Amy S.Y. Lee
mRNA translation in cellular differentiation and disease
A fundamental question in cell biology is how cells sharing the same DNA produce drastically distinct phenotypes. In one organism, the same genome allows for the development of different tissues, controlled cell cycle progression, and specialized responses to environmental stimuli. This occurs through a process known as gene regulation, where modulation of RNA transcription and protein synthesis allow the level of expression of a gene or its gene product to be controlled. The importance of gene regulation is further underscored by its disruption being associated with a myriad of human diseases ranging from developmental diseases to carcinogenesis.
We are focused on understanding how gene regulation occurs through novel mechanisms of mRNA translation. Specifically, we study how non-canonical translation pathways shape cell growth and differentiation. Accumulating evidence supports the essentiality of mRNA translation control in these cell fate decisions, including abundant genetic links between dysregulation of translation initiation factors with malignancy, inheritable diseases, and behavioral disorders.
During my postdoctoral research, I studied the translation mechanisms by which dysregulation of the eukaryotic initiation factor 3 (eIF3) leads to overactive cell proliferation. Using a genome-wide sequencing approach, I identified ~500 mRNA targets in human cells that bind directly to eIF3, with the major site of interaction in the 5′ UTR. By using in vitro biochemical and cell-based assays, I discovered that eIF3 binds to distinct stem loop structures, and this leads to either translation activation of cell proliferation mRNAs or repression of cell differentiation mRNAs. Gene ontology analyses of eIF3 targets stratify into functional categories that are implicated in carcinogenesis, including differentiation, cell cycling, and apoptosis. Circumventing eIF3 translational control in lung cancer cells overexpressing eIF3a is sufficient to reduce cell invasiveness, suggesting that targeting eIF3–RNA binding may be a therapeutic target. These results highlight the critical importance of translational control during cell growth regulation.
Our research is at the nexus of combining discovery and mechanism-based studies, and thus we use genome-wide and computational approaches together with molecular genetics, cell biology, biochemistry, and structural biology techniques. We aim to contribute to understanding the significance of translational control during cell growth decisions by addressing the following questions:
- How do we discover non-canonical translation pathways that shape the decisions of the cell to undergo cell growth, proliferation, or differentiation into different cell types?
- How are the functions of RNA-binding proteins and translation factors regulated by intra- and extracellular environmental signals?
- Why does dysregulation of transcript-specific translation lead to carcinogenesis and developmental diseases; and can we therapeutically target RNA-protein interactions for disease intervention?
- Bacterial cGAS-like enzymes synthesize diverse nucleotide signals. Whiteley AT, Eaglesham JB, de Oliveira Mann CC, Morehouse BR, Lowey B, Nieminen EA, Danilchanka O, King DS, Lee ASY, Mekalanos JJ*, Kranzusch PJ*. Nature. 2019; 567(7747), 194–199.
- Lee ASY, Kranzusch PJ, Doudna JA, Cate JH. eIF3d is an mRNA cap-binding protein required for specialized translation initiation.Nature. 2016 Aug 4; 10.1038/nature18954.
- Lee ASY, Kranzusch PJ, Cate JH (2015). “eIF3 targets cell proliferation mRNAs for translational activation or repression.” Nature. 2015 Jun 04; 522:111-114.
- Kranzusch PJ*, Wilson SC*, Lee ASY, Berger JM, Doudna JA, Vance RE (2015). “Ancient Origin of cGAS-STING reveals mechanism of universal 2’, 3’ cGAMP signaling.” Molecular Cell. 2015 Sept 17; 59(6): 891-903.
- Nuñez JK, Lee ASY, Engelman A, Doudna JA (2015). “Integrase-mediated spacer acquisition during CRISPR– Cas adaptive immunity.” Nature. 2015 Mar 12; 519:193-198.
- Lee ASY, Burdeinick-Kerr R, Whelan SP (2014). “Host factors required for vesicular stomatitis virus infection.” Journal of Virology. 2014 Aug 1; 88(15): 8355-8360.
- Kranzusch PJ, Lee ASY, Wilson SC, Solovykh MS, Vance RE, Berger JM, Doudna JA (2014). “Structure-Guided Reprogramming of Human cGAS Dinucleotide Linkage Specificity.” Cell. 2014 Aug 28; 158(5):1011-1021.
- Lee ASY, Burdeinick-Kerr R, Whelan SP (2013). “A ribosome-specialized translation initiation pathway is required for cap-dependent translation of vesicular stomatitis virus mRNAs.” Proc Natl Acad Sci USA. 2013 Jan 2; 110(1): 324-9.
- Kranzusch PJ, Lee ASY, Berger JM, Doudna JA (2013). “Structure of human cGAS reveals a conserved family of second-messenger enzymes in innate immunity.” Cell Reports. 2013 May 23; 3(5): 1362-1368.
- Brulois K, Chang H, Lee ASY, Ensser A, Wong LY, Toth Z, Lee SH, Lee HR, Myoung J, Ganem DE, Oh TK, Kim JF, Gao SG, Jung JU (2012). “Construction and manipulation of a new Kaposi’s sarcoma-associated herpesvirus bacterial artificial chromosome clone.” Journal of Virology. 2012 Sept; 86(18): 9708-9720.
- Dixit E, Boulant S, Zhang Y, Lee ASY, Odendall C, Shum B, Hacohen N, Chen ZJ, Whelan SP, Fransen M, Nibert ML, Superti-Furga G, Kagan JC (2010). “Peroxisomes are signaling platforms for antiviral innate immunity.” Cell. 2010 May 14;141(4):668-81.
- Ge Z, Lee A, Whary MT, Rogers AB, Maurer KJ, Taylor NS, Schauer DB, Fox JG (2008). “Helicobacter hepaticus urease is not required for intestinal colonization but promotes hepatic inflammation in male A/JCr mice.” Microbial Pathogenesis. 2008 Jul; 45(1): 18-24.
- Radioshitzky S, Kuhn J, Spiropoulous C, Albarino C, Nguyen D, Salazar-Bravo J, Dorfman T, Lee AS, Wang E, Ross S, Choe H, Farzan M (2008). “Receptor Determinants of Zoonotic Transmission of New World Hemorrhagic Fever Arenaviruses.” Proc Natl Acad Sci USA. 2008 Feb 19;105(7):2664-9.
- Ge Z, Rogers AB, Feng Y, Lee A, Xu S, Taylor NS, Fox JG (2007). “Bacterial cytolethal distending toxin promotes the development of dysplasia in a model of microbially induced hepatocarcinogenesis”. Cell Microbiology. 2007 Aug; 9(8): 2070-2080.