Our body contains hundreds of different cell types with specific developmental histories or lineages. We are interested in cell identity, and how cells transition from one type to another. In this context, we study embryonic stem cells, which represent a very early stage of mammalian development. Embryonic stem cells are pluripotent, and can generate all cell types of the body. As such, they can provide tremendous insight into development and disease. We use forward genetic screens in embryonic stem cells to learn about lineage maintenance, lineage transition, and the underlying genetic and epigenetic programs.
We are fascinated by using unbiased genetic screens to unravel biologic dependencies of biological processes. We think a data-driven approach to research facilitates discovery. Assumptions can limit our questions and insight – let biology tell the story. We like to use large scale, high-throughput methods to generate data that form a complete picture or answer to a particular question.
The core transcriptional circuitry defining embryonic stem cells has been elucidated over the last years, but we know much less about the genetic factors controlling entrance to and exit from pluripotency. We have developed novel screening approaches to uncover the genetic dependencies of reprogramming, differentiation, cell type identity, and epigenetic control of cellular state. Typically, changes in cell identity require time, involve several intermediate steps, and are often inefficient. We want to identify the genetic hierarchies governing these transitions positively or negatively, to gain further understanding of the processes as well as to establish a handle to modulate them.
As example, induced pluripotent stem cells (iPS cells) can be derived from differentiated cells by the forced expression of four transcription factors. This finding by Yamanaka and colleagues in 2006 revolutionized stem cell research. Overexpression of these lineage-defining activators may be sufficient to reawaken pluripotency, but the process is highly inefficient and rare. The molecular players within the cell guarding or enabling this cell identity change still remain elusive. We recently identified CAF-1 as a powerful roadblock of reprogramming and currently study novel guardians of cell identity.
We have empowered screening approaches in mammalian cells with the following advances:
- We derived haploid embryonic stem cells and optimized gene trap mutagenesis using a variety of different vectors. Haploid genetics is optimal for saturating recessive positive selection screens, as it combines the power of “yeast genetics” with the pluripotency om embryonic stem cells.
- We generated custom CRISPR libraries to perform genome editing based genetic screens that track single cell clones. This approach is very powerful for negative selection screens, to identify loss-of-function mutations that deplete from the pool, as well as for positive selection screens, to follow the expansion of specific mutant clones.
- We developed a biobank of 100 000 conditionally mutated ES cell lines to annotate gene function.
The identification of genes that safeguard lineage identity, as well as genes that are required for lineage transitions, is expected to reveal therapeutic targets for various diseases, such as cancer, diabetes, and neurodegeneration.
Elling, U., Penninger, JM. (2014). Genome wide functional genetics in haploid cells. FEBS Lett. 588(15):2415-21
Wirnsberger, G., Zwolanek, F., Stadlmann, J., Tortola, L., Liu, SW., Perlot, T., Järvinen, P., Dürnberger, G., Kozieradzki, I., Sarao, R., De Martino, A., Boztug, K., Mechtler, K., Kuchler, K., Klein, C., Elling, U., Penninger, JM. (2014). Jagunal homolog 1 is a critical regulator of neutrophil function in fungal host defense. Nat Genet. 46(9):1028-33
Elling, U., Taubenschmid, J., Wirnsberger, G., O'Malley, R., Demers, SP., Vanhaelen, Q., Shukalyuk, AI., Schmauss, G., Schramek, D., Schnuetgen, F., von Melchner, H., Ecker, JR., Stanford, WL., Zuber, J., Stark, A., Penninger, JM. (2011). Forward and reverse genetics through derivation of haploid mouse embryonic stem cells. Cell Stem Cell. 9(6):563-74