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Manou M, Loupis T, Vrachnos DM, Katsoulas N, Theocharis S, Kanakoglou DS, Basdra EK, Piperi C, Papavassiliou AG. Enhanced Transcriptional Signature and Expression of Histone-Modifying Enzymes in Salivary Gland Tumors. Cells 2023; 12:2437. [PMID: 37887281 PMCID: PMC10604940 DOI: 10.3390/cells12202437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Salivary gland tumors (SGTs) are rare and complex neoplasms characterized by heterogenous histology and clinical behavior as well as resistance to systemic therapy. Tumor etiology is currently under elucidation and an interplay of genetic and epigenetic changes has been proposed to contribute to tumor development. In this work, we investigated epigenetic regulators and histone-modifying factors that may alter gene expression and participate in the pathogenesis of SGT neoplasms. We performed a detailed bioinformatic analysis on a publicly available RNA-seq dataset of 94 ACC tissues supplemented with clinical data and respective controls and generated a protein-protein interaction (PPI) network of chromatin and histone modification factors. A significant upregulation of TP53 and histone-modifying enzymes SUV39H1, EZH2, PRMT1, HDAC8, and KDM5B, along with the upregulation of DNA methyltransferase DNMT3A and ubiquitin ligase UHRF1 mRNA levels, as well as a downregulation of lysine acetyltransferase KAT2B levels, were detected in ACC tissues. The protein expression of p53, SUV39H1, EZH2, and HDAC8 was further validated in SGT tissues along with their functional deposition of the repressive histone marks H3K9me3 and H3K27me3, respectively. Overall, this study is the first to detect a network of interacting proteins affecting chromatin structure and histone modifications in salivary gland tumor cells, further providing mechanistic insights in the molecular profile of SGTs that confer to altered gene expression programs.
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Affiliation(s)
- Maria Manou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (M.M.); (D.S.K.); (E.K.B.)
| | - Theodoros Loupis
- Haematology Research Laboratory, Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (T.L.); (D.M.V.)
| | - Dimitrios M. Vrachnos
- Haematology Research Laboratory, Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (T.L.); (D.M.V.)
| | - Nikolaos Katsoulas
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (N.K.); (S.T.)
| | - Stamatios Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (N.K.); (S.T.)
| | - Dimitrios S. Kanakoglou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (M.M.); (D.S.K.); (E.K.B.)
| | - Efthimia K. Basdra
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (M.M.); (D.S.K.); (E.K.B.)
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (M.M.); (D.S.K.); (E.K.B.)
| | - Athanasios G. Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (M.M.); (D.S.K.); (E.K.B.)
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Kanholm T, Rentia U, Hadley M, Karlow JA, Cox OL, Diab N, Bendall ML, Dawson T, McDonald JI, Xie W, Crandall KA, Burns KH, Baylin SB, Easwaran H, Chiappinelli KB. Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation at Transposable Element Loci. Cancer Res 2023; 83:2584-2599. [PMID: 37249603 PMCID: PMC10527578 DOI: 10.1158/0008-5472.can-22-3485] [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: 11/08/2022] [Revised: 03/30/2023] [Accepted: 05/25/2023] [Indexed: 05/31/2023]
Abstract
Transposable elements (TE) are typically silenced by DNA methylation and repressive histone modifications in differentiated healthy human tissues. However, TE expression increases in a wide range of cancers and is correlated with global hypomethylation of cancer genomes. We assessed expression and DNA methylation of TEs in fibroblast cells that were serially transduced with hTERT, SV40, and HRASR24C to immortalize and then transform them, modeling the different steps of the tumorigenesis process. RNA sequencing and whole-genome bisulfite sequencing were performed at each stage of transformation. TE expression significantly increased as cells progressed through transformation, with the largest increase in expression after the final stage of transformation, consistent with data from human tumors. The upregulated TEs were dominated by endogenous retroviruses [long terminal repeats (LTR)]. Most differentially methylated regions (DMR) in all stages were hypomethylated, with the greatest hypomethylation in the final stage of transformation. A majority of the DMRs overlapped TEs from the RepeatMasker database, indicating that TEs are preferentially demethylated. Many hypomethylated TEs displayed a concordant increase in expression. Demethylation began during immortalization and continued into transformation, while upregulation of TE transcription occurred in transformation. Numerous LTR elements upregulated in the model were also identified in The Cancer Genome Atlas datasets of breast, colon, and prostate cancer. Overall, these findings indicate that TEs, specifically endogenous retroviruses, are demethylated and transcribed during transformation. SIGNIFICANCE Analysis of epigenetic and transcriptional changes in a transformation model reveals that transposable element expression and methylation are dysregulated during oncogenic transformation.
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Affiliation(s)
- Tomas Kanholm
- The George Washington University Cancer Center (GWCC), Washington, DC, USA
- Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, USA
- The Institute for Biomedical Sciences at the George Washington University
| | - Uzma Rentia
- The George Washington University Cancer Center (GWCC), Washington, DC, USA
- Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Melissa Hadley
- The George Washington University Cancer Center (GWCC), Washington, DC, USA
- Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Jennifer A. Karlow
- Department of Pathology, Dana-Farber Cancer Institute / Harvard Medical School, Boston, MA, USA
| | - Olivia L. Cox
- The George Washington University Cancer Center (GWCC), Washington, DC, USA
- Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Noor Diab
- The George Washington University Cancer Center (GWCC), Washington, DC, USA
- Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, USA
- George Washington University School of Medicine and Health Sciences
| | - Matthew L. Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tyson Dawson
- The Institute for Biomedical Sciences at the George Washington University
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - James I. McDonald
- The George Washington University Cancer Center (GWCC), Washington, DC, USA
- Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Wenbing Xie
- Hefei National Laboratory for Physical Sciences at the Microscale, Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Keith A. Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Kathleen H. Burns
- Department of Pathology, Dana-Farber Cancer Institute / Harvard Medical School, Boston, MA, USA
| | - Stephen B. Baylin
- Department of Oncology, The Johns Hopkins School of Medicine, The Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Hari Easwaran
- Hefei National Laboratory for Physical Sciences at the Microscale, Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Katherine B. Chiappinelli
- The George Washington University Cancer Center (GWCC), Washington, DC, USA
- Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, USA
- The Institute for Biomedical Sciences at the George Washington University
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Metastatic mucoepidermoid carcinoma to the pleura: a case report. J Med Case Rep 2022; 16:69. [PMID: 35168684 PMCID: PMC8848957 DOI: 10.1186/s13256-022-03285-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/21/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Mucoepidermoid carcinoma is the most common malignant neoplasm arising from the salivary glands (Ali et al. in J Ayub Med Coll Abbottabad 20(2): 141-2, 2008, Xi et al. in World J Surg Oncol 10: 232, 2012). When arising from anatomic sites other than the salivary glands it can be a diagnostic challenge. Primary and metastatic mucoepidermoid carcinoma from and to the pleura are extremely rare entities that are frequently misdiagnosed as adenocarcinoma, adenosquamous carcinoma, or squamous cell carcinoma (Xi et al. in World J Surg Oncol 10: 232, 2012). CASE PRESENTATION We describe an unusual case of a 64-year-old Caucasian female patient with metastatic high-grade mucoepidermoid carcinoma to the pleura, morphologically resembling squamous cell carcinoma. Molecular studies of both the parotid gland and pleural tumors helped prove the metastatic nature of the pleural lesion. CONCLUSIONS Metastatic mucoepidermoid carcinoma to the pleura is a rare entity, frequently misdiagnosed as squamous cell carcinoma. Differentiating between a lung primary and a metastatic disease has treatment implications and prognostic significance for the patient. When morphologic and immunophenotypic overlap exists, molecular testing can help distinguish mucoepidermoid carcinoma from other neoplasms.
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