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Sarker B, Matiur Rahaman M, Alamin MH, Ariful Islam M, Nurul Haque Mollah M. Boosting edgeR (Robust) by dealing with missing observations and gene-specific outliers in RNA-Seq profiles and its application to explore biomarker genes for diagnosis and therapies of ovarian cancer. Genomics 2024; 116:110834. [PMID: 38527595 DOI: 10.1016/j.ygeno.2024.110834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 02/09/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Abstract
The edgeR (Robust) is a popular approach for identifying differentially expressed genes (DEGs) from RNA-Seq profiles. However, it shows weak performance against gene-specific outliers and is unable to handle missing observations. To address these issues, we proposed a pre-processing approach of RNA-Seq count data by combining the iLOO-based outlier detection and random forest-based missing imputation approach for boosting the performance of edgeR (Robust). Both simulation and real RNA-Seq count data analysis results showed that the proposed edgeR (Robust) outperformed than the conventional edgeR (Robust). To investigate the effectiveness of identified DEGs for diagnosis, and therapies of ovarian cancer (OC), we selected top-ranked 12 DEGs (IL6, XCL1, CXCL8, C1QC, C1QB, SNAI2, TYROBP, COL1A2, SNAP25, NTS, CXCL2, and AGT) and suggested hub-DEGs guided top-ranked 10 candidate drug-molecules for the treatment against OC. Hence, our proposed procedure might be an effective computational tool for exploring potential DEGs from RNA-Seq profiles for diagnosis and therapies of any disease.
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Affiliation(s)
- Bandhan Sarker
- Department of Statistics, Faculty of Science, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Md Matiur Rahaman
- Department of Statistics, Faculty of Science, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining 314400, China.
| | - Muhammad Habibulla Alamin
- Department of Statistics, Faculty of Science, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Md Ariful Islam
- Bioinformatics Laboratory (Dry), Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Nurul Haque Mollah
- Bioinformatics Laboratory (Dry), Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh.
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Jia H, Tang WJ, Sun L, Wan C, Zhou Y, Shen WZ. Pan-cancer analysis identifies proteasome 26S subunit, ATPase (PSMC) family genes, and related signatures associated with prognosis, immune profile, and therapeutic response in lung adenocarcinoma. Front Genet 2023; 13:1017866. [PMID: 36699466 PMCID: PMC9868736 DOI: 10.3389/fgene.2022.1017866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Background: Proteasome 26S subunit, ATPase gene (PSMC) family members play a critical role in regulating protein degradation and are essential for tumor development. However, little is known about the integrative function and prognostic significance of the PSMC gene family members in lung cancer. Methods: First, we assessed the expression and prognostic features of six PSMC family members in pan-cancer from The Cancer Genome Atlas (TCGA) dataset. Hence, by focusing on the relationship between PSMC genes and the prognostic, genomic, and tumor microenvironment features in lung adenocarcinoma (LUAD), a PSMC-based prognostic signature was established using consensus clustering and multiple machine learning algorithms, including the least absolute shrinkage and selection operator (LASSO) Cox regression, CoxBoost, and survival random forest analysis in TCGA and GSE72094. We then validated it in three independent cohorts from GEO and estimated the correlation between risk score and clinical features: genomic features (alterations, tumor mutation burden, and copy number variants), immune profiles (immune score, TIDE score, tumor-infiltrated immune cells, and immune checkpoints), sensitivity to chemotherapy (GDSC, GSE42127, and GSE14814), and immunotherapy (IMvigor210, GSE63557, and immunophenoscore). Twenty-one patients with LUAD were included in our local cohort, and tumor samples were submitted for evaluation of risk gene and PD-L1 expression. Results: Nearly all six PSMC genes were overexpressed in pan-cancer tumor tissues; however, in LUAD alone, they were all significantly correlated with overall survival. Notably, they all shared a positive association with increased TMB, TIDE score, expression of immune checkpoints (CD276 and PVR), and more M1 macrophages but decreased B-cell abundance. A PSMC-based prognostic signature was established based on five hub genes derived from the differential expression clusters of PSMC genes, and it was used to dichotomize LUAD patients into high- and low-risk groups according to the median risk score. The area under the curve (AUC) values for predicting survival at 1, 3, and 5 years in the training cohorts were all >.71, and the predictive accuracy was also robust and stable in the GSE72094, GSE31210, and GSE13213 datasets. The risk score was significantly correlated with advanced tumor, lymph node, and neoplasm disease stages as an independent risk factor for LUAD. Furthermore, the risk score shared a similar genomic and immune feature as PSMC genes, and high-risk tumors exhibited significant genomic and chromosomal instability, a higher TIDE score but lower immune score, and a decreased abundance of B and CD8+ T cells. Finally, high-risk patients were suggested to be less sensitive to immunotherapy but had a higher possibility of responding to platinum-based chemotherapy. The LUAD samples from the local cohort supported the difference in the expression levels of these five hub genes between tumor and normal tissues and the correlation between the risk score and PD-L1 expression. Conclusion: Overall, our results provide deep insight into PSMC genes in LUAD, especially the prognostic effect and related immune profile that may predict therapeutic responses.
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Affiliation(s)
- Hui Jia
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Wen-Jin Tang
- Department of Nursing, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Lei Sun
- Department of Interventional Radiology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Chong Wan
- Yangtze Delta Region Institute of Tsinghua University, Jiaxing, China
| | - Yun Zhou
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China,*Correspondence: Yun Zhou, ; Wei-Zhong Shen,
| | - Wei-Zhong Shen
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China,*Correspondence: Yun Zhou, ; Wei-Zhong Shen,
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Shuqing L, Zhiling Z. Patients with stage IA ovarian clear cell carcinoma do not require chemotherapy following surgery. Cancer Med 2022; 12:6668-6674. [PMID: 36416131 PMCID: PMC10067103 DOI: 10.1002/cam4.5453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 11/06/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Ovarian clear cell carcinoma (OCCC) is an infrequent histological subtype of epithelial ovarian cancer (EOC). The present study aimed to investigate whether chemotherapy is indispensable for patients with stage IA OCCC. METHODS Data were collected from the Surveillance, Epidemiology and End Results database between 2004 and 2015. All subjects were diagnosed with stage IA OCCC, according to their postoperative pathological reports. In the present study, 1038 patients were retrospectively investigated, among whom 692 patients received chemotherapy. Propensity score matching (PSM) was performed to prevent selection bias. The multivariate Cox proportional hazards model was used to analyze the correlation between variables and 5-year overall survival. RESULTS An equal number of patients (n = 346) who did or did not undergo chemotherapy after PSM were further enrolled in the study. The results showed that the mortality of OCCC increased for the patients aged ≥50 years. In addition, older age was associated with lower 5-year overall survival (p < 0.05). However, chemotherapy did not extend the 5-year overall survival (p = 0.524) of patients with stage IA OCCC, according to the multivariate Cox regression analysis. CONCLUSIONS Chemotherapy did not affect the overall survival of patients with stage IA OCCC following surgery.
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Affiliation(s)
- Li Shuqing
- Department of Obstetrics and Gynecology Obstetrics and Gynecology Hospital of Fudan University Shanghai China
| | - Zhu Zhiling
- Department of Obstetrics and Gynecology Obstetrics and Gynecology Hospital of Fudan University Shanghai China
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Wang PH, Yang ST, Chang WH, Liu CH, Lee FK, Lee WL. Endometriosis: Part I. Basic concept. Taiwan J Obstet Gynecol 2022; 61:927-934. [DOI: 10.1016/j.tjog.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2022] [Indexed: 11/23/2022] Open
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Kolev M, Das M, Gerber M, Baver S, Deschatelets P, Markiewski MM. Inside-Out of Complement in Cancer. Front Immunol 2022; 13:931273. [PMID: 35860237 PMCID: PMC9291441 DOI: 10.3389/fimmu.2022.931273] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 12/21/2022] Open
Abstract
The role of complement in cancer has received increasing attention over the last decade. Recent studies provide compelling evidence that complement accelerates cancer progression. Despite the pivotal role of complement in fighting microbes, complement seems to suppress antitumor immunity via regulation of host cell in the tumor microenvironment. Although most studies link complement in cancer to complement activation in the extracellular space, the discovery of intracellular activation of complement, raises the question: what is the relevance of this process for malignancy? Intracellular activation is pivotal for the survival of immune cells. Therefore, complement can be important for tumor cell survival and growth regardless of the role in immunosuppression. On the other hand, because intracellular complement (the complosome) is indispensable for activation of T cells, these functions will be essential for priming antitumor T cell responses. Here, we review functions of complement in cancer with the consideration of extra and intracellular pathways of complement activation and spatial distribution of complement proteins in tumors and periphery and provide our take on potential significance of complement as biomarker and target for cancer therapy.
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Affiliation(s)
- Martin Kolev
- Discovery, Apellis Pharmaceuticals, Waltham, MA, United States
- *Correspondence: Martin Kolev, ; Maciej M. Markiewski,
| | - Madhumita Das
- Discovery, Apellis Pharmaceuticals, Waltham, MA, United States
| | - Monica Gerber
- Legal Department, Apellis Pharmaceuticals, Waltham, MA, United States
| | - Scott Baver
- Medical Affairs, Apellis Pharmaceuticals, Waltham, MA, United States
| | | | - Maciej M. Markiewski
- Department of Immunotherapeutics and Biotechnology, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Abilene, TX, United States
- *Correspondence: Martin Kolev, ; Maciej M. Markiewski,
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Silva MC, Eugénio P, Faria D, Pesquita C. Ontologies and Knowledge Graphs in Oncology Research. Cancers (Basel) 2022; 14:cancers14081906. [PMID: 35454813 PMCID: PMC9029532 DOI: 10.3390/cancers14081906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/25/2022] [Accepted: 04/07/2022] [Indexed: 11/16/2022] Open
Abstract
The complexity of cancer research stems from leaning on several biomedical disciplines for relevant sources of data, many of which are complex in their own right. A holistic view of cancer—which is critical for precision medicine approaches—hinges on integrating a variety of heterogeneous data sources under a cohesive knowledge model, a role which biomedical ontologies can fill. This study reviews the application of ontologies and knowledge graphs in cancer research. In total, our review encompasses 141 published works, which we categorized under 14 hierarchical categories according to their usage of ontologies and knowledge graphs. We also review the most commonly used ontologies and newly developed ones. Our review highlights the growing traction of ontologies in biomedical research in general, and cancer research in particular. Ontologies enable data accessibility, interoperability and integration, support data analysis, facilitate data interpretation and data mining, and more recently, with the emergence of the knowledge graph paradigm, support the application of Artificial Intelligence methods to unlock new knowledge from a holistic view of the available large volumes of heterogeneous data.
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Wang CW, Lee YC, Chang CC, Lin YJ, Liou YA, Hsu PC, Chang CC, Sai AKO, Wang CH, Chao TK. A Weakly Supervised Deep Learning Method for Guiding Ovarian Cancer Treatment and Identifying an Effective Biomarker. Cancers (Basel) 2022; 14:cancers14071651. [PMID: 35406422 PMCID: PMC8996991 DOI: 10.3390/cancers14071651] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/14/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Ovarian cancer is a common malignant gynecological disease. Molecular target therapy, i.e., antiangiogenesis with bevacizumab, was found to be effective in some patients of epithelial ovarian cancer (EOC). Although careful patient selection is essential, there are currently no biomarkers available for routine therapeutic usage. To the authors’ best knowledge, this is the first automated precision oncology framework to effectively identify and select EOC and peritoneal serous papillary carcinoma (PSPC) patients with positive therapeutic effect. From March 2013 to January 2021, we have a database, containing four kinds of immunohistochemical tissue samples, including AIM2, c3, C5 and NLRP3, from patients diagnosed with EOC and PSPC and treated with bevacizumab in a hospital-based retrospective study. We developed a hybrid deep learning framework and weakly supervised deep learning models for each potential biomarker, and the experimental results show that the proposed model in combination with AIM2 achieves high accuracy 0.92, recall 0.97, F-measure 0.93 and AUC 0.97 for the first experiment (66% training and 34%testing) and high accuracy 0.86 ± 0.07, precision 0.9 ± 0.07, recall 0.85 ± 0.06, F-measure 0.87 ± 0.06 and AUC 0.91 ± 0.05 for the second experiment using five-fold cross validation, respectively. Both Kaplan-Meier PFS analysis and Cox proportional hazards model analysis further confirmed that the proposed AIM2-DL model is able to distinguish patients gaining positive therapeutic effects with low cancer recurrence from patients with disease progression after treatment (p < 0.005).
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Affiliation(s)
- Ching-Wei Wang
- Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology, Taipei 106335, Taiwan; (C.-W.W.); (Y.-A.L.); (C.-C.C.); (A.-K.-O.S.)
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 106335, Taiwan;
| | - Yu-Ching Lee
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 106335, Taiwan;
| | - Cheng-Chang Chang
- Department of Gynecology and Obstetrics, Tri-Service General Hospital, Taipei 11490, Taiwan; (C.-C.C.); (P.-C.H.)
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 11490, Taiwan
| | - Yi-Jia Lin
- Department of Pathology, Tri-Service General Hospital, Taipei 11490, Taiwan;
- Institute of Pathology and Parasitology, National Defense Medical Center, Taipei 11490, Taiwan
| | - Yi-An Liou
- Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology, Taipei 106335, Taiwan; (C.-W.W.); (Y.-A.L.); (C.-C.C.); (A.-K.-O.S.)
| | - Po-Chao Hsu
- Department of Gynecology and Obstetrics, Tri-Service General Hospital, Taipei 11490, Taiwan; (C.-C.C.); (P.-C.H.)
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 11490, Taiwan
| | - Chun-Chieh Chang
- Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology, Taipei 106335, Taiwan; (C.-W.W.); (Y.-A.L.); (C.-C.C.); (A.-K.-O.S.)
| | - Aung-Kyaw-Oo Sai
- Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology, Taipei 106335, Taiwan; (C.-W.W.); (Y.-A.L.); (C.-C.C.); (A.-K.-O.S.)
| | - Chih-Hung Wang
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, Taipei 11490, Taiwan;
- Department of Otolaryngology-Head and Neck Surgery, National Defense Medical Center, Taipei 11490, Taiwan
| | - Tai-Kuang Chao
- Department of Pathology, Tri-Service General Hospital, Taipei 11490, Taiwan;
- Institute of Pathology and Parasitology, National Defense Medical Center, Taipei 11490, Taiwan
- Correspondence:
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El Bairi K, Al Jarroudi O, Le Page C, Afqir S. Does the "Devil" originate from the fallopian tubes? Semin Cancer Biol 2021; 77:56-66. [PMID: 33766647 DOI: 10.1016/j.semcancer.2021.03.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/14/2021] [Accepted: 03/20/2021] [Indexed: 02/08/2023]
Abstract
Epithelial ovarian cancer (OC) is a heterogeneous disease and continues to be mostly diagnosed in advanced stages. The high lethality, the high rate of platinum-resistance, and the poor survival outcomes are the principal factors for categorizing OC among the most aggressive gynecological cancers. Only recently, a substantial progress has been made in our latest understanding of the origins of OC, particularly of high-grade serous histology. For a long time, the accumulation of genetic alterations in epithelial single layer cells of ovarian cysts caused by cyclic ovulations was considered as the most important driver and the long-standing dogma of ovarian tumorigenesis. Besides, the unique biological features and high histological heterogeneity of OC did not support this hypothesis. Indeed, various extra-ovarian cells of origin and multiple sites to each histotype were proposed, supported by cogent evidence from clinical cohorts and animal studies. In light of this enigma, this review was conducted to discuss the recent evidence supporting the revised origins of ovarian carcinoma histotypes with a particular focus on high-grade serous OC which may impact diagnostic and preventive approaches.
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Affiliation(s)
- Khalid El Bairi
- Department of Medical Oncology, Mohammed VI University Hospital, Oujda, Morocco; Faculty of Medicine and Pharmacy, Mohammed I(st) University, Oujda, Morocco.
| | - Ouissam Al Jarroudi
- Department of Medical Oncology, Mohammed VI University Hospital, Oujda, Morocco; Faculty of Medicine and Pharmacy, Mohammed I(st) University, Oujda, Morocco
| | - Cécile Le Page
- Research Institute of McGill University Health Center (RI-MUHC), Montréal, QC, Canada
| | - Said Afqir
- Department of Medical Oncology, Mohammed VI University Hospital, Oujda, Morocco; Faculty of Medicine and Pharmacy, Mohammed I(st) University, Oujda, Morocco
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Endometriosis-associated epithelial ovarian cancer is a more complicated disease than we suspected before. Taiwan J Obstet Gynecol 2021; 60:1112-1115. [PMID: 34794748 DOI: 10.1016/j.tjog.2021.09.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2020] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVE Endometriosis-associated epithelial ovarian cancer (EOC) often includes clear cell carcinoma and endometrioid-type carcinoma. Due to the low incidence of primary mucinous EOC and absence of association between endometriosis and primary mucinous EOC, we present an unusual endometriosis-associated mixed mucinous and endometrioid adenocarcinoma arising from the same ovary. CASE REPORT A 54-year-old woman had an abdominal palpable mass for months. Medical and surgical history, as well as preoperative surveys was unremarkable, except of presence of a pelvic mass. She underwent an exploration laparotomy, and a 22-cm right ovarian tumor was found. Grossly, right ovarian tumor containing brownish cloudy cystic fluid 2450 ml and an apparent 4 × 4 × 2 cm-sized papillary growth. Microscopically, a confluent glandular and infiltrative pattern presented endometrioid adenocarcinoma, and cells with intracytoplasmic mucin and stratified elongated epithelial cells presented mucinous adenocarcinoma. Surgico-pathological stage was FIGO IIIA due to tumor invading to the peritoneum above the pelvis. Postoperatively, the dose-dense chemotherapy was applied with uneventful outcome. CONCLUSION This is a rare case, composed with mixed mucinous and endometrioid adenocarcinoma of the same ovary, suggesting that careful pathological diagnosis of endometriosis-associated EOC is needed.
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Lee WL, Chang WH, Wang PH. Fever during chemotherapy: Hypersensitivity reactions. Taiwan J Obstet Gynecol 2021; 60:977-978. [PMID: 34794758 DOI: 10.1016/j.tjog.2021.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2021] [Indexed: 12/25/2022] Open
Affiliation(s)
- Wen-Ling Lee
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Medicine, Cheng-Hsin General Hospital, Taipei, Taiwan; Department of Nursing, Oriental Institute of Technology, New Taipei City, 220, Taiwan
| | - Wen-Hsun Chang
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; Department of Nursing, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Peng-Hui Wang
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; Female Cancer Foundation, Taipei, Taiwan; Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.
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Li YT, Lee WL, Wang PH. Is it possible to use the serum levels of alpha 1-antitrypsin as a serum biomarker to distinguish endometriosis and endometriosis-associated epithelial ovarian cancers? J Chin Med Assoc 2021; 84:985-986. [PMID: 34698690 DOI: 10.1097/jcma.0000000000000644] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Yiu-Tai Li
- Department of Obstetrics and Gynecology, Kuo General Hospital, Tainan, Taiwan, ROC
| | - Wen-Ling Lee
- Department of Medicine, Cheng-Hsin General Hospital, Taipei, Taiwan, ROC
- Department of Nursing, Oriental Institute of Technology, New Taipei City, Taiwan, ROC
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Peng-Hui Wang
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Female Cancer Foundation, Taipei, Taiwan, ROC
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, ROC
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Sun Y, Liu G. Endometriosis-associated Ovarian Clear Cell Carcinoma: A Special Entity? J Cancer 2021; 12:6773-6786. [PMID: 34659566 PMCID: PMC8518018 DOI: 10.7150/jca.61107] [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: 03/30/2021] [Accepted: 09/12/2021] [Indexed: 02/06/2023] Open
Abstract
Endometriosis is an estrogen-dependent disease, which serves as a precursor of ovarian cancer, especially clear cell carcinoma (OCCC) and endometrial carcinoma. Although micro-environmental factors such as oxidative stress, immune cell dysfunction, inflammation, steroid hormones, and stem cells required for malignant transformation have been found in endometriosis, the exact carcinogenic mechanism remains unclear. Recent research suggest that many putative driver genes and aberrant pathways including ARID1A mutations, PIK3CA mutations, MET activation, HNF-1β activation, and miRNAs dysfunction, play crucial roles in the malignant transformation of endometriosis to OCCC. The clinical features of OCCC are different from other histological types. Patients usually present with a large, unilateral pelvic mass, and occasionally have thromboembolic vascular complications. OCCC patients are easier to be resistant to chemotherapy, have a worse prognosis, and are usually difficult to treat. To improve the survival of OCCC patients, it is necessary to better understand its specific carcinogenic mechanism and explore new treatment strategy, including molecular target.
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Affiliation(s)
- Yue Sun
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, 300052, China.,Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin, 300052, China
| | - Guoyan Liu
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, 300052, China.,Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin, 300052, China
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Hsu PC, Chao TK, Chou YC, Yu MH, Wang YC, Lin YH, Lee YL, Liu LC, Chang CC. AIM2 Inflammasome in Tumor Cells as a Biomarker for Predicting the Treatment Response to Antiangiogenic Therapy in Epithelial Ovarian Cancer Patients. J Clin Med 2021; 10:jcm10194529. [PMID: 34640548 PMCID: PMC8509490 DOI: 10.3390/jcm10194529] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/08/2021] [Accepted: 09/29/2021] [Indexed: 01/10/2023] Open
Abstract
Antiangiogenic therapy, such as bevacizumab (BEV), has improved progression-free survival (PFS) and overall survival (OS) in high-risk patients with epithelial ovarian cancer (EOC) according to several clinical trials. Clinically, no reliable molecular biomarker is available to predict the treatment response to antiangiogenic therapy. Immune-related proteins can indirectly contribute to angiogenesis by regulating stromal cells in the tumor microenvironment. This study was performed to search biomarkers for prediction of the BEV treatment response in EOC patients. We conducted a hospital-based retrospective study from March 2013 to May 2020. Tissues from 78 Taiwanese patients who were newly diagnosed with EOC and peritoneal serous papillary carcinoma (PSPC) and received BEV therapy were collected. We used immunohistochemistry (IHC) staining and analyzed the expression of these putative biomarkers (complement component 3 (C3), complement component 5 (C5), and absent in melanoma 2 (AIM2)) based on the staining area and intensity of the color reaction to predict BEV efficacy in EOC patients. The immunostaining scores of AIM2 were significantly higher in the BEV-resistant group (RG) than in the BEV-sensitive group (SG) (355.5 vs. 297.1, p < 0.001). A high level of AIM2 (mean value > 310) conferred worse PFS after treatment with BEV than a low level of AIM2 (13.58 vs. 19.36 months, adjusted hazard ratio (HR) = 4.44, 95% confidence interval (CI) = 2.01–9.80, p < 0.001). There were no significant differences in C3 (p = 0.077) or C5 (p = 0.326) regarding BEV efficacy. AIM2 inflammasome expression can be a histopathological biomarker to predict the antiangiogenic therapy benefit in EOC patients. The molecular mechanism requires further investigation.
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Affiliation(s)
- Po-Chao Hsu
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (P.-C.H.); (M.-H.Y.); (Y.-C.W.); (Y.-H.L.); (Y.-L.L.); (L.-C.L.)
- Division of Obstetrics and Gynecology, Tri-Service General Hospital, Penghu Branch, Magong City 880, Taiwan
| | - Tai-Kuang Chao
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan;
| | - Yu-Ching Chou
- School of Public Health, National Defense Medical Center, Taipei 114, Taiwan;
| | - Mu-Hsien Yu
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (P.-C.H.); (M.-H.Y.); (Y.-C.W.); (Y.-H.L.); (Y.-L.L.); (L.-C.L.)
| | - Yu-Chi Wang
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (P.-C.H.); (M.-H.Y.); (Y.-C.W.); (Y.-H.L.); (Y.-L.L.); (L.-C.L.)
| | - Yi-Hsin Lin
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (P.-C.H.); (M.-H.Y.); (Y.-C.W.); (Y.-H.L.); (Y.-L.L.); (L.-C.L.)
| | - Yi-Liang Lee
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (P.-C.H.); (M.-H.Y.); (Y.-C.W.); (Y.-H.L.); (Y.-L.L.); (L.-C.L.)
| | - Li-Chun Liu
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (P.-C.H.); (M.-H.Y.); (Y.-C.W.); (Y.-H.L.); (Y.-L.L.); (L.-C.L.)
- Division of Obstetrics and Gynecology, Tri-Service General Hospital Songshan Branch, Taipei 105, Taiwan
| | - Cheng-Chang Chang
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (P.-C.H.); (M.-H.Y.); (Y.-C.W.); (Y.-H.L.); (Y.-L.L.); (L.-C.L.)
- Correspondence: ; Tel.: +886-2-8792-7205
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14
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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: 3] [Impact Index Per Article: 1.0] [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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15
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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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Zhu C, Xu Z, Zhang T, Qian L, Xiao W, Wei H, Jin T, Zhou Y. Updates of Pathogenesis, Diagnostic and Therapeutic Perspectives for Ovarian Clear Cell Carcinoma. J Cancer 2021; 12:2295-2316. [PMID: 33758607 PMCID: PMC7974897 DOI: 10.7150/jca.53395] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/30/2021] [Indexed: 12/15/2022] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is a special pathological type of epithelial ovarian carcinoma (EOC) and has a high prevalence in Asia without specific molecular subtype classification. Endometriosis is a recognized precancerous lesion that carries 3-fold increased risk of OCCC. Ovarian endometrioid carcinoma, which also originates from endometriosis, shares several features with OCCC, including platinum resistance and younger age at diagnosis. Patients with OCCC have about a 2.5 to 4 times greater risk of having a venous thromboembolism (VTE) compared with other EOC, and OCCC tends to metastasize through lymphatic vesicular and peritoneal spread as opposed to hematogenous metastasis. There is only mild elevation of the conventional biomarker CA125. Staging surgery or optimal cytoreduction combined with chemotherapy is a common therapeutic strategy for OCCC. However, platinum resistance commonly portends a poor prognosis, so novel treatments are urgently needed. Targeted therapy and immunotherapy are currently being studied, including PARP, EZH2, and ATR inhibitors combined with the synthetic lethality of ARID1A-dificiency, and MAPK/PI3K/HER2, VEGF/bFGF/PDGF, HNF1β, and PD-1/PD-L1 inhibitors. Advanced stage, suboptimal cytoreduction, platinum resistance, lymph node metastasis, and VTE are major prognostic predictors for OCCC. We focus on update pathogenesis, diagnostic methods and therapeutic approaches to provide future directions for clinical diagnosis and treatment of OCCC.
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Affiliation(s)
- Chenchen Zhu
- Department of Obstetrics and Gynecology, Anhui Provincial Hospital, Anhui Medical University, Hefei, 230001, China
| | - Zhihao Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Tianjiao Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Lili Qian
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Weihua Xiao
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China.,Institute of Immunology, University of Science and Technology of China, Hefei, China
| | - Haiming Wei
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China.,Institute of Immunology, University of Science and Technology of China, Hefei, China
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Ying Zhou
- Department of Obstetrics and Gynecology, Anhui Provincial Hospital, Anhui Medical University, Hefei, 230001, China.,Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
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Hsu YH, Wang PH, Chang CM. Functional Gene Clusters in Global Pathogenesis of Clear Cell Carcinoma of the Ovary Discovered by Integrated Analysis of Transcriptomes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17113951. [PMID: 32498447 PMCID: PMC7312065 DOI: 10.3390/ijerph17113951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/23/2020] [Accepted: 05/31/2020] [Indexed: 12/17/2022]
Abstract
Clear cell carcinoma of the ovary (ovarian clear cell carcinoma (OCCC)) is one epithelial ovarian carcinoma that is known to have a poor prognosis and a tendency for being refractory to treatment due to unclear pathogenesis. Published investigations of OCCC have mainly focused only on individual genes and lack of systematic integrated research to analyze the pathogenesis of OCCC in a genome-wide perspective. Thus, we conducted an integrated analysis using transcriptome datasets from a public domain database to determine genes that may be implicated in the pathogenesis involved in OCCC carcinogenesis. We used the data obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) DataSets. We found six interactive functional gene clusters in the pathogenesis network of OCCC, including ribosomal protein, eukaryotic translation initiation factors, lactate, prostaglandin, proteasome, and insulin-like growth factor. This finding from our integrated analysis affords us a global understanding of the interactive network of OCCC pathogenesis.
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Affiliation(s)
- Yueh-Han Hsu
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei 112, Taiwan; (Y.-H.H.); (P.-H.W.)
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan
| | - Peng-Hui Wang
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei 112, Taiwan; (Y.-H.H.); (P.-H.W.)
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan
- Institute of Clinical Medicine, National Yang-Ming University, Taipei 112, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung 440, Taiwan
- Female Cancer Foundation, Taipei 104, Taiwan
| | - Chia-Ming Chang
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei 112, Taiwan; (Y.-H.H.); (P.-H.W.)
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan
- Correspondence: ; Tel.: +886-2-2875-7826; Fax: +886-2-5570-2788
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