Whenever you find yourself on the side of the majority, it is time to pause and reflect. – Mark Twain
A) Developing high-throughput CRISPR based approaches to study the functions of lncRNAs
lncRNAs are a large group of genes (more than 100,000 annotated in the human genome), but their functional role in the cell remains a mystery. Until recently, the barrier to uncovering the biological role of lncRNAs was the lack of efficient methods to predict and identify their functionality. To overcome these limitations, we developed and are developing genome engineering approaches that are optimized for high-throughput functional assays of lncRNAs. Using modified CRISPR based technology we can change the “volume” of gene expression without the need to interfere with the sequence of the gene itself. Recently, we developed a CRISPR based platform to study thousands of genes in a single experiment. Using this approach, we identified lncRNAs that function in normal cells and lncRNAs affecting cancer development and treatment. These findings shed light on the biology of lncRNA gene function and regulation, and also may identify new cancer therapeutic targets.
B) Studying the functional role of lncRNAs in normal and malignant hematopoiesis
Hematopoiesis, the production of blood cells, is a multistep process. It start from undifferentiated stem cells that give rise to more than ten different blood cell types (lineages) with various functions. This prosses is tightly regulated, and any perturbation in the differentiation process may result in various diseases, including cancer. In recent years, genomic assays have identified many lncRNAs specifically expressed in the different types of blood cells. lncRNAs play important roles in the normal cellular functions, and abnormal lncRNA expression may affect cell differentiation and function, resulting in blood disorders and even cancer. Using genomic, genetic and molecular biology approaches, we study the molecular mechanisms of lncRNAs, their interactions with other cellular partners such as proteins, chromatin and other RNA molecules. We are interested in understanding how these interactions affect normal blood cells and how, when perturbed, do lncRNAs contribute to tumorigenicity.
C) Developing in vivo models to study the role of lncRNAs in hematopoiesis
Hematopoiesis starts in the bone marrow with the cells continuing their differentiation in other organs as well. This process involves specific microenvironments, chemicals and biological interactions that play critical roles in the behavior of the blood cells. lncRNAs, as regulators of gene expression and function, are also affected by the cellular microenvironment. Therefore, it is very important to generate new models that allow us to look into the biology of lncRNAs within the complex environment of the organism. To this end, we have optimized and generated genetically engineered mice models. These mice use different types of CRISPR systems in their hematopoietic cells. By breeding with other models, and by CRISPR engineering of the cells, we can generate a complex genetic model to study the interactions between lncRNAs, coding genes, and the cellular environment. We believe that uncovering these interactions is critical for a comprehensive understanding of normal blood development and its disorders.