3D imaging and quantitative analysis of intact tissues and organs

Embryonic development and tumor growth are highly complex and dynamic processes that exist in both time and space. To fully understand the molecular mechanisms that control these processes, it is crucial to study RNA expression and protein translation with single-cell spatiotemporal resolution. This is feasible by microscopic imaging that enables multidimensional assessments of cells, tissues, and organs. Here, a time-lapse calcium imaging and three-dimensional imaging was used to study physiological development of the brain or pathological development of cancer, respectively.

In Paper I, spatiotemporal calcium imaging revealed a new mechanism of neurogenesis during brain development. In Paper II, a new clearing method of clinically stored specimens, DIPCO (diagnosing immunolabeled paraffin-embedded cleared organs), was developed that allows better characterization and staging of intact human tumors. In Paper III, the DIPCO method was applied to determine tumor stage and characterize the microlymphatic system in bladder cancer. In Paper IV, a novel method for RNA labeling of volumetric specimens, DIIFCO (diagnosing in situ and immunofluorescence-labeled cleared onco-sample) was developed to study RNAs expression and localization in intact tumors.

Overall, the aim of the thesis was to demonstrate that multidimensional imaging extends the understanding of both physiological and pathological biological developmental processes.

List of scientific papers

I. Paola Rebellato*, Dagmara Kaczynska*, Shigeaki Kanatani, Ibrahim Al Rayyes, Songbai Zhang, Carlos Villaescusa, Anna Falk, Ernest Arenas, Ola Hermanson, Lauri Louhivuori, Per Uhlén. The T-type Ca2+ Channel Cav3.2 Regulates Differentiation of Neural Progenitor Cells during Cortical Development via Caspase-3. Neuroscience. 2019, 402, 78-89. *Contributed equally.
https://doi.org/10.1016/j.neuroscience.2019.01.015

II. Nobuyuki Tanaka*, Shigeaki Kanatani*, Raju Tomer, Cecilia Sahlgren, Pauliina Kronqvist, Dagmara Kaczynska, Lauri Louhivuori, Lorand Kis, Claes Lindh, Przemysław Mitura, Andrzej Stepulak, Sara Corvigno, Johan Hartman, Patrick Micke, Artur Mezheyeuski, Carina Strell, Joseph W. Carlson, Carlos Fernández Moro, Hanna Dahlstrand, Arne Östman, Kazuhiro Matsumoto, Peter Wiklund, Mototsugu Oya, Ayako Miyakawa, Karl Deisseroth and Per Uhlén. Whole-tissue biopsy phenotyping of three-dimensional tumours reveals patterns of cancer heterogeneity. Nature Biomedical Engineering. 2017, 1, 796-806. *Contributed equally.
https://doi.org/10.1038/s41551-017-0162-1

III. Tanaka Nobuyuki, Dagmara Kaczynska, Shigeaki Kanatani, Cecilia Sahlgren, Przemysław Mitura, Andrzej Stepulak, Ayako Miyakawa, Peter Wiklund, Per Uhlén. Mapping of the three-dimensional lymphatic microvasculature in bladder tumours using light-sheet microscopy. British Journal of Cancer. 2018, 118, 995-999.
https://doi.org/10.1038/s41416-018-0016-y

IV. Nobuyuki Tanaka*, Shigeaki Kanatani*, Dagmara Kaczynska*, Keishiro Fukumoto, Lauri Louhivuori, Tomohiro Mizutani, Oded Kopper, Pauliina Kronqvist, Stephanie Robertson, Claes Lindh, Lorand Kis, Robin Pronk, Naoya Niwa, Kazuhiro Matsumoto, Mototsugu Oya, Ayako Miyakawa, Anna Falk, Johan Hartman, Cecilia Sahlgren, Hans Clevers, and Per Uhlén. DIIFCO: A Single-Cell 3D Imaging Method to Analyze RNA and Protein Expressions in Intact Tumor Biopsies. *Contributed equally. [Accepted]
https://doi.org/10.1038/s41551-020-0576-z