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Noerman S, Johansson A, Shi L, Lehtonen M, Hanhineva K, Johansson I, Brunius C, Landberg R. Fasting plasma metabolites reflecting meat consumption and their associations with incident type 2 diabetes in two Swedish cohorts. Am J Clin Nutr 2024; 119:1280-1292. [PMID: 38403167 DOI: 10.1016/j.ajcnut.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/02/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024] Open
Abstract
BACKGROUND Consumption of processed red meat has been associated with increased risk of developing type 2 diabetes (T2D), but challenges in dietary assessment call for objective intake biomarkers. OBJECTIVES This study aimed to investigate metabolite biomarkers of meat intake and their associations with T2D risk. METHODS Fasting plasma samples were collected from a case-control study nested within Västerbotten Intervention Program (VIP) (214 females and 189 males) who developed T2D after a median follow-up of 7 years. Panels of biomarker candidates reflecting the consumption of total, processed, and unprocessed red meat and poultry were selected from the untargeted metabolomics data collected on the controls. Observed associations were then replicated in Swedish Mammography clinical subcohort in Uppsala (SMCC) (n = 4457 females). Replicated metabolites were assessed for potential association with T2D risk using multivariable conditional logistic regression in the discovery and Cox regression in the replication cohorts. RESULTS In total, 15 metabolites were associated with ≥1 meat group in both cohorts. Acylcarnitines 8:1, 8:2, 10:3, reflecting higher processed meat intake [r > 0.22, false discovery rate (FDR) < 0.001 for VIP and r > 0.05; FDR < 0.001 for SMCC) were consistently associated with higher T2D risk in both data sets. Conversely, lysophosphatidylcholine 17:1 and phosphatidylcholine (PC) 15:0/18:2 were associated with lower processed meat intake (r < -0.12; FDR < 0.023, for VIP and r < -0.05; FDR < 0.001, for SMCC) and with lower T2D risk in both data sets, except for PC 15:0/18:2, which was significant only in the VIP cohort. All associations were attenuated after adjustment for BMI (kg/m2). CONCLUSIONS Consistent associations of biomarker candidates involved in lipid metabolism between higher processed red meat intake with higher T2D risk and between those reflecting lower intake with the lower risk may suggest a relationship between processed meat intake and higher T2D risk. However, attenuated associations after adjusting for BMI indicates that such a relationship may at least partly be mediated or confounded by BMI.
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Affiliation(s)
- Stefania Noerman
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
| | - Anna Johansson
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Lin Shi
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden; School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Marko Lehtonen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Kati Hanhineva
- Department of Life Technologies, Food Sciences Unit, University of Turku, Turku, Finland; Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Ingegerd Johansson
- Department of Odontology, School of Dentistry, Cariology, Umeå University, Sweden
| | - Carl Brunius
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Rikard Landberg
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
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Catandi GD, Fresa KJ, Cheng MH, Whitcomb LA, Broeckling CD, Chen TW, Chicco AJ, Carnevale EM. Follicular metabolic alterations are associated with obesity in mares and can be mitigated by dietary supplementation. Sci Rep 2024; 14:7571. [PMID: 38555310 PMCID: PMC10981747 DOI: 10.1038/s41598-024-58323-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024] Open
Abstract
Obesity is a growing concern in human and equine populations, predisposing to metabolic pathologies and reproductive disturbances. Cellular lipid accumulation and mitochondrial dysfunction play an important role in the pathologic consequences of obesity, which may be mitigated by dietary interventions targeting these processes. We hypothesized that obesity in the mare promotes follicular lipid accumulation and altered mitochondrial function of oocytes and granulosa cells, potentially contributing to impaired fertility in this population. We also predicted that these effects could be mitigated by dietary supplementation with a combination of targeted nutrients to improve follicular cell metabolism. Twenty mares were grouped as: Normal Weight [NW, n = 6, body condition score (BCS) 5.7 ± 0.3], Obese (OB, n = 7, BCS 7.7 ± 0.2), and Obese Diet Supplemented (OBD, n = 7, BCS 7.7 ± 0.2), and fed specific feed regimens for ≥ 6 weeks before sampling. Granulosa cells, follicular fluid, and cumulus-oocyte complexes were collected from follicles ≥ 35 mm during estrus and after induction of maturation. Obesity promoted several mitochondrial metabolic disturbances in granulosa cells, reduced L-carnitine availability in the follicle, promoted lipid accumulation in cumulus cells and oocytes, and increased basal oocyte metabolism. Diet supplementation of a complex nutrient mixture mitigated most of the metabolic changes in the follicles of obese mares, resulting in parameters similar to NW mares. In conclusion, obesity disturbs the equine ovarian follicle by promoting lipid accumulation and altering mitochondrial function. These effects may be partially mitigated with targeted nutritional intervention, thereby potentially improving fertility outcomes in the obese female.
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Affiliation(s)
- Giovana D Catandi
- Equine Reproduction Laboratory, Department of Biomedical Sciences, Colorado State University, 3101 Rampart Road, Fort Collins, CO, 80521, USA
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Department of Veterinary Clinical Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Kyle J Fresa
- Equine Reproduction Laboratory, Department of Biomedical Sciences, Colorado State University, 3101 Rampart Road, Fort Collins, CO, 80521, USA
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Ming-Hao Cheng
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, CO, 80523, USA
| | - Luke A Whitcomb
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, 80523, USA
| | - Thomas W Chen
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, CO, 80523, USA
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, 80523, USA
| | - Adam J Chicco
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Elaine M Carnevale
- Equine Reproduction Laboratory, Department of Biomedical Sciences, Colorado State University, 3101 Rampart Road, Fort Collins, CO, 80521, USA.
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
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Huang Z, Peng C, Rong Z, Jiang L, Li Y, Feng Y, Chen S, Xie C, Jiang C. Longitudinal Mapping of Personal Biotic and Abiotic Exposomes and Transcriptome in Underwater Confined Space Using Wearable Passive Samplers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:5229-5243. [PMID: 38466915 DOI: 10.1021/acs.est.3c09379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Silicone-based passive samplers, commonly paired with gas chromatography-mass spectrometry (GC-MS) analysis, are increasingly utilized for personal exposure assessments. However, its compatibility with the biotic exposome remains underexplored. In this study, we introduce the wearable silicone-based AirPie passive sampler, coupled with nontargeted liquid chromatography with high-resolution tandem mass spectrometry (LC-HRMS/MS), GC-HRMS, and metagenomic shotgun sequencing methods, offering a comprehensive view of personalized airborne biotic and abiotic exposomes. We applied the AirPie samplers to 19 participants in a unique deep underwater confined environment, annotating 4,390 chemical and 2,955 microbial exposures, integrated with corresponding transcriptomic data. We observed significant shifts in environmental exposure and gene expression upon entering this unique environment. We noted increased exposure to pollutants, such as benzenoids, polycyclic aromatic hydrocarbons (PAHs), opportunistic pathogens, and associated antibiotic-resistance genes (ARGs). Transcriptomic analyses revealed the activation of neurodegenerative disease-related pathways, mostly related to chemical exposure, and the repression of immune-related pathways, linked to both biological and chemical exposures. In summary, we provided a comprehensive, longitudinal exposome map of the unique environment and underscored the intricate linkages between external exposures and human health. We believe that the AirPie sampler and associated analytical methods will have broad applications in exposome and precision medicine.
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Affiliation(s)
- Zinuo Huang
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China
| | - Chen Peng
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Zixin Rong
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Liuyiqi Jiang
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Yueer Li
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Yue Feng
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, China
| | | | | | - Chao Jiang
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China
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Joshi JR, Paudel D, Eddy E, Charkowski AO, Heuberger AL. Plant necrotrophic bacterial disease resistance phenotypes, QTL, and metabolites identified through integrated genetic mapping and metabolomics in Solanum species. FRONTIERS IN PLANT SCIENCE 2024; 15:1336513. [PMID: 38504885 PMCID: PMC10949924 DOI: 10.3389/fpls.2024.1336513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/12/2024] [Indexed: 03/21/2024]
Abstract
Most food crops are susceptible to necrotrophic bacteria that cause rotting and wilting diseases in fleshy organs and foods. All varieties of cultivated potato (Solanum tuberosum L.) are susceptible to diseases caused by Pectobacterium species, but resistance has been demonstrated in wild potato relatives including S. chacoense. Previous studies demonstrated that resistance is in part mediated by antivirulence activity of phytochemicals in stems and tubers. Little is known about the genetic basis of antivirulence traits, and the potential for inheritance and introgression into cultivated potato is unclear. Here, the metabolites and genetic loci associated with antivirulence traits in S. chacoense were elucidated by screening a sequenced S. tuberosum x S. chacoense recombinant inbred line (RIL) population for antivirulence traits of its metabolite extracts. Metabolite extracts from the RILs exhibited a quantitative distribution for two antivirulence traits that were positively correlated: quorum sensing inhibition and exo-protease inhibition, with some evidence of transgressive segregation, supporting the role of multiple loci and metabolites regulating these resistance-associated systems. Metabolomics was performed on the highly resistant and susceptible RILs that revealed 30 metabolites associated with resistance, including several alkaloids and terpenes. Specifically, several prenylated metabolites were more abundant in resistant RILs. We constructed a high-density linkage map with 795 SNPs mapped to 12 linkage groups, spanning a length of 1,507 cM and a density of 1 marker per 1.89 cM. Genetic mapping of the antivirulence and metabolite data identified five quantitative trait loci (QTLs) related to quorum sensing inhibition that explained 8-28% of the phenotypic variation and two QTLs for protease activity inhibition that explained 14-19% of the phenotypic variation. Several candidate genes including alkaloid, and secondary metabolite biosynthesis that are related to disease resistance were identified within these QTLs. Taken together, these data support that quorum sensing inhibition and exo-protease inhibition assays may serve as breeding targets to improve resistance to nectrotrophic bacterial pathogens in potato and other plants. The identified candidate genes and metabolites can be utilized in marker assisted selection and genomic selection to improve soft- rot and blackleg disease resistance.
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Affiliation(s)
- Janak R. Joshi
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, United States
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, United States
| | - Dev Paudel
- Department of Environmental Horticulture, University of Florida Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Ethan Eddy
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, United States
| | - Amy O. Charkowski
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Adam L. Heuberger
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, United States
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Pieper JR, Anthony BM, Chaparro JM, Prenni JE, Minas IS. Rootstock vigor dictates the canopy light environment that regulates metabolite profile and internal fruit quality development in peach. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108449. [PMID: 38503188 DOI: 10.1016/j.plaphy.2024.108449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/10/2024] [Accepted: 02/18/2024] [Indexed: 03/21/2024]
Abstract
Five rootstock cultivars of differing vigor: vigorous ('Atlas™' and 'Bright's Hybrid® 5'), standard ('Krymsk® 86' and 'Lovell') and dwarfing ('Krymsk® 1') grafted with 'Redhaven' as the scion were studied for their impact on productivity, mid-canopy photosynthetic active radiation transmission (i.e., light availability) and internal fruit quality. Αverage yield (kg per tree) and fruit count increased significantly with increasing vigor (trunk cross sectional area, TCSA). Α detailed peach fruit quality analysis on fruit of equal maturity (based on the index of absorbance difference, IAD) coming from trees with equal crop load (no. of fruit cm-2 of TCSA) characterized the direct impact of rootstock vigor on peach internal quality [dry matter content (DMC) and soluble solids concentration (SSC)]. DMC and SSC increased significantly with decreasing vigor and increasing light availability, potentially due to reduced intra-tree shading and better light distribution within the canopy. Physiologically characterized peach fruit mesocarp was further analyzed by non-targeted metabolite profiling using gas chromatography mass spectrometry (GC-MS). Metabolite distribution was associated with rootstock vigor class, mid-canopy light availability and fruit quality characteristics. Fructose, glucose, sorbose, neochlorogenic and quinic acids, catechin and sorbitol were associated with high light environments and enhanced quality traits, while sucrose, butanoic and malic acids related to low light conditions and inferior fruit quality. These outcomes show that while rootstock genotype and vigor are influencing peach tree productivity and yield, their effect on manipulating the light environment within the canopy also plays a significant role in fruit quality development.
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Affiliation(s)
- Jeff R Pieper
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA
| | - Brendon M Anthony
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jacqueline M Chaparro
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jessica E Prenni
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA
| | - Ioannis S Minas
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA.
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Hartvigsson O, Barman M, Rabe H, Sandin A, Wold AE, Brunius C, Sandberg AS. Associations of the placental metabolome with immune maturation up to one year of age in the Swedish NICE-cohort. Metabolomics 2024; 20:28. [PMID: 38407648 PMCID: PMC10896773 DOI: 10.1007/s11306-024-02092-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/26/2024] [Indexed: 02/27/2024]
Abstract
INTRODUCTION Allergies and other immune-mediated diseases are thought to result from incomplete maturation of the immune system early in life. We previously showed that infants' metabolites at birth were associated with immune cell subtypes during infancy. The placenta supplies the fetus with nutrients, but may also provide immune maturation signals. OBJECTIVES To examine the relationship between metabolites in placental villous tissue and immune maturation during the first year of life and infant and maternal characteristics (gestational length, birth weight, sex, parity, maternal age, and BMI). METHODS Untargeted metabolomics was measured using Liquid Chromatography-Mass Spectrometry. Subpopulations of T and B cells were measured using flow cytometry at birth, 48 h, one, four, and 12 months. Random forest analysis was used to link the metabolomics data with the T and B cell sub populations as well as infant and maternal characteristics. RESULTS Modest associations (Q2 = 0.2-0.3) were found between the placental metabolome and kappa-deleting recombination excision circles (KREC) at birth and naïve B cells and memory T cells at 12 months. Weak associations were observed between the placental metabolome and sex and parity. Still, most metabolite features of interest were of low intensity compared to associations previously found in cord blood, suggesting that underlying metabolites were not of placental origin. CONCLUSION Our results indicate that metabolomic measurements of the placenta may not effectively recognize metabolites important for immune maturation.
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Affiliation(s)
- Olle Hartvigsson
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Malin Barman
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden.
| | - Hardis Rabe
- Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Sandin
- Department of Clinical Sciences, Unit of Pediatrics, Umeå University, Umeå, Sweden
| | - Agnes E Wold
- Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Carl Brunius
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Ann-Sofie Sandberg
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
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Seitz VA, McGivem BB, Borton MA, Chaparro JM, Schipanski ME, Prenni JE, Wrighton KC. Cover Crop Root Exudates Impact Soil Microbiome Functional Trajectories in Agricultural Soils. RESEARCH SQUARE 2024:rs.3.rs-3956430. [PMID: 38410449 PMCID: PMC10896397 DOI: 10.21203/rs.3.rs-3956430/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Background Cover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and how these chemical messages selectively enrich specific microbial taxa and functionalities in agricultural soils. Results Here, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms where we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. We also identify broad changes in microbial nitrogen cycling in response chemical inputs. Conclusions We highlight that root exudate amendments alter microbial community function and phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally-relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, highlighting the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multiomics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production.
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Bodén S, Zheng R, Ribbenstedt A, Landberg R, Harlid S, Vidman L, Gunter MJ, Winkvist A, Johansson I, Van Guelpen B, Brunius C. Dietary patterns, untargeted metabolite profiles and their association with colorectal cancer risk. Sci Rep 2024; 14:2244. [PMID: 38278865 PMCID: PMC10817924 DOI: 10.1038/s41598-023-50567-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 12/21/2023] [Indexed: 01/28/2024] Open
Abstract
We investigated data-driven and hypothesis-driven dietary patterns and their association to plasma metabolite profiles and subsequent colorectal cancer (CRC) risk in 680 CRC cases and individually matched controls. Dietary patterns were identified from combined exploratory/confirmatory factor analysis. We assessed association to LC-MS metabolic profiles by random forest regression and to CRC risk by multivariable conditional logistic regression. Principal component analysis was used on metabolite features selected to reflect dietary exposures. Component scores were associated to CRC risk and dietary exposures using partial Spearman correlation. We identified 12 data-driven dietary patterns, of which a breakfast food pattern showed an inverse association with CRC risk (OR per standard deviation increase 0.89, 95% CI 0.80-1.00, p = 0.04). This pattern was also inversely associated with risk of distal colon cancer (0.75, 0.61-0.96, p = 0.01) and was more pronounced in women (0.69, 0.49-0.96, p = 0.03). Associations between meat, fast-food, fruit soup/rice patterns and CRC risk were modified by tumor location in women. Alcohol as well as fruit and vegetables associated with metabolite profiles (Q2 0.22 and 0.26, respectively). One metabolite reflecting alcohol intake associated with increased CRC risk, whereas three metabolites reflecting fiber, wholegrain, and fruit and vegetables associated with decreased CRC risk.
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Affiliation(s)
- Stina Bodén
- Department of Diagnostics and Intervention, Oncology, Umeå University, Umeå, Sweden.
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden.
| | - Rui Zheng
- Department of Surgical Sciences, The EpiHub, Uppsala University, Uppsala, Sweden
| | - Anton Ribbenstedt
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Rikard Landberg
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Sophia Harlid
- Department of Diagnostics and Intervention, Oncology, Umeå University, Umeå, Sweden
| | - Linda Vidman
- Department of Diagnostics and Intervention, Oncology, Umeå University, Umeå, Sweden
| | - Marc J Gunter
- International Agency for Research On Cancer, Nutrition and Metabolism Section, 69372, Lyon Cedex 08, France
- Cancer Epidemiology and Prevention Research Unit, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Anna Winkvist
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Sustainable Health, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Ingegerd Johansson
- Department of Odontology, Section of Cariology, Umeå University, Umeå, Sweden
| | - Bethany Van Guelpen
- Department of Diagnostics and Intervention, Oncology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Carl Brunius
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
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Chai YN, Qi Y, Goren E, Chiniquy D, Sheflin AM, Tringe SG, Prenni JE, Liu P, Schachtman DP. Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum. mSystems 2024; 9:e0119023. [PMID: 38132569 PMCID: PMC10804983 DOI: 10.1128/msystems.01190-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
The development of cereal crops with high nitrogen use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improving crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse Sorghum bicolor lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxon, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low N stress. This indicates that the shift in the sorghum microbiome due to low N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low N stress.IMPORTANCEThe development of crops that are more nitrogen use-efficient (NUE) is critical for the future of the enhanced sustainability of agriculture worldwide. This objective has been pursued mainly through plant breeding and plant molecular engineering, but these approaches have had only limited success. Therefore, a different strategy that leverages soil microbes needs to be fully explored because it is known that soil microbes improve plant growth through multiple mechanisms. To design approaches that use the soil microbiome to increase NUE, it will first be essential to understand the relationship among soil microbes, root metabolites, and crop productivity. Using this approach, we demonstrated that certain key metabolites and specific microbes are associated with high and low sorghum NUE in a field study. This important information provides a new path forward for developing crop genotypes that have increased NUE through the positive contribution of soil microbes.
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Affiliation(s)
- Yen Ning Chai
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Yunhui Qi
- Department of Statistics, Iowa State University, Ames, Iowa, USA
| | - Emily Goren
- Department of Statistics, Iowa State University, Ames, Iowa, USA
| | - Dawn Chiniquy
- Environmental Genomics and System Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amy M. Sheflin
- Department of Horticulture and Landscape Architecture, Colorado State University, Colorado State University, Fort Collins, Colorado, USA
| | - Susannah G. Tringe
- Environmental Genomics and System Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jessica E. Prenni
- Department of Horticulture and Landscape Architecture, Colorado State University, Colorado State University, Fort Collins, Colorado, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, Iowa, USA
| | - Daniel P. Schachtman
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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10
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Bresnahan DR, Catandi GD, Peters SO, Maclellan LJ, Broeckling CD, Carnevale EM. Maturation and culture affect the metabolomic profile of oocytes and follicular cells in young and old mares. Front Cell Dev Biol 2024; 11:1280998. [PMID: 38283993 PMCID: PMC10811030 DOI: 10.3389/fcell.2023.1280998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/22/2023] [Indexed: 01/30/2024] Open
Abstract
Introduction: Oocytes and follicular somatic cells within the ovarian follicle are altered during maturation and after exposure to culture in vitro. In the present study, we used a nontargeted metabolomics approach to assess changes in oocytes, cumulus cells, and granulosa cells from dominant, follicular-phase follicles in young and old mares. Methods: Samples were collected at three stages associated with oocyte maturation: (1) GV, germinal vesicle stage, prior to the induction of follicle/oocyte maturation in vivo; (2) MI, metaphase I, maturing, collected 24 h after induction of maturation in vivo; and (3) MIIC, metaphase II, mature with collection 24 h after induction of maturation in vivo plus 18 h of culture in vitro. Samples were analyzed using gas and liquid chromatography coupled to mass spectrometry only when all three stages of a specific cell type were obtained from the same mare. Results and Discussion: Significant differences in metabolite abundance were most often associated with MIIC, with some of the differences appearing to be linked to the final stage of maturation and others to exposure to culture medium. While differences occurred for many metabolite groups, some of the most notable were detected for energy and lipid metabolism and amino acid abundance. The study demonstrated that metabolomics has potential to aid in optimizing culture methods and evaluating cell culture additives to support differences in COCs associated with maternal factors.
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Affiliation(s)
- D R Bresnahan
- Department of Animal Sciences, Berry College, Mount Berry, GA, United States
| | - G D Catandi
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - S O Peters
- Department of Animal Sciences, Berry College, Mount Berry, GA, United States
| | - L J Maclellan
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - C D Broeckling
- Proteomic and Metabolomics Core Facility, Colorado State University, Fort Collins, CO, United States
| | - E M Carnevale
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
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11
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Zhao Y, Meijer J, Walker DI, Kim J, Portengen L, Jones DP, Saberi Hosnijeh F, Vlaanderen J, Vermeulen R. Dioxin(-like)-Related Biological Effects through Integrated Chemical-wide and Metabolome-wide Analyses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:258-268. [PMID: 38149779 PMCID: PMC10785760 DOI: 10.1021/acs.est.3c07588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/28/2023]
Abstract
Dioxin(-like) exposures are linked to adverse health effects, including cancer. However, metabolic alterations induced by these chemicals remain largely unknown. Beyond known dioxin(-like) compounds, we leveraged a chemical-wide approach to assess chlorinated co-exposures and parent compound products [termed dioxin(-like)-related compounds] among 137 occupational workers. Endogenous metabolites were profiled by untargeted metabolomics, namely, reversed-phase chromatography with negative electrospray ionization (C18-negative) and hydrophilic interaction liquid chromatography with positive electrospray ionization (HILIC-positive). We performed a metabolome-wide association study to select dioxin(-like) associated metabolic features using a 20% false discovery rate threshold. Metabolic features were then characterized by pathway enrichment analyses. There are no significant features associated with polychlorinated dibenzo-p-dioxins (PCDDs), a subgroup of known dioxin(-like) compounds. However, 3,110 C18-negative and 2,894 HILIC-positive features were associated with at least one of the PCDD-related compounds. Abundant metabolic changes were also observed for polychlorinated dibenzofuran-related and polychlorinated biphenyl-related compounds. These metabolic features were primarily enriched in pathways of amino acids, lipid and fatty acids, carbohydrates, cofactors, and nucleotides. Our study highlights the potential of chemical-wide analysis for comprehensive exposure assessment beyond targeted chemicals. Coupled with advanced endogenous metabolomics, this approach allows for an in-depth exploration of metabolic alterations induced by environmental chemicals.
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Affiliation(s)
- Yujia Zhao
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
| | - Jeroen Meijer
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
- Department
Environment & Health, Vrije Universiteit, Amsterdam 1081 HV, The Netherlands
| | - Douglas I. Walker
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Juni Kim
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Lützen Portengen
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
| | - Dean P. Jones
- Division
of Pulmonary, Allergy, Critical Care and Sleep Medicine, School of
Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Fatemeh Saberi Hosnijeh
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
| | - Jelle Vlaanderen
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
| | - Roel Vermeulen
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
- Julius
Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht 3584 CX, The Netherlands
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12
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Chahine Z, Abel S, Hollin T, Chung JH, Barnes GL, Daub ME, Renard I, Choi JY, Pratap V, Pal A, Alba-Argomaniz M, Banks CAS, Kirkwood J, Saraf A, Camino I, Castaneda P, Cuevas MC, De Mercado-Arnanz J, Fernandez-Alvaro E, Garcia-Perez A, Ibarz N, Viera-Morilla S, Prudhomme J, Joyner CJ, Bei AK, Florens L, Ben Mamoun C, Vanderwal CD, Le Roch KG. A Potent Kalihinol Analogue Disrupts Apicoplast Function and Vesicular Trafficking in P. falciparum Malaria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568162. [PMID: 38045341 PMCID: PMC10690269 DOI: 10.1101/2023.11.21.568162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Here we report the discovery of MED6-189, a new analogue of the kalihinol family of isocyanoterpene (ICT) natural products. MED6-189 is effective against drug-sensitive and -resistant P. falciparum strains blocking both intraerythrocytic asexual replication and sexual differentiation. This compound was also effective against P. knowlesi and P. cynomolgi. In vivo efficacy studies using a humanized mouse model of malaria confirms strong efficacy of the compound in animals with no apparent hemolytic activity or apparent toxicity. Complementary chemical biology, molecular biology, genomics and cell biological analyses revealed that MED6-189 primarily targets the parasite apicoplast and acts by inhibiting lipid biogenesis and cellular trafficking. Genetic analyses in P. falciparum revealed that a mutation in PfSec13, which encodes a component of the parasite secretory machinery, reduced susceptibility to the drug. The high potency of MED6-189 in vitro and in vivo, its broad range of efficacy, excellent therapeutic profile, and unique mode of action make it an excellent addition to the antimalarial drug pipeline.
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Affiliation(s)
- Z Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - S Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - T Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - JH Chung
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - GL Barnes
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - ME Daub
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - I Renard
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - JY Choi
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - V Pratap
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - A Pal
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - M Alba-Argomaniz
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - CAS Banks
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - J Kirkwood
- Metabolomics Core Facility, University of California, Riverside, CA 92521, USA
| | - A Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - I Camino
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - P Castaneda
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - MC Cuevas
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | | | | | - A Garcia-Perez
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - N Ibarz
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - S Viera-Morilla
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - J Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - CJ Joyner
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - AK Bei
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - L Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - C Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - CD Vanderwal
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - KG Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
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13
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Snider AP, Gomes RS, Summers AF, Tenley SC, Abedal-Majed MA, McFee RM, Wood JR, Davis JS, Cupp AS. Identification of Lipids and Cytokines in Plasma and Follicular Fluid before and after Follicle-Stimulating Hormone Stimulation as Potential Markers for Follicular Maturation in Cattle. Animals (Basel) 2023; 13:3289. [PMID: 37894013 PMCID: PMC10603728 DOI: 10.3390/ani13203289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
The process of follicle maturation leading to ovulation is a key milestone in female fertility. It is known that circulating lipids and cytokines play a role in the follicle's ability to go through follicular maturation and the ovulatory processes. However, the specific mechanisms are not well understood. We posit that dysregulation of granulosa cells influences the ovarian environment, which tries to adapt by changing released lipids and cytokines to achieve follicular maturation. Eleven non-lactating adult females underwent estrus synchronization with two injections of PGF2α 14 days apart. Daily blood samples were collected for 28 days to monitor steroid hormone production after the second injection. To understand the potential impacts of lipids and cytokines during ovulation, a low-dose FSH stimulation (FSHLow) was performed after resynchronization of cows, and daily blood samples were collected for 14 days to monitor steroid hormone production until ovariectomies. The lipidomic analysis demonstrated increased circulating diacylglycerides and triacylglycerides during the mid-luteal phase and after FSHLow treatment. Cholesteryl esters decreased in circulation but increased in follicular fluid (FF) after FSHLow. Increased circulating concentrations of TNFα and reduced CXCL9 were observed in response to FSHLow. Therefore, specific circulating lipids and cytokines may serve as markers of normal follicle maturation.
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Affiliation(s)
- Alexandria P. Snider
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA;
| | - Renata S. Gomes
- Department of Animal Science, University of Nebraska–Lincoln, 3940 Fair Street, Lincoln, NE 68583, USA; (R.S.G.); (J.R.W.)
| | | | - Sarah C. Tenley
- Department of Animal Science, University of Nebraska–Lincoln, 3940 Fair Street, Lincoln, NE 68583, USA; (R.S.G.); (J.R.W.)
| | - Mohamed A. Abedal-Majed
- Department of Animal Production, School of Agriculture, The University of Jordan, Amman 11942, Jordan;
| | - Renee M. McFee
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA;
| | - Jennifer R. Wood
- Department of Animal Science, University of Nebraska–Lincoln, 3940 Fair Street, Lincoln, NE 68583, USA; (R.S.G.); (J.R.W.)
| | - John S. Davis
- Olson Center for Women’s Health, University of Nebraska Medical Center, 983255 Nebraska Medical Center, Omaha, NE 68198, USA;
- VA Nebraska-Western Iowa Health Care System, Omaha, NE 68105, USA
| | - Andrea S. Cupp
- Department of Animal Science, University of Nebraska–Lincoln, 3940 Fair Street, Lincoln, NE 68583, USA; (R.S.G.); (J.R.W.)
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14
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Vidman L, Zheng R, Bodén S, Ribbenstedt A, Gunter MJ, Palmqvist R, Harlid S, Brunius C, Van Guelpen B. Untargeted plasma metabolomics and risk of colorectal cancer-an analysis nested within a large-scale prospective cohort. Cancer Metab 2023; 11:17. [PMID: 37849011 PMCID: PMC10583301 DOI: 10.1186/s40170-023-00319-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a leading cause of cancer-related death worldwide, but if discovered at an early stage, the survival rate is high. The aim of this study was to identify novel markers predictive of future CRC risk using untargeted metabolomics. METHODS This study included prospectively collected plasma samples from 902 CRC cases and 902 matched cancer-free control participants from the population-based Northern Sweden Health and Disease Study (NSHDS), which were obtained up to 26 years prior to CRC diagnosis. Using reverse-phase liquid chromatography-mass spectrometry (LC-MS), data comprising 5015 metabolic features were obtained. Conditional logistic regression was applied to identify potentially important metabolic features associated with CRC risk. In addition, we investigated if previously reported metabolite biomarkers of CRC risk could be validated in this study population. RESULTS In the univariable analysis, seven metabolic features were associated with CRC risk (using a false discovery rate cutoff of 0.25). Two of these could be annotated, one as pyroglutamic acid (odds ratio per one standard deviation increase = 0.79, 95% confidence interval, 0.70-0.89) and another as hydroxytigecycline (odds ratio per one standard deviation increase = 0.77, 95% confidence interval, 0.67-0.89). Associations with CRC risk were also found for six previously reported metabolic biomarkers of prevalent and/or incident CRC: sebacic acid (inverse association) and L-tryptophan, 3-hydroxybutyric acid, 9,12,13-TriHOME, valine, and 13-OxoODE (positive associations). CONCLUSIONS These findings suggest that although the circulating metabolome may provide new etiological insights into the underlying causes of CRC development, its potential application for the identification of individuals at higher risk of developing CRC is limited.
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Affiliation(s)
- Linda Vidman
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden.
| | - Rui Zheng
- Department of Surgical Sciences, Medical Epidemiology, Uppsala University, Uppsala, Sweden
| | - Stina Bodén
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
| | - Anton Ribbenstedt
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Chalmers Mass Spectrometry Infrastructure, Chalmers University of Technology, Gothenburg, Sweden
| | - Marc J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Richard Palmqvist
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Carl Brunius
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Chalmers Mass Spectrometry Infrastructure, Chalmers University of Technology, Gothenburg, Sweden
| | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
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15
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Das S, Helmus R, Dong Y, Beijer S, Praetorius A, Parsons JR, Jansen B. Organic contaminants in bio-based fertilizer treated soil: Target and suspect screening approaches. CHEMOSPHERE 2023; 337:139261. [PMID: 37379984 DOI: 10.1016/j.chemosphere.2023.139261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/11/2023] [Accepted: 06/16/2023] [Indexed: 06/30/2023]
Abstract
Using bio-based fertilizer (BBF) in agricultural soil can reduce the dependency on chemical fertilizer and increase sustainability by recycling nutrient-rich side-streams. However, organic contaminants in BBFs may lead to residues in the treated soil. This study assessed the presence of organic contaminants in BBF treated soils, which is essential for evaluating sustainability/risks of BBF use. Soil samples from two field studies amended with 15 BBFs from various sources (agricultural, poultry, veterinary, and sludge) were analyzed. A combination of QuEChERS-based extraction, liquid chromatography quadrupole time of flight mass spectrometry-based (LC-QTOF-MS) quantitative analysis, and an advanced, automated data interpretation workflow was optimized to extract and analyze organic contaminants in BBF-treated agricultural soil. The comprehensive screening of organic contaminants was performed using target analysis and suspect screening. Of the 35 target contaminants, only three contaminants were detected in the BBF-treated soil with concentrations ranging from 0.4 ng g-1 to 28.7 ng g-1; out of these three detected contaminants, two were also present in the control soil sample. Suspect screening using patRoon (an R-based open-source software platform) workflows and the NORMAN Priority List resulted in tentative identification of 20 compounds (at level 2 and level 3 confidence level), primarily pharmaceuticals and industrial chemicals, with only one overlapping compound in two experimental sites. The contamination profiles of the soil treated with BBFs sourced from veterinary and sludge were similar, with common pharmaceutical features identified. The suspect screening results suggest that the contaminants found in BBF-treated soil might come from alternative sources other than BBFs.
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Affiliation(s)
- Supta Das
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands.
| | - Rick Helmus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Yan Dong
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Steven Beijer
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Antonia Praetorius
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - John R Parsons
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Boris Jansen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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16
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Catandi GD, Bresnahan DR, Peters SO, Fresa KJ, Maclellan LJ, Broeckling CD, Carnevale EM. Equine maternal aging affects the metabolomic profile of oocytes and follicular cells during different maturation time points. Front Cell Dev Biol 2023; 11:1239154. [PMID: 37818125 PMCID: PMC10561129 DOI: 10.3389/fcell.2023.1239154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/28/2023] [Indexed: 10/12/2023] Open
Abstract
Introduction: Oocyte quality and fertility decline with advanced maternal age. During maturation within the ovarian follicle, the oocyte relies on the associated somatic cells, specifically cumulus and granulosa cells, to acquire essential components for developmental capacity. Methods: A nontargeted metabolomics approach was used to investigate the effects of mare age on different cell types within the dominant, follicular-phase follicle at three time points during maturation. Metabolomic analyses from single oocytes and associated cumulus and granulosa cells allowed correlations of metabolite abundance among cell types. Results and Discussion: Overall, many of the age-related changes in metabolite abundance point to Impaired mitochondrial metabolic function and oxidative stress in oocytes and follicular cells. Supporting findings include a higher abundance of glutamic acid and triglycerides and lower abundance of ceramides in oocytes and somatic follicular cells from old than young mares. Lower abundance of alanine in all follicular cell types from old mares, suggests limited anaerobic energy metabolism. The results also indicate impaired transfer of carbohydrate and free fatty acid substrates from cumulus cells to the oocytes of old mares, potentially related to disruption of transzonal projections between the cell types. The identification of age-associated alterations in the abundance of specific metabolites and their correlations among cells contribute to our understanding of follicular dysfunction with maternal aging.
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Affiliation(s)
- G. D. Catandi
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - D. R. Bresnahan
- Department of Animal Sciences, Berry College, Mount Berry, GA, United States
| | - S. O. Peters
- Department of Animal Sciences, Berry College, Mount Berry, GA, United States
| | - K. J. Fresa
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - L. J. Maclellan
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - C. D. Broeckling
- Proteomic and Metabolomics Core Facility, Colorado State University, Fort Collins, CO, United States
| | - E. M. Carnevale
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
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17
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Nordin E, Hellström PM, Vuong E, Ribbenstedt A, Brunius C, Landberg R. IBS randomized study: FODMAPs alter bile acids, phenolic- and tryptophan metabolites, while gluten modifies lipids. Am J Physiol Regul Integr Comp Physiol 2023; 325:R248-R259. [PMID: 37399002 DOI: 10.1152/ajpregu.00016.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/10/2023] [Accepted: 06/17/2023] [Indexed: 07/04/2023]
Abstract
Diet is considered a culprit for symptoms in irritable bowel syndrome (IBS), although the mechanistic understanding of underlying causes is lacking. Metabolomics, i.e., the analysis of metabolites in biological samples may offer a diet-responsive fingerprint for IBS. Our aim was to explore alterations in the plasma metabolome after interventions with fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) or gluten versus control in IBS, and to relate such alterations to symptoms. People with IBS (n = 110) were included in a double-blind, randomized, crossover study with 1-wk provocations of FODMAPs, gluten, or placebo. Symptoms were evaluated with the IBS severity scoring system (IBS-SSS). Untargeted metabolomics was performed on plasma samples using LC-qTOF-MS. Discovery of metabolite alterations by treatment was performed using random forest followed by linear mixed modeling. Associations were studied using Spearman correlation. The metabolome was affected by FODMAP [classification rate (CR) 0.88, P < 0.0001], but less by gluten intake CR 0.72, P = 0.01). FODMAP lowered bile acids, whereas phenolic-derived metabolites and 3-indolepropionic acid (IPA) were higher compared with placebo. IPA and some unidentified metabolites correlated weakly to abdominal pain and quality of life. Gluten affected lipid metabolism weakly, but with no interpretable relationship to IBS. FODMAP affected gut microbial-derived metabolites relating to positive health outcomes. IPA and unknown metabolites correlated weakly to IBS severity. Minor symptom worsening by FODMAP intake must be weighed against general positive health aspects of FODMAP. The gluten intervention affected lipid metabolism weakly with no interpretable association to IBS severity. Registration: www.clinicaltrials.gov as NCT03653689.NEW & NOTEWORTHY In irritable bowel syndrome (IBS), fermentable oligo-, di-, monosaccharides, and polyols (FODMAPs) affected microbial-derived metabolites relating to positive health outcomes such as reduced risk of colon cancer, inflammation, and type 2 diabetes, as shown in previous studies. The minor IBS symptom induction by FODMAP intake must be weighed against the positive health aspects of FODMAP consumption. Gluten affected lipids weakly with no association to IBS severity.
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Affiliation(s)
- Elise Nordin
- Department of Biology and Biological Engineering, Food and Nutrition Science, Chalmers University of Technology, Gothenburg, Sweden
| | - Per M Hellström
- Department of Medical Sciences, Gastroenterology/Hepatology, Uppsala University, Uppsala, Sweden
| | - Eddie Vuong
- Department of Biology and Biological Engineering, Food and Nutrition Science, Chalmers University of Technology, Gothenburg, Sweden
| | - Anton Ribbenstedt
- Department of Biology and Biological Engineering, Food and Nutrition Science, Chalmers University of Technology, Gothenburg, Sweden
| | - Carl Brunius
- Department of Biology and Biological Engineering, Food and Nutrition Science, Chalmers University of Technology, Gothenburg, Sweden
| | - Rikard Landberg
- Department of Biology and Biological Engineering, Food and Nutrition Science, Chalmers University of Technology, Gothenburg, Sweden
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18
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Bishop LM, Shen T, Fiehn O. Improving Quantitative Accuracy in Nontargeted Lipidomics by Evaluating Adduct Formation. Anal Chem 2023; 95:12683-12690. [PMID: 37582244 DOI: 10.1021/acs.analchem.3c01221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
For large-scale lipidomic analyses, accurate and reproducible quantification of endogenous lipids is crucial for comparing results within and across studies. Many lipids present in liquid chromatography-electrospray ionization-mass spectrometry form various adducts with buffer components. The mechanisms and conditions that dictate adduct formation are still poorly understood. In a positive mode, neutral lipids like mono-, di-, and triacylglycerides and cholesteryl esters typically generate [M + NH4]+ adduct ions, although [M + Na]+, [M + K]+, and other (more complex) species can also be significantly abundant in MS1 precursor ion spectra. Variations in the ratios of these adducts (within and between matrices) can lead to dramatic inaccuracies during quantification. Here, we examine 48 unique diacylglycerol (DAG) species across 2366 mouse samples for eight matrix-specific data sets of plasma, liver, kidney, brain, heart muscle, gastrocnemius muscle, gonadal, and inguinal fat. Typically, no single adduct ion species accounted for more than 60% of the total observed abundance across each data set. Even within a single matrix, DAGs showed a high variability of adduct ratios. The ratio of [M + NH4]+ adduct ions was increased for longer-chain DAGs and for polyunsaturated DAGs, at the expense of reduced ratios of [M + Na]+ adducts. When using three deuterated internal DAG standards, we found that absolute concentrations were estimated with up to 70% error when only one adduct ion was used instead of all adducts combined. Importantly, when combining [M + NH4]+ and [M + Na]+ adduct ions, quantification results were within 5% accuracy compared to all adduct ions combined. Additional variance can be caused by other factors, such as instrument conditions or matrix effects.
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Affiliation(s)
- Lauren M Bishop
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Tong Shen
- West Coast Metabolomics Center, 451 Health Sci. Drive, University of California Davis, Davis, California 95616, United States
| | - Oliver Fiehn
- West Coast Metabolomics Center, 451 Health Sci. Drive, University of California Davis, Davis, California 95616, United States
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19
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Perez de Souza L, Bitocchi E, Papa R, Tohge T, Fernie AR. Decreased metabolic diversity in common beans associated with domestication revealed by untargeted metabolomics, information theory, and molecular networking. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1021-1036. [PMID: 37272491 DOI: 10.1111/tpj.16277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/28/2023] [Accepted: 05/03/2023] [Indexed: 06/06/2023]
Abstract
The process of crop domestication leads to a dramatic reduction in the gene expression associated with metabolic diversity. Genes involved in specialized metabolism appear to be particularly affected. Although there is ample evidence of these effects at the genetic level, a reduction in diversity at the metabolite level has been taken for granted despite having never been adequately accessed and quantified. Here we leveraged the high coverage of ultra high performance liquid chromatography-high-resolution mass spectrometry based metabolomics to investigate the metabolic diversity in the common bean (Phaseolus vulgaris). Information theory highlights a shift towards lower metabolic diversity and specialization when comparing wild and domesticated bean accessions. Moreover, molecular networking approaches facilitated a broader metabolite annotation than achieved to date, and its integration with gene expression data uncovers a metabolic shift from specialized metabolism towards central metabolism upon domestication of this crop.
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Affiliation(s)
- Leonardo Perez de Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Elena Bitocchi
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Takayuki Tohge
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, Potsdam-Golm, 14476, Germany
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20
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Talvio K, Wagner VA, Minkeviciene R, Kirkwood JS, Kulinich AO, Umemori J, Bhatia A, Hur M, Käkelä R, Ethell IM, Castrén ML. An iPSC-derived astrocyte model of fragile X syndrome exhibits dysregulated cholesterol homeostasis. Commun Biol 2023; 6:789. [PMID: 37516746 PMCID: PMC10387075 DOI: 10.1038/s42003-023-05147-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 07/14/2023] [Indexed: 07/31/2023] Open
Abstract
Cholesterol is an essential membrane structural component and steroid hormone precursor, and is involved in numerous signaling processes. Astrocytes regulate brain cholesterol homeostasis and they supply cholesterol to the needs of neurons. ATP-binding cassette transporter A1 (ABCA1) is the main cholesterol efflux transporter in astrocytes. Here we show dysregulated cholesterol homeostasis in astrocytes generated from human induced pluripotent stem cells (iPSCs) derived from males with fragile X syndrome (FXS), which is the most common cause of inherited intellectual disability. ABCA1 levels are reduced in FXS human and mouse astrocytes when compared with controls. Accumulation of cholesterol associates with increased desmosterol and polyunsaturated phospholipids in the lipidome of FXS mouse astrocytes. Abnormal astrocytic responses to cytokine exposure together with altered anti-inflammatory and cytokine profiles of human FXS astrocyte secretome suggest contribution of inflammatory factors to altered cholesterol homeostasis. Our results demonstrate changes of astrocytic lipid metabolism, which can critically regulate membrane properties and affect cholesterol transport in FXS astrocytes, providing target for therapy in FXS.
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Affiliation(s)
- Karo Talvio
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Victoria A Wagner
- Division of Biomedical Sciences, and Neuroscience Graduate Program, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Rimante Minkeviciene
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jay S Kirkwood
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA, USA
| | - Anna O Kulinich
- Division of Biomedical Sciences, and Neuroscience Graduate Program, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Juzoh Umemori
- Gene and Cell Technology, A.I.Virtanen Institute, University of Eastern Finland, Kuopio, Finland
| | - Anil Bhatia
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA, USA
| | - Manhoi Hur
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA, USA
| | - Reijo Käkelä
- Helsinki University Lipidomics Unit, HiLIPID, Helsinki Institute of Life Science, HiLIFE, Biocenter Finland (Metabolomics), and Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Iryna M Ethell
- Division of Biomedical Sciences, and Neuroscience Graduate Program, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Maija L Castrén
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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21
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Liessi N, Tomati V, Capurro V, Loberto N, Garcia-Aloy M, Franceschi P, Aureli M, Pedemonte N, Armirotti A. The combination elexacaftor/tezacaftor/ivacaftor (ETI) modulates the de novo synthethic pathway of ceramides in a genotype-independent manner. J Cyst Fibros 2023; 22:680-682. [PMID: 37088636 DOI: 10.1016/j.jcf.2023.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
We report here how the triple combination of drugs elexacaftor/tezacaftor/ivacaftor (ETI) alters the balance of the de-novo synthethic pathway of sphingolipids in primary cells of human bronchial epithelium. The treatment with ETI roughly doubles the levels of dihydrosphingolipids, possibly by modulating the delta(4)-desaturase enzymes that convert dihydroceramides into ceramides. This appears to be an off-target effect of ETI, since it occurs in a genotype-independent manner, for both cystic fibrosis (CF) and non-CF subjects.
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Affiliation(s)
- Nara Liessi
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Valeria Tomati
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Valeria Capurro
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Nicoletta Loberto
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via F.lli Cervi 93, 20054 Segrate (MI)
| | - Mar Garcia-Aloy
- Centro di Ricerca e Innovazione, Fondazione Edmund Mach, Via Edmund Mach, 1, 38098 San Michele all'Adige, Trento, Italy
| | - Pietro Franceschi
- Centro di Ricerca e Innovazione, Fondazione Edmund Mach, Via Edmund Mach, 1, 38098 San Michele all'Adige, Trento, Italy
| | - Massimo Aureli
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via F.lli Cervi 93, 20054 Segrate (MI)
| | - Nicoletta Pedemonte
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Andrea Armirotti
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
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22
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Baygi SF, Kumar Y, Barupal DK. IDSL.CSA: Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets. Anal Chem 2023; 95:9480-9487. [PMID: 37311059 PMCID: PMC11080491 DOI: 10.1021/acs.analchem.3c00376] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Poor chemical annotation of high-resolution mass spectrometry data limits applications of untargeted metabolomics datasets. Our new software, the Integrated Data Science Laboratory for Metabolomics and Exposomics─Composite Spectra Analysis (IDSL.CSA) R package, generates composite mass spectra libraries from MS1-only data, enabling the chemical annotation of high-resolution mass spectrometry coupled with liquid chromatography peaks regardless of the availability of MS2 fragmentation spectra. We demonstrate comparable annotation rates for commonly detected endogenous metabolites in human blood samples using IDSL.CSA libraries versus MS/MS libraries in validation tests. IDSL.CSA can create and search composite spectra libraries from any untargeted metabolomics dataset generated using high-resolution mass spectrometry coupled to liquid or gas chromatography instruments. The cross-applicability of these libraries across independent studies may provide access to new biological insights that may be missed due to the lack of MS2 fragmentation data. The IDSL.CSA package is available in the R-CRAN repository at https://cran.r-project.org/package=IDSL.CSA. Detailed documentation and tutorials are provided at https://github.com/idslme/IDSL.CSA.
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Affiliation(s)
- Sadjad Fakouri Baygi
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yashwant Kumar
- Non-communicable Diseases Division, Translational Health Science and Technology Institute, Faridabad, Haryana, 121001, India
| | - Dinesh Kumar Barupal
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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23
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Baygi SF, Kumar Y, Barupal DK. IDSL.CSA: Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527886. [PMID: 36798308 PMCID: PMC9934657 DOI: 10.1101/2023.02.09.527886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Poor chemical annotation of high-resolution mass spectrometry data limit applications of untargeted metabolomics datasets. Our new software, the Integrated Data Science Laboratory for Metabolomics and Exposomics - Composite Spectra Analysis (IDSL.CSA) R package, generates composite mass spectra libraries from MS1-only data, enabling the chemical annotation of LC/HRMS peaks regardless of the availability of MS2 fragmentation spectra. We demonstrate comparable annotation rates for commonly detected endogenous metabolites in human blood samples using IDSL.CSA libraries versus MS/MS libraries in validation tests. IDSL.CSA can create and search composite spectra libraries from any untargeted metabolomics dataset generated using high-resolution mass spectrometry coupled to liquid or gas chromatography instruments. The cross-applicability of these libraries across independent studies may provide access to new biological insights that may be missed due to the lack of MS2 fragmentation data. The IDSL.CSA package is available in the R CRAN repository at https://cran.r-project.org/package=IDSL.CSA . Detailed documentation and tutorials are provided at https://github.com/idslme/IDSL.CSA . For Table of Contents Only
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Affiliation(s)
- Sadjad Fakouri Baygi
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yashwant Kumar
- Non-communicable Diseases Division, Translational Health Science and Technology Institute, Faridabad, Haryana, 121001, India
| | - Dinesh Kumar Barupal
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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24
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Walsh SC, Miles JR, Broeckling CD, Rempel LA, Wright-Johnson EC, Pannier AK. Secreted metabolome of porcine blastocysts encapsulated within in vitro 3D alginate hydrogel culture systems undergoing morphological changes provides insights into specific mechanisms involved in the initiation of porcine conceptus elongation. Reprod Fertil Dev 2023; 35:375-394. [PMID: 36780705 DOI: 10.1071/rd22210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/24/2023] [Indexed: 02/15/2023] Open
Abstract
CONTEXT The exact mechanisms regulating the initiation of porcine conceptus elongation are not known due to the complexity of the uterine environment. AIMS To identify contributing factors for initiation of conceptus elongation in vitro , this study evaluated differential metabolite abundance within media following culture of blastocysts within unmodified alginate (ALG) or Arg-Gly-Asp (RGD)-modified alginate hydrogel culture systems. METHODS Blastocysts were harvested from pregnant gilts, encapsulated within ALG or RGD or as non-encapsulated control blastocysts (CONT), and cultured. At the termination of 96h culture, media were separated into blastocyst media groups: non-encapsulated control blastocysts (CONT); ALG and RGD blastocysts with no morphological change (ALG- and RGD-); ALG and RGD blastocysts with morphological changes (ALG+ and RGD+) and evaluated for non-targeted metabolomic profiling by liquid chromatography (LC)-mass spectrometry (MS) techniques and gas chromatography-(GC-MS). KEY RESULTS Analysis of variance identified 280 (LC-MS) and 1 (GC-MS) compounds that differed (P <0.05), of which 134 (LC-MS) and 1 (GC-MS) were annotated. Metabolites abundance between ALG+ vs ALG-, RGD+ vs RGD-, and RGD+ vs ALG+ were further investigated to identify potential differences in metabolic processes during the initiation of elongation. CONCLUSIONS This study identified changes in phospholipid, glycosphingolipid, lipid signalling, and amino acid metabolic processes as potential RGD-independent mechanisms of elongation and identified changes in lysophosphatidylcholine and sphingolipid secretions during RGD-mediated elongation. IMPLICATIONS These results illustrate changes in phospholipid and sphingolipid metabolic processes and secretions may act as mediators of the RGD-integrin adhesion that promotes porcine conceptus elongation.
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Affiliation(s)
- Sophie C Walsh
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, P.O. Box 830726, Lincoln, NE 68583, USA
| | - Jeremy R Miles
- USDA, U.S. Meat Animal Research Center, P.O. Box 166, Clay Center, NE 68933, USA
| | - Corey D Broeckling
- Bioanalysis and Omics Center, Colorado State University, Fort Collins, CO, USA
| | - Lea A Rempel
- USDA, U.S. Meat Animal Research Center, P.O. Box 166, Clay Center, NE 68933, USA
| | | | - Angela K Pannier
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, P.O. Box 830726, Lincoln, NE 68583, USA
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25
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Anthony BM, Chaparro JM, Prenni JE, Minas IS. Carbon sufficiency boosts phenylpropanoid biosynthesis early in peach fruit development priming superior fruit quality. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:1019-1031. [PMID: 36898214 DOI: 10.1016/j.plaphy.2023.02.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Manipulating the crop load in peach trees determines carbon supply and optimum balance between fruit yield and quality potentials. The impact of carbon supply on peach fruit quality was assessed in three development stages (S2, S3, S4) on fruit of equal maturity from trees that were carbon (C) starved (unthinned) and sufficient (thinned). Previous studies determined that primary metabolites of peach fruit mesocarp are mainly linked with developmental processes, thus, the secondary metabolite profile was assessed using non-targeted liquid chromatography mass-spectrometry (LC-MS). Carbon sufficient (C-sufficient) fruit demonstrated superior quality attributes as compared to C-starved fruit. Early metabolic shifts in the secondary metabolome appear to prime quality at harvest. Enhanced C-availability facilitated the increased and consistent synthesis of flavonoids, like catechin, epicatechin and eriodyctiol, via the phenylpropanoid pathway, providing a link between the metabolome and fruit quality, and serving as signatures of C-sufficiency during peach fruit development.
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Affiliation(s)
- Brendon M Anthony
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, United States
| | - Jacqueline M Chaparro
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, United States
| | - Jessica E Prenni
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, United States
| | - Ioannis S Minas
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, United States.
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26
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Du X, Dastmalchi F, Ye H, Garrett TJ, Diller MA, Liu M, Hogan WR, Brochhausen M, Lemas DJ. Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software. Metabolomics 2023; 19:11. [PMID: 36745241 DOI: 10.1007/s11306-023-01974-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/20/2023] [Indexed: 02/07/2023]
Abstract
BACKGROUND Liquid chromatography-high resolution mass spectrometry (LC-HRMS) is a popular approach for metabolomics data acquisition and requires many data processing software tools. The FAIR Principles - Findability, Accessibility, Interoperability, and Reusability - were proposed to promote open science and reusable data management, and to maximize the benefit obtained from contemporary and formal scholarly digital publishing. More recently, the FAIR principles were extended to include Research Software (FAIR4RS). AIM OF REVIEW This study facilitates open science in metabolomics by providing an implementation solution for adopting FAIR4RS in the LC-HRMS metabolomics data processing software. We believe our evaluation guidelines and results can help improve the FAIRness of research software. KEY SCIENTIFIC CONCEPTS OF REVIEW We evaluated 124 LC-HRMS metabolomics data processing software obtained from a systematic review and selected 61 software for detailed evaluation using FAIR4RS-related criteria, which were extracted from the literature along with internal discussions. We assigned each criterion one or more FAIR4RS categories through discussion. The minimum, median, and maximum percentages of criteria fulfillment of software were 21.6%, 47.7%, and 71.8%. Statistical analysis revealed no significant improvement in FAIRness over time. We identified four criteria covering multiple FAIR4RS categories but had a low %fulfillment: (1) No software had semantic annotation of key information; (2) only 6.3% of evaluated software were registered to Zenodo and received DOIs; (3) only 14.5% of selected software had official software containerization or virtual machine; (4) only 16.7% of evaluated software had a fully documented functions in code. According to the results, we discussed improvement strategies and future directions.
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Affiliation(s)
- Xinsong Du
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Farhad Dastmalchi
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Hao Ye
- Health Science Center Libraries, University of Florida, Florida, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Florida, USA
| | - Matthew A Diller
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Mei Liu
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - William R Hogan
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Mathias Brochhausen
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Dominick J Lemas
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA.
- Department of Obstetrics and Gynecology, University of Florida College of Medicine, Florida, Gainesville, United States.
- Center for Perinatal Outcomes Research, University of Florida College of Medicine, Gainesville, United States.
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27
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Towards a harmonized identification scoring system in LC-HRMS/MS based non-target screening (NTS) of emerging contaminants. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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28
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Hissong R, Evans KR, Evans CR. Compound Identification Strategies in Mass Spectrometry-Based Metabolomics and Pharmacometabolomics. Handb Exp Pharmacol 2023; 277:43-71. [PMID: 36409330 DOI: 10.1007/164_2022_617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The metabolome is composed of a vast array of molecules, including endogenous metabolites and lipids, diet- and microbiome-derived substances, pharmaceuticals and supplements, and exposome chemicals. Correct identification of compounds from this diversity of classes is essential to derive biologically relevant insights from metabolomics data. In this chapter, we aim to provide a practical overview of compound identification strategies for mass spectrometry-based metabolomics, with a particular eye toward pharmacologically-relevant studies. First, we describe routine compound identification strategies applicable to targeted metabolomics. Next, we discuss both experimental (data acquisition-focused) and computational (software-focused) strategies used to identify unknown compounds in untargeted metabolomics data. We then discuss the importance of, and methods for, assessing and reporting the level of confidence of compound identifications. Throughout the chapter, we discuss how these steps can be implemented using today's technology, but also highlight research underway to further improve accuracy and certainty of compound identification. For readers interested in interpreting metabolomics data already collected, this chapter will supply important context regarding the origin of the metabolite names assigned to features in the data and help them assess the certainty of the identifications. For those planning new data acquisition, the chapter supplies guidance for designing experiments and selecting analysis methods to enable accurate compound identification, and it will point the reader toward best-practice data analysis and reporting strategies to allow sound biological and pharmacological interpretation.
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29
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Levina AV, Hoekenga OA, Gordin M, Broeckling C, De Jong WS. Applying network and genetic analysis to the potato metabolome. FRONTIERS IN PLANT SCIENCE 2023; 14:1108351. [PMID: 37152172 PMCID: PMC10154602 DOI: 10.3389/fpls.2023.1108351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/20/2023] [Indexed: 05/09/2023]
Abstract
Compositional traits in potato [Solanum tuberosum L.] are economically important but genetically complex, often controlled by many loci of small effect; new methods need to be developed to accelerate analysis and improvement of such traits, like chip quality. In this study, we used network analysis to organize hundreds of metabolic features detected by mass spectrometry into groups, as a precursor to genetic analysis. 981 features were condensed into 44 modules; module eigenvalues were used for genetic mapping and correlation analysis with phenotype data collected by the Solanaceae Coordinated Agricultural Project. Half of the modules were associated with at least one SNP according to GWAS; 11 of those modules were also significantly correlated with chip color. Within those modules features associated with chipping provide potential targets for selection in addition to selection for reduced glucose. Loci associated with module eigenvalues were not evenly distributed throughout the genome but were instead clustered on chromosomes 3, 7, and 8. Comparison of GWAS on single features and modules of clustered features often identified the same SNPs. However, features with related chemistries (for example, glycoalkaloids with precursor/product relationships) were not found to be near neighbors in the network analysis and did not share common SNPs from GWAS. Instead, the features within modules were often structurally disparate, suggesting that linkage disequilibrium complicates network analyses in potato. This result is consistent with recent genomic studies of potato showing that chromosomal rearrangements that create barriers to recombination are common in cultivated germplasm.
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Affiliation(s)
- Anna V. Levina
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | | | - Mikhail Gordin
- Department of Mechanical Engineering, Penn State University, State College, PA, United States
| | - Corey Broeckling
- Bioanalysis and Omics Team, Colorado State University, Fort Collins, CO, United States
| | - Walter S. De Jong
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- *Correspondence: Walter S. De Jong,
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30
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Peralbo-Molina Á, Solà-Santos P, Perera-Lluna A, Chicano-Gálvez E. Data Processing and Analysis in Mass Spectrometry-Based Metabolomics. Methods Mol Biol 2023; 2571:207-239. [PMID: 36152164 DOI: 10.1007/978-1-0716-2699-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Metabolomics is the latest of the omics sciences. It attempts to measure and characterize metabolites-small chemical compounds <1500 Da-on cells, tissue, or biofluids, which are usually products of biological reactions. As metabolic reactions are closer to the phenotype, metabolomics has emerged as an attractive science for various areas of research, including personalized medicine. However, due to the complexity of data obtained and the absence of curated databases for metabolite identification, data processing is the major bottleneck in this area since most technicians lack the required bioinformatics expertise to process datasets in a reliable and fast manner. The aim of this chapter is to describe the available tools for data processing that makes an inexperienced researcher capable of obtaining reliable results without having to undergo through huge parametrization steps.
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Affiliation(s)
- Ángela Peralbo-Molina
- IMIBIC Mass Spectrometry and Molecular Imaging Unit, Maimonides, Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba (UCO), Córdoba, Spain.
| | - Pol Solà-Santos
- B2SLab, Departament d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, Barcelona, Spain
- Networking Biomedical Research Centre in the Subject Area of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
- Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Alexandre Perera-Lluna
- B2SLab, Departament d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, Barcelona, Spain
- Networking Biomedical Research Centre in the Subject Area of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
- Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Eduardo Chicano-Gálvez
- IMIBIC Mass Spectrometry and Molecular Imaging Unit, Maimonides, Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba (UCO), Córdoba, Spain
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An Untargeted Metabolomics Approach on Carfilzomib-Induced Nephrotoxicity. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227929. [PMID: 36432029 PMCID: PMC9697636 DOI: 10.3390/molecules27227929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Carfilzomib (Cfz) is an anti-cancer drug related to cardiorenal adverse events, with cardiovascular and renal complications limiting its clinical use. Despite the important progress concerning the discovery of the underlying causes of Cfz-induced nephrotoxicity, the molecular/biochemical background is still not well clarified. Furthermore, the number of metabolomics-based studies concerning Cfz-induced nephrotoxicity is limited. METHODS A metabolomics UPLC-HRMS-DIA methodology was applied to three bio-sample types i.e., plasma, kidney, and urine, obtained from two groups of mice, namely (i) Cfz (8 mg Cfz/ kg) and (ii) Control (0.9% NaCl) (n = 6 per group). Statistical analysis, involving univariate and multivariate tools, was applied for biomarker detection. Furthermore, a sub-study was developed, aiming to estimate metabolites' correlation among bio-samples, and to enlighten potential mechanisms. RESULTS Cfz mostly affects the kidneys and urine metabolome. Fifty-four statistically important metabolites were discovered, and some of them have already been related to renal diseases. Furthermore, the correlations between bio-samples revealed patterns of metabolome alterations due to Cfz. CONCLUSIONS Cfz causes metabolite retention in kidney and dysregulates (up and down) several metabolites associated with the occurrence of inflammation and oxidative stress.
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El Abiead Y, Bueschl C, Panzenboeck L, Wang M, Doppler M, Seidl B, Zanghellini J, Dorrestein PC, Koellensperger G. Heterogeneous multimeric metabolite ion species observed in LC-MS based metabolomics data sets. Anal Chim Acta 2022; 1229:340352. [PMID: 36156231 DOI: 10.1016/j.aca.2022.340352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 08/08/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022]
Abstract
Covalent or non-covalent heterogeneous multimerization of molecules associated with extracts from biological samples analyzed via LC-MS are quite difficult to recognize/annotate and therefore the prevalence of multimerization remains largely unknown. In this study, we utilized 13C labeled and unlabeled Pichia pastoris extracts to recognize heterogeneous multimers. More specifically, between 0.8% and 1.5% of the biologically-derived features detected in our experiments were confirmed to be heteromers, about half of which we could successfully annotate with monomeric partners. Interestingly, we found specific chemical classes such as nucleotides to disproportionately contribute to heteroadducts. Furthermore, we compiled these compounds into the first MS/MS library that included data from heteromultimers to provide a starting point for other labs to improve the annotation of such ions in other metabolomics data sets. Then, the detected heteromers were also searched in publicly accessible LC-MS datasets available in Metabolights, Metabolomics WB and GNPS/MassIVE to demonstrate that these newly annotated ions are also relevant to other public datasets. Furthermore, in additional datasets (Triticum aestivum, Fusarium graminearum, and Trichoderma reesei) our developed workflow also detected 0.5%-4.9% of metabolite features to originate from heterodimers, demonstrating heteroadducts to be present in metabolomics studies at a low percentage.
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Affiliation(s)
- Yasin El Abiead
- Department of Analytical Chemistry, University of Vienna, 1090, Vienna, Austria.
| | - Christoph Bueschl
- Department of Analytical Chemistry, University of Vienna, 1090, Vienna, Austria; Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, 3430, Tulln, Austria
| | - Lisa Panzenboeck
- Department of Analytical Chemistry, University of Vienna, 1090, Vienna, Austria
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Maria Doppler
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, 3430, Tulln, Austria; Core Facility Bioactive Molecules: Screening and Analysis, University of Natural Resources and Life Sciences, Vienna, 3430, Tulln, Austria
| | - Bernhard Seidl
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, 3430, Tulln, Austria
| | - Jürgen Zanghellini
- Department of Analytical Chemistry, University of Vienna, 1090, Vienna, Austria
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA; Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Gunda Koellensperger
- Department of Analytical Chemistry, University of Vienna, 1090, Vienna, Austria.
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33
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Sedlacko EM, Heuberger AL, Chaparro JM, Cath TY, Higgins CP. Metabolomics reveals primary response of wheat (Triticum aestivum) to irrigation with oilfield produced water. ENVIRONMENTAL RESEARCH 2022; 212:113547. [PMID: 35660401 DOI: 10.1016/j.envres.2022.113547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/28/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The reuse of oilfield produced water (PW) for agricultural irrigation has received increased attention for utility in drought-stricken regions. It was recently demonstrated that PW irrigation can affect physiological processes in food crops. However, metabolomic evaluations are important to further discern specific mechanisms of how PW may contribute as a plant-environmental stressor. Herein, the primary metabolic responses of wheat irrigated with PW and matching salinity controls were investigated. Non-targeted gas chromatography mass spectrometry (GC-MS) metabolomics was combined with multivariate analysis and revealed that PW irrigation altered the primary metabolic profiles of both wheat leaf and grain. Over 600 compounds (183 annotated metabolites) were detected that varied between controls (salinity control and tap water) and PW irrigated plants. While some of these changed metabolites are related to salinity stress, over half were found to be unique to PW. The primary metabolites exhibiting changes in abundance in leaf and grain tissues were amines/amino acids, organic acids, and saccharides. Metabolite pathway analysis revealed that amino acid metabolism, sugar metabolism, and nitrogen remobilization are all impacted by PW irrigation, independent of regular plant responses to salinity stress. These data, when combined with prior physiological studies, support a multi-faceted, physio-metabolic response of wheat to the unique stressor imposed by irrigation with PW.
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Affiliation(s)
- Erin M Sedlacko
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, 80401, USA
| | - Adam L Heuberger
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jaqueline M Chaparro
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA; Analytical Resources Core - Bioanalysis and Omics, Colorado State University, Fort Collins, CO, 80523, USA
| | - Tzahi Y Cath
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, 80401, USA
| | - Christopher P Higgins
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, 80401, USA.
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34
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Magnuson JT, Caceres L, Sy N, Ji C, Tanabe P, Gan J, Lydy MJ, Schlenk D. The Use of Non-targeted Lipidomics and Histopathology to Characterize the Neurotoxicity of Bifenthrin to Juvenile Rainbow Trout ( Oncorhynchus mykiss). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11482-11492. [PMID: 35876619 PMCID: PMC9387103 DOI: 10.1021/acs.est.2c01542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/14/2022] [Accepted: 07/14/2022] [Indexed: 05/25/2023]
Abstract
Due to the detection frequencies and measured concentrations in surface water, the type I pyrethroid insecticide, bifenthrin, has been of particular concern within the Sacramento-San Joaquin Delta in California. Concentrations have been detected above levels previously reported to impair neuroendocrine function and induce neurotoxicity to several species of salmonids. Metabolomic and transcriptomic studies indicated impairment of cellular signaling within the brain of exposed animals and potential alteration of lipid metabolism. To better understand the potential impacts of bifenthrin on brain lipids, juvenile rainbow trout (Oncorhynchus mykiss) were exposed to mean bifenthrin concentrations of 28 or 48 ng/L for 14 days, and non-targeted lipidomic profiling in the brain was conducted. Brain tissue sections were also assessed for histopathological insult following bifenthrin treatment. Bifenthrin-exposed trout had a concentration-dependent decrease in the relative abundance of triglycerides (TGs) with levels of phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs) significantly altered following 48 ng/L bifenthrin exposure. An increased incidence of histopathological lesions, such as focal hemorrhages and congestion of blood vessels, was noted in the brains of bifenthrin-treated animals, suggesting an association between altered lipid metabolism and neuronal cell structure and integrity.
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Affiliation(s)
- Jason T. Magnuson
- Department
of Environmental Sciences, University of
California, Riverside, California 92521, United States
| | - Leslie Caceres
- Department
of Environmental Sciences, University of
California, Riverside, California 92521, United States
| | - Nathan Sy
- Department
of Environmental Sciences, University of
California, Riverside, California 92521, United States
| | - Chenyang Ji
- College
of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Philip Tanabe
- Department
of Environmental Sciences, University of
California, Riverside, California 92521, United States
| | - Jay Gan
- Department
of Environmental Sciences, University of
California, Riverside, California 92521, United States
| | - Michael J. Lydy
- Department
of Zoology, Center for Fisheries, Aquaculture and Aquatic Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Daniel Schlenk
- Department
of Environmental Sciences, University of
California, Riverside, California 92521, United States
- Institute
of Environmental Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
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35
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Yan S, Bhawal R, Yin Z, Thannhauser TW, Zhang S. Recent advances in proteomics and metabolomics in plants. MOLECULAR HORTICULTURE 2022; 2:17. [PMID: 37789425 PMCID: PMC10514990 DOI: 10.1186/s43897-022-00038-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/20/2022] [Indexed: 10/05/2023]
Abstract
Over the past decade, systems biology and plant-omics have increasingly become the main stream in plant biology research. New developments in mass spectrometry and bioinformatics tools, and methodological schema to integrate multi-omics data have leveraged recent advances in proteomics and metabolomics. These progresses are driving a rapid evolution in the field of plant research, greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment. Here, we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response, gene/protein function characterization, metabolic and signaling pathways exploration, and natural product discovery. We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology. This review is intended to provide readers with an overview of how advanced MS technology, and integrated application of proteomics and metabolomics can be used to advance plant system biology research.
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Affiliation(s)
- Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA
| | - Zhibin Yin
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | | | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA.
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36
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Berry JC, Qi M, Sonawane BV, Sheflin A, Cousins A, Prenni J, Schachtman DP, Liu P, Bart RS. Increased signal-to-noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components. eLife 2022; 11:70056. [PMID: 35819140 PMCID: PMC9275819 DOI: 10.7554/elife.70056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/29/2022] [Indexed: 12/11/2022] Open
Abstract
Environmental variability poses a major challenge to any field study. Researchers attempt to mitigate this challenge through replication. Thus, the ability to detect experimental signals is determined by the degree of replication and the amount of environmental variation, noise, within the experimental system. A major source of noise in field studies comes from the natural heterogeneity of soil properties which create microtreatments throughout the field. In addition, the variation within different soil properties is often nonrandomly distributed across a field. We explore this challenge through a sorghum field trial dataset with accompanying plant, microbiome, and soil property data. Diverse sorghum genotypes and two watering regimes were applied in a split-plot design. We describe a process of identifying, estimating, and controlling for the effects of spatially distributed soil properties on plant traits and microbial communities using minimal degrees of freedom. Importantly, this process provides a method with which sources of environmental variation in field data can be identified and adjusted, improving our ability to resolve effects of interest and to quantify subtle phenotypes.
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Affiliation(s)
- Jeffrey C Berry
- Donald Danforth Plant Science Center, St. Louis, United States
| | - Mingsheng Qi
- Donald Danforth Plant Science Center, St. Louis, United States
| | - Balasaheb V Sonawane
- School of Biological Sciences, Washington State University, Pullman, United States
| | - Amy Sheflin
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Asaph Cousins
- School of Biological Sciences, Washington State University, Pullman, United States
| | - Jessica Prenni
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, United States
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, United States
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, St. Louis, United States
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37
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Lichtner FJ, Jurick WM, Bradshaw M, Broeckling C, Bauchan G, Broders K. Penicillium raperi, a species isolated from Colorado cropping soils, is a potential biological control agent that produces multiple metabolites and is antagonistic against postharvest phytopathogens. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01812-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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38
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Metabolomic Profiles of Multidrug-Resistant Salmonella Typhimurium from Humans, Bovine, and Porcine Hosts. Animals (Basel) 2022; 12:ani12121518. [PMID: 35739855 PMCID: PMC9219436 DOI: 10.3390/ani12121518] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The global threat that is imposed by the resistance the pathogens develop to antimicrobial drugs is escalating. Tools to detect the resistance (with evidence on molecular and cellular outcomes) would reveal intricate mechanisms through which novel drugs could be developed. Approaches such as metabolomics, which involve metabolite detection, provide scientific evidence of metabolite expression of antimicrobial-resistant pathogens. The current study involved metabolomics of antimicrobial-resistant Salmonella Typhimurium collected from various hosts (human, porcine, bovine) and were exposed to antimicrobial drugs—ampicillin, chloramphenicol, streptomycin, sulfisoxazole, and tetracycline—as one set of the experiment. The same isolates were also cultured with no drug exposure as a comparison. There are certain pathways of metabolite expression that are impacted by drug exposure when compared to no drug exposure, meaning that the expressed metabolites could be potential targets for drug companies for the treatment of antimicrobial-resistant pathogens. Abstract Antimicrobial resistance (AMR) is a global public health threat, yet tools for detecting resistance patterns are limited and require advanced molecular methods. Metabolomic approaches produce metabolite profiles and help provide scientific evidence of differences in metabolite expressions between Salmonella Typhimurium from various hosts. This research aimed to evaluate the metabolomic profiles of S. Typhimurium associated with AMR and it compares profiles across various hosts. Three samples, each from bovine, porcine, and humans (total n = 9), were selectively chosen from an existing library to compare these nine isolates cultured under no drug exposure to the same isolates cultured in the presence of the antimicrobial drug panel ACSSuT (ampicillin, chloramphenicol, streptomycin, sulfisoxazole, tetracycline). This was followed by metabolomic profiling using UPLC and GC–mass spectrometry. The results indicated that the metabolite regulation was affected by antibiotic exposure, irrespective of the host species. When exposed to antibiotics, 59.69% and 40.31% of metabolites had increased and decreased expressions, respectively. The most significantly regulated metabolic pathway was aminoacyl-tRNA biosynthesis, which demonstrated increased expressions of serine, aspartate, alanine, and citric acid. Metabolites that showed decreased expressions included glutamate and pyruvate. This pathway and associated metabolites have known AMR associations and could be targeted for new drug discoveries and diagnostic methods.
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Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function. Appl Environ Microbiol 2022; 88:e0022622. [PMID: 35536051 DOI: 10.1128/aem.00226-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a high-sugar treatment (HST). To parse the response of the soil microbiome to different exudate regimens, laboratory soil reactors were amended with these root exudate treatments as well as a nonexudate control. Amplicon sequencing of the 16S rRNA gene illustrated distinct microbial diversity patterns and membership in response to HST, HOT, or control amendments. Exometabolite changes reflected these microbial community changes, and we observed enrichment of organic and amino acids, as well as possible phytohormones in the HST relative to the HOT and control. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multiomics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production. IMPORTANCE Decrypting the chemical interactions between plant roots and the soil microbiome is a gateway for future manipulation and management of the rhizosphere, a soil compartment critical to promoting plant fitness and yields. Our experimental results demonstrate how soil microbial community and genomic diversity is influenced by root exudates of differing chemical compositions and how changes in this microbiome result in altered production of plant-relevant metabolites. Together, these findings demonstrate the tractability of high-resolution multiomics tools to investigate soil microbiomes and provide new information on plant-soil environments useful for the development of efficient and precise microbiota management strategies in agricultural systems.
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40
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Walker DI, Juran BD, Cheung AC, Schlicht EM, Liang Y, Niedzwiecki M, LaRusso NF, Gores GJ, Jones DP, Miller GW, Lazaridis KN. High-Resolution Exposomics and Metabolomics Reveals Specific Associations in Cholestatic Liver Diseases. Hepatol Commun 2022; 6:965-979. [PMID: 34825528 PMCID: PMC9035559 DOI: 10.1002/hep4.1871] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/20/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022] Open
Abstract
Progress in development of prognostic and therapeutic options for the rare cholestatic liver diseases, primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC), is hampered by limited knowledge of their pathogeneses. In particular, the potential role of hepatotoxic and/or metabolism-altering environmental chemicals in the pathogenesis of these diseases remains relatively unstudied. Moreover, the extent to which metabolic pathways are altered due to ongoing cholestasis and subsequent liver damage or possibly influenced by hepatotoxic chemicals is poorly understood. In this study, we applied a comprehensive exposomics-metabolomics approach to uncover potential pathogenic contributors to PSC and PBC. We used untargeted high-resolution mass spectrometry to characterize a wide range of exogenous chemicals and endogenous metabolites in plasma and tested them for association with disease. Exposome-wide association studies (EWAS) identified environmental chemicals, including pesticides, additives and persistent pollutants, that were associated with PSC and/or PBC, suggesting potential roles for these compounds in disease pathogenesis. Metabolome-wide association studies (MWAS) found disease-associated alterations to amino acid, eicosanoid, lipid, co-factor, nucleotide, mitochondrial and microbial metabolic pathways, many of which were shared between PSC and PBC. Notably, this analysis implicates a potential role of the 5-lipoxygenase pathway in the pathogenesis of these diseases. Finally, EWAS × MWAS network analysis uncovered linkages between environmental agents and disrupted metabolic pathways that provide insight into potential mechanisms for PSC and PBC. Conclusion: This study establishes combined exposomics-metabolomics as a generalizable approach to identify potentially pathogenic environmental agents and enumerate metabolic alterations that may impact PSC and PBC, providing a foundation for diagnostic and therapeutic strategies.
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Affiliation(s)
- Douglas I. Walker
- Department of Environmental Medicine and Public HealthIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Brian D. Juran
- Division of Gastroenterology and HepatologyMayo ClinicRochesterMNUSA
| | - Angela C. Cheung
- Gastroenterology and HepatologyDepartment of MedicineThe Ottawa HospitalOttawaONCanada
| | - Erik M. Schlicht
- Division of Gastroenterology and HepatologyMayo ClinicRochesterMNUSA
| | - Yongliang Liang
- Clinical Biomarkers LaboratoryDivision of PulmonaryAllergyCritical Care and Sleep MedicineEmory UniversityAtlantaGAUSA
| | - Megan Niedzwiecki
- Department of Environmental Medicine and Public HealthIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | | | - Gregory J. Gores
- Division of Gastroenterology and HepatologyMayo ClinicRochesterMNUSA
| | - Dean P. Jones
- Clinical Biomarkers LaboratoryDivision of PulmonaryAllergyCritical Care and Sleep MedicineEmory UniversityAtlantaGAUSA
| | - Gary W. Miller
- Department of Environmental Health SciencesColumbia University Mailman School of Public HealthNew YorkNYUSA
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41
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Sikes KJ, McConnell A, Serkova N, Cole B, Frisbie D. Untargeted metabolomics analysis identifies creatine, myo-inositol, and lipid pathway modulation in a murine model of tendinopathy. J Orthop Res 2022; 40:965-976. [PMID: 34081345 PMCID: PMC8639838 DOI: 10.1002/jor.25112] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/12/2021] [Accepted: 05/31/2021] [Indexed: 02/04/2023]
Abstract
Tendinopathy has been broadly characterized as alterations in cell proliferation, extracellular matrix turnover/synthesis, and inflammatory alterations. However, the underlying glucose metabolism pathways which contribute to these responses have not been well explored. The potential link between glucose metabolism and tendon pathology is interesting from a global standpoint since the development of spontaneous tendinopathy is associated with systemic metabolic disorders including diabetes mellitus. Therefore, the overarching goal of this study was to understand the potential pathogenic role of glucose metabolism-driven mechanisms in the development of tendinopathy. To test this, we have utilized an untargeted metabolomics approach to discover pathways which may be altered following tendinopathic injury and treadmill running in an established murine model of TGF-β1 induced tendinopathy. While specific tendon glucose alterations were not observed via metabolomics or 18 F-fluoroeoxyglucose (FDG) positron emission tomography/microcomputed tomography imaging (18 F-FDG PET/CT), metabolites including creatinine, D-chiro-inositol, and lipids were dysregulated following tendon injury. As novel pathways for manipulation, the creatine pathway, myo-inositol pathway, and lipid signaling may lead to the development of enhanced preventative strategies and therapeutic options for all patients who suffer from tendon-related injuries.
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Affiliation(s)
- Katie J. Sikes
- Orthopaedic Research Center, Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523
| | - Anna McConnell
- Orthopaedic Research Center, Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523
| | - Natalie Serkova
- Department of Radiology, University of Colorado Denver, Denver, CO 80045
| | - Brian Cole
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL 60612
| | - David Frisbie
- Orthopaedic Research Center, Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523
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Hollin T, Abel S, Falla A, Pasaje CFA, Bhatia A, Hur M, Kirkwood JS, Saraf A, Prudhomme J, De Souza A, Florens L, Niles JC, Le Roch KG. Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum. Nat Commun 2022; 13:1275. [PMID: 35277503 PMCID: PMC8917122 DOI: 10.1038/s41467-022-28981-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/14/2022] [Indexed: 12/31/2022] Open
Abstract
The RAP (RNA-binding domain abundant in Apicomplexans) protein family has been identified in various organisms. Despite expansion of this protein family in apicomplexan parasites, their main biological functions remain unknown. In this study, we use inducible knockdown studies in the human malaria parasite, Plasmodium falciparum, to show that two RAP proteins, PF3D7_0105200 (PfRAP01) and PF3D7_1470600 (PfRAP21), are essential for parasite survival and localize to the mitochondrion. Using transcriptomics, metabolomics, and proteomics profiling experiments, we further demonstrate that these RAP proteins are involved in mitochondrial RNA metabolism. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (eCLIP-seq), we validate that PfRAP01 and PfRAP21 are true RNA-binding proteins and interact specifically with mitochondrial rRNAs. Finally, mitochondrial enrichment experiments followed by deep sequencing of small RNAs demonstrate that PfRAP21 controls mitochondrial rRNA expression. Collectively, our results establish the role of these RAP proteins in mitoribosome activity and contribute to further understanding this protein family in malaria parasites.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Alejandra Falla
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Anil Bhatia
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Manhoi Hur
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Jay S Kirkwood
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Amancio De Souza
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA.
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43
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Huang D, Zhang C, Chen J, Xiao Y, Li M, Sun L, Qiu S, Chen W. Computational Workflow to Study the Diversity of Secondary Metabolites in Fourteen Different Isatis Species. Cells 2022; 11:cells11050907. [PMID: 35269530 PMCID: PMC8909408 DOI: 10.3390/cells11050907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 11/22/2022] Open
Abstract
The screening of real features among thousands of ions remains a great challenge in the study of metabolomics. In this research, a workflow designed based on the MetaboFR tool and “feature-rating” rule was developed to screen the real features in large-scale data analyses. Seventy-four reference standards were used to test the feasibility, with 83.21% of real features being obtained after MetaboFR processing. Moreover, the full workflow was applied for systematic characterization of 14 species of the genus Isatis, with the result that 87.72% of real features were retained and 69.19% of the in-source fragments were removed. To gain insights into metabolite diversity within this plant family, 1697 real features were tentatively identified, including lipids, phenylpropanoids, organic acids, indole derivatives, etc. Indole derivatives were demonstrated to be the best chemical markers with which to differentiate different species. The rare existence of indole derivatives in Isatis cappadocica (cap) and Isatis cappadocica subsp. Steveniana (capS) indicates that the biosynthesis of indole derivatives could play a key role in driving the chemical diversity and evolution of genus Isatis. Our workflow provides the foundations for the exploration of real features in metabolomics, and has the potential to reveal the chemical composition and marker metabolites of secondary metabolites in plant fields.
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Affiliation(s)
- Doudou Huang
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (D.H.); (C.Z.); (J.C.); (Y.X.); (L.S.)
| | - Chen Zhang
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (D.H.); (C.Z.); (J.C.); (Y.X.); (L.S.)
| | - Junfeng Chen
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (D.H.); (C.Z.); (J.C.); (Y.X.); (L.S.)
| | - Ying Xiao
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (D.H.); (C.Z.); (J.C.); (Y.X.); (L.S.)
| | - Mingming Li
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200433, China;
| | - Lianna Sun
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (D.H.); (C.Z.); (J.C.); (Y.X.); (L.S.)
| | - Shi Qiu
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (D.H.); (C.Z.); (J.C.); (Y.X.); (L.S.)
- Correspondence: (S.Q.); (W.C.)
| | - Wansheng Chen
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (D.H.); (C.Z.); (J.C.); (Y.X.); (L.S.)
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200433, China;
- Correspondence: (S.Q.); (W.C.)
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44
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Graça G, Cai Y, Lau CHE, Vorkas PA, Lewis MR, Want EJ, Herrington D, Ebbels TMD. Automated Annotation of Untargeted All-Ion Fragmentation LC-MS Metabolomics Data with MetaboAnnotatoR. Anal Chem 2022; 94:3446-3455. [PMID: 35180347 PMCID: PMC8892435 DOI: 10.1021/acs.analchem.1c03032] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022]
Abstract
Untargeted metabolomics and lipidomics LC-MS experiments produce complex datasets, usually containing tens of thousands of features from thousands of metabolites whose annotation requires additional MS/MS experiments and expert knowledge. All-ion fragmentation (AIF) LC-MS/MS acquisition provides fragmentation data at no additional experimental time cost. However, analysis of such datasets requires reconstruction of parent-fragment relationships and annotation of the resulting pseudo-MS/MS spectra. Here, we propose a novel approach for automated annotation of isotopologues, adducts, and in-source fragments from AIF LC-MS datasets by combining correlation-based parent-fragment linking with molecular fragment matching. Our workflow focuses on a subset of features rather than trying to annotate the full dataset, saving time and simplifying the process. We demonstrate the workflow in three human serum datasets containing 599 features manually annotated by experts. Precision and recall values of 82-92% and 82-85%, respectively, were obtained for features found in the highest-rank scores (1-5). These results equal or outperform those obtained using MS-DIAL software, the current state of the art for AIF data annotation. Further validation for other biological matrices and different instrument types showed variable precision (60-89%) and recall (10-88%) particularly for datasets dominated by nonlipid metabolites. The workflow is freely available as an open-source R package, MetaboAnnotatoR, together with the fragment libraries from Github (https://github.com/gggraca/MetaboAnnotatoR).
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Affiliation(s)
- Gonçalo Graça
- Section
of Bioinformatics, Division of Systems Medicine, Department of Metabolism,
Digestion and Reproduction, Imperial College
London, South Kensington Campus, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
| | - Yuheng Cai
- Section
of Bioinformatics, Division of Systems Medicine, Department of Metabolism,
Digestion and Reproduction, Imperial College
London, South Kensington Campus, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
| | - Chung-Ho E. Lau
- Department
of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, U.K.
| | - Panagiotis A. Vorkas
- Section
of Biomolecular Medicine, Division of Systems Medicine, Department
of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
- Institute
of Applied Biosciences, Centre for Research
and Technology Hellas, Thessaloniki 57001, Greece
| | - Matthew R. Lewis
- Section
of Bioanalytical Chemistry and National Phenome Centre, Division of
Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building, London W12 0NN, U.K.
| | - Elizabeth J. Want
- Section
of Biomolecular Medicine, Division of Systems Medicine, Department
of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
| | - David Herrington
- Section on
Cardiovascular Medicine, Wake Forest School
of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Timothy M. D. Ebbels
- Section
of Bioinformatics, Division of Systems Medicine, Department of Metabolism,
Digestion and Reproduction, Imperial College
London, South Kensington Campus, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
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45
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Bauermeister A, Mannochio-Russo H, Costa-Lotufo LV, Jarmusch AK, Dorrestein PC. Mass spectrometry-based metabolomics in microbiome investigations. Nat Rev Microbiol 2022; 20:143-160. [PMID: 34552265 PMCID: PMC9578303 DOI: 10.1038/s41579-021-00621-9] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 02/08/2023]
Abstract
Microbiotas are a malleable part of ecosystems, including the human ecosystem. Microorganisms affect not only the chemistry of their specific niche, such as the human gut, but also the chemistry of distant environments, such as other parts of the body. Mass spectrometry-based metabolomics is one of the key technologies to detect and identify the small molecules produced by the human microbiota, and to understand the functional role of these microbial metabolites. This Review provides a foundational introduction to common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis. Data analysis remains an obstacle; therefore, the emphasis is placed on data analysis approaches and integrative analysis, including the integration of microbiome sequencing data.
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Affiliation(s)
- Anelize Bauermeister
- Institute of Biomedical Science, Universidade de São Paulo, São Paulo, SP, Brazil,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Helena Mannochio-Russo
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, SP, Brazil,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | | | - Alan K. Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA.,Department of Pediatrics, University of California, San Diego, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, CA, USA
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46
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Yu M, Dolios G, Petrick L. Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features. J Cheminform 2022; 14:6. [PMID: 35172886 PMCID: PMC8848943 DOI: 10.1186/s13321-022-00586-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/03/2022] [Indexed: 01/16/2023] Open
Abstract
Unknown features in untargeted metabolomics and non-targeted analysis (NTA) are identified using fragment ions from MS/MS spectra to predict the structures of the unknown compounds. The precursor ion selected for fragmentation is commonly performed using data dependent acquisition (DDA) strategies or following statistical analysis using targeted MS/MS approaches. However, the selected precursor ions from DDA only cover a biased subset of the peaks or features found in full scan data. In addition, different statistical analysis can select different precursor ions for MS/MS analysis, which make the post-hoc validation of ions selected following a secondary analysis impossible for precursor ions selected by the original statistical method. Here we propose an automated, exhaustive, statistical model-free workflow: paired mass distance-dependent analysis (PMDDA), for reproducible untargeted mass spectrometry MS2 fragment ion collection of unknown compounds found in MS1 full scan. Our workflow first removes redundant peaks from MS1 data and then exports a list of precursor ions for pseudo-targeted MS/MS analysis on independent peaks. This workflow provides comprehensive coverage of MS2 collection on unknown compounds found in full scan analysis using a “one peak for one compound” workflow without a priori redundant peak information. We compared pseudo-spectra formation and the number of MS2 spectra linked to MS1 data using the PMDDA workflow to that obtained using CAMERA and RAMclustR algorithms. More annotated compounds, molecular networks, and unique MS/MS spectra were found using PMDDA compared with CAMERA and RAMClustR. In addition, PMDDA can generate a preferred ion list for iterative DDA to enhance coverage of compounds when instruments support such functions. Finally, compounds with signals in both positive and negative modes can be identified by the PMDDA workflow, to further reduce redundancies. The whole workflow is fully reproducible as a docker image xcmsrocker with both the original data and the data processing template.
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Affiliation(s)
- Miao Yu
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Georgia Dolios
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lauren Petrick
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,The Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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47
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Sayre-Chavez B, Bettenhausen H, Windes S, Aron P, Cistué L, Fisk S, Helgerson L, Heuberger AL, Tynan S, Hayes P, Muñoz-Amatriaín M. Genetic basis of barley contributions to beer flavor. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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48
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Aron AT, Petras D, Schmid R, Gauglitz JM, Büttel I, Antelo L, Zhi H, Nuccio SP, Saak CC, Malarney KP, Thines E, Dutton RJ, Aluwihare LI, Raffatellu M, Dorrestein PC. Native mass spectrometry-based metabolomics identifies metal-binding compounds. Nat Chem 2022; 14:100-109. [PMID: 34795435 PMCID: PMC8959065 DOI: 10.1038/s41557-021-00803-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 08/27/2021] [Indexed: 11/09/2022]
Abstract
Although metals are essential for the molecular machineries of life, systematic methods for discovering metal-small molecule complexes from biological samples are limited. Here, we describe a two-step native electrospray ionization-mass spectrometry method, in which post-column pH adjustment and metal infusion are combined with ion identity molecular networking, a rule-based data analysis workflow. This method enabled the identification of metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion species with the same chromatographic profiles. As this native electrospray metabolomics approach is suited to the use of any liquid chromatography-mass spectrometry system to explore the binding of any metal, this method has the potential to become an essential strategy for elucidating metal-binding molecules in biology.
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Affiliation(s)
- Allegra T. Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, USA,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA,Present affiliation: CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, Tübingen, 72076, Germany
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, D-48149, Germany
| | - Julia M. Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, USA,Present affiliation: Sapient Bioanalytics, La Jolla, CA, 92093, USA
| | - Isabell Büttel
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, Mainz D-55128, Germany
| | - Luis Antelo
- Institute of Biotechnology and Drug Research (IBWF gGmbH), Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, Mainz D-55128, Germany
| | - Hui Zhi
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Sean-Paul Nuccio
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Christina C. Saak
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kien P. Malarney
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eckhard Thines
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, Mainz D-55128, Germany,Institute of Biotechnology and Drug Research (IBWF gGmbH), Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, Mainz D-55128, Germany
| | - Rachel J. Dutton
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA,Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lihini I. Aluwihare
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA,Chiba University-University of California San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, CA 92093, United States of America,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA,Correspondence to
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49
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Fuentes ZC, Schwartz YL, Robuck AR, Walker DI. Operationalizing the Exposome Using Passive Silicone Samplers. CURRENT POLLUTION REPORTS 2022; 8:1-29. [PMID: 35004129 PMCID: PMC8724229 DOI: 10.1007/s40726-021-00211-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/11/2021] [Indexed: 05/15/2023]
Abstract
The exposome, which is defined as the cumulative effect of environmental exposures and corresponding biological responses, aims to provide a comprehensive measure for evaluating non-genetic causes of disease. Operationalization of the exposome for environmental health and precision medicine has been limited by the lack of a universal approach for characterizing complex exposures, particularly as they vary temporally and geographically. To overcome these challenges, passive sampling devices (PSDs) provide a key measurement strategy for deep exposome phenotyping, which aims to provide comprehensive chemical assessment using untargeted high-resolution mass spectrometry for exposome-wide association studies. To highlight the advantages of silicone PSDs, we review their use in population studies and evaluate the broad range of applications and chemical classes characterized using these samplers. We assess key aspects of incorporating PSDs within observational studies, including the need to preclean samplers prior to use to remove impurities that interfere with compound detection, analytical considerations, and cost. We close with strategies on how to incorporate measures of the external exposome using PSDs, and their advantages for reducing variability in exposure measures and providing a more thorough accounting of the exposome. Continued development and application of silicone PSDs will facilitate greater understanding of how environmental exposures drive disease risk, while providing a feasible strategy for incorporating untargeted, high-resolution characterization of the external exposome in human studies.
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Affiliation(s)
- Zoe Coates Fuentes
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY USA
| | - Yuri Levin Schwartz
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY USA
| | - Anna R. Robuck
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY USA
| | - Douglas I. Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY USA
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50
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Tian Z, Liu F, Li D, Fernie AR, Chen W. Strategies for structure elucidation of small molecules based on LC–MS/MS data from complex biological samples. Comput Struct Biotechnol J 2022; 20:5085-5097. [PMID: 36187931 PMCID: PMC9489805 DOI: 10.1016/j.csbj.2022.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/03/2022] [Accepted: 09/03/2022] [Indexed: 11/06/2022] Open
Abstract
LC–MS/MS is a major analytical platform for metabolomics, which has become a recent hotspot in the research fields of life and environmental sciences. By contrast, structure elucidation of small molecules based on LC–MS/MS data remains a major challenge in the chemical and biological interpretation of untargeted metabolomics datasets. In recent years, several strategies for structure elucidation using LC–MS/MS data from complex biological samples have been proposed, these strategies can be simply categorized into two types, one based on structure annotation of mass spectra and for the other on retention time prediction. These strategies have helped many scientists conduct research in metabolite-related fields and are indispensable for the development of future tools. Here, we summarized the characteristics of the current tools and strategies for structure elucidation of small molecules based on LC–MS/MS data, and further discussed the directions and perspectives to improve the power of the tools or strategies for structure elucidation.
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