My lab is driven by two fundamental questions: (1) what is the mechanism by which microRNAs affect gene expression and (2) how does dysregulation of microRNA pathways influence oncogenesis? We described the first cell-free microRNA-mediated translation repression system which provided us with a unique tool to dissect the requirements for microRNA activity such as the requirement for target mRNAs to possess a physiological 7mG cap and thus showed that microRNAs can block translation initiation.
Using reverse genetic screening approaches we also showed that ribosomal protein genes (RPGs) as a class globally regulated microRNA-mediated repression of translation initiation. Reduced expression of any ribosomal protein selectively increased translation of microRNA-targeted mRNAs. This observation also led us to study a rare group of genetic diseases called ribosomopathies, characterized by reduced ribosome biogenesis and function, which include Diamond Blackfan Anemia (DBA) and Shwachman Diamond Syndrome (SDS). Clinically, these patients present with congenital anomalies, bone marrow failure (lineage-specific and pan-anemia) and cancer predisposition. It has been a long-standing mystery why patients present with this constellation of clinical findings. Because microRNAs frequently target body patterning genes, differentiation and developmental genes and oncogenes, we may have identified the molecular pathogenesis of ribosomopathies. We are currently using single cell RNA-seq of DBA- and SDS-patient bone marrow samples to investigate the mechanism by which reduced expression of ribosomal genes can promote cancers. Notably, an increasing number of cancers are characterized by reduced RPG expression. We are also investigating potential tumor suppressor roles for RPGs in a variety of cancers using combined biochemical and genomic approaches.
We are also investigating transcriptional regulation of microRNAs. Altered microRNA expression has been correlated with the tissue of origin, prognosis, and drug sensitivity of cancers and other diseases. Thus, it is critical to understand how microRNA expression is controlled in normal and disease contexts. MicroRNA expression is regulated by DNA methylation, as many microRNA genes exhibit aberrant promoter hypo- and hyper-methylation in cancer. To study the causes and consequences of inappropriate DNA methylation of microRNA genes, my lab is developing “epigenetic engineering” tools that will enable site-specific addition and removal of methyl groups on DNA. In contrast to genetically altering, sterically blocking, or transcriptionally activating target genes, epigenetically reprogramming target genes by site-specific DNA methylation or demethylation will lead to durable repression or activation, not requiring continuous expression of ectopic proteins.
We believe that epigenetic reprogramming of any gene of interest may be the next frontier in gene therapy. We are focused on targeted reprogramming of microRNA promoters and collaborate with other DFHCC members on epigenetic engineering of ovarian cancer genes (Dr. Drapkin), tumor-targeting immune cells or tumor-supporting stromal cells (Dr. Wucherpfennig), and putative tumor suppressor genes (Dr. Benjamin).