Cellular Technologies

Elimination of the “essential” warburg effect in mammalian cells through a multiplex genome engineering strategy

Tuesday, February 6
10:30 AM - 11:00 AM
Location: 6D

Innovative genome editing technologies are accumulating and are rapidly elucidating the genetic basis of many cell functions. However, many disease phenotypes and physiological processes are governed by complex networks involving many gene products. Thus, numerous phenotypes need to be unraveled using multiplex genome editing techniques and in silico analysis. Furthermore, these approaches must further leverage legacy knowledge to identify the genes involved and understand the cell response. As an example, we unraveled the core cellular network controlling the Warburg effect, also known as aerobic glycolysis. This effect involves the tendency of rapidly-proliferating cells to consume excess glucose and secrete copious amounts of lactic acid, despite having adequate oxygen for more efficient oxidative phosphorylation. This response is a hallmark of cancer, immune cell expansion, and other processes with rapidly proliferating cells. However, efforts to test the purpose of Warburg metabolism have been stymied by the difficulty to generate cell lines that are unable to produce lactic acid, since genes involved have proven to be essential or synthetic lethal in proliferating cells. We discovered a genetic circuit involving multiple genes that control lactic acid secretion, and using a multiplex genome editing with CRISPR, we successfully eliminated lactic acid secretion and enabled the deletion of multiple “essential” genes. Surprisingly, the cells show improved metabolic and growth phenotypes, despite the elimination of this fundamental metabolic activity. To understand how immortalized mammalian cells can cope without this seemingly essential metabolic process, we conducted a comprehensive analysis of these cell lines using time-course RNA-Seq, metabolomics, and a genome-scale metabolic network model we have developed for Chinese hamster ovary cells (1). Thus, through a multiplex metabolic engineering effort and comprehensive systems biology analysis, we have been able to engineer out a hallmark phenotype of proliferating cells and begin to understand now a cell can survive without a seemingly essential process.

1. Hefzi, H. et al. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Syst. 3, 434–443.e8 (2016).

Nathan E. Lewis

Assistant Professort of Pediatrics and Bioengineering
University of California, San Diego

Dr. Lewis is an Assistant Professor of Pediatrics and Bioengineering at the University of California, San Diego. He received his BS in biochemistry at Brigham Young University, and his PhD at UC San Diego, he focused on proteomics and developing novel approaches for analyzing biological big data using genome-scale systems biology modeling techniques. Dr. Lewis completed his postdoctoral training at the Wyss Institute at Harvard Medical School, where he worked on genome editing and the use of systems biology for the interpretation of genetic screens. Dr. Lewis' current lab integrates all of his previous work by focusing heavily on the use of systems biology and genome editing techniques to map out and engineer the cell pathways controlling mammalian cell growth, protein synthesis, and protein glycosylation.

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