Complex interactions between individual components of biological systems often generate unexpected outcomes that defy simple analysis. A fundamental challenge is to analyze the behaviors of highly-connected genetic and cellular networks and to understand how these networks can be perturbed or harnessed for mankind's benefits. Our lab develops and applies novel genome engineering tools to dissect regulatory networks underlying cell fate decisions. We are particularly interested in studying a fundamental biological process known as RNA editing, whereby genetically encoded information is modified after transcription. Since RNA editing is dysregulated in many human diseases, we hope that our research will open up new avenues of therapeutic interventions.
We are primarily interested in DNA and RNA editing, particularly in the context of cell identity. Although living cells have biological information hardwired into their genomes, this information can be naturally or artificially altered, either at the level of DNA where the changes can be permanent or at the level of RNA where the changes can be dynamic. The research activities in our laboratory are thus broadly classified into the following areas:
1) DNA editing
(a) Development of novel genome engineering technologies. The emergence of powerful genome editing tools, such as CRISPR-Cas9, have greatly enhanced our ability to modify the human genome. However, CRISPR-associated technologies currently suffer from three major problems, namely efficiency, specificity, and limited targeting range. These shortcomings must be adequately addressed before CRISPR-based technologies can be applied in the clinical setting, for example, to correct disease-causing mutations in patients. Our laboratory is actively pursuing different ways to improve the editing enzymes, with the goal of developing new human therapeutics. In addition, we are developing related technologies, such as inducible genome editing systems and CRISPR-based transcriptional or epigenetic regulators, for various biomedical and biotechnological applications.
(b) Application of genome engineering technologies to understand cell fate decisions. A human body contains many different types of cells, but yet they carry essentially the same DNA. How does a cell know what it should be? Our laboratory leverages on cutting edge genome engineering tools to investigate human stem cell biology. We not only carry out targeted genetic perturbations to gain insights into the underlying regulatory networks orchestrating mammalian development and stem cell differentiation but also perform unbiased high-throughput CRISPR-based screens to identify novel factors involved in cell fate decisions.
2) RNA editing
(a) Functions of RNA editing events. The most prevalent type of RNA editing in mammals is adenosine-to-inosine (A-to-I) editing catalyzed by the ADAR family of RNA-binding proteins. Since inosines are recognized by cellular machineries as guanosines, this type of editing effectively results in nucleotide changes. Next generation sequencing experiments have revealed that A-to-I editing is prevalent in human, but the functional consequences of most editing events are unknown. Our laboratory is interested in investigating the roles of A-to-I editing in stem cell differentiation and how defective editing can contribute to the pathogenesis of various diseases like cancer and neurodegeneration.
(b) Regulation of A-to-I editing. Our laboratory, together with others, has extensively profiled A-to-I editing in numerous normal and diseased tissues. Strikingly, diverse spatiotemporal patterns of editing can be readily detected. However, there are only three ADAR genes encoded in the mammalian genome and only ADAR1 and ADAR2 have been found to exhibit enzymatic activity. Hence, in order to account for the numerous editing patterns observed, other cellular factors must exist to regulate A-to-I editing besides the ADAR proteins. Our laboratory is employing genetic, biochemical, and cell biological approaches to map out the full repertoire of editing regulators, particularly in the context of human development and diseases, and to understand the different mechanisms of regulation.