15 September

Thesis defense Kim Boonekamp: Utilizing organoids to study general and tissue-specific adult stem cell profiles

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Kim Boonekamp, from the group of Hans Clevers, successfully defended her thesis “Utilizing organoids to study general and tissue-specific adult stem cell profiles: Exploiting organoid cultures for basic stem cell research” on the 15th of September. During her PhD, Boonekamp developed a new organoid model for mouse skin that is valuable for research into fundamental questions and can be used as a stem cell capacity test. Additionally, she explored the application of organoid models for studying the Wnt signaling pathway. Mutations in this pathway are associated with cancer.

Stem cells play a pivotal role in not only the development of the body, but also in keeping the internal state of the body stable, a mechanism called homeostasis. This is because stem cells have the ability to generate new cells to replace old ones. To renew tissue, they form functional daughter cells while also sustaining themselves. Various molecular signaling pathways regulate this process tightly to control tissue generation; dysregulation due to for example genetic mutations can lead to excessive tissue growth and can thereby result in cancer.

Organoid technology

Tissue regeneration takes place almost everywhere in the body. A concrete example can be found in the epidermis, the upper layer of the skin, which constantly sheds old skin cells that various stem cell populations replace with new ones. Previously, researchers mainly used mouse models in which stem cells are labeled in a fluorescent color to study these stem cell populations. This way, they were able to track the newly formed daughter cells.

More recently, organoid technology was developed, which enables the growth of stem cells in the lab. Organoid technology allows the isolation of stem cells from mature tissues, which can consequently be kept alive in a Petri dish. With the help of an extracellular matrix and various growth factors, these mini-organs of about 1 mm in size – ‘organoids’ – can be grown into 3D structures. Various types of organoids can be cultivated, including intestinal, gut and liver organoids. Additionally, organoids can be grown from both healthy and sick tissue.


Boonekamp focused on developing an organoid model for mouse skin. She deployed this model in combination with CRISPR/Cas9 technology to verify the effect of mutations in the Desmoplakin gene on epidermal homeostasis in living tissue. The Desmoplakin gene is generally involved in the formation and maintenance of the cornified epidermis – the outermost layer of the epidermis. In another project, Boonekamp and colleagues identified a protein called ‘Troy’ as a marker for stem cells that solely contribute to the squamous epithelium – a specific layer of tissue that can be found in the epidermis. In this project, she used the developed organoid system to address the stem cell capacity of the cells containing Troy. These stem cells are long-term contributors to the regeneration of the epidermis. With this discovery, Boonekamp and her team made epidermis-specific genetic alterations in mouse skin, which was not possible until now.

Wnt signaling pathway

Organoid models such as the one Boonekamp developed enable fundamental research into the signaling pathways of stem cells. These pathways regulate the maintenance of stem cells and play an important role in the facilitation of homeostasis and the prevention of stem cell depletion or excessive tissue growth. Mutations in one of the best-known signaling pathways – the Wnt pathway – are highly associated with various cancer types, including colorectal cancer. Boonekamp used various organoid models to identify genes that come to expression under influence of the Wnt signaling pathway. Additionally, she elaborated on the possibilities of using organoids to investigate rare cell types.

With her thesis, she emphasizes the broad spectrum of opportunities provided by organoid technology and illustrates how this cutting-edge technology can contribute to stem cell research.




Boonekamp worked as a PhD-candidate in the lab of Hans Clevers. Since completing her thesis, she has started a Postdoc position in the lab of Michael Boutros at the German Cancer Research Center (DKFZ) in Heidelberg, Germany.