Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies
(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.
(Less)
- author
- publishing date
- 2020-09
- 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
-
- scopus:85087027537
- pmid:32601394
- 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
- 2024-09-07 21:58:34
@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}}, }