Organoids are an excellent tool to define epithelial effector responses. Specific features such as organoid size, morphology, and cellular composition are essential parameters. These parameters identify whether a particular treatment leads to induction of repair processes that are needed after the loss of tissue due to damage or infection. Macrophages reside in virtually all organs and play a key role in host defense and tissue homeostasis. Tissue macrophages are particularly important in the gut where they defend the body against a wide variety of pathogens and toxic substances. However, gut macrophages also contribute to pathology. Aberrant activation of macrophages plays an important role in disorders such as inflammatory bowel disease (Ulcerative colitis and Crohn's disease).
Main objectives for the master thesis project:
- Establishment of human gut organoids to study intestinal niche.
- Establishment of ex vivo model to study inflammation in organoids- macrophages co-culture system.
Study design and methods:
Here, we will use mixed methods research to combine quantitative and qualitative data analysis to investigate different research objectives. For example, RNA-seq analysis will be helpful to combine quantitative transcriptome analysis. In addition, confocal laser scanning microscopy will be employed for both qualitative observation and quantitative measurement of different parameters of human gut duodenal and colon organoids. In the last four years, I have gained the necessary expertise in these techniques to study mouse intestinal epithelium and thus, it will be a smooth transition to now do human gut epithelium tissue-based studies. "Overall, master students will learn organoids culture from human gut tissue, Immunofluorescence microscopy, Immunohistochemistry, flow cytometry, real-time qRT-PCR, Western blotting, RNA isolation method for RNA sequencing and other techniques." As well as student will learn how to proceed with bioinformatics analysis of the Immunofluorescence images and how to interpret the data.
Routine workflow in our laboratory and for this master thesis project:
We work at the Department of Pathology, Rikshospitalet Oslo. We study the human gut under both normal and cancer conditions. To do this, we get human gut tissue from the surgery department at Rikshospitalet. After that, we isolate different cell types from the duodenum and colonic tissue depending on the projects. For this project, I separate duodenal and colonic crypts from tissue as the project involves generating and maintaining human gut organoids. After establishing organoid cultures from different patient tissue, downstream analysis using RNA techniques, immunohistochemistry, Immunofluorescent staining of organoids, and other methods are performed.
Figure 2: Routine workflow for organoids generation from human gut tissue in our laboratory.
Supervisor for this project: Naveen Parmar Ph.D. email: naveen.parmar@medisin.uio.no
Current position: Postdoctoral Fellow, Rikshospitalet, Department of Pathology, University of Oslo
Co-supervisor: Diana Domanska , Researcher
Group Leader: Frode Lars Jahnsen
Please read here more about our research: