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Analysis of cell-specific transcriptional responses in human colon tissue using CIBERSORTx

Diet is an important determinant of overall health, and has been linked to the risk of various cancers. To understand the mechanisms involved, transcriptomic responses from human intervention studies are very informative. However, gene expression analysis of human biopsy material only represents the...

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Autores principales: He, Yueqin, De Benedictis, Julia Nicole, Caiment, Florian, van Breda, Simone G. J., de Kok, Theo M. C. M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10600214/
https://www.ncbi.nlm.nih.gov/pubmed/37880448
http://dx.doi.org/10.1038/s41598-023-45582-6
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author He, Yueqin
De Benedictis, Julia Nicole
Caiment, Florian
van Breda, Simone G. J.
de Kok, Theo M. C. M.
author_facet He, Yueqin
De Benedictis, Julia Nicole
Caiment, Florian
van Breda, Simone G. J.
de Kok, Theo M. C. M.
author_sort He, Yueqin
collection PubMed
description Diet is an important determinant of overall health, and has been linked to the risk of various cancers. To understand the mechanisms involved, transcriptomic responses from human intervention studies are very informative. However, gene expression analysis of human biopsy material only represents the average profile of a mixture of cell types that can mask more subtle, but relevant cell-specific changes. Here, we use the CIBERSORTx algorithm to generate single-cell gene expression from human multicellular colon tissue. We applied the CIBERSORTx to microarray data from the PHYTOME study, which investigated the effects of different types of meat on transcriptional and biomarker changes relevant to colorectal cancer (CRC) risk. First, we used single-cell mRNA sequencing data from healthy colon tissue to generate a novel signature matrix in CIBERSORTx, then we determined the proportions and gene expression of each separate cell type. After comparison, cell proportion analysis showed a continuous upward trend in the abundance of goblet cells and stem cells, and a continuous downward trend in transit amplifying cells after the addition of phytochemicals in red meat products. The dietary intervention influenced the expression of genes involved in the growth and division of stem cells, the metabolism and detoxification of enterocytes, the translation and glycosylation of goblet cells, and the inflammatory response of innate lymphoid cells. These results show that our approach offers novel insights into the heterogeneous gene expression responses of different cell types in colon tissue during a dietary intervention.
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spelling pubmed-106002142023-10-27 Analysis of cell-specific transcriptional responses in human colon tissue using CIBERSORTx He, Yueqin De Benedictis, Julia Nicole Caiment, Florian van Breda, Simone G. J. de Kok, Theo M. C. M. Sci Rep Article Diet is an important determinant of overall health, and has been linked to the risk of various cancers. To understand the mechanisms involved, transcriptomic responses from human intervention studies are very informative. However, gene expression analysis of human biopsy material only represents the average profile of a mixture of cell types that can mask more subtle, but relevant cell-specific changes. Here, we use the CIBERSORTx algorithm to generate single-cell gene expression from human multicellular colon tissue. We applied the CIBERSORTx to microarray data from the PHYTOME study, which investigated the effects of different types of meat on transcriptional and biomarker changes relevant to colorectal cancer (CRC) risk. First, we used single-cell mRNA sequencing data from healthy colon tissue to generate a novel signature matrix in CIBERSORTx, then we determined the proportions and gene expression of each separate cell type. After comparison, cell proportion analysis showed a continuous upward trend in the abundance of goblet cells and stem cells, and a continuous downward trend in transit amplifying cells after the addition of phytochemicals in red meat products. The dietary intervention influenced the expression of genes involved in the growth and division of stem cells, the metabolism and detoxification of enterocytes, the translation and glycosylation of goblet cells, and the inflammatory response of innate lymphoid cells. These results show that our approach offers novel insights into the heterogeneous gene expression responses of different cell types in colon tissue during a dietary intervention. Nature Publishing Group UK 2023-10-25 /pmc/articles/PMC10600214/ /pubmed/37880448 http://dx.doi.org/10.1038/s41598-023-45582-6 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This 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/) .
spellingShingle Article
He, Yueqin
De Benedictis, Julia Nicole
Caiment, Florian
van Breda, Simone G. J.
de Kok, Theo M. C. M.
Analysis of cell-specific transcriptional responses in human colon tissue using CIBERSORTx
title Analysis of cell-specific transcriptional responses in human colon tissue using CIBERSORTx
title_full Analysis of cell-specific transcriptional responses in human colon tissue using CIBERSORTx
title_fullStr Analysis of cell-specific transcriptional responses in human colon tissue using CIBERSORTx
title_full_unstemmed Analysis of cell-specific transcriptional responses in human colon tissue using CIBERSORTx
title_short Analysis of cell-specific transcriptional responses in human colon tissue using CIBERSORTx
title_sort analysis of cell-specific transcriptional responses in human colon tissue using cibersortx
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10600214/
https://www.ncbi.nlm.nih.gov/pubmed/37880448
http://dx.doi.org/10.1038/s41598-023-45582-6
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