Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue specimens constitute a highly valuable source of clinical material for retrospective molecular studies. However, metabolomic assessment of such archival material remains still in its infancy. Hence, there is an urgent need for efficient methods enabling extraction and profiling of metabolites present in FFPE tissue specimens. Here we demonstrate the methodology for isolation of primary metabolites from archival tissues; either fresh-frozen, formalin-fixed or formalin-fixed and paraffin-embedded specimens of mouse kidney were analysed and compared in this work. We used gas chromatography followed by mass spectrometry (GC/MS approach) to identify about 80 metabolites (including amino acids, saccharides, carboxylic acids, fatty acids) present in such archive material. Importantly, about 75% of identified compounds were detected in all three types of specimens. Moreover, we observed that fixation with formalin itself (and their duration) did not affect markedly the presence of particular metabolites in tissue-extracted material, yet fixation for 24h could be recommended as a practical standard. Paraffin embedding influenced efficiency of extraction, which resulted in reduced quantities...Continue Reading
References
Aug 1, 1985·The Journal of Histochemistry and Cytochemistry : Official Journal of the Histochemistry Society·C H FoxP P Roller
Jun 23, 2004·The Journal of Histochemistry and Cytochemistry : Official Journal of the Histochemistry Society·Derek AtkinsStephan Störkel
Nov 17, 2006·Cancer Research·Carsten DenkertOliver Fiehn
Feb 9, 2008·Journal of Proteome Research·Haifeng XuBrian M Balgley
Jun 20, 2008·Molecular BioSystems·Niroshini J NirmalanRosamonde E Banks
May 27, 2009·Molecular & Cellular Proteomics : MCP·Robert W SprungDaniel C Liebler
Sep 8, 2009·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Thaer KhourySwati Kulkarni
Oct 16, 2009·Current Proteomics·Beth Ann ReimelTeresa A Brentnall
Jun 2, 2011·The Analyst·Mark J HackettPeter A Lay
Jun 3, 2011·Brain Pathology·Felix SahmAndreas von Deimling
Oct 11, 2011·PloS One·Andrew D KellyJohn M Asara
Jan 4, 2012·Proteomics. Clinical Applications·Alessandro TancaMaria Filippa Addis
Apr 14, 2012·Nature Protocols·Min YuanJohn M Asara
May 26, 2012·Cancer Research·Sheila GantiRobert H Weiss
Apr 18, 2013·Amino Acids·Evelyne MaesLiliane Schoofs
Dec 18, 2013·Proteomics·Carine SteinerPaul Cutler
Jan 15, 2014·Cancer Chemotherapy and Pharmacology·Ella S M NgAnthony M Magliocco
Jul 12, 2014·The Journal of Clinical Endocrinology and Metabolism·Susan RichterGraeme Eisenhofer
Citations
Feb 20, 2016·Scientific Reports·Arkadiusz D LiśkiewiczHalina Jędrzejowska-Szypułka
Apr 12, 2016·Analytical Chemistry·Achim BuckAxel Walch
Jul 16, 2016·Nature Protocols·Alice LyAxel Walch
Aug 10, 2016·Frontiers in Plant Science·Dawid PerlikowskiArkadiusz Kosmala
Sep 1, 2016·Scientific Reports·Tao HuanLiang Li
Jan 11, 2017·Molecular Genetics and Metabolism Reports·Edward KimRoderick J Clifton-Bligh
Jan 18, 2018·Proceedings of the National Academy of Sciences of the United States of America·Jie HanArianne L Theiss
Nov 24, 2019·Foods·Fabiane M NachtigallLeonardo S Santos
Oct 2, 2020·Metabolomics : Official Journal of the Metabolomic Society·Jéssica Gardone VitórioRicardo Santiago Gomez
Oct 23, 2019·International Journal of Oncology·Di FengMancang Gu
Sep 18, 2016·Der Pathologe·J Budczies
Mar 24, 2016·Proteomics·Monika PietrowskaPiotr Widłak
Jul 8, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Anna WojakowskaDorota Tarnawska
Jan 12, 2017·Molecular Cancer Research : MCR·Stefano CacciatoreMassimo Loda
Jan 27, 2021·Journal of Pharmaceutical and Biomedical Analysis·Magdalena Buszewska-ForajtaMichał J Markuszewski
Jul 18, 2020·Journal of the American Society for Mass Spectrometry·Vanna DentiAndrew Smith
Jun 27, 2020·Clinical Biochemistry·Akram Tayanloo-BeikBabak Arjmand