PubMed

Pestic Biochem Physiol. 2024 Aug;203:105983. doi: 10.1016/j.pestbp.2024.105983. Epub 2024 Jun 11.ABSTRACTThe "Cell Painting" technology utilizes multiplexed fluorescent staining of various cell organelles, to produce high-content microscopy images of cells for multidimensional phenotype assessment. The phenotypic profiles extracted from those images can be analyzed upon perturbations with biologically active molecules to annotate the mode of action or biological activity by comparison with reference profiles of already known mechanisms of action, ultimately enabling the determination of on-target and off-target effects. This approach is already described in various human cell cultures, the most commonly used being the U2OS cell line, yet allows broad applications in additional areas of chemical-biological research. Here we describe for the first time the application and adaptation of Cell Painting to an insect cell line, the Sf9 cells from Spodoptera frugiperda. By adjusting image acquisition and analysis models, specific phenotypic profiles were obtained in a dose-dependent manner for 20 reference compounds, including representatives for the most relevant insecticidal modes of action categories (nerve & muscle, respiration and growth & development). Through a dimensionality-reduction method, both calculations of phenotypic half maximal inhibition concentration (IC50) values as well as similarity analysis of the obtained profiles by hierarchical clustering were performed. By Cell Painting effects on the phenotype could be obtained at higher sensitivity than in other assay formats, such as cytotoxicity assessments. More importantly, these analyses provide insight into mechanistic determinants of biological activity. Compounds with similar modes of action showed a high degree of proximity in a hierarchical clustering analysis while being distinct from actives with an unrelated mode of action. In essence, we provide strong evidence on the impact of Cell Painting mechanistic understanding of insecticides with regards to determinants of efficacy and safety utilizing an insect cell model system.PMID:39084786 | DOI:10.1016/j.pestbp.2024.105983

Pestic Biochem Physiol. 2024 Aug;203:106022. doi: 10.1016/j.pestbp.2024.106022. Epub 2024 Jul 14.ABSTRACTThe extensive application of pesticides and antibiotics in agricultural production makes it possible for them to coexist in farmland, and the interaction of the two pollutants can lead to changes in environmental behavior and toxicity, creating uncertainty risks to soil and soil organisms. In this study, we explored the environmental behavior and the effects of earthworms under co-exposure to amoxicillin and boscalid and further explored the accumulation and toxic effects on earthworms. The results showed that amoxicillin increased the adsorption of boscalid in soil and inhibited its degradation. In addition, we noticed that the co-exposure of amoxicillin and boscalid caused intestinal barrier damage, which increased the bioaccumulation of earthworms for boscalid and led to more severe oxidative stress and metabolic disorders in earthworms. In summary, our findings indicate that amoxicillin can increase the ecological risk of boscalid in the environment and imply that the encounter between antibiotics and pesticides in the environment can amplify the toxic effects of pesticides, which provides new insights into the ecological risks of antibiotics.PMID:39084781 | DOI:10.1016/j.pestbp.2024.106022

Gut. 2024 Jul 30:gutjnl-2024-332407. doi: 10.1136/gutjnl-2024-332407. Online ahead of print.ABSTRACTOBJECTIVE: The specific breast milk-derived metabolites that mediate host-microbiota interactions and contribute to the onset of atopic dermatitis (AD) remain unknown and require further investigation.DESIGN: We enrolled 250 mother-infant pairs and collected 978 longitudinal faecal samples from infants from birth to 6 months of age, along with 243 maternal faecal samples for metagenomics. Concurrently, 239 corresponding breast milk samples were analysed for metabolomics. Animal and cellular experiments were conducted to validate the bioinformatics findings.RESULTS: The clinical findings suggested that a decrease in daily breastfeeding duration was associated with a reduced incidence of AD. This observation inspired us to investigate the effects of breast milk-derived fatty acids. We found that high concentrations of arachidonic acid (AA), but not eicosapentaenoic acid (EPA) or docosahexaenoic acid, induced gut dysbiosis in infants. Further investigation revealed that four specific bacteria degraded mannan into mannose, consequently enhancing the mannan-dependent biosynthesis of O-antigen and lipopolysaccharide. Correlation analysis confirmed that in infants with AD, the abundance of Escherichia coli under high AA concentrations was positively correlated with some microbial pathways (eg, 'GDP-mannose-derived O-antigen and lipopolysaccharide biosynthesis'). These findings are consistent with those of the animal studies. Additionally, AA, but not EPA, disrupted the ratio of CD4/CD8 cells, increased skin lesion area and enhanced the proportion of peripheral Th2 cells. It also promoted IgE secretion and the biosynthesis of prostaglandins and leukotrienes in BALB/c mice fed AA following ovalbumin immunostimulation. Moreover, AA significantly increased IL-4 secretion in HaCaT cells costimulated with TNF-α and INF-γ.CONCLUSIONS: This study demonstrates that AA is intimately linked to the onset of AD via gut dysbiosis.PMID:39084687 | DOI:10.1136/gutjnl-2024-332407

J Agric Food Chem. 2024 Jul 31. doi: 10.1021/acs.jafc.3c09535. Online ahead of print.ABSTRACTIntestinal stem cells (ISCs) are necessary to maintain intestinal renewal. Here, we found that the highland barley β-glucan (HBG) alleviated pathological symptoms and promoted the proliferation of intestinal stem cells in colitis mice. Notably, metabolomics studies showed that docosahexaenoic acid (DHA) was significantly increased by the HBG treatment. DHA is a ligand for peroxisome proliferator-activated receptor α (PPARα), which can promote ISC proliferation. Expectedly, HBG facilitated the expression of intestinal PPARα and the proliferation of ISCs in colitis mice. Further experiments verified that DHA significantly facilitated the expression of PPARα and the proliferation of ISCs in intestinal organoids. Intriguingly, the effect of DHA on ISC proliferation was reversed by the PPARα inhibitor. Together, our data indicate that HBG might accelerate PPARα-mediated ISC proliferation through DHA. This provides new insights into the effective application of polysaccharides in maintaining intestinal homeostasis.PMID:39084686 | DOI:10.1021/acs.jafc.3c09535

Anal Chem. 2024 Jul 31. doi: 10.1021/acs.analchem.4c01532. Online ahead of print.ABSTRACTUrine is an equally attractive biofluid for metabolomics analysis, as it is a challenging matrix analytically. Accurate urine metabolite concentration estimates by Nuclear Magnetic Resonance (NMR) are hampered by pH and ionic strength differences between samples, resulting in large peak shift variability. Here we show that calculating the spectra of original samples from mixtures of samples using linear algebra reduces the shift problems and makes various error estimates possible. Since the use of two-dimensional (2D) NMR to confirm metabolite annotations is effectively impossible to employ on every sample of large sample sets, stabilization of metabolite peak positions increases the confidence in identifying metabolites, avoiding the pitfall of oranges-to-apples comparisons.PMID:39084612 | DOI:10.1021/acs.analchem.4c01532

Bioresour Technol. 2024 Jul 29:131176. doi: 10.1016/j.biortech.2024.131176. Online ahead of print.ABSTRACTMicroalgae biotechnology holds great potential for mitigating CO2 emissions, yet faces challenges in commercialization due to suboptimal photosynthetic efficiency. This study presents an innovative approach to improve CO2 mass transfer efficiency in microalgae using carbonic anhydrase (CA) in an internal LED flexible air-lift photobioreactor. Optimal conditions initial inoculation with 3.55 × 106 cells/mL and 20 % CO2 concentration, complemented by white LED lighting in Chlorella sp. CA regulated intracellular composition, enhancing chlorophyll, lipid, and protein contents. Metabolomics revealed elevated malic and succinic acids, associated with increased Ribulose 1,5-bisphosphate carboxylase oxygenase (RuBisCO) and Acetoacetyl coenzyme A (Acetyl-CoA) activities, facilitating efficient carbon fixation. CA also mitigated cellular oxidative stress by reducing reactive oxygen species (ROS). Furthermore, CA improved extracellular electron acceptor with currents surpassed CK. This CA-based microalgae biotechnology provides a foundation for future commercial applications, addressing CO2 emissions.PMID:39084534 | DOI:10.1016/j.biortech.2024.131176

Int J Biol Macromol. 2024 Jul 29:134281. doi: 10.1016/j.ijbiomac.2024.134281. Online ahead of print.ABSTRACTCordyceps sinensis, a traditionally prized medicinal fungus, contains polysaccharides as one of its main bioactive constituents, known for their significant immunomodulatory properties. In this study, we systematically investigated the composition and structure of Cordyceps sinensis polysaccharide, followed by an evaluation of its therapeutic effect on depression using a chronic restraint stress-induced depression model. The polysaccharide CSWP-2, extracted via hot water, precipitated with ethanol, and purified using DEAE-cellulose column chromatography from Cordyceps sinensis, is primarily composed of glucose, mannose, and galactose, with α-1,4-D-glucan as its major structural component. Behavioral tests, immunological profiling, metabolomics, and gut microbiota analyses indicated a notable ameliorative effect of CSWP-2 on depressive-like symptoms in mice. Furthermore, the action of CSWP-2 may be attributed to the modulation of the gut microbiome's abundance and its metabolic impacts, thereby transmitting signals to the host immune system and exerting immunomodulatory activity, ultimately contributing to its antidepressant effects.PMID:39084447 | DOI:10.1016/j.ijbiomac.2024.134281

Int J Biol Macromol. 2024 Jul 29:134179. doi: 10.1016/j.ijbiomac.2024.134179. Online ahead of print.ABSTRACTThe butyrylcholinesterase (BChE) is an attractive target for treating Alzheimer's disease. In this study, we report the discovery of five new monoterpene indole alkaloids (MIAs) along with three known analogues from Uncaria sessilifructus Roxb. as BChE inhibitors using affinity ultrafiltration based metabolomic profiling directed isolation strategy. Their structures were well identified through comprehensive spectroscopic and chiroptical analyses. Compounds 1-2 featured unique glycosidic linkages with 1, 3-dioxane structure. All the compounds exhibited BChE inhibitory bioactivity without any cytotoxic effects. Enzymatic kinetic and molecular docking analyses of compounds 1 and 6 demonstrated their inhibiting mechanisms and binding patterns to BChE. These findings provide a valuable workflow for efficiently screening ligands that bind to proteins, and scientific recognition in the discovery of BChE inhibitors for treating neurodegenerative disorders.PMID:39084425 | DOI:10.1016/j.ijbiomac.2024.134179

Sci Total Environ. 2024 Jul 29:175134. doi: 10.1016/j.scitotenv.2024.175134. Online ahead of print.ABSTRACTAcrylamide exposure has become an emerging environmental and food safety issue, and its toxicity poses a potential threat to public health worldwide. However, limited studies have paid attention to the detrimental effects of parental exposure to acrylamide on the neurodevelopment in zebrafish offspring. In this study, the embryos were life-cycle exposed to acrylamide (0.125 and 0.25 mM) for 180 days. Subsequently, these zebrafish (F0) were allowed to mate, and their offspring (F1) were collected to culture in clean water from embryos to adults. We employed developmental and morphological observations, behavioral profiles, metabolomics analyses, and transcriptional level examinations to investigate the transgenerational neurotoxicity with parental exposure to acrylamide. Our results showed that parental exposure to acrylamide harms the birth, development, and behavior characterization of the F1 zebrafish larvae, including poor egg quality, increased mortality rates, abnormal heart rates, slowed swimming activity, and heightened anxiety behavior, and continuously disturbs mental health in F1 adult zebrafish. The transcriptional analysis showed that parental chronic exposure to acrylamide deteriorates the neurodevelopment in F1 larvae. In addition, metabolomics analyses revealed that sphingolipid metabolism disruption may be associated with the observed abnormal development and behavioral response in unexposed F1 offspring. Overall, the present study provides pioneer evidence that acrylamide induces transgenerational neurotoxicity via targeting and disrupting sphingolipid metabolism, which reveals intergenerational transmission of acrylamide exposure and unravels its spatiotemporal toxicological effect on neurodevelopment.PMID:39084380 | DOI:10.1016/j.scitotenv.2024.175134

Phytomedicine. 2024 Jul 20;133:155895. doi: 10.1016/j.phymed.2024.155895. Online ahead of print.ABSTRACTBACKGROUND: Shizao decoction (SZD) consisted of Euphorbia kansui (EK), Euphorbia pekinensis (EP), Daphne genkwa (DG), and Fructus Jujubae (FJ) is a classic Chinese herbal medicine formula for treating malignant ascites, which is closely related to the modulation of gut microbiota by our previous study. For water-expelling members (WEM) including EK, EP, and DG may have side effects on the intestine, FJ is employed for detoxification and effectivity enhancement of WEM. However, the underlying mechanism for the compatibility of WEM and FJ is still unknown.PURPOSE: To investigate the effect of the compatibility of WEM with FJ in SZD on malignant ascites and elucidate the potential mechanism from the perspective of the modulation of gut microbiota and related metabolic function.METHODS: Qualitative and quantitative evaluation of main components was conducted for comprehensive characterization of SZD and WEM. The effect of WEM and SZD was compared on malignant ascites effusion (MAE) rats. The intestinal injury was evaluated by HE staining and oxidative damage. Ascites weight, urine amount, fecal water content, the expression of aquaporins, and cytokines in ascites (IL-6, VEGF, and TNF-α) were measured to estimate the water-expelling activity. The intestinal flora was detected by 16S rDNA sequencing and the content of fecal short-chain fatty acids (SCFAs) was analyzed using gas chromatography-mass spectrometry. Pseudo-germ-free (PGF) and fecal bacteria transplantation animal experiments were subsequently employed to validate this finding. The fecal metabolomics and correlation analysis were finally conducted to explore the related metabolic changes.RESULTS: 51 and 33 components were identified in SZD and WEM, respectively. Compared to WEM alone, the compatibility with FJ remarkably reduced intestinal oxidative damage in MAE rats. Ascites was also relieved by downregulating the expression of AQP3 in the colon and decreasing the levels of IL-6, TNF-α and VEGF in ascites. The diversity of gut microbiota was reversed with an increase in Lactobacillus and Clostridia_UCG-014 while a decrease in Colidextribacter. Under the PGF condition, compatibility of WEM with FJ failed to reduce intestinal injury and alleviate MA significantly, but this effect was further enhanced after FMT. 23 potential fecal metabolites were finally identified. Correlation analysis further showed that Lactobacillus and Clostridia_UCG-014 were positively correlated with SCFAs and l-tryptophan. Colidextribacter was negatively correlated with thymidine but positively correlated with ursodeoxycholic acid and deoxycholic acid.CONCLUSION: FJ cooperated with WEM reduced intestinal injury and alleviated malignant ascites by modulating gut microbiota, short-chain fatty and tryptophan metabolism. These findings provide a scientific basis for the clinical application of FJ from SZD and the safe usage of SZD.PMID:39084184 | DOI:10.1016/j.phymed.2024.155895

Comp Biochem Physiol Part D Genomics Proteomics. 2024 Jul 29;52:101302. doi: 10.1016/j.cbd.2024.101302. Online ahead of print.ABSTRACTThe Alexandrine parakeet (Palaeornis eupatria), also known as the Alexandrine parrot, is a critically endangered species in the world and a national second class protected animal. Current knowledge on gut microbiome and metabolome of captive Alexandrine parrots is limited. In the current study, we characterized the effect of dietary change with pellet feeding on the gut microbiome and metaboliome in Alexandrine parrots using 16S gene sequencing and liquid chromatography with tandem mass spectrometry (LC-MS/MS). Total of 12 Alexandrine parrots were used in a cross-over study with each period for 10 days. The results showed that dietary change with pellet feeding did not affect alpha indices of gut microbiota. Cyanobacteria, Firmicutes and Proteobacteria were the predominant bacterial phyla in the gut of Alexandrine parrot with Cynobacteria being the highest. Change of diet significantly increased the relative abundance of Actinobacteria and decreased Spirochaetota. The relative abundance of Fusobacteriota tended to increase with pellet feeding. No treatment effects were observed between the control and pellet feeding groups at the genus level. Based on the annotation results from Clusters of Orthologous Genes (COG) database, dietary change with pellet feeding significantly increased the relative abundance of genes coding for extracellular structures and lipid transport and metabolism. Metabolomics analysis combined with enrichment analysis revealed that dietary change altered the concentrations of gut metabolites as well as the metabolic pattern, and significantly affected the concentrations of fecal metabolites involved in isoflavonoid biosynthesis, flavonoid biosynthesis, nucleotide metabolism etc. In summary, dietary changes with pellet feeding affected the gut microbial composition and metabolites to some extent. The relevance of current findings to Alexandrine parrots' health and potential zoonosis need further exploring.PMID:39084149 | DOI:10.1016/j.cbd.2024.101302

Biomed Eng Online. 2024 Jul 31;23(1):76. doi: 10.1186/s12938-024-01265-5.ABSTRACTBACKGROUND: Transcranial sonography (TCS) plays a crucial role in diagnosing Parkinson's disease. However, the intricate nature of TCS pathological features, the lack of consistent diagnostic criteria, and the dependence on physicians' expertise can hinder accurate diagnosis. Current TCS-based diagnostic methods, which rely on machine learning, often involve complex feature engineering and may struggle to capture deep image features. While deep learning offers advantages in image processing, it has not been tailored to address specific TCS and movement disorder considerations. Consequently, there is a scarcity of research on deep learning algorithms for TCS-based PD diagnosis.METHODS: This study introduces a deep learning residual network model, augmented with attention mechanisms and multi-scale feature extraction, termed AMSNet, to assist in accurate diagnosis. Initially, a multi-scale feature extraction module is implemented to robustly handle the irregular morphological features and significant area information present in TCS images. This module effectively mitigates the effects of artifacts and noise. When combined with a convolutional attention module, it enhances the model's ability to learn features of lesion areas. Subsequently, a residual network architecture, integrated with channel attention, is utilized to capture hierarchical and detailed textures within the images, further enhancing the model's feature representation capabilities.RESULTS: The study compiled TCS images and personal data from 1109 participants. Experiments conducted on this dataset demonstrated that AMSNet achieved remarkable classification accuracy (92.79%), precision (95.42%), and specificity (93.1%). It surpassed the performance of previously employed machine learning algorithms in this domain, as well as current general-purpose deep learning models.CONCLUSION: The AMSNet proposed in this study deviates from traditional machine learning approaches that necessitate intricate feature engineering. It is capable of automatically extracting and learning deep pathological features, and has the capacity to comprehend and articulate complex data. This underscores the substantial potential of deep learning methods in the application of TCS images for the diagnosis of movement disorders.PMID:39085884 | DOI:10.1186/s12938-024-01265-5

BMC Plant Biol. 2024 Jul 31;24(1):732. doi: 10.1186/s12870-024-05330-y.ABSTRACTBACKGROUND: Soybean is the main oil crop in Northeast China. Continuous monocropping is more commonly used for soybean production due to rising market demand and arable land constraints. However, autotoxic substances, such as phenolic acids, produced by continuously cropped soybean can reduce yield and quality. The mycorrhiza formed of Arbuscular mycorrhizal fungi (AMF) and plant roots regulate the metabolic activities of the host plant and increase its disease resistance. The main purpose of this study was to inhibit the production of phenolic acids and determine the adverse effects on the growth of continuous monocropping soybean by inoculating Funneliformis mosseae (F. mosseae).RESULTS: Transcriptomics results showed that the production of phenolic acids in continuous monocropping soybean roots was mainly regulated by the expression of the CHS6, PCL1, SAMT, SRG1, and ACO1 genes, and the expression of these genes was significantly downregulated after inoculation with F. mosseae. Metabolomics results showed that continuous monocropping soybean roots inoculated with F. mosseae inhibited phenolic acid production through the phenylpropane biosynthetic, α-linoleic acid, linoleic acid, and other metabolic pathways. Phenolic acids in the phenylpropane metabolic pathway, such as 4-hydroxybenzoic acid, phthalic acid, and vanillic acid, decreased significantly after inoculation with F. mosseae. The combined analysis of the two showed that genes such as YLS9 and ARF3 were positively correlated with 4-hydroxybenzoic acid and so on, while genes such as CHS6 and SRG1 were negatively correlated with butyric acid and so on.CONCLUSION: F. mosseae regulated the expression of functional genes and related phenolic acid metabolic pathways produced by continuous monocropping soybean roots, inhibiting the production of phenolic acid autotoxic substances in continuous cropped soybean, and slowing down the disturbance of continuous monocropping. This study provides a new solution for continuous monocropping of plants to overcome the autotoxicity barrier and provides a new basis for the development and utilization of AMF as a biological agent.PMID:39085801 | DOI:10.1186/s12870-024-05330-y

BMC Plant Biol. 2024 Jul 31;24(1):731. doi: 10.1186/s12870-024-05450-5.ABSTRACTBACKGROUND: In the field of ornamental horticulture, phenotypic mutations, particularly in leaf color, are of great interest due to their potential in developing new plant varieties. The introduction of variegated leaf traits in plants like Heliopsis helianthoides, a perennial herbaceous species with ecological adaptability, provides a rich resource for molecular breeding and research on pigment metabolism and photosynthesis. We aimed to explore the mechanism of leaf variegation of Heliopsis helianthoides (using HY2021F1-0915 variegated mutant named HY, and green-leaf control check named CK in 2020 April, May and June) by analyzing the transcriptome and metabolome.RESULTS: Leaf color and physiological parameters were found to be significantly different between HY and CK types. Chlorophyll content of HY was lower than that of CK samples. Combined with the result of Weighted Gene Co-expression Network Analysis (WGCNA), 26 consistently downregulated differentially expressed genes (DEGs) were screened in HY compared to CK subtypes. Among the DEGs, 9 genes were verified to be downregulated in HY than CK by qRT-PCR. The reduction of chlorophyll content in HY might be due to the downregulation of FSD2. Low expression level of PFE2, annotated as ferritin-4, might also contribute to the interveinal chlorosis of HY. Based on metabolome data, differential metabolites (DEMs) between HY and CK samples were significantly enriched on ABC transporters in three months. By integrating DEGs and DEMs, they were enriched on carotenoids pathway. Downregulation of four carotenoid pigments might be one of the reasons for HY's light color.CONCLUSION: FSD2 and PFE2 (ferritin-4) were identified as key genes which likely contribute to the reduced chlorophyll content and interveinal chlorosis observed in HY. The differential metabolites were significantly enriched in ABC transporters. Carotenoid biosynthesis pathway was highlighted with decreased pigments in HY individuals. These findings not only enhance our understanding of leaf variegation mechanisms but also offer valuable insights for future plant breeding strategies aimed at preserving and enhancing variegated-leaf traits in ornamental plants.PMID:39085772 | DOI:10.1186/s12870-024-05450-5

Mol Cell Pediatr. 2024 Aug 1;11(1):6. doi: 10.1186/s40348-024-00179-5.ABSTRACTBACKGROUND: As an indigestible component of human breast milk, Human Milk Oligosaccharides (HMOs) play an important role as a substrate for the establishing microbiome of the newborn. They have further been shown to have beneficial effects on the immune system, lung and brain development. For preterm infants HMO composition of human breast milk may be of particular relevance since the establishment of a healthy microbiome is challenged by multiple disruptive factors associated with preterm birth, such as cesarean section, hospital environment and perinatal antibiotic exposure. In a previous study it has been proposed that maternal probiotic supplementation during late stages of pregnancy may change the HMO composition in human milk. However, there is currently no study on pregnancies which are threatened to preterm birth. Furthermore, HMO composition has not been investigated in association with clinically relevant outcomes of vulnerable infants including inflammation-mediated diseases such as sepsis, necrotizing enterocolitis (NEC) or chronic lung disease.MAIN BODY: A randomized controlled intervention study (PROMO = probiotics for human milk oligosaccharides) has been designed to analyze changes in HMO composition of human breast milk after supplementation of probiotics (Lactobacillus acidophilus, Bifidobacterium lactis and Bifidobacterium infantis) in pregnancies at risk for preterm birth. The primary endpoint is HMO composition of 3-fucosyllactose and 3'-sialyllactose in expressed breast milk. We estimate that probiotic intervention will increase these two HMO levels by 50% according to the standardized mean difference between treatment and control groups. As secondary outcomes we will measure preterm infants' clinical outcomes (preterm birth, sepsis, weight gain growth, gastrointestinal complications) and effects on microbiome composition in the rectovaginal tract of mothers at delivery and in the gut of term and preterm infants by sequencing at high genomic resolution. Therefore, we will longitudinally collect bio samples in the first 4 weeks after birth as well as in follow-up investigations at 3 months, one year, and five years of age.CONCLUSIONS: We estimate that probiotic intervention will increase these two HMO levels by 50% according to the standardized mean difference between treatment and control groups. The PROMO study will gain insight into the microbiome-HMO interaction at the fetomaternal interface and its consequences for duration of pregnancy and outcome of infants.PMID:39085734 | DOI:10.1186/s40348-024-00179-5

Exp Mol Med. 2024 Aug 1. doi: 10.1038/s12276-024-01291-2. Online ahead of print.ABSTRACTTFE3-rearranged renal cell cancer (tRCC) is a rare form of RCC that involves chromosomal translocation of the Xp11.2 TFE3 gene. Despite its early onset and poor prognosis, the molecular mechanisms of the pathogenesis of tRCC remain elusive. This study aimed to identify novel therapeutic targets for patients with primary and recurrent tRCC. We collected 19 TFE3-positive RCC tissues that were diagnosed by immunohistochemistry and subjected them to genetic characterization to examine their genomic and transcriptomic features. Tumor-specific signatures were extracted using whole exome sequencing (WES) and RNA sequencing (RNA-seq) data, and the functional consequences were analyzed in a cell line with TFE3 translocation. Both a low burden of somatic single nucleotide variants (SNVs) and a positive correlation between the number of somatic variants and age of onset were observed. Transcriptome analysis revealed that four samples (21.1%) lacked the expected fusion event and clustered with the genomic profiles of clear cell RCC (ccRCC) tissues. The fusion event also demonstrated an enrichment of upregulated genes associated with mitochondrial respiration compared with ccRCC expression profiles. Comparison of the RNA expression profile with the TFE3 ChIP-seq pattern data indicated that PPARGC1A is a metabolic regulator of the oncogenic process. Cell proliferation was reduced when PPARGC1A and its related metabolic pathways were repressed by its inhibitor SR-18292. In conclusion, we demonstrate that PPARGC1A-mediated mitochondrial respiration can be considered a potential therapeutic target in tRCC. This study identifies an uncharacterized genetic profile of an RCC subtype with unique clinical features and provides therapeutic options specific to tRCC.PMID:39085357 | DOI:10.1038/s12276-024-01291-2

Commun Chem. 2024 Jul 31;7(1):168. doi: 10.1038/s42004-024-01252-w.ABSTRACTFragment screening is a popular strategy of generating viable chemical starting points especially for challenging targets. Although fragments provide a better coverage of chemical space and they have typically higher chance of binding, their weak affinity necessitates highly sensitive biophysical assays. Here, we introduce a screening concept that combines evolutionary optimized fragment pharmacophores with the use of a photoaffinity handle that enables high hit rates by LC-MS-based detection. The sensitivity of our screening protocol was further improved by a target-conjugated photocatalyst. We have designed, synthesized, and screened 100 diazirine-tagged fragments against three benchmark and three therapeutically relevant protein targets of different tractability. Our therapeutic targets included a conventional enzyme, the first bromodomain of BRD4, a protein-protein interaction represented by the oncogenic KRasG12D protein, and the yet unliganded N-terminal domain of the STAT5B transcription factor. We have discovered several fragment hits against all three targets and identified their binding sites via enzymatic digestion, structural studies and modeling. Our results revealed that this protocol outperforms screening traditional fully functionalized and photoaffinity fragments in better exploration of the available binding sites and higher hit rates observed for even difficult targets.PMID:39085342 | DOI:10.1038/s42004-024-01252-w

Sci Rep. 2024 Jul 31;14(1):17649. doi: 10.1038/s41598-024-64574-8.ABSTRACTCervical cancer (CC) remains a major health concern globally, much of the brunt of which is experienced by the low- and middle-income countries where screening in terms of cytology and DNA genotyping for the high-risk oncogenic subtypes of the human papilloma virus (hr-HPV) is either inadequate or performed rather late. In this study, we aimed to determine biomarkers or panels of biomarkers that are capable of diagnosing the precancerous cervical intraepithelial neoplasia (CIN) stages from healthy and CC patients via untargeted gas chromatography-mass spectrometry-based metabolomics. Various cross-comparisons were conducted from which differential metabolites were identified. The underlying metabolic pathways based on the differential metabolites identified from the various cross-comparisons mainly related to amino acids biosynthesis and metabolism and steroid hormone biosynthesis. From all cross-comparisons, two common metabolites namely, 2-methyl-1-propylamine (also known as isobutylamine) and estrone were found to possess excellent to good diagnostic abilities, especially in distinguishing the early stages of CIN (CIN I, CIN II) from healthy women and CC patients. These findings have clinical significance in the sense that, once validated the 2-biomarker panel could be adopted in clinical practice for early diagnosis of CIN and invasive carcinoma. This would therefore inform the choice of treatment to be initiated by the clinician.PMID:39085248 | DOI:10.1038/s41598-024-64574-8

Nat Commun. 2024 Jul 31;15(1):6463. doi: 10.1038/s41467-024-50752-9.ABSTRACTHyperuricemia is associated with an increased risk of gout, hypertension, diabetes, and cardiovascular diseases. Most mammals maintain normal serum uric acid (SUA) via urate oxidase (Uox), an enzyme that metabolizes poorly-soluble UA to highly-soluble allantoin. In contrast, Uox became a pseudogene in humans and apes over the long course of evolution. Here we demonstrate an atavistic strategy for treating hyperuricemia based on endogenous expression of Uox in hepatocytes mediated by mRNA (mUox) loaded with an ionizable lipid nanoparticle termed iLAND. mUox@iLAND allows effective transfection and protein expression in vitro. A single dose of mUox@iLAND lowers SUA levels for several weeks in two female murine models, including a novel long-lasting model, which is also confirmed by metabolomics analysis. Together with the excellent safety profiles observed in vivo, the proposed mRNA agent demonstrates substantial potential for hyperuricemia therapy and the prevention of associated conditions.PMID:39085241 | DOI:10.1038/s41467-024-50752-9

NPJ Biofilms Microbiomes. 2024 Aug 1;10(1):66. doi: 10.1038/s41522-024-00538-0.ABSTRACTThe clinical course of COVID-19 is variable and often unpredictable. To test the hypothesis that disease progression and inflammatory responses associate with alterations in the microbiome and metabolome, we analyzed metagenome, metabolome, cytokine, and transcriptome profiles of repeated samples from hospitalized COVID-19 patients and uninfected controls, and leveraged clinical information and post-hoc confounder analysis. Severe COVID-19 was associated with a depletion of beneficial intestinal microbes, whereas oropharyngeal microbiota disturbance was mainly linked to antibiotic use. COVID-19 severity was also associated with enhanced plasma concentrations of kynurenine and reduced levels of several other tryptophan metabolites, lysophosphatidylcholines, and secondary bile acids. Moreover, reduced concentrations of various tryptophan metabolites were associated with depletion of Faecalibacterium, and tryptophan decrease and kynurenine increase were linked to enhanced production of inflammatory cytokines. Collectively, our study identifies correlated microbiome and metabolome alterations as a potential contributor to inflammatory dysregulation in severe COVID-19.PMID:39085233 | DOI:10.1038/s41522-024-00538-0