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Fu M, Deng F, Chen J, Fu L, Lei J, Xu T, Chen Y, Zhou J, Gao Q, Ding H. Current data and future perspectives on DNA methylation in ovarian cancer (Review). Int J Oncol 2024; 64:62. [PMID: 38757340 PMCID: PMC11095605 DOI: 10.3892/ijo.2024.5650] [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: 11/23/2023] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Ovarian cancer (OC) represents the most prevalent malignancy of the female reproductive system. Its distinguishing features include a high aggressiveness, substantial morbidity and mortality, and a lack of apparent symptoms, which collectively pose significant challenges for early detection. Given that aberrant DNA methylation events leading to altered gene expression are characteristic of numerous tumor types, there has been extensive research into epigenetic mechanisms, particularly DNA methylation, in human cancers. In the context of OC, DNA methylation is often associated with the regulation of critical genes, such as BRCA1/2 and Ras‑association domain family 1A. Methylation modifications within the promoter regions of these genes not only contribute to the pathogenesis of OC, but also induce medication resistance and influence the prognosis of patients with OC. As such, a more in‑depth understanding of DNA methylation underpinning carcinogenesis could potentially facilitate the development of more effective therapeutic approaches for this intricate disease. The present review focuses on classical tumor suppressor genes, oncogenes, signaling pathways and associated microRNAs in an aim to elucidate the influence of DNA methylation on the development and progression of OC. The advantages and limitations of employing DNA methylation in the diagnosis, treatment and prevention of OC are also discussed. On the whole, the present literature review indicates that the DNA methylation of specific genes could potentially serve as a prognostic biomarker for OC and a therapeutic target for personalized treatment strategies. Further investigations in this field may yield more efficacious diagnostic and therapeutic alternatives for patients with OC.
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Affiliation(s)
- Mengyu Fu
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Fengying Deng
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jie Chen
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Li Fu
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jiahui Lei
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Ting Xu
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
- Department of Gynecology and Obstetrics, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, Jiangsu 215100, P.R. China
| | - Youguo Chen
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jinhua Zhou
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Qinqin Gao
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Hongmei Ding
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
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2
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Wang J, Ford JC, Mitra AK. Defining the Role of Metastasis-Initiating Cells in Promoting Carcinogenesis in Ovarian Cancer. BIOLOGY 2023; 12:1492. [PMID: 38132318 PMCID: PMC10740540 DOI: 10.3390/biology12121492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/23/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
Ovarian cancer is the deadliest gynecological malignancy with a high prevalence of transcoelomic metastasis. Metastasis is a multi-step process and only a small percentage of cancer cells, metastasis-initiating cells (MICs), have the capacity to finally establish metastatic lesions. These MICs maintain a certain level of stemness that allows them to differentiate into other cell types with distinct transcriptomic profiles and swiftly adapt to external stresses. Furthermore, they can coordinate with the microenvironment, through reciprocal interactions, to invade and establish metastases. Therefore, identifying, characterizing, and targeting MICs is a promising strategy to counter the spread of ovarian cancer. In this review, we provided an overview of OC MICs in the context of characterization, identification through cell surface markers, and their interactions with the metastatic niche to promote metastatic colonization.
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Affiliation(s)
- Ji Wang
- Indiana University School of Medicine-Bloomington, Indiana University, Bloomington, IN 47405, USA; (J.W.); (J.C.F.)
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN 46202, USA
| | - James C. Ford
- Indiana University School of Medicine-Bloomington, Indiana University, Bloomington, IN 47405, USA; (J.W.); (J.C.F.)
| | - Anirban K. Mitra
- Indiana University School of Medicine-Bloomington, Indiana University, Bloomington, IN 47405, USA; (J.W.); (J.C.F.)
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN 46202, USA
- Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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3
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Khella CA, Franciosa L, Rodirguez-Rodriguez L, Rajkarnikar R, Mythreye K, Gatza ML. HCK Promotes High-Grade Serous Ovarian Cancer Tumorigenesis through CD44 and NOTCH3 Signaling. Mol Cancer Res 2023; 21:1037-1049. [PMID: 37342066 DOI: 10.1158/1541-7786.mcr-22-0496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/05/2022] [Accepted: 06/15/2023] [Indexed: 06/22/2023]
Abstract
High-grade serous ovarian cancer (HGSOC) is a highly aggressive and lethal subtype of ovarian cancer. While most patients initially respond to standard-of-care treatment, the majority will eventually relapse and succumb to their disease. Despite significant advances in our understanding of this disease, the mechanisms that govern the distinctions between HGSOC with good and poor prognosis remain unclear. In this study, we implemented a proteogenomic approach to analyze gene expression, proteomic and phosphoproteomic profiles of HGSOC tumor samples to identify molecular pathways that distinguish HGSOC tumors relative to clinical outcome. Our analyses identify significant upregulation of hematopoietic cell kinase (HCK) expression and signaling in poor prognostic HGSOC patient samples. Analyses of independent gene expression datasets and IHC of patient samples confirmed increased HCK signaling in tumors relative to normal fallopian or ovarian samples and demonstrated aberrant expression in tumor epithelial cells. Consistent with the association between HCK expression and tumor aggressiveness in patient samples, in vitro phenotypic studies showed that HCK can, in part, promote cell proliferation, colony formation, and invasive capacity of cell lines. Mechanistically, HCK mediates these phenotypes, partly through CD44 and NOTCH3-dependent signaling, and inhibiting CD44 or NOTCH3 activity, either genetically or through gamma-secretase inhibitors, can revert HCK-driven phenotypes. IMPLICATIONS Collectively, these studies establish that HCK acts as an oncogenic driver of HGSOC through aberrant activation of CD44 and NOTCH3 signaling and identifies this network as a potential therapeutic opportunity in a subset of patients with aggressive and recurrent HGSOC.
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Affiliation(s)
- Christen A Khella
- Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, New Jersey
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
- School of Graduate Studies, Rutgers University, New Brunswick, New Jersey
| | | | | | - Resha Rajkarnikar
- Department of Pathology and O'Neal Comprehensive Cancer Center, Heersink School of Medicine, University of Alabama, Birmingham, Alabama
| | - Karthikeyan Mythreye
- Department of Pathology and O'Neal Comprehensive Cancer Center, Heersink School of Medicine, University of Alabama, Birmingham, Alabama
| | - Michael L Gatza
- Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, New Jersey
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
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4
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Keathley R, Kocherginsky M, Davuluri R, Matei D. Integrated Multi-Omic Analysis Reveals Immunosuppressive Phenotype Associated with Poor Outcomes in High-Grade Serous Ovarian Cancer. Cancers (Basel) 2023; 15:3649. [PMID: 37509311 PMCID: PMC10377286 DOI: 10.3390/cancers15143649] [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: 05/18/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
High-grade serous ovarian cancer (HGSOC) is characterized by a complex genomic landscape, with both genetic and epigenetic diversity contributing to its pathogenesis, disease course, and response to treatment. To better understand the association between genomic features and response to treatment among 370 patients with newly diagnosed HGSOC, we utilized multi-omic data and semi-biased clustering of HGSOC specimens profiled by TCGA. A Cox regression model was deployed to select model input features based on the influence on disease recurrence. Among the features most significantly correlated with recurrence were the promotor-associated probes for the NFRKB and DPT genes and the TREML1 gene. Using 1467 transcriptomic and methylomic features as input to consensus clustering, we identified four distinct tumor clusters-three of which had noteworthy differences in treatment response and time to disease recurrence. Each cluster had unique divergence in differential analyses and distinctly enriched pathways therein. Differences in predicted stromal and immune cell-type composition were also observed, with an immune-suppressive phenotype specific to one cluster, which associated with short time to disease recurrence. Our model features were additionally used as a neural network input layer to validate the previously defined clusters with high prediction accuracy (91.3%). Overall, our approach highlights an integrated data utilization workflow from tumor-derived samples, which can be used to uncover novel drivers of clinical outcomes.
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Affiliation(s)
- Russell Keathley
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; (R.K.); (M.K.)
- Driskill Graduate Program in Life Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Masha Kocherginsky
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; (R.K.); (M.K.)
- Department of Preventive Medicine (Biostatistics), Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Chicago, IL 60611, USA
| | - Ramana Davuluri
- Department of Biomedical Informatics, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA;
| | - Daniela Matei
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; (R.K.); (M.K.)
- Robert H. Lurie Comprehensive Cancer Center, Chicago, IL 60611, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
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5
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Sullivan AE. Epigenetic Control of Cell Potency and Fate Determination during Mammalian Gastrulation. Genes (Basel) 2023; 14:1143. [PMID: 37372324 DOI: 10.3390/genes14061143] [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: 04/21/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Pluripotent embryonic stem cells have a unique and characteristic epigenetic profile, which is critical for differentiation to all embryonic germ lineages. When stem cells exit the pluripotent state and commit to lineage-specific identities during the process of gastrulation in early embryogenesis, extensive epigenetic remodelling mediates both the switch in cellular programme and the loss of potential to adopt alternative lineage programmes. However, it remains to be understood how the stem cell epigenetic profile encodes pluripotency, or how dynamic epigenetic regulation helps to direct cell fate specification. Recent advances in stem cell culture techniques, cellular reprogramming, and single-cell technologies that can quantitatively profile epigenetic marks have led to significant insights into these questions, which are important for understanding both embryonic development and cell fate engineering. This review provides an overview of key concepts and highlights exciting new advances in the field.
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Affiliation(s)
- Adrienne E Sullivan
- Quantitative Stem Cell Biology Lab, Francis Crick Institute, London NW1 1AT, UK
- Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5000, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5000, Australia
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6
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Simon T, Riemer P, Jarosch A, Detjen K, Di Domenico A, Bormann F, Menne A, Khouja S, Monjé N, Childs LH, Lenze D, Leser U, Rossner F, Morkel M, Blüthgen N, Pavel M, Horst D, Capper D, Marinoni I, Perren A, Mamlouk S, Sers C. DNA methylation reveals distinct cells of origin for pancreatic neuroendocrine carcinomas and pancreatic neuroendocrine tumors. Genome Med 2022; 14:24. [PMID: 35227293 PMCID: PMC8886788 DOI: 10.1186/s13073-022-01018-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 01/28/2022] [Indexed: 02/07/2023] Open
Abstract
Background Pancreatic neuroendocrine neoplasms (PanNENs) fall into two subclasses: the well-differentiated, low- to high-grade pancreatic neuroendocrine tumors (PanNETs), and the poorly-differentiated, high-grade pancreatic neuroendocrine carcinomas (PanNECs). While recent studies suggest an endocrine descent of PanNETs, the origin of PanNECs remains unknown. Methods We performed DNA methylation analysis for 57 PanNEN samples and found that distinct methylation profiles separated PanNENs into two major groups, clearly distinguishing high-grade PanNECs from other PanNETs including high-grade NETG3. DNA alterations and immunohistochemistry of cell-type markers PDX1, ARX, and SOX9 were utilized to further characterize PanNECs and their cell of origin in the pancreas. Results Phylo-epigenetic and cell-type signature features derived from alpha, beta, acinar, and ductal adult cells suggest an exocrine cell of origin for PanNECs, thus separating them in cell lineage from other PanNENs of endocrine origin. Conclusions Our study provides a robust and clinically applicable method to clearly distinguish PanNECs from G3 PanNETs, improving patient stratification. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01018-w.
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Affiliation(s)
- Tincy Simon
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Pamela Riemer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Armin Jarosch
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Katharina Detjen
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hepatology and Gastroenterology, Berlin, Germany
| | | | | | - Andrea Menne
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Slim Khouja
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Nanna Monjé
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Liam H Childs
- Humboldt-Universität zu Berlin, Knowledge Management in Bioinformatics, Berlin, Germany
| | - Dido Lenze
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Ulf Leser
- Humboldt-Universität zu Berlin, Knowledge Management in Bioinformatics, Berlin, Germany
| | - Florian Rossner
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Markus Morkel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Nils Blüthgen
- Integrative Research Institute (IRI) Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marianne Pavel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hepatology and Gastroenterology, Berlin, Germany
| | - David Horst
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - David Capper
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neuropathology, Berlin, Germany.,German Cancer Consortium (DKTK); Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ilaria Marinoni
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Aurel Perren
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Soulafa Mamlouk
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany. .,German Cancer Consortium (DKTK); Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Christine Sers
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany. .,German Cancer Consortium (DKTK); Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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7
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USP13 promotes development and metastasis of high-grade serous ovarian carcinoma in a novel mouse model. Oncogene 2022; 41:1974-1985. [PMID: 35173307 PMCID: PMC8956511 DOI: 10.1038/s41388-022-02224-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/07/2022] [Accepted: 02/01/2022] [Indexed: 12/15/2022]
Abstract
Epithelial ovarian cancer is the most lethal gynecologic malignancy and one of the most common causes of cancer mortality among women worldwide. Ubiquitin-Specific Peptidase 13 (USP13) gene copy is strongly amplified in human epithelial ovarian cancer, and high USP13 expression is correlated with poor survival outcomes. Yet, its pathological contribution to ovarian tumorigenesis remains unknown. We crossed a conditional Usp13 overexpressing knock-in mouse with a conditional knockout of Trp53 and Pten mouse and generated a novel ovarian cancer genetically engineered mouse model (GEMM), which closely recapitulates the genetic changes driving ovarian cancer in humans. Overexpression of USP13 with deletion of Trp53 and Pten in murine ovarian surface epithelium accelerated ovarian tumorigenesis and led to decreased survival in mice. Notably, USP13 greatly enhanced peritoneal metastasis of ovarian tumors with frequent development of hemorrhagic ascites. The primary and metastatic tumors exhibited morphology and clinical behavior similar to human high-grade serous ovarian cancer. Co-inhibition of USP13 and AKT significantly decreased the viability of the primary murine ovarian cancer cells isolated from the GEMM. USP13 also increased the tumorigenic and metastatic abilities of primary murine ovarian cancer cells in a syngeneic mouse study. These findings suggest a critical role of USP13 in ovarian cancer development and reveal USP13 as a potential therapeutic target for ovarian cancer.
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8
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Fierheller CT, Guitton-Sert L, Alenezi WM, Revil T, Oros KK, Gao Y, Bedard K, Arcand SL, Serruya C, Behl S, Meunier L, Fleury H, Fewings E, Subramanian DN, Nadaf J, Bruce JP, Bell R, Provencher D, Foulkes WD, El Haffaf Z, Mes-Masson AM, Majewski J, Pugh TJ, Tischkowitz M, James PA, Campbell IG, Greenwood CMT, Ragoussis J, Masson JY, Tonin PN. A functionally impaired missense variant identified in French Canadian families implicates FANCI as a candidate ovarian cancer-predisposing gene. Genome Med 2021; 13:186. [PMID: 34861889 PMCID: PMC8642877 DOI: 10.1186/s13073-021-00998-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
Background Familial ovarian cancer (OC) cases not harbouring pathogenic variants in either of the BRCA1 and BRCA2 OC-predisposing genes, which function in homologous recombination (HR) of DNA, could involve pathogenic variants in other DNA repair pathway genes. Methods Whole exome sequencing was used to identify rare variants in HR genes in a BRCA1 and BRCA2 pathogenic variant negative OC family of French Canadian (FC) ancestry, a population exhibiting genetic drift. OC cases and cancer-free individuals from FC and non-FC populations were investigated for carrier frequency of FANCI c.1813C>T; p.L605F, the top-ranking candidate. Gene and protein expression were investigated in cancer cell lines and tissue microarrays, respectively. Results In FC subjects, c.1813C>T was more common in familial (7.1%, 3/42) than sporadic (1.6%, 7/439) OC cases (P = 0.048). Carriers were detected in 2.5% (74/2950) of cancer-free females though female/male carriers were more likely to have a first-degree relative with OC (121/5249, 2.3%; Spearman correlation = 0.037; P = 0.011), suggesting a role in risk. Many of the cancer-free females had host factors known to reduce risk to OC which could influence cancer risk in this population. There was an increased carrier frequency of FANCI c.1813C>T in BRCA1 and BRCA2 pathogenic variant negative OC families, when including the discovery family, compared to cancer-free females (3/23, 13%; OR = 5.8; 95%CI = 1.7–19; P = 0.005). In non-FC subjects, 10 candidate FANCI variants were identified in 4.1% (21/516) of Australian OC cases negative for pathogenic variants in BRCA1 and BRCA2, including 10 carriers of FANCI c.1813C>T. Candidate variants were significantly more common in familial OC than in sporadic OC (P = 0.04). Localization of FANCD2, part of the FANCI-FANCD2 (ID2) binding complex in the Fanconi anaemia (FA) pathway, to sites of induced DNA damage was severely impeded in cells expressing the p.L605F isoform. This isoform was expressed at a reduced level, destabilized by DNA damaging agent treatment in both HeLa and OC cell lines, and exhibited sensitivity to cisplatin but not to a poly (ADP-ribose) polymerase inhibitor. By tissue microarray analyses, FANCI protein was consistently expressed in fallopian tube epithelial cells and only expressed at low-to-moderate levels in 88% (83/94) of OC samples. Conclusions This is the first study to describe candidate OC variants in FANCI, a member of the ID2 complex of the FA DNA repair pathway. Our data suggest that pathogenic FANCI variants may modify OC risk in cancer families. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00998-5.
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Affiliation(s)
- Caitlin T Fierheller
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Laure Guitton-Sert
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Wejdan M Alenezi
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada.,Department of Medical Laboratory Technology, Taibah University, Medina, Saudi Arabia
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Kathleen K Oros
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Yuandi Gao
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Karine Bedard
- Laboratoire de Diagnostic Moléculaire, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Quebec, Canada.,Département de pathologie et biologie cellulaire, Université de Montréal, Montreal, Quebec, Canada
| | - Suzanna L Arcand
- Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Corinne Serruya
- Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Supriya Behl
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Liliane Meunier
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada
| | - Hubert Fleury
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada
| | - Eleanor Fewings
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Deepak N Subramanian
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Javad Nadaf
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Jeffrey P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rachel Bell
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Diane Provencher
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada.,Division of Gynecologic Oncology, Université de Montréal, Montreal, Quebec, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Zaki El Haffaf
- Centre de recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada.,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Paul A James
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,The Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Celia M T Greenwood
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Patricia N Tonin
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada. .,Department of Medicine, McGill University, Montreal, Quebec, Canada.
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9
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Barnes BM, Nelson L, Tighe A, Burghel GJ, Lin IH, Desai S, McGrail JC, Morgan RD, Taylor SS. Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes. Genome Med 2021; 13:140. [PMID: 34470661 PMCID: PMC8408985 DOI: 10.1186/s13073-021-00952-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 08/12/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Epithelial ovarian cancer (OC) is a heterogenous disease consisting of five major histologically distinct subtypes: high-grade serous (HGSOC), low-grade serous (LGSOC), endometrioid (ENOC), clear cell (CCOC) and mucinous (MOC). Although HGSOC is the most prevalent subtype, representing 70-80% of cases, a 2013 landmark study by Domcke et al. found that the most frequently used OC cell lines are not molecularly representative of this subtype. This raises the question, if not HGSOC, from which subtype do these cell lines derive? Indeed, non-HGSOC subtypes often respond poorly to chemotherapy; therefore, representative models are imperative for developing new targeted therapeutics. METHODS Non-negative matrix factorisation (NMF) was applied to transcriptomic data from 44 OC cell lines in the Cancer Cell Line Encyclopedia, assessing the quality of clustering into 2-10 groups. Epithelial OC subtypes were assigned to cell lines optimally clustered into five transcriptionally distinct classes, confirmed by integration with subtype-specific mutations. A transcriptional subtype classifier was then developed by trialling three machine learning algorithms using subtype-specific metagenes defined by NMF. The ability of classifiers to predict subtype was tested using RNA sequencing of a living biobank of patient-derived OC models. RESULTS Application of NMF optimally clustered the 44 cell lines into five transcriptionally distinct groups. Close inspection of orthogonal datasets revealed this five-cluster delineation corresponds to the five major OC subtypes. This NMF-based classification validates the Domcke et al. analysis, in identifying lines most representative of HGSOC, and additionally identifies models representing the four other subtypes. However, NMF of the cell lines into two clusters did not align with the dualistic model of OC and suggests this classification is an oversimplification. Subtype designation of patient-derived models by a random forest transcriptional classifier aligned with prior diagnosis in 76% of unambiguous cases. In cases where there was disagreement, this often indicated potential alternative diagnosis, supported by a review of histological, molecular and clinical features. CONCLUSIONS This robust classification informs the selection of the most appropriate models for all five histotypes. Following further refinement on larger training cohorts, the transcriptional classification may represent a useful tool to support the classification of new model systems of OC subtypes.
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Affiliation(s)
- Bethany M Barnes
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Louisa Nelson
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Anthony Tighe
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Oxford Road, Manchester, M13 9WL, UK
| | - I-Hsuan Lin
- Bioinformatics Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
| | - Sudha Desai
- Department of Histopathology, The Christie NHS Foundation Trust, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Joanne C McGrail
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Robert D Morgan
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Stephen S Taylor
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK.
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10
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Coughlan AY, Testa G. Exploiting epigenetic dependencies in ovarian cancer therapy. Int J Cancer 2021; 149:1732-1743. [PMID: 34213777 PMCID: PMC9292863 DOI: 10.1002/ijc.33727] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 01/02/2023]
Abstract
Ovarian cancer therapy has remained fundamentally unchanged for 50 years, with surgery and chemotherapy still the frontline treatments. Typically asymptomatic until advanced stages, ovarian cancer is known as “the silent killer.” Consequently, it has one of the worst 5‐year survival rates, as low as 30%. The most frequent driver mutations are found in well‐defined tumor suppressors, such as p53 and BRCA1/2. In recent years, it has become clear that, like the majority of other cancers, many epigenetic regulators are altered in ovarian cancer, including EZH2, SMARCA2/4 and ARID1A. Disruption of epigenetic regulators often leads to loss of transcriptional control, aberrant cell fate trajectories and disruption of senescence, apoptotic and proliferation pathways. These mitotically inherited epigenetic alterations are particularly promising targets for therapy as they are largely reversible. Consequently, many drugs targeting chromatin modifiers and other epigenetic regulators are at various stages of clinical trials for other cancers. Understanding the mechanisms by which ovarian cancer‐specific epigenetic processes are disrupted in patients can allow for informed targeting of epigenetic pathways tailored for each patient. In recent years, there have been groundbreaking new advances in disease modeling through ovarian cancer organoids; these models, alongside single‐cell transcriptomic and epigenomic technologies, allow the elucidation of the epigenetic pathways deregulated in ovarian cancer. As a result, ovarian cancer therapy may finally be ready to advance to next‐generation treatments. Here, we review the major developments in ovarian cancer, including genetics, model systems and technologies available for their study and the implications of applying epigenetic therapies to ovarian cancer.
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Affiliation(s)
- Aisling Y Coughlan
- Department of Experimental Oncology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Giuseppe Testa
- Department of Experimental Oncology, European Institute of Oncology, IRCCS, Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
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11
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Mei J, Tian H, Huang HS, Hsu CF, Liou Y, Wu N, Zhang W, Chu TY. Cellular models of development of ovarian high-grade serous carcinoma: A review of cell of origin and mechanisms of carcinogenesis. Cell Prolif 2021; 54:e13029. [PMID: 33768671 PMCID: PMC8088460 DOI: 10.1111/cpr.13029] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/19/2021] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
High-grade serous carcinoma (HGSC) is the most common and malignant histological type of epithelial ovarian cancer, the origin of which remains controversial. Currently, the secretory epithelial cells of the fallopian tube are regarded as the main origin and the ovarian surface epithelial cells as a minor origin. In tubal epithelium, these cells acquire TP53 mutations and expand to a morphologically normal 'p53 signature' lesion, transform to serous tubal intraepithelial carcinoma and metastasize to the ovaries and peritoneum where they develop into HGSC. This shifting paradigm of the main cell of origin has revolutionarily changed the focus of HGSC research. Various cell lines have been derived from the two cellular origins by acquiring immortalization via overexpression of hTERT plus disruption of TP53 and the CDK4/RB pathway. Malignant transformation was achieved by adding canonical driver mutations (such as gain of CCNE1) revealed by The Cancer Genome Atlas or by noncanonical gain of YAP and miR181a. Alternatively, because of the extreme chromosomal instability, spontaneous transformation can be achieved by long passage of murine immortalized cells, whereas in humans, it requires ovulatory follicular fluid, containing regenerating growth factors to facilitate spontaneous transformation. These artificially and spontaneously transformed cell systems in both humans and mice have been widely used to discover carcinogens, oncogenic pathways and malignant behaviours in the development of HGSC. Here, we review the origin, aetiology and carcinogenic mechanism of HGSC and comprehensively summarize the cell models used to study this fatal cancer having multiple cells of origin and overt genomic instability.
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Affiliation(s)
- Jie Mei
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Huixiang Tian
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Hsuan-Shun Huang
- Center for Prevention and Therapy of Gynecological Cancers, Department of Research, Buddhist Tzu Chi General Hospital, Hualien, Taiwan, ROC
| | - Che-Fang Hsu
- Center for Prevention and Therapy of Gynecological Cancers, Department of Research, Buddhist Tzu Chi General Hospital, Hualien, Taiwan, ROC
| | - Yuligh Liou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China
| | - Nayiyuan Wu
- Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Tang-Yuan Chu
- Center for Prevention and Therapy of Gynecological Cancers, Department of Research, Buddhist Tzu Chi General Hospital, Hualien, Taiwan, ROC.,Department of Obstetrics & Gynecology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan, ROC.,Department of Life Sciences, Tzu Chi University, Hualien, Taiwan, ROC
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