Differential genetic mutations of ectoderm, mesoderm, and endoderm-derived tumors in TCGA database
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PRIMARY RESEARCH
Cancer Cell International Open Access
Differential genetic mutations of ectoderm, mesoderm, and endoderm‑derived tumors in TCGA database Xingjie Gao1,2*, Xiaoteng Cui1,2,3, Xinxin Zhang1,2, Chunyan Zhao1,2, Nan Zhang1,2, Yan Zhao1,2, Yuanyuan Ren1,2, Chao Su1,2, Lin Ge1,2, Shaoyuan Wu1,2 and Jie Yang1,2*
Abstract Background: In terms of biological behavior, gene regulation, or signaling pathways, there is a certain similarity between tumorigenesis and embryonic development of humans. Three germ layer structure exhibits the distinct ability to form specific tissues and organs. Methods: The present study set out to investigate the genetic mutation characteristics of germ layer differentiationrelated genes using the tumor cases of the cancer genome atlas (TCGA) database. Results: These tumor samples were divided into three groups, including the ectoderm, mesoderm, and endoderm. Children cases less than 9 years old accounted for a larger proportion for the cases in the ectoderm and mesoderm groups; whereas the middle-aged and elderly individuals (from 50 to 89 years old) were more susceptible to tumors of endoderm. There was a better prognosis for the cases of mesoderm, especially the male with the race of White, compared with the other groups. A missense mutation was frequently detected for the cases of ectoderm and endoderm, while deletion mutation was common for that of mesoderm. We could not identify the ectoderm, mesoderm, or endoderm-specific mutated genes or variants with high mutation frequency. However, there was a relatively higher mutation incidence of endoderm markers (GATA6, FOXA2, GATA4, AFP) in the endoderm group, compared with the groups of ectoderm and mesoderm. Additionally, four members (SMO, GLI1, GLI2, GLI3) within the Hedgehog signaling pathway genes showed a relatively higher mutation rate in the endoderm group than the other two groups. Conclusions: TCGA tumors of ectoderm, mesoderm, and endoderm groups exhibit the distinct subject distribution, survival status, and genomic alteration characteristics. The synergistic mutation effect of specific genes closely related to embryonic development may contribute to the tumorigenesis of tissues or organs derived from the specific germ layers. This study provides a novel reference for exploring the functional connection between embryogenesis and tumorigenesis. Keywords: Ectoderm, Mesoderm, Endoderm, Tumor, TCGA, Genetic mutation
*Correspondence: [email protected]; [email protected] 1 Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Heping District Qixiangtai Road No.22, Tianjin 300070, People’s Republic of China Full list of author information is available at the end of the article
Background It has commonly been assumed that the embryonic period occurred in the first 3 months of human intrauterine development [1]. After the combination of the spermatozoa in males with the ovum in females, the formation and the followed first mitotic d
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