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Miao Z, Li S, Song X, Ren F, Jin H. Discovery of perfluoroalkyl sulfonyl quaternary ammonium substances in the environment and their environmental behaviors. WATER RESEARCH 2024; 263:122189. [PMID: 39096813 DOI: 10.1016/j.watres.2024.122189] [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: 05/24/2024] [Revised: 07/15/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Abstract
A variety of per- and polyfluoroalkyl substances (PFASs) have been released into the environment via wastewater treatment plant (WWTP) effluent, with current target and nontarget analytical methods typically focusing on negatively ionized PFASs while largely overlooking positively ionized ones. In this study, five cationic PFASs, perfluoroalkyl sulfonyl quaternary ammonium substances (PFAQASs), were first identified in surface water impacted by the WWTP effluent, applying a metabolomics-based nontarget analysis method. Environmental behaviors of identified novel PFAQASs were further investigated. In surface water, sediment, and fish (Coilia mystus) samples collected from the Yangtze River, 8:3 PFAQA was consistently the predominant PFAQASs, with the mean concentrations of 90 ng/L (< LOD-558 ng/L), 92 ng/g dw (< LOD-421 ng/g dw), and 2.3 ng/g ww (< LOD-4.6 ng/g ww), respectively. This study highlights the necessity to discover other cationic PFASs in the environment. Among PFAQASs, 8:4 PFAQA (4.2, range 3.4 - 4.6) had the highest mean sediment-water partitioning coefficient (log Koc), followed by 8:3 PFAQA (3.9, 2.8 - 4.5) and 6:3 PFAQA (3.7, 3.3 - 4.1). The log Koc of PFAQASs showed a general increase trend with the increasing carbon chain length. Mean bioaccumulation factor (BAF) values of PFAQASs calculated in the collected fish from the Yangtze River ranged from 1.9 ± 0.32 (4:3 PFAQA) to 2.9 ± 0.34 (8:4 PFAQA). The mean BAF values of PFAQASs generally increased with the carbon chain length. Further studies are warranted to elucidate the environmental fate, potential toxicity, and human exposure implications for these identified novel PFASs.
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Affiliation(s)
- Zhijia Miao
- Hebei Center for Ecological and Environmental Geology Research, Hebei GEO University, Shijiazhuang, 050031, PR China; School of Water Resources and Environment, Hebei GEO University, Shijiazhuang, 050031, PR China
| | - Shuoyang Li
- Hebei Center for Ecological and Environmental Geology Research, Hebei GEO University, Shijiazhuang, 050031, PR China; School of Water Resources and Environment, Hebei GEO University, Shijiazhuang, 050031, PR China
| | - Xueqiang Song
- Hebei Center for Ecological and Environmental Geology Research, Hebei GEO University, Shijiazhuang, 050031, PR China; School of Water Resources and Environment, Hebei GEO University, Shijiazhuang, 050031, PR China
| | - Fangfang Ren
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310032, PR China
| | - Hangbiao Jin
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310032, PR China.
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Zheng T, Zhang Z, Yu Z, Wang H, Lyu X, Han C. Investigation on the mechanisms of scorpion venom in hepatocellular carcinoma model mice via untargeted metabolomics profiling. Int Immunopharmacol 2024; 138:112578. [PMID: 38959539 DOI: 10.1016/j.intimp.2024.112578] [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: 01/28/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
Metabolic reprogramming is frequently accompanied by hepatocellular carcinoma (HCC) progression. Disrupted metabolites act as potential biomarkers and drug therapeutic targets for HCC. Peptide extract of scorpion venom (PESV) induces cytotoxic anti-proliferative effects and apoptosis in tumors. However, the action mechanisms of PESV remain unknown. This study aimed to explore the serum metabolic profiles of tumor-bearing mouse model. We generated an orthotopic HCC xenograft mouse model by implanting H22 cells into the left hepatic lobe of male C57BL/6 mice. After surgery, the mice were assigned to two groups randomly: PESV (PESV-treated 40 mg/kg daily, i.g.; n = 6) and control (treated with the solvent equally for 14 d, n = 6) groups. Based on an untargeted metabolomics approach using ultra-high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry, differential metabolites were screened via univariate and multivariate data analyses. A total of 48 differential metabolites in negative ion mode and 63 in positive ion mode were identified in the serum samples. Furthermore, metabolic pathway analysis revealed that aminoacyl-tRNA biosynthesis, amino acid pathway, glutathione metabolism, protein transports, protein digestion and absorption, and cAMP signaling pathways play vital roles in PESV-induced inhibition of tumors. These findings highlight the distinct changes in the metabolic profiles of HCC-bearing mice after PESV treatment, suggesting the potential of the identified metabolic molecules as therapeutic targets for HCC.
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Affiliation(s)
- Tiancheng Zheng
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Zhaoxiang Zhang
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Zishang Yu
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Hengxiao Wang
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Xinxing Lyu
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China; Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.
| | - Chen Han
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China; Department of clinical research center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.
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Yin Z, Huang W, Li K, Fernie AR, Yan S. Advances in mass spectrometry imaging for plant metabolomics-Expanding the analytical toolbox. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2168-2180. [PMID: 38990529 DOI: 10.1111/tpj.16924] [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: 04/30/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 07/12/2024]
Abstract
Mass spectrometry imaging (MSI) has become increasingly popular in plant science due to its ability to characterize complex chemical, spatial, and temporal aspects of plant metabolism. Over the past decade, as the emerging and unique features of various MSI techniques have continued to support new discoveries in studies of plant metabolism closely associated with various aspects of plant function and physiology, spatial metabolomics based on MSI techniques has positioned it at the forefront of plant metabolic studies, providing the opportunity for far higher resolution than was previously available. Despite these efforts, profound challenges at the levels of spatial resolution, sensitivity, quantitative ability, chemical confidence, isomer discrimination, and spatial multi-omics integration, undoubtedly remain. In this Perspective, we provide a contemporary overview of the emergent MSI techniques widely used in the plant sciences, with particular emphasis on recent advances in methodological breakthroughs. Having established the detailed context of MSI, we outline both the golden opportunities and key challenges currently facing plant metabolomics, presenting our vision as to how the enormous potential of MSI technologies will contribute to progress in plant science in the coming years.
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Affiliation(s)
- Zhibin Yin
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- Institute of Advanced Science Facilities, Shenzhen, 518107, Guangdong, China
| | - Wenjie Huang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Kun Li
- Guangdong Key Laboratory of Crop Genetic Improvement, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
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Magny R, Lefrère B, Roulland E, Auzeil N, Farah S, Richeval C, Gish A, Vodovar D, Labat L, Houzé P. Feature-Based Molecular Network for New Psychoactive Substance Identification: The Case of Synthetic Cannabinoids in a Seized e-Liquid and Biological Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39186500 DOI: 10.1021/jasms.4c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
The comprehensive detection of new psychoactive substances, including synthetic cannabinoids along with their associated metabolites in biological samples, remains an analytical challenge. To detect these chemicals, untargeted approaches using appropriate bioinformatic tools such as molecular networks are useful, albeit it necessitates as a prerequisite the identification of a node of interest within the cluster. To illustrate it, we reported in this study the identification of synthetic cannabinoids and some of their metabolites in seized e-liquid, urine, and hair collected from an 18-year-old poisoned patient hospitalized for neuropsychiatric disorders. A comprehensive analysis of the seized e-liquid was performed using gas chromatography coupled with electron ionization mass spectrometry, 1H NMR, and liquid chromatography coupled with high resolution tandem mass spectrometry combined with data processing based on molecular network strategy. It allowed researchers to detect in the e-liquid known synthetic cannabinoids including MDMB-4en-PINACA, EDMB-4en-PINACA, MMB-4en-PINACA, and MDMB-5F-PICA. Compounds corresponding to transesterification of MDMB-4en-PINACA with pentenol, glycerol, and propylene glycol were also identified. Regarding the urine sample of the patient, metabolites of MDMB-4en-PINACA were detected, including MDMB-4en-PINACA butanoic acid, dihydroxylated MDMB-4en-PINACA butanoic acid, and glucurono-conjugated MDMB-4en-PINACA butanoic acid. Hair analysis of the patient allowed the detection of MDMB-4en-PINACA and MDMB-5F-PICA in the two investigated hair segments. This untargeted analysis of seized materials and biological samples demonstrates the utility of the molecular network strategy in identifying closely related compounds and metabolites of synthetic cannabinoids. It also emphasizes the need for developing strategies to anchor molecular networks, especially for new psychoactive substances.
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Affiliation(s)
- Romain Magny
- Laboratoire de Toxicologie, Fédération de Toxicologie, AH-HP, Hôpital Lariboisière, 75010 Paris, France
- INSERM UMRS-1144, Université Paris Cité, 75006 Paris, France
| | - Bertrand Lefrère
- Laboratoire de Toxicologie, Fédération de Toxicologie, AH-HP, Hôpital Lariboisière, 75010 Paris, France
| | | | - Nicolas Auzeil
- CNRS, CiTCoM, Université Paris Cité, 75006 Paris, France
| | - Soha Farah
- Laboratoire de Toxicologie, Fédération de Toxicologie, AH-HP, Hôpital Lariboisière, 75010 Paris, France
- INSERM UMRS-1144, Université Paris Cité, 75006 Paris, France
| | - Camille Richeval
- CHRU Lille, Unité Fonctionnelle de Toxicologie, 59000 Lille, France
- ULR 4483-IMPECS-IMPact de l'Environnement Chimique sur la Santé humaine, Université de Lille, 59000 Lille, France
| | - Alexandr Gish
- CHRU Lille, Unité Fonctionnelle de Toxicologie, 59000 Lille, France
- ULR 4483-IMPECS-IMPact de l'Environnement Chimique sur la Santé humaine, Université de Lille, 59000 Lille, France
| | - Dominique Vodovar
- INSERM UMRS-1144, Université Paris Cité, 75006 Paris, France
- Centre antipoison de Paris, Hôpital Fernand Widal, AP-HP, 75010 Paris, France
| | - Laurence Labat
- Laboratoire de Toxicologie, Fédération de Toxicologie, AH-HP, Hôpital Lariboisière, 75010 Paris, France
- INSERM UMRS-1144, Université Paris Cité, 75006 Paris, France
| | - Pascal Houzé
- Laboratoire de Toxicologie, Fédération de Toxicologie, AH-HP, Hôpital Lariboisière, 75010 Paris, France
- INSERM UMRS-1144, Université Paris Cité, 75006 Paris, France
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Liu X, Peng T, Xu M, Lin S, Hu B, Chu T, Liu B, Xu Y, Ding W, Li L, Cao C, Wu P. Spatial multi-omics: deciphering technological landscape of integration of multi-omics and its applications. J Hematol Oncol 2024; 17:72. [PMID: 39182134 PMCID: PMC11344930 DOI: 10.1186/s13045-024-01596-9] [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: 05/22/2024] [Accepted: 08/09/2024] [Indexed: 08/27/2024] Open
Abstract
The emergence of spatial multi-omics has helped address the limitations of single-cell sequencing, which often leads to the loss of spatial context among cell populations. Integrated analysis of the genome, transcriptome, proteome, metabolome, and epigenome has enhanced our understanding of cell biology and the molecular basis of human diseases. Moreover, this approach offers profound insights into the interactions between intracellular and intercellular molecular mechanisms involved in the development, physiology, and pathogenesis of human diseases. In this comprehensive review, we examine current advancements in multi-omics technologies, focusing on their evolution and refinement over the past decade, including improvements in throughput and resolution, modality integration, and accuracy. We also discuss the pivotal contributions of spatial multi-omics in revealing spatial heterogeneity, constructing detailed spatial atlases, deciphering spatial crosstalk in tumor immunology, and advancing translational research and cancer therapy through precise spatial mapping.
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Affiliation(s)
- Xiaojie Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ting Peng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Miaochun Xu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shitong Lin
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bai Hu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tian Chu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Binghan Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yashi Xu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wencheng Ding
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Li Li
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Canhui Cao
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Peng Wu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Gupta I, Badrzadeh F, Tsentalovich Y, Gaykalova DA. Connecting the dots: investigating the link between environmental, genetic, and epigenetic influences in metabolomic alterations in oral squamous cell carcinoma. J Exp Clin Cancer Res 2024; 43:239. [PMID: 39169426 PMCID: PMC11337877 DOI: 10.1186/s13046-024-03141-5] [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: 05/20/2024] [Accepted: 07/28/2024] [Indexed: 08/23/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) accounts for around 90% of all oral cancers and is the eighth most common cancer worldwide. Despite progress in managing OSCC, the overall prognosis remains poor, with a survival rate of around 50-60%, largely due to tumor size and recurrence. The challenges of late-stage diagnosis and limitations in current methods emphasize the urgent need for less invasive techniques to enable early detection and treatment, crucial for improving outcomes in this aggressive form of oral cancer. Research is currently aimed at unraveling tumor-specific metabolite profiles to identify candidate biomarkers as well as discover underlying pathways involved in the onset and progression of cancer that could be used as new targets for diagnostic and therapeutic purposes. Metabolomics is an advanced technological approach to identify metabolites in different sample types (biological fluids and tissues). Since OSCC promotes metabolic reprogramming influenced by a combination of genetic predisposition and environmental factors, including tobacco and alcohol consumption, and viral infections, the identification of distinct metabolites through screening may aid in the diagnosis of this condition. Moreover, studies have shown the use of metabolites during the catalysis of epigenetic modification, indicating a link between epigenetics and metabolism. In this review, we will focus on the link between environmental, genetic, and epigenetic influences in metabolomic alterations in OSCC. In addition, we will discuss therapeutic targets of tumor metabolism, which may prevent oral tumor growth, metastasis, and drug resistance.
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Affiliation(s)
- Ishita Gupta
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Fariba Badrzadeh
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Yuri Tsentalovich
- International tomography center CB RAS, Institutskaya str. 3a, Novosibirsk, 630090, Russia
| | - Daria A Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
- Institute for Genome Sciences, 670 West Baltimore Street, Baltimore, MD, 21201, USA.
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7
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Toral PG, Hervás G, Frutos P. INVITED REVIEW: Research on ruminal biohydrogenation: Achievements, gaps in knowledge, and future approaches from the perspective of dairy science. J Dairy Sci 2024:S0022-0302(24)01070-1. [PMID: 39154717 DOI: 10.3168/jds.2023-24591] [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: 12/21/2023] [Accepted: 07/18/2024] [Indexed: 08/20/2024]
Abstract
Scientific knowledge about ruminal biohydrogenation (BH) has improved greatly since this metabolic process was empirically confirmed in 1951. For years, BH had mostly been perceived as a process to be avoided to increase the post-ruminal flow of UFA from the diet. Two milestones changed this perception and stimulated great interest in BH intermediates themselves: In 1987, the in vitro anticarcinogenic properties of CLA were described, and in 2000, the inhibition of milk fat synthesis by trans-10 cis-12 CLA was confirmed. Since then, numerous BH metabolites have been described in small and large ruminants, and the major deviation from the common BH pathway (i.e., the trans-10 shift) has been reasonably well established. However, there are some less well-characterized alterations, and the comprehensive description of new BH intermediates (e.g., using isotopic tracers) has not been coupled with research on their biological effects. In this regard, the low quality of some published fatty acid profiles may also be limiting the advance of knowledge in BH. Furthermore, although BH seems to no longer be considered a metabolic niche inhabited by a few bacterial species with a highly specific metabolic capability, researchers have failed to elucidate which specific microbial groups are involved in the process and the basis for alterations in BH pathways (i.e., changes in microbial populations or their activity). Unraveling both issues may be beneficial for the description of new microbial enzymes involved in ruminal lipid metabolism that have industrial interest. From the perspective of diary science, other knowledge gaps that require additional research in the coming years are evaluation of the relationship between BH and feed efficiency and enteric methane emissions, as well as improving our understanding of how alterations in BH are involved in milk fat depression. Addressing these issues will have relevant practical implications in dairy science.
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Affiliation(s)
- P G Toral
- Instituto de Ganadería de Montaña (CSIC-University of León), Finca Marzanas s/n, 24346 Grulleros, León, Spain.
| | - G Hervás
- Instituto de Ganadería de Montaña (CSIC-University of León), Finca Marzanas s/n, 24346 Grulleros, León, Spain
| | - P Frutos
- Instituto de Ganadería de Montaña (CSIC-University of León), Finca Marzanas s/n, 24346 Grulleros, León, Spain
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8
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Fan J, Wang D, Kaneko S, Shimizu K. Lipidomic Profiling of Flammulina velutipes (Curtis) Singer (Agaricomycetes) through Ultra-Performance Liquid Chromatography Coupled with Quadrupole Time-of-Flight Mass Spectrometry: Examining Lipid Dynamics Changes during Fruiting Body Formation and Development. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18271-18282. [PMID: 39074379 DOI: 10.1021/acs.jafc.4c03863] [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: 07/31/2024]
Abstract
Flammulina velutipes (enokitake) is widely recognized for its nutritional and medicinal properties. Understanding the biochemical processes, such as lipid metabolism during fruiting body formation, is essential for enhancing mushroom cultivation and utilization. This study aimed at elucidating the dynamic lipidomic changes during seven growth stages of F. velutipes using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Our results revealed significant increases in ceramides along with the growth and a sharp decline in phosphatidylinositols from mycelial to primordial stages. Fatty acid esters of hydroxy fatty acids, recently discovered for their bioactivities, showed high intensities in the mycelial and primordial stages but decreased rapidly thereafter. These findings provide profound insights into the lipid profiles associated with mushroom morphology and development. This lipidomics study establishes a foundational understanding for future research in agricultural and food chemistry applications, potentially improving industrial production and quality control of F. velutipes.
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Affiliation(s)
- Jiaxin Fan
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Dongmei Wang
- Department of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Shuhei Kaneko
- Japan Tree Doctors Association, Tokyo 113-0021, Japan
| | - Kuniyoshi Shimizu
- Department of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
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9
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Chen J, Wang W, Hu X, Yue Y, Lu X, Wang C, Wei B, Zhang H, Wang H. Medium-sized peptides from microbial sources with potential for antibacterial drug development. Nat Prod Rep 2024; 41:1235-1263. [PMID: 38651516 DOI: 10.1039/d4np00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Covering: 1993 to the end of 2022As the rapid development of antibiotic resistance shrinks the number of clinically available antibiotics, there is an urgent need for novel options to fill the existing antibiotic pipeline. In recent years, antimicrobial peptides have attracted increased interest due to their impressive broad-spectrum antimicrobial activity and low probability of antibiotic resistance. However, macromolecular antimicrobial peptides of plant and animal origin face obstacles in antibiotic development because of their extremely short elimination half-life and poor chemical stability. Herein, we focus on medium-sized antibacterial peptides (MAPs) of microbial origin with molecular weights below 2000 Da. The low molecular weight is not sufficient to form complex protein conformations and is also associated to a better chemical stability and easier modifications. Microbially-produced peptides are often composed of a variety of non-protein amino acids and terminal modifications, which contribute to improving the elimination half-life of compounds. Therefore, MAPs have great potential for drug discovery and are likely to become key players in the development of next-generation antibiotics. In this review, we provide a detailed exploration of the modes of action demonstrated by 45 MAPs and offer a concise summary of the structure-activity relationships observed in these MAPs.
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Affiliation(s)
- Jianwei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xubin Hu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yujie Yue
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xingyue Lu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chenjie Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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10
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Peter EK, Jaeger C, Lisec J, Peters RS, Mourot R, Rossel PE, Tranter M, Anesio AM, Benning LG. Endometabolic profiling of pigmented glacier ice algae: the impact of sample processing. Metabolomics 2024; 20:98. [PMID: 39123092 PMCID: PMC11315761 DOI: 10.1007/s11306-024-02147-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/24/2024] [Indexed: 08/12/2024]
Abstract
INTRODUCTION Glacier ice algae, mainly Ancylonema alaskanum and Ancylonema nordenskiöldi, bloom on Greenland Ice Sheet bare ice surfaces. They significantly decrease surface albedo due to their purple-brown pigmentation, thus increasing melt. Little is known about their metabolic adaptation and factors controlling algal growth dynamics and pigment formation. A challenge in obtaining such data is the necessity of melting samples, which delays preservation and introduces bias to metabolomic analysis. There is a need to evaluate the physiological response of algae to melting and establish consistent sample processing strategies for metabolomics of ice microbial communities. OBJECTIVES To address the impact of sample melting procedure on metabolic characterization and establish a processing and analytical workflow for endometabolic profiling of glacier ice algae. METHODS We employed untargeted, high-resolution mass spectrometry and tested the effect of sample melt temperature (10, 15, 20 °C) and processing delay (up to 49 h) on the metabolome and lipidome, and complemented this approach with cell counts (FlowCam), photophysiological analysis (PAM) and diversity characterization. RESULTS AND CONCLUSION We putatively identified 804 metabolites, with glycerolipids, glycerophospholipids and fatty acyls being the most prominent superclasses (> 50% of identified metabolites). Among the polar metabolome, carbohydrates and amino acid-derivatives were the most abundant. We show that 8% of the metabolome is affected by melt duration, with a pronounced decrease in betaine membrane lipids and pigment precursors, and an increase in phospholipids. Controlled fast melting at 10 °C resulted in the highest consistency, and is our recommendation for future supraglacial metabolomics studies.
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Affiliation(s)
- Elisa K Peter
- German Research Centre for Geosciences - GFZ, 14473, Potsdam, Germany.
- Department of Earth Sciences, Freie Universität Berlin, 12249, Berlin, Germany.
| | - Carsten Jaeger
- Bundesanstalt für Materialforschung und -prüfung (BAM), 12489, Berlin, Germany
| | - Jan Lisec
- Bundesanstalt für Materialforschung und -prüfung (BAM), 12489, Berlin, Germany
| | - R Sven Peters
- German Research Centre for Geosciences - GFZ, 14473, Potsdam, Germany
| | - Rey Mourot
- German Research Centre for Geosciences - GFZ, 14473, Potsdam, Germany
- Department of Earth Sciences, Freie Universität Berlin, 12249, Berlin, Germany
| | - Pamela E Rossel
- German Research Centre for Geosciences - GFZ, 14473, Potsdam, Germany
| | - Martyn Tranter
- Department of Environmental Science, Aarhus University, 4000, Roskilde, Denmark
| | - Alexandre M Anesio
- Department of Environmental Science, Aarhus University, 4000, Roskilde, Denmark
| | - Liane G Benning
- German Research Centre for Geosciences - GFZ, 14473, Potsdam, Germany.
- Department of Earth Sciences, Freie Universität Berlin, 12249, Berlin, Germany.
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11
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Zhu F, Ahchige MW, Wen W, Cheng Y, Alseekh S, Fernie AR. The natural variance of Arabidopsis secondary metabolism on extended darkness. Sci Data 2024; 11:841. [PMID: 39097666 PMCID: PMC11297995 DOI: 10.1038/s41597-024-03694-2] [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: 04/03/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024] Open
Abstract
In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0-and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the Zenodo database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.
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Affiliation(s)
- Feng Zhu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, National R&D Center for Citrus Preservation, Huazhong Agricultural University, 430070, Wuhan, China
- Hubei Hongshan Laboratory, 430070, Wuhan, China
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Micha Wijesingha Ahchige
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Weiwei Wen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, National R&D Center for Citrus Preservation, Huazhong Agricultural University, 430070, Wuhan, China
- Hubei Hongshan Laboratory, 430070, Wuhan, China
| | - Yunjiang Cheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, National R&D Center for Citrus Preservation, Huazhong Agricultural University, 430070, Wuhan, China
- Hubei Hongshan Laboratory, 430070, Wuhan, China
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
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12
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Shi C, Cheng L, Yu Y, Chen S, Dai Y, Yang J, Zhang H, Chen J, Geng N. Multi-omics integration analysis: Tools and applications in environmental toxicology. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 360:124675. [PMID: 39103035 DOI: 10.1016/j.envpol.2024.124675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/08/2024] [Accepted: 08/03/2024] [Indexed: 08/07/2024]
Abstract
Nowadays, traditional single-omics study is not enough to explain the causality between molecular alterations and toxicity endpoints for environmental pollutants. With the development of high-throughput sequencing technology and high-resolution mass spectrometry technology, the integrative analysis of multi-omics has become an efficient strategy to understand holistic biological mechanisms and to uncover the regulation network in specific biological processes. This review summarized sample preparation methods, integration analysis tools and the application of multi-omics integration analyses in environmental toxicology field. Currently, omics methods have been widely applied being as the sensitivity of early biological response, especially for low-dose and long-term exposure to environmental pollutants. Integrative omics can reveal the overall changes of genes, proteins, and/or metabolites in the cells, tissues or organisms, which provide new insights into revealing the overall toxicity effects, screening the toxic targets, and exploring the underlying molecular mechanism of pollutants.
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Affiliation(s)
- Chengcheng Shi
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Lin Cheng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Ying Yu
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Shuangshuang Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Yubing Dai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jiajia Yang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; College of Materials Science and Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Haijun Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jiping Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Ningbo Geng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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13
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Yu W, Wang K, He Y, Shang Y, Hu X, Deng X, Zhao L, Ma X, Mu X, Li R, Gao Z. The potential role of lung microbiota and lauroylcarnitine in T-cell activation associated with checkpoint inhibitor pneumonitis. EBioMedicine 2024; 106:105267. [PMID: 39098109 PMCID: PMC11334825 DOI: 10.1016/j.ebiom.2024.105267] [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: 03/19/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/06/2024] Open
Abstract
BACKGROUND Checkpoint inhibitor pneumonitis (CIP) is a potentially fatal adverse event characterized by new pulmonary infiltrates in cancer patients receiving immune checkpoint inhibitor therapy. This study aims to explore the interplay between lung microbiota, dysregulated metabolites, and host immunity in CIP. METHODS We recruited thirteen hospitalized CIP patients, eleven idiopathic pulmonary fibrosis (IPF) patients, and ten new-onset non-small cell lung cancer patients. Bronchoalveolar lavage fluid samples were collected for 16S rRNA gene sequencing. The percentages of immune cells were determined using manual counting and flow cytometry. Interactions among microbiota, metabolites, and lymphocytes were analyzed using cultured mouse splenocytes and human T cells. FINDINGS Proteobacteria emerged as the dominant phylum, notably abundant in both the CIP and IPF groups. Vibrio, Halomonas, Mangrovibacter, and Salinivibrio were the predominant microbiota because of their discriminative abundance patterns. Vibrio (r = 0.72, P-adj = 0.007) and Halomonas (r = 0.65, P-adj = 0.023) demonstrated strong correlations with lymphocytes. Vibrio metschnikovii and Mangrovibacter plantisponsors were more abundant in the CIP group than in the IPF group. Lauroylcarnitine, a key intermediary metabolite co-occurring with the predominant microbiota, exhibited a potent effect on cytokine secretion by mouse and human T cells, notably enhancing IFN-γ and TNF-α production from CD4 and CD8 cells in vitro. INTERPRETATION Lauroylcarnitine, co-occurring with the predominant lung microbiota in CIP, could activate T cells in vitro. These findings suggest potential involvement of lung microbiota and acylcarnitine metabolism dysregulation in the pathogenesis of CIP. FUNDING This work was supported by Peking University People's Hospital Scientific Research Development Funds (RDJ2022-15) and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine).
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Affiliation(s)
- Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Keqiang Wang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Yukun He
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Ying Shang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Xiaoyi Hu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Xinwei Deng
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Lili Zhao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Xinqian Ma
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Xinlin Mu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Ran Li
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China.
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China.
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14
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Gutschker S, Ruescher D, Rabbi IY, Rosado-Souza L, Pommerrenig B, Pauly M, Robertz S, van Doorn AM, Schlereth A, Neuhaus HE, Fernie AR, Reinert S, Sonnewald U, Zierer W. Carbon usage in yellow-fleshed Manihot esculenta storage roots shifts from starch biosynthesis to cell wall and raffinose biosynthesis via the myo-inositol pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2045-2062. [PMID: 38961707 DOI: 10.1111/tpj.16909] [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: 11/29/2023] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/05/2024]
Abstract
Cassava is a crucial staple crop for smallholder farmers in tropical Asia and Sub-Saharan Africa. Although high yield remains the top priority for farmers, the significance of nutritional values has increased in cassava breeding programs. A notable negative correlation between provitamin A and starch accumulation poses a significant challenge for breeding efforts. The negative correlation between starch and carotenoid levels in conventional and genetically modified cassava plants implies the absence of a direct genomic connection between the two traits. The competition among various carbon pathways seems to account for this relationship. In this study, we conducted a thorough analysis of 49 African cassava genotypes with varying levels of starch and provitamin A. Our goal was to identify factors contributing to differential starch accumulation. Considering carotenoid levels as a confounding factor in starch production, we found that yellow- and white-fleshed storage roots did not differ significantly in most measured components of starch or de novo fatty acid biosynthesis. However, genes and metabolites associated with myo-inositol synthesis and cell wall polymer production were substantially enriched in high provitamin A genotypes. These results indicate that yellow-fleshed cultivars, in comparison to their white-fleshed counterparts, direct more carbon toward the synthesis of raffinose and cell wall components. This finding is underlined by a significant rise in cell wall components measured within the 20 most contrasting genotypes for carotenoid levels. Our findings enhance the comprehension of the biosynthesis of starch and carotenoids in the storage roots of cassava.
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Affiliation(s)
- Sindy Gutschker
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
| | - David Ruescher
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
| | - Ismail Y Rabbi
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | | | - Markus Pauly
- Heinrich-Heine-University, Institute of Plant Cell Biology and Biotechnology, Düsseldorf, Germany
| | - Stefan Robertz
- Heinrich-Heine-University, Institute of Plant Cell Biology and Biotechnology, Düsseldorf, Germany
| | - Anna M van Doorn
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Armin Schlereth
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Stephan Reinert
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
| | - Uwe Sonnewald
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
| | - Wolfgang Zierer
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
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15
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Zhang Y, Gao L, Ai Q, Liu Y, Qiao L, Cheng X, Li J, Zhang L, Lyu B, Zheng M, Wu Y. Screening for compounds with bioaccumulation potential in breast milk using their retention behavior in two-dimensional gas chromatography. ENVIRONMENT INTERNATIONAL 2024; 190:108911. [PMID: 39067189 DOI: 10.1016/j.envint.2024.108911] [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: 03/20/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Discovery of emerging pollutants in breast milk will be helpful for understanding the hazards to human health. However, it is difficult to identify key compounds among thousands present in complex samples. In this study, a method for screening compounds with bioaccumulation potential was developed. The method can decrease the number of compounds needing structural identification because the partitioning properties of bioaccumulative compounds can be mapped onto GC×GC chromatograms through their retention behaviors. Twenty pooled samples from seven provinces in China were analyzed. 1,286 compounds with bioaccumulation potential were selected from over 3,000 compounds. Sixty-two compounds, including aromatic compounds, phthalates, and phenolics etc., were identified with a high level of confidence and then quantified. Among them, twenty-seven compounds were found for the first time in breast milk. Three phthalate plasticizers and two phenolic antioxidants were found in significantly higher concentrations than other compounds. A toxicological priority index approach was applied to prioritize the compounds considering their concentrations, detection frequencies and eight toxic effects. The prioritization indicated that 13 compounds, including bis(2-ethylhexyl) phthalate, dibutyl phthalate, 1,3-di-tert-butylbenzene, phenanthrene, 2,6-di-tert-butyl-1,4-benzoquinone, 2,4-di-tert-butylphenol, and others, showed higher health risks. Meanwhile, some compounds with high risk for a particular toxic effect, such as benzothiazole and geranylacetone, were still noteworthy. This study is important for assessing the risks of human exposure to organic compounds.
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Affiliation(s)
- Yingxin Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lirong Gao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310000, China.
| | - Qiaofeng Ai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Qiao
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Xin Cheng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingguang Li
- Research Unit of Food Safety, Chinese Academy of Medical Sciences (No. 2019RU014); NHC Key Lab of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment (CFSA), Beijing 100022, China
| | - Lei Zhang
- Research Unit of Food Safety, Chinese Academy of Medical Sciences (No. 2019RU014); NHC Key Lab of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment (CFSA), Beijing 100022, China.
| | - Bing Lyu
- Research Unit of Food Safety, Chinese Academy of Medical Sciences (No. 2019RU014); NHC Key Lab of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment (CFSA), Beijing 100022, China
| | - Minghui Zheng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310000, China
| | - Yongning Wu
- Research Unit of Food Safety, Chinese Academy of Medical Sciences (No. 2019RU014); NHC Key Lab of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment (CFSA), Beijing 100022, China
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16
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Tiozon RJN, Alseekh S, Fernie AR, Bonto AP, Yu J, Buenafe RJQ, Sreenivasulu N. Comprehensive lipidomic insights of differentially accumulating lipids in large pigmented rice sprout collection and the changes in the starch composition upon germination. Food Chem 2024; 460:140677. [PMID: 39102764 DOI: 10.1016/j.foodchem.2024.140677] [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: 06/12/2024] [Revised: 07/14/2024] [Accepted: 07/25/2024] [Indexed: 08/07/2024]
Abstract
Germination represents a vital bioprocess characterized by numerous biochemical transformations that significantly influence the nutritional characteristics of rice. The mobilization of starch and lipids during germination plays a pivotal role in altering the dietary profile of rice, thus potentially addressing the nutritional requirements of populations heavily reliant on rice as a staple food. To explore this potential, a comprehensive analysis encompassing lipidomics and starch composition was conducted on a diverse collection of pigmented rice sprouts. High-resolution mass spectrometry unveiled substantial shifts in the lipidome of pigmented rice sprouts, showcasing a notable enrichment in carotenoids and unsaturated triglycerides, with potential human health benefits. Notably, purple rice sprouts exhibited heightened levels of alpha- and beta-carotene. Analysis of starch composition revealed slight changes in amylose and amylopectin content; however, a consistent increase in digestible carbohydrates was observed across all rice varieties. Germination also led to a reduction in resistant starch content, with purple rice sprouts demonstrating a pronounced two-fold decrease (p < 0.05). These changes were corroborated by a 1.33% decrease in gelatinization enthalpy and a 0.40% reduction in the melting of the amylose-lipid complex. Furthermore, pasting property analysis indicated a substantial 42% decrease in the complexation index post-germination. We posit that the insights garnered from this study hold significant promise for the development of novel products enriched with health-promoting lipids and characterized by unique flour properties.
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Affiliation(s)
- Rhowell Jr N Tiozon
- Consumer-driven Grain Quality and Nutrition Center, Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños 4030, Philippines; Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
| | - Aldrin P Bonto
- Department of Chemistry, College of Science, De La Salle University, Manila, Philippines.
| | - Jazlyn Yu
- Consumer-driven Grain Quality and Nutrition Center, Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños 4030, Philippines
| | - Reuben James Q Buenafe
- Consumer-driven Grain Quality and Nutrition Center, Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños 4030, Philippines.
| | - Nese Sreenivasulu
- Consumer-driven Grain Quality and Nutrition Center, Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños 4030, Philippines.
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17
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Zhang Y, Wang G, Shao Y, Zheng P, Guo C, Liu Z, Shen L, Liu Z, Ding J, Zhang H. Simultaneous determination of 18 steroids in the hypothalamic pituitary gonadal axis based on UPLC-MS/MS with multimode ionization. Analyst 2024. [PMID: 39073090 DOI: 10.1039/d4an00524d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
To objectively quantify changes in steroid hormones in organisms caused by adverse environmental loads, we developed a simple and sensitive UPLC-MS/MS (ultra-performance liquid chromatography triple quadrupole mass spectrometry) method for the simultaneous determination of 18 steroid hormones on the HPG axis. This analytical method was based on liquid extraction and a multimode electrospray and atmospheric pressure chemical ionization (ESCi) source, which was optimized by mass spectrometry, liquid phase and pretreatment for the quantification of cholesterol (CH), aldosterone (A), cortisone (E), hydrocortisone (F), 21-deoxycortisol (21-DF), corticosterone (B), 11-deoxycortisol (11-DF), androstenedione (A2), estradiol (E2), estrone (E1), 2-methoxyestradiol (2-MeE2), 21-hydroxyprogesterone (21-OHP), 17-α hydroxyprogesterone (17α-OHP), testosterone (T), dehydroepiandrosterone (DHEA), progesterone (P4), dihydrotestosterone (DHT), and pregnenolone (P5). The method exhibits linearity in the analyte-concentration range 0.03-1000 μg mL-1 (r2 > 0.99), the spiked recoveries for the concentration range tested are 76.22-113.66%, and the relevant parameters of precision are 7.52-1.14%. Compared to other methods, this new method not only uses a small amount of serum (only 100 μL), but also permits the analysis of the challenging steroid, cholesterol. Furthermore, the method was successfully applied to the determination of steroids in Mus musculus, Carassius auratus, Rana catesbeiana Shaw, and Rana nigromaculata serum samples from randomly selected individuals. Therefore, this method is efficient and a very useful tool for assessing changes in steroid hormones.
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Affiliation(s)
- Yinan Zhang
- Hangzhou Normal University, 311121, Hangzhou, Zhejiang, China.
| | - Guanghui Wang
- Hangzhou Normal University, 311121, Hangzhou, Zhejiang, China.
| | - Yongjian Shao
- Hangzhou Normal University, 311121, Hangzhou, Zhejiang, China.
| | - Pei Zheng
- Daishan Branch of Ecological Environment Bureau, 316299, Zhoushan, Zhejiang, China
| | - Chunyan Guo
- Zhejiang Radiation Environment Monitoring Station (Technical Center for Radiation Environment Monitoring, Ministry of Ecology and Environment), 310012, Hangzhou, Zhejiang, China
| | - Zhiqun Liu
- Hangzhou Normal University, 311121, Hangzhou, Zhejiang, China.
| | - Lilai Shen
- Hangzhou Normal University, 311121, Hangzhou, Zhejiang, China.
| | - Zhiquan Liu
- Hangzhou Normal University, 311121, Hangzhou, Zhejiang, China.
| | - Jiafeng Ding
- Hangzhou Normal University, 311121, Hangzhou, Zhejiang, China.
| | - Hangjun Zhang
- Hangzhou Normal University, 311121, Hangzhou, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Urban Wetlands and Regional Change, 311121, Hangzhou, Zhejiang, China
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18
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Albores-Méndez EM, Carrasco-Vargas H, Alaniz Monreal S, Mayen Quinto RD, López García ED, Gutierrez Salmean G, Medina-Quero K, Vargas-Hernández MA, Ferreira Batista CV, López-Hernández Y, Winkler R. An intense 60-day weight-loss course leads to an 18 kg body weight reduction and metabolic reprogramming of soldiers with obesity. PeerJ 2024; 12:e17757. [PMID: 39076775 PMCID: PMC11285361 DOI: 10.7717/peerj.17757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/25/2024] [Indexed: 07/31/2024] Open
Abstract
Soldiers of the Mexican Army with obesity were subjected to an intense 60-day weight-loss course consisting of a controlled diet, daily physical training, and psychological sessions. The nutritional treatment followed the European Society of Cardiology (ESC) recommendations, incorporating elements of the traditional milpa diet in the nutritional intervention. The total energy intake was reduced by 200 kcal every 20 days, starting with 1,800 kcal and ending with 1,400 kcal daily. On average, the participants reduced their body weight by 18 kg. We employed an innovative approach to monitor the progress of the twelve soldiers who completed the entire program. We compared the untargeted metabolomics profiles of their urine samples, taken before and after the course. The data obtained through liquid chromatography and high-resolution mass spectrometry (LC-MS) provided insightful results. Classification models perfectly separated the profiles pre and post-course, indicating a significant reprogramming of the participants' metabolism. The changes were observed in the C1-, vitamin, amino acid, and energy metabolism pathways, primarily affecting the liver, biliary system, and mitochondria. This study not only demonstrates the potential of rapid weight loss and metabolic pathway modification but also introduces a non-invasive method for monitoring the metabolic state of individuals through urine mass spectrometry data.
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Affiliation(s)
- Exsal M. Albores-Méndez
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | - Humberto Carrasco-Vargas
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | | | - Rodolfo David Mayen Quinto
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | - Ernesto Diderot López García
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | | | - Karen Medina-Quero
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | - Marco A. Vargas-Hernández
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | - Cesar Vicente Ferreira Batista
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | - Yamilé López-Hernández
- Laboratorio de Proteómica y Metabolómica de la Unidad de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
| | - Robert Winkler
- Unidad de Genómica Avanzada, Cinvestav, Irapuato, Mexico
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Cowled MS, Phippen CBW, Kromphardt KJK, Clemmensen SE, Frandsen RJN, Frisvad JC, Larsen TO. Unveiling the fungal diversity and associated secondary metabolism on black apples. Appl Environ Microbiol 2024; 90:e0034224. [PMID: 38899884 PMCID: PMC11267942 DOI: 10.1128/aem.00342-24] [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: 03/02/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Black apples are the result of late-stage microbial decomposition after falling to the ground. This phenomenon is highly comparable from year to year, with the filamentous fungus Monilinia fructigena most commonly being the first invader, followed by Penicillium expansum. Motivated by the fact that only little chemistry has been reported from apple microbiomes, we set out to investigate the chemical diversity and potential ecological roles of secondary metabolites (SMs) in a total of 38 black apples. Metabolomics analyses were conducted on either whole apples or small excisions of fungal biomass derived from black apples. Annotation of fungal SMs in black apple extracts was aided by the cultivation of 15 recently isolated fungal strains on 9 different substrates in a One Strain Many Compounds (OSMAC) approach, leading to the identification of 3,319 unique chemical features. Only 6.4% were attributable to known compounds based on analysis of high-performance liquid chromatography-high-resolution mass spectrometry (HPLC-HRMS/MS) data using spectral library matching tools. Of the 1,606 features detected in the black apple extracts, 32% could be assigned as fungal-derived, due to their presence in the OSMAC-based training data set. Notably, the detection of several antifungal compounds indicates the importance of such compounds for the invasion of and control of other microbial competitors on apples. In conclusion, the diversity and abundance of microbial SMs on black apples were found to be much higher than that typically observed for other environmental microbiomes. Detection of SMs known to be produced by the six fungal species tested also highlights a succession of fungal growth following the initial invader M. fructigena.IMPORTANCEMicrobial secondary metabolites constitute a significant reservoir of biologically potent and clinically valuable chemical scaffolds. However, their usefulness is hampered by rapidly developing resistance, resulting in reduced profitability of such research endeavors. Hence, the ecological role of such microbial secondary metabolites must be considered to understand how best to utilize such compounds as chemotherapeutics. Here, we explore an under-investigated environmental microbiome in the case of black apples; a veritable "low-hanging fruit," with relatively high abundances and diversity of microbially produced secondary metabolites. Using both a targeted and untargeted metabolomics approach, the interplay between metabolites, other microbes, and the apple host itself was investigated. This study highlights the surprisingly low incidence of known secondary metabolites in such a system, highlighting the need to study the functionality of secondary metabolites in microbial interactions and complex microbiomes.
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Affiliation(s)
- Michael S. Cowled
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Christopher B. W. Phippen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kresten J. K. Kromphardt
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sidsel E. Clemmensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Rasmus J. N. Frandsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jens C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Thomas O. Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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20
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Mai Z, Han Y, Liang D, Mai F, Zheng H, Li P, Li Y, Ma C, Chen Y, Li W, Zhang S, Feng Y, Chen X, Wang Y. Gut-derived metabolite 3-methylxanthine enhances cisplatin-induced apoptosis via dopamine receptor D1 in a mouse model of ovarian cancer. mSystems 2024; 9:e0130123. [PMID: 38899930 PMCID: PMC11264688 DOI: 10.1128/msystems.01301-23] [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: 12/06/2023] [Accepted: 04/30/2024] [Indexed: 06/21/2024] Open
Abstract
Platinum-based chemotherapy failure represents a significant challenge in the management of ovarian cancer (OC) and contributes to disease recurrence and poor prognosis. Recent studies have shed light on the involvement of the gut microbiota in modulating anticancer treatments. However, the precise underlying mechanisms, by which gut microbiota regulates the response to platinum-based therapy, remain unclear. Here, we investigated the role of gut microbiota on the anticancer response of cisplatin and its underlying mechanisms. Our results demonstrate a substantial improvement in the anticancer efficacy of cisplatin following antibiotic-induced perturbation of the gut microbiota in OC-bearing mice. 16S rRNA sequencing showed a pronounced alteration in the composition of the gut microbiome in the cecum contents following exposure to cisplatin. Through metabolomic analysis, we identified distinct metabolic profiles in the antibiotic-treated group, with a notable enrichment of the gut-derived metabolite 3-methylxanthine in antibiotic-treated mice. Next, we employed a strategy combining transcriptome analysis and chemical-protein interaction network databases. We identified metabolites that shared structural similarity with 3-methylxanthine, which interacted with genes enriched in cancer-related pathways. It is identified that 3-methylxanthinesignificantly enhances the effectiveness of cisplatin by promoting apoptosis both in vivo and in vitro. Importantly, through integrative multiomics analyses, we elucidated the mechanistic basis of this enhanced apoptosis, revealing a dopamine receptor D1-dependent pathway mediated by 3-methylxanthine. This study elucidated the mechanism by which gut-derived metabolite 3-methylxanthine mediated cisplatin-induced apoptosis. Our findings highlight the potential translational significance of 3-methylxanthine as a promising adjuvant in conjunction with cisplatin, aiming to improve treatment outcomes for OC patients.IMPORTANCEThe precise correlation between the gut microbiota and the anticancer effect of cisplatin in OC remains inadequately understood. Our investigation has revealed that manipulation of the gut microbiota via the administration of antibiotics amplifies the efficacy of cisplatin through the facilitation of apoptosis in OC-bearing mice. Metabolomic analysis has demonstrated that the cecum content from antibiotic-treated mice exhibits an increase in the levels of 3-methylxanthine, which has been shown to potentially enhance the therapeutic effectiveness of cisplatin by an integrated multiomic analysis. This enhancement appears to be attributable to the promotion of cisplatin-induced apoptosis, with 3-methylxanthine potentially exerting its influence via the dopamine receptor D1-dependent pathway. These findings significantly contribute to our comprehension of the impact of the gut microbiota on the anticancer therapy in OC. Notably, the involvement of 3-methylxanthine suggests its prospective utility as a supplementary component for augmenting treatment outcomes in patients afflicted with ovarian cancer.
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Affiliation(s)
- Zhensheng Mai
- Obstetrics and Gynecology Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Department of Obstetrics & Gynecology, First people’s hospital of Foshan, Foshan, China
| | - Yubin Han
- Department of Obstetrics & Gynecology, First people’s hospital of Foshan, Foshan, China
| | - Dong Liang
- Department of Obstetrics & Gynecology, First people’s hospital of Foshan, Foshan, China
| | - Feihong Mai
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Huimin Zheng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang Province, China
| | - Pan Li
- Microbiome Research Centre, St. George and Sutherland Clinical School, UNSW, Sydney, New South Wales, Australia
| | - Yuan Li
- Department of Obstetrics & Gynecology, First people’s hospital of Foshan, Foshan, China
| | - Cong Ma
- Department of Obstetrics & Gynecology, First people’s hospital of Foshan, Foshan, China
| | - Yunqing Chen
- Department of Obstetrics & Gynecology, First people’s hospital of Foshan, Foshan, China
| | - Weifeng Li
- Department of Obstetrics & Gynecology, First people’s hospital of Foshan, Foshan, China
| | - Siyou Zhang
- Department of Obstetrics & Gynecology, First people’s hospital of Foshan, Foshan, China
| | - Yinglin Feng
- Department of Obstetrics, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, China
| | - Xia Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang Province, China
| | - Yifeng Wang
- Obstetrics and Gynecology Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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21
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Day F, O'Sullivan J, Ramzan F, Pook C. Polar metabolomics using trichloroacetic acid extraction and porous graphitic carbon stationary phase. Metabolomics 2024; 20:77. [PMID: 39014104 PMCID: PMC11252196 DOI: 10.1007/s11306-024-02146-7] [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: 12/21/2023] [Accepted: 06/24/2024] [Indexed: 07/18/2024]
Abstract
INTRODUCTION Accurately identifying and quantifying polar metabolites using untargeted metabolomics has proven challenging in comparison to mid to non-polar metabolites. Hydrophilic interaction chromatography and gas chromatography-mass spectrometry are predominantly used to target polar metabolites. OBJECTIVES This study aims to demonstrate a simple one-step extraction combined with liquid chromatography-mass spectrometry (LC-MS) that reliably retains polar metabolites. METHODS The method involves a MilliQ + 10% trichloroacetic acid extraction from 6 healthy individuals serum, combined with porous graphitic carbon liquid chromatography-mass spectrometry (LC-MS). The coefficient of variation (CV) assessed retention reliability of polar metabolites with logP as low as - 9. QreSS (Quantification, Retention, and System Suitability) internal standards determined the method's consistency and recovery efficiency. RESULTS The method demonstrated reliable retention (CV < 0.30) of polar metabolites within a logP range of - 9.1 to 5.6. QreSS internal standards confirmed consistent performance (CV < 0.16) and effective recovery (70-130%) of polar to mid-polar metabolites. Quality control dilution series demonstrated that ~ 80% of annotated metabolites could be accurately quantified (Pearson's correlation coefficient > 0.80) within their concentration range. Repeatability was demonstrated through clustering of repeated extractions from a single sample. CONCLUSION This LC-MS method is better suited to covering the polar segment of the metabolome than current methods, offering a reliable and efficient approach for accurate quantification of polar metabolites in untargeted metabolomics.
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Affiliation(s)
- Francesca Day
- Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Justin O'Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- Australian Parkinson's Mission, Garvan Institute of Medical Research, 384 Victoria Street, Sydney, Darlinghurst, NSW, 2010, Australia
- A*STAR Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Farha Ramzan
- Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Chris Pook
- Liggins Institute, The University of Auckland, Auckland, New Zealand.
- School of Chemical Sciences, University of Auckland, 23 Symonds St., Auckland, 1010, New Zealand.
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22
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Vich Vila A, Zhang J, Liu M, Faber KN, Weersma RK. Untargeted faecal metabolomics for the discovery of biomarkers and treatment targets for inflammatory bowel diseases. Gut 2024:gutjnl-2023-329969. [PMID: 39002973 DOI: 10.1136/gutjnl-2023-329969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 06/23/2024] [Indexed: 07/15/2024]
Abstract
The gut microbiome has been recognised as a key component in the pathogenesis of inflammatory bowel diseases (IBD), and the wide range of metabolites produced by gut bacteria are an important mechanism by which the human microbiome interacts with host immunity or host metabolism. High-throughput metabolomic profiling and novel computational approaches now allow for comprehensive assessment of thousands of metabolites in diverse biomaterials, including faecal samples. Several groups of metabolites, including short-chain fatty acids, tryptophan metabolites and bile acids, have been associated with IBD. In this Recent Advances article, we describe the contribution of metabolomics research to the field of IBD, with a focus on faecal metabolomics. We discuss the latest findings on the significance of these metabolites for IBD prognosis and therapeutic interventions and offer insights into the future directions of metabolomics research.
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Affiliation(s)
- Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Jingwan Zhang
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong (SAR), People's Republic of China
- Microbiota I-Center (MagIC), Hong Kong (SAR), People's Republic of China
| | - Moting Liu
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
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23
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House RRJ, Soper-Hopper MT, Vincent MP, Ellis AE, Capan CD, Madaj ZB, Wolfrum E, Isaguirre CN, Castello CD, Johnson AB, Escobar Galvis ML, Williams KS, Lee H, Sheldon RD. A diverse proteome is present and enzymatically active in metabolite extracts. Nat Commun 2024; 15:5796. [PMID: 38987243 PMCID: PMC11237058 DOI: 10.1038/s41467-024-50128-z] [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: 01/26/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024] Open
Abstract
Metabolite extraction is the critical first-step in metabolomics experiments, where it is generally regarded to inactivate and remove proteins. Here, arising from efforts to improve extraction conditions for polar metabolomics, we discover a proteomic landscape of over 1000 proteins within metabolite extracts. This is a ubiquitous feature across several common extraction and sample types. By combining post-resuspension stable isotope addition and enzyme inhibitors, we demonstrate in-extract metabolite interconversions due to residual transaminase activity. We extend these findings with untargeted metabolomics where we observe extensive protein-mediated metabolite changes, including in-extract formation of glutamate dipeptide and depletion of total glutathione. Finally, we present a simple extraction workflow that integrates 3 kDa filtration for protein removal as a superior method for polar metabolomics. In this work, we uncover a previously unrecognized, protein-mediated source of observer effects in metabolomics experiments with broad-reaching implications across all research fields using metabolomics and molecular metabolism.
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Affiliation(s)
- Rachel Rae J House
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, USA
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | | | | | - Abigail E Ellis
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Colt D Capan
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Zachary B Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Emily Wolfrum
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | | | | | - Amy B Johnson
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Martha L Escobar Galvis
- Office of the Cores, Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
| | - Kelsey S Williams
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Hyoungjoo Lee
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Ryan D Sheldon
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA.
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24
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Varzieva VG, Mesonzhnik NV, Ilgisonis IS, Belenkov YN, Kozhevnikova MV, Appolonova SA. Metabolomic biomarkers of multiple myeloma: A systematic review. Biochim Biophys Acta Rev Cancer 2024; 1879:189151. [PMID: 38986721 DOI: 10.1016/j.bbcan.2024.189151] [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: 11/21/2023] [Accepted: 07/03/2024] [Indexed: 07/12/2024]
Abstract
Multiple myeloma (MM) is an incurable malignancy of clonal plasma cells. Various diagnostic methods are used in parallel to accurately determine stage and severity of the disease. Identifying a biomarker or a panel of biomarkers could enhance the quality of medical care that patients receive by adopting a more personalized approach. Metabolomics utilizes high-throughput analytical platforms to examine the levels and quantities of biochemical compounds in biosamples. The aim of this review was to conduct a systematic literature search for potential metabolic biomarkers that may aid in the diagnosis and prognosis of MM. The review was conducted in accordance with PRISMA recommendations and was registered in PROSPERO. The systematic search was performed in PubMed, CINAHL, SciFinder, Scopus, The Cochrane Library and Google Scholar. Studies were limited to those involving people with clinically diagnosed MM and healthy controls as comparators. Articles had to be published in English and had no restrictions on publication date or sample type. The quality of articles was assessed according to QUADOMICS criteria. A total of 709 articles were collected during the literature search. Of these, 436 were excluded based on their abstract, with 26 more removed after a thorough review of the full text. Finally, 16 articles were deemed relevant and were subjected to further analysis of their data. A number of promising candidate biomarkers was discovered. Follow-up studies with large sample sizes are needed to determine their suitability for clinical applications.
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Affiliation(s)
- Valeria G Varzieva
- Department of Pharmacology, Sechenov First Moscow State Medical University (Sechenov University), Vernadskogo pr., 96, 119571 Moscow, Russia; Centre of Biopharmaceutical Analysis and Metabolomics, Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University (Sechenov University), Nakhimovsky pr., 45, 117418 Moscow, Russia.
| | - Natalia V Mesonzhnik
- Centre of Biopharmaceutical Analysis and Metabolomics, Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University (Sechenov University), Nakhimovsky pr., 45, 117418 Moscow, Russia.
| | - Irina S Ilgisonis
- Hospital Therapy No. 1 Department, Sechenov First Moscow State Medical University (Sechenov University), Bol'shaya Pirogovskaya st. 6/1, 119435 Moscow, Russia
| | - Yuri N Belenkov
- Hospital Therapy No. 1 Department, Sechenov First Moscow State Medical University (Sechenov University), Bol'shaya Pirogovskaya st. 6/1, 119435 Moscow, Russia
| | - Maria V Kozhevnikova
- Hospital Therapy No. 1 Department, Sechenov First Moscow State Medical University (Sechenov University), Bol'shaya Pirogovskaya st. 6/1, 119435 Moscow, Russia
| | - Svetlana A Appolonova
- Department of Pharmacology, Sechenov First Moscow State Medical University (Sechenov University), Vernadskogo pr., 96, 119571 Moscow, Russia; Centre of Biopharmaceutical Analysis and Metabolomics, Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University (Sechenov University), Nakhimovsky pr., 45, 117418 Moscow, Russia
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25
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Zemitis A, Vanags J, Fan J, Klavins K, Laganovska G. Metabolomic Disparities in Intraocular Fluid Across Varied Stages of Cataract Progression: Implications for the Analysis of Cataract Development. J Ocul Pharmacol Ther 2024. [PMID: 38976556 DOI: 10.1089/jop.2024.0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024] Open
Abstract
Introduction: The lens's metabolic demands are met through a continuous circulation of aqueous humor, encompassing a spectrum of components such as organic and inorganic ions, carbohydrates, glutathione, urea, amino acids, proteins, oxygen, carbon dioxide, and water. Metabolomics is a pivotal tool, offering an initial insight into the complexities of integrated metabolism. In this investigative study, we systematically scrutinize the composition of intraocular fluid in individuals afflicted with cataracts. Methods: The investigation involved a comprehensive analysis of aqueous humor samples from a cohort comprising 192 patients. These individuals were stratified by utilizing the SPONCS classification system, delineating distinct groups characterized by the hardness of cataracts. The analytical approach employed targeted quantitative metabolite analysis using HILIC-based liquid chromatography coupled with high-resolution mass spectrometric detection. The metabolomics data analysis was performed with MetaboAnalyst 5.0. Results: The results of the enrichment analysis have facilitated the inference that the discerned disparities among groups arise from disruptions in taurine and hypotaurine metabolism, variations in tryptophan metabolism, and modifications in mitochondrial beta-oxidation of short-chain saturated fatty acids and pyrimidine metabolism. Conclusion: A decline in taurine concentration precipitates diminished glutathione activity, prompting an elevated requirement for NAD+ and instigating tryptophan metabolism along the kynurenine pathway. Activation of this pathway is additionally prompted by interferon-gamma and UV radiation, leading to the induction of IDO. Concurrently, heightened mitochondrial beta-oxidation signifies a distinctive scenario in translocating fatty acids into the mitochondria, enhancing energy production.
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Affiliation(s)
- Arturs Zemitis
- Department of Ophthalmology, Riga Stradins University, Riga, Latvia
- Clinic of Ophthalmology, Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Juris Vanags
- Department of Ophthalmology, Riga Stradins University, Riga, Latvia
- Clinic of Ophthalmology, Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Jingzhi Fan
- Faculty of Natural Sciences and Technology, Institute of Biomaterials and Bioengineering, Riga Technical University, Riga, Latvia
| | - Kristaps Klavins
- Faculty of Natural Sciences and Technology, Institute of Biomaterials and Bioengineering, Riga Technical University, Riga, Latvia
| | - Guna Laganovska
- Department of Ophthalmology, Riga Stradins University, Riga, Latvia
- Clinic of Ophthalmology, Pauls Stradins Clinical University Hospital, Riga, Latvia
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26
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Liu J, Yang M, Chen F, Huang C, Xu X, Zhang F, Chen Y. Preparation of immunomagnetic composite nanostructures with bifunctional four-arm PEG derivatives as linkers for the ultrafast enrichment of zearalenone and its metabolites. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134321. [PMID: 38723478 DOI: 10.1016/j.jhazmat.2024.134321] [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: 01/30/2024] [Revised: 04/03/2024] [Accepted: 04/14/2024] [Indexed: 05/30/2024]
Abstract
It is challenging to prepare sample pretreatment materials with simple use, strong selectivity and satisfactory enrichment performance. In this study, the antibody (3D4) that can specifically recognize zearalenone (ZEN) and its metabolites was immobilized on the surface of gold-coated magnetic Fe3O4 nanoparticles (GMN) by streptavidin (SA)-biotin interaction using GMN as the substrate and our designed four-arm PEG derivative (HS-4ARMPEG10K-(CM)3) as the linker. The immunomagnetic nanoparticles (GMN-4ARMPEG10K-SA-3D4) prepared by this strategy can achieve rapid enrichment (only 5 min) of analytes directly in the matrix, and higher enrichment capacity compared with the previous immunomagnetic particles. The sensitive and accurate analysis of ZEN and its metabolites can be achieved coupled with HPLC-MS/MS. The LODs and LOQs were 0.02-0.05 μg/kg and 0.05-0.10 μg/kg, respectively. The recoveries were 84.13%-112.67%, and the RSDs were 1.09%-9.39%. The method can provide a powerful tool for highly sensitive and rapid monitoring of mycotoxins in complex matrices due to its' strong selectivity and resistance to matrix interference.
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Affiliation(s)
- Jiawei Liu
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China; Key Laboratory of Food Quality and Safety for State Market Regulation, Beijing 100176, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Minli Yang
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China; Key Laboratory of Food Quality and Safety for State Market Regulation, Beijing 100176, China
| | - Fengming Chen
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China; Key Laboratory of Food Quality and Safety for State Market Regulation, Beijing 100176, China
| | - Chenxi Huang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Xu
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China; Key Laboratory of Food Quality and Safety for State Market Regulation, Beijing 100176, China
| | - Feng Zhang
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China; Key Laboratory of Food Quality and Safety for State Market Regulation, Beijing 100176, China.
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Sun Z, Guo X, Kumar RMS, Huang C, Xie Y, Li M, Li J. Transcriptomic and metabolomic analyses reveal the importance of ethylene networks in mulberry fruit ripening. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 344:112084. [PMID: 38614360 DOI: 10.1016/j.plantsci.2024.112084] [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: 12/29/2023] [Revised: 03/21/2024] [Accepted: 04/02/2024] [Indexed: 04/15/2024]
Abstract
Mulberry (Morus alba L.) is a climacteric and highly perishable fruit. Ethylene has been considered to be an important trigger of fruit ripening process. However, the role of ethylene in the mulberry fruit ripening process remains unclear. In this study, we performed a comprehensive analysis of metabolomic and transcriptomic data of mulberry fruit and the physiological changes accompanying the fruit ripening process. Our study revealed that changes in the accumulation of specific metabolites at different stages of fruit development and ripening were closely correlated to transcriptional changes as well as underlying physiological changes and the development of taste biomolecules. The ripening of mulberry fruits was highly associated with the production of endogenous ethylene, and further application of exogenous ethylene assisted the ripening process. Transcriptomic analysis revealed that differential expression of diverse ripening-related genes was involved in sugar metabolism, anthocyanin biosynthesis, and cell wall modification pathways. Network analysis of transcriptomics and metabolomics data revealed that many transcription factors and ripening-related genes were involved, among which ethylene-responsive transcription factor 3 (MaERF3) plays a crucial role in the ripening process. The role of MaERF3 in ripening was experimentally proven in a transient overexpression assay in apples. Our study indicates that ethylene plays a vital role in modulating mulberry fruit ripening. The results provide a basis for guiding the genetic manipulation of mulberry fruits towards sustainable agricultural practices and improve post-harvest management, potentially enhancing the quality and shelf life of mulberry fruits for sustainable agriculture and forestry.
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Affiliation(s)
- Zhichao Sun
- Sericultural Research Insitute, Chengde Medical University, Chengde 067000, China; State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China.
| | - Xinmiao Guo
- Chengde College of Applied Technology, Chengde 067000, China.
| | - R M Saravana Kumar
- Department of Biotechnology, Saveetha School of Engineering, Saveetha University, Chennai, Tamil Nadu 602105, India.
| | - Chunying Huang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China.
| | - Yan Xie
- Sericultural Research Insitute, Chengde Medical University, Chengde 067000, China.
| | - Meng Li
- Sericultural Research Insitute, Chengde Medical University, Chengde 067000, China.
| | - Jisheng Li
- Sericultural Research Insitute, Chengde Medical University, Chengde 067000, China.
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28
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Hong H, Habib A, Bi L, Qais DS, Wen L. Hollow Cathode Discharge Ionization Mass Spectrometry: Detection, Quantification and Gas Phase Ion-Molecule Reactions of Explosives and Related Compounds. Crit Rev Anal Chem 2024; 54:148-174. [PMID: 35467991 DOI: 10.1080/10408347.2022.2067467] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Mass spectrometry (MS) has become an essential analytical method in every sector of science and technology. Because of its unique ability to provide direct molecular structure information on analytes, an extra method is rarely required. This review describes fabrication of a variable-pressure hollow cathode discharge (HCD) ion source for MS in detection, quantification and investigation of gas-phase ion molecule reactions of explosives and related compounds using air as a carrier gas. The HCD ion source has been designed in such a way that by altering the ion source pressures, the system can generate both HCD and conventional GD. This design enables for the selective detection and quantification of explosives at trace to ultra-trace levels. The pressure-dependent HCD ion source has also been used to investigate ion-molecule reactions in the gas phase of explosives and related compounds. The mechanism of ion formation in explosive reactions is also discussed.
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Affiliation(s)
- Huanhuan Hong
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - Ahsan Habib
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- Department of Chemistry, University of Dhaka, Dhaka, Bangladesh
| | - Lei Bi
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | | | - Luhong Wen
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
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29
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Owens DJ, Bennett S. An exercise physiologist's guide to metabolomics. Exp Physiol 2024; 109:1066-1079. [PMID: 38358958 PMCID: PMC11215473 DOI: 10.1113/ep091059] [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: 09/19/2023] [Accepted: 01/25/2024] [Indexed: 02/17/2024]
Abstract
The field of exercise physiology has undergone significant technological advancements since the pioneering works of exercise physiologists in the early to mid-20th century. Historically, the ability to detect metabolites in biofluids from exercising participants was limited to single-metabolite analyses. However, the rise of metabolomics, a discipline focused on the comprehensive analysis of metabolites within a biological system, has facilitated a more intricate understanding of metabolic pathways and networks in exercise. This review explores some of the pivotal technological and bioinformatic advancements that have propelled metabolomics to the forefront of exercise physiology research. Metabolomics offers a unique 'fingerprint' of cellular activity, offering a broader spectrum than traditional single-metabolite assays. Techniques, including mass spectrometry and nuclear magnetic resonance spectroscopy, have significantly improved the speed and sensitivity of metabolite analysis. Nonetheless, challenges persist, including study design and data interpretation issues. This review aims to serve as a guide for exercise physiologists to facilitate better research design, data analysis and interpretation within metabolomics. The potential of metabolomics in bridging the gap between genotype and phenotype is emphasised, underscoring the critical importance of careful study design and the selection of appropriate metabolomics techniques. Furthermore, the paper highlights the need to deeply understand the broader scientific context to discern meaningful metabolic changes. The emerging field of fluxomics, which seeks to quantify metabolic reaction rates, is also introduced as a promising avenue for future research.
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Affiliation(s)
- Daniel J. Owens
- Research Institute of Sport and Exercise Science (RISES)Liverpool John Moores UniversityLiverpoolUK
| | - Samuel Bennett
- Center for Biological Clocks Research, Department of BiologyTexas A&M UniversityCollege StationTexasUSA
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30
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Marina H, Arranz JJ, Suárez-Vega A, Pelayo R, Gutiérrez-Gil B, Toral PG, Hervás G, Frutos P, Fonseca PAS. Assessment of milk metabolites as biomarkers for predicting feed efficiency in dairy sheep. J Dairy Sci 2024; 107:4743-4757. [PMID: 38369116 DOI: 10.3168/jds.2023-23984] [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: 07/28/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024]
Abstract
Estimating feed efficiency (FE) in dairy sheep is challenging due to the high cost of systems that measure individual feed intake. Identifying proxies that can serve as effective predictors of FE could make it possible to introduce FE into breeding programs. Here, 39 Assaf ewes in first lactation were evaluated regarding their FE by 2 metrics, residual feed intake (RFI) and feed conversion ratio (FCR). The ewes were classified into high, medium and low groups for each metric. Milk samples of the 39 ewes were subjected to untargeted metabolomics analysis. The complete milk metabolomic signature was used to discriminate the FE groups using partial least squares discriminant analysis. A total of 41 and 26 features were selected as the most relevant features for the discrimination of RFI and FCR groups, respectively. The predictive ability when utilizing the complete milk metabolomic signature and the reduced data sets were investigated using 4 machine learning (ML) algorithms and a multivariate regression method. The orthogonal partial least squares algorithm outperformed other ML algorithms for FCR prediction in the scenarios using the complete milk metabolite signature (R2 = 0.62 ± 0.06) and the 26 selected features (R2 = 0.62 ± 0.15). Regarding RFI predictions, the scenarios using the 41 selected features outperformed the scenario with the complete milk metabolite signature, where the multilayer feedforward artificial neural network (R2 = 0.18 ± 0.14) and extreme gradient boosting (R2 = 0.17 ± 0.15) outperformed other algorithms. The functionality of the selected metabolites implied that the metabolism of glucose, galactose, fructose, sphingolipids, amino acids, insulin, and thyroid hormones was at play. Compared with the use of traditional methods, practical applications of these biomarkers might simplify and reduce costs in selecting feed-efficient ewes.
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Affiliation(s)
- H Marina
- Dpto. Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24007 León, Spain
| | - J J Arranz
- Dpto. Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24007 León, Spain.
| | - A Suárez-Vega
- Dpto. Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24007 León, Spain
| | - R Pelayo
- Dpto. Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24007 León, Spain
| | - B Gutiérrez-Gil
- Dpto. Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24007 León, Spain
| | - P G Toral
- Instituto de Ganadería de Montaña (CSIC-University of León), Finca Marzanas s/n, 24346 Grulleros, León, Spain
| | - G Hervás
- Instituto de Ganadería de Montaña (CSIC-University of León), Finca Marzanas s/n, 24346 Grulleros, León, Spain
| | - P Frutos
- Instituto de Ganadería de Montaña (CSIC-University of León), Finca Marzanas s/n, 24346 Grulleros, León, Spain
| | - P A S Fonseca
- Dpto. Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24007 León, Spain
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31
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Xie P, Luo M, Fan J, Xiong L. Multiomics Analysis Reveals Gut Virome-Bacteria-Metabolite Interactions and Their Associations with Symptoms in Patients with IBS-D. Viruses 2024; 16:1054. [PMID: 39066219 PMCID: PMC11281411 DOI: 10.3390/v16071054] [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: 05/27/2024] [Revised: 06/23/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
The gut microbiota is involved in the pathogenesis of diarrhea-predominant irritable bowel syndrome (IBS-D), but few studies have focused on the role of the gut virome in IBS-D. We aimed to explore the characteristics of the gut virome in patients with IBS-D, its interactions with bacteria and metabolites, and the associations between gut multiomics profiles and symptoms. This study enrolled twelve patients with IBS-D and eight healthy controls (HCs). The stool samples were subjected to metavirome sequencing, 16S rRNA gene sequencing, and untargeted metabolomic analysis. The participants completed relevant scales to assess the severity of their gastrointestinal symptoms, depression, and anxiety. The results revealed unique DNA and RNA virome profiles in patients with IBS-D with significant alterations in the abundance of contigs from Siphoviridae, Podoviridae, Microviridae, Picobirnaviridae, and Tombusviridae. Single-omics co-occurrence network analyses demonstrated distinct differences in the gut virus, bacteria, and metabolite network patterns between patients with IBS-D and HCs. Multiomics networks revealed that short-chain fatty acid-producing bacteria occupied more core positions in IBS-D networks, but had fewer links to viruses. Amino acids and their derivatives exhibit unique connectivity patterns and centrality features within the IBS-D network. The gastrointestinal and psychological symptom factors of patients with IBS-D were highly clustered in the symptom-multiomics network compared with those of HCs. Machine learning models based on multiomics data can distinguish IBS-D patients from HCs and predict the scores of gastrointestinal and psychological symptoms. This study provides insights into the interactions among gut viruses, bacteria, metabolites, and clinical symptoms in patients with IBS-D, indicating further classification and personalized treatment for IBS-D.
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Affiliation(s)
| | | | | | - Lishou Xiong
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
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32
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Zhong C, Hu C, Xu C, Zhang Z, Hu G. Metabolomics reveals changes in soil metabolic profiles during vegetation succession in karst area. Front Microbiol 2024; 15:1337672. [PMID: 38989027 PMCID: PMC11233535 DOI: 10.3389/fmicb.2024.1337672] [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: 01/23/2024] [Accepted: 06/13/2024] [Indexed: 07/12/2024] Open
Abstract
Soil metabolites are critical in regulating the dynamics of ecosystem structure and function, particularly in fragile karst ecosystems. Clarification of response of soil metabolism to vegetation succession in karst areas will contribute to the overall understanding and management of karst soils. Here, we investigated the metabolite characteristics of karst soils with different vegetation stages (grassland, brushwood, secondary forest and primary forest) based on untargeted metabolomics. We confirmed that the abundance and composition of soil metabolites altered with vegetation succession. Of the 403 metabolites we found, 157 had significantly varied expression levels across vegetation soils, including mainly lipids and lipid-like molecules, phenylpropanoids and polyketides, organic acids and derivatives. Certain soil metabolites, such as maltotetraose and bifurcose, were sensitive to vegetation succession, increasing significantly from grassland to brushwood and then decreasing dramatically in secondary and primary forests, making them possible indicators of karst vegetation succession. In addition, soil metabolic pathways, such as galactose metabolism and biosynthesis of unsaturated fatty acids, also changed with vegetation succession. This study characterized the soil metabolic profile in different vegetation stages during karst secondary succession, which would provide new insights for the management of karst soils.
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Affiliation(s)
| | | | | | - Zhonghua Zhang
- Key Laboratory of Wildlife Evolution and Conservation in Mountain Ecosystem of Guangxi, College of Environmental and Life Sciences, Nanning Normal University, Nanning, China
| | - Gang Hu
- Key Laboratory of Wildlife Evolution and Conservation in Mountain Ecosystem of Guangxi, College of Environmental and Life Sciences, Nanning Normal University, Nanning, China
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33
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Chen R, Chen X, Gao J. 3-O-acylated bile acids: disrupters or harmonizers of metabolism? Trends Mol Med 2024:S1471-4914(24)00161-8. [PMID: 38926031 DOI: 10.1016/j.molmed.2024.06.003] [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: 05/03/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Unveiling a metabolic mystery, this article explores how 3-O-acylated bile acids, specifically 3-O-succinylated cholic acid (3-sucCA) and 3-acetylated cholic acid (3-acetyCA), modified by gut microbes Bacteroides uniformis and Christensenella minuta, respectively, may either disrupt or harmonize our metabolic processes, offering novel therapeutic avenues for conditions such as metabolic dysfunction-associated steatohepatitis (MASH) and type 2 diabetes mellitus (T2D).
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Affiliation(s)
- Runzhi Chen
- Key BioAI Synthetica Lab for Natural Product Drug Discovery, College of Bee and Biomedical Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Xinhua Chen
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.
| | - Jiangtao Gao
- Key BioAI Synthetica Lab for Natural Product Drug Discovery, College of Bee and Biomedical Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.
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34
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Christopher MW, Klug AC, Lee JH, Ericson AC, Feizbakhsh Bazargani S, Dinglasan RR, Prentice BM, Garrett TJ. Indole-3-pyruvate: Analysis and Control of Tautomerism and Reactivity. Anal Chem 2024; 96:10399-10407. [PMID: 38858849 DOI: 10.1021/acs.analchem.4c01584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
It is well-known in biochemistry that structure confers function, meaning that chemical structural elucidation is critical to truly understanding the function of a given metabolite. Indole-3-pyruvate (IPyA) exists in an equilibrium between the keto and enol tautomeric forms. IPyA is suggested to play a role in immune function; however, determining whether the tautomeric forms function differently can only be studied if an analytical method is capable of distinguishing between the two forms. Herein, we describe the use of UHPLC-HRMS to gain insight into the physical variables that govern IPyA tautomer equilibrium, reactivity, and detection limit. We use hydrogen-deuterium exchange (HDX) to identify enol and keto peaks, and we show that tautomers exhibit a valley of fronting followed by a tailing peak shape (though separation is still attainable) and identical MS/MS spectra. We observed drastically different ratios of keto and enol forms in different solvents, which is an important consideration for in vitro studies. IPyA was found to be highly unstable with accelerated reactivity in peroxides. Through in vitro reactivity studies, IPyA produced a myriad of known and unknown metabolites via nonenzymatic processes, many of which were mapped in vivo via the analysis of human plasma. Finally, we show that vitamin C (ascorbic acid) can slow this reactivity and enable sensitive detection in whole blood.
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Affiliation(s)
- Michael W Christopher
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Alexander C Klug
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Jae Hwan Lee
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Aiden C Ericson
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | | | - Rhoel R Dinglasan
- Department of Infectious Disease and Immunology, University of Florida, College of Veterinary Medicine, Gainesville, Florida 32608, United States
| | - Boone M Prentice
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Timothy J Garrett
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, Florida 32608, United States
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35
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Luo J, Xiao S, Ma D, Xiang J, Wang B, Cai Y, Wang J. Investigating the Impact of Pineapple-Whey Protein Fermentation Products on Cefixime-Induced Intestinal Flora Dysbiosis in Mice Using 16S Sequencing and Untargeted Metabolomics Techniques. Foods 2024; 13:1927. [PMID: 38928868 PMCID: PMC11202880 DOI: 10.3390/foods13121927] [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: 04/19/2024] [Revised: 05/21/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
In our previous study, a new fermented food (PWF) created by utilizing pineapple by-products and whey proteins as a matrix via co-fermentation with lactic acid bacteria and yeast was developed, and, in the current study, we examined the impact of a pineapple-whey protein fermentation product on a cefixime-induced dysbiosis model in mice using 16S sequencing and untargeted metabolomics techniques. The results indicated that the pineapple-whey protein fermentation product played a positive role in restoring the intestinal flora. In this study, cefixime reduced the overall abundance of intestinal flora and decreased the relative abundance of probiotics in the gut, while also inhibiting amino acid metabolism. The addition of PWF normalized the intestinal flora to a steady state, significantly increasing the populations of Weissella, Lactococcus, Faecalibaculum, and Bacteroides acidophilus, while decreasing the numbers of Akkermansia and Escherichia-Shigella. Additionally, PWF modulated microbial metabolites, such as L-glutamate and L-threonine, and upregulated amino-acid-related metabolic pathways, including those involving glycine, serine, and threonine. In conclusion, PWF can alleviate intestinal flora dysbiosis and metabolic disturbances induced by antibiotic interventions. It is suggested that PWF could be a potential dietary strategy for patients with antibiotic-associated diarrhea.
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Affiliation(s)
- Jiawei Luo
- School of Life and Health Technology, Dongguan University of Technology, Dongguan 523808, China; (J.L.); (D.M.); (J.X.); (B.W.); (Y.C.); (J.W.)
- Dongguan Prefabricated Food Innovation Development and Quality Control Key Laboratory, Dongguan 523808, China
| | - Shan Xiao
- School of Life and Health Technology, Dongguan University of Technology, Dongguan 523808, China; (J.L.); (D.M.); (J.X.); (B.W.); (Y.C.); (J.W.)
- Dongguan Prefabricated Food Innovation Development and Quality Control Key Laboratory, Dongguan 523808, China
| | - Da Ma
- School of Life and Health Technology, Dongguan University of Technology, Dongguan 523808, China; (J.L.); (D.M.); (J.X.); (B.W.); (Y.C.); (J.W.)
- Dongguan Prefabricated Food Innovation Development and Quality Control Key Laboratory, Dongguan 523808, China
| | - Junhan Xiang
- School of Life and Health Technology, Dongguan University of Technology, Dongguan 523808, China; (J.L.); (D.M.); (J.X.); (B.W.); (Y.C.); (J.W.)
- Dongguan Prefabricated Food Innovation Development and Quality Control Key Laboratory, Dongguan 523808, China
| | - Bo Wang
- School of Life and Health Technology, Dongguan University of Technology, Dongguan 523808, China; (J.L.); (D.M.); (J.X.); (B.W.); (Y.C.); (J.W.)
- Dongguan Prefabricated Food Innovation Development and Quality Control Key Laboratory, Dongguan 523808, China
| | - Yanxue Cai
- School of Life and Health Technology, Dongguan University of Technology, Dongguan 523808, China; (J.L.); (D.M.); (J.X.); (B.W.); (Y.C.); (J.W.)
- Dongguan Prefabricated Food Innovation Development and Quality Control Key Laboratory, Dongguan 523808, China
| | - Jihui Wang
- School of Life and Health Technology, Dongguan University of Technology, Dongguan 523808, China; (J.L.); (D.M.); (J.X.); (B.W.); (Y.C.); (J.W.)
- Dongguan Prefabricated Food Innovation Development and Quality Control Key Laboratory, Dongguan 523808, China
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36
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Zhang Y, Ren H, Tang X, Liu Q, Xiao W, Zhang Z, Tian Y. A GC×GC-MS method based on solid-state modulator for non-targeted metabolomics: Comparison with traditional GC-MS method. J Pharm Biomed Anal 2024; 243:116068. [PMID: 38428247 DOI: 10.1016/j.jpba.2024.116068] [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: 12/19/2023] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
The formidable challenge posed by the presence of extremely high amounts of compounds and large differences in concentrations in plasma significantly complicates non-targeted metabolomics analyses. In this study, a comprehensive two-dimensional gas chromatography-quadrupole mass spectrometry (GC×GC-qMS) method with a solid-state modulator (SSM) for non-targeted metabolomics in beagle plasma was first established based on a GC-MS method, and the qualitative and quantitative performance of the two platforms were compared. Identification of detected compounds was accomplished utilizing NIST database match scores, retention indices (RIs) and standards. Semi-quantification involved the calculation of peak area ratios to internal standards. Metabolite identification sheets were generated for plasma samples on both analytical platforms, featuring 22 representative metabolites chosen for validating qualitative accuracy, and for conducting comparisons of linearity, accuracy, precision, and sensitivity. The outcomes revealed a threefold increase in the number of identifiable metabolites on the GC×GC-MS platform, with lower limits of quantitation (LLOQs) reduced to 0.5-0.05 times those achieved on the GC-MS platform. Accuracy in quantification for both GC×GC-MS and GC-MS fell within the range of 85-115%, and the vast majority of intra- and inter-day precisions were within the range of 20%. These findings underscore that relative to the conventional GC-MS method, the GC×GC-MS method developed in this study, combined with SSM, exhibits enhanced qualitative capabilities, heightened sensitivity, and comparable accuracy and precision, rendering it more suitable for non-targeted metabolomics analyses.
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Affiliation(s)
- Yueyi Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing 210009, PR China
| | - Haihui Ren
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing 210009, PR China
| | - Xiao Tang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing 210009, PR China
| | - Qiaorong Liu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing 210009, PR China
| | - Wen Xiao
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing 210009, PR China
| | - Zunjian Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing 210009, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China.
| | - Yuan Tian
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing 210009, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China.
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37
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Orban B, Tengölics R, Zavori L, Simon D, Erdo-Bonyar S, Molnar T, Schwarcz A, Csecsei P. The Difference in Serum Metabolomic Profiles between the Good and Poor Outcome Groups at 3 Months in the Early and Late Phases of Aneurysmal Subarachnoid Hemorrhage. Int J Mol Sci 2024; 25:6597. [PMID: 38928303 PMCID: PMC11203497 DOI: 10.3390/ijms25126597] [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: 05/19/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
We aimed to investigate the characteristics of serum metabolomics in aneurysmal subarachnoid hemorrhage patients (aSAH) with different 3-month outcomes (good = modified Rankin score: 0-3 vs. poor = mRS 4-6). We collected serum samples from 46 aSAH patients at 24 (D1) and 168 (D7) hours after injury for analysis by liquid chromatography-mass spectrometry. Ninety-six different metabolites were identified. Groups were compared using multivariate (orthogonal partial least squares discriminant analysis), univariate, and receiving operator characteristic (ROC) methods. We observed a marked decrease in serum homocysteine levels at the late phase (D7) compared to the early phase (D1). At both D1 and D7, mannose and sorbose levels were notably higher, alongside elevated levels of kynurenine (D1) and increased 2-hydroxybutyrate, methyl-galactoside, creatine, xanthosine, p-hydroxyphenylacetate, N-acetylalanine, and N-acetylmethionine (all D7) in the poor outcome group. Conversely, levels of guanidinoacetate (D7) and several amino acids (both D1 and D7) were significantly lower in patients with poor outcomes. Our results indicate significant changes in energy metabolism, shifting towards ketosis and alternative energy sources, both in the early and late phases, even with adequate enteral nutrition, particularly in patients with poor outcomes. The early activation of the kynurenine pathway may also play a role in this process.
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Affiliation(s)
- Brigitta Orban
- Department of Neurosurgery, Medical School, University of Pecs, 7632 Pecs, Hungary; (B.O.); (A.S.)
| | - Roland Tengölics
- Metabolomics Lab, Biological Research Centre, Hungarian Research Network, 6726 Szeged, Hungary;
- Core Facilities, Biological Research Centre, Hungarian Research Network, 6726 Szeged, Hungary
- Hungarian Centre of Excellence for Molecular Medicine—Biological Research Centre Metabolic Systems Biology Lab, 6726 Szeged, Hungary
| | - Laszlo Zavori
- Emergency Department, Saudi German Hospital, Dubai 391093, United Arab Emirates;
| | - Diana Simon
- Department of Immunology and Biotechnology, Medical School, University of Pecs, 7632 Pecs, Hungary; (D.S.); (S.E.-B.)
| | - Szabina Erdo-Bonyar
- Department of Immunology and Biotechnology, Medical School, University of Pecs, 7632 Pecs, Hungary; (D.S.); (S.E.-B.)
| | - Tihamer Molnar
- Department of Anaesthesiology and Intensive Care, Medical School, University of Pecs, 7632 Pecs, Hungary;
| | - Attila Schwarcz
- Department of Neurosurgery, Medical School, University of Pecs, 7632 Pecs, Hungary; (B.O.); (A.S.)
| | - Peter Csecsei
- Department of Neurosurgery, Medical School, University of Pecs, 7632 Pecs, Hungary; (B.O.); (A.S.)
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Curtis MA, Saferin N, Nguyen JH, Imami AS, Ryan WG, Neifer KL, Miller GW, Burkett JP. Developmental pyrethroid exposure in mouse leads to disrupted brain metabolism in adulthood. Neurotoxicology 2024; 103:87-95. [PMID: 38876425 DOI: 10.1016/j.neuro.2024.06.007] [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: 03/27/2024] [Revised: 05/24/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024]
Abstract
Environmental and genetic risk factors, and their interactions, contribute significantly to the etiology of neurodevelopmental disorders (NDDs). Recent epidemiology studies have implicated pyrethroid pesticides as an environmental risk factor for autism and developmental delay. Our previous research showed that low-dose developmental exposure to the pyrethroid pesticide deltamethrin in mice caused male-biased changes in the brain and in NDD-relevant behaviors in adulthood. Here, we used a metabolomics approach to determine the broadest possible set of metabolic changes in the adult male mouse brain caused by low-dose pyrethroid exposure during development. Using a litter-based design, we exposed mouse dams during pregnancy and lactation to deltamethrin (3 mg/kg or vehicle every 3 days) at a concentration well below the EPA-determined benchmark dose used for regulatory guidance. We raised male offspring to adulthood and collected whole brain samples for untargeted high-resolution metabolomics analysis. Developmentally exposed mice had disruptions in 116 metabolites which clustered into pathways for folate biosynthesis, retinol metabolism, and tryptophan metabolism. As a cross-validation, we integrated metabolomics and transcriptomics data from the same samples, which confirmed previous findings of altered dopamine signaling. These results suggest that pyrethroid exposure during development leads to disruptions in metabolism in the adult brain, which may inform both prevention and therapeutic strategies.
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Affiliation(s)
- Melissa A Curtis
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, United States
| | - Nilanjana Saferin
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, United States
| | - Jennifer H Nguyen
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, United States
| | - Ali S Imami
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, United States
| | - William G Ryan
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, United States
| | - Kari L Neifer
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, United States
| | - Gary W Miller
- Department of Environmental Health, Emory Rollins School of Public Health, Atlanta, GA 30322, United States; Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, United States
| | - James P Burkett
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, United States.
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Yang S, Fu J, Qin W, Wang R, Gu M, Huang Y, Liu W, Su H, Xu X, Chen W, Yiming A, Hu B, Huang L, Qian K, Wang H. Bile metabolic fingerprints distinguish biliary tract cancer from benign biliary diseases. Hepatology 2024:01515467-990000000-00907. [PMID: 38861680 DOI: 10.1097/hep.0000000000000957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND AND AIMS Biliary tract cancers are aggressive gastrointestinal malignancies characterized by a dismal 5-year overall survival rate <20%. Current diagnostic modalities suffer from limitations regarding sensitivity and specificity. This study aimed to develop a bile metabolite-based platform for precise discrimination between malignant and benign biliary diseases. APPROACH AND RESULTS Samples were collected from 336 patients with biliary tract cancer or benign biliary diseases across 3 independent cohorts. Untargeted metabolic fingerprinting was performed on 300 bile samples using novel nanoparticle-enhanced laser desorption/ionization mass spectrometry. Subsequently, a diagnostic assay was developed based on the exploratory cohort using a selected bile metabolic biomarker panel, with performance evaluated in the validation cohort. Further external validation of disease-specific metabolites from bile samples was conducted in a prospective cohort (n = 36) using quantitative analysis. As a result, we established a novel bile-based assay, BileMet, for the rapid and precise detection of malignancies in the biliary tract system with an AUC of 0.891. We identified 6-metabolite biomarker candidates and discovered the critical role of the chenodeoxycholic acid glycine conjugate as a protective metabolite associated with biliary tract cancer. CONCLUSIONS Our findings confirmed the improved diagnostic capabilities of BileMet assay in a clinical setting. If applied, the BileMet assay enables intraoperative testing and fast medical decision-making for cases with suspected malignancy where brush cytology detection fails to support malignancy, ultimately reducing the economic burden by over 90%.
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Affiliation(s)
- Shouzhi Yang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Jing Fu
- International Cooperation Laboratory on Signal Transduction, National Center for Liver Cancer, Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Eastern Hepatobiliary Surgery Hospital, Naval Military Medical University, Shanghai, P.R. China
| | - Wenhao Qin
- Department of Gastroenterology and Endoscopy, Eastern Hepatobiliary Surgery Hospital, Naval Military Medical University, Shanghai, P.R. China
| | - Ruimin Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Mingye Gu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yida Huang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Wanshan Liu
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Haiyang Su
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Xiaoyu Xu
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Wei Chen
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Ayizekeranmu Yiming
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Bing Hu
- Department of Gastroenterology and Endoscopy, Eastern Hepatobiliary Surgery Hospital, Naval Military Medical University, Shanghai, P.R. China
| | - Lin Huang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Kun Qian
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Hongyang Wang
- International Cooperation Laboratory on Signal Transduction, National Center for Liver Cancer, Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Eastern Hepatobiliary Surgery Hospital, Naval Military Medical University, Shanghai, P.R. China
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Li T, Wang A, Zhang Y, Chen W, Guo Y, Yuan X, Liu Y, Geng Y. Chemoproteomic Profiling of Signaling Metabolite Fructose-1,6-Bisphosphate Interacting Proteins in Living Cells. J Am Chem Soc 2024; 146:15155-15166. [PMID: 38775806 DOI: 10.1021/jacs.4c01335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Fructose-1,6-bisphosphate (FBP), a cellular endogenous sugar metabolite in the glycolytic pathway, has recently been reported to act as a signaling molecule to regulate various cellular events through the engagement of important proteins. Though tremendous progress has been made in identifying specific FBP-protein interactions, the comprehensive identification of FBP-interacting proteins and their regulatory mechanisms remains largely unexplored. Here, we describe a concise synthetic approach for the scalable preparation of a photoaffinity FBP probe that enables the quantitative chemoproteomic profiling of FBP-protein interactions based on photoaffinity labeling (PAL) directly in living cells. Using such a protocol, we captured known FBP targets including PKM2 and MDH2. Furthermore, among unknown FBP-interacting proteins, we identified a mitochondrial metabolic enzyme aldehyde dehydrogenase 2 (ALDH2), against which FBP showed inhibitory activity and resulted in cellular ROS upregulation accompanied by mitochondrial fragmentation. Our findings disclosed a new mode of glucose signaling mediating by the FBP-ALDH2-ROS axis.
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Affiliation(s)
- Tian Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Anhui Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yanling Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wei Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yanshen Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xia Yuan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuan Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yiqun Geng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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Maimone NM, Apaza-Castillo GA, Quecine MC, de Lira SP. Accessing the specialized metabolome of actinobacteria from the bulk soil of Paullinia cupana Mart. on the Brazilian Amazon: a promising source of bioactive compounds against soybean phytopathogens. Braz J Microbiol 2024; 55:1863-1882. [PMID: 38421597 PMCID: PMC11153476 DOI: 10.1007/s42770-024-01286-1] [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: 11/24/2023] [Accepted: 02/10/2024] [Indexed: 03/02/2024] Open
Abstract
The Amazon rainforest, an incredibly biodiverse ecosystem, has been increasingly vulnerable to deforestation. Despite its undeniable importance and potential, the Amazonian microbiome has historically received limited study, particularly in relation to its unique arsenal of specialized metabolites. Therefore, in this study our aim was to assess the metabolic diversity and the antifungal activity of actinobacterial strains isolated from the bulk soil of Paullinia cupana, a native crop, in the Brazilian Amazon Rainforest. Extracts from 24 strains were subjected to UPLC-MS/MS analysis using an integrative approach that relied on the Chemical Structural and Compositional Similarity (CSCS) metric, GNPS molecular networking, and in silico dereplication tools. This procedure allowed the comprehensive understanding of the chemical space encompassed by these actinobacteria, which consists of features belonging to known bioactive metabolite classes and several unannotated molecular families. Among the evaluated strains, five isolates exhibited bioactivity against a panel of soybean fungal phytopathogens (Rhizoctonia solani, Macrophomina phaseolina, and Sclerotinia sclerotiorum). A focused inspection led to the annotation of pepstatins, oligomycins, hydroxamate siderophores and dorrigocins as metabolites produced by these bioactive strains, with potentially unknown compounds also comprising their metabolomes. This study introduces a pragmatic protocol grounded in established and readily available tools for the annotation of metabolites and the prioritization of strains to optimize further isolation of specialized metabolites. Conclusively, we demonstrate the relevance of the Amazonian actinobacteria as sources for bioactive metabolites useful for agriculture. We also emphasize the importance of preserving this biome and conducting more in-depth studies on its microbiota.
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Affiliation(s)
- Naydja Moralles Maimone
- College of Agriculture "Luiz de Queiroz", Department of Exact Sciences, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Gladys Angélica Apaza-Castillo
- College of Agriculture "Luiz de Queiroz", Department of Genetics, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Maria Carolina Quecine
- College of Agriculture "Luiz de Queiroz", Department of Genetics, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Simone Possedente de Lira
- College of Agriculture "Luiz de Queiroz", Department of Exact Sciences, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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Song Y, Yao S, Li X, Wang T, Jiang X, Bolan N, Warren CR, Northen TR, Chang SX. Soil metabolomics: Deciphering underground metabolic webs in terrestrial ecosystems. ECO-ENVIRONMENT & HEALTH 2024; 3:227-237. [PMID: 38680731 PMCID: PMC11047296 DOI: 10.1016/j.eehl.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/05/2024] [Accepted: 03/04/2024] [Indexed: 05/01/2024]
Abstract
Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites, i.e., metabolomes, in the soil. Soil metabolites, including fatty acids, amino acids, lipids, organic acids, sugars, and volatile organic compounds, often contain essential nutrients such as nitrogen, phosphorus, and sulfur and are directly linked to soil biogeochemical cycles driven by soil microorganisms. This paper presents an overview of methods for analyzing soil metabolites and the state-of-the-art of soil metabolomics in relation to soil nutrient cycling. We describe important applications of metabolomics in studying soil carbon cycling and sequestration, and the response of soil organic pools to changing environmental conditions. This includes using metabolomics to provide new insights into the close relationships between soil microbiome and metabolome, as well as responses of soil metabolome to plant and environmental stresses such as soil contamination. We also highlight the advantage of using soil metabolomics to study the biogeochemical cycles of elements and suggest that future research needs to better understand factors driving soil function and health.
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Affiliation(s)
- Yang Song
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shi Yao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaona Li
- School of Environment and Ecology, Jiangnan University, Wuxi 225127, China
| | - Tao Wang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610299, China
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nanthi Bolan
- School of Agriculture and Environment, The University of Western Australia, Nedland, WA-6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Nedland, WA-6009, Australia
- Healthy Environments and Lives (HEAL) National Research Network, Australia
| | - Charles R. Warren
- School of Life and Environmental Sciences, University of Sydney, Heydon-Laurence Building A08, NSW 2006, Australia
| | - Trent R. Northen
- Environmental Genomics and System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Scott X. Chang
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta T6G 2E3, Canada
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Hilovsky D, Hartsell J, Young JD, Liu X. Stable Isotope Tracing Analysis in Cancer Research: Advancements and Challenges in Identifying Dysregulated Cancer Metabolism and Treatment Strategies. Metabolites 2024; 14:318. [PMID: 38921453 PMCID: PMC11205609 DOI: 10.3390/metabo14060318] [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: 05/07/2024] [Revised: 05/13/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024] Open
Abstract
Metabolic reprogramming is a hallmark of cancer, driving the development of therapies targeting cancer metabolism. Stable isotope tracing has emerged as a widely adopted tool for monitoring cancer metabolism both in vitro and in vivo. Advances in instrumentation and the development of new tracers, metabolite databases, and data analysis tools have expanded the scope of cancer metabolism studies across these scales. In this review, we explore the latest advancements in metabolic analysis, spanning from experimental design in stable isotope-labeling metabolomics to sophisticated data analysis techniques. We highlight successful applications in cancer research, particularly focusing on ongoing clinical trials utilizing stable isotope tracing to characterize disease progression, treatment responses, and potential mechanisms of resistance to anticancer therapies. Furthermore, we outline key challenges and discuss potential strategies to address them, aiming to enhance our understanding of the biochemical basis of cancer metabolism.
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Affiliation(s)
- Dalton Hilovsky
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; (D.H.); (J.H.)
| | - Joshua Hartsell
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; (D.H.); (J.H.)
| | - Jamey D. Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37212, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212, USA
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; (D.H.); (J.H.)
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Yu Y, Alseekh S, Zhu Z, Zhou K, Fernie AR. Multiomics and biotechnologies for understanding and influencing cadmium accumulation and stress response in plants. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38817148 DOI: 10.1111/pbi.14379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/04/2024] [Accepted: 05/03/2024] [Indexed: 06/01/2024]
Abstract
Cadmium (Cd) is one of the most toxic heavy metals faced by plants and, additionally, via the food chain, threatens human health. It is principally dispersed through agro-ecosystems via anthropogenic activities and geogenic sources. Given its high mobility and persistence, Cd, although not required, can be readily assimilated by plants thereby posing a threat to plant growth and productivity as well as animal and human health. Thus, breeding crop plants in which the edible parts contain low to zero Cd as safe food stuffs and harvesting shoots of high Cd-containing plants as a route for decontaminating soils are vital strategies to cope with this problem. Recently, multiomics approaches have been employed to considerably enhance our understanding of the mechanisms underlying (i) Cd toxicity, (ii) Cd accumulation, (iii) Cd detoxification and (iv) Cd acquisition tolerance in plants. This information can be deployed in the development of the biotechnological tools for developing plants with modulated Cd tolerance and detoxification to safeguard cellular and genetic integrity as well as to minimize food chain contamination. The aim of this review is to provide a current update about the mechanisms involved in Cd uptake by plants and the recent developments in the area of multiomics approach in terms of Cd stress responses, as well as in the development of Cd tolerant and low Cd accumulating crops.
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Affiliation(s)
- Yan Yu
- School of Agronomy, Anhui Agricultural University, Hefei, China
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Zonghe Zhu
- School of Agronomy, Anhui Agricultural University, Hefei, China
| | - Kejin Zhou
- School of Agronomy, Anhui Agricultural University, Hefei, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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Joblin-Mills A, Wu ZE, Sequeira-Bisson IR, Miles-Chan JL, Poppitt SD, Fraser K. Utilising a Clinical Metabolomics LC-MS Study to Determine the Integrity of Biological Samples for Statistical Modelling after Long Term -80 °C Storage: A TOFI_Asia Sub-Study. Metabolites 2024; 14:313. [PMID: 38921448 PMCID: PMC11205627 DOI: 10.3390/metabo14060313] [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: 04/16/2024] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Biological samples of lipids and metabolites degrade after extensive years in -80 °C storage. We aimed to determine if associated multivariate models are also impacted. Prior TOFI_Asia metabolomics studies from our laboratory established multivariate models of metabolic risks associated with ethnic diversity. Therefore, to compare multivariate modelling degradation after years of -80 °C storage, we selected a subset of aged (≥5-years) plasma samples from the TOFI_Asia study to re-analyze via untargeted LC-MS metabolomics. Samples from European Caucasian (n = 28) and Asian Chinese (n = 28) participants were evaluated for ethnic discrimination by partial least squares discriminative analysis (PLS-DA) of lipids and polar metabolites. Both showed a strong discernment between participants ethnicity by features, before (Initial) and after (Aged) 5-years of -80 °C storage. With receiver operator characteristic curves, sparse PLS-DA derived confusion matrix and prediction error rates, a considerable reduction in model integrity was apparent with the Aged polar metabolite model relative to Initial modelling. Ethnicity modelling with lipids maintained predictive integrity in Aged plasma samples, while equivalent polar metabolite models reduced in integrity. Our results indicate that researchers re-evaluating samples for multivariate modelling should consider time at -80 °C when producing predictive metrics from polar metabolites, more so than lipids.
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Affiliation(s)
- Aidan Joblin-Mills
- Food Chemistry & Structure Team, AgResearch, Palmerston North 4410, New Zealand; (Z.E.W.); (K.F.)
- High-Value Nutrition National Science Challenge, Auckland 1145, New Zealand; (I.R.S.-B.); (J.L.M.-C.); (S.D.P.)
| | - Zhanxuan E. Wu
- Food Chemistry & Structure Team, AgResearch, Palmerston North 4410, New Zealand; (Z.E.W.); (K.F.)
- High-Value Nutrition National Science Challenge, Auckland 1145, New Zealand; (I.R.S.-B.); (J.L.M.-C.); (S.D.P.)
- School of Food and Nutrition, Massey University, Palmerston North 4410, New Zealand
| | - Ivana R. Sequeira-Bisson
- High-Value Nutrition National Science Challenge, Auckland 1145, New Zealand; (I.R.S.-B.); (J.L.M.-C.); (S.D.P.)
- Human Nutrition Unit, School of Biological Sciences, University of Auckland, Auckland 1024, New Zealand
| | - Jennifer L. Miles-Chan
- High-Value Nutrition National Science Challenge, Auckland 1145, New Zealand; (I.R.S.-B.); (J.L.M.-C.); (S.D.P.)
- Human Nutrition Unit, School of Biological Sciences, University of Auckland, Auckland 1024, New Zealand
| | - Sally D. Poppitt
- High-Value Nutrition National Science Challenge, Auckland 1145, New Zealand; (I.R.S.-B.); (J.L.M.-C.); (S.D.P.)
- Human Nutrition Unit, School of Biological Sciences, University of Auckland, Auckland 1024, New Zealand
- Department of Medicine, University of Auckland, Auckland 1145, New Zealand
| | - Karl Fraser
- Food Chemistry & Structure Team, AgResearch, Palmerston North 4410, New Zealand; (Z.E.W.); (K.F.)
- High-Value Nutrition National Science Challenge, Auckland 1145, New Zealand; (I.R.S.-B.); (J.L.M.-C.); (S.D.P.)
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Curtis MA, Saferin N, Nguyen JH, Imami AS, Ryan WG, Neifer KL, Miller GW, Burkett JP. Developmental pyrethroid exposure in mouse leads to disrupted brain metabolism in adulthood. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.13.562226. [PMID: 37961675 PMCID: PMC10634990 DOI: 10.1101/2023.10.13.562226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Environmental and genetic risk factors, and their interactions, contribute significantly to the etiology of neurodevelopmental disorders (NDDs). Recent epidemiology studies have implicated pyrethroid pesticides as an environmental risk factor for autism and developmental delay. Our previous research showed that low-dose developmental exposure to the pyrethroid pesticide deltamethrin in mice caused male-biased changes in the brain and in NDD-relevant behaviors in adulthood. Here, we used a metabolomics approach to determine the broadest possible set of metabolic changes in the adult male mouse brain caused by low-dose pyrethroid exposure during development. Using a litter-based design, we exposed mouse dams during pregnancy and lactation to deltamethrin (3 mg/kg or vehicle every 3 days) at a concentration well below the EPA-determined benchmark dose used for regulatory guidance. We raised male offspring to adulthood and collected whole brain samples for untargeted high-resolution metabolomics analysis. Developmentally exposed mice had disruptions in 116 metabolites which clustered into pathways for folate biosynthesis, retinol metabolism, and tryptophan metabolism. As a cross-validation, we integrated metabolomics and transcriptomics data from the same samples, which confirmed previous findings of altered dopamine signaling. These results suggest that pyrethroid exposure during development leads to disruptions in metabolism in the adult brain, which may inform both prevention and therapeutic strategies.
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Affiliation(s)
- Melissa A. Curtis
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614
| | - Nilanjana Saferin
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614
| | - Jennifer H. Nguyen
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614
| | - Ali S. Imami
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614
| | - William G. Ryan
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614
| | - Kari L. Neifer
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614
| | - Gary W. Miller
- Department of Environmental Health, Emory Rollins School of Public Health, Atlanta, GA 30322
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032 (current)
| | - James P. Burkett
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614
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47
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Tang Q, Ratnayake R, Seabra G, Jiang Z, Fang R, Cui L, Ding Y, Kahveci T, Bian J, Li C, Luesch H, Li Y. Morphological profiling for drug discovery in the era of deep learning. Brief Bioinform 2024; 25:bbae284. [PMID: 38886164 PMCID: PMC11182685 DOI: 10.1093/bib/bbae284] [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: 03/09/2024] [Revised: 05/13/2024] [Accepted: 06/03/2024] [Indexed: 06/20/2024] Open
Abstract
Morphological profiling is a valuable tool in phenotypic drug discovery. The advent of high-throughput automated imaging has enabled the capturing of a wide range of morphological features of cells or organisms in response to perturbations at the single-cell resolution. Concurrently, significant advances in machine learning and deep learning, especially in computer vision, have led to substantial improvements in analyzing large-scale high-content images at high throughput. These efforts have facilitated understanding of compound mechanism of action, drug repurposing, characterization of cell morphodynamics under perturbation, and ultimately contributing to the development of novel therapeutics. In this review, we provide a comprehensive overview of the recent advances in the field of morphological profiling. We summarize the image profiling analysis workflow, survey a broad spectrum of analysis strategies encompassing feature engineering- and deep learning-based approaches, and introduce publicly available benchmark datasets. We place a particular emphasis on the application of deep learning in this pipeline, covering cell segmentation, image representation learning, and multimodal learning. Additionally, we illuminate the application of morphological profiling in phenotypic drug discovery and highlight potential challenges and opportunities in this field.
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Affiliation(s)
- Qiaosi Tang
- Calico Life Sciences, South San Francisco, CA 94080, United States
| | - Ranjala Ratnayake
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, United States
| | - Gustavo Seabra
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, United States
| | - Zhe Jiang
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, United States
| | - Ruogu Fang
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, United States
- J. Crayton Pruitt Family Department of Biomedical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL 32611, United States
| | - Lina Cui
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, United States
| | - Tamer Kahveci
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, United States
| | - Jiang Bian
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32611, United States
| | - Chenglong Li
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, United States
| | - Hendrik Luesch
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, United States
| | - Yanjun Li
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, United States
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, United States
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48
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Downie CG, Highland HM, Alotaibi M, Welch BM, Howard AG, Cheng S, Miller N, Jain M, Kaplan RC, Lilly AG, Long T, Sofer T, Thyagarajan B, Yu B, North KE, Avery CL. Genome-wide association study reveals shared and distinct genetic architecture underlying fatty acid and bioactive oxylipin metabolites in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.21.24307719. [PMID: 38826448 PMCID: PMC11142272 DOI: 10.1101/2024.05.21.24307719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Bioactive fatty acid-derived oxylipin molecules play key roles in mediating inflammation and oxidative stress, which underlie many chronic diseases. Circulating levels of fatty acids and oxylipins are influenced by both environmental and genetic factors; characterizing the genetic architecture of bioactive lipids could yield new insights into underlying biological pathways. Thus, we performed a genome wide association study (GWAS) of n=81 fatty acids and oxylipins in n=11,584 Hispanic Community Health Study/Study of Latinos (HCHS/SOL) participants with genetic and lipidomic data measured at study baseline (58.6% female, mean age = 46.1 years, standard deviation = 13.8 years). Additionally, given the effects of central obesity on inflammation, we examined interactions with waist circumference using two-degree-of-freedom joint tests. Heritability estimates ranged from 0% to 47.9%, and 48 of the 81oxylipins and fatty acids were significantly heritable. Moreover, 40 (49.4%) of the 81 oxylipins and fatty acids had at least one genome-wide significant (p< 6.94E-11) variant resulting in 19 independent genetic loci involved in fatty acid and oxylipin synthesis, as well as downstream pathways. Four loci (lead variant minor allele frequency [MAF] range: 0.08-0.50), including the desaturase-encoding FADS and the OATP1B1 transporter protein-encoding SLCO1B1, exhibited associations with four or more fatty acids and oxylipins. The majority of the 15 remaining loci (87.5%) (lead variant MAF range = 0.03-0.45, mean = 0.23) were only associated with one oxylipin or fatty acid, demonstrating evidence of distinct genetic effects. Finally, while most loci identified in two-degree-of-freedom tests were previously identified in our main effects analyses, we also identified an additional rare variant (MAF = 0.002) near CARS2, a locus previously implicated in inflammation. Our analyses revealed shared and distinct genetic architecture underlying fatty acids and oxylipins, providing insights into genetic factors and motivating future multi-omics work to characterize these compounds and elucidate their roles in disease pathways.
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Affiliation(s)
- Carolina G Downie
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Mona Alotaibi
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, San Diego, San Diego, CA
| | - Barrett M Welch
- School of Public Health, University of Nevada, Reno, Reno, NV
| | - Annie Green Howard
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Mohit Jain
- Sapient Bioanalytics, San Diego, CA
- Departments of Medicine and Pharmacology, University of California, San Diego, San Diego, CA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY; Public Health Sciences Division, Fred Hutchison Cancer Center, Seattle, WA
| | - Adam G Lilly
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Tao Long
- Sapient Bioanalytics, San Diego, CA
| | - Tamar Sofer
- CardioVascular Institute (CVI), Beth Israel Deaconess Medical Center, Boston, MA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical Center, Minneapolis, MN
| | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health, Houston, TX
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Chang C, Roh YS, Du M, Kuo YC, Zhang Y, Hardy M, Gahler R, Solnier J. Differences in Metabolite Profiles of Dihydroberberine and Micellar Berberine in Caco-2 Cells and Humans-A Pilot Study. Int J Mol Sci 2024; 25:5625. [PMID: 38891813 PMCID: PMC11171481 DOI: 10.3390/ijms25115625] [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: 04/15/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
We investigated the pharmacokinetic pathway of berberine and its metabolites in vitro, in Caco-2 cells, and in human participants following the administration of dihydroberberine (DHB) and micellar berberine (LipoMicel®, LMB) formulations. A pilot trial involving nine healthy volunteers was conducted over a 24 h period; blood samples were collected and subjected to Ultra High-Performance Liquid Chromatography-High Resolution Mass Spectrometry (UHPLC-HRMS) analyses to quantify the concentrations of berberine and its metabolites. Pharmacokinetic correlations indicated that berberrubine and thalifendine follow distinct metabolic pathways. Additionally, jatrorrhizine sulfate appeared to undergo metabolism differently compared to the other sulfated metabolites. Moreover, berberrubine glucuronide likely has a unique metabolic pathway distinct from other glucuronides. The human trial revealed significantly higher blood concentrations of berberine metabolites in participants of the DHB treatment group compared to the LMB treatment group-except for berberrubine glucuronide, which was only detected in the LMB treatment group. Similarly, results from in vitro investigations showed significant differences in berberine metabolite profiles between DHB and LMB. Dihydroberberine, dihydroxy-berberrubine/thalifendine and jatrorrhizine sulfate were detected in LMB-treated cells, but not in DHB-treated cells; thalifendine and jatrorrhizine-glucuronide were detected in DHB-treated cells only. While DHB treatment provided higher blood concentrations of berberine and most berberine metabolites, both in vitro (Caco-2 cells) and in vivo human studies showed that treatment with LMB resulted in a higher proportion of unmetabolized berberine compared to DHB. These findings suggest potential clinical implications that merit further investigation in future large-scale trials.
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Affiliation(s)
- Chuck Chang
- ISURA, Clinical Research, Burnaby, BC V3N 4S9, Canada; (C.C.); (Y.S.R.); (M.D.); (Y.C.K.); (Y.Z.)
| | - Yoon Seok Roh
- ISURA, Clinical Research, Burnaby, BC V3N 4S9, Canada; (C.C.); (Y.S.R.); (M.D.); (Y.C.K.); (Y.Z.)
| | - Min Du
- ISURA, Clinical Research, Burnaby, BC V3N 4S9, Canada; (C.C.); (Y.S.R.); (M.D.); (Y.C.K.); (Y.Z.)
| | - Yun Chai Kuo
- ISURA, Clinical Research, Burnaby, BC V3N 4S9, Canada; (C.C.); (Y.S.R.); (M.D.); (Y.C.K.); (Y.Z.)
| | - Yiming Zhang
- ISURA, Clinical Research, Burnaby, BC V3N 4S9, Canada; (C.C.); (Y.S.R.); (M.D.); (Y.C.K.); (Y.Z.)
| | - Mary Hardy
- Academy of Integrative and Holistic Medicine, San Diego, CA 92037, USA;
| | | | - Julia Solnier
- ISURA, Clinical Research, Burnaby, BC V3N 4S9, Canada; (C.C.); (Y.S.R.); (M.D.); (Y.C.K.); (Y.Z.)
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50
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Heuckeroth S, Damiani T, Smirnov A, Mokshyna O, Brungs C, Korf A, Smith JD, Stincone P, Dreolin N, Nothias LF, Hyötyläinen T, Orešič M, Karst U, Dorrestein PC, Petras D, Du X, van der Hooft JJJ, Schmid R, Pluskal T. Reproducible mass spectrometry data processing and compound annotation in MZmine 3. Nat Protoc 2024:10.1038/s41596-024-00996-y. [PMID: 38769143 DOI: 10.1038/s41596-024-00996-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 02/26/2024] [Indexed: 05/22/2024]
Abstract
Untargeted mass spectrometry (MS) experiments produce complex, multidimensional data that are practically impossible to investigate manually. For this reason, computational pipelines are needed to extract relevant information from raw spectral data and convert it into a more comprehensible format. Depending on the sample type and/or goal of the study, a variety of MS platforms can be used for such analysis. MZmine is an open-source software for the processing of raw spectral data generated by different MS platforms. Examples include liquid chromatography-MS, gas chromatography-MS and MS-imaging. These data might typically be associated with various applications including metabolomics and lipidomics. Moreover, the third version of the software, described herein, supports the processing of ion mobility spectrometry (IMS) data. The present protocol provides three distinct procedures to perform feature detection and annotation of untargeted MS data produced by different instrumental setups: liquid chromatography-(IMS-)MS, gas chromatography-MS and (IMS-)MS imaging. For training purposes, example datasets are provided together with configuration batch files (i.e., list of processing steps and parameters) to allow new users to easily replicate the described workflows. Depending on the number of data files and available computing resources, we anticipate this to take between 2 and 24 h for new MZmine users and nonexperts. Within each procedure, we provide a detailed description for all processing parameters together with instructions/recommendations for their optimization. The main generated outputs are represented by aligned feature tables and fragmentation spectra lists that can be used by other third-party tools for further downstream analysis.
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Affiliation(s)
| | - Tito Damiani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Olena Mokshyna
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Corinna Brungs
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ansgar Korf
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Joshua David Smith
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | | | - Louis-Félix Nothias
- University of Geneva, Geneva, Switzerland
- Université Côte d'Azur, CNRS, ICN, Nice, France
| | | | - Matej Orešič
- Örebro University, Örebro, Sweden
- University of Turku and Åbo Akademi University, Turku, Finland
| | - Uwe Karst
- University of Münster, Münster, Germany
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Daniel Petras
- University of Tuebingen, Tuebingen, Germany
- University of California Riverside, Riverside, CA, USA
| | - Xiuxia Du
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Justin J J van der Hooft
- Wageningen University & Research, Wageningen, the Netherlands
- University of Johannesburg, Johannesburg, South Africa
| | - Robin Schmid
- University of Münster, Münster, Germany.
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Tomáš Pluskal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
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