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Cores
Metabolism Core
Metabolic analysis requires identification and quantification of a large number of metabolites of widely differing biochemical classes from diverse biological samples, including cells, culture media, tissues, and biofluids. In most cases, a biochemical mechanism is needed, in which case it is necessary to introduce appropriate stable isotope tracers (e.g., 13C or 15N), which greatly increases the information content of the experiments, and with multiplexed tracing, enables extraction of maximal information from limited samples. The Core’s goal is to provide services for a wide coverage of metabolites, with isotopomer and isotopologue analysis, as efficiently as possible (1), Figure 1.
This Core leverages the University of Kentucky's existing Center for Environmental and System Biology (https://medicine.uky.edu/centers/cesb) and Resource Center for Stable Isotope-Resolved Metabolomics instrumentation for experiments. The CCM makes use of three major analytical platforms, namely, high-resolution NMR, high-resolution mass spectrometry (with or without chromatography (1), and Reverse Phase Protein Arrays (2). The Metabolism Core leaders consult on analytical methods and experimental design and provide standardized methods for particular problems (3). Additionally, core personnel develop new techniques to address issues of identification and quantification specific metabolites that are biologically important and relevant to the focus of CCM investigators (4-6).
Analytical Services include:
Stable isotope labeling strategies
High resolution NMR (Bruker 16.45 T Avance III spectrometer with a 1.7 mm inverse triple resonance cryoprobe)
Direct infusion ultrahigh resolution fourier transform mass spectrometry (Thermo Lumos) for lipid analyses
Ion chromatography coupled to FT-MS (Dionex-positive and negative ion separation)
GC coupled to FT-MS (Plasmion SICRIT for gases and derivatizable compounds)
ICP-MS (Agilent 8800 triple quad: elemental analysis)
Laser Ablation with ICP-MS (Teledyne Iridia: MS-based imaging)
Reverse Phase Protein Array (RPPA) (Marathon ArrayJet: protein analysis)
Drs. Lane, Higashi, and Fan assist CCM investigators with experimental design, sample preparation, optimal instrument use, data acquisition and reduction, as well as biochemical interpretation of the experimental results (1-4).
1. Lane, A.N., Higashi, R.M. and Fan, T.W.M. (2019) NMR and MS-based Stable Isotope-Resolved Metabolomics and applications in cancer metabolism. Trac-Trends in Analytical Chemistry, 120, 115322.
2. Fan, T.W.M., Bruntz, R.C., Yang, Y., Song, H., Chernyavskaya, Y., Deng, P., Zhang, Y., Shah, P.P., Beverly, L.J., Qi, Z. Mahan, A.L., Higashi, R.M., Dang, C.V., Lane, A.N. (2019) De novo synthesis of serine and glycine fuels purine nucleotide biosynthesis in human lung cancer tissues. J. Biol. Chem., 294, 13464-13477.
3. T. W-M. Fan, J. Islam, R. Higashi, P. Lin, C. Brainson, A.N. Lane. (2024) Matrix-dependent metabolic reprogramming modulated by EZH2. J. Biol. Chem. 300: 105485
4. T. W.-M. Fan, C. Lima Goncalves, J. Yan, J. Islam, P. Lin, M. M. Y. Kaddah, R. M. Higashi, A. N. Lane, X. Wang, and C. Zhu (2025). Probing metabolic reprogramming in individual breast cancer patients’ tumors using patient-derived organotypic tissue cultures. J. Biol. Chem 301: 108495
5. Yang. J.S., Fan, T. W-M., Brandon, J.A., Lane, A.N. & Higashi, R.M. (2021) Rapid analysis of S-Adenosylmethionine (SAM) and S-Adenosylhomocysteine (SAH) isotopologues in stable isotope-resolved metabolomics (SIRM) using direct infusion nanoelectrospray ultra-high-resolution Fourier transform mass spectrometry (DI-nESI-UHR-FTMS). Anal Chim Acta 118, 338873
6. S. Vicente-Munoz, P. Lin, T. Fan, A.N. Lane (2021) Chemoselection with isotopomer analysis using 15N Cholamine. Anal. Chem. 93:6629-6637
7. Scott, T.L; Zhu, J; Cassel, T.A; Vicente, S., Lin, P., Higashi, R.M; Lane, A.N; Fan, T.W-M (2022). A small-scale microwave-assisted acid hydrolysis method for glycogen determination and turnover in biological samples using Stable Isotope Resolved Metabolomics. Metabolites 12: 760
This Core leverages the University of Kentucky's existing Center for Environmental and System Biology (https://medicine.uky.edu/centers/cesb) and Resource Center for Stable Isotope-Resolved Metabolomics instrumentation for experiments. The CCM makes use of three major analytical platforms, namely, high-resolution NMR, high-resolution mass spectrometry (with or without chromatography (1), and Reverse Phase Protein Arrays (2). The Metabolism Core leaders consult on analytical methods and experimental design and provide standardized methods for particular problems (3). Additionally, core personnel develop new techniques to address issues of identification and quantification specific metabolites that are biologically important and relevant to the focus of CCM investigators (4-6).
Analytical Services include:
Stable isotope labeling strategies
High resolution NMR (Bruker 16.45 T Avance III spectrometer with a 1.7 mm inverse triple resonance cryoprobe)
Direct infusion ultrahigh resolution fourier transform mass spectrometry (Thermo Lumos) for lipid analyses
Ion chromatography coupled to FT-MS (Dionex-positive and negative ion separation)
GC coupled to FT-MS (Plasmion SICRIT for gases and derivatizable compounds)
ICP-MS (Agilent 8800 triple quad: elemental analysis)
Laser Ablation with ICP-MS (Teledyne Iridia: MS-based imaging)
Reverse Phase Protein Array (RPPA) (Marathon ArrayJet: protein analysis)
Drs. Lane, Higashi, and Fan assist CCM investigators with experimental design, sample preparation, optimal instrument use, data acquisition and reduction, as well as biochemical interpretation of the experimental results (1-4).
1. Lane, A.N., Higashi, R.M. and Fan, T.W.M. (2019) NMR and MS-based Stable Isotope-Resolved Metabolomics and applications in cancer metabolism. Trac-Trends in Analytical Chemistry, 120, 115322.
2. Fan, T.W.M., Bruntz, R.C., Yang, Y., Song, H., Chernyavskaya, Y., Deng, P., Zhang, Y., Shah, P.P., Beverly, L.J., Qi, Z. Mahan, A.L., Higashi, R.M., Dang, C.V., Lane, A.N. (2019) De novo synthesis of serine and glycine fuels purine nucleotide biosynthesis in human lung cancer tissues. J. Biol. Chem., 294, 13464-13477.
3. T. W-M. Fan, J. Islam, R. Higashi, P. Lin, C. Brainson, A.N. Lane. (2024) Matrix-dependent metabolic reprogramming modulated by EZH2. J. Biol. Chem. 300: 105485
4. T. W.-M. Fan, C. Lima Goncalves, J. Yan, J. Islam, P. Lin, M. M. Y. Kaddah, R. M. Higashi, A. N. Lane, X. Wang, and C. Zhu (2025). Probing metabolic reprogramming in individual breast cancer patients’ tumors using patient-derived organotypic tissue cultures. J. Biol. Chem 301: 108495
5. Yang. J.S., Fan, T. W-M., Brandon, J.A., Lane, A.N. & Higashi, R.M. (2021) Rapid analysis of S-Adenosylmethionine (SAM) and S-Adenosylhomocysteine (SAH) isotopologues in stable isotope-resolved metabolomics (SIRM) using direct infusion nanoelectrospray ultra-high-resolution Fourier transform mass spectrometry (DI-nESI-UHR-FTMS). Anal Chim Acta 118, 338873
6. S. Vicente-Munoz, P. Lin, T. Fan, A.N. Lane (2021) Chemoselection with isotopomer analysis using 15N Cholamine. Anal. Chem. 93:6629-6637
7. Scott, T.L; Zhu, J; Cassel, T.A; Vicente, S., Lin, P., Higashi, R.M; Lane, A.N; Fan, T.W-M (2022). A small-scale microwave-assisted acid hydrolysis method for glycogen determination and turnover in biological samples using Stable Isotope Resolved Metabolomics. Metabolites 12: 760
Imaging Core
Jianhang Jia, PhD
Because cancer research follows disease progression from tumor initiation to progression and metastasis, high-end imaging capabilities at specific stages are critically important to the CCM. The Imaging Core provides access to sophisticated and advanced imaging equipment beyond the capabilities of individual laboratories to acquire and operate themselves.
Our services span from basic microscope imaging to advanced imaging analysis using sophisticated methodologies. The Imaging Core team trains and assists users in operating instruments and analyzing imaging data. The Imaging Core provides key instrumentation and expertise via the following imaging systems:
Raman microscope SploRA Plus.
Nikon high content Ti2-E inverted live imaging system.
Nikon AX R confocal system with incubation system for live cell imaging.
Nikon A1+-Ti2 confocal system.
Lago optical in vivo imaging system.
Olympus FV1000 inverted confocal.
Nikon Ti-E fully automated inverted microscope system.
Nikon eclipse Ti-E with TIRF system.
GFP/RFP panoramic imaging system.
Xenogen IVIS spectrum imaging system.
Aperio ScanScope XT high-throughput digital slide scanner system (in partnership with the Center on Aging Pathology Core).
Because cancer research follows disease progression from tumor initiation to progression and metastasis, high-end imaging capabilities at specific stages are critically important to the CCM. The Imaging Core provides access to sophisticated and advanced imaging equipment beyond the capabilities of individual laboratories to acquire and operate themselves.
Our services span from basic microscope imaging to advanced imaging analysis using sophisticated methodologies. The Imaging Core team trains and assists users in operating instruments and analyzing imaging data. The Imaging Core provides key instrumentation and expertise via the following imaging systems:
Raman microscope SploRA Plus.
Nikon high content Ti2-E inverted live imaging system.
Nikon AX R confocal system with incubation system for live cell imaging.
Nikon A1+-Ti2 confocal system.
Lago optical in vivo imaging system.
Olympus FV1000 inverted confocal.
Nikon Ti-E fully automated inverted microscope system.
Nikon eclipse Ti-E with TIRF system.
GFP/RFP panoramic imaging system.
Xenogen IVIS spectrum imaging system.
Aperio ScanScope XT high-throughput digital slide scanner system (in partnership with the Center on Aging Pathology Core).
Administrative Core
Nathan Vanderford, PhD, MBA
The Administrative Core facilitates and enhances the scientific productivity of the CCM’s faculty (early-stage and pilot project leaders) by delivering coordinated administrative services across scientific projects and cores. The Administrative Core coordinates all CCM operations, promoting an integrated research and research support framework that promotes synergy, efficiency, effectiveness, and accountability while maximizing multidisciplinary interactions and optimizing core support.
The Administrative Core coordinates and implements all administrative activities of the CCM: daily center activities; program communications, fiscal processes, meeting organization, and advisory committee input; interactions among projects and cores; the CCM pilot project program; and program and project evaluation efforts.
The Administrative Core facilitates and enhances the scientific productivity of the CCM’s faculty (early-stage and pilot project leaders) by delivering coordinated administrative services across scientific projects and cores. The Administrative Core coordinates all CCM operations, promoting an integrated research and research support framework that promotes synergy, efficiency, effectiveness, and accountability while maximizing multidisciplinary interactions and optimizing core support.
The Administrative Core coordinates and implements all administrative activities of the CCM: daily center activities; program communications, fiscal processes, meeting organization, and advisory committee input; interactions among projects and cores; the CCM pilot project program; and program and project evaluation efforts.