Cargando…
Deep Metabolic Profiling Assessment of Tissue Extraction Protocols for Three Model Organisms
Metabolic profiling harbors the potential to better understand various disease entities such as cancer, diabetes, Alzheimer’s, Parkinson’s disease or COVID-19. To better understand such diseases and their intricate metabolic pathways in human studies, model animals are regularly used. There, standar...
Autores principales: | , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9083328/ https://www.ncbi.nlm.nih.gov/pubmed/35548679 http://dx.doi.org/10.3389/fchem.2022.869732 |
_version_ | 1784703397594660864 |
---|---|
author | Gegner, Hagen M. Mechtel, Nils Heidenreich, Elena Wirth, Angela Cortizo, Fabiola Garcia Bennewitz, Katrin Fleming, Thomas Andresen, Carolin Freichel, Marc Teleman, Aurelio A. Kroll, Jens Hell, Rüdiger Poschet, Gernot |
author_facet | Gegner, Hagen M. Mechtel, Nils Heidenreich, Elena Wirth, Angela Cortizo, Fabiola Garcia Bennewitz, Katrin Fleming, Thomas Andresen, Carolin Freichel, Marc Teleman, Aurelio A. Kroll, Jens Hell, Rüdiger Poschet, Gernot |
author_sort | Gegner, Hagen M. |
collection | PubMed |
description | Metabolic profiling harbors the potential to better understand various disease entities such as cancer, diabetes, Alzheimer’s, Parkinson’s disease or COVID-19. To better understand such diseases and their intricate metabolic pathways in human studies, model animals are regularly used. There, standardized rearing conditions and uniform sampling strategies are prerequisites towards a successful metabolomic study that can be achieved through model organisms. Although metabolomic approaches have been employed on model organisms before, no systematic assessment of different conditions to optimize metabolite extraction across several organisms and sample types has been conducted. We address this issue using a highly standardized metabolic profiling assay analyzing 630 metabolites across three commonly used model organisms (Drosophila, mouse, and zebrafish) to find an optimal extraction protocol for various matrices. Focusing on parameters such as metabolite coverage, concentration and variance between replicates we compared seven extraction protocols. We found that the application of a combination of 75% ethanol and methyl tertiary-butyl ether (MTBE), while not producing the broadest coverage and highest concentrations, was the most reproducible extraction protocol. We were able to determine up to 530 metabolites in mouse kidney samples, 509 in mouse liver, 422 in zebrafish and 388 in Drosophila and discovered a core overlap of 261 metabolites in these four matrices. To enable other scientists to search for the most suitable extraction protocol in their experimental context and interact with this comprehensive data, we have integrated our data set in the open-source shiny app “MetaboExtract”. Hereby, scientists can search for metabolites or compound classes of interest, compare them across the different tested extraction protocols and sample types as well as find reference concentration values. |
format | Online Article Text |
id | pubmed-9083328 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-90833282022-05-10 Deep Metabolic Profiling Assessment of Tissue Extraction Protocols for Three Model Organisms Gegner, Hagen M. Mechtel, Nils Heidenreich, Elena Wirth, Angela Cortizo, Fabiola Garcia Bennewitz, Katrin Fleming, Thomas Andresen, Carolin Freichel, Marc Teleman, Aurelio A. Kroll, Jens Hell, Rüdiger Poschet, Gernot Front Chem Chemistry Metabolic profiling harbors the potential to better understand various disease entities such as cancer, diabetes, Alzheimer’s, Parkinson’s disease or COVID-19. To better understand such diseases and their intricate metabolic pathways in human studies, model animals are regularly used. There, standardized rearing conditions and uniform sampling strategies are prerequisites towards a successful metabolomic study that can be achieved through model organisms. Although metabolomic approaches have been employed on model organisms before, no systematic assessment of different conditions to optimize metabolite extraction across several organisms and sample types has been conducted. We address this issue using a highly standardized metabolic profiling assay analyzing 630 metabolites across three commonly used model organisms (Drosophila, mouse, and zebrafish) to find an optimal extraction protocol for various matrices. Focusing on parameters such as metabolite coverage, concentration and variance between replicates we compared seven extraction protocols. We found that the application of a combination of 75% ethanol and methyl tertiary-butyl ether (MTBE), while not producing the broadest coverage and highest concentrations, was the most reproducible extraction protocol. We were able to determine up to 530 metabolites in mouse kidney samples, 509 in mouse liver, 422 in zebrafish and 388 in Drosophila and discovered a core overlap of 261 metabolites in these four matrices. To enable other scientists to search for the most suitable extraction protocol in their experimental context and interact with this comprehensive data, we have integrated our data set in the open-source shiny app “MetaboExtract”. Hereby, scientists can search for metabolites or compound classes of interest, compare them across the different tested extraction protocols and sample types as well as find reference concentration values. Frontiers Media S.A. 2022-04-25 /pmc/articles/PMC9083328/ /pubmed/35548679 http://dx.doi.org/10.3389/fchem.2022.869732 Text en Copyright © 2022 Gegner, Mechtel, Heidenreich, Wirth, Cortizo, Bennewitz, Fleming, Andresen, Freichel, Teleman, Kroll, Hell and Poschet. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Chemistry Gegner, Hagen M. Mechtel, Nils Heidenreich, Elena Wirth, Angela Cortizo, Fabiola Garcia Bennewitz, Katrin Fleming, Thomas Andresen, Carolin Freichel, Marc Teleman, Aurelio A. Kroll, Jens Hell, Rüdiger Poschet, Gernot Deep Metabolic Profiling Assessment of Tissue Extraction Protocols for Three Model Organisms |
title | Deep Metabolic Profiling Assessment of Tissue Extraction Protocols for Three Model Organisms |
title_full | Deep Metabolic Profiling Assessment of Tissue Extraction Protocols for Three Model Organisms |
title_fullStr | Deep Metabolic Profiling Assessment of Tissue Extraction Protocols for Three Model Organisms |
title_full_unstemmed | Deep Metabolic Profiling Assessment of Tissue Extraction Protocols for Three Model Organisms |
title_short | Deep Metabolic Profiling Assessment of Tissue Extraction Protocols for Three Model Organisms |
title_sort | deep metabolic profiling assessment of tissue extraction protocols for three model organisms |
topic | Chemistry |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9083328/ https://www.ncbi.nlm.nih.gov/pubmed/35548679 http://dx.doi.org/10.3389/fchem.2022.869732 |
work_keys_str_mv | AT gegnerhagenm deepmetabolicprofilingassessmentoftissueextractionprotocolsforthreemodelorganisms AT mechtelnils deepmetabolicprofilingassessmentoftissueextractionprotocolsforthreemodelorganisms AT heidenreichelena deepmetabolicprofilingassessmentoftissueextractionprotocolsforthreemodelorganisms AT wirthangela deepmetabolicprofilingassessmentoftissueextractionprotocolsforthreemodelorganisms AT cortizofabiolagarcia deepmetabolicprofilingassessmentoftissueextractionprotocolsforthreemodelorganisms AT bennewitzkatrin deepmetabolicprofilingassessmentoftissueextractionprotocolsforthreemodelorganisms AT flemingthomas deepmetabolicprofilingassessmentoftissueextractionprotocolsforthreemodelorganisms AT andresencarolin deepmetabolicprofilingassessmentoftissueextractionprotocolsforthreemodelorganisms AT freichelmarc deepmetabolicprofilingassessmentoftissueextractionprotocolsforthreemodelorganisms AT telemanaurelioa deepmetabolicprofilingassessmentoftissueextractionprotocolsforthreemodelorganisms AT krolljens deepmetabolicprofilingassessmentoftissueextractionprotocolsforthreemodelorganisms AT hellrudiger deepmetabolicprofilingassessmentoftissueextractionprotocolsforthreemodelorganisms AT poschetgernot deepmetabolicprofilingassessmentoftissueextractionprotocolsforthreemodelorganisms |