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Jurmeister P, Leitheiser M, Arnold A, Capilla EP, Mochmann LH, Zhdanovic Y, Schleich K, Jung N, Chimal EC, Jung A, Kumbrink J, Harter P, Prenißl N, Elezkurtaj S, Brcic L, Deigendesch N, Frank S, Hench J, Försch S, Breimer G, van Engen van Grunsven I, Lassche G, van Herpen C, Zhou F, Snuderl M, Agaimy A, Müller KR, von Deimling A, Capper D, Klauschen F, Ihrler S. DNA Methylation Profiling of Salivary Gland Tumors Supports and Expands Conventional Classification. Mod Pathol 2024; 37:100625. [PMID: 39332710 DOI: 10.1016/j.modpat.2024.100625] [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: 04/05/2024] [Revised: 08/05/2024] [Accepted: 09/13/2024] [Indexed: 09/29/2024]
Abstract
Tumors of the major and minor salivary glands histologically encompass a diverse and partly overlapping spectrum of frequent diagnostically challenging neoplasms. Despite recent advances in molecular testing and the identification of tumor-specific mutations or gene fusions, there is an unmet need to identify additional diagnostic biomarkers for entities lacking specific alterations. In this study, we collected a comprehensive cohort of 363 cases encompassing 20 different salivary gland tumor entities and explored the potential of DNA methylation to classify these tumors. We were able to show that most entities show specific epigenetic signatures and present a machine learning algorithm that achieved a mean balanced accuracy of 0.991. Of note, we showed that cribriform adenocarcinoma is epigenetically distinct from classical polymorphous adenocarcinoma, which could support risk stratification of these tumors. Myoepithelioma and pleomorphic adenoma form a uniform epigenetic class, supporting the theory of a single entity with a broad but continuous morphologic spectrum. Furthermore, we identified a histomorphologically heterogeneous but epigenetically distinct class that could represent a novel tumor entity. In conclusion, our study provides a comprehensive resource of the DNA methylation landscape of salivary gland tumors. Our data provide novel insight into disputed entities and show the potential of DNA methylation to identify new tumor classes. Furthermore, in future, our machine learning classifier could support the histopathologic diagnosis of salivary gland tumors.
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Affiliation(s)
- Philipp Jurmeister
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany; German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | | | - Alexander Arnold
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Emma Payá Capilla
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Liliana H Mochmann
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Yauheniya Zhdanovic
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Konstanze Schleich
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nina Jung
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Andreas Jung
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany; German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörg Kumbrink
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Patrick Harter
- German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Neuropathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Niklas Prenißl
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sefer Elezkurtaj
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Luka Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Nikolaus Deigendesch
- Department of Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Stephan Frank
- Department of Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Jürgen Hench
- Department of Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Sebastian Försch
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Gerben Breimer
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Gerben Lassche
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carla van Herpen
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Fang Zhou
- Department of Pathology, New York University Langone Health, School of Medicine, New York, New York
| | - Matija Snuderl
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nurnberg, University Hospital Erlangen, Erlangen, Germany
| | - Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nurnberg, University Hospital Erlangen, Erlangen, Germany
| | - Klaus-Robert Müller
- Machine Learning Group, Department of Software Engineering and Theoretical Computer Science, Technical University of Berlin, Berlin, Germany; Department of Artificial Intelligence, Korea University, Seoul, South Korea; Max Planck Institute for Informatics, Saarbrucken, Germany; BIFOLD-Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frederick Klauschen
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany; German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany; BIFOLD-Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
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Flick KM, Demirci H, Demirci FY. Epigenetics of Conjunctival Melanoma: Current Knowledge and Future Directions. Cancers (Basel) 2024; 16:3687. [PMID: 39518125 PMCID: PMC11544918 DOI: 10.3390/cancers16213687] [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: 09/19/2024] [Revised: 10/24/2024] [Accepted: 10/28/2024] [Indexed: 11/16/2024] Open
Abstract
The purpose of this article is to provide a literature review of the epigenetic understanding of conjunctival melanoma (CM), with a primary focus on current gaps in knowledge and future directions in research. CM is a rare aggressive cancer that predominantly affects older adults. Local recurrences and distant metastases commonly occur in CM patients; however, their prediction and management remain challenging. Hence, there is currently an unmet need for useful biomarkers and more effective treatments to improve the clinical outcomes of these patients. Like other cancers, CM occurrence and prognosis are believed to be influenced by multiple genetic and epigenetic factors that contribute to tumor development/progression/recurrence/spread, immune evasion, and primary/acquired resistance to therapies. Epigenetic alterations may involve changes in chromatin conformation/accessibility, post-translational histone modifications or the use of histone variants, changes in DNA methylation, alterations in levels/functions of short (small) or long non-coding RNAs (ncRNAs), or RNA modifications. While recent years have witnessed a rapid increase in available epigenetic technologies and epigenetic modulation-based treatment options, which has enabled the development/implementation of various epi-drugs in the cancer field, the epigenetic understanding of CM remains limited due to a relatively small number of epigenetic studies published to date. These studies primarily investigated DNA methylation, ncRNA (e.g., miRNA or circRNA) expression, or RNA methylation. While these initial epigenetic investigations have revealed some potential biomarkers and/or therapeutic targets, they had various limitations, and their findings warrant replication in independent and larger studies/samples. In summary, an in-depth understanding of CM epigenetics remains largely incomplete but essential for advancing our molecular knowledge and improving clinical management/outcomes of this aggressive disease.
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Affiliation(s)
- Kaylea M. Flick
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hakan Demirci
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - F. Yesim Demirci
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
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Scheurleer WFJ, van de Velde LJ, Devriese LA, de Ridder M, Louwman MWJ, Breimer GE, de Bree R, van Dijk BAC, Rijken JA. Sinonasal mucosal melanoma in The Netherlands between 2001 and 2021: a clinical and epidemiological overview of 320 cases. Eur Arch Otorhinolaryngol 2024; 281:5437-5446. [PMID: 38761218 PMCID: PMC11416361 DOI: 10.1007/s00405-024-08717-7] [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: 04/17/2024] [Accepted: 05/01/2024] [Indexed: 05/20/2024]
Abstract
PURPOSE Sinonasal mucosal melanoma (SNMM) is a rare malignancy, characterised by high (local) recurrence rates and poor survival. Comprehensive understanding of tumour etiology is currently lacking, which complicates adequate tumour treatment. Besides examining trends in incidence, this study aims to assess the association between clinical characteristics, treatment practices and patient outcomes, with the objective of establishing a baseline from which SNMM management can be enhanced. METHODS All newly diagnosed SNMM cases in The Netherlands between 2001 and 2021 were included using data from The Netherlands Cancer Registry (NCR). RESULTS A total of 320 patients were included. The annual incidence rate for the overall population was stable over the inclusion period with an annual percentage change (APC) of only - 0.01%. The 5-year overall survival (OS) and relative survival (RS) were 24.5 and 32.4%, respectively. Relative survival did not increase over time. The addition of adjuvant radiotherapy to surgery was not associated with a higher OS and RS compared to surgery alone. CONCLUSION Sinonasal mucosal melanoma is a rare disease with stable incidence rates in the Netherlands between 2001 and 2021. There has been no improvement in survival over the course of the inclusion period. The study reaffirms that adjuvant radiotherapy does not seem to improve patient outcomes. Given the generally poor outcomes for SNMM patients, novel therapeutic options ought to be considered in order to improve care.
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Affiliation(s)
- W F Julius Scheurleer
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
| | - Lise J van de Velde
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Lot A Devriese
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mischa de Ridder
- Department of Radiation Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marieke W J Louwman
- Comprehensive Cancer Center The Netherlands (IKNL), Department of Research and Development, Utrecht, The Netherlands
| | - Gerben E Breimer
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Remco de Bree
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Boukje A C van Dijk
- Comprehensive Cancer Center The Netherlands (IKNL), Department of Research and Development, Utrecht, The Netherlands
- Department of Epidemiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Johannes A Rijken
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
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Yang L, Wang G, Tian H, Jia S, Wang S, Cui R, Zhuang A. RBMS1 reflects a distinct microenvironment and promotes tumor progression in ocular melanoma. Exp Eye Res 2024; 246:109990. [PMID: 38969283 DOI: 10.1016/j.exer.2024.109990] [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: 03/22/2024] [Revised: 06/25/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Ocular melanoma, including uveal melanoma (UM) and conjunctival melanoma (CM), is the most common ocular cancer among adults with a high rate of recurrence and poor prognosis. Loss of epigenetic homeostasis disturbed gene expression patterns, resulting in oncogenesis. Herein, we comprehensively analyzed the DNA methylation, transcriptome profiles, and corresponding clinical information of UM patients through multiple machine-learning algorithms, finding that a methylation-driven gene RBMS1 was correlated with poor clinical outcomes of UM patients. RNA-seq and single-cell RNA-seq analyses revealed that RBMS1 reflected diverse tumor microenvironments, where high RBMS1 expression marked an immune active TME. Furthermore, we found that tumor cells were identified to have the higher communication probability in RBMS1+ state. The functional enrichment analysis revealed that RBMS1 was associated with pigment granule and melanosome, participating in cell proliferation as well as apoptotic signaling pathway. Biological experiments were performed and demonstrated that the silencing of RBMS1 inhibited ocular melanoma proliferation and promoted apoptosis. Our study highlighted that RBMS1 reflects a distinct microenvironment and promotes tumor progression in ocular melanoma, contributing to the therapeutic customization and clinical decision-making.
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Affiliation(s)
- Ludi Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, PR China
| | - Gaoming Wang
- Department of Medical Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, PR China
| | - Hao Tian
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, PR China
| | - Shichong Jia
- Tianjin Eye Hospital, Tianjin Key Lab of Ophthalmology and Visual Science, Nankai University Affiliated Eye Hospital, Tianjin Eye Institute, Tianjin, 300020, PR China
| | - Shaoyun Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, PR China.
| | - Ran Cui
- Department of Medical Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, PR China.
| | - Ai Zhuang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, PR China.
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5
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Cornejo KM, Goyal A, Valencia Guerrero A, Astudillo M, Dias-Santagata D, Johnson MM, Feldman AS, Hoang MP. Clinicopathological and Molecular Features of Penile Melanoma With a Proposed Staging System. Am J Surg Pathol 2024; 48:825-833. [PMID: 38808927 DOI: 10.1097/pas.0000000000002247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Penile melanomas (PM) are an exceedingly rare subtype of mucosal melanoma (MM), and we reviewed the clinicopathologic features and molecular profile in 8 PMs. The patient ages ranged from 46 to 78 (mean: 62.8) years with involvement on the glans (n=5; 62.5%), penile urethra (n=2; 25%), and foreskin (n=1, 12.5%). Tumor depth ranged from 1.6 to 10.0 (mean: 5.25) mm. Most of the patients underwent partial penectomy (n=6; 75%) and sentinel lymph node (LN) biopsy N=7; 87.5%). Seven patients had metastatic disease at diagnosis, 6 involving LNs and 1 the adrenal gland, and 4 died of disease with a mean follow-up period of 40.5 (2 to 95) months. Five of 7 (71%) cases identified 15 molecular alterations within KIT , CDKN2A , NF1 , PTEN , and APC (n=2 each), and NRAS , MAP3K1 , CDH1 , MSH6 , and TERT (n=1 each). Two cases were not found to harbor genetic aberrations, and 1 case failed testing. In addition, we reviewed the English literature and included 93 cases with a reported depth of invasion and follow-up. A total of 101 PMs were analyzed for prognostic parameters, and the overall survival was significantly worse in patients with LN metastasis (P=0.0008), distant metastasis (P=0.0016), and greater depth of invasion (P=0.0222) based upon T-stage. While T4 conferred substantially worse survival, the delineation of the survival curves between T2 and T3 was less clear, and combining T2+T3 disease had a strong prognostic impact ( P =0.0024). Prognostic parameters used in the staging of cutaneous melanomas may also be used in PMs. An alternative staging system expanding the inclusion criteria for T2 might provide a more accurate prognostic stratification.
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Affiliation(s)
- Kristine M Cornejo
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Amrita Goyal
- Department of Dermatology, University of Minnesota, Minneapolis, MN
| | | | | | - Dora Dias-Santagata
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | | | - Adam S Feldman
- Department of Urology, Massachusetts General Hospital, Boston, MA
| | - Mai P Hoang
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
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Henzinger H, Brčić I, Igrec J, Godschachner TM, Scheipl S, Szkandera J, Jurmeister P, Liegl-Atzwanger B. The Role of Methylation Analysis in Distinguishing Cellular Myxoma from Low-Grade Myxofibrosarcoma. Int J Mol Sci 2024; 25:5105. [PMID: 38791144 PMCID: PMC11121712 DOI: 10.3390/ijms25105105] [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: 03/27/2024] [Revised: 05/03/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Cellular myxoma is a benign soft tissue tumor frequently associated with GNAS mutation that may morphologically resemble low-grade myxofibrosarcoma. This study aimed to identify the undescribed methylation profile of cellular myxoma and compare it to myxofibrosarcoma. We performed molecular analysis on twenty cellular myxomas and nine myxofibrosarcomas and analyzed the results using the methylation-based DKFZ sarcoma classifier. A total of 90% of the cellular myxomas had GNAS mutations (four loci had not been previously described). Copy number variations were found in all myxofibrosarcomas but in none of the cellular myxomas. In the classifier, none of the cellular myxomas reached the 0.9 threshold. Unsupervised t-SNE analysis demonstrated that cellular myxomas form their own clusters, distinct from myxofibrosarcomas. Our study shows the diagnostic potential and the limitations of molecular analysis in cases where morphology and immunohistochemistry are not sufficient to distinguish cellular myxoma from myxofibrosarcoma, particularly regarding GNAS wild-type tumors. The DKFZ sarcoma classifier only provided a valid prediction for one myxofibrosarcoma case; this limitation could be improved by training the tool with a more considerable number of cases. Additionally, the classifier should be introduced to a broader spectrum of mesenchymal neoplasms, including benign tumors like cellular myxoma, whose distinct methylation pattern we demonstrated.
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Affiliation(s)
- Hanna Henzinger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria; (H.H.); (T.M.G.); (B.L.-A.)
| | - Iva Brčić
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria; (H.H.); (T.M.G.); (B.L.-A.)
| | - Jasminka Igrec
- Division of General Radiology, Department of Radiology, Medical University of Graz, 8010 Graz, Austria;
| | - Theresa Marie Godschachner
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria; (H.H.); (T.M.G.); (B.L.-A.)
| | - Susanne Scheipl
- Department of Orthopedics and Trauma, Medical University of Graz, 8010 Graz, Austria;
| | - Joanna Szkandera
- Division of Clinical Oncology, Department of Medicine, Medical University of Graz, 8010 Graz, Austria;
| | - Philipp Jurmeister
- Institute of Pathology, Ludwig Maximilians University Hospital Munich, 80336 Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, 80336 Munich, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Bernadette Liegl-Atzwanger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria; (H.H.); (T.M.G.); (B.L.-A.)
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Păsărică MA, Curcă PF, Dragosloveanu CDM, Grigorescu AC, Nisipașu CI. Pathological and Molecular Diagnosis of Uveal Melanoma. Diagnostics (Basel) 2024; 14:958. [PMID: 38732371 PMCID: PMC11083017 DOI: 10.3390/diagnostics14090958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
(1) Background: Uveal melanoma (UM) is a common malignant intraocular tumor that presents with significant genetic differences to cutaneous melanoma and has a high genetic burden in terms of prognosis. (2) Methods: A systematic literature search of several repositories on uveal melanoma diagnosis, prognosis, molecular analysis, and treatment was conducted. (3) Results: Recent genetic understanding of oncogene-initiation mutations in GNAQ, GNA11, PLCB4, and CYSLTR2 and secondary progression drivers of BAP1 inactivation and SF3B1 and EIF1AX mutations offers an appealing explanation to the high prognostic impact of adding genetic profiling to clinical UM classification. Genetic information could help better explain peculiarities in uveal melanoma, such as the low long-term survival despite effective primary tumor treatment, the overwhelming propensity to metastasize to the liver, and possibly therapeutic behaviors. (4) Conclusions: Understanding of uveal melanoma has improved step-by-step from histopathology to clinical classification to more recent genetic understanding of oncogenic initiation and progression.
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Affiliation(s)
- Mihai Adrian Păsărică
- Clinical Department of Ophthalmology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (M.A.P.); (C.D.M.D.)
- Department of Ophthalmology, Clinical Hospital for Ophthalmological Emergencies, 010464 Bucharest, Romania
| | - Paul Filip Curcă
- Clinical Department of Ophthalmology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (M.A.P.); (C.D.M.D.)
- Department of Ophthalmology, Clinical Hospital for Ophthalmological Emergencies, 010464 Bucharest, Romania
| | - Christiana Diana Maria Dragosloveanu
- Clinical Department of Ophthalmology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (M.A.P.); (C.D.M.D.)
- Department of Ophthalmology, Clinical Hospital for Ophthalmological Emergencies, 010464 Bucharest, Romania
| | | | - Cosmin Ionuț Nisipașu
- Department of Dental Medicine I, Implant-Prosthetic Therapy, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania;
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Ressler JM, Tomasich E, Hatziioannou T, Ringl H, Heller G, Silmbrod R, Gottmann L, Starzer AM, Zila N, Tschandl P, Hoeller C, Preusser M, Berghoff AS. DNA Methylation Signatures Correlate with Response to Immune Checkpoint Inhibitors in Metastatic Melanoma. Target Oncol 2024; 19:263-275. [PMID: 38401029 DOI: 10.1007/s11523-024-01041-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND DNA methylation profiles have emerged as potential predictors of therapeutic response in various solid tumors. OBJECTIVE This study aimed to analyze the DNA methylation profiles of patients with stage IV metastatic melanoma undergoing first-line immune checkpoint inhibitor treatment and evaluate their correlation with a radiological response according to immune-related Response Evaluation Criteria in Solid Tumors (iRECIST). METHODS A total of 81 tissue samples from 71 patients with metastatic melanoma (27 female, 44 male) were included in this study. We utilized Illumina Methylation EPIC Beadchips to retrieve their genome-wide methylation profile by interrogating >850,000 CpG sites. Clustering based on the 500 most differentially methylated genes was conducted to identify distinct methylation patterns associated with immune checkpoint inhibitor response. Results were further aligned with an independent, previously published data set. RESULTS The median progression-free survival was 8.5 months (range: 0-104.1 months), and the median overall survival was 30.6 months (range: 0-104.1 months). Objective responses were observed in 29 patients (40.8%). DNA methylation profiling revealed specific signatures that correlated with radiological response to immune checkpoint inhibitors. Three distinct clusters were identified based on the methylation patterns of the 500 most differentially methylated genes. Cluster 1 (12/12) and cluster 2 (12/24) exhibited a higher proportion of responders, while cluster 3 (39/45) predominantly consisted of non-responders. In the validation data set, responders also showed more frequent hypomethylation although differences in the data sets limit the interpretation. CONCLUSIONS These findings suggest that DNA methylation profiling of tumor tissues might serve as a predictive biomarker for immune checkpoint inhibitor response in patients with metastatic melanoma. Further validation studies are warranted to confirm the efficiency of DNA methylation profiling as a predictive tool in the context of immunotherapy for metastatic melanoma.
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Affiliation(s)
| | - Erwin Tomasich
- Department of Medicine I, Division of Oncology, Christian Doppler Laboratory for Personalized Immunotherapy, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Teresa Hatziioannou
- Department of Medicine I, Division of Oncology, Christian Doppler Laboratory for Personalized Immunotherapy, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Helmut Ringl
- Wiener Gesundheitsverbund, Klinik Donaustadt, Vienna, Austria
| | - Gerwin Heller
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Rita Silmbrod
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Lynn Gottmann
- Department of Medicine I, Division of Oncology, Christian Doppler Laboratory for Personalized Immunotherapy, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | | | - Nina Zila
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
- Division of Biomedical Science, University of Applied Sciences FH Campus Wien, Vienna, Austria
| | - Philipp Tschandl
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Christoph Hoeller
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Matthias Preusser
- Department of Medicine I, Division of Oncology, Christian Doppler Laboratory for Personalized Immunotherapy, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Anna Sophie Berghoff
- Department of Medicine I, Division of Oncology, Christian Doppler Laboratory for Personalized Immunotherapy, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria.
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Al Hmada Y, Brodell RT, Kharouf N, Flanagan TW, Alamodi AA, Hassan SY, Shalaby H, Hassan SL, Haikel Y, Megahed M, Santourlidis S, Hassan M. Mechanisms of Melanoma Progression and Treatment Resistance: Role of Cancer Stem-like Cells. Cancers (Basel) 2024; 16:470. [PMID: 38275910 PMCID: PMC10814963 DOI: 10.3390/cancers16020470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Melanoma is the third most common type of skin cancer, characterized by its heterogeneity and propensity to metastasize to distant organs. Melanoma is a heterogeneous tumor, composed of genetically divergent subpopulations, including a small fraction of melanoma-initiating cancer stem-like cells (CSCs) and many non-cancer stem cells (non-CSCs). CSCs are characterized by their unique surface proteins associated with aberrant signaling pathways with a causal or consequential relationship with tumor progression, drug resistance, and recurrence. Melanomas also harbor significant alterations in functional genes (BRAF, CDKN2A, NRAS, TP53, and NF1). Of these, the most common are the BRAF and NRAS oncogenes, with 50% of melanomas demonstrating the BRAF mutation (BRAFV600E). While the successful targeting of BRAFV600E does improve overall survival, the long-term efficacy of available therapeutic options is limited due to adverse side effects and reduced clinical efficacy. Additionally, drug resistance develops rapidly via mechanisms involving fast feedback re-activation of MAPK signaling pathways. This article updates information relevant to the mechanisms of melanoma progression and resistance and particularly the mechanistic role of CSCs in melanoma progression, drug resistance, and recurrence.
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Affiliation(s)
- Youssef Al Hmada
- Department of Pathology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA; (Y.A.H.); (R.T.B.)
| | - Robert T. Brodell
- Department of Pathology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA; (Y.A.H.); (R.T.B.)
| | - Naji Kharouf
- Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France; (N.K.); (Y.H.)
- Department of Operative Dentistry and Endodontics, Dental Faculty, University of Strasbourg, 67000 Strasbourg, France
| | - Thomas W. Flanagan
- Department of Pharmacology and Experimental Therapeutics, LSU Health Sciences Center, New Orleans, LA 70112, USA;
| | - Abdulhadi A. Alamodi
- College of Health Sciences, Jackson State University, 310 W Woodrow Wilson Ave Ste 300, Jackson, MS 39213, USA;
| | - Sofie-Yasmin Hassan
- Department of Pharmacy, Faculty of Science, Heinrich-Heine University Duesseldorf, 40225 Dusseldorf, Germany;
| | - Hosam Shalaby
- Department of Urology, Tulane University School of Medicine, New Orleans, LA 70112, USA;
| | - Sarah-Lilly Hassan
- Department of Chemistry, Faculty of Science, Heinrich-Heine University Duesseldorf, 40225 Dusseldorf, Germany;
| | - Youssef Haikel
- Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France; (N.K.); (Y.H.)
- Department of Operative Dentistry and Endodontics, Dental Faculty, University of Strasbourg, 67000 Strasbourg, France
- Pôle de Médecine et Chirurgie Bucco-Dentaire, Hôpital Civil, Hôpitaux Universitaire de Strasbourg, 67000 Strasbourg, France
| | - Mosaad Megahed
- Clinic of Dermatology, University Hospital of Aachen, 52074 Aachen, Germany;
| | - Simeon Santourlidis
- Epigenetics Core Laboratory, Medical Faculty, Institute of Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf, 40225 Dusseldorf, Germany;
| | - Mohamed Hassan
- Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France; (N.K.); (Y.H.)
- Department of Operative Dentistry and Endodontics, Dental Faculty, University of Strasbourg, 67000 Strasbourg, France
- Research Laboratory of Surgery-Oncology, Department of Surgery, Tulane University School of Medicine, New Orleans, LA 70112, USA
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10
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Guimarães LM, Baumhoer D, Andrei V, Friedel D, Koelsche C, Gomez RS, von Deimling A, Gomes CC. DNA methylation profile discriminates sporadic giant cell granulomas of the jaws and cherubism from their giant cell-rich histological mimics. J Pathol Clin Res 2023; 9:464-474. [PMID: 37555357 PMCID: PMC10556276 DOI: 10.1002/cjp2.337] [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: 03/05/2023] [Revised: 06/07/2023] [Accepted: 07/03/2023] [Indexed: 08/10/2023]
Abstract
Sporadic giant cell granulomas (GCGs) of the jaws and cherubism-associated giant cell lesions share histopathological features and microscopic diagnosis alone can be challenging. Additionally, GCG can morphologically closely resemble other giant cell-rich lesions, including non-ossifying fibroma (NOF), aneurysmal bone cyst (ABC), giant cell tumour of bone (GCTB), and chondroblastoma. The epigenetic basis of these giant cell-rich tumours is unclear and DNA methylation profiling has been shown to be clinically useful for the diagnosis of other tumour types. Therefore, we aimed to assess the DNA methylation profile of central and peripheral sporadic GCG and cherubism to test whether DNA methylation patterns can help to distinguish them. Additionally, we compared the DNA methylation profile of these lesions with those of other giant cell-rich mimics to investigate if the microscopic similarities extend to the epigenetic level. DNA methylation analysis was performed for central (n = 10) and peripheral (n = 10) GCG, cherubism (n = 6), NOF (n = 10), ABC (n = 16), GCTB (n = 9), and chondroblastoma (n = 10) using the Infinium Human Methylation EPIC Chip. Central and peripheral sporadic GCG and cherubism share a related DNA methylation pattern, with those of peripheral GCG and cherubism appearing slightly distinct, while central GCG shows overlap with both of the former. NOF, ABC, GCTB, and chondroblastoma, on the other hand, have distinct methylation patterns. The global and enhancer-associated CpG DNA methylation values showed a similar distribution pattern among central and peripheral GCG and cherubism, with cherubism showing the lowest and peripheral GCG having the highest median values. By contrast, promoter regions showed a different methylation distribution pattern, with cherubism showing the highest median values. In conclusion, DNA methylation profiling is currently not capable of clearly distinguishing sporadic and cherubism-associated giant cell lesions. Conversely, it could discriminate sporadic GCG of the jaws from their giant cell-rich mimics (NOF, ABC, GCTB, and chondroblastoma).
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Affiliation(s)
- Letícia Martins Guimarães
- Department of Pathology, Biological Science InstituteUniversidade Federal de Minas Gerais (UFMG)Belo HorizonteMinas GeraisBrazil
| | - Daniel Baumhoer
- Bone Tumor Reference Centre, Institute of PathologyUniversity Hospital Basel and University of BaselBaselSwitzerland
| | - Vanghelita Andrei
- Bone Tumor Reference Centre, Institute of PathologyUniversity Hospital Basel and University of BaselBaselSwitzerland
| | - Dennis Friedel
- Department of Neuropathology, Institute of PathologyHeidelberg University HospitalHeidelbergGermany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ)German Consortium for Translational Cancer Research (DKTK)HeidelbergGermany
| | - Christian Koelsche
- Department of Neuropathology, Institute of PathologyHeidelberg University HospitalHeidelbergGermany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ)German Consortium for Translational Cancer Research (DKTK)HeidelbergGermany
- Department of General Pathology, Institute of PathologyHeidelberg University HospitalHeidelbergGermany
- Institute of Pathology, Faculty of MedicineLMU MunichMunichGermany
| | - Ricardo Santiago Gomez
- Department of Oral Surgery and Pathology, School of DentistryUniversidade Federal de Minas Gerais (UFMG)Belo HorizonteMinas GeraisBrazil
| | - Andreas von Deimling
- Department of Neuropathology, Institute of PathologyHeidelberg University HospitalHeidelbergGermany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ)German Consortium for Translational Cancer Research (DKTK)HeidelbergGermany
| | - Carolina Cavalieri Gomes
- Department of Pathology, Biological Science InstituteUniversidade Federal de Minas Gerais (UFMG)Belo HorizonteMinas GeraisBrazil
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11
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Pašalić D, Nikuševa-Martić T, Sekovanić A, Kaštelan S. Genetic and Epigenetic Features of Uveal Melanoma-An Overview and Clinical Implications. Int J Mol Sci 2023; 24:12807. [PMID: 37628989 PMCID: PMC10454135 DOI: 10.3390/ijms241612807] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/09/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Uveal melanoma (UM) is rare, but it is the most common primary intraocular malignancy among adults. This review represents the molecular, genetic, and immunobiological mechanisms involved in UM carcinogenesis and progression, as well as data about the association of chromosomal changes, genetic mutations, selective proteins, and biochemical biomarkers with the clinical implications of UM. Genetic analysis has the potential to identify patients with a high risk of UM metastasis, enabling management that is more effective and allowing for the follow-up of patients. Advancements in molecular characterization of UM offer opportunities to develop targeted therapeutic strategies by focusing on relevant signaling pathways. Changes in miRNA expression could be useful in the diagnosis and prognosis of UM, due to unique miRNA profiles in melanoma cells or tissue and its association with metastasis. Although liver function tests do not provide enough data on the prognosis of UM, due to the high frequency of liver metastasis, liver function tests (LFTs) might be useful indicators; however, the absence of rising LFT values cannot lead to the exclusion of liver metastases. Molecular analysis of tumor tissue will allow us to identify patients with the added benefit of new therapeutic agents and provide a better insight into melanoma pathogenesis and its biological behavior.
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Affiliation(s)
- Daria Pašalić
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Tamara Nikuševa-Martić
- Department of Biology and Genetics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Ankica Sekovanić
- Institute for Medical Research and Occupational Health, 10000 Zagreb, Croatia;
| | - Snježana Kaštelan
- Department of Ophthalmology and Optometry, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
- Department of Ophthalmology, Clinical Hospital Dubrava, 10000 Zagreb, Croatia
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12
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Scheurleer WFJ, Braunius WW, Tijink BM, Suijkerbuijk KPM, Dierselhuis MP, Meijers RWJ, Blokx WAM, de Bree R, Breimer GE, Rijken JA. PRAME Staining in Sinonasal Mucosal Melanoma: A Single-Center Experience. Head Neck Pathol 2023; 17:401-408. [PMID: 36586078 PMCID: PMC10293483 DOI: 10.1007/s12105-022-01515-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/24/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND Sinonasal mucosal melanoma (MM) is a rare, aggressive melanoma subtype. Complete surgical excision, with or without adjuvant radiotherapy, remains the cornerstone of treatment and yields adequate locoregional control. Metastatic MM is managed similarly to metastatic cutaneous melanoma but with poorer survival. PReferentially expressed Antigen in MElanoma (PRAME) has been identified as a potential diagnostic marker and therapeutic target in the treatment of cutaneous melanoma. METHODS Retrospective analysis of the clinical characteristics and immunohistochemical features of all sinonasal MM patients referred to the department of Head and Neck Surgical Oncology, UMC Utrecht Cancer Center, between 2011 and 2021 was performed. Single nucleotide polymorphism (SNP) array and next-generation sequencing (NGS) were performed in selected cases. RESULTS A total of 26 patients with an MM were included. The median follow-up duration was 15 months. At the end of follow-up, 13 patients had died due to progression of their disease, and one patient died of intercurrent disease. PRAME immunohistochemistry was performed in 23 out of 26 cases, all displaying PRAME expression. In two cases PRAME expression was present both within the melanoma cells and in melanocytes in adjacent mucosa. SNP array showed ≥ 5 copy number variants (CNV) in all tested cases, with a median of 29.5 CNVs (IQR 23.25-40). The three most common mutations identified by NGS were NRAS (7 cases) and NF1 (2 cases). CONCLUSION We show that expression of PRAME is common in sinonasal MM, making PRAME a useful ancillary diagnostic tool and a potential therapeutic target in sinonasal MM. The demonstrated occurrence of extensive presence of PRAME-positive melanocytes in the surrounding mucosa of sinonasal MM might explain the multifocal nature of melanoma in the (sinonasal) mucosa, and would be an extra argument for a PRAME targeting treatment in preventing local disease recurrence.
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Affiliation(s)
- W F Julius Scheurleer
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - W Weibel Braunius
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Bernard M Tijink
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Ruud W J Meijers
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Willeke A M Blokx
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Remco de Bree
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gerben E Breimer
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johannes A Rijken
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
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13
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Yang L, Wang G, Shi H, Jia S, Ruan J, Cui R, Ge S. Methylation-driven gene DLL3 is a potential prognostic biomarker in ocular melanoma correlating with metastasis. Front Oncol 2022; 12:964902. [PMID: 36338696 PMCID: PMC9630341 DOI: 10.3389/fonc.2022.964902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/30/2022] [Indexed: 11/20/2022] Open
Abstract
Background Ocular melanoma is an aggressive malignancy with a high rate of metastasis and poor prognosis. Increasing evidence indicated that DNA methylation plays an important role in the occurrence and development of ocular melanoma. Hence, exploring new diagnostic and prognostic biomarkers at the genetic level may be beneficial to the prognosis of patients with ocular melanoma. Methods We collected DNA methylation and gene expression profiles of human UM (uveal melanoma) and CM (conjunctival melanoma) samples from various datasets. We conducted differential methylation and expression analyses to screen the potential biomarkers. Correlation analysis was performed to investigate the relationships between the expression level of DLL3 (delta-like protein 3) and the methylation level of its corresponding CpGs. We explored the prognostic and diagnostic value of DLL3 in UM and CM. Functional annotation and GSEA (gene set enrichment analysis) were applied to get insight into the possible biological roles of DLL3. A cohort of 60 ocular melanoma patients as well as UM and CM cell lines were used to validate our findings in bioinformatic analyses. Results We found that DLL3 was a methylation-driven gene correlating with UM metastasis. The CpGs of DLL3 are mainly located in the gene body and their methylation level positively correlated to DLL3 expression. Multivariate Cox regression analysis revealed that DLL3 was an independent protective factor for UM patients. High DLL3 expression significantly prolonged the overall survival and disease-free survival of UM patients. DLL3 also showed a promising power to distinguish CM from normal tissues. Functional annotation exhibited that DLL3 may suppress UM progression through modulating immune activities and down-regulating various signaling pathways. External datasets, biospecimens, and cell lines further validated the aberrant expression and prognostic role of DLL3 in ocular melanoma. Conclusion Methylation-driven gene DLL3 could serve as a new potential diagnostic and prognostic biomarker in ocular melanoma. Our findings may contribute to improving the clinical outcomes of patients with UM or CM.
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Affiliation(s)
- Ludi Yang
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Gaoming Wang
- Department of Hepatopancreatobiliary Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hanhan Shi
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Shichong Jia
- Tianjin Eye Hospital, Tianjin Key Lab of Ophthalmology and Visual Science, Nankai University Affiliated Eye Hospital, Tianjin Eye Institute, Tianjin, China
| | - Jing Ruan
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- *Correspondence: Jing Ruan, ; Ran Cui, ; Shengfang Ge,
| | - Ran Cui
- Department of Hepatopancreatobiliary Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Jing Ruan, ; Ran Cui, ; Shengfang Ge,
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- *Correspondence: Jing Ruan, ; Ran Cui, ; Shengfang Ge,
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14
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Gallenga CE, Franco E, Adamo GG, Violanti SS, Tassinari P, Tognon M, Perri P. Genetic Basis and Molecular Mechanisms of Uveal Melanoma Metastasis: A Focus on Prognosis. Front Oncol 2022; 12:828112. [PMID: 35480119 PMCID: PMC9037634 DOI: 10.3389/fonc.2022.828112] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/25/2022] [Indexed: 12/21/2022] Open
Abstract
Uveal melanoma (UM) is the most frequently found primary intraocular tumor, although it accounts for only 5% of all melanomas. Despite novel systemic therapies, patient survival has remained poor. Indeed, almost half of UM patients develop metastases from micro-metastases which were undetectable at diagnosis. Genetic analysis is crucial for metastatic risk prediction, as well as for patient management and follow-up. Several prognostic parameters have been explored, including tumor location, basal dimension and thickness, histopathologic cell type, vascular mimicry patterns, and infiltrating lymphocytes. Herein, the Authors review the available literature concerning cytogenetic prognostic markers and biochemical pathways correlated to UM metastasis development.
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Affiliation(s)
| | - Elena Franco
- Department of Translational Medicine and for Romagna, University of Ferrara, Ferrara, Italy
| | - Ginevra Giovanna Adamo
- Department of Specialized Surgery, Section of Ophthalmology, Sant’Anna University Hospital, Ferrara, Italy
| | - Sara Silvia Violanti
- Department of Head and Neck, Section of Ophthalmology, San Paolo Hospital, Savona, Italy
| | - Paolo Tassinari
- Department of Specialized Surgery, Section of Ophthalmology, Sant’Anna University Hospital, Ferrara, Italy
| | - Mauro Tognon
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Paolo Perri
- Department of Neuroscience and Rehabilitation, Section of Ophthalmology, University of Ferrara, Ferrara, Italy
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15
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Koelsche C, von Deimling A. Methylation classifiers: brain tumors, sarcomas and what's next. Genes Chromosomes Cancer 2022; 61:346-355. [PMID: 35388566 DOI: 10.1002/gcc.23041] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 11/09/2022] Open
Abstract
Tumor classification has evolved over the last decades with technical progress contributing much to our current concepts. Among diagnostic hallmark novelties were immunostaining, Fluorescence in situ hybridization, Sanger sequencing followed by massive parallel DNA sequencing and recently, epigenetic analyses have entered the stage. Although each of these techniques was revolutionary and, in some way, also disruptive in certain diagnostic fields, it took years to decades for broad implementation into standard pathological-diagnostic algorithms. In contrast, DNA methylation profiling has been accepted in short time as a game changer with lasting impact on brain tumor classification and with potential for classification of other tumor types. This review provides a brief introduction in DNA methylation-based tumor classification. We present why DNA methylation signatures are attractive diagnostic biomarkers, discuss present achievements and future aims and explain the integration of methylation-based classifiers in diagnostic procedure. Finally, we provide an outlook on the challenges and opportunities associated with DNA methylation-based tumor profiling. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Christian Koelsche
- Department of General Pathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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16
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Prouteau A, Mottier S, Primot A, Cadieu E, Bachelot L, Botherel N, Cabillic F, Houel A, Cornevin L, Kergal C, Corre S, Abadie J, Hitte C, Gilot D, Lindblad-Toh K, André C, Derrien T, Hedan B. Canine Oral Melanoma Genomic and Transcriptomic Study Defines Two Molecular Subgroups with Different Therapeutical Targets. Cancers (Basel) 2022; 14:cancers14020276. [PMID: 35053440 PMCID: PMC8774001 DOI: 10.3390/cancers14020276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 02/05/2023] Open
Abstract
Simple Summary In humans, mucosal melanoma (MM) is a rare and aggressive cancer. The canine model is frequently and spontaneously affected by MM, thus facilitating the collection of samples and the study of its genetic bases. Thanks to an integrative genomic and transcriptomic analysis of 32 canine MM samples, we identified two molecular subgroups of MM with a different microenvironment and structural variant (SV) content. We demonstrated that SVs are associated with recurrently amplified regions, and identified new candidate oncogenes (TRPM7, GABPB1, and SPPL2A) for MM. Our findings suggest the existence of two MM molecular subgroups that could benefit from dedicated therapies, such as immune checkpoint inhibitors or targeted therapies, for both human and veterinary medicine. Abstract Mucosal melanoma (MM) is a rare, aggressive clinical cancer. Despite recent advances in genetics and treatment, the prognosis of MM remains poor. Canine MM offers a relevant spontaneous and immunocompetent model to decipher the genetic bases and explore treatments for MM. We performed an integrative genomic and transcriptomic analysis of 32 canine MM samples, which identified two molecular subgroups with a different microenvironment and structural variant (SV) content. The overexpression of genes related to the microenvironment and T-cell response was associated with tumors harboring a lower content of SVs, whereas the overexpression of pigmentation-related pathways and oncogenes, such as TERT, was associated with a high SV burden. Using whole-genome sequencing, we showed that focal amplifications characterized complex chromosomal rearrangements targeting oncogenes, such as MDM2 or CDK4, and a recurrently amplified region on canine chromosome 30. We also demonstrated that the genes TRPM7, GABPB1, and SPPL2A, located in this CFA30 region, play a role in cell proliferation, and thus, may be considered as new candidate oncogenes for human MM. Our findings suggest the existence of two MM molecular subgroups that may benefit from dedicated therapies, such as immune checkpoint inhibitors or targeted therapies, for both human and veterinary medicine.
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Affiliation(s)
- Anais Prouteau
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Stephanie Mottier
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Aline Primot
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Edouard Cadieu
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Laura Bachelot
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Nadine Botherel
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Florian Cabillic
- Laboratoire de Cytogénétique et Biologie Cellulaire, CHU de Rennes, INSERM, INRA, University of Rennes 1, Nutrition Metabolisms and Cancer, 35000 Rennes, France; (F.C.); (L.C.)
| | - Armel Houel
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Laurence Cornevin
- Laboratoire de Cytogénétique et Biologie Cellulaire, CHU de Rennes, INSERM, INRA, University of Rennes 1, Nutrition Metabolisms and Cancer, 35000 Rennes, France; (F.C.); (L.C.)
| | - Camille Kergal
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Sébastien Corre
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Jérôme Abadie
- Laboniris, Department of Biology, Pathology and Food Sciences, Oniris, 44300 Nantes, France;
| | - Christophe Hitte
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - David Gilot
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA;
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Catherine André
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Thomas Derrien
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
- Correspondence: (T.D.); (B.H.); Tel.: +33-2-23-23-43-19 (B.H.)
| | - Benoit Hedan
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
- Correspondence: (T.D.); (B.H.); Tel.: +33-2-23-23-43-19 (B.H.)
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17
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Molecular Profiling and Novel Therapeutic Strategies for Mucosal Melanoma: A Comprehensive Review. Int J Mol Sci 2021; 23:ijms23010147. [PMID: 35008570 PMCID: PMC8745551 DOI: 10.3390/ijms23010147] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 01/15/2023] Open
Abstract
Mucosal melanoma is a rare and aggressive subtype of melanoma. Unlike its cutaneous counterpart, mucosal melanoma has only gained limited benefit from novel treatment approaches due to the lack of actionable driver mutations and poor response to immunotherapy. Over the last years, whole-genome and exome sequencing techniques have led to increased knowledge on the molecular landscape of mucosal melanoma. Molecular studies have underlined noteworthy findings with potential therapeutic implications, including the presence of KIT mutations, which are potential targets of tyrosine kinase inhibitors currently in use in the clinic (imatinib), but also SF3B1 mutation, CDK4 amplifications, and CDKN2A gene deletions, which are presently under investigation in clinical trials. Recent results from a pooled analysis of patients with mucosal melanoma treated with immunotherapy have suggested that the combination of immune checkpoint inhibitors might improve survival outcomes in this subset of patients, as compared with single-agent immunotherapy. However, these results are not confirmed across different studies, and combo-immunotherapy correlates with a higher rate of adverse events. In this review, we describe the clinical, biological, and genetic features of mucosal melanoma. We also provide an update on the results of approved systemic treatment in this setting and overview the therapeutic strategies currently under investigation in clinical trials.
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18
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Wrede N, Hoffmann I, Vollbrecht C, Koch I, Wolkenstein P, Klauschen F, Capper D, von Laffert M, Jurmeister P. Comparative investigation of cell cycle and immunomodulatory genes in mucosal and cutaneous melanomas: Preliminary data suggest a potential promising clinical role for p16 and the PD-1/PD-L1 axis. Pathol Res Pract 2021; 229:153689. [PMID: 34844086 DOI: 10.1016/j.prp.2021.153689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/12/2021] [Indexed: 02/03/2023]
Abstract
Mucosal melanomas arise from the mucosal lining of various organs. Their etiology is currently unknown and there are no tissue-based methods to differentiate it from cutaneous melanomas. Furthermore, prognostic and predictive markers (e.g. for immune checkpoint inhibition) are lacking. In this study, we aimed to assess the protein expression levels of cell cycle-associated proteins and immune checkpoint markers in a cohort of mucosal melanomas in comparison to cutaneous melanomas and evaluated the effect of potential regulatory mechanisms. We performed immunohistochemistry, DNA methylation analysis and copy number profiling of 47 mucosal and 28 cutaneous melanoma samples. Protein expression of CD117, Ki67 and p16 was higher in mucosal melanomas, while BCL2, Cyclin D1, PD-1 and PD-L1 were overexpressed in cutaneous melanomas. CDKN2A deletions were the most prevalent numeric chromosomal alterations in both mucosal and cutaneous melanoma and were associated with decreased p16 expression. KIT was frequently amplified in mucosal melanomas, but not associated with CD117 expression. On the other hand, amplification of CCND1 lead to Cyclin D1 overexpression. In mucosal melanoma patients high PD-1 expression and high PD-L1 promoter methylation levels were associated with improved survival. PD-L1 expression correlated with response to immune checkpoint inhibitor therapy in the combined group of melanoma patients. Mucosal and cutaneous melanomas show different expression levels of cell cycle-associated and immunomodulatory proteins that are partially regulated by DNA methylation and copy number alterations. PD-1 expression and PD-L1 promoter methylation levels might be a prognostic marker for mucosal melanomas.
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Affiliation(s)
- Niklas Wrede
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Inga Hoffmann
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Claudia Vollbrecht
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Ines Koch
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Peggy Wolkenstein
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Frederick Klauschen
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany; Institute of Pathology, Ludwig Maximilians University Hospital Munich, Thalkirchner Str. 36, 80337 Munich, Germany
| | - David Capper
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Maximilian von Laffert
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany; Institute of Pathology, University Hospital Leipzig, Leipzig, Germany
| | - Philipp Jurmeister
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany; Institute of Pathology, Ludwig Maximilians University Hospital Munich, Thalkirchner Str. 36, 80337 Munich, Germany.
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19
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Xing J, Zhai R, Wang C, Liu H, Zeng J, Zhou D, Zhang M, Wang L, Wu Q, Gu Y, Zhang Y. DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database. Nucleic Acids Res 2021; 50:D1208-D1215. [PMID: 34792145 PMCID: PMC8728278 DOI: 10.1093/nar/gkab1088] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 11/14/2022] Open
Abstract
DNA methylation has a growing potential for use as a biomarker because of its involvement in disease. DNA methylation data have also substantially grown in volume during the past 5 years. To facilitate access to these fragmented data, we proposed DiseaseMeth version 3.0 based on DiseaseMeth version 2.0, in which the number of diseases including increased from 88 to 162 and High-throughput profiles samples increased from 32 701 to 49 949. Experimentally confirmed associations added 448 pairs obtained by manual literature mining from 1472 papers in PubMed. The search, analyze and tools sections were updated to increase performance. In particular, the FunctionSearch now provides for the functional enrichment of genes from localized GO and KEGG annotation. We have also developed a unified analysis pipeline for identifying differentially DNA methylated genes (DMGs) from the original data stored in the database. 22 718 DMGs were found in 99 diseases. These DMGs offer application in disease evaluation using two self-developed online tools, Methylation Disease Correlation and Cancer Prognosis & Co-Methylation. All query results can be downloaded and can also be displayed through a box plot, heatmap or network module according to whichever search section is used. DiseaseMeth version 3.0 is freely available at http://diseasemeth.edbc.org/.
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Affiliation(s)
- Jie Xing
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Ruiyang Zhai
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Cong Wang
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Honghao Liu
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Jiaqi Zeng
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Dianshuang Zhou
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Mengyan Zhang
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Liru Wang
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Qiong Wu
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Yue Gu
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Yan Zhang
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China.,Guangzhou Institute of Respiratory health, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 510120, China
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