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

Tanaka, Nobuyuki ; Kanatani, Shigeaki ; Kaczynska, Dagmara ; Fukumoto, Keishiro ; Louhivuori, Lauri ; Mizutani, Tomohiro ; Kopper, Oded ; Kronqvist, Pauliina ; Robertson, Stephanie and Lindh, Claes , et al. (2020) In Nature Biomedical Engineering 4(9). p.875-888
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... (More)

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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publishing date
type
Contribution to journal
publication status
published
subject
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
in
Nature Biomedical Engineering
volume
4
issue
9
pages
14 pages
publisher
Nature Publishing Group
external identifiers
  • pmid:32601394
  • scopus:85087027537
ISSN
2157-846X
DOI
10.1038/s41551-020-0576-z
language
English
LU publication?
no
id
b8eb89e3-e25c-4b3b-8cd2-6511495f996c
date added to LUP
2021-08-09 14:13:10
date last changed
2024-05-18 12:19:47
@article{b8eb89e3-e25c-4b3b-8cd2-6511495f996c,
  abstract     = {{<p>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.</p>}},
  author       = {{Tanaka, Nobuyuki and Kanatani, Shigeaki and Kaczynska, Dagmara and Fukumoto, Keishiro and Louhivuori, Lauri and Mizutani, Tomohiro and Kopper, Oded and Kronqvist, Pauliina and Robertson, Stephanie and Lindh, Claes and Kis, Lorand and Pronk, Robin and Niwa, Naoya and Matsumoto, Kazuhiro and Oya, Mototsugu and Miyakawa, Ayako and Falk, Anna and Hartman, Johan and Sahlgren, Cecilia and Clevers, Hans and Uhlén, Per}},
  issn         = {{2157-846X}},
  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}},
  language     = {{eng}},
  number       = {{9}},
  pages        = {{875--888}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Nature Biomedical Engineering}},
  title        = {{Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies}},
  url          = {{http://dx.doi.org/10.1038/s41551-020-0576-z}},
  doi          = {{10.1038/s41551-020-0576-z}},
  volume       = {{4}},
  year         = {{2020}},
}