Research areas

Regulation of Hematopoietic Stem Cells and Development of Hematologic Malignancies

The best studied of adult stem cells is the hematopoietic (blood-forming) stem cell (HSC) that resides in the bone marrow.  Despite decades of work, little is known about the factors or mechanisms that regulate them.  We are using HSCs as a paradigm to understand the general mechanisms governing adult stem cells, and how dysregulation of some of these pathways leads to malignancy development.

DNMT3A in hematologic malignancy

DNMT3A is mutated in about 20 percent of hematologic malignancies, and is emerging as one of the most important tumor suppressors of the hematopoietic system.  How it exerts its role, considering the genome-wide activity, is an enigma.  We are using a combination of approaches including biochemistry, generation of novel mouse models, and examination of human samples, to study how DNMT3A mutation promotes malignancy development.  See Yang, Rau, Goodell, Nature Reviews Cancer, 2015.

Regulation of HSCs during aging

The biggest risk factor for malignancy development is age.  We are studying the cell intrinsic and environmental factors in mice that change with age and promote transformation in the hematopoietic system. In particular, we are interested in the epigenetic changes with age, and how mutations in epigenetic regulators affect this process (See Sun et al, Cell Stem Cell, 2014).

Epigenetic regulation of stem cell self-renewal and differentiation

How the decision of stem cells to self-renew or differentiate is still poorly understood. HSCs reside in a primarily quiescent state in the bone marrow and are rapidly activated to divide and give rise to the component cells of the blood when needed. If we can understand how stem cells are maintained, we could potentially expand HSC ex vivo allowing improved bone marrow transplantation and cancer treatments.

Our approach to this problem has been to identify genes that are candidates for regulating the stem cell, by determining the genes that change in their expressed levels while stem cells are undergoing a decision process.  We recently discovered that DNA methyltransferase 3a (DNMT3A) was highly and specifically expressed in HSCs.  In mouse embryonic stem (ES) cells, DNMT3A, along with DNMT3B, is required for differentiation, suggesting it may play a similar role in HSCs.   We found that when conditionally knocked out, DNMT3A-deficient HSCs expanded dramatically and lost their ability to differentiate (Challen, Nature Genetics 2012). The additional loss of DNMT3B causes further loss of differentiation and increase of self-renewal capacity (Challen, Cell Stem Cell 2014). This important finding, along with the involvement of DNMT3A in human hematologic malignancies, including both leukemias and lymphomas, has led us to focus on the role of DNMT3A in self-renewal and differentiation in stem cells more broadly.

We are looking at the mechanism of DNMT3A action in depth using mouse ES cells.  These interests have led us to develop genome-wide approaches to examine epigenetic regulation in small numbers of stem cells, including whole genome methylation profiling (using whole genome bisulfite sequencing, WGBS), ChIP sequencing, and RNA seq (Jeong, Nature Genetics, 2014). 

These studies led to the discovery of a new genome feature we call DNA methylation canyons, which are large stretches of very low DNA methylation (> 3.5 KB and < 10% DNA methylation) that harbor highly conserved developmental regulator genes (Jeong, Nature Genetics, 2014).