Kirkeby Group: Human Neural Development – University of Copenhagen

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Kirkeby Group: Human Neural Development

"We apply advanced stem cell models to study the detailed processes that control human brain development. In particular, we aim to understand traits of brain development which are unique to humans compared to brain development in commonly used animal models.

The human brain is a highly complex structure, consisting of hundreds of different subtypes of neural cells; each of which fulfil a specific function in the brain network. However, experimental evidence regarding the development of the human brain is highly restricted due to the limited availability of fetal brain tissue – instead, smaller model organisms have classically been applied for neurodevelopmental studies. In the Kirkeby lab, we aim to apply advanced human stem cells models to understand how the hundreds of human neural subtypes of cells are formed during embryo development. This knowledge will enable us with new tools to produce and study human nerve cells in the lab, and to use these for disease modelling, drug screening and transplantation therapies towards brain diseases.

The Kirkeby group studies the factors involved in human neural subtype specification in order to enable production of specific neurons for understanding and treating neurological diseases, (click on the image to enlarge).

Ongoing Projects

Creating a human fetal brain in the dish with microfluidics (the MISTR model)
This project is an interdisciplinary collaboration joining forces from the fields of bioengineering and stem cell biology with the aim of producing a novel model of early human neural tube patterning. Through microfluidic engineering techniques, we expose hESCs to morphogenic gradients in vitro, thereby building a microenvironment in which the stem cells are patterned into structures resembling the early stages of the rostral-to-caudal regionalised human neural tube. With this technique, the aim is to produce an anatomically relevant 3D in vitro model of the developing human brain corresponding to around weeks 2-10 of fetal development.

Mapping human neural subtype identities through single cell RNAseq
In this project, we apply unbiased single cell RNAseq techniques to map the complexity of human neural subtypes present during early and late neural specification. For this, we use our 3D stem cell models of human brain development, as well as validation in human fetal tissue. By mapping cells at a single cell level, we aim to identify the unique molecular signatures of different human neural subtypes and to dissect the multitude and variety of different subtypes present at different time points during development.

Identifying secreted factors from different human brain regions through proteomics
For this project, we will use our MISTR model to search for human-specific patterns of developmental growth factors through unbiased mass-spec (MS) proteomic analysis of the secreted proteins produced from different neural regions during development. Novel candidates identified from this approach will be explored for their biological function in directing neural cells towards specific neuronal subtypes and for inducing neuronal subtype maturation. 

Studying the functions of long non-coding RNAs in human neural cells
Long non-coding RNAs (lncRNAs) are highly abundant in the human genome, and for the vast majority of these their functions are unknown. Here, we apply CRISPR gene editing techniques in human pluripotent cells (CRISPR knockout, CRISPR activation and CRISPR inhibition) to investigate the functions of novel lncRNAs during human neural specification and differentiation. We aim to uncover both general functions in neural differentiation as well as more specific functions in regional subtype specification.

Selected publications

Nolbrant, S., Heuer, A., Parmar, M., and Kirkeby, A. (2017). Generation of high-purity human ventral midbrain dopaminergic progenitors for in vitro maturation and intracerebral transplantation. Nature Protocols 12, 1962-1979, doi:10.1038/nprot.2017.078.

Kirkeby, A., Nolbrant, S., Tiklova, K., Heuer, A., Kee, N., Cardoso, T., Ottosson, D.R., Lelos, M.J., Rifes, P., Dunnett, S.B., Grealish, S., Perlmann, T., and Parmar, M. (2017). Predictive Markers Guide Differentiation to Improve Graft Outcome in Clinical Translation of hESC-Based Therapy for Parkinson's Disease. Cell Stem Cell 20, 135-148, doi:10.1016/j.stem.2016.09.004.

Kee, N., Volakakis, N., Kirkeby, A., Dahl, L., Storvall, H., Nolbrant, S., Lahti, L., Björklund, Å.K., Gillberg, L., Joodmardi, E., Sandberg, R., Parmar, M., and Perlmann, T. (2017). Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages. Cell Stem Cell 20, 29-40, doi:10.1016/j.stem.2016.10.003.

Kirkeby, A., Parmar, M., and Barker, R.A. (2017). Strategies for bringing stem cell-derived dopamine neurons to the clinic: A European approach (STEM-PD). Progress in Brain Research, book series: Functional Neural Transplantation – IV, Elsevier, doi: 10.1016/bs.pbr.2016.11.011.

Grealish, S., Diguet, E., Kirkeby, A., Mattsson, B., Heuer, A., Bramoulle, Y., Van Camp, N., Perrier, A.L., Hantraye, P., Björklund, A., and Parmar, M. (2014). Human ESC-Derived Dopamine Neurons Show Similar Preclinical Efficacy and Potency to Fetal Neurons when grafted in a Rat Model of Parkinson’s Disease. Cell Stem Cell 15, 653-665, doi:10.1016/j.stem.2014.09.017.

Kirkeby, A., Grealish, S., Wolf, D.A., Nelander, J., Wood, J., Lundblad, M., Lindvall, O., and Parmar, M. (2012). Generation of Regionally Specified Neural Progenitors and Functional Neurons from Human Embryonic Stem Cells under Defined Conditions. Cell Reports 1, 703-714, doi:10.1016/j.celrep.2012.04.009

Pfisterer, U.*, Kirkeby*, A., Torper*, O., Wood, J., Nelander, J., Dufour, A., Björklund, A., Lindvall, O.,  Jakobsson, J., and Parmar, M. (2011). Direct conversion of human fibroblasts to dopaminergic neurons. Proceedings of the National Academy of Sciences 108, 10343-10348, doi:10.1073/pnas.1105135108. *contributed equally