PubMed

Nat Med. 2023 Mar 17. doi: 10.1038/s41591-023-02260-4. Online ahead of print.ABSTRACTCardiometabolic diseases have become a leading cause of morbidity and mortality globally. They have been tightly linked to microbiome taxonomic and functional composition, with diet possibly mediating some of the associations described. Both the microbiome and diet are modifiable, which opens the way for novel therapeutic strategies. High-throughput omics techniques applied on microbiome samples (meta-omics) hold the unprecedented potential to shed light on the intricate links between diet, the microbiome, the metabolome and cardiometabolic health, with a top-down approach. However, effective integration of complementary meta-omic techniques is an open challenge and their application on large cohorts is still limited. Here we review meta-omics techniques and discuss their potential in this context, highlighting recent large-scale efforts and the novel insights they provided. Finally, we look to the next decade of meta-omics research and discuss various translational and clinical pathways to improving cardiometabolic health.PMID:36932240 | DOI:10.1038/s41591-023-02260-4

J Heart Lung Transplant. 2023 Feb 23:S1053-2498(23)01534-6. doi: 10.1016/j.healun.2023.02.1492. Online ahead of print.ABSTRACTBACKGROUND: Assessment of myocardial viability during ex situ heart perfusion (ESHP) is based on the measurement of lactate concentrations. As this provides with limited information, we sought to investigate the metabolic signature associated with donation after circulatory death (DCD) and the impact of ESHP on the myocardial metabolome.METHODS: Porcine hearts were retrieved either after warm ischemia (DCD group, N = 6); after brain-stem death (BSD group, N = 6); or without DCD nor BSD (Control group, N = 6). Hearts were perfused using normothermic oxygenated blood for 240 minutes. Plasma and myocardial samples were collected respectively every 30 and 60 minutes, and analyzed by an untargeted metabolomic approach using liquid chromatography coupled to high-resolution mass spectrometry.RESULTS: Median duration of warm ischemia was 23 minutes [19-29] in DCD animals. Lactate level within myocardial biopsies was not significantly different between groups at T0 (p = 0.281), and remained stable over the 4-hour period of ESHP. More than 300 metabolites were detected in plasma and heart biopsy samples. Compared to BSD animals, metabolomics changes involving energy and nucleotide metabolisms were observed in plasma samples of DCD animals before initiation of ESHP, whereas 2 metabolites (inosine monophosphate and methylbutyrate) exhibited concentration changes in biopsy samples. Normalization of DCD metabolic profile was remarkable after 4 hours of ESHP.CONCLUSION: A specific metabolic profile was observed in DCD hearts, mainly characterized by an increased nucleotide catabolism. DCD and BSD metabolomes proved normalized during ESHP. Complementary investigations are needed to correlate these findings to cardiac performances.PMID:36931989 | DOI:10.1016/j.healun.2023.02.1492

Metab Eng. 2023 Mar 15:S1096-7176(23)00047-2. doi: 10.1016/j.ymben.2023.03.006. Online ahead of print.ABSTRACTThe nonproteinogenic cyclic metabolite l-pipecolic acid is a chiral precursor for the synthesis of various commercial drugs and functions as a cell-protective extremolyte and mediator of defense in plants, enabling high-value applications in the pharmaceutical, medical, cosmetic, and agrochemical markets. To date, the production of the compound is unfavorably fossil-based. Here, we upgraded the strain Corynebacterium glutamicum for l-pipecolic acid production using systems metabolic engineering. Heterologous expression of the l-lysine 6-dehydrogenase pathway, apparently the best route to be used in the microbe, yielded a family of strains that enabled successful de novo synthesis from glucose but approached a limit of performance at a yield of 0.18 mol mol-1. Detailed analysis of the producers at the transcriptome, proteome, and metabolome levels revealed that the requirements of the introduced route were largely incompatible with the cellular environment, which could not be overcome after several further rounds of metabolic engineering. Based on the gained knowledge, we based the strain design on l-l-lysine 6-aminotransferase instead, which enabled a substantially higher in vivo flux toward l-pipecolic acid. The tailormade producer C. glutamicum PIA-7 formed l-pipecolic acid up to a yield of 562 mmol mol-1, representing 75% of the theoretical maximum. Ultimately, the advanced mutant PIA-10B achieved a titer of 93 g L-1 in a fed-batch process on glucose, outperforming all previous efforts to synthesize this valuable molecule de novo and even approaching the level of biotransformation from l-lysine. Notably, the use of C. glutamicum allows the safe production of GRAS-designated l-pipecolic acid, providing extra benefit toward addressing the high-value pharmaceutical, medical, and cosmetic markets. In summary, our development sets a milestone toward the commercialization of biobased l-pipecolic acid.PMID:36931556 | DOI:10.1016/j.ymben.2023.03.006

J Ethnopharmacol. 2023 Mar 15:116385. doi: 10.1016/j.jep.2023.116385. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Propolis is a traditional natural medicine with various activities such as antioxidant and anti-inflammatory, immunomodulatory, anti-tumour, gastroenteritis treatment and prevention, anti-microbial and parasitic, as well as glucose regulation and anti-diabetes, and is expected to be an anti-diabetic candidate with few side effects, but the mechanism of action of propolis on type 2 diabetes mellitus (T2DM) has not been fully elucidated.AIM OF THE STUDY: The purpose of this study was to investigate the mechanism of the effect of ethanol extract of propolis (EEP) on the regulation of blood glucose in T2DM mice.MATERIALS AND METHODS: We studied the possible mechanism of EEP on T2DM using an animal model of T2DM induced by a combination of a high-fat diet and intraperitoneal injection of streptozotocin (STZ). The experiment was divided into four groups, namely, the normal group (HC), model group (T2DM), EEP and metformin group (MET). Biochemical indexes and cytokines were measured, and the differences of metabolites in the serum were compared by 1H-NMR. In addition, the diversity of intestinal flora in feces was studied by 16S rDNA amplicon sequencing.RESULTS: The results showed that following treatment with EEP and MET, the weight-loss trend of mice was alleviated, and the fasting blood glucose, insulin secretion level, insulin resistance index, C peptide level and oral glucose tolerance level decreased, whereas the insulin sensitivity index increased, thereby EEP effectively alleviated the occurrence of T2DM and insulin resistance. Compared with the T2DM group, the concentrations of pro-inflammatory cytokines interleukin-1 beta (IL-1β), interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) decreased significantly in EEP and MET groups, whereas the concentrations of anti-inflammatory cytokine interleukin-10 (IL-10) increased significantly. Metabolomics results revealed that EEP and MET regulate carbohydrate metabolism and restore amino acid and lipid metabolism. Correlation analysis of intestinal flora in mouse feces showed that compared with the HC group, harmful bacteria such as Bilophila, Eubacterium_ventriosum_group, Mucispirillum and Desulfovibrio were found in the T2DM group, whereas the abundance of beneficial bacteria such as Lactobacillus was significantly reduced. Parabacteroides, Akkermansia, Leuconostoc, and Alloprevotella were abundantly present in the EEP group; however, the MET group showed an increase in the genus Parasutterella, which could regulate energy metabolism and insulin sensitivity.CONCLUSIONS: The results showed that EEP and MET reduce fasting blood glucose in T2DM mice, followed by alleviating insulin resistance, improving the inflammatory reaction of mice, regulating the metabolism of mice, and affecting the steady state of gut microbiota. However, the overall therapeutic effect of EEP is better than that of MET.PMID:36931413 | DOI:10.1016/j.jep.2023.116385

Int Immunopharmacol. 2023 Mar 15;118:109946. doi: 10.1016/j.intimp.2023.109946. Online ahead of print.ABSTRACTSystemic lupus erythematosus (SLE) is a chronic multi-organ autoimmune disease characterized by clinical heterogeneity, unpredictable progression, and flare ups. Due to the heterogeneous nature of lupus, it has been challenging to identify sensitive and specific biomarkers for its diagnosis and monitoring. Despite the fact that the mechanism of SLE remains unknown, impressive progress has been made over the last decade towards understanding how different immune cells contribute to its pathogenesis. Research suggests that cellular metabolic programs could affect the immune response by regulating the activation, proliferation, and differentiation of innate and adaptive immune cells. Many studies have shown that the dysregulation of the immune system is associated with changes to metabolite profiles. The study of metabolite profiling may provide a means for mechanism exploration and novel biomarker discovery for disease diagnostic, classification, and monitoring. Here we review the latest advancements in understanding the role of immunometabolism in SLE, as well as the systemic metabolite profiling of this disease along with possible clinical application.PMID:36931174 | DOI:10.1016/j.intimp.2023.109946

Meat Sci. 2023 Mar 10;200:109160. doi: 10.1016/j.meatsci.2023.109160. Online ahead of print.ABSTRACTBlackcurrants are sources of phenolic compounds, such as anthocyanins, possessing strong antioxidant, antimicrobial and antifungal activity. Therefore, the addition of different blackcurrant pomace ingredients may affect the overall meat quality. The actual chemical profile and bioactivities of blackcurrant pomace ingredients may strongly depend on its preparation; for instance, in our study the highest values of the in vitro antioxidant capacity were determined for blackcurrant seeds after supercritical CO2 extraction. Starting from these background conditions, in this work, we evaluated the ability of three different concentrations (namely 1, 3, and 5% w/w) of blackcurrant (BC) seeds following EtOH/water extraction (BC-AE), before supercritical fluid CO2 extraction (BC-RS), and after supercritical fluid CO2 extraction (BC-ASC) to affect different quality parameters of pork meatballs. These latter were stored considering three different time-points, namely 1, 3 and 6 days at 4 °C packed under modified atmosphere (i.e., 70% N2 and 30% CO2). Untargeted metabolomics allowed to identify several lipid and protein-related oxidation products involved in redox reactions, such as 13-L-hydroperoxylinoleic acid, (12S,13S)-epoxylinolenic acid, 9,10-epoxyoctadecenoic acid, glutathione, glutathione disulfide, L-carnosine, l-ascorbic acid, and tocotrienols. Besides, multivariate statistics applied on the metabolomics dataset confirmed that the chemical profile of meatballs was an exclusive combination of both BC inclusion levels and type of BC-ingredients considered. Our findings showed that the higher the concentration of BC seed ingredients in meatballs, the lower the cooking loss and the higher the fibre content. Also, all the ingredients significantly affected the colour parameters.PMID:36931151 | DOI:10.1016/j.meatsci.2023.109160

Comp Biochem Physiol Part D Genomics Proteomics. 2023 Mar 11;46:101071. doi: 10.1016/j.cbd.2023.101071. Online ahead of print.ABSTRACTOlfaction, a universal form of chemical communication, is a powerful channel for animals to obtain social and environmental cues. The mechanisms by which fish olfaction affects reproduction, breeding and disease control are not yet clear. To evaluate metabolites profiles, plasma from anosmic and control black porgy during reproduction was analyzed by non-targeted metabolomics using ultra high-performance liquid chromatography-mass spectrometry and multivariate statistical analysis techniques, including principal component analysis and orthogonal partial least squares discriminant analysis. The metabolite profiles of anosmia and control groups were found to be significantly separated. Ten different differential metabolites, mainly including amino acids, such as isoleucine and methionine, and lipids, such as phosphatidylserine, were screened based on the combined analysis of variable importance in the projection and p values. In addition, six key differential metabolic pathways were analyzed using the Kyoto Encyclopedia of Genes and Genomes and enriched for four metabolic pathways including the citrate acid (TCA) cycle, tyrosine metabolism, arginine and proline metabolism, and arginine synthesis. The TCA cycle enhances fertility through the reduction of pyruvate kinase, and intermediate derivatives (acetyl CoA, malonyl CoA) act as signaling factors that regulate immune cell function. The tyrosine cycle can indirectly participate and promote reproduction in black porgy through melanin-concentrating hormone. Arginine and proline metabolism can promote reproduction by promoting growth hormone and enhance immunity in anosmic black porgy by stimulating T lymphocytes. Our metabolomic study revealed that anosmia in black porgy played an active role in immunity and reproduction and provided theoretical support for breeding and disease control.PMID:36931130 | DOI:10.1016/j.cbd.2023.101071

Biomed Pharmacother. 2023 Mar 15;161:114535. doi: 10.1016/j.biopha.2023.114535. Online ahead of print.ABSTRACTThe pharmacological inhibition of sodium-glucose cotransporter 2 (SGLT2) has emerged as a treatment for patients with type 2 diabetes mellitus (T2DM), cardiovascular disease and/or other metabolic disturbances, although some of the mechanisms implicated in their beneficial effects are unknown. The SGLT2 inhibitor (SGLT2i) empagliflozin has been suggested as a regulator of adiposity, energy metabolism, and systemic inflammation in adipose tissue. The aim of our study was to evaluate the impact of a 6-week-empagliflozin treatment on the lipidome of visceral (VAT) and subcutaneous adipose tissue (SAT) from diabetic obese Zucker Diabetic Fatty (ZDF) rats using an untargeted metabolomics approach. We found that empagliflozin increases the content of diglycerides and oxidized fatty acids (FA) in VAT, while in SAT, it decreases the levels of several lysophospholipids and increases 2 phosphatidylcholines. Empagliflozin also reduces the expression of the cytokines interleukin-1 beta (IL-1β), IL-6, tumor necrosis factor-alpha (TNFα), monocyte-chemotactic protein-1 (MCP-1) and IL-10, and of Cd86 and Cd163 M1 and M2 macrophage markers in VAT, with no changes in SAT, except for a decrease in IL-1β. Empagliflozin treatment also shows an effect on lipolysis increasing the expression of hormone-sensitive lipase (HSL) in SAT and VAT and of adipose triglyceride lipase (ATGL) in VAT, together with a decrease in the adipose content of the FA transporter cluster of differentiation 36 (CD36). In conclusion, our data highlighted differences in the VAT and SAT lipidomes, inflammatory profiles and lipolytic function, which suggest a distinct metabolism of these two white adipose tissue depots after the empagliflozin treatment.PMID:36931025 | DOI:10.1016/j.biopha.2023.114535

Food Chem. 2023 Mar 15;417:135895. doi: 10.1016/j.foodchem.2023.135895. Online ahead of print.ABSTRACTUntargeted Liquid chromatography tandem mass spectrometry (LC-MS) based metabolomics in combination with UV-visible and colorimeter was applied in identifying critical colored enzymatically oxidized products of (-)-epigallocatechin gallate (EGCG). Pearson correlation coefficient analysis between marker compounds and a* value was conducted, and then a series of colored oxidation products were targeted and subsequently identified by diode array detection and mass fragmentation ions. The quinone of oolongtheanin 3-O'-gallate degraded product with quasi-molecular mass ion at m/z 711 was identified as a critical colored oxidation product of single EGCG. To explore the effect of chlorogenic acid on the formation of colored EGCG enzymatic oxidation products, the variation of oxidation products on the oolongtheanin pathway was semi-quantitatively determined. The result showed chlorogenic acid significantly inhibited the formation of colored oxidation products, thus lightened the color of EGCG oxidation mixture. The addition of chlorogenic acid influences the process of tea polyphenols' enzymatic oxidation.PMID:36931012 | DOI:10.1016/j.foodchem.2023.135895

J Proteome Res. 2023 Mar 17. doi: 10.1021/acs.jproteome.2c00736. Online ahead of print.ABSTRACTIntracellular purine- and pyrimidine-related derivatives are vital molecules for preserving genetic information and are essential for cellular bioenergetics and signal transduction. This study developed a practical liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for quantifying intracellular purine- and pyrimidine-related derivatives. To solve the distorted peak shape related to di- and triphosphate nucleotides, in-sample addition of medronic acid and ammonium phosphate was performed. Using the BEH-amide column, the results showed that adding 0.5 mM medronic acid to the sample significantly improved the peak shape without causing an obvious ion suppressive effect. Method validation confirmed that the coefficients of determination (R2) values for linearity evaluation were above 0.94 for all analytes. The intraday and interday accuracies ranged from 85.1 to 128.4%, with the precision below 16.6%. The validated method was successfully applied in characterizing the alterations of purine- and pyrimidine-related derivatives in the A549 cell line with perturbed mitochondrial fission or blockade of the electron transport chain. Collectively, this study demonstrates that the strategy of in-sample medronic acid addition is effective in improving the quantification of intracellular purine- and pyrimidine-related derivatives. We believe that our proposed platform can facilitate the development of novel drugs targeting purine and pyrimidine metabolism in the future.PMID:36930966 | DOI:10.1021/acs.jproteome.2c00736

PLoS One. 2023 Mar 17;18(3):e0283118. doi: 10.1371/journal.pone.0283118. eCollection 2023.ABSTRACTPre-existing and gestationally-developed diabetes mellitus have been linked with impairments in placental villous trophoblast cell metabolic function, that are thought to underlie the development of metabolic diseases early in the lives of the exposed offspring. Previous research using placental cell lines and ex vivo trophoblast preparations have highlighted hyperglycemia is an important independent regulator of placental function. However, it is poorly understood if hyperglycemia directly influences aspects of placental metabolic function, including nutrient storage and mitochondrial respiration, that are altered in term diabetic placentae. The current study examined metabolic and mitochondrial function as well as nutrient storage in both undifferentiated cytotrophoblast and differentiated syncytiotrophoblast BeWo cells cultured under hyperglycemia conditions (25 mM glucose) for 72 hours to further characterize the direct impacts of placental hyperglycemic exposure. Hyperglycemic-exposed BeWo trophoblasts displayed increased glycogen and triglyceride nutrient stores, but real-time functional readouts of metabolic enzyme activity and mitochondrial respiratory activity were not altered. However, specific investigation into mitochondrial dynamics highlighted increased expression of markers associated with mitochondrial fission that could indicate high glucose-exposed trophoblasts are transitioning towards mitochondrial dysfunction. To further characterize the impacts of independent hyperglycemia, the current study subsequently utilized a multi-omics approach and evaluated the transcriptomic and metabolomic signatures of BeWo cytotrophoblasts. BeWo cytotrophoblasts exposed to hyperglycemia displayed increased mRNA expression of ACSL1, HSD11B2, RPS6KA5, and LAP3 and reduced mRNA expression of CYP2F1, and HK2, concomitant with increased levels of: lactate, malonate, and riboflavin metabolites. These changes highlighted important underlying alterations to glucose, glutathione, fatty acid, and glucocorticoid metabolism in BeWo trophoblasts exposed to hyperglycemia. Overall, these results demonstrate that hyperglycemia is an important independent regulator of key areas of placental metabolism, nutrient storage, and mitochondrial function, and these data continue to expand our knowledge on mechanisms governing the development of placental dysfunction.PMID:36930661 | DOI:10.1371/journal.pone.0283118

Proc Natl Acad Sci U S A. 2023 Mar 21;120(12):e2217383120. doi: 10.1073/pnas.2217383120. Epub 2023 Mar 17.ABSTRACTThis year marks the 25th anniversary of the coinage of the term metabolome [S. G. Oliver et al., Trends Biotech. 16, 373-378 (1998)]. As the field rapidly advances, it is important to take stock of the progress which has been made to best inform the disciplines future. While a medical-centric perspective on metabolomics has recently been published [M. Giera et al., Cell Metab. 34, 21-34 (2022)], this largely ignores the pioneering contributions made by the plant and microbial science communities. In this perspective, we provide a contemporary overview of all fields in which metabolomics is employed with particular emphasis on both methodological and application breakthroughs made in plant and microbial sciences that have shaped this evolving research discipline from the very early days of its establishment. This will not cover all types of metabolomics assays currently employed but will focus mainly on those utilizing mass spectrometry-based measurements since they are currently by far the most prominent. Having established the historical context of metabolomics, we will address the key challenges currently facing metabolomics and offer potential approaches by which these can be faced. Most salient among these is the fact that the vast majority of mass features are as yet not annotated with high confidence; what we may refer to as definitive identification. We discuss the potential of both standard compound libraries and artificial intelligence technologies to address this challenge and the use of natural variance-based approaches such as genome-wide association studies in attempt to assign specific functions to the myriad of structurally similar and complex specialized metabolites. We conclude by stating our contention that as these challenges are epic and that they will need far greater cooperative efforts from biologists, chemists, and computer scientists with an interest in all kingdoms of life than have been made to date. Ultimately, a better linkage of metabolome and genome data will likely also be needed particularly considering the Earth BioGenome Project.PMID:36930598 | DOI:10.1073/pnas.2217383120

J Anim Sci. 2023 Mar 17:skad080. doi: 10.1093/jas/skad080. Online ahead of print.ABSTRACTTwo experiments were carried out to evaluate the effects of betaine (BET) supplementation in diets with reduced net energy (NE) levels on growth performance, nutrient digestibility and serum metabolomic profiles in growing pigs. In Exp. 1, 24 growing pigs (initial body weight, BW, 30.83 ± 2.50 kg) were allotted to one of the four treatments (six replications with one pig per pen) in a 2 × 2 factorial arrangement, including two dietary NE levels (2475 [N-NE] or 2395 [R80-NE] kcal/kg) and two BET doses (0 or 1500 mg/kg). In Exp. 2, 72 growing pigs were used in a 2 × 3 factorial arrangement, including three dietary NE levels (2475 [N-NE], 2415 [R60-NE] or 2355 [R120-NE] kcal/kg) and two BET doses (0 or 1500 mg/kg). Pigs with initial BW of 31.44 ± 1.65 kg were divided to one of the six treatments (six replications with two pigs per pen). In Exp. 1, lowing NE concentrations increased average daily feed intake (ADFI) by 10.69% in pigs fed the diet without BET (P > 0.05). BET significant increased ADFI in N-NE diet (P < 0.05) but had no influence on ADFI in R80-NE diet (P > 0.05). BET enhanced the apparent digestibility of crude protein (CP), dry matter (DM), organic matter (OM), gross energy (GE) and ether extract (EE) in R80-NE diet (P < 0.05). In Exp. 2, lowing NE concentrations enhanced ADFI (P > 0.05) and decreased average daily gain (ADG) (P < 0.05). The reduction in feed intake by BET was further enhanced as NE concentrations decreased from 2415 to 2355 kcal/kg (P < 0.10). BET reversed the elevation of serum triglyceride, alkaline phosphatase, aspartate aminotransferase and alanine aminotransferase levels caused by R120-NE diet (P < 0.05). The concentrations of cholecystokinin and glucagon-like peptide 1 were increased by BET in pigs fed R120-NE diet (P < 0.05). Serum metabolomics reveals that lowing dietary NE concentrations affected mainly amino acid biosynthetic pathways (P < 0.05). BET supplementation in R120-NE diet up-regulated serum BET levels and down-regulated homocysteine, DL-carnitine and four amino acid secondary metabolites (P < 0.05). In conclusion, lowing dietary NE contents reduced the growth performance and caused metabolic abnormalities in growing pigs. However, BET decreased feed intake to a certain extent and improved the metabolic health of pigs fed low-NE diets, which may be related to the dual regulation of amino acid metabolism and the secretion of appetite related hormones by BET.PMID:36930062 | DOI:10.1093/jas/skad080

J AOAC Int. 2023 Mar 17:qsad039. doi: 10.1093/jaoacint/qsad039. Online ahead of print.ABSTRACTBACKGROUND: Schizonepetae Herba (SH, Jingjie) and Schizonepetae Herba Carbonisata (SHC, Jingjie Tan) are two different forms of the same herbal material, with SHC being the processed product of SH. The different clinical efficacies of SH and SHC may be caused by changes in their chemical compositions. Despite this, there have been few studies that have reported on the comparative identification of SH and SHC. Therefore, the aims of this experiment are to investigate the differential changes of non-volatile and volatile components before and after SH processing.OBJECTIVES: To establish combination strategies for identifying the chemical markers in SH and SHC, ultra-high-performance liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-Q-TOF-MS) and headspace gas chromatography mass spectrometry (HS-GC-MS) to use.METHODS: An untargeted metabolomics approach using UHPLC-Q-TOF-MS and HS-GC-MS was utilized to comprehensively discriminate between SH and SHC. To identify chemical markers, principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) were performed on 14 batches of SH and SHC.RESULTS: A total of 71 non-volatile compounds and 81 volatile compounds were tentatively identified in SH and SHC. Among these, 14 non-volatile compounds and 18 volatile oils were found to be potential characteristic markers that can differentiate between SH and SHC.CONCLUSIONS: The present work provides valuable information for understanding the chemical differences between SH and SHC. The results obtained from this research may serve as a scientific foundation for comprehensively revealing the mechanisms involved in the carbonizing processing method of stir-frying SH.HIGHLIGHTS: The chemical changes that occur before and after carbonizing Schizonepetae Herba were investigated using integrated methods based on LC-MS and GC-MS, and chemical markers in SH and SHC were identified.PMID:36929943 | DOI:10.1093/jaoacint/qsad039

Metabolomics. 2023 Mar 16;19(4):19. doi: 10.1007/s11306-023-01995-y.NO ABSTRACTPMID:36929444 | DOI:10.1007/s11306-023-01995-y

Methods Mol Biol. 2023;2629:247-269. doi: 10.1007/978-1-0716-2986-4_12.ABSTRACTIn this chapter, we review the cutting-edge statistical and machine learning methods for missing value imputation, normalization, and downstream analyses in mass spectrometry metabolomics studies, with illustration by example datasets. The missing peak recovery includes simple imputation by zero or limit of detection, regression-based or distribution-based imputation, and prediction by random forest. The batch effect can be removed by data-driven methods, internal standard-based, and quality control sample-based normalization. We also summarize different types of statistical analysis for metabolomics and clinical outcomes, such as inference on metabolic biomarkers, clustering of metabolomic profiles, metabolite module building, and integrative analysis with transcriptome.PMID:36929081 | DOI:10.1007/978-1-0716-2986-4_12

Methods Mol Biol. 2023;2629:1-9. doi: 10.1007/978-1-0716-2986-4_1.ABSTRACTIn the current era of multi-omics, new sequencing and molecular profiling technologies have facilitated our quest for a deeper and broader understanding of the variations and dynamic regulations in human genomes. However, analyzing and integrating data generated from diverse platforms, modalities, and large-scale heterogeneous samples to extract functional and clinically valuable information remains a significant challenge. Here, we first discuss recent advances in methods and algorithms for analyzing data at the genome, transcriptome, proteome, metabolome, and microbiome levels, followed by emerging methods for leveraging single-cell sequencing and spatial transcriptomic data. We also highlight the mechanistic insights that these advances can bring to the field, as well as the current challenges and outlooks relating to their translational and reproducible adoption at the population level. It is evident that novel statistical methods, which were inspired by new assays, will enable the associated molecular profiling pipelines and experimental designs to continuously improve our understanding of the human genome and the downstream consequences in the transcriptome, epigenome, proteome, metabolome, regulome, and microbiome.PMID:36929070 | DOI:10.1007/978-1-0716-2986-4_1

JAMA Otolaryngol Head Neck Surg. 2023 Mar 16. doi: 10.1001/jamaoto.2023.0052. Online ahead of print.ABSTRACTIMPORTANCE: Persistent tinnitus is common, disabling, and difficult to treat.OBJECTIVE: To evaluate the association between circulating metabolites and persistent tinnitus.DESIGN, SETTING, AND PARTICIPANTS: This was a population-based case-control study of 6477 women who were participants in the Nurses' Health Study (NHS) and NHS II with metabolomic profiles and tinnitus data. Information on tinnitus onset and frequency was collected on biennial questionnaires (2009-2017). For cases, metabolomic profiles were measured (2015-2021) in blood samples collected after the date of the participant's first report of persistent tinnitus (NHS, 1989-1999 and 2010-2012; NHS II, 1996-1999). Data analyses were performed from January 24, 2022, to January 14, 2023.EXPOSURES: In total, 466 plasma metabolites from 488 cases of persistent tinnitus and 5989 controls were profiled using 3 complementary liquid chromatography tandem mass spectrometry approaches.MAIN OUTCOMES AND MEASURES: Logistic regression was used to estimate odds ratios (ORs) of persistent tinnitus (per 1 SD increase in metabolite values) and 95% CIs for each individual metabolite. Metabolite set enrichment analysis was used to identify metabolite classes enriched for associations with tinnitus.RESULTS: Of the 6477 study participants (mean [SD] age, 52 [9] years; 6477 [100%] female; 6121 [95%] White individuals) who were registered nurses, 488 reported experiencing daily persistent (≥5 minutes) tinnitus. Compared with participants with no tinnitus (5989 controls), those with persistent tinnitus were slightly older (53.0 vs 51.8 years) and more likely to be postmenopausal, using oral postmenopausal hormone therapy, and have type 2 diabetes, hypertension, and/or hearing loss at baseline. Compared with controls, homocitrulline (OR, 1.32; (95% CI, 1.16-1.50); C38:6 phosphatidylethanolamine (PE; OR, 1.24; 95% CIs, 1.12-1.38), C52:6 triglyceride (TAG; OR, 1.22; 95% CIs, 1.10-1.36), C36:4 PE (OR, 1.22; 95% CIs, 1.10-1.35), C40:6 PE (OR, 1.22; 95% CIs, 1.09-1.35), and C56:7 TAG (OR, 1.21; 95% CIs, 1.09-1.34) were positively associated, whereas α-keto-β-methylvalerate (OR, 0.68; 95% CIs, 0.56-0.82) and levulinate (OR, 0.60; 95% CIs, 0.46-0.79) were inversely associated with persistent tinnitus. Among metabolite classes, TAGs (normalized enrichment score [NES], 2.68), PEs (NES, 2.48), and diglycerides (NES, 1.65) were positively associated, whereas phosphatidylcholine plasmalogens (NES, -1.91), lysophosphatidylcholines (NES, -2.23), and cholesteryl esters (NES,-2.31) were inversely associated with persistent tinnitus.CONCLUSIONS AND RELEVANCE: This population-based case-control study of metabolomic profiles and tinnitus identified novel plasma metabolites and metabolite classes that were significantly associated with persistent tinnitus, suggesting that metabolomic studies may help improve understanding of tinnitus pathophysiology and identify therapeutic targets for this challenging disorder.PMID:36928544 | DOI:10.1001/jamaoto.2023.0052

Int J Surg. 2023 Mar 17. doi: 10.1097/JS9.0000000000000006. Online ahead of print.ABSTRACTBACKGROUND: Multiple primary lung cancer (MPLC) is becoming increasingly common in clinical practice. Imaging examination is sometimes difficult to differentiate from intrapulmonary metastasis (IM) or single primary lung cancer (SPLC) before surgery. There is a lack of effective blood biomarkers as an auxiliary diagnostic method.PARTICIPANTS AND METHODS: A total of 179 patients who were hospitalized and operated in our department from January to June 2019 were collected, and they were divided into SPLC with 136 patients, MPLC with 24 patients, and IM with 19 patients. In total, 96 healthy people without lung cancer were enrolled. Medical history, imaging, and pathology data were assembled from all participants. Plasma metabolomics analysis was performed by quadrupole time-of-flight tandem mass spectrometry, and data were analyzed using SPSS19.0/Simca 14.1/MetaboAnalyst5.0 software. Significant metabolites were selected by variable importance in projection, P value, and fold change. The area under the receiver operating characteristic curve was used to evaluate their diagnostic ability.RESULTS: There were significant differences in plasma metabolite profiles between IM and MPLC. Seven metabolites were screened out. Two metabolites had higher levels in IM, and five metabolites had higher levels in MPLC. All had favorable discriminating capacity. Phosphatidyl ethanolamine (38:5) showed the highest sensitivity (0.95) and specificity (0.92). It was followed by l-histidine with sensitivity 0.92 and specificity 0.84. l-tyrosine can be used to identify SPLC and MPLC. The panel composed of related metabolites exhibited higher diagnostic ability. Eight principal metabolites caused remarkable differences between healthy people and MPLC, and five of them had area under the curves greater than 0.85, showing good discriminating power.CONCLUSION: Through the study of plasma metabolomics, it was found that there were obvious differences in the metabolite profiles of MPLC, IM, SPLC, and the healthy population. Some discovered metabolites possessed excellent diagnostic competence with high sensitivity and specificity. They had the potential to act as biomarkers for the screening and differential diagnosis of MPLCs.PMID:36928390 | DOI:10.1097/JS9.0000000000000006

NPJ Sci Food. 2023 Mar 16;7(1):7. doi: 10.1038/s41538-023-00187-1.ABSTRACTThe geographic origin of agri-food products contributes greatly to their quality and market value. Here, we developed a robust method combining metabolomics and machine learning (ML) to authenticate the geographic origin of Wuyi rock tea, a premium oolong tea. The volatiles of 333 tea samples (174 from the core region and 159 from the non-core region) were profiled using gas chromatography time-of-flight mass spectrometry and a series of ML algorithms were tested. Wuyi rock tea from the two regions featured distinct aroma profiles. Multilayer Perceptron achieved the best performance with an average accuracy of 92.7% on the training data using 176 volatile features. The model was benchmarked with two independent test sets, showing over 90% accuracy. Gradient Boosting algorithm yielded the best accuracy (89.6%) when using only 30 volatile features. The proposed methodology holds great promise for its broader applications in identifying the geographic origins of other valuable agri-food products.PMID:36928372 | DOI:10.1038/s41538-023-00187-1