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, 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 CleversPer Uhlén

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

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
DOIs	https://doi.org/10.1038/s41551-020-0576-z
Publication status	Published - 2020 Sept
Externally published	Yes

Subject classification (UKÄ)

Cancer and Oncology
Radiology, Nuclear Medicine and Medical Imaging

Free keywords

Animals
Biomarkers, Tumor/genetics
Biopsy
Embryo, Mammalian/metabolism
Humans
Imaging, Three-Dimensional
Immunohistochemistry
In Situ Hybridization, Fluorescence
Mice
Multimodal Imaging
Neoplasms/metabolism
Phenotype
RNA/metabolism
Single-Cell Analysis

UN SDGs

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

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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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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.",

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author = "Nobuyuki Tanaka and Shigeaki Kanatani and Dagmara Kaczynska and Keishiro Fukumoto and Lauri Louhivuori and Tomohiro Mizutani and Oded Kopper and Pauliina Kronqvist and Stephanie Robertson and Claes Lindh and Lorand Kis and Robin Pronk and Naoya Niwa and Kazuhiro Matsumoto and Mototsugu Oya and Ayako Miyakawa and Anna Falk and Johan Hartman and Cecilia Sahlgren and Hans Clevers and Per Uhl{\'e}n",

year = "2020",

month = sep,

doi = "10.1038/s41551-020-0576-z",

language = "English",

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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

TY - JOUR

T1 - Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies

AU - Tanaka, Nobuyuki

AU - Kanatani, Shigeaki

AU - Kaczynska, Dagmara

AU - Fukumoto, Keishiro

AU - Louhivuori, Lauri

AU - Mizutani, Tomohiro

AU - Kopper, Oded

AU - Kronqvist, Pauliina

AU - Robertson, Stephanie

AU - Lindh, Claes

AU - Kis, Lorand

AU - Pronk, Robin

AU - Niwa, Naoya

AU - Matsumoto, Kazuhiro

AU - Oya, Mototsugu

AU - Miyakawa, Ayako

AU - Falk, Anna

AU - Hartman, Johan

AU - Sahlgren, Cecilia

AU - Clevers, Hans

AU - Uhlén, Per

PY - 2020/9

Y1 - 2020/9

N2 - 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.

AB - 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.

KW - Animals

KW - Biomarkers, Tumor/genetics

KW - Biopsy

KW - Embryo, Mammalian/metabolism

KW - Humans

KW - Imaging, Three-Dimensional

KW - Immunohistochemistry

KW - In Situ Hybridization, Fluorescence

KW - Mice

KW - Multimodal Imaging

KW - Neoplasms/metabolism

KW - Phenotype

KW - RNA/metabolism

KW - Single-Cell Analysis

U2 - 10.1038/s41551-020-0576-z

DO - 10.1038/s41551-020-0576-z

M3 - Article

C2 - 32601394

SN - 2157-846X

VL - 4

SP - 875

EP - 888

JO - Nature Biomedical Engineering

JF - Nature Biomedical Engineering

IS - 9

ER -

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

Abstract

Subject classification (UKÄ)

Free keywords

UN SDGs

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Cite this