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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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Herzog C, Jones A, Evans I, Reisel D, Olaitan A, Doufekas K, MacDonald N, Rådestad AF, Gemzell-Danielsson K, Zikan M, Cibula D, Dostálek L, Paprotka T, Leimbach A, Schmitt M, Ryan A, Gentry-Maharaj A, Apostolidou S, Rosenthal AN, Menon U, Widschwendter M. Plasma cell-free DNA methylation analysis for ovarian cancer detection: Analysis of samples from a case-control study and an ovarian cancer screening trial. Int J Cancer 2024; 154:679-691. [PMID: 37861205 DOI: 10.1002/ijc.34757] [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: 05/22/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]
Abstract
Analysis of cell-free DNA methylation (cfDNAme), alone or combined with CA125, could help to detect ovarian cancers earlier and may reduce mortality. We assessed cfDNAme in regions of ZNF154, C2CD4D and WNT6 via targeted bisulfite sequencing in diagnostic and early detection (preceding diagnosis) settings. Diagnostic samples were obtained via prospective blood collection in cell-free DNA tubes in a convenience series of patients with a pelvic mass. Early detection samples were matched case-control samples derived from the UK Familial Ovarian Cancer Screening Study (UKFOCSS). In the diagnostic set (ncases = 27, ncontrols = 41), the specificity of cfDNAme was 97.6% (95% CI: 87.1%-99.9%). High-risk cancers were detected with a sensitivity of 80% (56.3%-94.3%). Combination of cfDNAme and CA125 resulted in a sensitivity of 94.4% (72.7%-99.9%) for high-risk cancers. Despite technical issues in the early detection set (ncases = 29, ncontrols = 29), the specificity of cfDNAme was 100% (88.1%-100.0%). We detected 27.3% (6.0%-61.0%) of high-risk cases with relatively lower genomic DNA (gDNA) contamination. The sensitivity rose to 33.3% (7.5%-70.1%) in samples taken <1 year before diagnosis. We detected ovarian cancer in several patients up to 1 year before diagnosis despite technical limitations associated with archival samples (UKFOCSS). Combined cfDNAme and CA125 assessment may improve ovarian cancer screening in high-risk populations, but future large-scale prospective studies will be required to validate current findings.
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Affiliation(s)
- Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Austria
| | - Allison Jones
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| | - Iona Evans
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| | - Adeola Olaitan
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| | - Konstantinos Doufekas
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| | - Nicola MacDonald
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| | - Angelique Flöter Rådestad
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Kristina Gemzell-Danielsson
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Michal Zikan
- Department of Gynecology and Obstetrics, Charles University in Prague, First Faculty of Medicine and Hospital, Na Bulovce, Czech Republic
| | - David Cibula
- Department of Gynaecology, Obstetrics and Neonatology, First Faculty of Medicine, Charles University, Prague and, General University Hospital, Prague, Czech Republic
| | - Lukáš Dostálek
- Department of Gynaecology, Obstetrics and Neonatology, First Faculty of Medicine, Charles University, Prague and, General University Hospital, Prague, Czech Republic
| | | | | | - Markus Schmitt
- Eurofins Genomics Europe Sequencing GmbH, Konstanz, Germany
| | - Andy Ryan
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, University College London, London, UK
| | - Aleksandra Gentry-Maharaj
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, University College London, London, UK
| | - Sophia Apostolidou
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, University College London, London, UK
| | - Adam N Rosenthal
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| | - Usha Menon
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, University College London, London, UK
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Austria
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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Bao S, Sun N, Li Y, Shu J, Xu J, Zhang Y, Qiu X. BRCA mutation status and pathological characterization of breast cancer in Zhoushan Islands, China. J Int Med Res 2024; 52:3000605231223426. [PMID: 38263931 PMCID: PMC10807394 DOI: 10.1177/03000605231223426] [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: 05/31/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
OBJECTIVE To investigate BRCA1/2 gene mutations and their relationship with clinicopathological features in patients with breast cancer in Zhoushan Islands. METHODS High-throughput whole-exome gene sequencing was used to detect BRCA1/2 mutations in 776 breast cancer patients in Zhoushan Islands. RESULTS The BRCA1/2 mutation rate of breast cancer patients in Zhoushan Islands was 4.38% (34/776). BRCA1 mutations were significantly correlated with age, molecular type, and family history of breast and ovarian cancers. BRCA2 mutations were most commonly found in invasive lobular carcinoma. Moreover, the BRCA2 mutation rate of cancers with molecular type luminal B (receptor protein-tyrosine kinase [HER2]-negative) was also relatively high. CONCLUSION The rate of BRCA1/2 mutations in breast cancer patients from Zhoushan Islands is approximately 4.38%, and BRCA1 mutation is related to age, molecular type, and family history of breast and ovarian cancers.
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Affiliation(s)
- Shuhui Bao
- Surgery Department, Zhoushan Hospital of Traditional Chinese Medicine, Zhejiang, China
- Department of Breast Surgery, Zhoushan Hospital, Zhejiang, China
| | - Nini Sun
- Surgery Department, Zhoushan Hospital of Traditional Chinese Medicine, Zhejiang, China
| | - Yaling Li
- Surgery Department, Zhoushan Hospital of Traditional Chinese Medicine, Zhejiang, China
| | - Jiaojie Shu
- Surgery Department, Zhoushan Hospital of Traditional Chinese Medicine, Zhejiang, China
| | - Jing Xu
- Surgery Department, Zhoushan Hospital of Traditional Chinese Medicine, Zhejiang, China
| | - Yong Zhang
- Surgery Department, Zhoushan Hospital of Traditional Chinese Medicine, Zhejiang, China
| | - Xia Qiu
- Surgery Department, Zhoushan Hospital of Traditional Chinese Medicine, Zhejiang, China
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4
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Avramenko AS, Flanagan JM. An epigenetic hypothesis for ovarian cancer prevention by oral contraceptive pill use. Clin Epigenetics 2023; 15:165. [PMID: 37853473 PMCID: PMC10585871 DOI: 10.1186/s13148-023-01584-9] [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: 06/28/2023] [Accepted: 10/09/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND Ovarian cancer is the second most common gynecological cancer type after uterine cancers. In 2020, according to worldwide statistics, there were more than 313,000 new cases of ovarian cancer. Most concerning with ovarian cancer is the poor overall survival, with only 30% of patients surviving for longer than 5 years after diagnosis. The reason for this poor outcome includes late diagnosis due to non-specific symptoms and a lack of any highly effective biomarkers of the early stages of ovarian carcinogenesis. However, it is important to note that some modifiable lifestyle factors can be preventative [pregnancy, breastfeeding and combined oral contraceptives pill (COCP) use]. RESULTS There is now increasing data reporting the role of epigenetic changes, which are detectable in ovarian cancer tumors, suggesting the possibility that epigenetics may also play a key role in the mechanism of long-term effective prevention of ovarian cancer. To our knowledge, there is a lack of high-quality data on the molecular mechanisms of ovarian cancer prevention, although several hypotheses have been proposed. CONCLUSIONS This review focusses on the evidence for a proposed novel hypothesis-that COCPs act as a chemoprevention through the impact on the epigenome of the cells of origin of ovarian cancer-fallopian tubes epithelium.
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Affiliation(s)
- Anna S Avramenko
- Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, 4th Floor IRDB, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - James M Flanagan
- Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, 4th Floor IRDB, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
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5
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Wisztorski M, Aboulouard S, Roussel L, Duhamel M, Saudemont P, Cardon T, Narducci F, Robin YM, Lemaire AS, Bertin D, Hajjaji N, Kobeissy F, Leblanc E, Fournier I, Salzet M. Fallopian tube lesions as potential precursors of early ovarian cancer: a comprehensive proteomic analysis. Cell Death Dis 2023; 14:644. [PMID: 37775701 PMCID: PMC10541450 DOI: 10.1038/s41419-023-06165-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/08/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
Ovarian cancer is the leading cause of death from gynecologic cancer worldwide. High-grade serous carcinoma (HGSC) is the most common and deadliest subtype of ovarian cancer. While the origin of ovarian tumors is still debated, it has been suggested that HGSC originates from cells in the fallopian tube epithelium (FTE), specifically the epithelial cells in the region of the tubal-peritoneal junction. Three main lesions, p53 signatures, STILs, and STICs, have been defined based on the immunohistochemistry (IHC) pattern of p53 and Ki67 markers and the architectural alterations of the cells, using the Sectioning and Extensively Examining the Fimbriated End Protocol. In this study, we performed an in-depth proteomic analysis of these pre-neoplastic epithelial lesions guided by mass spectrometry imaging and IHC. We evaluated specific markers related to each preneoplastic lesion. The study identified specific lesion markers, such as CAVIN1, Emilin2, and FBLN5. We also used SpiderMass technology to perform a lipidomic analysis and identified the specific presence of specific lipids signature including dietary Fatty acids precursors in lesions. Our study provides new insights into the molecular mechanisms underlying the progression of ovarian cancer and confirms the fimbria origin of HGSC.
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Affiliation(s)
- Maxence Wisztorski
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Soulaimane Aboulouard
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Lucas Roussel
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Marie Duhamel
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Philippe Saudemont
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Tristan Cardon
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Fabrice Narducci
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Yves-Marie Robin
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Anne-Sophie Lemaire
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Delphine Bertin
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Nawale Hajjaji
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Medical Oncology Department, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Firas Kobeissy
- Department of Neurobiology, Center for Neurotrauma, Multiomics & Biomarkers (CNMB), MorehouseSchool of Medicine, Atlanta, GA, 30310, USA
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Eric Leblanc
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France.
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France.
| | - Isabelle Fournier
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France.
- Institut Universitaire de France, 75000, Paris, France.
| | - Michel Salzet
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France.
- Institut Universitaire de France, 75000, Paris, France.
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Ferrari AJ, Rawat P, Rendulich HS, Annapragada AV, Kinose Y, Zhang X, Devins K, Budina A, Scharpf RB, Mitchell MA, Tanyi JL, Morgan MA, Schwartz LE, Soong TR, Velculescu VE, Drapkin R. H2Bub1 loss is an early contributor to clear cell ovarian cancer progression. JCI Insight 2023; 8:e164995. [PMID: 37345659 PMCID: PMC10371241 DOI: 10.1172/jci.insight.164995] [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: 08/31/2022] [Accepted: 05/04/2023] [Indexed: 06/23/2023] Open
Abstract
Epigenetic aberrations, including posttranslational modifications of core histones, are major contributors to cancer. Here, we define the status of histone H2B monoubiquitylation (H2Bub1) in clear cell ovarian carcinoma (CCOC), low-grade serous carcinoma, and endometrioid carcinomas. We report that clear cell carcinomas exhibited profound loss, with nearly all cases showing low or negative H2Bub1 expression. Moreover, we found that H2Bub1 loss occurred in endometriosis and atypical endometriosis, which are established precursors to CCOCs. To examine whether dysregulation of a specific E3 ligase contributes to the loss of H2Bub1, we explored expression of ring finger protein 40 (RNF40), ARID1A, and UBR7 in the same case cohort. Loss of RNF40 was significantly and profoundly correlated with loss of H2Bub1. Using genome-wide DNA methylation profiles of 230 patients with CCOC, we identified hypermethylation of RNF40 in CCOC as a likely mechanism underlying the loss of H2Bub1. Finally, we demonstrated that H2Bub1 depletion promoted cell proliferation and clonogenicity in an endometriosis cell line. Collectively, our results indicate that H2Bub1 plays a tumor-suppressive role in CCOCs and that its loss contributes to disease progression.
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Affiliation(s)
- Adam J. Ferrari
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
- Graduate Program in Cell and Molecular Biology; and
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Priyanka Rawat
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Hannah S. Rendulich
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Akshaya V. Annapragada
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yasuto Kinose
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Xiaoming Zhang
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle Devins
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anna Budina
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Robert B. Scharpf
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Marilyn A. Mitchell
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Janos L. Tanyi
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Mark A. Morgan
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Lauren E. Schwartz
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - T. Rinda Soong
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Victor E. Velculescu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
- Graduate Program in Cell and Molecular Biology; and
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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7
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Bogaerts JMA, van Bommel MHD, Hermens RPMG, Steenbeek MP, de Hullu JA, van der Laak JAWM, Simons M. Consensus based recommendations for the diagnosis of serous tubal intraepithelial carcinoma: an international Delphi study. Histopathology 2023. [PMID: 36939551 DOI: 10.1111/his.14902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 02/25/2023] [Indexed: 03/21/2023]
Abstract
AIM Reliably diagnosing or safely excluding serous tubal intraepithelial carcinoma (STIC), a precursor lesion of tubo-ovarian high-grade serous carcinoma (HGSC), is crucial for individual patient care, for better understanding the oncogenesis of HGSC, and for safely investigating novel strategies to prevent tubo-ovarian carcinoma. To optimize STIC diagnosis and increase its reproducibility, we set up a three-round Delphi study. METHODS AND RESULTS In round 1, an international expert panel of 34 gynecologic pathologists, from 11 countries, was assembled to provide input regarding STIC diagnosis, which was used to develop a set of statements. In round 2, the panel rated their level of agreement with those statements on a 9-point Likert scale. In round 3, statements without previous consensus were rated again by the panel while anonymously disclosing the responses of the other panel members. Finally, each expert was asked to approve or disapprove the complete set of consensus statements. The panel indicated their level of agreement with 64 statements. A total of 27 statements (42%) reached consensus after three rounds. These statements reflect the entire diagnostic work-up for pathologists, regarding processing and macroscopy (three statements); microscopy (eight statements); immunohistochemistry (nine statements); interpretation and reporting (four statements); and miscellaneous (three statements). The final set of consensus statements was approved by 85%. CONCLUSION This study provides an overview of current clinical practice regarding STIC diagnosis amongst expert gynecopathologists. The experts' consensus statements form the basis for a set of recommendations, which may help towards more consistent STIC diagnosis.
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Affiliation(s)
- Joep M A Bogaerts
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Majke H D van Bommel
- Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rosella P M G Hermens
- IQ Healthcare, Radboud Institute of Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Miranda P Steenbeek
- Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Joanne A de Hullu
- Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jeroen A W M van der Laak
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.,Center for Medical Image Science and Visualization, Linköping University, Linköping, Sweden
| | | | - Michiel Simons
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
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8
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Lehtinen M, Pimenoff VN, Nedjai B, Louvanto K, Verhoef L, Heideman DAM, El‐Zein M, Widschwendter M, Dillner J. Assessing the risk of cervical neoplasia in the post-HPV vaccination era. Int J Cancer 2023; 152:1060-1068. [PMID: 36093582 PMCID: PMC10091767 DOI: 10.1002/ijc.34286] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 01/21/2023]
Abstract
This review is based on the recent EUROGIN scientific session: "Assessing risk of cervical cancer in the post-vaccination era," which addressed the demands of cervical intraepithelial neoplasia (CIN)/squamous intraepithelial lesion (SIL) triage now that the prevalence of vaccine-targeted oncogenic high-risk (hr) human papillomaviruses (HPVs) is decreasing. Change in the prevalence distribution of oncogenic HPV types that follows national HPV vaccination programs is setting the stage for loss of positive predictive value of conventional but possibly also new triage modalities. Understanding the contribution of the latter, most notably hypermethylation of cellular and viral genes in a new setting where most oncogenic HPV types are no longer present, requires studies on their performance in vaccinated women with CIN/SIL that are associated with nonvaccine HPV types. Lessons learned from this research may highlight the potential of cervical cells for risk prediction of all women's cancers.
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Affiliation(s)
- Matti Lehtinen
- Medical FacultyTampere UniversityTampereFinland
- Department of Laboratory MedicineKarolinska InstituteStockholmSweden
| | - Ville N. Pimenoff
- Department of Laboratory MedicineKarolinska InstituteStockholmSweden
| | - Belinda Nedjai
- Wolfson Institute of Population HealthQueen Mary University of LondonLondonUK
| | - Karolina Louvanto
- Medical FacultyTampere UniversityTampereFinland
- Department of Obstetrics and GynecologyTampere University HospitalTampereFinland
| | - Lisanne Verhoef
- Department of PathologyAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
- Cancer Center Amsterdam, Imaging and BiomarkersAmsterdamThe Netherlands
| | - Daniëlle A. M. Heideman
- Department of PathologyAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
- Cancer Center Amsterdam, Imaging and BiomarkersAmsterdamThe Netherlands
| | - Mariam El‐Zein
- Division of Cancer EpidemiologyMcGill UniversityMontrealCanada
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) InstituteUniversität InnsbruckHall in TirolAustria
- Research Institute for Biomedical Aging ResearchUniversität InnsbruckInnsbruckAustria
- Department of Women's Cancer, UCL EGA Institute for Women's HealthUniversity College LondonLondonUK
- Department of Women's and Children's Health, Division of Obstetrics and GynecologyKarolinska Institute and Karolinska University HospitalStockholmSweden
| | - Joakim Dillner
- Department of Laboratory MedicineKarolinska InstituteStockholmSweden
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9
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Ibrahim J, Peeters M, Van Camp G, Op de Beeck K. Methylation biomarkers for early cancer detection and diagnosis: Current and future perspectives. Eur J Cancer 2023; 178:91-113. [PMID: 36427394 DOI: 10.1016/j.ejca.2022.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/11/2022] [Accepted: 10/17/2022] [Indexed: 11/25/2022]
Abstract
The increase in recent scientific studies on cancer biomarkers has brought great new insights into the field. Moreover, novel technological breakthroughs such as long read sequencing and microarrays have enabled high throughput profiling of many biomarkers, while advances in bioinformatic tools have made the possibility of developing highly reliable and accurate biomarkers a reality. These changes triggered renewed interest in biomarker research and provided tremendous opportunities for enhancing cancer management and improving early disease detection. DNA methylation alterations are known to accompany and contribute to carcinogenesis, making them promising biomarkers for cancer, namely due to their stability, frequency and accessibility in bodily fluids. The advent of newer minimally invasive experimental methods such as liquid biopsies provide the perfect setting for methylation-based biomarker development and application. Despite their huge potential, accurate and robust biomarkers for the conclusive diagnosis of most cancer types are still not routinely used, hence a strong need for sustained research in this field is still needed. This review provides a brief exposition of current methylation biomarkers for cancer diagnosis and early detection, including markers already in clinical use as well as various upcoming ones. It also outlines how recent big data and novel technologies will revolutionise the next generation of cancer tests in supplementing or replacing currently existing invasive techniques.
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Affiliation(s)
- Joe Ibrahim
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Marc Peeters
- Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium; Department of Medical Oncology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium.
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10
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Konishi I, Abiko K, Hayashi T, Yamanoi K, Murakami R, Yamaguchi K, Hamanishi J, Baba T, Matsumura N, Mandai M. Peritoneal dissemination of high-grade serous ovarian cancer: pivotal roles of chromosomal instability and epigenetic dynamics. J Gynecol Oncol 2022; 33:e83. [PMID: 36032027 PMCID: PMC9428305 DOI: 10.3802/jgo.2022.33.e83] [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: 06/02/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 12/02/2022] Open
Abstract
Epithelial ovarian cancer remains the lethal gynecological malignancy in women. The representative histotype is high-grade serous carcinoma (HGSC), and most patients with HGSC present at advanced stages with peritoneal dissemination. Since the peritoneal dissemination is the most important factor for poor prognosis of the patients, complete exploration for its molecular mechanisms is mandatory. In this narrative review, being based on the clinical, pathologic, and genomic findings of HGSC, chromosomal instability and epigenetic dynamics have been discussed as the potential drivers for cancer development in the fallopian tube, acquisition of cancer stem cell (CSC)-like properties, and peritoneal metastasis of HGSC. The natural history of carcinogenesis with clonal evolution, and adaptation to microenvironment of peritoneal dissemination of HGSC should be targeted in the novel development of strategies for prevention, early detection, and precision treatment for patients with HGSC.
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Affiliation(s)
- Ikuo Konishi
- Department of Obstetrics and Gynecology, National Hospital Organization Kyoto Medical Center, Kyoto, Japan.,Clinical Research Center, National Hospital Organization Kyoto Medical Center, Kyoto, Japan.,Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | - Kaoru Abiko
- Department of Obstetrics and Gynecology, National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Takuma Hayashi
- Clinical Research Center, National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Koji Yamanoi
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryusuke Murakami
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ken Yamaguchi
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Junzo Hamanishi
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tsukasa Baba
- Department of Obstetrics and Gynecology, Iwate Medical University School of Medicine, Morioka, Japan
| | - Noriomi Matsumura
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osakasayama, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
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11
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Liberto JM, Chen SY, Shih IM, Wang TH, Wang TL, Pisanic TR. Current and Emerging Methods for Ovarian Cancer Screening and Diagnostics: A Comprehensive Review. Cancers (Basel) 2022; 14:2885. [PMID: 35740550 PMCID: PMC9221480 DOI: 10.3390/cancers14122885] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 02/04/2023] Open
Abstract
With a 5-year survival rate of less than 50%, ovarian high-grade serous carcinoma (HGSC) is one of the most highly aggressive gynecological malignancies affecting women today. The high mortality rate of HGSC is largely attributable to delays in diagnosis, as most patients remain undiagnosed until the late stages of -disease. There are currently no recommended screening tests for ovarian cancer and there thus remains an urgent need for new diagnostic methods, particularly those that can detect the disease at early stages when clinical intervention remains effective. While diagnostics for ovarian cancer share many of the same technical hurdles as for other cancer types, the low prevalence of the disease in the general population, coupled with a notable lack of sensitive and specific biomarkers, have made the development of a clinically useful screening strategy particularly challenging. Here, we present a detailed review of the overall landscape of ovarian cancer diagnostics, with emphasis on emerging methods that employ novel protein, genetic, epigenetic and imaging-based biomarkers and/or advanced diagnostic technologies for the noninvasive detection of HGSC, particularly in women at high risk due to germline mutations such as BRCA1/2. Lastly, we discuss the translational potential of these approaches for achieving a clinically implementable solution for screening and diagnostics of early-stage ovarian cancer as a means of ultimately improving patient outcomes in both the general and high-risk populations.
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Affiliation(s)
- Juliane M. Liberto
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; (J.M.L.); (I.-M.S.); (T.-L.W.)
| | - Sheng-Yin Chen
- School of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan;
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; (J.M.L.); (I.-M.S.); (T.-L.W.)
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA;
| | - Tza-Huei Wang
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA;
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tian-Li Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; (J.M.L.); (I.-M.S.); (T.-L.W.)
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA;
| | - Thomas R. Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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12
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Lu H, Liu Y, Wang J, Fu S, Wang L, Huang C, Li J, Xie L, Wang D, Li D, Zhou H, Rao Q. Detection of ovarian cancer using plasma cell-free DNA methylomes. Clin Epigenetics 2022; 14:74. [PMID: 35681212 PMCID: PMC9185905 DOI: 10.1186/s13148-022-01285-9] [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] [Accepted: 05/09/2022] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Ovarian cancer (OC) is a highly lethal gynecologic cancer, and it is hard to diagnose at an early stage. Clinically, there are no ovarian cancer-specific markers for early detection. Here, we demonstrate the use of cell-free DNA (cfDNA) methylomes to detect ovarian cancer, especially the early-stage OC. EXPERIMENTAL DESIGN Plasma from 74 epithelial ovarian cancer patients, 86 healthy volunteers, and 20 patients with benign pelvic masses was collected. The cfDNA methylomes of these samples were generated by cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq). The differentially methylated regions (DMRs) were identified by the contrasts between tumor and non-tumor groups, and the discrimination performance was evaluated with the iterative training and testing method. RESULTS The DMRs identified for cfDNA methylomes can well discriminate tumor groups and non-tumor groups (ROC values from 0.86 to 0.98). The late-stage top 300 DMRs are more late-stage-specific and failed to detect early-stage OC. However, the early-stage markers have the potential to discriminate all-stage OCs from non-tumor samples. CONCLUSIONS This study demonstrates that cfDNA methylomes generated with cfMeDIP-seq could be used to identify OC-specific biomarkers for OC, especially early OC detection. To detect early-stage OC, the biomarkers should be directly identified from early OC plasma samples rather than mix-stage ones. Further exploration of DMRs from a k larger early-stage OC cohort is warranted.
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Affiliation(s)
- Huaiwu Lu
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yunyun Liu
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jingyu Wang
- Shanghai Danbei Medical Technology Co., Ltd, Shanghai, China
| | - Shaliu Fu
- Shanghai Danbei Medical Technology Co., Ltd, Shanghai, China
| | - Lingping Wang
- Shanghai Danbei Medical Technology Co., Ltd, Shanghai, China
| | - Chunxian Huang
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jing Li
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lingling Xie
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Dongyan Wang
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Dan Li
- Shanghai Danbei Medical Technology Co., Ltd, Shanghai, China
| | - Hui Zhou
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Qunxian Rao
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China.
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13
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Yao Z, Zhu G, Too J, Duan M, Wang Z. Feature Selection of OMIC Data by Ensemble Swarm Intelligence Based Approaches. Front Genet 2022; 12:793629. [PMID: 35350819 PMCID: PMC8957794 DOI: 10.3389/fgene.2021.793629] [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: 10/12/2021] [Accepted: 12/22/2021] [Indexed: 12/28/2022] Open
Abstract
OMIC datasets have high dimensions, and the connection among OMIC features is very complicated. It is difficult to establish linkages among these features and certain biological traits of significance. The proposed ensemble swarm intelligence-based approaches can identify key biomarkers and reduce feature dimension efficiently. It is an end-to-end method that only relies on the rules of the algorithm itself, without presets such as the number of filtering features. Additionally, this method achieves good classification accuracy without excessive consumption of computing resources.
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Affiliation(s)
- Zhaomin Yao
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, China.,College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, China
| | - Gancheng Zhu
- Key Laboratory of Symbolic Computation, College of Computer Science and Technology, Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Jingwei Too
- Faculty of Electrical Engineering, Universiti Teknikal Malaysia Melaka, Hang Tuah Jaya, Melaka, Malaysia
| | - Meiyu Duan
- Key Laboratory of Symbolic Computation, College of Computer Science and Technology, Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Zhiguo Wang
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, China.,College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, China
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14
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Toward More Comprehensive Homologous Recombination Deficiency Assays in Ovarian Cancer, Part 1: Technical Considerations. Cancers (Basel) 2022; 14:cancers14051132. [PMID: 35267439 PMCID: PMC8909526 DOI: 10.3390/cancers14051132] [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: 01/21/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary High-grade serous ovarian cancer (HGSOC) is the most frequent and lethal form of ovarian cancer and is associated with homologous recombination deficiency (HRD) in 50% of cases. This specific alteration is associated with sensitivity to PARP inhibitors (PARPis). Despite vast prognostic improvements due to PARPis, current molecular assays assessing HRD status suffer from several limitations, and there is an urgent need for a more accurate evaluation. In these companion reviews (Part 1: Technical considerations; Part 2: Medical perspectives), we develop an integrative review to provide physicians and researchers involved in HGSOC management with a holistic perspective, from translational research to clinical applications. Abstract High-grade serous ovarian cancer (HGSOC), the most frequent and lethal form of ovarian cancer, exhibits homologous recombination deficiency (HRD) in 50% of cases. In addition to mutations in BRCA1 and BRCA2, which are the best known thus far, defects can also be caused by diverse alterations to homologous recombination-related genes or epigenetic patterns. HRD leads to genomic instability (genomic scars) and is associated with PARP inhibitor (PARPi) sensitivity. HRD is currently assessed through BRCA1/2 analysis, which produces a genomic instability score (GIS). However, despite substantial clinical achievements, FDA-approved companion diagnostics (CDx) based on GISs have important limitations. Indeed, despite the use of GIS in clinical practice, the relevance of such assays remains controversial. Although international guidelines include companion diagnostics as part of HGSOC frontline management, they also underscore the need for more powerful and alternative approaches for assessing patient eligibility to PARP inhibitors. In these companion reviews, we review and present evidence to date regarding HRD definitions, achievements and limitations in HGSOC. Part 1 is dedicated to technical considerations and proposed perspectives that could lead to a more comprehensive and dynamic assessment of HR, while Part 2 provides a more integrated approach for clinicians.
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15
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Kim S, Hwang S. G-Quadruplex Matters in Tissue-Specific Tumorigenesis by BRCA1 Deficiency. Genes (Basel) 2022; 13:genes13030391. [PMID: 35327946 PMCID: PMC8948836 DOI: 10.3390/genes13030391] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/14/2022] Open
Abstract
How and why distinct genetic alterations, such as BRCA1 mutation, promote tumorigenesis in certain tissues, but not others, remain an important issue in cancer research. The underlying mechanisms may reveal tissue-specific therapeutic vulnerabilities. Although the roles of BRCA1, such as DNA damage repair and stalled fork stabilization, obviously contribute to tumor suppression, these ubiquitously important functions cannot explain tissue-specific tumorigenesis by BRCA1 mutations. Recent advances in our understanding of the cancer genome and fundamental cellular processes on DNA, such as transcription and DNA replication, have provided new insights regarding BRCA1-associated tumorigenesis, suggesting that G-quadruplex (G4) plays a critical role. In this review, we summarize the importance of G4 structures in mutagenesis of the cancer genome and cell type-specific gene regulation, and discuss a recently revealed molecular mechanism of G4/base excision repair (BER)-mediated transcriptional activation. The latter adequately explains the correlation between the accumulation of unresolved transcriptional regulatory G4s and multi-level genomic alterations observed in BRCA1-associated tumors. In summary, tissue-specific tumorigenesis by BRCA1 deficiency can be explained by cell type-specific levels of transcriptional regulatory G4s and the role of BRCA1 in resolving it. This mechanism would provide an integrated understanding of the initiation and development of BRCA1-associated tumors.
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Affiliation(s)
- Sanghyun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Sungnam 13488, Korea;
| | - Sohyun Hwang
- Department of Biomedical Science, College of Life Science, CHA University, Sungnam 13488, Korea;
- Department of Pathology, CHA Bundang Medical Center, CHA University School of Medicine, Sungnam 13496, Korea
- Correspondence:
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16
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Barrett JE, Jones A, Evans I, Reisel D, Herzog C, Chindera K, Kristiansen M, Leavy OC, Manchanda R, Bjørge L, Zikan M, Cibula D, Widschwendter M. The DNA methylome of cervical cells can predict the presence of ovarian cancer. Nat Commun 2022; 13:448. [PMID: 35105887 PMCID: PMC8807742 DOI: 10.1038/s41467-021-26615-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 10/04/2021] [Indexed: 02/03/2023] Open
Abstract
The vast majority of epithelial ovarian cancer arises from tissues that are embryologically derived from the Müllerian Duct. Here, we demonstrate that a DNA methylation signature in easy-to-access Müllerian Duct-derived cervical cells from women with and without ovarian cancer (i.e. referred to as the Women's risk IDentification for Ovarian Cancer index or WID-OC-index) is capable of identifying women with an ovarian cancer in the absence of tumour DNA with an AUC of 0.76 and women with an endometrial cancer with an AUC of 0.81. This and the observation that the cervical cell WID-OC-index mimics the epigenetic program of those cells at risk of becoming cancerous in BRCA1/2 germline mutation carriers (i.e. mammary epithelium, fallopian tube fimbriae, prostate) further suggest that the epigenetic misprogramming of cervical cells is an indicator for cancer predisposition. This concept has the potential to advance the field of risk-stratified cancer screening and prevention.
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Affiliation(s)
- James E Barrett
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Allison Jones
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Iona Evans
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
| | - Kantaraja Chindera
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Mark Kristiansen
- UCL Genomics, Zayed Centre for Research into Rare Disease in Children, University College London, London, WC1N 1DZ, UK
| | - Olivia C Leavy
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
- Department of Non-communicable Disease Epidemiology, The London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Ranjit Manchanda
- Department of Gynaecological Oncology, Barts Health NHS Trust, Royal London Hospital, London, E1 1BB, UK
- Centre for Prevention, Detection & Diagnosis, Wolfson Institute of Population Health, Queen Mary University of London, London, EC1M 6BQ, UK
- Department of Health Services Research, The London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Line Bjørge
- Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Michal Zikan
- Hospital Na Bulovce, Prague, Czech Republic
- Department of Obstetrics and Gynecology, General University Hospital in Prague, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - David Cibula
- Department of Obstetrics and Gynecology, General University Hospital in Prague, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria.
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria.
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK.
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
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17
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Zoo: Selecting Transcriptomic and Methylomic Biomarkers by Ensembling Animal-Inspired Swarm Intelligence Feature Selection Algorithms. Genes (Basel) 2021; 12:genes12111814. [PMID: 34828418 PMCID: PMC8621246 DOI: 10.3390/genes12111814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 02/03/2023] Open
Abstract
Biological omics data such as transcriptomes and methylomes have the inherent “large p small n” paradigm, i.e., the number of features is much larger than that of the samples. A feature selection (FS) algorithm selects a subset of the transcriptomic or methylomic biomarkers in order to build a better prediction model. The hidden patterns in the FS solution space make it challenging to achieve a feature subset with satisfying prediction performances. Swarm intelligence (SI) algorithms mimic the target searching behaviors of various animals and have demonstrated promising capabilities in selecting features with good machine learning performances. Our study revealed that different SI-based feature selection algorithms contributed complementary searching capabilities in the FS solution space, and their collaboration generated a better feature subset than the individual SI feature selection algorithms. Nine SI-based feature selection algorithms were integrated to vote for the selected features, which were further refined by the dynamic recursive feature elimination framework. In most cases, the proposed Zoo algorithm outperformed the existing feature selection algorithms on transcriptomics and methylomics datasets.
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18
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Han Y, Huang L, Zhou F. A dynamic recursive feature elimination framework (dRFE) to further refine a set of OMIC biomarkers. Bioinformatics 2021; 37:2183-2189. [PMID: 33515240 DOI: 10.1093/bioinformatics/btab055] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/23/2020] [Accepted: 01/25/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION A feature selection algorithm may select the subset of features with the best associations with the class labels. The recursive feature elimination (RFE) is a heuristic feature screening framework and has been widely used to select the biological OMIC biomarkers. This study proposed a dynamic recursive feature elimination (dRFE) framework with more flexible feature elimination operations. The proposed dRFE was comprehensively compared with 11 existing feature selection algorithms and five classifiers on the eight difficult transcriptome datasets from a previous study, the ten newly collected transcriptome datasets and the five methylome datasets. RESULTS The experimental data suggested that the regular RFE framework did not perform well, and dRFE outperformed the existing feature selection algorithms in most cases. The dRFE-detected features achieved Acc=1.0000 for the two methylome datasets GSE53045 and GSE66695. The best prediction accuracies of the dRFE-detected features were 0.9259, 0.9424, and 0.8601 for the other three methylome datasets GSE74845, GSE103186, and GSE80970, respectively. Four transcriptome datasets received Acc=1.0000 using the dRFE-detected features, and the prediction accuracies for the other six newly collected transcriptome datasets were between 0.6301 and 0.9917. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yuanyuan Han
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, China, 130012
| | - Lan Huang
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, China, 130012
| | - Fengfeng Zhou
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, China, 130012
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19
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Assessing ZNF154 methylation in patient plasma as a multicancer marker in liquid biopsies from colon, liver, ovarian and pancreatic cancer patients. Sci Rep 2021; 11:221. [PMID: 33420235 PMCID: PMC7794477 DOI: 10.1038/s41598-020-80345-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/08/2020] [Indexed: 12/21/2022] Open
Abstract
One epigenetic hallmark of many cancer types is differential DNA methylation occurring at multiple loci compared to normal tissue. Detection and assessment of the methylation state at a specific locus could be an effective cancer diagnostic. We assessed the effectiveness of hypermethylation at the CpG island of ZNF154, a previously reported multi-cancer specific signature for use in a blood-based cancer detection assay. To predict its effectiveness, we compared methylation levels of 3698 primary tumors encompassing 11 solid cancers, 724 controls, 2711 peripheral blood cell samples, and 350 noncancer disease tissues from publicly available methylation array datasets. We performed a single-molecule high-resolution DNA melt analysis on 71 plasma samples from cancer patients and 20 noncancer individuals to assess ZNF154 methylation as a candidate diagnostic metric in liquid biopsy and compared results to KRAS mutation frequency in the case of pancreatic carcinoma. We documented ZNF154 hypermethylation in early stage tumors, which did not increase in most noncancer disease or with respect to age or sex in peripheral blood cells, suggesting it is a promising target in liquid biopsy. ZNF154 cfDNA methylation discriminated cases from healthy donor plasma samples in minimal plasma volumes and outperformed KRAS mutation frequency in pancreatic cancer.
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20
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Nené NR, Barrett J, Jones A, Evans I, Reisel D, Timms JF, Paprotka T, Leimbach A, Franchi D, Colombo N, Bjørge L, Zikan M, Cibula D, Widschwendter M. DNA methylation signatures to predict the cervicovaginal microbiome status. Clin Epigenetics 2020; 12:180. [PMID: 33228781 PMCID: PMC7686703 DOI: 10.1186/s13148-020-00966-7] [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: 07/29/2020] [Accepted: 11/03/2020] [Indexed: 01/21/2023] Open
Abstract
Background The composition of the microbiome plays an important role in human health and disease. Whether there is a direct association between the cervicovaginal microbiome and the host’s epigenome is largely unexplored.
Results Here we analyzed a total of 448 cervicovaginal smear samples and studied both the DNA methylome of the host and the microbiome using the Illumina EPIC array and next-generation sequencing, respectively. We found that those CpGs that are hypo-methylated in samples with non-lactobacilli (O-type) dominating communities are strongly associated with gastrointestinal differentiation and that a signature consisting of 819 CpGs was able to discriminate lactobacilli-dominating (L-type) from O-type samples with an area under the receiver operator characteristic curve (AUC) of 0.84 (95% CI = 0.77–0.90) in an independent validation set. The performance found in samples with more than 50% epithelial cells was further improved (AUC 0.87) and in women younger than 50 years of age was even higher (AUC 0.91). In a subset of 96 women, the buccal but not the blood cell DNA showed the same trend as the cervicovaginal samples in discriminating women with L- from O-type cervicovaginal communities. Conclusions These findings strongly support the view that the epithelial epigenome plays an essential role in hosting specific microbial communities.
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Affiliation(s)
- Nuno R Nené
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, London, UK.,Department of Mathematics, University College London, London, UK
| | - James Barrett
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, London, UK.,European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria.,Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
| | - Allison Jones
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, London, UK
| | - Iona Evans
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, London, UK
| | - Daniel Reisel
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, London, UK
| | - John F Timms
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, London, UK
| | | | | | | | - Nicoletta Colombo
- Europeo Di Oncologia, IRCCS, Milan, Italy.,University of Milano-Bicocca, Milan, Italy
| | - Line Bjørge
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway.,Centre for Cancer Biomarkers, Department of Clinical Science, CCBIO, University of Bergen, Bergen, Norway
| | - Michal Zikan
- Hospital Na Bulovce, Prague, Czech Republic.,Department of Obstetrics and Gynecology, General University Hospital in Prague, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - David Cibula
- Department of Obstetrics and Gynecology, General University Hospital in Prague, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Widschwendter
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, London, UK. .,European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria. .,Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria.
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21
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Cai J, Xu Y, Zhang W, Ding S, Sun Y, Lyu J, Duan M, Liu S, Huang L, Zhou F. A comprehensive comparison of residue-level methylation levels with the regression-based gene-level methylation estimations by ReGear. Brief Bioinform 2020; 22:5921981. [PMID: 33048108 DOI: 10.1093/bib/bbaa253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/10/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION DNA methylation is a biological process impacting the gene functions without changing the underlying DNA sequence. The DNA methylation machinery usually attaches methyl groups to some specific cytosine residues, which modify the chromatin architectures. Such modifications in the promoter regions will inactivate some tumor-suppressor genes. DNA methylation within the coding region may significantly reduce the transcription elongation efficiency. The gene function may be tuned through some cytosines are methylated. METHODS This study hypothesizes that the overall methylation level across a gene may have a better association with the sample labels like diseases than the methylations of individual cytosines. The gene methylation level is formulated as a regression model using the methylation levels of all the cytosines within this gene. A comprehensive evaluation of various feature selection algorithms and classification algorithms is carried out between the gene-level and residue-level methylation levels. RESULTS A comprehensive evaluation was conducted to compare the gene and cytosine methylation levels for their associations with the sample labels and classification performances. The unsupervised clustering was also improved using the gene methylation levels. Some genes demonstrated statistically significant associations with the class label, even when no residue-level methylation features have statistically significant associations with the class label. So in summary, the trained gene methylation levels improved various methylome-based machine learning models. Both methodology development of regression algorithms and experimental validation of the gene-level methylation biomarkers are worth of further investigations in the future studies. The source code, example data files and manual are available at http://www.healthinformaticslab.org/supp/.
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22
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Pisanic TR, Wang Y, Sun H, Considine M, Li L, Wang TH, Wang TL, Shih IM. Methylomic Landscapes of Ovarian Cancer Precursor Lesions. Clin Cancer Res 2020; 26:6310-6320. [PMID: 32817081 DOI: 10.1158/1078-0432.ccr-20-0270] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/11/2020] [Accepted: 08/12/2020] [Indexed: 12/21/2022]
Abstract
PURPOSE The current paradigm in the development of high-grade serous ovarian carcinoma (HGSC) proposes that the majority of HGSCs arise from precursor serous tubal intraepithelial carcinoma (STIC) lesions of the fallopian tube. Here we survey genome-wide methylation in HGSC precursor lesions to identify genomic regions that exhibit high-specificity differential hypermethylation for potential use as biomarkers for detecting STIC and HGSC at stages when curative intervention likely remains feasible. EXPERIMENTAL DESIGN We first identified quality control criteria for performing reliable methylomic analysis of DNA-limited tubal precursor lesions with the Illumina Infinium MethylationEPIC array. We then used this platform to compare genome-wide methylation among 12 STICs with paired adjacent-normal epithelia, one p53 signature lesion and two samples of concurrent HGSC. The resulting methylomic data were analyzed by unsupervised hierarchical clustering and multidimensional analysis. Regions of high-confidence STIC-specific differential hypermethylation were identified using selective bioinformatic criteria and compared with published MethylationEPIC data from 23 HGSC tumors and 11 healthy fallopian tube mucosae. RESULTS Unsupervised analysis showed that STICs largely clustered with HGSCs, but were clearly distinct from adjacent-normal fallopian tube epithelia. Forty-two genomic regions exhibited high-confidence STIC-specific differential hypermethylation, of which 17 (40.5%) directly overlapped with HGSC-specific differentially methylated regions. Methylation at these shared loci was able to completely distinguish STIC and HGSC samples from normal and adjacent-normal specimens. CONCLUSIONS Our results suggest that most STICs are epigenetically similar to HGSCs and share regions of differential hypermethylation that warrant further evaluation for potential use as biomarkers for early detection of ovarian HGSC.See related commentary by Ishak and De Carvalho, p. 6083.
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Affiliation(s)
- Thomas R Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.
| | - Yeh Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hanru Sun
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
| | - Michael Considine
- Department of Biostatistics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lihong Li
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tza-Huei Wang
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Tian-Li Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland. .,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
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23
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Integrative Transcriptome Analyses of the Human Fallopian Tube: Fimbria and Ampulla-Site of Origin of Serous Carcinoma of the Ovary. Cancers (Basel) 2020; 12:cancers12051090. [PMID: 32349388 PMCID: PMC7281286 DOI: 10.3390/cancers12051090] [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: 03/31/2020] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 01/15/2023] Open
Abstract
Epithelial ovarian cancer represents a group of heterogeneous diseases with high grade serous cancer (HGSC) representing the most common histotype. Molecular profiles of precancerous lesions found in the fallopian tube have implicated this tissue as the presumptive site of origin of HGSC. Precancerous lesions are primarily found in the distal fallopian tube (fimbria), near the ovary relative to the proximal tissue (ampulla), nearer to the uterus. The proximity of the fimbria to the ovary and the link between ovulation, through follicular fluid release, and ovarian cancer risk led us to examine transcriptional responses of fallopian tube epithelia (FTE) at the different anatomical sites of the human fallopian tube. Gene expression profiles of matched FTE from the fimbria and from premenopausal women resulted in differentially expressed genes (DEGs): CYYR1, SALL1, FOXP2, TAAR1, AKR1C2/C3/C4, NMBR, ME1 and GSTA2. These genes are part of the antioxidant, stem and inflammation pathways. Comparisons between the luteal phase (post-ovulation) to the follicular phase (pre-ovulation) demonstrated greater differences in DEGs than a comparison between fimbria and fallopian tube anatomical differences alone. This data suggests that cyclical transcriptional changes experienced in pre-menopause are inherent physiological triggers that expose the FTE in the fimbria to cytotoxic stressors. These cyclical exposures induce transcriptional changes reflective of genotoxic and cytotoxic damage to the FTE in the fimbria which are closely related to transcriptional and genomic alterations observed in ovarian cancer.
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24
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Reavis HD, Drapkin R. The tubal epigenome - An emerging target for ovarian cancer. Pharmacol Ther 2020; 210:107524. [PMID: 32197795 DOI: 10.1016/j.pharmthera.2020.107524] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 02/07/2023]
Abstract
Ovarian cancer is the most lethal gynecologic malignancy in the United States. The mortality of this disease is primarily attributed to challenges in early detection and therapeutic resistance. Recent studies indicate that the majority of high-grade serous ovarian carcinomas (HGSCs) originate from aberrant fallopian tube epithelial (FTE) cells. This shift in thinking about ovarian cancer pathogenesis has been met with an effort to identify the early genetic and epigenetic changes that underlie the transformation of normal FTE cells and prompt them to migrate and colonize the ovary, ultimately giving rise to aggressive HGSC. While identification of these early changes is important for biomarker discovery, the emergence of epigenetic alterations in FTE chromatin may also provide new opportunities for early detection, prevention, and therapeutic intervention. Here we provide a comprehensive overview of the current knowledge regarding early epigenetic reprogramming that precedes HGSC tumor development, the way that these alterations affect both intrinsic and extrinsic tumor properties, and how the epigenome may be targeted to thwart HGSC tumorigenesis.
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Affiliation(s)
- Hunter D Reavis
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Graduate Program in Cell and Molecular Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Graduate Program in Cell and Molecular Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
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25
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Non-Surgical Cancer Risk Reduction in BRCA1 Mutation Carriers: Disabling the Remote Control. Cancers (Basel) 2020; 12:cancers12030547. [PMID: 32120796 PMCID: PMC7139938 DOI: 10.3390/cancers12030547] [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: 01/30/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 11/23/2022] Open
Abstract
Women-specific cancers are a major health issue, particularly those associated with the BRCA1 germline mutation carrier state, which include triple-negative basal breast carcinomas and high-grade serous ovarian carcinomas (referred to as extra-uterine Müllerian carcinomas). Whereas many chronic diseases can currently be prevented (e.g., cardiovascular diseases), no recent tangible progress was made in cancer prevention of BRCA1 mutation carriers apart from surgical resections of at-risk organs. This lack of progress is largely due to (1) poor understanding of the initiating events triggered by known risk factors in the development of these cancers, (2) the fact that current preventive measures rely on evidence obtained from adjuvant breast cancer treatment that fail to protect against poor prognostic cancers, and (3) problems with using cancer incidence in high-risk women as an ethically justifiable endpoint in cancer prevention trials. Here, we propose that cancer predisposition in BRCA1 mutation carriers is driven, at least in part, by cell-nonautonomous mechanisms (i.e., driven by consequences of this carrier state on hormonal and other systemic factors controlled in organs other than those that are cancer-prone) and that biomarkers of epigenomic reprogramming, hypothesized to be a direct consequence of such cell-nonautonomous mechanisms, are attractive as intermediate surrogate endpoints to assess the efficacy of cancer risk-reducing strategies targeting these mechanisms.
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26
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Differential DNA methylation in high-grade serous ovarian cancer (HGSOC) is associated with tumor behavior. Sci Rep 2019; 9:17996. [PMID: 31784612 PMCID: PMC6884482 DOI: 10.1038/s41598-019-54401-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/13/2019] [Indexed: 12/21/2022] Open
Abstract
The epigenome offers an additional facet of cancer that can help categorize patients into those at risk of disease, recurrence, or treatment failure. We conducted a retrospective, nested, case-control study of advanced and recurrent high-grade serous ovarian cancer (HGSOC) patients in which we assessed epigenome-wide association using Illumina methylationEPIC arrays to characterize DNA methylation status and RNAseq to evaluate gene expression. Comparing HGSOC tumors with normal fallopian tube tissues we observe global hypomethylation but with skewing towards hypermethylation when interrogating gene promoters. In total, 5,852 gene interrogating probes revealed significantly different methylation. Within HGSOC, 57 probes highlighting 17 genes displayed significant differential DNA methylation between primary and recurrent disease. Between optimal vs suboptimal surgical outcomes 99 probes displayed significantly different methylation but only 29 genes showed an inverse correlation between methylation status and gene expression. Overall, differentially methylated genes point to several pathways including RAS as well as hippo signaling in normal vs primary HGSOC; valine, leucine, and isoleucine degradation and endocytosis in primary vs recurrent HGSOC; and pathways containing immune driver genes in optimal vs suboptimal surgical outcomes. Thus, differential DNA methylation identified numerous genes that could serve as potential biomarkers and/or therapeutic targets in HGSOC.
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27
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Singh A, Gupta S, Sachan M. Epigenetic Biomarkers in the Management of Ovarian Cancer: Current Prospectives. Front Cell Dev Biol 2019; 7:182. [PMID: 31608277 PMCID: PMC6761254 DOI: 10.3389/fcell.2019.00182] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer (OC) causes significant morbidity and mortality as neither detection nor screening of OC is currently feasible at an early stage. Difficulty to promptly diagnose OC in its early stage remains challenging due to non-specific symptoms in the early-stage of the disease, their presentation at an advanced stage and poor survival. Therefore, improved detection methods are urgently needed. In this article, we summarize the potential clinical utility of epigenetic signatures like DNA methylation, histone modifications, and microRNA dysregulation, which play important role in ovarian carcinogenesis and discuss its application in development of diagnostic, prognostic, and predictive biomarkers. Molecular characterization of epigenetic modification (methylation) in circulating cell free tumor DNA in body fluids offers novel, non-invasive approach for identification of potential promising cancer biomarkers, which can be performed at multiple time points and probably better reflects the prevailing molecular profile of cancer. Current status of epigenetic research in diagnosis of early OC and its management are discussed here with main focus on potential diagnostic biomarkers in tissue and body fluids. Rapid and point of care diagnostic applications of DNA methylation in liquid biopsy has been precluded as a result of cumbersome sample preparation with complicated conventional methods of isolation. New technologies which allow rapid identification of methylation signatures directly from blood will facilitate sample-to answer solutions thereby enabling next-generation point of care molecular diagnostics. To date, not a single epigenetic biomarker which could accurately detect ovarian cancer at an early stage in either tissue or body fluid has been reported. Taken together, the methodological drawbacks, heterogeneity associated with ovarian cancer and non-validation of the clinical utility of reported potential biomarkers in larger ovarian cancer populations has impeded the transition of epigenetic biomarkers from lab to clinical settings. Until addressed, clinical implementation as a diagnostic measure is a far way to go.
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Affiliation(s)
- Alka Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
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28
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Reavis H, Drapkin R. H2Bub1: Guardian of chromatin accessibility in ovarian cancer. Oncoscience 2019; 6:349-350. [PMID: 31608296 PMCID: PMC6768845 DOI: 10.18632/oncoscience.484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/14/2019] [Indexed: 12/13/2022] Open
Affiliation(s)
- Hunter Reavis
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Ronny Drapkin
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
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29
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Kumar R, Paul AM, Rameshwar P, Pillai MR. Epigenetic Dysregulation at the Crossroad of Women's Cancer. Cancers (Basel) 2019; 11:cancers11081193. [PMID: 31426393 PMCID: PMC6721458 DOI: 10.3390/cancers11081193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
An increasingly number of women of all age groups are affected by cancer, despite substantial progress in our understanding of cancer pathobiology, the underlying genomic alterations and signaling cascades, and cellular-environmental interactions. Though our understanding of women’s cancer is far more complete than ever before, there is no comprehensive model to explain the reasons behind the increased incidents of certain reproductive cancer among older as well as younger women. It is generally suspected that environmental and life-style factors affecting hormonal and growth control pathways might help account for the rise of women’s cancers in younger age, as well, via epigenetic mechanisms. Epigenetic regulators play an important role in orchestrating an orderly coordination of cellular signals in gene activity in response to upstream signaling and/or epigenetic modifiers present in a dynamic extracellular milieu. Here we will discuss the broad principles of epigenetic regulation of DNA methylation and demethylation, histone acetylation and deacetylation, and RNA methylation in women’s cancers in the context of gene expression, hormonal action, and the EGFR family of cell surface receptor tyrosine kinases. We anticipate that a better understanding of the epigenetics of women’s cancers may provide new regulatory leads and further fuel the development of new epigenetic biomarkers and therapeutic approaches.
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Affiliation(s)
- Rakesh Kumar
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India.
- Department of Medicine, Division of Hematology-Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA.
| | - Aswathy Mary Paul
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India
- Graduate Degree Program, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Pranela Rameshwar
- Department of Medicine, Division of Hematology-Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - M Radhakrishna Pillai
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India
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30
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Abstract
PURPOSE OF REVIEW Both conventional and novel approaches to early detection of ovarian cancer are reviewed in the context of new developments in our understanding of ovarian cancer biology. RECENT FINDINGS While CA125 as a single value lacks adequate specificity or sensitivity for screening, large studies have shown that a 2-stage strategy which tracks CA125 change over time and prompts transvaginal ultrasound (TVS) for a small subset of women with abnormally rising biomarker values achieves adequate specificity and detects a higher fraction of early-stage disease. Sensitivity could clearly be improved in both blood tests and in imaging. Metastasis can occur from ovarian cancers too small to increase blood levels of protein antigens and a significant fraction of ovarian cancers arise from the fimbriae of fallopian tubes that cannot be imaged with TVS. Autoantibodies, miRNA, ctDNA, DNA methylation in blood, and cervical mucus might improve sensitivity of the initial phase and magnetic relaxometry and autofluorescence could improve imaging in the second phase. Enhancing the sensitivity of two-stage strategies for early detection could reduce mortality from ovarian cancer.
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Affiliation(s)
- Denise R Nebgen
- Division of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Karen H Lu
- Division of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Robert C Bast
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.
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31
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Martínez-Cano J, Campos-Sánchez E, Cobaleda C. Epigenetic Priming in Immunodeficiencies. Front Cell Dev Biol 2019; 7:125. [PMID: 31355198 PMCID: PMC6635466 DOI: 10.3389/fcell.2019.00125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/26/2019] [Indexed: 12/17/2022] Open
Abstract
Immunodeficiencies (IDs) are disorders of the immune system that increase susceptibility to infections and cancer, and are therefore associated with elevated morbidity and mortality. IDs can be primary (not caused by other condition or exposure) or secondary due to the exposure to different agents (infections, chemicals, aging, etc.). Most primary immunodeficiencies (PIDs) are of genetic origin, caused by mutations affecting genes with key roles in the development or function of the cells of the immune system. A large percentage of PIDs are associated with a defective development and/or function of lymphocytes and, especially, B cells, the ones in charge of generating the different types of antibodies. B-cell development is a tightly regulated process in which many different factors participate. Among the regulators of B-cell differentiation, a correct epigenetic control of cellular identity is essential for normal cell function. With the advent of next-generation sequencing (NGS) techniques, more and more alterations in different types of epigenetic regulators are being described at the root of PIDs, both in humans and in animal models. At the same time, it is becoming increasingly clear that epigenetic alterations triggered by the exposure to environmental agents have a key role in the development of secondary immunodeficiencies (SIDs). Due to their largely reversible nature, epigenetic modifications are quickly becoming key therapeutic targets in other diseases where their contribution has been known for more time, like cancer. Here, we establish a parallelism between IDs and the nowadays accepted role of epigenetics in cancer initiation and progression, and propose that epigenetics forms a "third axis" (together with genetics and external agents) to be considered in the etiology of IDs, and linking PIDs and SIDs at the molecular level. We therefore postulate that IDs arise due to a variable contribution of (i) genetic, (ii) environmental, and (iii) epigenetic causes, which in fact form a continuum landscape of all possible combinations of these factors. Additionally, this implies the possibility of a fully epigenetically triggered mechanism for some IDs. This concept would have important prophylactic and translational implications, and would also imply a more blurred frontier between primary and secondary immunodeficiencies.
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Affiliation(s)
| | | | - César Cobaleda
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas –Universidad Autónoma de Madrid), Madrid, Spain
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32
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Pisanic TR, Asaka S, Lin SF, Yen TT, Sun H, Bahadirli-Talbott A, Wang TH, Burns KH, Wang TL, Shih IM. Long Interspersed Nuclear Element 1 Retrotransposons Become Deregulated during the Development of Ovarian Cancer Precursor Lesions. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:513-520. [PMID: 30553834 PMCID: PMC6412403 DOI: 10.1016/j.ajpath.2018.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/20/2018] [Accepted: 11/19/2018] [Indexed: 11/30/2022]
Abstract
There is growing evidence that most high-grade serous ovarian carcinomas likely arise from local dissemination of precursor lesions of the fallopian tube. Evolution of these lesions from early p53 signatures to latter-stage, serous tubal intraepithelial carcinomas (STICs) is characterized by cytologic atypia, accumulation of somatic mutations, and genomic instability, the etiologies of which remain unclear. Long interspersed element 1 (LINE-1) retrotransposon is expressed in many carcinomas, including high-grade serous ovarian carcinoma, where it contributes to genomic instability; however, the timing of LINE-1 activation during this evolution has yet to be elucidated. In this study, we assessed LINE-1 open reading frame 1 protein expression in 12 p53 signature lesions, 32 STICs, and 112 various types of ovarian cancers via immunohistochemical staining and examined LINE-1 promoter methylation in representative cases. We found that 78% and 57% of STICs, with and without concurrent ovarian carcinomas, respectively, exhibited intense LINE-1 immunoreactivity compared with adjacent, normal-appearing fallopian tube epithelium. Hypomethylation of the LINE-1 promoter was found in all STICs exhibiting overexpression. None of the 12 p53 signatures demonstrated significant LINE-1 expression. In ovarian cancer, 84 (75%) of 112 ovarian carcinomas overexpressed LINE-1. Our results indicate that LINE-1 retrotransposons often become deregulated during progression of ovarian cancer precursor lesions from the p53 signature to STIC stages and remain highly expressed in carcinoma.
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Affiliation(s)
- Thomas R Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
| | - Shiho Asaka
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Shiou-Fu Lin
- Department of Pathology, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Ting-Tai Yen
- Department of Gynecology and Obstetrics, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Hanru Sun
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
| | | | - Tza-Huei Wang
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland; Department of Biomedical Engineering, Johns Hopkins Medical Institutions, Baltimore, Maryland; Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Kathleen H Burns
- Department of Pathology, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Tian-Li Wang
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland; Department of Pathology, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland; Department of Gynecology and Obstetrics, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Ie-Ming Shih
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland; Department of Pathology, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland; Department of Gynecology and Obstetrics, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland.
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33
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Vicente-Dueñas C, Hauer J, Cobaleda C, Borkhardt A, Sánchez-García I. Epigenetic Priming in Cancer Initiation. Trends Cancer 2019; 4:408-417. [PMID: 29860985 DOI: 10.1016/j.trecan.2018.04.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 12/17/2022]
Abstract
Recent evidence from hematopoietic and epithelial tumors revealed that the contribution of oncogenes to cancer development is mediated mainly through epigenetic priming of cancer-initiating cells, suggesting that genetic lesions that initiate the cancer process might be dispensable for the posterior tumor progression and maintenance. Epigenetic priming may remain latent until it is later triggered by endogenous or environmental stimuli. This Opinion article addresses the impact of epigenetic priming in cancer development and in the design of new therapeutic approaches.
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Affiliation(s)
| | - Julia Hauer
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Heinrich Heine University Düsseldorf, Medical Faculty, Düsseldorf, Germany; Equal first author
| | - César Cobaleda
- Department of Cell Biology and Immunology, Centro de Biologia Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; Equal senior author.
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Heinrich Heine University Düsseldorf, Medical Faculty, Düsseldorf, Germany; Equal senior author.
| | - Isidro Sánchez-García
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain; Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Campus M. de Unamuno s/n, 37007 Salamanca, Spain; Equal senior author.
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34
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Hentze JL, Høgdall CK, Høgdall EV. Methylation and ovarian cancer: Can DNA methylation be of diagnostic use? Mol Clin Oncol 2019; 10:323-330. [PMID: 30847169 DOI: 10.3892/mco.2019.1800] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/04/2018] [Indexed: 12/31/2022] Open
Abstract
Ovarian cancer is a silent killer and, due to late diagnosis and frequent chemo resistance in patients, the primary cause of fatality amongst the various types of gynecological cancer. The discovery of a specific and sensitive biomarker for ovarian cancer could improve early diagnosis, thereby saving lives. Biomarkers could also improve treatment, by predicting which patients will benefit from specific treatment strategies. DNA methylation is an epigenetic mechanism, and 'methylation imbalance' is characteristic of cancer. Previous research suggests that changes in DNA methylation can be used diagnostically, and that they may predict resistance to treatment. This paper gives an up-to-date overview of research investigating the potential of DNA methylation-based markers for diagnostics, prognostics, screening and prediction of drug resistance for ovarian cancer patients. DNA methylation cancer-biomarkers may be useful for cancer treatment, particularly since they are chemically stable and since cancer-associated changes in methylation typically precedes tumor growth. DNA methylation markers could improve diagnosis and treatment and might even be used for screening in the future. Furthermore, DNA methylation biomarkers could facilitate the development of precision medicine. However, at this point no biomarkers for ovarian cancer have a sufficient combination of sensitivity and specificity in a clinical setting. A reason for this is that most studies have focused on a single or a few methylation sites. More large screenings and genome-wide studies must be performed to increase the chance of identifying a DNA methylation marker which can identify ovarian cancer.
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Affiliation(s)
- Julie L Hentze
- Department of Pathology, Herlev Hospital, University of Copenhagen, 2730 Herlev, Denmark
| | - Claus K Høgdall
- Department of Gynecology, The Juliane Marie Centre, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Estrid V Høgdall
- Department of Pathology, Herlev Hospital, University of Copenhagen, 2730 Herlev, Denmark
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35
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Campos-Sanchez E, Martínez-Cano J, Del Pino Molina L, López-Granados E, Cobaleda C. Epigenetic Deregulation in Human Primary Immunodeficiencies. Trends Immunol 2018; 40:49-65. [PMID: 30509895 DOI: 10.1016/j.it.2018.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022]
Abstract
Primary immunodeficiencies (PIDs) are immune disorders resulting from defects in genes involved in immune regulation, and manifesting as an increased susceptibility to infections, autoimmunity, and cancer. However, the molecular basis of some prevalent entities remains poorly understood. Epigenetic control is essential for immune functions, and epigenetic alterations have been identified in different PIDs, including syndromes such as immunodeficiency-centromeric-instability-facial-anomalies, Kabuki, or Wolf-Hirschhorn, among others. Although the epigenetic changes may differ among these PIDs, the reversibility of epigenetic modifications suggests that they might become potential therapeutic targets. Here, we review recent mechanistic advances in our understanding of epigenetic alterations associated with certain PIDs, propose that a fully epigenetically driven mechanism might underlie some PIDs, and discuss the possible prophylactic and therapeutic implications.
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Affiliation(s)
- Elena Campos-Sanchez
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; These authors contributed equally to this work
| | - Jorge Martínez-Cano
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; These authors contributed equally to this work
| | - Lucía Del Pino Molina
- Clinical Immunology Department, Hospital Universitario, La Paz Institute of Biomedical Research, 28046, Madrid, Spain; Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, 28046 Madrid, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, Hospital Universitario, La Paz Institute of Biomedical Research, 28046, Madrid, Spain; Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, 28046 Madrid, Spain.
| | - Cesar Cobaleda
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain.
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36
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Pisanic TR, Cope LM, Lin SF, Yen TT, Athamanolap P, Asaka R, Nakayama K, Fader AN, Wang TH, Shih IM, Wang TL. Methylomic Analysis of Ovarian Cancers Identifies Tumor-Specific Alterations Readily Detectable in Early Precursor Lesions. Clin Cancer Res 2018; 24:6536-6547. [PMID: 30108103 DOI: 10.1158/1078-0432.ccr-18-1199] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/12/2018] [Accepted: 08/09/2018] [Indexed: 12/22/2022]
Abstract
PURPOSE High-grade serous ovarian carcinoma (HGSOC) typically remains undiagnosed until advanced stages when peritoneal dissemination has already occurred. Here, we sought to identify HGSOC-specific alterations in DNA methylation and assess their potential to provide sensitive and specific detection of HGSOC at its earliest stages. EXPERIMENTAL DESIGN MethylationEPIC genome-wide methylation analysis was performed on a discovery cohort comprising 23 HGSOC, 37 non-HGSOC malignant, and 36 histologically unremarkable gynecologic tissue samples. The resulting data were processed using selective bioinformatic criteria to identify regions of high-confidence HGSOC-specific differential methylation. Quantitative methylation-specific real-time PCR (qMSP) assays were then developed for 8 of the top-performing regions and analytically validated in a cohort of 90 tissue samples. Lastly, qMSP assays were used to assess and compare methylation in 30 laser-capture microdissected (LCM) fallopian tube epithelia samples obtained from cancer-free and serous tubal intraepithelial carcinoma (STIC) positive women. RESULTS Bioinformatic selection identified 91 regions of robust, HGSOC-specific hypermethylation, 23 of which exhibited an area under the receiver-operator curve (AUC) value ≥ 0.9 in the discovery cohort. Seven of 8 top-performing regions demonstrated AUC values between 0.838 and 0.968 when analytically validated by qMSP in a 90-patient cohort. A panel of the 3 top-performing genes (c17orf64, IRX2, and TUBB6) was able to perfectly discriminate HGSOC (AUC 1.0). Hypermethylation within these loci was found exclusively in LCM fallopian tube epithelia from women with STIC lesions, but not in cancer-free fallopian tubes. CONCLUSIONS A panel of methylation biomarkers can be used to accurately identify HGSOC, even at precursor stages of the disease.
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Affiliation(s)
- Thomas R Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.
| | - Leslie M Cope
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Oncology and Biostatistics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Shiou-Fu Lin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ting-Tai Yen
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Pornpat Athamanolap
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ryoichi Asaka
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kentaro Nakayama
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo, Japan
| | - Amanda N Fader
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tza-Huei Wang
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Ie-Ming Shih
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tian-Li Wang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland. .,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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37
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Zheng SC, Webster AP, Dong D, Feber A, Graham DG, Sullivan R, Jevons S, Lovat LB, Beck S, Widschwendter M, Teschendorff AE. A novel cell-type deconvolution algorithm reveals substantial contamination by immune cells in saliva, buccal and cervix. Epigenomics 2018; 10:925-940. [DOI: 10.2217/epi-2018-0037] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: An outstanding challenge in epigenome studies is the estimation of cell-type proportions in complex epithelial tissues. Materials & methods: Here, we construct and validate a DNA methylation reference and algorithm for complex tissues that contain epithelial, immune and nonimmune stromal cells. Results: Using this reference, we show that easily accessible tissues such as saliva, buccal and cervix exhibit substantial variation in immune cell (IC) contamination. We further validate our reference in the context of oral cancer, where it correctly predicts an increased IC infiltration in cancer but suppressed in patients with highest smoking exposure. Finally, our method can improve the specificity of differentially methylated CpG calls in epithelial cancer. Conclusion: The degree and variation of IC contamination in complex epithelial tissues is substantial. We provide a valuable resource and tool for assessing the epithelial purity and IC contamination of samples and for identifying differential methylation in such complex tissues.
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Affiliation(s)
- Shijie C Zheng
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, 320 Yue Yang Road, Shanghai 200031, PR China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, PR China
| | - Amy P Webster
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Danyue Dong
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, 320 Yue Yang Road, Shanghai 200031, PR China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, PR China
| | - Andy Feber
- Division of Surgery & Interventional Science, UCL, London WC1E 6BT, UK
| | - David G Graham
- Division of Surgery & Interventional Science, UCL, London WC1E 6BT, UK
| | - Roisin Sullivan
- Division of Surgery & Interventional Science, UCL, London WC1E 6BT, UK
| | - Sarah Jevons
- Division of Surgery & Interventional Science, UCL, London WC1E 6BT, UK
| | - Laurence B Lovat
- Division of Surgery & Interventional Science, UCL, London WC1E 6BT, UK
| | - Stephan Beck
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Martin Widschwendter
- Department of Women's Cancer, University College London, 74 Huntley Street, London WC1E 6AU, UK
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, 320 Yue Yang Road, Shanghai 200031, PR China
- Department of Women's Cancer, University College London, 74 Huntley Street, London WC1E 6AU, UK
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38
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Vicente-Dueñas C, González-Herrero I, Sehgal L, García-Ramírez I, Rodríguez-Hernández G, Pintado B, Blanco O, Criado FJG, Cenador MBG, Green MR, Sánchez-García I. Dnmt1 links BCR-ABLp210 to epigenetic tumor stem cell priming in myeloid leukemia. Leukemia 2018; 33:249-278. [PMID: 29955131 PMCID: PMC6326950 DOI: 10.1038/s41375-018-0192-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/20/2018] [Accepted: 05/30/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Inés González-Herrero
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-USAL, Campus M. de Unamuno s/n, Salamanca, Spain
| | - Lalit Sehgal
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Idoia García-Ramírez
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-USAL, Campus M. de Unamuno s/n, Salamanca, Spain
| | - Guillermo Rodríguez-Hernández
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-USAL, Campus M. de Unamuno s/n, Salamanca, Spain
| | - Belén Pintado
- Transgenesis Facility CNB-CBMSO, CSIC-UAM, Madrid, Spain
| | - Oscar Blanco
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Departamento de Anatomía Patológica, Universidad de Salamanca, Salamanca, Spain
| | - Francisco Javier García Criado
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Departamento de Cirugía, Universidad de Salamanca, Salamanca, Spain
| | - María Begoña García Cenador
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Departamento de Cirugía, Universidad de Salamanca, Salamanca, Spain
| | - Michael R Green
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Isidro Sánchez-García
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. .,Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-USAL, Campus M. de Unamuno s/n, Salamanca, Spain.
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39
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Taking the Tube: From Normal Fallopian Tube Epithelium to Ovarian High-grade Serous Carcinoma. Clin Obstet Gynecol 2018; 60:697-710. [PMID: 29045296 DOI: 10.1097/grf.0000000000000313] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Detailed pathologic studies over the past decade suggest a distal fallopian tube origin for the majority of "ovarian" high-grade serous carcinomas (HGSC). This review will summarize molecular alterations observed in tubal precursors for HGSC, namely p53 signatures and serous tubal intraepithelial carcinomas, and in nonmalignant fallopian tube epithelial cells obtained from women at increased genetic risk for HGSC. Recent experiments investigating the impact of follicular fluid exposure and retrograde menstruation on tumor development in the fallopian tube will also be discussed. These data will be reconciled with traditional ovarian cancer risk factors related to reproductive history.
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40
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Abstract
Due to the clonal nature of human leukemia evolution, all leukemic cells carry the same leukemia-initiating genetic lesions, independently of the intrinsic tumoral cellular heterogeneity. However, the latest findings have shown that the mode of action of oncogenes is not homogeneous throughout the developmental history of leukemia. Studies on different types of hematopoietic tumors have shown that the contribution of oncogenes to leukemia is mainly mediated through the epigenetic reprogramming of the leukemia-initiating target cell. This driving of cancer by a malignant epigenetic stem cell rewiring is, however, not exclusive of the hematopoietic system, but rather represents a common tumoral mechanism that is also at work in epithelial tumors. Tumoral epigenetic reprogramming is therefore a new type of interaction between genes and their target cells, in which the action of the oncogene modifies the epigenome to prime leukemia development by establishing a new pathological tumoral cellular identity. This reprogramming may remain latent until it is triggered by either endogenous or environmental stimuli. This new view on the making of leukemia not only reveals a novel function for oncogenes, but also provides evidence for a previously unconsidered model of leukemogenesis, in which the programming of the leukemia cellular identity has already occurred at the level of stem cells, therefore showing a role for oncogenes in the timing of leukemia initiation.
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41
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Widschwendter M, Jones A, Evans I, Reisel D, Dillner J, Sundström K, Steyerberg EW, Vergouwe Y, Wegwarth O, Rebitschek FG, Siebert U, Sroczynski G, de Beaufort ID, Bolt I, Cibula D, Zikan M, Bjørge L, Colombo N, Harbeck N, Dudbridge F, Tasse AM, Knoppers BM, Joly Y, Teschendorff AE, Pashayan N. Epigenome-based cancer risk prediction: rationale, opportunities and challenges. Nat Rev Clin Oncol 2018; 15:292-309. [PMID: 29485132 DOI: 10.1038/nrclinonc.2018.30] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The incidence of cancer is continuing to rise and risk-tailored early diagnostic and/or primary prevention strategies are urgently required. The ideal risk-predictive test should: integrate the effects of both genetic and nongenetic factors and aim to capture these effects using an approach that is both biologically stable and technically reproducible; derive a score from easily accessible biological samples that acts as a surrogate for the organ in question; and enable the effectiveness of risk-reducing measures to be monitored. Substantial evidence has accumulated suggesting that the epigenome and, in particular, DNA methylation-based tests meet all of these requirements. However, the development and implementation of DNA methylation-based risk-prediction tests poses considerable challenges. In particular, the cell type specificity of DNA methylation and the extensive cellular heterogeneity of the easily accessible surrogate cells that might contain information relevant to less accessible tissues necessitates the use of novel methods in order to account for these confounding issues. Furthermore, the engagement of the scientific community with health-care professionals, policymakers and the public is required in order to identify and address the organizational, ethical, legal, social and economic challenges associated with the routine use of epigenetic testing.
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Affiliation(s)
- Martin Widschwendter
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Allison Jones
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Iona Evans
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Daniel Reisel
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Sundström
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Ewout W Steyerberg
- Center for Medical Decision Sciences, Department of Public Health, Erasmus MC, Rotterdam, Netherlands.,Department of Biomedical Data Sciences, LUMC, Leiden, Netherlands
| | - Yvonne Vergouwe
- Center for Medical Decision Sciences, Department of Public Health, Erasmus MC, Rotterdam, Netherlands
| | - Odette Wegwarth
- Max Planck Institute for Human Development, Harding Center for Risk Literacy, Berlin, Germany.,Max Planck Institute for Human Development, Center for Adaptive Rationality, Berlin, Germany
| | - Felix G Rebitschek
- Max Planck Institute for Human Development, Harding Center for Risk Literacy, Berlin, Germany
| | - Uwe Siebert
- Institute of Public Health, Medical Decision Making and Health Technology Assessment, Department of Public Health, Health Services Research, and HTA, UMIT-University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria.,Harvard T. C. Chan School of Public Health, Center for Health Decision Science, Department of Health Policy and Management, Boston, MA, USA.,Oncotyrol: Center for Personalized Medicine, Innsbruck, Austria
| | - Gaby Sroczynski
- Institute of Public Health, Medical Decision Making and Health Technology Assessment, Department of Public Health, Health Services Research, and HTA, UMIT-University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria
| | - Inez D de Beaufort
- Department of Medical Ethics and Philosophy of Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - Ineke Bolt
- Department of Medical Ethics and Philosophy of Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - David Cibula
- Department of Obstetrics and Gynaecology, First Medical Faculty of the Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Michal Zikan
- Department of Obstetrics and Gynaecology, First Medical Faculty of the Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Line Bjørge
- Department of Obstetrics and Gynecology, Haukeland University Hospital, and Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Nicoletta Colombo
- European Institute of Oncology and University Milan-Bicocca, Milan, Italy
| | - Nadia Harbeck
- Breast Center, Department of Gynaecology and Obstetrics, University of Munich (LMU), Munich, Germany
| | - Frank Dudbridge
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.,Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anne-Marie Tasse
- Public Population Project in Genomics and Society, McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | | | - Yann Joly
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Andrew E Teschendorff
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Nora Pashayan
- Department of Applied Health Research, Institute of Epidemiology and Healthcare, University College London, UK
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42
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Saini U, Suarez AA, Naidu S, Wallbillich JJ, Bixel K, Wanner RA, Bice J, Kladney RD, Lester J, Karlan BY, Goodfellow PJ, Cohn DE, Selvendiran K. STAT3/PIAS3 Levels Serve as "Early Signature" Genes in the Development of High-Grade Serous Carcinoma from the Fallopian Tube. Cancer Res 2018; 78:1739-1750. [PMID: 29339537 DOI: 10.1158/0008-5472.can-17-1671] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/13/2017] [Accepted: 01/10/2018] [Indexed: 01/23/2023]
Abstract
The initial molecular events that lead to malignant transformation of the fimbria of the fallopian tube (FT) through high-grade serous ovarian carcinoma (HGSC) remain poorly understood. In this study, we report that increased expression of signal transducer and activator of transcription 3 (pSTAT3 Tyr705) and suppression or loss of protein inhibitor of activated STAT3 (PIAS3) in FT likely drive HGSC. We evaluated human tissues-benign normal FT, tubal-peritoneal junction (TPJ), p53 signature FT tissue, tubal intraepithelial lesion in transition (TILT), serous tubal intraepithelial carcinoma (STIC) without ovarian cancer, and HGSC for expression of STAT3/PIAS3 (compared with their known TP53 signature) and their target proliferation genes. We observed constitutive activation of STAT3 and low levels or loss of PIAS3 in the TPJ, p53 signature, TILT, and STIC through advanced stage IV (HGSC) tissues. Elevated expression of pSTAT3 Tyr705 and decreased levels of PIAS3 appeared as early as TPJ and the trend continued until very advanced stage HGSC (compared with high PIAS3 and low pSTAT3 expression in normal benign FT). Exogenous expression of STAT3 in FT cells mediated translocation of pSTAT3 and c-Myc into the nucleus. In vivo experiments demonstrated that overexpression of STAT3 in FT secretory epithelial cells promoted tumor progression and metastasis, mimicking the clinical disease observed in patients with HGSC. Thus, we conclude that the STAT3 pathway plays a role in the development and progression of HGSC from its earliest premalignant states.Significance: Concomitant gain of pSTAT3 Tyr705 and loss of PIAS3 appear critical for initiation and development of high-grade serous carcinoma. Cancer Res; 78(7); 1739-50. ©2018 AACR.
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Affiliation(s)
- Uksha Saini
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Adrian A Suarez
- Department of Pathology, Gynecological Pathology and Cytopathology Unit, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Shan Naidu
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - John J Wallbillich
- Division of Gynecologic Oncology, Department of OB/GYN, Georgia Cancer Center, Augusta University, Augusta, Georgia
| | - Kristin Bixel
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Ross A Wanner
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Jason Bice
- Pathology Core Lab, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Raleigh D Kladney
- Pathology Core Lab, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Jenny Lester
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars Sinai Medical Center, Los Angeles, California
| | - Beth Y Karlan
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars Sinai Medical Center, Los Angeles, California
| | - Paul J Goodfellow
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - David E Cohn
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Karuppaiyah Selvendiran
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, the Ohio State University Wexner Medical Center, Columbus, Ohio.
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Widschwendter M, Zikan M, Wahl B, Lempiäinen H, Paprotka T, Evans I, Jones A, Ghazali S, Reisel D, Eichner J, Rujan T, Yang Z, Teschendorff AE, Ryan A, Cibula D, Menon U, Wittenberger T. The potential of circulating tumor DNA methylation analysis for the early detection and management of ovarian cancer. Genome Med 2017; 9:116. [PMID: 29268796 PMCID: PMC5740748 DOI: 10.1186/s13073-017-0500-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/24/2017] [Indexed: 02/07/2023] Open
Abstract
Background Despite a myriad of attempts in the last three decades to diagnose ovarian cancer (OC) earlier, this clinical aim still remains a significant challenge. Aberrant methylation patterns of linked CpGs analyzed in DNA fragments shed by cancers into the bloodstream (i.e. cell-free DNA) can provide highly specific signals indicating cancer presence. Methods We analyzed 699 cancerous and non-cancerous tissues using a methylation array or reduced representation bisulfite sequencing to discover the most specific OC methylation patterns. A three-DNA-methylation-serum-marker panel was developed using targeted ultra-high coverage bisulfite sequencing in 151 women and validated in 250 women with various conditions, particularly in those associated with high CA125 levels (endometriosis and other benign pelvic masses), serial samples from 25 patients undergoing neoadjuvant chemotherapy, and a nested case control study of 172 UKCTOCS control arm participants which included serum samples up to two years before OC diagnosis. Results The cell-free DNA amount and average fragment size in the serum samples was up to ten times higher than average published values (based on samples that were immediately processed) due to leakage of DNA from white blood cells owing to delayed time to serum separation. Despite this, the marker panel discriminated high grade serous OC patients from healthy women or patients with a benign pelvic mass with specificity/sensitivity of 90.7% (95% confidence interval [CI] = 84.3–94.8%) and 41.4% (95% CI = 24.1–60.9%), respectively. Levels of all three markers plummeted after exposure to chemotherapy and correctly identified 78% and 86% responders and non-responders (Fisher’s exact test, p = 0.04), respectively, which was superior to a CA125 cut-off of 35 IU/mL (20% and 75%). 57.9% (95% CI 34.0–78.9%) of women who developed OC within two years of sample collection were identified with a specificity of 88.1% (95% CI = 77.3–94.3%). Sensitivity and specificity improved further when specifically analyzing CA125 negative samples only (63.6% and 87.5%, respectively). Conclusions Our data suggest that DNA methylation patterns in cell-free DNA have the potential to detect a proportion of OCs up to two years in advance of diagnosis and may potentially guide personalized treatment. The prospective use of novel collection vials, which stabilize blood cells and reduce background DNA contamination in serum/plasma samples, will facilitate clinical implementation of liquid biopsy analyses. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0500-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Widschwendter
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK.
| | - Michal Zikan
- Gynaecologic Oncology Center, Department of Obstetrics & Gynaecology, First Faculty of Medicine & General University Hospital, Charles University, Prague, Czech Republic
| | - Benjamin Wahl
- GATC Biotech AG, Jakob-Stadler-Platz 7, 78467, Konstanz, Germany
| | | | - Tobias Paprotka
- GATC Biotech AG, Jakob-Stadler-Platz 7, 78467, Konstanz, Germany
| | - Iona Evans
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Allison Jones
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Shohreh Ghazali
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | | | - Tamas Rujan
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - Zhen Yang
- CAS Max-Planck Partner Institute for Computational Biology, Shanghai Institute of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andrew E Teschendorff
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK.,CAS Max-Planck Partner Institute for Computational Biology, Shanghai Institute of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andy Ryan
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - David Cibula
- Gynaecologic Oncology Center, Department of Obstetrics & Gynaecology, First Faculty of Medicine & General University Hospital, Charles University, Prague, Czech Republic
| | - Usha Menon
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
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Hentze JL, Høgdall C, Kjær SK, Blaakær J, Høgdall E. Searching for new biomarkers in ovarian cancer patients: Rationale and design of a retrospective study under the Mermaid III project. Contemp Clin Trials Commun 2017; 8:167-174. [PMID: 29696206 PMCID: PMC5898550 DOI: 10.1016/j.conctc.2017.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/28/2017] [Accepted: 10/04/2017] [Indexed: 02/06/2023] Open
Abstract
Ovarian cancer is a silent killer and, due to late diagnosis, the primary cause of death amongst gynecological cancers, killing approximately 376 women annually in Denmark. The discovery of a specific and sensitive biomarker for ovarian cancer could improve early diagnosis, but also treatment, by predicting which patients will benefit from specific treatment strategies. The Mermaid III project is consisting of 3 parts including "Early detection, screening and long-term survival," "Biomarkers and/or prognostic markers" and "The infection theory." The present paper gives an overview of the part regarding biomarkers and/or prognostic markers, with a focus on rationale and design. The study described has 3 major branches: microRNAs, epigenetics and Next Generation Sequencing. Tissue and blood from ovarian cancer patients, already enrolled in the prospective ongoing pelvic mass cohort, will be examined. Relevant microRNAs and DNA methylation patterns will be investigated using array technology. Patient exomes will be fully sequenced, and identified genetic variations will be validated with Next Generation Sequencing. In all cases, data will be correlated with clinical information on the patient, in order to identify possible biomarkers. A thorough investigation of biomarkers in ovarian cancer, including large numbers of different markers, has never been done before. Besides from improving diagnosis and treatment, other outcomes could be markers for screening, knowledge of the molecular aspects of cancer and the discovery of new drugs. Moreover, biomarkers are a prerequisite for the development of precision medicine. This study will attack the ovarian cancer problem from several angles, thereby increasing the chance of successfully contributing to saving lives.
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Key Words
- CA125, Cancer Antigen 125
- CPH-I, Copenhagen Index
- DGCD, Danish Gynecologic Cancer Database
- Diagnostic/prognostic biomarkers
- Epigenetics
- FFPE, Formalin fixed and paraffin embedded
- FIGO, International Federation of Gynecology and Obstetrics
- HE4, Human Epididymis Protein 4
- MALOVA, MALignant OVArian cancer study
- MicroRNA
- NGS, Next Generation Sequencing
- Next Generation Sequencing
- O.C.T., Optimal cutting temperature
- OC, Ovarian cancer
- OS, Overall survival
- Ovarian cancer
- PARP, poly(adenosine diphosphate [ADP]-ribose) polymerase
- PFS, Progression free survival
- RMI, Risk of Malignancy Index
- ROCA, Risk of Ovarian Cancer Algorithm
- ROMA, Risk of Ovarian Malignancy Algorithm
- UKCTOCS, UK Collaborative Trial of OC Screening
- miRNAs, MicroRNAs
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Affiliation(s)
- Julie L. Hentze
- Department of Pathology, Herlev Hospital, Herlev, Copenhagen University Hospital, Denmark
| | - Claus Høgdall
- Department of Gynecology, The Juliane Marie Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Susanne K. Kjær
- Department of Gynecology, The Juliane Marie Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Unit of Virus, Lifestyle, and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Jan Blaakær
- Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev Hospital, Herlev, Copenhagen University Hospital, Denmark
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Kobayashi H, Ogawa K, Kawahara N, Iwai K, Niiro E, Morioka S, Yamada Y. Sequential molecular changes and dynamic oxidative stress in high-grade serous ovarian carcinogenesis. Free Radic Res 2017; 51:755-764. [PMID: 28931330 DOI: 10.1080/10715762.2017.1383605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The mechanism of high-grade serous ovarian cancer (HGSC) development remains elusive. This review outlines recent advances in the understanding of sequential molecular changes associated with the development of HGSC, as well as describes oxidative stress-induced genomic instability and carcinogenesis. This article reviews the English language literature between 2005 and 2017. Clinicopathological features analysis provides a sequential progression of fallopian tubal epithelium to precursor lesions to type 2 HGSC. HGSC may develop over a long time after incessant ovulation and repeated retrograde menstruation via stepwise accumulation of genetic alterations, including PAX2, ALDH1A1, STMN1, EZH2 and CCNE1, which confer positive selection of cells with growth advantages through acquiring driver mutations such as BRCA1/2, p53 or PTEN/PIK3CA. Haemoglobin and iron-induced oxidative stress leads to the emergence of genetic alterations in fallopian tubal epithelium via increased DNA damage and impaired DNA repair. Serous tubal intraepithelial carcinoma (STIC), the likely precursor of HGSC, may be susceptible to DNA double-strand breaks, exhibit DNA replication stress and increase genomic instability. The induction of genomic instability is considered to be a driving mechanism of reactive oxygen species (ROS)-induced carcinogenesis. HGSC exemplifies the view of stepwise cancer development. We describe how genetic alterations emerge during HGSC carcinogenesis related to oxidative stress.
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Affiliation(s)
- Hiroshi Kobayashi
- a Department of Obstetrics and Gynecology , Nara Medical University , Nara , Japan
| | - Kenji Ogawa
- a Department of Obstetrics and Gynecology , Nara Medical University , Nara , Japan
| | - Naoki Kawahara
- a Department of Obstetrics and Gynecology , Nara Medical University , Nara , Japan
| | - Kana Iwai
- a Department of Obstetrics and Gynecology , Nara Medical University , Nara , Japan
| | - Emiko Niiro
- a Department of Obstetrics and Gynecology , Nara Medical University , Nara , Japan
| | - Sachiko Morioka
- a Department of Obstetrics and Gynecology , Nara Medical University , Nara , Japan
| | - Yuki Yamada
- a Department of Obstetrics and Gynecology , Nara Medical University , Nara , Japan
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Meserve EEK, Brouwer J, Crum CP. Serous tubal intraepithelial neoplasia: the concept and its application. Mod Pathol 2017; 30:710-721. [PMID: 28106106 DOI: 10.1038/modpathol.2016.238] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 12/04/2016] [Accepted: 12/05/2016] [Indexed: 12/11/2022]
Abstract
In recent years it has become clear that many extra-uterine (pelvic) high-grade serous carcinomas (serous carcinomas) are preceded by a precursor lesion in the distal fallopian tube. Precursors range from small self-limited 'p53 signatures' to expansile serous tubal intraepithelial neoplasms that include both serous tubal epithelial proliferations (or lesions) of uncertain significance and serous tubal intraepithelial carcinomas. These precursors can be considered from three perspectives. The first is biologic underpinnings, which are multifactorial, and include the intersection of DNA damage with Tp53 mutations and disturbances in transcriptional regulation that increase with age. The second perspective is the morphologic discovery and classification of intraepithelial neoplasms that are intercepted early in their natural history, either incidentally or in risk-reduction surgeries for germline mutations. For the practicing pathologist, as well as the investigators, a distinction between a primary intraepithelial neoplasm and an intramucosal carcinoma must be made to avoid misinterpreting (or underestimating) the significance of these proliferations. The third perspective is the application of this information to intervention, devising strategies that will actually lower the ovarian cancer death rate by opportunistic salpingectomy, widespread comprehensive genetic screening and early detection. Central to this issue are the questions of (1) whether some STICs are metastatic, (2) whether lower-grade epithelial proliferations can invade prior to evolving into intraepithelial carcinoma, or (3) metastasize and become malignant elsewhere ('precursor escape'). An important caveat is the persistent and unsettling reality that many high-grade serous carcinomas are not associated with an obvious point of initiation in the fallopian tube. The pathologist sits squarely in the midst of all of these issues, and has a pivotal role in managing expectations for stemming the death rate from this lethal disease.
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Affiliation(s)
- Emily E K Meserve
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham and Women's Hospital, Boston, MA USA
| | - Jan Brouwer
- Department of Gynecologic Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Christopher P Crum
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham and Women's Hospital, Boston, MA USA
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Chen F, Gaitskell K, Garcia MJ, Albukhari A, Tsaltas J, Ahmed AA. Serous tubal intraepithelial carcinomas associated with high-grade serous ovarian carcinomas: a systematic review. BJOG 2017; 124:872-878. [DOI: 10.1111/1471-0528.14543] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2016] [Indexed: 01/21/2023]
Affiliation(s)
- F Chen
- Ovarian Cancer Cell Laboratory; The Weatherall Institute of Molecular Medicine; University of Oxford; Headington Oxford UK
- School of Clinical Sciences; Monash University; Clayton Melbourne Victoria Australia
| | - K Gaitskell
- Ovarian Cancer Cell Laboratory; The Weatherall Institute of Molecular Medicine; University of Oxford; Headington Oxford UK
- Cancer Epidemiology Unit; Nuffield Department of Population Health; University of Oxford; Oxford UK
| | - MJ Garcia
- Human Genetics Group; Spanish National Cancer Research Center (CNIO); Madrid Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER); Valencia Spain
| | - A Albukhari
- Ovarian Cancer Cell Laboratory; The Weatherall Institute of Molecular Medicine; University of Oxford; Headington Oxford UK
- Biochemistry Department; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
| | - J Tsaltas
- School of Clinical Sciences; Monash University; Clayton Melbourne Victoria Australia
| | - AA Ahmed
- Ovarian Cancer Cell Laboratory; The Weatherall Institute of Molecular Medicine; University of Oxford; Headington Oxford UK
- Nuffield Department of Obstetrics and Gynaecology; University of Oxford; Women's Centre; John Radcliffe Hospital; Oxford UK
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48
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Role of Fallopian Tubes in the Development of Ovarian Cancer. J Minim Invasive Gynecol 2017; 24:230-234. [DOI: 10.1016/j.jmig.2016.12.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/09/2016] [Accepted: 12/10/2016] [Indexed: 12/30/2022]
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