Areas of Research: Quantitative and comprehensive understanding of metabolism.
- Chemistry and the Lewis-Sigler Institute for Integrative Genomics
241 Carl Icahn Laboratory
Towards a Holistic Understanding of Cellular Metabolism
The 20th century saw remarkable progress in understanding key biochemical structures and processes, such as the enzymatic pathway by which glucose is used to generate ATP and the mechanism of replication of genetic material. Until very recently, however, chemical biology focused almost exclusively on understanding biological processes in relative isolation, with minimal attention to the mechanisms by which the complete chemical constituents of cells, or even more dauntingly multi-cellular organisms, function together. With newfound knowledge of the full genetic sequences of multiple organisms, chemical biology is for the first time beginning to investigate the means by which the integrated functioning of the full complement of biological chemicals yields life.
To succeed in developing a complete chemical model of even a simple organism, it is necessary to gain a comprehensive understanding of the molecular constituents involved, including their function, production, consumption, and geometrical organization. These constituents can be broadly divided into large molecule biopolymers such as DNA, RNA, and proteins, and small molecules such metabolic intermediates and membrane lipids. Currently, progress towards a complete understanding of biopolymers is progressing with remarkable speed, largely due to the advent of powerful new analytical tools such as DNA microarrays.
A critical complement to the current holistic studies of cellular large molecules is comparably comprehensive study of the dynamics of the intracellular metabolites. Currently, methods for comprehensive characterization of small molecule concentrations and fluxes in living cells lag behind those for biopolymer expression. The overall goal of our lab is to develop robust means of measuring the concentrations and fluxes of numerous intracellular metabolites in parallel.
Scientific and Biomedical Applications
In our research, beyond developing analytical tools, we apply our metabolite concentration and flux measurement capabilities in three areas:
- Quantitative modeling of the complete metabolic reaction network, using iterative series of computer simulations and experiments;
- Exploration of the linkages between perturbation of the cellular environment (e.g., nutrient deprivation), metabolic response, and gene expression response; and
- Discovery of improved metabolic inhibitors (a large number of important drugs, including some antibiotics, anticancer agents, and cholesterol lowering drugs, function by blocking specific metabolic reactions)
- Guo, J. Y., Teng, X., Laddha, S. V., Ma S., Van Nostrand, S. C., Yang Y., Khor, S., Chan C. S., Rabinowitz, J. D., White, E. (2016) Autophagy provides metabolic substrates to maintain energy charge and nucleotide pools in Ras-driven lung cancer cells. Gene Dev., 30(15): 1704-17. Pubmed
- Frederick, D. W., Loro, E., Liu, L., Davila, A. Jr., Chellappa, K., Silverman, I. M., Quinn, W. J. 3rd, Gosai, S. J., Tichy, E. D., Davis, J. G., Mourkioti, F., Gregory, B. D., Dellinger, R. W., Redpath, P., Migaud, M. E., Nakamaru-Ogiso, E., Rabinowitz, J. D., Khurana, T. S., Baur, J. A. (2016) Loss of NAD homeostasis leads to progressive and reversible degeneration of skeletal muscle. Cell Metab., 24(2): 269-82. Pubmed
- Ron-Harel, N., Santos, D., Ghergurovich, J. M., Sage, P. T., Reddy, A., Lovitch, S. B., Dephoure, N., Satterstrom, F. K., Sheffer, M., Spinelli, J. B., Gygi, S., Rabinowitz, J. D., Sharpe, A. H., Haigis, M. C. (2016) Mitochondrial biogenesis and proteome remodeling promote one-carbon metabolism for T cell. Cell Metab., 24(1): 104-17. Pubmed
- Teng, X., Emmett, M. J., Lazar, M. A., Goldberg, E., Rabinowitz, J. D. (2016) Lactate dehydrogenase C produces s-2-hydroxyglutarate in mouse testis. ACS Cem. Biol., 2016 Jul 7 [Epub ahead of print]. Pubmed
- Titchenell, P. M., Quinn, W. J., Lu, M., Chu, Q., Lu, W., Li, C., Chen, H., Monks, B. R., Chen, J., Rabinowitz, J. D., Birnbaum, M. J. (2016) Direct hepatocyte insulin signaling is required for lipogenesis but is dispensable for the suppression of glucose production. Cell Metab., pii: S1550-4131(16)30174-7. Pubmed
- Ducker, G. S., Chen, L., Morscher, R. J., Ghergurovich, J. M., Esposito, M., Teng, X., Kang, Y., Rabinowitz, J. D. (2016) Reversal of cytosolic one-carbon flux compensates for loss of the mitochondrial folate pathway. Cell Metab., 2016 May 18. pii: S1550-4131(16)30168-1. Pubmed
- Bren, A., Park, J. O., Towbin, B. D., Dekel, E., Rabinowitz, J. D., Alon, U. (2016) Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP. Sci Rep., 6:24834. Pubmed
- Rabinowitz, J. D., Coller, H. A. (2016) Partners in the Warburg effect. Elife, 5: e15938. Pubmed
- Liu, L., Shah, S., Fan, J., Park, J. O., Wellen, K. E., Rabinowitz, J. D. (2016) Malic enzyme tracers reveal hypoxia-induced switch in adipocyte NADPH pathway usage. Nat. Chem. Biol., 12(5): 345-52. Pubmed
- Koivunen, P., Fell, S. M., Lu, W., Rabinowitz, J. D., Kung, A. L., Schlisio, S. (2016) The 2-oxoglutarate analog 3-oxoglutarate decreases normoxic hypoxia-inducible factor 1α in cancer cells, induces cell death, and reduces tumor xenograft growth. Hypoxia, 4: 15-27.
- Jang, C., Oh, S. F., Wada, S., Rowe, G. C., Liu, L., Chan, M. C., Rhee, J., Hoshino, A., Kim, B., Ibrahim, A., Baca, L.G., Kim, E., Ghosh, C. C., Parikh, S. M., Jiang, A., Chu, Q., Forman, D. E., Lecker, S. H., Krishnaiah, S., Rabinowitz, J. D., Weljie, A. M., Baur, J. A., Kasper, D. L., Arany, Z. (2016) A branched-chain amino acid metabolite drives vascular fatty acid transport and causes insulin resistance. Nat. Med., 22(4): 421-6. Pubmed
- Zong, WX, Rabinowitz, JD, White, E. (2016) Mitochondria and cancer. Mol. Cell, 61(5): 667-76. Pubmed
- Bott, AJ, Peng, IC, Fan, Y, Faubert, B, Zhao, L, Li, J, Neidler, S, Sun, Y, Jaber, N, Krokowski, D, Lu, W, Pan, JA, Powers, S, Rabinowitz, J, Hatzoglou, M, Murphy, DJ, Jones, R, Wu, S, Girnun, G, Zong, WX. (2015) Oncogenic Myc induces expression of glutamine synthetase through promoter demethylation. Cell Metab., 22(6): 1068-77. Pubmed
- Su, X, Wellen, KE, Rabinowitz, JD. (2015) Metabolic control of methylation and acetylation. Curr. Opin. Chem. Biol., 30: 52-60. Pubmed
View complete list of Publications.