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Goehring L, Keegan S, Lahiri S, Xia W, Kong M, Jimenez-Sainz J, Gupta D, Drapkin R, Jensen RB, Smith DJ, Rothenberg E, Fenyö D, Huang TT. Dormant origin firing promotes head-on transcription-replication conflicts at transcription termination sites in response to BRCA2 deficiency. Nat Commun 2024; 15:4716. [PMID: 38830843 PMCID: PMC11148086 DOI: 10.1038/s41467-024-48286-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
BRCA2 is a tumor suppressor protein responsible for safeguarding the cellular genome from replication stress and genotoxicity, but the specific mechanism(s) by which this is achieved to prevent early oncogenesis remains unclear. Here, we provide evidence that BRCA2 acts as a critical suppressor of head-on transcription-replication conflicts (HO-TRCs). Using Okazaki-fragment sequencing (Ok-seq) and computational analysis, we identified origins (dormant origins) that are activated near the transcription termination sites (TTS) of highly expressed, long genes in response to replication stress. Dormant origins are a source for HO-TRCs, and drug treatments that inhibit dormant origin firing led to a reduction in HO-TRCs, R-loop formation, and DNA damage. Using super-resolution microscopy, we showed that HO-TRC events track with elongating RNA polymerase II, but not with transcription initiation. Importantly, RNase H2 is recruited to sites of HO-TRCs in a BRCA2-dependent manner to help alleviate toxic R-loops associated with HO-TRCs. Collectively, our results provide a mechanistic basis for how BRCA2 shields against genomic instability by preventing HO-TRCs through both direct and indirect means occurring at predetermined genomic sites based on the pre-cancer transcriptome.
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Affiliation(s)
- Liana Goehring
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Sarah Keegan
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Institute for Systems Genetics, New York University School of Medicine, New York University School of Medicine, New York, NY, USA
| | - Sudipta Lahiri
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Wenxin Xia
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Michael Kong
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | | | - Dipika Gupta
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ryan B Jensen
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Duncan J Smith
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Eli Rothenberg
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - David Fenyö
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Institute for Systems Genetics, New York University School of Medicine, New York University School of Medicine, New York, NY, USA
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
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2
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Constantinescu DR, Sorop A, Ghionescu AV, Lixandru D, Herlea V, Bacalbasa N, Dima SO. EM-transcriptomic signature predicts drug response in advanced stages of high-grade serous ovarian carcinoma based on ascites-derived primary cultures. Front Pharmacol 2024; 15:1363142. [PMID: 38510654 PMCID: PMC10953505 DOI: 10.3389/fphar.2024.1363142] [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: 12/29/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction: High-grade serous ovarian carcinoma (HGSOC) remains a medical challenge despite considerable improvements in the treatment. Unfortunately, over 75% of patients have already metastasized at the time of diagnosis. Advances in understanding the mechanisms underlying how ascites cause chemoresistance are urgently needed to derive novel therapeutic strategies. This study aimed to identify the molecular markers involved in drug sensitivity and highlight the use of ascites as a potential model to investigate HGSOC treatment options. Methods: After conducting an in silico analysis, eight epithelial-mesenchymal (EM)-associated genes related to chemoresistance were identified. To evaluate differences in EM-associated genes in HGSOC samples, we analyzed ascites-derived HGSOC primary cell culture (AS), tumor (T), and peritoneal nodule (NP) samples. Moreover, in vitro experiments were employed to measure tumor cell proliferation and cell migration in AS, following treatment with doxorubicin (DOX) and cisplatin (CIS) and expression of these markers. Results: Our results showed that AS exhibits a mesenchymal phenotype compared to tumor and peritoneal nodule samples. Moreover, DOX and CIS treatment leads to an invasive-intermediate epithelial-to-mesenchymal transition (EMT) state of the AS by different EM-associated marker expression. For instance, the treatment of AS showed that CDH1 and GATA6 decreased after CIS exposure and increased after DOX treatment. On the contrary, the expression of KRT18 has an opposite pattern. Conclusion: Taken together, our study reports a comprehensive investigation of the EM-associated genes after drug exposure of AS. Exploring ascites and their associated cellular and soluble components is promising for understanding the HGSOC progression and treatment response at a personalized level.
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Affiliation(s)
| | - Andrei Sorop
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | | | - Daniela Lixandru
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
| | - Vlad Herlea
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
- Department of Pathology-Fundeni Clinical Institute, Bucharest, Romania
| | - Nicolae Bacalbasa
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Simona Olimpia Dima
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
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3
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Azzalini E, Stanta G, Canzonieri V, Bonin S. Overview of Tumor Heterogeneity in High-Grade Serous Ovarian Cancers. Int J Mol Sci 2023; 24:15077. [PMID: 37894756 PMCID: PMC10606847 DOI: 10.3390/ijms242015077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Ovarian cancers encompass a group of neoplasms originating from germinal tissues and exhibiting distinct clinical, pathological, and molecular features. Among these, epithelial ovarian cancers (EOCs) are the most prevalent, comprising five distinct tumor histotypes. Notably, high-grade serous ovarian cancers (HGSOCs) represent the majority, accounting for over 70% of EOC cases. Due to their silent and asymptomatic behavior, HGSOCs are generally diagnosed in advanced stages with an evolved and complex genomic state, characterized by high intratumor heterogeneity (ITH) due to chromosomal instability that distinguishes HGSOCs. Histologically, these cancers exhibit significant morphological diversity both within and between tumors. The histologic patterns associated with solid, endometrioid, and transitional (SET) and classic subtypes of HGSOCs offer prognostic insights and may indicate specific molecular profiles. The evolution of HGSOC from primary to metastasis is typically characterized by clonal ITH, involving shared or divergent mutations in neoplastic sub-clones within primary and metastatic sites. Disease progression and therapy resistance are also influenced by non-clonal ITH, related to interactions with the tumor microenvironment and further genomic changes. Notably, significant alterations occur in nonmalignant cells, including cancer-associated fibroblast and immune cells, during tumor progression. This review provides an overview of the complex nature of HGSOC, encompassing its various aspects of intratumor heterogeneity, histological patterns, and its dynamic evolution during progression and therapy resistance.
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Affiliation(s)
- Eros Azzalini
- Department of Medical Sciences (DSM), University of Trieste, 34149 Trieste, Italy; (E.A.); (G.S.); (V.C.)
| | - Giorgio Stanta
- Department of Medical Sciences (DSM), University of Trieste, 34149 Trieste, Italy; (E.A.); (G.S.); (V.C.)
| | - Vincenzo Canzonieri
- Department of Medical Sciences (DSM), University of Trieste, 34149 Trieste, Italy; (E.A.); (G.S.); (V.C.)
- Pathology Unit, Centro di Riferimento Oncologico (CRO) IRCCS, Aviano-National Cancer Institute, 33081 Pordenone, Italy
| | - Serena Bonin
- Department of Medical Sciences (DSM), University of Trieste, 34149 Trieste, Italy; (E.A.); (G.S.); (V.C.)
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4
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Planas-Paz L, Pliego-Mendieta A, Hagedorn C, Aguilera-Garcia D, Haberecker M, Arnold F, Herzog M, Bankel L, Guggenberger R, Steiner S, Chen Y, Kahraman A, Zoche M, Rubin MA, Moch H, Britschgi C, Pauli C. Unravelling homologous recombination repair deficiency and therapeutic opportunities in soft tissue and bone sarcoma. EMBO Mol Med 2023; 15:e16863. [PMID: 36779660 PMCID: PMC10086583 DOI: 10.15252/emmm.202216863] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 02/14/2023] Open
Abstract
Defects in homologous recombination repair (HRR) in tumors correlate with poor prognosis and metastases development. Determining HRR deficiency (HRD) is of major clinical relevance as it is associated with therapeutic vulnerabilities and remains poorly investigated in sarcoma. Here, we show that specific sarcoma entities exhibit high levels of genomic instability signatures and molecular alterations in HRR genes, while harboring a complex pattern of chromosomal instability. Furthermore, sarcomas carrying HRDness traits exhibit a distinct SARC-HRD transcriptional signature that predicts PARP inhibitor sensitivity in patient-derived sarcoma cells. Concomitantly, HRDhigh sarcoma cells lack RAD51 nuclear foci formation upon DNA damage, further evidencing defects in HRR. We further identify the WEE1 kinase as a therapeutic vulnerability for sarcomas with HRDness and demonstrate the clinical benefit of combining DNA damaging agents and inhibitors of DNA repair pathways ex vivo and in the clinic. In summary, we provide a personalized oncological approach to treat sarcoma patients successfully.
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Affiliation(s)
- Lara Planas-Paz
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Alicia Pliego-Mendieta
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Catherine Hagedorn
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Domingo Aguilera-Garcia
- Molecular Tumor Profiling Laboratory, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Martina Haberecker
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Fabian Arnold
- Molecular Tumor Profiling Laboratory, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Marius Herzog
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Lorenz Bankel
- Department of Medical Oncology and Haematology, University Hospital Zurich, Zurich, Switzerland
| | - Roman Guggenberger
- Diagnostic and Interventional Radiology, University Hospital Zurich, Zurich, Switzerland
| | - Sabrina Steiner
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Yanjiang Chen
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Abdullah Kahraman
- Molecular Tumor Profiling Laboratory, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Zoche
- Molecular Tumor Profiling Laboratory, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Mark A Rubin
- Precision Oncology Laboratory, Department for Biomedical Research, Bern Center for Precision Medicine, Bern, Switzerland
| | - Holger Moch
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Christian Britschgi
- Department of Medical Oncology and Haematology, University Hospital Zurich, Zurich, Switzerland
| | - Chantal Pauli
- Laboratory for Systems Pathology and Functional Tumor Pathology, Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.,Medical Faculty, University of Zurich, Zurich, Switzerland
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5
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Chang YH, Chu TY, Ding DC. Spontaneous Transformation of a p53 and Rb-Defective Human Fallopian Tube Epithelial Cell Line after Long Passage with Features of High-Grade Serous Carcinoma. Int J Mol Sci 2022; 23:ijms232213843. [PMID: 36430324 PMCID: PMC9695839 DOI: 10.3390/ijms232213843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/28/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
Ovarian cancer is one of the most lethal gynecological cancers, and 80% are high-grade serous carcinomas (HGSOC). Despite advances in chemotherapy and the development of targeted therapies, the survival rate of HGSOC has only moderately improved. Therefore, a cell model that reflects the pathogenesis and clinical characteristics of this disease is urgently needed. We previously developed a human fallopian tube epithelial cell line (FE25) with p53 and Rb deficiencies. After long-term culture in vitro, cells at high-passage numbers showed spontaneous transformation (FE25L). This study aimed to compare FE25 cells cultured in vitro for low (passage 16-31) and high passages (passage 116-139) to determine whether these cells can serve as an ideal cell model of HGSOC. Compared to the cells at low passage, FE25L cells showed increased cell proliferation, clonogenicity, polyploidy, aneuploidy, cell migration, and invasion. They also showed more resistance to chemotherapy and the ability to grow tumors in xenografts. RNA-seq data also showed upregulation of hypoxia, epithelial-mesenchymal transition (EMT), and the NF-κB pathway in FE25L compared to FE25 cells. qRT-PCR confirmed the upregulation of EMT, cytokines, NF-κB, c-Myc, and the Wnt/β-catenin pathway. Cross-platform comparability found that FE25L cells could be grouped with the other most likely HGSOC lines, such as TYKNU and COV362. In conclusion, FE25L cells showed more aggressive malignant behavior than FE25 cells and hence might serve as a more suitable model for HGSOC research.
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Affiliation(s)
- Yu-Hsun Chang
- Department of Pediatrics, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Tzu Chi University, Hualien 97005, Taiwan
| | - Tang-Yuan Chu
- Department of Obstetrics and Gynecology, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Tzu Chi University, Hualien 97005, Taiwan
- Institute of Medical Sciences, Collagen of Medicine, Tzu Chi University, Hualien 97005, Taiwan
| | - Dah-Ching Ding
- Department of Obstetrics and Gynecology, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Tzu Chi University, Hualien 97005, Taiwan
- Institute of Medical Sciences, Collagen of Medicine, Tzu Chi University, Hualien 97005, Taiwan
- Correspondence: ; Tel.: +886-3856-1825 (ext. 13383); Fax: +886-3857-7161
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6
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Punzón-Jiménez P, Lago V, Domingo S, Simón C, Mas A. Molecular Management of High-Grade Serous Ovarian Carcinoma. Int J Mol Sci 2022; 23:13777. [PMID: 36430255 PMCID: PMC9692799 DOI: 10.3390/ijms232213777] [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] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) represents the most common form of epithelial ovarian carcinoma. The absence of specific symptoms leads to late-stage diagnosis, making HGSOC one of the gynecological cancers with the worst prognosis. The cellular origin of HGSOC and the role of reproductive hormones, genetic traits (such as alterations in P53 and DNA-repair mechanisms), chromosomal instability, or dysregulation of crucial signaling pathways have been considered when evaluating prognosis and response to therapy in HGSOC patients. However, the detection of HGSOC is still based on traditional methods such as carbohydrate antigen 125 (CA125) detection and ultrasound, and the combined use of these methods has yet to support significant reductions in overall mortality rates. The current paradigm for HGSOC management has moved towards early diagnosis via the non-invasive detection of molecular markers through liquid biopsies. This review presents an integrated view of the relevant cellular and molecular aspects involved in the etiopathogenesis of HGSOC and brings together studies that consider new horizons for the possible early detection of this gynecological cancer.
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Affiliation(s)
- Paula Punzón-Jiménez
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
| | - Victor Lago
- Department of Gynecologic Oncology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
- Department of Obstetrics and Gynecology, CEU Cardenal Herrera University, 46115 Valencia, Spain
| | - Santiago Domingo
- Department of Gynecologic Oncology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Universidad de Valencia, 46010 Valencia, Spain
| | - Carlos Simón
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Universidad de Valencia, 46010 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Harvard University, Boston, MA 02215, USA
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aymara Mas
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
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7
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Xu J, Fang Y, Chen K, Li S, Tang S, Ren Y, Cen Y, Fei W, Zhang B, Shen Y, Lu W. Single-Cell RNA Sequencing Reveals the Tissue Architecture in Human High-Grade Serous Ovarian Cancer. Clin Cancer Res 2022; 28:3590-3602. [PMID: 35675036 PMCID: PMC9662915 DOI: 10.1158/1078-0432.ccr-22-0296] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/16/2022] [Accepted: 06/06/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE The heterogeneity of high-grade serous ovarian cancer (HGSOC) is not well studied, which severely hinders clinical treatment of HGSOC. Thus, it is necessary to characterize the heterogeneity of HGSOC within its tumor microenvironment (TME). EXPERIMENTAL DESIGN The tumors of 7 treatment-naïve patients with HGSOC at early or late stages and five age-matched nonmalignant ovarian samples were analyzed by deep single-cell RNA sequencing (scRNA-seq). RESULTS A total of 59,324 single cells obtained from HGSOC and nonmalignant ovarian tissues were sequenced by scRNA-seq. Among those cells, tumor cells were characterized by a set of epithelial-to-mesenchymal transition (EMT)-associated gene signatures, in which a combination of NOTCH1, SNAI2, TGFBR1, and WNT11 was further selected as a genetic panel to predict the poor outcomes of patients with HGSOC. Matrix cancer-associated fibroblasts (mCAF) expressing α-SMA, vimentin, COL3A, COL10A, and MMP11 were the dominant CAFs in HGSOC tumors and could induce EMT properties of ovarian cancer cells in the coculture system. Specific immune cell subsets such as C7-APOBEC3A M1 macrophages, CD8+ TRM, and TEX cells were preferentially enriched in early-stage tumors. In addition, an immune coinhibitory receptor TIGIT was highly expressed on CD8+ TEX cells and TIGIT blockade could significantly reduce ovarian cancer tumor growth in mouse models. CONCLUSIONS Our transcriptomic results analyzed by scRNA-seq delineate an ecosystemic landscape of HGSOC at early or late stages with a focus on its heterogeneity with TME. The major applications of our findings are a four-EMT gene model for prediction of HGSOC patient outcomes, mCAFs' capability of enhancing ovarian cancer cell invasion and potential therapeutic value of anti-TIGIT treatment.
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Affiliation(s)
- Junfen Xu
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China.,Corresponding Authors: Junfen Xu, Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, No. 1 Xueshi Road, Hangzhou, Zhejiang 310006, P.R. China. Phone: 8657-1870-61501; Fax: 8657-1870-61878; E-mail: (lead contact); Weiguo Lu, ; and Yuanming Shen,
| | - Yifeng Fang
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Kelie Chen
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Sen Li
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Sangsang Tang
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Yan Ren
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Yixuan Cen
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Weidong Fei
- Department of Pharmacy, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, P.R. China
| | - Bo Zhang
- Novel Bioinformatics Co., Ltd, Shanghai, P.R. China
| | - Yuanming Shen
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China.,Corresponding Authors: Junfen Xu, Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, No. 1 Xueshi Road, Hangzhou, Zhejiang 310006, P.R. China. Phone: 8657-1870-61501; Fax: 8657-1870-61878; E-mail: (lead contact); Weiguo Lu, ; and Yuanming Shen,
| | - Weiguo Lu
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China.,Center of Uterine Cancer Diagnosis and Therapy of Zhejiang Province, Hangzhou, Zhejiang, P.R. China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, P.R. China.,Corresponding Authors: Junfen Xu, Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, No. 1 Xueshi Road, Hangzhou, Zhejiang 310006, P.R. China. Phone: 8657-1870-61501; Fax: 8657-1870-61878; E-mail: (lead contact); Weiguo Lu, ; and Yuanming Shen,
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8
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Chen J, Shi X, Xiao L, Li Z, Li Z, Sun L. Better or worse? The prognostic role of the mesenchymal subtype in patients with high-grade serous ovarian carcinoma: A systematic review and meta-analysis. Cancer Med 2022; 11:3761-3770. [PMID: 35434908 PMCID: PMC9582683 DOI: 10.1002/cam4.4752] [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: 11/18/2021] [Revised: 02/23/2022] [Accepted: 04/04/2022] [Indexed: 12/24/2022] Open
Abstract
Background Tumor characteristics can be prognostically relevant in patients with high‐grade serous ovarian carcinoma (HGSOC). This study aimed to determine whether different subtypes of HGSOC, especially the mesenchymal subtype, are associated with overall survival (OS) or progression‐free survival (PFS) in patients with HGSOC. Methods PubMed, Embase, and the Cochrane Library were searched for studies published up to September 2020. The eligibility criteria were (1) population: patients with HGSOG with molecular subtyping of their tumor, (2) exposure: mesenchymal subtype, (3) non‐exposure: differentiated, immunoreactive, proliferative, and other non‐mesenchymal subtypes, (4) outcome: survival, with hazard ratios (HRs), and (5) English language. Results The mesenchymal subtype showed no statistically significant difference in OS compared with the immunoreactive subtype (HR = 1.47, 95% CI: 0.78–2.78, p = 0.238; I2 = 81.2%, pheterogeneity = 0.005) or all non‐mesenchymal subtypes (HR = 1.65, 95% CI: 0.97–2.80, p = 0.063; I2 = 79.4%, pheterogeneity = 0.008). The mesenchymal subtype showed no statistically significant difference in PFS compared with the immunoreactive subtype (HR = 1.19, 95% CI: 0.71–2.00, p = 0.514; I2 = 71.6%, pheterogeneity = 0.030) but a significant differences was observed when using all non‐mesenchymal subtypes as reference (HR = 1.51, 95% CI: 1.00–2.28, p = 0.049). The results were robust according to the sensitivity analyses. Conclusions There are no statistically significant differences in OS between the mesenchymal subtype of HGSOC and other subtypes of HGSOC. Because of statistical power, this meta‐analysis cannot conclude about non‐inferiority, and the relationship between the molecular subtypes and HGSOC prognosis remains controversial. Based on one study, the mesenchymal subtype could have a poorer PFS than the non‐mesenchymal subtypes of HGSOC, but this conclusion requires further evidence.
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Affiliation(s)
- Juan Chen
- Department of Obstetrics & Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaoyan Shi
- Central Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lan Xiao
- Department of Obstetrics & Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zelian Li
- Department of Obstetrics & Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhimin Li
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Lei Sun
- Department of Obstetrics & Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, China
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9
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Wang Z, Yang L, Huang Z, Li X, Xiao J, Qu Y, Huang L, Wang Y. Identification of Prognosis Biomarkers for High-Grade Serous Ovarian Cancer Based on Stemness. Front Genet 2022; 13:861954. [PMID: 35360863 PMCID: PMC8964092 DOI: 10.3389/fgene.2022.861954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/23/2022] [Indexed: 12/20/2022] Open
Abstract
In this paper, high-grade serous ovarian cancer (HGSOC) is studied, which is the most common histological subtype of ovarian cancer. We use a new analytical procedure to combine the bulk RNA-Seq sample for ovarian cancer, mRNA expression-based stemness index (mRNAsi), and single-cell data for ovarian cancer. Through integrating bulk RNA-Seq sample of cancer samples from TCGA, UCSC Xena and single-cell RNA-Seq (scRNA-Seq) data of HGSOC from GEO, and performing a series of computational analyses on them, we identify stemness markers and survival-related markers, explore stem cell populations in ovarian cancer, and provide potential treatment recommendation. As a result, 171 key genes for capturing stem cell characteristics are screened and one vital cancer stem cell subpopulation is identified. Through further analysis of these key genes and cancer stem cell subpopulation, more critical genes can be obtained as LCP2, FCGR3A, COL1A1, COL1A2, MT-CYB, CCT5, and PAPPA, are closely associated with ovarian cancer. So these genes have the potential to be used as prognostic biomarkers for ovarian cancer.
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Affiliation(s)
- Zhihang Wang
- Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Lili Yang
- Department of Obstetrics, The First Hospital of Jilin University, Changchun, China
| | - Zhenyu Huang
- Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Xuan Li
- Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Juan Xiao
- Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Yinwei Qu
- Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Lan Huang
- Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Yan Wang
- Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China.,College of Artificial Intelligence, Jilin University, Changchun, China
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Nagasawa S, Ikeda K, Shintani D, Yang C, Takeda S, Hasegawa K, Horie K, Inoue S. Identification of a Novel Oncogenic Fusion Gene SPON1-TRIM29 in Clinical Ovarian Cancer That Promotes Cell and Tumor Growth and Enhances Chemoresistance in A2780 Cells. Int J Mol Sci 2022; 23:689. [PMID: 35054873 PMCID: PMC8776205 DOI: 10.3390/ijms23020689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/04/2023] Open
Abstract
Gene structure alterations, such as chromosomal rearrangements that develop fusion genes, often contribute to tumorigenesis. It has been shown that the fusion genes identified in public RNA-sequencing datasets are mainly derived from intrachromosomal rearrangements. In this study, we explored fusion transcripts in clinical ovarian cancer specimens based on our RNA-sequencing data. We successfully identified an in-frame fusion transcript SPON1-TRIM29 in chromosome 11 from a recurrent tumor specimen of high-grade serous carcinoma (HGSC), which was not detected in the corresponding primary carcinoma, and validated the expression of the identical fusion transcript in another tumor from a distinct HGSC patient. Ovarian cancer A2780 cells stably expressing SPON1-TRIM29 exhibited an increase in cell growth, whereas a decrease in apoptosis was observed, even in the presence of anticancer drugs. The siRNA-mediated silencing of SPON1-TRIM29 fusion transcript substantially impaired the enhanced growth of A2780 cells expressing the chimeric gene treated with anticancer drugs. Moreover, a subcutaneous xenograft model using athymic mice indicated that SPON1-TRIM29-expressing A2780 cells rapidly generated tumors in vivo compared to control cells, whose growth was significantly repressed by the fusion-specific siRNA administration. Overall, the SPON1-TRIM29 fusion gene could be involved in carcinogenesis and chemotherapy resistance in ovarian cancer, and offers potential use as a diagnostic and therapeutic target for the disease with the fusion transcript.
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Affiliation(s)
- Saya Nagasawa
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan;
| | - Kazuhiro Ikeda
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
| | - Daisuke Shintani
- Department of Gynecologic Oncology, Saitama Medical University International Medical Center, Hidaka, Saitama 350-1298, Japan; (D.S.); (K.H.)
| | - Chiujung Yang
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan;
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan;
| | - Kosei Hasegawa
- Department of Gynecologic Oncology, Saitama Medical University International Medical Center, Hidaka, Saitama 350-1298, Japan; (D.S.); (K.H.)
| | - Kuniko Horie
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
| | - Satoshi Inoue
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo 173-0015, Japan
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