Role of DYRK1A in atypical neurodevelopment in Down syndrome

Proteomic landscape of trisomy 21 cerebral organoid proteomics reveals signatures of dysregulated cortical development.

Human trisomy 21 (Down syndrome) is the most common genetic cause of intellectual disability, and is characterized by a complex spectrum of clinical manifestations that includes intellectual disability, cardiovascular and craniofacial abnormalities, and early onset Alzheimer’s-like neurodegeneration (2). Paradoxically, Down syndrome individuals are at increased risk of childhood leukemias, but have a remarkably reduced risk of solid tumors (3). Understanding how an extra copy of chromosome 21 contributes to these pathologies will help pave the way to new therapeutics that increase the quality of life for individuals with Down syndrome. Moreover, research in these areas promises to further our collective understanding of diseases like cancer and neurodegeneration.

We are currently investigating the role of the chromosome 21 encoded protein kinase, DYRK1A, in altered neuropathologies in Down syndrome. We are using biochemical approaches, CRISPR-Cas9 gene editing, and mass spectrometry based approaches to map DYRK1A substrates and interaction partners. The list of proteins that interact with and are phosphorylated by DYRK1A is steadily increasing, but no efforts have systematically mapped DYRK1A targets in a disease relevant model system. Our group is undertaking such an effort.

Our recent data indicates that DYRK1A interacts with and phosphorylates tissue-specific transcription factors, splicing factors and chromatin remodelers important in neurodevelopment, cell growth and cancer progression. To identify these tissue-specific substrates and interaction partners, we are using a variety of cell line and organoid model systems.

Systems pharmacology approaches to identify novel mechanisms of action

Multi-omic perturbation profiling for unknown mechanisms of action.

We have developed multi-omic profiling methods for drug perturbation studies, and a microfluidic platform technology for proteome-wide thermal shift profiling. These approaches facilitate unbiased identification of drug targets and pathway/network level mechanisms. This technology greatly improves the reproducibility of thermal shift assays, and identifies drug-induced alterations in protein interactions, aggregation, and post-translational modifications. We are using microCETSA to investigate cellular perturbations in neuroblastoma cell lines and iPSC-derived model systems of neurodegenerative disorders.

Model systems

In 2007, Kazutoshi Takahashi and Shinya Yamanaka first reported that human skin cells could be reprogrammed into a stem cell-like, pluripotent state with the potential to become any cell type in the body, which they named induced pluripotent stem cells (iPSC) (4, 5). In the short span of one decade since this ground-breaking discovery, we now have the knowledge to differentiate human iPSC into many of the different cell types in the human body, and even grow 3D forms of human tissues in the lab, called organoids (6). Patient derived iPSC can now be grown in the lab into neuronal tissue, or cerebral organoids, that recapitulate many of the key cellular features in the developing human brain (7, 8), and even aspects of human genetic disorders that affect brain development (9). We can now create living models of ourselves: the cells, tissues and organs that cooperate in our health but conspire against us in aging and disease. This has opened up new frontiers in the search for therapeutics targeting diseases previously considered untreatable. We are currently using cerebral organoids and other cancer cell line models identify new therapeutic avenues in Down syndrome, neurodegeneration, and cancer.

Cerebral organoid, treated with an ALK kinase inhibitor, visualizing axons projecting out into the extracellular matrix in response to drug.

Cited References

1.    McClure-Begley, T. D., Ebmeier, C. C., Ball, K. E., Jacobsen, J. R., Kogut, I., Bilousova, G., Klymkowsky, M. K., and Old, W. M. (2018) Cerebral organoid proteomics reveals signatures of dysregulated cortical development associated with human trisomy 21. bioRxiv

2.    Lott, I. T., and Dierssen, M. (2010) Cognitive deficits and associated neurological complications in individuals with Down's syndrome. Lancet Neurol 9, 623-633

3.    Hasle, H., Clemmensen, I. H., and Mikkelsen, M. (2000) Risks of leukaemia and solid tumours in individuals with Down's syndrome. Lancet 355, 165-169

4.    Takahashi, K., and Yamanaka, S. (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663-676

5.    Takahashi, K., Tanabe, K., Ohnuki, M., Narita, M., Ichisaka, T., Tomoda, K., and Yamanaka, S. (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861-872

6.    Lancaster, M. A., and Knoblich, J. A. (2014) Organogenesis in a dish: modeling development and disease using organoid technologies. Science 345, 1247125

7.    Lancaster, M. A., Renner, M., Martin, C. A., Wenzel, D., Bicknell, L. S., Hurles, M. E., Homfray, T., Penninger, J. M., Jackson, A. P., and Knoblich, J. A. (2013) Cerebral organoids model human brain development and microcephaly. Nature 501, 373-379

8.    Camp, J. G., Badsha, F., Florio, M., Kanton, S., Gerber, T., Wilsch-Brauninger, M., Lewitus, E., Sykes, A., Hevers, W., Lancaster, M., Knoblich, J. A., Lachmann, R., Paabo, S., Huttner, W. B., and Treutlein, B. (2015) Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. Proceedings of the National Academy of Sciences of the United States of America 112, 15672-15677

9.    Bershteyn, M., Nowakowski, T. J., Pollen, A. A., Di Lullo, E., Nene, A., Wynshaw-Boris, A., and Kriegstein, A. R. (2017) Human iPSC-Derived Cerebral Organoids Model Cellular Features of Lissencephaly and Reveal Prolonged Mitosis of Outer Radial Glia. Cell stem cell