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...

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Published in:Scientific reports 2023-08, Vol.13 (1), p.13214-13214, Article 13214
Main Authors: Kitamura, Kazuki, Yamamoto, Takayoshi, Ochi, Haruki, Suzuki, Makoto, Suzuki, Nanoka, Igawa, Takeshi, Yoshida, Tadashi, Futakuchi, Mitsuru, Ogino, Hajime, Michiue, Tatsuo
Format: Article
Language:English
Subjects:
631/136/334/1874
631/337/2019
631/67/1857
631/67/395
c-Met protein
Cancer
Cancer therapies
Collagen
Extracellular matrix
Gene expression
Humanities and Social Sciences
Keratan sulfate
multidisciplinary
Science
Science (multidisciplinary)
Tissues
Tumor suppressor genes
Tumorigenesis
Tumors
Xenopus tropicalis
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Summary: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.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-023-40193-7