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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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2
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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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3
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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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4
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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:e0034224. [PMID: 38899884 DOI: 10.1128/aem.00342-24] [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: 03/02/2024] [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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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:e0130123. [PMID: 38899930 DOI: 10.1128/msystems.01301-23] [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: 12/06/2023] [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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6
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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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7
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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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8
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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. [PMID: 38858849 DOI: 10.1021/acs.analchem.4c01584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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9
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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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10
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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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11
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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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12
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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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13
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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] [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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14
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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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15
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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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16
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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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17
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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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18
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Wang J, Qiu Z, Zeng H, Tan Y, Huang Y, Luo J, Shu W. Long-Term Consumption of Purified Water Altered Amino Acid, Fatty Acid and Energy Metabolism in Livers of Rats. Metabolites 2024; 14:289. [PMID: 38786766 PMCID: PMC11122726 DOI: 10.3390/metabo14050289] [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: 04/24/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
The consumption of low-mineral water has been increasing worldwide. Drinking low-mineral water is associated with cardiovascular disease, osteopenia, and certain neurodegenerative diseases. However, the specific mechanism remains unclear. The liver metabolic alterations in rats induced by drinking purified water for 3 months were investigated with a metabolomics-based strategy. Compared with the tap water group, 74 metabolites were significantly changed in the purified water group (6 increased and 68 decreased), including 29 amino acids, 11 carbohydrates, 10 fatty acids, 7 short chain fatty acids (SCFAs), and 17 other biomolecules. Eight metabolic pathways were significantly changed, namely aminoacyl-tRNA biosynthesis; nitrogen metabolism; alanine, aspartate and glutamate metabolism; arginine and proline metabolism; histidine metabolism; biosynthesis of unsaturated fatty acids; butanoate metabolism; and glycine, serine and threonine metabolism. These changes suggested that consumption of purified water induced negative nitrogen balance, reduced expression of some polyunsaturated fatty acids and SCFAs, and disturbed energy metabolism in rats. These metabolic disturbances may contribute to low-mineral-water-associated health risks. The health risk of consuming low-mineral water requires attention.
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Affiliation(s)
- Jia Wang
- Department of Medical English, College of Basic Medicine, Army Medical University, Chongqing 400038, China;
| | - Zhiqun Qiu
- Department of Environmental Hygiene, College of Preventive Medicine, Army Medical University, Chongqin 400038, China; (Z.Q.); (H.Z.); (Y.T.); (Y.H.)
| | - Hui Zeng
- Department of Environmental Hygiene, College of Preventive Medicine, Army Medical University, Chongqin 400038, China; (Z.Q.); (H.Z.); (Y.T.); (Y.H.)
| | - Yao Tan
- Department of Environmental Hygiene, College of Preventive Medicine, Army Medical University, Chongqin 400038, China; (Z.Q.); (H.Z.); (Y.T.); (Y.H.)
| | - Yujing Huang
- Department of Environmental Hygiene, College of Preventive Medicine, Army Medical University, Chongqin 400038, China; (Z.Q.); (H.Z.); (Y.T.); (Y.H.)
| | - Jiaohua Luo
- Department of Environmental Hygiene, College of Preventive Medicine, Army Medical University, Chongqin 400038, China; (Z.Q.); (H.Z.); (Y.T.); (Y.H.)
| | - Weiqun Shu
- Department of Environmental Hygiene, College of Preventive Medicine, Army Medical University, Chongqin 400038, China; (Z.Q.); (H.Z.); (Y.T.); (Y.H.)
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19
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Jiang F, Li M, Huang L, Wang H, Bai Z, Niu L, Zhang Y. Metabolite Profiling and Biological Activity Assessment of Paeonia ostii Anthers and Pollen Using UPLC-QTOF-MS. Int J Mol Sci 2024; 25:5462. [PMID: 38791503 PMCID: PMC11121493 DOI: 10.3390/ijms25105462] [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: 03/19/2024] [Revised: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Paeonia ostii is an important economic oil and medicinal crop. Its anthers are often used to make tea in China with beneficial effects on human health. However, the metabolite profiles, as well as potential biological activities of P. ostii anthers and the pollen within anthers have not been systematically analyzed, which hinders the improvement of P. ostii utilization. With comprehensive untargeted metabolomic analysis using UPLC-QTOF-MS, we identified a total of 105 metabolites in anthers and pollen, mainly including phenylpropanoids, polyketides, organic acids, benzenoids, lipids, and organic oxygen compounds. Multivariate statistical analysis revealed the metabolite differences between anthers and pollen, with higher carbohydrates and flavonoids content in pollen and higher phenolic content in anthers. Meanwhile, both anthers and pollen extracts exhibited antioxidant activity, antibacterial activity, α-glucosidase and α-amylase inhibitory activity. In general, the anther stage of S4 showed the highest biological activity among all samples. This study illuminated the metabolites and biological activities of anthers and pollen of P. ostii, which supports the further utilization of them.
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Affiliation(s)
- Fengfei Jiang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling District, Xianyang 712100, China; (F.J.); (M.L.); (L.H.); (H.W.); (Z.B.)
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling District, Xianyang 712100, China
| | - Mengchen Li
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling District, Xianyang 712100, China; (F.J.); (M.L.); (L.H.); (H.W.); (Z.B.)
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling District, Xianyang 712100, China
| | - Linbo Huang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling District, Xianyang 712100, China; (F.J.); (M.L.); (L.H.); (H.W.); (Z.B.)
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling District, Xianyang 712100, China
| | - Hui Wang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling District, Xianyang 712100, China; (F.J.); (M.L.); (L.H.); (H.W.); (Z.B.)
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling District, Xianyang 712100, China
| | - Zhangzhen Bai
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling District, Xianyang 712100, China; (F.J.); (M.L.); (L.H.); (H.W.); (Z.B.)
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling District, Xianyang 712100, China
| | - Lixin Niu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling District, Xianyang 712100, China; (F.J.); (M.L.); (L.H.); (H.W.); (Z.B.)
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling District, Xianyang 712100, China
| | - Yanlong Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling District, Xianyang 712100, China; (F.J.); (M.L.); (L.H.); (H.W.); (Z.B.)
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling District, Xianyang 712100, China
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20
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Yu J, Yang Y, Luo L, Feng F, Saeed S, Luo J, Fang C, Zhou J, Li K. Photoperiod-Dependent Nutrient Accumulation in Rice Cultivated in Plant Factories: A Comparative Metabolomic Analysis. Foods 2024; 13:1544. [PMID: 38790844 PMCID: PMC11121446 DOI: 10.3390/foods13101544] [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: 03/18/2024] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Plant factories offer a promising solution to some of the challenges facing traditional agriculture, allowing for year-round rapid production of plant-derived foods. However, the effects of conditions in plant factories on metabolic nutrients remain to be explored. In this study, we used three rice accessions (KongYu131, HuangHuaZhan, and Kam Sweet Rice) as objectives, which were planted in a plant factory with strict photoperiods that are long-day (12 h light/12 h dark) or short-day (8 h light/16 h dark). A total of 438 metabolites were detected in the harvested rice grains. The difference in photoperiod leads to a different accumulation of metabolites in rice grains. Most metabolites accumulated significantly higher levels under the short-day condition than the long-day condition. Differentially accumulated metabolites were enriched in the amino acids and vitamin B6 pathway. Asparagine, pyridoxamine, and pyridoxine are key metabolites that accumulate at higher levels in rice grains harvested from the short-day photoperiod. This study reveals the photoperiod-dependent metabolomic differences in rice cultivated in plant factories, especially the metabolic profiling of taste- and nutrition-related compounds.
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Affiliation(s)
- Jingyao Yu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (J.Y.); (Y.Y.); (J.L.); (C.F.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570288, China;
| | - Yu Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (J.Y.); (Y.Y.); (J.L.); (C.F.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570288, China;
| | - Lanjun Luo
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570288, China;
| | - Fang Feng
- Wuhan Greenfafa Institute of Novel Genechip R&D Co., Ltd., Wuhan 430070, China;
| | - Sana Saeed
- Department of Plant Breeding & Genetics, University of Sargodha, Sargodha 40100, Pakistan;
| | - Jie Luo
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (J.Y.); (Y.Y.); (J.L.); (C.F.)
| | - Chuanying Fang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (J.Y.); (Y.Y.); (J.L.); (C.F.)
| | - Junjie Zhou
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (J.Y.); (Y.Y.); (J.L.); (C.F.)
- School of Life and Health Sciences, Hainan University, Haikou 570288, China
| | - Kang Li
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (J.Y.); (Y.Y.); (J.L.); (C.F.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570288, China;
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21
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Ovbude ST, Sharmeen S, Kyei I, Olupathage H, Jones J, Bell RJ, Powers R, Hage DS. Applications of chromatographic methods in metabolomics: A review. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1239:124124. [PMID: 38640794 DOI: 10.1016/j.jchromb.2024.124124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 03/11/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024]
Abstract
Chromatography is a robust and reliable separation method that can use various stationary phases to separate complex mixtures commonly seen in metabolomics. This review examines the types of chromatography and stationary phases that have been used in targeted or untargeted metabolomics with methods such as mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. General considerations for sample pretreatment and separations in metabolomics are considered, along with the various supports and separation formats for chromatography that have been used in such work. The types of liquid chromatography (LC) that have been most extensively used in metabolomics will be examined, such as reversed-phase liquid chromatography and hydrophilic liquid interaction chromatography. In addition, other forms of LC that have been used in more limited applications for metabolomics (e.g., ion-exchange, size-exclusion, and affinity methods) will be discussed to illustrate how these techniques may be utilized for new and future research in this field. Multidimensional LC methods are also discussed, as well as the use of gas chromatography and supercritical fluid chromatography in metabolomics. In addition, the roles of chromatography in NMR- vs. MS-based metabolomics are considered. Applications are given within the field of metabolomics for each type of chromatography, along with potential advantages or limitations of these separation methods.
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Affiliation(s)
- Susan T Ovbude
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Sadia Sharmeen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Isaac Kyei
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Harshana Olupathage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Jacob Jones
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Richard J Bell
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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22
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Hill CJ, Phelan MM, Dutton PJ, Busuulwa P, Maclean A, Davison AS, Drury JA, Tempest N, Horne AW, Gutiérrez EC, Hapangama DK. Diagnostic utility of clinicodemographic, biochemical and metabolite variables to identify viable pregnancies in a symptomatic cohort during early gestation. Sci Rep 2024; 14:11172. [PMID: 38750192 PMCID: PMC11096363 DOI: 10.1038/s41598-024-61690-3] [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: 03/04/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024] Open
Abstract
A significant number of pregnancies are lost in the first trimester and 1-2% are ectopic pregnancies (EPs). Early pregnancy loss in general can cause significant morbidity with bleeding or infection, while EPs are the leading cause of maternal mortality in the first trimester. Symptoms of pregnancy loss and EP are very similar (including pain and bleeding); however, these symptoms are also common in live normally sited pregnancies (LNSP). To date, no biomarkers have been identified to differentiate LNSP from pregnancies that will not progress beyond early gestation (non-viable or EPs), defined together as combined adverse outcomes (CAO). In this study, we present a novel machine learning pipeline to create prediction models that identify a composite biomarker to differentiate LNSP from CAO in symptomatic women. This prospective cohort study included 370 participants. A single blood sample was prospectively collected from participants on first emergency presentation prior to final clinical diagnosis of pregnancy outcome: LNSP, miscarriage, pregnancy of unknown location (PUL) or tubal EP (tEP). Miscarriage, PUL and tEP were grouped together into a CAO group. Human chorionic gonadotrophin β (β-hCG) and progesterone concentrations were measured in plasma. Serum samples were subjected to untargeted metabolomic profiling. The cohort was randomly split into train and validation data sets, with the train data set subjected to variable selection. Nine metabolite signals were identified as key discriminators of LNSP versus CAO. Random forest models were constructed using stable metabolite signals alone, or in combination with plasma hormone concentrations and demographic data. When comparing LNSP with CAO, a model with stable metabolite signals only demonstrated a modest predictive accuracy (0.68), which was comparable to a model of β-hCG and progesterone (0.71). The best model for LNSP prediction comprised stable metabolite signals and hormone concentrations (accuracy = 0.79). In conclusion, serum metabolite levels and biochemical markers from a single blood sample possess modest predictive utility in differentiating LNSP from CAO pregnancies upon first presentation, which is improved by variable selection and combination using machine learning. A diagnostic test to confirm LNSP and thus exclude pregnancies affecting maternal morbidity and potentially life-threatening outcomes would be invaluable in emergency situations.
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Affiliation(s)
- Christopher J Hill
- Department of Women's and Children's Health, Centre for Women's Health Research, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool, L8 7SS, UK
| | - Marie M Phelan
- High Field NMR Facility, Liverpool Shared Research Facilities, University of Liverpool, Liverpool, L69 7TX, UK
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Philip J Dutton
- Department of Women's and Children's Health, Centre for Women's Health Research, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool, L8 7SS, UK
- Liverpool Women's Hospital NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool, L8 7SS, UK
| | - Paula Busuulwa
- Department of Women's and Children's Health, Centre for Women's Health Research, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool, L8 7SS, UK
- Liverpool Women's Hospital NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool, L8 7SS, UK
| | - Alison Maclean
- Department of Women's and Children's Health, Centre for Women's Health Research, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool, L8 7SS, UK
| | - Andrew S Davison
- Department of Women's and Children's Health, Centre for Women's Health Research, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool, L8 7SS, UK
- Department of Clinical Biochemistry and Metabolic Medicine, Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Foundation Trust, Liverpool, L7 8SP, UK
| | - Josephine A Drury
- Department of Women's and Children's Health, Centre for Women's Health Research, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool, L8 7SS, UK
| | - Nicola Tempest
- Department of Women's and Children's Health, Centre for Women's Health Research, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool, L8 7SS, UK
- Liverpool Women's Hospital NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool, L8 7SS, UK
| | - Andrew W Horne
- Centre for Reproductive Health, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Eva Caamaño Gutiérrez
- High Field NMR Facility, Liverpool Shared Research Facilities, University of Liverpool, Liverpool, L69 7TX, UK
- Computational Biology Facility, Liverpool Shared Research Facilities, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Dharani K Hapangama
- Department of Women's and Children's Health, Centre for Women's Health Research, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool, L8 7SS, UK.
- Liverpool Women's Hospital NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool, L8 7SS, UK.
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23
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Ware I, Franke K, Frolov A, Bureiko K, Kysil E, Yahayu M, El Enshasy HA, Wessjohann LA. Comparative metabolite analysis of Piper sarmentosum organs approached by LC-MS-based metabolic profiling. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:30. [PMID: 38743199 PMCID: PMC11093948 DOI: 10.1007/s13659-024-00453-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024]
Abstract
Piper sarmentosum Roxb. (Piperaceae) is a traditional medicinal and food plant widely distributed in the tropical and subtropical regions of Asia, offering both health and culinary benefits. In this study the secondary metabolites in different organs of P. sarmentosum were identified and their relative abundances were characterized. The metabolic profiles of leaves, roots, stems and fruits were comprehensively investigated by liquid chromatography high-resolution mass spectrometry (LC-HR-MS) and the data subsequently analyzed using multivariate statistical methods. Manual interpretation of the tandem mass spectrometric (MS/MS) fragmentation patterns revealed the presence of 154 tentatively identified metabolites, mostly represented by alkaloids and flavonoids. Principle component analysis and hierarchical clustering indicated the predominant occurrence of flavonoids, lignans and phenyl propanoids in leaves, aporphines in stems, piperamides in fruits and lignan-amides in roots. Overall, this study provides extensive data on the metabolite composition of P. sarmentosum, supplying useful information for bioactive compounds discovery and patterns of their preferential biosynthesis or storage in specific organs. This can be used to optimize production and harvesting as well as to maximize the plant's economic value as herbal medicine or in food applications.
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Affiliation(s)
- Ismail Ware
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), 81310 Johor Bahru, Johor, Malaysia
| | - Katrin Franke
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany.
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, 06108, Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| | - Kseniia Bureiko
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| | - Elana Kysil
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| | - Maizatulakmal Yahayu
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), 81310 Johor Bahru, Johor, Malaysia
| | - Hesham Ali El Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), 81310 Johor Bahru, Johor, Malaysia
- City of Scientific Research and Technology Applications, New Borg Al Arab, Alexandria, 21934, Egypt
| | - Ludger A Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.
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24
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Yu W, Gong F, Xu H, Zhou X. Molecular Mechanism of Exogenous ABA to Enhance UV-B Resistance in Rhododendron chrysanthum Pall. by Modulating Flavonoid Accumulation. Int J Mol Sci 2024; 25:5248. [PMID: 38791294 PMCID: PMC11121613 DOI: 10.3390/ijms25105248] [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: 04/10/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
With the depletion of the ozone layer, the intensity of ultraviolet B (UV-B) radiation reaching the Earth's surface increases, which in turn causes significant stress to plants and affects all aspects of plant growth and development. The aim of this study was to investigate the mechanism of response to UV-B radiation in the endemic species of Rhododendron chrysanthum Pall. (R. chrysanthum) in the Changbai Mountains and to study how exogenous ABA regulates the response of R. chrysanthum to UV-B stress. The results of chlorophyll fluorescence images and OJIP kinetic curves showed that UV-B radiation damaged the PSII photosystem of R. chrysanthum, and exogenous ABA could alleviate this damage to some extent. A total of 2148 metabolites were detected by metabolomics, of which flavonoids accounted for the highest number (487, or 22.67%). KEGG enrichment analysis of flavonoids that showed differential accumulation by UV-B radiation and exogenous ABA revealed that flavonoid biosynthesis and flavone and flavonol biosynthesis were significantly altered. GO analysis showed that most of the DEGs produced after UV-B radiation and exogenous ABA were distributed in the cellular process, cellular anatomical entity, and catalytic activity. Network analysis of key DFs and DEGs associated with flavonoid synthesis identified key flavonoids (isorhamnetin-3-O-gallate and dihydromyricetin) and genes (TRINITY_DN2213_c0_g1_i4-A1) that promote the resistance of R. chrysanthum to UV-B stress. In addition, multiple transcription factor families were found to be involved in the regulation of the flavonoid synthesis pathway under UV-B stress. Overall, R. chrysanthum actively responded to UV-B stress by regulating changes in flavonoids, especially flavones and flavonols, while exogenous ABA further enhanced its resistance to UV-B stress. The experimental results not only provide a new perspective for understanding the molecular mechanism of the response to UV-B stress in the R. chrysanthum, but also provide a valuable theoretical basis for future research and application in improving plant adversity tolerance.
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Affiliation(s)
| | | | - Hongwei Xu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping 136000, China
| | - Xiaofu Zhou
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping 136000, China
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25
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Szűcs Z, Cziáky Z, Volánszki L, Máthé C, Vasas G, Gonda S. Production of Polyphenolic Natural Products by Bract-Derived Tissue Cultures of Three Medicinal Tilia spp.: A Comparative Untargeted Metabolomics Study. PLANTS (BASEL, SWITZERLAND) 2024; 13:1288. [PMID: 38794359 PMCID: PMC11124948 DOI: 10.3390/plants13101288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024]
Abstract
Medicinal plant tissue cultures are potential sources of bioactive compounds. In this study, we report the chemical characterization of the callus cultures of three medicinal Tilia spp. (Tilia cordata, Tilia vulgaris and Tilia tomentosa), along with the comparison to bracts and flowers of the same species. Our aim was to show that calli of Tilia spp. are good alternatives to the calli of T. americana for the production of polyphenols and are better sources of a subset of polyphenolic metabolites, compared to the original organs. Calli were initiated from young bracts and grown on woody plant medium containing 1 mg L-1 2,4-D and 0.1 mg L-1 BAP. For chemical characterization, a quality-controlled untargeted metabolomics approach and the quantification of several bioactive compounds was performed with the use of LC-ESI-MS/MS. While bracts and flowers contained flavonoid glycosides (astragalin, isoquercitrin) as major polyphenols, calli of all species contained catechins, coumarins (fraxin, esculin and scopoletin) and flavane aglyca. T. tomentosa calli contained 5397 µg g DW-1 catechin, 201 µg g DW-1 esculin, 218 µg g DW-1 taxifolin and 273 µg g DW-1 eriodictyol, while calli from other species contained lower amounts. T. cordata and T. tomentosa flowers were rich in isoquercitrin, containing 8134 and 6385 µg g DW-1, respectively. The currently tested species contained many of the bioactive metabolites described from T. americana. The production of catechin was shown to be comparable to the most efficient tissue cultures reported. Flowers and bracts contained flavonoid glycosides, including tiliroside, resembling bioactive fractions of T. americana. In addition, untargeted metabolomics has shown fingerprint-like differences among species, highlighting possible chemotaxonomic and quality control applications, especially for bracts.
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Affiliation(s)
- Zsolt Szűcs
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (Z.S.); (C.M.); (G.V.)
- Healthcare Industry Institute, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Zoltán Cziáky
- Agricultural and Molecular Research and Service Institute, University of Nyíregyháza, Sóstói út 31/b, 4400 Nyíregyháza, Hungary;
| | - László Volánszki
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (Z.S.); (C.M.); (G.V.)
- Doctoral School of Pharmaceutical Sciences, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Csaba Máthé
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (Z.S.); (C.M.); (G.V.)
| | - Gábor Vasas
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (Z.S.); (C.M.); (G.V.)
- Balaton Limnological Research Institute, HUN-REN (Hungarian Research Network), Klebelsberg K. u. 3, 8237 Tihany, Hungary
| | - Sándor Gonda
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (Z.S.); (C.M.); (G.V.)
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26
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Kuang Z, Kong M, Yan N, Ma X, Wu M, Li J. Precision Cardio-oncology: Update on Omics-Based Diagnostic Methods. Curr Treat Options Oncol 2024; 25:679-701. [PMID: 38676836 PMCID: PMC11082000 DOI: 10.1007/s11864-024-01203-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2024] [Indexed: 04/29/2024]
Abstract
OPINION STATEMENT Cardio-oncology is an emerging interdisciplinary field dedicated to the early detection and treatment of adverse cardiovascular events associated with anticancer treatment, and current clinical management of anticancer-treatment-related cardiovascular toxicity (CTR-CVT) remains limited by a lack of detailed phenotypic data. However, the promise of diagnosing CTR-CVT using deep phenotyping has emerged with the development of precision medicine, particularly the use of omics-based methodologies to discover sensitive biomarkers of the disease. In the future, combining information produced by a variety of omics methodologies could expand the clinical practice of cardio-oncology. In this review, we demonstrate how omics approaches can improve our comprehension of CTR-CVT deep phenotyping, discuss the positive and negative aspects of available omics approaches for CTR-CVT diagnosis, and outline how to integrate multiple sets of omics data into individualized monitoring and treatment. This will offer a reliable technical route for lowering cardiovascular morbidity and mortality in cancer patients and survivors.
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Affiliation(s)
- Ziyu Kuang
- Oncology Department, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Miao Kong
- Oncology Department, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ningzhe Yan
- Oncology Department, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Xinyi Ma
- Oncology Department, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Min Wu
- Cardiovascular Department, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Jie Li
- Oncology Department, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.
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27
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Santos AA, Delgado TC, Marques V, Ramirez-Moncayo C, Alonso C, Vidal-Puig A, Hall Z, Martínez-Chantar ML, Rodrigues CM. Spatial metabolomics and its application in the liver. Hepatology 2024; 79:1158-1179. [PMID: 36811413 PMCID: PMC11020039 DOI: 10.1097/hep.0000000000000341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/05/2023] [Indexed: 02/24/2023]
Abstract
Hepatocytes work in highly structured, repetitive hepatic lobules. Blood flow across the radial axis of the lobule generates oxygen, nutrient, and hormone gradients, which result in zoned spatial variability and functional diversity. This large heterogeneity suggests that hepatocytes in different lobule zones may have distinct gene expression profiles, metabolic features, regenerative capacity, and susceptibility to damage. Here, we describe the principles of liver zonation, introduce metabolomic approaches to study the spatial heterogeneity of the liver, and highlight the possibility of exploring the spatial metabolic profile, leading to a deeper understanding of the tissue metabolic organization. Spatial metabolomics can also reveal intercellular heterogeneity and its contribution to liver disease. These approaches facilitate the global characterization of liver metabolic function with high spatial resolution along physiological and pathological time scales. This review summarizes the state of the art for spatially resolved metabolomic analysis and the challenges that hinder the achievement of metabolome coverage at the single-cell level. We also discuss several major contributions to the understanding of liver spatial metabolism and conclude with our opinion on the future developments and applications of these exciting new technologies.
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Affiliation(s)
- André A. Santos
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa C. Delgado
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Bizkaia, Spain
- Congenital Metabolic Disorders, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Vanda Marques
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Carmen Ramirez-Moncayo
- Institute of Clinical Sciences, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | | | - Antonio Vidal-Puig
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Centro Investigation Principe Felipe, Valencia, Spain
| | - Zoe Hall
- Division of Systems Medicine, Imperial College London, London, UK
| | - María Luz Martínez-Chantar
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain
| | - Cecilia M.P. Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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Kelly JT, McNamara LE, Hoover ME, Rubenstein HM, Houthuijs K, Martens J. Development of Nontargeted Workflow of Occupational Exposure by Infrared Ion Spectroscopy and Silicone Wristbands' Passive Sampling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:829-833. [PMID: 38564189 DOI: 10.1021/jasms.3c00400] [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: 04/04/2024]
Abstract
A new approach using orthogonal analytical techniques is developed for chemical identification. High resolution mass spectrometry and infrared ion spectroscopy are applied through a 5-level confidence paradigm to demonstrate the effectiveness of nontargeted workflow for the identification of hazardous organophosphates. Triphenyl phosphate is used as a surrogate organophosphate for occupational exposure, and silicone wristbands are used to represent personal samplers. Spectral data of a target compound is combined with spectral data of the sodium adduct and quantum chemical calculations to achieve a confirmed identification. Here, we demonstrate a nontargeted workflow that identifies organophosphate exposure and provides a mechanism for selecting validated methods for quantitative analyses.
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Affiliation(s)
- John T Kelly
- Savannah River National Laboratory, 301 Gateway Drive, Aiken, South Carolina 29803, United States
| | - Louis E McNamara
- Savannah River National Laboratory, 301 Gateway Drive, Aiken, South Carolina 29803, United States
| | - Megan E Hoover
- Savannah River National Laboratory, 301 Gateway Drive, Aiken, South Carolina 29803, United States
| | - H Mitchell Rubenstein
- United States Air Force - Air Force Research Laboratory, 711th Human Performance Wing, 2510 Fifth Street, Area B, Building 840, Wright-Patterson AFB, Ohio 45433, United States
| | - Kas Houthuijs
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
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29
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Deng W, He Q, Zhang W. Analysis of the mechanism of curcumin against osteoarthritis using metabolomics and transcriptomics. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:3313-3329. [PMID: 37938371 PMCID: PMC11074044 DOI: 10.1007/s00210-023-02785-y] [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: 08/28/2023] [Accepted: 10/12/2023] [Indexed: 11/09/2023]
Abstract
Curcumin, a polyphenolic compound derived from the turmeric plant (Curcuma longa), has been extensively studied for its anti-inflammatory and anti-proliferative properties. The safety and efficacy of curcumin have been thoroughly validated. Nevertheless, the underlying mechanism for treating osteoarthritis remains ambiguous. This study aims to reveal the potential mechanism of curcumin in treating osteoarthritis by using metabolomics and transcriptomics. Firstly, we validated the effect of curcumin on inflammatory factors in human articular chondrocytes. Secondly, we explored the cellular metabolism mechanism of curcumin against osteoarthritis using cell metabolomics. Thirdly, we assessed the differences in gene expression of human articular chondrocytes through transcriptomics. Lastly, to evaluate the essential targets and elucidate the potential mechanism underlying the therapeutic effects of curcumin in osteoarthritis, we conducted a screening of the proteins within the shared pathway of metabolomics and transcriptomics. Our results demonstrated that curcumin significantly decreased the levels of inflammatory markers, such as IL-β, IL-6, and TNF-α, in human articular chondrocytes. Cell metabolomics identified 106 differential metabolites, including beta-aminopropionitrile, 3-amino-2-piperidone, pyrrole-2-carboxaldehyde, and various other components. The transcriptomic analysis yielded 1050 differential mRNAs. Enrichment analysis showed that the differential metabolites and mRNAs were significantly enriched in seven pathways, including glycine, serine, and threonine metabolism; pentose and glucuronate interconversions; glycerolipid metabolism; histidine metabolism; mucin-type o-glycan biosynthesis; inositol phosphate metabolism; and cysteine and methionine metabolism. A total of 23 key targets were identified to be involved in these pathways. We speculate that curcumin may alleviate osteoarthritis by targeting key proteins involved in glycine, serine, and threonine metabolism; inhibiting pyruvate production; and modulating glycolysis.
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Affiliation(s)
- Wenxiang Deng
- College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China
| | - Qinghu He
- Department of Rehabilitation and Healthcare, Hunan University of Medicine, Huaihua, 418000, Hunan, China.
- College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China.
| | - Wenan Zhang
- College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China
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30
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Ponce LF, Bishop SL, Wacker S, Groves RA, Lewis IA. SCALiR: A Web Application for Automating Absolute Quantification of Mass Spectrometry-Based Metabolomics Data. Anal Chem 2024; 96:6566-6574. [PMID: 38642077 DOI: 10.1021/acs.analchem.3c04988] [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: 04/22/2024]
Abstract
Quantitative liquid chromatography-mass spectrometry (LC-MS)-based metabolomics is becoming an important approach for studying complex biological systems but presents several technical challenges that limit its widespread use. Computing metabolite concentrations using standard curves generated from standard mixtures of known concentrations is a labor-intensive process that is often performed manually. Currently, there are few options for open-source software tools that can automatically calculate metabolite concentrations. Herein, we introduce SCALiR (standard curve application for determining linear ranges), a new web-based software tool specifically built for this task, which allows users to automatically transform LC-MS signals into absolute quantitative data (https://www.lewisresearchgroup.org/software). SCALiR uses an algorithm that automatically finds the equation of the line of best fit for each standard curve and uses this equation to calculate compound concentrations from the LC-MS signal. Using a standard mix containing 77 metabolites, we show a close correlation between the concentrations calculated by SCALiR and the expected concentrations of each compound (R2 = 0.99 for a y = x curve fitting). Moreover, we demonstrate that SCALiR reproducibly calculates concentrations of midrange standards across ten analytical batches (average coefficient of variation 0.091). SCALiR can be used to calculate metabolite concentrations either using external calibration curves or by using internal standards to correct for matrix effects. This open-source and vendor agnostic software offers users several advantages in that (1) it requires only 10 s of analysis time to compute concentrations of >75 compounds, (2) it facilitates automation of quantitative workflows, and (3) it performs deterministic evaluations of compound quantification limits. SCALiR therefore provides the metabolomics community with a simple and rapid tool that enables rigorous and reproducible quantitative metabolomics studies.
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Affiliation(s)
- Luis F Ponce
- Alberta Centre for Advanced Diagnostics, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Stephanie L Bishop
- Alberta Centre for Advanced Diagnostics, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Soren Wacker
- Alberta Centre for Advanced Diagnostics, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Ryan A Groves
- Alberta Centre for Advanced Diagnostics, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Ian A Lewis
- Alberta Centre for Advanced Diagnostics, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
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Perez de Souza L, Fernie AR. Computational methods for processing and interpreting mass spectrometry-based metabolomics. Essays Biochem 2024; 68:5-13. [PMID: 37999335 PMCID: PMC11065554 DOI: 10.1042/ebc20230019] [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: 09/15/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
Metabolomics has emerged as an indispensable tool for exploring complex biological questions, providing the ability to investigate a substantial portion of the metabolome. However, the vast complexity and structural diversity intrinsic to metabolites imposes a great challenge for data analysis and interpretation. Liquid chromatography mass spectrometry (LC-MS) stands out as a versatile technique offering extensive metabolite coverage. In this mini-review, we address some of the hurdles posed by the complex nature of LC-MS data, providing a brief overview of computational tools designed to help tackling these challenges. Our focus centers on two major steps that are essential to most metabolomics investigations: the translation of raw data into quantifiable features, and the extraction of structural insights from mass spectra to facilitate metabolite identification. By exploring current computational solutions, we aim at providing a critical overview of the capabilities and constraints of mass spectrometry-based metabolomics, while introduce some of the most recent trends in data processing and analysis within the field.
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Affiliation(s)
- Leonardo Perez de Souza
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
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32
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Xu Y, Cao L, Chen Y, Zhang Z, Liu W, Li H, Ding C, Pu J, Qian K, Xu W. Integrating Machine Learning in Metabolomics: A Path to Enhanced Diagnostics and Data Interpretation. SMALL METHODS 2024:e2400305. [PMID: 38682615 DOI: 10.1002/smtd.202400305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/07/2024] [Indexed: 05/01/2024]
Abstract
Metabolomics, leveraging techniques like NMR and MS, is crucial for understanding biochemical processes in pathophysiological states. This field, however, faces challenges in metabolite sensitivity, data complexity, and omics data integration. Recent machine learning advancements have enhanced data analysis and disease classification in metabolomics. This study explores machine learning integration with metabolomics to improve metabolite identification, data efficiency, and diagnostic methods. Using deep learning and traditional machine learning, it presents advancements in metabolic data analysis, including novel algorithms for accurate peak identification, robust disease classification from metabolic profiles, and improved metabolite annotation. It also highlights multiomics integration, demonstrating machine learning's potential in elucidating biological phenomena and advancing disease diagnostics. This work contributes significantly to metabolomics by merging it with machine learning, offering innovative solutions to analytical challenges and setting new standards for omics data analysis.
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Affiliation(s)
- Yudian Xu
- Department of Traditional Chinese Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Linlin Cao
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Yifan Chen
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Ziyue Zhang
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Wanshan Liu
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - He Li
- Department of Traditional Chinese Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Chenhuan Ding
- Department of Traditional Chinese Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Jun Pu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Wei Xu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
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33
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Shamjana U, Vasu DA, Hembrom PS, Nayak K, Grace T. The role of insect gut microbiota in host fitness, detoxification and nutrient supplementation. Antonie Van Leeuwenhoek 2024; 117:71. [PMID: 38668783 DOI: 10.1007/s10482-024-01970-0] [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: 07/06/2023] [Accepted: 04/15/2024] [Indexed: 05/01/2024]
Abstract
Insects are incredibly diverse, ubiquitous and have successfully flourished out of the dynamic and often unpredictable nature of evolutionary processes. The resident microbiome has accompanied the physical and biological adaptations that enable their continued survival and proliferation in a wide array of environments. The host insect and microbiome's bidirectional relationship exhibits their capability to influence each other's physiology, behavior and characteristics. Insects are reported to rely directly on the microbial community to break down complex food, adapt to nutrient-deficit environments, protect themselves from natural adversaries and control the expression of social behavior. High-throughput metagenomic approaches have enhanced the potential for determining the abundance, composition, diversity and functional activities of microbial fauna associated with insect hosts, enabling in-depth investigation into insect-microbe interactions. We undertook a review of some of the major advances in the field of metagenomics, focusing on insect-microbe interaction, diversity and composition of resident microbiota, the functional capability of endosymbionts and discussions on different symbiotic relationships. The review aims to be a valuable resource on insect gut symbiotic microbiota by providing a comprehensive understanding of how insect gut symbionts systematically perform a range of functions, viz., insecticide degradation, nutritional support and immune fitness. A thorough understanding of manipulating specific gut symbionts may aid in developing advanced insect-associated research to attain health and design strategies for pest management.
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Affiliation(s)
- U Shamjana
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Deepa Azhchath Vasu
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Preety Sweta Hembrom
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Karunakar Nayak
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Tony Grace
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India.
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34
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Meiser J, Frezza C. Presenting metabolomics analyses: what's in a number? EMBO J 2024:10.1038/s44318-024-00098-1. [PMID: 38664540 DOI: 10.1038/s44318-024-00098-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 05/09/2024] Open
Affiliation(s)
- Johannes Meiser
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg.
| | - Christian Frezza
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University Hospital Cologne, Cologne, Germany.
- Institute of Genetics, Faculty of Mathematics and Natural Sciences, Faculty of Medicine, University of Cologne, Cologne, Germany.
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35
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Yang C, Yu H, Li W, Lin H, Wu H, Deng C. High-Throughput Metabolic Pattern Screening Strategy for Early Colorectal and Gastric Cancers Based on Covalent Organic Frameworks-Assisted Laser Desorption/Ionization Mass Spectrometry. Anal Chem 2024; 96:6264-6274. [PMID: 38600676 DOI: 10.1021/acs.analchem.3c05527] [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: 04/12/2024]
Abstract
Precise early diagnosis and staging are conducive to improving the prognosis of colorectal cancer (CRC) and gastric cancer (GC) patients. However, due to intrusive inspections and limited sensitivity, the prevailing diagnostic methods impede precisely large-scale screening. In this work, we reported a high-throughput serum metabolic patterns (SMP) screening strategy based on covalent organic frameworks-assisted laser desorption/ionization mass spectrometry (hf-COFsLDI-MS) for early diagnosis and staging of CRC and GC. Notably, 473 high-quality SMP were extracted without any tedious sample pretreatment and coupled with multiple machine learning algorithms; the area under the curve (AUC) value is 0.938 with 96.9% sensitivity for early CRC diagnosis, and the AUC value is 0.974 with 100% sensitivity for early GC diagnosis. Besides, the discrimination of CRC and GC is accomplished with an AUC value of 0.966 for the validation set. Also, the screened-out features were identified by MS/MS experiments, and 8 metabolites were identified as the biomarkers for CRC and GC. Finally, the corresponding disordered metabolic pathways were revealed, and the staging of CRC and GC was completed. This work provides an alternative high-throughput screening strategy for CRC and GC and highlights the potential of metabolic molecular diagnosis in clinical applications.
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Affiliation(s)
- Chenjie Yang
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Hailong Yu
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Weihong Li
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Hairu Lin
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Hao Wu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chunhui Deng
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China
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36
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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. [PMID: 38651516 DOI: 10.1039/d4np00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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37
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Lu H, Zheng S, Ma C, Gao X, Ji J, Luo J, Hua H, Cui J. Integrated Omics Analysis Reveals Key Pathways in Cotton Defense against Mirid Bug ( Adelphocoris suturalis Jakovlev) Feeding. INSECTS 2024; 15:254. [PMID: 38667384 PMCID: PMC11049813 DOI: 10.3390/insects15040254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/05/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024]
Abstract
The recent dominance of Adelphocoris suturalis Jakovlev as the primary cotton field pest in Bt-cotton-cultivated areas has generated significant interest in cotton pest control research. This study addresses the limited understanding of cotton defense mechanisms triggered by A. suturalis feeding. Utilizing LC-QTOF-MS, we analyzed cotton metabolomic changes induced by A. suturalis, and identified 496 differential positive ions (374 upregulated, 122 downregulated) across 11 categories, such as terpenoids, alkaloids, phenylpropanoids, flavonoids, isoflavones, etc. Subsequent iTRAQ-LC-MS/MS analysis of the cotton proteome revealed 1569 differential proteins enriched in 35 metabolic pathways. Integrated metabolome and proteome analysis highlighted significant upregulation of 17 (89%) proteases in the α-linolenic acid (ALA) metabolism pathway, concomitant with a significant increase in 14 (88%) associated metabolites. Conversely, 19 (73%) proteases in the fructose and mannose biosynthesis pathway were downregulated, with 7 (27%) upregulated proteases corresponding to the downregulation of 8 pathway-associated metabolites. Expression analysis of key regulators in the ALA pathway, including allene oxidase synthase (AOS), phospholipase A (PLA), allene oxidative cyclase (AOC), and 12-oxophytodienoate reductase3 (OPR3), demonstrated significant responses to A. suturalis feeding. Finally, this study pioneers the exploration of molecular mechanisms in the plant-insect relationship, thereby offering insights into potential novel control strategies against this cotton pest.
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Affiliation(s)
- Hui Lu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant, Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Green Agricultural Products Safety and Warning Laboratory, Research Center of Soil Resource Comprehensive Utilization and Ecological Environment in Western Inner Mongolia, Hetao College, Bayannur 015000, China
| | - Shuaichao Zheng
- Henan Institute of Science and Technology, College of Life Science, Hualan St. 90, Xinxiang 453003, China;
| | - Chao Ma
- Anhui Provincial Center for Disease Control and Prevention, Hefei 230601, China;
| | - Xueke Gao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Jichao Ji
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Junyu Luo
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Hongxia Hua
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant, Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Jinjie Cui
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
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38
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Li S, Looby N, Chandran V, Kulasingam V. Challenges in the Metabolomics-Based Biomarker Validation Pipeline. Metabolites 2024; 14:200. [PMID: 38668328 PMCID: PMC11051909 DOI: 10.3390/metabo14040200] [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: 03/01/2024] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 04/28/2024] Open
Abstract
As end-products of the intersection between the genome and environmental influences, metabolites represent a promising approach to the discovery of novel biomarkers for diseases. However, many potential biomarker candidates identified by metabolomics studies fail to progress beyond analytical validation for routine implementation in clinics. Awareness of the challenges present can facilitate the development and advancement of innovative strategies that allow improved and more efficient applications of metabolite-based markers in clinical settings. This minireview provides a comprehensive summary of the pre-analytical factors, required analytical validation studies, and kit development challenges that must be resolved before the successful translation of novel metabolite biomarkers originating from research. We discuss the necessity for strict protocols for sample collection, storage, and the regulatory requirements to be fulfilled for a bioanalytical method to be considered as analytically validated. We focus especially on the blood as a biological matrix and liquid chromatography coupled with tandem mass spectrometry as the analytical platform for biomarker validation. Furthermore, we examine the challenges of developing a commercially viable metabolomics kit for distribution. To bridge the gap between the research lab and clinical implementation and utility of relevant metabolites, the understanding of the translational challenges for a biomarker panel is crucial for more efficient development of metabolomics-based precision medicine.
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Affiliation(s)
- Shenghan Li
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Nikita Looby
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Division of Orthopaedic Surgery, Osteoarthritis Research Program, Schroeder Arthritis Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Vinod Chandran
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Division of Clinical Biochemistry, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
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Liu Y, Zhang X, Wang Y, Wang J, Wei H, Zhang C, Zhang Q. Cyclocodon lancifolius fruit prolongs the lifespan of Caenorhabditis elegans via antioxidation and regulation of purine metabolism. Food Funct 2024; 15:3353-3364. [PMID: 38481358 DOI: 10.1039/d3fo02931j] [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: 04/04/2024]
Abstract
Cyclocodon lancifolius fruit is a promising commercial fruit with antioxidant activity and is rich in polyphenolic compounds. In this study, the anti-aging activity of C. lancifolius fruit extract (CF) on Caenorhabditis elegans (C. elegans) was evaluated by observing the longevity, stress response, reproduction, oscillation, lipofuscin, and antioxidant enzymes of worms. Moreover, the effects and potential mechanisms of CF on delaying C. elegans senescence at the mRNA and metabolite levels were investigated. The results showed that CF treatment significantly increased the lifespan and stress resistance, decreased the levels of lipofuscin and reactive oxygen species (ROS), and improved the antioxidant system of C. elegans. The extension of the lifespan of C. elegans was remarkably correlated with the upregulation of mtl-1 and Hsp-16.2, along with the downregulation of age-1, daf-2, and akt-1. Metabolomics analysis revealed that purine metabolism is a key regulatory pathway for CF to exert anti-aging effects. The present study suggests that C. lancifolius fruit has potential for use as a functional food to enhance antioxidant capacity and delay aging.
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Affiliation(s)
- Yihan Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Xudong Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Yan Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Jianxia Wang
- School of Pharmaceutical Sciences, Jishou University, Jishou 416000, China
| | - Hua Wei
- School of Pharmaceutical Sciences, Jishou University, Jishou 416000, China
| | - Cunli Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Qiang Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
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Mukherjee A, Abraham S, Singh A, Balaji S, Mukunthan KS. From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies. Mol Biotechnol 2024:10.1007/s12033-024-01133-6. [PMID: 38565775 DOI: 10.1007/s12033-024-01133-6] [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: 12/27/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
In the dynamic landscape of targeted therapeutics, drug discovery has pivoted towards understanding underlying disease mechanisms, placing a strong emphasis on molecular perturbations and target identification. This paradigm shift, crucial for drug discovery, is underpinned by big data, a transformative force in the current era. Omics data, characterized by its heterogeneity and enormity, has ushered biological and biomedical research into the big data domain. Acknowledging the significance of integrating diverse omics data strata, known as multi-omics studies, researchers delve into the intricate interrelationships among various omics layers. This review navigates the expansive omics landscape, showcasing tailored assays for each molecular layer through genomes to metabolomes. The sheer volume of data generated necessitates sophisticated informatics techniques, with machine-learning (ML) algorithms emerging as robust tools. These datasets not only refine disease classification but also enhance diagnostics and foster the development of targeted therapeutic strategies. Through the integration of high-throughput data, the review focuses on targeting and modeling multiple disease-regulated networks, validating interactions with multiple targets, and enhancing therapeutic potential using network pharmacology approaches. Ultimately, this exploration aims to illuminate the transformative impact of multi-omics in the big data era, shaping the future of biological research.
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Affiliation(s)
- Arnab Mukherjee
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Suzanna Abraham
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Akshita Singh
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - S Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - K S Mukunthan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India.
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Jiang W, Yang L, Dang Y, Jiang X, Wu L, Tong X, Guo J, Bao Y. Metabolomic profiling of deep vein thrombosis. Phlebology 2024; 39:154-168. [PMID: 37992130 PMCID: PMC10938490 DOI: 10.1177/02683555231215199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Deep vein thrombosis (DVT) of the lower extremities is one of the most common peripheral vascular diseases, with significant complications and sequelae. Metabolomics aims to identify small molecules in biological samples. It can serve as a promising method for screening compounds that can be used for early disease detection, diagnosis, treatment response prediction, and prognosis. In addition, high-throughput metabolomics screening can yield significant insights into the pathophysiological pathways of DVT. Currently, the metabolomic profiles of DVT have yielded inconsistent expression patterns. This article examines the recent advancements in metabolomic studies of DVT and analyzes the factors that may influence the results.
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Affiliation(s)
- Weiguang Jiang
- Chifeng Clinical Medical College of Inner Mongolia Medical University, Chifeng, China
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
| | - Liu Yang
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
| | - Yongkang Dang
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
| | - Xuechao Jiang
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
| | - Lan Wu
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
| | - Xiangyang Tong
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
| | - Jianquan Guo
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
| | - Yongtao Bao
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
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42
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Ho PY, Nguyen TH, Sanchez JM, DeFelice BC, Huang KC. Resource competition predicts assembly of gut bacterial communities in vitro. Nat Microbiol 2024; 9:1036-1048. [PMID: 38486074 DOI: 10.1038/s41564-024-01625-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 01/26/2024] [Indexed: 04/06/2024]
Abstract
Microbial community dynamics arise through interspecies interactions, including resource competition, cross-feeding and pH modulation. The individual contributions of these mechanisms to community structure are challenging to untangle. Here we develop a framework to estimate multispecies niche overlaps by combining metabolomics data of individual species, growth measurements in spent media and mathematical models. We applied our framework to an in vitro model system comprising 15 human gut commensals in complex media and showed that a simple model of resource competition accounted for most pairwise interactions. Next, we built a coarse-grained consumer-resource model by grouping metabolomic features depleted by the same set of species and showed that this model predicted the composition of 2-member to 15-member communities with reasonable accuracy. Furthermore, we found that incorporation of cross-feeding and pH-mediated interactions improved model predictions of species coexistence. Our theoretical model and experimental framework can be applied to characterize interspecies interactions in bacterial communities in vitro.
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Affiliation(s)
- Po-Yi Ho
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- School of Engineering, Westlake University, Hangzhou, China.
| | - Taylor H Nguyen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | | | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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Çiçek SS, Mangoni A, Hanschen FS, Agerbirk N, Zidorn C. Essentials in the acquisition, interpretation, and reporting of plant metabolite profiles. PHYTOCHEMISTRY 2024; 220:114004. [PMID: 38331135 DOI: 10.1016/j.phytochem.2024.114004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/10/2024]
Abstract
Plant metabolite profiling reveals the diversity of secondary or specialized metabolites in the plant kingdom with its hundreds of thousands of species. Specialized plant metabolites constitute a vast class of chemicals posing significant challenges in analytical chemistry. In order to be of maximum scientific relevance, reports dealing with these compounds and their source species must be transparent, make use of standards and reference materials, and be based on correctly and traceably identified plant material. Essential aspects in qualitative plant metabolite profiling include: (i) critical review of previous literature and a reasoned sampling strategy; (ii) transparent plant sampling with wild material documented by vouchers in public herbaria and, optimally, seed banks; (iii) if possible, inclusion of generally available reference plant material; (iv) transparent, documented state-of-the art chemical analysis, ideally including chemical reference standards; (v) testing for artefacts during preparative extraction and isolation, using gentle analytical methods; (vi) careful chemical data interpretation, avoiding over- and misinterpretation and taking into account phytochemical complexity when assigning identification confidence levels, and (vii) taking all previous scientific knowledge into account in reporting the scientific data. From the current stage of the phytochemical literature, selected comments and suggestions are given. In the past, proposed revisions of botanical taxonomy were sometimes based on metabolite profiles, but this approach ("chemosystematics" or "chemotaxonomy") is outdated due to the advent of DNA sequence-based phylogenies. In contrast, systematic comparisons of plant metabolite profiles in a known phylogenetic framework remain relevant. This approach, known as chemophenetics, allows characterizing species and clades based on their array of specialized metabolites, aids in deducing the evolution of biosynthetic pathways and coevolution, and can serve in identifying new sources of rare and economically interesting natural products.
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Affiliation(s)
- Serhat S Çiçek
- Department of Biotechnology, Hamburg University of Applied Sciences, Ulmenliet 20, 21033, Hamburg, Germany
| | - Alfonso Mangoni
- Dipartimento di Farmacia, Università di Napoli Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy
| | - Franziska S Hanschen
- Plant Quality and Food Security, Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e. V., Theodor-Echtermeyer-Weg 1, 14979, Grossbeeren, Germany
| | - Niels Agerbirk
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Christian Zidorn
- Pharmazeutisches Institut, Abteilung Pharmazeutische Biologie, Christian-Albrechts- Universität zu Kiel, Gutenbergstraße 76, 24118, Kiel, Germany.
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Lazar SM, Challman TD, Myers SM. Etiologic Evaluation of Children with Autism Spectrum Disorder. Pediatr Clin North Am 2024; 71:179-197. [PMID: 38423715 DOI: 10.1016/j.pcl.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Autism spectrum disorder (ASD) is clinically and etiologically heterogeneous. A causal genetic variant can be identified in approximately 20% to 25% of affected individuals with current clinical genetic testing, and all patients with an ASD diagnosis should be offered genetic etiologic evaluation. We suggest that exome sequencing with copy number variant coverage should be the first-line etiologic evaluation for ASD. Neuroimaging, neurophysiologic, metabolic, and other biochemical evaluations can provide insight into the pathophysiology of ASD but should be recommended in the appropriate clinical circumstances.
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Affiliation(s)
- Steven M Lazar
- Section of Pediatric Neurology and Developmental Neuroscience, Meyer Center for Developmental Pediatrics & Autism, Baylor College of Medicine - Texas Children's Hospital, 6701 Fannin Street Suite 1250, Houston, TX 77030, USA.
| | - Thomas D Challman
- Geisinger Autism & Developmental Medicine Institute, Geisinger Commonwealth School of Medicine, 120 Hamm Drive, Suite 2A, Lewisburg, PA 17837, USA
| | - Scott M Myers
- Geisinger Autism & Developmental Medicine Institute, Geisinger Commonwealth School of Medicine, 120 Hamm Drive, Suite 2A, Lewisburg, PA 17837, USA
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45
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Tkalec Ž, Antignac JP, Bandow N, Béen FM, Belova L, Bessems J, Le Bizec B, Brack W, Cano-Sancho G, Chaker J, Covaci A, Creusot N, David A, Debrauwer L, Dervilly G, Duca RC, Fessard V, Grimalt JO, Guerin T, Habchi B, Hecht H, Hollender J, Jamin EL, Klánová J, Kosjek T, Krauss M, Lamoree M, Lavison-Bompard G, Meijer J, Moeller R, Mol H, Mompelat S, Van Nieuwenhuyse A, Oberacher H, Parinet J, Van Poucke C, Roškar R, Togola A, Trontelj J, Price EJ. Innovative analytical methodologies for characterizing chemical exposure with a view to next-generation risk assessment. ENVIRONMENT INTERNATIONAL 2024; 186:108585. [PMID: 38521044 DOI: 10.1016/j.envint.2024.108585] [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: 08/18/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024]
Abstract
The chemical burden on the environment and human population is increasing. Consequently, regulatory risk assessment must keep pace to manage, reduce, and prevent adverse impacts on human and environmental health associated with hazardous chemicals. Surveillance of chemicals of known, emerging, or potential future concern, entering the environment-food-human continuum is needed to document the reality of risks posed by chemicals on ecosystem and human health from a one health perspective, feed into early warning systems and support public policies for exposure mitigation provisions and safe and sustainable by design strategies. The use of less-conventional sampling strategies and integration of full-scan, high-resolution mass spectrometry and effect-directed analysis in environmental and human monitoring programmes have the potential to enhance the screening and identification of a wider range of chemicals of known, emerging or potential future concern. Here, we outline the key needs and recommendations identified within the European Partnership for Assessment of Risks from Chemicals (PARC) project for leveraging these innovative methodologies to support the development of next-generation chemical risk assessment.
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Affiliation(s)
- Žiga Tkalec
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia.
| | | | - Nicole Bandow
- German Environment Agency, Laboratory for Water Analysis, Colditzstraße 34, 12099 Berlin, Germany.
| | - Frederic M Béen
- Vrije Universiteit Amsterdam, Amsterdam Institute for Life and Environment (A-LIFE), Section Chemistry for Environment and Health, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands; KWR Water Research Institute, Nieuwegein, The Netherlands.
| | - Lidia Belova
- Toxicological Center, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Jos Bessems
- Flemish Institute for Technological Research (VITO), Mol, Belgium.
| | | | - Werner Brack
- Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Effect-Directed Analysis, Permoserstraße 15, 04318 Leipzig, Germany; Goethe University Frankfurt, Department of Evolutionary Ecology and Environmental Toxicology, Max-von-Laue-Strasse 13, 60438 Frankfurt, Germany.
| | | | - Jade Chaker
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.
| | - Adrian Covaci
- Toxicological Center, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Nicolas Creusot
- INRAE, French National Research Institute For Agriculture, Food & Environment, UR1454 EABX, Bordeaux Metabolome, MetaboHub, Gazinet Cestas, France.
| | - Arthur David
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.
| | - Laurent Debrauwer
- Toxalim (Research Centre in Food Toxicology), INRAE UMR 1331, ENVT, INP-Purpan, Paul Sabatier University (UPS), Toulouse, France.
| | | | - Radu Corneliu Duca
- Unit Environmental Hygiene and Human Biological Monitoring, Department of Health Protection, Laboratoire National de Santé (LNS), 1 Rue Louis Rech, L-3555 Dudelange, Luxembourg; Environment and Health, Department of Public Health and Primary Care, Katholieke Universiteit of Leuven (KU Leuven), 3000 Leuven, Belgium.
| | - Valérie Fessard
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory of Fougères, Toxicology of Contaminants Unit, 35306 Fougères, France.
| | - Joan O Grimalt
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Catalonia, Spain.
| | - Thierry Guerin
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Strategy and Programs Department, F-94701 Maisons-Alfort, France.
| | - Baninia Habchi
- INRS, Département Toxicologie et Biométrologie Laboratoire Biométrologie 1, rue du Morvan - CS 60027 - 54519, Vandoeuvre Cedex, France.
| | - Helge Hecht
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic.
| | - Juliane Hollender
- Swiss Federal Institute of Aquatic Science and Technology - Eawag, 8600 Dübendorf, Switzerland; Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland.
| | - Emilien L Jamin
- Toxalim (Research Centre in Food Toxicology), INRAE UMR 1331, ENVT, INP-Purpan, Paul Sabatier University (UPS), Toulouse, France.
| | - Jana Klánová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic.
| | - Tina Kosjek
- Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia.
| | - Martin Krauss
- Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Effect-Directed Analysis, Permoserstraße 15, 04318 Leipzig, Germany.
| | - Marja Lamoree
- Vrije Universiteit Amsterdam, Amsterdam Institute for Life and Environment (A-LIFE), Section Chemistry for Environment and Health, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Gwenaelle Lavison-Bompard
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory for Food Safety, Pesticides and Marine Biotoxins Unit, F-94701 Maisons-Alfort, France.
| | - Jeroen Meijer
- Vrije Universiteit Amsterdam, Amsterdam Institute for Life and Environment (A-LIFE), Section Chemistry for Environment and Health, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Ruth Moeller
- Unit Medical Expertise and Data Intelligence, Department of Health Protection, Laboratoire National de Santé (LNS), 1 Rue Louis Rech, L-3555 Dudelange, Luxembourg.
| | - Hans Mol
- Wageningen Food Safety Research - Part of Wageningen University and Research, Akkermaalsbos 2, 6708 WB, Wageningen, The Netherlands.
| | - Sophie Mompelat
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory of Fougères, Toxicology of Contaminants Unit, 35306 Fougères, France.
| | - An Van Nieuwenhuyse
- Environment and Health, Department of Public Health and Primary Care, Katholieke Universiteit of Leuven (KU Leuven), 3000 Leuven, Belgium; Department of Health Protection, Laboratoire National de Santé (LNS), 1 Rue Louis Rech, L-3555 Dudelange, Luxembourg.
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Insbruck, 6020 Innsbruck, Austria.
| | - Julien Parinet
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory for Food Safety, Pesticides and Marine Biotoxins Unit, F-94701 Maisons-Alfort, France.
| | - Christof Van Poucke
- Flanders Research Institute for Agriculture, Fisheries And Food (ILVO), Brusselsesteenweg 370, 9090 Melle, Belgium.
| | - Robert Roškar
- University of Ljubljana, Faculty of Pharmacy, Slovenia.
| | - Anne Togola
- BRGM, 3 avenue Claude Guillemin, 45060 Orléans, France.
| | | | - Elliott J Price
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic.
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Jiang J, Hu D, Pei E. Integrated omics analysis reveals a correlation between gut microbiota and egg production in captive African penguins (Spheniscus demersus). Anim Reprod Sci 2024; 263:107448. [PMID: 38428346 DOI: 10.1016/j.anireprosci.2024.107448] [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: 11/02/2023] [Revised: 01/24/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
The egg production of captive African penguins differs considerably between individuals. An understanding of the physiological differences in African penguins with relatively greater and lesser egg production is meaningful for the captive breeding program of this endangered species. The objective of this study was to investigate differential microbial composition and metabolites in captive African penguins with different egg production. Fecal samples were collected from captive female African penguins during the breeding season. The results of 16 S rRNA gene sequencing showed that African penguins with different egg production had similar microbial diversities, whereas a significant difference was observed between their microbial community structure. African penguins with relatively greater egg production exhibited a higher relative abundance of Alphaproteobacteria, Rhizobiales, Bradyrhizobiaceae, Bradyrhizobium and Bosea. Meanwhile, penguins with relatively lesser egg production had an increased proportion of Klebsiella and Plesiomonas. We further identified a total of 1858 metabolites in female African penguins by liquid chromatography-mass spectrometry analysis. Among these metabolites, 13 kinds of metabolites were found to be significantly differential between African penguins with different egg production. In addition, the correlation analysis revealed that the egg production had significant correlations with most of the differential microbial bacteria and metabolites. Our findings might aid in understanding the potential mechanism underlying the phenomenon of abnormal egg production in captive African penguins, and provide novel insights into the relationship between gut microbiota and reproduction in penguins.
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Affiliation(s)
- Jingle Jiang
- Shanghai Endangered Species Conservation and Research Centre, Shanghai Zoo, Shanghai 200335, China
| | - Di Hu
- Shanghai Endangered Species Conservation and Research Centre, Shanghai Zoo, Shanghai 200335, China
| | - Enle Pei
- Shanghai Endangered Species Conservation and Research Centre, Shanghai Zoo, Shanghai 200335, China.
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Olanrewaju OS, Glick BR, Babalola OO. Metabolomics-guided utilization of beneficial microbes for climate-resilient crops. Curr Opin Chem Biol 2024; 79:102427. [PMID: 38290195 DOI: 10.1016/j.cbpa.2024.102427] [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: 04/26/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 02/01/2024]
Abstract
In the rhizosphere, plants and microbes communicate chemically, especially under environmental stress. Over millions of years, plants and their microbiome have coevolved, sharing various chemicals, including signaling molecules. This mutual exchange impacts bacterial communication and influences plant metabolism. Inter-kingdom signal crosstalk affects bacterial colonization and plant fitness. Beneficial microbes and their metabolomes offer eco-friendly ways to enhance plant resilience and agriculture. Plant metabolites are pivotal in this dynamic interaction between host plants and their interacting beneficial microbes. Understanding these associations is key to engineering a robust microbiome for stress mitigation and improved plant growth. This review explores mechanisms behind plant-microbe interactions, the role of beneficial microbes and metabolomics, and the practical applications for addressing climate change's impact on agriculture. Integrating beneficial microbes' activities and metabolomics' application to study metabolome-driven interaction between host plants and their corresponding beneficial microbes holds promise for enhancing crop resilience and productivity.
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Affiliation(s)
- Oluwaseyi Samuel Olanrewaju
- Unit for Environmental Sciences and Management, Potchefstroom Campus, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho 2735, South Africa.
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Liu X, Song L, Xue B, Chi Z, Wang Y, Wen S, Lv W, Hu Q, Guo Q, Wang S, Wu D, Liang G, Jing D. Organic acid and sugar components accumulation and flavor associated metabolites dynamic changes in yellow- and white-fleshed seedless loquats ( Eriobotrya japonica). Food Chem X 2024; 21:101046. [PMID: 38173902 PMCID: PMC10762357 DOI: 10.1016/j.fochx.2023.101046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/27/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
Triploid loquats are divided into yellow- and white-fleshed cultivars. To better understand taste variations in triploid loquat fruits, we used a UPLC-ESI-QTRAP-MS/MS-based widely targeted metabolomic analysis to examine the metabolic composition of two different color fleshed triploid loquats with a sample size of 54 and external validation method within a confidence level of P<0.05. We identified key flavor-related differentially accumulated metabolites using the variable importance in projection (VIP) value (VIP ≥ 1.0) and fold change ≥ 2 or ≤ 0.5. Furthermore, the results of the HPLC analysis showed that white-fleshed loquats had a low malic acid content. We also performed the UPLC-MS/MS system to investigate the carotenoids contents and lipidome in four triploid cultivars. In the fruits of white-fleshed varieties, the carotenoids contents were significantly downregulated, but the contents of most glycerolphospholipids were increased. Our results reveal the metabolomic changes between the yellow- and white-fleshed cultivars.
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Affiliation(s)
- Xinya Liu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Liqin Song
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Baogui Xue
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
- Jiuquan Forest Fruit Service Center, Jiuquan, Gansu 735000, China
| | - Zhuoheng Chi
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Yuan Wang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Songqin Wen
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Wenjuan Lv
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Qiankun Hu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Qigao Guo
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Shuming Wang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Di Wu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Guolu Liang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Danlong Jing
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
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P. Gomes PW, Mannochio-Russo H, Mao J, Zhao HN, Ancira J, Tipton CD, Dorrestein PC, Li M. Co-occurrence network analysis reveals the alterations of the skin microbiome and metabolome in adults with mild to moderate atopic dermatitis. mSystems 2024; 9:e0111923. [PMID: 38319107 PMCID: PMC10949451 DOI: 10.1128/msystems.01119-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
Skin microbiome can be altered in patients with atopic dermatitis (AD). An understanding of the changes from healthy to atopic skin can help develop new targets for treatment by identifying microbial and molecular biomarkers. This study investigates the skin microbiome and metabolome of healthy adult subjects and lesion (ADL) and non-lesion (ADNL) of AD patients by 16S rRNA gene sequencing and mass spectrometry, respectively. Samples from AD patients showed alterations in the diversity and composition of the skin microbiome, with ADL skin having the greatest divergence. Staphylococcus species, especially S. aureus, were significantly increased in AD patients. Metabolomic profiles were also different between the groups. Dipeptide derivatives are more abundant in ADL, which may be related to skin inflammation. Co-occurrence network analysis of the microbiome and metabolomics data revealed higher co-occurrence of metabolites and bacteria in healthy ADNL compared to ADL. S. aureus co-occurred with dipeptide derivatives in ADL, while phytosphingosine-derived compounds showed co-occurrences with commensal bacteria, for example, Paracoccus sp., Pseudomonas sp., Prevotella bivia, Lactobacillus iners, Anaerococcus sp., Micrococcus sp., Corynebacterium ureicelerivorans, Corynebacterium massiliense, Streptococcus thermophilus, and Roseomonas mucosa, in healthy and ADNL groups. Therefore, these findings provide valuable insights into how AD affects the human skin metabolome and microbiome.IMPORTANCEThis study provides valuable insight into changes in the skin microbiome and associated metabolomic profiles in an adult population with mild to moderate atopic dermatitis. It also identifies new therapeutic targets that may be useful for developing personalized treatments for individuals with atopic dermatitis based on their unique skin microbiome and metabolic profiles.
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Affiliation(s)
- Paulo Wender P. Gomes
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Helena Mannochio-Russo
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Junhong Mao
- Colgate−Palmolive Company, Piscataway, New Jersey, USA
| | - Haoqi Nina Zhao
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | | | | | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California, San Diego, California, USA
| | - Min Li
- Colgate−Palmolive Company, Piscataway, New Jersey, USA
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Calabrese V, Brunet TA, Degli-Esposti D, Chaumot A, Geffard O, Salvador A, Clément Y, Ayciriex S. Electron-activated dissociation (EAD) for the complementary annotation of metabolites and lipids through data-dependent acquisition analysis and feature-based molecular networking, applied to the sentinel amphipod Gammarus fossarum. Anal Bioanal Chem 2024:10.1007/s00216-024-05232-w. [PMID: 38492024 DOI: 10.1007/s00216-024-05232-w] [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: 12/12/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/18/2024]
Abstract
The past decades have marked the rise of metabolomics and lipidomics as the -omics sciences which reflect the most phenotypes in living systems. Mass spectrometry-based approaches are acknowledged for both quantification and identification of molecular signatures, the latter relying primarily on fragmentation spectra interpretation. However, the high structural diversity of biological small molecules poses a considerable challenge in compound annotation. Feature-based molecular networking (FBMN) combined with database searches currently sets the gold standard for annotation of large datasets. Nevertheless, FBMN is usually based on collision-induced dissociation (CID) data, which may lead to unsatisfying information. The use of alternative fragmentation methods, such as electron-activated dissociation (EAD), is undergoing a re-evaluation for the annotation of small molecules, as it gives access to additional fragmentation routes. In this study, we apply the performances of data-dependent acquisition mass spectrometry (DDA-MS) under CID and EAD fragmentation along with FBMN construction, to perform extensive compound annotation in the crude extracts of the freshwater sentinel organism Gammarus fossarum. We discuss the analytical aspects of the use of the two fragmentation modes, perform a general comparison of the information delivered, and compare the CID and EAD fragmentation pathways for specific classes of compounds, including previously unstudied species. In addition, we discuss the potential use of FBMN constructed with EAD fragmentation spectra to improve lipid annotation, compared to the classic CID-based networks. Our approach has enabled higher confidence annotations and finer structure characterization of 823 features, including both metabolites and lipids detected in G. fossarum extracts.
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Affiliation(s)
- Valentina Calabrese
- Universite Claude Bernard Lyon1, ISA, UMR 5280, CNRS, 5 Rue de La Doua, 69100, Villeurbanne, France.
| | - Thomas Alexandre Brunet
- Universite Claude Bernard Lyon1, ISA, UMR 5280, CNRS, 5 Rue de La Doua, 69100, Villeurbanne, France
| | | | - Arnaud Chaumot
- Laboratoire d'écotoxicologie, INRAE, UR RiverLy, 69625, Villeurbanne, France
| | - Olivier Geffard
- Laboratoire d'écotoxicologie, INRAE, UR RiverLy, 69625, Villeurbanne, France
| | - Arnaud Salvador
- Universite Claude Bernard Lyon1, ISA, UMR 5280, CNRS, 5 Rue de La Doua, 69100, Villeurbanne, France
| | - Yohann Clément
- Universite Claude Bernard Lyon1, ISA, UMR 5280, CNRS, 5 Rue de La Doua, 69100, Villeurbanne, France
| | - Sophie Ayciriex
- Universite Claude Bernard Lyon1, ISA, UMR 5280, CNRS, 5 Rue de La Doua, 69100, Villeurbanne, France.
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