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Kontogianni G, Voutetakis K, Piroti G, Kypreou K, Stefanaki I, Vlachavas EI, Pilalis E, Stratigos A, Chatziioannou A, Papadodima O. A Comprehensive Analysis of Cutaneous Melanoma Patients in Greece Based on Multi-Omic Data. Cancers (Basel) 2023; 15:cancers15030815. [PMID: 36765773 PMCID: PMC9913631 DOI: 10.3390/cancers15030815] [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: 12/13/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Abstract
Cutaneous melanoma (CM) is the most aggressive type of skin cancer, and it is characterised by high mutational load and heterogeneity. In this study, we aimed to analyse the genomic and transcriptomic profile of primary melanomas from forty-six Formalin-Fixed, Paraffin-Embedded (FFPE) tissues from Greek patients. Molecular analysis for both germline and somatic variations was performed in genomic DNA from peripheral blood and melanoma samples, respectively, exploiting whole exome and targeted sequencing, and transcriptomic analysis. Detailed clinicopathological data were also included in our analyses and previously reported associations with specific mutations were recognised. Most analysed samples (43/46) were found to harbour at least one clinically actionable somatic variant. A subset of samples was profiled at the transcriptomic level, and it was shown that specific melanoma phenotypic states could be inferred from bulk RNA isolated from FFPE primary melanoma tissue. Integrative bioinformatics analyses, including variant prioritisation, differential gene expression analysis, and functional and gene set enrichment analysis by group and per sample, were conducted and molecular circuits that are implicated in melanoma cell programmes were highlighted. Integration of mutational and transcriptomic data in CM characterisation could shed light on genes and pathways that support the maintenance of phenotypic states encrypted into heterogeneous primary tumours.
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Affiliation(s)
- Georgia Kontogianni
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
- Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | | | - Georgia Piroti
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Katerina Kypreou
- 1st Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, 16121 Athens, Greece
| | - Irene Stefanaki
- 1st Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, 16121 Athens, Greece
| | | | | | - Alexander Stratigos
- 1st Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, 16121 Athens, Greece
| | - Aristotelis Chatziioannou
- Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- e-NIOS Applications Private Company, 17671 Kallithea, Greece
- Correspondence: (A.C.); (O.P.); Tel.: +30-210-727-3721 (A.C. & O.P.)
| | - Olga Papadodima
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
- Correspondence: (A.C.); (O.P.); Tel.: +30-210-727-3721 (A.C. & O.P.)
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Maglogiannis I, Kontogianni G, Papadodima O, Karanikas H, Billiris A, Chatziioannou A. An Integrated Platform for Skin Cancer Heterogenous and Multilayered Data Management. J Med Syst 2021; 45:10. [PMID: 33404959 DOI: 10.1007/s10916-020-01679-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 11/23/2020] [Indexed: 01/22/2023]
Abstract
Electronic health record (EHR) systems improve health care services by allowing the combination of health data with clinical decision support features and clinical image analyses. This study presents a modular and distributed platform that is able to integrate and accommodate heterogeneous, multidimensional (omics, histological images and clinical) data for the multi-angled portrayal and management of skin cancer patients. The proposed design offers a layered analytical framework as an expansion of current EHR systems, which can integrate high-volume molecular -omics data, imaging data, as well as relevant clinical observations. We present a case study in the field of dermatology, where we attempt to combine the multilayered information for the early detection and characterization of melanoma. The specific architecture aspires to lower the barrier for the introduction of personalized therapeutic approaches, towards precision medicine. The paper describes the technical issues of implementation, along with an initial evaluation of the system and discussion.
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Affiliation(s)
- Ilias Maglogiannis
- Department of Digital Systems, University of Piraeus, 126 Grigoriou Lambraki, 18534, Piraeus, Greece.
| | - Georgia Kontogianni
- Department of Digital Systems, University of Piraeus, 126 Grigoriou Lambraki, 18534, Piraeus, Greece
- National Hellenic Research Foundation, 48 Vassileos Constantinou Ave, 11635, Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Olga Papadodima
- National Hellenic Research Foundation, 48 Vassileos Constantinou Ave, 11635, Athens, Greece
| | | | | | - Aristotelis Chatziioannou
- National Hellenic Research Foundation, 48 Vassileos Constantinou Ave, 11635, Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
- e-NIOS Applications Private Company, 17671, Kallithea, Greece
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3
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Loss-of-function variants in FSIP1 identified by targeted sequencing are associated with one particular subtype of mucosal melanoma. Gene 2020; 759:144964. [PMID: 32717308 DOI: 10.1016/j.gene.2020.144964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/04/2020] [Accepted: 07/13/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Mucosal melanoma is a tumor caused by the malignant transformation of pigment-producing cells and can arise from any mucosal tissue where melanocytes are present. Due to its rarity, the mucosal melanoma subtype is poorly described, and its genetic characteristics are infrequently studied. The discovery or confirmation of new mucosal melanoma susceptibility genes will provide important insights for the study of its pathogenesis. MATERIALS AND METHODS We performed deep targeted sequencing of 100 previously reported melanoma-related genes in 39 mucosal melanoma samples and a gene-level loss-of-function (LOF) variant enrichment analysis for mucosal melanoma from different incidence sites. RESULTS We detected 7,589 variants in these samples, and 484 were LOF variants (gain or loss of a stop codon, missense, and splice site). Four different gene-level enrichment analyses revealed that FSIP1 (fibrous sheath interacting protein 1) is a susceptibility gene for oral mucosal melanoma (OR = 0.33, PChi = 4.05 × 10-2, Pburden = 3.06 × 10-2, Pskat = 3.01 × 10-2, Pskato = 3.01 × 10-2), whereas the different methods did not detect a significant susceptibility gene for the other subtypes. CONCLUSIONS In our study, a susceptibility gene for oral mucosal melanoma was confirmed in a Chinese Han population, and these findings contribute to a better genetic understanding of mucosal melanoma of different subtypes.
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Wuthrick EJ, Chablani P. Do Not Forget About the Importance of Loco-Regional Therapy in Melanoma Management. Semin Radiat Oncol 2019; 29:166-170. [PMID: 30827455 DOI: 10.1016/j.semradonc.2018.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Immunotherapy agents have significantly changed the landscape of melanoma treatment over the past decade. Paradigm shifts in treatment require reanalysis of the treatment algorithms in melanoma. Despite surgical excision, certain high risk patients with desmoplastic melanoma remain at high risk for local recurrence and retrospective data suggests improvement in local control with adjuvant radiation therapy. Likewise, despite surgical excision and effective systemic therapy agents, patients with extracapsular extension and other high risk features are at substantial risk of nodal basin (regional) recurrence. Adjuvant radiation therapy has been demonstrated to reduce the local recurrence risk. Despite these benefits, adjuvant radiation therapy in melanoma remains controversial in part because its use has not been definitively demonstrated to improve overall or disease-free survival in a randomized prospective study.
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Affiliation(s)
- Evan J Wuthrick
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL.
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5
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Vescovi R, Monti M, Moratto D, Paolini L, Consoli F, Benerini L, Melocchi L, Calza S, Chiudinelli M, Rossi G, Bugatti M, Maio M, Fonsatti E, Farisoglio C, Simbolo M, Almici C, Verardi R, Scarpa A, Bergese P, Manganoni A, Facchetti F, Vermi W. Collapse of the Plasmacytoid Dendritic Cell Compartment in Advanced Cutaneous Melanomas by Components of the Tumor Cell Secretome. Cancer Immunol Res 2019; 7:12-28. [PMID: 30401679 DOI: 10.1158/2326-6066.cir-18-0141] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/16/2018] [Accepted: 11/01/2018] [Indexed: 11/16/2022]
Abstract
Melanoma is an immunogenic neoplasm infiltrated by T cells, although these adaptive T cells usually fail to eradicate the tumor. Plasmacytoid dendritic cells (PDCs) are potent regulators of the adaptive immune response and can eliminate melanoma cells via TLR-mediated effector functions. The PDC compartment is maintained by progressively restricted bone marrow progenitors. Terminally differentiated PDCs exit the bone marrow into the circulation, then home to lymph nodes and inflamed peripheral tissues. Infiltration by PDCs is documented in various cancers. However, their role within the melanoma immune contexture is not completely known. We found that in locoregional primary cutaneous melanoma (PCM), PDC infiltration was heterogeneous, occurred early, and was recurrently localized at the invasive margin, the site where PDCs interact with CD8+ T cells. A reduced PDC density was coupled with an increased Breslow thickness and somatic mutations at the NRAS p.Q61 codon. Compared with what was seen in PCM, high numbers of PDCs were found in regional lymph nodes, as also identified by in silico analysis. In contrast, in metastatic melanoma patients, PDCs were mostly absent in the tumor tissues and were significantly reduced in the circulation, particularly in the advanced M1c group. Exposure of circulating PDCs to melanoma cell supernatant (SN-mel) depleted of extracellular vesicles resulted in significant PDC death. SN-mel exposure also resulted in a defect of PDC differentiation from CD34+ progenitors. These findings indicate that soluble components released by melanoma cells support the collapse of the PDC compartment, with clinical implications for refining TLR agonist-based trials.
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Affiliation(s)
- Raffaella Vescovi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Matilde Monti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Daniele Moratto
- Laboratory of Genetic Disorders of Childhood, "Angelo Nocivelli" Institute for Molecular Medicine, Spedali Civili, Brescia, Italy
| | - Lucia Paolini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | | | - Luisa Benerini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Laura Melocchi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Stefano Calza
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Mariella Chiudinelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Giulio Rossi
- Pathology Unit, Azienda Romagna, Hospital Santa Maria delle Croci, Ravenna, Italy
| | - Mattia Bugatti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Michele Maio
- Medical Oncology and Immunotherapy, University Hospital of Siena, Istituto Toscano Tumori, Siena, Italy
| | - Ester Fonsatti
- Medical Oncology and Immunotherapy, University Hospital of Siena, Istituto Toscano Tumori, Siena, Italy
| | | | - Michele Simbolo
- ARC-Net Research Centre and Department of Diagnostics and Public Health, Section of Pathology, Università degli Studi di Verona, Verona, Italy
| | - Camillo Almici
- Department of Transfusion Medicine, Laboratory for Stem Cells Manipulation and Cryopreservation, ASST Spedali Civili, Brescia, Italy
| | - Rosanna Verardi
- Department of Transfusion Medicine, Laboratory for Stem Cells Manipulation and Cryopreservation, ASST Spedali Civili, Brescia, Italy
| | - Aldo Scarpa
- ARC-Net Research Centre and Department of Diagnostics and Public Health, Section of Pathology, Università degli Studi di Verona, Verona, Italy
| | - Paolo Bergese
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | | | - Fabio Facchetti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - William Vermi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
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Ji K, Zhang J, Fan R, Yang S, Dong C. Differential expression of lncRNAs and predicted target genes in normal mouse melanocytes and B16 cells. Exp Dermatol 2018; 27:1230-1236. [DOI: 10.1111/exd.13768] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/26/2018] [Accepted: 08/08/2018] [Indexed: 01/23/2023]
Affiliation(s)
- Kaiyuan Ji
- College of Animal Science and Veterinary Medicine; Shanxi Agricultural University; Taigu China
| | - Junzhen Zhang
- College of Animal Science and Veterinary Medicine; Shanxi Agricultural University; Taigu China
| | - Ruiwen Fan
- College of Animal Science and Veterinary Medicine; Shanxi Agricultural University; Taigu China
| | - Shanshan Yang
- College of Animal Science and Veterinary Medicine; Shanxi Agricultural University; Taigu China
| | - Changsheng Dong
- College of Animal Science and Veterinary Medicine; Shanxi Agricultural University; Taigu China
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7
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Dissecting the Mutational Landscape of Cutaneous Melanoma: An Omic Analysis Based on Patients from Greece. Cancers (Basel) 2018; 10:cancers10040096. [PMID: 29596374 PMCID: PMC5923351 DOI: 10.3390/cancers10040096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/20/2018] [Accepted: 03/27/2018] [Indexed: 12/21/2022] Open
Abstract
Melanoma is a lethal type of skin cancer, unless it is diagnosed early. Formalin-fixed, paraffin-embedded (FFPE) tissue is a valuable source for molecular assays after diagnostic examination, but isolated nucleic acids often suffer from degradation. Here, for the first time, we examine primary melanomas from Greek patients, using whole exome sequencing, so as to derive their mutational profile. Application of a bioinformatic framework revealed a total of 10,030 somatic mutations. Regarding the genes containing putative protein-altering mutations, 73 were common in at least three patients. Sixty-five of these 73 top common genes have been previously identified in melanoma cases. Biological processes related to melanoma were affected by varied genes in each patient, suggesting differences in the components of a pathway possibly contributing to pathogenesis. We performed a multi-level analysis highlighting a short list of candidate genes with a probable causative role in melanoma.
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8
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Pampena MB, Barrio MM, Juliá EP, Blanco PA, von Euw EM, Mordoh J, Levy EM. Early Events of the Reaction Elicited by CSF-470 Melanoma Vaccine Plus Adjuvants: An In Vitro Analysis of Immune Recruitment and Cytokine Release. Front Immunol 2017; 8:1342. [PMID: 29109725 PMCID: PMC5660290 DOI: 10.3389/fimmu.2017.01342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/03/2017] [Indexed: 11/13/2022] Open
Abstract
In a previous work, we showed that CSF-470 vaccine plus bacillus Calmette–Guerin (BCG) and granulocyte macrophage colony-stimulating factor (GM-CSF) as adjuvants resulted in a significant benefit in the distant metastasis-free survival when comparing vaccinated vs. IFN-α2b-treated high-risk cutaneous melanoma patients in a Phase II study. Immune monitoring demonstrated an increase in anti-tumor innate and adaptive immunities of vaccinated patients, with a striking increase in IFN-γ secreting lymphocytes specific for melanoma antigens (Ags). In an effort to dissect the first steps of the immune response elicited by CSF-470 vaccine plus adjuvants, we evaluated, in an in vitro model, leukocyte migration, cytokine production, and monocyte phagocytosis of vaccine cells. Our results demonstrate that leukocytes recruitment, mostly from the innate immune system, is an early event after CSF-470 vaccine plus BCG plus GM-CSF interaction with immune cells, possibly explained by the high expression of CCL2/MCP-1 and other chemokines by vaccine cells. Early release of TNF-α and IL-1β pro-inflammatory cytokines and efficient tumor Ags phagocytosis by monocytes take place and would probably create a favorable context for Ag processing and presentation. Although the presence of the vaccine cells hampered cytokines production stimulated by BCG in a mechanism partially mediated by TGF-β and IL-10, still significant levels of TNF-α and IL-1β could be detected. Thus, BCG was required to induce local inflammation in the presence of CSF-470 vaccine cells.
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Affiliation(s)
- María B Pampena
- Centro de Investigaciones Oncológicas-Fundación Cáncer, Buenos Aires, Argentina
| | - María M Barrio
- Centro de Investigaciones Oncológicas-Fundación Cáncer, Buenos Aires, Argentina
| | - Estefanía P Juliá
- Centro de Investigaciones Oncológicas-Fundación Cáncer, Buenos Aires, Argentina
| | - Paula A Blanco
- Centro de Investigaciones Oncológicas-Fundación Cáncer, Buenos Aires, Argentina
| | - Erika M von Euw
- UCLA JCCC-Translational Oncology Research Labs, Los Angeles, CA, United States
| | - José Mordoh
- Centro de Investigaciones Oncológicas-Fundación Cáncer, Buenos Aires, Argentina.,Instituto Médico Especializado Alexander Fleming, Buenos Aires, Argentina.,Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
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9
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Stark MS, Bonazzi VF. Gene Expression Array Analysis to Identify Candidate Tumor Suppressor Genes in Melanoma. Methods Mol Biol 2017. [PMID: 28770491 DOI: 10.1007/7651_2017_54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Melanoma is a complex multifactorial disease; therefore, a combination of various approaches is necessary to girt all aspects of its biology and identify the many different genes and factors involved in its etiology.Epigenetic regulation of tumor suppressor genes (TSGs) has been shown to play a central role in melanomagenesis. Here, we describe a new pipeline based on an integrative and comparative analysis of several array platform, post-demethylation treatment expression data, methylation array, and constitutive mRNA expression analysis to identify novel TSGs frequently methylated in melanoma.
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Affiliation(s)
- Mitchell S Stark
- Dermatology Research Centre, The University of Queensland, Woolloongabba, QLD, Australia
| | - Vanessa F Bonazzi
- Endometrial Cancer Laboratory, Translational Research Institute, Queensland University of Technology, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
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10
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Phan NN, Wang CY, Chen CF, Sun Z, Lai MD, Lin YC. Voltage-gated calcium channels: Novel targets for cancer therapy. Oncol Lett 2017; 14:2059-2074. [PMID: 28781648 PMCID: PMC5530219 DOI: 10.3892/ol.2017.6457] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 04/13/2017] [Indexed: 01/11/2023] Open
Abstract
Voltage-gated calcium channels (VGCCs) comprise five subtypes: The L-type; R-type; N-type; P/Q-type; and T-type, which are encoded by α1 subunit genes. Calcium ion channels also have confirmed roles in cellular functions, including mitogenesis, proliferation, differentiation, apoptosis and metastasis. An association between VGCCs, a reduction in proliferation and an increase in apoptosis in prostate cancer cells has also been reported. Therefore, in the present study, the online clinical database Oncomine was used to identify the alterations in the mRNA expression level of VGCCs in 19 cancer subtypes. Overall, VGCC family genes exhibited under-expression in numerous types of cancer, including brain, breast, kidney and lung cancers. Notably, the majority of VGCC family members (CACNA1C, CACNA1D, CACNA1A, CACNA1B, CACNA1E, CACNA1H and CACNA1I) exhibited low expression in brain tumors, with mRNA expression levels in the top 1–9% of downregulated gene rankings. A total of 5 VGCC family members (CACNA1A, CACNA1B, CACNA1E, CACNA1G and CACNA1I) were under-expressed in breast cancer, with a gene ranking in the top 1–10% of the low-expressed genes compared with normal tissue. In kidney and lung cancers, CACNA1S, CACNA1C, CACNA1D, CACNA1A and CACNA1H exhibited low expression, with gene rankings in the top 1–8% of downregulated genes. In conclusion, the present findings may contribute to the development of new cancer treatment approaches by identifying target genes involved in specific types of cancer.
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Affiliation(s)
- Nam Nhut Phan
- Faculty of Applied Sciences, Ton Duc Thang University, Tan Phong Ward, Ho Chi Minh 700000, Vietnam
| | - Chih-Yang Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, R.O.C.,Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, R.O.C.,Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Chien-Fu Chen
- School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung 84001, Taiwan, R.O.C
| | - Zhengda Sun
- Department of Radiology, University of California, San Francisco, CA 94143, USA
| | - Ming-Derg Lai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, R.O.C.,Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, R.O.C
| | - Yen-Chang Lin
- Graduate Institute of Biotechnology, Chinese Culture University, Taipei 1114, Taiwan, R.O.C
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11
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Shim JH, Shin HT, Park J, Park JH, Lee JH, Yang JM, Kim DH, Jang KT, Lee DY. Mutational profiling of acral melanomas in Korean populations. Exp Dermatol 2017; 26:883-888. [DOI: 10.1111/exd.13321] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Joon Ho Shim
- Department of Dermatology; Samsung Medical Center; Sungkyunkwan University School of Medicine; Seoul Korea
- Samsung Genome Institute; Samsung Medical Center; Seoul Korea
| | - Hyun-Tae Shin
- Samsung Genome Institute; Samsung Medical Center; Seoul Korea
| | - Jiho Park
- Department of Health Sciences and Technology; Samsung Advanced Institute for Health Sciences and Technology; Sungkyunkwan University; Seoul Korea
| | - Ji-Hye Park
- Department of Dermatology; Samsung Medical Center; Sungkyunkwan University School of Medicine; Seoul Korea
| | - Jong-Hee Lee
- Department of Dermatology; Samsung Medical Center; Sungkyunkwan University School of Medicine; Seoul Korea
- Department of Medical Device Management & Research; Samsung Advanced Institute for Health Sciences and Technology; Sungkyunkwan University; Seoul Korea
| | - Jun-Mo Yang
- Department of Dermatology; Samsung Medical Center; Sungkyunkwan University School of Medicine; Seoul Korea
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology; Samsung Biomedical Research Institute; Sungkyunkwan University School of Medicine; Suwon Korea
| | - Kee-Taek Jang
- Department of Pathology; Samsung Medical Center; Sungkyunkwan University School of Medicine; Seoul Korea
| | - Dong-Youn Lee
- Department of Dermatology; Samsung Medical Center; Sungkyunkwan University School of Medicine; Seoul Korea
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12
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Non-reproducible sequence artifacts in FFPE tissue: an experience report. J Cancer Res Clin Oncol 2017; 143:1199-1207. [PMID: 28314930 DOI: 10.1007/s00432-017-2399-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Recent advances in sequencing technologies supported the development of molecularly targeted therapy in cancer patients. Thus, genomic analyses are becoming a routine part in clinical practice and accurate detection of actionable mutations is essential to assist diagnosis and therapy choice. However, this is often challenging due to major problems associated with DNA from formalin-fixed paraffin-embedded tissue which is usually the primary source for genetic testing. OBJECTIVES Here we want to share our experience regarding major problems associated with FFPE DNA used for PCR-based sequencing as illustrated by the mutational analysis of ERBB4 in melanoma. We want to focus on two major problems including extensive DNA fragmentation and hydrolytic deamination as source of non-reproducible sequence artifacts. Further, we provide potential explanations and possible strategies to minimize these difficulties and improve the detection of targetable mutations. METHODS Genomic DNA from formalin-fixed paraffin-embedded tumor samples was isolated followed by PCR amplification, Sanger sequencing and statistical analysis. RESULTS Analysis of Sanger sequencing data revealed a total of 46 ERBB4 mutations in 27 of 96 samples including the identification of 11 mutations at three previously unknown mutational hotspots. Unfortunately, we were not able to confirm any assumed hotspot mutation within repeated sequencing of relevant amplicons suggesting the detection of sequence artifacts most likely caused by DNA lesions associated with FFPE tissues. CONCLUSION Since DNA from FFPE tissue is usually the primary source for mutational analyses, appropriate measures must be implemented in the workflow to assess DNA damage in formalin-fixed tissue to ensure accurate detection of actionable mutations and minimize the occurrence of sequence artifacts.
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13
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Lineage-specific roles of the cytoplasmic polyadenylation factor CPEB4 in the regulation of melanoma drivers. Nat Commun 2016; 7:13418. [PMID: 27857118 PMCID: PMC5120223 DOI: 10.1038/ncomms13418] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 10/03/2016] [Indexed: 02/07/2023] Open
Abstract
Nuclear 3'-end-polyadenylation is essential for the transport, stability and translation of virtually all eukaryotic mRNAs. Poly(A) tail extension can also occur in the cytoplasm, but the transcripts involved are incompletely understood, particularly in cancer. Here we identify a lineage-specific requirement of the cytoplasmic polyadenylation binding protein 4 (CPEB4) in malignant melanoma. CPEB4 is upregulated early in melanoma progression, as defined by computational and histological analyses. Melanoma cells are distinct from other tumour cell types in their dependency on CPEB4, not only to prevent mitotic aberrations, but to progress through G1/S cell cycle checkpoints. RNA immunoprecipitation, sequencing of bound transcripts and poly(A) length tests link the melanoma-specific functions of CPEB4 to signalling hubs specifically enriched in this disease. Essential in these CPEB4-controlled networks are the melanoma drivers MITF and RAB7A, a feature validated in clinical biopsies. These results provide new mechanistic links between cytoplasmic polyadenylation and lineage specification in melanoma. Cytoplasmic polyadenylated transcripts have been poorly characterized, particularly in cancer. Here the authors identify a lineage-specific requirement of the cytoplasmic polyadenylation binding protein 4 (CPEB4) in malignant melanoma and show that it controls melanoma drivers MITF and RAB27A.
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14
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Wurth L, Papasaikas P, Olmeda D, Bley N, Calvo GT, Guerrero S, Cerezo-Wallis D, Martinez-Useros J, García-Fernández M, Hüttelmaier S, Soengas MS, Gebauer F. UNR/CSDE1 Drives a Post-transcriptional Program to Promote Melanoma Invasion and Metastasis. Cancer Cell 2016; 30:694-707. [PMID: 27908735 DOI: 10.1016/j.ccell.2016.10.004] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 06/13/2016] [Accepted: 10/03/2016] [Indexed: 12/11/2022]
Abstract
RNA binding proteins (RBPs) modulate cancer progression through poorly understood mechanisms. Here we show that the RBP UNR/CSDE1 is overexpressed in melanoma tumors and promotes invasion and metastasis. iCLIP sequencing, RNA sequencing, and ribosome profiling combined with in silico studies unveiled sets of pro-metastatic factors coordinately regulated by UNR as part of RNA regulons. In addition to RNA steady-state levels, UNR was found to control many of its targets at the level of translation elongation/termination. Key pro-oncogenic targets of UNR included VIM and RAC1, as validated by loss- and gain-of-function studies. Our results identify UNR as an oncogenic modulator of melanoma progression, unravel the underlying molecular mechanisms, and identify potential targets for this therapeutically challenging malignancy.
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Affiliation(s)
- Laurence Wurth
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Panagiotis Papasaikas
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - David Olmeda
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Nadine Bley
- Section Molecular Cell Biology, Institute of Molecular Medicine (IMM), Martin-Luther-University (MLU), 06120 Halle, Germany
| | - Guadalupe T Calvo
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Santiago Guerrero
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Daniela Cerezo-Wallis
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Javier Martinez-Useros
- Translational Oncology Division, Oncohealth Institute - Health Research Institute - University Hospital "Fundacion Jimenez Diaz", 28040 Madrid, Spain
| | - María García-Fernández
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Stefan Hüttelmaier
- Section Molecular Cell Biology, Institute of Molecular Medicine (IMM), Martin-Luther-University (MLU), 06120 Halle, Germany
| | - Maria S Soengas
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
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15
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RAB7 counteracts PI3K-driven macropinocytosis activated at early stages of melanoma development. Oncotarget 2016; 6:11848-62. [PMID: 26008978 PMCID: PMC4494909 DOI: 10.18632/oncotarget.4055] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 04/20/2015] [Indexed: 12/28/2022] Open
Abstract
Derailed endolysosomal trafficking is emerging as a widespread feature of aggressive neoplasms. However, the oncogenic signals that alter membrane homeostasis and their specific contribution to cancer progression remain unclear. Understanding the upstream drivers and downstream regulators of aberrant vesicular trafficking is distinctly important in melanoma. This disease is notorious for its inter- and intra-tumoral heterogeneity. Nevertheless, melanomas uniformly overexpress a cluster of endolysosomal genes, being particularly addicted to the membrane traffic regulator RAB7. Still, the underlying mechanisms and temporal determinants of this dependency have yet to be defined. Here we addressed these questions by combining electron microscopy, real time imaging and mechanistic analyses of vesicular trafficking in normal and malignant human melanocytic cells. This strategy revealed Class I PI3K as the key trigger of a hyperactive influx of macropinosomes that melanoma cells counteract via RAB7-mediated lysosomal degradation. In addition, gain- and loss-of-function in vitro studies followed by histopathological validation in clinical biopsies and genetically-engineered mouse models, traced back the requirement of RAB7 to the suppression of premature cellular senescence traits elicited in melanocytes by PI3K-inducing oncogenes. Together, these results provide new insight into the regulators and modes of action of RAB7, broadening the impact of endosomal fitness on melanoma development.
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16
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Taber JM, Aspinwall LG, Stump TK, Kohlmann W, Champine M, Leachman SA. Genetic test reporting enhances understanding of risk information and acceptance of prevention recommendations compared to family history-based counseling alone. J Behav Med 2015; 38:740-53. [PMID: 26178773 PMCID: PMC4568160 DOI: 10.1007/s10865-015-9648-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 05/15/2015] [Indexed: 11/25/2022]
Abstract
It is unknown whether or why genetic test reporting confers benefits in the understanding and management of cancer risk beyond what patients learn from counseling based on family history. A prospective nonexperimental control group study compared participants from melanoma-prone families who underwent CDKN2A/p16 (p16) genetic testing (27 carriers, 38 noncarriers) to participants from equivalently melanoma-prone families known not to carry a deleterious p16 mutation (31 no-test controls). All participants received equivalent counseling concerning elevated lifetime melanoma risk and corresponding recommendations for prevention and screening. Both immediately and 1 month after counseling, participants receiving a genetic test result reported greater understanding of their risk, decreased derogation of the risk information, and greater personal applicability of prevention recommendations than no-test controls. Decreased derogation of risk information after test reporting predicted further increases in understanding of melanoma risk and applicability of prevention recommendations 1 month later. Results suggest unique benefits of genetic test reporting in promoting understanding and acceptance of information about hereditary cancer risk and its management.
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Affiliation(s)
- Jennifer M Taber
- Department of Psychology, University of Utah, 380 South 1530 East, Room 502, Salt Lake City, UT, 84112-0251, USA
| | - Lisa G Aspinwall
- Department of Psychology, University of Utah, 380 South 1530 East, Room 502, Salt Lake City, UT, 84112-0251, USA.
| | - Tammy K Stump
- Department of Psychology, University of Utah, 380 South 1530 East, Room 502, Salt Lake City, UT, 84112-0251, USA
| | - Wendy Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Marjan Champine
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
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17
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Zhang D, Zhu R, Zhang H, Zheng CH, Xia J. MGDB: a comprehensive database of genes involved in melanoma. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav097. [PMID: 26424083 PMCID: PMC4589692 DOI: 10.1093/database/bav097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/07/2015] [Indexed: 12/14/2022]
Abstract
The Melanoma Gene Database (MGDB) is a manually curated catalog of molecular genetic data relating to genes involved in melanoma. The main purpose of this database is to establish a network of melanoma related genes and to facilitate the mechanistic study of melanoma tumorigenesis. The entries describing the relationships between melanoma and genes in the current release were manually extracted from PubMed abstracts, which contains cumulative to date 527 human melanoma genes (422 protein-coding and 105 non-coding genes). Each melanoma gene was annotated in seven different aspects (General Information, Expression, Methylation, Mutation, Interaction, Pathway and Drug). In addition, manually curated literature references have also been provided to support the inclusion of the gene in MGDB and establish its association with melanoma. MGDB has a user-friendly web interface with multiple browse and search functions. We hoped MGDB will enrich our knowledge about melanoma genetics and serve as a useful complement to the existing public resources. Database URL:http://bioinfo.ahu.edu.cn:8080/Melanoma/index.jsp
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Affiliation(s)
- Di Zhang
- Institute of Health Sciences, School of Computer Science and Technology
| | - Rongrong Zhu
- Institute of Health Sciences, School of Computer Science and Technology
| | - Hanqian Zhang
- Institute of Health Sciences, School of Computer Science and Technology
| | - Chun-Hou Zheng
- College of Electrical Engineering and Automation and Center of Information Support and Assurance Technology, Anhui University, Hefei, Anhui 230601, China
| | - Junfeng Xia
- Institute of Health Sciences, School of Computer Science and Technology, Center of Information Support and Assurance Technology, Anhui University, Hefei, Anhui 230601, China
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18
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Shitara D, Tell-Martí G, Badenas C, Enokihara MMSS, Alós L, Larque AB, Michalany N, Puig-Butille JA, Carrera C, Malvehy J, Puig S, Bagatin E. Mutational status of naevus-associated melanomas. Br J Dermatol 2015; 173:671-80. [PMID: 25857817 DOI: 10.1111/bjd.13829] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2015] [Indexed: 01/02/2023]
Abstract
BACKGROUND The origin of melanoma has always been a debated subject, as well as the role of adjacent melanocytic naevi. Epidemiological and histopathological studies point to melanomas arising either de novo or from a naevus. OBJECTIVES To evaluate the presence of mutations in genes from well-known melanomagenesis pathways in a large series of naevus-associated melanomas. MATERIALS AND METHODS Sixty-one melanomas found in association with a pre-existing naevus were microdissected, after careful selection of cell subpopulations, and submitted to Sanger sequencing of the BRAF, NRAS, c-KIT, PPP6C, STK19 and RAC1 genes. Each gene was evaluated twice in all samples by sequencing or by sequencing and another confirmation method, allele-specific fluorescent polymerase chain reaction (PCR) and capillary electrophoresis detection or by SNaPshot analysis. Only mutations confirmed via two different molecular methods or twice by sequencing were considered positive. RESULTS The majority of cases presented concordance of mutational status between melanoma and the associated naevus for all six genes (40 of 60; 66.7%). Nine cases presented concomitant BRAF and NRAS mutations, including one case in which both the melanoma and the adjacent naevus harboured V600E and Q61K double mutations. In two cases, both melanoma and associated naevus located on acral sites were BRAF mutated, including an acral lentiginous melanoma. CONCLUSIONS To our knowledge this is the largest naevus-associated melanoma series evaluated molecularly. The majority of melanomas and adjacent naevi in our sample share the same mutational profile, corroborating the theory that the adjacent naevus and melanoma are clonally related and that the melanoma originated within a naevus.
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Affiliation(s)
- D Shitara
- Department of Dermatology, Federal University of São Paulo, São Paulo, Brazil.,Melanoma Unit, Dermatology, Biochemistry and Molecular Genetics Departments, Hospital Clinic of Barcelona, IDIBAPS, Barcelona, Spain
| | - G Tell-Martí
- Melanoma Unit, Dermatology, Biochemistry and Molecular Genetics Departments, Hospital Clinic of Barcelona, IDIBAPS, Barcelona, Spain.,CIBER de Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
| | - C Badenas
- Melanoma Unit, Dermatology, Biochemistry and Molecular Genetics Departments, Hospital Clinic of Barcelona, IDIBAPS, Barcelona, Spain.,CIBER de Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
| | - M M S S Enokihara
- Department of Dermatology, Federal University of São Paulo, São Paulo, Brazil.,Department of Pathology, Federal University of São Paulo, São Paulo, Brazil
| | - L Alós
- Melanoma Unit, Pathology Service, Hospital Clinic of Barcelona, IDIBAPS, Barcelona, Spain
| | - A B Larque
- Melanoma Unit, Pathology Service, Hospital Clinic of Barcelona, IDIBAPS, Barcelona, Spain
| | - N Michalany
- Department of Dermatology, Federal University of São Paulo, São Paulo, Brazil.,Department of Pathology, Federal University of São Paulo, São Paulo, Brazil
| | - J A Puig-Butille
- Melanoma Unit, Dermatology, Biochemistry and Molecular Genetics Departments, Hospital Clinic of Barcelona, IDIBAPS, Barcelona, Spain.,CIBER de Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
| | - C Carrera
- Melanoma Unit, Dermatology, Biochemistry and Molecular Genetics Departments, Hospital Clinic of Barcelona, IDIBAPS, Barcelona, Spain.,CIBER de Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain.,University of Barcelona, Barcelona, Spain
| | - J Malvehy
- Melanoma Unit, Dermatology, Biochemistry and Molecular Genetics Departments, Hospital Clinic of Barcelona, IDIBAPS, Barcelona, Spain.,CIBER de Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain.,University of Barcelona, Barcelona, Spain
| | - S Puig
- Melanoma Unit, Dermatology, Biochemistry and Molecular Genetics Departments, Hospital Clinic of Barcelona, IDIBAPS, Barcelona, Spain.,CIBER de Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain.,University of Barcelona, Barcelona, Spain
| | - E Bagatin
- Department of Dermatology, Federal University of São Paulo, São Paulo, Brazil
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19
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Stockman DL, Curry JL, Torres-Cabala CA, Watson IR, Siroy AE, Bassett RL, Zou L, Patel KP, Luthra R, Davies MA, Wargo JA, Routbort MA, Broaddus RR, Prieto VG, Lazar AJ, Tetzlaff MT. Use of clinical next-generation sequencing to identify melanomas harboringSMARCB1mutations. J Cutan Pathol 2015; 42:308-17. [DOI: 10.1111/cup.12481] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 02/01/2015] [Indexed: 12/26/2022]
Affiliation(s)
- David L. Stockman
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Jonathan L. Curry
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Carlos A. Torres-Cabala
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Ian R. Watson
- Department of Genomic Medicine; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Alan E. Siroy
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Roland L. Bassett
- Department of Biostatistics; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Lihua Zou
- The Eli and Edythe L. Broad Institute of Massachusetts; Institute of Technology and Harvard University; Cambridge Massachusetts USA
| | - Keyur P. Patel
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Rajyalakshmi Luthra
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Michael A. Davies
- Department of Melanoma Medical Oncology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Jennifer A. Wargo
- Department of Surgery; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Mark A. Routbort
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Russell R. Broaddus
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Victor G. Prieto
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Alexander J. Lazar
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Michael T. Tetzlaff
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
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20
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Valavanis I, Maglogiannis I, Chatziioannou AA. Exploring Robust Diagnostic Signatures for Cutaneous Melanoma Utilizing Genetic and Imaging Data. IEEE J Biomed Health Inform 2015; 19:190-8. [DOI: 10.1109/jbhi.2014.2336617] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Barbour AP, Tang YH, Armour N, Dutton-Regester K, Krause L, Loffler KA, Lambie D, Burmeister B, Thomas J, Smithers BM, Hayward NK. BRAF mutation status is an independent prognostic factor for resected stage IIIB and IIIC melanoma: implications for melanoma staging and adjuvant therapy. Eur J Cancer 2014; 50:2668-76. [PMID: 25070294 DOI: 10.1016/j.ejca.2014.06.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/13/2014] [Accepted: 06/13/2014] [Indexed: 02/09/2023]
Abstract
BACKGROUND 5-year survival for melanoma metastasis to regional lymph nodes (American Joint Committee on Cancer stage III) is <50%. Knowledge of outcomes following therapeutic lymphadenectomy for stage III melanoma related to BRAF status may guide adjuvant use of BRAF/MEK inhibitors along with established and future therapies. AIMS To determine patterns of melanoma recurrence and survival following therapeutic lymph node dissection (TLND) associated with oncogenic mutations. METHODS DNA was obtained from patients who underwent TLND and had ⩾2 positive nodes, largest node >3cm or extracapsular invasion. Mutations were detected using an extended Sequenom MelaCARTA panel. RESULTS Mutations were most commonly detected in BRAF (57/124 [46%] patients) and NRAS (26/124 [21%] patients). Patients with BRAF mutations had higher 3-year recurrence rate (77%) versus 54% for BRAF wild-type patients (hazard ratio (HR) 1.8, p=0.008). The only prognostically significant mutations occurred in BRAF: median recurrence-free (RFS) and disease-specific survival (DSS) for BRAF mutation patients was 7 months and 16 months, versus 19 months and not reached for BRAF wild-type patients, respectively. Multivariate analysis identified BRAF mutant status and number of positive lymph nodes as the only independent prognostic factors for RFS and DSS. CONCLUSIONS Patients with BRAF mutations experienced rapid progression of metastatic disease with locoregional recurrence rarely seen in isolation, supporting incorporation of BRAF status into melanoma staging and use of BRAF/MEK inhibitors post-TLND.
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Affiliation(s)
- Andrew P Barbour
- Surgical Oncology Group, School of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia; Queensland Melanoma Project, Discipline of Surgery, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, QLD, Australia.
| | - Yue Hang Tang
- Surgical Oncology Group, School of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Nicola Armour
- Surgical Oncology Group, School of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Ken Dutton-Regester
- QIMR Berghofer Medical Research Institute, Oncogenomics Laboratory, Brisbane, QLD, Australia
| | - Lutz Krause
- QIMR Berghofer Medical Research Institute, Oncogenomics Laboratory, Brisbane, QLD, Australia
| | - Kelly A Loffler
- Surgical Oncology Group, School of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Duncan Lambie
- Department of Pathology, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Bryan Burmeister
- Queensland Melanoma Project, Discipline of Surgery, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Janine Thomas
- Queensland Melanoma Project, Discipline of Surgery, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - B Mark Smithers
- Queensland Melanoma Project, Discipline of Surgery, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, Oncogenomics Laboratory, Brisbane, QLD, Australia
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22
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Xia J, Jia P, Hutchinson KE, Dahlman KB, Johnson D, Sosman J, Pao W, Zhao Z. A meta-analysis of somatic mutations from next generation sequencing of 241 melanomas: a road map for the study of genes with potential clinical relevance. Mol Cancer Ther 2014; 13:1918-28. [PMID: 24755198 DOI: 10.1158/1535-7163.mct-13-0804] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Next generation sequencing (NGS) has been used to characterize the overall genomic landscape of melanomas. Here, we systematically examined mutations from recently published melanoma NGS data involving 241 paired tumor-normal samples to identify potentially clinically relevant mutations. Melanomas were characterized according to an in-house clinical assay that identifies well-known specific recurrent mutations in five driver genes: BRAF (affecting V600), NRAS (G12, G13, and Q61), KIT (W557, V559, L576, K642, and D816), GNAQ (Q209), and GNA11 (Q209). Tumors with none of these mutations are termed "pan negative." We then mined the driver mutation-positive and pan-negative melanoma NGS data for mutations in 632 cancer genes that could influence existing or emerging targeted therapies. First, we uncovered several genes whose mutations were more likely associated with BRAF- or NRAS-driven melanomas, including TP53 and COL1A1 with BRAF, and PPP6C, KALRN, PIK3R4, TRPM6, GUCY2C, and PRKAA2 with NRAS. Second, we found that the 69 "pan-negative" melanoma genomes harbored alternate infrequent mutations in the five known driver genes along with many mutations in genes encoding guanine nucleotide binding protein α-subunits. Third, we identified 12 significantly mutated genes in "pan-negative" samples (ALK, STK31, DGKI, RAC1, EPHA4, ADAMTS18, EPHA7, ERBB4, TAF1L, NF1, SYK, and KDR), including five genes (RAC1, ADAMTS18, EPHA7, TAF1L, and NF1) with a recurrent mutation in at least two "pan-negative" tumor samples. This meta-analysis provides a road map for the study of additional potentially actionable genes in both driver mutation-positive and pan-negative melanomas.
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Affiliation(s)
- Junfeng Xia
- Authors' Affiliations: Department of Biomedical Informatics
| | - Peilin Jia
- Authors' Affiliations: Department of Biomedical Informatics; Center for Quantitative Sciences
| | | | | | - Douglas Johnson
- Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jeffrey Sosman
- Vanderbilt-Ingram Cancer Center; and Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - William Pao
- Vanderbilt-Ingram Cancer Center; and Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Zhongming Zhao
- Authors' Affiliations: Department of Biomedical Informatics; Center for Quantitative Sciences; Department of Cancer Biology; Vanderbilt-Ingram Cancer Center; and
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23
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Abstract
A 52-year-old man has unresectable locally recurrent melanoma of the left foot (Fig 1) and pulmonary metastases. Nine months before this presentation, he underwent a wide local excision and sentinel node biopsy for an acral melanoma on his left heel. Pathology disclosed Breslow thickness of 4.8 mm, Clark level IV, and tumor ulceration with a mitotic rate of 37 mitoses/mm(2). Both sentinel nodes in the left groin were positive for melanoma cells, which expressed S100, HMB45, and melan A. At subsequent left inguinal dissection, seven more nodes showed no additional nodal metastases. Within 3 months of his original surgery, the patient developed a local recurrence in the foot, and over the subsequent 6 months, he underwent serial local excisions and topical diphencyprone treatment. A recent staging scan showed at least 20 foci of in-transit disease in the left lower leg and foot, as well as a solitary lung metastasis (12 mm). His Eastern Cooperative Oncology Group performance status is 1, with no significant comorbidities. High-resolution melt followed by sequencing of an in-transit metastasis showed there is no BRAF exon 15 mutation. However, Sanger sequencing of KIT exons 9, 11, 13, and 17, performed as screening for a clinical trial enrolling patients with metastatic acral and mucosal melanomas, showed an exon 13 K642E mutation.
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Affiliation(s)
- Megan Lyle
- Melanoma Institute Australia, Sydney, New South Wales, Australia
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24
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Cifola I, Pietrelli A, Consolandi C, Severgnini M, Mangano E, Russo V, De Bellis G, Battaglia C. Comprehensive genomic characterization of cutaneous malignant melanoma cell lines derived from metastatic lesions by whole-exome sequencing and SNP array profiling. PLoS One 2013; 8:e63597. [PMID: 23704925 PMCID: PMC3660556 DOI: 10.1371/journal.pone.0063597] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 04/04/2013] [Indexed: 02/08/2023] Open
Abstract
Cutaneous malignant melanoma is the most fatal skin cancer and although improved comprehension of its pathogenic pathways allowed to realize some effective molecular targeted therapies, novel targets and drugs are still needed. Aiming to add genetic information potentially useful for novel targets discovery, we performed an extensive genomic characterization by whole-exome sequencing and SNP array profiling of six cutaneous melanoma cell lines derived from metastatic patients. We obtained a total of 3,325 novel coding single nucleotide variants, including 2,172 non-synonymous variants. We catalogued the coding mutations according to Sanger COSMIC database and to a manually curated list including genes involved in melanoma pathways identified by mining recent literature. Besides confirming the presence of known melanoma driver mutations (BRAF(V600E), NRAS(Q61R) ), we identified novel mutated genes involved in signalling pathways crucial for melanoma pathogenesis and already addressed by current targeted therapies (such as MAPK and glutamate pathways). We also identified mutations in four genes (MUC19, PAICS, RBMXL1, KIF23) never reported in melanoma, which might deserve further investigations. All data are available to the entire research community in our Melanoma Exome Database (at https://155.253.6.64/MExDB/). In summary, these cell lines are valuable biological tools to improve the genetic comprehension of this complex cancer disease and to study functional relevance of individual mutational events, and these findings could provide insights potentially useful for identification of novel therapeutic targets for cutaneous malignant melanoma.
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Affiliation(s)
- Ingrid Cifola
- Institute for Biomedical Technologies, National Research Council, Milan, Italy.
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25
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Perrot CY, Javelaud D, Mauviel A. Insights into the Transforming Growth Factor-β Signaling Pathway in Cutaneous Melanoma. Ann Dermatol 2013; 25:135-44. [PMID: 23717002 PMCID: PMC3662904 DOI: 10.5021/ad.2013.25.2.135] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transforming growth factor-β (TGF-β) is a pleiotropic growth factor with broad tissue distribution that plays critical roles during embryonic development, normal tissue homeostasis, and cancer. While its cytostatic activity on normal epithelial cells initially defined TGF-β signaling as a tumor suppressor pathway, there is ample evidence indicating that TGF-β is a potent pro-tumorigenic agent, acting via autocrine and paracrine mechanisms to promote peri-tumoral angiogenesis, together with tumor cell migration, immune escape, and dissemination to metastatic sites. This review summarizes the current knowledge on the implication of TGF-β signaling in melanoma.
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Affiliation(s)
- Carole Yolande Perrot
- Institut Curie, Team "TGF-β and Oncogenesis", Equipe Labellisée Ligue Contre le Cancer, Orsay, France
- INSERM U1021 Orsay, France
- CNRS UMR 3347, Orsay, France
| | - Delphine Javelaud
- Institut Curie, Team "TGF-β and Oncogenesis", Equipe Labellisée Ligue Contre le Cancer, Orsay, France
- INSERM U1021 Orsay, France
- CNRS UMR 3347, Orsay, France
| | - Alain Mauviel
- Institut Curie, Team "TGF-β and Oncogenesis", Equipe Labellisée Ligue Contre le Cancer, Orsay, France
- INSERM U1021 Orsay, France
- CNRS UMR 3347, Orsay, France
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Kim GH, Levy A, Compoginis G. Neutrophilic panniculitis developing after treatment of metastatic melanoma with vemurafenib. J Cutan Pathol 2013; 40:667-9. [DOI: 10.1111/cup.12149] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 03/10/2013] [Accepted: 03/11/2013] [Indexed: 11/29/2022]
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27
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Schlegel J, Sambade MJ, Sather S, Moschos SJ, Tan AC, Winges A, DeRyckere D, Carson CC, Trembath DG, Tentler JJ, Eckhardt SG, Kuan PF, Hamilton RL, Duncan LM, Miller CR, Nikolaishvili-Feinberg N, Midkiff BR, Liu J, Zhang W, Yang C, Wang X, Frye SV, Earp HS, Shields JM, Graham DK. MERTK receptor tyrosine kinase is a therapeutic target in melanoma. J Clin Invest 2013; 123:2257-67. [PMID: 23585477 DOI: 10.1172/jci67816] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/21/2013] [Indexed: 01/09/2023] Open
Abstract
Metastatic melanoma is one of the most aggressive forms of cutaneous cancers. Although recent therapeutic advances have prolonged patient survival, the prognosis remains dismal. C-MER proto-oncogene tyrosine kinase (MERTK) is a receptor tyrosine kinase with oncogenic properties that is often overexpressed or activated in various malignancies. Using both protein immunohistochemistry and microarray analyses, we demonstrate that MERTK expression correlates with disease progression. MERTK expression was highest in metastatic melanomas, followed by primary melanomas, while the lowest expression was observed in nevi. Additionally, over half of melanoma cell lines overexpressed MERTK compared with normal human melanocytes; however, overexpression did not correlate with mutations in BRAF or RAS. Stimulation of melanoma cells with the MERTK ligand GAS6 resulted in the activation of several downstream signaling pathways including MAPK/ERK, PI3K/AKT, and JAK/STAT. MERTK inhibition via shRNA reduced MERTK-mediated downstream signaling, reduced colony formation by up to 59%, and diminished tumor volume by 60% in a human melanoma murine xenograft model. Treatment of melanoma cells with UNC1062, a novel MERTK-selective small-molecule tyrosine kinase inhibitor, reduced activation of MERTK-mediated downstream signaling, induced apoptosis in culture, reduced colony formation in soft agar, and inhibited invasion of melanoma cells. This work establishes MERTK as a therapeutic target in melanoma and provides a rationale for the continued development of MERTK-targeted therapies.
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Affiliation(s)
- Jennifer Schlegel
- Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
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28
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Klinac D, Gray ES, Millward M, Ziman M. Advances in personalized targeted treatment of metastatic melanoma and non-invasive tumor monitoring. Front Oncol 2013; 3:54. [PMID: 23515890 PMCID: PMC3601325 DOI: 10.3389/fonc.2013.00054] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 02/28/2013] [Indexed: 12/19/2022] Open
Abstract
Despite extensive scientific progress in the melanoma field, treatment of advanced stage melanoma with chemotherapeutics and biotherapeutics has rarely provided response rates higher than 20%. In the past decade, targeted inhibitors have been developed for metastatic melanoma, leading to the advent of more personalized therapies of genetically characterized tumors. Here we review current melanoma treatments and emerging targeted molecular therapies. In particular we discuss the mutant BRAF inhibitors Vemurafenib and Dabrafenib, which markedly inhibit tumor growth and advance patients' overall survival. However this response is almost inevitably followed by complete tumor relapse due to drug resistance hampering the encouraging initial responses. Several mechanisms of resistance within and outside the MAPK pathway have now been uncovered and have paved the way for clinical trials of combination therapies to try and overcome tumor relapse. It is apparent that personalized treatment management will be required in this new era of targeted treatment. Circulating tumor cells (CTCs) provide an easily accessible means of monitoring patient relapse and several new approaches are available for the molecular characterization of CTCs. Thus CTCs provide a monitoring tool to evaluate treatment efficacy and early detection of drug resistance in real time. We detail here how advances in the molecular analysis of CTCs may provide insight into new avenues of approaching therapeutic options that would benefit personalized melanoma management.
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Affiliation(s)
- Dragana Klinac
- School of Medical Sciences, Edith Cowan UniversityPerth, WA, Australia
| | - Elin S. Gray
- School of Medical Sciences, Edith Cowan UniversityPerth, WA, Australia
| | - Michael Millward
- School of Medicine and Pharmacology, University of Western AustraliaCrawley, WA, Australia
| | - Mel Ziman
- School of Medical Sciences, Edith Cowan UniversityPerth, WA, Australia
- School of Pathology and Laboratory Medicine, University of Western AustraliaCrawley, WA, Australia
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29
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Read J. Recent advances in cutaneous melanoma: towards a molecular model and targeted treatment. Australas J Dermatol 2013; 54:163-72. [DOI: 10.1111/ajd.12013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 10/28/2012] [Indexed: 12/14/2022]
Affiliation(s)
- Jazlyn Read
- Wesley Clinical School; The Wesley Hospital; Brisbane; Queensland; Australia
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30
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Feng Y, Lau E, Scortegagna M, Ruller C, De SK, Barile E, Krajewski S, Aza-Blanc P, Williams R, Pinkerton AB, Jackson M, Chin L, Pellecchia M, Bosenberg M, Ronai ZA. Inhibition of melanoma development in the Nras((Q61K)) ::Ink4a(-/-) mouse model by the small molecule BI-69A11. Pigment Cell Melanoma Res 2012; 26:136-42. [PMID: 23035722 DOI: 10.1111/pcmr.12033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 09/26/2012] [Indexed: 11/30/2022]
Abstract
To date, there are no effective therapies for tumors bearing NRAS mutations, which are present in 15-20% of human melanomas. Here we extend our earlier studies where we demonstrated that the small molecule BI-69A11 inhibits the growth of melanoma cell lines. Gene expression analysis revealed the induction of interferon- and cell death-related genes that were associated with responsiveness of melanoma cell lines to BI-69A11. Strikingly, the administration of BI-69A11 inhibited melanoma development in genetically modified mice bearing an inducible form of activated Nras and a deletion of the Ink4a gene (Nras((Q61K)) ::Ink4a(-/-) ). Biweekly administration of BI-69A11 starting at 10 weeks or as late as 24 weeks after the induction of mutant Nras expression inhibited melanoma development (100 and 36%, respectively). BI-69A11 treatment did not inhibit the development of histiocytic sarcomas, which constitute about 50% of the tumors in this model. BI-69A11-resistant Nras((Q61K)) ::Ink4a(-/-) tumors exhibited increased CD45 expression, reflective of immune cell infiltration and upregulation of gene networks associated with the cytoskeleton, DNA damage response, and small molecule transport. The ability to attenuate the development of NRAS mutant melanomas supports further development of BI-69A11 for clinical assessment.
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Affiliation(s)
- Yongmei Feng
- Signal Transduction Program, Cancer Center, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
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31
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Soengas MS. Mitophagy or how to control the Jekyll and Hyde embedded in mitochondrial metabolism: implications for melanoma progression and drug resistance. Pigment Cell Melanoma Res 2012; 25:721-31. [DOI: 10.1111/pcmr.12021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- María S. Soengas
- Melanoma Laboratory, Molecular Pathology Programme; Centro Nacional de Investigaciones Oncológicas (Spanish National Cancer Research Centre); Madrid; Spain
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32
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Mathieu V, Pirker C, Schmidt WM, Spiegl-Kreinecker S, Lötsch D, Heffeter P, Hegedus B, Grusch M, Kiss R, Berger W. Aggressiveness of human melanoma xenograft models is promoted by aneuploidy-driven gene expression deregulation. Oncotarget 2012; 3:399-413. [PMID: 22535842 PMCID: PMC3380575 DOI: 10.18632/oncotarget.473] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Melanoma is a devastating skin cancer characterized by distinct biological subtypes. Besides frequent mutations in growth- and survival-promoting genes like BRAF and NRAS, melanomas additionally harbor complex non-random genomic alterations. Using an integrative approach, we have analysed genomic and gene expression changes in human melanoma cell lines (N=32) derived from primary tumors and various metastatic sites and investigated the relation to local growth aggressiveness as xenografts in immuno-compromised mice (N=22). Although the vast majority >90% of melanoma models harbored mutations in either BRAF or NRAS, significant differences in subcutaneous growth aggressiveness became obvious. Unsupervised clustering revealed that genomic alterations rather than gene expression data reflected this aggressive phenotype, while no association with histology, stage or metastatic site of the original melanoma was found. Genomic clustering allowed separation of melanoma models into two subgroups with differing local growth aggressiveness in vivo. Regarding genes expressed at significantly altered levels between these subgroups, a surprising correlation with the respective gene doses (>85% accordance) was found. Genes deregulated at the DNA and mRNA level included well-known cancer genes partly already linked to melanoma (RAS genes, PTEN, AURKA, MAPK inhibitors Sprouty/Spred), but also novel candidates like SIPA1 (a Rap1GAP). Pathway mining further supported deregulation of Rap1 signaling in the aggressive subgroup e.g. by additional repression of two Rap1GEFs. Accordingly, siRNA-mediated down-regulation of SIPA1 exerted significant effects on clonogenicity, adherence and migration in aggressive melanoma models. Together our data suggest that an aneuploidy-driven gene expression deregulation drives local aggressiveness in human melanoma.
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Affiliation(s)
- Véronique Mathieu
- Laboratory of Toxicology, Faculty of Pharmacy, Université Libre de Bruxelles, Brussels, Belgium
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Gorkin DU, Lee D, Reed X, Fletez-Brant C, Bessling SL, Loftus SK, Beer MA, Pavan WJ, McCallion AS. Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Res 2012; 22:2290-301. [PMID: 23019145 PMCID: PMC3483558 DOI: 10.1101/gr.139360.112] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We take a comprehensive approach to the study of regulatory control of gene expression in melanocytes that proceeds from large-scale enhancer discovery facilitated by ChIP-seq; to rigorous validation in silico, in vitro, and in vivo; and finally to the use of machine learning to elucidate a regulatory vocabulary with genome-wide predictive power. We identify 2489 putative melanocyte enhancer loci in the mouse genome by ChIP-seq for EP300 and H3K4me1. We demonstrate that these putative enhancers are evolutionarily constrained, enriched for sequence motifs predicted to bind key melanocyte transcription factors, located near genes relevant to melanocyte biology, and capable of driving reporter gene expression in melanocytes in culture (86%; 43/50) and in transgenic zebrafish (70%; 7/10). Next, using the sequences of these putative enhancers as a training set for a supervised machine learning algorithm, we develop a vocabulary of 6-mers predictive of melanocyte enhancer function. Lastly, we demonstrate that this vocabulary has genome-wide predictive power in both the mouse and human genomes. This study provides deep insight into the regulation of gene expression in melanocytes and demonstrates a powerful approach to the investigation of regulatory sequences that can be applied to other cell types.
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Affiliation(s)
- David U Gorkin
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Lau E, Ronai ZA. ATF2 - at the crossroad of nuclear and cytosolic functions. J Cell Sci 2012; 125:2815-24. [PMID: 22685333 DOI: 10.1242/jcs.095000] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
An increasing number of transcription factors have been shown to elicit oncogenic and tumor suppressor activities, depending on the tissue and cell context. Activating transcription factor 2 (ATF2; also known as cAMP-dependent transcription factor ATF-2) has oncogenic activities in melanoma and tumor suppressor activities in non-malignant skin tumors and breast cancer. Recent work has shown that the opposing functions of ATF2 are associated with its subcellular localization. In the nucleus, ATF2 contributes to global transcription and the DNA damage response, in addition to specific transcriptional activities that are related to cell development, proliferation and death. ATF2 can also translocate to the cytosol, primarily following exposure to severe genotoxic stress, where it impairs mitochondrial membrane potential and promotes mitochondrial-based cell death. Notably, phosphorylation of ATF2 by the epsilon isoform of protein kinase C (PKCε) is the master switch that controls its subcellular localization and function. Here, we summarize our current understanding of the regulation and function of ATF2 in both subcellular compartments. This mechanism of control of a non-genetically modified transcription factor represents a novel paradigm for 'oncogene addiction'.
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Affiliation(s)
- Eric Lau
- Signal Transduction Program, Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Rd, La Jolla, CA 92130, USA.
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36
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Madorsky-Rowdo FP, Lacreu ML, Mordoh J. Melanoma vaccines and modulation of the immune system in the clinical setting: building from new realities. Front Immunol 2012; 3:103. [PMID: 22566975 PMCID: PMC3343264 DOI: 10.3389/fimmu.2012.00103] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 04/16/2012] [Indexed: 01/09/2023] Open
Abstract
To endow the immune system with the capacity to fight cancer has always attracted attention, although the clinical results obtained have been until recently disappointing. Cutaneous melanoma is a highly immunogenic tumor; therefore most of the attempts to produce cancer vaccines have been addressed to this disease. New advances in the comprehension of the mechanisms of antigen presentation by dendritic cells, in the immune responses triggered by adjuvants, as well as the understanding of the role of immunosuppressor molecules such as cytotoxic T-lymphocyte antigen-4 (CTLA-4), which led to the recent approval of the anti-CTLA-4 monoclonal antibody ipilimumab, have opened new hopes about the installment of immunotherapy as a new modality to treat cancer.
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