultsUsing 12 chicken embryos (6 x wildtype (Wt) and 6 x Na) RNA was extracted from the M. complexus of each embryo and sequenced. The resulting differential expression analyses led to the discovery of 461 differentially expressed (DE) genes in the M. complexus of the experimental group. Among those, 77 genes were of uncertain function (LOC symbols), with 31 were classified as uncharacterised. The regulation of a number of pathways involved in normal embryonic development, were found to be negatively influenced by the Na genotype. Further pathways involved in cell-cell adhesion, cell signalling pathways, and amino acid (AA) metabolism/transport were also observed. GDF7 (alias BMP12), whose localised overexpression in the neck skin causes the Na/Na phenotype, was significantly overexpressed in the M. complexus of Na/Na embryos, and shows a significant increase in the number of binding sites for the transcription factor PITX2 was also observed.ConclusionIn Na chickens, GDF7 is under the control of a mutated cis-regulatory element, whose actions are known to suppress the development and distribution of feathers through the sensitizing action of retinoic acid. In this study, a number of DE genes with over 10 retinoic acid response elements (RAREs) in close proximity were observed, indicating changes to the retinol metabolism. With the understanding that the Na/Na mutation leads to increased retinoic acid activity, this indicates a high likelihood of GDF7 excerpting a direct pleiotropic effect, not just in the observed reduction in feather patterning, but also impacting the development of the M.complexus, and consequently leading to the reduced hatchability observed in birds with the Na/Na genotype.Furthermore, the enrichment of PITX2 binding sites in proximity to DE genes in the M. complexus, also indicates that muscle development is still ongoing in Na embryos. This suggests that the M. complexus is not yet fully developed, further increasing the potential for late embryonic mortality in Na chicks at hatching.

Comparative Transcriptome Analysis Reveals the Impact of a High-Fat Diet on Hepatic Metabolic Function in Tilapia (Oreochromis niloticus).

Hepatic steatosis is prevalent among cultured fish, yet the molecular mechanisms remain incompletely understood. This study aimed to assess changes in hepatic metabolic function in tilapia and to explore the underlying molecular mechanisms through transcriptomic analyses. Tilapia were allocated into two groups: a normal control (Ctr)-fed group and a high-fat diet (HFD)-fed group. Serum biochemical analyses revealed that HFD feeding led to liver damage and lipid accumulation, characterized by elevated levels of glutamic-pyruvic transaminase (GPT), glutamic-oxaloacetic transaminase (GOT), triglycerides (TGs), and total cholesterol (TC). Transcriptome analysis showed that 538 genes were significantly downregulated, and 460 genes were significantly upregulated in the HFD-fed fish. Gene Ontology (GO) enrichment analysis showed that these differentially expressed genes (DEGs) were apparently involved in the lipid metabolic process and monocarboxylic acid metabolic process. Meanwhile, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated significant alterations in pathways of steroid biosynthesis, porphyrin metabolism, terpenoid backbone biosynthesis, and retinol metabolism after HFD feeding. Additionally, results from Gene Set Enrichment Analysis (GSEA) revealed that gene expression patterns in pathways including oxidative phosphorylation, protein export, protein processing in the endoplasmic reticulum, and ribosome biogenesis were positively enriched in the HFD-fed tilapia. These findings provide novel insights into the mechanisms underlying HFD-induced hepatic dysfunction in fish, contributing to the optimization of feeding strategies in aquaculture.

Identification of Sequential Molecular Mechanisms and Key Biomarkers in Early Glaucoma by Integrated Bioinformatics Analysis.

Glaucoma is a neurodegenerative disease characterized by progressive optic nerve degeneration and retinal ganglion cell (RGC) loss. In early glaucoma, before obvious axon loss, highly organized pathological processes in RGCs occur sequentially, involving axons, dendrites and synaptic terminals. The optic nerve head (ONH) is the critical structure of early glaucomatous neurodegeneration. Taking advantage of high-throughput data from the ONH and the weighted gene coexpression network analysis (WGCNA) method, the current study aims to gain insight into the full scope of pathological events in early glaucoma and define their chronological sequence. The expression profiles of GSE26299, GSE110019, and GSE139605, which measure ONH gene expression in different glaucoma models, were downloaded from the Gene Expression Omnibus (GEO) database. In GSE26299, which uses 10.5-month-old DBA/2J mice, WGCNA was utilized to construct a gene coexpression network, and the most significant modules of early (NOE), moderate (MOD) and severe (SEV) glaucoma were identified. The differentially expressed genes (DEGs) of GSE110019 and GSE139605 significantly overlapped with the correlated module of the MOD group, so the 3 gene sets were analyzed together. Pathway enrichment analysis via the GO, KEGG, and Reactome pathways was subsequently performed, followed by protein‒protein interaction (PPI) analysis to screen key genes associated with each stage. Several hub gene expression patterns were identified in a glucocorticoid-induced glaucoma (GIG) model via quantitative PCR and immunostaining. The pink module was positively correlated with the NOE group (r = 0.48, p = 4e-04) and negatively correlated with the glaucoma stage (r = -0.88, p = 3e-17). The genes in the pink module were enriched in the synaptic transmission and axonal transport pathways. The tan module was negatively correlated with the NOE group (r = -0.43, p = 0.002) and positively correlated with the glaucoma stage (r = 0.77, p = 7e-11). The genes in the tan module were associated with pathways such as tight junctions, retinol metabolism, and linoleic acid metabolism. The purple module was positively correlated with the MOD group (r = 0.64, p = 5e-07). The common genes among the purple module and the DEGs of the two other datasets were enriched in pathways related to mitotic cell division, cytokine activity, and the extracellular matrix (ECM). The hub genes identified by PPI included Nrn1, Cplx1, Timp1, and Cdk1. Quantitative PCR and immunostaining confirmed that Limk1 expression was increased in the ONH of GIG mice. In early glaucomatous neuropathy, intrinsic changes in RGCs precede the activation of glial cells and ECM remodeling. These latter events are common pathological changes observed in the ONH in both cats and mice. Our study may provide new targets for the early detection and treatment of glaucoma.

LNX1-AS2 as a Key Prognostic and Immunotherapy Response Biomarker for Lung Adenocarcinoma.

The role of LNX1 antisense RNA 2 (LNX1-AS2) in lung adenocarcinoma (LUAD) remains unclear. This study aimed to investigate the association between LNX1-AS2 and LUAD by employing bioinformatics analysis and experimental validation. Statistical analysis and database interrogation were utilized to assess correlations among LNX1-AS2 expression, clinical characteristics of LUAD patients, prognostic factors, regulatory networks, and immune infiltration. LNX1-AS2 expression in LUAD cell lines was quantified using quantitative real-time polymerase chain reaction (qRT-PCR). The study found significantly elevated levels of LNX1-AS2 expression in patients with LUAD. Furthermore, elevated LNX1-AS2 expression in LUAD patients did not significantly correlate with gender (p = 0.041) or race (p = 0.049). Importantly, high LNX1-AS2 expression levels were associated with poorer overall survival (OS, p = 0.042) and disease-specific survival (DSS, p = 0.040) in LUAD patients. Additionally, high LNX1-AS2 expression (p = 0.015) was independently correlated with OS in LUAD patients. The phenotype characterized by high LNX1-AS2 expression was also found to be enriched for asthma, allograft rejection, drug metabolism cytochrome P450, metabolism of xenobiotics by cytochrome P450, olfactory transduction, renin-angiotensin system, retinol metabolism, pentose and glucuronate interconversions, and porphyrin and chlorophyll metabolism. A significant correlation was identified between the expression levels of LNX1-AS2 and immune infiltration in the context of LUAD. Elevated expression of LNX1-AS2 was notably detected in LUAD cell lines as opposed to Beas-2B. A noteworthy relationship was established among increased LNX1-AS2 expression in LUAD patients, unfavorable prognosis, and heightened immune infiltration. These findings suggest that the LNX1-AS2 gene could serve as a valuable prognostic indicator for LUAD and a potential predictor of response to immunotherapy.

Innovative Vegetable Chips: Harnessing the Nutritional Power of Underutilized Leafy Greens

This study investigates the acceptability of spinach-cabbage chips in three flavor variants: plain, cheese, and barbeque, specifically targeting preschoolers as the primary evaluators. A sensory evaluation was conducted, assessing the chips based on appearance, color, texture, taste, aroma, and overall acceptability. Data were analyzed using One-Way Analysis of Variance (ANOVA) to identify the most preferred nutri-chip formulation, while Kramer's Rank-Sum Test determined the favored variant among the participants. The study utilized fresh spinach and cabbage, focusing on their nutritional profiles and the production process for the chips. Key methodologies included sensory evaluations, cost analysis of ingredients, and calculations of theoretical vitamin A content, along with the percentage of the Recommended Nutrient Intake (RENI) for vitamin A per 50-gram serving for children aged 4-10 years. Results indicated that the optimal formulation comprised 200 grams of spinach and 100 grams of cabbage, with no significant differences at the 5% level in appearance and color between formulations. However, significant differences were noted in texture, taste, aroma, and overall acceptability. The spinach-cabbage nutri-chips contained 512 μg of Retinol Equivalents (RE) of vitamin A, translating to 12.8% of the daily recommended intake for preschoolers. The findings suggest that spinach-cabbage nutri-chips can serve as a nutritious snack option to enhance vitamin A intake among preschoolers and may be beneficial for supplementary feeding programs. Recommendations for production, packaging, and further research into the product's shelf life and applicability in school feeding initiatives are provided.

Study on Active Components and Mechanism of Lettuce Latex Against Spodoptera Litura.

Plant latex is a sticky emulsion exuded from laticifers once the plant is damaged. Latex is an essential component of plant defense against herbivores. Lettuce (Lactuca sativa L.) in the Compositae family has relatively fewer insect herbivores compared with other leaf vegetables. The larvae of a generalist lepidopteran pest Spodoptera litura (Fabricius) avoided feeding on living lettuce plants. However, the larvae rapidly damaged the excised leaves that were unable to produce latex. Six compounds were isolated from lettuce latex. They were identified as 2,5-dihydroxybenzaldehyde (1), 3β-hydroxy-4,15-dehydrograndolide (2), annuolide D (3), lactucin (4), lactucopicrin (5), and hanphyllin (6). Bioassays showed that the inhibition rate of compound 1 (2,5-dihydroxybenzaldehyde) and 6 (hanphyllin, a sesquiterpene lactone) on the weight gain of S. litura were 52.4 % and 10 %, respectively, at the concentration of 100 μg/g. RNA-seq analyses showed that larval exposure to compound 1 down-regulated the genes associated with heterobiotic metabolism including drug metabolism-cytochrome P450, metabolism of xenobiotics by cytochrome P450, retinol metabolism, glutathione metabolism, and drug metabolism-other enzymes (mainly uridine diphosphate glucuronyltransferase, UGTs). RT-qPCR further confirmed that 33 genes in the family of carboxylesterase (CarE), P450s and UGTs were down-regulated by compound 1. The activities of CarE, P450s and UGTs in the larvae fed on diets containing compound 1 were significantly lower than those fed on control diets, with the inhibition for the three detoxification enzymes being 55.4 %, 53.9 %, and 52.9 %. These findings suggest that secondary metabolites including 2,5-dihydroxybenzaldehyde in the latex play a key role in protecting lettuce from insect herbivory.

FBXO family genes promotes hepatocellular carcinoma via ubiquitination of p53

FBXO protein family plays an essential role in the ubiquitination process acting as E3 ligases, which may contribute to the progression of cancers. However, the molecular functions of FBXOs in hepatocellular carcinoma (HCC) remain incompletely understood. Here, we investigated the overlapping genes between the FBXOs and differentially expressed genes (DEGs) of HCC identified by utilizing The Cancer Genome Atlas (TCGA) dataset, then, a prognostic model with effective predictive capacity was constructed based on the uni-cox and LASSO regression analyses. To elucidate the underlying mechanism of the FBXO model genes, KEGG analysis was carried out. Drug metabolism-cytochrome P450 and retinol metabolism were revealed as the potential pathway, which Increased the credibility of subsequent drug prediction research. Meanwhile, patients divided by the prognostic model showed a different immune infiltrating status and we also found FBXO model genes may ubiquitinate P53, inducing TP53 more prone to mutations, thereby promoting the occurrence and development of tumors. Consistent with these findings, the result of immunohistochemistry (IHC) validated an elevated expression of these model genes in HCC tissues than in the adjacent tissues. The primary aim of this investigation is to formulate a prognostic model while exploring the underlying mechanisms associated with FBXO genes in HCC. These findings offer initial research perspectives on the involvement of FBXO genes in HCC and contribute to the discovery of dependable biomarkers for the management, prognostication, and early detection of HCC in patients.

Toxicity of parental co-exposure of microplastic and bisphenol compounds on adult zebrafish: Multi-omics investigations on offspring

In recent years, the widespread use of bisphenol compounds and microplastics (MP) have attracted attention due to their harmful effects. Here, individual and combined effects of MP and bisphenol compounds, were assessed on adult zebrafish after co-exposure of bisphenol A (BPA) or bisphenol S (BPS) and 25 μm polyethylene MP. Impacts on their offspring (the F1 generation) were also investigated. The reproductive toxicity in adult zebrafish impacted exerted by bisphenol compounds were aggravated by the co-presence of MP. Transcriptomics and metabolomics further showed single or co-exposure of bisphenol compounds and MP could together regulate apoptosis, calcium signaling pathway and glycerophospholipid signaling pathways. Our results also showed the different toxicity mechanisms on transcriptional and metabolic profiles in the combination effects of bisphenol compounds and MP. The co-exposure of BPA and MP predominantly influenced neurotoxicity via the MAPK signaling pathway and voltage-dependent calcium channels, whereas the co-exposure of BPS and MP principally affected visual development through phototransduction and retinol metabolism. The co-exposure of BPA and MP, as well as BPS and MP, specifically regulate lipid metabolism and carbohydrate metabolism in zebrafish offspring, respectively. Overall, this study provided a deep understanding of the toxicity differences between co-exposure and single exposure of bisphenol compound and MP in zebrafish, as well as the transgenerational effects and potential molecular mechanisms of bisphenol compounds and MP in zebrafish offspring.

Lycium barbarum leaf flavonoids ameliorate high fructose induced insulin resistance in mice by regulating blood glucose and gut microbiota composition

Insulin resistance is an increasingly severe public health issue worldwide, affecting millions and significantly raising the risk of diabetes and cardiovascular diseases. Despite this, current treatment options remain limited, which has heightened interest in exploring interventions based on natural compounds. This study investigates the potential of Lycium barbarum leaf flavonoids (LBLF) to improve insulin resistance induced by high fructose in mice, with a focus on the mechanisms related to blood glucose regulation and gut microbiota composition. Research results show that, compared to the high fructose model group, treatment with metformin hydrochloride and rutin reduced fasting blood glucose levels by 32.06% and 18.94%, respectively. LBLF treatment at various doses decreased fasting blood glucose levels by 12.29%, 19.02%, and 32.98%, and insulin levels by 26.50%, 11.04%, and 28.23%, respectively, demonstrating its effective ability to regulate blood glucose levels. It was also found that LBLF effectively regulated lipid disorders, significantly reduced oxidative stress in the liver, and protected liver function. Liver transcriptomic analysis suggests that LBLF may improve insulin resistance by regulating gene expression in the MAPK and retinol metabolism signaling pathways. Additionally, gut microbiota diversity analysis revealed that LBLF treatment reduced the Firmicutes/Bacteroidetes (F/B) ratio, which is associated with obesity and metabolic disorders, thereby optimizing the gut microbiota structure disrupted by high fructose intake. These results highlight the therapeutic potential of LBLF in managing insulin resistance and associated metabolic disorders, providing a theoretical basis for further research into its broader applications.

Proteomic analysis of HeLa cells after stable transfection with the Chlamydia trachomatis CT143 gene

BackgroundThe CT143 protein of Chlamydia trachomatis (Ct) is a key immunodominant antigen and candidate type-III secretion substrate. Although CT143 expression has not been detected in the cytosol of infected cells, it is known to interfere with the physiological behavior of HeLa cells. This study aims to investigate how the CT143 protein affects the protein expression profile of HeLa cells, providing a basis for further research into Ct’s pathogenic mechanisms. MethodsWe constructed a stably transfected HeLa cell line, pCD513B-1-CT143-HeLa, and a control cell line, pCD513B-1-HeLa. Protein expression profiles of these cell lines were determined using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Differentially expressed proteins were identified, constructed into a database, and verified using parallel reaction monitoring (PRM). Bioinformatics software facilitated the preliminary analysis of the biological functions of these differential proteins. ResultsA total of 221 host proteins were differentially expressed, with 68 upregulated and 153 downregulated. These variations influence the regulation of peptidase activity and are crucial in biological processes such as cell secretion and protease activity. Significant changes were noted in protein processing, alcohol dehydrogenase activity, Aldo-Keto reductase activity, and peptidase regulator activity. Furthermore, alterations were observed in cellular components like the plasma membrane and cell periphery. Pathways involving the hematopoietic system, glycosaminoglycan degradation, retinol metabolism, and cytochrome P450-mediated exogenous drug metabolism were notably affected. Indirect interactions among differentially expressed proteins included three key nodal proteins: C3, IFIT3, and IFIT1. ConclusionThe successful construction of a host differential protein expression profile was achieved through stable transfection of HeLa cells with the CT143 gene. The differential proteins identified are implicated in regulating various biological processes such as intracellular signal transduction, cell secretion, protein processing, hydrolysis, and enzyme activity. These findings suggest that the CT143 protein may influence the host cell’s biological behavior by altering host protein expression, potentially hindering Ct growth and development.

Evaluation and the mechanism of ShengXian and JinShuiLiuJun decoction in the treatment of silicotic fibrosis: An integrated network pharmacology, life omics, and experimental validation study

BackgroundSilicosis is a systemic disease characterized by extensive fibrosis due to prolonged exposure to silica dust, with rising incidence rates significantly impacting global public health. ShengXian and JinShuiLiuJun Decoction (SXD) is a Chinese medicinal preparation containing a variety of medicinal plants. It has shown notable clinical efficacy in treating silicotic fibrosis in China. However, the precise mechanisms underlying its therapeutic effects remain unclear. This study integrates network pharmacology, multi-omics analysis, and experimental validation to investigate the potential mechanisms by which SXD treats silicotic fibrosis. ObjectiveThe study aims to investigate the therapeutic efficacy of SXD in treating silicotic fibrosis and to elucidate its underlying molecular mechanisms. MethodsHPLC-Q-TOF-MS was used to identify the active components of SXD, and combined with network pharmacology, metabolomics, and transcriptomics, the mechanism of SXD in treating silicotic fibrosis was explored from multiple perspectives. The therapeutic effect of SXD was assessed through HE staining, Masson staining, Micro CT imaging, pulmonary function tests, and hydroxyproline content in lung tissue. Finally, network pharmacology and multi-omics findings were validated using molecular docking. CETSA, immunofluorescence, SPR, and Western blotting were used to analyze key factors in the NF-κB pathway at the animal, cellular, and molecular levels. ResultsSXD treatment improved lung function in silicosis rats, reduced inflammatory cell infiltration, collagen deposition, fibrosis and other pathological changes, and inhibited the protein expression of TNF-α, IL-17A, and IL-1β, and NF-κB in lung tissue. HPLC-Q-TOF-MS combined with network pharmacology identified key compounds such as Liquiritigenin, 3-Methoxynobiletin, Isomangiferin, Hesperidin, shogaol, and Ligustroflavone, which likely exert therapeutic effects through the TNF, IL-17, NF-κB, and TGF-β signaling pathways. Transcriptomics and metabolomics results revealed that SXD up-regulated the expression of NF-κB pathway-related genes (NFKBIA, NFKBIZ) and key regulators of the retinol metabolism pathway, while down-regulating pro-inflammatory genes (IL1B, IL17A, IL6). Experimental findings confirmed that SXD suppressed the expression of NF-κB pathway-related proteins and upstream activators TNF-α, IL-17A, and IL-1β, as well as their receptors, in both lung tissue and cellular models. Additionally, SXD-containing serum had a direct, non-toxic effect on MRC-5 cells, effectively inhibiting collagen expression and TGF-β secretion. SXD also had a positive effect on collagen production and extracellular matrix (ECM) aggregation in fibroblasts. Molecular dynamics studies showed that SXD directly binds to NF-κB and IκB. ConclusionSXD exerts therapeutic effects on silicotic fibrosis by inhibiting NF-κB signaling transduction mediated by TNF-α, IL-17A, and IL-1β, and suppressing fibroblast activation.

Methodology for Studying Interactions of Vitamin A Membrane Receptors and Opsin Protein with their Ligands in Generating the Retinylidene Protein.

Distribution of dietary vitamin A/all-trans retinol (ROL) throughout the body is critical for maintaining retinoid function in peripheral tissues and generating the retinylidene protein for visual function. RBP4-ROL is the complex of ROL with retinol-binding protein 4 (RBP4), which is present in the blood. Two membrane receptors, Retinol Binding Protein 4 Receptor 2 (RBPR2) in the liver and STimulated by Retinoic Acid 6 Retinol (STRA6) in the eye, bind circulatory RBP4 and this mechanism is critical for internalizing ROL into cells. Establishing methods to investigate receptor-ligand kinetics is essential in understanding the physiological function of vitamin A receptors for retinoid homeostasis. Using Surface Plasmon Resonance (SPR) assays, we can analyze the binding affinities and kinetic parameters of vitamin A membrane receptors with its physiological ligand RBP4. These methodologies can reveal new structural and biochemical information of RBP4-binding motifs in RBPR2 and STRA6, which are critical for understanding pathological states of vitamin A deficiency. In the eye, internalized ROL is metabolized to 11-cis retinal, the visual chromophore that binds to opsin in photoreceptors to form the retinylidene protein, rhodopsin. The absorbance of light causes the cis-to-trans isomerization of 11-cis retinal, inducing conformational changes in rhodopsin and the subsequent activation of the phototransduction cascade. Decreased concentrations of serum and ocular ROL can impact retinylidene protein formation, which in turn can cause rhodopsin mislocalization, apoprotein opsin accumulation, night blindness, and photoreceptor outer segment degeneration, leading to Retinitis Pigmentosa or Leber Congenital Amaurosis. Therefore, spectrophotometric methodologies to quantify the G protein-coupled receptor opsin-11-cis retinal complex in the retina are critical for understanding mechanisms of retinal cell degeneration in the above-mentioned pathological states. With these comprehensive methodologies, investigators will be able to better assess dietary vitamin A supply in maintaining systemic and ocular retinoid homeostasis, which is critical for generating and maintaining retinylidene protein concentrations in photoreceptors, which is critical for sustaining visual function in humans.

Retinol metabolism signaling participates in microbiota-regulated fat deposition in obese mice

Obesity is a global pandemic threatening public health, excess fat accumulation and overweight are its characteristics. In this study, the interplay between gut microbiota and retinol metabolism in modulating fat accumulation was verified. We observed gut microbiota depletion reduced the body weight (P<0.05) and the ratios of white adipose tissues (WATs) to body weight (P<0.05) in high-fat diet (HFD) fed-mice. Both the hepatic metabolomics and transcriptomics analyses confirmed that gut microbiota modulated fat accumulation in obese mice. Besides, the kyoto encyclopedia of genes and genomes (KEGG) analysis and protein-protein interaction (PPI) network of RNA-seq results indicated that retinol metabolism signaling may be involved in the microbiota-regulated fat deposition. Furthermore, activated retinol metabolism signaling by all-trans retinoic acid (atRA) supplementation reduced body weight (P<0.05) and WAT accumulation in obese mice. On the other hand, 16S rRNA gene sequencing of the ileal microbiota suggested that atRA supplementation, in turn, increased the microbial diversity and induced the growth of beneficial bacteria including Parabacteroides, Bacteroides, Clostridium_XVIII, Bifidobacterium, Enterococcus, Bacillus, Leuconostoc, and Lactobacillus in obese mice. Spearman correlation showed that atRA decreased the bacteria (Parvibacter, Asaccharobacter, Romboutsia, and Clostridium_IV) that were positively associated with body and WAT weights, whereas increased the bacteria (Lactobacillus) that were negatively associated with body and WAT weights. Together, this study reveals the interaction between the gut microbiota and retinol metabolism signaling in regulating adipose accumulation and obesity. It is expected of this finding to provide new insights to prevent and develop therapeutic measures of obesity-related metabolic syndrome.