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 Clevers

Per Uhlén

^*Korresponderande författare för detta arbete

Forskningsoutput: Tidskriftsbidrag › Artikel › Vetenskaplig › Peer review

32 Citeringar (Scopus)

Sammanfattning

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.

Originalspråk	Engelska
Sidor (från-till)	875-888
Antal sidor	14
Tidskrift	Nature Biomedical Engineering
Volym	4
Nummer	9
DOI	https://doi.org/10.1038/s41551-020-0576-z
Status	Publicerad - 2020
MoE-publikationstyp	A1 Tidskriftsartikel-refererad

Finansiering

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.

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10.1038/s41551-020-0576-z

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CellMech: Center of Excellence in Cellular Mechanostasis
Sahlgren, C. (Ansvarig forskare), Sistonen, L. (Ansvarig forskare), Eriksson, J. (Ansvarig forskare), Toivola, D. (Ansvarig forskare), Meinander, A. (Ansvarig forskare), Cheng, F. (Ansvarig forskare) & Jacquemet, G. (Ansvarig forskare)
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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., ... 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

@article{e1d37d553bb44817ac90492ae133d8d6,

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

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.",

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",

note = "Funding Information: We thank A. {\"O}stman 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 Hagel{\'e}n 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. Publisher Copyright: {\textcopyright} 2020, The Author(s), under exclusive licence to Springer Nature Limited. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",

year = "2020",

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

language = "English",

volume = "4",

pages = "875--888",

journal = "Nature Biomedical Engineering",

issn = "2157-846X",

publisher = "Nature Research",

number = "9",

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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, nr. 9, s. 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

N1 - Funding Information: 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. Publisher Copyright: © 2020, The Author(s), under exclusive licence to Springer Nature Limited. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2020

Y1 - 2020

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.

UR - https://www.scopus.com/pages/publications/85087027537

U2 - 10.1038/s41551-020-0576-z

DO - 10.1038/s41551-020-0576-z

M3 - Article

C2 - 32601394

AN - SCOPUS:85087027537

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

Sammanfattning

Finansiering

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Projekt

CellMech: Center of Excellence in Cellular Mechanostasis

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