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Hrbac T, Kopkova A, Siegl F, Vecera M, Ruckova M, Kazda T, Jancalek R, Hendrych M, Hermanova M, Vybihal V, Fadrus P, Smrcka M, Sokol F, Kubes V, Lipina R, Slaby O, Kren L, Sana J. HLA-E and HLA-F Are Overexpressed in Glioblastoma and HLA-E Increased After Exposure to Ionizing Radiation. Cancer Genomics Proteomics 2022; 19:151-162. [PMID: 35181585 PMCID: PMC8865046 DOI: 10.21873/cgp.20311] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/08/2021] [Accepted: 01/21/2022] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND/AIM Glioblastoma (GBM) is one of the deadliest human cancers responding very poorly to therapy. Although the central nervous system has been traditionally considered an immunologically privileged site with an enhanced immune response, GBM appears to benefit from this immunosuppressive milieu. Immunomodulatory molecules play an important role in immune tumor-host interactions. Non-classical human leukocyte antigens (HLA) class Ib molecules HLA-E, HLA-F, and HLA-G have been previously described to be involved in protecting semi-allogeneic fetal allografts from the maternal immune response and in transplant tolerance as well as tumoral immune escape. Unfortunately, their role in GBM remains poorly understood. Our study, therefore, aimed to characterize the relationship between the expression of these molecules in GBM on the transcriptional level and clinicopathological and molecular features of GBM as well as the effect of ionizing radiation. MATERIALS AND METHODS We performed the analysis of HLA-E, HLA-F, and HLA-G mRNA expression in 69 GBM tissue samples and 21 non-tumor brain tissue samples (controls) by reverse transcription polymerase chain reaction. Furthermore, two primary GBM cell cultures had been irradiated to identify the effect of ionizing radiation on the expression of non-classical HLA molecules. RESULTS Analyses revealed that both HLA-E and HLA-F are significantly up-regulated in GBM samples. Subsequent survival analysis showed a significant association between low expression of HLA-E and shorter survival of GBM patients. The dysregulated expression of both molecules was also observed between patients with methylated and unmethylated O-6-methylguanine-DNA methyltransferase (MGMT) promoter. Finally, we showed that ionizing radiation increased HLA-E expression level in GBM cells in vitro. CONCLUSION HLA-E and HLA-F play an important role in GBM biology and could be used as diagnostic biomarkers, and in the case of HLA-E also as a prognostic biomarker.
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Affiliation(s)
- Tomas Hrbac
- Department of Neurosurgery, University Hospital Ostrava, Ostrava, Czech Republic
| | - Alena Kopkova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Frantisek Siegl
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Marek Vecera
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michaela Ruckova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tomas Kazda
- Department of Radiation Oncology, Masaryk Memorial Cancer Institute and Faculty of Medicine of Masaryk University, Brno, Czech Republic
| | - Radim Jancalek
- Department of Neurosurgery, St. Anne's University Hospital and Faculty of Medicine of Masaryk University, Brno, Czech Republic
| | - Michal Hendrych
- First Department of Pathology, St. Anne's University Hospital and Faculty of Medicine of Masaryk University, Brno, Czech Republic
| | - Marketa Hermanova
- First Department of Pathology, St. Anne's University Hospital and Faculty of Medicine of Masaryk University, Brno, Czech Republic
| | - Vaclav Vybihal
- Department of Neurosurgery, University Hospital Brno, Brno, Czech Republic
| | - Pavel Fadrus
- Department of Neurosurgery, University Hospital Brno, Brno, Czech Republic
| | - Martin Smrcka
- Department of Neurosurgery, University Hospital Brno, Brno, Czech Republic
| | - Filip Sokol
- Department of Pathology, University Hospital Brno, Brno, Czech Republic
| | - Vaclav Kubes
- Department of Pathology, University Hospital Brno, Brno, Czech Republic
| | - Radim Lipina
- Department of Neurosurgery, University Hospital Ostrava, Ostrava, Czech Republic
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine of Masaryk University, Brno, Czech Republic
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Leos Kren
- Department of Pathology, University Hospital Brno, Brno, Czech Republic;
| | - Jiri Sana
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic;
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
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2
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Tonella L, Pala V, Ponti R, Rubatto M, Gallo G, Mastorino L, Avallone G, Merli M, Agostini A, Fava P, Bertero L, Senetta R, Osella-Abate S, Ribero S, Fierro MT, Quaglino P. Prognostic and Predictive Biomarkers in Stage III Melanoma: Current Insights and Clinical Implications. Int J Mol Sci 2021; 22:4561. [PMID: 33925387 PMCID: PMC8123895 DOI: 10.3390/ijms22094561] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 01/19/2023] Open
Abstract
Melanoma is one of the most aggressive skin cancers. The 5-year survival rate of stage III melanoma patients ranges from 93% (IIIA) to 32% (IIID) with a high risk of recurrence after complete surgery. The introduction of target and immune therapies has dramatically improved the overall survival, but the identification of patients with a high risk of relapse who will benefit from adjuvant therapy and the determination of the best treatment choice remain crucial. Currently, patient prognosis is based on clinico-pathological features, highlighting the urgent need of predictive and prognostic markers to improve patient management. In recent years, many groups have focused their attention on identifying molecular biomarkers with prognostic and predictive potential. In this review, we examined the main candidate biomarkers reported in the literature.
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Affiliation(s)
- Luca Tonella
- Department of Medical Sciences, Dermatologic Clinic, University of Turin, 10126 Turin, Italy; (V.P.); (R.P.); (M.R.); (G.G.); (L.M.); (G.A.); (M.M.); (A.A.); (P.F.); (S.R.); (M.T.F.); (P.Q.)
| | - Valentina Pala
- Department of Medical Sciences, Dermatologic Clinic, University of Turin, 10126 Turin, Italy; (V.P.); (R.P.); (M.R.); (G.G.); (L.M.); (G.A.); (M.M.); (A.A.); (P.F.); (S.R.); (M.T.F.); (P.Q.)
| | - Renata Ponti
- Department of Medical Sciences, Dermatologic Clinic, University of Turin, 10126 Turin, Italy; (V.P.); (R.P.); (M.R.); (G.G.); (L.M.); (G.A.); (M.M.); (A.A.); (P.F.); (S.R.); (M.T.F.); (P.Q.)
| | - Marco Rubatto
- Department of Medical Sciences, Dermatologic Clinic, University of Turin, 10126 Turin, Italy; (V.P.); (R.P.); (M.R.); (G.G.); (L.M.); (G.A.); (M.M.); (A.A.); (P.F.); (S.R.); (M.T.F.); (P.Q.)
| | - Giuseppe Gallo
- Department of Medical Sciences, Dermatologic Clinic, University of Turin, 10126 Turin, Italy; (V.P.); (R.P.); (M.R.); (G.G.); (L.M.); (G.A.); (M.M.); (A.A.); (P.F.); (S.R.); (M.T.F.); (P.Q.)
| | - Luca Mastorino
- Department of Medical Sciences, Dermatologic Clinic, University of Turin, 10126 Turin, Italy; (V.P.); (R.P.); (M.R.); (G.G.); (L.M.); (G.A.); (M.M.); (A.A.); (P.F.); (S.R.); (M.T.F.); (P.Q.)
| | - Gianluca Avallone
- Department of Medical Sciences, Dermatologic Clinic, University of Turin, 10126 Turin, Italy; (V.P.); (R.P.); (M.R.); (G.G.); (L.M.); (G.A.); (M.M.); (A.A.); (P.F.); (S.R.); (M.T.F.); (P.Q.)
| | - Martina Merli
- Department of Medical Sciences, Dermatologic Clinic, University of Turin, 10126 Turin, Italy; (V.P.); (R.P.); (M.R.); (G.G.); (L.M.); (G.A.); (M.M.); (A.A.); (P.F.); (S.R.); (M.T.F.); (P.Q.)
| | - Andrea Agostini
- Department of Medical Sciences, Dermatologic Clinic, University of Turin, 10126 Turin, Italy; (V.P.); (R.P.); (M.R.); (G.G.); (L.M.); (G.A.); (M.M.); (A.A.); (P.F.); (S.R.); (M.T.F.); (P.Q.)
| | - Paolo Fava
- Department of Medical Sciences, Dermatologic Clinic, University of Turin, 10126 Turin, Italy; (V.P.); (R.P.); (M.R.); (G.G.); (L.M.); (G.A.); (M.M.); (A.A.); (P.F.); (S.R.); (M.T.F.); (P.Q.)
| | - Luca Bertero
- Department of Oncology, Pathology Unit, University of Turin, 10126 Turin, Italy; (L.B.); (R.S.); (S.O.-A.)
| | - Rebecca Senetta
- Department of Oncology, Pathology Unit, University of Turin, 10126 Turin, Italy; (L.B.); (R.S.); (S.O.-A.)
| | - Simona Osella-Abate
- Department of Oncology, Pathology Unit, University of Turin, 10126 Turin, Italy; (L.B.); (R.S.); (S.O.-A.)
| | - Simone Ribero
- Department of Medical Sciences, Dermatologic Clinic, University of Turin, 10126 Turin, Italy; (V.P.); (R.P.); (M.R.); (G.G.); (L.M.); (G.A.); (M.M.); (A.A.); (P.F.); (S.R.); (M.T.F.); (P.Q.)
| | - Maria Teresa Fierro
- Department of Medical Sciences, Dermatologic Clinic, University of Turin, 10126 Turin, Italy; (V.P.); (R.P.); (M.R.); (G.G.); (L.M.); (G.A.); (M.M.); (A.A.); (P.F.); (S.R.); (M.T.F.); (P.Q.)
| | - Pietro Quaglino
- Department of Medical Sciences, Dermatologic Clinic, University of Turin, 10126 Turin, Italy; (V.P.); (R.P.); (M.R.); (G.G.); (L.M.); (G.A.); (M.M.); (A.A.); (P.F.); (S.R.); (M.T.F.); (P.Q.)
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3
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Eisenstein A, Gonzalez EC, Raghunathan R, Xu X, Wu M, McLean EO, McGee J, Ryu B, Alani RM. Emerging Biomarkers in Cutaneous Melanoma. Mol Diagn Ther 2018; 22:203-218. [PMID: 29411301 DOI: 10.1007/s40291-018-0318-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Earlier identification of aggressive melanoma remains a goal in the field of melanoma research. With new targeted and immune therapies that have revolutionized the care of patients with melanoma, the ability to predict progression and monitor or predict response to therapy has become the new focus of research into biomarkers in melanoma. In this review, promising biomarkers are highlighted. These biomarkers have been used to diagnose melanoma as well as predict progression to advanced disease and response to therapy. The biomarkers take various forms, including protein expression at the level of tissue, genetic mutations of cancer cells, and detection of circulating DNA. First, a brief description is provided about the conventional tissue markers used to stage melanoma, including tumor depth. Next, protein biomarkers, which provide both diagnostic and prognostic information, are described. This is followed by a discussion of important genetic mutations, microRNA, and epigenetic modifications that can provide therapeutic and prognostic material. Finally, emerging serologic biomarkers are reviewed, including circulating melanoma cells and exosomes. Overall the goal is to identify biomarkers that aid in the earlier identification and improved treatment of aggressive melanoma.
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Affiliation(s)
- Anna Eisenstein
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA, 02118, USA
| | - Estela Chen Gonzalez
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA, 02118, USA
| | - Rekha Raghunathan
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA, 02118, USA
| | - Xixi Xu
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA, 02118, USA
| | - Muzhou Wu
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA, 02118, USA
| | - Emily O McLean
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA, 02118, USA
| | - Jean McGee
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA, 02118, USA
| | - Byungwoo Ryu
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA, 02118, USA.
| | - Rhoda M Alani
- Department of Dermatology, Boston University School of Medicine, 609 Albany Street, Boston, MA, 02118, USA.
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4
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Dai J, Lu Y, Wang J, Yang L, Han Y, Wang Y, Yan D, Ruan Q, Wang S. A four-gene signature predicts survival in clear-cell renal-cell carcinoma. Oncotarget 2018; 7:82712-82726. [PMID: 27779101 PMCID: PMC5347726 DOI: 10.18632/oncotarget.12631] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/25/2016] [Indexed: 01/20/2023] Open
Abstract
Clear-cell renal-cell carcinoma (ccRCC) is the most common pathological subtype of renal cell carcinoma (RCC), accounting for about 80% of RCC. In order to find potential prognostic biomarkers in ccRCC, we presented a four-gene signature to evaluate the prognosis of ccRCC. SurvExpress and immunohistochemical (IHC) staining of tissue microarrays were used to analyze the association between the four genes and the prognosis of ccRCC. Data from TCGA dataset revealed a prognostic prompt function of the four genes (PTEN, PIK3C2A, ITPA and BCL3). Further discovery suggested that the four-gene signature predicted survival better than any of the four genes alone. Moreover, IHC staining demonstrated a consistent result with TCGA, indicating that the signature was an independent prognostic factor of survival in ccRCC. Univariate and multivariate Cox proportional hazard regression analysis were conducted to verify the association of clinicopathological variables and the four genes' expression levels with survival. The results further testified that the risk (four-gene signature) was an independent prognostic factors of both Overall Survival (OS) and Disease-free Survival (DFS) (P<0.05). In conclusion, the four-gene signature was correlated with the survival of ccRCC, and therefore, may help to provide significant clinical implications for predicting the prognosis of patients.
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Affiliation(s)
- Jun Dai
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuchao Lu
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinyu Wang
- Department of Orthopaedics and Traumatology, Prince of Wales Hospital, The Chinese University of Hong Kong SAR, Hong Kong, China
| | - Lili Yang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingyan Han
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Wang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dan Yan
- Department of Pathology, Medical College, Wuhan University of Science and Technology, Wuhan, China
| | - Qiurong Ruan
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaogang Wang
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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5
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Lee RJ, Gremel G, Marshall A, Myers KA, Fisher N, Dunn JA, Dhomen N, Corrie PG, Middleton MR, Lorigan P, Marais R. Circulating tumor DNA predicts survival in patients with resected high-risk stage II/III melanoma. Ann Oncol 2018; 29:490-496. [PMID: 29112704 PMCID: PMC5834029 DOI: 10.1093/annonc/mdx717] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background Patients with high-risk stage II/III resected melanoma commonly develop distant metastases. At present, we cannot differentiate between patients who will recur or those who are cured by surgery. We investigated if circulating tumor DNA (ctDNA) can predict relapse and survival in patients with resected melanoma. Patients and methods We carried out droplet digital polymerase chain reaction to detect BRAF and NRAS mutations in plasma taken after surgery from 161 stage II/III high-risk melanoma patients enrolled in the AVAST-M adjuvant trial. Results Mutant BRAF or NRAS ctDNA was detected (≥1 copy of mutant ctDNA) in 15/132 (11%) BRAF mutant patient samples and 4/29 (14%) NRAS mutant patient samples. Patients with detectable ctDNA had a decreased disease-free interval [DFI; hazard ratio (HR) 3.12; 95% confidence interval (CI) 1.79-5.47; P < 0.0001] and distant metastasis-free interval (DMFI; HR 3.22; 95% CI 1.80-5.79; P < 0.0001) versus those with undetectable ctDNA. Detectable ctDNA remained a significant predictor after adjustment for performance status and disease stage (DFI: HR 3.26, 95% CI 1.83-5.83, P < 0.0001; DMFI: HR 3.45, 95% CI 1.88-6.34, P < 0.0001). Five-year overall survival rate for patients with detectable ctDNA was 33% (95% CI 14%-55%) versus 65% (95% CI 56%-72%) for those with undetectable ctDNA. Overall survival was significantly worse for patients with detectable ctDNA (HR 2.63; 95% CI 1.40-4.96); P = 0.003) and remained significant after adjustment for performance status (HR 2.50, 95% CI 1.32-4.74, P = 0.005). Conclusion ctDNA predicts for relapse and survival in high-risk resected melanoma and could aid selection of patients for adjuvant therapy. Clinical trial number ISRCTN 81261306.
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Affiliation(s)
- R J Lee
- Molecular Oncology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - G Gremel
- Molecular Oncology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - A Marshall
- Warwick Clinical Trials Unit, University of Warwick, Coventry, UK
| | - K A Myers
- Oxford Experimental Cancer Medicine Centre, University of Oxford, Oxford, UK
| | - N Fisher
- Oxford Experimental Cancer Medicine Centre, University of Oxford, Oxford, UK
| | - J A Dunn
- Warwick Clinical Trials Unit, University of Warwick, Coventry, UK
| | - N Dhomen
- Molecular Oncology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - P G Corrie
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - M R Middleton
- Oxford Experimental Cancer Medicine Centre, University of Oxford, Oxford, UK
| | - P Lorigan
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; Department of Medical Oncology, Christie NHS Foundation Trust, Manchester, UK
| | - R Marais
- Molecular Oncology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK.
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6
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Bracalente C, Ibañez IL, Berenstein A, Notcovich C, Cerda MB, Klamt F, Chernomoretz A, Durán H. Reprogramming human A375 amelanotic melanoma cells by catalase overexpression: Upregulation of antioxidant genes correlates with regression of melanoma malignancy and with malignant progression when downregulated. Oncotarget 2018; 7:41154-41171. [PMID: 27206673 PMCID: PMC5173049 DOI: 10.18632/oncotarget.9273] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 04/02/2016] [Indexed: 12/18/2022] Open
Abstract
Reactive oxygen species (ROS) are implicated in tumor transformation. The antioxidant system (AOS) protects cells from ROS damage. However, it is also hijacked by cancers cells to proliferate within the tumor. Thus, identifying proteins altered by redox imbalance in cancer cells is an attractive prognostic and therapeutic tool. Gene expression microarrays in A375 melanoma cells with different ROS levels after overexpressing catalase were performed. Dissimilar phenotypes by differential compensation to hydrogen peroxide scavenging were generated. The melanotic A375-A7 (A7) upregulated TYRP1, CNTN1 and UCHL1 promoting melanogenesis. The metastatic A375-G10 (G10) downregulated MTSS1 and TIAM1, proteins absent in metastasis. Moreover, differential coexpression of AOS genes (EPHX2, GSTM3, MGST1, MSRA, TXNRD3, MGST3 and GSR) was found in A7 and G10. Their increase in A7 improved its AOS ability and therefore, oxidative stress response, resembling less aggressive tumor cells. Meanwhile, their decrease in G10 revealed a disruption in the AOS and therefore, enhanced its metastatic capacity. These gene signatures, not only bring new insights into the physiopathology of melanoma, but also could be relevant in clinical prognostic to classify between non aggressive and metastatic melanomas.
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Affiliation(s)
- Candelaria Bracalente
- Departamento de Micro y Nanotecnología, Comisión Nacional de Energía Atómica, San Martín, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Irene L Ibañez
- Departamento de Micro y Nanotecnología, Comisión Nacional de Energía Atómica, San Martín, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Ariel Berenstein
- Fundación Instituto Leloir and Departamento de Física, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cintia Notcovich
- Departamento de Micro y Nanotecnología, Comisión Nacional de Energía Atómica, San Martín, Buenos Aires, Argentina
| | - María B Cerda
- Departamento de Micro y Nanotecnología, Comisión Nacional de Energía Atómica, San Martín, Buenos Aires, Argentina
| | - Fabio Klamt
- Laboratório de Bioquímica Celular, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil
| | - Ariel Chernomoretz
- Fundación Instituto Leloir and Departamento de Física, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Hebe Durán
- Departamento de Micro y Nanotecnología, Comisión Nacional de Energía Atómica, San Martín, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina.,Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
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7
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Falkenius J, Johansson H, Tuominen R, Frostvik Stolt M, Hansson J, Egyhazi Brage S. Presence of immune cells, low tumor proliferation and wild type BRAF mutation status is associated with a favourable clinical outcome in stage III cutaneous melanoma. BMC Cancer 2017; 17:584. [PMID: 28851300 PMCID: PMC5576332 DOI: 10.1186/s12885-017-3577-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 08/22/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The variable prognosis in stage III cutaneous melanoma is partially due to unknown prognostic factors. Improved prognostic tools are required to define patients with an increased risk of developing metastatic disease who might benefit from adjuvant therapies. The aim was to examine if cellular immune markers in association with tumor proliferation rate and BRAF mutation status have an impact on prognosis in stage III melanoma. METHODS We have used two sets of case series with stage III disease: 23 patients with short survival (≤ 13 months) and 19 patients with long survival (≥ 60 months). Lymph node metastases were analyzed for Ki67, CD8 and FOXP3 protein expression using immunohistochemistry. BRAF mutation status was analyzed in a previous study on the same samples. RESULTS Low tumor proliferation rate was significantly associated with a better prognosis (p = 0.013). Presence of FOXP3+ T cells was not correlated to adverse clinical outcome. A highly significant trend for a longer survival was found in the presence of an increasing number of markers; CD8+ and FOXP3+ T cells, low tumor proliferation and BRAF wildtype status (p = 0.003). Presence of at least three of these four markers was found to be an independent favorable prognostic factor (OR 19.4, 95% CI 1.9-197, p = 0.012), when adjusting for ulceration and number of lymph node metastases. Proliferation alone remained significant in multivariate analyses (OR 26.1, 95% CI 2.0-344, p = 0.013) but with a wider confidence interval. This panel still remained independent when also adjusting for a previously identified prognostic glycolytic-pigment panel. CONCLUSIONS We have demonstrated that presence of immune cells in association with tumor proliferation and BRAF mutation status may further contribute to identify stage III melanoma patients with high risk of relapse.
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Affiliation(s)
- Johan Falkenius
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Karolinska University Hospital, 171 76 Solna, Stockholm Sweden
| | - Hemming Johansson
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Karolinska University Hospital, 171 76 Solna, Stockholm Sweden
| | - Rainer Tuominen
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Karolinska University Hospital, 171 76 Solna, Stockholm Sweden
| | - Marianne Frostvik Stolt
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Karolinska University Hospital, 171 76 Solna, Stockholm Sweden
| | - Johan Hansson
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Karolinska University Hospital, 171 76 Solna, Stockholm Sweden
| | - Suzanne Egyhazi Brage
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Karolinska University Hospital, 171 76 Solna, Stockholm Sweden
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8
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Abstract
Malignant melanoma remains the skin cancer with the highest number of mortalities worldwide. While early diagnosis and complete surgical excision remain the best possibility for curing disease, prognosis at the stage of metastasis is still poor. Recent years have brought about considerable advances in terms of understanding the pathogenesis of melanoma and treating advanced disease. The discovery of activating BRAF mutations in around 50% of tumors has led to the introduction of targeted therapies downregulating BRAF signaling output. These have been further refined as combination therapies, which by targeting multiple targets have further improved the clinical outcome. A comparable, potentially even superior therapeutic alternative has been the introduction of immunotherapeutic approaches, including PD-1 and CTLA-4 checkpoint blockade therapies. Despite all genetic knowledge acquired in recent years, a clearly applicable prognostic signature of clinical value has not been established. General prognostic assessment of cutaneous melanoma remains based on clinical and pathological criteria (most importantly tumor thickness). The main challenges lying ahead are to establish a reliable prognostic test effectively determining which tumors will metastasize. Additionally establishing biomarkers which will allow patients to be stratified according to the most promising systemic therapy (immunotherapies and/or BRAF inhibitor therapies) is of utmost importance for patients with metastasized disease. Identifying serum biomarkers enabling disease to be monitored as well as determining tumor properties (i.e. resistance) would also be of great value. While initial results have proven promising, there remains much work to be done.
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Affiliation(s)
- Klaus G Griewank
- a Department of Dermatology , University Hospital Essen , Essen , Germany
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9
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Yao J, Caballero OL, Huang Y, Lin C, Rimoldi D, Behren A, Cebon JS, Hung MC, Weinstein JN, Strausberg RL, Zhao Q. Altered Expression and Splicing of ESRP1 in Malignant Melanoma Correlates with Epithelial-Mesenchymal Status and Tumor-Associated Immune Cytolytic Activity. Cancer Immunol Res 2016; 4:552-61. [PMID: 27045022 DOI: 10.1158/2326-6066.cir-15-0255] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/03/2016] [Indexed: 11/16/2022]
Abstract
Melanoma is one of the major cancer types for which new immune-based cancer treatments have achieved promising results. However, anti-PD-1 and anti-CTLA-4 therapies are effective only in some patients. Hence, predictive molecular markers for the development of clinical strategies targeting immune checkpoints are needed. Using The Cancer Genome Atlas (TCGA) RNAseq data, we found that expression of ESRP1, encoding a master splicing regulator in the epithelial-mesenchymal transition (EMT), was inversely correlated with tumor-associated immune cytolytic activity. That association holds up across multiple TCGA tumor types, suggesting a link between tumor EMT status and infiltrating lymphocyte activity. In melanoma, ESRP1 mainly exists in a melanocyte-specific truncated form transcribed from exon 13. This was validated by analyzing CCLE cell line data, public CAGE data, and RT-PCR in primary cultured melanoma cell lines. Based on ESRP1 expression, we divided TCGA melanoma cases into ESRP1-low, -truncated, and -full-length groups. ESRP1-truncated tumors comprise approximately two thirds of melanoma samples and reside in an apparent transitional state between epithelial and mesenchymal phenotypes. ESRP1 full-length tumors express epithelial markers and constitute about 5% of melanoma samples. In contrast, ESRP1-low tumors express mesenchymal markers and are high in immune cytolytic activity as well as PD-L2 and CTLA-4 expression. Those tumors are associated with better patient survival. Results from our study suggest a path toward the use of ESRP1 and other EMT markers as informative biomarkers for immunotherapy. Cancer Immunol Res; 4(6); 552-61. ©2016 AACR.
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Affiliation(s)
- Jun Yao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Otavia L Caballero
- Ludwig Collaborative Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland. Orygen Biotecnologia, SA., São Paulo, SP, Brazil
| | - Ying Huang
- Regeneron Pharmaceuticals Inc., Tarrytown, New York
| | - Calvin Lin
- Regeneron Pharmaceuticals Inc., Tarrytown, New York
| | - Donata Rimoldi
- Clinical Tumor Biology and Immunotherapy Unit, Ludwig Center, University of Lausanne, Switzerland, Lausanne, Switzerland
| | - Andreas Behren
- Cancer Immunobiology Laboratory, Olivia Newton-John Cancer Research Institute, Victoria, Australia
| | - Jonathan S Cebon
- Cancer Immunobiology Laboratory, Olivia Newton-John Cancer Research Institute, Victoria, Australia
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Qi Zhao
- Ludwig Collaborative Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland. Regeneron Pharmaceuticals Inc., Tarrytown, New York.
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10
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Cirenajwis H, Ekedahl H, Lauss M, Harbst K, Carneiro A, Enoksson J, Rosengren F, Werner-Hartman L, Törngren T, Kvist A, Fredlund E, Bendahl PO, Jirström K, Lundgren L, Howlin J, Borg Å, Gruvberger-Saal SK, Saal LH, Nielsen K, Ringnér M, Tsao H, Olsson H, Ingvar C, Staaf J, Jönsson G. Molecular stratification of metastatic melanoma using gene expression profiling: Prediction of survival outcome and benefit from molecular targeted therapy. Oncotarget 2016; 6:12297-309. [PMID: 25909218 PMCID: PMC4494939 DOI: 10.18632/oncotarget.3655] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/27/2015] [Indexed: 01/02/2023] Open
Abstract
Melanoma is currently divided on a genetic level according to mutational status. However, this classification does not optimally predict prognosis. In prior studies, we have defined gene expression phenotypes (high-immune, pigmentation, proliferative and normal-like), which are predictive of survival outcome as well as informative of biology. Herein, we employed a population-based metastatic melanoma cohort and external cohorts to determine the prognostic and predictive significance of the gene expression phenotypes. We performed expression profiling on 214 cutaneous melanoma tumors and found an increased risk of developing distant metastases in the pigmentation (HR, 1.9; 95% CI, 1.05-3.28; P=0.03) and proliferative (HR, 2.8; 95% CI, 1.43-5.57; P=0.003) groups as compared to the high-immune response group. Further genetic characterization of melanomas using targeted deep-sequencing revealed similar mutational patterns across these phenotypes. We also used publicly available expression profiling data from melanoma patients treated with targeted or vaccine therapy in order to determine if our signatures predicted therapeutic response. In patients receiving targeted therapy, melanomas resistant to targeted therapy were enriched in the MITF-low proliferative subtype as compared to pre-treatment biopsies (P=0.02). In summary, the melanoma gene expression phenotypes are highly predictive of survival outcome and can further help to discriminate patients responding to targeted therapy.
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Affiliation(s)
- Helena Cirenajwis
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Henrik Ekedahl
- Department of Clinical Sciences, Division of Surgery, Lund University, Lund, Sweden
| | - Martin Lauss
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Katja Harbst
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Ana Carneiro
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Oncology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Jens Enoksson
- Department of Clinical Pathology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Frida Rosengren
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Linda Werner-Hartman
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Therese Törngren
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Anders Kvist
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Erik Fredlund
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Pär-Ola Bendahl
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Karin Jirström
- Department of Clinical Pathology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Lotta Lundgren
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Oncology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Jillian Howlin
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Åke Borg
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Sofia K Gruvberger-Saal
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Lao H Saal
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Kari Nielsen
- Department of Dermatology, Helsingborg General Hospital, Helsingborg, Sweden
| | - Markus Ringnér
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Hensin Tsao
- Department of Dermatology, Harvard Medical School, Boston, USA.,Wellman Center for Photomedicine, MGH Cancer Center, Massachusetts General Hospital, Boston, USA
| | - Håkan Olsson
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Oncology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Christian Ingvar
- Department of Clinical Sciences, Division of Surgery, Lund University, Lund, Sweden
| | - Johan Staaf
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Göran Jönsson
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
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11
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Foth M, Wouters J, de Chaumont C, Dynoodt P, Gallagher WM. Prognostic and predictive biomarkers in melanoma: an update. Expert Rev Mol Diagn 2015; 16:223-37. [PMID: 26620320 DOI: 10.1586/14737159.2016.1126511] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Malignant melanoma is one of the most aggressive cancers. Several new therapeutic strategies that focus on immuno- and/or targeted therapy have been developed, which have entered clinical trials or already been approved. This review provides an update on prognostic and predictive biomarkers in melanoma that may be used to improve the clinical management of patients. Prognostic markers include conventional histopathological characteristics, chromosomal aberrations, gene expression patterns and miRNA profiles. There is a trend towards multi-marker assays and whole-genome molecular screening methods to determine the prognosis of individual patients. Predictive biomarkers, including targeted components of signal transduction, developmental or transcriptional pathways, can be used to determine patient response towards a particular treatment or combination thereof. The rapid evolution of sequencing technologies and multi-marker screening will change the spectrum of patients who become candidates for therapeutic agents, and in addition create new ethical and regulatory challenges.
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Affiliation(s)
- Mona Foth
- a OncoMark Ltd., NovaUCD, Bellfield , University College Dublin , Dublin , Ireland.,b Cancer Research UK, Beatson Institute , Glasgow , United Kingdom
| | - Jasper Wouters
- a OncoMark Ltd., NovaUCD, Bellfield , University College Dublin , Dublin , Ireland.,c Translational Cell & Tissue Research , Department of Imaging and Pathology, Katholieke Universiteit Leuven , Leuven , Belgium
| | - Ciaran de Chaumont
- a OncoMark Ltd., NovaUCD, Bellfield , University College Dublin , Dublin , Ireland.,d Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Peter Dynoodt
- a OncoMark Ltd., NovaUCD, Bellfield , University College Dublin , Dublin , Ireland
| | - William M Gallagher
- a OncoMark Ltd., NovaUCD, Bellfield , University College Dublin , Dublin , Ireland.,e UCD Cancer Biology and Therapeutics Laboratory, School of Biomolecular and Biomedical Science, Conway Institute of Biomolecular and Biomedical Research , University College Dublin , Dublin , Ireland
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12
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Mactier S, Kaufman KL, Wang P, Crossett B, Pupo GM, Kohnke PL, Thompson JF, Scolyer RA, Yang JY, Mann GJ, Christopherson RI. Protein signatures correspond to survival outcomes of AJCC stage III melanoma patients. Pigment Cell Melanoma Res 2014; 27:1106-16. [PMID: 24995518 PMCID: PMC4285183 DOI: 10.1111/pcmr.12290] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 07/02/2014] [Indexed: 11/28/2022]
Abstract
Summary Outcomes for melanoma patients with stage III disease differ widely even within the same subcategory. Molecular signatures that more accurately predict prognosis are needed to stratify patients according to risk. Proteomic analyses were used to identify differentially abundant proteins in extracts of surgically excised samples from patients with stage IIIc melanoma lymph node metastases. Analysis of samples from patients with poor (n = 14, <1 yr) and good (n = 19, >4 yr) survival outcomes identified 84 proteins that were differentially abundant between prognostic groups. Subsequent selected reaction monitoring analysis verified 21 proteins as potential biomarkers for survival. Poor prognosis patients are characterized by increased levels of proteins involved in protein metabolism, nucleic acid metabolism, angiogenesis, deregulation of cellular energetics and methylation processes, and decreased levels of proteins involved in apoptosis and immune response. These proteins are able to classify stage IIIc patients into prognostic subgroups (P < 0.02). This is the first report of potential prognostic markers from stage III melanoma using proteomic analyses. Validation of these protein markers in larger patient cohorts should define protein signatures that enable better stratification of stage III melanoma patients.
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Affiliation(s)
- Swetlana Mactier
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
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13
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Jönsson G. Advances in molecular profiling of malignant melanoma: ready for clinical practice? Melanoma Manag 2014; 1:3-6. [DOI: 10.2217/mmt.14.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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14
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Jayawardana K, Schramm SJ, Haydu L, Thompson JF, Scolyer RA, Mann GJ, Müller S, Yang JYH. Determination of prognosis in metastatic melanoma through integration of clinico-pathologic, mutation, mRNA, microRNA, and protein information. Int J Cancer 2014; 136:863-74. [DOI: 10.1002/ijc.29047] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 06/06/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Kaushala Jayawardana
- School of Mathematics & Statistics; The University of Sydney; Sydney NSW Australia
| | - Sarah-Jane Schramm
- Sydney Medical School; The University of Sydney at Westmead Millennium Institute for Medical Research; Westmead NSW Australia
- Melanoma Institute Australia; Sydney NSW Australia
| | - Lauren Haydu
- Melanoma Institute Australia; Sydney NSW Australia
| | - John F. Thompson
- Melanoma Institute Australia; Sydney NSW Australia
- Discipline of Surgery; The University of Sydney; Sydney NSW Australia
| | - Richard A. Scolyer
- Melanoma Institute Australia; Sydney NSW Australia
- Discipline of Pathology; The University of Sydney; Sydney NSW Australia
- Tissue Pathology and Diagnostic Oncology; Royal Prince Alfred Hospital; Camperdown NSW Australia
| | - Graham J. Mann
- Sydney Medical School; The University of Sydney at Westmead Millennium Institute for Medical Research; Westmead NSW Australia
- Melanoma Institute Australia; Sydney NSW Australia
| | - Samuel Müller
- School of Mathematics & Statistics; The University of Sydney; Sydney NSW Australia
| | - Jean Yee Hwa Yang
- School of Mathematics & Statistics; The University of Sydney; Sydney NSW Australia
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15
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Andrews MC, Woods K, Cebon J, Behren A. Evolving role of tumor antigens for future melanoma therapies. Future Oncol 2014; 10:1457-68. [DOI: 10.2217/fon.14.84] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
ABSTRACT: Human tumor rejection antigens recognized by T lymphocytes were first defined in the early 1990s and the identification of shared tumor-restricted antigens sparked hopes for the development of a therapeutic vaccination to treat cancer, including melanoma. Despite decades of intense preclinical and clinical research, the success of anticancer vaccines based on these antigens has been limited. While melanoma is a highly immunogenic tumor, the ability to prime immunity with vaccines has not generally translated into objective disease regression. However, with the development of small molecules targeting oncogenic proteins, such as V600-mutated BRAF, and immune checkpoint inhibitors with demonstrable long-lasting clinical benefit, new opportunities for antigen-targeted directed therapies are emerging.
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Affiliation(s)
- Miles C Andrews
- Ludwig Institute for Cancer Research Ltd, Olivia Newton-John Cancer & Wellness Centre, Cancer Immunobiology, Heidelberg, VIC, Australia
- Medical Oncology, Joint Ludwig–Austin Oncology Unit, Austin Health, Victoria, Australia
| | - Katherine Woods
- Ludwig Institute for Cancer Research Ltd, Olivia Newton-John Cancer & Wellness Centre, Cancer Immunobiology, Heidelberg, VIC, Australia
| | - Jonathan Cebon
- Ludwig Institute for Cancer Research Ltd, Olivia Newton-John Cancer & Wellness Centre, Cancer Immunobiology, Heidelberg, VIC, Australia
- Medical Oncology, Joint Ludwig–Austin Oncology Unit, Austin Health, Victoria, Australia
| | - Andreas Behren
- Ludwig Institute for Cancer Research Ltd, Olivia Newton-John Cancer & Wellness Centre, Cancer Immunobiology, Heidelberg, VIC, Australia
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16
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Griewank KG, Scolyer RA, Thompson JF, Flaherty KT, Schadendorf D, Murali R. Genetic alterations and personalized medicine in melanoma: progress and future prospects. J Natl Cancer Inst 2014; 106:djt435. [PMID: 24511108 DOI: 10.1093/jnci/djt435] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
High-throughput sequencing technologies are providing new insights into the genetic alterations involved in melanomagenesis. It appears likely that most genetic events important in the pathogenesis of melanoma will be discovered over the next few years. Genetic analysis is also increasingly being used to direct patient care. In parallel with the discovery of new genes and the elucidation of molecular pathways important in the development of melanoma, therapies targeting these pathways are becoming available. In other words, the age of personalized medicine has arrived, characterized by molecular profiling of melanoma to identify the relevant genetic alterations and the abnormal signaling mechanisms involved, followed by selection of optimal, individualized therapies. In this review, we summarize the key genetic alterations in melanoma and the development of targeted agents against melanomas bearing specific mutations. These developments in melanoma serve as a model for the implementation of personalized medicine for patients with all cancers.
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Affiliation(s)
- Klaus G Griewank
- Affiliations of authors: Department of Dermatology, University Hospital, University Duisburg-Essen, Essen, Germany (KGG, DS); Royal Prince Alfred Hospital, Camperdown, NSW, Australia (RAS); University of Sydney, Camperdown, NSW, Australia (RAS, JFT); Melanoma Institute Australia, North Sydney, NSW, Australia (RAS, JFT); Center for Melanoma, Massachusetts General Hospital Cancer Center, Boston, MA (KTF); Department of Pathology, and Center for Molecular Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (RM)
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17
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Mandalà M, Massi D. Tissue prognostic biomarkers in primary cutaneous melanoma. Virchows Arch 2014; 464:265-81. [PMID: 24487785 DOI: 10.1007/s00428-013-1526-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 12/03/2013] [Indexed: 01/04/2023]
Abstract
Cutaneous melanoma (CM) causes the greatest number of skin cancer-related deaths worldwide. Predicting CM prognosis is important to determine the need for further investigation, counseling of patients, to guide appropriate management (particularly the need for postoperative adjuvant therapy), and for assignment of risk status in groups of patients entering clinical trials. Since recurrence rate is largely independent from stages defined by morphological and morphometric criteria, there is a strong need for identification of additional robust prognostic factors to support decision-making processes. Most data on prognostic biomarkers in melanoma have been evaluated in tumor tissue samples by conventional morphology and immunohistochemistry (IHC) as well as DNA and RNA analyses. In the present review, we critically summarize main high-quality studies investigating IHC-based protein biomarkers of melanoma outcome according to Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK)-derived criteria. Pathways have been classified and conveyed in the "biologic road" previously described by Hanahan and Weinberg. Data derived from genomic and transcriptomic technologies have been critically reviewed to better understand if any of investigated proteins or gene signatures should be incorporated into clinical practice or still remain a field of melanoma research. Despite a wide body of research, no molecular prognostic biomarker has yet been translated into clinical practice. Conventional tissue biomarkers, such as Breslow thickness, ulceration, mitotic rate and lymph node positivity, remain the backbone prognostic indicators in melanoma.
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Affiliation(s)
- Mario Mandalà
- Unit of Clinical and Translational Research, Medical Oncology, Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy
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18
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Tremante E, Ginebri A, Lo Monaco E, Benassi B, Frascione P, Grammatico P, Cappellacci S, Catricalà C, Arcelli D, Natali PG, Di Filippo F, Mottolese M, Visca P, Benevolo M, Giacomini P. A melanoma immune response signature including Human Leukocyte Antigen-E. Pigment Cell Melanoma Res 2014; 27:103-12. [PMID: 24011128 DOI: 10.1111/pcmr.12164] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 08/27/2013] [Indexed: 12/29/2022]
Abstract
Paired cultures of early-passage melanoma cells and melanocytes were established from metastatic lesions and the uninvolved skin of five patients. In this stringent autologous setting, cDNA profiling was used to analyze a subset of 1477 genes selected by the Gene Ontology term 'immune response'. Human Leukocyte Antigen E (HLA-E) was ranked 19th among melanoma-overexpressed genes and was embedded in a transformation signature including its preferred peptide ligand donors HLA-A, HLA-B, HLA-C, and HLA-G. Mostly undetectable in normal skin and 39 nevi (including rare and atypical lesions), HLA-E was detected by immunohistochemistry in 17/30 (57%) and 32/48 (67%) primary and metastatic lesions, respectively. Accordingly, surface HLA-E was higher on melanoma cells than on melanocytes and protected the former (6/6 cell lines) from lysis by natural killer (NK) cells, functionally counteracting co-expressed triggering ligands. Although lacking HLA-E, melanocytes (4/4 cultures) were nevertheless (and surprisingly) fully protected from NK cell lysis.
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Affiliation(s)
- Elisa Tremante
- Laboratory of Immunology, Regina Elena National Cancer Institute, Rome, Italy
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19
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Quintana E, Piskounova E, Shackleton M, Weinberg D, Eskiocak U, Fullen DR, Johnson TM, Morrison SJ. Human melanoma metastasis in NSG mice correlates with clinical outcome in patients. Sci Transl Med 2013; 4:159ra149. [PMID: 23136044 PMCID: PMC4501487 DOI: 10.1126/scitranslmed.3004599] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Studies of human cancer metastasis have been limited by a lack of experimental assays in which cancer cells from patients metastasize in vivo in a way that correlates with clinical outcome. This makes it impossible to study intrinsic differences in the metastatic properties of cancers from different patients. We recently developed an assay in which human melanomas readily engraft in nonobese diabetic/severe combined immunodeficient interleukin-2 receptor-γ chain null (NSG) mice. We show that melanomas from 25 patients exhibited reproducible differences in the rate of spontaneous metastasis after transplantation into NSG mice and that these differences correlated with clinical outcome in the patients. Stage IIIB/C melanomas that formed distant metastases within 22 months in patients also formed tumors that metastasized widely in NSG mice, whereas stage IIIB/C melanomas that did not form distant metastases within 22 to 50 months in patients metastasized more slowly in NSG mice. These differences in the efficiency of metastasis correlated with the presence of circulating melanoma cells in the blood of NSG mice, suggesting that the rate of entry into the blood is one factor that limits the rate of metastasis. The study of NSG mice can therefore yield information about the metastasis of human melanomas in vivo, in this case revealing intrinsic differences among stage III melanomas in their ability to circulate/survive in the blood and to metastasize.
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Affiliation(s)
- Elsa Quintana
- Howard Hughes Medical Institute, Life Sciences Institute, Department of Internal Medicine, and Center for Stem Cell Biology, University of Michigan, Ann Arbor, MI 48109-2216, USA
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20
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Simone PD, Pavlov YI, Borgstahl GEO. ITPA (inosine triphosphate pyrophosphatase): from surveillance of nucleotide pools to human disease and pharmacogenetics. Mutat Res 2013; 753:131-146. [PMID: 23969025 DOI: 10.1016/j.mrrev.2013.08.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/31/2013] [Accepted: 08/02/2013] [Indexed: 01/08/2023]
Abstract
Cellular nucleotide pools are often contaminated by base analog nucleotides which interfere with a plethora of biological reactions, from DNA and RNA synthesis to cellular signaling. An evolutionarily conserved inosine triphosphate pyrophosphatase (ITPA) removes the non-canonical purine (d)NTPs inosine triphosphate and xanthosine triphosphate by hydrolyzing them into their monophosphate form and pyrophosphate. Mutations in the ITPA orthologs in model organisms lead to genetic instability and, in mice, to severe developmental anomalies. In humans there is genetic polymorphism in ITPA. One allele leads to a proline to threonine substitution at amino acid 32 and causes varying degrees of ITPA deficiency in tissues and plays a role in patients' response to drugs. Structural analysis of this mutant protein reveals that the protein is destabilized by the formation of a cavity in its hydrophobic core. The Pro32Thr allele is thought to cause the observed dominant negative effect because the resulting active enzyme monomer targets both homo- and heterodimers to degradation.
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Affiliation(s)
- Peter D Simone
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Youri I Pavlov
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, USA; Department of Genetics, St-Petersburg University, St-Petersburg, 199034, Russia
| | - Gloria E O Borgstahl
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, USA; Department of Pharmaceutical Sciences, University of Nebraska Medical Center, USA.
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21
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Schramm SJ, Li SS, Jayaswal V, Fung DCY, Campain AE, Pang CNI, Scolyer RA, Yang YH, Mann GJ, Wilkins MR. Disturbed protein-protein interaction networks in metastatic melanoma are associated with worse prognosis and increased functional mutation burden. Pigment Cell Melanoma Res 2013; 26:708-22. [PMID: 23738911 DOI: 10.1111/pcmr.12126] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/30/2013] [Indexed: 12/15/2022]
Abstract
For disseminated melanoma, new prognostic biomarkers and therapeutic targets are urgently needed. The organization of protein-protein interaction networks was assessed via the transcriptomes of four independent studies of metastatic melanoma and related to clinical outcome and MAP-kinase pathway mutations (BRAF/NRAS). We also examined patient outcome-related differences in a predicted network of microRNAs and their targets. The 32 hub genes with the most reproducible survival-related disturbances in co-expression with their protein partner genes included oncogenes and tumor suppressors, previously known correlates of prognosis, and other proteins not previously associated with melanoma outcome. Notably, this network-based gene set could classify patients according to clinical outcomes with 67-80% accuracy among cohorts. Reproducibly disturbed networks were also more likely to have a higher functional mutation burden than would be expected by chance. The disturbed regions of networks are therefore markers of clinically relevant, selectable tumor evolution in melanoma which may carry driver mutations.
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Affiliation(s)
- Sarah-Jane Schramm
- Sydney Medical School, The University of Sydney at Westmead Millennium Institute for Medical Research, Sydney, NSW, Australia
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22
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Fruci D, Benevolo M, Cifaldi L, Lorenzi S, Lo Monaco E, Tremante E, Giacomini P. Major histocompatibility complex class i and tumour immuno-evasion: how to fool T cells and natural killer cells at one time. ACTA ACUST UNITED AC 2013; 19:39-41. [PMID: 22328841 DOI: 10.3747/co.19.945] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cytotoxic T lymphocytes (ctls) and natural killer (nk) cells lyse tumours expressing and lacking, respectively, properly conformed class i molecules of the major histocompatibility complex [mhc-i (Figure 1)] [...]
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Affiliation(s)
- D Fruci
- IRCCS, Ospedale Pediatrico Bambino Gesù, Oncohaematology Department, Rome, Italy
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23
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Liu W, Peng Y, Tobin DJ. A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis. PeerJ 2013; 1:e49. [PMID: 23638386 PMCID: PMC3628745 DOI: 10.7717/peerj.49] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/20/2013] [Indexed: 12/16/2022] Open
Abstract
Genome-wide microarray technology has facilitated the systematic discovery of diagnostic biomarkers of cancers and other pathologies. However, meta-analyses of published arrays often uncover significant inconsistencies that hinder advances in clinical practice. Here we present an integrated microarray analysis framework, based on a genome-wide relative significance (GWRS) and genome-wide global significance (GWGS) model. When applied to five microarray datasets on melanoma published between 2000 and 2011, this method revealed a new signature of 200 genes. When these were linked to so-called ‘melanoma driver’ genes involved in MAPK, Ca2+, and WNT signaling pathways we were able to produce a new 12-gene diagnostic biomarker signature for melanoma (i.e., EGFR, FGFR2, FGFR3, IL8, PTPRF, TNC, CXCL13, COL11A1, CHP2, SHC4, PPP2R2C, and WNT4). We have begun to experimentally validate a subset of these genes involved in MAPK signaling at the protein level, including CXCL13, COL11A1, PTPRF and SHC4 and found these to be over-expressed in metastatic and primary melanoma cells in vitro and in situ compared to melanocytes cultured from healthy skin epidermis and normal healthy human skin. While SHC4 has been reported previously to be associated to melanoma, this is the first time CXCL13, COL11A1, and PTPRF have been associated with melanoma on experimental validation. Our computational evaluation indicates that this 12-gene biomarker signature achieves excellent diagnostic power in distinguishing metastatic melanoma from normal skin and benign nevus. Further experimental validation of the role of these 12 genes in a new signaling network may provide new insights into the underlying biological mechanisms driving the progression of melanoma.
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Affiliation(s)
- Wanting Liu
- Department of Computing, University of Bradford , Great Britain ; Centre of Skin Sciences, University of Bradford , Great Britain
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An attempt at a molecular prediction of metastasis in patients with primary cutaneous melanoma. PLoS One 2012; 7:e49865. [PMID: 23166783 PMCID: PMC3498185 DOI: 10.1371/journal.pone.0049865] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 10/15/2012] [Indexed: 12/31/2022] Open
Abstract
Background Current prognostic clinical and morphological parameters are insufficient to accurately predict metastasis in individual melanoma patients. Several studies have described gene expression signatures to predict survival or metastasis of primary melanoma patients, however the reproducibility among these studies is disappointingly low. Methodology/Principal Findings We followed extended REMARK/Gould Rothberg criteria to identify gene sets predictive for metastasis in patients with primary cutaneous melanoma. For class comparison, gene expression data from 116 patients with clinical stage I/II (no metastasis) and 72 with III/IV primary melanoma (with metastasis) at time of first diagnosis were used. Significance analysis of microarrays identified the top 50 differentially expressed genes. In an independent data set from a second cohort of 28 primary melanoma patients, these genes were analyzed by multivariate Cox regression analysis and leave-one-out cross validation for association with development of metastatic disease. In a multivariate Cox regression analysis, expression of the genes Ena/vasodilator-stimulated phosphoprotein-like (EVL) and CD24 antigen gave the best predictive value (p = 0.001; p = 0.017, respectively). A multivariate Cox proportional hazards model revealed these genes as a potential independent predictor, which may possibly add (both p = 0.01) to the predictive value of the most important morphological indicator, Breslow depth. Conclusion/Significance Combination of molecular with morphological information may potentially enable an improved prediction of metastasis in primary melanoma patients. A strength of the gene expression set is the small number of genes, which should allow easy reevaluation in independent data sets and adequately designed clinical trials.
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BRAF mutation, NRAS mutation, and the absence of an immune-related expressed gene profile predict poor outcome in patients with stage III melanoma. J Invest Dermatol 2012; 133:509-17. [PMID: 22931913 DOI: 10.1038/jid.2012.283] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Prediction of outcome for melanoma patients with surgically resected macroscopic nodal metastases is very imprecise. We performed a comprehensive clinico-pathologic assessment of fresh-frozen macroscopic nodal metastases and the preceding primary melanoma, somatic mutation profiling, and gene expression profiling to identify determinants of outcome in 79 melanoma patients. In addition to disease stage <II at initial presentation, the following clinical and pathologic factors were independent predictors of improved outcome (odds ratios for survival >4 years, 90% confidence interval): the presence of a nodular component in the primary melanoma (6.8, 0.6-76.0), and small cell size (11.1, 0.8-100.0) or low pigmentation (3.0, 0.8-100.0) in the nodal metastases. Absence of BRAF mutation (20.0, 1.0-1000.0) or NRAS mutation (16.7, 0.6-1000.0) were both favorable prognostic factors. A 46-gene expression signature with strong overrepresentation of immune response genes was predictive of better survival (10.9, 0.4-325.6); in the full cohort, median survival was >100 months in those with the signature, but 10 months in those without. This relationship was validated in two previously published independent stage III melanoma data sets. We conclude that the presence of BRAF mutation, NRAS mutation, and the absence of an immune-related expressed gene profile predict poor outcome in melanoma patients with macroscopic stage III disease.
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Tremante E, Ginebri A, Lo Monaco E, Frascione P, Di Filippo F, Terrenato I, Benevolo M, Mottolese M, Pescarmona E, Visca P, Natali PG, Giacomini P. Melanoma molecular classes and prognosis in the postgenomic era. Lancet Oncol 2012; 13:e205-11. [PMID: 22554548 DOI: 10.1016/s1470-2045(12)70003-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Gene expression profiling is a powerful method to classify human tumours on the basis of biological aggressiveness, response to therapy, and outcome for the patient, but its application in melanoma lags behind that of other cancers. From more than 100 articles available on the topic, we selected 14 focusing on patients' outcome. We review and briefly discuss salient findings, and list ten reasons why melanoma molecular classes are not yet used in clinical diagnosis and prognosis. The available evidence suggests that we are on the verge of creating a framework for the use of melanoma molecular classes in prognosis, but so far there is little consensus to put together informative diagnostic and prognostic gene sets.
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Affiliation(s)
- Elisa Tremante
- Laboratory of Immunology, Regina Elena National Cancer Institute, Rome, Italy
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27
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Kren L, Valkovsky I, Dolezel J, Capak I, Pacik D, Poprach A, Lakomy R, Redova M, Fabian P, Krenova Z, Slaby O. HLA-G and HLA-E specific mRNAs connote opposite prognostic significance in renal cell carcinoma. Diagn Pathol 2012; 7:58. [PMID: 22640987 PMCID: PMC3408319 DOI: 10.1186/1746-1596-7-58] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Accepted: 05/29/2012] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Renal cell carcinoma (RCC) is characterized by its resistance to radiotherapy and/or chemotherapy. On the other hand, it is an immunogenic tumor - it is able to stimulate antitumor responses. A prognostic significance of HLA-G expression by neoplastic cells in RCC is not well characterized; significance HLA-E expression in RCC is not characterized at all. METHODS In our study, we evaluated the expression of HLA-G and HLA-E specific mRNA transcripts produced by neoplastic cells in 38 cases of RCC and in 10 samples of normal kidney parenchyma. The results were statistically correlated with various clinico-pathological parameters. RESULTS We confirmed that HLA-G is downregulated in normal kidney tissue; if it is up-regulated in RCC, then it is connected to worse prognosis. On the other hand, HLA-E mRNA transcripts were present in both normal kidney tissue and RCC and their increasing concentrations counterintuitively carried better prognosis, more favorable pT stage and lower nuclear Fuhrmann's grade. CONCLUSION Considering the fact that there is known aberrant activation of HLA-G and HLA-E expression by interferons, identification of HLA-G and HLA-E status could contribute to better selection of RCC patients who could possibly benefit from more tailored neoadjuvant biological/immunological therapy. Thus, these molecules could represent useful prognostic biomarkers in RCC, and the expression of both these molecules in RCC deserves further study. THE VIRTUAL: Slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/7383071387016614.
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Affiliation(s)
- Leos Kren
- Department of Pathology, Faculty of Medicine, University Hospital Brno, Masaryk University, Jihlavska 20, Brno, 625 00, Czech Republic
| | - Ivo Valkovsky
- Faculty Hospital Ostrava, Clinic of Internal Medicine, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Jan Dolezel
- Department of Oncological Urology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ivo Capak
- Department of Oncological Urology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Dalibor Pacik
- Department of Urology, Faculty of Medicine, University Hospital Brno, Masaryk University, Brno, Czech Republic
| | - Alexandr Poprach
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Radek Lakomy
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Martina Redova
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pavel Fabian
- Department of Oncological and Experimental Pathology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Zdenka Krenova
- Department of Childrens’ Oncology, Faculty of Medicine, University Hospital Brno, Masaryk University, Brno, Czech Republic
| | - Ondrej Slaby
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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Cell cycle gene networks are associated with melanoma prognosis. PLoS One 2012; 7:e34247. [PMID: 22536322 PMCID: PMC3335030 DOI: 10.1371/journal.pone.0034247] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 02/24/2012] [Indexed: 11/19/2022] Open
Abstract
Background Our understanding of the molecular pathways that underlie melanoma remains incomplete. Although several published microarray studies of clinical melanomas have provided valuable information, we found only limited concordance between these studies. Therefore, we took an in vitro functional genomics approach to understand melanoma molecular pathways. Methodology/Principal Findings Affymetrix microarray data were generated from A375 melanoma cells treated in vitro with siRNAs against 45 transcription factors and signaling molecules. Analysis of this data using unsupervised hierarchical clustering and Bayesian gene networks identified proliferation-association RNA clusters, which were co-ordinately expressed across the A375 cells and also across melanomas from patients. The abundance in metastatic melanomas of these cellular proliferation clusters and their putative upstream regulators was significantly associated with patient prognosis. An 8-gene classifier derived from gene network hub genes correctly classified the prognosis of 23/26 metastatic melanoma patients in a cross-validation study. Unlike the RNA clusters associated with cellular proliferation described above, co-ordinately expressed RNA clusters associated with immune response were clearly identified across melanoma tumours from patients but not across the siRNA-treated A375 cells, in which immune responses are not active. Three uncharacterised genes, which the gene networks predicted to be upstream of apoptosis- or cellular proliferation-associated RNAs, were found to significantly alter apoptosis and cell number when over-expressed in vitro. Conclusions/Significance This analysis identified co-expression of RNAs that encode functionally-related proteins, in particular, proliferation-associated RNA clusters that are linked to melanoma patient prognosis. Our analysis suggests that A375 cells in vitro may be valid models in which to study the gene expression modules that underlie some melanoma biological processes (e.g., proliferation) but not others (e.g., immune response). The gene expression modules identified here, and the RNAs predicted by Bayesian network inference to be upstream of these modules, are potential prognostic biomarkers and drug targets.
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Journe F, Id Boufker H, Van Kempen L, Galibert MD, Wiedig M, Salès F, Theunis A, Nonclercq D, Frau A, Laurent G, Awada A, Ghanem G. TYRP1 mRNA expression in melanoma metastases correlates with clinical outcome. Br J Cancer 2011; 105:1726-32. [PMID: 22045183 PMCID: PMC3242608 DOI: 10.1038/bjc.2011.451] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background: Clinical outcome of patients with high-risk melanoma cannot be reliably predicted on the basis of classical histopathological examination. Our study aimed to determine in melanoma metastases a gene expression profile associated with patient survival, and to identify and validate marker(s) of poor clinical outcome. Methods: Skin and lymph node metastases from melanoma patients (training population) were used to identify candidate prognostic marker(s) based on DNA microarray analysis. Additional skin metastases (validation population) were used to assess the prognostic value of the first ranked gene by real-time PCR. Results: We performed microarray analysis in the training population and generated a list of 278 probe sets associated with a shorter survival. We used the first ranked gene, tyrosinase-related protein 1 (TYRP1), further measured its expression in the validation population by real-time PCR and found it to be significantly correlated with distant metastasis-free survival (DMFS), overall survival (OS) and Breslow thickness. We also found that it was fairly well conserved in the course of the disease regardless of the delay to metastasis occurrence. Finally, although Tyrp1 protein (immunohistochemistry (IHC)) was only detected in about half of the samples, we showed that its expression also correlated with Breslow thickness. Conclusion: Our data indicate that TYRP1 mRNA expression level, at least in skin metastases, is a prognostic marker for melanoma, and is particularly useful when prognostic pathology parameters at the primary lesion are lacking. Its conserved expression further supports its use as a target for therapy.
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Affiliation(s)
- F Journe
- Laboratoire d'Oncologie et de Chirurgie Expérimentale, Institut Jules Bordet, Université Libre de Bruxelles, 1 rue Heger-Bordet, Brussels, Belgium
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30
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Benevolo M, Mottolese M, Tremante E, Rollo F, Diodoro MG, Ercolani C, Sperduti I, Monaco EL, Cosimelli M, Giacomini P. High expression of HLA-E in colorectal carcinoma is associated with a favorable prognosis. J Transl Med 2011; 9:184. [PMID: 22032294 PMCID: PMC3219584 DOI: 10.1186/1479-5876-9-184] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 10/27/2011] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Human Leukocyte Antigen (HLA)-E is a non-classical class I HLA molecule that can be stabilized by ligands donated by other classical (HLA-A, -B, -C) and non-classical (HLA-G) family members. HLA-E engages a variety of immune receptors expressed by cytotoxic T lymphocytes (CTLs), Natural killer (NK) cells and NK-CTLs. In view of the opposing outcomes (activation or inhibition) of the different HLA-E receptors, the preferred role (if any) of HLA-E expressed in vivo on tumor cells remains to be established. METHODS Taking advantage of MEM-E/02, a recently characterized antibody to denatured HLA-E molecules, HLA-E expression was assessed by immunohistochemistry on an archival collection (formalin-fixed paraffin-embedded) of 149 colorectal primary carcinoma lesions paired with their morphologically normal mucosae. Lymphoid infiltrates were assessed for the expression of the HLA-E-specific, inhibitory, non-rearranging receptor NKG2A. RESULTS High HLA-E expression did not significantly correlate with the expression of classical HLA-B and HLA-C molecules, but it did correlate with high expression of its preferential ligand donor HLA-A. In addition, it correlated with lymphoid cell infiltrates expressing the inhibitory NKG2A receptor, and was an independent predictor of good prognosis, particularly in a subset of patients whose tumors express HLA-A levels resembling those of their paired normal counterparts (HLA-A). Thus, combination phenotypes (HLA-Elo-int/HLA-AE and HLA-Ehi/HLA-AE) of classical and non-classical class I HLA molecules mark two graded levels of good prognosis. CONCLUSIONS These results suggest that HLA-E favors activating immune responses to colorectal carcinoma. They also provide evidence in humans that tumor cells entertain extensive negotiation with the immune system until a compromise between recognition and escape is reached. It is implied that this process occurs stepwise, as predicted by the widely accepted 'immunoediting' model.
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Affiliation(s)
- Maria Benevolo
- Department of Pathology, Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144 Rome, Italy
| | - Marcella Mottolese
- Department of Pathology, Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144 Rome, Italy
| | - Elisa Tremante
- Laboratory of Immunology, Regina Elena National Cancer Institute, Via delle Messi d'Oro 156, 00158 Rome, Italy
| | - Francesca Rollo
- Department of Pathology, Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144 Rome, Italy
| | - Maria Grazia Diodoro
- Department of Pathology, Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144 Rome, Italy
| | - Cristiana Ercolani
- Department of Pathology, Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144 Rome, Italy
| | - Isabella Sperduti
- Biostatistics Unit, Istituti Fisioterapici Ospitalieri, Via E. Chianesi 53, 00144 Rome, Italy
| | - Elisa Lo Monaco
- Laboratory of Immunology, Regina Elena National Cancer Institute, Via delle Messi d'Oro 156, 00158 Rome, Italy
| | - Maurizio Cosimelli
- Hepato-Biliary-Pancreatic Surgery, Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144 Rome, Italy
| | - Patrizio Giacomini
- Laboratory of Immunology, Regina Elena National Cancer Institute, Via delle Messi d'Oro 156, 00158 Rome, Italy
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Review and cross-validation of gene expression signatures and melanoma prognosis. J Invest Dermatol 2011; 132:274-83. [PMID: 21956122 DOI: 10.1038/jid.2011.305] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In melanoma, there is an urgent need to identify novel biomarkers with prognostic performance superior to traditional clinical and histological parameters. Gene expression-based prognostic signatures offer promise, but studies have been challenged by sample scarcity, cohort heterogeneity, and doubts about the efficacy of such signatures relative to current clinical practices. Motivated by new studies that have begun to address these challenges, we reviewed prognostic signatures derived from gene expression microarray analysis of human melanoma tissue. We used REMARK-based criteria to select the most relevant studies and directly compared their signature gene lists. Through functional ontology enrichment analysis, we observed that these independent data sets converge in part upon immune response processes and the G-protein signaling NRAS-regulation pathway, both important in melanoma development and progression. The signatures correctly predicted patient outcome in independent gene expression data sets with some notably low misclassification rates, particularly among studies involving more advanced-stage tumors. This successful cross-validation indicates that gene expression analysis-based signatures are becoming translationally relevant to care of melanoma patients, as well as improving understanding of the aspects of melanoma biology that determine patient outcome.
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32
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Monaco EL, Tremante E, Cerboni C, Melucci E, Sibilio L, Zingoni A, Nicotra MR, Natali PG, Giacomini P. Human leukocyte antigen E contributes to protect tumor cells from lysis by natural killer cells. Neoplasia 2011; 13:822-30. [PMID: 21969815 PMCID: PMC3182274 DOI: 10.1593/neo.101684] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 07/22/2011] [Accepted: 07/28/2011] [Indexed: 01/03/2023]
Abstract
The nonclassic class I human leukocyte antigen E (HLA-E) molecule engages the inhibitory NKG2A receptor on several cytotoxic effectors, including natural killer (NK) cells. Its tissue distribution was claimed to be wider in normal than in neoplastic tissues, and surface HLA-E was undetectable in most tumor cell lines. Herein, these issues were reinvestigated taking advantage of HLA-E-specific antibodies, immunohistochemistry, and biochemical methods detecting intracellular and surface HLA-E regardless of conformation. Contrary to published evidence, HLA-E was detected in a few normal epithelia and in a large fraction (approximately 1/3) of solid tumors, including those derived from HLA-E-negative/low-normal counterparts. Remarkably, HLA-E was detected in 30 of 30 tumor cell lines representative of major lymphoid and nonlymphoid lineages, and in 11 of 11, it was surface-expressed, although in a conformation poorly reactive with commonly used antibodies. Coexpression of HLA-E and HLA class I ligand donors was not required for surface expression but was associated with NKG2A-mediated protection from lysis by the cytotoxic cell line NKL and polyclonal NK cells from healthy donors, as demonstrated by antibody-mediated relief of protection in 10% to 20% of the tested target-effector combinations. NKG2A-mediated protection of additional targets became evident on NK effector blocking with antibodies to activating receptors (DNAM-1, natural cytotoxicity receptors, and NKG2D). Thus, initial evidence that the long-elusive HLA-E molecule is enhanced by malignant transformation and is functional in tumor cells is presented here, although its importance and precise functional role remain to be addressed in the context of a general understanding of the NK ligand-receptor network.
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Affiliation(s)
- Elisa Lo Monaco
- Laboratory of Immunology, Regina Elena Cancer Institute CRS, Rome, Italy
| | - Elisa Tremante
- Laboratory of Immunology, Regina Elena Cancer Institute CRS, Rome, Italy
| | - Cristina Cerboni
- Department of Molecular Medicine, University “La Sapienza,” Rome, Italy
| | - Elisa Melucci
- Department of Pathology, Regina Elena Cancer Institute, Rome, Italy
| | - Leonardo Sibilio
- Laboratory of Immunology, Regina Elena Cancer Institute CRS, Rome, Italy
| | | | - Maria Rita Nicotra
- Laboratory of Immunology, Regina Elena Cancer Institute CRS, Rome, Italy
| | - Pier Giorgio Natali
- Consorzio Interuniversitario Nazionale per la Bio-Oncologia Laboratories, University “Gabriele d'Annunzio,” Chieti, Italy
| | - Patrizio Giacomini
- Laboratory of Immunology, Regina Elena Cancer Institute CRS, Rome, Italy
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Hofmann MA, Schicke B, Fritsch A, Biesold S, Gussmann F, Küchler I, Voit C, Trefzer U. Impact of lymph node metastases on serum level of melanoma inhibitory activity in stage III melanoma patients. J Dermatol 2011; 38:880-6. [PMID: 21658116 DOI: 10.1111/j.1346-8138.2011.01219.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Melanoma patients in stage III have a considerable recurrence rate. The 10-year survival in this stage depends on the number and size of affected nodes. Currently, there is no optimal serum marker for early detection of relapse available. The goal of the study was to assess the utility of melanoma inhibitory activity (MIA) serum marker in the follow up and primary diagnosis of stage III melanoma patients. One hundred and thirty-eight melanoma patients in stage III at time of primary diagnosis were analyzed at time of primary diagnosis and during periodical routine follow up both for serum MIA using an enzyme-linked immunosorbent assay and for serum lactate dehydrogenase (LDH). Results were correlated with the positivity of the sentinel lymph node (SLN) and the number of lymph node metastases in the completion lymph node dissection at time of primary diagnosis. During follow up, the overall survival time was assessed using the Kaplan-Meier method in terms of elevated MIA (>12 ng/mL) values. Regarding SLN status, significant differences of MIA values (P = 0.024) and LDH (P = 0.007) were found, both within the normal cut-off. Having lymph node metastases in the completion lymph node dissection, significantly higher MIA values (12.55 ng/mL [±0.48], P < 0.0001) were found. In patients with three or more tumor-positive nodes, MIA values were significantly higher when compared to patients with one or two affected nodes (P = 0.024). In the routine follow-up, stage III patients with an MIA value of more than 12 ng/mL had a five times higher risk for developing recurrences (P < 0.0001). Patients with relapsing disease had a significantly (P < 0.0001) higher mean MIA value (13.76 ng/mL) compared to patients without relapse (7.52 ng/mL). The MIA serum marker can be helpful in patients undergoing lymph node dissection. Furthermore, during follow up, patients showing relapsing diseases can have an elevated MIA value.
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Affiliation(s)
- Maja A Hofmann
- Department of Dermatology and Allergy, Melanoma Center Department of Biomedical Statistics, Charité-Universitätsmedizin Berlin, Germany.
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Serão NVL, Delfino KR, Southey BR, Beever JE, Rodriguez-Zas SL. Cell cycle and aging, morphogenesis, and response to stimuli genes are individualized biomarkers of glioblastoma progression and survival. BMC Med Genomics 2011; 4:49. [PMID: 21649900 PMCID: PMC3127972 DOI: 10.1186/1755-8794-4-49] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 06/07/2011] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Glioblastoma is a complex multifactorial disorder that has swift and devastating consequences. Few genes have been consistently identified as prognostic biomarkers of glioblastoma survival. The goal of this study was to identify general and clinical-dependent biomarker genes and biological processes of three complementary events: lifetime, overall and progression-free glioblastoma survival. METHODS A novel analytical strategy was developed to identify general associations between the biomarkers and glioblastoma, and associations that depend on cohort groups, such as race, gender, and therapy. Gene network inference, cross-validation and functional analyses further supported the identified biomarkers. RESULTS A total of 61, 47 and 60 gene expression profiles were significantly associated with lifetime, overall, and progression-free survival, respectively. The vast majority of these genes have been previously reported to be associated with glioblastoma (35, 24, and 35 genes, respectively) or with other cancers (10, 19, and 15 genes, respectively) and the rest (16, 4, and 10 genes, respectively) are novel associations. Pik3r1, E2f3, Akr1c3, Csf1, Jag2, Plcg1, Rpl37a, Sod2, Topors, Hras, Mdm2, Camk2g, Fstl1, Il13ra1, Mtap and Tp53 were associated with multiple survival events.Most genes (from 90 to 96%) were associated with survival in a general or cohort-independent manner and thus the same trend is observed across all clinical levels studied. The most extreme associations between profiles and survival were observed for Syne1, Pdcd4, Ighg1, Tgfa, Pla2g7, and Paics. Several genes were found to have a cohort-dependent association with survival and these associations are the basis for individualized prognostic and gene-based therapies. C2, Egfr, Prkcb, Igf2bp3, and Gdf10 had gender-dependent associations; Sox10, Rps20, Rab31, and Vav3 had race-dependent associations; Chi3l1, Prkcb, Polr2d, and Apool had therapy-dependent associations. Biological processes associated glioblastoma survival included morphogenesis, cell cycle, aging, response to stimuli, and programmed cell death. CONCLUSIONS Known biomarkers of glioblastoma survival were confirmed, and new general and clinical-dependent gene profiles were uncovered. The comparison of biomarkers across glioblastoma phases and functional analyses offered insights into the role of genes. These findings support the development of more accurate and personalized prognostic tools and gene-based therapies that improve the survival and quality of life of individuals afflicted by glioblastoma multiforme.
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Affiliation(s)
- Nicola VL Serão
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kristin R Delfino
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan E Beever
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sandra L Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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35
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Abstract
For in-transit melanoma confined to the extremities, regional chemotherapy in the form of hyperthermic isolated limb perfusion and isolated limb infusion are effective treatment modalities carrying superior response rates to current standard systemic therapy. Despite high response rates, most patients will eventually recur, supporting the role for novel research aimed at improving durable responses and minimizing toxicity. Although the standard cytotoxic agent for regional chemotherapy is melphalan, alternative agents such as temozolomide are currently being tested, with promising preliminary results. Current strategies for improving chemosensitivity to regional chemotherapy are aimed at overcoming classic resistance mechanisms such as drug metabolism and DNA repair, increasing drug delivery, inhibiting tumor-specific angiogenesis, and decreasing the apoptotic threshold of melanoma cells. Concurrent with development and testing of these agents, genomic profiling and biomolecular analysis of acquired tumor tissue may define patterns of tumor resistance and sensitivity from which personalized treatment may be tailored to optimize efficacy. In this article rational strategies for treatment of in-transit melanoma are outlined, with special emphasis on current translational and clinical research efforts.
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Sigalotti L, Fratta E, Bidoli E, Covre A, Parisi G, Colizzi F, Coral S, Massarut S, Kirkwood JM, Maio M. Methylation levels of the "long interspersed nucleotide element-1" repetitive sequences predict survival of melanoma patients. J Transl Med 2011; 9:78. [PMID: 21615918 PMCID: PMC3123580 DOI: 10.1186/1479-5876-9-78] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 05/26/2011] [Indexed: 11/19/2022] Open
Abstract
Background The prognosis of cutaneous melanoma (CM) differs for patients with identical clinico-pathological stage, and no molecular markers discriminating the prognosis of stage III individuals have been established. Genome-wide alterations in DNA methylation are a common event in cancer. This study aimed to define the prognostic value of genomic DNA methylation levels in stage III CM patients. Methods Overall level of genomic DNA methylation was measured using bisulfite pyrosequencing at three CpG sites (CpG1, CpG2, CpG3) of the Long Interspersed Nucleotide Element-1 (LINE-1) sequences in short-term CM cultures from 42 stage IIIC patients. The impact of LINE-1 methylation on overall survival (OS) was assessed using Cox regression and Kaplan-Meier analysis. Results Hypomethylation (i.e., methylation below median) at CpG2 and CpG3 sites significantly associated with improved prognosis of CM, CpG3 showing the strongest association. Patients with hypomethylated CpG3 had increased OS (P = 0.01, log-rank = 6.39) by Kaplan-Meyer analysis. Median OS of patients with hypomethylated or hypermethylated CpG3 were 31.9 and 11.5 months, respectively. The 5 year OS for patients with hypomethylated CpG3 was 48% compared to 7% for patients with hypermethylated sequences. Among the variables examined by Cox regression analysis, LINE-1 methylation at CpG2 and CpG3 was the only predictor of OS (Hazard Ratio = 2.63, for hypermethylated CpG3; 95% Confidence Interval: 1.21-5.69; P = 0.01). Conclusion LINE-1 methylation is identified as a molecular marker of prognosis for CM patients in stage IIIC. Evaluation of LINE-1 promises to represent a key tool for driving the most appropriate clinical management of stage III CM patients.
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Affiliation(s)
- Luca Sigalotti
- Cancer Bioimmunotherapy Unit, Centro di Riferimento Oncologico, Istituto di Ricovero e Cura a Carattere Scientifico, Aviano, Italy
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Decoding melanoma metastasis. Cancers (Basel) 2010; 3:126-63. [PMID: 24212610 PMCID: PMC3756353 DOI: 10.3390/cancers3010126] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 12/22/2010] [Accepted: 12/23/2010] [Indexed: 12/18/2022] Open
Abstract
Metastasis accounts for the vast majority of morbidity and mortality associated with melanoma. Evidence suggests melanoma has a predilection for metastasis to particular organs. Experimental analyses have begun to shed light on the mechanisms regulating melanoma metastasis and organ specificity, but these analyses are complicated by observations of metastatic dormancy and dissemination of melanocytes that are not yet fully malignant. Additionally, tumor extrinsic factors in the microenvironment, both at the site of the primary tumor and the site of metastasis, play important roles in mediating the metastatic process. As metastasis research moves forward, paradigms explaining melanoma metastasis as a step-wise process must also reflect the temporal complexity and heterogeneity in progression of this disease. Genetic drivers of melanoma as well as extrinsic regulators of disease spread, particularly those that mediate metastasis to specific organs, must also be incorporated into newer models of melanoma metastasis.
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Affiliation(s)
- Ryan J Sullivan
- Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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Minutilli E. New research advances for treating metastatic melanoma. Int J Dermatol 2010; 49:712-4. [PMID: 20618481 DOI: 10.1111/j.1365-4632.2009.04428.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Jönsson G, Busch C, Knappskog S, Geisler J, Miletic H, Ringnér M, Lillehaug JR, Borg A, Lønning PE. Gene expression profiling-based identification of molecular subtypes in stage IV melanomas with different clinical outcome. Clin Cancer Res 2010; 16:3356-67. [PMID: 20460471 DOI: 10.1158/1078-0432.ccr-09-2509] [Citation(s) in RCA: 182] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE The incidence of malignant melanoma is increasing worldwide in fair-skinned populations. Melanomas respond poorly to systemic therapy, and metastatic melanomas inevitably become fatal. Although spontaneous regression, likely due to immune defense activation, rarely occurs, we lack a biological rationale and predictive markers in selecting patients for immune therapy. EXPERIMENTAL DESIGN We performed unsupervised hierarchical clustering of global gene expression data from stage IV melanomas in 57 patients. For further characterization, we used immunohistochemistry of selected markers, genome-wide DNA copy number analysis, genetic and epigenetic analysis of the CDKN2A locus, and NRAS/BRAF mutation screening. RESULTS The analysis revealed four distinct subtypes with gene signatures characterized by expression of immune response, pigmentation differentiation, proliferation, or stromal composition genes. Although all subtypes harbored NRAS and BRAF mutations, there was a significant difference between subtypes (P < 0.01), with no BRAF/NRAS wild-type samples in the proliferative subtype. Additionally, the proliferative subtype was characterized by a high frequency of CDKN2A homozygous deletions (P < 0.01). We observed a different prognosis between the subtypes (P = 0.01), with a particularly poor survival for patients harboring tumors of the proliferative subtype compared with the others (P = 0.003). Importantly, the clinical relevance of the subtypes was validated in an independent cohort of 44 stage III and IV melanomas. Moreover, low expression of an a priori defined gene set associated with immune response signaling was significantly associated with poor outcome (P = 0.001). CONCLUSIONS Our data reveal a biologically based taxonomy of malignant melanomas with prognostic effect and support an influence of the antitumoral immune response on outcome.
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Affiliation(s)
- Göran Jönsson
- Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden
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Augustine CK, Jung SH, Sohn I, Yoo JS, Yoshimoto Y, Olson JA, Friedman HS, Ali-Osman F, Tyler DS. Gene expression signatures as a guide to treatment strategies for in-transit metastatic melanoma. Mol Cancer Ther 2010; 9:779-90. [PMID: 20371714 DOI: 10.1158/1535-7163.mct-09-0764] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In-transit metastatic melanoma, which typically presents as multifocal lesions, provides a unique setting to evaluate the utility of gene signatures for defining optimal regional therapeutic strategies and assessing the efficacy of treatment. The goal of this study was to determine whether a single multifocal lesion is representative of residual tumor burden in terms of gene expression signatures predictive of response to therapy. Using microarray-based gene expression profiling, we examined 55 in-transit melanoma lesions across 29 patients with multifocal disease. Principal component analysis, unsupervised hierarchical clustering, one-way ANOVA, binary regression analysis, and gene signatures predictive of oncogenic pathway activation were used to compare patterns of gene expression across all multifocal lesions from a patient. Patterns of gene expression were highly similar (P < 0.006; average r = 0.979) across pretreatment lesions from a single patient compared with the significantly different patterns observed across patients (P < 0.05). The findings presented in this study show that individual melanoma tumor nodules in patients with multifocal disease harbor similar patterns of gene expression and a single lesion can be used to predict response to chemotherapy, evaluate the activation status of oncogenic signaling pathways, and characterize other aspects of the biology of an individual patient's disease. These results will facilitate the use of gene expression profiling in melanoma regional therapy clinical trials to not only select optimal regional chemotherapeutic agents but to also allow for a more rational identification of candidates for specific targeted therapies and evaluation of their therapeutic efficacy. Mol Cancer Ther; 9(4); 779-90. (c)2010 AACR.
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Gene signature of the metastatic potential of cutaneous melanoma: too much for too little? Clin Exp Metastasis 2010; 27:371-87. [DOI: 10.1007/s10585-010-9307-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Accepted: 01/28/2010] [Indexed: 10/19/2022]
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Identification and functional validation of therapeutic targets for malignant melanoma. Crit Rev Oncol Hematol 2009; 72:194-214. [DOI: 10.1016/j.critrevonc.2009.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 02/04/2009] [Accepted: 02/19/2009] [Indexed: 12/12/2022] Open
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Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival. Proc Natl Acad Sci U S A 2009; 106:20429-34. [PMID: 19915147 DOI: 10.1073/pnas.0905139106] [Citation(s) in RCA: 286] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Although remission rates for metastatic melanoma are generally very poor, some patients can survive for prolonged periods following metastasis. We used gene expression profiling, mitotic index (MI), and quantification of tumor infiltrating leukocytes (TILs) and CD3+ cells in metastatic lesions to search for a molecular basis for this observation and to develop improved methods for predicting patient survival. We identified a group of 266 genes associated with postrecurrence survival. Genes positively associated with survival were predominantly immune response related (e.g., ICOS, CD3d, ZAP70, TRAT1, TARP, GZMK, LCK, CD2, CXCL13, CCL19, CCR7, VCAM1) while genes negatively associated with survival were cell proliferation related (e.g., PDE4D, CDK2, GREF1, NUSAP1, SPC24). Furthermore, any of the 4 parameters (prevalidated gene expression signature, TILs, CD3, and in particular MI) improved the ability of Tumor, Node, Metastasis (TNM) staging to predict postrecurrence survival; MI was the most significant contributor (HR = 2.13, P = 0.0008). An immune response gene expression signature and presence of TILs and CD3+ cells signify immune surveillance as a mechanism for prolonged survival in these patients and indicate improved patient subcategorization beyond current TNM staging.
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Halaban R, Krauthammer M, Pelizzola M, Cheng E, Kovacs D, Sznol M, Ariyan S, Narayan D, Bacchiocchi A, Molinaro A, Kluger Y, Deng M, Tran N, Zhang W, Picardo M, Enghild JJ. Integrative analysis of epigenetic modulation in melanoma cell response to decitabine: clinical implications. PLoS One 2009; 4:e4563. [PMID: 19234609 PMCID: PMC2642998 DOI: 10.1371/journal.pone.0004563] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2008] [Accepted: 01/06/2009] [Indexed: 12/31/2022] Open
Abstract
Decitabine, an epigenetic modifier that reactivates genes otherwise suppressed by DNA promoter methylation, is effective for some, but not all cancer patients, especially those with solid tumors. It is commonly recognized that to overcome resistance and improve outcome, treatment should be guided by tumor biology, which includes genotype, epigenotype, and gene expression profile. We therefore took an integrative approach to better understand melanoma cell response to clinically relevant dose of decitabine and identify complementary targets for combined therapy. We employed eight different melanoma cell strains, determined their growth, apoptotic and DNA damage responses to increasing doses of decitabine, and chose a low, clinically relevant drug dose to perform whole-genome differential gene expression, bioinformatic analysis, and protein validation studies. The data ruled out the DNA damage response, demonstrated the involvement of p21(Cip1) in a p53-independent manner, identified the TGFbeta pathway genes CLU and TGFBI as markers of sensitivity to decitabine and revealed an effect on histone modification as part of decitabine-induced gene expression. Mutation analysis and knockdown by siRNA implicated activated beta-catenin/MITF, but not BRAF, NRAS or PTEN mutations as a source for resistance. The importance of protein stability predicted from the results was validated by the synergistic effect of Bortezomib, a proteasome inhibitor, in enhancing the growth arrest of decitabine in otherwise resistant melanoma cells. Our integrative analysis show that improved therapy can be achieved by comprehensive analysis of cancer cells, identified biomarkers for patient's selection and monitoring response, as well as targets for improved combination therapy.
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Affiliation(s)
- Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, United States of America.
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