Dan Raftery

• Professor,  Department of Anesthesiology and Pain Medicine

• Adjunct Professor, Department of Chemistry

• Member, Fred Hutchinson Cancer Research Center

• Director, Northwest Metabolomics Research Center

Research Interests

My research group focuses on the development of new methods in and applications of metabolite profiling using a combination of mass spectrometry and NMR platforms which provide a broad based approach for biomarker discovery and systems biology research. We have worked closely with a large number of scientific and clinical collaborators and biostatisticians on various metabolomics projects such as the identification of cancer biomarkers for early detection, recurrence monitoring and therapy prediction. We are also involved in studies of diabetes and heart diseases as well as nutrition based disease prevention and aging. Our group has a strong interest in expanding the understanding of disease risk factors using metabolite profiling approaches. We have extensive experience in the quantitative determination of metabolite concentrations in a variety of samples including serum/plasma, urine, cells and tissue extracts. In conjunction with the Northwest Metabolomics Research Center that we established several years ago, we have developed a large number of assays and approaches for metabolite profiling. We utilize a range of platforms including targeted LC-MS/MS for broad based and quantitative profiling and targeted pathway assays, LC-MS for global aqueous profiling and lipidomics, and GC-MS and NMR global profiling methods that provide excellent coverage of the metabolome. We also perform isotope tracer analysis using GC-MS and NMR based approaches. We have significant experience and expertise in the use of a number of multivariate statistical methods as well as metabolic pathway analysis tools. My group has experience running large metabolomics sample sets that incorporate a number of quality control measures to ensure reliability of large datasets.

• Metabolite profiling, methods development and applications
• Disease diagnostics development and systems biology research
• NMR spectroscopy and mass spectrometry

Education

• A.B.:Harvard College, 1984
• Visiting Scientist: CERN, Geneva Switzerland, 1985
• Ph.D.: University of California, Berkeley, 1991
• Postdoctoral Scientist: University of Pennsylvania 1992-94

Honors and Awards

• 1982-84 Harvard College Scholarship
• 1987-88 Chateaubriand International Research Scholarship
• 1997-99 Research Corporation Cottrell Scholars Award
• 1999-01 Alfred P. Sloan Research Fellow
• 2011 Purdue School of Science Engagement Award

Selected Publications

Metabolomics Methods Development:

• L. Paudel, G.A. Nagana Gowda, D. Raftery, “Extractive Ratio Analysis NMR Spectroscopy for Metabolite Identification in Complex Biological Mixtures,” Anal. Chem., 2019 in press.
• G.A. Nagana Gowda, D. Djukovic, L. Bettcher, H. Gu, D. Raftery, “NMR-Guided Mass Spectrometry for Absolute Quantitation of Human Blood Metabolites,” Anal. Chem., 90(3):2001-09 (2018).

• A. Nagana Gowda, L. Abell, C.F. Lee, R. Tian, D. Raftery, “Simultaneous Analysis of Major Coenzymes of Cellular Redox Reactions and Energy Using Ex Vivo ¹H NMR Spectroscopy,” Anal. Chem. 88, 4817-24 (2016).
• A. Nagana Gowda, Y.N. Gowda, D. Raftery, “Expanding the Limits of Human Blood Metabolite Quantitation using NMR Spectroscopy,” Anal. Chem. 87, 706-15 (2015).
• Gu, P. Zhang, D. Raftery, “Globally Optimized Targeted Mass Spectrometry (GOT-MS): Reliable Metabolomics Analysis with Broad Coverage,” Anal. Chem. 87, 12355-62 (2015).

Cancer Biomarker Discovery:

• Baniasadi, G.A. Nagana Gowda, H. Gu, A. Zeng, S. Zhuang, N. Skill, M. Maluccio, and D. Raftery, “Targeted Metabolic Profiling of Hepatocellular Carcinoma and Hepatitis C using LC-MS/MS,” Electrophoresis 34, 29-2917 (2013).
• Zhu, D. Djukovic, L. Deng, H. Gu, F. Himmati, E.G. Chiorean, M.A. Zaid, D. Raftery: Targeted Serum Metabolite Profiling for Colorectal Cancer Progression Monitoring,” Anal. Bioanal. Chem. 407, 7857-63, (2015).
• Zhu, D. Djukovic, L. Deng, H. Gu, F. Himmati, E.G. Chiorean, D. Raftery, “Colorectal Cancer Detection using Targeted Serum Metabolic Profiling.” J. Proteome Res. 13, 4120-30 (2014).
• Asiago, L. Alvarado, N. Shanaiah, K. Owusu-Sarfo, G. A. Nagana Gowda, R. Ballas, and D. Raftery, “Early Detection of Recurrent Breast Cancer Using Metabolite Profiling,” Cancer Res. 70, 8309-18 (2010).

Statistical Methods Development:

• Wei, J. Zhang, L. Liu, T. Ye, G.A. Nagana Gowda, F. Tayyari, D.Raftery, “Ratio Analysis NMR Spectroscopy (RANSY) for Selective Metabolite Identification in Complex Samples,” Anal. Chem. 83, 7616-23 (2011).
• Gu, G. A. Nagana Gowda, F. Carnevale Neto, M. R. Opp, D. Raftery, “RAMSY: Ratio Analysis of Mass Spectrometry to Improve Compound Identification,” Anal. Chem. 85, 10771-79 (2013).
• Chen, L. Deng, S. Wei, G.A. Nagana Gowda, H. Gu, E.G. Chiorean, M. Abu Zaid, M. Harrison, J. Pekny, P. Loehrer, D. Zhang, M. Zhang, D. Raftery, “Exploring Metabolic Profile Differences between Colorectal Polyp Patients and Controls Using Seemingly Unrelated Regression,” Proteome Res. 14, 2492-2499 (2015).

Metabolomics of Cancer Cell Metabolism:

• Carroll, D. Diolaiti, L. McFerrin, H. Gu, D. Djukovic, D. Du, P.F. Cheng, S. Anderson, M. Ulrich, J.B. Hurley, D. Raftery, D.E. Ayer, R.N. Eisenman, “Deregulated Myc Requires MondoA/Mlx for Metabolic Reprogramming and Tumorigenesis,” Cancer Cell 27, 271-285 (2015).
• Zhou, W. Zheng, G.A. Nagana Gowda, D. Raftery, S.S. Donkin, B. Bequette, D. Teegarden, “1,25-Dihydroxyvitamin D Inhibits Glutamine Metabolism in Harvey-ras Transformed MCF10A Human Breast Epithelial Cells,” J. Steroid Biochem Mol. Biol. 163, 147-56 (2016).
• Zheng, F. Tayyari, G.A. Nagana Gowda, D. Raftery, E.S. McLamore, J. Shi, D.M. Porterfield, B. Bequette, S. Donkin, D. Teegarden, “Altered Glucose Metabolism in Harvey-ras Transformed MCF10A Cells,” Mol Carcinogenesis 54, 111-120 (2015).
• G.A. Nagana Gowda, G.A. Barding Jr., J. Dai, H. Gu, D.H. Margineantu, D.M. Hockenbery, D. Raftery, “A Metabolomics Study of BPTES Altered Metabolism in Human Breast Cancer Cell Lines,” Frontiers Mol. Biosci. 5, 49 (2018).

Collaborative Metabolomics Projects:

• D. Shao, O. Villet, Z. Zhang, S.W. Choi, J. Yan, J. Ritterhoff, H. Gu, D. Djukovic, D. Christodoulou, S. Kolwicz, D. Raftery, R. Tian, “Glucose Promotes Cell Growth by Suppressing Branched-Chain Amino Acid Degradation,” Nature Comm. 9:2935 (2018).
• M.S. Nadjsombati, J.W. McGinty, M.R. Lyons-Cohen, J.B. Jaffe, L. DiPeso, C. Schneider, C.N. Miller, J.L. Pollack, G.A. Nagana Gowda, D.J. Erle, M.S. Anderson, R.M. Locksley, D. Raftery, J. von Moltke, “Detection of Succinate by Intestinal Tuft Cells Triggers a Type 2 Innate Immune Circuit,” Immunity 49(1):33 (2018).
• P. Lohavanichbutr. Y. Zhang. P. Wang. H. Gu, G.A. Nagana Gowda, D. Djukovic, M.F. Buas, D. Raftery, C. Chen, “Salivary Metabolite Profiling Distinguishes Patients with Oral Cavity Squamous Cell Carcinoma from Normal Controls,” PLoS One (13):e0204249 (2018).
• R.J. Davis, M. Gonen, D.H. Margineantu, S. Handeli, J. Swanger, J.E. Grim, H. Gu, D. Raftery, D.M. Hockenbery, A. Margolin, B.E. Clurman, “Pan-Cancer Transcriptional Signatures Predictive of Oncogenic Mutations Reveal that Fbw7 Regulates Cancer Cell Oxidative Metabolism,” PNAS 115, 5462-67 (2018).
• B. Roshanravan, L.R. Zelnick, D. Djukovic, H. Gu, J.A. Alvarez, T.R. Ziegler, J.L. Gamboa, K. Utzschneider, B. Kestenbaum, J. Himmelfarb, S.E. Kahn, D. Raftery, I.H. de Boer, “Chronic Kidney Disease Attenuates the Plasma Metabolome Response to Insulin. Chronic kidney Disease Attenuates the Plasma Metabolome Response to Insulin, JCI Insight. 23(16) (2018).
• K.A. Ederer, K. Jin, S. Bouslog, L. Wang, G.S. Gorman, G.C. Rowe, P. Abadir, D. Raftery, D. Moellering, D. Promislow, P. Jumbo-Lucioni, M. De Luca, “Age- and Genotype-Specific Effects of the Angiotensin-Converting Enzyme Inhibitor Lisinopril on Mitochondrial and Metabolic Parameters in Drosophila melanogaster,” Int J Mol Sci 19(11): pii: E3351, 2018.
• D. F. Wang, L. Cheng, Q. Fei, H. Gu, D. Raftery, B. Cao, C. Zhang, X. Sun, J. Yan, J.Y. Cui, J. Wang, “Metabolic Profiling Identifies Phospholipids as Potential Serum Biomarkers for Schizophrenia,” Psychiatry Res. 272:18-29 (2018).
• B.N.R. Ginos, S.L. Navarro, Y. Schwarz, H. Gu, D.F. Wang, T.W. Randolph, A. Shojaie, M. Kratz, M.A.J. Hullar, M.A.J., P.D. Lampe, M.L. Neuhouser, D. Raftery, J.W. Lampe, “Circulating bile acids in healthy adults respond differently to a dietary pattern characterized by whole grains, legumes and fresh fruits and vegetables compared to a diet high in refined grains and added sugars: a randomized, controlled, crossover feeding study,” Metabolism 83:197-204 (2018).
• M.F. Buas, H. Gu, D. Djukovic, J. Zhu, L. Onstad, B.J. Reid, D. Raftery, T.L. Vaughan, “Identification of Novel Candidate Serum Metabolite Biomarkers for Distinguishing between Gastro-Esophageal Reflux Disease, Barrett’s Esophagus, and High-Grade Dysplasia/Esophageal Adenocarcinoma,” Metabolomics 13, 27 (2017).
• T. Li, Z. Zhang, S.C. Kolwicz, Jr., L. Abell, N.D. Roe, M. Kim, B. Zhou, Y. Cao, J. Ritterhoff, H. Gu, D. Raftery, H. Sun, R. Tian, “Defective Branched-Chain Amino Catabolism Disrupts Glucose Metabolism and Sensitizes the Heart to Ischemia-reperfusion Injury,” Cell Metabolism 25:374-385 (2017).
• H. Sperber, J.  Mathieu, Y. Wang, A. Ferreccio, J. Hesson, Z. Xu, K.A. Fischer, A., Devi, D. Detraux, H. Gu, et al., “The Metabolome Regulates the Epigenetic Landscape during Naïve to Primed Human Embryonic Stem Cell Transition,” Nature Cell Biol. 17, 1523-35 (2015). PMCID: PMC4662931

 List of Published Work in MyBibliography (from over 190):

http://www.ncbi.nlm.nih.gov/sites/myncbi/daniel.raftery.1/bibliography/40922798/public/

Laboratory

• Raftery Lab Research