Metabolic profiling of formalin-fixed paraffin-embedded tissues discriminates normal colon from colorectal cancer

Kota Arima, Mai Chan Lau, Melissa Zhao, Koichiro Haruki, Keisuke Kosumi, Kosuke Mima, Mancang Gu, Juha P. Väyrynen, Tyler S. Twombly, Yoshifumi Baba, Kenji Fujiyoshi, Junko Kishikawa, Chunguang Guo, Hideo Baba, William G. Richards, Andrew T. Chan, Reiko Nishihara, Jeffrey A. Meyerhardt, Jonathan A. Nowak, Marios GiannakisCharles S. Fuchs, Shuji Ogino

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


Accumulating evidence suggests that metabolic reprogramming has a critical role in carcinogenesis and tumor progression. The usefulness of formalin-fixed paraffin-embedded (FFPE) tissue material for metabolomics analysis as compared with fresh frozen tissue material remains unclear. LC/MS-MS-based metabolomics analysis was performed on 11 pairs of matched tumor and normal tissues in both FFPE and fresh frozen tissue materials from patients with colorectal carcinoma. Permutation t test was applied to identify metabolites with differential abundance between tumor and normal tissues. A total of 200 metabolites were detected in the FFPE samples and 536 in the fresh frozen samples. The preservation of metabolites in FFPE samples was diverse according to classes and chemical characteristics, ranging from 78% (energy) to 0% (peptides). Compared with the normal tissues, 34 (17%) and 174 (32%) metabolites were either accumulated or depleted in the tumor tissues derived from FFPE and fresh frozen samples, respectively. Among them, 15 metabolites were common in both FFPE and fresh frozen samples. Notably, branched chain amino acids were highly accumulated in tumor tissues. Using KEGG pathway analyses, glyoxylate and dicarboxylate metabolism, arginine and proline, glycerophospholipid, and glycine, serine, and threonine metabolism pathways distinguishing tumor from normal tissues were found in both FFPE and fresh frozen samples. This study demonstrates that informative data of metabolic profiles can be retrieved from FFPE tissue materials. Implications: Our findings suggest potential value of metabolic profiling using FFPE tumor tissues and may help to shape future translational studies through developing treatment strategies targeting metabolites.

Original languageEnglish
Pages (from-to)883-890
Number of pages8
JournalMolecular Cancer Research
Issue number6
StatePublished - 1 Jun 2020
Externally publishedYes


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