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Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis
Colorectal cancer (CRC) is the most common gastrointestinal malignancy and a leading cause of cancer deaths in the United States. More than half of CRC patients develop metastatic disease (mCRC) with an average 5-year survival rate of 13%. Circular RNAs (circRNAs) have recently emerged as important...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10198730/ https://www.ncbi.nlm.nih.gov/pubmed/37213253 http://dx.doi.org/10.1093/narcan/zcad021 |
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author | Zhao, Sidi Ly, Amy Mudd, Jacqueline L Rozycki, Emily B Webster, Jace Coonrod, Emily Othoum, Ghofran Luo, Jingqin Dang, Ha X Fields, Ryan C Maher, Christopher A |
author_facet | Zhao, Sidi Ly, Amy Mudd, Jacqueline L Rozycki, Emily B Webster, Jace Coonrod, Emily Othoum, Ghofran Luo, Jingqin Dang, Ha X Fields, Ryan C Maher, Christopher A |
author_sort | Zhao, Sidi |
collection | PubMed |
description | Colorectal cancer (CRC) is the most common gastrointestinal malignancy and a leading cause of cancer deaths in the United States. More than half of CRC patients develop metastatic disease (mCRC) with an average 5-year survival rate of 13%. Circular RNAs (circRNAs) have recently emerged as important tumorigenesis regulators; however, their role in mCRC progression remains poorly characterized. Further, little is known about their cell-type specificity to elucidate their functions in the tumor microenvironment (TME). To address this, we performed total RNA sequencing (RNA-seq) on 30 matched normal, primary and metastatic samples from 14 mCRC patients. Additionally, five CRC cell lines were sequenced to construct a circRNA catalog in CRC. We detected 47 869 circRNAs, with 51% previously unannotated in CRC and 14% novel candidates when compared to existing circRNA databases. We identified 362 circRNAs differentially expressed in primary and/or metastatic tissues, termed circular RNAs associated with metastasis (CRAMS). We performed cell-type deconvolution using published single-cell RNA-seq datasets and applied a non-negative least squares statistical model to estimate cell-type specific circRNA expression. This predicted 667 circRNAs as exclusively expressed in a single cell type. Collectively, this serves as a valuable resource, TMECircDB (accessible at https://www.maherlab.com/tmecircdb-overview), for functional characterization of circRNAs in mCRC, specifically in the TME. |
format | Online Article Text |
id | pubmed-10198730 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-101987302023-05-20 Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis Zhao, Sidi Ly, Amy Mudd, Jacqueline L Rozycki, Emily B Webster, Jace Coonrod, Emily Othoum, Ghofran Luo, Jingqin Dang, Ha X Fields, Ryan C Maher, Christopher A NAR Cancer Cancer-specific RNAs and RNA Processing Colorectal cancer (CRC) is the most common gastrointestinal malignancy and a leading cause of cancer deaths in the United States. More than half of CRC patients develop metastatic disease (mCRC) with an average 5-year survival rate of 13%. Circular RNAs (circRNAs) have recently emerged as important tumorigenesis regulators; however, their role in mCRC progression remains poorly characterized. Further, little is known about their cell-type specificity to elucidate their functions in the tumor microenvironment (TME). To address this, we performed total RNA sequencing (RNA-seq) on 30 matched normal, primary and metastatic samples from 14 mCRC patients. Additionally, five CRC cell lines were sequenced to construct a circRNA catalog in CRC. We detected 47 869 circRNAs, with 51% previously unannotated in CRC and 14% novel candidates when compared to existing circRNA databases. We identified 362 circRNAs differentially expressed in primary and/or metastatic tissues, termed circular RNAs associated with metastasis (CRAMS). We performed cell-type deconvolution using published single-cell RNA-seq datasets and applied a non-negative least squares statistical model to estimate cell-type specific circRNA expression. This predicted 667 circRNAs as exclusively expressed in a single cell type. Collectively, this serves as a valuable resource, TMECircDB (accessible at https://www.maherlab.com/tmecircdb-overview), for functional characterization of circRNAs in mCRC, specifically in the TME. Oxford University Press 2023-05-19 /pmc/articles/PMC10198730/ /pubmed/37213253 http://dx.doi.org/10.1093/narcan/zcad021 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of NAR Cancer. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Cancer-specific RNAs and RNA Processing Zhao, Sidi Ly, Amy Mudd, Jacqueline L Rozycki, Emily B Webster, Jace Coonrod, Emily Othoum, Ghofran Luo, Jingqin Dang, Ha X Fields, Ryan C Maher, Christopher A Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis |
title | Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis |
title_full | Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis |
title_fullStr | Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis |
title_full_unstemmed | Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis |
title_short | Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis |
title_sort | characterization of cell-type specific circular rnas associated with colorectal cancer metastasis |
topic | Cancer-specific RNAs and RNA Processing |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10198730/ https://www.ncbi.nlm.nih.gov/pubmed/37213253 http://dx.doi.org/10.1093/narcan/zcad021 |
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