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Wang Q, Cao SH, Li YY, Zhang JB, Yang XH, Zhang B. Advances in precision therapy of low-grade serous ovarian cancer: A review. Medicine (Baltimore) 2024; 103:e34306. [PMID: 38669365 PMCID: PMC11049748 DOI: 10.1097/md.0000000000034306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/19/2023] [Indexed: 04/28/2024] Open
Abstract
Low-grade serous ovarian carcinoma (LGSOC) is a rare subtype of ovarian cancer that accounts for approximately 6% to 10% of serous ovarian cancers. The clinical treatment of LGSOC is similar to that of high-grade serous ovarian carcinoma, however, its clinical and molecular characteristics are different from those of high-grade serous ovarian carcinoma. This article reviews the research on gene diagnosis, surgical treatment, chemotherapy, and biological therapy of LGSOC, providing reference for clinical diagnosis and treatment of LGSOC. Surgery is the cornerstone of LGSOC treatment and maximum effort must be made to achieve R0 removal. Although LGSOC is not sensitive to chemotherapy, postoperative platinum-based combination chemotherapy remains the first-line treatment option for LGSOC. Additional clinical trials are needed to confirm the clinical benefits of chemotherapy and explore new chemotherapy protocols. Hormone and targeted therapies may also play important roles. Some patients, particularly those with residual lesions after treatment, may benefit from hormone maintenance therapy after chemotherapy. Targeted therapies, such as MEKi, show good application prospects and are expected to change the treatment pattern of LGSOC. Continuing to further study the genomics of LGSOC, identify its specific gene changes, and combine traditional treatment methods with precision targeted therapy based on second-generation sequencing may be the direction for LGSOC to overcome the treatment bottleneck. In future clinical work, comprehensive genetic testing should be carried out for LGSOC patients to accumulate data for future scientific research, in order to find more effective methods and drugs for the treatment of LGSOC.
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Affiliation(s)
- Qing Wang
- Department of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Sheng-Han Cao
- Graduate School of Bengbu Medical University, Bengbu, Anhui, China
| | - Yan-Yu Li
- Department of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Jing-Bo Zhang
- Department of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Xin-Hui Yang
- Department of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Bei Zhang
- Department of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
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2
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Lee M, Ahmad SF, Xu J. Regulation and function of transposable elements in cancer genomes. Cell Mol Life Sci 2024; 81:157. [PMID: 38556602 PMCID: PMC10982106 DOI: 10.1007/s00018-024-05195-2] [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: 12/03/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 04/02/2024]
Abstract
Over half of human genomic DNA is composed of repetitive sequences generated throughout evolution by prolific mobile genetic parasites called transposable elements (TEs). Long disregarded as "junk" or "selfish" DNA, TEs are increasingly recognized as formative elements in genome evolution, wired intimately into the structure and function of the human genome. Advances in sequencing technologies and computational methods have ushered in an era of unprecedented insight into how TE activity impacts human biology in health and disease. Here we discuss the current views on how TEs have shaped the regulatory landscape of the human genome, how TE activity is implicated in human cancers, and how recent findings motivate novel strategies to leverage TE activity for improved cancer therapy. Given the crucial role of methodological advances in TE biology, we pair our conceptual discussions with an in-depth review of the inherent technical challenges in studying repeats, specifically related to structural variation, expression analyses, and chromatin regulation. Lastly, we provide a catalog of existing and emerging assays and bioinformatic software that altogether are enabling the most sophisticated and comprehensive investigations yet into the regulation and function of interspersed repeats in cancer genomes.
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Affiliation(s)
- Michael Lee
- Department of Pediatrics, Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA.
| | - Syed Farhan Ahmad
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place - MS 345, Memphis, TN, 38105, USA
| | - Jian Xu
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place - MS 345, Memphis, TN, 38105, USA.
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3
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Perkiö A, Pradhan B, Genc F, Pirttikoski A, Pikkusaari S, Erkan EP, Falco MM, Huhtinen K, Narva S, Hynninen J, Kauppi L, Vähärautio A. Locus-specific LINE-1 expression in clinical ovarian cancer specimens at the single-cell level. Sci Rep 2024; 14:4322. [PMID: 38383551 PMCID: PMC10881972 DOI: 10.1038/s41598-024-54113-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 02/08/2024] [Indexed: 02/23/2024] Open
Abstract
Long interspersed nuclear elements (LINE-1s/L1s) are a group of retrotransposons that can copy themselves within a genome. In humans, it is the most successful transposon in nucleotide content. L1 expression is generally mild in normal human tissues, but the activity has been shown to increase significantly in many cancers. Few studies have examined L1 expression at single-cell resolution, thus it is undetermined whether L1 reactivation occurs solely in malignant cells within tumors. One of the cancer types with frequent L1 activity is high-grade serous ovarian carcinoma (HGSOC). Here, we identified locus-specific L1 expression with 3' single-cell RNA sequencing in pre- and post-chemotherapy HGSOC sample pairs from 11 patients, and in fallopian tube samples from five healthy women. Although L1 expression quantification with the chosen technique was challenging due to the repetitive nature of the element, we found evidence of L1 expression primarily in cancer cells, but also in other cell types, e.g. cancer-associated fibroblasts. The expression levels were similar in samples taken before and after neoadjuvant chemotherapy, indicating that L1 transcriptional activity was unaffected by clinical platinum-taxane treatment. Furthermore, L1 activity was negatively associated with the expression of MYC target genes, a finding that supports earlier literature of MYC being an L1 suppressor.
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Affiliation(s)
- Anna Perkiö
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Barun Pradhan
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Fatih Genc
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Anna Pirttikoski
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Sanna Pikkusaari
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Erdogan Pekcan Erkan
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Matias Marin Falco
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Kaisa Huhtinen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku and Turku University Hospital, 20521, Turku, Finland
| | - Sara Narva
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, 20521, Turku, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, 20521, Turku, Finland
| | - Liisa Kauppi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
| | - Anna Vähärautio
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
- Foundation for the Finnish Cancer Institute (FCI), Helsinki, Finland.
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4
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Mendez-Dorantes C, Burns KH. LINE-1 retrotransposition and its deregulation in cancers: implications for therapeutic opportunities. Genes Dev 2023; 37:948-967. [PMID: 38092519 PMCID: PMC10760644 DOI: 10.1101/gad.351051.123] [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] [Indexed: 12/28/2023]
Abstract
Long interspersed element 1 (LINE-1) is the only protein-coding transposon that is active in humans. LINE-1 propagates in the genome using RNA intermediates via retrotransposition. This activity has resulted in LINE-1 sequences occupying approximately one-fifth of our genome. Although most copies of LINE-1 are immobile, ∼100 copies are retrotransposition-competent. Retrotransposition is normally limited via epigenetic silencing, DNA repair, and other host defense mechanisms. In contrast, LINE-1 overexpression and retrotransposition are hallmarks of cancers. Here, we review mechanisms of LINE-1 regulation and how LINE-1 may promote genetic heterogeneity in tumors. Finally, we discuss therapeutic strategies to exploit LINE-1 biology in cancers.
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Affiliation(s)
- Carlos Mendez-Dorantes
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
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5
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Taylor MS, Wu C, Fridy PC, Zhang SJ, Senussi Y, Wolters JC, Cajuso T, Cheng WC, Heaps JD, Miller BD, Mori K, Cohen L, Jiang H, Molloy KR, Chait BT, Goggins MG, Bhan I, Franses JW, Yang X, Taplin ME, Wang X, Christiani DC, Johnson BE, Meyerson M, Uppaluri R, Egloff AM, Denault EN, Spring LM, Wang TL, Shih IM, Fairman JE, Jung E, Arora KS, Yilmaz OH, Cohen S, Sharova T, Chi G, Norden BL, Song Y, Nieman LT, Pappas L, Parikh AR, Strickland MR, Corcoran RB, Mustelin T, Eng G, Yilmaz ÖH, Matulonis UA, Chan AT, Skates SJ, Rueda BR, Drapkin R, Klempner SJ, Deshpande V, Ting DT, Rout MP, LaCava J, Walt DR, Burns KH. Ultrasensitive Detection of Circulating LINE-1 ORF1p as a Specific Multicancer Biomarker. Cancer Discov 2023; 13:2532-2547. [PMID: 37698949 PMCID: PMC10773488 DOI: 10.1158/2159-8290.cd-23-0313] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/09/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023]
Abstract
Improved biomarkers are needed for early cancer detection, risk stratification, treatment selection, and monitoring treatment response. Although proteins can be useful blood-based biomarkers, many have limited sensitivity or specificity for these applications. Long INterspersed Element-1 (LINE-1) open reading frame 1 protein (ORF1p) is a transposable element protein overexpressed in carcinomas and high-risk precursors during carcinogenesis with negligible expression in normal tissues, suggesting ORF1p could be a highly specific cancer biomarker. To explore ORF1p as a blood-based biomarker, we engineered ultrasensitive digital immunoassays that detect mid-attomolar (10-17 mol/L) ORF1p concentrations in plasma across multiple cancers with high specificity. Plasma ORF1p shows promise for early detection of ovarian cancer, improves diagnostic performance in a multianalyte panel, provides early therapeutic response monitoring in gastroesophageal cancers, and is prognostic for overall survival in gastroesophageal and colorectal cancers. Together, these observations nominate ORF1p as a multicancer biomarker with potential utility for disease detection and monitoring. SIGNIFICANCE The LINE-1 ORF1p transposon protein is pervasively expressed in many cancers and is a highly specific biomarker of multiple common, lethal carcinomas and their high-risk precursors in tissue and blood. Ultrasensitive ORF1p assays from as little as 25 μL plasma are novel, rapid, cost-effective tools in cancer detection and monitoring. See related commentary by Doucet and Cristofari, p. 2502. This article is featured in Selected Articles from This Issue, p. 2489.
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Affiliation(s)
- Martin S. Taylor
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
| | - Connie Wu
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Peter C. Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York
| | - Stephanie J. Zhang
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Yasmeen Senussi
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Justina C. Wolters
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tatiana Cajuso
- Department of Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Wen-Chih Cheng
- Department of Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - John D. Heaps
- Department of Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Bryant D. Miller
- Department of Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Kei Mori
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- Healthcare Optics Research Laboratory, Canon U.S.A., Inc., Cambridge, Massachusetts
| | - Limor Cohen
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York
| | | | - Irun Bhan
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Joseph W. Franses
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Xiaoyu Yang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Xinan Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - David C. Christiani
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Bruce E. Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Ravindra Uppaluri
- Department of Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ann Marie Egloff
- Department of Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Elyssa N. Denault
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Laura M. Spring
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Tian-Li Wang
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ie-Ming Shih
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Euihye Jung
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kshitij S. Arora
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
| | - Osman H. Yilmaz
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Sonia Cohen
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Tatyana Sharova
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Gary Chi
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Bryanna L. Norden
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Yuhui Song
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Linda T. Nieman
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Leontios Pappas
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Aparna R. Parikh
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Matthew R. Strickland
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ryan B. Corcoran
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - George Eng
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Ömer H. Yilmaz
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Ursula A. Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit and Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Steven J. Skates
- MGH Biostatistics, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Bo R. Rueda
- Department of Obstetrics and Gynecology, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Ronny Drapkin
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Samuel J. Klempner
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Vikram Deshpande
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
| | - David T. Ting
- Mass General Cancer Center and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, the Netherlands
| | - David R. Walt
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Kathleen H. Burns
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
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6
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Boeke JD, Burns KH, Chiappinelli KB, Classon M, Coffin JM, DeCarvalho DD, Dukes JD, Greenbaum B, Kassiotis G, Knutson SK, Levine AJ, Nath A, Papa S, Rios D, Sedivy J, Ting DT. Proceedings of the inaugural Dark Genome Symposium: November 2022. Mob DNA 2023; 14:18. [PMID: 37990347 PMCID: PMC10664479 DOI: 10.1186/s13100-023-00306-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/08/2023] [Indexed: 11/23/2023] Open
Abstract
In November 2022 the first Dark Genome Symposium was held in Boston, USA. The meeting was hosted by Rome Therapeutics and Enara Bio, two biotechnology companies working on translating our growing understanding of this vast genetic landscape into therapies for human disease. The spirit and ambition of the meeting was one of shared knowledge, looking to strengthen the network of researchers engaged in the field. The meeting opened with a welcome from Rosana Kapeller and Kevin Pojasek followed by a first session of field defining talks from key academics in the space. A series of panels, bringing together academia and industry views, were then convened covering a wide range of pertinent topics. Finally, Richard Young and David Ting gave their views on the future direction and promise for patient impact inherent in the growing understanding of the Dark Genome.
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Affiliation(s)
- Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, 10016, USA
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Katherine B Chiappinelli
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Marie Classon
- Pfizer Centre for Therapeutic Innovation, San Diego, USA
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, 02111, USA
| | - Daniel D DeCarvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Joseph D Dukes
- Enara Bio Limited, Magdalen Centre, 1 Robert Robinson Avenue, The Oxford Science Park, Oxford, OX4 4GA, UK
| | - Benjamin Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Sarah K Knutson
- Rome Therapeutics, 201 Brookline Avenue, Suite 1001, Boston, MA, USA
| | - Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
| | - Avindra Nath
- Section for Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sophie Papa
- Enara Bio Limited, Magdalen Centre, 1 Robert Robinson Avenue, The Oxford Science Park, Oxford, OX4 4GA, UK.
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.
| | - Daniel Rios
- Rome Therapeutics, 201 Brookline Avenue, Suite 1001, Boston, MA, USA
| | - John Sedivy
- Center on the Biology of Aging, Brown University, Providence, RI, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - David T Ting
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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7
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Fu J, Qin T, Li C, Zhu J, Ding Y, Zhou M, Yang Q, Liu X, Zhou J, Chen F. Research progress of LINE-1 in the diagnosis, prognosis, and treatment of gynecologic tumors. Front Oncol 2023; 13:1201568. [PMID: 37546391 PMCID: PMC10399582 DOI: 10.3389/fonc.2023.1201568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
The retrotransposon known as long interspersed nuclear element-1 (LINE-1), which is currently the sole autonomously mobile transposon in the human genome, can result in insertional mutations, chromosomal rearrangements, and genomic instability. In recent years, numerous studies have shown that LINE-1 is involved in the development of various diseases and also plays an important role in the immune regulation of the organism. The expression of LINE-1 in gynecologic tumors suggests that it is expected to be an independent indicator for early diagnosis and prognosis, and also, as a therapeutic target, LINE-1 is closely associated with gynecologic tumor prognosis. This article discusses the function of LINE-1 in the diagnosis, treatment, and prognosis of ovarian, cervical, and endometrial malignancies, as well as other gynecologic malignancies. It offers fresh perspectives on the early detection of tumors and the creation of novel anti-tumor medications.
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Affiliation(s)
- Jiaojiao Fu
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Tiansheng Qin
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
- The First Clinical Medical School, Lanzhou University, Lanzhou, Gansu, China
- National Health Commission (NHC) Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Chaoming Li
- The First People’s Hospital of Longnan, Longnan City Hospital, Longnan, Gansu, China
| | - Jiaojiao Zhu
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Yaoyao Ding
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Meiying Zhou
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Qing Yang
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Xiaofeng Liu
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Juanhong Zhou
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Fan Chen
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
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8
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Taylor MS, Connie W, Fridy PC, Zhang SJ, Senussi Y, Wolters JC, Cheng WC, Heaps J, Miller BD, Mori K, Cohen L, Jiang H, Molloy KR, Norden BL, Chait BT, Goggins M, Bhan I, Franses JW, Yang X, Taplin ME, Wang X, Christiani DC, Johnson BE, Meyerson M, Uppaluri R, Egloff AM, Denault EN, Spring LM, Wang TL, Shih IM, Jung E, Arora KS, Zukerberg LR, Yilmaz OH, Chi G, Matulonis UA, Song Y, Nieman L, Parikh AR, Strickland M, Corcoran RB, Mustelin T, Eng G, Yilmaz ÃMH, Skates SJ, Rueda BR, Drapkin R, Klempner SJ, Deshpande V, Ting DT, Rout MP, LaCava J, Walt DR, Burns KH. Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525462. [PMID: 36747644 PMCID: PMC9900799 DOI: 10.1101/2023.01.25.525462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Improved biomarkers are needed for early cancer detection, risk stratification, treatment selection, and monitoring treatment response. While proteins can be useful blood-based biomarkers, many have limited sensitivity or specificity for these applications. Long INterspersed Element-1 (LINE-1, L1) open reading frame 1 protein (ORF1p) is a transposable element protein overexpressed in carcinomas and high-risk precursors during carcinogenesis with negligible detectable expression in corresponding normal tissues, suggesting ORF1p could be a highly specific cancer biomarker. To explore the potential of ORF1p as a blood-based biomarker, we engineered ultrasensitive digital immunoassays that detect mid-attomolar (10-17 M) ORF1p concentrations in patient plasma samples across multiple cancers with high specificity. Plasma ORF1p shows promise for early detection of ovarian cancer, improves diagnostic performance in a multi-analyte panel, and provides early therapeutic response monitoring in gastric and esophageal cancers. Together, these observations nominate ORF1p as a multi-cancer biomarker with potential utility for disease detection and monitoring.
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9
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Desaulniers D, Cummings-Lorbetskie C, Leingartner K, Meier MJ, Pickles JC, Yauk CL. DNA methylation changes from primary cultures through senescence-bypass in Syrian hamster fetal cells initially exposed to benzo[a]pyrene. Toxicology 2023; 487:153451. [PMID: 36754249 DOI: 10.1016/j.tox.2023.153451] [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: 12/06/2022] [Revised: 01/27/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
Current chemical testing strategies are limited in their ability to detect non-genotoxic carcinogens (NGTxC). Epigenetic anomalies develop during carcinogenesis regardless of whether the molecular initiating event is associated with genotoxic (GTxC) or NGTxC events; therefore, epigenetic markers may be harnessed to develop new approach methodologies that improve the detection of both types of carcinogens. This study used Syrian hamster fetal cells to establish the chronology of carcinogen-induced DNA methylation changes from primary cells until senescence-bypass as an essential carcinogenic step. Cells exposed to solvent control for 7 days were compared to naïve primary cultures, to cells exposed for 7 days to benzo[a]pyrene, and to cells at the subsequent transformation stages: normal colonies, morphologically transformed colonies, senescence, senescence-bypass, and sustained proliferation in vitro. DNA methylation changes identified by reduced representation bisulphite sequencing were minimal at day-7. Profound DNA methylation changes arose during cellular senescence and some of these early differentially methylated regions (DMRs) were preserved through the final sustained proliferation stage. A set of these DMRs (e.g., Pou4f1, Aifm3, B3galnt2, Bhlhe22, Gja8, Klf17, and L1l) were validated by pyrosequencing and their reproducibility was confirmed across multiple clones obtained from a different laboratory. These DNA methylation changes could serve as biomarkers to enhance objectivity and mechanistic understanding of cell transformation and could be used to predict senescence-bypass and chemical carcinogenicity.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
| | | | - Karen Leingartner
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
| | - Matthew J Meier
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
| | | | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
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10
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Sato S, Gillette M, de Santiago PR, Kuhn E, Burgess M, Doucette K, Feng Y, Mendez-Dorantes C, Ippoliti PJ, Hobday S, Mitchell MA, Doberstein K, Gysler SM, Hirsch MS, Schwartz L, Birrer MJ, Skates SJ, Burns KH, Carr SA, Drapkin R. LINE-1 ORF1p as a candidate biomarker in high grade serous ovarian carcinoma. Sci Rep 2023; 13:1537. [PMID: 36707610 PMCID: PMC9883229 DOI: 10.1038/s41598-023-28840-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/25/2023] [Indexed: 01/29/2023] Open
Abstract
Long interspersed element 1 (LINE-1) open reading frame 1 protein (ORF1p) expression is a common feature of many cancer types, including high-grade serous ovarian carcinoma (HGSOC). Here, we report that ORF1p is not only expressed but also released by ovarian cancer and primary tumor cells. Immuno-multiple reaction monitoring-mass spectrometry assays showed that released ORF1p is confidently detectable in conditioned media, ascites, and patients' plasma, implicating ORF1p as a potential biomarker. Interestingly, ORF1p expression is detectable in fallopian tube (FT) epithelial precursors of HGSOC but not in benign FT, suggesting that ORF1p expression in an early event in HGSOC development. Finally, treatment of FT cells with DNA methyltransferase inhibitors led to robust expression and release of ORF1p, validating the regulatory role of DNA methylation in LINE-1 repression in non-tumorigenic tissue.
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Affiliation(s)
- Sho Sato
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Michael Gillette
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Pamela R de Santiago
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Eric Kuhn
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Michael Burgess
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kristen Doucette
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yi Feng
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | | | - Paul J Ippoliti
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sara Hobday
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Marilyn A Mitchell
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Kai Doberstein
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Stefan M Gysler
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Lauren Schwartz
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael J Birrer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Steven J Skates
- Harvard Medical School, Boston, MA, 02115, USA.,Biostatistics and Computational Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Kathleen H Burns
- Harvard Medical School, Boston, MA, 02115, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA. .,Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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11
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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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12
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Vang R, Shih IM. Serous tubal intraepithelial carcinoma: What Do We Really Know at this Point? Histopathology 2022; 81:542-555. [PMID: 35859323 DOI: 10.1111/his.14722] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/18/2022] [Accepted: 06/23/2022] [Indexed: 11/27/2022]
Abstract
Serous tubal intraepithelial carcinoma (STIC) is the earliest morphologically recognizable step in the development of invasive high-grade serous carcinoma of the fallopian tube. Lesions occurring prior to STIC within the carcinogenic sequence for the pathogenesis of invasive high-grade serous carcinoma include the p53 signature and secretory cell outgrowth (SCOUT). Variable histologic criteria have been used for diagnosing STIC, but a combination of morphology and immunohistochemistry for p53/Ki-67 improves interobserver agreement. Half of all carcinomas identified in risk-reducing salpingo-oophorectomy specimens are in the form of STIC; however, STIC also may be incidentally found on occasion in specimens from women at low or average risk of ovarian/tubal/peritoneal carcinoma. TP53 mutation is the earliest known DNA sequence alteration in STIC and almost all invasive high-grade serous carcinomas of the ovary and peritoneum. Data on the clinical behavior of STIC are limited. While the short-term follow-up in the prior literature suggests a low risk of malignant progression, a more recent meta-analysis indicates a 10-year risk of 28%. STIC probably should be best regarded as a lesion with uncertain malignant potential at present, and future molecular analysis will help classify those with higher risk of dissemination. This review article provides an update on the current knowledge of STIC and related issues.
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Affiliation(s)
- Russell Vang
- Departments of Pathology (Division of Gynecologic Pathology), The Johns Hopkins University School of Medicine; Baltimore, MD, USA.,Gynecology & Obstetrics, The Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Ie-Ming Shih
- Departments of Pathology (Division of Gynecologic Pathology), The Johns Hopkins University School of Medicine; Baltimore, MD, USA.,Gynecology & Obstetrics, The Johns Hopkins University School of Medicine; Baltimore, MD, USA.,Oncology, The Johns Hopkins University School of Medicine; Baltimore, MD, USA
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13
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Berrino E, Miglio U, Bellomo SE, Debernardi C, Bragoni A, Petrelli A, Cascardi E, Giordano S, Montemurro F, Marchiò C, Venesio T, Sapino A. The Tumor-Specific Expression of L1 Retrotransposons Independently Correlates with Time to Relapse in Hormone-Negative Breast Cancer Patients. Cells 2022; 11:cells11121944. [PMID: 35741073 PMCID: PMC9221920 DOI: 10.3390/cells11121944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Long-Interspersed Nuclear Element (L1) retrotransposons are silenced in healthy tissues but unrepressed in cancer. Even if L1 reactivation has been associated with reduced overall survival in breast cancer (BC) patients, a comprehensive correlation with clinicopathological features is still missing. METHODS Using quantitative, reverse-transcription PCR, we assessed L1 mRNA expression in 12 BC cells, 210 BC patients and in 47 normal mammary tissues. L1 expression was then correlated with molecular and clinicopathological data. RESULTS We identified a tumor-exclusive expression of L1s, absent in normal mammary cells and tissues. A positive correlation between L1 expression and tumor dedifferentiation, lymph-node involvement and increased immune infiltration was detected. Molecular subtyping highlighted an enrichment of L1s in basal-like cells and cancers. By exploring disease-free survival, we identified L1 overexpression as an independent biomarker for patients with a high risk of recurrence in hormone-receptor-negative BCs. CONCLUSIONS Overall, L1 reactivation identified BCs with aggressive features and patients with a worse clinical fate.
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Affiliation(s)
- Enrico Berrino
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Umberto Miglio
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
| | - Sara Erika Bellomo
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Oncology, University of Turin, 10124 Turin, Italy
| | - Carla Debernardi
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Alberto Bragoni
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Annalisa Petrelli
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
| | - Eliano Cascardi
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Silvia Giordano
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Oncology, University of Turin, 10124 Turin, Italy
| | - Filippo Montemurro
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Tiziana Venesio
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Correspondence: ; Tel.: +39-011-9933547; Fax: +39-011-9933480
| | - Anna Sapino
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
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14
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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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15
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Cen Y, Fang Y, Ren Y, Hong S, Lu W, Xu J. Global characterization of extrachromosomal circular DNAs in advanced high grade serous ovarian cancer. Cell Death Dis 2022; 13:342. [PMID: 35418185 PMCID: PMC9007969 DOI: 10.1038/s41419-022-04807-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 03/21/2022] [Accepted: 03/30/2022] [Indexed: 01/02/2023]
Abstract
High grade serous ovarian cancer (HGSOC) is the most aggressive subtype of ovarian cancer and HGSOC patients often appear with metastasis, leading to the poor prognosis. Up to date, the extrachromosomal circular DNAs (eccDNAs) have been shown to be involved in cancer genome remodeling but the roles of eccDNAs in metastatic HGSOC are still not clear. Here we explored eccDNA profiles in HGSOC by Circle-Sequencing analysis using four pairs of primary and metastatic tissues of HGSOC patients. Within the differentially expressed eccDNAs screened out by our analysis, eight candidates were validated by outward PCR and qRT-PCR analysis. Among them, DNMT1circle10302690-10302961 was further confirmed by FISH assay and BaseScope assay, as the most significantly down-regulated eccDNA in metastatic tumors of HGSOC. Lower expression of DNMT1circle10302690-10302961 in both primary and metastatic tumors was associated with worse prognosis of HGSOC. Taken together, our finding firstly demonstrated the eccDNAs landscape of primary and metastatic tissues of HGSOC. The eccDNA DNMT1circle10302690-10302961 can be considered as a potential biomarker or a therapeutically clinical target of HGSOC metastasis and prognosis.
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Affiliation(s)
- Yixuan Cen
- Women's Reproductive Health Laboratory of Zhejiang Province; Women's Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Yifeng Fang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Yan Ren
- Women's Reproductive Health Laboratory of Zhejiang Province; Women's Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Shiyuan Hong
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, China.
| | - Weiguo Lu
- Women's Reproductive Health Laboratory of Zhejiang Province; Women's Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006, China. .,Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China. .,Cancer Center, Zhejiang University, Hangzhou, 310058, China.
| | - Junfen Xu
- Women's Reproductive Health Laboratory of Zhejiang Province; Women's Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006, China. .,Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
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16
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Leveraging Genomics, Transcriptomics, and Epigenomics to Understand the Biology and Chemoresistance of Ovarian Cancer. Cancers (Basel) 2021; 13:cancers13164029. [PMID: 34439181 PMCID: PMC8391219 DOI: 10.3390/cancers13164029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/31/2022] Open
Abstract
Ovarian cancer is a major cause of fatality due to a gynecological malignancy. This lethality is largely due to the unspecific clinical manifestations of ovarian cancer, which lead to late detection and to high resistance to conventional therapies based on platinum. In recent years, we have advanced our understanding of the mechanisms provoking tumor relapse, and the advent of so-called omics technologies has provided exceptional tools to evaluate molecular mechanisms leading to therapy resistance in ovarian cancer. Here, we review the contribution of genomics, transcriptomics, and epigenomics techniques to our knowledge about the biology and molecular features of ovarian cancers, with a focus on therapy resistance. The use of these technologies to identify molecular markers and mechanisms leading to chemoresistance in these tumors is discussed, as well as potential further applications.
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17
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Mukherjee K, Sur D, Singh A, Rai S, Das N, Sekar R, Narindi S, Dhingra VK, Jat B, Balraam KVV, Agarwal SP, Mandal PK. Robust expression of LINE-1 retrotransposon encoded proteins in oral squamous cell carcinoma. BMC Cancer 2021; 21:628. [PMID: 34044801 PMCID: PMC8161598 DOI: 10.1186/s12885-021-08174-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/07/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Oral Squamous Cell Carcinoma (OSCC) results from a series of genetic alteration in squamous cells. This particular type of cancer considers one of the most aggressive malignancies to control because of its frequent local invasions to the regional lymph node. Although several biomarkers have been reported, the key marker used to predict the behavior of the disease is largely unknown. Here we report Long INterpersed Element-1 (LINE1 or L1) retrotransposon activity in post-operative oral cancer samples. L1 is the only active retrotransposon occupying around 17% of the human genome with an estimated 500,000 copies. An active L1 encodes two proteins (L1ORF1p and L1ORF2p); both of which are critical in the process of retrotransposition. Several studies report that the L1 retrotransposon is highly active in many cancers. L1 activity is generally determined by assaying L1ORF1p because of its high expression and availability of the antibody. However, due to its lower expression and unavailability of a robust antibody, detection of L1ORF2p has been limited. L1ORF2p is the crucial protein in the process of retrotransposition as it provides endonuclease and reverse transcriptase (RT) activity. METHODS Immunohistochemistry and Western blotting were performed on the post-operative oral cancer samples and murine tissues. RESULTS Using in house novel antibodies against both the L1 proteins (L1ORF1p and L1ORF2p), we found L1 retrotransposon is extremely active in post-operative oral cancer tissues. Here, we report a novel human L1ORF2p antibody generated using an 80-amino-acid stretch from the RT domain, which is highly conserved among different species. The antibody detects significant L1ORF2p expression in human oral squamous cell carcinoma (OSCC) samples and murine germ tissues. CONCLUSIONS We report exceptionally high L1ORF1p and L1ORF2p expression in post-operative oral cancer samples. The novel L1ORF2p antibody reported in this study will serve as a useful tool to understand why L1 activity is deregulated in OSCC and how it contributes to the progression of this particular cancer. Cross-species reactivity of L1ORF2p antibody due to the conserved epitope will be useful to study the retrotransposon biology in mice and rat germ tissues.
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Affiliation(s)
- Koel Mukherjee
- Department of Biotechnology, IIT Roorkee, Roorkee, Uttarakhand India
| | - Debpali Sur
- Department of Biotechnology, IIT Roorkee, Roorkee, Uttarakhand India
| | - Abhijeet Singh
- Department of Head-Neck Surgery and Oncology, AIIMS Rishikesh, Rishikesh, Uttarakhand India
| | - Sandhya Rai
- Department of Biotechnology, IIT Roorkee, Roorkee, Uttarakhand India
| | | | - Rakshanya Sekar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | | | - Vandana Kumar Dhingra
- Department of Head-Neck Surgery and Oncology, AIIMS Rishikesh, Rishikesh, Uttarakhand India
| | - Bhinyaram Jat
- Department of Head-Neck Surgery and Oncology, AIIMS Rishikesh, Rishikesh, Uttarakhand India
| | | | - Satya Prakash Agarwal
- Department of Head-Neck Surgery and Oncology, AIIMS Rishikesh, Rishikesh, Uttarakhand India
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18
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Grundy EE, Diab N, Chiappinelli KB. Transposable element regulation and expression in cancer. FEBS J 2021; 289:1160-1179. [PMID: 33471418 DOI: 10.1111/febs.15722] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/08/2021] [Accepted: 01/14/2021] [Indexed: 12/11/2022]
Abstract
Approximately 45% of the human genome is composed of transposable elements (TEs). Expression of these elements is tightly regulated during normal development. TEs may be expressed at high levels in embryonic stem cells but are epigenetically silenced in terminally differentiated cells. As part of the global 'epigenetic dysregulation' that cells undergo during transformation from normal to cancer, TEs can lose epigenetic silencing and become transcribed, and, in some cases, active. Here, we summarize recent advances detailing the consequences of TE activation in cancer and describe how these understudied residents of our genome can both aid tumorigenesis and potentially be harnessed for anticancer therapies.
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Affiliation(s)
- Erin E Grundy
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA.,The GW Cancer Center, The George Washington University, Washington, DC, USA.,The Institute for Biomedical Sciences at The George Washington University, Washington, DC, USA
| | - Noor Diab
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA.,The GW Cancer Center, The George Washington University, Washington, DC, USA
| | - Katherine B Chiappinelli
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA.,The GW Cancer Center, The George Washington University, Washington, DC, USA
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19
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Shih IM, Wang Y, Wang TL. The Origin of Ovarian Cancer Species and Precancerous Landscape. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 191:26-39. [PMID: 33011111 DOI: 10.1016/j.ajpath.2020.09.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/31/2020] [Accepted: 09/09/2020] [Indexed: 12/14/2022]
Abstract
Unlike other human cancers, in which all primary tumors arise de novo, ovarian epithelial cancers are primarily imported from either endometrial or fallopian tube epithelium. The prevailing paradigm in the genesis of high-grade serous carcinoma (HGSC), the most common ovarian cancer, posits to its development in fallopian tubes through stepwise tumor progression. Recent progress has been made not only in gathering terabytes of omics data but also in detailing the histologic-molecular correlations required for looking into, and making sense of, the tissue origin of HGSC. This emerging paradigm is changing many facets of ovarian cancer research and routine gynecology practice. The precancerous landscape in fallopian tubes contains multiple concurrent precursor lesions, including serous tubal intraepithelial carcinoma (STIC), with genetic heterogeneity providing a platform for HGSC evolution. Mathematical models imply that a prolonged time (decades) elapses from the development of a TP53 mutation, the earliest known molecular alteration, to an STIC, followed by a shorter span (6 years) for progression to an HGSC. Genetic predisposition accelerates the trajectory. This timeline may allow for the early diagnosis of HGSC and STIC, followed by intent-to-cure surgery. This review discusses the recent advances in this tubal paradigm and its biological and clinical implications, alongside the promise and challenge of studying STIC and other precancerous lesions of HGSC.
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Affiliation(s)
- Ie-Ming Shih
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Pathobiology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Yeh Wang
- Pathobiology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tian-Li Wang
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Pathobiology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
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20
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Matei D, Nephew KP. Epigenetic Attire in Ovarian Cancer: The Emperor's New Clothes. Cancer Res 2020; 80:3775-3785. [PMID: 32381656 PMCID: PMC7501210 DOI: 10.1158/0008-5472.can-19-3837] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/01/2020] [Accepted: 05/04/2020] [Indexed: 12/15/2022]
Abstract
Ovarian cancer is an aggressive epithelial tumor that remains a major cause of cancer morbidity and mortality in women. Epigenetic alterations including DNA methylation and histone modifications are being characterized in ovarian cancer and have been functionally linked to processes involved in tumor initiation, chemotherapy resistance, cancer stem cell survival, and tumor metastasis. The epigenetic traits of cancer cells and of associated tumor microenvironment components have been shown to promote an immunosuppressive tumor milieu. However, DNA methylation and histone modifications are reversible, and therapies targeting the epigenome have been implicated in potential reinvigoration of the antitumor immunity. In this review, we provide an overview specifically of DNA methylation and histone modifications as "clothes of the ovarian cancer genome" in relationship to their functional effects and highlight recent developments in the field. We also address the clinical implications of therapeutic strategies to remove or alter specific articles of genomic "clothing" and restore normal cellular function. As the clothes of the genome continue to be deciphered, we envision that the epigenome will become an important therapeutic target for cancer.
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Affiliation(s)
- Daniela Matei
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.
- Robert H Lurie Comprehensive Cancer Center, Chicago, Illinois
- Jesse Brown VA Medical Center, Chicago, Illinois
| | - Kenneth P Nephew
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana.
- Department of Anatomy, Cell Biology and Physiology; Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
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21
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Burns KH. Our Conflict with Transposable Elements and Its Implications for Human Disease. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 15:51-70. [PMID: 31977294 DOI: 10.1146/annurev-pathmechdis-012419-032633] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Our genome is a historic record of successive invasions of mobile genetic elements. Like other eukaryotes, we have evolved mechanisms to limit their propagation and minimize the functional impact of new insertions. Although these mechanisms are vitally important, they are imperfect, and a handful of retroelement families remain active in modern humans. This review introduces the intrinsic functions of transposons, the tactics employed in their restraint, and the relevance of this conflict to human pathology. The most straightforward examples of disease-causing transposable elements are germline insertions that disrupt a gene and result in a monogenic disease allele. More enigmatic are the abnormal patterns of transposable element expression in disease states. Changes in transposon regulation and cellular responses to their expression have implicated these sequences in diseases as diverse as cancer, autoimmunity, and neurodegeneration. Distinguishing their epiphenomenal from their pathogenic effects may provide wholly new perspectives on our understanding of disease.
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Affiliation(s)
- Kathleen H Burns
- Department of Pathology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
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22
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Sharp CN, Korte EA, Hosseinejad K, Pitman J, Lavasanifar A, Eichenberger DJ, Sephton S, Cash E, Jortani SA. ELISA-based detection of Open Reading Frame protein 1 in patients at risk of developing lung cancer. Clin Chim Acta 2020; 507:1-6. [PMID: 32275987 DOI: 10.1016/j.cca.2020.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/24/2020] [Accepted: 04/06/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Early detection of lung cancer significantly improves survival outcomes. Thus, lung cancer screening for high-risk individuals using low-dose CT scan (LDCT) is recommended. LDCT has several limitations, and often requires invasive follow up. Previously, we have developed an ELISA for measurement of Open Reading Frame 1 protein (ORF1p) in serum. We assessed whether ORF1p can be used as a risk assessment biomarker for patients at high risk for developing lung cancer. PATIENTS Patients with risk factors for lung cancer were enrolled in our study with consent under IRB approval. A total of 122 patients were included. The lung cancer cohort consisted of 38 patients with varying stages of cancer undergoing treatment. METHODS ORF1p quantification was performed using our ELISA assay on serum samples. RESULTS ORF1p was significantly increased in the serum of patients with identified lung nodules compared to those without nodules (P = 0.0007). ORF1p was also significantly increased in patients who were recommended for follow up (P = 0.0004). When comparing the at-risk cohort to patients with lung cancer, there was not a significant difference in ORF1p levels. CONCLUSION ORF1p can be used to identify patients at high risk of developing lung cancer and may provide an effective, non-invasive risk assessment marker to complement LDCT screening.
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Affiliation(s)
- Cierra N Sharp
- Department of Pathology and Laboratory Medicine, University of Louisville, 511 South Floyd Street, Louisville, KY 40202, United States
| | - Erik A Korte
- Department of Pathology and Laboratory Medicine, University of Louisville, 511 South Floyd Street, Louisville, KY 40202, United States
| | - Keivan Hosseinejad
- Department of Pathology and Laboratory Medicine, University of Louisville, 511 South Floyd Street, Louisville, KY 40202, United States
| | - Jennifer Pitman
- Department of Pathology and Laboratory Medicine, University of Louisville, 511 South Floyd Street, Louisville, KY 40202, United States
| | - Afsaneh Lavasanifar
- Department of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | | | - Sandra Sephton
- Department of Psychological and Brain Sciences, University of Louisville, 322A Life Sciences Building, Louisville, KY 40292, United States
| | - Elizabeth Cash
- Department of Otolaryngology-Head and Neck Surgery and Communicative Disorders, University of Louisville School of Medicine, 401 E Chestnut St # 170, Louisville, KY 40202, United States
| | - Saeed A Jortani
- Department of Pathology and Laboratory Medicine, University of Louisville, 511 South Floyd Street, Louisville, KY 40202, United States.
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23
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Zhang W, Klinkebiel D, Barger CJ, Pandey S, Guda C, Miller A, Akers SN, Odunsi K, Karpf AR. Global DNA Hypomethylation in Epithelial Ovarian Cancer: Passive Demethylation and Association with Genomic Instability. Cancers (Basel) 2020; 12:cancers12030764. [PMID: 32213861 PMCID: PMC7140107 DOI: 10.3390/cancers12030764] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 03/19/2020] [Indexed: 02/08/2023] Open
Abstract
A hallmark of human cancer is global DNA hypomethylation (GDHO), but the mechanisms accounting for this defect and its pathological consequences have not been investigated in human epithelial ovarian cancer (EOC). In EOC, GDHO was associated with advanced disease and reduced overall and disease-free survival. GDHO (+) EOC tumors displayed a proliferative gene expression signature, including FOXM1 and CCNE1 overexpression. Furthermore, DNA hypomethylation in these tumors was enriched within genomic blocks (hypomethylated blocks) that overlapped late-replicating regions, lamina-associated domains, PRC2 binding sites, and the H3K27me3 histone mark. Increased proliferation coupled with hypomethylated blocks at late-replicating regions suggests a passive hypomethylation mechanism. This hypothesis was further supported by our observation that cytosine DNA methyltransferases (DNMTs) and UHRF1 showed significantly reduced expression in GDHO (+) EOC after normalization to canonical proliferation markers, including MKI67. Finally, GDHO (+) EOC tumors had elevated chromosomal instability (CIN), and copy number alterations (CNA) were enriched at the DNA hypomethylated blocks. Together, these findings implicate a passive DNA demethylation mechanism in ovarian cancer that is associated with genomic instability and poor prognosis.
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Affiliation(s)
- Wa Zhang
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198, USA; (W.Z.); (C.J.B.)
| | - David Klinkebiel
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; (D.K.); (C.G.)
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Carter J. Barger
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198, USA; (W.Z.); (C.J.B.)
| | - Sanjit Pandey
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Chittibabu Guda
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; (D.K.); (C.G.)
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Austin Miller
- Department of Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Stacey N. Akers
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (S.N.A.); (K.O.)
| | - Kunle Odunsi
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (S.N.A.); (K.O.)
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Adam R. Karpf
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198, USA; (W.Z.); (C.J.B.)
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; (D.K.); (C.G.)
- Correspondence: ; Tel.: +1-402-559-6115; Fax: +1-402-599-4651
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24
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Ishak CA, De Carvalho DD. Reactivation of Endogenous Retroelements in Cancer Development and Therapy. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2020. [DOI: 10.1146/annurev-cancerbio-030419-033525] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Domesticated retroelements contribute extensively as regulatory elements within host gene networks. Upon germline integration, retroelement mobilization is restricted through epigenetic silencing, mutational degradation, and innate immune defenses described as the viral mimicry response. Recent discoveries reveal how early events in tumorigenesis reactivate retroelements to facilitate onco-exaptation, replication stress, retrotransposition, mitotic errors, and sterile inflammation, which collectively disrupt genome integrity. The characterization of altered epigenetic homeostasis at retroelements in cancer cells also reveals new epigenetic targets whose inactivation can bolster responses to cancer therapies. Recent discoveries reviewed here frame reactivated retroelements as both drivers of tumorigenesis and therapy responses, where their reactivation by emerging epigenetic therapies can potentiate immune checkpoint blockade, cancer vaccines, and other standard therapies.
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Affiliation(s)
- Charles A. Ishak
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Daniel D. De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
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25
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Ardeljan D, Steranka JP, Liu C, Li Z, Taylor MS, Payer LM, Gorbounov M, Sarnecki JS, Deshpande V, Hruban RH, Boeke JD, Fenyö D, Wu PH, Smogorzewska A, Holland AJ, Burns KH. Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication. Nat Struct Mol Biol 2020; 27:168-178. [PMID: 32042151 PMCID: PMC7080318 DOI: 10.1038/s41594-020-0372-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 12/31/2019] [Indexed: 12/18/2022]
Abstract
LINE-1 retrotransposon overexpression is a hallmark of human cancers. We identified a colorectal cancer wherein a fast-growing tumor subclone downregulated LINE-1, prompting us to examine how LINE-1 expression affects cell growth. We find that nontransformed cells undergo a TP53-dependent growth arrest and activate interferon signaling in response to LINE-1. TP53 inhibition allows LINE-1+ cells to grow, and genome-wide-knockout screens show that these cells require replication-coupled DNA-repair pathways, replication-stress signaling and replication-fork restart factors. Our findings demonstrate that LINE-1 expression creates specific molecular vulnerabilities and reveal a retrotransposition-replication conflict that may be an important determinant of cancer growth.
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Affiliation(s)
- Daniel Ardeljan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Jared P Steranka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chunhong Liu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zhi Li
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York City, NY, USA
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Lindsay M Payer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mikhail Gorbounov
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jacob S Sarnecki
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Ralph H Hruban
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York City, NY, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York City, NY, USA
| | - Pei-Hsun Wu
- Johns Hopkins Physical Sciences Oncology Center, Johns Hopkins University, Baltimore, MD, USA
- Institute for NanoBiotechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York City, NY, USA
| | - Andrew J Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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26
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Ardeljan D, Wang X, Oghbaie M, Taylor MS, Husband D, Deshpande V, Steranka JP, Gorbounov M, Yang WR, Sie B, Larman HB, Jiang H, Molloy KR, Altukhov I, Li Z, McKerrow W, Fenyö D, Burns KH, LaCava J. LINE-1 ORF2p expression is nearly imperceptible in human cancers. Mob DNA 2019; 11:1. [PMID: 31892958 PMCID: PMC6937734 DOI: 10.1186/s13100-019-0191-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/22/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Long interspersed element-1 (LINE-1, L1) is the major driver of mobile DNA activity in modern humans. When expressed, LINE-1 loci produce bicistronic transcripts encoding two proteins essential for retrotransposition, ORF1p and ORF2p. Many types of human cancers are characterized by L1 promoter hypomethylation, L1 transcription, L1 ORF1p protein expression, and somatic L1 retrotransposition. ORF2p encodes the endonuclease and reverse transcriptase activities required for L1 retrotransposition. Its expression is poorly characterized in human tissues and cell lines. RESULTS We report mass spectrometry-based tumor proteome profiling studies wherein ORF2p eludes detection. To test whether ORF2p could be detected with specific reagents, we developed and validated five rabbit monoclonal antibodies with immunoreactivity for specific epitopes on the protein. These reagents readily detect ectopic ORF2p expressed from bicistronic L1 constructs. However, endogenous ORF2p is not detected in human tumor samples or cell lines by western blot, immunoprecipitation, or immunohistochemistry despite high levels of ORF1p expression. Moreover, we report endogenous ORF1p-associated interactomes, affinity isolated from colorectal cancers, wherein we similarly fail to detect ORF2p. These samples include primary tumors harboring hundreds of somatically acquired L1 insertions. The new data are available via ProteomeXchange with identifier PXD013743. CONCLUSIONS Although somatic retrotransposition provides unequivocal genetic evidence for the expression of ORF2p in human cancers, we are unable to directly measure its presence using several standard methods. Experimental systems have previously indicated an unequal stoichiometry between ORF1p and ORF2p, but in vivo, the expression of these two proteins may be more strikingly uncoupled. These findings are consistent with observations that ORF2p is not tolerable for cell growth.
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Affiliation(s)
- Daniel Ardeljan
- McKusick Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Xuya Wang
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - Mehrnoosh Oghbaie
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065 USA
| | - Martin S. Taylor
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - David Husband
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - Jared P. Steranka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Mikhail Gorbounov
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Wan Rou Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Brandon Sie
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - H. Benjamin Larman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065 USA
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065 USA
| | - Ilya Altukhov
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Russia
| | - Zhi Li
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - Wilson McKerrow
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - David Fenyö
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - Kathleen H. Burns
- McKusick Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065 USA
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, 9713 AV The Netherlands
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27
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Chang YH, Dubnau J. The Gypsy Endogenous Retrovirus Drives Non-Cell-Autonomous Propagation in a Drosophila TDP-43 Model of Neurodegeneration. Curr Biol 2019; 29:3135-3152.e4. [PMID: 31495585 PMCID: PMC6783360 DOI: 10.1016/j.cub.2019.07.071] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/11/2019] [Accepted: 07/23/2019] [Indexed: 12/16/2022]
Abstract
A hallmark of neurodegenerative disease is focal onset of pathological protein aggregation, followed by progressive spread of pathology to connected brain regions. In amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), pathology is often associated with aggregation of TAR DNA-binding protein 43 (TDP-43). Although aggregated TDP-43 protein moves between cells, it is not clear whether and how this movement propagates the degeneration. Here, we have established a Drosophila model of human TDP-43 in which we initiated toxic expression of human TDP-43 focally within small groups of glial cells. We found that this focal onset kills adjacent neurons. Surprisingly, we show that this spreading death is caused by an endogenous retrovirus within the glia, which leads to DNA damage and death in adjacent neurons. These findings suggest a possible mechanism by which human retroviruses such as HERV-K might contribute to TDP-43-mediated propagation of neurodegeneration.
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Affiliation(s)
- Yung-Heng Chang
- Department of Anesthesiology, Stony Brook School of Medicine, NY 11794, USA
| | - Josh Dubnau
- Department of Anesthesiology, Stony Brook School of Medicine, NY 11794, USA; Department of Neurobiology and Behavior, Stony Brook University, NY 11794, USA.
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28
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Xia Z, Cochrane DR, Tessier-Cloutier B, Leung S, Karnezis AN, Cheng AS, Farnell DA, Magrill J, Schmidt D, Kommoss S, Kommoss FKF, Kommoss F, McAlpine JN, Gilks CB, Koebel M, Rabban JT, Huntsman DG. Expression of L1 retrotransposon open reading frame protein 1 in gynecologic cancers. Hum Pathol 2019; 92:39-47. [PMID: 31220479 DOI: 10.1016/j.humpath.2019.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/24/2022]
Abstract
LINE-1 (L1) retrotransposons are mobile genetic elements capable of "copy-and-pasting" their own sequences into random genomic loci, and one of the proteins it uses to achieve mobility is LINE-1 open reading frame 1 protein (L1ORF1p). L1ORF1p expression is found across many epithelial cancers, including small cohorts of ovarian and endometrial cancers, and is highly expressed in cancers with mutant p53 expressions. Here we aimed to gain insights into L1ORF1p expression levels within specific histotypes of ovarian cancers: high-grade serous (n = 585), low-grade serous (n = 26), clear cell (n = 132), endometrioid (n = 148), and mucinous (n = 32) ovarian cancers, as well as endometrial cancers (n = 607) using tissue microarray (TMA's). We demonstrated that L1ORF1p expression is associated with advanced stage and serous histotype in gynecological cancers. Like previous studies, we found a higher proportion of L1ORF1p expression in cases with aberrant p53 expression. We evaluated the expression of L1ORF1p in serous tubal intraepithelial carcinomas (STICs) (n = 6) and p53 signature lesions (n = 2) in fallopian tubes. Three STIC cases displayed aberrant p53 overexpression with corresponding L1ORF1p expression in the same tissues, but such correlation was not seen in the two p53 signature lesions, suggesting that L1 protein may be expressed after dysplastic transformation. The remaining three STIC cases have TP53 nonsense mutations with absent p53 expression but a strong and clear L1ORF1p expression within the STIC lesions. While L1ORF1p may not be prognostic in gynecological cancers, it may be useful clinically as a diagnostic IHC marker for p53 null STIC lesions and this warrants further investigation.
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Affiliation(s)
- Zhouchunyang Xia
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
| | - Dawn R Cochrane
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z 4E6, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
| | - Samuel Leung
- Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC V6H 3Z6, Canada
| | - Anthony N Karnezis
- Department of Pathology and Laboratory Medicine, University of California, Davis, CA 95817, USA
| | - Angela S Cheng
- Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC V6H 3Z6, Canada
| | - David A Farnell
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
| | - Jamie Magrill
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z 4E6, Canada
| | | | - Stefan Kommoss
- Department of Obstetrics and Gynecology, University of Tübingen, 72076, Germany
| | - Felix K F Kommoss
- Institute of Pathology, Heidelberg University Hospital, 69120, Germany
| | - Friederich Kommoss
- Institute of Pathology, Medizin Campus Bodensee, Friedrichshafen, 88048, Germany
| | - Jessica N McAlpine
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
| | - Martin Koebel
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB T2N 2T9, Canada
| | - Joseph T Rabban
- Department of Pathology and Laboratory Medicine, University of California, San Francisco, CA 94158, USA
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1L3, Canada; Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
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