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Zhang Y, Wong G, Mann G, Muller S, Yang JYH. SurvBenchmark: comprehensive benchmarking study of survival analysis methods using both omics data and clinical data. Gigascience 2022; 11:6652188. [PMID: 35906887 PMCID: PMC9338425 DOI: 10.1093/gigascience/giac071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/16/2022] [Accepted: 06/22/2022] [Indexed: 11/24/2022] Open
Abstract
Survival analysis is a branch of statistics that deals with both the tracking of time and the survival status simultaneously as the dependent response. Current comparisons of survival model performance mostly center on clinical data with classic statistical survival models, with prediction accuracy often serving as the sole metric of model performance. Moreover, survival analysis approaches for censored omics data have not been thoroughly investigated. The common approach is to binarize the survival time and perform a classification analysis. Here, we develop a benchmarking design, SurvBenchmark, that evaluates a diverse collection of survival models for both clinical and omics data sets. SurvBenchmark not only focuses on classical approaches such as the Cox model but also evaluates state-of-the-art machine learning survival models. All approaches were assessed using multiple performance metrics; these include model predictability, stability, flexibility, and computational issues. Our systematic comparison design with 320 comparisons (20 methods over 16 data sets) shows that the performances of survival models vary in practice over real-world data sets and over the choice of the evaluation metric. In particular, we highlight that using multiple performance metrics is critical in providing a balanced assessment of various models. The results in our study will provide practical guidelines for translational scientists and clinicians, as well as define possible areas of investigation in both survival technique and benchmarking strategies.
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Affiliation(s)
- Yunwei Zhang
- School of Mathematics and Statistics, The University of Sydney, Sydney 2006, Australia.,Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia
| | - Germaine Wong
- Sydney School of Public Health, The University of Sydney, NSW, Sydney 2006, Australia.,Centre for Kidney Research, Kids Research Institute, The Children's Hospital at Westmead, NSW, 2145, Sydney, Australia.,Centre for Transplant and Renal Research, Westmead Hospital, NSW, 2145, Sydney, Australia
| | - Graham Mann
- John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia.,Melanoma Institute Australia, North Sydney, NSW 2065, Australia
| | - Samuel Muller
- School of Mathematics and Statistics, The University of Sydney, Sydney 2006, Australia.,Department of Mathematics and Statistics, Macquarie University, Sydney 2109, Australia
| | - Jean Y H Yang
- School of Mathematics and Statistics, The University of Sydney, Sydney 2006, Australia.,Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia.,Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
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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: 19] [Impact Index Per Article: 6.3] [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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Kupczyk P, Simiczyjew A, Marczuk J, Dratkiewicz E, Beberok A, Rok J, Pieniazek M, Biecek P, Nevozhay D, Slowikowski B, Chodaczek G, Wrzesniok D, Nowak D, Donizy P. PARP1 as a Marker of an Aggressive Clinical Phenotype in Cutaneous Melanoma-A Clinical and an In Vitro Study. Cells 2021; 10:286. [PMID: 33572647 PMCID: PMC7911865 DOI: 10.3390/cells10020286] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 01/12/2023] Open
Abstract
(1) Background: Poly(ADP-ribose) polymerase 1) (PARP1) is a pleiotropic enzyme involved in several cellular processes, e.g., DNA damage repair, regulation of mitosis, and immune response. Little is known about the role of PARP1 in melanoma development and progression. We aimed to investigate the prognostic significance of PARP1 expression in cutaneous melanoma through evaluation of mRNA and protein levels of PARP1 in normal melanocytes and melanoma cell lines, as well as in patients' tissue material from surgical resections. (2) Methods: An in vitro model was based on two types of normal human melanocytes (HEMn-DP and HEMn-LP) and four melanoma cell lines (A375, WM1341D, Hs294T, and WM9). PARP1 mRNA gene expression was estimated using real-time polymerase chain reaction (RT-PCR), whereas the protein level of PARP1 was evaluated by fluorescence confocal microscopy and then confirmed by Western Blotting analysis. The expression of PARP1 was also assessed by immunohistochemistry in formalin-fixed paraffin-embedded tissues of 128 primary cutaneous melanoma patients and correlated with follow-up and clinicopathologic features. (3) Results: The in vitro study showed that melanoma cells exhibited significantly higher PARP1 expression at mRNA and protein levels than normal melanocytes. High PARP1 expression was also associated with the invasiveness of tumor cells. Elevated nuclear PARP1 expression in patients without nodal metastases strongly correlated with significantly shorter disease-free survival (p = 0.0015) and revealed a trend with shorter cancer-specific overall survival (p = 0.05). High PARP1 immunoreactivity in the lymph node-negative group of patients was significantly associated with higher Breslow tumor thickness, presence of ulceration, and a higher mitotic index (p = 0.0016, p = 0.023, and p < 0.001, respectively). In patients with nodal metastases, high PARP1 expression significantly correlated with the presence of microsatellitosis (p = 0.034), but we did not confirm the prognostic significance of PARP1 expression in these patients. In the entire analyzed group of patients (with and without nodal metastases at the time of diagnosis), PARP1 expression was associated with a high mitotic index (p = 0.001) and the presence of ulceration (p = 0.036). Moreover, in patients with elevated PARP1 expression, melanoma was more frequently located in the skin of the head and neck region (p = 0.015). In multivariate analysis, high PARP1 expression was an independent unfavorable prognosticator in lymph node-negative cutaneous melanoma patients. (4) Conclusions: In vitro molecular biology approaches demonstrated enhanced PARP1 expression in cutaneous melanoma. These results were confirmed by the immunohistochemical study with clinical parameter analysis, which showed that a high level of PARP1 correlated with unfavorable clinical outcome. These observations raise the potential role of PARP1 inhibitor-based therapy in cutaneous melanoma.
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Affiliation(s)
- Piotr Kupczyk
- Department of Pathomorphology, Wroclaw Medical University, 50-368 Wroclaw, Poland;
| | - Aleksandra Simiczyjew
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland; (A.S.); (E.D.); (D.N.)
| | - Jakub Marczuk
- Department of Dermatology, Research and Development Center, Regional Specialized Hospital, 51-124 Wroclaw, Poland;
| | - Ewelina Dratkiewicz
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland; (A.S.); (E.D.); (D.N.)
| | - Artur Beberok
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 41-200 Sosnowiec, Poland; (A.B.); (J.R.); (D.W.)
| | - Jakub Rok
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 41-200 Sosnowiec, Poland; (A.B.); (J.R.); (D.W.)
| | - Malgorzata Pieniazek
- Department of Clinical Oncology, Tadeusz Koszarowski Regional Oncology Centre, 45-061 Opole, Poland;
| | - Przemyslaw Biecek
- Faculty of Mathemathics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland;
| | - Dmitry Nevozhay
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
- School of Biomedicine, Far Eastern Federal University, 690950 Vladivostok, Russia
| | - Bartosz Slowikowski
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 60-781 Poznan, Poland;
| | - Grzegorz Chodaczek
- Laboratory of Bioimaging, Łukasiewicz Research Network—PORT Polish Center for Technology Development, 54-066 Wroclaw, Poland;
| | - Dorota Wrzesniok
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 41-200 Sosnowiec, Poland; (A.B.); (J.R.); (D.W.)
| | - Dorota Nowak
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland; (A.S.); (E.D.); (D.N.)
| | - Piotr Donizy
- Department of Pathomorphology and Oncological Cytology, Wroclaw Medical University, 50-556 Wroclaw, Poland
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García-Silva S, Benito-Martín A, Sánchez-Redondo S, Hernández-Barranco A, Ximénez-Embún P, Nogués L, Mazariegos MS, Brinkmann K, Amor López A, Meyer L, Rodríguez C, García-Martín C, Boskovic J, Letón R, Montero C, Robledo M, Santambrogio L, Sue Brady M, Szumera-Ciećkiewicz A, Kalinowska I, Skog J, Noerholm M, Muñoz J, Ortiz-Romero PL, Ruano Y, Rodríguez-Peralto JL, Rutkowski P, Peinado H. Use of extracellular vesicles from lymphatic drainage as surrogate markers of melanoma progression and BRAF V600E mutation. J Exp Med 2019; 216:1061-1070. [PMID: 30975894 PMCID: PMC6504207 DOI: 10.1084/jem.20181522] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/22/2018] [Accepted: 03/12/2019] [Indexed: 12/19/2022] Open
Abstract
García-Silva et al. show for the first time that extracellular vesicles isolated from the exudative seroma obtained from the lymphatic drainage implanted in melanoma patients after lymphadenectomy can be interrogated for melanoma markers and BRAF mutations. Profiling the BRAFV600E mutation in this biofluid is a novel approach to predict disease relapse. Liquid biopsies from cancer patients have the potential to improve diagnosis and prognosis. The assessment of surrogate markers of tumor progression in circulating extracellular vesicles could be a powerful non-invasive approach in this setting. We have characterized extracellular vesicles purified from the lymphatic drainage also known as exudative seroma (ES) of stage III melanoma patients obtained after lymphadenectomy. Proteomic analysis showed that seroma-derived exosomes are enriched in proteins resembling melanoma progression. In addition, we found that the BRAFV600E mutation can be detected in ES-derived extracellular vesicles and its detection correlated with patients at risk of relapse.
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Affiliation(s)
- Susana García-Silva
- Microenvironment and Metastasis Laboratory, Molecular Oncology Program, Spanish National Cancer Research Center, Madrid, Spain
| | - Alberto Benito-Martín
- Children's Cancer and Blood Foundation Laboratories, Department of Pediatrics, Weill Cornell Medicine, New York, NY
| | - Sara Sánchez-Redondo
- Microenvironment and Metastasis Laboratory, Molecular Oncology Program, Spanish National Cancer Research Center, Madrid, Spain
| | - Alberto Hernández-Barranco
- Microenvironment and Metastasis Laboratory, Molecular Oncology Program, Spanish National Cancer Research Center, Madrid, Spain
| | - Pilar Ximénez-Embún
- Proteomics Unit-ProteoRed-Instituto de Salud Carlos III, Spanish National Cancer Research Center, Madrid, Spain
| | - Laura Nogués
- Microenvironment and Metastasis Laboratory, Molecular Oncology Program, Spanish National Cancer Research Center, Madrid, Spain
| | - Marina S Mazariegos
- Microenvironment and Metastasis Laboratory, Molecular Oncology Program, Spanish National Cancer Research Center, Madrid, Spain
| | | | - Ana Amor López
- Microenvironment and Metastasis Laboratory, Molecular Oncology Program, Spanish National Cancer Research Center, Madrid, Spain
| | - Lisa Meyer
- Exosome Diagnostics, GmbH, Martinsried, Germany
| | - Carlos Rodríguez
- Electron Microscopy Unit, Spanish National Cancer Research Center, Madrid, Spain
| | - Carmen García-Martín
- Electron Microscopy Unit, Spanish National Cancer Research Center, Madrid, Spain
| | - Jasminka Boskovic
- Electron Microscopy Unit, Spanish National Cancer Research Center, Madrid, Spain
| | - Rocío Letón
- Hereditary Endocrine Group, Spanish National Cancer Research Center, Madrid, Spain
| | - Cristina Montero
- Hereditary Endocrine Group, Spanish National Cancer Research Center, Madrid, Spain
| | - Mercedes Robledo
- Hereditary Endocrine Group, Spanish National Cancer Research Center, Madrid, Spain
| | - Laura Santambrogio
- Department of Pathology, Microbiology & Immunology, Albert Einstein College of Medicine, New York, NY
| | | | - Anna Szumera-Ciećkiewicz
- Maria Sklodowska-Curie Institute-Oncology Center, Department of Pathology and Laboratory Medicine, Warsaw, Poland
| | - Iwona Kalinowska
- Maria Sklodowska-Curie Institute-Oncology Center, Department of Soft Tissue/Bone Sarcoma and Melanoma, Warsaw, Poland
| | | | | | - Javier Muñoz
- Proteomics Unit-ProteoRed-Instituto de Salud Carlos III, Spanish National Cancer Research Center, Madrid, Spain
| | - Pablo L Ortiz-Romero
- Department of Dermatology, Medical school, Universidad Complutense de Madrid, Instituto i+12, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Yolanda Ruano
- Department of Pathology, Medical school, Universidad Complutense de Madrid, Instituto i+12, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - José L Rodríguez-Peralto
- Department of Pathology, Medical school, Universidad Complutense de Madrid, Instituto i+12, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Piotr Rutkowski
- Maria Sklodowska-Curie Institute-Oncology Center, Department of Soft Tissue/Bone Sarcoma and Melanoma, Warsaw, Poland
| | - Héctor Peinado
- Microenvironment and Metastasis Laboratory, Molecular Oncology Program, Spanish National Cancer Research Center, Madrid, Spain
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5
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Betancourt LH, Pawłowski K, Eriksson J, Szasz AM, Mitra S, Pla I, Welinder C, Ekedahl H, Broberg P, Appelqvist R, Yakovleva M, Sugihara Y, Miharada K, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Wieslander E, Horvatovich P, Malm J, Jönsson G, Marko-Varga G. Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data. Sci Rep 2019; 9:5154. [PMID: 30914758 PMCID: PMC6435712 DOI: 10.1038/s41598-019-41625-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 03/13/2019] [Indexed: 12/18/2022] Open
Abstract
Metastatic melanoma is one of the most common deadly cancers, and robust biomarkers are still needed, e.g. to predict survival and treatment efficiency. Here, protein expression analysis of one hundred eleven melanoma lymph node metastases using high resolution mass spectrometry is coupled with in-depth histopathology analysis, clinical data and genomics profiles. This broad view of protein expression allowed to identify novel candidate protein markers that improved prediction of survival in melanoma patients. Some of the prognostic proteins have not been reported in the context of melanoma before, and few of them exhibit unexpected relationship to survival, which likely reflects the limitations of current knowledge on melanoma and shows the potential of proteomics in clinical cancer research.
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Affiliation(s)
| | - Krzysztof Pawłowski
- Lund University, Lund, Sweden.
- Warsaw University of Life Sciences SGGW, Warszawa, Poland.
| | | | - A Marcell Szasz
- Lund University, Lund, Sweden
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Semmelweis University, Budapest, Hungary
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Peter Horvatovich
- Lund University, Lund, Sweden
- University of Groningen, Groningen, The Netherlands
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6
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Lim SY, Lee JH, Diefenbach RJ, Kefford RF, Rizos H. Liquid biomarkers in melanoma: detection and discovery. Mol Cancer 2018; 17:8. [PMID: 29343260 PMCID: PMC5772714 DOI: 10.1186/s12943-018-0757-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/02/2018] [Indexed: 12/18/2022] Open
Abstract
A vast array of tumor-derived genetic, proteomic and cellular components are constantly released into the circulation of cancer patients. These molecules including circulating tumor DNA and RNA, proteins, tumor and immune cells are emerging as convenient and accurate liquid biomarkers of cancer. Circulating cancer biomarkers provide invaluable information on cancer detection and diagnosis, prognosticate patient outcomes, and predict treatment response. In this era of effective molecular targeted treatments and immunotherapies, there is now an urgent need to implement use of these circulating biomarkers in the clinic to facilitate personalized therapy. In this review, we present recent findings in circulating melanoma biomarkers, examine the challenges and promise of evolving technologies used for liquid biomarker discovery, and discuss future directions and perspectives in melanoma biomarker research.
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Affiliation(s)
- Su Yin Lim
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, Sydney, NSW, Australia
| | - Jenny H Lee
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, Sydney, NSW, Australia
| | - Russell J Diefenbach
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, Sydney, NSW, Australia
| | - Richard F Kefford
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, Sydney, NSW, Australia.,Department of Medical Oncology, Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, NSW, Australia
| | - Helen Rizos
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia. .,Melanoma Institute Australia, Sydney, NSW, Australia. .,Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, Sydney, NSW, 2109, Australia.
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7
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Sykes EK, McDonald CE, Ghazanfar S, Mactier S, Thompson JF, Scolyer RA, Yang JY, Mann GJ, Christopherson RI. A 14-Protein Signature for Rapid Identification of Poor Prognosis Stage III Metastatic Melanoma. Proteomics Clin Appl 2017; 12:e1700094. [PMID: 29227041 DOI: 10.1002/prca.201700094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/08/2017] [Indexed: 11/10/2022]
Abstract
PURPOSE To validate differences in protein levels between good and poor prognosis American Joint Committee on Cancer (AJCC) stage III melanoma patients and compile a protein panel to stratify patient risk. EXPERIMENTAL DESIGN Protein extracts from melanoma metastases within lymph nodes in patients with stage III disease with good (n = 16, >4 years survival) and poor survival (n = 14, <2 years survival) were analyzed by selected reaction monitoring (SRM). Diagonal Linear Discriminant Analysis (DLDA) was performed to generate a protein biomarker panel. RESULTS SRM analysis identified ten proteins that were differentially abundant between good and poor prognosis stage III melanoma patients. The ten differential proteins were combined with 22 proteins identified in our previous work. A panel of 14 proteins was selected by DLDA that was able to accurately classify patients into prognostic groups based on levels of these proteins. CONCLUSIONS AND CLINICAL RELEVANCE The ten differential proteins identified by SRM have biological significance in cancer progression. The final signature of 14 proteins identified by SRM could be used to identify AJCC stage III melanoma patients likely to have poor outcomes who may benefit from adjuvant systemic therapy.
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Affiliation(s)
- Erin K Sykes
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | | | - Shila Ghazanfar
- School of Mathematics and Statistics, University of Sydney, NSW, Australia
| | - Swetlana Mactier
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - John F Thompson
- Melanoma Institute Australia, University of Sydney, North Sydney, NSW, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,University of Sydney at Westmead Millennium Institute, Westmead, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, University of Sydney, North Sydney, NSW, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Jean Y Yang
- School of Mathematics and Statistics, University of Sydney, NSW, Australia
| | - Graham J Mann
- Melanoma Institute Australia, University of Sydney, North Sydney, NSW, Australia.,University of Sydney at Westmead Millennium Institute, Westmead, NSW, Australia
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8
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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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9
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Thurgood LA, Chataway TK, Lower KM, Kuss BJ. From genome to proteome: Looking beyond DNA and RNA in chronic lymphocytic leukemia. J Proteomics 2017; 155:73-84. [PMID: 28069558 DOI: 10.1016/j.jprot.2017.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/11/2016] [Accepted: 01/03/2017] [Indexed: 02/07/2023]
Abstract
Chronic lymphocytic leukemia (CLL) remains the most common leukemia in the Western world. Whilst its disease course is extremely heterogeneous (ranging from indolent to aggressive), current methods are unable to accurately predict the clinical journey of each patient. There is clearly a pressing need for both improved prognostication and treatment options for patients with this disease. Whilst molecular studies have analyzed both genetic mutations and gene expression profiles of these malignant B-cells, and as a result have shed light on the pathogenesis of CLL, proteomic studies have been largely overlooked to date. This review summarizes our current knowledge of the proteomics of CLL, and discusses some of the issues in CLL proteomic research, such as reproducibility and data interpretation. In addition, we look ahead to how proteomics may significantly help in the development of a successful treatment for this currently incurable disease.
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Affiliation(s)
- Lauren A Thurgood
- Department of Haematology and Genetic Pathology, Flinders University, Adelaide, South Australia, Australia.
| | - Tim K Chataway
- Department of Physiology, Flinders University, Adelaide, South Australia, Australia
| | - Karen M Lower
- Department of Haematology and Genetic Pathology, Flinders University, Adelaide, South Australia, Australia
| | - Bryone J Kuss
- Department of Haematology and Genetic Pathology, Flinders University, Adelaide, South Australia, Australia
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10
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Mahar AL, Compton C, Halabi S, Hess KR, Gershenwald JE, Scolyer RA, Groome PA. Critical Assessment of Clinical Prognostic Tools in Melanoma. Ann Surg Oncol 2016; 23:2753-61. [DOI: 10.1245/s10434-016-5212-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Indexed: 12/13/2022]
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11
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Vogelsang M, Wilson M, Kirchhoff T. Germline determinants of clinical outcome of cutaneous melanoma. Pigment Cell Melanoma Res 2016; 29:15-26. [PMID: 26342156 PMCID: PMC5024571 DOI: 10.1111/pcmr.12418] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/02/2015] [Indexed: 12/12/2022]
Abstract
Cutaneous melanoma (CM) is the most lethal form of skin cancer. Despite the constant increase in melanoma incidence, which is in part due to incremental advances in early diagnostic modalities, mortality rates have not improved over the last decade and for advanced stages remain steadily high. While conventional prognostic biomarkers currently in use find significant utility for predicting overall general survival probabilities, they are not sensitive enough for a more personalized clinical assessment on an individual level. In recent years, the advent of genomic technologies has brought the promise of identification of germline DNA alterations that may associate with CM outcomes and hence represent novel biomarkers for clinical utilization. This review attempts to summarize the current state of knowledge of germline genetic factors studied for their impact on melanoma clinical outcomes. We also discuss ongoing problems and hurdles in validating such surrogates, and we also project future directions in discovery of more powerful germline genetic factors with clinical utility in melanoma prognostication.
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Affiliation(s)
- Matjaz Vogelsang
- Perlmutter Cancer Center, New York University School of Medicine, New York, USA
- Departments of Population Health and Environmental Medicine, New York University School of Medicine, New York, USA
- The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, USA
| | - Melissa Wilson
- Perlmutter Cancer Center, New York University School of Medicine, New York, USA
- Department of Medicine, New York University School of Medicine, New York, USA
- The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, USA
| | - Tomas Kirchhoff
- Perlmutter Cancer Center, New York University School of Medicine, New York, USA
- Departments of Population Health and Environmental Medicine, New York University School of Medicine, New York, USA
- The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, USA
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12
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Huang PY, Mactier S, Armacki N, Giles Best O, Belov L, Kaufman KL, Pascovici D, Mulligan SP, Christopherson RI. Protein profiles distinguish stable and progressive chronic lymphocytic leukemia. Leuk Lymphoma 2015; 57:1033-43. [DOI: 10.3109/10428194.2015.1094692] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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13
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Welinder C, Pawłowski K, Sugihara Y, Yakovleva M, Jönsson G, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Jansson B, Laurell T, Fehniger T, Döme B, Malm J, Wieslander E, Nishimura T, Marko-Varga G. A protein deep sequencing evaluation of metastatic melanoma tissues. PLoS One 2015; 10:e0123661. [PMID: 25874936 PMCID: PMC4395420 DOI: 10.1371/journal.pone.0123661] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/21/2015] [Indexed: 12/13/2022] Open
Abstract
Malignant melanoma has the highest increase of incidence of malignancies in the western world. In early stages, front line therapy is surgical excision of the primary tumor. Metastatic disease has very limited possibilities for cure. Recently, several protein kinase inhibitors and immune modifiers have shown promising clinical results but drug resistance in metastasized melanoma remains a major problem. The need for routine clinical biomarkers to follow disease progression and treatment efficacy is high. The aim of the present study was to build a protein sequence database in metastatic melanoma, searching for novel, relevant biomarkers. Ten lymph node metastases (South-Swedish Malignant Melanoma Biobank) were subjected to global protein expression analysis using two proteomics approaches (with/without orthogonal fractionation). Fractionation produced higher numbers of protein identifications (4284). Combining both methods, 5326 unique proteins were identified (2641 proteins overlapping). Deep mining proteomics may contribute to the discovery of novel biomarkers for metastatic melanoma, for example dividing the samples into two metastatic melanoma "genomic subtypes", ("pigmentation" and "high immune") revealed several proteins showing differential levels of expression. In conclusion, the present study provides an initial version of a metastatic melanoma protein sequence database producing a total of more than 5000 unique protein identifications. The raw data have been deposited to the ProteomeXchange with identifiers PXD001724 and PXD001725.
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Affiliation(s)
- Charlotte Welinder
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
| | | | - Yutaka Sugihara
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Maria Yakovleva
- National Korányi Institute of Pulmonology, Budapest, Hungary
- Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, Lund, Sweden
| | - Göran Jönsson
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Christian Ingvar
- Surgery, Dept. of Clinical Sciences, Lund University, Skåne University Hospital, Lund, Sweden
| | - Lotta Lundgren
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
- Skåne University Hospital, Lund, Sweden
| | - Bo Baldetorp
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Håkan Olsson
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
- Skåne University Hospital, Lund, Sweden
- Cancer Epidemiology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, Lund, Sweden
| | - Bo Jansson
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Thomas Laurell
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, Lund, Sweden
| | - Thomas Fehniger
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
| | - Balazs Döme
- National Korányi Institute of Pulmonology, Budapest, Hungary
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Johan Malm
- Section for Clinical Chemistry, Dept. of Laboratory Medicine, Lund University, Skåne University Hospital in Malmö, Malmö, Sweden
| | - Elisabet Wieslander
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Toshihide Nishimura
- Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- First Dept. of Surgery, Tokyo Medical University, Tokyo, Japan
| | - György Marko-Varga
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, Lund, Sweden
- First Dept. of Surgery, Tokyo Medical University, Tokyo, Japan
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