PubMed

J Dairy Sci. 2023 Nov 1:S0022-0302(23)00777-4. doi: 10.3168/jds.2023-24154. Online ahead of print.ABSTRACTConstipation is directly related to the intestinal microenvironment, in which the promotion of gastrointestinal (GI) motility and improvement of gut microbiota distribution are important for alleviating symptoms. Herein, after the intervention of probiotic fermented milk (FMMIX) containing Lacticaseibacillus paracasei JY062 and Lactobacillus gasseri JM1 for 14 d in Kunming mice with loperamide-induced constipation, the results indicated that FMMIX significantly increased the secretion of serum motilin (MTL), gastrin (GAS) and 5-hydroxytryptamine (5-HT) and decreased those of peptide YY (PYY), vasoactive intestinal peptide (VIP) and nitric oxide (NO) in mice. As determined by immunohistochemical analysis, FMMIX promoted an augmentation in the quantity of Cajal interstitial cells (ICC). And mRNA and protein expression of c-kit and SCF was upregulated to facilitate intestinal motility. High-throughput sequencing and gas chromatography techniques revealed that FMMIX led to an increase in the relative abundance of beneficial bacteria (Lactobacillus, Oscillospira, Ruminococcus, Coprococcus, and Akkermansia), reduced the presence of harmful bacteria (Prevotella), and resulted in elevated levels of short-chain fatty acids (SCFAs) with a superior improvement compared with UFM. Untargeted metabolomics revealed significant upregulation of functional metabolites such as L-pipecolinic acid, DL-phenylalanine and naringenin in FMMIX, presumably playing a potential role in constipation relief. In conclusion, FMMIX had the potential to alleviate constipation symptoms in mice by improving the secretion of serum GI regulatory peptides and neurotransmitters, increasing the expression of c-kit and SCF proteins, and modulating the gut microbiota structure and SCFAs levels, and may be associated with an increase in the above functional components in FMMIX. This suggested that FMMIX could be a promising adjunctive strategy for managing constipation symptoms and could contribute to the development of functional foods aimed at improving gut health.PMID:37923200 | DOI:10.3168/jds.2023-24154

J Lipid Res. 2023 Nov 1:100469. doi: 10.1016/j.jlr.2023.100469. Online ahead of print.ABSTRACTDeletion of the nuclear hormone receptor small heterodimer partner (Shp) ameliorates the development of obesity and nonalcoholic steatohepatitis (NASH) in mice. Liver-specific SHP plays a significant role in this amelioration. The gut microbiota has been associated with these metabolic disorders, and the interplay between bile acids (BAs) and gut microbiota contributes to various metabolic disorders. Since hepatic SHP is recognized as a critical regulator in BA synthesis, we assessed the involvement of gut microbiota in the anti-obesity and anti-NASH phenotype of Shp-/- mice. Shp deletion significantly altered the levels of a few conjugated BAs. Sequencing the 16S ribosomal RNA gene in fecal samples collected from separately housed mice revealed apparent dysbiosis in Shp-/- mice. Cohousing Shp-/- mice with wild-type (WT) mice during a western diet (WD) regimen impaired their metabolic improvement and effectively disrupted their distinctive microbiome structure, which became indistinguishable from that of WT mice. While the WD challenge significantly increased lipopolysaccharide (LPS) and phenylacetic acid (PAA) levels in the blood of WT mice, their levels were not increased in Shp-/- mice. PAA was strongly associated with hepatic peroxisome proliferator-activated receptor gamma isoform 2 (Pparg2) activation in mice, which may represent the basis of the molecular mechanism underlying the association of gut bacteria and hepatic steatosis. Shp deletion reshapes the gut microbiota possibly by altering BAs. While LPS and PAA are the major driving forces derived from gut microbiota for NASH development, Shp deletion decreases these signaling molecules via dysbiosis, thereby partially protecting mice from diet-induced metabolic disorders.PMID:37922990 | DOI:10.1016/j.jlr.2023.100469

Mar Environ Res. 2023 Oct 27;192:106241. doi: 10.1016/j.marenvres.2023.106241. Online ahead of print.ABSTRACTBiofouling is a specific lifestyle including both marine prokaryotic and eukaryotic communities. Hydrodynamics are poorly studied parameters affecting biofouling formation. This study aimed to investigate how water dynamics in the Etel Estuary (Northwest Atlantic coasts of France) influences the colonization of artificial substrates. Hydrodynamic conditions, mainly identified as shear stress, were characterized by measuring current velocity, turbulence intensity and energy using Acoustic Doppler Current Profiler (ADCP). One-month biofouling was analyzed by coupling metabarcoding (16S rRNA, 18S rRNA and COI genes), untargeted metabolomics (liquid chromatography coupled with high-resolution mass spectrometry, LC-HRMS) and characterization of the main biochemical components of the microbial exopolymeric matrix. A higher richness was observed for biofouling communities (prokaryotes and eukaryotes) exposed to the strongest currents. Ectopleura (Cnidaria) and its putative symbionts Endozoicomonas (Gammaproteobacteria) were dominant in the less dynamic conditions. Eukaryotes assemblages were specifically shaped by shear stress, leading to drastic changes in metabolite profiles. Under high hydrodynamic conditions, the exopolymeric matrix increased and was composed of 6 times more polysaccharides than proteins, these latter playing a crucial role in the adhesion and cohesion properties of biofilms. This original multidisciplinary approach demonstrated the importance of shear stress on both the structure of marine biofouling and the metabolic response of these complex communities.PMID:37922705 | DOI:10.1016/j.marenvres.2023.106241

Biochem Biophys Res Commun. 2023 Oct 26;686:149169. doi: 10.1016/j.bbrc.2023.149169. Online ahead of print.ABSTRACTMetals have been used for many years in medicine, particularly for the treatment of cancer. Cisplatin is one of the most used drugs in the treatment of cancer. Although platinum-containing therapeutics have unparalleled efficacy in cancer treatment, they are coupled with adverse effects and the development of tumour resistance. This has led to the exploration of other metal-based modalities including ruthenium-based compounds. Thus, in our previous study, we synthesized and characterized a novel ruthenium (II) complex (referred to herein as GA113) containing a bis-amino-phosphine ligand. The complex was subsequently screened for its anti-cancerous potential against a human malignant melanoma A375 cell line and findings revealed favourable cytotoxicity. In the current study, a nuclear magnetic resonance (NMR)-based cellular metabolomics approach was applied to probe the possible mechanism of GA113 in A375 cells. In addition, other biological assays including light microscopy, Hoechst-33258 and MitoTracker Orange CM-H2TMRos stain were used to assess cellular viability and apoptosis in GA113-treated cells. Consequently, multivariate statistical data analysis was applied to the metabolomic data to identify potential biomarkers. Six signatory metabolites were altered after treatment. Changes in these metabolites were linked to two metabolic pathways, which include the alanine, aspartate, and glutamate metabolic pathway as well as the glycine, serine, and threonine pathway. By means of an NMR-based metabolomic approach, we identified the potential mechanism of action of complex GA113 in A375 cancer cells thus providing new insights into the metabolic pathways affected by complex GA113 and establishing a foundation for further development, research, and eventual application in cancer.PMID:37922571 | DOI:10.1016/j.bbrc.2023.149169

Dig Liver Dis. 2023 Nov 1:S1590-8658(23)00994-5. doi: 10.1016/j.dld.2023.10.006. Online ahead of print.ABSTRACTBACKGROUND: Alcohol-Associated Liver Disease (ALD) is a leading cause of liver mortality. Mechanisms responsible for severe ALD and the roles of gut microbiota are not fully understood. Multi-omics tools have enabled a better understanding of metabolic alterations and can aid in identifying metabolites as biomarkers for severe ALD.AIMS: Examine differences between cirrhotic and non-cirrhotic ALD, investigate microbial contributions to such changes, and identify potential diagnostic and prognostic metabolites for severe ALD.METHODS: Untargeted metabolomics were performed on the serum of 11 non-cirrhotic and 11 cirrhotic ALD patients. Data were analyzed using MetOrigin and Metaboanalyst to identify enriched pathways.RESULTS: Increased methylated nucleotides, gamma-glutamyl amino acids, bile acids, and specific metabolites kynurenine and campesterol were increased in ALD cirrhosis, whereas branched-chain amino acids, serotonin, and xanthurenate were decreased. Microbial contributions included increases in the short-chain fatty acid indolebutyrate and methionine sulfoxide in ALD cirrhosis. The analysis also identified the potential for serum levels of 3-ureidopropionate, cis-3,3-methyleneheptanoylglycine, retinol, and valine to be used as biomarkers for clinical assessment of alcohol-associated cirrhosis.CONCLUSION: We have identified a set of metabolites that are differentially altered in cirrhotic compared to non-cirrhotic ALD that can potentially be used as biomarkers for the severity of the disease.PMID:37923598 | DOI:10.1016/j.dld.2023.10.006

Small Methods. 2023 Nov 3:e2301192. doi: 10.1002/smtd.202301192. Online ahead of print.ABSTRACTIn vitro diagnosis (IVD) is pivotal in modern medicine, enabling early disease detection and treatment optimization. Omics technologies, particularly proteomics and metabolomics, offer profound insights into IVD. Despite its significance, omics analyses for IVD face challenges, including low analyte concentrations and the complexity of biological environments. In addition, the direct omics analysis by mass spectrometry (MS) is often hampered by issues like large sample volume requirements and poor ionization efficiency. Through manipulating their size, surface charge, and functionalization, as well as the nanoparticle-fluid incubation conditions, nanomaterials have emerged as a promising solution to extract biomolecules and enhance the desorption/ionization efficiency in MS detection. This review delves into the last five years of nanomaterial applications in omics, focusing on their role in the enrichment, separation, and ionization analysis of proteins and metabolites for IVD. It aims to provide a comprehensive update on nanomaterial design and application in omics, highlighting their potential to revolutionize IVD.PMID:37922520 | DOI:10.1002/smtd.202301192

Adv Healthc Mater. 2023 Nov 3:e2302128. doi: 10.1002/adhm.202302128. Online ahead of print.ABSTRACTPeripheral nerve injuries (PNI) can lead to mitochondrial dysfunction and energy depletion within the affected microenvironment. Our objective was to investigate the potential of transplanting mitochondria to reshape the neural regeneration microenvironment. High-purity functional mitochondria with an intact structure were extracted from human umbilical cord-derived mesenchymal stem cells (hUCMSCs) using the Dounce homogenization combined with ultracentrifugation. Results showed that when hUCMSC-derived mitochondria (hUCMSC-Mitos) were co-cultured with Schwann cells (SCs), they promoted the proliferation, migration, and respiratory capacity of SCs. Acellular nerve allografts (ANAs) have shown promise in nerve regeneration, however, their therapeutic effect is not satisfactory enough. The incorporation of hUCMSC-Mitos within ANAs (referred to as Mito-ANAs) has the potential to remodel the regenerative microenvironment. This approach demonstrated satisfactory outcomes in terms of tissue regeneration and functional recovery. Particularly, we propose for the first time the use of metabolomics and bioenergetic profiling to analyze the energy metabolism microenvironment after PNI. This remodeling occurs through the enhancement of the tricarboxylic acid (TCA) cycle and the regulation of associated metabolites, resulting in increased energy synthesis. Overall, the hUCMSC-Mito-loaded ANAs exhibited high functionality to promote nerve regeneration, providing a novel regenerative strategy based on improving energy metabolism for neural repair. This article is protected by copyright. All rights reserved.PMID:37922434 | DOI:10.1002/adhm.202302128

Arch Toxicol. 2023 Nov 3. doi: 10.1007/s00204-023-03622-0. Online ahead of print.ABSTRACTGlyphosate is a widely used active ingredient in agricultural herbicides, inhibiting the biosynthesis of aromatic amino acids in plants by targeting their shikimate pathway. Our gut microbiota also facilitates the shikimate pathway, making it a vulnerable target when encountering glyphosate. Dysbiosis in the gut microbiota may impair the gut-brain axis, bringing neurological outcomes. To evaluate the neurotoxicity and biochemical changes attributed to glyphosate, we exposed mice with the reference dose (RfD) set by the U.S. EPA (1.75 mg/Kg-BW/day) and its hundred-time-equivalence (175 mg/Kg-BW/day) chronically via drinking water, then compared a series of neurobehaviors and their fecal/serum metabolomic profile against the non-exposed vehicles (n = 10/dosing group). There was little alteration in the neurobehavior, including motor activities, social approach, and conditioned fear, under glyphosate exposure. Metabolomic differences attributed to glyphosate were observed in the feces, corresponding to 68 and 29 identified metabolites with dysregulation in the higher and lower dose groups, respectively, compared to the vehicle-control. There were less alterations observed in the serum metabolome. Under 175 mg/Kg-BW/day of glyphosate exposure, the aromatic amino acids (phenylalanine, tryptophan, and tyrosine) were reduced in the feces but not in the serum of mice. We further focused on how tryptophan metabolism was dysregulated based on the pathway analysis, and identified the indole-derivatives were more altered compared to the serotonin and kynurenine derivatives. Together, we obtained a three-dimensional data set that records neurobehavioral, fecal metabolic, and serum biomolecular dynamics caused by glyphosate exposure at two different doses. Our data showed that even under the high dose of glyphosate irrelevant to human exposure, there were little evidence that supported the impairment of the gut-brain axis.PMID:37922104 | DOI:10.1007/s00204-023-03622-0

Vet Q. 2023 Nov 3:1-41. doi: 10.1080/01652176.2023.2280041. Online ahead of print.ABSTRACTEpigallocatechin gallate (EGCG) is a main component in green tea extract, which possesses multiple bioactivities. The present research studied the effects of EGCG on the laying performance, egg quality, immune status, antioxidant capacity, and hepatic metabolome of Linwu laying ducks reared under high temperature. A total of 180 42-w-old healthy Linwu laying ducks were allocated into control or EGCG-treated groups. Each treatment had 6 replicates with 15 ducks in each replicate. Diets for the two groups were basal diets supplemented with 0 or 300 mg/kg EGCG, respectively. All ducks were raised in the high temperature condition (35 ± 2 °C for 6 h from 10:00 to 16:00, and 28 ± 2 °C for the other 18 h from 16:00 to 10:00 the next day) for 21 days. Results showed that EGCG increased the egg production rate (P = 0.014). and enhanced the immunocompetence by improving serum levels of immunoglobulin A (P = 0.008) and immunoglobulin G (P = 0.006). EGCG also fortified the antioxidant capacity by activating superoxide dismutase (P = 0.012), catalase (P = 0.009), and glutathione peroxidase (P = 0.021), and increasing the level of heat-shock protein 70 (P = 0.003) in laying ducks' liver. At the same time, hepatic metabolomics result suggested that EGCG increased the concentration of several key metabolites, such as spermidine (P = 0.031), tetramethylenediamine (P = 0.009), hyoscyamine (P = 0.026), β-nicotinamide adenine dinucleotide phosphate (P = 0.038), and pantothenic acid (P = 0.010), which were involved in the metabolic pathways of glutathione metabolism, arginine and proline metabolism, β-alanine metabolism, and tropane, piperidine and pyridine alkaloid biosynthesis. In conclusion, 300 mg/kg dietary EGCG showed protection effects on the laying ducks reared in high temperature by improving the immune and antioxidant capacities, which contributed to the increase of laying performance of ducks. The potential mechanism could be that EGCG modulate the synthesis of key metabolites and associated metabolic pathways.PMID:37921498 | DOI:10.1080/01652176.2023.2280041

Microbiol Spectr. 2023 Nov 3:e0274323. doi: 10.1128/spectrum.02743-23. Online ahead of print.ABSTRACTPlants of the genus Otoba have been the basis for the treatment of tropical diseases in indigenous communities of countries like Colombia. Despite the lack of knowledge about their bioactive principles, endophytic fungi derived from medicinal plants are a prolific source of innovative chemistry. We systematically investigated the secondary metabolite production of a previously undescribed species of Diaporthe, herein introduced as Diaporthe caliensis sp. nov., using different metabolomics approaches together with classical chemical screening. To get an outline of the chemical space produced by this fungus, an exploratory molecular networking (MN) analysis was undertaken. A major molecular family was found to contain the known 10-membered lactone phomol (1), together with other putative congeners as compound 3. After isolation by preparative high-performance liquid chromatography, we confirmed phomol (1) as the main reason for the antimicrobial activity of the crude extract. The unknown absolute configuration of 1 was determined by the synthesis of α-methoxy-α-trifluoromethylphenylacetyl (MTPA)-esters and chemical degradation experiments. Moreover, caliensolides A (2) and B (3) were isolated, and their structures were elucidated as novel butenolides structurally unrelated to 1. Overall, the initial MN analysis incorrectly clustered compounds 1 and 3 within a single molecular family, despite evident differences in chemical structures and biosynthetic origin. Contrariwise, the unsupervised substructure discovery algorithm MS2LDA provided a deeper understanding of the fragmentation patterns and correctly clustered the polyketide-lactones produced by D. caliensis sp. nov. Our findings encourage the exploration of Colombian fungal diversity, which as demonstrated here could result in the discovery of new natural products.IMPORTANCEThe integration of metabolomics-based approaches into the discovery pipeline has enabled improved mining and prioritization of prolific secondary metabolite producers such as endophytic fungi. However, relying on automated untargeted analysis tools might lead to misestimation of the chemical complexity harbored in these organisms. Our study emphasizes the importance of isolation and structure elucidation of the respective metabolites in addition to deep metabolome analysis for the correct interpretation of untargeted metabolomics approaches such as molecular networking. Additionally, it encourages the further exploration of endophytic fungi from traditional medicinal plants for the discovery of natural products.PMID:37921483 | DOI:10.1128/spectrum.02743-23

Clin Sci (Lond). 2023 Nov 3:CS20230704. doi: 10.1042/CS20230704. Online ahead of print.ABSTRACTSepsis is known to cause damage to the intestinal mucosa, leading to bacterial translocation, and exacerbation of both local and remote organ impairments. In this study, fecal samples were collected from both septic and healthy individuals. Analysis through 16s rRNA sequencing of the fecal microbiota revealed that sepsis disrupts the balance of the gut microbial community. Recent research has highlighted the association of lipid metabolism with disease. By analyzing the fecal metabolome, four lipid metabolites that showed significant differences between the two groups were identified: PE(O-16:0/0:0), PE(17:0/0:0), PE(0:0/14:0), and PE(12:0/20:5(5Z, 8Z, 11Z, 14Z, 17Z)). Notably, the serum levels of PE(0:0/14:0) were higher in the healthy group. Subsequent in vitro and in vivo experiments demonstrated the protective effects of this compound against sepsis-induced intestinal barrier damage. Label-free proteomic analysis showed significant differences in the expression levels of the aryl hydrocarbon receptor (AHR), a protein implicated in sepsis pathogenesis, between the LPS-Caco-2 and LPS-Caco-2 + PE(0:0/14:0) groups. Further analysis, with the help of Discovery Studio 3.5 software and co-immunoprecipitation assays, confirmed the direct interaction between AHR and PE(0:0/14:0). In the cecal ligation and puncture (CLP) model, treatment with PE(0:0 /14:0) was found to upregulate the expression of tight junction proteins through the AhR/Cytochrome P450, family 1, subfamily A, polypeptide 1 (CYP1A1) pathway. This highlights the potential therapeutic use of PE(0:0/14:0) in addressing sepsis-induced intestinal barrier damage.PMID:37921121 | DOI:10.1042/CS20230704

Mol Med Rep. 2023 Dec;28(6):232. doi: 10.3892/mmr.2023.13119. Epub 2023 Nov 3.ABSTRACTTelomeres are major contributors to cell fate and aging through their involvement in cell cycle arrest and senescence. The accelerated attrition of telomeres is associated with aging‑related diseases, and agents able to maintain telomere length (TL) through telomerase activation may serve as potential treatment strategies. The aim of the present study was to assess the potency of a novel telomerase activator on TL and telomerase activity in vivo. The administration of a nutraceutical formulation containing Centella asiatica extract, vitamin C, zinc and vitamin D3 in 18‑month‑old rats for a period of 3 months reduced the telomere shortening rate at the lower supplement dose and increased mean the TL at the higher dose, compared to pre‑treatment levels. TL was determined using the Q‑FISH method in peripheral blood mononuclear cells collected from the tail vein of the rats and cultured with RPMI‑1640 medium. In both cases, TLs were significantly longer compared to the untreated controls (P≤0.001). In addition, telomerase activity was increased in the peripheral blood mononuclear cells of both treatment groups. On the whole, the present study demonstrates that the nutraceutical formulation can maintain or even increase TL and telomerase activity in middle‑aged rats, indicating a potential role of this formula in the prevention and treatment of aging‑related diseases.PMID:37921058 | DOI:10.3892/mmr.2023.13119

Cancer Commun (Lond). 2023 Nov 2. doi: 10.1002/cac2.12502. Online ahead of print.ABSTRACTBACKGROUND: Metabolism reprogramming plays a vital role in glioblastoma (GBM) progression and recurrence by producing enough energy for highly proliferating tumor cells. In addition, metabolic reprogramming is crucial for tumor growth and immune-escape mechanisms. Epidermal growth factor receptor (EGFR) amplification and EGFR-vIII mutation are often detected in GBM cells, contributing to the malignant behavior. This study aimed to investigate the functional role of the EGFR pathway on fatty acid metabolism remodeling and energy generation.METHODS: Clinical GBM specimens were selected for single-cell RNA sequencing and untargeted metabolomics analysis. A metabolism-associated RTK-fatty acid-gene signature was constructed and verified. MK-2206 and MK-803 were utilized to block the RTK pathway and mevalonate pathway induced abnormal metabolism. Energy metabolism in GBM with activated EGFR pathway was monitored. The antitumor effect of Osimertinib and Atorvastatin assisted by temozolomide (TMZ) was analyzed by an intracranial tumor model in vivo.RESULTS: GBM with high EGFR expression had characteristics of lipid remodeling and maintaining high cholesterol levels, supported by the single-cell RNA sequencing and metabolomics of clinical GBM samples. Inhibition of the EGFR/AKT and mevalonate pathways could remodel energy metabolism by repressing the tricarboxylic acid cycle and modulating ATP production. Mechanistically, the EGFR/AKT pathway upregulated the expressions of acyl-CoA synthetase short-chain family member 3 (ACSS3), acyl-CoA synthetase long-chain family member 3 (ACSL3), and long-chain fatty acid elongation-related gene ELOVL fatty acid elongase 2 (ELOVL2) in an NF-κB-dependent manner. Moreover, inhibition of the mevalonate pathway reduced the EGFR level on the cell membranes, thereby affecting the signal transduction of the EGFR/AKT pathway. Therefore, targeting the EGFR/AKT and mevalonate pathways enhanced the antitumor effect of TMZ in GBM cells and animal models.CONCLUSIONS: Our findings not only uncovered the mechanism of metabolic reprogramming in EGFR-activated GBM but also provided a combinatorial therapeutic strategy for clinical GBM management.PMID:37920878 | DOI:10.1002/cac2.12502

Comput Struct Biotechnol J. 2023 Oct 19;21:5136-5143. doi: 10.1016/j.csbj.2023.10.033. eCollection 2023.ABSTRACTPURPOSE: Meta-analyses failed to accurately identify patients with non-metastatic breast cancer who are likely to benefit from chemotherapy, and metabolomics could provide new answers. In our previous published work, patients were clustered using five different unsupervised machine learning (ML) methods resulting in the identification of three clusters with distinct clinical and simulated survival data. The objective of this study was to evaluate the survival outcomes, with extended follow-up, using the same 5 different methods of unsupervised machine learning.EXPERIMENTAL DESIGN: Forty-nine patients, diagnosed between 2013 and 2016, with non-metastatic BC were included retrospectively. Median follow-up was extended to 85.8 months. 449 metabolites were extracted from tumor resection samples by combined Liquid chromatography-mass spectrometry (LC-MS). Survival analyses were reported grouping together Cluster 1 and 2 versus cluster 3. Bootstrap optimization was applied.RESULTS: PCA k-means, K-sparse and Spectral clustering were the most effective methods to predict 2-year progression-free survival with bootstrap optimization (PFSb); as bootstrap example, with PCA k-means method, PFSb were 94% for cluster 1&2 versus 82% for cluster 3 (p = 0.01). PCA k-means method performed best, with higher reproducibility (mean HR=2 (95%CI [1.4-2.7]); probability of p ≤ 0.05 85%). Cancer-specific survival (CSS) and overall survival (OS) analyses highlighted a discrepancy between the 5 ML unsupervised methods.CONCLUSION: Our study is a proof-of-principle that it is possible to use unsupervised ML methods on metabolomic data to predict PFS survival outcomes, with the best performance for PCA k-means. A larger population study is needed to draw conclusions from CSS and OS analyses.PMID:37920813 | PMC:PMC10618114 | DOI:10.1016/j.csbj.2023.10.033

Can J Kidney Health Dis. 2023 Oct 30;10:20543581231209012. doi: 10.1177/20543581231209012. eCollection 2023.ABSTRACTPURPOSE OF REVIEW: Diabetic kidney disease (DKD) is a leading cause of chronic kidney disease (CKD) for which many treatments exist that have been shown to prevent CKD progression and kidney failure. However, DKD is a complex and heterogeneous etiology of CKD with a spectrum of phenotypes and disease trajectories. In this narrative review, we discuss precision medicine approaches to DKD, including genomics, metabolomics, proteomics, and their potential role in the management of diabetes mellitus and DKD. A patient and caregivers of patients with lived experience with CKD were involved in this review.SOURCES OF INFORMATION: Original research articles were identified from MEDLINE and Google Scholar using the search terms "diabetes," "diabetic kidney disease," "diabetic nephropathy," "chronic kidney disease," "kidney failure," "dialysis," "nephrology," "genomics," "metabolomics," and "proteomics."METHODS: A focused review and critical appraisal of existing literature regarding the precision medicine approaches to the diagnosis, prognosis, and treatment of diabetes and DKD framed by a patient partner's/caregiver's lived experience.KEY FINDINGS: Distinguishing diabetic nephropathy from CKD due to other types of DKD and non-DKD is challenging and typically requires a kidney biopsy for a diagnosis. Biomarkers have been identified to assist with the prediction of the onset and progression of DKD, but they have yet to be incorporated and evaluated relative to clinical standard of care CKD and kidney failure risk prediction tools. Genomics has identified multiple causal genetic variants for neonatal diabetes mellitus and monogenic diabetes of the young that can be used for diagnostic purposes and to specify antiglycemic therapy. Genome-wide-associated studies have identified genes implicated in DKD pathophysiology in the setting of type 1 and 2 diabetes but their translational benefits are lagging beyond polygenetic risk scores. Metabolomics and proteomics have been shown to improve diagnostic accuracy in DKD, have been used to identify novel pathways involved in DKD pathogenesis, and can be used to improve the prediction of CKD progression and kidney failure as well as predict response to DKD therapy.LIMITATIONS: There are a limited number of large, high-quality prospective observational studies and no randomized controlled trials that support the use of precision medicine based approaches to improve clinical outcomes in adults with or at risk of diabetes and DKD. It is unclear which patients may benefit from the clinical use of genomics, metabolomics and proteomics along the spectrum of DKD trajectory.IMPLICATIONS: Additional research is needed to evaluate the role of the use of precision medicine for DKD management, including diagnosis, differentiation of diabetic nephropathy from other etiologies of DKD and CKD, short-term and long-term risk prognostication kidney outcomes, and the prediction of response to and safety of disease-modifying therapies.PMID:37920777 | PMC:PMC10619345 | DOI:10.1177/20543581231209012

Front Plant Sci. 2023 Oct 18;14:1259561. doi: 10.3389/fpls.2023.1259561. eCollection 2023.ABSTRACTThe type and content of carbohydrates in konjac corms are an essential factors in determining the quality of konjac; however, the pattern of carbohydrate changes and the mechanism regulating the development of mother and daughter corms in the "relay growth" process of Amorphophallus muelleri remain unclear. This study aimed to investigate changes in corm carbohydrates during the growth cycle of A. muelleri and to compare the carbohydrate composition and the expression of related genes between mother and daughter corms. Integrated metabolome and RNA-seq analyses identified 37 differential metabolites as well as 8074 genes that were differentially expressed between mother and daughter corms, the majority of which were involved in starch and sucrose metabolism. More than 80% of the differential metabolites, including sucrose and starch, tended to accumulate in the mother corms; however, konjac glucomannan (KGM), as one of the most important carbohydrates and its major component of the corm, accumulated in higher amounts in the daughter corms. In addition, the expression of invertase and alpha-amylase that promote the breakdown of sucrose and starch was 351.78- and 15.63-fold higher, respectively, in the daughter corm, whereas that of the starch synthesis gene AkWAXY was only 0.096 times as high as in the mother corms. Furthermore, the level of cellulose synthase-like protein G, which promotes KGM synthesis, was 3.85 times higher in daughter corms compared to mother corms. Thus, we inferred that the daughter and mother corms had two distinct carbohydrate utilization strategies. This study provides insights into temporal changes in carbohydrates during the growth cycle of A. muelleri.PMID:37920719 | PMC:PMC10619727 | DOI:10.3389/fpls.2023.1259561

Front Med (Lausanne). 2023 Oct 18;10:1247851. doi: 10.3389/fmed.2023.1247851. eCollection 2023.ABSTRACTAshitaba seems to improve glucose intolerance and decrease triglyceride (TG) and total cholesterol (TC), which contribute to the development of non-alcoholic fatty liver disease (NAFLD). However, it remains to be explored the mechanism of Ashitaba in managing NAFLD. We determined the impact of Ashitaba on NAFLD, particularly its underlying mechanisms at the bioinformatic level. The established NAFLD mouse model was treated with or without Ashitaba, and the underlying mechanism was explored using transcriptomics paired with metabolomics. Ashitaba reduced obesity and liver steatosis in NAFLD mice. It identified 429 differentially expressed genes (DEGs) and verified 45 differential metabolites, especially those that alleviate NAFLD via the FXR signaling pathway. Our data may provide insight into the therapeutic impact of Ashitaba in the management of NAFLD and may be useful in clinical interventions for NAFLD.PMID:37920601 | PMC:PMC10618682 | DOI:10.3389/fmed.2023.1247851

PNAS Nexus. 2023 Oct 31;2(10):pgad326. doi: 10.1093/pnasnexus/pgad326. eCollection 2023 Oct.ABSTRACTPlants produce specialized metabolites with defensive properties that are often synthesized through the coordinated regulation of metabolic genes by transcription factors in various biological contexts. In this study, we investigated the regulatory function of the transcription factor PhERF1 from petunia (Petunia hybrida), which belongs to a small group of ETHYLENE RESPONSE FACTOR (ERF) family members that regulate the biosynthesis of bioactive alkaloids and terpenoids in various plant lineages. We examined the effects of transiently overexpressing PhERF1 in petunia leaves on the transcriptome and metabolome, demonstrating the production of a class of specialized steroids, petuniolides, and petuniasterones in these leaves. We also observed the activation of many metabolic genes, including those involved in sterol biosynthesis, as well as clustered genes that encode new metabolic enzymes, such as cytochrome P450 oxidoreductases, 2-oxoglutarate-dependent dioxygenases, and BAHD acyltransferases. Furthermore, we determined that PhERF1 transcriptionally induces downstream metabolic genes by recognizing specific cis-regulatory elements in their promoters. This study highlights the potential of evolutionarily conserved transcriptional regulators to induce the production of specialized products through transcriptional reprogramming.PMID:37920550 | PMC:PMC10619512 | DOI:10.1093/pnasnexus/pgad326

Heliyon. 2023 Oct 21;9(11):e21392. doi: 10.1016/j.heliyon.2023.e21392. eCollection 2023 Nov.ABSTRACTImproved biosynthesis of commercially and pharmacologically relevant phytometabolites through genetic and metabolic engineering is a lucrative strategy for crop improvement. However, identifying appropriate biosynthetic pathways pertaining to specific bioactivities has been challenging since the major metabolic pathways remain closely interconnected. Here we propose a reverse association strategy in which, based on the phytochemical profile, putative target metabolic pathways could be identified for increased production of phytochemicals. Dried seed fruits of Coriandrum sativum, Trachyspermum ammi, Cuminum cyminum, and Foeniculum vulgare (family Apiaceae) were subjected to untargeted gas chromatography-mass spectrometry-based phytochemical profiling followed by evaluation of the overall antioxidant profile using multiple antioxidant assays. Using bioinformatics approaches, specific phytochemical classes and the enrichment of their respective biosynthetic pathways were identified. Collectively, the data suggest enrichment of isoprenoids and fatty acids biosynthetic pathways. The close association of metabolic pathways with antioxidant capacities indicated a need for enrichment of specific yet closely-related metabolic pathways to achieve an improved quality of spices for better antioxidant effects.PMID:37920519 | PMC:PMC10618831 | DOI:10.1016/j.heliyon.2023.e21392

Heliyon. 2023 Oct 19;9(11):e21011. doi: 10.1016/j.heliyon.2023.e21011. eCollection 2023 Nov.ABSTRACTAging is associated with gradual changes in liver structure, altered metabolites and other physiological/pathological functions in hepatic cells. However, its characterized phenotypes based on altered metabolites and the underlying biological mechanism are unclear. Advancements in high-throughput omics technology provide new opportunities to understand the pathological process of aging. Here, in our present study, both metabolomics and phosphoproteomics were applied to identify the altered metabolites and phosphorylated proteins in liver of young (the WTY group) and naturally aged (the WTA group) mice, to find novel biomarkers and pathways, and uncover the biological mechanism. Analysis showed that the body weights, alanine aminotransferase (ALT) and aspartate aminotransferase (AST) increased in the WTA group. The grips decreased with age, while the triglyceride (TG) and cholesterol (TC) did not change significantly. The increase of fibrosis, accumulation of inflammatory cells, hepatocytes degeneration, the deposition of lipid droplets and glycogen, the damaged mitochondria, and deduction of endoplasmic reticulum were observed in the aging liver under optical and electron microscopes. In addition, a network of metabolites and phosphorylated proteomes of the aging liver was established. Metabolomics detected 970 metabolites in the positive ion mode and 778 metabolites in the negative ion mode. A total of 150 pathways were pooled. Phosphoproteomics identified 2618 proteins which contained 16621 phosphosites. A total of 164 pathways were detected. 65 common pathways were detected in two omics. Phosphorylated protein heat shock protein HSP 90-alpha (HSP90A) and v-raf murine viral oncogene homolog B1(BRAF), related to cancer pathway, were significantly upregulated in aged mice liver. Western blot verified that protein expression of MEK and ERK, downstream of BRAF pathway were elevated in the liver of aging mice. However, the protein expression of BRAF was not a significant difference. Overall, these findings revealed a close link between aging and cancer and contributed to our understanding of the multi-omics changes in natural aging.PMID:37920504 | PMC:PMC10618800 | DOI:10.1016/j.heliyon.2023.e21011