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Jung SH, Park HC, Choi YJ, Song SY, Chung YJ, Lee SH. Molecular genetic evidence supporting diverse histogenic origins of germ cell tumors. J Pathol 2021; 256:38-49. [PMID: 34561860 DOI: 10.1002/path.5799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/24/2021] [Accepted: 09/20/2021] [Indexed: 11/10/2022]
Abstract
Germ cell tumors (GCTs) originate during the histogenesis of primordial germ cells to mature gametes. Previous studies identified five histogenic mechanisms in ovarian mature teratomas (type I: failure of meiosis I; type II: failure of meiosis II; type III: duplication of the genome of a mature gamete; type IV: no meiosis; and type V: fusion of two different ova), but those of other GCTs remain elusive. In this study, we analyzed 84 GCTs of various pathologic types to identify the histogenesis using single-nucleotide polymorphism array by analyzing copy-neutral loss of heterozygosity (CN-LOH) and copy number alterations (CNAs). We detected types I and II in ovarian teratomas, type III in ovarian teratomas and yolk sac tumors (YSTs), and type IV in all GCT types. The GCTs with multiple-type histogenesis (I-IV) (ovarian mature/immature teratomas and YST) show meiotic CN-LOH with scant CNAs. Type IV-only GCTs are either with mitotic CN-LOH and abundant CNAs (seminoma, dysgerminoma, testicular mixed GCTs) or with scant CNAs and no CN-LOH (pediatric testicular and mediastinal teratomas). The development sequences of CN-LOH and CNA are different between the multiple type (I-IV) GCTs and type IV-only GCTs. We analyzed two different histologic areas in eight GCTs (one mature teratoma with a mucin-secreting adenoma, two immature teratomas, and five mixed GCTs). We found that GCTs (mature teratoma, immature teratoma, and mixed GCT) showed different genomic alterations between histologic areas, suggesting that genomic differences within a GCT could accompany histologic differentiation. Of note, we found evidence for collision tumors in a mixed GCT. Our data indicate that GCTs may have various histogenesis and intratumoral genomic differences, which might provide important information for the identification of GCTs, especially for those with different histologic areas. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Seung-Hyun Jung
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Precision Medicine Research Center/IRCGP, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyeon-Chun Park
- Department of Precision Medicine Research Center/IRCGP, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Youn Jin Choi
- Department of Obstetrics/Gynecology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sang Yong Song
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Yeun-Jun Chung
- Department of Precision Medicine Research Center/IRCGP, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sug Hyung Lee
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Zhao Q, Zhang Y, Shao S, Sun Y, Lin Z. Identification of hub genes and biological pathways in hepatocellular carcinoma by integrated bioinformatics analysis. PeerJ 2021; 9:e10594. [PMID: 33552715 PMCID: PMC7821758 DOI: 10.7717/peerj.10594] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/26/2020] [Indexed: 12/18/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC), the main type of liver cancer in human, is one of the most prevalent and deadly malignancies in the world. The present study aimed to identify hub genes and key biological pathways by integrated bioinformatics analysis. Methods A bioinformatics pipeline based on gene co-expression network (GCN) analysis was built to analyze the gene expression profile of HCC. Firstly, differentially expressed genes (DEGs) were identified and a GCN was constructed with Pearson correlation analysis. Then, the gene modules were identified with 3 different community detection algorithms, and the correlation analysis between gene modules and clinical indicators was performed. Moreover, we used the Search Tool for the Retrieval of Interacting Genes (STRING) database to construct a protein protein interaction (PPI) network of the key gene module, and we identified the hub genes using nine topology analysis algorithms based on this PPI network. Further, we used the Oncomine analysis, survival analysis, GEO data set and random forest algorithm to verify the important roles of hub genes in HCC. Lastly, we explored the methylation changes of hub genes using another GEO data (GSE73003). Results Firstly, among the expression profiles, 4,130 up-regulated genes and 471 down-regulated genes were identified. Next, the multi-level algorithm which had the highest modularity divided the GCN into nine gene modules. Also, a key gene module (m1) was identified. The biological processes of GO enrichment of m1 mainly included the processes of mitosis and meiosis and the functions of catalytic and exodeoxyribonuclease activity. Besides, these genes were enriched in the cell cycle and mitotic pathway. Furthermore, we identified 11 hub genes, MCM3, TRMT6, AURKA, CDC20, TOP2A, ECT2, TK1, MCM2, FEN1, NCAPD2 and KPNA2 which played key roles in HCC. The results of multiple verification methods indicated that the 11 hub genes had highly diagnostic efficiencies to distinguish tumors from normal tissues. Lastly, the methylation changes of gene CDC20, TOP2A, TK1, FEN1 in HCC samples had statistical significance (P-value < 0.05). Conclusion MCM3, TRMT6, AURKA, CDC20, TOP2A, ECT2, TK1, MCM2, FEN1, NCAPD2 and KPNA2 could be potential biomarkers or therapeutic targets for HCC. Meanwhile, the metabolic pathway, the cell cycle and mitotic pathway might played vital roles in the progression of HCC.
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Affiliation(s)
- Qian Zhao
- College of Information Science and Technology, Dalian Martime University, Dalian, Liaoning, China
| | - Yan Zhang
- College of Information Science and Technology, Dalian Martime University, Dalian, Liaoning, China
| | - Shichun Shao
- College of Environmental Science and Engineering, Dalian Martime University, Dalian, Liaoning, China
| | - Yeqing Sun
- College of Environmental Science and Engineering, Dalian Martime University, Dalian, Liaoning, China
| | - Zhengkui Lin
- College of Information Science and Technology, Dalian Martime University, Dalian, Liaoning, China
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Tamura D, Maeda D, Sato T, Sugawara T, Shirasawa H, Shimizu D, Sato N, Goto A, Terada Y. An extragonadal yolk sac tumor presumed to be of postmeiotic germ cell origin by genetic zygosity analysis via single nucleotide polymorphism array. Genes Chromosomes Cancer 2019; 59:209-213. [DOI: 10.1002/gcc.22817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/15/2019] [Indexed: 01/19/2023] Open
Affiliation(s)
- Daisuke Tamura
- Department of Obstetrics and Gynecology, Graduate School of MedicineAkita University Akita Japan
- Department of GynecologyAkita Red Cross Hospital Akita Japan
| | - Daichi Maeda
- Department of Clinical Genomics, Graduate School of MedicineOsaka University Osaka Japan
| | - Toshiharu Sato
- Department of Obstetrics and Gynecology, Graduate School of MedicineAkita University Akita Japan
| | - Tae Sugawara
- Department of Obstetrics and Gynecology, Graduate School of MedicineAkita University Akita Japan
| | - Hiromitsu Shirasawa
- Department of Obstetrics and Gynecology, Graduate School of MedicineAkita University Akita Japan
| | - Dai Shimizu
- Department of Obstetrics and Gynecology, Graduate School of MedicineAkita University Akita Japan
| | - Naoki Sato
- Department of Obstetrics and Gynecology, Graduate School of MedicineAkita University Akita Japan
| | - Akiteru Goto
- Department of Cellular and Organ Pathology, Graduate School of MedicineAkita University Akita Japan
| | - Yukihiro Terada
- Department of Obstetrics and Gynecology, Graduate School of MedicineAkita University Akita Japan
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Feichtinger J, McFarlane RJ. Meiotic gene activation in somatic and germ cell tumours. Andrology 2019; 7:415-427. [PMID: 31102330 PMCID: PMC6766858 DOI: 10.1111/andr.12628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 12/20/2022]
Abstract
Background Germ cell tumours are uniquely associated with the gametogenic tissues of males and females. A feature of these cancers is that they can express genes that are normally tightly restricted to meiotic cells. This aberrant gene expression has been used as an indicator that these cancer cells are attempting a programmed germ line event, meiotic entry. However, work in non‐germ cell cancers has also indicated that meiotic genes can become aberrantly activated in a wide range of cancer types and indeed provide functions that serve as oncogenic drivers. Here, we review the activation of meiotic factors in cancers and explore commonalities between meiotic gene activation in germ cell and non‐germ cell cancers. Objectives The objectives of this review are to highlight key questions relating to meiotic gene activation in germ cell tumours and to offer possible interpretations as to the biological relevance in this unique cancer type. Materials and Methods PubMed and the GEPIA database were searched for papers in English and for cancer gene expression data, respectively. Results We provide a brief overview of meiotic progression, with a focus on the unique mechanisms of reductional chromosome segregation in meiosis I. We then offer detailed insight into the role of meiotic chromosome regulators in non‐germ cell cancers and extend this to provide an overview of how this might relate to germ cell tumours. Conclusions We propose that meiotic gene activation in germ cell tumours might not indicate an unscheduled attempt to enter a full meiotic programme. Rather, it might simply reflect either aberrant activation of a subset of meiotic genes, with little or no biological relevance, or aberrant activation of a subset of meiotic genes as positive tumour evolutionary/oncogenic drivers. These postulates provide the provocation for further studies in this emerging field.
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Affiliation(s)
- J Feichtinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria.,OMICS Center Graz, BioTechMed Graz, Graz, Austria
| | - R J McFarlane
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, UK
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Usui H, Nakabayashi K, Kaku H, Maehara K, Hata K, Shozu M. Elucidation of the developmental mechanism of ovarian mature cystic teratomas using B allele-frequency plots of single nucleotide polymorphism array data. Genes Chromosomes Cancer 2018; 57:409-419. [PMID: 29700881 DOI: 10.1002/gcc.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 04/21/2018] [Accepted: 04/22/2018] [Indexed: 12/15/2022] Open
Abstract
Ovarian mature cystic teratomas (MCTs) originate from post-meiotic germ cells. Conventional methods such as karyotyping or short tandem repeat-polymorphism analysis may be used to better classify MCTs, although such data would be insufficient. The aim of this study was to elucidate the origin of ovarian MCTs using B allele-frequency (BAF) plots of single nucleotide polymorphism array data. MCTs can be classified in terms of the zygosity of the centromeres and distal chromosome regions. We evaluated the zygosity of all chromosomes from 38 MCT specimens using BAF plot data. BAF plots were used to determine the homozygous and heterozygous regions over the whole genome. Theoretically, MCTs originated from the fusion of two ova (previously referred to as type V MCTs) should have a mixed pattern of centromeric zygosity, that is, a combination of heterozygous and homozygous regions in the centromeric regions. However, no MCTs in this study met this criterion. We identified 13 type I MCTs, 14 type II MCTs, and 11 type III MCTs. In addition, BAF plots facilitated the construction of recombination maps at the whole-genome level for type I and II MCTs. No crossover, especially in the short arms, contributed to the failure of meiosis I, resulting in type I MCTs. Crossover in all arms might assure the normal progress of meiosis in human oocytes. In conclusion, our findings indicate that BAF plots can elucidate the developmental mechanism of MCTs, and further serve as useful analytical tools for analyzing human oocyte meiosis, and related aberrations.
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Affiliation(s)
- Hirokazu Usui
- Department of Reproductive Medicine, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya, Tokyo, Japan
| | - Hiroshi Kaku
- Department of Reproductive Medicine, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Kayoko Maehara
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya, Tokyo, Japan
| | - Makio Shozu
- Department of Reproductive Medicine, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
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Stuart D. Sorting out meiosis. Cytometry A 2014; 85:474-6. [PMID: 24664871 DOI: 10.1002/cyto.a.22468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 03/06/2014] [Accepted: 03/12/2014] [Indexed: 01/06/2023]
Affiliation(s)
- David Stuart
- University of Alberta, Department of Biochemistry, Edmonton, Alberta, Canada
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Age-related biological features of germ cell tumors. Genes Chromosomes Cancer 2013; 53:215-27. [DOI: 10.1002/gcc.22131] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 11/06/2013] [Indexed: 12/15/2022] Open
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