Education / Training

Princeton University, Department of Molecular Biology. Postdoctoral research with Drs. Eric Wieschaus and Michael Cole, 2001-2006.

Johns Hopkins University, Department of Biology. PhD, conferred 2002.

Carnegie Mellon University, B.S. in Biology, 1995.

Research Overview: Molecular genetics and genomics of cancer

Excessive accumulation of the Myc oncoprotein leads to tumorigenesis and is present in 50% of all human tumors. Myc is a DNA-binding protein that is able to both activate and repress transcription of many genes, and is capable of binding to over 10% of all genes in the human genome. While Myc induces dramatic changes in expression in vivo, Myc is a weak transcriptional activator in vitro, and repression by Myc does not clearly require Myc binding to DNA.

My lab is interested in understanding how Myc induces such dramatic changes in gene expression, especially during embryogenesis when Myc levels are normally high. We use the Drosophila embryo for our work, which allows us to rapidly obtain thousands of genetically manipulated embryos for our experiments.   We have discovered several nuclear, chromatin remodeling proteins that are involved in Myc's ability to both activate and repress its targets (Polycomb, Ash1, Pho, Su(z)2). These proteins have well-known roles in cell fate specification, and we are interested in understanding the mechanism by which these proteins, and others, affect Myc activity in different cell types and in general.

Transcriptional activation and repression by Myc in the Drosophila embryo

Ectopic Myc in the Drosophila embryo increases expression of many genes (red) and decreases expression of many genes (green). Genes whose levels rise or fall with ectopic Myc change during embryonic development, and we study this developmental control of a genome's response to ectopic Myc. Chromatin structure, sequence elements, modifier proteins and non-coding RNAs are all potential mediators of the response to Myc, as they are for all transcription factors. We use genetic, genomic and molecular biological tools to address the question of what controls a genome's response to Myc.

Myc Auto-Repression

In 1989, Rosenbaum and colleagues reported that transgenic mice over-expressing one of two myc homologs in B cells, either c-myc or N-myc, obtained lymphoid tumors. In tumor cells derived from either N-myc or c-myc transgenic mice, all endogenous N-myc and c-myc loci were transcriptionally silent (Rosenbaum et al. 1989). These experiments revealed the functional equivalence of c-Myc and N-Myc in cancer formation and in Myc-induced repression of both myc genes. Later, Penn and colleagues described the phenomenon of auto-repression in culture cells, which occurs at the level of transcription initiation, is induced by physiological levels of Myc protein, and requires cellular cofactors in addition to Myc (Penn et al. 1990). At the same time, Grignani and others showed that this auto-repression is disrupted in all cancer lines tested (Grignani et al. 1990).

Years later, we began investigating auto-repression in Drosophila because it appeared to involve an epigenetic component. Once Myc protein levels drop, eliminating the trigger for auto-repression, the silenced endogenous loci remain silenced (Mango et al. 1989). Because the trigger for auto-repression necessarily goes away, and yet transcriptional repression remains, we hypothesized that epigenetic regulation must be involved in auto-repression. Drosophila melanogaster was the dominant biological tool for epigenetic research at the time, and therefore we decided to investigate auto-repression in a system with superior genetic and epigenetic tools.

Consistent with our hypothesis that auto-repression involves an epigenetic component, we have shown previously that the chromatin binding repressor Polycomb (Pc) is required for Myc to repress its own gene, dmyc, in Drosophila (Goodliffe et al. 2005). Polycomb Group (PcG) proteins are known for their role in regulation of gene expression necessary for cellular differentiation, stem cell maintenance, and avoidance of tumorigenesis (Schwartz and Pirrotta 2007; Sauvageau and Sauvageau 2008). Polycomb group proteins work in large, multi-subunit complexes that bind to and modify chromatin, silencing hundreds of loci from flies to mammals (Boyer et al. 2006; Bracken et al. 2006; Lee et al. 2006; Negre et al. 2006; Schwartz et al. 2006; Tolhuis et al. 2006; Schuettengruber et al. 2007; Schwartz and Pirrotta 2007). Pc RNAi in the Drosophila embryo results in the loss of the majority of trans-repression by Myc, among many other gene expression changes (Goodliffe et al. 2005; Goodliffe et al. 2007).

Dramatic auto-repression during embryogenesis results in reduced dmyc expression overall, and a dm phenotype (Gal4; UAS dmyc larva). Su(z)2 completely rescues this phenotype (Gal4; Su(z)2XP; UAS dmyc). From Khan et. al., 2009.

Along with the decrease in repression by Myc upon Polycomb RNAi, we have shown increase in levels of Su(z)2, a PcG related protein (Brunk et al. 1991a; Brunk et al. 1991b; Rastelli et al. 1993; Sharp et al. 1994) that is required for ectopic Myc-induced overgrowth in the Drosophila eye (Secombe et al. 2007). An increase in Su(z)2 alone disrupts auto-repression by Myc, but not Myc repression of other targets. As a consequence of the loss of auto-repression, we have shown that elevated levels of ectopic Myc lead to an increase in Myc activation of its targets (Khan et al. 2009). These data provide the first evidence for a protein that interferes with Myc auto-repression, leading to elevated Myc levels and subsequent increases in activation by Myc.

Su(z)2 has two mammalian homologs: Bmi-1 and Mel-18 (Brunk et al. 1991a; van Lohuizen et al. 1991a). Bmi-1 was originally isolated as a collaborator with Myc in tumorigenesis (Haupt et al. 1991; van Lohuizen et al. 1991b), and Myc has been shown to directly activate Bmi-1 (Guney et al. 2006). Interestingly, Mel-18 behaves as a tumor suppressor by repressing oncogenes Bmi-1 and c-myc in mammals (Guo et al. 2007a; Guo et al. 2007b). However, Mel-18 and Bmi-1 have both been shown to increase proliferation and survival of cancer cells (Wiederschain et al. 2007). We are interested in understanding whether Su(z)2’s modulation of myc auto-repression is relevant to Bmi-1 and/or Mel-18 biology in mammals.

Lab Members

Kaveh Daneshvar, PhD student

Abid Khan, PhD student

Sam Vaughan, MA student

Wesley Shover, Research Technician

Akram Alami, undergraduate (second degree seeker)

Casey Rimland, undergraduate

Nina Tran, undergraduate

Courses

Biology 3166, Genetics. Next time I teach 3166 will be Spring of 2011.

Biology 4000 (Spring 2010) or 6000/8000 (Fall 2009): Stem Cells.

Recent Publications

Abid Khan, Wesley Shover, Julie M. Goodliffe. 2009. Su(z)2 Antagonizes Auto-Repression by Myc in Drosophila, Increasing Myc Levels and Subsequent Trans-Activation. 2009. PLoS ONE. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005076

Julie M. Goodliffe, Michael Cole and Eric Wieschaus. 2007. Coordinated Regulation of Myc Trans-activation Targets by Polycomb and the Trithorax Group Protein Ash1. BMC Molecular Biology, 8:40.

Michelle Beaucher*, Julie Goodliffe*, Evelyn Hersperger, Svetlana Trunova, Horacio Frydman and Allen Shearn. 2007. Drosophila brain tumor metastases express both neuronal and glial cell type markers. Developmental Biology, Jan 1;301(1) 287-97. *Authors contributed equally.

Julie M. Goodliffe, Eric Wieschaus and Michael Cole. 2005. Polycomb mediates Myc autorepression and its transcriptional control of many loci in Drosophila. Genes & Development, 2005 Dec 15;19(24) 2941.