1
|
Eiger-Moscovich M, Shields CL, Eagle RC, Milman T. BRCA-associated protein1 (BAP1) immunohistochemical stain reliability in postbrachytherapy uveal melanoma enucleation specimens. Indian J Ophthalmol 2024; 72:S459-S467. [PMID: 38324631 DOI: 10.4103/ijo.ijo_648_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 12/21/2023] [Indexed: 02/09/2024] Open
Abstract
PURPOSE The BRCA-associated protein1 (BAP1) immunohistochemical (IHC) stain has emerged as a powerful and inexpensive prognostic tool in uveal melanoma (UM), correlating with UM genetics and outcome. The data on the reliability of BAP1 immunohistochemistry in previously irradiated UM is scant. We aim to assess BAP1 IHC in post-Iodine-125 plaque brachytherapy-treated UM-enucleated eyes. METHODS In a case-control study, the medical records of all patients who underwent enucleation for UM at a major Ocular Oncology Service from December 1 st , 2007 to December 31 st , 2014 were reviewed. All cases with either chromosome 3 (ch3) status or sufficient follow-up (>5 years or metastasis) were selected. Nuclear BAP1 (nBAP1) immunoreactivity was interpreted as intact (positive in >90% of nuclei), lost (positive in <5% of nuclei), or heterogeneous (positive in 5-90% of nuclei). Retina and intratumoral blood vessels served as internal positive controls. RESULTS A comparison of 34 postbrachytherapy UM secondary-enucleated eyes with 47 nonbrachytherapy primary enucleated controls revealed no significant difference with respect to nBAP1 IHC (lost in 41% vs 51%, P = 0.19), ch3 status (ch3 monosomy in 59% vs 60%, P = 0.48), and outcome (metastatic disease in 44% vs 47%, P = 0.8). Association of nBAP1 IHC with ch3 status and outcome [intact nBAP1/(ch3 disomy and/or no metastasis) and lost nBAP1 (ch3 monosomy and/or metastasis)] in post-brachytherapy UM was significantly lower when compared with non-brachytherapy tumors [21/30 (70%) vs 41/44 (93%), P = 0.004*]. CONCLUSION Although nBAP1 IHC stain is a strong prognostic tool in UM, its association with ch3 status, and outcome in postbrachytherapy UM was significantly lower compared with nonbrachytherapy tumors due to pitfalls in the interpretation of nBAP1 immunoreactivity in irradiated UM. This test should be used judiciously in the prognostication of postbrachytherapy-enucleated UM.
Collapse
Affiliation(s)
- Maya Eiger-Moscovich
- Department of Pathology, Wills Eye Hospital, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, USA
- Department of Ophthalmology, Hadassah Medical Center, Jerusalem, Israel
| | - Carol L Shields
- Ocular Oncology Service, Wills Eye Hospital, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, USA
| | - Ralph C Eagle
- Department of Pathology, Wills Eye Hospital, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, USA
| | - Tatyana Milman
- Department of Pathology, Wills Eye Hospital, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, USA
| |
Collapse
|
2
|
Donizy P, Spytek M, Krzyziński M, Kotowski K, Markiewicz A, Romanowska-Dixon B, Biecek P, Hoang MP. Ki67 is a better marker than PRAME in risk stratification of BAP1-positive and BAP1-loss uveal melanomas. Br J Ophthalmol 2023:bjo-2023-323816. [PMID: 37734766 DOI: 10.1136/bjo-2023-323816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/06/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND Accurate risk stratification of uveal melanoma (UM) patients is important for determining the interval and frequency of surveillance. Loss of BAP1 expression has been shown to be strongly associated with UM-related death and metastasis. METHODS In this study of 164 enucleated UMs, we assessed the prognostic role of preferentially expressed antigen in melanoma (PRAME) expression and Ki67 proliferation index measured by digital quantitation using QuPath programme in patients with BAP1-positive and BAP1-loss UMs. RESULTS In univariate analyses with log-rank tests and Kaplan-Meier curves, PRAME further stratified only overall survival (OS) in BAP1-positive and BAP1-loss tumour groups. However, Ki67 further stratified both OS and disease-free survival (DFS) in BAP1-positive and BAP1-loss tumour groups. In multivariate analyses, Ki67 percentage and BAP1 were independent survival predictors for both OS and DFS, whereas PRAME was not a significant covariate. In model comparisons, combined Ki67 and BAP1 performed better than combined PRAME and BAP1 in risk-stratifying patients for both OS and DFS. Ki67 was better than PRAME in risk stratification of BAP1-positive UMs. Low Ki67 index correlated with significantly prolonged DFS in BAP1-loss UMs. CONCLUSION A panel of Ki67 and BAP1 could be a helpful risk stratification strategy for UM.
Collapse
Affiliation(s)
- Piotr Donizy
- Department of Clinical and Experimental Pathology, Wroclaw Medical University, Wroclaw, Poland
- Department of Pathology and Clinical Cytology, Jan Mikulicz-Radecki University Hospital, Wroclaw, Poland
| | - Mikołaj Spytek
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Mateusz Krzyziński
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Krzysztof Kotowski
- Department of Clinical and Experimental Pathology, Wroclaw Medical University, Wroclaw, Poland
| | - Anna Markiewicz
- Department of Ophthalmology and Ocular Oncology, Jagiellonian University Medical College, Kraków, Poland
| | - Bozena Romanowska-Dixon
- Department of Ophthalmology and Ocular Oncology, Jagiellonian University Medical College, Kraków, Poland
| | - Przemyslaw Biecek
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Mai P Hoang
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
3
|
Wan Y, Shen J, Hong Y, Liu J, Shi T, Cai J. Mapping knowledge landscapes and emerging trends of the biomarkers in melanoma: a bibliometric analysis from 2004 to 2022. Front Oncol 2023; 13:1181164. [PMID: 37427124 PMCID: PMC10327294 DOI: 10.3389/fonc.2023.1181164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Background Melanoma is a skin tumor with a high mortality rate, and early diagnosis and effective treatment are the key to reduce its mortality rate. Therefore, more and more attention has been paid for biomarker identification for early diagnosis, prognosis prediction and prognosis evaluation of melanoma. However, there is still a lack of a report that comprehensively and objectively evaluates the research status of melanoma biomarkers. Therefore, this study aims to intuitively analyze the research status and trend of melanoma biomarkers through the methods of bibliometrics and knowledge graph. Objective This study uses bibliometrics to analyze research in biomarkers in melanoma, summarize the field's history and current status of research, and predict future research directions. Method Articles and Reviews related to melanoma biomarkers were retrieved by using Web of Science core collection subject search. Bibliometric analysis was performed in Excel 365, CiteSpace, VOSviewer and Bibliometrix (R-Tool of R-Studio). Result A total of 5584 documents from 2004 to 2022 were included in the bibliometric analysis. The results show that the number of publications and the frequency of citations in this field are increasing year by year, and the frequency of citations has increased rapidly after 2018. The United States is the most productive and influential country in this field, with the largest number of publications and institutions with high citation frequency. Caroline Robert, F. Stephen Hodi, Suzanne L. Topalian and others are authoritative authors in this field, and The New England Journal of Medicine, Journal of Clinical Oncology and Clinical Cancer Research are the most authoritative journals in this field. Biomarkers related to the diagnosis, treatment and prognosis of melanoma are hot topics and cutting-edge hotspots in this field. Conclusion For the first time, this study used the bibliometric method to visualize the research in the field of melanoma biomarkers, revealing the trends and frontiers of melanoma biomarkers research, which provides a useful reference for scholars to find key research issues and partners.
Collapse
Affiliation(s)
- Yantong Wan
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Junyi Shen
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yinghao Hong
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jinghua Liu
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, China
| | - Junwei Cai
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| |
Collapse
|
4
|
Li Y, Xiong C, Wu LL, Zhang BY, Wu S, Chen YF, Xu QH, Liao HF. Tumor subtypes and signature model construction based on chromatin regulators for better prediction of prognosis in uveal melanoma. Pathol Oncol Res 2023; 29:1610980. [PMID: 37362244 PMCID: PMC10287976 DOI: 10.3389/pore.2023.1610980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
Background: Uveal Melanoma (UM) is the most prevalent primary intraocular malignancy in adults. This study assessed the importance of chromatin regulators (CRs) in UM and developed a model to predict UM prognosis. Methods: Gene expression data and clinical information for UM were obtained from public databases. Samples were typed according to the gene expression of CRs associated with UM prognosis. The prognostic key genes were further screened by the protein interaction network, and the risk model was to predict UM prognosis using the least absolute shrinkage and selection operator (LASSO) regression analysis and performed a test of the risk mode. In addition, we performed gene set variation analysis, tumor microenvironment, and tumor immune analysis between subtypes and risk groups to explore the mechanisms influencing the development of UM. Results: We constructed a signature model consisting of three CRs (RUVBL1, SIRT3, and SMARCD3), which was shown to be accurate, and valid for predicting prognostic outcomes in UM. Higher immune cell infiltration in poor prognostic subtypes and risk groups. The Tumor immune analysis and Tumor Immune Dysfunction and Exclusion (TIDE) score provided a basis for clinical immunotherapy in UM. Conclusion: The risk model has prognostic value for UM survival and provides new insights into the treatment of UM.
Collapse
Affiliation(s)
- Yue Li
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Chao Xiong
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Li Li Wu
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Bo Yuan Zhang
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Sha Wu
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Yu Fen Chen
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Qi Hua Xu
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Hong Fei Liao
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| |
Collapse
|
5
|
Han LM, Lee KW, Uludag G, Seider MI, Afshar AR, Bloomer MM, Pekmezci M. Prognostic Value of BAP1 and Preferentially Expressed Antigen in Melanoma (PRAME) Immunohistochemistry in Uveal Melanomas. Mod Pathol 2023; 36:100081. [PMID: 36788079 DOI: 10.1016/j.modpat.2022.100081] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/21/2022] [Accepted: 12/11/2022] [Indexed: 01/11/2023]
Abstract
Uveal melanoma (UM) is the most common primary intraocular tumor in adults, and despite excellent local control, more than 50% of patients develop and die from metastatic disease. Loss of BAP1 nuclear staining, a surrogate marker of BAP1 mutation, and preferentially expressed antigen in melanoma (PRAME) messenger RNA overexpression, as assessed using qPCR, have previously been shown to correlate with increased metastasis rate in UM. In this study, we demonstrated that UM could be successfully risk-stratified using a combination of BAP1 and PRAME immunohistochemical (IHC) stains. We retrospectively reviewed 318 UM cases with sufficient tissue and performed BAP1 and PRAME IHC to stratify them as BAP1+/PRAME- (group 1, n = 135), BAP1+/PRAME+ (group 2, n = 43), BAP1-/PRAME- (group 3, n = 94), and BAP1-/PRAME+ (group 4, n = 46). Increasing the study risk group on the basis of loss of BAP1 expression and positive PRAME staining was associated with a higher rate of metastasis and disease-specific death and lower metastasis-free survival (MFS) and disease-specific survival (DSS). Among tumors with loss of BAP1 staining, PRAME positivity was associated with shorter MFS (P = .018) and showed a trend toward shorter DSS (P = .061). Among tumors with retained BAP1 staining, PRAME positivity was associated with shorter MFS and DSS (P = .001 and P = .021, respectively). In summary, a combination of BAP1 and PRAME IHC can be used for risk stratification of UMs.
Collapse
Affiliation(s)
- Lucy M Han
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Kar Wan Lee
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California
| | - Gunay Uludag
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Michael I Seider
- Department of Ophthalmology, Kaiser Permanente San Francisco, San Francisco, California
| | - Armin R Afshar
- Ocular Oncology Service, Department of Ophthalmology, Wayne & Gladys Valley Center for Vision, University of California San Francisco, San Francisco, California
| | - Michele M Bloomer
- Department of Pathology, University of California San Francisco, San Francisco, California; Department of Ophthalmology, University of California San Francisco, San Francisco, California
| | - Melike Pekmezci
- Department of Pathology, University of California San Francisco, San Francisco, California; Department of Ophthalmology, University of California San Francisco, San Francisco, California; San Francisco Veterans Affairs Medical Center, San Francisco, California.
| |
Collapse
|
6
|
Cole YC, Zhang YZ, Gallo B, Januszewski AP, Nastase A, Essex DJ, Thaung CMH, Cohen VML, Sagoo MS, Bowcock AM. Correlation between BAP1 Localization, Driver Mutations, and Patient Survival in Uveal Melanoma. Cancers (Basel) 2022; 14:cancers14174105. [PMID: 36077643 PMCID: PMC9454448 DOI: 10.3390/cancers14174105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 12/02/2022] Open
Abstract
Uveal melanoma (UM) is an uncommon but highly aggressive ocular malignancy. Poor overall survival is associated with deleterious BAP1 alterations, which frequently occur with monosomy 3 (LOH3) and a characteristic gene expression profile. Tumor DNA from a cohort of 100 UM patients from Moorfields Biobank (UK) that had undergone enucleation were sequenced for known UM driver genes (BAP1, SF3B1, EIF1AX, GNAQ, and GNA11). Immunohistochemical staining of BAP1 and interphase FISH for chromosomes 3 and 8 was performed, and cellular localization of BAP1 was correlated with BAP1 mutations. Wildtype (WT) BAP1 staining was characterized by nBAP1 expression with <10% cytoplasmic BAP1 (cBAP1). Tumors exhibited heterogeneity with respect to BAP1 staining with different percentages of nBAP1 loss: ≥25% loss of nuclear BAP1 (nBAP1) was superior to chr8q and LOH3 as a prognostic indicator. Of the successfully sequenced UMs, 38% harbored oncogenic mutations in GNA11 and 48% harbored mutations in GNAQ at residues 209 or 183. Of the secondary drivers, 39% of mutations were in BAP1, 11% were in EIF1AX, and 20% were in the SF3B1 R625 hotspot. Most tumors with SF3B1 or EIF1AX mutations retained nuclear BAP1 (nBAP1). The majority of tumor samples with likely pathogenic BAP1 mutations, regardless of mutation class, displayed ≥25% loss of nBAP1. This included all tumors with truncating mutations and 80% of tumors with missense mutations. In addition, 60% of tumors with truncating mutations and 82% of tumors with missense mutations expressed >10% cBAP1.
Collapse
Affiliation(s)
- Yasemin C. Cole
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
| | - Yu-Zhi Zhang
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London SW3 6NP, UK
| | - Beatrice Gallo
- Ocular Oncology Service, Moorfields Eye Hospital & St. Bartholomew’s Hospital, London EC1V 2PD, UK
| | - Adam P. Januszewski
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
| | - Anca Nastase
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
| | - David J. Essex
- Ocular Oncology Service, Moorfields Eye Hospital & St. Bartholomew’s Hospital, London EC1V 2PD, UK
| | - Caroline M. H. Thaung
- Moorfields Eye Hospital, London EC1V 2PD, UK
- Department of Eye Pathology, UCL Institute of Ophthalmology, London EC1V 9EL, UK
| | - Victoria M. L. Cohen
- Ocular Oncology Service, Moorfields Eye Hospital & St. Bartholomew’s Hospital, London EC1V 2PD, UK
- Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Mandeep S. Sagoo
- Ocular Oncology Service, Moorfields Eye Hospital & St. Bartholomew’s Hospital, London EC1V 2PD, UK
- Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Anne M. Bowcock
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
- Departments of Oncological Sciences, Dermatology and Genetics & Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence: ; Tel.: +1-212-659-8256
| |
Collapse
|
7
|
Piaggio F, Croce M, Reggiani F, Monti P, Bernardi C, Ambrosio M, Banelli B, Dogrusöz M, Jockers R, Bordo D, Puzone R, Viaggi S, Coviello D, Lanza FB, Bartolucci M, Petretto A, Mosci C, Gangemi R, van der Velden PA, Jager MJ, Pfeffer U, Amaro A. In uveal melanoma Gα-protein GNA11 mutations convey a shorter disease-specific survival and are more strongly associated with loss of BAP1 and chromosomal alterations than Gα-protein GNAQ mutations. Eur J Cancer 2022; 170:27-41. [DOI: 10.1016/j.ejca.2022.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/08/2022] [Accepted: 04/04/2022] [Indexed: 12/21/2022]
|
8
|
Fan Z, Duan J, Luo P, Shao L, Chen Q, Tan X, Zhang L, Xu X. SLC25A38 as a novel biomarker for metastasis and clinical outcome in uveal melanoma. Cell Death Dis 2022; 13:330. [PMID: 35411037 PMCID: PMC9001737 DOI: 10.1038/s41419-022-04718-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 02/18/2022] [Accepted: 03/09/2022] [Indexed: 01/03/2023]
Abstract
Risk of metastasis is increased by the presence of chromosome 3 monosomy in uveal melanoma (UM). This study aimed to identify more accurate biomarker for risk of metastasis in UM. A total of 80 patients with UM from TCGA were assigned to two groups based on the metastatic status, and bioinformatic analyses were performed to search for critical genes for risk of metastasis. SLC25A38, located on chromosome 3, was the dominant downregulated gene in metastatic UM patients. Low expression of SLC25A38 was an independent predictive and prognostic factor in UM. The predictive potential of SLC25A38 expression was superior to that of pervious reported biomarkers in both TCGA cohort and GSE22138 cohort. Subsequently, its role in promoting metastasis was explored in vitro and in vivo. Knock-out of SLC25A38 could enhance the migration ability of UM cells, and promote distant metastasis in mice models. Through the inhibition of CBP/HIF-mediated pathway followed by the suppression of pro-angiogenic factors, SLC25A38 was situated upstream of metastasis-related pathways, especially angiogenesis. Low expression of SLC25A38 promotes angiogenesis and metastasis, and identifies increased metastatic risk and worse survival in UM patients. This finding may further improve the accuracy of prognostic prediction for UM.
Collapse
Affiliation(s)
- Zhongyi Fan
- Department of Oncology and Bio-therapeutic Center, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Research Center for Communicable Disease Diagnosis and Treatment, Shenzhen, 518112, China.,Department of Oncology, The First Medical Center, General Hospital of PLA, Beijing, 100853, China
| | - Jingjing Duan
- Department of Gastrointestinal Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Pu Luo
- Department of Oncology and Bio-therapeutic Center, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Research Center for Communicable Disease Diagnosis and Treatment, Shenzhen, 518112, China
| | - Ling Shao
- Department of Oncology and Bio-therapeutic Center, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Research Center for Communicable Disease Diagnosis and Treatment, Shenzhen, 518112, China
| | - Qiong Chen
- Department of Oncology and Bio-therapeutic Center, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Research Center for Communicable Disease Diagnosis and Treatment, Shenzhen, 518112, China
| | - Xiaohua Tan
- Department of Oncology and Bio-therapeutic Center, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Research Center for Communicable Disease Diagnosis and Treatment, Shenzhen, 518112, China.
| | - Lei Zhang
- Department of Ophthalmology, Xuanwu Hospital Attached to the Capital Medical University, Beijing, 100053, China.
| | - Xiaojie Xu
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, 100850, China.
| |
Collapse
|
9
|
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: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
10
|
Ida CM, Pulido J, Greipp PT, Garcia JJ, Olsen TW, Dalvin L, Salomão DR. BAP1 Immunostain Status in Intraocular Biopsy Specimens for Uveal Melanoma Highly Correlates with Other Prognostic Markers. Ocul Oncol Pathol 2022; 8:22-29. [PMID: 35356602 PMCID: PMC8914242 DOI: 10.1159/000515858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/14/2021] [Indexed: 02/03/2023] Open
Abstract
Introduction Loss of BAP1 protein expression emerged as a negative prognostic marker in uveal melanoma (UM) and has primarily been studied in enucleations. Intraocular biopsy is frequently performed prior to UM globe-conserving therapy. Methods We retrospectively evaluated BAP1 immunostaining of UM in 16 biopsies and 8 subsequent enucleations, and results were correlated with the UM-specific gene expression profile (GEP; n = 11), chromosome 3 status by FISH and/or chromosomal microarray (n = 12; 9 also had GEP), and clinical outcomes. Results UM involved the choroid in 15 (of 16) cases. Biopsy was performed for prognostication (n = 12) or diagnosis (n = 4). Treatment included brachytherapy (n = 13; 5 followed by enucleation) or enucleation only (n = 3). BAP1 nuclear immunostaining was positive in 9, negative in 4, and equivocal in 3 biopsies. For the 3 equivocal biopsies, BAP1 immunostaining was positive in 2 (of 3) subsequent enucleations. BAP1 immunostaining was concordant between all 5 remaining biopsies and enucleations. BAP1-positive biopsies had disomy 3 (n = 6) or 3p loss (n = 1) and class 1 GEP (n = 6). BAP1-negative biopsies had monosomy 3 (n = 3) and class 2 GEP (n = 2). Median follow-up was 62.5 months (range, 17-150). For BAP1-positive UM patients, 8 were alive (7 without metastatic disease) and 3 had died (1 melanoma-related death). Among BAP1-negative UM patients, 2 were alive (1 with metastatic disease) and 3 had melanoma-related deaths. Conclusion BAP1 immunostaining in biopsies highly correlates with results in subsequent enucleations and with well-established UM prognostic markers, representing a potential additional prognostic tool for UM biopsies.
Collapse
Affiliation(s)
- Cristiane M. Ida
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jose Pulido
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Patricia T. Greipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Joaquin J. Garcia
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Timothy W. Olsen
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Lauren Dalvin
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Diva Regina Salomão
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA,Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA,*Diva Regina Salomão,
| |
Collapse
|
11
|
Wang T, Liu D, Wang L, Liu M, Duan W, Yi J, Yi Y, Kanat O. DNA Repair Genes Are Associated with Subtype Classification, Prognosis, and Immune Infiltration in Uveal Melanoma. Journal of Oncology 2022; 2022:1-18. [PMID: 35096056 PMCID: PMC8791741 DOI: 10.1155/2022/1965451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/27/2021] [Indexed: 11/18/2022]
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. DNA repair genes play a vital role in cancer development. However, there has been very little research about DNA repair genes in UM. This study aimed to evaluate the importance of DNA repair genes and established a signature for predicting prognosis and immune features of UM. In this study, we mined TCGA database through bioinformatics analysis, and the intersect was taken between DNA repair genes and prognosis related genes and yielded 52 genes. We divided 80 UM patients into C1 and C2 subtypes. GSEA results indicated that abundant cancer-promoting functions and signaling pathways were activated in C2 subtype and the proportion of SNVs was higher in C2 than in C1 which suggested a worse prognosis. We built a six DNA repair genes model including ITPA, CETN2, CCNO, POLR2J, POLD1, and POLA1 by LASSO regression to predict prognosis of UM patients and utilized the median value of risk scores as the cutoff point to differentiate high risk and low risk group. The survival analyses and the receiver operating characteristic (ROC) curves in the validation group and entire data set confirmed the accuracy of this model. We also constructed a nomogram based on age and risk scores to evaluate the relationship between risk scores and clinical outcome. The calibration curve of the overall survival (OS) indicated that the performance of this model is steady and robust. Finally, the enrichment analysis showed that there were complex regulatory mechanisms in UM patients. The immune infiltration analysis indicated that the immune infiltration in C2 in the high risk group was different from that in the low risk group. Our findings indicated that the DNA repair genes may be related to UM prognosis and provide new insight into the underlying mechanisms.
Collapse
|
12
|
Tabuenca Del Barrio L, Nova-Camacho LM, Zubicoa Enériz A, Martínez de Espronceda Ezquerro I, Córdoba Iturriagagoitia A, Borque Rodríguez-Maimón E, García-Layana A. Prognostic Factor Utility of BAP1 Immunohistochemistry in Uveal Melanoma: A Single Center Study in Spain. Cancers (Basel) 2021; 13:cancers13215347. [PMID: 34771510 PMCID: PMC8582434 DOI: 10.3390/cancers13215347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/17/2021] [Accepted: 10/21/2021] [Indexed: 11/21/2022] Open
Abstract
Simple Summary As uveal melanoma metastasis rates are still very high, the mechanisms by which it spreads need to be evaluated. Our research sought to determine which pathological and clinical features were correlated with the prognosis of uveal melanoma in a Spanish community. BAP1 (BRCA1-Associated Protein 1) gene mutation is one of the strongest predictors for metastasis in uveal melanoma. The BAP1 protein has a tumor suppressor function and the presence of the BAP1 protein can be shown using immunohistochemical staining. Our study showed that nuclear BAP1 immunostaining had a significant correlation with survival rate in our sample, and patients with a lack of nuclear BAP1 immunostaining should be considered high-risk and receive a close follow-up. This stain can be used as routine technique in the pathological examination of uveal melanoma. Abstract Even today, the mortality rate for uveal melanoma (UM) remains very high. In our research, we sought to determine which pathological and clinical features were correlated with the prognosis of UM. BAP1 (BRCA1-Associated Protein 1) gene mutation has been analyzed as one of the strongest predictors for metastasis in UM. The BAP1 gene codifies the BAP1 protein which has a tumor suppressor function. The presence of this protein can be determined by BAP1 immunohistochemical staining. Eighty-four uveal melanoma patients and forty enucleated eyeballs were examined. Metastasis was present in 24 patients. Nuclear BAP1 staining was low in 23 patients. The presence of a higher large basal diameter tumor (p < 0.001), tumor infiltrating lymphocytes (p = 0.020), and a lack of nuclear BAP1 immunostaining (p = 0.001) ocurred significantly more often in the metastatic group. Metastasis-free survival was lower in patients with low nuclear BAP1 staining (p = 0.003). In conclusion, to the best of our knowledge, this is the first time that BAP1 staining has been studied in uveal melanoma in a Spanish community. We believe that this technique should become routine in the pathological examination of uveal melanoma in order to allow adequate classification of patients and to establish an individual follow-up plan.
Collapse
Affiliation(s)
- Laura Tabuenca Del Barrio
- Complejo Hospitalario de Navarra, Department of Ophthalmology, Calle Irunlarrea s/n, 31008 Pam-plona, Spain; (A.Z.E.); (E.B.R.-M.)
- IdiSNA, Navarra Institute for Health Research, Calle Irunlarrea s/n, 31008 Pamplona, Spain; (I.M.d.E.E.); (A.G.-L.)
- Correspondence:
| | - Luiz Miguel Nova-Camacho
- Complejo Hospitalario de Navarra, Department of Pathology, Calle Irunlarrea s/n, 31008 Pamplo-na, Spain; (L.M.N.-C.); (A.C.I.)
| | - Alicia Zubicoa Enériz
- Complejo Hospitalario de Navarra, Department of Ophthalmology, Calle Irunlarrea s/n, 31008 Pam-plona, Spain; (A.Z.E.); (E.B.R.-M.)
- IdiSNA, Navarra Institute for Health Research, Calle Irunlarrea s/n, 31008 Pamplona, Spain; (I.M.d.E.E.); (A.G.-L.)
| | - Iñigo Martínez de Espronceda Ezquerro
- IdiSNA, Navarra Institute for Health Research, Calle Irunlarrea s/n, 31008 Pamplona, Spain; (I.M.d.E.E.); (A.G.-L.)
- Complejo Hospitalario de Navarra, Department of Dermatology, Calle Irunlarrea s/n, 31008 Pamplo-na, Spain
| | - Alicia Córdoba Iturriagagoitia
- Complejo Hospitalario de Navarra, Department of Pathology, Calle Irunlarrea s/n, 31008 Pamplo-na, Spain; (L.M.N.-C.); (A.C.I.)
| | - Enrique Borque Rodríguez-Maimón
- Complejo Hospitalario de Navarra, Department of Ophthalmology, Calle Irunlarrea s/n, 31008 Pam-plona, Spain; (A.Z.E.); (E.B.R.-M.)
| | - Alfredo García-Layana
- IdiSNA, Navarra Institute for Health Research, Calle Irunlarrea s/n, 31008 Pamplona, Spain; (I.M.d.E.E.); (A.G.-L.)
- Department of Ophthalmology, Clínica Universidad de Navarra, Avenida de Pio XII 36, 31008 Pam-plona, Spain
- Instituto de Salud Carlos III, 28029 Madrid, Spain
| |
Collapse
|
13
|
van Poppelen NM, de Bruyn DP, Bicer T, Verdijk R, Naus N, Mensink H, Paridaens D, de Klein A, Brosens E, Kiliҫ E. Genetics of Ocular Melanoma: Insights into Genetics, Inheritance and Testing. Int J Mol Sci 2020; 22:E336. [PMID: 33396957 PMCID: PMC7795687 DOI: 10.3390/ijms22010336] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/04/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022] Open
Abstract
Ocular melanoma consists of posterior uveal melanoma, iris melanoma and conjunctival melanoma. These malignancies derive from melanocytes in the uveal tract or conjunctiva. The genetic profiles of these different entities differ from each other. In uveal melanoma, GNAQ and GNA11 gene mutations are frequently found and prognosis is based on mutation status of BAP1, SF3B1 and EIF1AX genes. Iris melanoma, also originating from the uvea, has similarities to the genetic makeups of both posterior uveal melanoma (UM) and conjunctival melanoma since mutations in GNAQ and GNA11 are less common and genes involved in conjunctival melanoma such as BRAF have been described. The genetic spectrum of conjunctival melanoma, however, includes frequent mutations in the BRAF, NRAS and TERT promoter genes, which are found in cutaneous melanoma as well. The BRAF status of the tumor is not correlated to prognosis, whereas the TERT promoter gene mutations are. Clinical presentation, histopathological characteristics and copy number alterations are associated with survival in ocular melanoma. Tissue material is needed to classify ocular melanoma in the different subgroups, which creates a need for the use of noninvasive techniques to prognosticate patients who underwent eye preserving treatment.
Collapse
Affiliation(s)
- Natasha M. van Poppelen
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (A.d.K.); (E.B.)
| | - Daniël P. de Bruyn
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (A.d.K.); (E.B.)
| | - Tolga Bicer
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
- Department of Ophthalmology, University of Health Sciences Diskapi Training and Research Hospital, Ankara 06330, Turkey
| | - Rob Verdijk
- Department of Pathology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands;
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Nicole Naus
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
| | - Hanneke Mensink
- Department of Ophthalmic Oncology, The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands;
| | - Dion Paridaens
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
- Department of Ophthalmic Oncology, The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands;
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (A.d.K.); (E.B.)
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (A.d.K.); (E.B.)
| | - Emine Kiliҫ
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
| |
Collapse
|
14
|
Yu H, Cheng Y, Li W, Li Z, Wu P, Qiu S, Zeng B, Huang B. A novel lncRNA-miRNA-mRNA competitive endogenous RNA network for uveal melanoma prognosis constructed by weighted gene co-expression network analysis. Life Sci 2020; 260:118409. [PMID: 32926921 DOI: 10.1016/j.lfs.2020.118409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 02/07/2023]
Abstract
AIMS Uveal melanoma (UM) is the most common and aggressive intraocular tumor in adults, and long-term survival of UM patients remains poor. Abnormal competitive endogenous RNA (ceRNA) networks promote the initiation and progression of many tumors and may thus serve as useful prognostic indicators. Here, we do a comprehensive analysis of long non-coding RNA (lncRNA)-microRNA (miRNA)-mRNA ceRNA networks as prognostic markers for UM. MATERIALS AND METHODS The Cancer Genome Atlas UM dataset was used to identify survival-related mRNA and lncRNA modules through weighted gene co-expression network analysis (WGCNA). Prognostic miRNAs were identified using univariate Cox proportional hazard regression. We then used Cox and least absolute shrinkage and selection operator regression to screen for prognostic hub mRNAs and establish a hub ceRNA network. A nomogram of five hub mRNAs was constructed and Kaplan-Meier survival analysis performed. KEY FINDINGS Six mRNA modules were constructed, two of which involved 1490 mRNAs that significantly correlated with survival. Among the three lncRNA modules constructed, one involved 199 survival-related lncRNAs. Five hub prognostic mRNAs were identified and a hub ceRNA network constructed, consisting of six lncRNAs, four miRNAs, and five mRNAs, with high prognostic value. SIGNIFICANCE We describe a hub ceRNA network of survival-associated lncRNAs, miRNAs, and mRNA that may underlie a critical post-translational regulatory mechanism determining UM aggression. These hub RNAs may be valuable prognostic markers and therapeutic targets in UM.
Collapse
Affiliation(s)
- Huan Yu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Yaqi Cheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Weihua Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Zhiquan Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Peixin Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Sujuan Qiu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Baozhu Zeng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Bing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China.
| |
Collapse
|
15
|
Thornton S, Kalirai H, Aughton K, Coupland SE. Unpacking the genetic etiology of uveal melanoma. Expert Review of Ophthalmology 2020. [DOI: 10.1080/17469899.2020.1785872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Sophie Thornton
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Liverpool Clinical Laboratories, Liverpool University Hospitals Foundation Trusts, Liverpool, UK
| | - Helen Kalirai
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Liverpool Clinical Laboratories, Liverpool University Hospitals Foundation Trusts, Liverpool, UK
| | - Karen Aughton
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Sarah E. Coupland
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Liverpool Clinical Laboratories, Liverpool University Hospitals Foundation Trusts, Liverpool, UK
| |
Collapse
|
16
|
Abstract
Immunohistochemistry represents an indispensable complement to an epidemiology and morphology-driven approach to tumor diagnosis and site of origin assignment. This review reflects the state of my current practice, based on 15-years' experience in Pathology and a deep-dive into the literature, always striving to be better equipped to answer the age old questions, "What is it, and where is it from?" The tables and figures in this manuscript are the ones I "pull up on the computer" when I am teaching at the microscope and turn to myself when I am (frequently) stuck. This field is so exciting because I firmly believe that, through the application of next-generation immunohistochemistry, we can provide better answers than ever before. Specific topics covered in this review include (1) broad tumor classification and associated screening markers; (2) the role of cancer epidemiology in determining pretest probability; (3) broad-spectrum epithelial markers; (4) noncanonical expression of broad tumor class screening markers; (5) a morphologic pattern-based approach to poorly to undifferentiated malignant neoplasms; (6) a morphologic and immunohistochemical approach to define 4 main carcinoma types; (7) CK7/CK20 coordinate expression; (8) added value of semiquantitative immunohistochemical stain assessment; algorithmic immunohistochemical approaches to (9) "garden variety" adenocarcinomas presenting in the liver, (10) large polygonal cell adenocarcinomas, (11) the distinction of primary surface ovarian epithelial tumors with mucinous features from metastasis, (12) tumors presenting at alternative anatomic sites, (13) squamous cell carcinoma versus urothelial carcinoma, and neuroendocrine neoplasms, including (14) the distinction of pheochromocytoma/paraganglioma from well-differentiated neuroendocrine tumor, site of origin assignment in (15) well-differentiated neuroendocrine tumor and (16) poorly differentiated neuroendocrine carcinoma, and (17) the distinction of well-differentiated neuroendocrine tumor G3 from poorly differentiated neuroendocrine carcinoma; it concludes with (18) a discussion of diagnostic considerations in the broad-spectrum keratin/CD45/S-100-"triple-negative" neoplasm.
Collapse
|
17
|
See TR, Stålhammar G, Phillips S, Grossniklaus HE. BAP1 Immunoreactivity Correlates with Gene Expression Class in Uveal Melanoma. Ocul Oncol Pathol 2019; 6:129-137. [PMID: 32258021 DOI: 10.1159/000502550] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022] Open
Abstract
Background Uveal melanoma (UM) is the most common intraocular tumour in adults. Currently there are different tests available to determine the risk of UM for metastasis, among which include BRCA1-associated protein-1 (BAP1) immunohistochemistry (IHC) and gene expression profiling (GEP). BAP1 is a deubiquitylating enzyme (DUB) that has tumour suppressor activity, the loss of which therefore is associated with higher risk for tumour growth and metastasis. Objectives To compare and correlate the prognostic significance of BAP1-IHC staining patterns and GEP in the prediction of UM's risk for metastasis. Methods This is a retrospective chart review with prospective follow-up of patients with primary UM who underwent enucleation from the year 2008 to 2018. Clinical history, histopathologic findings, GEP classification, BAP1-IHC of the formalin-fixed paraffin-embedded tissues, and follow-up data for metastasis were collected and statistically analysed. Results A total of 30 enucleated eyes with UM were included in the study. All class 1a tumours had high nuclear BAP1 expression and all class 2 had low nuclear BAP1 expression. Fifty percent of the class 1b tumours had low nuclear BAP1 expression. Among the tumours with low nuclear BAP1 expression, 68% developed metastasis, while 9% developed metastasis among high nuclear expression. Fifty-five percent developed metastasis in tumours with high cytoplasmic expression and 42% for low cytoplasmic expression. Predictive values for metastasis (positive predictive value, negative predictive value) are as follows: (1) nuclear BAP1-IHC (68%, 91%), (2) cytoplasmic BAP1-IHC (55%, 58%), and (3) GEP (73%, 80%). Nuclear BAP1-IHC and GEP had the same accuracy rate of 77% and cytoplasmic BAP1-IHC had an accuracy of 57%. Conclusion Low nuclear BAP1-IHC strongly correlates with GEP class 2 and was equally accurate in the prediction of metastasis.
Collapse
Affiliation(s)
- Thonnie Rose See
- Department of Ophthalmology and Pathology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Gustav Stålhammar
- Department of Ophthalmology and Pathology, Emory University School of Medicine, Atlanta, Georgia, USA.,Oncology and Pathology Service, St. Erik Eye Hospital, Stockholm, Sweden.,Department of Clinical Neurosciences, Karolinska Institutet, Stockholm, Sweden
| | - Stephen Phillips
- Department of Ophthalmology and Pathology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Hans E Grossniklaus
- Department of Ophthalmology and Pathology, Emory University School of Medicine, Atlanta, Georgia, USA
| |
Collapse
|
18
|
Xue M, Shang J, Chen B, Yang Z, Song Q, Sun X, Chen J, Yang J. Identification of Prognostic Signatures for Predicting the Overall Survival of Uveal Melanoma Patients. J Cancer 2019; 10:4921-4931. [PMID: 31598164 PMCID: PMC6775505 DOI: 10.7150/jca.30618] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 07/20/2019] [Indexed: 12/28/2022] Open
Abstract
Uveal melanoma (UM) is an aggressive cancer which has a high percentage of metastasis and with a poor prognosis. Identifying the potential prognostic markers of uveal melanoma may provide information for early detection of metastasis and treatment. In this work, we analyzed 80 uveal melanoma samples from The Cancer Genome Atlas (TCGA). We developed an 18-gene signature which can significantly predict the prognosis of UM patients. Firstly, we performed a univariate Cox regression analysis to identify significantly prognostic genes in uveal melanoma (P<0.01). Then the glmnet Cox analysis was used to generate a powerful prognostic gene model. Further, we established a risk score formula for every patient based on the 18-gene prognostic model with multivariate Cox regression. We stratified patients into high- and low-risk subtypes with median risk score and found that patients in high-risk group had worse prognosis than patients in low-risk group. Multivariate Cox regression analysis demonstrated that 18-gene model risk score was independent of clinical prognostic factors. We identified four genes whose mutations were closely to UM patients' prognosis or risk score. We also explored the relationship between copy number variation and risk score and found that high risk group showed more chromosome aberrations than low risk group. Gene Set Enrichment Analysis (GSEA) analysis showed that the different biological pathways and functions between low and high risk group. In summary, our findings constructed an 18-gene signature for estimating overall survival (OS) of UM. Patients were categorized into two subtypes based on the risk score and we found that high risk group showed more chromosome aberrations than low risk group.
Collapse
Affiliation(s)
- Meijuan Xue
- Department of Dermatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Binglin Chen
- Department of Dermatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zuyi Yang
- Department of Hematology, The First Affiliated Hospital of Soochow University, Shizijie Campus: NO.188, Shizijie Road, Suzhou 215006, P. R. China
| | - Qian Song
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, China
| | - Xiaoyan Sun
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jianing Chen
- Department of Hematology, The First Affiliated Hospital of Soochow University, Shizijie Campus: NO.188, Shizijie Road, Suzhou 215006, P. R. China
| | - Ji Yang
- Department of Dermatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| |
Collapse
|
19
|
Anbunathan H, Verstraten R, Singh AD, Harbour JW, Bowcock AM. Integrative Copy Number Analysis of Uveal Melanoma Reveals Novel Candidate Genes Involved in Tumorigenesis Including a Tumor Suppressor Role for PHF10/BAF45a. Clin Cancer Res 2019; 25:5156-5166. [PMID: 31227497 DOI: 10.1158/1078-0432.ccr-18-3052] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 04/23/2019] [Accepted: 06/17/2019] [Indexed: 12/18/2022]
Abstract
PURPOSE Uveal melanoma is a primary malignancy of the eye with oncogenic mutations in GNAQ, GNA11, or CYSLTR2, and additional mutations in BAP1 (usually associated with LOH of Chr 3), SF3B1, or EIF1AX. There are other characteristic chromosomal alterations, but their significance is not clear. EXPERIMENTAL DESIGN To investigate genes driving chromosomal alterations, we integrated copy number, transcriptome, and mutation data from three cohorts and followed up key findings. RESULTS We observed significant enrichment of transcripts on chromosomes 1p, 3, 6, 8, and 16q and identified seven shared focal copy number alterations (FCNAs) on Chr 1p36, 2q37, 3, 6q25, 6q27, and 8q24. Integrated analyses revealed clusters of genes in focal copy number regions whose expression was associated with metastasis and worse overall survival. This included genes from Chr 1p36, 3p21, and 8q24.3. At Chr 6q27, we identified two tumors with homozygous deletion of PHF10/BAF45a and one with a frameshift mutation with concomitant loss of the wild-type allele. Downregulation of PHF10 in uveal melanoma cell lines and tumors altered a number of biological pathways including development and adhesion. These findings provide support for a role for PHF10 as a novel tumor suppressor at Chr 6q27. CONCLUSIONS Integration of copy number, transcriptome, and mutation data revealed novel candidate genes playing a role in uveal melanoma pathogenesis and a potential tumor suppressor role for PHF10.
Collapse
Affiliation(s)
- Hima Anbunathan
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Ruth Verstraten
- National Heart and Lung Institute, Imperial College, London, United Kingdom.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Arun D Singh
- Department of Ophthalmic Oncology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio
| | - J William Harbour
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Anne M Bowcock
- National Heart and Lung Institute, Imperial College, London, United Kingdom. .,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Departments of Dermatology and Genetics & Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| |
Collapse
|
20
|
Abstract
One of the most attractive cancer-related genes under investigation is BAP1. Reasons of this growing interest are related to the wide spectrum of pathways directly or indirectly modulated by this gene and shared by several solid tumors. Programmed cell-death, cell metabolisms, immune cells development, ferroptosis and defects in DNA damage response are only some of the multitude of processes depending on BAP1. Loss of this gene seems to occur in different times of tumor history. Moreover, times of BAP1 loss strongly diverge among primary tumors suggesting the presence of several and different triggering factors. Regardless of when it happens, BAP1 loss usually results in prognosis worsening and in the acquisition of more aggressive clinical features by cancer cells.
Collapse
Affiliation(s)
| | - Giorgio Frega
- Oncology Unit, Department of Experimental, Diagnostic & Specialty Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Matteo Santoni
- Department of Oncology, Macerata Hospital, Macerata, Italy
| | - Lidia Gatto
- Oncology Unit, Department of Experimental, Diagnostic & Specialty Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Michelangelo Fiorentino
- Pathology Service, Addarii Institute of Oncology, S-Orsola-Malpighi Hospital, Bologna, Italy
| | - Rodolfo Montironi
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, Ancona, Italy
| | | | - Giovanni Brandi
- Oncology Unit, Department of Experimental, Diagnostic & Specialty Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | | |
Collapse
|
21
|
Li Y, Yang X, Yang J, Wang H, Wei W. An 11-gene-based prognostic signature for uveal melanoma metastasis based on gene expression and DNA methylation profile. J Cell Biochem 2019; 120:8630-8639. [PMID: 30556166 DOI: 10.1002/jcb.28151] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/05/2018] [Indexed: 01/24/2023]
Abstract
Uveal melanoma (UM) is the most common intraocular tumor worldwide. We proposed to identify a vital gene signature that has prognostic value for UM metastasis. For this purpose, we obtained a published DNA methylation and gene expression data set associated with UM from the Gene Expression Omnibus. The genes whose aberrant expression significantly associated with UM patients' metastasis-free survival (MFS) were identified by applying a univariate Cox proportional hazards model to the gene expression data set followed by a robust likelihood-based survival analysis to screen the optimal prognostic gene signatures (PGS). A formula for calculating the risk score that represents UM metastasis risk was constructed by including the PGSs' expression values weighted by their regression coefficients, which were obtained by a multivariate Cox regression analysis. As a result, aberrant expression of 2884 genes were found to be significantly associated with UM patients' MFS, which were referred to as MFSGs, and 11 out of those MFSGs, GJC1, TCEA1, MFSD3, FAF2, TLCD1, GPAA1, CYC1, ASAP1, JPH1, LDB3, and KDELR3, were identified as PGSs through which we could accurately separate UM samples with shorter MFS from those with longer MFS. By combining the DNA methylation data set and MFSGs, we further identified 265 MFSGs, which contained CpG sites that significantly hyper- or hypo-methylated in UM samples compared with control samples. Functional enrichment analysis and pathway crosstalk analysis of those genes indicated significant enrichment of cancer-related pathways. In conclusion, we identified an 11-gene-based prognostic signature and several gene biomarkers for UM metastasis, which should be helpful for selecting an appropriate treatment method for specific patients with UM.
Collapse
Affiliation(s)
- Yang Li
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xuan Yang
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jingyan Yang
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Heng Wang
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wenbin Wei
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| |
Collapse
|