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2015 Scientific Report

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Van Andel Research

Van Andel Research Institute | Scientific Report 2015 Jeffrey P. MacKeigan, Ph.D. Laboratory of Systems Biology Dr. MacKeigan received his Ph.D. in microbiology and immunology at the University of North Carolina Lineberger Comprehensive Cancer Center in 2002 and then held a postdoctoral fellowship in the Department of Cell Biology at Harvard Medical School. In 2004, he joined Novartis Institutes for Biomedical Research in Cambridge, Massachusetts, as an investigator and project leader in the Molecular and Developmental Pathways expertise platform. Dr. MacKeigan joined VARI in 2006 as an Assistant Professor and was promoted to Associate Professor in 2010. He leads the Laboratory of Systems Biology and directs the Pathway of Hope research initiative. From left, back row: MacKeigan, Burgenske, Merrill, Doppel, Sisson, Webb, Solitro, Nelson, Bagchi; kneeling: Kortus, Lanning, Kerk Staff Students Adjunct Faculty Nicole Doppel, B.S. Vanessa Fogg, Ph.D. Sam Kerk, B.S. Jennifer Kordich, M.S. Matt Kortus, M.S. Nate Lanning, Ph.D. Brendan Looyenga, Ph.D. Katie Martin, Ph.D. Amy Nelson Juliana Sacoman, Ph.D. Aaron Sayfie, B.A. Kellie Sisson, B.S. Jennifer Webb, B.A. Aditi Bagchi, M.D. Dani Burgenske, B.S. Megan Goodall, Ph.D. Nate Merrill, B.S. Anna Plantinga, B.S. Abbey Solitro, B.S. Laura Westrate, Ph.D. Brian Lane, M.D., Ph.D. 18

MacKeigan Research Interests Systems biology integrates disciplines such as biochemistry, mathematics, and genetics to investigate biological questions. The Laboratory of Systems Biology focuses on identifying and understanding the genes and signaling pathways that, when mutated, contribute to the pathophysiology of cancer and neurodegeneration. Our lab has two major research programs: cancer metabolism and the evasion of apoptosis, and PI3K-mTOR and the autophagy signaling network. We use tools such as RNA interference (RNAi), quantitative proteomics, and in silico screening to investigate the kinases and phosphatases that mediate the pro-apoptotic and cell survival functions of mitochondria, as well as those that regulate lipid signaling and autophagy. The laboratory’s primary scientific objectives are to investigate the molecular details of cancer and tumor diseases; develop therapeutics for high-priority targets; reposition drugs into cancer and neurodegenerative diseases; and map genes to disease. Cancer metabolism and the evasion of apoptosis A wealth of experimental evidence connects the regulation of cellular metabolism with the development of cancer. Metabolic changes are considered key events in the transition from a normal cell to a cancer cell. Such changes reprogram cells to provide the fuel and energy required for rapid malignant proliferation. To identify genes crucial in cancer cell metabolism, we developed a novel, high-throughput method to comprehensively screen all known nuclear-encoded genes whose protein products localize to mitochondria. Our screen also included other metabolic genes and used cellular ATP levels as a readout. The screen was performed under both glycolytic and oxidative phosphorylation–restricted conditions to define genes contributing to ATP production in each bioenergetic state. From our screen, we identified several genes that drive cancer cell bioenergetics and that cancer cells rely on for survival and proliferation. A substantial proportion of the genes we identified as novel targets were dysregulated in tumors from glioma patients, and their expression and copy number significantly correlated with patient survival. One such gene was for a mitochondrial adenylate kinase (AK4), which regulates cellular ATP levels and AMPK signaling. We also identified a mechanism by which electron transport chain changes under glycolytic conditions increased ATP production through enhanced glycolytic flux, highlighting the cellular potential for metabolic plasticity. This study has comprehensively mapped the bioenergetic landscape of all mitochondrial proteins in the context of varied metabolic substrates and thus has begun to link key metabolic genes to clinical outcomes. PI3K-mTOR and the autophagy signaling network Autophagy is a cellular catabolic process that generates internal nutrients by targeting portions of cytosol for lysosomal degradation. During times of stress, autophagy is activated as a way to generate energy, clear damaged organelles, and delay or prevent cell death. Accordingly, autophagy is often activated by oncogenic transformation (e.g., KRAS) and is crucial for tumor survival and progression as an adaptation to stressors such as chemotherapy. Mechanistically, autophagy is directly inhibited by mTOR; therefore, molecular-targeted therapies that block PI3K-AKT-mTOR signaling induce autophagy, providing a counterproductive mechanism of cell survival and drug resistance. In addition, compounds not directly impinging on that pathway can generate intracellular stress signals that activate autophagy by less direct mechanisms. Understanding the effects of a compound on autophagy is crucial to improving its therapeutic efficacy. We have identified a potent activator of autophagy in cancer cells. To further this discovery, we used RNAi to target the human kinome and also a set of genes encoding proteins having likely roles in the regulation of autophagy. We developed a robust, microscopy-based assay to quantitatively measure autophagy and we demonstrated that drug-induced autophagy required two genes. One was an expected finding due to its central role in autophagy; the other was a novel finding with no previous connections to autophagy. We used these two genes as leads in a second RNAi screen. We confirmed that knockdown of the novel gene selectively decreased the viability of the oncogenic KRAS line, making this gene a promising target for further research. 19

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