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Su KM, Gao HW, Chang CM, Lu KH, Yu MH, Lin YH, Liu LC, Chang CC, Li YF, Chang CC. Synergistic AHR Binding Pathway with EMT Effects on Serous Ovarian Tumors Recognized by Multidisciplinary Integrated Analysis. Biomedicines 2021; 9:866. [PMID: 34440070 PMCID: PMC8389648 DOI: 10.3390/biomedicines9080866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/12/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
Epithelial ovarian cancers (EOCs) are fatal and obstinate among gynecological malignancies in advanced stage or relapsed status, with serous carcinomas accounting for the vast majority. Unlike EOCs, borderline ovarian tumors (BOTs), including serous BOTs, maintain a semimalignant appearance. Using gene ontology (GO)-based integrative analysis, we analyzed gene set databases of serous BOTs and serous ovarian carcinomas for dysregulated GO terms and pathways and identified multiple differentially expressed genes (DEGs) in various aspects. The SRC (SRC proto-oncogene, non-receptor tyrosine kinase) gene and dysfunctional aryl hydrocarbon receptor (AHR) binding pathway consistently influenced progression-free survival and overall survival, and immunohistochemical staining revealed elevated expression of related biomarkers (SRC, ARNT, and TBP) in serous BOT and ovarian carcinoma samples. Epithelial-mesenchymal transition (EMT) is important during tumorigenesis, and we confirmed the SNAI2 (Snail family transcriptional repressor 2, SLUG) gene showing significantly high performance by immunohistochemistry. During serous ovarian tumor formation, activated AHR in the cytoplasm could cooperate with SRC, enter cell nuclei, bind to AHR nuclear translocator (ARNT) together with TATA-Box Binding Protein (TBP), and act on DNA to initiate AHR-responsive genes to cause tumor or cancer initiation. Additionally, SNAI2 in the tumor microenvironment can facilitate EMT accompanied by tumorigenesis. Although it has not been possible to classify serous BOTs and serous ovarian carcinomas as the same EOC subtype, the key determinants of relevant DEGs (SRC, ARNT, TBP, and SNAI2) found here had a crucial role in the pathogenetic mechanism of both tumor types, implying gradual evolutionary tendencies from serous BOTs to ovarian carcinomas. In the future, targeted therapy could focus on these revealed targets together with precise detection to improve therapeutic effects and patient survival rates.
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Affiliation(s)
- Kuo-Min Su
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan; (K.-M.S.); (M.-H.Y.)
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (Y.-H.L.); (L.-C.L.); (C.-C.C.)
| | - Hong-Wei Gao
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan;
| | - Chia-Ming Chang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan;
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Kai-Hsi Lu
- Department of Medical Research and Education, Cheng-Hsin General Hospital, Taipei 112, Taiwan;
| | - Mu-Hsien Yu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan; (K.-M.S.); (M.-H.Y.)
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (Y.-H.L.); (L.-C.L.); (C.-C.C.)
| | - Yi-Hsin Lin
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (Y.-H.L.); (L.-C.L.); (C.-C.C.)
| | - Li-Chun Liu
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (Y.-H.L.); (L.-C.L.); (C.-C.C.)
- Division of Obstetrics and Gynecology, Tri-Service General Hospital Songshan Branch, National Defense Medical Center, Taipei 105, Taiwan
| | - Chia-Ching Chang
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (Y.-H.L.); (L.-C.L.); (C.-C.C.)
| | - Yao-Feng Li
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan;
| | - Cheng-Chang Chang
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan; (K.-M.S.); (M.-H.Y.)
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (Y.-H.L.); (L.-C.L.); (C.-C.C.)
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Dysregulated Immunological Functionome and Dysfunctional Metabolic Pathway Recognized for the Pathogenesis of Borderline Ovarian Tumors by Integrative Polygenic Analytics. Int J Mol Sci 2021; 22:ijms22084105. [PMID: 33921111 PMCID: PMC8071470 DOI: 10.3390/ijms22084105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 12/20/2022] Open
Abstract
The pathogenesis and molecular mechanisms of ovarian low malignant potential (LMP) tumors or borderline ovarian tumors (BOTs) have not been fully elucidated to date. Surgery remains the cornerstone of treatment for this disease, and diagnosis is mainly made by histopathology to date. However, there is no integrated analysis investigating the tumorigenesis of BOTs with open experimental data. Therefore, we first utilized a functionome-based speculative model from the aggregated obtainable datasets to explore the expression profiling data among all BOTs and two major subtypes of BOTs, serous BOTs (SBOTs) and mucinous BOTs (MBOTs), by analyzing the functional regularity patterns and clustering the separate gene sets. We next prospected and assembled the association between these targeted biomolecular functions and their related genes. Our research found that BOTs can be accurately recognized by gene expression profiles by means of integrative polygenic analytics among all BOTs, SBOTs, and MBOTs; the results exhibited the top 41 common dysregulated biomolecular functions, which were sorted into four major categories: immune and inflammatory response-related functions, cell membrane- and transporter-related functions, cell cycle- and signaling-related functions, and cell metabolism-related functions, which were the key elements involved in its pathogenesis. In contrast to previous research, we identified 19 representative genes from the above classified categories (IL6, CCR2 for immune and inflammatory response-related functions; IFNG, ATP1B1, GAS6, and PSEN1 for cell membrane- and transporter-related functions; CTNNB1, GATA3, and IL1B for cell cycle- and signaling-related functions; and AKT1, SIRT1, IL4, PDGFB, MAPK3, SRC, TWIST1, TGFB1, ADIPOQ, and PPARGC1A for cell metabolism-related functions) that were relevant in the cause and development of BOTs. We also noticed that a dysfunctional pathway of galactose catabolism had taken place among all BOTs, SBOTs, and MBOTs from the analyzed gene set databases of canonical pathways. With the help of immunostaining, we verified significantly higher performance of interleukin 6 (IL6) and galactose-1-phosphate uridylyltransferase (GALT) among BOTs than the controls. In conclusion, a bioinformatic platform of gene-set integrative molecular functionomes and biophysiological pathways was constructed in this study to interpret the complicated pathogenic pathways of BOTs, and these important findings demonstrated the dysregulated immunological functionome and dysfunctional metabolic pathway as potential roles during the tumorigenesis of BOTs and may be helpful for the diagnosis and therapy of BOTs in the future.
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Su KM, Lin TW, Liu LC, Yang YP, Wang ML, Tsai PH, Wang PH, Yu MH, Chang CM, Chang CC. The Potential Role of Complement System in the Progression of Ovarian Clear Cell Carcinoma Inferred from the Gene Ontology-Based Immunofunctionome Analysis. Int J Mol Sci 2020; 21:E2824. [PMID: 32316695 PMCID: PMC7216156 DOI: 10.3390/ijms21082824] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/27/2020] [Accepted: 04/15/2020] [Indexed: 02/07/2023] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is the second most common epithelial ovarian carcinoma (EOC). It is refractory to chemotherapy with a worse prognosis after the preliminary optimal debulking operation, such that the treatment of OCCC remains a challenge. OCCC is believed to evolve from endometriosis, a chronic immune/inflammation-related disease, so that immunotherapy may be a potential alternative treatment. Here, gene set-based analysis was used to investigate the immunofunctionomes of OCCC in early and advanced stages. Quantified biological functions defined by 5917 Gene Ontology (GO) terms downloaded from the Gene Expression Omnibus (GEO) database were used. DNA microarray gene expression profiles were used to convert 85 OCCCs and 136 normal controls into to the functionome. Relevant offspring were as extracted and the immunofunctionomes were rebuilt at different stages by machine learning. Several dysregulated pathogenic functions were found to coexist in the immunopathogenesis of early and advanced OCCC, wherein the complement-activation-alternative-pathway may be the headmost dysfunctional immunological pathway in duality for carcinogenesis at all OCCC stages. Several immunological genes involved in the complement system had dual influences on patients' survival, and immunohistochemistrical analysis implied the higher expression of C3a receptor (C3aR) and C5a receptor (C5aR) levels in OCCC than in controls.
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Affiliation(s)
- Kuo-Min Su
- Department of Obstetrics and Gynecology, Tri-service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (K.-M.S.); (L.-C.L.); (M.-H.Y.)
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Tzu-Wei Lin
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (T.-W.L.); (Y.-P.Y.); (M.-L.W.); (P.-H.T.)
| | - Li-Chun Liu
- Department of Obstetrics and Gynecology, Tri-service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (K.-M.S.); (L.-C.L.); (M.-H.Y.)
- Division of Obstetrics and Gynecology, Tri-Service General Hospital Songshan Branch, National Defense Medical Center, Taipei 105, Taiwan
| | - Yi-Pin Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (T.-W.L.); (Y.-P.Y.); (M.-L.W.); (P.-H.T.)
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan;
| | - Mong-Lien Wang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (T.-W.L.); (Y.-P.Y.); (M.-L.W.); (P.-H.T.)
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan;
| | - Ping-Hsing Tsai
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (T.-W.L.); (Y.-P.Y.); (M.-L.W.); (P.-H.T.)
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan;
| | - Peng-Hui Wang
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan;
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung 404, Taiwan
| | - Mu-Hsien Yu
- Department of Obstetrics and Gynecology, Tri-service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (K.-M.S.); (L.-C.L.); (M.-H.Y.)
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Chia-Ming Chang
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan;
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Cheng-Chang Chang
- Department of Obstetrics and Gynecology, Tri-service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (K.-M.S.); (L.-C.L.); (M.-H.Y.)
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan
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Ho CH, Chang CM, Li HY, Shen HY, Lieu FK, Wang PSG. Dysregulated immunological and metabolic functions discovered by a polygenic integrative analysis for PCOS. Reprod Biomed Online 2019; 40:160-167. [PMID: 31780352 DOI: 10.1016/j.rbmo.2019.09.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/22/2019] [Accepted: 09/23/2019] [Indexed: 12/28/2022]
Abstract
RESEARCH QUESTION Polycystic ovary syndrome (PCOS) is a complex disease and its pathophysiology is still unclear. This polygenic study may provide some clues. DESIGN A polygenic, functionome-based study with the ovarian gene expression profiles downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database, including 48 PCOS and 181 normal control samples. These profiles were converted to the gene set regularity (GSR) indices, which were computed by the modified differential rank conversion algorithm and were defined by the gene ontology terms. RESULTS Machine learning could accurately recognize the patterns of functional regularities between PCOS and normal controls. The significantly aberrant functions in PCOS included transporter activity, catalytic activity, the receptor signalling pathway via signal transducer and activator of transcription (STAT), the cellular metabolic process, and immune response. CONCLUSION This study provided a comprehensive view of the dysregulated functions and information for further studies on the management of PCOS.
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Affiliation(s)
- Chi-Hong Ho
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei Taiwan, Republic of China; Institute of Physiology, School of Medicine, National Yang-Ming University, Taipei Taiwan, Republic of China
| | - Chia-Ming Chang
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei Taiwan, Republic of China; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei Taiwan, Republic of China
| | - Hsin-Yang Li
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei Taiwan, Republic of China
| | - Heng-Yi Shen
- Department of Rehabilitation, Cheng Hsin General Hospital, Taipei Taiwan, Republic of China; Department of Physical Medicine and Rehabilitation, National Defense Medical Center, Taipei Taiwan, Republic of China
| | - Fu-Kong Lieu
- Department of Rehabilitation, Cheng Hsin General Hospital, Taipei Taiwan, Republic of China; Department of Physical Medicine and Rehabilitation, National Defense Medical Center, Taipei Taiwan, Republic of China
| | - Paulus Shyi-Gang Wang
- Institute of Physiology, School of Medicine, National Yang-Ming University, Taipei Taiwan, Republic of China; Medical Center of Ageing Research, China Medical University Hospital, Taichung Taiwan, Republic of China; Department of Biotechnology, College of Health Science, Asia University, Taichung Taiwan, Republic of China; Department of Medical Research, Taipei Veterans General Hospital, Taipei Taiwan, Republic of China.
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Chang CC, Su KM, Lu KH, Lin CK, Wang PH, Li HY, Wang ML, Lin CK, Yu MH, Chang CM. Key Immunological Functions Involved in the Progression of Epithelial Ovarian Serous Carcinoma Discovered by the Gene Ontology-Based Immunofunctionome Analysis. Int J Mol Sci 2018; 19:ijms19113311. [PMID: 30356023 PMCID: PMC6274992 DOI: 10.3390/ijms19113311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/19/2018] [Accepted: 10/23/2018] [Indexed: 11/16/2022] Open
Abstract
Serous carcinoma (SC) is the most common and lethal subtype of epithelial ovarian carcinoma; immunotherapy is a potential treatment for SC, however, the global immunological functions of SC as well as their change during the progression of SC have not been investigated in detail till now. We conducted a genome-wide integrative analysis to investigate the immunofunctionomes of SC at four tumor stages by quantifying the immunological functions defined by the Gene Ontology gene sets. DNA microarray gene expression profiles of 1100 SCs and 136 normal ovarian tissue controls were downloaded from the Gene Expression Omnibus database and converted to the functionome. Then the immunofunctionomes were reconstructed by extracting the offspring from the functionome for the four SC staging groups. The key immunological functions extracted from immunofunctionomes with a series of filters revealed that the immunopathy of SC consisted of a group of deregulated functions with the core members including B cell activation and differentiation, regulation of leukocyte chemotaxis/cellular extravasation, antigen receptor mediated signaling pathway, T helper mediated immunity and macrophage activation; and the auxiliary elements included leukocyte mediated immunity, regulation of inflammatory response, T cell differentiation, mononuclear cell migration, megakaryocyte differentiation, complement activation and cytokine production. These deregulated immunological functions reveal the candidates to target in the immunotherapy.
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Affiliation(s)
- Cheng-Chang Chang
- Department of Obstetrics and Gynecology, Tri-service General Hospital, National Defense Medical Center, Taipei 114, Taiwan.
| | - Kuo-Min Su
- Department of Obstetrics and Gynecology, Tri-service General Hospital, National Defense Medical Center, Taipei 114, Taiwan.
| | - Kai-Hsi Lu
- Department of Medical Research and Education, Cheng-Hsin Hospital, Taipei 112, Taiwan.
| | - Chi-Kang Lin
- Department of Obstetrics and Gynecology, Tri-service General Hospital, National Defense Medical Center, Taipei 114, Taiwan.
| | - Peng-Hui Wang
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan.
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei 112, Taiwan.
- Department of Medical Research, China Medical University Hospital, Taichung 404, Taiwan.
| | - Hsin-Yang Li
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan.
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei 112, Taiwan.
| | - Mong-Lien Wang
- Department of Medical Research and Education, Cheng-Hsin Hospital, Taipei 112, Taiwan.
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan.
| | - Cheng-Kuo Lin
- Department of Obstetrics and Gynecology, Taoyuan Armed Forces General Hospital, Taoyuan 325, Taiwan.
| | - Mu-Hsien Yu
- Department of Obstetrics and Gynecology, Tri-service General Hospital, National Defense Medical Center, Taipei 114, Taiwan.
| | - Chia-Ming Chang
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan.
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei 112, Taiwan.
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Chang CM, Wang ML, Lu KH, Yang YP, Juang CM, Wang PH, Hsu RJ, Yu MH, Chang CC. Integrating the dysregulated inflammasome-based molecular functionome in the malignant transformation of endometriosis-associated ovarian carcinoma. Oncotarget 2017; 9:3704-3726. [PMID: 29423077 PMCID: PMC5790494 DOI: 10.18632/oncotarget.23364] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/29/2017] [Indexed: 11/30/2022] Open
Abstract
The coexistence of endometriosis (ES) with ovarian clear cell carcinoma (CCC) or endometrioid carcinoma (EC) suggested that malignant transformation of ES leads to endometriosis associated ovarian carcinoma (EAOC). However, there is still lack of an integrating data analysis of the accumulated experimental data to provide the evidence supporting the hypothesis of EAOC transformation. Herein we used a function-based analytic model with the publicly available microarray datasets to investigate the expression profiling between ES, CCC, and EC. We analyzed the functional regularity pattern of the three type of samples and hierarchically clustered the gene sets to identify key mechanisms regulating the malignant transformation of EAOC. We identified a list of 18 genes (NLRP3, AIM2, PYCARD, NAIP, Caspase-4, Caspase-7, Caspase-8, TLR1, TLR7, TOLLIP, NFKBIA, TNF, TNFAIP3, INFGR2, P2RX7, IL-1B, IL1RL1, IL-18) closely related to inflammasome complex, indicating an important role of inflammation/immunity in EAOC transformation. We next explore the association between these target genes and patient survival using Gene Expression Omnibus (GEO), and found significant correlation between the expression levels of the target genes and the progression-free survival. Interestingly, high expression levels of AIM2 and NLRP3, initiating proteins of inflammasomes, were significantly correlated with poor progression-free survival. Immunohistochemistry staining confirmed a correlation between high AIM2 and high Ki-67 in clinical EAOC samples, supporting its role in disease progression. Collectively, we established a bioinformatic platform of gene-set integrative molecular functionome to dissect the pathogenic pathways of EAOC, and demonstrated a key role of dysregulated inflammasome in modulating the malignant transformation of EAOC.
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Affiliation(s)
- Chia-Ming Chang
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Mong-Lien Wang
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Kai-Hsi Lu
- Department of Medical Research and Education, Cheng-Hsin Hospital, Taipei, Taiwan
| | - Yi-Ping Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chi-Mou Juang
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Peng-Hui Wang
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Ren-Jun Hsu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.,Biobank Management Center of Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Mu-Hsien Yu
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Cheng-Chang Chang
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
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Chang CM, Wang PH, Horng HC. Gene set-based analysis of mucinous ovarian carcinoma. Taiwan J Obstet Gynecol 2017; 56:210-216. [PMID: 28420510 DOI: 10.1016/j.tjog.2016.12.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2016] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Mucinous ovarian carcinoma (MOC) is an uncommon subtype of epithelial ovarian cancers, and the pathogenesis is still poorly understood because of its rarity. We conducted a gene set-based analysis to investigate the pathogenesis of MOC by integrating microarray gene expression datasets based on the regularity of functions defined by gene ontology or canonical pathway databases. MATERIALS AND METHODS Forty-five pairs of MOC and normal ovarian tissue sample gene expression profiles were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus database. The gene expression profiles were converted to the gene set regularity indexes by measuring the change of gene expression ordering in a gene set. Then the pathogenesis of MOC was investigated with the differences of function regularity with the gene set regularity indexes between the MOC and normal control samples. RESULTS The informativeness of the gene set regularity indexes was sufficient for machine learning to accurately recognize and classify the functional regulation patterns with an accuracy of 99.44%. The statistical analysis revealed that the GTPase regulators and receptor tyrosine kinase erbB-2 (ERBB2) were the most important aberrations; the exploratory factor analysis revealed phosphoinositide 3-kinase-activating kinase, G-protein coupled receptor pathway, oxidoreductase activity, immune response, peptidase activity, regulation of translation, and transport and channel activity were also involved in the pathogenesis of MOC. CONCLUSION Investigating the pathogenesis of MOC with the functionome provided a comprehensive view of the deregulated functions of this disease. In addition to GTPase regulators and ERBB2, a plenty of deregulated functions such as phosphoinositide 3-kinase, G-protein coupled receptor pathway, and immune response also participated in the interaction network of MOC pathogenesis.
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Affiliation(s)
- Chia-Ming Chang
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; Institute of Oral Biology, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, National Yang-Ming University, Taipei, Taiwan
| | - Peng-Hui Wang
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; Department of Obstetrics and Gynecology, National Yang-Ming University, Taipei, Taiwan; Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan; Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Huann-Cheng Horng
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; Department of Obstetrics and Gynecology, National Yang-Ming University, Taipei, Taiwan.
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Discovering the Deregulated Molecular Functions Involved in Malignant Transformation of Endometriosis to Endometriosis-Associated Ovarian Carcinoma Using a Data-Driven, Function-Based Analysis. Int J Mol Sci 2017; 18:ijms18112345. [PMID: 29113136 PMCID: PMC5713314 DOI: 10.3390/ijms18112345] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/03/2017] [Accepted: 11/04/2017] [Indexed: 12/12/2022] Open
Abstract
The clinical characteristics of clear cell carcinoma (CCC) and endometrioid carcinoma EC) are concomitant with endometriosis (ES), which leads to the postulation of malignant transformation of ES to endometriosis-associated ovarian carcinoma (EAOC). Different deregulated functional areas were proposed accounting for the pathogenesis of EAOC transformation, and there is still a lack of a data-driven analysis with the accumulated experimental data in publicly-available databases to incorporate the deregulated functions involved in the malignant transformation of EOAC. We used the microarray gene expression datasets of ES, CCC and EC downloaded from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO) database. Then, we investigated the pathogenesis of EAOC by a data-driven, function-based analytic model with the quantified molecular functions defined by 1454 Gene Ontology (GO) term gene sets. This model converts the gene expression profiles to the functionome consisting of 1454 quantified GO functions, and then, the key functions involving the malignant transformation of EOAC can be extracted by a series of filters. Our results demonstrate that the deregulated oxidoreductase activity, metabolism, hormone activity, inflammatory response, innate immune response and cell-cell signaling play the key roles in the malignant transformation of EAOC. These results provide the evidence supporting the specific molecular pathways involved in the malignant transformation of EAOC.
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Gene Set-Based Integrative Analysis Revealing Two Distinct Functional Regulation Patterns in Four Common Subtypes of Epithelial Ovarian Cancer. Int J Mol Sci 2016; 17:ijms17081272. [PMID: 27527159 PMCID: PMC5000670 DOI: 10.3390/ijms17081272] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/22/2016] [Accepted: 07/27/2016] [Indexed: 01/04/2023] Open
Abstract
Clear cell (CCC), endometrioid (EC), mucinous (MC) and high-grade serous carcinoma (SC) are the four most common subtypes of epithelial ovarian carcinoma (EOC). The widely accepted dualistic model of ovarian carcinogenesis divided EOCs into type I and II categories based on the molecular features. However, this hypothesis has not been experimentally demonstrated. We carried out a gene set-based analysis by integrating the microarray gene expression profiles downloaded from the publicly available databases. These quantified biological functions of EOCs were defined by 1454 Gene Ontology (GO) term and 674 Reactome pathway gene sets. The pathogenesis of the four EOC subtypes was investigated by hierarchical clustering and exploratory factor analysis. The patterns of functional regulation among the four subtypes containing 1316 cases could be accurately classified by machine learning. The results revealed that the ERBB and PI3K-related pathways played important roles in the carcinogenesis of CCC, EC and MC; while deregulation of cell cycle was more predominant in SC. The study revealed that two different functional regulation patterns exist among the four EOC subtypes, which were compatible with the type I and II classifications proposed by the dualistic model of ovarian carcinogenesis.
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