Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies

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; Per Uhlén

doi:10.1038/s41551-020-0576-z

Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies

Nobuyuki Tanaka (Corresponding author)
, 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

Per Uhlén (Corresponding author)

Research output: Contribution to journal › Article › Academic › peer-review

31 Citations (Scopus)

Abstract

Microscopy analysis of tumour samples is commonly performed on fixed, thinly sectioned and protein-labelled tissues. However, these examinations do not reveal the intricate three-dimensional structures of tumours, nor enable the detection of aberrant transcripts. Here, we report a method, which we name DIIFCO (for diagnosing in situ immunofluorescence-labelled cleared oncosamples), for the multimodal volumetric imaging of RNAs and proteins in intact tumour volumes and organoids. We used DIIFCO to spatially profile the expression of diverse coding RNAs and non-coding RNAs at the single-cell resolution in a variety of cancer tissues. Quantitative single-cell analysis revealed spatial niches of cancer stem-like cells, and showed that the niches were present at a higher density in triple-negative breast cancer tissue. The improved molecular phenotyping and histopathological diagnosis of cancers may lead to new insights into the biology of tumours of patients.

Original language	English
Pages (from-to)	875-888
Number of pages	14
Journal	Nature Biomedical Engineering
Volume	4
Issue number	9
Early online date	29 Jun 2020
DOIs	https://doi.org/10.1038/s41551-020-0576-z
Publication status	Published - 1 Sept 2020

Funding

We thank A. Östman for discussions. This study was supported by the Swedish Research Council (grant nos. 2009-3364, 2013-3189 and 2017-00815, to P.U.), the Swedish Cancer Society (grant nos. CAN 2016-801, 19 0544 Pj and 19 0545 Us, to P.U.), the Swedish Childhood Cancer Foundation (grant no. PR2018-0123, to P.U.), the Swedish Brain Foundation (grant nos. FO2018-0209, to P.U., and FO2018-0281, to A.F.), the Olle Engkvist foundation (to P.U.), the David and Astrid Hagelén Foundation (to N.T.), the Karolinska Institutet Research Foundation (to N.T., S.K. and P.U.), the Takeda Science Foundation (to N.T.), Grant-in-Aid for Scientific Research (KAKENHI 18H04906, 18K19482 and 19H03792, to N.T.), the Kobayashi Foundation for Cancer Research (to N.T.), the Keio Gijuku Academic Development Funds (to N.T.), the Scandinavia-Japan Sasakawa Foundation (to N.T., K.F. and S.K.), and the Wenner-Gren Foundation (to S.K.). The light-sheet microscopy infrastructure used in this research received grants from the Strategic Research Area in Neuroscience (StratNeuro) and the Strategic Research Area in Stem Cells and Regenerative Medicine (StratRegen), supported by the Swedish government.

Funders	Funder number
Karolinska Institutet
Vetenskapsrådet	2017-00815, 2009-3364, 2013-3189

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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10.1038/s41551-020-0576-z

Cite this

Tanaka, N., Kanatani, S., Kaczynska, D., Fukumoto, K., Louhivuori, L., Mizutani, T., Kopper, O., Kronqvist, P., Robertson, S., Lindh, C., Kis, L., Pronk, R., Niwa, N., Matsumoto, K., Oya, M., Miyakawa, A., Falk, A., Hartman, J., Sahlgren, C., ... Uhlén, P. (2020). Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies. Nature Biomedical Engineering, 4(9), 875-888. https://doi.org/10.1038/s41551-020-0576-z

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Tanaka, N, Kanatani, S, Kaczynska, D, Fukumoto, K, Louhivuori, L, Mizutani, T, Kopper, O, Kronqvist, P, Robertson, S, Lindh, C, Kis, L, Pronk, R, Niwa, N, Matsumoto, K, Oya, M, Miyakawa, A, Falk, A, Hartman, J, Sahlgren, C, Clevers, H & Uhlén, P 2020, 'Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies', Nature Biomedical Engineering, vol. 4, no. 9, pp. 875-888. https://doi.org/10.1038/s41551-020-0576-z

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AU - Kronqvist, Pauliina

AU - Robertson, Stephanie

AU - Lindh, Claes

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AU - Pronk, Robin

AU - Niwa, Naoya

AU - Matsumoto, Kazuhiro

AU - Oya, Mototsugu

AU - Miyakawa, Ayako

AU - Falk, Anna

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AU - Sahlgren, Cecilia

AU - Clevers, Hans

AU - Uhlén, Per

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Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies

Abstract

Funding

UN SDGs

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-Karolinska Institutet: New 3D imaging method for tumour samples to be used for studying COVID-19

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Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies

Abstract

Funding

UN SDGs

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-Karolinska Institutet: New 3D imaging method for tumour samples to be used for studying COVID-19

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