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Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis

Cancer treatment is still challenging because the disease is often caused by multiple mutations. Although genomic studies have identified many oncogenes and tumor suppressor genes, gene sets involved in tumorigenesis remain poorly understood. Xenopus, a genus of aquatic frogs, is a useful model to i...

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Autores principales: Kitamura, Kazuki, Yamamoto, Takayoshi, Ochi, Haruki, Suzuki, Makoto, Suzuki, Nanoka, Igawa, Takeshi, Yoshida, Tadashi, Futakuchi, Mitsuru, Ogino, Hajime, Michiue, Tatsuo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10425369/
https://www.ncbi.nlm.nih.gov/pubmed/37580380
http://dx.doi.org/10.1038/s41598-023-40193-7
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author Kitamura, Kazuki
Yamamoto, Takayoshi
Ochi, Haruki
Suzuki, Makoto
Suzuki, Nanoka
Igawa, Takeshi
Yoshida, Tadashi
Futakuchi, Mitsuru
Ogino, Hajime
Michiue, Tatsuo
author_facet Kitamura, Kazuki
Yamamoto, Takayoshi
Ochi, Haruki
Suzuki, Makoto
Suzuki, Nanoka
Igawa, Takeshi
Yoshida, Tadashi
Futakuchi, Mitsuru
Ogino, Hajime
Michiue, Tatsuo
author_sort Kitamura, Kazuki
collection PubMed
description Cancer treatment is still challenging because the disease is often caused by multiple mutations. Although genomic studies have identified many oncogenes and tumor suppressor genes, gene sets involved in tumorigenesis remain poorly understood. Xenopus, a genus of aquatic frogs, is a useful model to identify gene sets because it can be genetically and experimentally analyzed. Here, we analyzed gene expression in tumor tissues of three individuals in Xenopus tropicalis and identified 55 differentially expressed genes (DEGs). Gene ontology (GO) analysis showed that the upregulated genes in the tumor tissues were enriched in GO terms related to the extracellular matrix and collagen fibril organization. Hierarchical clustering showed that the gene expression patterns of tumor tissues in X. tropicalis were comparable to those of human connective, soft, and subcutaneous tissue-derived cancers. Additionally, pathway analysis revealed that these DEGs were associated with multiple pathways, including the extracellular matrix, collagen fibril organization, MET signaling, and keratan sulfate. We also found that the expression tendency of some DEGs that have not been well analyzed in the cancer field clearly determines the prognosis of human cancer patients. This study provides a remarkable reference for future experimental work on X. tropicalis to identify gene sets involved in human cancer.
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spelling pubmed-104253692023-08-16 Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis Kitamura, Kazuki Yamamoto, Takayoshi Ochi, Haruki Suzuki, Makoto Suzuki, Nanoka Igawa, Takeshi Yoshida, Tadashi Futakuchi, Mitsuru Ogino, Hajime Michiue, Tatsuo Sci Rep Article Cancer treatment is still challenging because the disease is often caused by multiple mutations. Although genomic studies have identified many oncogenes and tumor suppressor genes, gene sets involved in tumorigenesis remain poorly understood. Xenopus, a genus of aquatic frogs, is a useful model to identify gene sets because it can be genetically and experimentally analyzed. Here, we analyzed gene expression in tumor tissues of three individuals in Xenopus tropicalis and identified 55 differentially expressed genes (DEGs). Gene ontology (GO) analysis showed that the upregulated genes in the tumor tissues were enriched in GO terms related to the extracellular matrix and collagen fibril organization. Hierarchical clustering showed that the gene expression patterns of tumor tissues in X. tropicalis were comparable to those of human connective, soft, and subcutaneous tissue-derived cancers. Additionally, pathway analysis revealed that these DEGs were associated with multiple pathways, including the extracellular matrix, collagen fibril organization, MET signaling, and keratan sulfate. We also found that the expression tendency of some DEGs that have not been well analyzed in the cancer field clearly determines the prognosis of human cancer patients. This study provides a remarkable reference for future experimental work on X. tropicalis to identify gene sets involved in human cancer. Nature Publishing Group UK 2023-08-14 /pmc/articles/PMC10425369/ /pubmed/37580380 http://dx.doi.org/10.1038/s41598-023-40193-7 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
Kitamura, Kazuki
Yamamoto, Takayoshi
Ochi, Haruki
Suzuki, Makoto
Suzuki, Nanoka
Igawa, Takeshi
Yoshida, Tadashi
Futakuchi, Mitsuru
Ogino, Hajime
Michiue, Tatsuo
Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis
title Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis
title_full Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis
title_fullStr Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis
title_full_unstemmed Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis
title_short Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis
title_sort identification of tumor-related genes via rna sequencing of tumor tissues in xenopus tropicalis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10425369/
https://www.ncbi.nlm.nih.gov/pubmed/37580380
http://dx.doi.org/10.1038/s41598-023-40193-7
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