PubMed

Anal Chem. 2023 Dec 19. doi: 10.1021/acs.analchem.3c01380. Online ahead of print.ABSTRACTUrine is one of the most widely used biofluids in metabolomic studies because it can be collected noninvasively and is available in large quantities. However, it shows large heterogeneity in sample concentration and consequently requires normalization to reduce unwanted variation and extract meaningful biological information. Biological samples like urine are commonly measured with electrospray ionization (ESI) coupled to a mass spectrometer, producing data sets for positive and negative modes. Combining these gives a more complete picture of the total metabolites present in a sample. However, the effect of this data merging on subsequent data analysis, especially in combination with normalization, has not yet been analyzed. To address this issue, we conducted a neutral comparison study to evaluate the performance of eight postacquisition normalization methods under different data merging procedures using 1029 urine samples from the Food Chain plus (FoCus) cohort. Samples were measured with a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS). Normalization methods were evaluated by five criteria capturing the ability to remove sample concentration variation and preserve relevant biological information. Merging data after normalization was generally favorable for quality control (QC) sample similarity, sample classification, and feature selection for most of the tested normalization methods. Merging data after normalization and the usage of probabilistic quotient normalization (PQN) in a similar setting are generally recommended. Relying on a single analyte to capture sample concentration differences, like with postacquisition creatinine normalization, seems to be a less preferable approach, especially when data merging is applied.PMID:38113356 | DOI:10.1021/acs.analchem.3c01380

J Med Chem. 2023 Dec 19. doi: 10.1021/acs.jmedchem.3c01779. Online ahead of print.ABSTRACTScreening of ultra-low-molecular weight ligands (MiniFrags) successfully identified viable chemical starting points for a variety of drug targets. Here we report the electrophilic analogues of MiniFrags that allow the mapping of potential binding sites for covalent inhibitors by biochemical screening and mass spectrometry. Small electrophilic heterocycles and their N-quaternized analogues were first characterized in the glutathione assay to analyze their electrophilic reactivity. Next, the library was used for systematic mapping of potential covalent binding sites available in human histone deacetylase 8 (HDAC8). The covalent labeling of HDAC8 cysteines has been proven by tandem mass spectrometry measurements, and the observations were explained by mutating HDAC8 cysteines. As a result, screening of electrophilic MiniFrags identified three potential binding sites suitable for the development of allosteric covalent HDAC8 inhibitors. One of the hit fragments was merged with a known HDAC8 inhibitor fragment using different linkers, and the linker length was optimized to result in a lead-like covalent inhibitor.PMID:38113354 | DOI:10.1021/acs.jmedchem.3c01779

Mov Disord. 2023 Dec;38(12):2322-2323. doi: 10.1002/mds.29639.NO ABSTRACTPMID:38113318 | DOI:10.1002/mds.29639

Brief Bioinform. 2023 Nov 22;25(1):bbad453. doi: 10.1093/bib/bbad453.ABSTRACTResearchers increasingly turn to explainable artificial intelligence (XAI) to analyze omics data and gain insights into the underlying biological processes. Yet, given the interdisciplinary nature of the field, many findings have only been shared in their respective research community. An overview of XAI for omics data is needed to highlight promising approaches and help detect common issues. Toward this end, we conducted a systematic mapping study. To identify relevant literature, we queried Scopus, PubMed, Web of Science, BioRxiv, MedRxiv and arXiv. Based on keywording, we developed a coding scheme with 10 facets regarding the studies' AI methods, explainability methods and omics data. Our mapping study resulted in 405 included papers published between 2010 and 2023. The inspected papers analyze DNA-based (mostly genomic), transcriptomic, proteomic or metabolomic data by means of neural networks, tree-based methods, statistical methods and further AI methods. The preferred post-hoc explainability methods are feature relevance (n = 166) and visual explanation (n = 52), while papers using interpretable approaches often resort to the use of transparent models (n = 83) or architecture modifications (n = 72). With many research gaps still apparent for XAI for omics data, we deduced eight research directions and discuss their potential for the field. We also provide exemplary research questions for each direction. Many problems with the adoption of XAI for omics data in clinical practice are yet to be resolved. This systematic mapping study outlines extant research on the topic and provides research directions for researchers and practitioners.PMID:38113073 | DOI:10.1093/bib/bbad453

Eur Rev Med Pharmacol Sci. 2023 Dec;27(6 Suppl):64-76. doi: 10.26355/eurrev_202312_34691.ABSTRACTOBJECTIVE: Anorexia nervosa (AN), a severe psychiatric disorder primarily affecting adolescents and young adults, is characterized by extreme dietary restriction and distorted body image. While the psychological aspects of AN are well-documented, its intricate metabolic underpinnings remain less explored. We think that metabolomic analysis of hair samples emerges as a promising tool to unveil the complex physiological alterations in AN. This study aims to comprehensively profile amino acid concentrations in hair samples from AN patients and healthy controls. Additionally, it seeks to elucidate potential correlations between amino acid alterations and appetite dysregulation in AN, thereby shedding light on the physiological basis of this debilitating disorder.PATIENTS AND METHODS: A total of 25 AN patients and 25 age-matched healthy controls were recruited for this study. Hair samples were collected, and metabolites were extracted and analyzed using high-resolution liquid chromatography-mass spectrometry. Clinical data and biochemical markers were also gathered to characterize participants' demographic and clinical profiles.RESULTS: Metabolomic analysis revealed significant alterations in amino acid concentrations in AN patients compared to healthy controls. Notably, deficiencies in essential amino acids (EAAs) and branched-chain amino acids (BCAAs) were observed, highlighting potential contributors to muscle wasting and appetite dysregulation. Further analysis identified specific amino acids as robust biomarkers capable of distinguishing AN patients with high sensitivity and specificity.CONCLUSIONS: This study unveils the complex metabolic disturbances associated with AN and underscores the role of amino acid dysregulation in the disorder's pathophysiology. The identified biomarkers hold promise for diagnostic screening and potential therapeutic interventions, opening avenues for personalized approaches in AN treatment. Ultimately, this research contributes to our understanding of chronic disorders through the lens of metabolomics and the chemosensory underpinnings of appetite regulation.PMID:38112949 | DOI:10.26355/eurrev_202312_34691

Planta. 2023 Dec 19;259(1):27. doi: 10.1007/s00425-023-04306-w.ABSTRACTIntegrated transcriptome and metabolome analysis have unveiled the physiological and molecular responses of rhubarb to infection by smut fungi. Rhubarb is an important medicinal plant that is easily infected by smut fungi during its growth. Thus far, no research on the influence of smut fungi on the growth of rhubarb and its secondary metabolism has been conducted. In this study, petioles of Chinese rhubarb (Rheum officinale) [healthy or infected with smut fungus (Thecaphora schwarzmaniana)] were characterized. Microscopic structure, global gene expression profiling, global metabolic profiling, and key enzyme activity and metabolite levels in infected plants were analyzed. Infection by smut fungi resulted in numerous holes inside the petiole tissue and led to visible tumors on the external surface of the petiole. Through metabolic changes, T. schwarzmaniana induced the production of specific sugars, lipids, and amino acids, and inhibited the metabolism of phenolics and flavonoids in R. officinale. The concentrations of key medicinal compounds (anthraquinones) were decreased because of smut fungus infection. In terms of gene expression, the presence of T. schwarzmaniana led to upregulation of the genes associated with nutrient (sugar, amino acid, etc.) transport and metabolism. The gene expression profiling showed a stimulated cell division activity (the basis of tumor formation). Although plant antioxidative response was enhanced, the plant defense response against pathogen was suppressed by T. schwarzmaniana, as indicated by the expression profiling of genes involved in biotic and abiotic stress-related hormone signaling and the synthesis of plant disease resistance proteins. This study demonstrated physiological and molecular changes in R. officinale under T. schwarzmaniana infection, reflecting the survival tactics employed by smut fungus for parasitizing rhubarb.PMID:38112830 | DOI:10.1007/s00425-023-04306-w

J Agric Food Chem. 2023 Dec 19. doi: 10.1021/acs.jafc.3c05879. Online ahead of print.ABSTRACTExogenous substances (ESs) can regulate plant growth and respond to environmental stress, but the effects of different ESs on blueberry fruit quality under soil cadmium (Cd) toxicity and related metabolic mechanisms are still unclear. In this study, four ES treatments [salicylic acid (SA), spermidine (Spd), 2,4-epibrassinolide (EBR), and melatonin (MT)] significantly increased blueberry fruit size, single-fruit weight, sweetness, and anthocyanin content under soil Cd toxicity and effectively reduced fruit Cd content to safe consumption levels by promoting mineral uptake (Ca, Mg, Mn, Cu and Zn). Furthermore, a total of 445, 360, 429, and 554 differentially abundant metabolites (DAMs) (LC-MS) and 63, 48, 79, and 73 DAMs (GC-MS) were identified from four comparison groups (SA/CK, Spd/CK, EBR/CK and MT/CK), respectively. The analyses revealed that ESs improved blueberry fruit quality and tolerance to Cd toxicity mainly by regulating the changes in metabolites related to ABC transporters, the TCA cycle, flavonoid biosynthesis, and phenylpropanoid biosynthesis.PMID:38112527 | DOI:10.1021/acs.jafc.3c05879

mSystems. 2023 Dec 19:e0099123. doi: 10.1128/msystems.00991-23. Online ahead of print.ABSTRACTIt was found that with the increase of drug use years, the content of tryptamine associated with neuropsychiatric disorders gradually increased. The prediction models based on oral microbiome and metabolome could effectively predict the methamphetamine (METH) smoking. Our study provides novel insights into the exploration of the molecular mechanisms regulating the toxic damage and addiction of METH as well as new ideas for early prevention and treatment strategies of METH addiction.PMID:38112416 | DOI:10.1128/msystems.00991-23

J Agric Food Chem. 2023 Dec 19. doi: 10.1021/acs.jafc.3c05837. Online ahead of print.ABSTRACTUntargeted nuclear magnetic resonance (NMR) metabolomics was used to evaluate compositional changes during yogurt fermentation upon lupin enrichment compared to traditional conditions. Lupin significantly changed the sample metabolic profile and its time course dynamics, seemingly delaying microbial action. The levels of organic and amino acids were significantly altered, along with those of some sugars, nucleotides, and choline compounds. Lupin seemed to favor acetate and formate synthesis, compared to that of citrate and fumarate; a higher formate levels may suggest increased levels of Streptococcus thermophilus action, compared toLactobacillus bulgaricus. Lupin-yogurt was poorer in hippurate, lactose (and hence lactate), galactose, glucose-1-phosphate, and galactose-1-phosphate, containing higher orotate levels (possibly related to increased uridine derivatives), among other differences. Trigonelline was confirmed as a lupin marker, possibly together with glutamate and histidine. Other metabolite trajectories remained unchanged upon lupin addition, unveiling unaffected underlying processes. These results demonstrate the usefulness of untargeted NMR metabolomics to understand/develop new foodstuffs and their production processes, highlighting the identity of a variety of bioactive metabolites with importance for human health.PMID:38112332 | DOI:10.1021/acs.jafc.3c05837

J Diabetes. 2023 Dec 19. doi: 10.1111/1753-0407.13514. Online ahead of print.ABSTRACTBACKGROUND: Pravastatin is an oral lipid-lowering drug, commonly used by patients with diabetes that is positively correlated with the occurrence of vascular calcification (VC), but the mechanism is unclear.METHODS: In this study, 16S rRNA sequencing and qRT-PCR wereused to detect the differential gut bacteria. Metabolomics and ELISA were used to analyze the differential metabolites. qRT-PCR and western blotting (WB) were used to detect genes expression. Flow cytometry was used to analyze macrophage phenotype. Immunohistochemistry was used to analyze aortic calcification.RESULTS: We found that gut Bacteroides fragilis (BF) increased significantly in patients who took pravastatin or type 2 diabetes (T2D) mice treated with pravastatin. In vitro experiments showed that pravastatin had little effect on BF but significantly promoted BF proliferation in vivo. Further analysis showed that ArsR was an important gene for pravastatin to regulate the activation of BF, and overexpression of ArsR significantly promoted the secretion of 3,4,5-trimethoxycinnamic acid (TMCA). Importantly, pravastatin significantly promoted BF secretion of TMCA and significantly increased TMCA secretion in T2D patients or T2D mice. TMCA had little effect on vascular smooth muscle cell calcification but significantly promoted macrophage M1 polarization, which we had demonstrated that M1 macrophages promoted T2D VC. In vivo studies found that pravastatin significantly upregulated TMCA levels in the feces and serum of T2D mice transplanted with BF and promoted the macrophage M1 polarization in bone marrow and the osteoblastic differentiation of aortic cells. Similar results were obtained in T2D mice after intravenous infusion of TMCA.CONCLUSIONS: Promoting intestinal BF to secrete TMCA, which leads to macrophage M1 polarization, is an important mechanism by which pravastatin promotes calcification, and the result will be used for the optimization of clinical medication strategies of pravastatin supplying a theoretical basis and experimental basis.PMID:38112268 | DOI:10.1111/1753-0407.13514

Neuropathol Appl Neurobiol. 2023 Dec 19:e12950. doi: 10.1111/nan.12950. Online ahead of print.ABSTRACTOBJECTIVE: Filipin complex is an autooxidation-prone fluorescent histochemical stain used in the diagnosis of Niemann-Pick Disease Type C (NP-C), a neurodegenerative lysosomal storage disorder. It is also widely used by researchers examining the distribution and accumulation of unesterified cholesterol in cell and animal models of neurodegenerative diseases including NP-C and Sanfilippo syndrome (mucopolysaccharidosis IIIA; MPS IIIA). Recently, it has been suggested to be useful in studying Alzheimer's and Huntington's disease. Given filipin's susceptibility to photobleaching, we sought to establish a quantitative biochemical method for free cholesterol measurement.METHODS: Brain tissue from mice with MPS IIIA was stained with filipin. Total and free cholesterol in brain homogenates was measured using a commercially available kit and a quantitative LC-MS/MS assay was developed. Gangliosides GM1, GM2 and GM3 were also quantified using LC-MS/MS.RESULTS: As anticipated, the MPS IIIA mouse brain displayed large numbers of filipin-positive intra-cytoplasmic inclusions, presumptively endo-lysosomes. Challenging the prevailing dogma, however, we found no difference in the amount of free cholesterol in MPS IIIA mouse brain homogenates cf. control tissue, using either the fluorometric kit or LC-MS/MS assay. Filipin has previously been reported to bind to GM1 ganglioside, however, this lipid does not accumulate in MPS IIIA cells/tissues. Using a fluorometric assay, we demonstrate for the first time that filipin cross-reacts with both GM2 and GM3 gangliosides, explaining the filipin-reactive inclusions observed in MPS IIIA brain cells.CONCLUSION: Filipin is not specific for free cholesterol, and positive staining in any setting should be interpreted with caution.PMID:38112248 | DOI:10.1111/nan.12950

Obesity (Silver Spring). 2023 Dec 19. doi: 10.1002/oby.23964. Online ahead of print.ABSTRACTOBJECTIVE: The aim of this study was to identify the differential metabolic characteristics of children with overweight and obesity and understand their potential mechanism in different age stratifications.METHODS: Four hundred seventy-three children were recruited and divided into two age stratifications: >4 years (older children) and ≤4 years (younger children), and overweight and obesity were defined according to their BMI percentile. A one dimensional proton nuclear magnetic resonance (1 H-NMR)-based metabolomics strategy combined with pattern recognition methods was used to identify the metabolic characteristics of childhood overweight and obesity.RESULTS: Four and sixteen potential biomarkers related to overweight and two and twenty potential biomarkers related to obesity were identified from younger and older children, respectively. Fluctuations in phenylalanine, tyrosine, glutamine, leucine, histidine, and ascorbate co-occurred in children with obesity at two age stratifications. The disturbances in biosynthesis and metabolism of amino acids, lipid metabolism, and galactose metabolism disturbance were mainly involved in children with overweight and obesity.CONCLUSIONS: The metabolic disturbances show a significant progression from overweight to obesity in children, and different metabolic characteristics were demonstrated in age stratifications. The changes in the levels of phenylalanine, tyrosine, glutamine, leucine, histidine, and ascorbate were tracked with the persistence of childhood obesity. These findings will promote the mechanistic understanding of childhood overweight and obesity.PMID:38112246 | DOI:10.1002/oby.23964

Circ Res. 2023 Dec 19. doi: 10.1161/CIRCRESAHA.123.323651. Online ahead of print.ABSTRACTBACKGROUND: Age-related cardiac fibrosis is a risk factor for heart failure and a marker for heart aging. However, the mechanisms underlying age-related cardiac fibrosis remain unclear. Ischemia and hypoxia are inevitable events in the aging process, which are direct causes of mitochondrial dysfunction and metabolic alterations. In this study, we identified metabolic changes and determined the mechanisms by which succinate (a tricarboxylic acid cycle intermediate) accumulation promotes fibroblast activation and apoptosis resistance in the aging heart. We also assessed its significance in relation to cardiac fibrosis and diastolic dysfunction.METHODS: We first investigated how aging promotes persistent cardiac fibrosis. Following this, the metabolic alterations of the aging heart were identified by untargeted metabolomics, and the succinate level was verified via quantitative analysis. Furthermore, the correlations between succinate and fibrosis or diastolic dysfunction in older mice/people were assessed. We also described the role of succinate and its receptor SUCNR1/GPR91 in establishing a fibrosis network during diastolic dysfunction with age using SUCNR1-/- mouse model and an AAV9-based approach. We further identified the specific mechanisms involved in PKM2 dimerization, which regulate fibroblast activation and apoptosis resistance.RESULTS: We demonstrated that aging promotes fibrogenesis and diastolic dysfunction, which are linked to fibroblast activation and apoptosis resistance in the heart. Succinate levels were correlated with diastolic dysfunction and cardiac fibrosis in older mice and people. Functionally, succinate promoted fibroblast activation and apoptosis resistance, which aggravate cardiac fibrosis formation in both young and old mice. This was attributed to the ability of succinate to stimulate PKM2 dimerization via succinate receptor SUCNR1. Furthermore, dimeric PKM2 translocated to the nucleus and mitochondria, where it promoted fibroblast activation and apoptosis resistance, respectively. Accumulated PKM2 in the nucleus interacted with HIF-1α, increasing the DNA binding of HIF-1α and the expression of fibrogenic genes, resulting in fibroblast activation. In the mitochondria, accumulated PKM2 phosphorylated VDAC1 at T93 and increased VDAC1 degradation by promoting SYVN1-based E3 ligase binding to VDAC1, which is associated with increased apoptosis resistance and fibrosis persistence. We found that targeting succinate accumulation by metformin can inhibit fibroblast activation and apoptosis resistance in mice, which is a potential strategy to control age-related cardiac fibrosis and diastolic dysfunction.CONCLUSIONS: Our findings indicate that targeting metabolic dysregulation has significant implications for the treatment of age-related cardiac fibrosis and diastolic dysfunction. We further demonstrate a novel mechanism by which succinate induces fibroblast activation and apoptosis resistance by promoting PKM2 dimerization. Hence, inhibiting succinate generation or blocking its downstream effects is potentially a promising new strategy for slowing the heart aging.PMID:38112098 | DOI:10.1161/CIRCRESAHA.123.323651

Hypertension. 2023 Dec 19. doi: 10.1161/HYPERTENSIONAHA.123.21710. Online ahead of print.ABSTRACTHypertension affects >1 billion people worldwide. Complications of hypertension include stroke, renal failure, cardiac hypertrophy, myocardial infarction, and cardiac failure. Despite the development of various antihypertensive drugs, the number of people with uncontrolled hypertension continues to rise. While the lack of compliance associated with frequent side effects to medication is a contributory issue, there has been a failure to consider the diverse nature of hypertensive populations. Instead, we propose that hypertension can only be truly managed by precision. A precision medicine approach would consider each patient's unique factors. In this review, we discuss the progress toward precision medicine for hypertension with more predictiveness and individualization of treatment. We will highlight the advances in data science, omics (genomics, metabolomics, proteomics, etc), artificial intelligence, gene therapy, and gene editing and their application to precision hypertension.PMID:38112080 | DOI:10.1161/HYPERTENSIONAHA.123.21710

J Agric Food Chem. 2023 Dec 19. doi: 10.1021/acs.jafc.3c05949. Online ahead of print.ABSTRACTAlzheimer's disease (AD) is distinguished by cognitive dysfunction and neuroinflammation in the brain. 2'-Fucosyllactose (2'-FL) is a major human milk oligosaccharide (HMO) that is abundantly present in breast milk and has been demonstrated to exhibit immunomodulatory effects. However, the role of 2'-FL and HMO in gut microbiota modulation in relation to AD remains insufficiently investigated. This study aimed to elucidate the preventive effect of the 2'-FL and HMO impact of AD and the relevant mechanism involved. Here, the behavioral results showed that 2'-FL and HMO intervention decreased the expression of Tau phosphorylation and amyloid-β (Aβ), inhibited neuroinflammation, and restored cognitive impairment in AD mice. The metagenomic analysis proved that 2'-FL and HMO intervention restored the dysbiosis of the gut microbiota in AD. Notably, 2'-FL and HMO intervention significantly enhanced the relative abundance of Clostridium and Akkermansia. The metabolomics results showed that 2'-FL and HMO enhanced the oleoyl-l-carnitine metabolism as potential drivers. More importantly, the levels of oleoyl-l-carnitine were positively correlated with the abundances of Clostridium and Akkermansia. These results indicated that 2'-FL and HMO had therapeutic potential to prevent AD-induced cognitive impairment, which is of great significance for the treatment of AD.PMID:38112024 | DOI:10.1021/acs.jafc.3c05949

Front Endocrinol (Lausanne). 2023 Dec 4;14:1266527. doi: 10.3389/fendo.2023.1266527. eCollection 2023.ABSTRACTHepatocyte Nuclear Factor 4α (HNF4α), a master regulator of hepatocyte differentiation, is regulated by two promoters (P1 and P2) which drive the expression of different isoforms. P1-HNF4α is the major isoform in the adult liver while P2-HNF4α is thought to be expressed only in fetal liver and liver cancer. Here, we show that P2-HNF4α is indeed expressed in the normal adult liver at Zeitgeber time (ZT)9 and ZT21. Using exon swap mice that express only P2-HNF4α we show that this isoform orchestrates a distinct transcriptome and metabolome via unique chromatin and protein-protein interactions, including with different clock proteins at different times of the day leading to subtle differences in circadian gene regulation. Furthermore, deletion of the Clock gene alters the circadian oscillation of P2- (but not P1-)HNF4α RNA, revealing a complex feedback loop between the HNF4α isoforms and the hepatic clock. Finally, we demonstrate that while P1-HNF4α drives gluconeogenesis, P2-HNF4α drives ketogenesis and is required for elevated levels of ketone bodies in female mice. Taken together, we propose that the highly conserved two-promoter structure of the Hnf4a gene is an evolutionarily conserved mechanism to maintain the balance between gluconeogenesis and ketogenesis in the liver in a circadian fashion.PMID:38111711 | PMC:PMC10726135 | DOI:10.3389/fendo.2023.1266527

Front Endocrinol (Lausanne). 2023 Dec 4;14:1232132. doi: 10.3389/fendo.2023.1232132. eCollection 2023.ABSTRACTINTRODUCTION: The pathogenesis of diabetic nephropathy (DN) is complex, inflammation is the central link among the inducing factors in the existing research, and the gutkidney axis could scientifically explain the reasons for the accumulation of chronic low-grade inflammation. As both a medicine and food, corn silk contains abundant polysaccharides. Historical studies and modern research have both confirmed its intervention effect on diabetes and DN, but the mechanism of action is unclear.METHODS: In this study, a DN rat model was generated, and the therapeutic effect of corn silk polysaccharides (CSPs) was evaluated based on behavioral, histopathological and biochemical indicators. We attempted to fully understand the interactions between CSPs, the gut microbiota and the host at the systemic level from a gut microbiota metabolomics perspective to fundamentally elucidate the mechanisms of action that can be used to intervene in DN.RESULTS: Research has found that the metabolic pathways with a strong correlation with CSPs were initially identified as glycerophosphate, fatty acid, bile acid, tyrosine, tryptophan and phenylalanine metabolism and involved Firmicutes, Bacteroides, Lachnospiraceae-NK4A136- group and Dubosiella, suggesting that the effect of CSPs on improving DN is related to changes in metabolite profiles and gut microbiota characteristics.DISCUSSION: CSPs could be harnessed to treat the abnormal metabolism of endogenous substances such as bile acids and uremic toxins caused by changes in gut microbiota, thus alleviating kidney damage caused by inflammation. In view of its natural abundance, corn silk is safe and nontoxic and can be used for the prevention and treatment of diabetes and DN.PMID:38111708 | PMC:PMC10726137 | DOI:10.3389/fendo.2023.1232132

Front Microbiol. 2023 Dec 4;14:1280485. doi: 10.3389/fmicb.2023.1280485. eCollection 2023.ABSTRACTMutualistic ectomycorrhizal symbiosis requires the exchange of signals even before direct contact of the partners. Volatiles, and specifically volatile terpenoids, can be detected at a distance and may trigger downstream signaling and reprogramming of metabolic responses. The late-stage ectomycorrhizal fungus Tricholoma vaccinum shows high host specificity with its main host spruce, Picea abies, while rarely associations can be found with pine, Pinus sylvestris. Hence, a comparison of the host and the low-compatibility host's responses can untangle differences in early signaling during mycorrhiza formation. We investigated sesquiterpenes and identified different patterns of phytohormone responses with spruce and pine. To test the specific role of volatiles, trees were exposed to the complete volatilome of the fungus versus volatiles present when terpene synthases were inhibited by rosuvastatin. The pleiotropic response in spruce included three non-identified products, a pyridine derivative as well as two diterpenes. In pine, other terpenoids responded to the fungal signal. Using exposure to the fungal volatilome with or without terpene synthesis inhibited, we could find a molecular explanation for the longer time needed to establish the low-compatibility interaction.PMID:38111643 | PMC:PMC10725908 | DOI:10.3389/fmicb.2023.1280485

Cancer Metab. 2023 Dec 18;11(1):27. doi: 10.1186/s40170-023-00311-5.ABSTRACTBACKGROUND: Hepatocellular carcinoma (HCC) is a principal type of liver cancer with high incidence and mortality rates. Regorafenib is a novel oral multikinase inhibitor for second-line therapy for advanced HCC. However, resistance to regorafenib is gradually becoming a dilemma for HCC and the mechanism remains unclear. In this study, we aimed to reveal the metabolic profiles of regorafenib-resistant cells and the key role and mechanism of the most relevant metabolic pathway in regorafenib resistance.METHODS: Metabolomics was performed to detect the metabolic alteration between drug-sensitive and regorafenib-resistant cells. Colony formation assay, CCK-8 assay and flow cytometry were applied to observe cell colony formation, cell proliferation and apoptosis, respectively. The protein and mRNA levels were detected by western blot and RT-qPCR. Cell lines of Glucose-6-phosphate dehydrogenase(G6PD) knockdown in regorafenib-resistant cells or G6PD overexpression in HCC cell lines were stably established by lentivirus infection technique. G6PD activity, NADPH level, NADPH/NADP+ ratio, the ratio of ROS positive cells, GSH level, and GSH/GSSG ratio were detected to evaluate the anti-oxidative stress ability of cells. Phosphorylation levels of NADK were evaluated by immunoprecipitation.RESULTS: Metabonomics analysis revealed that pentose phosphate pathway (PPP) was the most relevant metabolic pathway in regorafenib resistance in HCC. Compared with drug-sensitive cells, G6PD enzyme activity, NADPH level and NADPH/NADP+ ratio were increased in regorafenib-resistant cells, but the ratio of ROS positive cells and the apoptosis rate under the conditions of oxidative stress were decreased. Furthermore, G6PD suppression using shRNA or an inhibitor, sensitized regorafenib-resistant cells to regorafenib. In contrast, G6PD overexpression blunted the effects of regorafenib to drug-sensitive cells. Mechanistically, G6PD, the rate-limiting enzyme of PPP, regulated the PI3K/AKT activation. Furthermore, PI3K/AKT inhibition decreased G6PD protein expression, G6PD enzymatic activity and the capacity of PPP to anti-oxidative stress possibly by inhibited the expression and phosphorylation of NADK.CONCLUSION: Taken together, a feedback loop of PPP and PI3K/AKT signal pathway drives regorafenib-resistance in HCC and targeting the feedback loop could be a promising approach to overcome drug resistance.PMID:38111012 | DOI:10.1186/s40170-023-00311-5

J Transl Med. 2023 Dec 18;21(1):918. doi: 10.1186/s12967-023-04801-4.ABSTRACTBACKGROUND: Early diagnosis of hepatocellular carcinoma (HCC) is essential towards the improvement of prognosis and patient survival. Circulating markers such as α-fetoprotein (AFP) and micro-RNAs represent useful tools but still have limitations. Identifying new markers can be fundamental to improve both diagnosis and prognosis. In this approach, we harness the potential of metabolomics and lipidomics to uncover potential signatures of HCC.METHODS: A combined untargeted metabolomics and lipidomics plasma profiling of 102 HCV-positive patients was performed by HILIC and RP-UHPLC coupled to Mass Spectrometry. Biochemical parameters of liver function (AST, ALT, GGT) and liver cancer biomarkers (AFP, CA19.9 e CEA) were evaluated by standard assays.RESULTS: HCC was characterized by an elevation of short and long-chain acylcarnitines, asymmetric dimethylarginine, methylguanine, isoleucylproline and a global reduction of lysophosphatidylcholines. A supervised PLS-DA model showed that the predictive accuracy for HCC class of metabolomics and lipidomics was superior to AFP for the test set (100.00% and 94.40% vs 55.00%). Additionally, the model was applied to HCC patients with AFP values < 20 ng/mL, and, by using only the top 20 variables selected by VIP scores achieved an Area Under Curve (AUC) performance of 0.94.CONCLUSION: These exploratory findings highlight how metabo-lipidomics enables the distinction of HCC from chronic HCV conditions. The identified biomarkers have high diagnostic potential and could represent a viable tool to support and assist in HCC diagnosis, including AFP-negative patients.PMID:38110968 | DOI:10.1186/s12967-023-04801-4