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Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model

BACKGROUND: Intra-tumor heterogeneity (ITH) encompasses cellular differences in tumors and is related to clinical outcomes such as drug resistance. However, little is known about the dynamics of ITH, owing to the lack of time-series analysis at the single-cell level. Mouse models that recapitulate c...

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Autores principales: Ono, Hanako, Arai, Yasuhito, Furukawa, Eisaku, Narushima, Daichi, Matsuura, Tetsuya, Nakamura, Hiromi, Shiokawa, Daisuke, Nagai, Momoko, Imai, Toshio, Mimori, Koshi, Okamoto, Koji, Hippo, Yoshitaka, Shibata, Tatsuhiro, Kato, Mamoru
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8456589/
https://www.ncbi.nlm.nih.gov/pubmed/34548081
http://dx.doi.org/10.1186/s12915-021-01147-5
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author Ono, Hanako
Arai, Yasuhito
Furukawa, Eisaku
Narushima, Daichi
Matsuura, Tetsuya
Nakamura, Hiromi
Shiokawa, Daisuke
Nagai, Momoko
Imai, Toshio
Mimori, Koshi
Okamoto, Koji
Hippo, Yoshitaka
Shibata, Tatsuhiro
Kato, Mamoru
author_facet Ono, Hanako
Arai, Yasuhito
Furukawa, Eisaku
Narushima, Daichi
Matsuura, Tetsuya
Nakamura, Hiromi
Shiokawa, Daisuke
Nagai, Momoko
Imai, Toshio
Mimori, Koshi
Okamoto, Koji
Hippo, Yoshitaka
Shibata, Tatsuhiro
Kato, Mamoru
author_sort Ono, Hanako
collection PubMed
description BACKGROUND: Intra-tumor heterogeneity (ITH) encompasses cellular differences in tumors and is related to clinical outcomes such as drug resistance. However, little is known about the dynamics of ITH, owing to the lack of time-series analysis at the single-cell level. Mouse models that recapitulate cancer development are useful for controlled serial time sampling. RESULTS: We performed single-cell exome and transcriptome sequencing of 200 cells to investigate how ITH is generated in a mouse colorectal cancer model. In the model, a single normal intestinal cell is grown into organoids that mimic the intestinal crypt structure. Upon RNAi-mediated downregulation of a tumor suppressor gene APC, the transduced organoids were serially transplanted into mice to allow exposure to in vivo microenvironments, which play relevant roles in cancer development. The ITH of the transcriptome increased after the transplantation, while that of the exome decreased. Mutations generated during organoid culture did not greatly change at the bulk-cell level upon the transplantation. The RNA ITH increase was due to the emergence of new transcriptional subpopulations. In contrast to the initial cells expressing mesenchymal-marker genes, new subpopulations repressed these genes after the transplantation. Analyses of colorectal cancer data from The Cancer Genome Atlas revealed a high proportion of metastatic cases in human subjects with expression patterns similar to the new cell subpopulations in mouse. These results suggest that the birth of transcriptional subpopulations may be a key for adaptation to drastic micro-environmental changes when cancer cells have sufficient genetic alterations at later tumor stages. CONCLUSIONS: This study revealed an evolutionary dynamics of single-cell RNA and DNA heterogeneity in tumor progression, giving insights into the mesenchymal-epithelial transformation of tumor cells at metastasis in colorectal cancer. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-021-01147-5.
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spelling pubmed-84565892021-09-22 Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model Ono, Hanako Arai, Yasuhito Furukawa, Eisaku Narushima, Daichi Matsuura, Tetsuya Nakamura, Hiromi Shiokawa, Daisuke Nagai, Momoko Imai, Toshio Mimori, Koshi Okamoto, Koji Hippo, Yoshitaka Shibata, Tatsuhiro Kato, Mamoru BMC Biol Research Article BACKGROUND: Intra-tumor heterogeneity (ITH) encompasses cellular differences in tumors and is related to clinical outcomes such as drug resistance. However, little is known about the dynamics of ITH, owing to the lack of time-series analysis at the single-cell level. Mouse models that recapitulate cancer development are useful for controlled serial time sampling. RESULTS: We performed single-cell exome and transcriptome sequencing of 200 cells to investigate how ITH is generated in a mouse colorectal cancer model. In the model, a single normal intestinal cell is grown into organoids that mimic the intestinal crypt structure. Upon RNAi-mediated downregulation of a tumor suppressor gene APC, the transduced organoids were serially transplanted into mice to allow exposure to in vivo microenvironments, which play relevant roles in cancer development. The ITH of the transcriptome increased after the transplantation, while that of the exome decreased. Mutations generated during organoid culture did not greatly change at the bulk-cell level upon the transplantation. The RNA ITH increase was due to the emergence of new transcriptional subpopulations. In contrast to the initial cells expressing mesenchymal-marker genes, new subpopulations repressed these genes after the transplantation. Analyses of colorectal cancer data from The Cancer Genome Atlas revealed a high proportion of metastatic cases in human subjects with expression patterns similar to the new cell subpopulations in mouse. These results suggest that the birth of transcriptional subpopulations may be a key for adaptation to drastic micro-environmental changes when cancer cells have sufficient genetic alterations at later tumor stages. CONCLUSIONS: This study revealed an evolutionary dynamics of single-cell RNA and DNA heterogeneity in tumor progression, giving insights into the mesenchymal-epithelial transformation of tumor cells at metastasis in colorectal cancer. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-021-01147-5. BioMed Central 2021-09-21 /pmc/articles/PMC8456589/ /pubmed/34548081 http://dx.doi.org/10.1186/s12915-021-01147-5 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Ono, Hanako
Arai, Yasuhito
Furukawa, Eisaku
Narushima, Daichi
Matsuura, Tetsuya
Nakamura, Hiromi
Shiokawa, Daisuke
Nagai, Momoko
Imai, Toshio
Mimori, Koshi
Okamoto, Koji
Hippo, Yoshitaka
Shibata, Tatsuhiro
Kato, Mamoru
Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model
title Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model
title_full Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model
title_fullStr Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model
title_full_unstemmed Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model
title_short Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model
title_sort single-cell dna and rna sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8456589/
https://www.ncbi.nlm.nih.gov/pubmed/34548081
http://dx.doi.org/10.1186/s12915-021-01147-5
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