RRC ID 76891
Author Kazuki Kitamura, Takayoshi Yamamoto, Haruki Ochi, Makoto Suzuki, Nanoka Suzuki, Takeshi Igawa, Tadashi Yoshida, Mitsuru Futakuchi, Hajime Ogino, Tatsuo Michiue
Title Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis
Journal Scientific Reports
Abstract 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.
Volume 13
Published 2023-8-14
DOI 10.1038/s41598-023-40193-7
PMID 37580380
PMC PMC10425369
MeSH Animals Biomarkers, Tumor / genetics Collagen / genetics Collagen / metabolism Computational Biology Gene Expression Profiling* Gene Expression Regulation, Neoplastic Gene Ontology Genes, Neoplasm* Humans Sequence Analysis, RNA Xenopus / genetics Xenopus / metabolism
IF 3.998
Clawed frogs / Newts Xenopus tropicalis