Metabolomics and Tissue Imaging

Activities and Methods:

Metabolomics is the youngest family member of functional genomics and is devoted to the identification and quantitation of as many small molecule compounds (i.e., metabolites) as possible in biological systems in response to genetic modifications and environmental perturbations. The major focus of in-house metabolomics technology development is on designing and validating new and innovative analytical methods by UPLC-MRM/MS, UPLC-ultrahigh-resolution Fourier transform (FT) MS and chromatography-free FTMS for more comprehensive and in-depth determination of metabolites and lipids in blood, urine, cells, tissues and plants, as well as other compounds such as naphthenic acids in environmental samples. With the successful and continuing development of an assay of new UPLC-MRM/MS and UPLC-FTMS methods, we provide both targeted and untargeted metabolomics services, as the Victoria node of Genome Canada-funded TMIC (The Metabolomics Innovation Centre,, on a cost-recovery or collaborative basis, for domestic and international researchers and industrial clients.
The focus of in-house tissue imaging research is on developing novel and enhanced MALDI-MS techniques for high-throughput and multiplexed in situ detection and imaging of both small and large biomolecules in tissues and plants. With successful screening of a series of new MALDI matrices and invention of a novel technique, i.e., MCAEF (Matrix Coating Assisted by an Electric Field; patent pending), we are able to detect and image >800 metabolites and lipids and about 240 proteins in tissues by MALDI-FTICR/MS and MALDI-TOF/MS. Currently, we are continuing to develop new methods and are applying these techniques for clinical tissue imaging.

Cost-recovery and Collaborative Services

Targeted Metabolomics (Targeted Metabolite Analysis and Metabolic Profiling)
- Amino acids, biogenic amines, and intermediates of amino acid metabolism and urine cycle
- Metabolites involved in central carbon metabolism (glycolysis, gluconeogenesis, pentose phosphate pathway, the TCA cycle) --- sugar phosphates, nucleosides, enzyme cofactors, D/L-2-hydroxyglutarate and so on.
- Low-molecular weight aldoses and ketoses
- Bile acids, dihydroxy cholestenoic acid (DHCA), trihydroxy cholestanoic acid (THCA), and >40 potentially unknown bile acids
- Bioactive carboxylates, hydroxyl- and keto-carboxylates
- Short-, medium- and long-chain fatty acids; acyl-carnitines; acetyl-coenzymes; acyl-glycines
- Selected steroid hormones and sterols involved in cholesterol and steroid anabolism and catabolism: cortisol, 6β-OH cortisol, DHEA, DHEA sulphate, estrogens and androgens, etc.
- Oxidative stress biomarkers in relation to lipid, protein and DNA/RNA peroxidation
- Neurotransmitters
- Thyroid hormones
- Vitamin D and metabolites
- Polyphenols
- Naphthenic acids (>400)

Untargeted Metabolomics (Metabolic Fingerprinting and Metabolic Footprinting)
- UPLC-FTMS and UPLC-MS/MS, in combination with multiple RP, ion-pairing and HILIC methods and multivariate statistics
- Direct infusion-FTICR MS

MALDI Imaging
- Protein imaging by MALDI-TOF/MS
- Metabolite, lipid and peptide imaging by MALDI-FTICR/MS
- Quantitative imaging by MALDI-MRM/MS

Research Highlights

1. Han J, Liu Y, Wang R, Yang J, Ling V, Borchers CH. Metabolic profiling of bile acids in human and mouse blood by LC-MS/MS in combination with phospholipid-depletion solid-phase extraction. Anal Chem. 2014 Dec 12. [Epub ahead of print]

2. Han J, Lin K, Sequeira C, Borchers CH. An isotope-labeled chemical derivatization method for the quantitation of short-chain fatty acids in human feces by liquid chromatography-tandem mass spectrometry. Anal Chim Acta. 2015 Jan 7; 854:86-94.

3. Ichu TA, Han J, Borchers CH, Lesperance M, Helbing CC. Metabolomic insights into system-wide coordination of vertebrate metamorphosis. BMC Dev Biol. 2014, 14:5.

4. Antunes LC, Han J, Pan J, Moreira CJ, Azambuja P, Borchers CH, Carels N. Metabolic signatures of triatomine vectors of Trypanosoma cruzi unveiled by metabolomics. PLoS One. 2013, 8(10):e77283.

5. Eckle T, Brodsky K, Bonney M, Packard T, Han J, Borchers CH, Mariani TJ, Kominsky DJ, Mittelbronn M, Eltzschig HK. HIF1A reduces acute lung injury by optimizing carbohydrate metabolism in the alveolar epithelium. PLoS Biol. 2013, 11(9):e1001665.

6. Han J, Tschernutter V, Yang J, Eckle T, Borchers CH. Analysis of selected sugars and sugar phosphates in mouse heart tissue by reductive amination and liquid chromatography-electrospray ionization mass spectrometry. Anal Chem. 2013,85(12):5965-73.

7. Han J, Gagnon S, Eckle T, Borchers CH. Metabolomic analysis of key central carbon metabolism carboxylic acids as their 3-nitrophenylhydrazones by UPLC/ESI-MS. Electrophoresis. 2013, 34(19):2891-900.

8. Nyakas A, Han J, Peru KM, Headley JV, Borchers CH. Comprehensive analysis of oil sands processed water by direct-infusion Fourier-transform ion cyclotron resonance mass spectrometry with and without offline UHPLC sample prefractionation. Environ Sci Technol. 2013, 47(9):4471-9.

9. Eckle T, Hartmann K, Bonney S, Reithel S, Mittelbronn M, Walker LA, Lowes BD, Han J, Borchers CH, Buttrick PM, Kominsky DJ, Colgan SP, Eltzschig HK. Adora2b-elicited Per2 stabilization promotes a HIF-dependent metabolic switch crucial for myocardial adaptation to ischemia. Nature Medicine. 2012, 18(5):774-82.

10. Han J, Kalyan, S, Prior JC, Borchers CH. Quantitation of Urinary 6β-Hydroxycortisol and Free Cortisol by Ultra-Performance Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry. Clinical and Experimental Pharmacology. Clin Exp Pharmacol. 2011, S5

11. Antunes LC, Arena ET, Menendez A, Han J, Ferreira RB, Buckner MM, Lolic P, Madilao LL, Bohlmann J, Borchers CH, Finlay BB. Impact of salmonella infection on host hormone metabolism revealed by metabolomics. Infect Immun. 2011, 79(4):1759-69.

12. Antunes LC, Han J, Ferreira RB, Lolić P, Borchers CH, Finlay BB. Effect of antibiotic treatment on the intestinal metabolome. Antimicrob Agents Chemother. 2011, 55(4):1494-503.

13. Han J, Antunes LC, Finlay BB, Borchers CH. Metabolomics: towards understanding host-microbe interactions. Future Microbiol. 2010, 5(2):153-61.

14. Han J, Datla R, Chan S, Borchers CH. Mass spectrometry-based technologies for high-throughput metabolomics. Bioanalysis. 2009, 1(9):1665-84.

15. Han J, Danell RM, Patel JR, Gumerov DR, Scarlett CO, Speir JP, Parker CE, Rusyn I, Zeisel S, Borchers CH. Towards high-throughput metabolomics using ultrahigh-field Fourier transform ion cyclotron resonance mass spectrometry. Metabolomics. 2008, 4(2):128-140.

Tissue Imaging

16. Wang X, Han J, Yang J, Pan J, Borchers CH. Matrix coating assisted by an electric field (MCAEF) for enhanced tissue imaging by MALDI-MS. Chem. Sci. 2015, 6: 729–738.

17. Wang X, Han J, Pan J, Borchers CH. Comprehensive imaging of porcine adrenal gland lipids by MALDI-FTMS using quercetin as a matrix. Anal Chem. 2014, 86(1):638-46.

18. Le CH, Han J, Borchers CH. Dithranol as a matrix for matrix assisted laser desorption/ionization imaging on a fourier transform ion cyclotron resonance mass spectrometer. J Vis Exp. 2013, (81):e50733. 19. Wang X, Han J, Chou A, Yang J, Pan J, Borchers CH. Hydroxyflavones as a new family of matrices for MALDI tissue imaging. Anal Chem. 2013, 85(15):7566-73.

20. Le CH, Han J, Borchers CH. Dithranol as a MALDI matrix for tissue imaging of lipids by Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem. 2012, 84(19):8391-8.

21. Clemis EJ, Smith DS, Camenzind AG, Danell RM, Parker CE, Borchers CH. Quantitation of spatially-localized proteins in tissue samples using MALDI-MRM imaging. Anal Chem. 2012, 84(8):3514-22.

Group Members:

Jun Han, PhD, group leader
Xiaodong Wang, postdoc
Karen Lin, research associate