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Tai YT, Lin WC, Ye J, Ting-Hsian Chen D, Chen KC, Yi-Te Wang D, Tan TZ, Wei LH, Yun-Ju Huang R. Spatial profiling of ovarian clear cell carcinoma reveals immune-hot features. Mod Pathol 2024:100630. [PMID: 39395637 DOI: 10.1016/j.modpat.2024.100630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/20/2024] [Accepted: 09/27/2024] [Indexed: 10/14/2024]
Abstract
Ovarian clear cell carcinoma (OCCC) has a high incidence in Asia, with frequent occurrence at an early stage, but without sufficient data on molecular stratification for high-risk patients. Recently, immune-hot features have been proposed as indicators of poor prognosis in early stage OCCC. Specific patterns of intratumoral heterogeneity associated with immune-hot features must be defined. NanoString Digital Spatial Profiling technology was used to decipher the spatial distribution of the 18-plex protein panel. ROIs were collected based on the reference hematoxylin and eosin (H&E)-stained morphology. Areas of illumination (AOIs) were defined according to the ROI segmentation using the fluorescence signals of the visualization markers pan-cytokeratin (PanCK), CD45, or DNA. Unsupervised hierarchical clustering of 595 AOIs from 407 ROIs showed that the PanCK segments expressed different combinations of immune markers, suggestive of immune mimicry. Three immune-hot clusters were identified: granzyme B high (GZMB), immune signal high (IH), and immune-like cells (IL); two immune-cold clusters were identified: fibronectin high (FN) and immune checkpoint high cells (IC). In tumor samples at FIGO stage IC1/2 experiencing recurrence, there was an increased occurrence of PanCK+ AOIs with IH and IL groups in the papillary morphology surrounded by macrophage lineage tumor-infiltrating immune cells (TIIs). In contrast, for tumor samples at FIGO stage IC3/II with recurrence, PanCK + AOIs were prevalent in the FN group, particularly those with tubulocystic morphology surrounded by lymphoid lineage non-TIIs. Our work on the spatial profiling of early stage OCCC tumors revealed that the immune mimicry of tumor cells, presence of TIIs, and morphological patterns were associated with recurrence, which switched during tumor progression.
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Affiliation(s)
- Ya-Ting Tai
- Department of Obstetrics & Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wei-Chou Lin
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Jieru Ye
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Denis Ting-Hsian Chen
- School of Medicine, College of Medicine, Keele University, Newcastle, the United Kingdom
| | - Ko-Chen Chen
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Duncan Yi-Te Wang
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore 117599
| | - Lin-Hung Wei
- Department of Obstetrics & Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ruby Yun-Ju Huang
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan; Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Obstetrics & Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077.
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Lin TY, Gu SY, Lin YH, Shih JH, Lin JH, Chou TY, Lee YC, Chang SF, Lang YD. Paclitaxel-resistance facilitates glycolytic metabolism via Hexokinase-2-regulated ABC and SLC transporter genes in ovarian clear cell carcinoma. Biomed Pharmacother 2024; 180:117452. [PMID: 39341074 DOI: 10.1016/j.biopha.2024.117452] [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: 05/13/2024] [Revised: 09/16/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
Ovarian clear cell carcinoma (OCCC) frequently develops resistance to platinum-based therapies, which is regarded as an aggressive subtype. However, metabolic changes in paclitaxel resistance remain unclear. Herein, we present the metabolic alternations of paclitaxel resistance in bioenergetic profiling in OCCC. Paclitaxel-resistant OCCC cells were developed and metabolically active with oxygen consumption rates (OCR) compared to parental cells. Metabolite profiling analysis revealed that paclitaxel-resistant OCCC cells reduced intracellular ATP and GTP influx rates, increasing the NADH/NAD+ ratio. We further demonstrated that paclitaxel-resistant OCCC cells led to characteristic alternations of metabolite levels in energy-requiring and energy-releasing steps of glycolysis and their corresponding glycolytic enzymes. Copy number alterations and RNA sequencing analysis demonstrated that ATP-binding cassette (ABC) transporters and solute carrier (SLC) transporter genes involved in glycolysis metabolism and molecular transport were enriched in paclitaxel-resistant OCCC cells. We first identified that Hexokinase 2 (HK2) expression is upregulated in paclitaxel-resistant OCCC cells to determine the quantity of glucose entering glycolysis. Utilizing proteolysis-targeting chimera (PROTAC) HK2 degraders, we also found that paclitaxel sensitivity, viability, and oxygen consumption rates under paclitaxel treatment were restored by HK2 degraders treatment, and decreased downstream expression of the ABC and SLC transporters was shown in OCCC cells. Taken together, these findings highlight the paclitaxel resistance in OCCC elucidates metabolic alternation, including ABC- and SLC- drug transporters, thereby affecting glycolysis metabolism in response to paclitaxel resistance, and HK2 may become a novel potential therapeutic target for paclitaxel resistance.
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Affiliation(s)
- Tsai-Yu Lin
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Shin-Yuan Gu
- Department of Medical Research, Taipei Medical University Hospital, Taipei, Taiwan; Department of Pathology and Precision Medicine Research Center, Taipei Medical University Hospital and Precision Health Center, Taipei Medical University, Taipei, Taiwan
| | - Yi-Hui Lin
- Department of Obstetrics and Gynecology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Jou-Ho Shih
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jiun-Han Lin
- Department of Industrial Technology, Ministry of Economic Affairs, Taipei, Taiwan; Food Industry Research and Development Institute, Hsinchu City, Taiwan
| | - Teh-Ying Chou
- Department of Pathology and Precision Medicine Research Center, Taipei Medical University Hospital and Precision Health Center, Taipei Medical University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Ching Lee
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
| | - Shwu-Fen Chang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yaw-Dong Lang
- Department of Medical Research, Taipei Medical University Hospital, Taipei, Taiwan; Department of Pathology and Precision Medicine Research Center, Taipei Medical University Hospital and Precision Health Center, Taipei Medical University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
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3
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Ma Y, Field NR, Xie T, Briscas S, Kokinogoulis EG, Skipper TS, Alghalayini A, Sarker FA, Tran N, Bowden NA, Dickson KA, Marsh DJ. Aberrant SWI/SNF Complex Members Are Predominant in Rare Ovarian Malignancies-Therapeutic Vulnerabilities in Treatment-Resistant Subtypes. Cancers (Basel) 2024; 16:3068. [PMID: 39272926 PMCID: PMC11393890 DOI: 10.3390/cancers16173068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 08/30/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024] Open
Abstract
SWI/SNF (SWItch/Sucrose Non-Fermentable) is the most frequently mutated chromatin-remodelling complex in human malignancy, with over 20% of tumours having a mutation in a SWI/SNF complex member. Mutations in specific SWI/SNF complex members are characteristic of rare chemoresistant ovarian cancer histopathological subtypes. Somatic mutations in ARID1A, encoding one of the mutually exclusive DNA-binding subunits of SWI/SNF, occur in 42-67% of ovarian clear cell carcinomas (OCCC). The concomitant somatic or germline mutation and epigenetic silencing of the mutually exclusive ATPase subunits SMARCA4 and SMARCA2, respectively, occurs in Small cell carcinoma of the ovary, hypercalcaemic type (SCCOHT), with SMARCA4 mutation reported in 69-100% of SCCOHT cases and SMARCA2 silencing seen 86-100% of the time. Somatic ARID1A mutations also occur in endometrioid ovarian cancer (EnOC), as well as in the chronic benign condition endometriosis, possibly as precursors to the development of the endometriosis-associated cancers OCCC and EnOC. Mutation of the ARID1A paralogue ARID1B can also occur in both OCCC and SCCOHT. Mutations in other SWI/SNF complex members, including SMARCA2, SMARCB1 and SMARCC1, occur rarely in either OCCC or SCCOHT. Abrogated SWI/SNF raises opportunities for pharmacological inhibition, including the use of DNA damage repair inhibitors, kinase and epigenetic inhibitors, as well as immune checkpoint blockade.
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Affiliation(s)
- Yue Ma
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Natisha R Field
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Tao Xie
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Sarina Briscas
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Emily G Kokinogoulis
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Tali S Skipper
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Amani Alghalayini
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Farhana A Sarker
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Nham Tran
- School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Nikola A Bowden
- Drug Repurposing and Medicines Research Program, Hunter Medical Research Institute, Newcastle, NSW 2289, Australia
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW 2289, Australia
| | - Kristie-Ann Dickson
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Deborah J Marsh
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
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Wijaya ST, Ngoi NY, Loh JW, Tan TZ, Lim D, Khan IS, Thian YL, Lai A, Ang BW, Tong P, Ng J, Low JJ, Ilancheran A, Lim SE, Lim YW, Tan DS. Comprehensive characterization of genomic features and clinical outcomes following targeted therapy and secondary cytoreductive surgery in OCCC: a single center experience. J Gynecol Oncol 2024; 35:e69. [PMID: 38606821 PMCID: PMC11390249 DOI: 10.3802/jgo.2024.35.e69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 11/03/2023] [Accepted: 02/11/2024] [Indexed: 04/13/2024] Open
Abstract
OBJECTIVE Ovarian clear cell carcinoma (OCCC) is associated with chemoresistance. Limited data exists regarding the efficacy of targeted therapies such as immune checkpoint inhibitors (ICI) and bevacizumab, and the role of secondary cytoreductive surgery (SCS). METHODS We retrospectively analyzed genomic features and treatment outcomes of 172 OCCC patients treated at our institution from January 2000 to May 2022. Next-generation sequencing (NGS) was performed where sufficient archival tissue was available. RESULTS 64.0% of patients were diagnosed at an early stage, and 36.0% at an advanced stage. Patients with advanced/relapsed OCCC who received platinum-based chemotherapy plus bevacizumab followed by maintenance bevacizumab had a median first-line progression-free survival (PFS) of 12.2 months, compared with 9.3 months for chemotherapy alone (hazard ratio=0.69; 95% confidence interval [CI]=0.33, 1.45). In 27 patients who received an ICI, the overall response rate was 18.5% and median duration of response was 7.4 months (95% CI=6.5, 8.3). In 17 carefully selected patients with fewer than 3 sites of relapse, median PFS was 35 months (95% CI=0, 73.5) and median overall survival was 96.8 months (95% CI=44.6, 149.0) after SCS. NGS on 58 tumors revealed common mutations in ARID1A (48.3%), PIK3CA (46.6%), and KRAS (20.7%). Pathogenic alterations in PIK3CA, FGFR2, and NBN were associated with worse survival outcomes. Median tumor mutational burden was 3.78 (range, 0-16). All 26 patients with available loss of heterozygosity (LOH) scores had LOH <16%. CONCLUSION Our study demonstrates encouraging outcomes with bevacizumab and ICI, and SCS in select relapsed OCCC patients. Prospective trials are warranted.
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Affiliation(s)
- Silvana Talisa Wijaya
- Department of Haematology-Oncology, National University Cancer Institute Singapore, Singapore
| | - Natalie Yl Ngoi
- Department of Haematology-Oncology, National University Cancer Institute Singapore, Singapore
| | - Jerold Wz Loh
- Department of Haematology-Oncology, National University Cancer Institute Singapore, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Genomics and Data Analytics Core (GeDaC), Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Diana Lim
- Department of Pathology, National University Health System, Singapore
| | - Irfan Sagir Khan
- Department of Pathology, National University Health System, Singapore
| | - Yee Liang Thian
- Department of Diagnostic Imaging, National University Health System, Singapore
| | - Alexa Lai
- Department of Haematology-Oncology, National University Cancer Institute Singapore, Singapore
| | - Bertrand Wl Ang
- Department of Diagnostic Imaging, National University Health System, Singapore
| | - Pearl Tong
- Division of Gynaecologic Oncology, Department of Obstetrics & Gynaecology, National University Hospital, Singapore
| | - Joseph Ng
- Division of Gynaecologic Oncology, Department of Obstetrics & Gynaecology, National University Hospital, Singapore
| | - Jeffrey Jh Low
- Division of Gynaecologic Oncology, Department of Obstetrics & Gynaecology, National University Hospital, Singapore
| | - Arunachalam Ilancheran
- Division of Gynaecologic Oncology, Department of Obstetrics & Gynaecology, National University Hospital, Singapore
| | - Siew Eng Lim
- Department of Haematology-Oncology, National University Cancer Institute Singapore, Singapore
| | - Yi Wan Lim
- Department of Haematology-Oncology, National University Cancer Institute Singapore, Singapore
| | - David Sp Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore.
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5
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Kamaraj US, Gautam P, Cheng T, Chin TS, Tay SK, Ho TH, Nadarajah R, Goh RCH, Wong SL, Mantoo S, Busmanis I, Li H, Le MT, Li QJ, Lim EH, Loh YH. Deciphering tumour microenvironment and elucidating the origin of cancer cells in ovarian clear cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606821. [PMID: 39149248 PMCID: PMC11326226 DOI: 10.1101/2024.08.06.606821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Ovarian clear cell carcinoma (CCC) has an East Asian preponderance. It is associated with endometriosis, a benign condition where endometrial (inner lining of the uterus) tissue is found outside the uterus and on the peritoneal surface, in the abdominal or pelvic space. CCC is relatively more resistant to conventional chemotherapy compared to other ovarian cancer subtypes and is associated with a poorer prognosis. In this study, we recruited and obtained tumour tissues from seven patients across the four stages of CCC. The tumour and the tumour microenvironment (TME) from 7 CCC patients spanning clinical stages 1-4 were transcriptionally profiled using high-resolution scRNA-seq to gain insight into CCC's biological mechanisms. Firstly, we built a scRNA-seq resource for the CCC tumour microenvironment (TME). Secondly, we identified the different cell type proportions and found high levels of immune infiltration in CCC. Thirdly, since CCC is associated with endometriosis, we compared CCC with two publicly available endometriosis scRNA-seq datasets. The CCC malignant cells showed similarities with glandular secretory and ciliated epithelial cells found in endometriosis. Finally, we determined the differences in cell-cell communication between various cell types present in CCC TME and endometriosis conditions to gain insights into the transformations in CCC.
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Affiliation(s)
- Uma S Kamaraj
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Pradeep Gautam
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Terence Cheng
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Tham Su Chin
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Sun Kuie Tay
- Department of Obstetrics & Gynaecology, Singapore General Hospital, Outram Road, Singapore 169608
| | - Tew Hong Ho
- Department of Obstetrics & Gynaecology, Singapore General Hospital, Outram Road, Singapore 169608
| | - Ravichandran Nadarajah
- Department of Obstetrics & Gynaecology, Singapore General Hospital, Outram Road, Singapore 169608
| | - Ronald Chin Hong Goh
- Department of Anatomical Pathology, Singapore General Hospital, Academia, College Road, Singapore 169856
| | - Shing Lih Wong
- Department of Anatomical Pathology, Singapore General Hospital, Academia, College Road, Singapore 169856
| | - Sangeeta Mantoo
- Department of Anatomical Pathology, Singapore General Hospital, Academia, College Road, Singapore 169856
| | - Inny Busmanis
- Department of Anatomical Pathology, Singapore General Hospital, Academia, College Road, Singapore 169856
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Minh Tn Le
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Qi-Jing Li
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Elaine Hsuen Lim
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore 168583
| | - Yuin-Han Loh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
- Department of Physiology, NUS Yong Loo Lin School of Medicine, 2 Medical Drive, MD9, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- NUS Graduate School's Integrative Sciences and Engineering Programme, National University of Singapore, 28 Medical Drive, Singapore, Singapore
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6
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Chen C, Ren W, Pei L, Sun J, Bai T. Status and development of research on clear cell carcinoma of the ovary-a visualization-based bibliometric analysis. Transl Cancer Res 2024; 13:2950-2970. [PMID: 38988907 PMCID: PMC11231787 DOI: 10.21037/tcr-23-2351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/24/2024] [Indexed: 07/12/2024]
Abstract
Background Clear cell carcinoma of the ovary (CCCO) is a relatively rare type of epithelial ovarian cancer (EOC) that has unique biological characteristics and clinical features. Researchers have paid less attention to this disease than to other types of EOCs. However, in recent years, research in this area has still progressed. In this paper, a bibliometric analysis is used to integrate and analyse the literature in the field of CCCO in the past 20 years to determine research development, better understand the current status of research, and provide a reference for future study directions in this field. Methods With CCCO as the research subject, relevant publications indexed in the Web of Science (WOS) core dataset from September 2003 to September 2023 were retrieved. After screening the publications, we used EXCEL, VOSviewer, CiteSpace, Charticulator, Gephi, OriginPro and other tools to perform in-depth analyses of and to visualize the data. Results Through a comprehensive analysis of the literature in this field, we found that research on CCCO experienced a relatively rapid increase in 2006 and is now in a period of relatively high fluctuation. The quality of the literature in this field is generally high. In this field, countries in East Asia and North America play core roles, with Japan accounting for the most studies. A stable research group has been formed in this field, and extensive collaboration has occurred among the various research groups. In the past 20 years, basic research and clinical research in the field of CCCO have developed together, and a healthy development model in which basic and clinical research promote each other has formed. Research in this field has been continuously developed from a preliminary understanding of clinical features to in-depth explorations of the pathogenesis and the continuous optimization of treatment methods. The key molecular events in the pathogenesis and development of this disease and the application of novel antitumour drugs for this disease are the current research focuses and the future development direction in this field. Conclusions Research on CCCO has progressed significantly in the past 20 years, but there are still many important issues regarding its pathogenesis and treatment that need to be addressed, and therefore, more research in this area should be conducted in the future. The study of key molecular events and the use of novel antitumour drugs are future development directions in this field.
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Affiliation(s)
- Chao Chen
- Department of Gynecology and Obstetrics, General Hospital of Northern Theater, Shenyang, China
| | - Wei Ren
- Department of Gynecology and Obstetrics, General Hospital of Northern Theater, Shenyang, China
| | - Lipeng Pei
- Department of Gynecology and Obstetrics, General Hospital of Northern Theater, Shenyang, China
| | - Jingli Sun
- Department of Gynecology and Obstetrics, General Hospital of Northern Theater, Shenyang, China
| | - Tianmei Bai
- Department of Gynecology and Obstetrics, General Hospital of Northern Theater, Shenyang, China
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Yue L, Gong T, Jiang W, Qian L, Gong W, Sun Y, Cai X, Xu H, Liu F, Wang H, Li S, Zhu Y, Zheng Z, Wu Q, Guo T. Proteomic profiling of ovarian clear cell carcinomas identifies prognostic biomarkers for chemotherapy. Proteomics 2024; 24:e2300242. [PMID: 38171885 DOI: 10.1002/pmic.202300242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
Clear cell ovarian carcinoma (CCOC) is a relatively rare subtype of ovarian cancer (OC) with high degree of resistance to standard chemotherapy. Little is known about the underlying molecular mechanisms, and it remains a challenge to predict its prognosis after chemotherapy. Here, we first analyzed the proteome of 35 formalin-fixed paraffin-embedded (FFPE) CCOC tissue specimens from a cohort of 32 patients with CCOC (H1 cohort) and characterized 8697 proteins using data-independent acquisition mass spectrometry (DIA-MS). We then performed proteomic analysis of 28 fresh frozen (FF) CCOC tissue specimens from an independent cohort of 24 patients with CCOC (H2 cohort), leading to the identification of 9409 proteins with DIA-MS. After bioinformatics analysis, we narrowed our focus to 15 proteins significantly correlated with the recurrence free survival (RFS) in both cohorts. These proteins are mainly involved in DNA damage response, extracellular matrix (ECM), and mitochondrial metabolism. Parallel reaction monitoring (PRM)-MS was adopted to validate the prognostic potential of the 15 proteins in the H1 cohort and an independent confirmation cohort (H3 cohort). Interferon-inducible transmembrane protein 1 (IFITM1) was observed as a robust prognostic marker for CCOC in both PRM data and immunohistochemistry (IHC) data. Taken together, this study presents a CCOC proteomic data resource and a single promising protein, IFITM1, which could potentially predict the recurrence and survival of CCOC.
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Affiliation(s)
- Liang Yue
- School of Life Sciences, Fudan University, Shanghai, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Tingting Gong
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University
| | - Wenhao Jiang
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Liujia Qian
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Wangang Gong
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Yaoting Sun
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Xue Cai
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Heli Xu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Fanghua Liu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - He Wang
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Sainan Li
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China
| | - Yi Zhu
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Zhiguo Zheng
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Qijun Wu
- Department of Clinical Epidemiology, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
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Collins KE, Wang X, Klymenko Y, Davis NB, Martinez MC, Zhang C, So K, Buechlein A, Rusch DB, Creighton CJ, Hawkins SM. Transcriptomic analyses of ovarian clear-cell carcinoma with concurrent endometriosis. Front Endocrinol (Lausanne) 2023; 14:1162786. [PMID: 37621654 PMCID: PMC10445169 DOI: 10.3389/fendo.2023.1162786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/17/2023] [Indexed: 08/26/2023] Open
Abstract
Introduction Endometriosis, a benign inflammatory disease whereby endometrial-like tissue grows outside the uterus, is a risk factor for endometriosis-associated ovarian cancers. In particular, ovarian endometriomas, cystic lesions of deeply invasive endometriosis, are considered the precursor lesion for ovarian clear-cell carcinoma (OCCC). Methods To explore this transcriptomic landscape, OCCC from women with pathology-proven concurrent endometriosis (n = 4) were compared to benign endometriomas (n = 4) by bulk RNA and small-RNA sequencing. Results Analysis of protein-coding genes identified 2449 upregulated and 3131 downregulated protein-coding genes (DESeq2, P< 0.05, log2 fold-change > |1|) in OCCC with concurrent endometriosis compared to endometriomas. Gene set enrichment analysis showed upregulation of pathways involved in cell cycle regulation and DNA replication and downregulation of pathways involved in cytokine receptor signaling and matrisome. Comparison of pathway activation scores between the clinical samples and publicly-available datasets for OCCC cell lines revealed significant molecular similarities between OCCC with concurrent endometriosis and OVTOKO, OVISE, RMG1, OVMANA, TOV21G, IGROV1, and JHOC5 cell lines. Analysis of miRNAs revealed 64 upregulated and 61 downregulated mature miRNA molecules (DESeq2, P< 0.05, log2 fold-change > |1|). MiR-10a-5p represented over 21% of the miRNA molecules in OCCC with endometriosis and was significantly upregulated (NGS: log2fold change = 4.37, P = 2.43e-18; QPCR: 8.1-fold change, P< 0.05). Correlation between miR-10a expression level in OCCC cell lines and IC50 (50% inhibitory concentration) of carboplatin in vitro revealed a positive correlation (R2 = 0.93). MiR-10a overexpression in vitro resulted in a significant decrease in proliferation (n = 6; P< 0.05) compared to transfection with a non-targeting control miRNA. Similarly, the cell-cycle analysis revealed a significant shift in cells from S and G2 to G1 (n = 6; P< 0.0001). Bioinformatic analysis predicted that miR-10a-5p target genes that were downregulated in OCCC with endometriosis were involved in receptor signaling pathways, proliferation, and cell cycle progression. MiR-10a overexpression in vitro was correlated with decreased expression of predicted miR-10a target genes critical for proliferation, cell-cycle regulation, and cell survival including [SERPINE1 (3-fold downregulated; P< 0.05), CDK6 (2.4-fold downregulated; P< 0.05), and RAP2A (2-3-fold downregulated; P< 0.05)]. Discussion These studies in OCCC suggest that miR-10a-5p is an impactful, potentially oncogenic molecule, which warrants further studies.
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Affiliation(s)
- Kaitlyn E. Collins
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Xiyin Wang
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, United States
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Yuliya Klymenko
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Noah B. Davis
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Maria C. Martinez
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Chi Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Kaman So
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Aaron Buechlein
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, United States
| | - Douglas B. Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, United States
| | - Chad J. Creighton
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Shannon M. Hawkins
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, United States
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9
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Spagnolo E, Martinez A, Mascarós-Martínez A, Marí-Alexandre J, Carbonell M, González-Cantó E, Pena-Burgos EM, Mc Cormack BA, Tomás-Pérez S, Gilabert-Estellés J, López-Carrasco A, Hidalgo P, Ángeles MA, Redondo A, Gallego A, Hernández A. Evaluation of Immune Infiltrates in Ovarian Endometriosis and Endometriosis-Associated Ovarian Cancer: Relationship with Histological and Clinical Features. Int J Mol Sci 2023; 24:12083. [PMID: 37569458 PMCID: PMC10418839 DOI: 10.3390/ijms241512083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND the association between ovarian endometriosis (OE) and endometriosis-associated ovarian cancer (EAOC) is extensively documented, and misfunction of the immune system might be involved. The primary objective of this study was to identify and compare the spatial distribution of tumour-infiltrating lymphocytes (TILs) and tumour-associated macrophages (TAMs) in OE and EAOC. Secondary objectives included the analysis of the relationship between immunosuppressive populations and T-cell exhaustion markers in both groups. METHODS TILs (CD3, CD4, and CD8) and macrophages (CD163) were assessed by immunochemistry. Exhaustion markers (PD-1, TIM3, CD39, and FOXP3) and their relationship with tumour-associated macrophages (CD163) were assessed by immunofluorescence on paraffin-embedded samples from n = 43 OE and n = 54 EAOC patients. RESULTS we observed a predominantly intraepithelial CD3+ distribution in OE but both an intraepithelial and stromal pattern in EAOC (p < 0.001). TILs were more abundant in OE (p < 0.001), but higher TILs significantly correlated with a longer overall survival and disease-free survival in EAOC (p < 0.05). CD39 and FOXP3 significantly correlated with each other and CD163 (p < 0.05) at the epithelial level in moderate/intense CD4 EAOC, whereas in moderate/intense CD8+, PD-1+ and TIM3+ significantly correlated (p = 0.009). Finally, T-cell exhaustion markers FOXP3-CD39 were decreased and PD-1-TIM3 were significantly increased in EAOC (p < 0.05). CONCLUSIONS the dysregulation of TILs, TAMs, and T-cell exhaustion might play a role in the malignization of OE to EAOC.
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Affiliation(s)
- Emanuela Spagnolo
- Department of Gynecology, La Paz University Hospital, 28046 Madrid, Spain; (E.S.); (M.C.); (A.L.-C.); (A.H.)
- Research Institute “IdiPaz”, La Paz University Hospital, 28046 Madrid, Spain
| | - Alejandra Martinez
- Department of Surgical Oncology, Institut Claudius Regaud-Institut Universitaire du Cancer du Toulouse (IUCT) Oncopole, 31059 Toulouse, France; (A.M.); (M.A.Á.)
- Centre de Recherches en Cancérologie de Toulouse, UMR 1037 INSERM, 31100 Toulouse, France
| | | | - Josep Marí-Alexandre
- Department of Pathology, General University Hospital of Valencia, 46014 Valencia, Spain;
- Research Laboratory in Biomarkers in Reproduction, Obstetrics and Gynecology, Research Foundation, General University Hospital of Valencia, 46014 Valencia, Spain; (E.G.-C.); (B.A.M.C.); (S.T.-P.); (J.G.-E.)
| | - María Carbonell
- Department of Gynecology, La Paz University Hospital, 28046 Madrid, Spain; (E.S.); (M.C.); (A.L.-C.); (A.H.)
- Research Institute “IdiPaz”, La Paz University Hospital, 28046 Madrid, Spain
| | - Eva González-Cantó
- Research Laboratory in Biomarkers in Reproduction, Obstetrics and Gynecology, Research Foundation, General University Hospital of Valencia, 46014 Valencia, Spain; (E.G.-C.); (B.A.M.C.); (S.T.-P.); (J.G.-E.)
| | | | - Bárbara Andrea Mc Cormack
- Research Laboratory in Biomarkers in Reproduction, Obstetrics and Gynecology, Research Foundation, General University Hospital of Valencia, 46014 Valencia, Spain; (E.G.-C.); (B.A.M.C.); (S.T.-P.); (J.G.-E.)
| | - Sarai Tomás-Pérez
- Research Laboratory in Biomarkers in Reproduction, Obstetrics and Gynecology, Research Foundation, General University Hospital of Valencia, 46014 Valencia, Spain; (E.G.-C.); (B.A.M.C.); (S.T.-P.); (J.G.-E.)
| | - Juan Gilabert-Estellés
- Research Laboratory in Biomarkers in Reproduction, Obstetrics and Gynecology, Research Foundation, General University Hospital of Valencia, 46014 Valencia, Spain; (E.G.-C.); (B.A.M.C.); (S.T.-P.); (J.G.-E.)
- Department of Obstetrics and Gynecology, General University Hospital of Valencia, 46014 Valencia, Spain
- Department of Paediatrics, Obstetrics and Gynaecology, University of Valencia, 46010 Valencia, Spain
| | - Ana López-Carrasco
- Department of Gynecology, La Paz University Hospital, 28046 Madrid, Spain; (E.S.); (M.C.); (A.L.-C.); (A.H.)
- Research Institute “IdiPaz”, La Paz University Hospital, 28046 Madrid, Spain
| | - Paula Hidalgo
- Department of Radiology, La Paz University Hospital, 28046 Madrid, Spain;
| | - Martina Aida Ángeles
- Department of Surgical Oncology, Institut Claudius Regaud-Institut Universitaire du Cancer du Toulouse (IUCT) Oncopole, 31059 Toulouse, France; (A.M.); (M.A.Á.)
| | - Andrés Redondo
- Department of Medical Oncology, La Paz University Hospital, 28046 Madrid, Spain; (A.R.); (A.G.)
| | - Alejandro Gallego
- Department of Medical Oncology, La Paz University Hospital, 28046 Madrid, Spain; (A.R.); (A.G.)
| | - Alicia Hernández
- Department of Gynecology, La Paz University Hospital, 28046 Madrid, Spain; (E.S.); (M.C.); (A.L.-C.); (A.H.)
- Research Institute “IdiPaz”, La Paz University Hospital, 28046 Madrid, Spain
- Department of Obstetrics and Gynaecology, Universidad Autónoma Madrid, 28049 Madrid, Spain
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10
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Huang RYJ, Huang KJ, Chen KC, Hsiao SM, Tan TZ, Wu CJ, Hsu C, Chang WC, Pan CY, Sheu BC, Wei LH. Immune-Hot tumor features associated with recurrence in early-stage ovarian clear cell carcinoma. Int J Cancer 2023; 152:2174-2185. [PMID: 36629283 DOI: 10.1002/ijc.34428] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/03/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023]
Abstract
Ovarian clear cell carcinoma (OCCC) is a distinct histotype of ovarian cancer, which usually presages a worse prognosis upon recurrence. Identifying patients at risk for relapse is an unmet need to improve outcomes. A retrospective cohort analysis of 195 early-stage OCCC patients diagnosed between January 2011 and December 2019 at National Taiwan University Hospital was conducted to identify prognostic factors for recurrence, progression-free survival (PFS) and overall survival (OS). Molecular profiling of tumors was performed in a case-controlled cohort matched for adjuvant therapy for biomarker discovery. Multivariate Cox proportional hazard model revealed that paclitaxel-based chemotherapy was associated with better PFS than nonpaclitaxel chemotherapy (HR = 0.19, P = .006). The addition of bevacizumab was associated with better PFS, compared to no bevacizumab (HR = 0.09, P = .02). Neither showed significant improvement in OS. Recurrence is associated with an Immune-Hot tumor feature (P = .03), the CTLA-4-high subtype (P = .01) and increased infiltration of immune cells in general. The Immune-Hot feature (HR = 3.39, P = .005) and the CTLA-4-high subtype (HR = 2.13, P = .059) were associated with worse PFS. Immune-Hot tumor features could prognosticate recurrence in early-stage OCCC.
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Affiliation(s)
- Ruby Yun-Ju Huang
- School of Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Kuan-Ju Huang
- Department of Obstetrics and Gynecology, National Taiwan University Hospital & National Taiwan University College of Medicine, Taipei, Taiwan.,National Taiwan University Hospital Yunlin Branch, Douliu City, Taiwan
| | - Ko-Chen Chen
- School of Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Sheng-Mou Hsiao
- Department of Obstetrics and Gynecology, Far Eastern Memorial Hospital, New Taipei, Taiwan.,Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan, Taiwan
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore
| | - Chin-Jui Wu
- National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan
| | - Ching Hsu
- Department of Obstetrics and Gynecology, National Taiwan University Hospital & National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wen-Chun Chang
- Department of Obstetrics and Gynecology, National Taiwan University Hospital & National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chen-Yu Pan
- Department of Obstetrics and Gynecology, National Taiwan University Hospital & National Taiwan University College of Medicine, Taipei, Taiwan
| | - Bor-Ching Sheu
- Department of Obstetrics and Gynecology, National Taiwan University Hospital & National Taiwan University College of Medicine, Taipei, Taiwan
| | - Lin-Hung Wei
- Department of Obstetrics and Gynecology, National Taiwan University Hospital & National Taiwan University College of Medicine, Taipei, Taiwan
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11
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Chien W, Tyner JW, Gery S, Zheng Y, Li LY, Gopinatha Pillai MS, Nam C, Bhowmick NA, Lin DC, Koeffler HP. Treatment for ovarian clear cell carcinoma with combined inhibition of WEE1 and ATR. J Ovarian Res 2023; 16:80. [PMID: 37087441 PMCID: PMC10122390 DOI: 10.1186/s13048-023-01160-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 04/10/2023] [Indexed: 04/24/2023] Open
Abstract
BACKGROUND Standard platinum-based therapy for ovarian cancer is inefficient against ovarian clear cell carcinoma (OCCC). OCCC is a distinct subtype of epithelial ovarian cancer. OCCC constitutes 25% of ovarian cancers in East Asia (Japan, Korea, China, Singapore) and 6-10% in Europe and North America. The cancer is characterized by frequent inactivation of ARID1A and 10% of cases of endometriosis progression to OCCC. The aim of this study was to identify drugs that are either FDA-approved or in clinical trials for the treatment of OCCC. RESULTS High throughput screening of 166 compounds that are either FDA-approved, in clinical trials or are in pre-clinical studies identified several cytotoxic compounds against OCCC. ARID1A knockdown cells were more sensitive to inhibitors of either mTOR (PP242), dual mTOR/PI3K (GDC0941), ATR (AZD6738) or MDM2 (RG7388) compared to control cells. Also, compounds targeting BH3 domain (AZD4320) and SRC (AZD0530) displayed preferential cytotoxicity against ARID1A mutant cell lines. In addition, WEE1 inhibitor (AZD1775) showed broad cytotoxicity toward OCCC cell lines, irrespective of ARID1A status. CONCLUSIONS In a selection of 166 compounds we showed that inhibitors of ATR and WEE1 were cytotoxic against a panel of OCCC cell lines. These two drugs are already in other clinical trials, making them ideal candidates for treatment of OCCC.
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Affiliation(s)
- Wenwen Chien
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA, 90048, USA.
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Oregon Health and Science University, 2720 S.W. Moody Avenue, Portland, OR, 97201, USA
| | - Sigal Gery
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA, 90048, USA
| | - Yueyuan Zheng
- Clinical Big Data Research Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, 518107, P. R. China
| | - Li-Yan Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, Guandong Province, P. R. China
| | - Mohan Shankar Gopinatha Pillai
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA, 90048, USA
| | - Chehyun Nam
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Neil A Bhowmick
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA, 90048, USA
| | - De-Chen Lin
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - H Phillip Koeffler
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA, 90048, USA
- Department of Hematology-Oncology, National University Cancer Institute of Singapore, National University Hospital, Singapore, 119074, Singapore
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12
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Guo N, Yang A, Farooq FB, Kalaria S, Moss E, DeVorkin L, Lesperance M, Bénard F, Wilson D, Tinker AV, Nathoo FS, Hamilton PT, Lum JJ. CD8 + T cell infiltration is associated with improved survival and negatively correlates with hypoxia in clear cell ovarian cancer. Sci Rep 2023; 13:6530. [PMID: 37085560 PMCID: PMC10121667 DOI: 10.1038/s41598-023-30655-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 02/27/2023] [Indexed: 04/23/2023] Open
Abstract
Unlike other histological types of epithelial ovarian carcinoma, clear cell ovarian carcinoma (CCOC) has poor response to therapy. In many other carcinomas, expression of the hypoxia-related enzyme Carbonic anhydrase IX (CAIX) by cancer cells is associated with poor prognosis, while the presence of CD8 + tumor-infiltrating lymphocytes (TIL) is positively prognostic. We employed [18F]EF5-PET/CT imaging, transcriptome profiling, and spatially-resolved histological analysis to evaluate relationships between CAIX, CD8, and survival in CCOC. Tissue microarrays (TMAs) were evaluated for 218 cases in the Canadian COEUR study. Non-spatial relationships between CAIX and CD8 were investigated using Spearman rank correlation, negative binomial regression and gene set enrichment analysis. Spatial relationships at the cell level were investigated using the cross K-function. Survival analysis was used to assess the relationship of CAIX and CD8 with patient survival for 154 cases. CD8 + T cell infiltration positively predicted survival with estimated hazard ratio 0.974 (95% CI 0.950, 1000). The negative binomial regression analysis found a strong TMA effect (p-value < 0.0001). It also indicated a negative association between CD8 and CAIX overall (p-value = 0.0171) and in stroma (p-value = 0.0050) but not in tumor (p-value = 0.173). Examination of the spatial association between the locations of CD8 + T cells and CAIX cells found a significant amount of heterogeneity in the first TMA, while in the second TMA there was a clear signal indicating negative spatial association in stromal regions. These results suggest that hypoxia may contribute to immune exclusion, primarily mediated by effects in stroma.
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Affiliation(s)
- Nancy Guo
- Department of Mathematics and Statistics, University of Victoria, STN CSC, PO BOX 1700, Victoria, BC, V8W 2Y2, Canada
| | - Aijun Yang
- Department of Mathematics and Statistics, University of Victoria, STN CSC, PO BOX 1700, Victoria, BC, V8W 2Y2, Canada
| | | | - Shreena Kalaria
- Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, 2410 Lee Avenue, 3rd Floor, Victoria, BC, V8R 6V5, Canada
| | - Elena Moss
- Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, 2410 Lee Avenue, 3rd Floor, Victoria, BC, V8R 6V5, Canada
| | - Lindsay DeVorkin
- Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, 2410 Lee Avenue, 3rd Floor, Victoria, BC, V8R 6V5, Canada
| | - Mary Lesperance
- Department of Mathematics and Statistics, University of Victoria, STN CSC, PO BOX 1700, Victoria, BC, V8W 2Y2, Canada
| | - François Bénard
- Department of Radiology, University of British Columbia, Vancouver, Canada
| | - Don Wilson
- Functional Imaging, BC Cancer Vancouver, Vancouver, Canada
| | - Anna V Tinker
- Medical Oncology, BC Cancer Vancouver, Vancouver, Canada
| | - Farouk S Nathoo
- Department of Mathematics and Statistics, University of Victoria, STN CSC, PO BOX 1700, Victoria, BC, V8W 2Y2, Canada.
| | - Phineas T Hamilton
- Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, 2410 Lee Avenue, 3rd Floor, Victoria, BC, V8R 6V5, Canada.
| | - Julian J Lum
- Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, 2410 Lee Avenue, 3rd Floor, Victoria, BC, V8R 6V5, Canada.
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada.
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13
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Lansbergen MF, Khelil M, Etten-Jamaludin FSV, Bijlsma MF, van Laarhoven HWM. Poor-prognosis molecular subtypes in adenocarcinomas of pancreato-biliary and gynecological origin: A systematic review. Crit Rev Oncol Hematol 2023; 185:103982. [PMID: 37004743 DOI: 10.1016/j.critrevonc.2023.103982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023] Open
Abstract
Pancreato-biliary and gynecological adenocarcinomas need better tools to predict clinical outcome. Potential prognostic mesenchymal(-like) transcriptome-based subtypes have been identified in these cancers. In this systematic review, we include studies into molecular subtyping and summarize biological and clinical features of the subtypes within and across sites of origin, searching for suggestions to improve classification and prognostication. PubMed and Embase were searched for original research articles describing potential mesenchymal(-like) mRNA-based subtypes in pancreato-biliary or gynecological adenocarcinomas. Studies limited to supervised clustering were excluded. Fourty-four studies, discussing cholangiocarcinomas, gallbladder, ampullary, pancreatic, ovarian, and endometrial adenocarcinomas were included. There was overlap in molecular and clinical features in mesenchymal(-like) subtypes across all adenocarcinomas. Approaches including microdissection were more likely to identify prognosis-associating subtypes. To conclude, molecular subtypes in pancreato-biliary and gynecological adenocarcinomas share biological and clinical characteristics. Furthermore, separation of stromal and epithelial signals should be applied in future studies into biliary and gynecological adenocarcinomas.
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Affiliation(s)
- Marjolein F Lansbergen
- Amsterdam UMC location University of Amsterdam, Medical Oncology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam UMC location University of Amsterdam, Center for Experimental Molecular Medicine, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, the Netherlands.
| | - Maryam Khelil
- University of Amsterdam, Spui 21, 1012 WX Amsterdam, the Netherlands
| | - Faridi S van Etten-Jamaludin
- Amsterdam UMC location University of Amsterdam, Research Support Medical Library, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Maarten F Bijlsma
- Amsterdam UMC location University of Amsterdam, Center for Experimental Molecular Medicine, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, the Netherlands; Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Hanneke W M van Laarhoven
- Amsterdam UMC location University of Amsterdam, Medical Oncology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, the Netherlands
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14
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Hollis RL. Molecular characteristics and clinical behaviour of epithelial ovarian cancers. Cancer Lett 2023; 555:216057. [PMID: 36627048 DOI: 10.1016/j.canlet.2023.216057] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
Ovarian carcinoma (OC) is an umbrella term for multiple distinct diseases (histotypes), each with their own developmental origins, clinical behaviour and molecular profile. Accordingly, OC management is progressing away from a one-size-fits all approach, toward more molecularly-driven, histotype-specific management strategies. Our knowledge of driver events in high grade serous OC, the most common histotype, has led to major advances in treatments, including PARP inhibitor use. However, these agents are not suitable for all patients, most notably for many of those with rare OC histotypes. Identification of additional targeted therapeutic strategies will require a detailed understanding of the molecular landscape in each OC histotype. Until recently, tumour profiling studies in rare histotypes were sparse; however, significant advances have been made over the last decade. In particular, reports of genomic characterisation in endometrioid, clear cell, mucinous and low grade serous OC have significantly expanded our understanding of mutational events in these tumour types. Nonetheless, substantial knowledge gaps remain. This review summarises our current understanding of each histotype, highlighting recent advances in these unique diseases and outlining immediate research priorities for accelerating progress toward improving patient outcomes.
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Affiliation(s)
- Robert L Hollis
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, UK.
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15
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Fonseca MAS, Haro M, Wright KN, Lin X, Abbasi F, Sun J, Hernandez L, Orr NL, Hong J, Choi-Kuaea Y, Maluf HM, Balzer BL, Fishburn A, Hickey R, Cass I, Goodridge HS, Truong M, Wang Y, Pisarska MD, Dinh HQ, El-Naggar A, Huntsman DG, Anglesio MS, Goodman MT, Medeiros F, Siedhoff M, Lawrenson K. Single-cell transcriptomic analysis of endometriosis. Nat Genet 2023; 55:255-267. [PMID: 36624343 PMCID: PMC10950360 DOI: 10.1038/s41588-022-01254-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/28/2022] [Indexed: 01/11/2023]
Abstract
Endometriosis is a common condition in women that causes chronic pain and infertility and is associated with an elevated risk of ovarian cancer. We profiled transcriptomes of >370,000 individual cells from endometriomas (n = 8), endometriosis (n = 28), eutopic endometrium (n = 10), unaffected ovary (n = 4) and endometriosis-free peritoneum (n = 4), generating a cellular atlas of endometrial-type epithelial cells, stromal cells and microenvironmental cell populations across tissue sites. Cellular and molecular signatures of endometrial-type epithelium and stroma differed across tissue types, suggesting a role for cellular restructuring and transcriptional reprogramming in the disease. Epithelium, stroma and proximal mesothelial cells of endometriomas showed dysregulation of pro-inflammatory pathways and upregulation of complement proteins. Somatic ARID1A mutation in epithelial cells was associated with upregulation of pro-angiogenic and pro-lymphangiogenic factors and remodeling of the endothelial cell compartment, with enrichment of lymphatic endothelial cells. Finally, signatures of ciliated epithelial cells were enriched in ovarian cancers, reinforcing epidemiologic associations between these two diseases.
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Affiliation(s)
- Marcos A S Fonseca
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Marcela Haro
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kelly N Wright
- Division of Minimally Invasive Gynecologic Surgery, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xianzhi Lin
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Forough Abbasi
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jennifer Sun
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lourdes Hernandez
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Natasha L Orr
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
| | - Jooyoon Hong
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
| | - Yunhee Choi-Kuaea
- Cancer Prevention and Control Program, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Horacio M Maluf
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bonnie L Balzer
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Aaron Fishburn
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ryan Hickey
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ilana Cass
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Obstetrics and Gynecology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Helen S Goodridge
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mireille Truong
- Division of Minimally Invasive Gynecologic Surgery, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yemin Wang
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Margareta D Pisarska
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Huy Q Dinh
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Amal El-Naggar
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Pathology, Faculty of Medicine, Menoufia University, Menoufia Governorate, Egypt
| | - David G Huntsman
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Michael S Anglesio
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
- British Columbia's Gynecological Cancer Research (OVCARE) Program, University of British Columbia, Vancouver General Hospital, and BC Cancer, Vancouver, British Columbia, Canada
| | - Marc T Goodman
- Cancer Prevention and Control Program, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Fabiola Medeiros
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Matthew Siedhoff
- Division of Minimally Invasive Gynecologic Surgery, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Cancer Prevention and Control Program, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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16
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Wang CK, Chen TJ, Tan GY, Chang FP, Sridharan S, Yu CHA, Chang YH, Chen YJ, Cheng LT, Hwang-Verslues WW. MEX3A Mediates p53 Degradation to Suppress Ferroptosis and Facilitate Ovarian Cancer Tumorigenesis. Cancer Res 2023; 83:251-263. [PMID: 36354374 PMCID: PMC9845988 DOI: 10.1158/0008-5472.can-22-1159] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/24/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022]
Abstract
Epithelial ovarian cancer is a highly heterogeneous and malignant female cancer with an overall low survival rate. Mutations in p53 are prevalent in the major ovarian cancer histotype, high-grade serous ovarian carcinoma (HGSOC), while p53 mutations are much less frequent in other ovarian cancer subtypes, particularly in ovarian clear cell carcinoma (OCCC). Advanced stage OCCC with wild-type (WT) p53 has a worse prognosis and increased drug resistance, metastasis, and recurrence than HGSOC. The mechanisms responsible for driving the aggressiveness of WT p53-expressing ovarian cancer remain poorly understood. Here, we found that upregulation of MEX3A, a dual-function protein containing a RING finger domain and an RNA-binding domain, was critical for tumorigenesis in WT p53-expressing ovarian cancer. MEX3A overexpression enhanced the growth and clonogenicity of OCCC cell lines. In contrast, depletion of MEX3A in OCCC cells, as well as ovarian teratocarcinoma cells, reduced cell survival and proliferative ability. MEX3A depletion also inhibited tumor growth and prolonged survival in orthotopic xenograft models. MEX3A depletion did not alter p53 mRNA level but did increase p53 protein stability. MEX3A-mediated p53 protein degradation was crucial to suppress ferroptosis and enhance tumorigenesis. Consistently, p53 knockdown reversed the effects of MEX3A depletion. Together, our observations identified MEX3A as an important oncogenic factor promoting tumorigenesis in ovarian cancer cells expressing WT p53. SIGNIFICANCE Degradation of p53 mediated by MEX3A drives ovarian cancer growth by circumventing p53 tumor suppressive functions, suggesting targeting MEX3A as a potential strategy for treating of ovarian cancer expressing WT p53.
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Affiliation(s)
- Cheng-Kai Wang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Tzu-Jou Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Grace Y.T. Tan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Fang-Pei Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | | | - Yen-Hou Chang
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Jen Chen
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Li-Tzu Cheng
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Wendy W. Hwang-Verslues
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Corresponding Author: Wendy W. Hwang-Verslues, Genomics Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei 115, Taiwan. Phone: +886-2-2787-1246; Fax: +886-2-2789-9924; E-mail:
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17
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Ji JX, Cochrane DR, Negri GL, Colborne S, Spencer Miko SE, Hoang LN, Farnell D, Tessier-Cloutier B, Huvila J, Thompson E, Leung S, Chiu D, Chow C, Ta M, Köbel M, Feil L, Anglesio M, Goode EL, Bolton K, Morin GB, Huntsman DG. The proteome of clear cell ovarian carcinoma. J Pathol 2022; 258:325-338. [PMID: 36031730 PMCID: PMC9649886 DOI: 10.1002/path.6006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/05/2022] [Accepted: 08/26/2022] [Indexed: 01/19/2023]
Abstract
Clear cell ovarian carcinoma (CCOC) is the second most common subtype of epithelial ovarian carcinoma. Late-stage CCOC is not responsive to gold-standard chemotherapy and results in suboptimal outcomes for patients. In-depth molecular insight is urgently needed to stratify the disease and drive therapeutic development. We conducted global proteomics for 192 cases of CCOC and compared these with other epithelial ovarian carcinoma subtypes. Our results showed distinct proteomic differences in CCOC compared with other epithelial ovarian cancer subtypes including alterations in lipid and purine metabolism pathways. Furthermore, we report potential clinically significant proteomic subgroups within CCOC, suggesting the biologic plausibility of stratified treatment for this cancer. Taken together, our results provide a comprehensive understanding of the CCOC proteomic landscape to facilitate future understanding and research of this disease. © 2022 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Jennifer X Ji
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Dawn R Cochrane
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Shane Colborne
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Sandra E Spencer Miko
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Lynn N Hoang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - David Farnell
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jutta Huvila
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
- Department of Biomedicine, University of Turku, Turku, Finland
| | - Emily Thompson
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Samuel Leung
- Genetic Pathology Evaluation Center, Vancouver, BC, Canada
| | - Derek Chiu
- Genetic Pathology Evaluation Center, Vancouver, BC, Canada
| | - Christine Chow
- Genetic Pathology Evaluation Center, Vancouver, BC, Canada
| | - Monica Ta
- Genetic Pathology Evaluation Center, Vancouver, BC, Canada
| | - Martin Köbel
- Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Lucas Feil
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Michael Anglesio
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Ellen L Goode
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Kelly Bolton
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
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18
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Bolton KL, Chen D, Corona de la Fuente R, Fu Z, Murali R, Köbel M, Tazi Y, Cunningham JM, Chan IC, Wiley BJ, Moukarzel LA, Winham SJ, Armasu SM, Lester J, Elishaev E, Laslavic A, Kennedy CJ, Piskorz A, Sekowska M, Brand AH, Chiew YE, Pharoah P, Elias KM, Drapkin R, Churchman M, Gourley C, DeFazio A, Karlan B, Brenton JD, Weigelt B, Anglesio MS, Huntsman D, Gayther S, Konner J, Modugno F, Lawrenson K, Goode EL, Papaemmanuil E. Molecular Subclasses of Clear Cell Ovarian Carcinoma and Their Impact on Disease Behavior and Outcomes. Clin Cancer Res 2022; 28:4947-4956. [PMID: 35816189 PMCID: PMC9777703 DOI: 10.1158/1078-0432.ccr-21-3817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/24/2022] [Accepted: 07/07/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE To identify molecular subclasses of clear cell ovarian carcinoma (CCOC) and assess their impact on clinical presentation and outcomes. EXPERIMENTAL DESIGN We profiled 421 primary CCOCs that passed quality control using a targeted deep sequencing panel of 163 putative CCOC driver genes and whole transcriptome sequencing of 211 of these tumors. Molecularly defined subgroups were identified and tested for association with clinical characteristics and overall survival. RESULTS We detected a putative somatic driver mutation in at least one candidate gene in 95% (401/421) of CCOC tumors including ARID1A (in 49% of tumors), PIK3CA (49%), TERT (20%), and TP53 (16%). Clustering of cancer driver mutations and RNA expression converged upon two distinct subclasses of CCOC. The first was dominated by ARID1A-mutated tumors with enriched expression of canonical CCOC genes and markers of platinum resistance; the second was largely comprised of tumors with TP53 mutations and enriched for the expression of genes involved in extracellular matrix organization and mesenchymal differentiation. Compared with the ARID1A-mutated group, women with TP53-mutated tumors were more likely to have advanced-stage disease, no antecedent history of endometriosis, and poorer survival, driven by their advanced stage at presentation. In women with ARID1A-mutated tumors, there was a trend toward a lower rate of response to first-line platinum-based therapy. CONCLUSIONS Our study suggests that CCOC consists of two distinct molecular subclasses with distinct clinical presentation and outcomes, with potential relevance to both traditional and experimental therapy responsiveness. See related commentary by Lheureux, p. 4838.
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Affiliation(s)
- Kelly L. Bolton
- Washington University School of Medicine, St. Louis, Missouri
| | - Denise Chen
- Philadelphia College of Osteopathic Medicine, Philadelphia, Pennsylvania
| | | | - Zhuxuan Fu
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | | | - Martin Köbel
- The University of Calgary, Calgary, Alberta, Canada
| | - Yanis Tazi
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | | | | | - Brian J. Wiley
- Washington University School of Medicine, St. Louis, Missouri
| | | | | | | | - Jenny Lester
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California
| | - Esther Elishaev
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Angela Laslavic
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Catherine J. Kennedy
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Anna Piskorz
- University of Cambridge, Cambridge, United Kingdom
| | | | - Alison H. Brand
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
| | - Yoke-Eng Chiew
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Paul Pharoah
- University of Cambridge, Cambridge, United Kingdom
| | | | - Ronny Drapkin
- University of Pennsylvania, Philadelphia, Pennsylvania
| | | | | | - Anna DeFazio
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, New South Wales, Australia
| | - Beth Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California
| | | | - Britta Weigelt
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | | | - David Huntsman
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Simon Gayther
- Cedars-Sinai Medical Center, Los Angeles, California
| | - Jason Konner
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Francesmary Modugno
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
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19
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Nath A, Cosgrove PA, Chang JT, Bild AH. Predicting clinical response to everolimus in ER+ breast cancers using machine-learning. Front Mol Biosci 2022; 9:981962. [PMID: 36304922 PMCID: PMC9592823 DOI: 10.3389/fmolb.2022.981962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
Endocrine therapy remains the primary treatment choice for ER+ breast cancers. However, most advanced ER+ breast cancers ultimately develop resistance to endocrine. This acquired resistance to endocrine therapy is often driven by the activation of the PI3K/AKT/mTOR signaling pathway. Everolimus, a drug that targets and inhibits the mTOR complex has been shown to improve clinical outcomes in metastatic ER+ breast cancers. However, there are no biomarkers currently available to guide the use of everolimus in the clinic for progressive patients, where multiple therapeutic options are available. Here, we utilized gene expression signatures from 9 ER+ breast cancer cell lines and 23 patients treated with everolimus to develop and validate an integrative machine learning biomarker of mTOR inhibitor response. Our results show that the machine learning biomarker can successfully distinguish responders from non-responders and can be applied to identify patients that will most likely benefit from everolimus treatment.
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Affiliation(s)
- Aritro Nath
- City of Hope Comprehensive Cancer Center, Department of Medical Oncology and Therapeutics, Monrovia, CA, United States
- *Correspondence: Aritro Nath, ; Andrea H. Bild,
| | - Patrick A. Cosgrove
- City of Hope Comprehensive Cancer Center, Department of Medical Oncology and Therapeutics, Monrovia, CA, United States
| | - Jeffrey T. Chang
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Andrea H. Bild
- City of Hope Comprehensive Cancer Center, Department of Medical Oncology and Therapeutics, Monrovia, CA, United States
- *Correspondence: Aritro Nath, ; Andrea H. Bild,
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20
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Takahashi N, Hatakeyama K, Nagashima T, Ohshima K, Urakami K, Yamaguchi K, Hirashima Y. Characterization of rare histological subtypes of ovarian cancer based on molecular profiling. Cancer Med 2022; 12:387-395. [PMID: 35676859 PMCID: PMC9844652 DOI: 10.1002/cam4.4927] [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: 01/13/2022] [Revised: 05/08/2022] [Accepted: 05/24/2022] [Indexed: 01/26/2023] Open
Abstract
OBJECTIVE Pan-cancer analysis across The Cancer Genome Atlas has revealed the molecular profiles of major types of carcinomas. High-grade serous carcinomas (HGSCs) have been characterized; however, in ovarian cancer, the profile of carcinoma with minor histopathological changes remains unclear. This study aimed to perform the molecular profiling of rare malignant ovarian tumors, including non-epithelial tumors (NETs; germ cell tumors and sex cord tumors) and clear cell carcinoma (CCC), to determine how they differ from the major HGSCs. METHODS Sixty-nine malignant ovarian tumors surgically resected at the Shizuoka Cancer Center between January 2014 and March 2019 were classified based on their histopathological types. The germline and somatic mutations in these carcinomas, including NETs, were determined using next-generation sequencing. Gene expression analysis was performed to investigate the major pathways of drug resistance, which is a characteristic of CCC. RESULTS NETs harbored copy-neutral loss of heterozygosity, accompanied by a high homologous recombination deficiency score; germline mutations of PALB2 and BARD1 were identified in two patients with NET. In chemoresistant CCC, the epithelial-mesenchymal transition pathway was activated regardless of ABC transporter expression. CONCLUSION This study revealed some genomic characteristics of rare malignant ovarian tumors, including NETs and CCC.
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Affiliation(s)
| | - Keiichi Hatakeyama
- Medical Genetics DivisionShizuoka Cancer Center Research InstituteSunto‐gunShizuokaJapan
| | - Takeshi Nagashima
- Cancer Diagnostics Research DivisionShizuoka Cancer Center Research InstituteSunto‐gunShizuokaJapan,SRL Inc.Shinjuku‐kuTokyoJapan
| | - Keiichi Ohshima
- Medical Genetics DivisionShizuoka Cancer Center Research InstituteSunto‐gunShizuokaJapan
| | - Kenichi Urakami
- Cancer Diagnostics Research DivisionShizuoka Cancer Center Research InstituteSunto‐gunShizuokaJapan
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21
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Khalique S, Nash S, Natrajan R. Definitive study shows no association between ARID1A mutation status and clinical outcome in endometriosis related ovarian cancers. J Pathol 2022; 258:1-3. [PMID: 35647895 PMCID: PMC9540905 DOI: 10.1002/path.5973] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 11/23/2022]
Abstract
The ARID1A tumour suppressor protein is a component of the SWI/SNF chromatin remodelling complex, which is mutated in approximately 20% of all human cancers. ARID1A mutational status is considered to hold prognostic significance in a range of solid malignancies, yet in endometriosis‐related ovarian carcinomas there has been a lack of clarity of its prognostic role. Moreover, the relationship between ARID1A status and immune infiltrate is also poorly understood. In a recent issue of The Journal of Pathology, a large comprehensive study by Heinze, Nazeran et al addressed these areas by reviewing 1,623 endometriosis‐associated ovarian carcinomas and correlating ARID1A status using standardised immunohistochemistry to infer mutation status, with comprehensive clinicopathological features, mismatch repair status and CD8+ tumour infiltrating lymphocytes. The study definitively showed that ARID1A status does not provide any independent prognostic value in endometriosis‐associated ovarian carcinomas. ARID1A loss was, however, shown to be associated with mismatch repair deficiency and increased CD8+ tumour infiltrating lymphocytes in endometrioid ovarian carcinoma, which may be relevant for future studies. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Saira Khalique
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
| | - Sarah Nash
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
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22
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Ye S, Li Q, Wu Y, Jiang W, Zhou S, Zhou X, Yang W, Tu X, Shan B, Huang S, Yang H. Integrative genomic and transcriptomic analysis reveals immune subtypes and prognostic markers in ovarian clear cell carcinoma. Br J Cancer 2022; 126:1215-1223. [PMID: 35043008 PMCID: PMC9023449 DOI: 10.1038/s41416-022-01705-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/18/2021] [Accepted: 01/07/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND We performed an integrative genomic and transcriptomic profiling to identify molecular subtypes and prognostic markers with special focus on immune-related pathways. METHODS Totally, 50 Chinese patients were subjected to targeted next-generation sequencing and transcriptomic sequencing. RESULTS Two distinct subgroups were identified as immune (22.0%) and non-immune (78.0%) based on the immune-pathway related hierarchical clustering. Surprisingly, patients with immune subtype had a significantly worse survival. The prognostic capacity was validated in external cohorts. The immune group had higher expression of genes involved in pro-inflammation and checkpoints. PD-1 signalling pathway was enriched in the immune subtype. Besides, the immune cluster presented enriched expression of genes involved in epithelial-mesenchymal transition, angiogenesis and PI3K-AKT-mTOR signalling, while the non-immune subtype had higher expression of metabolic pathways. The immune subtype had a higher mutation rate of PIK3CA though significance was not achieved. Lastly, we established a prognostic immune signature for overall survival. Interestingly, the immune signature could also be applied to renal clear cell carcinoma, but not to other histologic subtype of ovarian cancer. CONCLUSIONS An immune subtype of OCCC was identified with poor survival and enrichment of PD-1 and PI3K-AKT-mTOR signalling. We constructed and validated a robust prognostic immune signature of OCCC patients.
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Affiliation(s)
- Shuang Ye
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qin Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yutuan Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Jiang
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shuling Zhou
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaoyan Zhou
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wentao Yang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaoyu Tu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Boer Shan
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Shenglin Huang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Huijuan Yang
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Tamura R, Yoshihara K, Enomoto T. Therapeutic Strategies Focused on Cancer-Associated Hypercoagulation for Ovarian Clear Cell Carcinoma. Cancers (Basel) 2022; 14:2125. [PMID: 35565252 PMCID: PMC9099459 DOI: 10.3390/cancers14092125] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 02/04/2023] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is associated with chemotherapy resistance and poor prognosis, especially in advanced cases. Although comprehensive genomic analyses have clarified the significance of genomic alterations such as ARID1A and PIK3CA mutations in OCCC, therapeutic strategies based on genomic alterations have not been confirmed. On the other hand, OCCC is clinically characterized by a high incidence of thromboembolism. Moreover, OCCC specifically shows high expression of tissue factor and interleukin-6, which play a critical role in cancer-associated hypercoagulation and may be induced by OCCC-specific genetic alterations or the endometriosis-related tumor microenvironment. In this review, we focused on the association between cancer-associated hypercoagulation and molecular biology in OCCC. Moreover, we reviewed the effectiveness of candidate drugs targeting hypercoagulation, such as tissue factor- or interleukin-6-targeting drugs, anti-inflammatory drugs, anti-hypoxia signaling drugs, anticoagulants, and combined immunotherapy with these drugs for OCCC. This review is expected to contribute to novel basic research and clinical trials for the prevention, early detection, and treatment of OCCC focused on hypercoagulation.
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Affiliation(s)
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan; (R.T.); (T.E.)
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Kawabata A, Hayashi T, Akasu-Nagayoshi Y, Yamada A, Shimizu N, Yokota N, Nakato R, Shirahige K, Okamoto A, Akiyama T. CRISPR/Cas9 Screening for Identification of Genes Required for the Growth of Ovarian Clear Cell Carcinoma Cells. Curr Issues Mol Biol 2022; 44:1587-1596. [PMID: 35723366 PMCID: PMC9164056 DOI: 10.3390/cimb44040108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022] Open
Abstract
Epithelial ovarian cancer is classified into four major histological subtypes: serous, clear cell, endometrioid and mucinous. Ovarian clear cell carcinoma (OCCC) responds poorly to conventional chemotherapies and shows poor prognosis. Thus, there is a need to develop new drugs for the treatment of OCCC. In this study, we performed CRISPR/Cas9 screens against OCCC cell lines and identified candidate genes important for their proliferation. We found that quite different genes are required for the growth of ARID1A and PIK3CA mutant and wild-type OCCC cell lines, respectively. Furthermore, we found that the epigenetic regulator KDM2A and the translation regulator PAIP1 may play important roles in the growth of ARID1A and PIK3CA mutant, but not wild-type, OCCC cells. The results of our CRISPR/Cas9 screening may be useful in elucidating the molecular mechanism of OCCC tumorigenesis and in developing OCCC-targeted drugs.
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Affiliation(s)
- Ayako Kawabata
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (A.K.); (Y.A.-N.); (A.Y.); (N.S.)
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo 105-8461, Japan;
| | - Tomoatsu Hayashi
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (A.K.); (Y.A.-N.); (A.Y.); (N.S.)
| | - Yoko Akasu-Nagayoshi
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (A.K.); (Y.A.-N.); (A.Y.); (N.S.)
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo 105-8461, Japan;
| | - Ai Yamada
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (A.K.); (Y.A.-N.); (A.Y.); (N.S.)
| | - Naomi Shimizu
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (A.K.); (Y.A.-N.); (A.Y.); (N.S.)
| | - Naoko Yokota
- Laboratory of Computational Genetics, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (N.Y.); (R.N.)
| | - Ryuichiro Nakato
- Laboratory of Computational Genetics, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (N.Y.); (R.N.)
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan;
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo 105-8461, Japan;
| | - Tetsu Akiyama
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (A.K.); (Y.A.-N.); (A.Y.); (N.S.)
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25
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Heinze K, Nazeran TM, Lee S, Krämer P, Cairns ES, Chiu DS, Leung SC, Kang EY, Meagher NS, Kennedy CJ, Boros J, Kommoss F, Vollert HW, Heitze F, du Bois A, Harter P, Grube M, Kraemer B, Staebler A, Kommoss FK, Heublein S, Sinn HP, Singh N, Laslavic A, Elishaev E, Olawaiye A, Moysich K, Modugno F, Sharma R, Brand AH, Harnett PR, DeFazio A, Fortner RT, Lubinski J, Lener M, Tołoczko-Grabarek A, Cybulski C, Gronwald H, Gronwald J, Coulson P, El-Bahrawy MA, Jones ME, Schoemaker MJ, Swerdlow AJ, Gorringe KL, Campbell I, Cook L, Gayther SA, Carney ME, Shvetsov YB, Hernandez BY, Wilkens LR, Goodman MT, Mateoiu C, Linder A, Sundfeldt K, Kelemen LE, Gentry-Maharaj A, Widschwendter M, Menon U, Bolton KL, Alsop J, Shah M, Jimenez-Linan M, Pharoah PD, Brenton JD, Cushing-Haugen KL, Harris HR, Doherty JA, Gilks B, Ghatage P, Huntsman DG, Nelson GS, Tinker AV, Lee CH, Goode EL, Nelson BH, Ramus SJ, Kommoss S, Talhouk A, Köbel M, Anglesio MS. Validated biomarker assays confirm that ARID1A loss is confounded with MMR deficiency, CD8 + TIL infiltration, and provides no independent prognostic value in endometriosis-associated ovarian carcinomas. J Pathol 2022; 256:388-401. [PMID: 34897700 PMCID: PMC9544180 DOI: 10.1002/path.5849] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/12/2021] [Accepted: 12/10/2021] [Indexed: 11/11/2022]
Abstract
ARID1A (BAF250a) is a component of the SWI/SNF chromatin modifying complex, plays an important tumour suppressor role, and is considered prognostic in several malignancies. However, in ovarian carcinomas there are contradictory reports on its relationship to outcome, immune response, and correlation with clinicopathological features. We assembled a series of 1623 endometriosis-associated ovarian carcinomas, including 1078 endometrioid (ENOC) and 545 clear cell (CCOC) ovarian carcinomas, through combining resources of the Ovarian Tumor Tissue Analysis (OTTA) Consortium, the Canadian Ovarian Unified Experimental Resource (COEUR), local, and collaborative networks. Validated immunohistochemical surrogate assays for ARID1A mutations were applied to all samples. We investigated associations between ARID1A loss/mutation, clinical features, outcome, CD8+ tumour-infiltrating lymphocytes (CD8+ TILs), and DNA mismatch repair deficiency (MMRd). ARID1A loss was observed in 42% of CCOCs and 25% of ENOCs. We found no associations between ARID1A loss and outcomes, stage, age, or CD8+ TIL status in CCOC. Similarly, we found no association with outcome or stage in endometrioid cases. In ENOC, ARID1A loss was more prevalent in younger patients (p = 0.012) and was associated with MMRd (p < 0.001) and the presence of CD8+ TILs (p = 0.008). Consistent with MMRd being causative of ARID1A mutations, in a subset of ENOCs we also observed an association with ARID1A loss-of-function mutation as a result of small indels (p = 0.035, versus single nucleotide variants). In ENOC, the association with ARID1A loss, CD8+ TILs, and age appears confounded by MMRd status. Although this observation does not explicitly rule out a role for ARID1A influence on CD8+ TIL infiltration in ENOC, given current knowledge regarding MMRd, it seems more likely that effects are dominated by the hypermutation phenotype. This large dataset with consistently applied biomarker assessment now provides a benchmark for the prevalence of ARID1A loss-of-function mutations in endometriosis-associated ovarian cancers and brings clarity to the prognostic significance. © 2021 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Karolin Heinze
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, BC, Canada
- University of British Columbia, Vancouver General Hospital, and BC Cancer. British Columbia’s Gynecological Cancer Research Team (OVCARE), Vancouver, BC, Canada
| | - Tayyebeh M. Nazeran
- University of British Columbia, Vancouver General Hospital, and BC Cancer. British Columbia’s Gynecological Cancer Research Team (OVCARE), Vancouver, BC, Canada
| | - Sandra Lee
- University of Calgary, Department of Pathology and Laboratory Medicine, Calgary, AB, Canada
| | - Pauline Krämer
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, BC, Canada
- University Hospital Tübingen, Department of Women’s Health, Tübingen, Germany
| | - Evan S. Cairns
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, BC, Canada
| | - Derek S. Chiu
- University of British Columbia, Vancouver General Hospital, and BC Cancer. British Columbia’s Gynecological Cancer Research Team (OVCARE), Vancouver, BC, Canada
| | - Samuel C.Y. Leung
- University of British Columbia, Vancouver General Hospital, and BC Cancer. British Columbia’s Gynecological Cancer Research Team (OVCARE), Vancouver, BC, Canada
| | - Eun Young Kang
- University of Calgary, Department of Pathology and Laboratory Medicine, Calgary, AB, Canada
| | - Nicola S. Meagher
- University of New South Wales, Adult Cancer Program, Lowy Cancer Research Centre, Sydney, New South Wales, Australia
- University of New South Wales, School of Women’s and Children’s Health, Sydney, New South Wales, Australia
| | - Catherine J. Kennedy
- The University of Sydney, Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Westmead Hospital, Department of Gynaecological Oncology, Sydney, New South Wales, Australia
| | - Jessica Boros
- The University of Sydney, Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Westmead Hospital, Department of Gynaecological Oncology, Sydney, New South Wales, Australia
| | - Friedrich Kommoss
- Medizin Campus Bodensee, Institute of Pathology, Friedrichshafen, Germany
| | - Hans-Walter Vollert
- Medizin Campus Bodensee, Department of Gynecology and Obstetrics, Friedrichshafen, Germany
| | - Florian Heitze
- Kliniken Essen Mitte, Department of Gynecology and Gynecologic Oncology, Essen, Germany
| | - Andreas du Bois
- Kliniken Essen Mitte, Department of Gynecology and Gynecologic Oncology, Essen, Germany
| | - Philipp Harter
- Kliniken Essen Mitte, Department of Gynecology and Gynecologic Oncology, Essen, Germany
| | - Marcel Grube
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, BC, Canada
- University Hospital Tübingen, Department of Women’s Health, Tübingen, Germany
| | - Bernhard Kraemer
- University Hospital Tübingen, Department of Women’s Health, Tübingen, Germany
| | - Annette Staebler
- University Hospital Tübingen, Institute of Pathology and Neuropathology, Tübingen, Germany
| | - Felix K.F. Kommoss
- University Hospital Heidelberg, Institute of Pathology, Heidelberg, Germany
| | - Sabine Heublein
- University Hospital Heidelberg and National Center for Tumor Diseases, Department of Obstetrics and Gynecology, Heidelberg, Germany
| | - Hans-Peter Sinn
- University Hospital Heidelberg, Institute of Pathology, Heidelberg, Germany
| | - Naveena Singh
- Barts Health National Health Service Trust, Department of Pathology, London, UK
| | - Angela Laslavic
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, PA, USA
| | - Esther Elishaev
- University of Pittsburgh School of Medicine, Department of Pathology, PA, USA
| | - Alex Olawaiye
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, PA, USA
| | - Kirsten Moysich
- Roswell Park Cancer Institute, Department of Cancer Prevention and Control, Buffalo, NY, USA
| | - Francesmary Modugno
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, PA, USA
| | - Raghwa Sharma
- Westmead Hospital, Tissue Pathology and Diagnostic Oncology, Sydney, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
- Western Sydney University, Sydney, New South Wales, Australia
| | - Alison H. Brand
- Westmead Hospital, Department of Gynaecological Oncology, Sydney, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
| | - Paul R. Harnett
- Westmead Hospital, Department of Gynaecological Oncology, Sydney, New South Wales, Australia
- Westmead Hospital, Crown Princess Mary Cancer Centre, Sydney, New South Wales, Australia
| | - Anna DeFazio
- The University of Sydney, Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Westmead Hospital, Department of Gynaecological Oncology, Sydney, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, New South Wales, Australia
| | - Renée T. Fortner
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Jan Lubinski
- Pomeranian Medical University, Department of Genetics and Pathology, International Hereditary Cancer Centre, Szczecin, Poland
| | - Marcin Lener
- Pomeranian Medical University, Department of Genetics and Pathology, International Hereditary Cancer Centre, Szczecin, Poland
| | - Aleksandra Tołoczko-Grabarek
- Pomeranian Medical University, Department of Genetics and Pathology, International Hereditary Cancer Centre, Szczecin, Poland
| | - Cezary Cybulski
- Pomeranian Medical University, Department of Genetics and Pathology, International Hereditary Cancer Centre, Szczecin, Poland
| | - Helena Gronwald
- Pomeranian Medical University, Department of Propaedeutics, Physical Diagnostics and Dental Physiotherapy, Szczecin, Poland
| | - Jacek Gronwald
- Pomeranian Medical University, Department of Genetics and Pathology, International Hereditary Cancer Centre, Szczecin, Poland
| | - Penny Coulson
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London, UK
| | - Mona A El-Bahrawy
- Imperial College London, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, London, UK
| | - Michael E. Jones
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London, UK
| | - Minouk J. Schoemaker
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London, UK
| | - Anthony J. Swerdlow
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London, UK
- The Institute of Cancer Research, Division of Breast Cancer Research, London, UK
| | - Kylie L. Gorringe
- The University of Melbourne, Sir Peter MacCallum Department of Oncology, Melbourne, Australia
- Peter MacCallum Cancer Centre, Women’s Cancer Program, Melbourne, Australia
| | - Ian Campbell
- The University of Melbourne, Sir Peter MacCallum Department of Oncology, Melbourne, Australia
- Peter MacCallum Cancer Centre, Cancer Genetics Laboratory, Research Division, Melbourne, Australia
| | - Linda Cook
- The University of New Mexico, Division of Epidemiology and Biostatistics, Albuquerque, NM, USA
| | - Simon A. Gayther
- Cedars-Sinai Medical Center, Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core, Los Angeles, CA, USA
| | - Michael E. Carney
- John A. Burns School of Medicine, University of Hawaii, Honolulu, Department of Obstetrics and Gynecology, HI, USA
| | - Yurii B. Shvetsov
- University of Hawaii Cancer Center, Epidemiology Program, Honolulu, HI, USA
| | | | - Lynne R. Wilkens
- University of Hawaii Cancer Center, Epidemiology Program, Honolulu, HI, USA
| | - Marc T. Goodman
- Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Los Angeles, CA, USA
| | - Constantina Mateoiu
- Sahlgrenska Academy at Gothenburg University, Sahlgrenska Center for Cancer Research, Department of Obstetrics and Gynecology, Gothenburg, Sweden
| | - Anna Linder
- Sahlgrenska Academy at Gothenburg University, Sahlgrenska Center for Cancer Research, Department of Obstetrics and Gynecology, Gothenburg, Sweden
| | - Karin Sundfeldt
- Sahlgrenska Academy at Gothenburg University, Sahlgrenska Center for Cancer Research, Department of Obstetrics and Gynecology, Gothenburg, Sweden
| | - Linda E. Kelemen
- Medical University of South Carolina, Hollings Cancer Center and Department of Public Health Sciences, Charleston, SC, USA
| | - Aleksandra Gentry-Maharaj
- University College London, MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, London, UK
- University College London, Department of Women’s Cancer, Institute for Women’s Health, London, UK
| | | | - Usha Menon
- University College London, MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, London, UK
| | - Kelly L. Bolton
- Washington University School of Medicine, Department of Hematology and Oncology, Division of Oncology, St. Louis, MO, USA
| | - Jennifer Alsop
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | - Mitul Shah
- Addenbrookes Hospital, Department of Histopathology, Cambridge, UK
| | | | - Paul D.P. Pharoah
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - James D. Brenton
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Kara L. Cushing-Haugen
- Fred Hutchinson Cancer Research Center, Program in Epidemiology, Division of Public Health Sciences, Seattle, WA, USA
| | - Holly R. Harris
- Fred Hutchinson Cancer Research Center, Program in Epidemiology, Division of Public Health Sciences, Seattle, WA, USA
| | - Jennifer A. Doherty
- University of Utah, Huntsman Cancer Institute, Department of Population Health Sciences, Salt Lake City, UT, USA
| | - Blake Gilks
- University of British Columbia, Vancouver General Hospital, and BC Cancer. British Columbia’s Gynecological Cancer Research Team (OVCARE), Vancouver, BC, Canada
| | - Prafull Ghatage
- University of Calgary, Department of Oncology, Division of Gynecologic Oncology, Calgary, AB, Canada
| | - David G. Huntsman
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, BC, Canada
- University of British Columbia, Vancouver General Hospital, and BC Cancer. British Columbia’s Gynecological Cancer Research Team (OVCARE), Vancouver, BC, Canada
| | - Gregg S. Nelson
- University of Calgary, Department of Oncology, Division of Gynecologic Oncology, Calgary, AB, Canada
| | - Anna V. Tinker
- University of British Columbia, Vancouver General Hospital, and BC Cancer. British Columbia’s Gynecological Cancer Research Team (OVCARE), Vancouver, BC, Canada
- University of British Columbia, Department of Medicine, Vancouver, BC, Canada
| | - Cheng-Han Lee
- University of Alberta, Department of Laboratory Medicine and Pathology, Edmonton, AB, Canada
| | - Ellen L. Goode
- Mayo Clinic, Department of Health Science Research, Division of Epidemiology, Rochester, MN, USA
| | - Brad H. Nelson
- Trev & Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, BC, Canada
| | - Susan J. Ramus
- University of New South Wales, Adult Cancer Program, Lowy Cancer Research Centre, Sydney, New South Wales, Australia
- University of New South Wales, School of Women’s and Children’s Health, Sydney, New South Wales, Australia
| | - Stefan Kommoss
- University Hospital Tübingen, Department of Women’s Health, Tübingen, Germany
| | - Aline Talhouk
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, BC, Canada
- University of British Columbia, Vancouver General Hospital, and BC Cancer. British Columbia’s Gynecological Cancer Research Team (OVCARE), Vancouver, BC, Canada
| | - Martin Köbel
- University of Calgary, Department of Pathology and Laboratory Medicine, Calgary, AB, Canada
| | - Michael S. Anglesio
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, BC, Canada
- University of British Columbia, Vancouver General Hospital, and BC Cancer. British Columbia’s Gynecological Cancer Research Team (OVCARE), Vancouver, BC, Canada
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Yee C, Dickson KA, Muntasir MN, Ma Y, Marsh DJ. Three-Dimensional Modelling of Ovarian Cancer: From Cell Lines to Organoids for Discovery and Personalized Medicine. Front Bioeng Biotechnol 2022; 10:836984. [PMID: 35223797 PMCID: PMC8866972 DOI: 10.3389/fbioe.2022.836984] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/19/2022] [Indexed: 12/11/2022] Open
Abstract
Ovarian cancer has the highest mortality of all of the gynecological malignancies. There are several distinct histotypes of this malignancy characterized by specific molecular events and clinical behavior. These histotypes have differing responses to platinum-based drugs that have been the mainstay of therapy for ovarian cancer for decades. For histotypes that initially respond to a chemotherapeutic regime of carboplatin and paclitaxel such as high-grade serous ovarian cancer, the development of chemoresistance is common and underpins incurable disease. Recent discoveries have led to the clinical use of PARP (poly ADP ribose polymerase) inhibitors for ovarian cancers defective in homologous recombination repair, as well as the anti-angiogenic bevacizumab. While predictive molecular testing involving identification of a genomic scar and/or the presence of germline or somatic BRCA1 or BRCA2 mutation are in clinical use to inform the likely success of a PARP inhibitor, no similar tests are available to identify women likely to respond to bevacizumab. Functional tests to predict patient response to any drug are, in fact, essentially absent from clinical care. New drugs are needed to treat ovarian cancer. In this review, we discuss applications to address the currently unmet need of developing physiologically relevant in vitro and ex vivo models of ovarian cancer for fundamental discovery science, and personalized medicine approaches. Traditional two-dimensional (2D) in vitro cell culture of ovarian cancer lacks critical cell-to-cell interactions afforded by culture in three-dimensions. Additionally, modelling interactions with the tumor microenvironment, including the surface of organs in the peritoneal cavity that support metastatic growth of ovarian cancer, will improve the power of these models. Being able to reliably grow primary tumoroid cultures of ovarian cancer will improve the ability to recapitulate tumor heterogeneity. Three-dimensional (3D) modelling systems, from cell lines to organoid or tumoroid cultures, represent enhanced starting points from which improved translational outcomes for women with ovarian cancer will emerge.
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Affiliation(s)
- Christine Yee
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Kristie-Ann Dickson
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Mohammed N. Muntasir
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Yue Ma
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Deborah J. Marsh
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
- Northern Clinical School, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
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27
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Cunningham JM, Winham SJ, Wang C, Weiglt B, Fu Z, Armasu SM, McCauley BM, Brand AH, Chiew YE, Elishaev E, Gourley C, Kennedy CJ, Laslavic A, Lester J, Piskorz A, Sekowska M, Brenton JD, Churchman M, DeFazio A, Drapkin R, Elias KM, Huntsman DG, Karlan BY, Köbel M, Konner J, Lawrenson K, Papaemmanuil E, Bolton KL, Modugno F, Goode EL. DNA Methylation Profiles of Ovarian Clear Cell Carcinoma. Cancer Epidemiol Biomarkers Prev 2022; 31:132-141. [PMID: 34697060 PMCID: PMC8755592 DOI: 10.1158/1055-9965.epi-21-0677] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Ovarian clear cell carcinoma (OCCC) is a rare ovarian cancer histotype that tends to be resistant to standard platinum-based chemotherapeutics. We sought to better understand the role of DNA methylation in clinical and biological subclassification of OCCC. METHODS We interrogated genome-wide methylation using DNA from fresh frozen tumors from 271 cases, applied nonsmooth nonnegative matrix factorization (nsNMF) clustering, and evaluated clinical associations and biological pathways. RESULTS Two approximately equally sized clusters that associated with several clinical features were identified. Compared with Cluster 2 (N = 137), Cluster 1 cases (N = 134) presented at a more advanced stage, were less likely to be of Asian ancestry, and tended to have poorer outcomes including macroscopic residual disease following primary debulking surgery (P < 0.10). Subset analyses of targeted tumor sequencing and IHC data revealed that Cluster 1 tumors showed TP53 mutation and abnormal p53 expression, and Cluster 2 tumors showed aneuploidy and ARID1A/PIK3CA mutation (P < 0.05). Cluster-defining CpGs included 1,388 CpGs residing within 200 bp of the transcription start sites of 977 genes; 38% of these genes (N = 369 genes) were differentially expressed across cluster in transcriptomic subset analysis (P < 10-4). Differentially expressed genes were enriched for six immune-related pathways, including IFNα and IFNγ responses (P < 10-6). CONCLUSIONS DNA methylation clusters in OCCC correlate with disease features and gene expression patterns among immune pathways. IMPACT This work serves as a foundation for integrative analyses that better understand the complex biology of OCCC in an effort to improve potential for development of targeted therapeutics.
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Affiliation(s)
- Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
| | - Stacey J Winham
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Chen Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Britta Weiglt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zhuxuan Fu
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Sebastian M Armasu
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Bryan M McCauley
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Alison H Brand
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
| | - Yoke-Eng Chiew
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Esther Elishaev
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Catherine J Kennedy
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Angela Laslavic
- Womens Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Jenny Lester
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California
| | - Anna Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Magdalena Sekowska
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Michael Churchman
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Anna DeFazio
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - David G Huntsman
- British Columbia's Ovarian Cancer Research (OVCARE) Program, BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Beth Y Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California
| | - Martin Köbel
- Department of Laboratory and Pathology Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jason Konner
- Weill Cornell Medical College of Cornell University, New York, New York
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Kate Lawrenson
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Women's Cancer Program at the Samuel Oschin Cancer Institute Cedars-Sinai Medical Center, Los Angeles, California
| | - Elli Papaemmanuil
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kelly L Bolton
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Francesmary Modugno
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
- Womens Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, Pennsylvania
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ellen L Goode
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
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28
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Pérez-Mies B, Carretero-Barrio I, Palacios J. Immune-related gene expression signatures: A step forward in the stratification of patients with ovarian clear cell carcinoma. J Pathol 2021; 256:366-368. [PMID: 34908168 DOI: 10.1002/path.5850] [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: 11/15/2021] [Accepted: 12/13/2021] [Indexed: 11/10/2022]
Abstract
Clear cell carcinoma of the ovary (CCC) is one of the five major histological types of ovarian cancer and presents specific clinicopathological features, such as a higher prevalence in Asian population and a poor response to conventional chemotherapy. In a recent publication in The Journal of Pathology, Heong and coworkers demonstrated the heterogeneity of the immune landscape of CCC. They reported the immune signatures observed in a large cohort of CCC, including tumours from both Asian and Caucasian women. The authors analysed three cohorts from Europe, Japan and Singapore with a total of 246 tumours, and evaluated 730 immune related genes using NanoString technology. The study revealed four main transcriptional subtypes characterised by the expression of specific sets of genes: PD1-high (11%), CTLA4-high (29%), antigen-presentation (42%), and a pro-angiogenic subtype (18%). The two main conclusions of the study are: 1) CCC in women of Asian and Caucasian descent share significant molecular similarities, since all four molecular signatures are present in all the cohorts analysed, without any evident differences in frequency; and 2) the PD1-high and CTLA4-high subtypes were associated with worse clinical outcomes and may be useful when stratifying treatment in early-stage tumours. The immune signature could represent a promising biomarker of immunotherapy response if future prospective studies confirm it. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Belén Pérez-Mies
- Pathology Department, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain.,Faculty of Medicine, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain.,CIBERONC, Madrid, Spain
| | - Irene Carretero-Barrio
- Pathology Department, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain.,Faculty of Medicine, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
| | - José Palacios
- Pathology Department, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain.,Faculty of Medicine, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain.,CIBERONC, Madrid, Spain
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29
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Tamura R, Yoshihara K, Matsuo K, Yachida N, Miyoshi A, Takahashi K, Sugino K, Yamaguchi M, Mori Y, Suda K, Ishiguro T, Okuda S, Motoyama T, Nakaoka H, Kikuchi A, Ueda Y, Inoue I, Enomoto T. Proposing a molecular classification associated with hypercoagulation in ovarian clear cell carcinoma. Gynecol Oncol 2021; 163:327-333. [PMID: 34452748 DOI: 10.1016/j.ygyno.2021.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/12/2021] [Accepted: 08/14/2021] [Indexed: 01/26/2023]
Abstract
BACKGROUND Although ovarian clear cell carcinoma (CCC) is associated with high incidence of thromboembolism, the clinicopathological and biological significance of hypercoagulable status in CCC remains unclear. MATERIALS AND METHODS We retrospectively analyzed pretreatment D-dimer levels, thromboembolic status, and clinical outcome of 125 CCCs in the discovery set and 143 CCCs in two other independent validation sets. Next, we performed RNA sequencing of 93 CCCs and compared coagulation-related gene profiles with 2492 pan-cancer data. We investigated differences in molecular characteristics of CCC subclasses based on coagulation status. RESULTS In the discovery dataset, D-dimer elevation above the normal range was significantly associated with shorter progression-free and overall survival, irrespective to thromboembolic status. Multivariate analysis identified D-dimer elevation and clinical stage as an independent prognostic factors. We confirmed the prognostic significance of D-dimer elevation in the validation sets. Tissue factor and IL6, which are considered key elements of cancer-induced hypercoagulation, were highly expressed in CCC than in other cancers regardless of D-dimer level. Higher activity of various oncogenic pathways was observed in CCC with compared to without D-dimer elevation. Moreover, hierarchical cluster analysis divided 57 CCCs with D-dimer elevation into immunologically hot and cold tumor subtypes. Hot tumors were characterized by enrichment of T-cell inflamed phenotype, inflammation, the epithelial-mesenchymal transition, and high serum levels of CRP, and cold tumors by enrichment of cell cycle and MYC pathways. CONCLUSIONS CCC represents hypercoagulable disease and elevate D-dimer is a prognostic factor for decreased survival in CCC. D-dimer high CCC has distinct molecular characteristics into the inflammatory-driven pathway (hot tumor) and the immune-suppressive pathway (cold tumor). Treatment implication of our proposed molecular classification merits further investigation.
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Affiliation(s)
- Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
| | - Koji Matsuo
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Nozomi Yachida
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ai Miyoshi
- Department of Obstetrics and Gynecology, Osaka University School of Medicine, Suita, Japan
| | - Kotaro Takahashi
- Department of Gynecology, Niigata Cancer Center Hospital, Niigata, Japan
| | - Kentaro Sugino
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Manako Yamaguchi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yutaro Mori
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kazuaki Suda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shujiro Okuda
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Japan; Medical AI Center, Niigata University School of Medicine, Niigata, Japan
| | - Teiichi Motoyama
- Department of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Tokyo, Japan
| | - Akira Kikuchi
- Department of Gynecology, Niigata Cancer Center Hospital, Niigata, Japan
| | - Yutaka Ueda
- Department of Obstetrics and Gynecology, Osaka University School of Medicine, Suita, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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30
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Leary A, Tan D, Ledermann J. Immune checkpoint inhibitors in ovarian cancer: where do we stand? Ther Adv Med Oncol 2021; 13:17588359211039899. [PMID: 34422119 PMCID: PMC8377306 DOI: 10.1177/17588359211039899] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022] Open
Abstract
Numerous retrospective studies have demonstrated that the density of intra-tumoral immune cell infiltration is prognostic in epithelial ovarian cancer (OC). These observations together with reports of programmed death ligand-1 (PD-L1) expression in advanced OC provided the rationale for investigating the benefit of programmed death-1 (PD1) or PD-L1 inhibition in OC. Unfortunately clinical trials to date evaluating PD1/PD-L1 inhibition in patients with relapsed OC have been disappointing. In this review we will discuss early results from single agent PD1/PD-L1 inhibitors and the strategies to enhance benefit from immune-oncology agents in OC, including proposing anti-PD-L1 in combination with other agents (cytotoxics, anti-angiogenics, poly(ADP-ribose) polymerase. (PARP) inhibitors, targeted therapies or other immunotherapies), as well as evaluating these agents earlier in the disease course, or in biomarker selected patients.
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Affiliation(s)
- Alexandra Leary
- Institut Gustave Roussy, 114 rue Edouard Vaillant, Villejuif 94805, France, Université Paris-Saclay, INSERM U981, Villejuif, France
| | - David Tan
- Department of Haematology–Oncology, National University Cancer Institute, Singapore, Cancer Science Institute, National University of Singapore, Singapore
| | - Jonathan Ledermann
- UCL Cancer Institute, Cancer Research UK and UCL Trials Centre, London, UK
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31
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Khalique S, Nash S, Mansfield D, Wampfler J, Attygale A, Vroobel K, Kemp H, Buus R, Cottom H, Roxanis I, Jones T, von Loga K, Begum D, Guppy N, Ramagiri P, Fenwick K, Matthews N, Hubank MJF, Lord CJ, Haider S, Melcher A, Banerjee S, Natrajan R. Quantitative Assessment and Prognostic Associations of the Immune Landscape in Ovarian Clear Cell Carcinoma. Cancers (Basel) 2021; 13:3854. [PMID: 34359755 PMCID: PMC8345766 DOI: 10.3390/cancers13153854] [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: 07/01/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is a rare subtype of epithelial ovarian cancer characterised by a high frequency of loss-of-function ARID1A mutations and a poor response to chemotherapy. Despite their generally low mutational burden, an intratumoural T cell response has been reported in a subset of OCCC, with ARID1A purported to be a biomarker for the response to the immune checkpoint blockade independent of micro-satellite instability (MSI). However, assessment of the different immune cell types and spatial distribution specifically within OCCC patients has not been described to date. Here, we characterised the immune landscape of OCCC by profiling a cohort of 33 microsatellite stable OCCCs at the genomic, gene expression and histological level using targeted sequencing, gene expression profiling using the NanoString targeted immune panel, and multiplex immunofluorescence to assess the spatial distribution and abundance of immune cell populations at the protein level. Analysis of these tumours and subsequent independent validation identified an immune-related gene expression signature associated with risk of recurrence of OCCC. Whilst histological quantification of tumour-infiltrating lymphocytes (TIL, Salgado scoring) showed no association with the risk of recurrence or ARID1A mutational status, the characterisation of TILs via multiplexed immunofluorescence identified spatial differences in immunosuppressive cell populations in OCCC. Tumour-associated macrophages (TAM) and regulatory T cells were excluded from the vicinity of tumour cells in low-risk patients, suggesting that high-risk patients have a more immunosuppressive microenvironment. We also found that TAMs and cytotoxic T cells were also excluded from the vicinity of tumour cells in ARID1A-mutated OCCCs compared to ARID1A wild-type tumours, suggesting that the exclusion of these immune effectors could determine the host response of ARID1A-mutant OCCCs to therapy. Overall, our study has provided new insights into the immune landscape and prognostic associations in OCCC and suggest that tailored immunotherapeutic approaches may be warranted for different subgroups of OCCC patients.
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Affiliation(s)
- Saira Khalique
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - Sarah Nash
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - David Mansfield
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London SW3 6JB, UK; (D.M.); (A.M.)
| | - Julian Wampfler
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; (J.W.); (A.A.); (K.V.)
| | - Ayoma Attygale
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; (J.W.); (A.A.); (K.V.)
- Department of Histopathology, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Katherine Vroobel
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; (J.W.); (A.A.); (K.V.)
- Department of Histopathology, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Harriet Kemp
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - Richard Buus
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - Hannah Cottom
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - Ioannis Roxanis
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - Thomas Jones
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; (T.J.); (M.J.F.H.)
| | - Katharina von Loga
- Biomedical Research Centre, The Royal Marsden NHS Foundation Trust, London SM2 5PT, UK; (K.v.L.); (D.B.)
| | - Dipa Begum
- Biomedical Research Centre, The Royal Marsden NHS Foundation Trust, London SM2 5PT, UK; (K.v.L.); (D.B.)
| | - Naomi Guppy
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - Pradeep Ramagiri
- Tumour Profiling Unit, The Institute of Cancer Research, London SW3 6JB, UK; (P.R.); (K.F.); (N.M.)
| | - Kerry Fenwick
- Tumour Profiling Unit, The Institute of Cancer Research, London SW3 6JB, UK; (P.R.); (K.F.); (N.M.)
| | - Nik Matthews
- Tumour Profiling Unit, The Institute of Cancer Research, London SW3 6JB, UK; (P.R.); (K.F.); (N.M.)
| | - Michael J. F. Hubank
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; (T.J.); (M.J.F.H.)
| | - Christopher J. Lord
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Syed Haider
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - Alan Melcher
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London SW3 6JB, UK; (D.M.); (A.M.)
| | - Susana Banerjee
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; (J.W.); (A.A.); (K.V.)
- Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK
| | - Rachael Natrajan
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
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32
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Heong V, Tan TZ, Miwa M, Ye J, Lim D, Herrington CS, Iida Y, Yano M, Yasuda M, Ngoi NY, Wong SJ, Okamoto A, Gourley C, Hasegawa K, Tan DS, Huang RY. A multi-ethnic analysis of immune-related gene expression signatures in patients with ovarian clear cell carcinoma. J Pathol 2021; 255:285-295. [PMID: 34322886 PMCID: PMC9539643 DOI: 10.1002/path.5769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/07/2021] [Accepted: 07/23/2021] [Indexed: 11/23/2022]
Abstract
Little is known about the immune environment of ovarian clear cell carcinoma (OCCC) and its impact on various ethnic backgrounds. The aim of this OCCC immune‐related gene expression signatures (irGES) study was to address the interaction between tumour and immune environment of ethnically‐diverse Asian and Caucasian populations and to identify relevant molecular subsets of biological and clinical importance. Our study included 264 women from three different countries (Singapore, Japan, and the UK) and identified four novel immune subtypes (PD1‐high, CTLA4‐high, antigen‐presentation, and pro‐angiogenic subtype) with differentially expressed pathways, and gene ontologies using the NanoString nCounter PanCancer Immune Profiling Panel. The PD1‐high and CTLA4‐high subtypes demonstrated significantly higher PD1, PDL1, and CTLA4 expression, and were associated with poorer clinical outcomes. Mismatch repair (MMR) protein expression, assessed by immunohistochemistry, revealed that about 5% of OCCCs had deficient MMR expression. The prevalence was similar across the three countries and appeared to cluster in the CTLA4‐high subtype. Our results suggest that OCCC from women of Asian and Caucasian descent shares significant clinical and molecular similarities. To our knowledge, our study is the first study to include both Asian and Caucasian women with OCCC and helps to shine light on the impact of ethnic differences on the immune microenvironment of OCCC. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Valerie Heong
- Department of Medical Oncology, Tan Tock Seng Hospital, Singapore
| | - Tuan Z Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Maiko Miwa
- Department of Gynecologic Oncology, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Jieru Ye
- School of Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Diana Lim
- Department of Pathology, National University Hospital, Singapore
| | - C Simon Herrington
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - Yasushi Iida
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - Mitsutake Yano
- Department of Pathology, Saitama Medical University International Medical Center, Hidaka-shi, Japan
| | - Masanori Yasuda
- Department of Pathology, Saitama Medical University International Medical Center, Hidaka-shi, Japan
| | - Natalie Yl Ngoi
- Department of Haematology and Oncology, National University Cancer Institute Singapore, Singapore
| | - Sb Justin Wong
- Department of Pathology, National University Hospital, Singapore
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo, Japan
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - Kosei Hasegawa
- Department of Gynecologic Oncology, Saitama Medical University International Medical Center, Hidaka, Japan
| | - David Sp Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Haematology and Oncology, National University Cancer Institute Singapore, Singapore
| | - Ruby Yj Huang
- School of Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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33
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Hsu Lin L, Zamuco RL, Sharma Shukla P. Intratumoural Budding is Associated with Poor Clinical Outcome in Early-Stage Clear Cell Carcinoma of Ovary. Histopathology 2021; 79:1018-1029. [PMID: 34292622 DOI: 10.1111/his.14459] [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] [Received: 05/31/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 11/26/2022]
Abstract
AIMS Clear cell carcinoma of ovary (CCC) is considered a high-grade malignancy by default and the role of histological grading for assessing clinical outcome is not established. We aimed to evaluate histopathological features associated with clinical outcome in CCC patients. Seventy-six cases of CCC with available clinical follow-up information were studied. Histopathological features including tumour size, architectural patterns, nuclear atypia, mitotic activity, intraumoural and peritumoral inflammation, presence of endometriosis, peritumoural and intratumoural budding were evaluated. Multivariate analysis was performed with logistic regression and Kaplan-Meier survival curves with log rank test were used for survival analysis. METHODS AND RESULTS Forty cases (53%) presented at stage I. Complete response to treatment was achieved in 65%, while 35% of patients had tumor recurrence or progression of disease despite treatment. At last follow-up, 13% had died of disease, 20% were alive with disease and 67% had no evidence of disease. Higher stage (p=0.0016) and presence of intratumoural budding (p=0.0454) were independently associated with recurrence/disease progression. Advanced stage (p=0.0011), presence of lymph node involvement (p=0.0003), intratumoural budding (p=0.0023) and peritumoural budding (p=0.0334) were significantly associated with shorter survival. Intratumoural budding was significantly associated with recurrent/progressive disease (p=0.0195) and shorter survival (p=0.0277) within the cohort of low-stage (I/II) patients as well. CONCLUSIONS We have shown that besides the classic prognostic factors of stage and lymph node status, presence of tumour budding is associated with poorer outcome in patients with CCC. Specifically, evaluation of intratumoural budding may help to better predict prognosis in patients with early-stage disease.
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34
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Mori S, Gotoh O, Kiyotani K, Low SK. Genomic alterations in gynecological malignancies: histotype-associated driver mutations, molecular subtyping schemes, and tumorigenic mechanisms. J Hum Genet 2021; 66:853-868. [PMID: 34092788 DOI: 10.1038/s10038-021-00940-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/14/2021] [Accepted: 05/25/2021] [Indexed: 02/08/2023]
Abstract
There are numerous histological subtypes (histotypes) of gynecological malignancies, with each histotype considered to largely reflect a feature of the "cell of origin," and to be tightly linked with the clinical behavior and biological phenotype of the tumor. The recent advances in massive parallel sequencing technologies have provided a more complete picture of the range of the genomic alterations that can persist within individual tumors, and have highlighted the types and frequencies of driver-gene mutations and molecular subtypes often associated with these histotypes. Several large-scale genomic cohorts, including the Cancer Genome Atlas (TCGA), have been used to characterize the genomic features of a range of gynecological malignancies, including high-grade serous ovarian carcinoma, uterine corpus endometrial carcinoma, uterine cervical carcinoma, and uterine carcinosarcoma. These datasets have also been pivotal in identifying clinically relevant molecular targets and biomarkers, and in the construction of molecular subtyping schemes. In addition, the recent widespread use of clinical sequencing for the more ubiquitous types of gynecological cancer has manifested in a series of large genomic datasets that have allowed the characterization of the genomes, driver mutations, and histotypes of even rare cancer types, with sufficient statistical power. Here, we review the field of gynecological cancer, and seek to describe the genomic features by histotype. We also will demonstrate how these are linked with clinicopathological attributes and highlight the potential tumorigenic mechanisms.
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Affiliation(s)
- Seiichi Mori
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.
| | - Osamu Gotoh
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kazuma Kiyotani
- Project for Immunogenomics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Siew Kee Low
- Project for Immunogenomics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
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35
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Lapke N, Chen CH, Chang TC, Chao A, Lu YJ, Lai CH, Tan KT, Chen HC, Lu HY, Chen SJ. Genetic alterations and their therapeutic implications in epithelial ovarian cancer. BMC Cancer 2021; 21:499. [PMID: 33947352 PMCID: PMC8097933 DOI: 10.1186/s12885-021-08233-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 04/21/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Genetic alterations for epithelial ovarian cancer are insufficiently characterized. Previous studies are limited regarding included histologies, gene numbers, copy number variant (CNV) detection, and interpretation of pathway alteration patterns of individual patients. METHODS We sequenced 410 genes to analyze mutations and CNV of 82 ovarian carcinomas, including high-grade serous (n = 37), endometrioid (n = 22) and clear cell (n = 23) histologies. Eligibility for targeted therapy was determined for each patient by a pathway-based approach. The analysis covered DNA repair, receptor tyrosine kinase, PI3K/AKT/MTOR, RAS/MAPK, cell cycle, and hedgehog pathways, and included 14 drug targets. RESULTS Postulated PARP, MTOR, and CDK4/6 inhibition sensitivity were most common. BRCA1/2 alterations, PTEN loss, and gain of PIK3CA and CCND1 were characteristic for high-grade serous carcinomas. Mutations of ARID1A, PIK3CA, and KRAS, and ERBB2 gain were enriched in the other histologies. PTEN mutations and high tumor mutational burden were characteristic for endometrioid carcinomas. Drug target downstream alterations impaired actionability in all histologies, and many alterations would not have been discovered by key gene mutational analysis. Individual patients often had more than one actionable drug target. CONCLUSIONS Genetic alterations in ovarian carcinomas are complex and differ among histologies. Our results aid the personalization of therapy and biomarker analysis for clinical studies, and indicate a high potential for combinations of targeted therapies.
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MESH Headings
- Adenocarcinoma, Clear Cell/genetics
- Adenocarcinoma, Clear Cell/pathology
- Adenocarcinoma, Clear Cell/therapy
- Carcinoma/genetics
- Carcinoma/pathology
- Carcinoma/therapy
- Carcinoma, Endometrioid/genetics
- Carcinoma, Endometrioid/pathology
- Carcinoma, Endometrioid/therapy
- Carcinoma, Ovarian Epithelial/genetics
- Carcinoma, Ovarian Epithelial/pathology
- Carcinoma, Ovarian Epithelial/therapy
- Cell Cycle/genetics
- DNA Copy Number Variations
- DNA Mutational Analysis/methods
- DNA Repair/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Hedgehog Proteins/genetics
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Mutation
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/pathology
- Ovarian Neoplasms/therapy
- Precision Medicine
- Retrospective Studies
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Affiliation(s)
- Nina Lapke
- ACT Genomics, Co. Ltd., 3F., No.345, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan
- ACT Genomics, Co. Ltd., Units 803 - 807, 8F, Building 15W, No.15 Science Park West Avenue, Hong Kong Science Park, Pak Shek Kok. NT, Hong Kong, Hong Kong
| | - Chien-Hung Chen
- ACT Genomics, Co. Ltd., 3F., No.345, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan
| | - Ting-Chang Chang
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital and Chang Gung University, Linkou Medical Center, 5 Fushin St., Guishan District, Taoyuan, 333, Taiwan
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, 5 Fushin St., Guishan District, Taoyuan, 333, Taiwan
| | - Angel Chao
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital and Chang Gung University, Linkou Medical Center, 5 Fushin St., Guishan District, Taoyuan, 333, Taiwan
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, 5 Fushin St., Guishan District, Taoyuan, 333, Taiwan
| | - Yen-Jung Lu
- ACT Genomics, Co. Ltd., 3F., No.345, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan.
| | - Chyong-Huey Lai
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital and Chang Gung University, Linkou Medical Center, 5 Fushin St., Guishan District, Taoyuan, 333, Taiwan
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, 5 Fushin St., Guishan District, Taoyuan, 333, Taiwan
| | - Kien Thiam Tan
- ACT Genomics, Co. Ltd., 3F., No.345, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan
| | - Hua-Chien Chen
- ACT Genomics, Co. Ltd., 3F., No.345, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan
| | - Hsiao-Yun Lu
- ACT Genomics, Co. Ltd., 3F., No.345, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan
| | - Shu-Jen Chen
- ACT Genomics, Co. Ltd., 3F., No.345, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan
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Takahashi K, Takenaka M, Okamoto A, Bowtell DDL, Kohno T. Treatment Strategies for ARID1A-Deficient Ovarian Clear Cell Carcinoma. Cancers (Basel) 2021; 13:1769. [PMID: 33917230 PMCID: PMC8068058 DOI: 10.3390/cancers13081769] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/27/2021] [Accepted: 03/31/2021] [Indexed: 02/06/2023] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is a histological subtype of ovarian cancer that is more frequent in Asian countries (~25% of ovarian cancers) than in US/European countries (less than 10%). OCCC is refractory to conventional platinum-based chemotherapy, which is effective against high-grade serous carcinoma (HGSC), a major histological subtype of ovarian cancer. Notably, deleterious mutations in SWI/SNF chromatin remodeling genes, such as ARID1A, are common in OCCC but rare in HGSC. Because this complex regulates multiple cellular processes, including transcription and DNA repair, molecularly targeted therapies that exploit the consequences of SWI/SNF deficiency may have clinical efficacy against OCCC. Three such strategies have been proposed to date: prioritizing a gemcitabine-based chemotherapeutic regimen, synthetic lethal therapy targeting vulnerabilities conferred by SWI/SNF deficiency, and immune checkpoint blockade therapy that exploits the high mutational burden of ARID1A-deficient tumor. Thus, ARID1A deficiency has potential as a biomarker for precision medicine of ovarian cancer.
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Affiliation(s)
- Kazuaki Takahashi
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo 105-8461, Japan; (K.T.); (M.T.); (A.O.)
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia;
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Masataka Takenaka
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo 105-8461, Japan; (K.T.); (M.T.); (A.O.)
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo 105-8461, Japan; (K.T.); (M.T.); (A.O.)
| | - David D. L. Bowtell
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia;
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
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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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38
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Zhang Y, Zhang R, Liang F, Zhang L, Liang X. Identification of Metabolism-Associated Prostate Cancer Subtypes and Construction of a Prognostic Risk Model. Front Oncol 2020; 10:598801. [PMID: 33324566 PMCID: PMC7726320 DOI: 10.3389/fonc.2020.598801] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
Background Despite being the second most common tumor in men worldwide, the tumor metabolism-associated mechanisms of prostate cancer (PCa) remain unclear. Herein, this study aimed to investigate the metabolism-associated characteristics of PCa and to develop a metabolism-associated prognostic risk model for patients with PCa. Methods The activity levels of PCa metabolic pathways were determined using mRNA expression profiling of The Cancer Genome Atlas Prostate Adenocarcinoma cohort via single-sample gene set enrichment analysis (ssGSEA). The analyzed samples were divided into three subtypes based on the partitioning around medication algorithm. Tumor characteristics of the subsets were then investigated using t-distributed stochastic neighbor embedding (t-SNE) analysis, differential analysis, Kaplan–Meier survival analysis, and GSEA. Finally, we developed and validated a metabolism-associated prognostic risk model using weighted gene co-expression network analysis, univariate Cox analysis, least absolute shrinkage and selection operator, and multivariate Cox analysis. Other cohorts (GSE54460, GSE70768, genotype-tissue expression, and International Cancer Genome Consortium) were utilized for external validation. Drug sensibility analysis was performed on Genomics of Drug Sensitivity in Cancer and GSE78220 datasets. In total, 1,039 samples and six cell lines were concluded in our work. Results Three metabolism-associated clusters with significantly different characteristics in disease-free survival (DFS), clinical stage, stemness index, tumor microenvironment including stromal and immune cells, DNA mutation (TP53 and SPOP), copy number variation, and microsatellite instability were identified in PCa. Eighty-four of the metabolism-associated module genes were narrowed to a six-gene signature associated with DFS, CACNG4, SLC2A4, EPHX2, CA14, NUDT7, and ADH5 (p <0.05). A risk model was developed, and external validation revealed the strong robustness our risk model possessed in diagnosis and prognosis as well as the association with the cancer feature of drug sensitivity. Conclusions The identified metabolism-associated subtypes reflected the pathogenesis, essential features, and heterogeneity of PCa tumors. Our metabolism-associated risk model may provide clinicians with predictive values for diagnosis, prognosis, and treatment guidance in patients with PCa.
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Affiliation(s)
- Yanlong Zhang
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, China.,First Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Ruiqiao Zhang
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, China.,First Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Fangzhi Liang
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, China.,First Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Liyun Zhang
- Department of Rheumatology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Taiyuan, China
| | - Xuezhi Liang
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, China
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Zhang Z, Chen J, Zhu S, Zhu D, Xu J, He G. Construction and Validation of a Cell Cycle-Related Robust Prognostic Signature in Colon Cancer. Front Cell Dev Biol 2020; 8:611222. [PMID: 33304907 PMCID: PMC7701219 DOI: 10.3389/fcell.2020.611222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/28/2020] [Indexed: 01/05/2023] Open
Abstract
Colon cancer is one of the most common cancers, great progress was taken place in the treatment of colon cancer, however, the prognostic assessment system remains lagging. Cell cycle plays a vital role in the whole procedure of cancers. In this study, we firstly identified cell cycle-related genes specific in colon cancer. Functional enrichment analysis proved our analysis reliable. Furthermore, we constructed a robust signature based on the cell cycle-related genes. The AUC of the signature to predict the overall survival was 0.808, 0.807, and 0.831 of AUC at 1, 3, and 5 years, respectively. Internal and external validation proved the signature efficient. The 9 genes involved in the signature also showed a great job in molecular subgrouping which indicated the significant value of the 9 genes for further experimental research. In conclusion, the present research provided a novel robust signature predicting the prognosis of colon cancer.
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Affiliation(s)
- Zhiyuan Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jingwen Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shichao Zhu
- Department of Cardiac Surgery, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dexiang Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guodong He
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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40
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Characterization of Mutational Status, Spheroid Formation, and Drug Response of a New Genomically-Stable Human Ovarian Clear Cell Carcinoma Cell Line, 105C. Cells 2020; 9:cells9112408. [PMID: 33153119 PMCID: PMC7693681 DOI: 10.3390/cells9112408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/22/2020] [Accepted: 10/28/2020] [Indexed: 12/16/2022] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is a rare subtype of gynecological cancer for which well-characterized and authenticated model systems are scarce. We provide an extensive characterization of ‘105C’, a cell line generated from an adenocarcinoma of the clear cell histotype using targeted next-generation sequencing, cytogenetic microarrays, along with analyses of AKT/mTOR signaling. We report that that the 105C cell line is a bona fide OCCC cell line, carrying PIK3CA, PTEN, and ARID1A gene mutations, consistent with OCCC, yet maintain a stable genome as reflected by low copy number variation. Unlike KOC-7c, TOV-21G, and RMG-V OCCC lines also mutated for the above genes, the 105C cells do not carry mutations in mismatch repair genes. Importantly, we show that 105C cells exhibit greater resistance to mTOR inhibition and carboplatin treatment compared to 9 other OCCC cell lines in 3D spheroid cultures. This resistance may be attributed to 105C cells remaining dormant in suspension culture which surprisingly, contrasts with several other OCCC lines which continue to proliferate in long-term suspension culture. 105C cells survive xenotransplantation but do not proliferate and metastasize. Collectively, we show that the 105C OCCC cell line exhibits unique properties useful for the pre-clinical investigation of OCCC pathobiology.
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41
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Khan T, Sullivan MA, Gunter JH, Kryza T, Lyons N, He Y, Hooper JD. Revisiting Glycogen in Cancer: A Conspicuous and Targetable Enabler of Malignant Transformation. Front Oncol 2020; 10:592455. [PMID: 33224887 PMCID: PMC7667517 DOI: 10.3389/fonc.2020.592455] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023] Open
Abstract
Once thought to be exclusively a storage hub for glucose, glycogen is now known to be essential in a range of physiological processes and pathological conditions. Glycogen lies at the nexus of diverse processes that promote malignancy, including proliferation, migration, invasion, and chemoresistance of cancer cells. It is also implicated in processes associated with the tumor microenvironment such as immune cell effector function and crosstalk with cancer-associated fibroblasts to promote metastasis. The enzymes of glycogen metabolism are dysregulated in a wide variety of malignancies, including cancers of the kidney, ovary, lung, bladder, liver, blood, and breast. Understanding and targeting glycogen metabolism in cancer presents a promising but under-explored therapeutic avenue. In this review, we summarize the current literature on the role of glycogen in cancer progression and discuss its potential as a therapeutic target for cancer treatment.
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Affiliation(s)
- Tashbib Khan
- Mater Research Institute—The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Mitchell A. Sullivan
- Mater Research Institute—The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Jennifer H. Gunter
- Faculty of Health, Australian Prostate Cancer Research Centre-Queensland, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Thomas Kryza
- Mater Research Institute—The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Nicholas Lyons
- Mater Research Institute—The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Yaowu He
- Mater Research Institute—The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - John D. Hooper
- Mater Research Institute—The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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42
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Iida Y, Okamoto A, Hollis RL, Gourley C, Herrington CS. Clear cell carcinoma of the ovary: a clinical and molecular perspective. Int J Gynecol Cancer 2020; 31:605-616. [PMID: 32948640 DOI: 10.1136/ijgc-2020-001656] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
Clear cell carcinoma of the ovary has distinct biology and clinical behavior. There are significant geographical and racial differences in the incidence of clear cell carcinoma compared with other epithelial ovarian tumors. Patients with clear cell carcinoma are younger, tend to present at an early stage, and their tumors are commonly associated with endometriosis, which is widely accepted as a direct precursor of clear cell carcinoma and has been identified pathologically in approximately 50% of clear cell carcinoma cases. The most frequent and important specific gene alterations in clear cell carcinoma are mutations of AT-rich interaction domain 1A (ARID1A) (~50% of cases) and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) (~50% cases). More broadly, subgroups of clear cell carcinoma have been identified based on C-APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) and C-AGE (age-related) mutational signatures. Gene expression profiling shows upregulation of hepatocyte nuclear factor 1-beta (HNF1β) and oxidative stress-related genes, and has identified epithelial-like and mesenchymal-like tumor subgroups. Although the benefit of platinum-based chemotherapy is not clearly defined it remains the mainstay of first-line therapy. Patients with early-stage disease have a favorable clinical outcome but the prognosis of patients with advanced-stage or recurrent disease is poor. Alternative treatment strategies are required to improve patient outcome and the development of targeted therapies based on molecular characteristics is a promising approach. Improved specificity of the histological definition of this tumor type is helping these efforts but, due to the rarity of clear cell carcinoma, international collaboration will be essential to design appropriately powered, large-scale clinical trials.
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Affiliation(s)
- Yasushi Iida
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
| | - Robert L Hollis
- University of Edinburgh Cancer Research UK Centre, Edinburgh, UK
| | - Charlie Gourley
- University of Edinburgh Cancer Research UK Centre, Edinburgh, UK
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Liu N, Liu Z, Liu X, Duan X, Huang Y, Jin Z, Niu Y, Zhang L, Chen H. Identification of an Immune-Related Prognostic Signature Associated With Immune Infiltration in Melanoma. Front Genet 2020; 11:1002. [PMID: 33005180 PMCID: PMC7484056 DOI: 10.3389/fgene.2020.01002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/06/2020] [Indexed: 12/29/2022] Open
Abstract
Melanoma is the leading cause of cancer-related death among skin tumors, with an increasing incidence worldwide. Few studies have effectively investigated the significance of an immune-related gene (IRG) signature for melanoma prognosis. Here, we constructed an IRGs prognostic signature using bioinformatics methods and evaluated and validated its predictive capability. Then, immune cell infiltration and tumor mutation burden (TMB) landscapes associated with this signature in melanoma were analyzed comprehensively. With the 10-IRG prognostic signature, melanoma patients in the low-risk group showed better survival with distinct features of high immune cell infiltration and TMB. Importantly, melanoma patients in this subgroup were significantly responsive to MAGE-A3 in the validation cohort. This immune-related prognostic signature is thus a reliable tool to predict melanoma prognosis; as the underlying mechanism of this signature is associated with immune infiltration and mutation burden, it might reflect the benefit of immunotherapy to patients.
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Affiliation(s)
- Nian Liu
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zijian Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinxin Liu
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoru Duan
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqiong Huang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zilin Jin
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Niu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liling Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongxiang Chen
- Department of Dermatology, The 6th Affifiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
- Department of Dermatology, Union Shenzhen Hospital, Huazhong University of Science and Technology, Shenzhen, China
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Ngoi NY, Heong V, Ow S, Chay WY, Kim HS, Choi CH, Goss G, Goh JC, Tai BC, Lim DG, Kaliaperumal N, Au VB, Connolly JE, Kim JW, Friedlander M, Kim K, Tan DS. A multicenter phase II randomized trial of durvalumab (MEDI-4736) versus physician's choice chemotherapy in recurrent ovarian clear cell adenocarcinoma (MOCCA). Int J Gynecol Cancer 2020; 30:1239-1242. [PMID: 32591370 PMCID: PMC7418587 DOI: 10.1136/ijgc-2020-001604] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The optimal treatment of recurrent ovarian clear cell carcinoma remains unknown. There is increasing rationale to support the role of immune checkpoint inhibitors targeting the programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1) axis in ovarian clear cell carcinoma. PRIMARY OBJECTIVE To evaluate the efficacy of durvalumab (MEDI-4736) compared with standard chemotherapy in patients with recurrent ovarian clear cell carcinoma. STUDY HYPOTHESIS Patients with recurrent ovarian clear cell carcinoma treated with durvalumab will have improved progression-free survival compared with those treated with chemotherapy of physician's choice. TRIAL DESIGN The MOCCA study is a multicenter, open-label, randomized phase II trial in patients with recurrent ovarian clear cell carcinoma, which recruited from eight sites across Gynecologic Cancer Group Singapore (GCGS), Korean Gynecologic-Oncology Group (KGOG), and Australia New Zealand Gynecological Oncology Group (ANZGOG). Enrolled patients were randomized in a 2:1 ratio to receive durvalumab or physician's choice of chemotherapy until disease progression, intolerable toxicity, or withdrawal of patient consent. MAJOR INCLUSION/EXCLUSION CRITERIA Eligible patients required histologically documented diagnosis of recurrent ovarian clear cell carcinoma, as evidenced by WT1 negativity. All patients must have been of Eastern Cooperative Oncology Group (ECOG) performance status 2 or better, and have had previous treatment with, and progressed or recurred after prior platinum-based chemotherapy. No more than four prior lines of treatment were allowed and prior immune checkpoint inhibitor treatment was not permitted. PRIMARY ENDPOINTS The primary endpoint was the median progression-free survival following treatment with durvalumab, compared with physician's choice of chemotherapy. Progression-free survival was defined as the time from the first day of treatment to the first observation of disease progression, or death due to any cause, or last follow-up. SAMPLE SIZE The target sample size was 46 patients. ESTIMATED DATES FOR COMPLETING ACCRUAL AND PRESENTING RESULTS Accrual has been completed and results are expected to be presented by mid-2021. TRIAL REGISTRATION Clinicaltrials.gov: NCT03405454.
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Affiliation(s)
- Natalie Yl Ngoi
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - Valerie Heong
- Department of Medical Oncology, Tan Tock Seng Hospital, Singapore
| | - Samuel Ow
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - Wen Yee Chay
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Hee Seung Kim
- Department of Obstetrics and Gynecology, Seoul National University, Seoul, Republic of Korea
| | - Chel Hun Choi
- Department of Obstetrics and Gynecology, Samsung Medical Center, Seoul, Republic of Korea
| | | | - Jeffrey C Goh
- Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
- The University of Queensland, Saint Lucia, Queensland, Australia
| | - Bee Choo Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Diana Gz Lim
- Department of Pathology, National University Hospital, Singapore
| | - Nivashini Kaliaperumal
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Veonice B Au
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - John E Connolly
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
- Institute of Biomedical Studies, Baylor University, Waco, Texas, USA
| | - Jae-Weon Kim
- Department of Obstetrics and Gynecology, Seoul National University, Seoul, Republic of Korea
| | - Michael Friedlander
- The Prince of Wales Hospital, Randwick, New South Wales, Australia
- Prince of Wales Clinical School University of New South Wales, Randwick, New South Wales, Australia
| | - Kidong Kim
- Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - David Sp Tan
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cancer Science Institute Singapore, Singapore
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45
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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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